A Disclaimer for Behe?
by BilboWarning: If anyone posts something I consider off topic on this thread, I will send their comments to the memory hole. If you want to continue discussing weasels, go two threads down.
Yesterday, I read and e-mailed Behe's latest post at his blog. Afterwards, it occurred to me that my friends would notice that his blog now flies under the banner, "Uncommon Descent," and wonder if Behe has now rejected the theory of common descent. Behe has reacted with frustration in the past when his critics have expressed surprised that he accepts common descent. Perhaps he should understand that they may wonder if he's changed his mind. I suggest that he add a disclaimer to his profile. Something simple, such as:
"Even though my blog is now here at Uncommon Descent, where many of the contributors commonly argue against the theory of common descent, I still accept common descent, and believe that there is no good reason to reject it."
It might help prevent future misunderstandings. Maybe.
September 17th, 2009 at 5:56 pm
Let me offer some context, Rock. After reading Behe's The Edge of Evolution, Jerry Coyne (and maybe some other reviewers) expressed surprise that Behe accepted the theory of common descent. Behe replied in obvious frustration that they should have known that he accepted it, since he said so in his book, Darwin's Black Box. Now, Behe has his blog at a place called, "Uncommon Descent." The uninformed reader, such as the person I sent a copy of Behe's latest post to, might presume that such a place dissented from the theory of common descent. And if they read one or two of the threads there, they would almost certainly conclude that the blog was for those who disagreed with common descent. Then, seeing Behe has his own blog at UD, they might — reasonably, I think — conclude that Behe disagreed with common descent.
In such a situation, if Behe wanted to make sure people knew that he hadn't changed his mind, and still accepted common descent, then putting a disclaimer in his profile might help. Otherwise, what should he expect people to believe about him?
This does not mean that Behe is "cutting off free expression and free exchange of information, ideas, beliefs" of those who disagree with common descent. He's just informing the reader of his own views.
Comment by Bilbo — September 17, 2009 @ 5:56 pm
September 17th, 2009 at 6:46 pm
What you're demanding from Behe sounds silly. Darwinism is not only Darwin's 19th century views but many views. Have you seen anybody demanding from these people holding unorthodox Darwinian viewpoints to issue a disclaimer that they still are true Darwinians???
Comment by neddy — September 17, 2009 @ 6:46 pm
September 17th, 2009 at 8:24 pm
Why does Behe have to cater to people who are too lazy or too ill-informed to read what he writes (repeatedly)? This sets a bad precedent. Your views are not known by prominent critic so and so and some less prominent people might not know either so start making disclaimers, not about scientific data, but about your beliefs. I think Rock, an active researcher, is right on this. This type of expectation could have a chilling effect on free expression. Hey Rock, you may be fairly well known on that blog TT but since we do not know about you why not issue a disclaimer on ID so people don't think you are a creationist. After all we all know what those kind of people are like.
Comment by Bradford — September 17, 2009 @ 8:24 pm
September 17th, 2009 at 11:37 pm
Consider this:
John ID Doe states his belief that God created multiple unicellular organisms, front loaded their cellular properties to make evolution in the direction of ever increasing complexity inevitable and then let creation take its course which was descent from common multiple lines of initial organisms. He considers this uncommon descent. Others would ascribe the more commonly used phrase common descent to the same scenario. Does John ID Doe need to issue a disclaimer? Assume he is well known. Now is a disclaimer needed?
Comment by Bradford — September 17, 2009 @ 11:37 pm
September 18th, 2009 at 1:06 am
Bilbo,
http://www.uncommondescent.com...
Wouldn't this be close to what you're asking for?
Comment by nullasalus — September 18, 2009 @ 1:06 am
September 18th, 2009 at 5:41 am
From the link supplied by Nullasalus:
Given that the website Behe writes for makes explicit its distinction of ID from CD, I see even less cause for confusion. Again, there is no remedy for not devoting the time to read things. If inattention is the cause for confusion then that's on the inattentive.
Comment by Bradford — September 18, 2009 @ 5:41 am
September 18th, 2009 at 12:03 pm
I apologize for any role I had in hijacking your thread, and I must say your approach of surrendering the thread and starting a fresh one was very innovative.
But I thought the original topic was pretty much covered with this post:
"Uncommon Descent" has become a banner for opponents of the mainstream theories about evolution. I'm not sure where the term came from, but in addition to the web site, it was also used as the title of a book editted by Dembski to which Behe contributed a chapter. So Behe's been marching under that flag for a while.
I interpret it as "Un-Common" Descent, not Un-"Common Descent", meaning that the opposition isn't to descent from a common ancestor, but rather opposing the idea that the descent was ordinary or, as IDers like to put it, "just happened".
I don't recall Dembski's position vis-a-vis descent from a common ancestor. I always thought "uncommon descent" originated with him; if so, what he thought about common descent might be illuminating.
Comment by don provan — September 18, 2009 @ 12:03 pm
September 18th, 2009 at 3:19 pm
Good comment, Don Provan.
Dembski no longer believes in universal common descent.
http://www.uncommondescent.com...
Comment by Pez — September 18, 2009 @ 3:19 pm
September 18th, 2009 at 4:41 pm
I'm not demanding anything of Behe. I'm suggesting that if he wants to avoid more confusion over his views, that he should include a disclaimer in his profile.
He doesn't have to cater to them. But unless they read his books, or go out of their way to find out more, they will most likely conclude that Behe rejects common descent. Of course, if Behe wants to appeal to the Creationist crowd, he would probably want that, anyway.
If John want to make sure people distinguish his version of uncommon descent from other versions, then John should issue a disclaimer. If John doesn't care, then he shouldn't worry about it. Does Behe care if people know that he accepts CD? I thought he did. But maybe he doesn't care. Of maybe he wants fellow scientists to know it, but doesn't care if non-scientists know it?
Sure. Now if Behe wants to make sure people know he accepts CD, he should post this at his profile, and let them know he's one of the IDists who accepts CD. If he doesn't care, then he can do what he likes.
OK, that sounds good. But unless one is devoting a lot of time to trying to tease apart the various meanings of Uncommon Descent, one will probably miss the distinction. Again, how much does Behe want to help people know what his views on CD are?
Thanks for the info, Pez. I didn't know that about Dembski. Now the need for Behe to make a distinction becomes more apparent — assuming he wants everyone to know what his views are. Of course, he may prefer buttering both sides of the bread, if you know what I mean.
Comment by Bilbo — September 18, 2009 @ 4:41 pm
September 18th, 2009 at 5:06 pm
I wrote:
Let me add, that I hope he doesn't prefer that. I have great respect for Behe, and I would hate to think that he is being duplicitous in anyway.
Comment by Bilbo — September 18, 2009 @ 5:06 pm
September 18th, 2009 at 5:08 pm
OK, that seems reasonable. I think a critic making this point would get shouted down, but if, as someone that seems friendly to ID, you think "uncommon descent" is a confusing moniker, Behe might want to consider your suggestion.
Comment by don provan — September 18, 2009 @ 5:08 pm
September 18th, 2009 at 7:48 pm
Why would that be when some writers at UD accept CD?
That's an unfounded innuendo. Behe made his views apparent in DBB and many times since. He has never contradicted them AFAIK. The "creationist crowd" most likely includes many good people at the church he attends. They may find Behe appealing simply because he has the balls to swim against the current and is not a mindless sheep. Or maybe because he is a nice guy and most people recognize there is more to personal character than one's views on ID, CD…
Comment by Bradford — September 18, 2009 @ 7:48 pm
September 19th, 2009 at 2:46 am
I always took the name of the blog "Uncommon Descent" as a pun, "descent" = "dissent," Since the main focus of the blog is dissenting opinions on Darwinism.
Comment by Jehu — September 19, 2009 @ 2:46 am
September 19th, 2009 at 9:39 am
Bilbo:
Darwin's CD hypothesis (ToL) is having a hard time in the context of theoretical justification as we can easily spot in the recent scientific literature, but I don't see anybody like Woese issuing a disclaimer about his findings going against Darwin's CD idea.
Comment by neddy — September 19, 2009 @ 9:39 am
September 19th, 2009 at 12:12 pm
Hey Bilbo,
Should all the pro-evolution posters at Antievolution.org also issue disclaimers?
Comment by Daniel Smith — September 19, 2009 @ 12:12 pm
September 19th, 2009 at 2:45 pm
You have a very good, very interesting blog, neddy. I can’t get enuf of that sciency-stuff!
What exactly is “Darwin's CD hypothesis (ToL)”?
I need to know so I know what disclaimers I should be issuing.
Comment by Rock — September 19, 2009 @ 2:45 pm
September 19th, 2009 at 5:24 pm
Rock:
Not to speak for neddy but, I believe CD is Common Descent and ToL is Tree of Life… Darwin's "hypothesis" [i.e., Theory] 'On The Origin of Species' an all that jazz.
Comment by Rob R. — September 19, 2009 @ 5:24 pm
September 20th, 2009 at 4:21 pm
Ditto, Rob R.
Comment by neddy — September 20, 2009 @ 4:21 pm
September 20th, 2009 at 4:47 pm
You're right. I apologize for insinuating it.
Does Woese still accept Darwin's CD hypothesis (ToL)?
Comment by Bilbo — September 20, 2009 @ 4:47 pm
September 21st, 2009 at 9:04 am
don provan,
The title of the book is "Uncommon Dissent".
Comment by ID guy — September 21, 2009 @ 9:04 am
September 21st, 2009 at 9:10 am
Bilbo asked, "Does Woese still accept Darwin's CD hypothesis (ToL)?"
No, and he hasn't for several years. "The time has come," Woese wrote in 2002, "for biology to go beyond the Doctrine of Common Descent." Go here for more:
http://www.pnas.org/content/99...
This paper is open access.
Comment by P A Nelson — September 21, 2009 @ 9:10 am
September 21st, 2009 at 4:33 pm
Then he certainly wouldn't need to issue a disclaimer saying that he does accept it, would he? Behe, on the other hand, if he wants to make sure people understand that his blog being at UD in no way implies that he has changed his mind about common descent, should issue a disclaimer.
Comment by Bilbo — September 21, 2009 @ 4:33 pm
September 21st, 2009 at 4:37 pm
I've never been to that website. Are you saying that there are members at an antievolution blog, who get to post their own threads, and they are pro-evolution? Would the content of their threads often make that clear?
Comment by Bilbo — September 21, 2009 @ 4:37 pm
September 21st, 2009 at 5:00 pm
Antievolution.org needs to define what it means by "evolution".
IOW they do need a disclaimer- or something that clarifies their agenda.
Comment by ID guy — September 21, 2009 @ 5:00 pm
September 21st, 2009 at 6:00 pm
I see that Paul Nelson is still repeating the long-discredited DI line that Woese rejects Darwin's hypothesis of common descent. Nice try, Paul.
Evan Ratcliff, a contributor to Wired and the New Yorker, called Woese in 2004 to ask what he thought of these half-truths by the DI. Here is what transpired.
No, Paul, Woese does not reject common descent in the sense you, guys, do. He just says that you can't trace lineages beyond the point where horizontal gene transfer played the dominant role. Here is an excerpt from Woese's review article A New Biology for a New Century in Microbiol. Mol. Biol. Rev., 68, 173 (2004), doi:10.1128/MMBR.68.2.173-186.2004.
Comment by olegt — September 21, 2009 @ 6:00 pm
September 21st, 2009 at 7:50 pm
olegt,
Paul is saying tha Woese rejects the tree of life version of common descent.
However it is obvious that Woese doesn't understand ID.
Comment by ID guy — September 21, 2009 @ 7:50 pm
September 22nd, 2009 at 9:22 am
Oleg wrote:
Here is Darwin (1859, p. 484):
Here is Woese (2002, p. 8746):
3 > 1. Woese argues that all organisms are not related by descent [do the set theory], nor do they stem from a single common ancestor (i.e., a discrete cell).
Only by equivocating on the meaning of “ancestor” can one say that Woese accepts universal common ancestry, or Darwin’s single Tree of Life. Claiming that a population of cells with independent origins is an “ancestor” is like saying that Oleg’s biological parents are the nation of Russia.
Google "Woese," "Darwin," "common descent," etc., and you'll get hits like this, a news story (not from the DI) that came out at the time of Woese's 2002 paper:
http://www.unisci.com/stories/...
Note the title of the story.
Comment by P A Nelson — September 22, 2009 @ 9:22 am
September 22nd, 2009 at 10:29 am
Notice the "probably". The data was weak for universal common ancestry.
It is clear that Darwin's ideas on Common Descent allowed for multiple origins. And after it was pointed out that the claim of universal ancestry was too strong, later editions added appropriate caveats.
And this is consistent with Woese's position.
Comment by Zachriel — September 22, 2009 @ 10:29 am
September 22nd, 2009 at 10:56 am
I was going to quote Darwin as admitting the possibility of multiple origins also, although the very idea has been widely discounted.
I believe, there is empirical reasons to believe, that the LUCA was derived from independently evolved lineages via symbiosis. (Which themselves may have been so derived.) So I was asking about "disclaimers" I should be issuing.
I suspect that disclaimers should be issued by persons who insist that everything be simple, unnuanced, black-and-white, or fit neatly into the popsci formulae they are so used to dealing with.
Comment by Rock — September 22, 2009 @ 10:56 am
September 22nd, 2009 at 11:44 am
Recall that, for Darwin, the origin of the first cell(s) was qualitatively different, as an historical event, from what he called "ordinary generation" (descent with modification). In the 2nd ed. of the Origin, he adds "breathed by the Creator" to the passage I cited above, and although he later grumbled privately about making the change, he never took it out of the subsequent four editions of the Origin.
If one is going to posit divine creation for one primordial cell, there's not a great difference inferentially in positing multiple such origins. Whatever God can do once, he can do more than once. In any case, the possibility of multiple aboriginal cells does not survive into textbook neo-Darwinism, in which universal monophyly (a single Tree of Life, rooted in a common ancestor [cell]) is orthodoxy. In that sense, Woese's ideas indeed challenge "Darwin," as the latter's theory came into the 20th century.
However, allowing for multiple origins where the originating process requires natural abiogenesis in multiple independent settings (Rock's scenario, Woese's ideas) is a very different kettle of fish. Ordinary criteria of homology — i.e., the very markers of material descent, in conventional evolutionary reasoning — are cast into doubt. Whatever nature can do once, she can do more than once.
For Richard Dawkins, however, the existence of a universal genetic code (for instance) indicates the common ancestry, at a historical singularity, of the frozen accident of a single cell, for all organisms on Earth. This is of course the standard neo-Darwinian view.
Not so for Woese and his co-workers. The universality of the code is not to be explained by invoking a frozen accident or historical singularity of a single cell:
Cited from this paper:
http://arxiv.org/abs/q-bio/070...
See it and subsequent publications from the same group.
But if the code could have arisen multiple times independently…well, think about it. Follow the implications. The consequences for conventional evolutionary reasoning are not minor.
Comment by P A Nelson — September 22, 2009 @ 11:44 am
September 22nd, 2009 at 12:31 pm
Technically, all of you are off topic, but a discussion of common descent is close enough to the topic, that I'll allow it to proceed.
However, Dr. Nelson, may I ask what your points on common descent have to do with Behe's claims from his book, The Edge of Evolution, and with my argument that if he wants to make his claim regarding common descent clear (while his blog flies under the banner "Uncommon Descent, " where people such as yourself frequently argue against common descent, though most of them fail to show the same degree of civility that you do), he should have a disclaimer in his profile?
Comment by Bilbo — September 22, 2009 @ 12:31 pm
September 22nd, 2009 at 1:09 pm
Hi Bilbo,
Sorry for going off topic, but you did ask about Woese, which drew me in to comment. To your questions:
The blog banner "Uncommon Descent" is a double entendre, where "uncommon" can mean either "universal common ancestry is false" [which Behe does not accept] or “common ancestry was intelligently designed, hence ‘uncommon’” [for which he argues vigorously]. I know this because “Uncommon Descent” was the candidate title for a book on ID in biology (incl. the ideas of Behe), which Steve Meyer, Bill Dembski and I were going to write in the mid-1990s, until our collaboration fell apart. Bill later took the unused title for the group blog he started.
I don’t see why Behe needs to have a disclaimer. His support for common descent is well-known, and fully compatible with ID (as Mike understands it). Here’s a blog post from a few years ago, where I spell this out:
http://www.idthefuture.com/200...
It’s true that theories of undirected evolution via universal common ancestry come in for a lot of criticism at UD, but then one can find lively debate within the evolutionary biology community over the proposals of Carl Woese, W. Ford Doolittle, Eugene Koonin, and so on (skeptics of the single Tree of Life picture).
Disclaimers are too much trouble. Look at the data, draw hypotheses, critique them. Rinse and repeat.
Multiple competing hypotheses may be disorienting at times, but that’s healthy.
Comment by P A Nelson — September 22, 2009 @ 1:09 pm
September 22nd, 2009 at 11:09 pm
There seem to be two Paul Nelsons here. One writes:
Another Paul Nelson does the exact opposite. He seems only interested in sound bytes:
Note the title of the story? Of a pop science article? Is that your way of looking at data, Paul?
Well, let's look at what Woese actually said:
Let me compress that for you, Paul. Prior to a critical point, primitive life forms exchanged genes via horizontal gene transfer. Darwin's picture of common descent did not apply. When organisms became multicellular, Darwinian vertical development took over. It's pretty simple actually. I am sure you understand that.
I can appreciate Woese's point made in response to this kind of quote mining:
The parallel is quite striking. Classical physics, too, holds only down to a certain scale. It works for macroscopic objects but fails when we apply it to atoms and subatomic particles. On the microscale we have to switch to quantum physics. That, however, does not invalidate Newtonian mechanics. It remains valid science even though its range of applicability is limited.
Likewise, Darwin's theory may not be applicable to the earliest life forms because their method of procreation wasn't descent with modification solely, they exchanged genes by other means. But it still applies above the Darwinian threshold.
To make it simple, Woese is not questioning common ancestry of man and chimpanze, or man and mouse, or man and birds, or man and fish, or man and insects. He is only saying that genealogical lines become fuzzy and eventually indiscernible when you get down to the level of primitive, single-cell organisms.
That's the story. The headline is bullshit.
Comment by olegt — September 22, 2009 @ 11:09 pm
September 23rd, 2009 at 12:03 am
olegt,
you thought that the alcohol 'cousin' of their corresponding hydrocarbon was just as stable.
So I'd be concerned about anything you say.
Comment by GringoRoyale — September 23, 2009 @ 12:03 am
September 23rd, 2009 at 10:00 am
Oleg wrote:
I noted the headline to refute your claim that only the DI cited Woese, misleadingly, as challenging Darwinian reasoning. The author of the story, Jim Barlow, was not a DI staffer, nor (to my knowledge) does he have any ID sympathies. Rather, Barlow correctly understood that denying the universal common ancestry of life on Earth (from a single cell) does challenge textbook neo-Darwinism, where the Tree of Life terminates in a last universal common ancestor (an actual cell). 3 > 1; this is not a minor point.
Of course Woese does not question the common ancestry of groups higher in the Tree, such as the animals. But by severing the link between molecular homology and common ancestry — e.g., by arguing that the “universal” genetic code did not evolve from a single common ancestor, via a frozen accident, but rather had multiple independent origins — Woese and his reasearch group radically undermine fundamental lines of evolutionary reasoning. (The ribosome and its associated machinery, on this view, also evolve polyphyletically. Mull that for a bit.)
The corrosive effect on the structure of entire Tree is impossible to stop. For example: the characters used to unite the groups you list — all bilaterians — are molecular. But if molecular characters can evolve independently, there is no reason to postulate common ancestry to explain their distribution. The Tree of Life then comes apart from the bottom, once one has severed the inferential link between homology and common ancestry.
As I wrote above, the theoretical consequences of Woese’s viewpoint are far-reaching.
Thus, the parallel between Newton and Einstein, and Darwin and Woese, while suggestive, is inaccurate.
Comment by P A Nelson — September 23, 2009 @ 10:00 am
September 23rd, 2009 at 11:07 am
First, disclaimers aren't too much trouble. Behe already has a profile right next to his blog, that anybody can read. Including a simple statement, such as, "I accept the theory of common descent," wouldn't be too much trouble.
Second, as you point out, "Uncommon Descent" is a double entendre, having two meanings. Someone unfamiliar with UD, and unfamiliar with Behe' views might easily be confused as to which meaning is intended.
But I don't mind people being confused over what Behe believes. It's Behe who has expressed displeasure when people are confused over what he believes about common descent. If he wants to avoid future displeasure, a simple disclaimer might help.
But I must admit that I suspect that certain people at UD, such as Dembski, O'Leary, Hunter, or even you, might experience some displeasure if Behe decided to include a disclaimer. I suspect you want to cover up Behe's views on common descent from the conservative Christian audience, to which you are trying to make yourselves most appealing. A disclaimer would be an embarrassment to your blog and to your movement. I don't think it's an accident that Stephen Meyer excluded all mention of Behe's book, The Edge of Evolution, even from his bibilography.
Comment by Bilbo — September 23, 2009 @ 11:07 am
September 23rd, 2009 at 11:52 am
Clearly, Darwin didn't "posit" in the sense of proposing a scientific hypothesis, but was merely waxing poetic in the final words of his book.
Your use of the term "independent" does not correctly characterize Woese's position. In fact, he posits common descent of all life from a tightly knit cellular community where the notion of a well-defined organism may not apply. These interactions do not denote independence, but strong dependence.
Comment by Zachriel — September 23, 2009 @ 11:52 am
September 23rd, 2009 at 11:53 am
Bilbo wrote:
That's crazy talk. I regularly tell church audiences that Mike Behe accepts common descent, as do Dembski and Meyer, when they speak in such venues. The audience, as far as I can judge, doesn't much care, given that (when I introduce ID as an idea) I've already explained ID's internal diversity, on questions such as common descent, theology, and so on. Mike's views are pretty well-known, even among lay audiences.
It's good for ID as a theory-in-gestation to have differences of opinion about common descent. Knowledge in science arises in part from the back-and-forth of competing interpretations of data.
In any case, it wouldn't bother me in the least if Mike added a disclaimer about common descent to his UD profile, although such statements seem oddly like creedal forms (e.g., I believe in God the Father Almighty) and limiting on one's freedom as a scientist.
You write here under a pseudonym, Bilbo, so please don't be offended by this question (but I have no other way of finding out, given that I don't know your identity) — do you know Behe, Dembski, Meyer, or any of the other better-known ID / DI guys personally?
I ask, because then you'd understand that the reason Meyer doesn't cite Edge of Evolution in his Signature in the Cell has nothing to do with Behe and common descent, or being embarrassed by Mike's views on all that.
Comment by P A Nelson — September 23, 2009 @ 11:53 am
September 23rd, 2009 at 12:17 pm
That may be the idea but the descent origins are murky when independent lines are posited and this raises more questions than it answers. Independent, multiple origin lines would infer an abiogenic process that is robust with respect to its capacity to generate life but narrow in terms of the scope of its end products. Or it could infer independent design templates.
Comment by Bradford — September 23, 2009 @ 12:17 pm
September 23rd, 2009 at 12:20 pm
Zachriel wrote:
According to Woese and co-workers, when the three primary domains evolved from a common pre-cellular milieu, they did so independently, via what they call "a brief series of major evolutionary saltations" (2008, 13953). Thus, ribosomes and their associated machinery exhibit fundamental molecular differences, "RNA signatures," between (for instance) Bacteria and Archaea:
This means that when arguably the major system of terrestrial life (i.e., translation) booted up, it did so polyphyletically — i.e., as spatiotemporally separate events. The reason Woese et al. do not link the cellular architectures of the domains to a common cellular ancestor is they do not believe it is biologically possible to do so.
See E. Roberts et al., "Molecular signatures of ribosomal evolution," PNAS 105 (2008):13953-58. If you don't have access to this paper, I'd be happy to send it to you (don't know — it may be open access at the PNAS site now, can't check at the moment).
Comment by P A Nelson — September 23, 2009 @ 12:20 pm
September 23rd, 2009 at 12:29 pm
Paul Nelson in 2004:
Dr Nelson, have you your theory, yet?
Comment by Alan Fox — September 23, 2009 @ 12:29 pm
September 23rd, 2009 at 12:44 pm
Alan Fox to Paul Nelson:
Thomas Huxley, who coined the term abiogenesis to denote the idea that life evolved from non-living matter, gave a lecture at Edinburgh in 1868 called "On the Physical Basis of Life." In it he posited the term protoplasm as a fundamental substance to life. In the ensuing years can you cite a well supported theory for life from non-life?
Comment by Bradford — September 23, 2009 @ 12:44 pm
September 23rd, 2009 at 1:24 pm
According Woese, they only later became independent deriving from a highly interactive common ancestral state, not "natural abiogenesis in multiple independent settings".
This is precisely contrary to Woese's hypothesis which entails a "communal evolutionary dynamic" — the very opposite of independence.
Comment by Zachriel — September 23, 2009 @ 1:24 pm
September 23rd, 2009 at 2:52 pm
Molecular Signatures Of Ribosomal Evolution
Comment by chunkdz — September 23, 2009 @ 2:52 pm
September 23rd, 2009 at 4:12 pm
Yes, I can believe that you are forthright about Behe's views. I find it more difficult to believe that Dembski and Meyer are, and very difficult to believe that Behe's views are pretty well-known among lay audiences.
Agreed.
I'm glad it wouldn't bother you. Again, I suggest a disclaimer if Behe wants to avoid confusion over his views on common descent. He's always free to change his mind on the issue.
No, I don't know any of them personally.
Then what was the reason?
Comment by Bilbo — September 23, 2009 @ 4:12 pm
September 23rd, 2009 at 4:42 pm
Let me add that even if Dembski and Meyer are forthright about Behe's views, I doubt people like O'Leary or Hunter are. And I doubt O'Leary or Hunter would be happy with a disclaimer by Behe.
Comment by Bilbo — September 23, 2009 @ 4:42 pm
September 23rd, 2009 at 5:12 pm
Bilbo asked, re the absence of citations to Behe's Edge of Evolution in Meyer's Signature in the Cell:
Relevance. Mike was looking at the efficacy of mutation and selection in existing organisms; Steve was asking about the origin of biological information itself. (Okay — there's some overlap, but it's pretty slender, in light of Steve's main focus in his book.)
Bilbo — I'd suggest contacting O'Leary and Hunter, privately. I don't think either especially worries about Behe's support of common ancestry. The folks who hang out at UD, and post there, are a heterogeneous lot, united mostly by their feisty personalities, not by any shared doctrine.
Chunkdz, thanks so much for linking to the Molecular Signatures paper, which is easily one of the most interesting papers I've read in a long time.
Comment by P A Nelson — September 23, 2009 @ 5:12 pm
September 23rd, 2009 at 5:22 pm
Sorry, not buying it. Meyer devotes a great deal of the latter part of his book to the question of evolution in existing organisms. The Edge of Evolution would have been extremely pertinent.
Comment by Bilbo — September 23, 2009 @ 5:22 pm
September 23rd, 2009 at 9:09 pm
P A Nelson wrote:
Headlines aren't usually written by the authors themselves, they are the responsibility of a copy editor. You are thus quoting someone who is twice removed from the scientist. So by design a headline can't be an accurate depiction of the actual research findings. Don't use them to back up your argument.
Of course this is a major point, this is why Woese is famous. If you stopped there I would have no problem with you.
That's where you go off the rails, Paul. Woese does not make such a claim. We can very well trace common ancestry by comparing genomes anywhere in the tree of life except for its tangled roots. And even in the tangled genetic web of prokaryotes, vertical trends (common descent) can be untangled from horizontal gene transfer. [See this paper, for instance: P. Puigbò, Y. I. Wolf, and E. V. Koonin, Search for a 'Tree of Life' in the thicket of the phylogenetic forest, J. Biol. 8, 59 (2009). doi:10.1186/jbiol159.]
You're exaggerating, Paul. Biologists figured out that the tree of life is not a tree at its root and you are trying to suggest that the entire tree has been taken down. Well, no, it hasn't. Woese was specifically asked to comment on that, he laughed at the suggestion, and anyone can see why: because the argument is about the topology of the root, the tree itself is not controversial.
Again, that doesn't compute. Woese's work indeed has far-reaching consequences, but you misrepresent them (surprise, surprise). Woese called the DI's bluff and yes, you do look exactly like crackpots who claim that Einstein invalidated Newtonian physics. Such misrepresentations won't win you any friends among scientists. That's hardly a revelation for you since scientists aren't the intended audience for ID.
Comment by olegt — September 23, 2009 @ 9:09 pm
September 24th, 2009 at 9:08 am
Need to correct the Woese and Goldenfeld link, given above. This is the correct citation:
http://www.pnas.org/content/10...
Sorry for the incorrect link.
Oleg, we're just going round and round. Of course, above the level of the domains, Woese's thinking is (more or less) conventional evolution — the vertical descent of familiar monophyletic groups (the eukaryotes, the Metazoa, etc). But the theoretical consequences of breaking the inferential link between molecular homology and common ancestry are not conventional, and extend well beyond the domains themselves — my "corrosive" point, above. This is the case whether Woese himself sees it or not.
Comment by P A Nelson — September 24, 2009 @ 9:08 am
September 24th, 2009 at 11:17 am
olegt:
How can they differentiate between common ancestry, common design and convergnce?
Comment by ID guy — September 24, 2009 @ 11:17 am
September 24th, 2009 at 5:21 pm
Well, since everybody else is off-topic, I might as well go off-topic also. Behe's test was finding similar mistakes in the genome. Thus finding a pseudogene in both chimps and humans that has exactly the same mutations in the same places was compelling evidence for him of common ancestry. Why design the same exact mistakes twice? How likely to converge on the same exact mistakes twice? That the mistakes happened once and were passed on to common descendants seems much more likely.
Comment by Bilbo — September 24, 2009 @ 5:21 pm
September 24th, 2009 at 6:23 pm
P A Nelson wrote:
Au contraire, Paul, we are finally making progress.
You've admitted that your claim (about the broken link between molecular homology and common ancestry) is not supported by Woese. I can't find any support for that in Koonin's writings, either; quite the opposite, his article in the Journal of Biology that I linked to seems to suggest otherwise.
So tell us which professional biologists support this claim.
Comment by olegt — September 24, 2009 @ 6:23 pm
September 25th, 2009 at 8:56 am
Bilbo,
Seeing there are only four possible nucleotides to choose from convergence can find the same target very easily.
Don't you think that it stretches credibility that a mistake would remain unaltered over many, many generations?
Or that it would become fixed such that it could be used as a marker?
In "The Design of Life" they presented a case in which humans and guinea pigs share the same mistake. (page 133) the GULO pseudogene.
Also we know there are mutational "hot spots". That would increase the chances of convergence.
Comment by ID guy — September 25, 2009 @ 8:56 am
September 25th, 2009 at 9:03 am
olegt:
If it isn't a tree at its root, and the tree grows from their roots, then why would we expect a tree at all?
Was HGT predicted to stop at some specified evolutionary stage?
Was HGT predicted at all?
And where do marine invertebrates fit on this alleged tree?
Comment by ID guy — September 25, 2009 @ 9:03 am
September 25th, 2009 at 9:55 am
Oleg wrote:
Start with Woese himself. Here’s your homework assignment:
1. Read pages 408-410 of Dawkins’s new book, The Greatest Show on Earth (or, if you don’t have that book, any evolutionary biology textbook, where the evidence for the monophyly of life on Earth is presented). Summarize Dawkins’s explanation for the universality of the genetic code, and what it indicates about common ancestry. Pay particular attention to whether the Tree of Life terminates in a single organism — an actual cell — or something else.
2. Then, read the paper by Woese, Vestigian, and Goldenfeld, linked above and here:
http://www.pnas.org/content/10...
With paper and pencil, try to draw a cladogram representing their explanation for the origin of the code. Locate the node at which the code evolves (if possible). Ask yourself if that topology is congruent with Dawkins’s picture, or any textbook treatment of the same question.
3. Compare standard evolutionary biology textbook treatments of the origin of protein fold homology to Koonin’s 2007 argument that modern protein folds have “independent and polyphyletic origins”:
Koonin’s paper is open access:
http://www.biology-direct.com/...
4. Read this 2000 paper by WF Doolittle. Pay careful attention to the following section:
5. Ask yourself, in the light of all this, if — as Doolittle argues — “homology” is now a word with “no precise meaning.”
Get back to me when you’ve done that.
Comment by P A Nelson — September 25, 2009 @ 9:55 am
September 25th, 2009 at 10:31 am
There is evidence that 10 genes of the MHC remained clustered for 700 million years and can be found in modern species, not a mistake but definitely just as amazing.
Comment by Guts — September 25, 2009 @ 10:31 am
September 25th, 2009 at 11:17 am
P A Nelson wrote:
I'm sorry, Paul, but I don't think you're qualified to teach biology.
As I have said several times, the controversy about the tree of life applies to the level of single-cell organisms. You are trying to stretch it to include metazoa. I asked you to provide support for that by quoting professional biologists. So far you have failed: all of the articles you have cited deal with microbial genomes.
To provide further support for my position, I'll quote a paper by W. F. Doolittle and E. Bapteste, Pattern pluralism and the Tree of Life hypothesis, PNAS 104, 2043 (2007); doi:0.1073/pnas.0610699104. In that article Doolittle quotes Woese. That quote should make it clear where both of them stand on the issue. (The emphasis is mine.)
Woese's words can't be any clearer. Lateral (horizontal) gene transfer is an important factor in the evolution of single-cell organisms. It is precisely the HGT that spoils the tree-like phylogenies, hence the controversy. As any of these authors will agree, the HGT's role is insignificant in multicellular organisms. Above that Darwinian threshold, molecular homology works. You seem to argue against that, but so far you have not provided any support for your position.
Comment by olegt — September 25, 2009 @ 11:17 am
September 25th, 2009 at 12:12 pm
There is a broader point to be made than sheer controversy. Nelson had previously written:
The controversy on a unicellular level is traced to misaligning molecular signatures to possible causal origins. Interpretation of eukaryotic molecular signatures is as accurate as our ability to accurately align them to causal sources. The corrosive effect alluded to can refer to this tenuous linkage. Transposon events (or other yet unidentified phenomenon) may be less randomly generated than believed. If they were generated as part of undiscovered mechanisms- even faulty ones- then resulting molecular signatures among distinct species could be misinterpreted.
Comment by Bradford — September 25, 2009 @ 12:12 pm
September 25th, 2009 at 12:12 pm
Olegt:
That still remains to be seen, it may be the rule rather than the exception for DNA-based transposons.
Comment by Guts — September 25, 2009 @ 12:12 pm
September 25th, 2009 at 12:27 pm
Oleg wrote:
So what changes at the "Darwinian threshold" to make molecular homology a reliable indicator of common ancestry [organismal descent] above that point, but not below?
You focus on lateral gene transfer, but that's not where the problem lies. Still need to do your homework:
1. Does molecular homology indicate descent from a common ancestral organism (an actual cell) or not?
2. How many times did the molecular characters that define Woese's three domains [Bacteria, Archaea, Eukarya] evolve?
Correction to your post: all three papers I cited bear on the entire Tree of Life, not simply microbial groups.
Comment by P A Nelson — September 25, 2009 @ 12:27 pm
September 25th, 2009 at 3:23 pm
Evolution doesn't have a direction.
Therefore any "tree of life" would be due to what Mike Shermer calls "patternicity".
As for HGT/ LGT and metazoans- anyone see "The Fly"?
Comment by ID guy — September 25, 2009 @ 3:23 pm
September 25th, 2009 at 3:33 pm
On shared mistakes- I remember talk of a common mechanism- that is similar genes behave similarly.
For example a similar/ same envornmental cues cause similar/ same mutations to occur.
Comment by ID guy — September 25, 2009 @ 3:33 pm
September 25th, 2009 at 9:00 pm
P A Nelson wrote:
I've said that multiple times, Paul: the role of HGT in evolution diminishes and vertical evolution takes over. I did not make this up, read Woese.
Yes, it is HGT that causes the departure from the vertical evolution by common descent to the communal descent. Vetsigian, Woese, and Goldenfeld, whom you cited above, make precisely that point. Here is an excerpt (with my emphasis):
One more passage from the same article explaining what causes the transition:
But back to your comment:
These questions are irrelevant to the point you were trying to make, but no, vertical evolution cannot be traced all the way to a single ancestor cell: the process fails at the Darwinian threshold. Yet this does not invalidate the applicability of molecular homology to metazoa, the group located above the Darwinian threshold. That was the point you were trying to make but have been unable to back up.
Patently untrue. For example, here are Vetsigian et al. describing the scope of their paper:
The paper is narrowly focused on the first phase, where the actors are microbes and the evolution is dominated by the HGT.
We can play a few more rounds of this game but I don't expect that the pattern will change: Paul will keep quoting scientific literature out of context and I will keep correcting him. Anyone wanna bet?
Comment by olegt — September 25, 2009 @ 9:00 pm
September 26th, 2009 at 1:34 pm
It's quite revealing how much this discussion is dominated, not by evidence or scientific inquiry, but by an appeal to the positions and beliefs of the individuals cited.
Whenever a scientist outlines weaknesses in the traditional mechanisms of evolution and his words are cited by a creationist or IDist, the materialist crowd immediately counters with "Yes, but he still believes the theory of evolution is correct", as if that somehow negates the expressed concerns.
Whenever an ID scientist expresses agreement with a tenet of the ToE, and is cited by a materialist, the creationist/ID crowd counters with "Yes, but he still believes materialist mechanisms are insufficient in accounting for life".
The evidence be damned – it's the interpretation that matters!
The truth of the matter is this: most people see things according to their own biases. It's true of Supreme Court Justices, it's true of scientists and it's certainly true of internet posters. The evidence – in every case – is the same, whether it's a case before the Supreme Court, a science experiment, or an internet forum. The interpretation of that evidence is predictable – based on the biases of the parties involved. Going into a Supreme Court case, we often know that the decision will be 5-4, that the liberals will be on one side and the conservatives on the other and that the deciding vote will be the moderate (and this by men and women ordered by law and sworn to be impartial). Going into a lab experiment, we know that an atheist will not see evidence of the hand of God in biological life while the creationist will see evidence in all of its aspects. And we know beforehand that don provan, Alan Fox, olegt, Zachriel, etc. will oppose the views and interpretations of Bradford, Guts, JAD, and anyone else who leaves a door open for God in science.
It's all very predictable people!
Comment by Daniel Smith — September 26, 2009 @ 1:34 pm
September 26th, 2009 at 2:47 pm
Your observations are acurate and very germane, but they lead me to a different conclusion: although everyone can see weakness in the traditional mechanisms of evolution, in the end those weaknesses don't undermine the fundamental support for those mechanisms. Pointing out things biologists can't explain or having other reasons to conclude "intelligent design" does nothing to overturn the massive amounts of evidence that show mainstream theory is essentially correct as far as it goes. Some ID supporters seem to think that all it takes is one unexplainable feature, such as flagella, to overturn the foundation of biology.
(I mention flagella because it's an example of many seem to think of as such a linchpin, not because I think Behe himself is one of these people. I could be wrong, but from what I know about Behe, while he sees hiumself challenging mainstream theory, I don't think he thinks he is overturning mainstream theory as a whole. Typically he seems to acknowledge that much of the mainstream is undeniable but incomplete.)
Unlike you, I do not think that people are incapable of rising above their biases. But, on the other hand, I do agree that we should not pretend that everyone or anyone will rise above them in any specific situation.
But that's exactly what science is for. In science, you must clearly report your findings and conclusions for scrutiny. Others can confirm your evidence and criticize you logic. Science is designed to overcome, as best we humans can, the undeniable impact of bias. This extends to all levels, from standards for individual behavior such as publication to institutional checks and balances such as "The Academy".
In other words, our civilization is way ahead of you in recognizing the problem of bias. If you think bias in science is a problem, you'll need to do better than just observe it's a potential problem and then offer as your only proof that is actually is a problem the fact that it rejects your favorite idea.
I agree there's something disturbing about this trend of 5-4 decisions in the Supreme Court, but there are, at least, some mitigating causes. For one thing, the narrow decisions are reported more often since 9-0 decisions aren't typically as newsworthy. But I think that's a different topic.
Nope, sorry. I'm open to any interpretation those noted scientists Bradford, Guts, and JAD want to make. I simply insist that their observations are accurate and that their conclusion are logical. Well, none of them make any observations,of course, but others still inform them of observations made by others that they are overlooking. And Alan, olegt, Zachriel, aiguy, I, and others regularly explain why their conclusions are not logical, so don't pretend we simply reject them because of our own biases. More often than not, we reveal their biases. Perhaps your biases make it difficult to see that. Let's start with your bias that anyone that opposes ID is opposing God.
Comment by don provan — September 26, 2009 @ 2:47 pm
September 26th, 2009 at 2:58 pm
I disagree that they have successfully done this, at least when it comes to my arguments (i have not followed each and every debate that has taken place here at TT), but that is something to be hashed out in respective threads.
Comment by Guts — September 26, 2009 @ 2:58 pm
September 26th, 2009 at 3:25 pm
dp:
Don is correct to infer that the absence of explanations do not confer default status to mainstream or competing theories.
Most conclusions debated are not about hard data. They are about things like consciousness is the hard problem and we're working on origin of life theories and we're gaining ever increasing knowledge of cosmology. In short they are focused on areas where explanations are inconclusive and must therefore entail some personal opinions thrown into the mix. So while aiguy is quite knowledgeable about AI his assertions about consciousness are as speculative as anyone else's. The same applies to other mentioned names and their views on the origin of life and the universe. What is illogical is the concession that explanations are lacking juxtaposed to claims that opinions being asserted by the gang of five are authoratative.
Comment by Bradford — September 26, 2009 @ 3:25 pm
September 26th, 2009 at 3:31 pm
The point is that we don't just reject the application of God, we try to explain the reasons for our objections so that any bias on our point can be identified. I agree that whether they are successful arguments is another matter. I, of course, think they generally are.
The reason counter-arguments such as Daniel's don't sway me is that they typically provide little or no counter-reasoning, often depending on nothing more than rejecting the arguments by claiming bias, just as we see in Daniel's post to which I was reponding. In order to argue on nothing but the basis of bias, one must ignore the possibility that their own bias is the problem.
Of course, in the broader world, God is closed out of science entirely for very good practical reasons. But there's not much point in mentioning that global decision here at TT, and I don't recall critics bringing it up very often. TT is largely focused on rehashing those practical reasons which the rest of science already accepts. And I'm fine with that: the conclusion against God in science is a very big one, so it's very reasonable for people interested in it to rehash the arguments endlessly in case there really is a problem with the conclusion. As hard as it probably is for you to imagine, one reason I participate at TT is that some actual argument for God in science might be brought up. If it is, I want to be here to see it.
Comment by don provan — September 26, 2009 @ 3:31 pm
September 26th, 2009 at 3:51 pm
Don, the only thing you are qualified to coach is tard-like behavior.
Comment by Bradford — September 26, 2009 @ 3:51 pm
September 26th, 2009 at 5:43 pm
dp:
Define "God" and give me one practical reason.
dp:
How do you suspect an argument for "God" could be brought up for consideration if it is previously "closed out" for "practical reasons?" Wouldn't you have to reject those "practical reasons" first to even allow an argument for "God in science?" Or, is that actually what you are asking for — an argument against those "practical reasons" in the first place?
Furthermore, if one of those "practical reasons" happens to be that "God" can be conjured to explain anything, I'm sure you would agree that infinite universes/multiverses should also be closed out of science for the same practical reason.
Just checking to see if you are at least consistent.
But let's move our focus onto ID now. Has science also "closed out" the study of intelligent systems, lawful systems, randomness/chance and their respective effects for "practical reasons?"
P.S. remember that ID Theory is only about the discovery of specific patterns in relation to intelligence, so there is no basis to any claim that "intelligence can be used to explain anything." ID Theory itself states that is not so. There are patterns that one should *not* use intelligence to explain since in those cases, intelligence is not a necessary condition and other causes are sufficient.
Comment by CJYman — September 26, 2009 @ 5:43 pm
September 27th, 2009 at 2:09 am
As fascinating as the discussion between Paul Nelson and olegt has been, it misses the point of this thread– that Michael Behe believes is common descent, but is skeptical of natural selection.
Indeed, he points out that even Ernst Mayr argued that that common descent and natural selection should be seen as separate theories. If they are separate then one does not prove the other. In other words, if we accept common descent as true (as Behe does) it does not follow that natural selection is also true.
As Bilbo pointed out on another thread, in EoE Behe wrote:
"The bottom line is this. Common descent is true; yet the explanation of common descent — even the common descent of humans and chimps — although fascinating, is in a profound sense trivial. It says merely that commonalities were there from the start, present in a common ancestor. It does not even begin to explain where those commonalities came from, or how humans subsequently acquired remarkable differences. Something that is nonrandom must account for the common descent of life." (p 72)
I believe there are even some non-ID biologists who accept common descent but are skeptical of the robustness of natural selection to effect macro-evolutionary change. However, at the moment I can’t think of any. But, maybe Paul is aware of some.
Comment by JOHN_A_DESIGNER — September 27, 2009 @ 2:09 am
September 27th, 2009 at 3:04 am
JAD,
Fairly certain Lynn Margulis fits into that camp. If I recall right, she asserts NS certainly exists, but it's not a source of "novelty". How that fits in with typical macro-evolutionary change claims, I'm not sure, but she's the first one to come to mind.
Comment by nullasalus — September 27, 2009 @ 3:04 am
September 27th, 2009 at 9:29 am
That is so thoroughly wrong, it is hard to know where to begin. That humans and other organisms share a common ancestor is one of the most profound findings of biology—unifying and explaining a vast array of data.
Natural selection is not posited to be the source of novelty.
Margulis is a self-proclaimed Darwinist, that is, she accepts that natural selection is essential to adaptation. However, she disputes Neodarwinism, rejecting its naïve view of mutation as sufficient to explain the data. She posits the importance of horizontal mechanisms, and stresses that selection may act to enhance cooperation rather than competition.
Comment by Zachriel — September 27, 2009 @ 9:29 am
September 27th, 2009 at 9:36 am
Hi Oleg,
I was away at my younger daughter's volleyball tournament Fri and Sat.
Thanks for your latest, to which I'll reply later today. I was going to say, it looks like no one else is reading this thread, so you and I would have a seminar of two, but then several other people contributed (which is encouraging).
John A Designer wrote:
Many biologists fit this description. Try looking, for instance, at the work of Michael Lynch (Indiana Univ). I'll link to some of his stuff later today.
Comment by P A Nelson — September 27, 2009 @ 9:36 am
September 27th, 2009 at 10:07 am
That would be most biologists, including Darwin. Evolution requires variation as well as selection. Perhaps you mean adaptation. The vast majority of modern biologists understand that there are non-adaptionist mechanisms at play—including Michael Lynch.
Lynch, The frailty of adaptive hypotheses for the origins of organismal complexity, PNAS 2007. Here's a few exerpts.
Notice that Lynch is stating that evolution is due to these non-telic mechanisms and that this is well supported at the empirical level. In addition, he talks about the latter three mechanisms being stochastic.
Comment by Zachriel — September 27, 2009 @ 10:07 am
September 27th, 2009 at 1:33 pm
Actually, one of the things he points out is that there is evidence for mutational pressure, for example, toward AT and away from GC. But if you have GC at one site in a genome and AT in another, recombination will produce higher GC in regions with high recombination rates, and thus better translation of mRNA into protein.
There is also a hypothesized "force" (mutational pressure) that increases the number of tandem DNA sequence repeats (when other things are considered), which can later be co-opted for the various functions of the cell.
Another thing he talks about, is when you have a gene that has more than one function, and it gets duplicated. Inactivating mutations would most likely only effect one of the functions, so now you have more functional genes to play with.
There's a whole lot more of course but in general, variation isn't really random because it is tinkering with what already exists. What this suggests is that evolution may in fact be rather telic.
Comment by Guts — September 27, 2009 @ 1:33 pm
September 27th, 2009 at 1:56 pm
Variation is only random with respect to fitness and is highly constrained by evolutionary history, and ofttimes not subject to selection at all.
Funny how that completely eludes Lynch who clearly states otherwise. In any case, the idea that variation is constrained by history is intrinsic to evolution, variations being modifications of what already exists in the line.
Comment by Zachriel — September 27, 2009 @ 1:56 pm
September 27th, 2009 at 1:57 pm
Guts:
Yes. Start with a replicating system having built-in adaptive mechanisms and guess what happens next? Of course anti-telicians posit that non-telic forces led to a cellular replicator having robust adaptive properties. They are entitled to that belief. They can make that assumption without any knowledge required of the workings of the hypothesized precellular process. By doing so they become in effect de facto front loaders- conceptually front loading required adaptive machanisms into an ancient cellular replicator and then arguing for a non-telic evolutionary process by begging the FL causal issue.
Comment by Bradford — September 27, 2009 @ 1:57 pm
September 27th, 2009 at 2:10 pm
I'm not rejecting any arguments by claiming bias. I'm merely pointing out that all of our arguments are predictable based on our own biases. I knew you'd oppose me on this because you are biased against my position (even though you think yourself unbiased).
Their conclusions are not logical to you. That also is a predictable response based on your readily apparent, yet unacknowledged, bias.
Comment by Daniel Smith — September 27, 2009 @ 2:10 pm
September 27th, 2009 at 2:13 pm
This is not at all surprising. The telic nature would be evidenced by a front loading process which Lynch presumes to be non-telic, Guts and I presume it to be telic and empirical data is not directing either way.
Comment by Bradford — September 27, 2009 @ 2:13 pm
September 27th, 2009 at 2:27 pm
I thought the following passage from Lynch’s paper was interesting.
However he doesn’t really go on to explain how multicelluarity arose. But of course that undoubtedly would require a paper (if not book) of it own. Does he know? Does anybody?
Earlier he wrote:
So Lynch is willing to concede that NS + RM alone are are insufficient to explain evolution. But, then he seems to go on and argue that the other two “fundamental forces: recombination and genetic drift (along with NS + RM) are sufficient to explain all evolutionary change. How can you make such a claim, while there are major unanswered questions like the emergence of multi-celluarity.
He may be correct, but how would he know that?
Why is it necessary to posit an apriori assumption? Why not simply admit, that we don’t know?
Comment by JOHN_A_DESIGNER — September 27, 2009 @ 2:27 pm
September 27th, 2009 at 2:27 pm
This whole discussion boils down to competing lists of "who's for us and who's against us?" Lists based solely on opinions.
Comment by Daniel Smith — September 27, 2009 @ 2:27 pm
September 27th, 2009 at 2:52 pm
Daniel, the thread topic concerns views on Common Descent.
There is no reasonable doubt about the basic outlines of Common Descent, that life evolved and diversified from a common ancestral population, and that this leads to non-trivial predictions about everything from molecular biology to the content of geological strata. If you want to discuss the specifics, we could start with the nested hierarchy.
Comment by Zachriel — September 27, 2009 @ 2:52 pm
September 27th, 2009 at 2:55 pm
As you know Don, in the What is an Intelligent Cause? thread, I proposed that we: A) presume biological life to be designed, B) presume biological life to be a novel creation, C) examine biological life as if it were an artifact found on another planet, and D) attempt to define a designer based on this empirical evidence alone.
While this is not an argument for God in science, it is an argument that could empirically lead to the conclusion that only someone like God could create biological life on earth.
Comment by Daniel Smith — September 27, 2009 @ 2:55 pm
September 27th, 2009 at 2:58 pm
I'd love to. Show me where I can see the entire "nested hierarchy" – fleshed out in it's all-inclusive glory – and we'll discuss it.
Comment by Daniel Smith — September 27, 2009 @ 2:58 pm
September 27th, 2009 at 2:59 pm
Making a presumption and testing the entailed consequences is reasonable—as long as the presumption leads to specific and distinguishing empirical predictions, at least in principle. What have you come up with so far?
Comment by Zachriel — September 27, 2009 @ 2:59 pm
September 27th, 2009 at 3:03 pm
There's an entire field dedicated to the subject. Try the journal Cladistics.
Comment by Zachriel — September 27, 2009 @ 3:03 pm
September 27th, 2009 at 7:41 pm
It might have started with all of these characteristics .
Comment by Guts — September 27, 2009 @ 7:41 pm
September 28th, 2009 at 6:41 pm
The only prediction I've made so far is that a serious study of the qualities required to design and create biological life will lead to the conclusion that the being had to be omniscient. I base this on my own (admittedly limited) study of biology – specifically biochemistry.
Comment by Daniel Smith — September 28, 2009 @ 6:41 pm
September 28th, 2009 at 7:01 pm
I'm not real familiar with the field but I've heard that there are lots of disagreements between molecular (genetic) and morphological phylogenic classifications and that there's quite a bit of resistance to molecular classification.
I also have this paper in my possession: RECONSTRUCTING THE ANCESTRAL ANGIOSPERM FLOWER AND ITS INITIAL SPECIALIZATIONS.
This paper gives 19 phylogenic trees – all different – based on morphological and molecular traits.
From the abstract:
From this I gather that the nested hierarchy is not as neat and clean as many evolution proponents make it out to be.
Comment by Daniel Smith — September 28, 2009 @ 7:01 pm
September 28th, 2009 at 8:00 pm
It's a question of resolution. Specific details, especially concerning very ancient and rapid diversifications, can be difficult to discern. However, the broad outlines are clear, as are many individual branchings.
With respect to Angiosperms, they didn't just pop into existence, but evolved from seed-bearing plants, which in turn evolved from vascular plants. The paper you cited concerns whether Archaefructus is basal to flowering plants. Not surprisingly, it can be difficult to discern, based on fragmentary evidence, to distinguish between an ancestor and a close relative.
Comment by Zachriel — September 28, 2009 @ 8:00 pm
September 28th, 2009 at 10:46 pm
P A Nelson wrote:
Sure, Paul, take your time. I'll check back next month.
Comment by olegt — September 28, 2009 @ 10:46 pm
September 29th, 2009 at 10:34 am
Hi Oleg,
"Next month" is Thursday (10/1/09), so I beat that deadine by two days. Thanks for your patience.
First, a correction to your correction. Any argument dealing with the origin(s) of a molecular (or any) biological character necessarily bears on all instances of that character. Thus, the argument of Vestigian et al. 2006 that the universal genetic code did not originate in a frozen accident (in an actual cell), but arose communally, entails that n instances of the universal code (say, in H. sapiens, E. coli, and any archaean) do not indicate common ancestry from an actual cell — contra Dawkins, and most biology textbooks. As I noted, the arguments of Vestigian et al. 2006 therefore apply to the entire Tree of Life.
About the Darwinian threshold. Above, I asked the following:
You replied, “no, vertical evolution cannot be traced all the way to a single ancestor cell.” But I also asked this question:
You didn't answer this question, but said that molecular homology does indicate vertical descent (common ancestry from an actual cell) in Metazoa, “the group located above the Darwinian threshold.” [Clarification: Metazoa, or the animals, properly speaking, occur in Earth history long after Woese’s Darwinian threshold. The groups arising at the Darwinian threshold, on Woese’s hypothesis, are the three domains: Bacteria, Archaea, and Eukarya (the Metazoa stem within this last domain, and are a much smaller clade).]
So let's deal just with Eukarya. If the molecular characters that define this domain allow phylogenetically reliable inferences to organismal common ancestry — that is, not to communally distributed (i.e., arising) traits, which are not diagnostic, but rather to vertical descent from unique (token) cells — then we need to know how many times those characters arose (came to be).
Here is a helpful, if inexact, parallel. One could not uniquely identify a criminal suspect on the grounds that he or she possesses a bellybutton (an umbilicus). Every member of Homo sapiens has a bellybutton. One can identify criminal suspects, however, using molecular characters, the probability of whose origin is sufficiently low, e.g., short tandem repeats in DNA.
How many times, then, did the molecular characters that define Eukarya evolve? Put another way, how many organismal lineages carrying those characters crossed the Darwinian threshold?
Comment by P A Nelson — September 29, 2009 @ 10:34 am
September 29th, 2009 at 9:55 pm
Paul,
You turned in your homework two days early, but it is missing a critical link. This statement of yours—the arguments of Vestigian et al. 2006 therefore apply to the entire Tree of Life—is not valid. It applies to the microbial evolution but not to evolution of metazoa. (I explained why.) Your chain of arguments falls apart.
Since you are into inexact but helpful parallels, here is mine. I spent part of the last summer in Dresden. Dresden is connected by train to Prague in the south and Berlin in the north. Heavy rains in the Czech Republic disrupted the train link between Prague and Dresden. So one could not take a train between Berlin and Prague, but there was no problem going from Berlin to Dresden.
The analogy is obvious. If you want to say that man's evolution cannot be traced down to a single cell (Berlin to Prague), I have no argument with that and I said so many times. However, it seems to me that you want to stretch this and cast doubt onto the common descent of man and other animals (Berlin to Dresden). That simply does not follow from the works of Woese, Koonin, Doolittle, and others.
You still have two days before the deadline, so go ahead and try to make the connection. Just having the word therefore in a sentence is not a satisfactory argument.
Comment by olegt — September 29, 2009 @ 9:55 pm
September 29th, 2009 at 10:47 pm
Oleg wrote:
We agree that no universal Tree of Life exists. (If one argues, as do Vestigian et al. 2006 about the genetic code, that a biological character has come to be multiple times independently, that character cannot be used to establish monophyly, in this instance, the monophyly of life on Earth.) Let's move on.
You've argued above, following Woese's theory, that at the "Darwinian threshold" molecular homology becomes a reliable indicator of vertical descent (i.e., common ancestry from a discrete cell). According to Woese and colleagues, the Darwinian threshold is the point in evolutionary history when the three domains, Bacteria, Archaea, and Eukarya, "crystallize" (Woese's term, 1998) their cellular architectures, which then become refractory to HGT.
On this view, all eukaryotes share common ancestry. There IS a eukaryotic Tree of Life (plants, fungi, protists, Metazoa, chordates, vertebrates, mammals, etc., all stem from a common ancestor).
So — how many times did the molecular (or cellular) characters that define Eukarya arise, as that clade evolved and crossed the Darwinian threshold?
Comment by P A Nelson — September 29, 2009 @ 10:47 pm
September 30th, 2009 at 12:14 pm
P A Nelson wrote:
According to Vetsigian et al., these characters evolved once and did so through communal evolution. Even though you can see many distinct populations crossing this or that threshold vertically, the innovations were developing slowly in the vertical direction and rapidly shared horizontally. So while a threshold may have been crossed multiple times, the crossings weren't independent.
Are we done with this? For I am going to pound—again—on your failure to establish a logical link from the lack of a tree-like structure in early microbial evolution to the supposed failure of common ancestry between man and apes (or fish or insects). Here is Doolittle, one of the most vocal opponents of the Tree of Life, in The practice of classification and the theory of evolution, and what the demise of Charles Darwin's tree of life hypothesis means for both of them, Phil. Trans. R. Soc. B 364, 2221 (2009); doi:10.1098/rstb.2009.0032:
Stop asking questions and start providing answers, Paul.
Comment by olegt — September 30, 2009 @ 12:14 pm
September 30th, 2009 at 2:06 pm
Zachriel:
That humans and other organisms share a common design is one of the most profound findings of biology—unifying and explaining a vast array of data.
Comment by ID guy — September 30, 2009 @ 2:06 pm
September 30th, 2009 at 2:12 pm
Zachriel:
Evolution does not predict a nested hierarchy.
Common descent does not predict a nested hierarchy.
Descent with modification does not predict a nested hierarchy.
Cladograms are not nested hierarchies because cladograms are not beholden to the same rules as a nested hierarchy.
Prediction- Zachriel will continue to ignore all of that and blather on.
Comment by ID guy — September 30, 2009 @ 2:12 pm
September 30th, 2009 at 2:17 pm
True.
Comment by Bradford — September 30, 2009 @ 2:17 pm
September 30th, 2009 at 3:51 pm
Are you denying that humans and other land vertebrates share a common ancestor?
Comment by Zachriel — September 30, 2009 @ 3:51 pm
September 30th, 2009 at 3:53 pm
Haven't we had this conversation before? I would be curious if any ID supporter disputes these statements.
Comment by Zachriel — September 30, 2009 @ 3:53 pm
September 30th, 2009 at 4:09 pm
Zachriel:
How can that premise be tested with the exclusion of all alternatives?
Comment by ID guy — September 30, 2009 @ 4:09 pm
September 30th, 2009 at 4:12 pm
I said:
Evolution does not predict a nested hierarchy.
Common descent does not predict a nested hierarchy.
Descent with modification does not predict a nested hierarchy.
Cladograms are not nested hierarchies because cladograms are not beholden to the same rules as a nested hierarchy.
Yes we have. You were shown to be wrong then also.
So why do you still persist with well-refuted nonsense?
I would be curious to see if anyone disputes what I say and the reasoning behind their dispute(s).
Anyone?
Comment by ID guy — September 30, 2009 @ 4:12 pm
September 30th, 2009 at 4:14 pm
Yay! Let's play!
Comment by chunkdz — September 30, 2009 @ 4:14 pm
September 30th, 2009 at 4:19 pm
Oleg wrote:
So we have the following:
1. At t0, an indeterminate number (n) of “cell-like entities” exist, exchanging genetic information horizontally. These entities do not share common ancestry (vertical descent from a single cell), but have come to be independently from prebiotic precursors, in a population of unknown size and composition. Call this the ancestral population.
2. At t1, some fraction of the ancestral population evolves the molecular and cellular characters that define Eukarya. This is a “Darwinian threshold” or “transition,” the point at which molecular homology now reliably indicates organismal, or vertical, descent:
3. Although the Darwinian threshold for Eukarya “may have been crossed multiple times, the crossings weren’t independent” – the characters defining Eukarya evolved “once.”
What does “once” mean here?
– The events described in (2) occurred at a spatiotemporally unique location, in a single cell (or organism). We ordinarily use “once” in this sense to refer (for example) to the birth and death of individual organisms.
– The events described in (2) occurred during a particular interval of time, but without spatiotemporal uniqueness, e.g., “once, during the year 1859, the average height of European males was 1.8 m.” In this case, n cells evolve the characters defining Eukarya.
I ask because your summary is unclear: the threshold may have been crossed “multiple times,” but this happened “once.” Please clarify.
Oleg also wrote:
About what?
To recap: I joined this thread to answer a question about Woese’s views concerning Darwin’s Tree of Life (he rejects it, insofar as the TOL is rooted in a last universal common ancestor, which he judges to be biologically impossible). You said I misrepresented Woese. I replied that when molecular homology is decoupled from organismal (vertical) descent, as Woese and others have done for universally-shared characters such as the genetic code, unexpected consequences follow for inferences about the branches of the Tree of Life. You then cited publications where Woese, Doolittle, and others, affirm their faith in the monophyly of Eukarya, Metazoa, chimps and humans, whatever.
But I’ve never said that Woese or other universal TOL skeptics doubted the common ancestry of most of the Tree of Life (they don’t). I’ve said, rather, that their decoupling of molecular homology from organismal descent, once allowed at the base of the TOL, entails corrosive consequences for phylogenetic inference higher up in the branches – namely, that once the TOL breaks apart at its root, the fracturing is impossible to stop.
I’m now trying to show you that, by following out the consequences of Woese’s theory about the origin of the genetic code and the three domains.
Comment by P A Nelson — September 30, 2009 @ 4:19 pm
September 30th, 2009 at 4:44 pm
Darwin has a diagram in his book that looks essentially like some our constructed phylogenetic trees. Not exactly correct because branches merge at times, but essentially correct. You see this when you study for example, artiodactyls. The interesting thing is that when you study the distribution based on RNase, you find that all the active-site residues were conserved after gene duplication, as was the RNA-binding site. Which means that the ancestral RNase genes were not pseudogenes that evolved functions, but vice versa, proteins with functions that became pseudogenes in some lineages.
Comment by Guts — September 30, 2009 @ 4:44 pm
September 30th, 2009 at 5:13 pm
Paul:
I may be interpreting you wrong, but are you saying that because of the tacit admission that the genetic code and ribosomes and the like evolved multiple times, pretty much anything can evolve that many times independently and therefore the logic used to infer molecular homology, namely that homology is the only logical way to explain the molecular uniformity when there are so many different ways in principle to evolve these structures, is wrong.
This is the longest running sentence I ever made. I think I deserve a reward.
Comment by Guts — September 30, 2009 @ 5:13 pm
September 30th, 2009 at 5:53 pm
Guts,
You're right — that's some sentence. Almost Germanic in its complex clauses…
If you don't mind, I'd like to see Oleg's reply before I comment on your question.
Comment by P A Nelson — September 30, 2009 @ 5:53 pm
September 30th, 2009 at 7:04 pm
Guts:
Comment by Bradford — September 30, 2009 @ 7:04 pm
September 30th, 2009 at 7:09 pm
They haven't come to be independently. They are highly interdependent.
Yes, you've said that. But I have no idea what support you have for that claim. Are you saying it is a priori? That doesn't seem plausible. We can certainly imagine appropriate topologies that preserve the few main trunks of life that have their origin in a common population.
Comment by Zachriel — September 30, 2009 @ 7:09 pm
September 30th, 2009 at 7:30 pm
Bradford,
haha you haven't seen anything, go read some of my posts on ISCID for run on sentence madness.
Comment by Guts — September 30, 2009 @ 7:30 pm
September 30th, 2009 at 7:37 pm
How many trunks does one tree have?
I believe Paul is talking about "the" alleged tree of life.
And if you have this tangled web at the root then there isn't any saying that you would only get one trunk to emerge.
Furthermore even from many trunks we could still have convergences, as well as divergences.
Comment by ID guy — September 30, 2009 @ 7:37 pm
September 30th, 2009 at 7:50 pm
This pretty much sums up the materialist's case.
How can you argue with "imagination"?
Zachriel, I can "imagine a scenario" whereby natural forces created Stonehenge. All of the natural forces – earthquakes, floods, whirlpools, and hydro-turbulence – are known to have existed at the time Stonehenge came to be. All are still observed today. I can make specific predictions that somewhere on this earth there are rocks that have been sheered by earthquakes into a block-like shape, that there are places where floods have deposited heavy stones miles from where they originated, that a whirlpool will leave the objects it carries in a circular pattern, that hydro-turbulence can stand a heavy stone on edge, and that places exist where evidence of past heavy water flow is found far from existing rivers. All of these predictions can and have been verified. So, how is my imagined scenario any different from yours?
Comment by Daniel Smith — September 30, 2009 @ 7:50 pm
September 30th, 2009 at 10:07 pm
The contrary position to 'not possible' is 'possible'. It's an empirical question that could be resolved either way (the evidence strongly supporting most aspects of the phylogenetic tree). In any case, I'm not sure of P A Nelson's reason for thinking that horizontal mechanisms at the root of the phylogenetic tree means that the rest of the topology can't form a well-defined branching pattern.
I noticed that no ID supporter has bothered to correct your misunderstanding of phylogenies. The dicussion concerns Woese's hypothesis that there are three well-defined trees emerging from a common ancestral population. They still share common descent; not from a single organism, but from a community of highly interdependent protocells. All life has its root in that ancestral pool.
Comment by Zachriel — September 30, 2009 @ 10:07 pm
September 30th, 2009 at 11:06 pm
P A Nelson wrote:
Not sure what's behind this triangulation, Paul, but here is my reply.
That's the essence of communal evolution, where horizontal gene transfer dominates. If bacteria formed genealogical trees, evolving vertically, it would makes sense to speak of multiple independent threshold crossings: different lineages would reach the threshold at different times. However, when primitive organisms readily swap their genetic material, and with it the latest innovations, they all cross the threshold simultaneously and certainly not independently. The crossing happens once and involves a large population not related by vertical descent.
And I joined to point out that Woese's call "to go beyond the Doctrine of Common Descent" has nothing in common with your attempts to discredit common descent of man and apes. Not even close.
Woese et al. had good reasons to doubt the TOL picture at early stages of life. They were able to point out a mechanism that disrupts vertical evolution: the horizontal gene transfer. Their ideas are rooted in empirical studies. They also realize that eventually communal evolution stops and changes to the Darwinian mode because the mechanism responsible for it (HGT) becomes less efficient in complex organisms. After that point the tree-like genealogies are not disputed—by scientists that is.
Creationists, on the other hand, are trying to manufacture a controversy out of this and that's precisely what you are doing here. You vaguely warn of serious consequences to the entire tree of life, but what exactly is your argument? So far you keep asking questions and triangulating. Come on, Paul, spit it out, let us know what you really think!
That's precisely what I mean. Vague assertions of corrosive consequences and fracturing that is impossible to stop. Sounds very scary and the italics are adding to the impression. Yet I would like to hear from you exactly what mechanism gets in the way of vertical evolution in the upper branches of the tree. Would you care to explain at long last?
Comment by olegt — September 30, 2009 @ 11:06 pm
October 1st, 2009 at 7:27 am
Zachriel,
The discussion is about the ONE alleged tree of life.
My alleged misunderstanding is all in your head.
IOW Zachriel you have failed to show that I have a misunderstanding of phylogenies.
All you have is a bald assertion.
Comment by ID guy — October 1, 2009 @ 7:27 am
October 1st, 2009 at 7:30 am
That is a very bold claim.
Do you have some scientific data to substantiate it?
Or is your "say-so" all we get?
Why did HGT/ LGT stop at some threshold?
IOW olegt complains that Paul is providing vague assertions and just look what he presents.
Comment by ID guy — October 1, 2009 @ 7:30 am
October 1st, 2009 at 7:41 am
Daniel,
You are starting to find out that "imagination" is interchangeable with "scientific data" with people like Zachriel.
For all his bluster about scientific methodology "imagination" is always his fallback position.
Comment by ID guy — October 1, 2009 @ 7:41 am
October 1st, 2009 at 8:37 am
We're discussing the work of Carl Woese. If might behoove you to make yourself familiar with his work.
(By the way, as long as IDers refuse to correct egregious errors in other IDers, it is difficult to take them seriously. The hypotheses of Woese and ilk have all been subjected to continuous and intensive skepticism, criticism and testing. This demonstrates yet again the intellectual vacuity and scientific sterility of ID.)
Comment by Zachriel — October 1, 2009 @ 8:37 am
October 1st, 2009 at 8:50 am
Zachriel,
Why don't you just answer the questions?
And seeing that I correct all of you eregious errors I would think you should thank me.
We have all witnessed your scientific vacuity. So why do you insist on exposing it with every post?
Comment by ID guy — October 1, 2009 @ 8:50 am
October 1st, 2009 at 2:44 pm
So, by your logic, it is 'possible' that Stonehenge was formed by natural forces and – since 'the evidence strongly supports' the specific predictions I made – my imagined conclusion has strong merit.
I noticed that he ignored most of my argument. Perhaps he 'imagined' that I didn't make it.
Comment by Daniel Smith — October 1, 2009 @ 2:44 pm
October 1st, 2009 at 4:34 pm
Your imagined conclusion has no scientific merit, nor does misrepresenting a question posed to elicit a clarification represent an argument. The question concerned whether P A Nelson was suggesting that having a complex root has a *necessary consequence* of a fractured tree. You might address the actual position rather than the strawman.
Comment by Zachriel — October 1, 2009 @ 4:34 pm
October 1st, 2009 at 5:45 pm
What PA Nelson actually said:
Comment by ID guy — October 1, 2009 @ 5:45 pm
October 1st, 2009 at 7:47 pm
Why not?
I made specific predictions based on my (imagined) hypothesis. When put to the test, these predictions were all verified by strong evidence.
I'll ask again: how is my imagined scenario any different from yours?
Comment by Daniel Smith — October 1, 2009 @ 7:47 pm
October 1st, 2009 at 9:38 pm
And maybe lightning carved them where they stood.
Your so-called predictions are not entailed in the hypothesis, nor did you connect cause and effect. Meanwhile, there is strong evidence that humans erected Stonehenge, just like humans have erected many other lithic monuments.
Comment by Zachriel — October 1, 2009 @ 9:38 pm
October 2nd, 2009 at 8:27 am
Sigh. I guess not. Something that is inherently different between ID and science: In science, if you make an error, you can be sure someone will point it out. And that's the way it should be. I'd hate to think I kept repeating the same error over and over again because no one bothered to correct me. I consider it a sign of respect that someone would take the time to do so. Indeed, I try to learn from my mistakes, and have acquired quite an education thereby.
Of course it does. Darwin has only one diagram in Origin of Species, a branching illustration of phylogeny.
I'm not even sure you know what a set is.
Comment by Zachriel — October 2, 2009 @ 8:27 am
October 2nd, 2009 at 8:49 am
Obviously Zachriel cannot learn from his continued mistakes.
Darwin's diagram is not one of a nested hierarchy.
A nested hierarchy demands a direction. One of additive defining characteristics.
Evolution does not have a direction.
Characteristics can be lost. And once a characteristic is lost the set loses containment.
Cladagrams do not require that defining characteristics be additive.
Again if yiou start with a population A that gives rise to two other populations A1 and A2, you don't have a nested hierarchy unless A1 shares all the defining characteristics of A PLUS at least one other defining characteristic.
However, as I said and all educated people understand, evolution is not like that.
So what is Zachriel's problem? Is it that he doesn't understand evolution? Or is it that he doesn't understand nested hierarchies? Or both?
Comment by ID guy — October 2, 2009 @ 8:49 am
October 2nd, 2009 at 8:57 am
Also nested hierarchies demand distinct categories.
With evolution we wouldn't expect that- transitional organisms violate the distinct categories demanded by NH.
Now I have been over this and over this yet Zachriel doesn't appear to be able to understand such a simple concept.
Comment by ID guy — October 2, 2009 @ 8:57 am
October 2nd, 2009 at 9:28 am
Two questions for Zachriel that can resolve this issue:
1- Does evolution have a direction? (yes or no)
2- Does a nested hierarchy require a direction? (yes or no)
If you answer "yes" to the first question then you don't understand evolution.
If you answer "no" to the second question then you don't understand nested hierarchy.
And the only possible way for evolution to give us a nested hierarchy if the answer to both questions is the same.
So Zachriel you cannot learn from your mistakes unless you are man enough to admit to them.
Comment by ID guy — October 2, 2009 @ 9:28 am
October 2nd, 2009 at 9:53 am
Of course it is. Each subset is strictly contained within its superset. You can cut the diagram at any node, and the sub-diagram is still a nested hierarchy.
A nested hierarchy is a mathematical structure. The "direction" is distance from the trunk measured in number of branchings. The leaves on a tree form a nested hierarchy (when grouped by branch and limb). A taxonomy is a type of nested hierarchy based on a classification scheme, such as a biological classification.
The categories are defined by the branching from common ancestors. The common ancestor of any two distinct species is a node of the nested hierarchy. There are far more nodes in nature than is shown in a typical Linnaean classification. But because of the nature of a nested hierarchy, the structure remains a nested hierarchy whether we consider only the broad categories, or every distinct species.
tetrapods.. dinosaurs
.... birds
.. mammals
.... rodents
.... apes
But if we look more closely, each class also forms a nested hierarchy.
birds.. waterfowl
.. perchers
.... robins
.. falconiformes
.... falcons
.... eagles
.... hawks
Or we can look more broadly.
eukaryotes.. animals
.... Bilateria
...... humans
...... trout
.... radiata
.. plants
.... algae
.... vascular
.. fungi
We can even cut or ignore some branches and it's still a nested hierarchy. Each scheme forms a nested hierarchy that is a subset of what is known as the Tree of Life.
Comment by Zachriel — October 2, 2009 @ 9:53 am
October 2nd, 2009 at 10:16 am
ID guy asks Zachriel:
Answers:
1- Yes, although the direction is vague. CD infers that descendents are like their parents. Selection infers differences due to variation. Speciation would fix some varied properties within sub-groups. If evolution does not entail all of the foregoing then how would it be alternatively described?
2- Yes, in the sense that a nested hierarchy fulfills a particular definition of direction namely, an area of development having a tendency toward a particular end or goal. In this case that end or goal would be a relational structure.
Comment by Bradford — October 2, 2009 @ 10:16 am
October 2nd, 2009 at 10:24 am
Zachriel,
Darwin's diagram does not describe a nested hierarchy for the very reason it isn't based on characteristics and does not illustrate a set within set configuration.
Nested hierarchies are built on defining characteristics. Descent is not a defining characteristic.
Darwin's diagram just demonstrates descent with modification.
That modification can include the loss of characteristics.
A loss of characteristics means a loss of containment.
A nested hierarchy demands a direction. One of additive defining characteristics.
OK so you don't understand nested hierarchies. I knew that but thank you for proving it.
Yes it is obvious that you don't understand nested hierarchies.
And you think you can force your misconceptio onto others.
Wrong again.
With nested hierarchies the categories are defined by characteristics.
You start with a superset that is defined by a specific set of characteristics.
Every subset includes those characteristics PLUS at least one more at each level.
IOW in nested hierarchies every subset contains the defining characteristics of the set above it- from which it was derived.
BTW Linnean classification was used for the Created Kinds.
Evolutionists, not being very bright, stole his scheme and just renamed it.
And you, not being very bright, think that because they seem to have gotten away with it that evolution predicted it.
With evolution one may expect to create a Venn diagram, maybe even a lineage. But neither of those is to be confused with a nested hierarchy which demands strict containment and distinct categories.
Comment by ID guy — October 2, 2009 @ 10:24 am
October 2nd, 2009 at 10:33 am
ID guy to Zachriel:
I have no doubt that Zachriel and others could identify defining characteristics of organisms within nested hierarchies. They would do this by identifying the common designs of such organisms, making them closet IDists.
Comment by Bradford — October 2, 2009 @ 10:33 am
October 2nd, 2009 at 10:34 am
Bradford,
When I was out for a walk I realized that someone would say what you did about evolution having a direction- one generation giving rise to the next.
But at least you qualified it with "vague".
My point is that, with evolution, whatever survives to produce the next generation is whatever survives to produce the next generation.
As for nested hierarchies think containment set.
yahoo search for nested hierarchy reveals-
Wikipedia :
ISSS.org has the following:
Comment by ID guy — October 2, 2009 @ 10:34 am
October 2nd, 2009 at 10:35 am
Joe is hopelessly stuck in a category error. A nested hierarchy, exemplified by a genealogy of dividing cells, is ordered in the time direction: each cell has exactly one parent. A nested hierarchy need not be ordered in any other direction. When we say "evolution has no preferred direction" we refer not to the time (from parent to child) direction, but to the direction characterizing the appearance of new features*.
To use a simple geometrical analogy, a particle can move uniformly along the horizontal direction and at the same time perform a random walk along the vertical direction. One does not exclude the other.
My suggestion to Zachriel and Bradford is not to waste their mental effort trying to help Joe. My experience shows that it is impossible. He can't acknowledge that he is wrong. He'll curse you and insist that he is right till he is blue in the face. Visit his blog and see for yourselves.
*I am neglecting the existence of a preferred direction in the particular fitness landscape.
Comment by olegt — October 2, 2009 @ 10:35 am
October 2nd, 2009 at 11:28 am
How do dividing cells exemplify a nested hierarchy?
What criteria/ critereon are/ is used?
nested hierarchies involve levels which consist of, and contain, lower levels.
How do dividing cells meet that criteria?
And yes I agree it is impossible for ignorant people to "help" anyone.
So you cannot help anyone in this case.
Also we have covered the "time direction" drivel.
People like olegt act like they do when they have nothing else to support their position.
Always blame the opponent when all he really has to do is support his claims.
I have supported mine.
Comment by ID guy — October 2, 2009 @ 11:28 am
October 2nd, 2009 at 11:32 am
See what I mean?
Comment by olegt — October 2, 2009 @ 11:32 am
October 2nd, 2009 at 11:44 am
ID guy quoting from an International Society for the Systems Sciences source:
As an IDist two things stand out from my perspective. First, is it conceptually likely that one would design an outcome that is consistent with a nested hierarchy description? Could there be rational reasons for doing so and could an NH be incidental to a designed process?
Secondly, could process x be designed in such a way as to make a NA inevitable? IOW, is there any reason to believe that nested hierachies are incompatible with design?
Comment by Bradford — October 2, 2009 @ 11:44 am
October 2nd, 2009 at 12:05 pm
Bradford,
I would say the only way to get a nested hierarchy is by design.
Comment by ID guy — October 2, 2009 @ 12:05 pm
October 2nd, 2009 at 12:07 pm
olegt,
Thank you for proving my point- again.
BTW your projections are duly noted.
Comment by ID guy — October 2, 2009 @ 12:07 pm
October 2nd, 2009 at 12:11 pm
Another imagined scenario! Great, work up some predictions.
Of course my predictions are entailed in the hypothesis, and cause and effect are obvious. My imagined hypothesis is just as detailed and connected as any abiogenesis hypothesis or any hypothesis detailing the evolution of a major biological structure.
Ah, but introducing a designer brings with it a myriad of complications. What were the mechanisms used to carve, transport and erect the structure? Can we place these technologies at the time of Stonehenge's erection?
We know that my mechanisms were around then and that they have the power to do what my imaginary scenario outlines. Science must therefore favor my imaginary natural scenario over any 'design' scenario.
Isn't this how science works?
Comment by Daniel Smith — October 2, 2009 @ 12:11 pm
October 2nd, 2009 at 12:34 pm
Zachriel:
Zach, you say no ID supporter disputes these statements, but then you use exactly my argument when I addressed the issue. That is rather bizarre, but not surprising.
Comment by Guts — October 2, 2009 @ 12:34 pm
October 2nd, 2009 at 12:52 pm
There is no evidence that lightning created Stonehenge. Nor is there evidence that it was created by flood waters.
As I said, Stonehenge is only one of many lithic monuments made by humans. Maybe if we explore the surrounding areas, we can find evidence of these humans.
Of course, you can always handwave away anything that doesn't meet your definition of "major". Though you might think it of no consequence, the spontaneous evolution of antibiotic resistance in bacteria is very major from the point of view of a bacterium.
The evolution of the horse, the radiation of dinosaurs, or the adaptations in the Galápagos tortoise show the changes that can occur. Take a simple example, the mammalian middle ear, tiny bones in precise alignment that couple and amplify miniscule pressure waves. We have fossil and embryonic evidence that supports a gradual, selectable pathway.
Comment by Zachriel — October 2, 2009 @ 12:52 pm
October 2nd, 2009 at 2:19 pm
I read your comment, and mulled over whether it represented a gentle disagreement. It was not directed at ID guy, or specific enough to indicate a clear disputation. All four claims at issue refer to the nested hierarchy, which you don't even mention. Here they are again:
Later ID guy says "Darwin's diagram is not one of a nested hierarchy." His understanding of phylogenies and nested hierarchies is completely muddled. It isn't necessary to be wed to a particular terminology, but I'm not even sure he understands the concept of a set.
Comment by Zachriel — October 2, 2009 @ 2:19 pm
October 2nd, 2009 at 2:33 pm
I mentioned Darwin's diagram and said that it is similar to the trees we construct today, and even gave an example, and how to go about actually constructing one. Or do you disagree that any of my examples represent a nested hierarchy?
By the way, do you dispute this ? I don't see any comment from you about that, if you want to talk about correcting errors.
Comment by Guts — October 2, 2009 @ 2:33 pm
October 2nd, 2009 at 3:05 pm
Darwin’s diagram (1859, 116) is not a nested hierarchy, or at any rate not a universally inclusive hierarchy. Although there are graphical hints, in the dotted lines, that the 11 starting nodes (A-L, minus J, which does not exist as a character in Latin) may converge to earlier ancestors, they are not linked in the diagram. This visual ambiguity directly reflects Darwin’s uncertainty (1859, pp. 483-4) about whether evidence supported one or more common ancestors at the root of the Tree(s) of life.
Biology Direct just posted two articles of interest to our discussion:
http://www.biology-direct.com/...
http://www.biology-direct.com/...
I awakened early this morning thinking about easy (quick) ways to illustrate the problems with inferring the monophyly of Woese’s domains, at his postulated “Darwinian threshold,” but I have a looming book MS deadline. Should be possible to do this, however, just with a sheet of regular graph paper and a pencil. Let me try it myself over the weekend, and I’ll post the thought experiment here.
Comment by Paul Nelson — October 2, 2009 @ 3:05 pm
October 2nd, 2009 at 3:22 pm
I don't. ID guy apparently doesn't understand that a tree diagram is a representation of a nested hierarchy. As I said, I mulled over your statement. I'm not sure if ID guy would have considered it as disputing his position, but I am happy to correct my previous misstatement. You expressed disagreement with ID guy on this point.
However, the evidence for Common Descent is so fundamental to the Theory of Evolution, this problem cannot simply be glazed over.
What am I supposed to dispute?
Comment by Zachriel — October 2, 2009 @ 3:22 pm
October 2nd, 2009 at 3:27 pm
Do you agree with Olegt that the paper he references shows that Systems Biology has never "figured out how to make the vague ideas into a theoretical framework that would be useful in science. " ?
Comment by Guts — October 2, 2009 @ 3:27 pm
October 2nd, 2009 at 3:34 pm
Zachriel hasn't even shown he understands what a nested hierarchy is.
Nested hierarchies follow strict rules.
Trees do not have to follow those strict rules.
Zachriel's failure to address any of the reasons why evolution doesn't expect a nested hierarchy is also very telling.
Comment by ID guy — October 2, 2009 @ 3:34 pm
October 2nd, 2009 at 3:47 pm
Yet we don't even know the genes involved.
IOW we can't take a reptilian embryo, and tinker with its DNA such that we can control the "evolution" of the middle ear to a mammalian-like ear.
If universal common descent is so central to biology we should be able to test the premise to the exclusion of common design and convergence.
Yet we cannot.
Comment by ID guy — October 2, 2009 @ 3:47 pm
October 2nd, 2009 at 4:00 pm
Paul Nelson Says: Should be possible to do this, however, just with a sheet of regular graph paper and a pencil. Let me try it myself over the weekend, and I’ll post the thought experiment here.
Consider this
http://genetic-code.narod.ru/t...
This is both a phyletic tree and a nested hierarchy. Nonetheless, it certainly challenges common assumptions about how both should be represented graphically. But, as was pointed out, so was Darwin's famous "Tree of Life," "challenging," which apparently no one ever paid much attention to, because its trees, not a tree (or the tree), nor is it one nested hierarchy, but several.
LOL Maybe Darwin is one who should be (or should have) issued some disclaimer…
Disclaimers? What disclaimers should I be issuing?
I'm whacky? A creationist? Anti-evolutionist?
Comment by Rock — October 2, 2009 @ 4:00 pm
October 2nd, 2009 at 4:45 pm
Rock,
What is the criteria for Darwin's alleged nested hierarchy?
All he has in his diagram are descent lines.
Or are you also saying that descent, ie "who's your mamma and daddy?" is a defining characteristic?
Comment by ID guy — October 2, 2009 @ 4:45 pm
October 2nd, 2009 at 4:55 pm
Charles Darwin in chapter 6 of "On the Origins of Species:
The point being as I said before- transitionals spoil the distinct categories required by nested hierachies but they would fit in perfectly well with a Venn diagram.
Prediction- Zachriel and olegt will continue to ignore all refutations and blather on unfazed.
Comment by ID guy — October 2, 2009 @ 4:55 pm
October 2nd, 2009 at 4:57 pm
Ummm. Just had some proteomics for dinner. Delicious. Would have helped my cholesterol level though if I had only foregone the saturated mutants.
Comment by Bradford — October 2, 2009 @ 4:57 pm
October 2nd, 2009 at 5:11 pm
By the way, I didn't comment on it at the time because I didn't see it before you brought it to my attention. Please note that I didn't join the thread for more than a week after olegt's comment.
Systems Biology has been in stamp collecting mode for some time. It holds a great deal of promise, though, and many new ideas are percolating concerning how global structure relates to self-organizing complex systems. Systems Biology is in "observe some aspect of the world" mode, that must lead at some point to testable predictions. Some valid discoveries have been made, so it is probably better grounded than String Theory, which is still stuck in "devise some explanation to explain the data" mode. New computational methods, the huge amount of available data, and the limitations of reductionism are leading to increased interest in Systems Biology.
Molecular Systems Biology
The last sentence of the article in question "We're not exactly sure what the future holds, but the prospects are very exciting," emphasizes the current limitations of the field.
Comment by Zachriel — October 2, 2009 @ 5:11 pm
October 2nd, 2009 at 5:17 pm
Under the section WIDE APPLICATION
The article shows that these techniques are starting to come of age. They're beginning to yield novel insights that couldn't be gained by traditional approaches. Completely the opposite of what Olegt claimed. But I'll note your "gentle disagreement" and move on.
zach:
It already is .
Comment by Guts — October 2, 2009 @ 5:17 pm
October 2nd, 2009 at 6:23 pm
Spare me the bullshit, ID guy.
You're not arguing with Darwin, Zachriel, or olegt, now.
You're arguing with me.
Comment by Rock — October 2, 2009 @ 6:23 pm
October 2nd, 2009 at 6:58 pm
The bullshit is all yours Rock.
All I did was ask you a couple of questions.
You know for clarification purposes.
Comment by ID guy — October 2, 2009 @ 6:58 pm
October 2nd, 2009 at 7:39 pm
Noooo, buddy. You didn't ask any questions.
I asked questons. You did not.
That's the difference between me and you, the IDers and their critics.
I ask questions. You don't.
You guys have all the answers.
You are not scientists.
Comment by Rock — October 2, 2009 @ 7:39 pm
October 2nd, 2009 at 8:22 pm
By that standard, there is no evidence that life arose from non-life, nor is there evidence that any major system evolved via undirected mechanisms.
Evolution is central to the survival of bacteria. The fact that they evolve rapidly is a testament to their design.
It's a vague, undefined pathway with no experimental evidence to back it up. It's no better than my 'floodwater Stonehenge' in that regard. I can take a car, a little red wagon, and a lawnmower, posit 'relatedness' based on similarities, arrange them in a 'progression' and theorize that one descended from the other – all with no need to mention a mechanism that brings about said changes.
Your middle ear is the same thing – a group of similar structures arranged to imply progression with no real mechanism – other than the handwave "variation and selection" to connect them.
Just because things look related doesn't mean they are, there has to be a connection.
Comment by Daniel Smith — October 2, 2009 @ 8:22 pm
October 2nd, 2009 at 9:14 pm
Guts wrote:
Systems biology is a field that's still in its infancy, Guts. You can't argue with that. Here is an excerpt from a recent (Nov. 2006) editorial introduction to a special issue of Nature Cell Biology entitled Systems biology: a user's guide:
The lady doth protest too much, methinks.
Comment by olegt — October 2, 2009 @ 9:14 pm
October 2nd, 2009 at 10:34 pm
The term "coming of age" means more than a child, but not quite an adult. That would be a fair description. I have great sympathy for systems approaches, but most hypotheses are still very tentative. But as you say, the field is still maturing.
Rather like a teenager insisting on being treated as a grownup.
Comment by Zachriel — October 2, 2009 @ 10:34 pm
October 2nd, 2009 at 10:39 pm
There's no complete theory of abiogenesis, but that isn't the same as that there isn't any evidence.
That wasn't your claim. You said your imagined hypothesis was just as detailed as any hypothesis detailing the evolution of a major biological structure. When I pointed to well-known evolutionary pathways for antibiotic resistance, you change the subject and wave your hands.
The embryonic evidence predicted the fossil evidence decades before the discovery of the fossils.
Comment by Zachriel — October 2, 2009 @ 10:39 pm
October 2nd, 2009 at 10:58 pm
Olegt is a bitch, I think.
Comment by GringoRoyale — October 2, 2009 @ 10:58 pm
October 3rd, 2009 at 12:14 am
Olegt, your own 2009 reference contradicts your initial assertion that it is like String Theory, it even claims that these techniques made successful predictions. Lots of progress has obviously been made since 2006 (check out the blue box which one of the headings reads "WIDE APPLICATION"), but even your own 2006 reference states:
It's rather odd that you claimed Systems Biology has not made any "inroads" that are useful to science, and that the 2009 reference supports your erroneous assertion. Do you not understand your own references? Will you admit that you were wrong? Or are you no different than those whom you criticize? Your refusal to admit otherwise has vast implications for pretty much everything you have written in this forum (and elsewhere).
zach:
All hypotheses in science are tentative, that's the nature of science.
Comment by Guts — October 3, 2009 @ 12:14 am
October 3rd, 2009 at 8:33 am
Guts,
I did note at the onset that omics approaches had been useful. It seems to me descriptors like "a field in its infancy" and "coming of age" indicate that this cake is still half-baked.
Comment by olegt — October 3, 2009 @ 8:33 am
October 3rd, 2009 at 8:36 am
Hey Rock,
Thought you might be interested in this paper (if you haven't already seen it):
Delarue M (2007). An asymmetric underlying rule in the assignment of codons: Possible clue to a quick early evolution of the genetic code via successive binary choices. RNA 13(2): 161–169.
http://ukpmc.ac.uk/articlerend...
Comment by KC — October 3, 2009 @ 8:36 am
October 3rd, 2009 at 8:41 am
Rock,
I asked you two questions because you said something without support that contradicted what both I and Paul Nelson said.
Comment by ID guy — October 3, 2009 @ 8:41 am
October 3rd, 2009 at 8:53 am
Except that there isn't any evidence that a RNA World ever existed.
Comment by ID guy — October 3, 2009 @ 8:53 am
October 3rd, 2009 at 9:22 am
There isn't any evidence that non-living matter and energy can give rise to living organisms through undirected/ non-goal oriented processes.
And there isn't any evidence that those types of processes can give rise to the diversity of living organisms we observe on Earth.
Comment by ID guy — October 3, 2009 @ 9:22 am
October 3rd, 2009 at 9:35 am
And does it seem to you that descriptors like "crusty old discipline" and "forever holding forth promise of breakthroughs" would indicate that the origin of life field is a moldy excuse for dessert?
Comment by Bradford — October 3, 2009 @ 9:35 am
October 3rd, 2009 at 9:54 am
Hi Bradford,
Since you put those descriptors in quotes, would you care to point us to their source(s)?
And somewhat off-topic, it looks like one of your guests threw up on the carpet last night. It might be a good idea to clean up after him.
Comment by olegt — October 3, 2009 @ 9:54 am
October 3rd, 2009 at 10:08 am
You are confused on this. A-L represent "species of a genus large in its own country". Darwin doesn't connect them in the diagram as he is showing a point about how a divergent genus (something observed) can generate new species and even new genera. From this he then extrapolates that the various species of the genus diverged through a similar process, and so to larger taxonomic groupings, such as orders and families.
In other words, the ambiguity in the diagram is not due to his uncertainty concerning the very base of the Tree of Life. That uncertainty is due to limited data on which to reach a strong conclusion. In this case, the nested hierarchy of the genus is not drawn, but it's implied at the bottom of the diagram.
In Darwin's diagram, the sets are formed by shared ancestry. The "green and budding twigs" represent extant species. You might read Darwin's Origin of Species where he discusses his diagram and the simile of the Tree of Life.
In other words, the nested hierarchy of the observed Linnaean taxonomy is explained as due to the nested hierarchy of the posited descent from common ancestors. This leads to non-trivial predictions.
Comment by Zachriel — October 3, 2009 @ 10:08 am
October 3rd, 2009 at 10:25 am
Consider artificial evolution from random sequences inspired by origin of life research. Abiogenetics has been quite fertile in terms of scientific advances, including new technologies with therapeutic potential.
Comment by Zachriel — October 3, 2009 @ 10:25 am
October 3rd, 2009 at 11:03 am
Olegt:
No one is denying that that its application to biology using large-scale "omics"-type technologies is relatively new, but that is completely different from denying that it has been able to make any applications at all, which is what you claimed.
Comment by Guts — October 3, 2009 @ 11:03 am
October 3rd, 2009 at 11:18 am
zach:
"However, this frequency is still low enough to emphasize the magnitude of the problem faced by those attempting de novo protein design."
weak ATP binding, that is hardly a true biological function, and the process they used for the stronger binders is hardly stochastic. This is why systems biology is so important it puts things in it's proper context.
Comment by Guts — October 3, 2009 @ 11:18 am
October 3rd, 2009 at 12:02 pm
ATP binding was just the initial experiment. Many other proteins have been artificially evolved, including families not seen in nature. The random sequences have to have some function for evolution to proceed.
Evolution is hardly random, but the initial sequences and variations in these experiments are. Turns out that there is "CSI" in a reasonable proportion of random sequences. That is relevant to abiogenetics, and to an understanding of enzyme structure. In any case, abiogenetics has been a fruitful area of research—which was what was being addressed.
Comment by Zachriel — October 3, 2009 @ 12:02 pm
October 3rd, 2009 at 12:18 pm
zach:
They got proteins that weakly bind ATP. That's not biologically relevant. They then tweaked the proteins and got a stronger binder, it wasn't truly random.
It has no relevance to abiogenesis, "no known biological nucleotide-binding domain is a zinc-stabilized structure."
Comment by Guts — October 3, 2009 @ 12:18 pm
October 3rd, 2009 at 12:39 pm
Read it again. Generating random sequences and then identifying new enzymes and their properties is an active area of research.
Evolution isn't random. That's sort of the point of evolution. The initial random sequences can have biological capabilities.
The Keefe and Szostak paper makes clear that this is related abiogenetic research in that the relevant hypothesis is that primordial proteins formed from random sequences. They were trying to determine how often random sequences fold into functional proteins. Turns out well-within the parameters to support the hypothesis.
Comment by Zachriel — October 3, 2009 @ 12:39 pm
October 3rd, 2009 at 2:38 pm
What is the criteria for Darwin's alleged nested hierarchy?
All he has in his diagram are descent lines.
So there isn't any nested hierarchy at all.
Thank you for finally admitting that.
Nested hierarchy is determined by defining characteristics, not descent.
So again I thank you for proving you don't understand how to construct a nested hierarchy.
And if you want I am more than willing to put some money on it so we can settle this once and for all.
Comment by ID guy — October 3, 2009 @ 2:38 pm
October 3rd, 2009 at 2:41 pm
The problem with the "random sequence" scenario is no one can get those sequences to form without agency intervention.
Geez it takes agency intervention just two get a couple of nucleotides.
And it took quite a bit of agency intervention to synthesize RNA that can catalyze one bond.
So if we leave fantasy-land behind and use our observations and experience, ie knowledge, abiogenesis by way of undirected processes is "impossible".
Comment by ID guy — October 3, 2009 @ 2:41 pm
October 3rd, 2009 at 2:46 pm
zach, the focus of the paper is centered on these 4 families that bind ATP. It started out with random amino acids and then they selected for the ones that bind ATP. I have no idea what you are referring to here, did you even read the paper?
zach:
The claim is "functional proteins are suffciently common in protein sequence space (roughly 1 in 10^11) that they may be discovered by entirely stochastic means," if you get stronger binders via a non-random process, you essentially undercut that claim. If you're saying evolution works in the way that they evolved the stronger binders, well, naturally, I have no qualms with that.
zach:
What they got is something different from extant life. ATP-binding is universal and so it is also probably very ancient. So any experiement that purports to be relevant to the origin of life shouldn't come up with something that works differently. Furthermore, the only thing they got through a truly stochastic process was weak ATP binders, it would be far more impressive if they generated ATP-dependent interacting proteins. As far as being "well-within the parameters", I don't think so, even the author admits that the frequency is rather low. All that energy wasted to make thousands and thousands of proteins only to yield weak ATP-binders. Evolution doesn't even work that way, it more often reuses rather than depend on de-novo generation. So this suggests that relevant protein functions are not all that common.
Comment by Guts — October 3, 2009 @ 2:46 pm
October 3rd, 2009 at 3:58 pm
Zachriel,
If descent with modification leads to a nested hierarchy then we should be able to build a nested hierarchy out of a family tree.
Family tree- with a trunk, limbs, leaves and buds.
So what do you say Zachriel- Is a family tree a nested hierarchy?
Do the parents consist of and contain* all of their descendents?
* Nested and non-nested hierarchies: nested hierarchies involve levels which consist of, and contain, lower levels.
Comment by ID guy — October 3, 2009 @ 3:58 pm
October 3rd, 2009 at 5:06 pm
A biological taxonomy is a classification scheme based on character traits. A nested hierarchy is a mathematical structure, an ordered set such that each subset is strictly contained within its superset. In this case, each set of the nested hierarchy is defined by the posited common ancestor. The key to Darwin's argument is that the nested hierarchy of the taxonomy is explained by the nested hierarchy of the posited descent from common ancestors. As I said, this leads to non-trivial predictions.
Comment by Zachriel — October 3, 2009 @ 5:06 pm
October 3rd, 2009 at 5:33 pm
You said there "is no evidence" that Stonehenge "was created by flood waters". I say that there is just as much evidence, (and of the same sort), that Stonehenge was created by flood waters as there is that life rose from non-life, or that some major biological system arose from a series of accidents.
Think about it. The "evidence" that life arose from non-life is not direct evidence but simply circumstantial evidence of the kind 'look, here's evidence that it could have happened'. This is the kind of evidence I cited for my imaginary flood water Stonehenge theory.
The same is true of virtually every imagined scenario for the evolution of some major biological system, be it bat wings, feathers, or eyeballs, all of them are merely 'just-so' stories about how it might have happened.
My imaginary Stonehenge hypothesis is as good (or better) than anything you can cite in support of your position.
And I'm pointing out that – while antibiotic resistance may be 'major' to a bacteria – it is not the evolution of a major system by any definition of the term except yours. The evolution of antibiotic resistance is merely designed variation. Now if bacteria became multicellular in order to fight antibiotics, that would qualify as the evolution of a major system.
Ever read Schindewolf? Just because evolution can be chronicled does not mean that the mechanism was 'Darwinian' in nature. Schindewolf chronicled hundreds of cases of evolution that defy accidental mechanisms. Think about it. Why did the mammalian inner ear evolve the way it did? Was it just a series of happy coincidental accidents that caused all the right bones to evolve just the right way? Or does evolution proceed according to an unseen plan? How is it that everything that goes into producing these bones evolved just enough to make the next step possible?
Your position – that all of life's myriad systems are just due to a series of happy accidents – is foolhardy at best and disingenuous at worst. It's an attempt to deny God by an atheist who doesn't want there to be any evidence for God, lest he be accountable to him. It's no different than my imaginary Stonehenge scenario. You're ignoring obvious design in favor of an imagined series of improbable accidents for which the evidence is scant at best.
Comment by Daniel Smith — October 3, 2009 @ 5:33 pm
October 3rd, 2009 at 5:41 pm
Yes, and since the paper was written a veritable industry has developed. A large library of novel proteins have been created, with binding, enzymatic and antibody activities.
Of course, for engineering purposes, purely random libraries are being replaced by libraries with specific distributional skews. For instance, abiogenetic theory suggests that limiting the amino acids in the random sequences to those posited to have evolved first in primordial organisms would improve the rate of foldable proteins while maintaining diversity.
That's exactly what's predicted. Weak activity provides an advantage. Evolution then causes optimization of the function. But evolution requires the initial function, so it was posited that random sequences would be capable of various functions. That was what was tested. And that was what was found.
Considering researchers don't have oceans of organic molecules with millions of microenvironments for millions of years, it is quite a remarkable finding. Some random RNA sequences even have autocatalytic properties.
Comment by Zachriel — October 3, 2009 @ 5:41 pm
October 3rd, 2009 at 5:49 pm
Ever notice how the critical links – the evolution of new genera, new families, etc., via a series of necessary speciations – are missing from every phylogenic tree?
There's no fossil evidence for any of this. All we have for these crucial steps are dotted lines. Hmm… what does that tell us?
PS. Why are the Preview and Edit functions not working?
Comment by Daniel Smith — October 3, 2009 @ 5:49 pm
October 3rd, 2009 at 5:53 pm
A human family tree is not a nested hierarchy because there is crossing between lineages during mating. However, the male lineage and the female lineage each form a separate nested hierarchy as represented by the y-chromosome and the mitochondrial DNA respectively.
DNA testing for tracing one's ethnic heritage is quite a fad nowadays. It's based on the nesting inherent in uncrosssed, branching descent from common ancestors.
Comment by Zachriel — October 3, 2009 @ 5:53 pm
October 3rd, 2009 at 5:58 pm
Yet these vast oceans of organic molecules in their millions of microenvironments were somehow able to find each other (in literal oceans mind you) combine all their resources (we're talking about molecular structures – not Titanic sized ships) through HGT and the like (I prefer the scientific term 'swapping spit' myself) to produce the LUCA with its universal DNA!
It's an amazing story Zach! Tell us more!
Comment by Daniel Smith — October 3, 2009 @ 5:58 pm
October 3rd, 2009 at 6:09 pm
zach:
Probably best to include references of what you are actually talking about rather than provide a reference that doesn't show what you think it shows.
zach:
Various functions? What they found was strong ATP binding, and the stronger binders were gotten through mutagenic PCR. They then continued the original rounds of selection.
Regardless, it's not relevant.
zach:
Eh? That has nothing to do with what I wrote.
Comment by Guts — October 3, 2009 @ 6:09 pm
October 3rd, 2009 at 6:39 pm
All you are doing is handwaving. I gave the example of the evolution of the mammalian middle ear. You said it's "a vague, undefined pathway with no experimental evidence to back it up." In fact, it's specific, well-defined, and the embryonic data predicted the fossil data.
Comment by Zachriel — October 3, 2009 @ 6:39 pm
October 3rd, 2009 at 7:30 pm
You said trees form a nested hierarchy.
A family tree isn't any different than the tree of life/ trees or life.
There is mating going on in those trees.
A lineage cannot form a nested hierarchy. That is because well, it's a lineage.
You have absolutely no clue what a nested hierarchy is do you?
Lines do not form nested hierarchies.
Nested hierarchies are formed by defined characteristics.
Comment by ID guy — October 3, 2009 @ 7:30 pm
October 3rd, 2009 at 7:35 pm
I know.
That is what I have been telling you.
With evolution we would expect transitional forms would would defy containment.
With evolution there can be a loss of defining characteristics which would lead to a loss of containment.
You don't appear to be bright enough to understand any of that.
The best one can expect from genealogy is a partially ordered set.
However you don't seem to understand sets so that could be the whole problem.
Comment by ID guy — October 3, 2009 @ 7:35 pm
October 3rd, 2009 at 7:38 pm
What gene/ genes were involved?
We should be able to take embryos and mess with tem to get these alleged changes to appear- that is if your claim wants to be scientific and all.
Otherwise all you have is a bald declaration based on a specific PoV.
Comment by ID guy — October 3, 2009 @ 7:38 pm
October 3rd, 2009 at 8:30 pm
I thought we agreed that recently that there was no evidence that “cumulative selection” could be used as an explanation for chemical evolution under abiotic conditions. If cumulative selection is not plausible then we have to rely on a stochastic process to explain how functional protein sequences were “discovered” by some “dumb luck” type of process. However, this brings up another problem. To “find” a the functional protein sequence in a protein of say a 100 aa length we have to search though 20e100 = 1.2676506e130 possible sequences to find a subset that will provide the function that we need. And, that brings up yet another question, what percentage of the 1.2676506e130 possible sequences are functional? How can we make any type of definitive claim without answering that question?
Comment by JOHN_A_DESIGNER — October 3, 2009 @ 8:30 pm
October 3rd, 2009 at 9:43 pm
Leaving such egregious errors unchallenged is one of several reasons why ID will never be taken seriously outside the cloister.
The Tree of Life is a simile. In any case, the twigs on the typical tree do form a nested hierarchy when grouped naturally by branch and limb.
We define the sets such that each species is grouped with its descendent species. This forms an ordered set such that each subset is strictly contained within its superset.
That is incorrect. As long as lineages never overlap, then branching descent creates a nested hierarchy.
Unless we restrict our consideration to just the male or female lineages, of course.
Comment by Zachriel — October 3, 2009 @ 9:43 pm
October 3rd, 2009 at 10:18 pm
Selection may have some influence even in prebiotic conditions, but that isn't the issue here.
Take a look at the Keefe and Szostak paper. Random sequences (of nucleotides and of amino acids) can and do form functional ribozymes and proteins. They determined that about 10^-11 sequences have biological function. This experiment generated ATP binding proteins, but the technology has been extended and a variety of products have been produced, e.g. antibody-mimics. This dusty paper is particularly relevant.
Bartel & Szostak, Isolation of new ribozymes from a large pool of random sequences, Science 1993.
Comment by Zachriel — October 3, 2009 @ 10:18 pm
October 3rd, 2009 at 10:41 pm
Zachriel:
Zachriel, you previously stated "Selection may have some influence even in prebiotic conditions, but that isn't the issue here." I would argue that assigning selection a fitting role is the issue. You can cite random sequences leading to functional ribozymes and proteins but function occurs within a larger context. If that larger context is meaningful in an evolutionary context it must be replicated. Selection and function cannot be referenced in biological vacuums.
Comment by Bradford — October 3, 2009 @ 10:41 pm
October 3rd, 2009 at 10:45 pm
Based on what criteria?
IOW in what way do the twigs on a typical tree involve levels which consist of, and contain, lower levels.?
Please be specific.
A lineage cannot form a nested hierarchy.
We? As if you are part of it. LoL!!
But anyway nested hierarchies are formed by characteristics, not descent.
That is because descent is not a characteristic.
Also you said that a family tree does not form a nested hierarchy.
You seem to be all over the place. That is because you don't know what you are talking about and you aren't man enough to admit it.
Lineages cannot do that. It is a mathematical impossibility.
With evolution we would expect transitional forms would would defy containment.
Darwin agrees with me. And again it is a mathematical impossibility for a lineage to form a nested hierarchy.
Are you retarded or just dishonest?
The best one can expect from genealogy is a partially ordered set.
Just because you say so. Got it.
You don't seem to be capable of original thought Zachriel.
You don't understand how to construct a nested hierarchy.
You are clueless about sets and containment.
And you think your ignorance some how refutes the facts.
Comment by ID guy — October 3, 2009 @ 10:45 pm
October 3rd, 2009 at 10:49 pm
Charles Darwin in chapter 6 of "On the Origins of Species":
With evolution we would expect to see confusion, not order.
Comment by ID guy — October 3, 2009 @ 10:49 pm
October 3rd, 2009 at 10:54 pm
It may be an issue, but it wasn't the issue here. JOHN_A_DESIGNER was concerned about the probability of random sequences forming by some "dumb luck" type of process. Turns out dumb luck works.
Yes, it's a very important advance, and one consistent with abiogenetic theory.
Of course they can (though it may not represent a complete theory).
Comment by Zachriel — October 3, 2009 @ 10:54 pm
October 3rd, 2009 at 11:07 pm
The Chapter on difficulties on theory. What is Darwin's answer to these rhetorical questions?
A nested hierarchy is a mathematical structure, an ordered set such that each subset is strictly contained within its superset. You agreed to this definition. Sets can be formed by any rule (e.g. the contents of Sam of Ballyvourney's pocket can be considered as a set, even if his pocket is empty, as it often is.)
In this case, we are forming sets such that each species is grouped with all of its descendent species. Or in the case of a tree, twigs by branch and limb. In taxonomy, we use character traits. Darwin proposes that the nested hierarchy of Linnaean taxonomy is due to the nested hierarchy of descent. If the terminology confuses you, just call it something different. But we can map these various ordered sets, the posited common ancestry, the taxonomy, the archetypal tree, to one another.
Comment by Zachriel — October 3, 2009 @ 11:07 pm
October 4th, 2009 at 9:10 am
Darwin's answer was that DEATH provided the distinct categories, not descent.
A nested hierarchy is a CONTAIMENT set.
Containments set is contrasted with a partially ordered set. Genealogy, ie descent, gives us a partially ordered set.
Except that taxonomy is based on CHARACTERISTICS.
Descent is not a characteristic.
And Darwin attributed what we observe to death not descent.
Darwin said we should see confusion, not order.
If you were correct then a family tree would be a nested hierarchy. It isn't.
If you were correct any and all sequences would be a nested hierarchy- they are not.
For example:
Is a, b, c, d, e, f, g, h, i, j, k a nested hierarchy?
According to you it is.
IOW Zachriel you are not only ignorant you aren't even man enough to admit that you are wrong.
And it is very telling that you can't support your claims with valid references.
OTOH I have supported my claims with valid references.
Comment by ID guy — October 4, 2009 @ 9:10 am
October 4th, 2009 at 9:44 am
Well, not quite. It takes branching descent *and* competition leading to extinction.
That's correct.
Darwin posed a rhetorical question about the distinctiveness of species—which he then answered. Why are you misrepresenting his views?
Sexually reproducing populations do not form nested hierarchies. That's because the lines cross. However, once species become reproductively isolated, they don't cross. They form the characteristic branching pattern.
Darwin posits that they evolved from a common ancestor through a process that resembles the rest of the diagram. Hence, though the relationships are not shown in the diagram, they are part of the containing superset rooted in their common ancestor.
Comment by Zachriel — October 4, 2009 @ 9:44 am
October 4th, 2009 at 9:56 am
We are talking about sexually reproducing populations.
IOW Zachriel you just admitted that the alleged tree of life is not a nested hierarchy.
Are you saying they become asexual after becoming isolated?
LoL!!! You are just grasping for anything here.
Is a, b, c, d, e, f, g, h, i, j, k a nested hierarchy?
Darwin said the English alphabet evolved from a common ancestor?
RotFLMAO!!!!!!
But thank you for continuing to prove that you area clueless tool.
Comment by ID guy — October 4, 2009 @ 9:56 am
October 4th, 2009 at 10:07 am
Species that are reproductively isolated are separate populations. That is what Darwin is talking about.
No, but species that are reproductively isolated do not cross. That's what we mean by reproductively isolated.
We were discussing Darwin's diagram which begins with a-l. (No j though, as Paul Nelson pointed out. Ah, memories of the evolution of the letter j.)
You are an excellent representative for ID. Thank you.
Comment by Zachriel — October 4, 2009 @ 10:07 am
October 4th, 2009 at 10:08 am
Joe,
When you're done flaunting your ignorance on this thread, go read Evolution 101 on an educational website developed by biologists at the University of California at Berkeley (I am sure you have heard of this great institution). They explain in very clear terms how clades form a nested hierarchy. They even have color figures!
Come back and let us know what you have learned.
Comment by olegt — October 4, 2009 @ 10:08 am
October 4th, 2009 at 10:21 am
olegt,
My name is Jim.
And I have read that website.
Thay are wrong.
You should read "Evolution: A Theory in Crisis". It contains a chapter that thoroughly refutes the premise that evolution predicts a nested hierarchy.
And I have refuted that premise.
OTOH you appear to be totally clueless.
And you think you ignorance has some sort of meaning.
Strange.
Comment by ID guy — October 4, 2009 @ 10:21 am
October 4th, 2009 at 10:26 am
Yes they are but that still doesn't help your claim.
Nested hierarchies are built on characteristics. Descent is NOT a characteristic.
You appear confused on that point.
They don't form a nested hierarchy either.
In order to be a nested hierarchy one population must consist of and contain that isolated population.
It does not.
Darwin said the English alphabet evolved from a common ancestor?
Nope I just picked out a sequence of letters.
And according to you that sequence should form a nested hierarchy.
It does not.
You lose.
Comment by ID guy — October 4, 2009 @ 10:26 am
October 4th, 2009 at 10:33 am
From UC Berkley's site:
Zachriel has already admitted that a family tree is not a nested hierarchy.
A nested hierarchies involve levels which consist of, and contain, lower levels.
CONSISTS OF AND CONTAINS- do you not understand what that means?
Do you not understand that transitional forms violate the distinct categories nested hierarchy requires?
Do you really think that a LINEAGE can be represented as a nested hierarchy?
Tell you what oleg- I will put up $20,000.00 (US) against your $20,000.00 (US) and we can see who is correct.
Comment by ID guy — October 4, 2009 @ 10:33 am
October 4th, 2009 at 10:41 am
ID guy wrote:
Wow, we've got 2 bald-faced lies and one unsupported claim in just 3 sentences!
Let's see, the web site was developed by Roy Caldwell and David R. Lindberg, professors in the Department of Integrative Biology at Berkeley. On the other hand we have Mr. Joe G., a layman with zero background in biology and mathematics, who claims that they are wrong without further explanation.
I'm impressed!
Comment by olegt — October 4, 2009 @ 10:41 am
October 4th, 2009 at 10:47 am
Joe,
When you have read that web page click on the link saying next.
You may send the $20K to my business address. A fee of $50 will be assessed for every bounced check.
Comment by olegt — October 4, 2009 @ 10:47 am
October 4th, 2009 at 10:48 am
olegt the ignorant,
I have explained why the site is wrong.
It is like this- nested hierarchies are built on defined characteristics. Descent is not a characteristic.
With evolution we would expect confusion, not order, just as Darwin stated.
With evolution transitionals violate the distinct categories nested hierarchy requires.
With evolution there isn't any direction of additive characteristics.
Nested hierarchy demands a direction of additive characteristics.
And once again I am willing to throw down $20,000.00 (US) against yiu any time.
I will also show you my ID at that debate.
Comment by ID guy — October 4, 2009 @ 10:48 am
October 4th, 2009 at 10:50 am
olegt the ignorant,
Where on the pages you linked to does it say that descent with modification leads to a nested hierarchy?
Hint- it doesn't.
As a matter of fact you haven't demonstrated that you even know what a nested hierarchy is.
And you think that your ignorance is some sort of refutation.
Comment by ID guy — October 4, 2009 @ 10:50 am
October 4th, 2009 at 10:52 am
So here is the challenge-
Olegt and myself in front of a panel of biologists and mathematicians.
We both ante up $20,000 (US).
We both present our cases. And we let the panel decide.
Comment by ID guy — October 4, 2009 @ 10:52 am
October 4th, 2009 at 10:54 am
A nested hierarchy is just a mathematical structure as defined above. A taxonomy is a type of nested hierarchy classification based on character traits.
In phylogeny, we build our sets based on the posited common ancestor.
{a, b, c, d, e, f, g, h, i, j, k}is not a nested hierarchy as there are no defined subsets.However,
{a, b, c, {d, {e, f}}, {g, {h, {i, j}}}, k}is a nested hierarchy.Comment by Zachriel — October 4, 2009 @ 10:54 am
October 4th, 2009 at 10:55 am
ID guy,
OK, I nominate biologists Caldwell and Lindberg to the panel.
P. S. And Joe, when you are pretending to be someone else, don't use your characteristic punctuation (oleg- I will) and your trademark insults.
Comment by olegt — October 4, 2009 @ 10:55 am
October 4th, 2009 at 10:59 am
http://evolution.berkeley.edu/...
That does not make it a nested hierarchy.
No it isn't.
Thank you for proving that you don't understand the concept- again.
How does the subset {d,{e,f}} contain a, b, c?
It does not.
Comment by ID guy — October 4, 2009 @ 10:59 am
October 4th, 2009 at 11:01 am
And I will nominate biologist Michael Denton and biologist Tim Allen- author of A SUMMARY OF THE PRINCIPLES OF HIERARCHY THEORY.
Now for some mathematicians.
Comment by ID guy — October 4, 2009 @ 11:01 am
October 4th, 2009 at 11:05 am
That answers both your objections.
Please quit misrepresenting Darwin's rhetorical question as a statement.
Comment by Zachriel — October 4, 2009 @ 11:05 am
October 4th, 2009 at 11:11 am
Zachriel,
That quote does not say that descent with modification leads to a nested hierarchy.
And I am not misrepresenting Darwin. He knew there should be confusion.
However you are misrepresenting everything.
But that is because you appear to be uneducated.
Comment by ID guy — October 4, 2009 @ 11:11 am
October 4th, 2009 at 11:13 am
When people think that descent is a defining characteristic you know they are totally clueless.
Population A gives rise to pop[ulations A1 and A2.
A1 and A2 are isolated from each other and also from A.
Does population A consit of and contain populations A1 and A2? No it does not.
Therefore there isn't a nested hierarchy based on descent.
Comment by ID guy — October 4, 2009 @ 11:13 am
October 4th, 2009 at 11:14 am
{d,{e,f}}is a subset of the superset {a, b, c, {d, {e, f}}, {g, {h, {i, j}}}, k}. We will name the sets as follows:A = {a, b, c, {d, {e, f}}, {g, {h, {i, j}}}, k}D = {d, {e, f}}
E = {e,g}
G = {g, {h, {i, j}}}
H = {h, {i, j}}}
I = {i, j}
I is strictly contained in
Hwhich is strictly contained inGwhich is strictly contained inA.Eis strictly contained inDwhich is strictly contained inA. Each subset is strictly contained within its superset, hence is meets the definition of a nested hierarchy to which you agree above.We might represent it as tree like this:
ab
c
d
.. e
.. f
g
.. h
.... i
.... j
k
We *define* the set as the common ancestor and all its descendants (living and extinct).
Comment by Zachriel — October 4, 2009 @ 11:14 am
October 4th, 2009 at 11:25 am
ID guy wrote:
Joe, read the entire Evolution 101, it's a short course. Then connect the dots. Here are Cliffs Notes.
I'd like to collect my $20K.
Comment by olegt — October 4, 2009 @ 11:25 am
October 4th, 2009 at 11:38 am
Zachriel,
You have no idea what a nested hierarchy is even though I linked to the summary of the accepted standards of a nested hierarchy.
Except that you said a family tree does not form a nested hierarchy and all the alleged tree of life is is a family tree.
Comment by ID guy — October 4, 2009 @ 11:38 am
October 4th, 2009 at 11:38 am
Olegt:
I take it you're ignoring your own advice to not engage Joe.
Comment by Bradford — October 4, 2009 @ 11:38 am
October 4th, 2009 at 11:41 am
OlegT,
You are not even addressing any of the refuting arguments.
You appear proud to be ignorant.
Unfortunately there isn't any help for the willfully ignorant.
However I will write an email to that website and see if they will respond.
Perhaps they are not as cowardly as you.
One can only hope…
Comment by ID guy — October 4, 2009 @ 11:41 am
October 4th, 2009 at 11:42 am
Yeah, Bradford, I'm doing it against my better judgment.
But only because none of the ID people seem willing to point out to Joe how wrong-headed he looks.
Comment by olegt — October 4, 2009 @ 11:42 am
October 4th, 2009 at 11:44 am
Again:
First to understand NH you have to understand the meaning of consist and contain.
And example was provided. That example suppoorts my position and refutes the moron twins' position.
Will that mean anything to them?
Comment by ID guy — October 4, 2009 @ 11:44 am
October 4th, 2009 at 11:46 am
Clades, Joe! It's clades that form a nested hierarchy in evolution! Write that down.
Comment by olegt — October 4, 2009 @ 11:46 am
October 4th, 2009 at 11:50 am
It is the Linnean system that produces a nested hierarchy.
That is because it is involve(s) levels which consist of, and contain, lower levels.
Comment by ID guy — October 4, 2009 @ 11:50 am
October 4th, 2009 at 11:51 am
1- That was never my argument.
2- Clades are not beholden to the same rules as a nested hierarchy
3- With evolution characteristics can be lost
4- Lose a charcteristic means you lose containment
This is all explained by Denton in "Evolution: A Theory in Crisis".
But I do thank you for proving that you are indeed clueless.
Comment by ID guy — October 4, 2009 @ 11:51 am
October 4th, 2009 at 11:54 am
Sigh. And I'm here double-counting curly brackets {} like it's going to make a difference. (They say you have to hit rock bottom before you recognize the need to seek help.)
I wish to thank the ID Community once again for allowing ID guy to be their public representative. There's someone named Joseph over at Uncommon Descent who fills the same role.
By the way, Caldwell and Lindberg were sued. They won.
Comment by Zachriel — October 4, 2009 @ 11:54 am
October 4th, 2009 at 11:56 am
My claims:
1- Based on the fact that evolution does not have a direction of immutatble and additive characteristics and nested hierarchy demands that direction.
2- See 1
3- See 1
4- Cladograms are based on shared characteristics not necessarily immutable and additive
Comment by ID guy — October 4, 2009 @ 11:56 am
October 4th, 2009 at 11:59 am
Any onlooker can see that neither Zachriel nor olegt has responded to the refutations that I and Michael Denton- and others I am sure- have presented.
They think that their bloviations are meaningful.
Heck olegt obviously didn't even understand what I was talking about.
And Zachriel- as everyone who has ever dealt with knows- is just a bag of air.
Your parents must be very proud of you.
Comment by ID guy — October 4, 2009 @ 11:59 am
October 4th, 2009 at 12:02 pm
As we can't agree on the nature of a nested hierarchy, discussing your claims in that form would be unproductive.
Uncrossed, branching descent predicts nested clades.
That's a taxonomy. A clade is a grouping that includes a common ancestor and all the descendents (living and extinct) of that ancestor. This was mentioned a few times already.
Angels are created beings.
-
edit
Comment by Zachriel — October 4, 2009 @ 12:02 pm
October 4th, 2009 at 12:18 pm
ID guy wrote:
Will some of the onlookers have the courage to tell Joe how he is doing on this thread? Pretty please?
Comment by olegt — October 4, 2009 @ 12:18 pm
October 4th, 2009 at 2:48 pm
No it does not.
Nested hierarchies are not determined by descent, which produces a lineage.
Cladistics do not have to follow the rules of a nested hierarchy.
Comment by ID guy — October 4, 2009 @ 2:48 pm
October 4th, 2009 at 2:49 pm
Will they have the courage to tell you that you have completely shit the bed?
Obviously you don't have the courage to address the refutations presented.
Comment by ID guy — October 4, 2009 @ 2:49 pm
October 4th, 2009 at 3:25 pm
It is quite clear that discussing anything with you is unproductive.
Comment by ID guy — October 4, 2009 @ 3:25 pm
October 4th, 2009 at 4:35 pm
Talk about a pot/kettle moment!
Comment by Daniel Smith — October 4, 2009 @ 4:35 pm
October 4th, 2009 at 6:33 pm
What is the definition of a clade?
Comment by Zachriel — October 4, 2009 @ 6:33 pm
October 4th, 2009 at 6:58 pm
The book Uncommon Dissent was edited by Bill Dembski. It had a separate website.
See: http://www.uncommondissent.com...
which is linked to the Discovery Institute. Notice, the original word was "dissent"!
The phrase: "Uncommon Descent" was obviously a play on words for that original phrase "Uncommon Dissent".
Members who were recruited into the "Uncommon Descent" did not necessarily reject universal common ancestry, the most notable was DaveScot Springer.
I spoke to Behe at the DI book release party for "edge of evolution" a couple years back. Behe still accepted common descent back then but said somethng of the order of "I accept common descent, but if it isn't true it isn't true, my book focuses on ……."
For behe to change his mind, he would need compelling evidence to the contrary. Even creationists admit there is compelling evidence for certain kinds of common ancestry, the best articulated survey of evidence in favor of common anscestry is by the YEC Todd Wood:
The Chimpanzee Genome and the Probelm of Biological Similarity
Comment by Salvador T. Cordova — October 4, 2009 @ 6:58 pm
October 4th, 2009 at 7:07 pm
OK I see my mistake.
Uncrossed, branching descent does not predict a nested hierarchy.
Nested clades could be produced depending on what was alive at the time the clade was named.
It would also depend on whether or not characteristics were changed.
So it would all depend.
And if there is only one branch you would have a clad, not nested clades.
Clade:
Imagine that- just as I have been saying for years…
Comment by ID guy — October 4, 2009 @ 7:07 pm
October 4th, 2009 at 8:04 pm
Joe, you're making progress. However, this is wrong:
Clades may include extinct species as well. Furthermore, they are not based on characteristics but solely on ancestry. See this table for a comparison of the Linnaean taxonomy and cladistics: Summary of criticisms of cladistics.
Comment by olegt — October 4, 2009 @ 8:04 pm
October 4th, 2009 at 8:32 pm
OlegT,
Unfortunately you still don't know what is being debated, even though I spelled it out.
And you still haven't addressed any of the refutations I have presented.
You think your cowardess is some type of cunning tactic.
Weird.
I would have thought that to show one his/ her "wrong-headedness" you would have to actually address what that person is saying.
Silly me.
Regardless-
With clades the ancestry is assumed depending on shared characteristic traits.
The more shared characteristics allegedly the closer the ancestry.
My point about the transitionals being alive is that then they could become buds as opposed to being on any one line.
Also as I have said characteristics can be lost. And even then regained at some later time.
Therefore unless you directly observed the split you couldn't correctly place them on a cladogram.
Comment by ID guy — October 4, 2009 @ 8:32 pm
October 4th, 2009 at 8:47 pm
With cladistics, why only two paths from any node?
How is that supposed to mirror what can really happen?
"Well we couldn't keep using the Linnean System because people are starting to realize that we just stole it from the Creationists and just changed the names. So we developed cladistics to help illustrate the tree patterns Darwin drew. But we knew if we made it resemble how evolution really works no one would understand it so we fudged it just a little. (chortle)" anonymous biologist
Comment by ID guy — October 4, 2009 @ 8:47 pm
October 4th, 2009 at 9:00 pm
It's called polytomy. They can occur in a cladogram due to insufficient resolution of the evolutionary divergence, or due to simultaneous speciations (e.g. adaptive radiation).
Comment by Zachriel — October 4, 2009 @ 9:00 pm
October 5th, 2009 at 7:14 am
With cladistics, why only two paths from any node?
Wrong- a polytomy is not that cladistics can only have two branches from any particular node.
But anyway this (polytomy) proves my point that cladistics assumes common ancestry by way of shared characteristics
Comment by ID guy — October 5, 2009 @ 7:14 am
October 5th, 2009 at 7:45 am
Contrary to the presupposition implicit in your question, a cladogram can have more than two branches from a node. This is called a polytomy, as opposed to a dichotomy.
Note that there are two cases, a soft dichotomy wherein there is insufficient data to resolve the order of events, and a hard dichotomy where there were multiple, simultaneous branchings in fact.
Comment by Zachriel — October 5, 2009 @ 7:45 am
October 5th, 2009 at 8:00 am
The data may come from shared characteristics, but a cladogram is a representation of hypothesized evolutionary relationships.
Comment by Zachriel — October 5, 2009 @ 8:00 am
October 5th, 2009 at 8:27 am
I know that.
It's just that all the examples never portray that.
Old news.
Exactly what I said- common ancestry is assumed depending on the number of shared characteristics.
Now how about responding to my refutations of your claim that my claims are all wrong.
Here they are again:
1- Based on the fact that evolution does not have a direction of immutatble and additive characteristics and nested hierarchy demands that direction.
2- See 1
3- See 1
4- Cladograms are based on shared characteristics not necessarily immutable and additive
OR admit that you were wrong and my claims are correct.
Comment by ID guy — October 5, 2009 @ 8:27 am
October 5th, 2009 at 9:27 am
There are a number of ways to define a clade. However, all cladograms represent evolutionary descent. By the way, what is the definition of a clade? And is a clade a set?
As we can't agree on the nature of a nested hierarchy, discussing your claims in that form would be unproductive. Perhaps you could restate them without reference to the nested hierarchy.
Comment by Zachriel — October 5, 2009 @ 9:27 am
October 5th, 2009 at 9:39 am
They assume evolutionary descent.
I provided a link to the definition of "clade" above.
And yes a clade is a set.
However not all sets can form a nested hierarchy.
In order to be a nested hierarchy it must involve levels which consist of, and contain, lower levels.
It is a very simple concept.
Perhaps that is why you are unable to wiggle around it.
Translation- Zachriel is a coward.
The point is Zachriel, you don't have any idea what a nested hierarchy is even though I have provided all the information necessary for doing so.
And that you think your ignorance is some sort of refutation is very amusing.
Comment by ID guy — October 5, 2009 @ 9:39 am
October 5th, 2009 at 9:41 am
Evolution does not predict a nested hierarchy.
Common descent does not predict a nested hierarchy.
Descent with modification does not predict a nested hierarchy.
Cladograms are not nested hierarchies because cladograms are not beholden to the same rules as a nested hierarchy.
Seeing that nested hierarchy is what is being debated why would I want to not reference it?
All YOU have to do, Zachriel, is provide a valid/ verified nested hierarchy that does not follow the rules that I linked to.
Good luck with that…
Comment by ID guy — October 5, 2009 @ 9:41 am
October 5th, 2009 at 10:16 am
You linked to Wikipedia
Okay. And as you know, there are no crossings in a cladogram. Hence, each child has one-and-only-one parent, though a parent can have more than one child (typically two). Is this correct?
Our agreed definition of a nested hierarchy is an ordered set such that each subset is strictly contained within its superset. You seem to believe that a nested hierarchy requires rigid ranking, such as seen in Linnaean taxonomy. Is that correct? Is a containment hierarchy the same as a nested hierarchy?
Comment by Zachriel — October 5, 2009 @ 10:16 am
October 5th, 2009 at 10:36 am
Zachriel,
I know what I linked to.
Just because there aren't any crossings in a cladogram does not mean there aren't any crossings in real life.
Most animals have two parents.
But if you are calling a population a "parent" 1- that is misleading and 2- the parent populkation does not consist of and contain all subsequent child populations.
I use the definition provided by the ISSS.
If you use anything else you are not using the correct definition.
According to the ISSS it does.
Anyone who thinks otherwise needs to support that with valid references.
Once again-
In order to be a nested hierarchy it must involve levels which consist of, and contain, lower levels.
So why should anyone listen to "Zachriel" over the The International Society for the Systems Sciences?
(no a containment hierarchy is not the same as a nested hierarchy- however they do have similarities)
Comment by ID guy — October 5, 2009 @ 10:36 am
October 5th, 2009 at 11:00 am
That's a possibility, but that's a separate issue at this point (though hybridization is an important element, especially in plants). I'm just trying resolve some definitional issues.
A parent is defined as the immediate ancestor, the child as the immediate descendent.
No, but the clade does. That's why I keep asking you to repeat the definition.
That's a discussion of some principles of hierarchy theory, not a concise definition. You had agreed to the set definition. Have you changed your mind?
The levels in a cladogram are determined by the distance measured in branching events, not by an arbitrary ranking system. What would you call the geometry of the tree-like structure of a cladogram?
Here's Wikipedia on the Nested Hierarchy: A nested hierarchy is the name given to the classification of objects into a hierarchical structure of "groups within groups" or "branches from a trunk".
Comment by Zachriel — October 5, 2009 @ 11:00 am
October 5th, 2009 at 11:34 am
Zachriel wrote:
Zachriel, I am afraid this clarification won't help because Joe still doesn't understand what a clade is.
Comment by olegt — October 5, 2009 @ 11:34 am
October 5th, 2009 at 11:49 am
Then there would be two parents- in most cases.
the parent population does not consist of and contain all subsequent child populations.
The clade isn't a nested hierarchy.
I use the definition provided by the ISSS.
Sure it does. I even quoted it.
And what I quoted is more concise than what you have presented.
In order to be a nested hierarchy it must involve levels which consist of, and contain, lower levels.
That doesn't have anything to do with what I said.
I am talking about NESTED HIERARCHIES.
That clades can be nested does not make them nested hierarchies.
It also appears that the word "nested" in cladistics isn't used how the rest of the world uses the word. See nested.
IOW cladistics says they are "nested" if they share a common ancestor, yet ancestors do not contain their descendents.
So the bottom line is you don't know what a nested hierarchy entails and you think your ignorance some how refutes what I said.
Comment by ID guy — October 5, 2009 @ 11:49 am
October 5th, 2009 at 11:50 am
olegt,
Are you proud of yourself that you can fart bald asserttions?
You act just like all cowards.
Why is that?
Comment by ID guy — October 5, 2009 @ 11:50 am
October 5th, 2009 at 11:54 am
And if you cannot understand those principles there isn't any way you can understand what a nested hierarchy is.
And you have not shown any indication that you understand those principles.
My claims adhere to those principles.
Zachriel sez to screw those priniciples a nested hierarchy is what I say it is.
All the while olegt acts as Zachriel's cheerleader.
Thelma and Louise would be proud…
Comment by ID guy — October 5, 2009 @ 11:54 am
October 5th, 2009 at 12:03 pm
Again, we're only talking about the abstraction called a cladogram. In a cladogram, each child has one-and-only-one parent. Is that correct?
That's not a complete definition. In any case, a cladogram meets that requirement. A clade is a common ancestor and all its descendents. Those descendents along with their descendents also form clades. Hence, the higher level clade consists of and contains the lower level clades.
No, but the clade does. Can you give us the definition of a clade?
Comment by Zachriel — October 5, 2009 @ 12:03 pm
October 5th, 2009 at 3:02 pm
Zachriel,
We are talking about what evolution, universal common descent and descent with modification predict.
And it does not predict a nested hierarchy for all the reasons provided.
The reasons you ignore as if ignorance is some sort of refutation.
We are not talking about what we can do to classify organisms.
We are not talking about forcing our assumptions into a classification scheme.
For example a normal cladogram has Aves "nested" in the reptile clade.
However in doing so the word "nested" is not the same as the word "nested" in nested hierarchy.
The word "nested" when it comes to cladistics means something else entirely.
Comment by ID guy — October 5, 2009 @ 3:02 pm
October 5th, 2009 at 3:16 pm
ID guy wrote:
Joe, you're doing it wrong! Nested hierarchy works for monophyletic groups. Reptiles is a paraphyletic group. It is obtained by removing clades Aves and Synapsida (which includes Mammalia) from Amniota. The result is not a clade. That's why it's not a nested hierarchy.
Comment by olegt — October 5, 2009 @ 3:16 pm
October 5th, 2009 at 4:22 pm
olegt,
You are still in the wrong ballpark.
Once again you didn't even address what I posted.
I was just talking about the word "nested".
I said the way the word "nested" is used in cladistics is not the same way as it is used in nested hierarchy.
Aves are nested under reptiles in cladistics.
Notice I never said there was a nested hierarchy.
But again that is my point- that the way the word "nested" is used is different.
cladistics
According to that aves have an ancestor of reptiles.
See aves reptiles monophyly in yellow.
Comment by ID guy — October 5, 2009 @ 4:22 pm
October 5th, 2009 at 4:25 pm
But anyway olegt you still haven't addressed my initial claims.
You think that by dancing around people will forget what it is that is being disputed.
Comment by ID guy — October 5, 2009 @ 4:25 pm
October 5th, 2009 at 9:28 pm
ID guy wrote:
You know, Joe, no offense but this stuff really does seem to be above your head. It's okay, we all have limitations. I can't wrap my brain around philosophical arguments and I don't get worked up about it.
The term nested in cladistics is used precisely in the same sense as in nested hierarchy. You attempted to use Reptilia and Aves as an counter example but you failed because Reptilia is not a clade. The Wikipedia article on reptiles provides this nice explanation from science writer (with a degree in biology) Colin Tudge:
Because Reptilia is not a clade, your counter argument falls apart: we do not expect a nested hierarchy in this group.
No, it's the same—as long as we are talking about clades. If you have a valid counter example show us, otherwise concede that clades form a nested hierarchy.
Here are your claims, Joe (emphasis in the original):
Joe, you are fubar. I pointed you to an educational web site, where two full professors of biology at Berkeley explain in simple terms that common descent implies a nested hierarchy of clades. I even provided a helpful summary of their arguments in this thread. (And you claimed that you had previously read the site!) If you can't follow that simple explanation, there is nothing anyone can do for you. It's above your head. Sorry.
Comment by olegt — October 5, 2009 @ 9:28 pm
October 6th, 2009 at 7:30 am
No it does not.
Just you saying it is the same doesn't make it so.
I demonstrated how they are not the same- aves are not "nested" in reptiles in the same way mammals are nested in vertevrata (in Linnean Classification)
I never said reptilia was a clade.
I said by the cladogram provided aves have reptiles for an ancestor.
Are you retarded?
That doesn't have anything to do with what I am saying.
Also "nested" in cladistics just means that someone put them there as an ancestor.
They are not nested by any means of the definition of "nested".
Geez I even provided a definition of nested for the context we are using.
Also if a nested hierarchy is formed it is there at any two or more levels.
I provided a link to the principles of hierarchy and even provided a valid definition of nested hierarchy.
That you are too stupid to understand what it says doesn't mean it is wrong.
So what we have is olegt being retarded and misrepresenting my claims.
As I said you must be very proud of yourself.
Comment by ID guy — October 6, 2009 @ 7:30 am
October 6th, 2009 at 7:45 am
Just so we are clear:
That is not my argument.
My claims were very, very clear.
Not one of my claims said that common descent does not imply a nested hierarchy of clades.
However olegt has proven that cladograms are not nested hierarchies because cladograms are not beholden to the same rules as a nested hierarchy.
If they were then Aves would be nested under reptiles.
The bottom line is olegt is FUBAR and his only recourse is to attack me.
Comment by ID guy — October 6, 2009 @ 7:45 am
October 6th, 2009 at 7:46 am
ID guy wrote:
Yes, you did, Joe. In your own words:
That has never been in dispute.
You failed to point out how clades do not satisfy the definition of a nested hierarchy. You attempted to do so with Reptiles but it did not work out. So we are still waiting for a valid counter example.
Comment by olegt — October 6, 2009 @ 7:46 am
October 6th, 2009 at 7:52 am
Look at the cladogram and tell me why reptiles and aves are not in the same clade.
If we look at the definition of clade- A clade is a group, consisting of a single organism and all of its descendants.- my premise is correct as aves are a descendent of reptiles- that is if we go by the cladogram…
Comment by ID guy — October 6, 2009 @ 7:52 am
October 6th, 2009 at 8:03 am
ID guy wrote:
Lol! Joe, two lines above that you said "common descent does not predict a nested hierarchy," period. You thus deny a nested hierarchy of any kind! Including that of clades.
Keep embarrassing yourself!
Comment by olegt — October 6, 2009 @ 8:03 am
October 6th, 2009 at 8:09 am
So you get to tell me what my claim is?
I don't think so.
However seeing that Aves is not nested in reptiles your strawman of my claims holds true.
Comment by ID guy — October 6, 2009 @ 8:09 am
October 6th, 2009 at 8:12 am
Sure it is. It just means that one set is a proper subset of another, a hierarchy, series, or sequence of with each member, element, or set contained in or containing the next. That is, to fit compactly within another, like an egg in a bird's nest.
In cladistics, Mammalia and Dinosauria are strictly contained in (proper subsets of) Amniota. Amniota is a superset that consists of and contains Mammalia, Dinosauria, etc. Mammalia consists of and contains Eutheria, Marsupialia, etc. Hence, Dinosauria and Mammalia are properly nested within the higher-level classification, Amniota. We have a nested hierarchical arrangement.
Comment by Zachriel — October 6, 2009 @ 8:12 am
October 6th, 2009 at 8:32 am
In cladistics, Aves is nested in Reptilia through Diapsida. Linnaean taxonomy is also a nested hierarchy, but he had very limited knowledge of Reptiles and he set Reptiles as a separate class of Animals; therefore the class is not monophyletic.
Comment by Zachriel — October 6, 2009 @ 8:32 am
October 6th, 2009 at 8:39 am
Zachriel,
In order to be a proper subset it must contain ALL the characteristics of the superset.
Aves do not contain all the characteristics of reptiles.
Also aves is not nested in repltilia- olegt has said that.
So you don't understand nested hierarchies and you still think your ignorance means something.
Classic.
Also you and olegt need to get your stories straight.
Comment by ID guy — October 6, 2009 @ 8:39 am
October 6th, 2009 at 8:42 am
olegt,
In order to be a nested hierarchy, and therefore refute my claims, it must be a nested hierarchy through-n-through.
And to be nested doesn't just mean someone placed it there.
Comment by ID guy — October 6, 2009 @ 8:42 am
October 6th, 2009 at 8:45 am
{a, b, c, {d, {e, f}}, {g, {h, {i, j}}}, k}is also a nested hierarchy.Comment by Zachriel — October 6, 2009 @ 8:45 am
October 6th, 2009 at 8:50 am
Only to an ignoramus who doesn't understand nested hiearchies.
Comment by ID guy — October 6, 2009 @ 8:50 am
October 6th, 2009 at 8:54 am
Is your understanding that a nested hierarchy is the same as a taxonomy?
Is a nested hierarchy the same as a containment hierarchy?
Above, you agreed that a nested hierarchy is a mathematical structure, an ordered set such that each subset is strictly contained within its superset. The set
{a, b, c, {d, {e, f}}, {g, {h, {i, j}}}, k}meets that definition. Yet now you say it is not a nested hierarchy. Have you changed your mind concerning your acceptance of the definition you had agreed to above?Comment by Zachriel — October 6, 2009 @ 8:54 am
October 6th, 2009 at 9:03 am
Zachriel,
Read the ISSS link.
It explains exactly what it takes to be a nested hierarchy.
If you ate too stupid to understand that page then just give up.
Your alphabet example- the superset characteristics must be observed in EVERY lower level.
Obviously they are not.
Therefore you are an ignoramus and apparently proud of it.
Comment by ID guy — October 6, 2009 @ 9:03 am
October 6th, 2009 at 9:11 am
I don't see a concise definition, but a general discussion of some of the principles of hierarchies. "Nested hierarchies involve levels which consist of, and contain, lower levels." Cladograms, Linnaean Taxonomy and
set Aall have this characteristic.You had agreed to the set definition, but now you can't seem to be able to say one way or another. Is your understanding that a nested hierarchy is the same as a taxonomy? Is a nested hierarchy the same as a containment hierarchy? Are you rejecting the definition you had agreed to above?
It does. What would you call such an arrangement such that each subset is strictly contained within its superset?
Comment by Zachriel — October 6, 2009 @ 9:11 am
October 6th, 2009 at 9:21 am
Zachriel,
If you cannot understand what is written in the ISSS website article you don't belong in a discussion about nested hierarchies.
And if you think your alphabet example is an example of a nested hierarchy then discussing nested hierarchies with you is a waste of time.
Comment by ID guy — October 6, 2009 @ 9:21 am
October 6th, 2009 at 9:24 am
Please provide an example.
Comment by Tom MH — October 6, 2009 @ 9:24 am
October 6th, 2009 at 9:25 am
Send an email with your alphabet example to the author of the ISSS article.
Ask him if it represents a nested hierarchy.
Just so that you know- I have sent such an email to Dr Allen.
Comment by ID guy — October 6, 2009 @ 9:25 am
October 6th, 2009 at 9:36 am
I've asked you a few questions so as to understand your position better. But you keep refusing to answer.
You had agreed to the set definition, but now you can't seem to be able to say one way or another. Is your understanding that a nested hierarchy is the same as a taxonomy? Is a nested hierarchy the same as a containment hierarchy? Are you rejecting the definition you had agreed to above?
It really doesn't matter what you call it. What would you call an arrangement such that each subset is strictly contained within its superset?
Comment by Zachriel — October 6, 2009 @ 9:36 am
October 6th, 2009 at 9:55 am
A = {a, b, c, {d, {e, f}}, {g, {h, {i, j}}}, k}D = {d, {e, f}}
E = {e,g}
G = {g, {h, {i, j}}}
H = {h, {i, j}}}
I = {i, j}
A = mammals.. a = deer
.. b = rodents
.. c = primates
.. D = bovines.... e = cows
.... f = yak
.. G = carnivores.... g = cats
.... H = canines...... h = wolves
...... I = dogs
........ i = poodles
........ j = shepherds
.. k = kangaroosComment by Zachriel — October 6, 2009 @ 9:55 am
October 6th, 2009 at 10:26 am
Zachriel,
Send an email to Dr Allen and ask him if the English alphabet can be represented as a nested hierarchy.
If you refuse to do so then that alone proves that you are a coward.
And when you run with the goalposts from the English alphabet to:
It also proves that you are a coward.
"Mammals" are defined by characteristics, not descent.
Poodles are defined by characteristsics, not descent.
IOW all your latest example has done is support my claim.
Thank you.
Comment by ID guy — October 6, 2009 @ 10:26 am
October 6th, 2009 at 10:33 am
I answered that already Zachriel.
I said the are not identical but they do have similarities.
Linnean classification is a nested hierarchy as all subsets consist of and contain all of the characteristics of their supersets.
Animals have a set of specific characteristics.
Vertebrate contain all of those characteristics plus more.
Mammals contain all of the characteristics of vertebrates plus more.
With evolution, common descent, descent with modification, characteristics are not immutable and additive.
There wouldn't any distinct catgories- ie containment would be lost.
You seem incapable of understanding those simple concepts.
It appears that your only purpose is to deceive and confuse.
And you appear to be proud of yourself for doing so.
Now as I said earlier you and olegt can't even agree.
Comment by ID guy — October 6, 2009 @ 10:33 am
October 6th, 2009 at 10:34 am
ID guy, you have repeatedly refused to answer any relevant questions.
It really doesn't matter what you call it. What would you call an arrangement such that each subset is strictly contained within its superset?
{a, b, c, {d, {e, f}}, {g, {h, {i, j}}}, k}So you're saying a nested hierarchy is the same as a taxonomy (rather than a taxonomy being a type of nested hierarchy)?
Comment by Zachriel — October 6, 2009 @ 10:34 am
October 6th, 2009 at 10:54 am
ID guy wrote:
Joe, there is no disagreement between Zachriel and me. You are misinterpreting my words, either willingly or not. You tried to call Reptilia a clade and I pointed out that that was wrong. I never said anything about aves being "nested in reptilia."
So tell us, does common descent predict a nested hierarchy of clades or not?
Comment by olegt — October 6, 2009 @ 10:54 am
October 6th, 2009 at 11:28 am
olegt,
You don't appear to understand what a nested hierarchy is.
In order to be a nested hierarchy the scheme must be a nested hierarchy through-n-through.
Reptile and aves are in the same clade.
However aves are not nested in reptiles as they do not contain and consist of all the characteristics of reptiles.
The way "nested" is used in cladistics the only nesting is because someone put it there.
If the criteria is only of descent then there isn't a nested hierarchy.
Descent = genealogy and genealogy is a partially ordered set.
Comment by ID guy — October 6, 2009 @ 11:28 am
October 6th, 2009 at 11:32 am
Zachriel,
You have repeatedly failed to support your position.
You have proven that you don't understand nested hierarchies.
OTOH I have answered your questions even though you claim otherwise.
Now how about that email to Dr Allen?
Have you sent it?
I have already provided a reference that says cladistics is not the same as Linnean classification, yet you seem to conflate the two.
Comment by ID guy — October 6, 2009 @ 11:32 am
October 6th, 2009 at 11:35 am
Tell me how you are defining the word "nested".
If they are "nested" only by assumed descent then that does not meet the criteria of "nested" in the ISSS version of nested hierarchy.
Comment by ID guy — October 6, 2009 @ 11:35 am
October 6th, 2009 at 11:38 am
Joe, be specific: indicate which criterion is not met and which clade violates it.
Comment by olegt — October 6, 2009 @ 11:38 am
October 6th, 2009 at 12:08 pm
Well, I would like some clarification.
Are you saying a nested hierarchy is the same as a taxonomy (rather than a taxonomy being a type of nested hierarchy)?
What would you call an arrangement such that each subset is strictly contained within its superset?
{a, b, c, {d, {e, f}}, {g, {h, {i, j}}}, k}Comment by Zachriel — October 6, 2009 @ 12:08 pm
October 7th, 2009 at 10:29 am
If anyone is still reading this thread — here’s an easy way to see why Woese’s (or any) theory of communal evolution causes intractable problems for inferring monophyly, i.e., vertical descent from a discrete cell.
Take a regular notebook sheet of graph paper, and divide it into three sectors vertically, by drawing lines across the page from the left to right margin. (Graph paper isn’t necessary, but the pre-ruled lines help greatly in visualizing the problem.) Label the sectors, from bottom, respectively (1) communal evolution, (2) Darwinian transition / threshold, and (3) vertical descent. Time in the figure runs from (1) to (3).
At several — let’s say, 10 — of the vertices of the pre-ruled lines in (1), make a dot. These 10 dots will represent the “pre-cellular entities” of Woese’s theory: “organisms” (hard to say what these entities are, exactly, but we can call them organisms for lack of a better word) exchanging genetic information both laterally / horizontally, and vertically. The pre-ruled lines linking the entities horizonally show that information is passing between them.
Now, at 10 vertices in (3), make a dot. These 10 dots represent bona fide cells, in the region following what Woese calls the Darwinian threshold. Here, vertical descent dominates, so that the probability of horizontal or lateral transfer is significantly diminished.
OK, here’s the exercise:
Try to draw a figure connecting the 10 dots in (3) to a single, or unique dot in (1), so that any other such tree, or set of trees, is justifiably excluded.
Comment by Paul Nelson — October 7, 2009 @ 10:29 am
October 7th, 2009 at 11:10 am
Hello Paul,
Long time no C.
Zachriel and I have been so looking forward to your return. In the process we had to make a piñata out of Joe Gallien just to keep ourselves awake. Now you come back and you offer us this?
This is so lame! Neither of us is claiming that one can trace ancestry from (3) to (1). We asked you to explain how that fact presents a difficulty to tracing ancestry in (3), particularly among the upper branches (Animalia). Come on Paul, back up your ominous warnings about the corrosive effects with something.
To use my imprecise but useful analogy: you are still arguing about the lack of communication between Prague and Dresden. We know about that, we're not arguing about it. Explain why this poses a problem for travel between Dresden and Berlin.
Meanwhile, where's Joe?
Comment by olegt — October 7, 2009 @ 11:10 am
October 7th, 2009 at 11:34 am
Hi Oleg,
If you did the exercise, you'll see it is impossible to establish common ancestry (a unique tree) for the points in (3) to any point in (1). Indeed you say that "neither of us is claiming that one can trace ancestry from (3) to (1)." Thus, Eukarya may be polyphyletic.
OK, next step. Using another sheet of graph paper, rename the three sectors, as follows:
(1) Eukarya [sector 3 in the first exercise now becomes sector 1]
(2) Metazoa
(3) Chordata
Populate the sectors with multiple dots, as before. Time runs from (1) to (3), as before.
Then, draw a tree from (3) to (1), such that any other tree or set of trees is justifiably excluded. If you did the first exercise, Eukarya, sector (1), should have multiple dots terminating independently at the sector's lower margin.
Comment by Paul Nelson — October 7, 2009 @ 11:34 am
October 7th, 2009 at 12:26 pm
Nice try, Paul.
Can you tell me why Eukarya, sector (1), should be drawn as "multiple dots terminating independently at the sector's lower margin?" They aren't really independent at the Darwinian threshold. I would rather draw them as a single line. I then would run my ancestry lines from Chordata (3) down to Metazoa (2) and from Metazoa to the ground line (1).
Then there are several possible scenarios. In one, all metazoa came from a small vicinity of one point on the line. The rest of the eukarya line gave rise to descendants who died out. That would be the standard scenario of the tree of life with a slight modification at the root level (prior to the Darwinian threshold).
In another scenario, different branches of the tree would terminate at sufficiently well separated points on the ground line (1). That would mean that different metazoa came from different eukarya. Sort of like an aspen colony where all trees are distinct above the ground but share the root system.
Neither of these scenarios bothers me. The upper branches (Chordata) still form a single tree. Where are the corrosive consequences?
Comment by olegt — October 7, 2009 @ 12:26 pm
October 7th, 2009 at 12:49 pm
Oleg wrote:
Please clarify, in terms of the exercise, because you appear to be contradicting what you said above — namely, that ancestry cannot be traced from (3) to (1).
Eukarya is populated with multiple points. Do the lines of descent to those points (coming up from sector [2]) arise from a single point (vertex) in 2, or from multiple points?
It's unclear what you mean when you say "I would rather draw them as a single line."
How many lines cross the upper boundary of the Darwinian threshold, the line separating (2) and (3)?
Comment by Paul Nelson — October 7, 2009 @ 12:49 pm
October 7th, 2009 at 1:02 pm
Paul,
Let me clarify it. My depiction of eukarya in the new graph begins with the old (2), the Darwinian threshold. At that point these organisms are still related by HGT, so we draw the entire population as a single horizontal line. They are all related, not at all independent.
The second picture suggested by you starts with this horizontal line, the Darwinian threshold. Let's call it (0). Upwards from it we have vertical lines going through eukarya (1), metazoa (2), and finally chordata (3). They all begin at the ground level, which represents the end of the communal stage, and then propagate vertically as trees. In this picture chordata are still traceable to a unique branch originating at the ground level (0).
Comment by olegt — October 7, 2009 @ 1:02 pm
October 7th, 2009 at 1:04 pm
Here's a somewhat fanciful schematic of Woese's modified tree of life. Notice that other than the addition of organelles, eukaryotes are monophyletic. Animals are monophyletic regardless.
Comment by Zachriel — October 7, 2009 @ 1:04 pm
October 7th, 2009 at 3:24 pm
Oleg wrote:
If I understand you correctly, then, any cell within Eukarya may stem from any point (organism) on the whole horizontal (ground) line. The line depicts a population of cells, sharing the characters that define Eukarya (e.g., a membrane-bound nucleus), but which did not descend from an ancestral cell in (2) or (1).
How many cells (points) lie on your horizontal, or ground, line?
Zachriel, thanks for the picture, but that depicts WF Doolittle's ideas, not Woese's, iirc. I don't think their ideas are entirely congruent (with respect to the origin of the genetic code, for instance).
Comment by Paul Nelson — October 7, 2009 @ 3:24 pm
October 7th, 2009 at 3:57 pm
Indeed, you do recall correctly!
However, the discussion concerns the overall geometry. We can have a complex root and still have monophyletic trees emerging. Where does the schematic not suffice in this regard?
Comment by Zachriel — October 7, 2009 @ 3:57 pm
October 7th, 2009 at 4:32 pm
P A Nelson wrote:
Since the line is at the Darwinian threshold, I would imagine that there should be nearly continuous variation along that line: HGT washes out distinctions between lineages during the communal stage of evolution. Hence a continuous line instead of well-defined points.
Comment by olegt — October 7, 2009 @ 4:32 pm
October 7th, 2009 at 4:48 pm
Oleg wrote:
But HGT occurs between discrete cellular entities, by definition. Thus there must be distinguishable points (cells) on the line, whatever the degree of variation between them.
So, at the Darwinian threshold for Eukarya, you infer a population of n entities, unrelated by common ancestry (vertical descent) from an earlier cell, but sharing the characters that define Eukarya, such as a membrane-bound nucleus.
Comment by Paul Nelson — October 7, 2009 @ 4:48 pm
October 7th, 2009 at 4:52 pm
That's a good summary, Paul. Go on. (Zachriel will correct me if necessary.)
Comment by olegt — October 7, 2009 @ 4:52 pm
October 7th, 2009 at 5:09 pm
I had read the paper KC. Fits in well with my own ideas (none of which are original). I have been fiddling with Jimenez-Montoya’s six digit binary code. In particular I was interested in any patterns indicative of “trading-off” stabilityflexibility or adaptability. (E.g., taking the average weight, all the “complications,” all departures from symmetry, occur in average (“weightless”) or negatively weighted family boxes.)
Interesting result from graph theory (and the theory of parallel computing) is that any balanced color-coded tree (see figures 4&5?) may be embedded in a hypercube of the same dimension w/o “fudging.” Actually the results are limited to trees of 64 nodes. So far. Leaving the question of picking the origin unsolved. But I like Delarue’s choice of the origin very much! (Wish I’d thought of it!)
Comment by Rock — October 7, 2009 @ 5:09 pm
October 7th, 2009 at 6:11 pm
I wrote:
Oleg replied:
Then, for any extant eukaryote, there exists, not one, but n possible cellular ancestors at the Darwinian threshold (when Eukarya first evolved). This may be a very large number; in any case, n > 1.
In other words, the taxonomic character "possesses a membrane-bound nucleus" does not define a clade whose first representative was a discrete cell. Pick any eukaryotic species (say, the ciliated protozoan Tetrahymena thermophila) — one cannot be certain that a member of that species shares common ancestry, from a discrete cell, with a member of any other eukaryotic species (say, Drosophila melanogaster). In terms of the graph paper exercise I suggested, this can be represented by drawing lines of ancestry from any point (i.e., cell, at a vertex) in Eukarya through the horizontal or ground interval proposed by Oleg. Given that these lines of ancestry do not converge to a point, but pass through an interval of indeterminate width into a communal state, the set of ancestors of any eukaryote will not include a universally shared organismal member (usually referred to the literature as the last eukaryotic common ancestor, LECA).
In short, Eukarya is not a tree with a discrete root, arising from a unique cell, but a forest. If n possible ancestors exist at the Darwinian threshold, Eukarya has multiple origins.
Eukarya comes apart, from the bottom up. QED. The same will be the case for the clades nesting within Eukarya, if their defining characters are inferred to originate not in discrete cells, but communally (whatever that means — I don't know, except that Woese disallows inferences to discrete ancestors). The character "multicellularity," for instance, has been widely argued to arise all over the eukaryotic tree. We can repeat the exercise if you like for Metazoa, Chordata, etc.
Of interest, in the overall theme of this thread, if not the immediately preceding discussion, this new paper from Mike Arnold at the Univ. of Georgia:
http://www.mdpi.com/1422-0067/...
Comment by Paul Nelson — October 7, 2009 @ 6:11 pm
October 7th, 2009 at 8:04 pm
Not necessarily.*
Natural selection was alive and well before the Darwinian threshold. It is certainly reasonable to suppose that there were many episodes where innovations occurred which quickly came to dominate the population, one of those innovative bouts forming the root of Eukarya. The evidence supports Eukaryotic monophyly.
I'm not sure what you mean by communally here, but in orthodox evolution, we're dealing with populations. The population itself is the base of the branch. I think you're saying that if a population gives rise to a new species, that some of the new population will have variations among the population inherited from the old population. Population dynamics (e.g. bottlenecks, rapid adaptive episodes) tends to eliminate most of those variations, and we are typically left with a strong monophyletic signal. *Indeed, it will often be indistinguishable from n=1 (leaving aside hybridization, retroviruses, etc.).
Comment by Zachriel — October 7, 2009 @ 8:04 pm
October 7th, 2009 at 8:05 pm
Paul Nelson wrote:
Nothing new here. We all agree that vertical evolution does not work below the Darwinian threshold.
Nope. These n possible ancestors are not independent entities. Their genomes have formed through slow vertical evolution (innovation) and fast horizontal transfer (knowledge sharing). That is why I insisted on drawing a single horizontal line at the Darwinian threshold instead of a set of discrete points. Along that line we have numerous organisms with a shared origin. They crossed the threshold together, not independently of one another. That's the essence of communal evolution. In that sense eukarya originated once.
No, it doesn't. Below the threshold HGT keeps everyone's genomes developing together. The roots intertwine and form a single trunk at the ground level. Above the threshold HGT becomes ineffective and formerly interdependent organisms begin to evolve vertically. The trunk branches out.
I agree, you don't seem to understand the concept of communal evolution. You want to picture multiple independent eukarya crossing the Darwinian threshold, but they are strongly related through HGT.
Again, I fail to see the problem with vertical descent above the threshold. We've heard multiple times that ancestral lines of eukarya do not lead to a single ancestral cell. The same is true of any clades within eukarya. But in the umpteenth time, the interruption of the tree occurs at the Darwinian threshold, while above it the tree stays intact.
If the exercise will amount to going back to the Darwinian threshold and repeating that eukarya arose many times independently, spare the effort. We've heard your line, it's not what biologists are saying, and that point in time is irrelevant to the structure of clades from eukarya on up.
So Paul, if you keep repeating the same things over and over, I'm eventually going to tune out. Tell us something new.
Comment by olegt — October 7, 2009 @ 8:05 pm
October 7th, 2009 at 8:32 pm
And in that sense, Eukarya has a common ancestor. Only the common ancestor was a communal population. The interesting question is what happened in that primordial epoch.
Comment by Zachriel — October 7, 2009 @ 8:32 pm
October 8th, 2009 at 12:16 am
Er, do I really need to remind people that this Darwinian threshold is a speculative hypothesis?
Could someone summarize the evidence for the Darwinian threshold?
Also, what finding would falsify it?
Thanks.
Comment by MikeGene — October 8, 2009 @ 12:16 am
October 8th, 2009 at 7:11 am
Yes, Mike, we are aware that we are discussing a theory.
Thanks for your concern.
Comment by olegt — October 8, 2009 @ 7:11 am
October 8th, 2009 at 7:15 am
olegt has refused to answer my question. I will ask again- keeping the context:
Tell me how you are defining the word "nested".
If they are "nested" only by assumed descent then that does not meet the criteria of "nested" in the ISSS version of nested hierarchy.
The reason I ask is because nested hierarchies are built by defined characteristics.
Cladograms are also built on characteristics with the descent being assumed.
Neither olegt nor Zachriel seem to understand that concept.
IOW if any "nesting" exists in cladograms it is either by characteristics or just because someone placed things in the same group.
The bottom line is descent does not lead to a nested hierarchy- that is if we go by the ISSS.
Comment by ID guy — October 8, 2009 @ 7:15 am
October 8th, 2009 at 7:21 am
Except that you are so uncoordinated neither one of you has hit a thing.
Not only that neither one of you understands the concept of a nested hierarchy.
That you think your ignorance is some sort of refutation of my claims is hilarious.
Now answer the questions or asdmit that you are a coward.
BTW the $20,000 challenge still stands.
Comment by ID guy — October 8, 2009 @ 7:21 am
October 8th, 2009 at 7:25 am
I have already been over this:
Linnean classification is a nested hierarchy.
It is a nested hierarchy because it conforms to the principles put forth by the ISSS.
OTOH your alphabet is not a nested hierarchy.
However if you change your alphabet to be the Linnean classification- which you did earlier- then you are being deceptive.
But I undersatnd that is your only recourse.
Comment by ID guy — October 8, 2009 @ 7:25 am
October 8th, 2009 at 7:30 am
1- It would depend on how/ why they are contained.
2- Nested hierarchies involve levels which consist of, and contain, lower levels.
IOW containment isn't the only thing.
As I said with nested hierarchies it is the defined characteristics that are used- regardless of what is being discussed- biology, transportation, etc.
Comment by ID guy — October 8, 2009 @ 7:30 am
October 8th, 2009 at 7:31 am
Hi ID guy,
For the purposes of discussion, what should we call an ordered set such that each subset is strictly contained within its superset?
You forgot to give us a name to call it.
Comment by Zachriel — October 8, 2009 @ 7:31 am
October 8th, 2009 at 7:36 am
I don't care what you call it.
To be a nested hierarchy it must use the ISSS prinicles only as they are the only principles which are accepted by scientists and mathematicians.
That you want to not use the ISSS principles tells me that you are ignorant and dishonest.
Comment by ID guy — October 8, 2009 @ 7:36 am
October 8th, 2009 at 7:40 am
Are you saying there is no such thing as an ordered set such that each subset is strictly contained within its superset? Or are you saying no one has ever named it before? This is our chance! Priority! Priority!
In any case, we can give it a name for the purposes of the discussion. Do you understand the concepts of
set,superset,subset,strict containment (proper subset of)?Comment by Zachriel — October 8, 2009 @ 7:40 am
October 8th, 2009 at 7:47 am
That's fine. According to your reference, we can arrange arbitrary soldiers into groups within groups. Hence we should be able to arrange arbitrary letters into groups within groups.
{a, b, c, {d, {e, f}}, {g, {h, {i, j}}}, k}.We will name the sets as follows:
A = {a, b, c, {d, {e, f}}, {g, {h, {i, j}}}, k}D = {d, {e, f}}
E = {e,g}
G = {g, {h, {i, j}}}
H = {h, {i, j}}}
I = {i, j}
Ais the Army.a, b, c, D, G, kare the Corps.EandHare Divisions.Eis a Division ofDCorps.His a Division ofGcorps.Iis the Regiment of H division.iandjare Battalions inIRegiment.Comment by Zachriel — October 8, 2009 @ 7:47 am
October 8th, 2009 at 7:48 am
More distractions Zachriel? Is that all you have?
Why is it that you cannot stick with what the ISSS states about nested hierarchy?
That's right if we do that then your "argument" vanishes.
Comment by ID guy — October 8, 2009 @ 7:48 am
October 8th, 2009 at 7:49 am
Obviously better than you do.
However that is irrelevant as a nested hierarchy is more than a set, more than a superset, more than a subset, and more than strict containment.
Comment by ID guy — October 8, 2009 @ 7:49 am
October 8th, 2009 at 7:54 am
Joe, welcome back!
As Zachriel pointed out, ISSS does not provide a formal definition of a nested hierarchy. But let's go by what you think is the definition: nested hierarchies involve levels which consist of, and contain, lower levels. (It's a property of a nested hierarchy, not a definition, in case you're interested.)
Let's take a figure from Wikipedia's article on reptiles showing the root levels of the clade Vertebrates. The clade consists of and contains the clades Pisces and Tetrapoda. In turn, Tetrapoda consists of and contains Amphibia and Amniota. Amniota consists of and contains Synapsida and Sauropsida. And so on. Do you have any objection to this? Are there clades that do not have this property? Which ones?
Comment by olegt — October 8, 2009 @ 7:54 am
October 8th, 2009 at 7:54 am
Because we don't need to quibble over semantics. The structure that is important to continue the discussion is an ordered set such that each subset is strictly contained within its superset. It would just be handy to give it a name. Does it have a name? Per standard practice, we can give it any name we want for the purposes of discussion. Like in algebra, we say "Let T be time and D be distance."
Comment by Zachriel — October 8, 2009 @ 7:54 am
October 8th, 2009 at 7:57 am
Except the soldiers are where they in the Army via a set of definitions.
Those definitions lock the soldier(s) into very specific categories.
The alphabet is not a nested hierarchy.
Now if you want the alphabet to represent something other than the alphabet then that is a different story.
It is also decption.
So it appears that deception is your only "tool" in this discussion.
The $20,000 challenge goes for you too.
Comment by ID guy — October 8, 2009 @ 7:57 am
October 8th, 2009 at 7:58 am
It provides more than enough information so that a person can properly construct one.
Well that is an educated person.
How does it consist and contain the clades? By what criteria?
As I said cladograms are derived from shared characteristics and common ancestry is then ASSUMED.
Why can't you understand such a simple concept?
Comment by ID guy — October 8, 2009 @ 7:58 am
October 8th, 2009 at 7:59 am
Tell me how you are defining the word "nested".
If they are "nested" only by assumed descent then that does not meet the criteria of "nested" in the ISSS version of nested hierarchy.
The reason I ask is because nested hierarchies are built by defined characteristics.
Cladograms are also built on characteristics with the descent being assumed.
Neither olegt nor Zachriel seem to understand that concept.
IOW if any "nesting" exists in cladograms it is either by characteristics or just because someone placed things in the same group.
The bottom line is descent does not lead to a nested hierarchy- that is if we go by the ISSS.
Comment by ID guy — October 8, 2009 @ 7:59 am
October 8th, 2009 at 8:00 am
Neither are soldiers, unless and until we arrange them into groups. And then we can rearrange them as need be. There is no intrinsic characteristic of a soldier that makes him a member of a particular Regiment and platoon. It's arbitrary.
Comment by Zachriel — October 8, 2009 @ 8:00 am
October 8th, 2009 at 8:07 am
Joe, forget biology. Look at the figure and tell us whether that figure represents a nested hierarchy.
Comment by olegt — October 8, 2009 @ 8:07 am
October 8th, 2009 at 8:12 am
ID guy wrote:
Joe, you forgot to include two professors of biology from Berkeley, who also think that clades form a nested hierarchy. Actually, you forgot to include pretty much every biologist on the planet. Boy, this is a battle of epic proportions: a refrigerator repairman against the entrenched conspiracy of Darwinists!
Comment by olegt — October 8, 2009 @ 8:12 am
October 8th, 2009 at 8:13 am
Yes, descent is assumed, as in a hypothesis being a tentative assumption proposed for the purpose of testing its entailed empirical consequences. The cladogram is made by arbitrarily "placing things in the same group," But then, it is *tested* against the evidence. In modern systematics, a very large number of characteristics are used to test a very large number of proposed cladograms looking for the best fit under the principle of parsimony.
Comment by Zachriel — October 8, 2009 @ 8:13 am
October 8th, 2009 at 8:17 am
Have they said why it is a nested hierarchy or did they just declare it?
They didn't say why so it must be science via declaration.
I don't think that is so.
Dr Allen is a biologist- he wrote that ISSS article.
Also if you cannpt tell us why they are nested it is a safe bet they aren't nested by the criteria put forth by the ISSS.
Comment by ID guy — October 8, 2009 @ 8:17 am
October 8th, 2009 at 8:19 am
The alphabet is not a nested hierarchy.
We arrange them based on a set/ sets of definition(s) that lock the soldiers into place- a specific army, corps, division, etc.
Comment by ID guy — October 8, 2009 @ 8:19 am
October 8th, 2009 at 8:23 am
Zachriel,
Cladograms are based on characteristics.
In order for your claim to hold water cladograms must be constructed on common ancestry only. However they are not.
As I said if descent led to a nested hierarchy then if we start wiuth population A that gives rise to A1 and A2 then population A would consist of and contain populations A1 and A2.
Seeing that populations A1 and A2 are not contained by A there isn't a nested hierarchy.
It is a very simple concept actually.
Comment by ID guy — October 8, 2009 @ 8:23 am
October 8th, 2009 at 8:28 am
There isn't anything that speaks of criteria- a set of characteristics that define a group.
In order to be a nested hierarchy that specific criteria has to be met.
Also as I said before reptiles and aves are in the same clade, with aves being a descendent of reptiles.
So in order to be a nested hierarchy aves must consist of and contain ALL the characteristics of reptiles.
They do not therefore there isn't any nested hierarchy.
Comment by ID guy — October 8, 2009 @ 8:28 am
October 8th, 2009 at 8:39 am
ID guy wrote:
I have explained previously why this objection does not work. One more time, Joe. Reptiles is not a clade. Do you understand that?
Comment by olegt — October 8, 2009 @ 8:39 am
October 8th, 2009 at 8:44 am
trollegt,
I said reptiles and aves are in the same clade.
But anyway if we go by the diagram on wikipedia- reptilia is a clade and it includes aves.
A clade is a group, consisting of a single organism and all of its descendants.
Comment by ID guy — October 8, 2009 @ 8:44 am
October 8th, 2009 at 8:50 am
ID guy wrote:
LOL! Joe, this is an own goal. By this definition, reptilia is not a clade. A clade contains all of an organism's descendants. Aves are descendants of reptiles, but they are excluded from reptilia, so reptilia is not a clade. Think about that.
Comment by olegt — October 8, 2009 @ 8:50 am
October 8th, 2009 at 9:01 am
trollegt,
Clades are/ can be named by the nodes. Reptilia is a node.
Comment by ID guy — October 8, 2009 @ 9:01 am
October 8th, 2009 at 9:06 am
Joe, this article on Wikipedia should clear up your confusion: Paraphyly. (The illustration you linked to is from that article.)
Comment by olegt — October 8, 2009 @ 9:06 am
October 8th, 2009 at 9:10 am
The Linnaean classification Reptiles is marked in the blue and excludes Aves. Hence it is not a clade.
Comment by Zachriel — October 8, 2009 @ 9:10 am
October 8th, 2009 at 9:17 am
The wiki diagram that ID guy linked to is misleading in that it places reptilia in the position where one might normally find the clade sauropsida, and indicates that reptilia is a monophyletic group. That might be a cladists view of how the nomenclature should be applied, but tradition holds that reptilia does not include aves and so is not a clade.
Comment by Tom MH — October 8, 2009 @ 9:17 am
October 8th, 2009 at 9:17 am
trollegt,
If descent with modification led to a nested hierarchy then aves would be nested with reptiles- that is if we go by the cladogram that shows reptiles are an ancestor or aves.
That you agree that aves are not nested with reptiles means you support my claim.
Comment by ID guy — October 8, 2009 @ 9:17 am
October 8th, 2009 at 9:21 am
Linnean classification has nothing to do with clades.
Cladistics is different than Linnean classification.
In cladistics whatever is an ancestor of another is in the same clade as that "parent".
Comment by ID guy — October 8, 2009 @ 9:21 am
October 8th, 2009 at 9:22 am
Why is trollegt ignoring the following?:
Tell me how you are defining the word "nested".
If they are "nested" only by assumed descent then that does not meet the criteria of "nested" in the ISSS version of nested hierarchy.
The reason I ask is because nested hierarchies are built by defined characteristics.
Cladograms are also built on characteristics with the descent being assumed.
Neither olegt nor Zachriel seem to understand that concept.
IOW if any "nesting" exists in cladograms it is either by characteristics or just because someone placed things in the same group.
The bottom line is descent does not lead to a nested hierarchy- that is if we go by the ISSS.
Comment by ID guy — October 8, 2009 @ 9:22 am
October 8th, 2009 at 9:30 am
The confusion is all yours because the explanation supports my claim.
My claim being that evolution, common descent and descent with modification does not lead to a mested hierarchy.
That cladograms/ cladistics are not beholden to the same rules as a nested hierarchy.
Comment by ID guy — October 8, 2009 @ 9:30 am
October 8th, 2009 at 9:33 am
Consider the set of A and its descendents
{A, {A1, A2}}. Let's call{A, {A1, A2}}"mammalia", A1 "eutheria" and A2 "marsupialia". A, A1 and A2 are all members of the superset "mammalia", A being the ancestor of A1 and A2.It is misleading, but there is a clade Tetrapoda > Reptiliomorpha > Amniota > Reptilia. But this is not the same classification as the Linnaean Reptiles. Here's another look at the tree.
Comment by Zachriel — October 8, 2009 @ 9:33 am
October 8th, 2009 at 9:48 am
Yes, and we can do the same with letters. We can even use rigid ranking. We can even call them corps and divisions! They're just words. It's not the naming convention that makes it a nested hierarchy. It's the arrangement!
By the way, you never answered me. The structure that is important to continue the discussion is an ordered set such that each subset is strictly contained within its superset. It would just be handy to give it a name. Does it have a name? Can we call it a containment hierarchy?
Comment by Zachriel — October 8, 2009 @ 9:48 am
October 8th, 2009 at 9:54 am
Oh my. I think I agree with you (sorta). I should have taken olegt's advice. Oy vey!
Comment by Zachriel — October 8, 2009 @ 9:54 am
October 8th, 2009 at 10:03 am
So if you misrepresent what I said then you may get a nested hierarchy.
IOW if you have a nested hierarchy then you can represent it as a nested hierarchy.
Comment by ID guy — October 8, 2009 @ 10:03 am
October 8th, 2009 at 10:07 am
It's the arrangemnet IF AND ONLY IF said arrangement abides by the principles put forth in the ISSS article.
No Zachriel you never answer me.
Instead of answering me you always post an irrelevant distraction.
It is only a nested hierarchy if it abides by the principles put forth by the ISSS- period, end of story.
Comment by ID guy — October 8, 2009 @ 10:07 am
October 8th, 2009 at 10:11 am
You said, "we start with population A that gives rise to A1 and A2 then population A would consist of and contain populations A1 and A2." But that is not how clades are defined. A clade is a parent and *all* of its descendents. So the clade would be
{A, {A1, A2}}—by definition. And now we can see the nesting. IfA1then gives rise toB1, B2, then the new clade would be{A1, {B1, B2}}. And this is nested within the first clade{A, {{A1, {B1, B2}}, A2}}. And so on.Comment by Zachriel — October 8, 2009 @ 10:11 am
October 8th, 2009 at 10:12 am
oleg's "advice" is that seeing that you two are ignorant of nested hierarchies you should try to help someone understand them.
That is sound advice.
Comment by ID guy — October 8, 2009 @ 10:12 am
October 8th, 2009 at 10:14 am
"we start with population A that gives rise to A1 and A2 then population A would consist of and contain populations A1 and A2."
Yet clades are configured by characteristics, not descent.
Common ancestry is ASSUMED depending on the number of SHARED CHARACTERISTICS.
If the characteristics never changed there would only be one population in the cladogram.
Comment by ID guy — October 8, 2009 @ 10:14 am
October 8th, 2009 at 10:23 am
Oleg wrote:
I thought that using a graph paper exercise might get us past the verbal equivocations, but -– no such luck. The equivocations are prospering, and having offspring.
In Oleg’s statement, the following terms and words carry multiple, logically incompatible meanings:
– numerous organisms with a shared origin
– crossed the threshold together
– communal evolution
– eukarya
– once
In this Lewis Carroll world, cells (which are not really cells as we see them today) share (and yet do not share) common ancestry. “Organisms” swap genetic information laterally, yet these “organisms” cannot be distinguished or counted as individuals. Hence, Oleg draws a horizontal line to indicate the origin of Eukarya, but it is a line with no internal points, allowing him both to assert and deny the monophyly of the clade. The line represents a population, but -– magically -– one with no discrete members.
Logic takes a holiday, to paraphrase Wittgenstein. The Eukarya share a common ancestor, but it’s not an actual organism; rather, it’s a population. OK, did that population itself share a common ancestor? Can’t say. Well, did the population cross the Darwinian threshold once, with a first eukaryote arising as a spatiotemporally unique event (e.g., Oleg was born once in Russia), or as multiple discrete entities during an interval of time (e.g., European males were once x meters tall, on average). Don’t know: the theory of communal evolution is rather different from the biology we actually understand.
Zachriel illustrates the confusion, with his comment:
“Ancestor,” you see, ordinarily denotes an actual organism, but while the word is away on logical vacation, it can also denote a population. In this manner, one can assert and deny common ancestry, as needed.
As I noted before, way up in the thread, this is equivalent to saying that Oleg’s biological parents are the nation of Russia.
Elliott Sober (2008, p. 269) explains why this notion of “population ancestry” is biologically incoherent, if one wishes simultaneously to claim common ancestry for the same group:
I think Sober has yet to meet the magic of communal evolution, however.
Oleg wrote:
OK.
Reference
E. Sober, 2008. Evidence and Evolution: The Logic Behind the Science (Cambridge Univ. Press).
Comment by Paul Nelson — October 8, 2009 @ 10:23 am
October 8th, 2009 at 10:27 am
(Emphasis mine.)
I think we're done here.
Comment by Tom MH — October 8, 2009 @ 10:27 am
October 8th, 2009 at 11:06 am
Tom MH,
It (cladistics) uses shared characteristics to determine common ancestry.
Common ancestry is ASSUMED depending on the number of SHARED CHARACTERISTICS.
cladistics:
Comment by ID guy — October 8, 2009 @ 11:06 am
October 8th, 2009 at 11:37 am
That's what I thought. You are presenting a logical argument, not an empirical one. That's fine.
The basic model under consideration is a collection of closely related cells sharing subcellular components. These cells would not necessarily be homogeneous, but represent differing combinations of the various subcellular components. At some point, a combination results in Eukarya.
That's correct. We can trace common ancestry to the origin of Eukarya, but there are problems resolving the tree before that time. It's as if different components of the cell have different evolutionary histories. The simple model above is consistent with that data, though for some reason you claim it is logically inconsistent.
Comment by Zachriel — October 8, 2009 @ 11:37 am
October 8th, 2009 at 12:19 pm
ID guy, from your link to the New World Encyclopedia:
The latter approach characterizes cladistics. Your claim
seems to be more in line with numerical taxonomy.
BTW, further along in the NWE entry, terms are defined:
This is consistent with Zachriel's definition.
Also:
Thus it is not necessary for all taxa in the clade to share all characteristics, nor is it necessary for all taxa demonstrating the characteristc to be forced into the clade.
Comment by Tom MH — October 8, 2009 @ 12:19 pm
October 8th, 2009 at 2:56 pm
Tom MH,
1- You are jumping into the middle of something
My claims are the following:
I know what a clade is.
What I am saying is that how ancestry is determined is via shared characteristics.
That it is not necessary for all taxa in the clade to share all characteristics supports my claim that cladistics is not beholden to the same rules as a nested hierarchy.
Do you agree?
Comment by ID guy — October 8, 2009 @ 2:56 pm
October 8th, 2009 at 4:02 pm
Finally getting there, arn´t we.
First, the NWE article reflects more closely what is written in the german Wiki article, which is spot on concerning cladistics, since it is only about Hennigs approach (Tom MH confirmed that this is, what biologists call cladistics and that is what I was taught).
Anyway a few remarks on the subject:
In biology cladistics is an analytical approach to a defined set of taxa. The set of taxa has to be monophyletic to be analysed in a cladistic approach. Monophyletic means, that all taxa in the set share at least one characteristic. So the monophylic clade of metazoa contains only multicellular liveforms, this also defines the mentioned outgroups of taxa from protozoa and prokaryota. Since Linean taxonomie is based on common traits, it can serve as defining characteristic for the set of taxa, but other common denominators can be chosen – it does not matter as long as the set shares at least one common trait.
Cladistics analyses only live taxa, so traits/characteristis that are reproduceable an observable go into it. All traits/characteristics of live taxa are observed to be inheritable and this is the connection to common decent. If a trait is inheritable today, can we not assume it was inheritable in the past? Anyone can argue actualism at this point – feel free to do so.
So cladistics is a reductive method, stripping a defined set of taxa, that have for sure one trait in common, of all distinguishing, autapomorphic traits to arrive at sets of plesiomorphic traits that are common to all taxa in the monophylitic clade. Sometimes, all you are left with is the trait, that was used to define the clade to start with. You will get larger subsets of traits that contain all plesiomorphic traits plus synapomorphic traits that form grouping of larger subsets of taxa in the clade.
Cladistics is defined as nested hirarchy of traits, this nested hirarchy takes into account the fact, that traits are inheritable and constructs a line of ancestry from the earliest ancestor with the basic set of pleisiomorphic traits inherited to todays taxa via intermediate generations with added synapomorphic traits over time. It is therefore a method to falsify proposed hereditry lines of taxa, if the proposed decent with modification is true. If the nested hirarchy does not conform the proposed decend with modification line, you will have to say good by to the proposal.
So what do we have:
- is cladistics a nested hirarchy – definitly yes, that is how it is set up, all taxa to be included in the set are diveded into subsets. That´s what the ruele says.
- does cladistic presuppose common decent – no, it presupposes inheridibility of traits
- does cladistics provide a mean of testing suggested decent – yes, it is a falsification method
to be honest, i was at a loss, because the wiki-pedia definition presented on this thread ist not a reflection on what cladistics realy represents in terms of what is beeing taught at universitys in Germany and the summary of which is presented at wiki.de
Thanks to TOM HM for your comment, it encouraged me to post in this forum again against all odds.
And grudgingly thanks to ID guy, because you provided the NWE page, which is far supperior to the Wiki.org and more consistend with Wiki.de page, so that i dont have to translate this. Grudging, because I think you are unneccessarly rude and aggressive, you have no style and put down people, who try to give you things to think about. I do not have it in for ID proponents, but I do not support people like you, who do only halve the research about the topic without thinking about what has been really said.
You were as wrong as other people on the thread – but you were really intollerable in your choice of commentary.
peace to everyone else, no offence ment to any other party but ID guy
and he can declare himself, if he wants to
all the best
Karla
Comment by Karla — October 8, 2009 @ 4:02 pm
October 8th, 2009 at 4:26 pm
By whom? IOW who defines caldistics that way?
I know that Linnean classification is a nested hierarchy of charcteristic traits.
It has already been demonstrated that aves do not share all the traits of a reptile even though aves are descendents of reptiles.
Denton goes over this stuff in "Evolution: A Theory in Crisis"- transitional forms violate the nest just by their very nature. And there isn't anything that says characteristics cannot be lost.
And if you think I am rude and aggresive then perhaps you should look beyond my behaviour for I am a counter-puncher.
That has always been the nature of my beast.
Comment by ID guy — October 8, 2009 @ 4:26 pm
October 8th, 2009 at 4:40 pm
I loves me some Karla
Comment by chunkdz — October 8, 2009 @ 4:40 pm
October 8th, 2009 at 5:07 pm
Yet a tree (set theory) is defined as a partially ordered set.
And you were the one saying that trees are nested hierarchies…
Comment by ID guy — October 8, 2009 @ 5:07 pm
October 8th, 2009 at 5:51 pm
I bow to Karla.
ID guy, to answer your question: no, I do not agree with you about nested hierarchies and clades. Somehow I think you have read more into Professor Allen's discussion (the ISSS primer) than is really there. I could very well be wrong, however — did he ever respond to your email?
And, oh yeah:
You owe me for making me slap my forehead.
Comment by Tom MH — October 8, 2009 @ 5:51 pm
October 8th, 2009 at 7:17 pm
Tom MH,
Do nested hierarchies allow for the loss of traits?
If you look at the Linnean classification the species is a compilation of all of its supersets.
All sets are distinct.
The same with an Army.
One soldier cannot belong to two Corps any more than one species can belong to two Phyla.
With evolution there isn't any direction meaning there isn't any expectation (prediction) that traits would be immutable and additive.
This is discussed in Dr Denton's "Evolution: A Theory in Crisis".
Even if I didn't have the ISSS the arguments put forth by Denton are more than enough to support my claims.
Just think of the definition of a "transitional"- transitionals would blur the distinct boundaries that nested hierarchies require. A Venn diagram, however may depict common descent.
But again you still need changing characteristics.
Comment by ID guy — October 8, 2009 @ 7:17 pm
October 8th, 2009 at 9:15 pm
Yes. A tree is well-ordered in the down direction, and branching only occurs upward. So?
No. Because we define the set as the ancestor and all its descendents. Let's consider a case. Here's a typical arrangement. You can probably recognize the groupings; vertebrates, tetrapods, mammals, placentals.
{fish, {frog, {kangaroo, {cat, dog}}}}Now, where would you put the common ancestor of dogs and cats? It would be in the set of placentals.
{fish, {frog, {kangaroo, {1st.placental, cat, dog}}}}Notice we still have an aggregating hierarchy. (We'll use that term to denote an ordered set such that each subset is contained within its superset.) There is no difficulty in including the common ancestor. And this is done on the basis of characteristics; vertebrae, tetrapodal, mammaries, placentas.
Comment by Zachriel — October 8, 2009 @ 9:15 pm
October 8th, 2009 at 9:22 pm
A tree is a partially ordered set and you prattled on about ordered sets.
You messed up- admit it.
Who is "we"?
Also ancestors to not contain and consist of their descendents.
You seem to have great difficulties with tat simple concept.
Then you show me a set that is constructed on CHARACTERISTICS, not decent.
And you think that helps your case how?
Comment by ID guy — October 8, 2009 @ 9:22 pm
October 8th, 2009 at 9:38 pm
The term may be ambiguous, but it is certainly correct and should be clear from context. A tree is not totally ordered, and is well-ordered only in the one direction. I explained this to you many times before like this: A successor has one-and-only-one predecessor, but a predecessor can have more than one successor.
Of course not. The set is defined as the ancestor and all its descendents.
That's what you insisted upon.
Comment by Zachriel — October 8, 2009 @ 9:38 pm
October 8th, 2009 at 10:12 pm
Hello Paul,
I have been busy today and will continue to be busy in the coming days. So I'll respond briefly and return to make more detailed comments.
Your response offers no new support for your claims about the supposed corrosive influences of the complex root structure of the tree of life on the upper branches of the tree.
The subject of Sober's criticism is not "population ancestry" in general but specifically the designation of a species as the original ancestor. If you read the quote in context, it is clear that he is having a problem with defining a species at that time point. There is no such problem with defining a population of organisms, so no, Sober does not say that "population ancestry" is incoherent. (Quote mining? You don't say!)
And if you read a few pages beyond that quote, it's quite clear that, unlike you, Sober is able to wrap his mind around the picture of communal evolution. I'll provide relevant quotes later.
Lastly, your rant against my use of a continuum model looks out of place. In physics we model gases and liquids (and even solids) as continuous media—even though we know very well that they consist of discrete atoms. Representing a diverse population of organisms at the Darwinian threshold as discrete points seems hardly justified: what do these points represent? Are they distinct organisms? Billions upon billions? That would be essentially a continuous line. Are they groups of organisms? How would you delineate such groups in the presence of strong HGT? Your points don't make sense.
I'm off to finish preparations for tomorrow's lecture. Meanwhile, it would be great if you could finally explain what the problems are in the upper branches of the TOL.
Comment by olegt — October 8, 2009 @ 10:12 pm
October 9th, 2009 at 7:17 am
Well then how does that account for any divergence?
IOW from your description all we ahve is one set under another- like a lineage.
And THAT is not a nested hierarchy.
So once again you expose your ignorance about nested hierarchy.
Then you show me a set that is constructed on CHARACTERISTICS, not decent.
That is nested hierarchies insist upon.
However that is moot because according to YOU DESCVENT leads to a nested hierarchy even though it doesn't.
Comment by ID guy — October 9, 2009 @ 7:17 am
October 9th, 2009 at 8:35 am
You claimed that we couldn't include a transitional in an aggregating hierarchy constructed on trait characters. I showed you how it works. You just repeat the same verbiage over and over again. Try this. Can we group these organisms by character traits?
Fish, frog, kangaroo, cat, dog. If we do, do we have sets nested within sets? Now where would you place the first placental?Otherwise, perhaps you can have someone else from the Telic Thoughts Community explain your point.
Comment by Zachriel — October 9, 2009 @ 8:35 am
October 9th, 2009 at 10:16 am
Oleg wrote:
I’ll take up your reading of Sober when you return to the thread. Sober’s point is quite general, however, and not restricted to the species concept as you imply. “Population ancestry” is a notion that works best when one does not think about it too closely. I wish to analyze it carefully, however.
Oleg wrote:
Gases, liquids, solids, and atoms =/ organisms.
Oleg wrote:
These are your problems to solve. Recall that you are defending the coherence of Woese’s theory, as a solution to the problem of phylogenetic discordance at the root of the Tree of Life, with normal Hennigian clades (Eukarya, Metazoa, Chordata, etc.) somehow magically returning after the Darwinian threshold.
Thus far, you have resisted following out the consequences of Woese’s theory by producing an impenetrable (logical) fog at the origin of Eukarya. I propose to take the matter one step at a time. When you say, for instance, that organisms at the Darwinian threshold cannot be distinguished, as discrete biological objects – yet those same organisms are somehow transferring genetic information, viably – that’s a contradictory mess needing to be disentangled. (DNA is moving between what? Entities capable of taking it up, presumably. Can we describe these entities? Yes: well, OK, they’re cells, more or less as we understand them today. No: then frankly we have absolutely no idea what we are talking about.)
Oleg wrote:
One step at a time. A data dump now about problems with metazoan (or chordate or mammalian) phylogeny would be getting ahead of the discussion. Let’s sort out the origin of Eukarya, according to Woese, first.
Suggested reading, re HGT and its evidential support.
P.S. I have a book MS (with Scott Minnich) due next week, so will be away from this discussion over the weekend and early next week.
Comment by Paul Nelson — October 9, 2009 @ 10:16 am
October 9th, 2009 at 11:12 am
Descent with modification would likewise prevent a species from belonging to two different clades at the same level, thus fulfilling (what I understand to be) the requirement of a nested hierarchy. If that fails, either the clade (an assumption of common descent) is wrong OR descent with modification itself is wrong. The discovery of cats that lay eggs would show that descent with modifcation is no longer in play, or is so poorly understood that we might as well start all over; new physics are at work.
BTW I said "clade" instead of "phylum" because the problem I see with Linnaean taxonomy is that it organizes the taxa on the basis of morphology BUT MAKES NO PREDICTIONS. Mere stamp collecting. Furthermore, it insists on defining the same set of levels (phylum – class – order – family etc.) for each and every taxon, with no underlying reason for this orthodoxy. Even armies are not so constrained: the infantry may be organized by corp – division – regiment – batallion – etc. but the combat support units (for example) may follow a different organization.
Cladisitics organizes the taxa on the basis of morphology and then tries to make predictions of the pattern of descent that yielded those taxa. With the rise of molecular genetics, I imagine the predictions that can be made here are very powerful. It is possible that you could even assemble the molecular data into a digital file and let a computer find the best (most parsimonious) cladogram that fits the results.
(WARNING: there is a wealth of ignorance behind the previous paragraph. OPINIONS OF AN ELECTRICAL ENGINEER. Be afraid, be very afraid…but feel free to correct me, O TT Commentariat, if I am wrong.)
If by "loss of traits" you are referring to something discussed in Denton's work, then I am afraid I will not be able to follow further until I have read it. Descent with modification would presume that traits are preserved in the clade (cladisitcs assume the traits are inheritable, so by definition all members of the clade had or inherited that trait). Is there a specific failure of containment of a trait that you had in mind?
I would expect inheritable features to be able to be modified (descent with modification), of course. Even to a vestigial form, or re-purposed in a way that simple morphological analysis might have overlooked (jaw bones into ear bones). Yet another hypothesis, so look at the molecular data, look at embryology, look for fossil artifacts — tiktaalik!
And now I must apologize for taking up so much space on this ever-growing slow-to-load thread. Brighter minds than mine are here; I'll shut up for a while and listen.
Comment by Tom MH — October 9, 2009 @ 11:12 am
October 9th, 2009 at 10:14 pm
I said we couldn't build a nested hierarchy because transitionals would violate the distinct categories.
Comment by ID guy — October 9, 2009 @ 10:14 pm
October 9th, 2009 at 10:26 pm
Can we group these organisms by character traits?
Fish, frog, kangaroo, cat, dog. If we do, do we have sets nested within sets? Now where would you place the first placental?Comment by Zachriel — October 9, 2009 @ 10:26 pm
October 10th, 2009 at 8:08 am
Zachriel,
YOUR claim is that DESCENT leads to a nested hierarchy.
It does not.
You lose.
Comment by ID guy — October 10, 2009 @ 8:08 am
October 10th, 2009 at 8:13 am
ONE requirement.
However if clades are built on traits then convergence can screw up the descent premise.
Loss of traits happen.
Loss of legs, loss of eyes, loss of tails, loss of teeth, change from cold-blooded to warm-blooded, loss of scales, etc.
And once traits are lost so is containment.
BTW Denton's book was published in 1987 so you are only 22 years behind.
Comment by ID guy — October 10, 2009 @ 8:13 am
October 10th, 2009 at 8:14 am
Well then how does that account for any divergence?
IOW from your description all we ahve is one set under another- like a lineage.
And THAT is not a nested hierarchy.
Why did you ignore that?
Comment by ID guy — October 10, 2009 @ 8:14 am
October 10th, 2009 at 9:23 am
Yet, you can't or won't group a few common organisms into sets by character traits for consideration. This is pretty basic, ID guy. You have repeatedly refused to consider how we might group organisms by biological traits, even the simplest classifications, yet you wave your hands about the nested hierarchy.
Let's make it simple. Just one set. Are these all reasonably categorized as vertebrates;
{fish, frog, kangaroo, cat, dog}? If that is too complicated, can we form a set comprised of the contents of Sam of Ballyvourney's pocket (even if his pocket is empty, as it often is)?Comment by Zachriel — October 10, 2009 @ 9:23 am
October 10th, 2009 at 9:58 am
Paul Nelson wrote:
Sober argues narrowly against a species as the last ancestor. Here is the quote from Sober in context:
Your careful cropping of Sober's quote conceals his specific objections to the species as an ancestor. Replace a species with a population of early eukaryotes—organisms related both vertically and horizontally—and neither objection stands.
Yes, they have just emerged as cells more or less as we know them today.
One step at a time? You haven't made a single step in the direction of explaining your own position vis a vis the upper branches. I am starting to doubt that we'll see any.
Comment by olegt — October 10, 2009 @ 9:58 am
October 10th, 2009 at 10:04 am
Of course. I imagine it's rather important in cladistics to be able to differentiate between homologous traits and analogous traits. Bats, birds, and turtles — which is the outgroup? ("Well, both bats and birds have wings…")
Incorrecly built clades will yield incorrect conclusions on descent. This is a positive feature of cladistics – it's falsifiable! So what is your point?
Comment by Tom MH — October 10, 2009 @ 10:04 am
October 10th, 2009 at 10:33 am
I can and have.
But that is NOT the point.
Your point is that DESCENT ALONE creates a nested hierarchy.
Also it is very telling tat you keep ignoring your egregious error:
Well then how does that account for any divergence?
IOW from your description all we ahve is one set under another- like a lineage.
And THAT is not a nested hierarchy.
Comment by ID guy — October 10, 2009 @ 10:33 am
October 10th, 2009 at 10:34 am
Tom MH,
Bat wings and bird wings are not an example of convergence.
Comment by ID guy — October 10, 2009 @ 10:34 am
October 10th, 2009 at 11:09 am
Argumentum googleum.
Comment by Tom MH — October 10, 2009 @ 11:09 am
October 10th, 2009 at 11:38 am
Good. Then you won't mind going through a few examples so that we can see how the sets work or don't work with regards to common ancestry. But to do that we have to have a few agreed definitions.
It's just a set! It isn't meant to provide an "account". However, it is clear that each descendent can also be an ancestor with its own descendents contained within the larger superset.
Sets can contain other sets. One set 'under' another set is called a subset with the containing set called the superset. Every element of a subset is contained within the superset.
Let's start with a very simple example. Let vertebrates =
{fish, frog, kangaroo, cat, dog}and mammals ={kangaroo, cat, dog}. We say that mammals is contained within vertebrates. Mammals are a subset of vertebrates.Comment by Zachriel — October 10, 2009 @ 11:38 am
October 10th, 2009 at 12:17 pm
ID guy, we can argue about convergent evolution later. Zachriel is apparently as curious about your issues wth clades, sets, and divergence as I am. I'll sit back and listen.
Comment by Tom MH — October 10, 2009 @ 12:17 pm
October 10th, 2009 at 8:11 pm
I like that!
Seems to me that the same can be said about most every imagined evolutionary pathway and every abiogenesis story to boot!
Comment by Daniel Smith — October 10, 2009 @ 8:11 pm
October 11th, 2009 at 9:31 am
Well, let's look at one. The first tetrapods in the fossil record are dated at about 360 million years ago or so. Based on that, researchers located exposed strata from just before that period. Problem was, the strata was in an Arctic wasteland. Several years later, they found Tiktaalik. "Thinking closely" about the evolutionary pathway—and perseverance—is exactly what led the researchers to this discovery.
Comment by Zachriel — October 11, 2009 @ 9:31 am
October 11th, 2009 at 10:09 am
The sets work on CHARACTERISTICS not DESCENT.
>
A nested hierarchy is much more than a set.
I provided the principles a nested hierarchy must follow.
Why is it that YOU cannot follow them?
Zachriel:
Sets can contain other sets. One set 'under' another set is called a subset with the containing set called the superset. Every element of a subset is contained within the superset.
Level of organization: this type of level fits into its hierarchy by virtue of set of definitions that lock the level in question to those above and below.
The ordering of levels: there are several criteria whereby other levels reside above lower levels. These criteria often run in parallel, but sometimes only one or a few of them apply. Upper levels are above lower levels by virtue of: 1) being the context of, 2) offering constraint to, 3) behaving more slowly at a lower frequency than, 4) being populated by entities with greater integrity and higher bond strength than, and 5), containing and being made of – lower levels.
Nested and non-nested hierarchies: nested hierarchies involve levels which consist of, and contain, lower levels. Non-nested hierarchies are more general in that the requirement of containment of lower levels is relaxed. For example, an army consists of a collection of soldiers and is made up of them. Thus an army is a nested hierarchy. On the other hand, the general at the top of a military command does not consist of his soldiers and so the military command is a non-nested hierarchy with regard to the soldiers in the army. Pecking orders and a food chains are also non-nested hierarchies.
Zachriel:
Let's start with a very simple example. Let vertebrates = {fish, frog, kangaroo, cat, dog} and mammals = {kangaroo, cat, dog}. We say that mammals is contained within vertebrates. Mammals are a subset of vertebrates.
Comment by ID guy — October 11, 2009 @ 10:09 am
October 11th, 2009 at 11:02 am
I read your reply, but didn't see an answer to my simple question.
Let's start with a very simple example. Let
V = {fish, frog, kangaroo, cat, dog}andM = {kangaroo, cat, dog}.Is
Va set? IsMa set? IsMa subset ofV?Can we form a set of all the stuff in Sam of Ballyvourney's pocket (even if his pocket is empty, as it often is)? Can we form a set of all the pocket-stuff in County Cork?
Comment by Zachriel — October 11, 2009 @ 11:02 am
October 11th, 2009 at 11:10 am
Eventually, we will build aggregating sets built on character traits, and aggregating sets built on our posited evolutionary relationships. Then we show how they conform, and how this conformity leads to testable consequences.
Of course, that sort of discussion is impossible with ID guy. He doesn't understand that we can form sets by a variety of different criteria, so it is impossible to show him that aggregating sets of character traits and of evolutionary relationships conform in this way. It suffices to show that his ID Friends won't attempt to help him with this. ID isn't grounded in the evidence, so from their perspective, it really doesn't matter if they do or they don't.
Comment by Zachriel — October 11, 2009 @ 11:10 am
October 11th, 2009 at 6:53 pm
We have "walking" fish today… are mudskippers ancestral to humans too?
Use your imagination Zachriel!
Comment by Daniel Smith — October 11, 2009 @ 6:53 pm
October 11th, 2009 at 7:05 pm
What evidence?
Oh you mean THE evidence!
The evidence that–when design is excluded–only supports natural causes.
THAT evidence?
It's kinda funny how THAT evidence–when viewed within the context of design–fully supports THAT position.
Hmm, how can that be? How can THE SAME evidence support two contrary views?
Could it have something to do with INTERPRETATION?
I don't know – it's a mystery.
Comment by Daniel Smith — October 11, 2009 @ 7:05 pm
October 11th, 2009 at 7:21 pm
Mudskippers don't walk. They crutch, meaning they jerk forward on their pectoral fins. Their fused pectoral fins are not ancestral to wrists.
Design is not excluded from science a priori. Notice that while actual researchers find very rare fossils by "thinking closely" about the evolutionary pathway, you counter with handwaving.
Comment by Zachriel — October 11, 2009 @ 7:21 pm
October 11th, 2009 at 7:42 pm
A better example than the mudskipper would be the coelacanths, or lobe-fin fish which, along with lungfish, diverged about the same time as tetrapods (as supported by genetic evidence).
Comment by Zachriel — October 11, 2009 @ 7:42 pm
October 12th, 2009 at 8:52 am
Do you agree that the Army contains the General, as one of its constituent soldiers? That is, can we define the Army as:
Army = {General, {I Corps}, {II Corps}, {III Corps}}
Likewise, each Corps contains the commanding officer (a Lieutenant General, usually) and several Divisions:
Corps = {LTGEN, {1 Div}, {2 Div}, {3 Div}}
…and so on. Thus the Army is a nested hierarchy. It consists of, and contains, lower levels. A Corps is a lower level of the Army. The commanding General is also a lower level of the Army. He is the highest level of the chain of command, of course — but we are not depocting the chain of command here, just the Army itself.
Yes, the ancestor would be like the General. The clade contains the ancestor just as the Army contains the General. The ancestor does not consist of nor contain its descendents just as the General does not consist of nor contain the Corps under his command.
Comment by Tom MH — October 12, 2009 @ 8:52 am
October 14th, 2009 at 1:35 pm
Wrong again Zach- I understand that sets can be anything at all- that is anything any person wants to put in a set is a set.
YOUR problem is that you don't seem to be able to understand NESTED HIERARCHIES.
And what you still don't realize is that by using CHARACTERISTIC TRAITS you are conforming to the way I told you nested hierarchies are constructed.
They are not constructed by descent.
Your claim is that descent with modification leads to a nested hierarchy yet you have failed to support that claim.
All you can do is misrepresent my knowledge and misrepresent nested hierarchies and you think you have accomplished something.
Comment by ID guy — October 14, 2009 @ 1:35 pm
October 14th, 2009 at 1:39 pm
A General can be part of an Army.
I know it is. The ISSS article said it was.
However not how you depict it.
As you have it the Gebn or Lt Gen would have to contain and consist of all those other sets.
Comment by ID guy — October 14, 2009 @ 1:39 pm
October 14th, 2009 at 1:49 pm
Okay, then how would you depict it? I suggested:
What would you suggest instead?
Comment by Tom MH — October 14, 2009 @ 1:49 pm
October 14th, 2009 at 2:02 pm
That doesn't answer the question. You do understand that everyone can see that you won't answer?
Let
V = {fish, frog, kangaroo, cat, dog}andM = {kangaroo, cat, dog}. IsVa set? IsMa set? IsMa subset ofV?Can we consider the set of an ancestor and all of its descendents?
Comment by Zachriel — October 14, 2009 @ 2:02 pm
October 14th, 2009 at 2:10 pm
What intrinsic characteristic puts one private in I Corps and another in II Corps?
Comment by Zachriel — October 14, 2009 @ 2:10 pm
October 14th, 2009 at 2:34 pm
Zachriel,
It is you who won't answer questions- starting with the basics:
1- Do nested hierarchies require a direction of immutable and additive characteristics?
2- Does evolution/ descent with modification/ universal common descent have a direction of immutable and additive characteristics?
Tom MH feel free to answer those also.
Comment by ID guy — October 14, 2009 @ 2:34 pm
October 14th, 2009 at 2:41 pm
I understand that sets can be anything at all- that is anything any person wants to put in a set is a set.
I wasn't responding to a question.
I was responding to your nonsensical accusation.
Now for your other drivel:
1- fish, frog, kangaroo, cat, dog are all so called because of specific sets or sets of characteristics.
2- As I said anything anyone wants to put in {} is a set.
3- V is a set
4- Anyone can also put anything they want as a subset of a set just by adding more {}
5- M would therefore be a subset of V
Nothing else to consider until you answer those two questions:
Comment by ID guy — October 14, 2009 @ 2:41 pm
October 14th, 2009 at 2:45 pm
That fossil says nothing about the mechanism of evolution.
Think closely about that.
Comment by Daniel Smith — October 14, 2009 @ 2:45 pm
October 14th, 2009 at 2:48 pm
{fish, frog, kangaroo, cat, dog}
Are fish cold blooded?
Are frogs cold blooded?
Are kangaroos cold blooded?
Are cats cold blooded?
Are dogs cold blooded?
Are characteristics immutable?
Comment by ID guy — October 14, 2009 @ 2:48 pm
October 14th, 2009 at 2:52 pm
Danial,
The fossil doesn't say anything about "evolution" at all.
All fossils can say is that such organisms existed at one point in time.
When we look to genetics to try to find an answer to the question of what causes the changes- for example from water to land animal- we are at a loss.
We know only a small fraction of genes influence development but we can't find what determines the final form.
Alas- the evolutionary "holy grail"-"The Island of Dr Moreau"- is still fiction.
Comment by ID guy — October 14, 2009 @ 2:52 pm
October 14th, 2009 at 3:47 pm
Okay: yes, and yes. If I understand your terms.
Let's take the Army first, as an example of a nested hierarchy. I'll use MY set definition above, since you haven't provided one yet (harrumph).
Army = {General, {I Corps}, {II Corps}, {III Corps}}
The Army consists of the General and the three CORPS. They each share the characteristic of BEING PART OF THE ARMY. Every subset of them also share that characteristic.
Now take I CORPS. It consists of the LTGEN and three divisions.
I Corps = {LTGEN, {1 Div}, {2 Div}, {3 Div}}
They each share the characteristics of BEING PART OF THE ARMY and BEING PART OF I CORPS. Note that they have not lost the first characteristic, and have added a second characteristic. Note also that none of the members of II CORPS or III CORPS share this second characteristic, though they do share the first.
And so on for Division, Regiment, Battalion, etc.. A nested hierarchy, with additive and immutable characteristics. So far, so good?
Now take Amniota. (Disclaimer: not being a cladistician, there may be errors of nomenclature here. So be it.) It consists of the common ancestor to all modern amniotes, and all of its descendants, so the characteristic is BEING RELATED BY DESCENT TO THE COMMON ANCESTOR OF ALL AMNIOTES. Note that the ancestor is related to itself, so it is also included in the set.
So we hypothesize that all amniotes are descended from a common ancestor. We further hypothesize that the descendants form two groups: Synapsida and Sauropsida.
Amniota = {common ancestor, Synapsida, Sauropsida}
The Sauropsids have the characteristics of BEING RELATED BY DESCENT TO THE COMMON ANCESTOR OF ALL AMNIOTES and BEING RELATED BY DESCENT TO THE COMMON ANCESTOR OF ALL SAUROPSIDS. Two characteristics, and note that they are immutable and additive. And note that the synapsids do not share this second characteristic.
We further hypothesize that the descendents of the common ancestor of the Sauropsids form two groups: Testudina and Diapsida.
Sauropsida = {common ancestor, Testudina, Diapsida}
And so on. A nested hierarchy, with additive and immutable characteristics.
Note that per this scheme, the characteristics for Testudina are:
- BEING RELATED BY DESCENT TO THE C.A. OF ALL AMNIOTES
- BEING RELATED BY DESCENT TO THE C.A. OF ALL SAUROPSIDS
- BEING RELATED BY DESCENT TO THE C.A. OF ALL TESTUDINES
and not
- LOOKS LIKE A TURTLE.
That would be morphological (Linnaean) classification.
[Boy I hope Karla shows up before I drive this thing into a ditch!!]
Comment by Tom MH — October 14, 2009 @ 3:47 pm
October 14th, 2009 at 3:52 pm
As we don't agree on the meaning of the terms, it is not possible to give an unambiguous answer. That's why we're starting with basics.
So
M = {kangaroo, cat, dog}is a subset ofV = {fish, frog, kangaroo, cat, dog}. That only took a few weeks. But you forgot to answer this question: Can we consider the set of an ancestor and all of its descendents? If the terms are unclear, then I would be happy to clarify them for you.Comment by Zachriel — October 14, 2009 @ 3:52 pm
October 14th, 2009 at 3:56 pm
1- Do nested hierarchies require a direction of immutable and additive characteristics?
2- Does evolution/ descent with modification/ universal common descent have a direction of immutable and additive characteristics?
Tom MH feel free to answer those also.
No terms- either traits can never be lost and they are also additive OR traits can be lost and they don't have to be additive.
For example cold bloodedness- a defining characteristic trait.
Limbs are also a defining characteristic.
The point being that any and everyone who knows anything about the theory of evolution knows there isn't any direction save for "whatever survives and reproduces".
Next you prove you don't understand nested hierarchies:
According to that the General has to consist of and conatain all 3 Corps.
Does he?
Also there isn't any such characteristic of "BEING RELATED BY DESCENT ".
But I take it that you think you are smart by posting something so stupid.
Comment by ID guy — October 14, 2009 @ 3:56 pm
October 14th, 2009 at 3:57 pm
Now you say …
That wasn't the issue you raised. We were discussing evolutionary pathways. And we showed how "thinking closely" about evolutionary pathways leads to new discoveries.
Comment by Zachriel — October 14, 2009 @ 3:57 pm
October 14th, 2009 at 4:03 pm
No. That's not what that means.
Generalis a single *element* of the supersetArmy.Armyconsists of and contains the elementGeneraland the subsetsI Corps, II Corps, III Corps.Comment by Zachriel — October 14, 2009 @ 4:03 pm
October 14th, 2009 at 4:06 pm
1- Do nested hierarchies require a direction of immutable and additive characteristics?
My question is starting with the basics.
If you don't understand that nested hierarchies demand a direction of immutable and additive characteristics you aren't even worth my time.
IOW you are proving that you are ignorant pertaining to nested hierarchies and you think your ignorance somehow supports your position.
That is a genealogy and genalogies are partially ordered sets.
IOW it is a family tree which you have already admitted is not a nested hierarchy.
2- Does evolution/ descent with modification/ universal common descent have a direction of immutable and additive characteristics?
Answer that question.
Comment by ID guy — October 14, 2009 @ 4:06 pm
October 14th, 2009 at 4:06 pm
No, according to that the General is part of the Army (which you earlier agreed to). Please offer what you think is the correct expression.
Comment by Tom MH — October 14, 2009 @ 4:06 pm
October 14th, 2009 at 4:07 pm
What I said is exactly what it means.
Substitute "Kingdom" for "General" and 3 Phlya for the 3 Corps- the Kingdom consists of and contains the three phyla.
IOW all you are doing is to continue to prove your ignorance.
Comment by ID guy — October 14, 2009 @ 4:07 pm
October 14th, 2009 at 4:11 pm
Tom MH,
The General is part of the Army. But in order for what you presented to be a nested hierarchy that General must consist of and contain the three Corps.
However first you need an education so that you will understand nested hierarchies.
Send an email to Dr Allen and present your case.
See what he says.
Comment by ID guy — October 14, 2009 @ 4:11 pm
October 14th, 2009 at 4:12 pm
What new discoveries?
And how can we "think closely" about something that we haven't a clue about?
Comment by ID guy — October 14, 2009 @ 4:12 pm
October 14th, 2009 at 4:17 pm
Fine. Please draw out the nested hierarchy for the Army, including the General. I've answered your questions; please answer mine.
Comment by Tom MH — October 14, 2009 @ 4:17 pm
October 14th, 2009 at 4:18 pm
Correct expression:
{Army, {Corps I}, {Corps II}, {Corps III}} – each corps would have at least two divisions, each division at least two regiments, each regiment at least two battalions, each battalion at least two companies and so on down to the squad or troop.
Comment by ID guy — October 14, 2009 @ 4:18 pm
October 14th, 2009 at 4:19 pm
The basics are how to form and manipulate sets. The problem is you think you know, but don't, so you can't learn.
D = {Kingdom, {I Phylum}, {II Phylum}, {III Phylum}}. Sorry, but in this case,Kingdomdoes not consist of and contains the three phyla.It should be
Kingdom = {{I Phylum}, {II Phylum}, {III Phylum}}. NowKingdomconsists of and contains the three phyla.That is incorrect. If
Armyconsists of and contains the three corps, then it should beArmy = {{Corps I}, {Corps II}, {Corps III}}.Comment by Zachriel — October 14, 2009 @ 4:19 pm
October 14th, 2009 at 4:21 pm
Can't draw what cannot exist.
That is like asking me to make apple juice from a bushel of oranges.
Comment by ID guy — October 14, 2009 @ 4:21 pm
October 14th, 2009 at 4:24 pm
No it isn't.
Nested hierarchies are much more than sets and manipulated sets.
They have to follow the rules- the rules you refuse to understand.
The problem is you are ignorant and willfully so.
Just saying so doesn't mean anything.
You need something to support that claim.
However we all know that you won't provide anything.
Comment by ID guy — October 14, 2009 @ 4:24 pm
October 14th, 2009 at 4:55 pm
Thank you for answering my question.
The above "correct expression" does not describe the Army as a set. You apparently don't know what a set is, and that is a comprehension problem for you because a nested hierarchy is a set.
Comment by Tom MH — October 14, 2009 @ 4:55 pm
October 14th, 2009 at 7:35 pm
The "pathway" spells out HOW we get from point A to point B. That has everything to do with mechanism. Your example has nothing to do with it.
Otto Schindewolf chronicled example after example of evolution that could not be the result of Darwinian mechanisms. He showed quite explicitly that evolution follows patterns set at early stages. His ideas were ignored by most scientists because A) he published exclusively in German, and B) his ideas threw a gigantic monkey wrench into the wheels of the Darwinian revolution and its march to eliminate God from the equation (although Schindewolf himself did not view evolution as a teleological process).
What he did show however was that random variation and natural selection are incapable of accounting for ALL of the evidence. This is why people like you harp on and on about certain organisms that fit your preconceived ideas of how evolution works and ignore the rest.
Comment by Daniel Smith — October 14, 2009 @ 7:35 pm
October 14th, 2009 at 7:45 pm
zach:
The Keefe and Szostak paper you referenced has nothing to do with biologically relevant functional proteins, as I showed.
zach:
Simply not true, weak ATP binding is not a biologically relevant function, as I already explained. They aren't even similar to anything we see in Biology. They even had trouble characterizing them, and required the help of an actual biological protein:
Really what these type of experiments show is how one can rationally exploit chance, the starting conditions made all the difference, followed by tweaking the periphery in order to strengthen the binding. This is essentially what we see when we look at the bacterial porin and the MTS .
Comment by Guts — October 14, 2009 @ 7:45 pm
October 14th, 2009 at 8:28 pm
You can follow a path by walking, running or taking a car. The researchers looked at the sequence of known historical events, then predicted based on Common Descent, where to find a rare fossil organism. That discovery is a brute fact that won't go away because you wave your hands.
That's why ID will never have scientific relevance. They don't do anything. These scientists searched in the rocks of an Arctic wasteland for years before finding Tiktaalik. They put their "thinking closely" to the test.
Comment by Zachriel — October 14, 2009 @ 8:28 pm
October 14th, 2009 at 8:29 pm
It's a folded protein that binds with ATP. Of course it's relevant. (Clue: There is a reason why the paper is titled, Functional proteins from a random-sequence library.)
For more recent work, try searching for "in vitro display technology".
The starting conditions can be random sequences. (Of course, the pressing goal is producing novel therapeutics, so the engineering has become specialized to explore interesting regions of sequence space.)
Not tweaked, but artificially evolved. The researchers don't need to know how the peptide works, just that is has the desired function.
Comment by Zachriel — October 14, 2009 @ 8:29 pm
October 14th, 2009 at 8:41 pm
Zachriel:
The title is irrelevant, the arguments need to be addressed. Biological functions require context . Stuff that just weakly binds to ATP don't do anything. There are no consequences.
zach:
And an ATP molecule that is used as "bait".
zach:
The desired function was set out from the get go, binding to ATP. The tweaking came in later, with mutagenic PCR, again you have to actually read the paper.
Comment by Guts — October 14, 2009 @ 8:41 pm
October 14th, 2009 at 9:06 pm
The question was "how frequently functional, or even folded, proteins occur in collections of random sequences," which answered Bradford's question about the ability of abiogenetics to guide research. Szostak et al. made a scientifically significant finding while advancing in vitro display technology that is already finding application in medical research. By scientifically significant, we mean widely cited, of course.
That's the idea, to mutate the sequences then amplify them for study.
Comment by Zachriel — October 14, 2009 @ 9:06 pm
October 14th, 2009 at 9:18 pm
zach:
I am questioning their conclusion:
"frequency of occurrence of functional proteins"
I wrote:
zach:
They did it by holding the sequence in place for 3 rounds. That's artificial.
Comment by Guts — October 14, 2009 @ 9:18 pm
October 14th, 2009 at 9:45 pm
They used PCR amplification, then mutagenic PCR amplification, then PCR amplification. It doesn't matter to the point, because one of the original random sequences already had function. Amplification is required to detect the products, and of course, is essential to practical protein engineering.
The paper has been around for quite some time, has been tested many times, and in many different ways.
Comment by Zachriel — October 14, 2009 @ 9:45 pm
October 14th, 2009 at 9:53 pm
zach:
The function was weak ATP binding, not strong ATP binding which was gotten through mutagenic PCR. So no, the function was not "already there".
zach:
That doesn't answer my argument.
Comment by Guts — October 14, 2009 @ 9:53 pm
October 14th, 2009 at 10:00 pm
Right.
I haven't seen an argument. You don't 'like' ATP binding as a test of a functional protein. I suggested you do a search for "in vitro display technology" for other examples. (The starting conditions can be random sequences, though the pressing goal is producing novel therapeutics, so the engineering has become specialized to explore interesting regions of sequence space.)
Rothe, Hosse & Powers, In vitro display technologies reveal novel biopharmaceutics, FASEB Journal 2006.
Sergeeva et al., Display technologies: application for the discovery of drug and gene delivery agents, Adv Drug Deliv Rev. 2006: Combinatorial peptide libraries comprised either by completely random peptides or by backbones randomized in defined positions have served to identify protein binding sites. Excellent reviews summarize the experience with using random and semi-random peptide libraries in the context of various display platforms.
(Follow through some of the cites for more.)
Comment by Zachriel — October 14, 2009 @ 10:00 pm
October 14th, 2009 at 10:16 pm
zach:
It's not that I don't "like" it, it's just that I don't see how it is biologically relevant. As a design methodology that makes intelligent use of an existing architecture, it's great. Like I said, put it in it's prebiotic context and I'll be impressed, get ATP dependent interacting proteins, even better, something that contributes to the systems of a cell. Selective binding in and of itself, isn't really something that I would consider relevant.
Comment by Guts — October 14, 2009 @ 10:16 pm
October 15th, 2009 at 7:53 am
{Army, {Corps I}, {Corps II}, {Corps III}}
Everything in {} is a set.
So apparently you don't know what a set is.
Comment by ID guy — October 15, 2009 @ 7:53 am
October 15th, 2009 at 7:58 am
Zachriel,
The theory of evolution doesn't have any scientific relevance because not one of its grand claims can be objectively tested.
The transition from water to land exists only in the minds of those who require it.
Comment by ID guy — October 15, 2009 @ 7:58 am
October 15th, 2009 at 8:46 am
{Army, {Corps I}, {Corps II}, {Corps III}}
That means that Army is the superset which consists of and contains the three Corps.
Comment by ID guy — October 15, 2009 @ 8:46 am
October 15th, 2009 at 9:22 am
ID guy wrote:
No, Joe, this line describes a set that consists of Army and three sets that consist of Corps I, II, and III. It does not indicate that the Corps are subsets of Army.
Comment by olegt — October 15, 2009 @ 9:22 am
October 15th, 2009 at 7:56 pm
Exactly my point. Thinking closely about these things allows us to determine the "HOW?" and the "WHY?".
I'm not waving my hands. I'm asking you if you ever 'think closely' about HOW anything relevant actually evolved? I don't think you have.
Bully for them. Now, explain to me (to the best of your ability) HOW and WHY the evolution of wrists occurred. Think closely about it. Don't just wave your magic RV+NS wand.
Comment by Daniel Smith — October 15, 2009 @ 7:56 pm
October 15th, 2009 at 8:18 pm
Yes, but that doesn't salvage your suggestion that a posited evolutionary pathway is a notion that works best when one doesn't think about it too closely. In fact, thinking closely about has led to wonderful new discoveries. When confronted with these sorts of verifiable predictions from the Theory of Common Descent you change the subject.
Comment by Zachriel — October 15, 2009 @ 8:18 pm
October 16th, 2009 at 7:12 am
Do you have something to support your claim?
Or is bald declaration the best you have?
Or is this format better:
{Army, {{Corps I}, {Corps II}, {Corps III}}}
I ask because I have seen the biological classification depicted as such- that is IKingdom would be where the "Army" is and thge Phyla wouold replace the three corps, but perhaps I didn't include enough {} in my original.
Comment by ID guy — October 16, 2009 @ 7:12 am
October 16th, 2009 at 7:13 am
Zachriel,
How can one tell the difference between common descent and common design?
IOW what is the objective test that separates the two?
Comment by ID guy — October 16, 2009 @ 7:13 am
October 16th, 2009 at 7:55 am
The brackets define the set. The notation does not indicate that
Armyis a superset of anything. IfX1 = {Army, {Corps I}, {Corps II}, {Corps III}}, then Army is just an element of the set X1, while X1 is a superset of Army and the Corps subsets. Notice that Army is within the outer brackets, but doesn't bracket anything else.No better. Army is still just an element of the superset. It needs to be written like this: Army = {{Corps I}, {Corps II}, {Corps III}}.
Armyis now the name of the set that contains and consists of the subsetCorps.It an archetypal army, the Generals are soldiers within a Corps:
Army = {General, other soldiers of I Corps}, {General, other soldiers of II Corps}, {General, other soldiers III Corps}}.Comment by Zachriel — October 16, 2009 @ 7:55 am
October 16th, 2009 at 8:17 am
Zachriel,
In order to be a nested hierarcht the Army has to be part of the set.
Yes they are, so what?
However I have noticed that you cannot provide a valid reference to support your claims.
That you think your word is all that is required is hilarious to say the least.
Comment by ID guy — October 16, 2009 @ 8:17 am
October 16th, 2009 at 8:19 am
X1 = {Army, {Corps I}, {Corps II}, {Corps III}}
X1 just names the set. It is not part of the set and it is not a superset.
Army = {{Corps I}, {Corps II}, {Corps III}}
Army is no longer in the set, it is just the name.
Comment by ID guy — October 16, 2009 @ 8:19 am
October 16th, 2009 at 8:31 am
X1 just names the set.
X1 is not part of the set.
X1 is the superset of
Army, {Corps I}, {Corps II} and {Corps III}.Whenever you see X1, just think
{Army, {Corps I}, {Corps II}, {Corps III}}. "X1 is the superset" means exactly that "{Army, {Corps I}, {Corps II}, {Corps III}}is the superset."That's right.
Armyis not in the setArmy. Whenever you seeArmy, think{{Corps I}, {Corps II}, {Corps III}}.Armyconsists of and contains{Corps I}, {Corps II} and {Corps III}.Comment by Zachriel — October 16, 2009 @ 8:31 am
October 16th, 2009 at 8:42 am
Zachriel,
Either provide a valid reference that supports your claims or admit that you are a coward.
Army has to be in the set in order to construct a nested hierarchjy of that Army.
So the question is why does Zachriel think his bald assertions are a substitute for a valdi reference?
Comment by ID guy — October 16, 2009 @ 8:42 am
October 16th, 2009 at 9:43 am
A nested hierarchy is not part of a set. A nested hierarchy is a set.
Your set
is not a nested hierarchy because a soldier can be in the set {Army} and also be in the set {Corps I}. You've placed {Army} at the same level as {Corps}, violating the assymetric relationship required of a partially ordered set.
Comment by Tom MH — October 16, 2009 @ 9:43 am
October 16th, 2009 at 10:32 am
Joe, how about first learning the basics of set theory and then asking questions about it? I hear this is the more efficient way.
Comment by olegt — October 16, 2009 @ 10:32 am
October 16th, 2009 at 10:37 am
In order to be a nested hierarcht the Army has to be part of the set.
That doesn't have anything to do with what I said.
I know a nested hierarchy is a set- a very specific set.
Wjat I said is that in order for the Army to be part of the nested hierarchy it must be included in the set.
{Army, {Corps I}, {Corps II}, {Corps III}}
Actually I believe the correct representation is:
{Army, {{Corps I}, {Corps II}, {Corps III}}}
And yes the point is the soldier is part of the Army, Corps, Division, etc just as a human is an animal, chordate, etc.
Then you copy the definition of a HIERARCHY as if that is supposed to mean something.
Comment by ID guy — October 16, 2009 @ 10:37 am
October 16th, 2009 at 10:39 am
trollegt,
Perhaps you should first demonstrate knowledge of something before you pontificate about it.
I hear that is the correct way.
I also hear that in order to refute someone you have to actually provide something, that is other than your say-so, to do it. Something like an example, data, references- give it a try as opposed to just telling someone they are wrong.
Comment by ID guy — October 16, 2009 @ 10:39 am
October 16th, 2009 at 10:48 am
Joe,
That was just a suggestion. You can keep entertaining us if you prefer.
Comment by olegt — October 16, 2009 @ 10:48 am
October 16th, 2009 at 11:11 am
trollegt,
Mine was also just a suggestion.
However I understand that you and your ilk prefer bald assertions to actual data.
BTW imbeciles are usually entertained by what they cannot comprehend.
Comment by ID guy — October 16, 2009 @ 11:11 am
October 16th, 2009 at 11:39 am
The ISSS primer on nested hierarchies gives the Army as an example of a nested hierarchy, not part of a nested hierarchy. You seem unable to describe in set notation the Army as a nested hierarchy. This:
ain't it.
a. The Army is an example of a nested hierarchy.
b. A nested hierarchy is a set.
c. You are unable to descibe in set notation the Army as a nested hierarchy.
Prove me wrong.
Comment by Tom MH — October 16, 2009 @ 11:39 am
October 16th, 2009 at 12:03 pm
In order to be an example of a nested hierarchy it has to be part of it.
Army is the superset just as animal kingdom is the superset.
The Army consists of and contains all the Corps, Divisions, etc just as the animal kingdom consists of and contains all of its Phyla, Classes, Orders, etc.
Just your say so isn't enough Tom.
It sure can be if set up properly.
A very specific type of set.
Except for the fact that I have- that is just to the "Corps" level.
BTW I don't have to prove you are wrong if you don't have anything to support your claim that you are right.
Comment by ID guy — October 16, 2009 @ 12:03 pm
October 16th, 2009 at 1:00 pm
From here.
So let's examine your set, ID guy.
It consists of two elements:
Army
and another subset
{{Corps I}, {Corps II}, {Corps III}}
which in turn consists of three subsets: {Corps I}, {Corps II}, and {Corps III}.
So either you've just defined a set that consists of an Army and a group of three additional Corps (an Army Group perhaps?) or you've started to define the power set of Army, which is the set of all subsets of Army, and which is fine as well. But neither of those are the Army as a nested hierarchy. Represented as a nested hierarchies, each of the subsets within Army should be a proper subset.
Comment by Tom MH — October 16, 2009 @ 1:00 pm
October 16th, 2009 at 2:20 pm
Tom MH,
There isn't anything in your link that shows us how to contstruct a nested hierarchy using {}.
And there isn't anything in that link that supports your claim.
The outer {} contain the superset.
The next {} are the next level/ subsets with their entities- specified subsets in that subset- in {}.
But if you are saying my first depiction is correct- {Army, {Corps I}, {Corps II}, {Corps III}}- that could be.
However all that is moot because descent is not a defining characteristic, evolution does noit have a direction and nested hierarchies demand a direction of additive characteristics.
Comment by ID guy — October 16, 2009 @ 2:20 pm
October 16th, 2009 at 6:51 pm
You don't even have a fundamental understanding of set notation.
Comment by Zachriel — October 16, 2009 @ 6:51 pm
October 16th, 2009 at 8:41 pm
You obviously mean "No".
How "closely" do you have to think about an evolutionary pathway to figure out that proto-wrists would come before actual wrists? You're completely missing my point Zach! Which is probably why you ignored the rest of my post:
Comment by Daniel Smith — October 16, 2009 @ 8:41 pm
October 16th, 2009 at 11:06 pm
You talked about pathways, and when provided an example of how a posited pathway led to specific and verified empirical predictions, you change the subject. If instead of changing the subject, you are indicating a change in position, you should state so explicitly.
Comment by Zachriel — October 16, 2009 @ 11:06 pm
October 17th, 2009 at 9:41 am
Paul Nelson wrote 8 days ago:
Paul, kicking Joe around has been boring lately. Come back and liven up the thread.
Comment by olegt — October 17, 2009 @ 9:41 am
October 17th, 2009 at 11:46 am
And you are a liar and a sore loser.
Comment by ID guy — October 17, 2009 @ 11:46 am
October 17th, 2009 at 11:49 am
trolleg,
How do you define "kicking"?
It must be that you think "kicking" is your throwing a hissy fit and never supporting your claims.
You and Zachriel are pros at both of those.
The $20,000 challenge still stands you coward.
Comment by ID guy — October 17, 2009 @ 11:49 am
October 17th, 2009 at 11:56 am
{{{}, {{}}, {{}}}, {{{}, {}, {}}, {{}, {{{}, {}}, {{}, {}}}}}, {{}, {{}, {{}, {}, {}}, {{}, {}, {{}}}}, {{{}, {{}}, {}}, {}}}}Just sayin'.
Comment by Zachriel — October 17, 2009 @ 11:56 am
October 17th, 2009 at 4:02 pm
This is pointless. I cannot get you to look closely at how evolution works because you, apparently, are afraid to do so. You're afraid your world will crumble I guess. Why else would you avoid every attempt I've made to discuss the mechanisms of evolution?
One more try:
Now, explain to me (to the best of your ability) HOW and WHY the evolution of wrists occurred. Think closely about it. Don't just wave your magic RV+NS wand.
Comment by Daniel Smith — October 17, 2009 @ 4:02 pm
October 17th, 2009 at 6:15 pm
You had said that evolutionary pathways work best when one doesn't think too closely about it. I provided an example that shows how thinking about those pathways leads to novel discoveries. You then changed the subject. One can't discuss the mechanisms of evolution by ignoring the history of evolution, the pathways by which organisms diverged.
Comment by Zachriel — October 17, 2009 @ 6:15 pm
October 17th, 2009 at 6:35 pm
Just in case you are really interested, you might read this paper. It doesn't discuss the entire transition, but does cover an important intermediate.
Shubin, Daeschler & Jenkins,The pectoral fin of Tiktaalik roseae and the origin of the tetrapod limb, Nature 2005.
Comment by Zachriel — October 17, 2009 @ 6:35 pm
October 17th, 2009 at 7:19 pm
WHAT are you sayin' Zachriel?
The following is what I posted:
{Army, {Corps I}, {Corps II}, {Corps III}}
and
{Army, {{Corps I}, {Corps II}, {Corps III}}}
all my { have the correct corresponding }
So I take it you are just sayin' you can misrepresent my posts?
I am pretty sure everyone who has ever dealt with you understands that is all you have.
Comment by ID guy — October 17, 2009 @ 7:19 pm
October 17th, 2009 at 7:30 pm
Let's recap:
Zachriel says that nested hierarchies are ordered sets.
He also sez that trees are/ form a nested hierarchy.
However Zachriel also sez a family tree is not a tree because it doesn't form a nested hierarchy.
So I hit him with:
He just hand waves that away.
And he sez I don't have a fundamental understanding.
Comment by ID guy — October 17, 2009 @ 7:30 pm
October 17th, 2009 at 7:35 pm
I read that paper.
I must have missed the part that ties the genetics to the fins and limbs.
Oh, that's right, there wasn't anything about what mutations in what genes and/ or regulatory networks are linked to what changes.
Don't you find it a little strange that we can't even test the premise that fins can change into limbs, complete with wrists?
Or are you one of those guys that PT Barnum was talking about?
Comment by ID guy — October 17, 2009 @ 7:35 pm
October 17th, 2009 at 9:42 pm
An example of the set order up one "branch" of the superset:
Fire and maneuver team ⊂ fireteam ⊂ squad ⊂ section ⊂ platoon ⊂ company ⊂ battalion ⊂ regiment ⊂ brigade ⊂ division ⊂ corps ⊂ army
Comment by ID guy — October 17, 2009 @ 9:42 pm
October 17th, 2009 at 10:00 pm
We can also do:
H. sapiens ⊂ Homo ⊂ Primates ⊂ Mammalia ⊂ Animalia
(yes I see that sets are missing)
Comment by ID guy — October 17, 2009 @ 10:00 pm
October 17th, 2009 at 10:19 pm
That's funny.
Comment by Zachriel — October 17, 2009 @ 10:19 pm
October 17th, 2009 at 11:40 pm
Yes it is funny that you always have to be cryptic.
It is also funny that you guys think being obtuse is a virtue.
And what is REALLY funny is when you tell people they are wrong but never support that claim.
Comment by ID guy — October 17, 2009 @ 11:40 pm