More Egg on Miller's Face
by MikeGeneAccording to Jonathan Witt's report, we read:
Also, in yesterday's testimony, Miller called attention to a factual error in Pandas. In today's questioning, he conceded that the "elephant" edition of his own high school biology textbook contained an error, describing evolution as a "random and undirected process." Miller said that that wasn't a scientific statement, and it was removed from subsequent editions.
I'm glad that Ken Miller has officially admitted that his science textbook was propagating non-scientific statements about reality. But Ken's explanation is not good enough. Here are more questions that naturally follow:
1. How did Miller find out about this error? Did he catch it himself? Or did someone else point it out to him? Who was the first to notice this error?
2. More importantly, how did this "error" get into his science text? Did it poof into existence? Was he looking away while typing and his fingers randomly typed in "random and undirected process?"
3. Why, of all the words in the English language, did this "error" happen to coincide nicely with what mainstream scientists tell us about evolution: "evolution is understood to be the result of an unguided, unplanned process of random variation and natural selection."
4. Was it another error for Miller's textbook to teach "evolution works without either plan or purpose?" If so, how did this error occur?
5. If there was no ID movement, would Dr. Miller still be claiming there were "errors?"
September 27th, 2005 at 9:55 pm
At least Miller can admit to error. Can Dembski? Can Behe?
Comment by ericmurphy — September 27, 2005 @ 9:55 pm
September 27th, 2005 at 10:28 pm
You miss the point. I'd like to know how this error happened.
Comment by MikeGene — September 27, 2005 @ 10:28 pm
September 27th, 2005 at 10:46 pm
I was pretty sure your point was to imply that without ID watching over those crafty evolutionists, their mistakes would never come to light. Was I mistaken?
My point was to imply that science (whatever the foibles of individual scientists) is inherently self-correcting, in that errors are pointed out by other scientists, or become refuted by subsequent inquiry. I've seen precious little evidence that ID proponents like Mssrs. Dembski or Behe are capable of admitting error, which is a problem for their scientific credibility.
But I am curious as to what you're implying by wondering about the source of Mr. Miller's error. Are you implying that because he's made an error, all of his work then becomes suspect? Or are you implying that his statement was not an error at all, but a deliberate attempt to mislead? The former is a weak inference, but the latter is a serious charge, at least when leveled at a scientist.
In any event, since I can't tell from the quote what exactly the error was, it's difficult to decide what to make of this admission. Is the entire statement erroneous, i.e., evolution is a "non-random and intelligently directed process" Or is it possibly not entirely random, but still undirected? Possibly it's deterministic, but still undirected. All are possibilities, but without follow-up from the cross-examiner, we can't tell which Miller meant.
Comment by ericmurphy — September 27, 2005 @ 10:46 pm
September 27th, 2005 at 11:00 pm
You keep missing the point. I'd like to know how this error happened. Did it poof into existence? Was he looking away while typing and his fingers randomly typed in "random and undirected process?"
Comment by MikeGene — September 27, 2005 @ 11:00 pm
September 27th, 2005 at 11:30 pm
I have to say, I think I'm still missing the point. I guess if you really wanted to know, you'd have to ask Ken himself (assuming he even knows). But my point, or maybe it's more of a question, is why is the answer to this particular question so important? Isn't it more important to find out exactly what Mr. Miller thinks the error is? If Miller thinks the error is only that evolution isn't entirely random (most evolutionists would say that natural selection, for example, is non-random), I think your point will end up being less strong than you think it is. If, on the other hand, Miller means he was mistaken about evolution being undirected, I think we've got a much bigger issue here.
In any event, I'm pretty sure that neither of your guesses is close. My guess is either than he wasn't thinking clearly, or that he overstated his case and on thinking about it later realized he should probably rephrase himself. But all of this is speculation, and at the moment I'm wondering if it's pointless speculation. I'm pretty sure that your real question is not how the error occurred, but why.
Comment by ericmurphy — September 27, 2005 @ 11:30 pm
September 27th, 2005 at 11:46 pm
No, I would like to know how it happened. Errors have a cause, right?
Comment by MikeGene — September 27, 2005 @ 11:46 pm
September 28th, 2005 at 12:12 am
Mike,
I'm looking for the article that I just read. Miller says he overlooked what his co-author wrote. Unfortunately, I can't seem to find the article anymore! It may have been part of the court testimony.
I'm a little disappointed the defense isn't tearing into Miller more.
Salvador
Comment by Salvador T. Cordova — September 28, 2005 @ 12:12 am
September 28th, 2005 at 12:56 am
I think we can probably both agree that the error had some cause. Why don't you send Ken an e-mail? Again, assuming he knows.
But aside from knowing what caused the error, wouldn't you also like to know the exact nature of the cause?
Comment by ericmurphy — September 28, 2005 @ 12:56 am
September 28th, 2005 at 12:57 am
Oops. I meant to say, the nature of the error.
(You shouldn't compose comments while talking on the phone…)
Comment by ericmurphy — September 28, 2005 @ 12:57 am
September 28th, 2005 at 2:07 am
Eric…the error is obvious to anybody who follows the controversy. Basically, Miller argues that "science" is silent regarding questions of purpose, and regarding the possibility that God might have any role in directing the universe in any way. So, when he wrote that evolution is "random and undirected," he overstepped the bounds of "science," and made a philosophical/religious assertion.
Now, with that understanding, how would you respond to Mike's question as to how that "error" came about?
Comment by ryan — September 28, 2005 @ 2:07 am
September 28th, 2005 at 2:55 am
Yes, I got that part. Miller finds himself contradicting himself, which is why I guessed that the "error" was in overstepping the bounds of what he believes he can reasonably attest to. My question is, why is the cause of the error important to Mike? The only thing I can think of is that Mike is implying that it isn't actually an "error," it was intentional, and Ken only retracted it when he got "caught" by the ID community.
Again, this is not a question about "how" the error happened, but "why." The "how" is a matter of mechanics.
And the "error" is only an "error" in certain contexts. Many evolutionary biologists would no doubt maintain that evolution is in fact undirected, that the evidence points that way, and would disagree with the second half of Miller's "correction." Miller may believe himself that it's an "error" to claim that evolution is undirected, but that doesn't mean it really is an error to so state, or that all (or even most) evolutionary biologists agree with him.
Comment by ericmurphy — September 28, 2005 @ 2:55 am
September 28th, 2005 at 4:08 am
Eric, the source of Miller's "error" is pretty clear – he listened to Eugenie Scott. The real question is, "What combination of pressure and bad logic made Eugenie Scott say that calling evolution a random and undirected process was unscientific?"
Since everything we know about mutations leads us to believe that they are random (with regard to fitness) and undirected and since there is NO evidence to the contrary, the real question is why did Eugenie make her mistake.
I tend to think that she was trying to assuage the fears of religionists by trying to convince them that their cause is not as hopeless as it really is.
Since many in the ID community think that evolution IS directed, I would ask them to list their evidence for this belief here. And "It looks designed to me" does not count as evidence. It looks undesigned to me, so our opinions cancel out. What evidence does ID have for unnatural direction in evolution?
Comment by DataDoc — September 28, 2005 @ 4:08 am
September 28th, 2005 at 8:13 am
That's some sophistry right there. Obviously, if Miller wrote it on purpose, the "how" it got there is different from if he wrote it on accident (however much sense that makes), or if his cowriter wrote it, and he just somehow missed it (however believable that is).
Yes, but we're only concerned with Miller's context here. He must regard it as an "error", because if it wasn't, then he was being duplicitious when responding to the Cardinal, and in other places where he has said that questions of purpose are outside the scope of science, an argument he uses to try and get Christians to accept Darwinism, and to keep ID out of science.
Comment by Deuce — September 28, 2005 @ 8:13 am
September 28th, 2005 at 8:57 am
You know boys it's possible Miller only had the philosophical nature of his textbook statement pointed out after it was made. He may have personally disagreed with it at the time but thought that that was *the* acceptable inference to draw from evolution. Of course it's also possible he knew from day 1 that it was a philosophical statement outside the bounds of scientific "testing" and put it anyway!
It's funny though — I think Miller is trying to please everyone. He believes in God and doesn't want to join the atheists, but he doesn't want to offend their comfortable naturalistic dominance of the biological sciences. To dare suggest that design is a real part of the cosmos and that certain features may not be reducible to purely mechanistic forces alone, in a universe he believes was 'built by God'? Never!!
Comment by Plump-DJ — September 28, 2005 @ 8:57 am
September 28th, 2005 at 9:09 am
Good question. Maybe we should all just be agnostic then. I think one indicator would be wether or not biological systems would have an increased appearence or connection to designed systems, the more we knew about them. Do we need greater amounts of teleological concepts and analogies to understand them?
There must come a point where the poor old ID-ists 'personal incredulity' get's overtaken by the poor old skeptics "personal credulity"! What is that point I don't know.
One thing I will say though — To suggest random mutations are random therefore Evolution is random is somewhat tautological. Who really knows the scope through which evolution wss allowed to drive? Did we watch it unfold? I don't think we did.
Comment by Plump-DJ — September 28, 2005 @ 9:09 am
September 28th, 2005 at 11:39 am
DD
I think the reason that Eugenie Scott make that statement is that to claim that "evolution was an undirected process" was a scientific claim would mean that detecting direction/non-direction in nature was a legitimate scientific endeavor. This sounds remarkably like one of the core claims of ID.
Comment by daveb — September 28, 2005 @ 11:39 am
September 28th, 2005 at 12:13 pm
Good point daveb. I think you've got it. I don't think Miller changed his mind about evolution being random and undirected, but he realized that to so state it goes beyond the bounds of science and into philosophy, and comes perilously close to being an outright assertion of atheism as fact, therefore it would violate the church/state clause in the case of education, which will rebound unpleasantly back on them.
I am in the mood to stick my neck all the way out. Since I'm no doubt the least educated or qualified person here, I can afford to be foolish. I think the idea that random mutations are largely responsible for the genomes of some 100 million life forms is surely the most absurd concoction that man has ever dreamed up with which to fool himself. Its silliness may never again be matched.
How did it happen? Man the storyteller likes to have a comfortable myth to live by. Not at all happy without one. Darwin proposed small changes in the generations. No knowledge of genetics. But once they adjusted to that idea, it wasn't long before the Aha! moment. Voila!
The problem is, as becomes increasingly clear, it is an inadequate explanation. Why not suppose that we are now in a situation similar to Darwinians before the advent of genetics? In other words, stop insisting on genetic mutations as the source of life forms and assume instead that there is at least one very major mechanism driving evolution, of whose existence we are not yet aware? Why pretend to more understanding than we have?
From my point of view, I don't think that when those mechanism(s) are discovered, that they will be random and undirected, but the evolutionists can certainly hold out the hope that it will be.
Comment by onething — September 28, 2005 @ 12:13 pm
September 28th, 2005 at 12:41 pm
I keep wondering why IDists insist that gradual change over time is an inadequate explanation for the diversity of life, and therefore that evolution is a theory in crisis.
Let's have a look at the two other great scientific theories, general relativity and quantum physics. How well do these two theories fare when we get back to the beginning of time? Not very well. Both theories break down at the extremes present at the beginning of time. Both theories (at least currently) appear to be incompatible with each other. Quantum theory mispredicts the cosmological constant by about 120 orders of magnitude, which surely must rank as one of the greatest theoretical failings of all time. The standard model of particle physics makes no predictions as to most of the physical constants; they have to be put into the model by hand.
And yet no one describes either general relativity or quantum physics as "theories in crisis," despite the fact that both theories are known to be incomplete descriptions of reality.
Could it be that neither theory strikes fear in the hearts of the religious the way evolution does? Just a thought.
Comment by ericmurphy — September 28, 2005 @ 12:41 pm
September 28th, 2005 at 1:55 pm
ericmurphy said:
Actually, the Standard Model of physics is currently suffering from "Unitary Crisis," in that it spews gibberish at currently achievable energy levels. Of course, the SM is also known as RQFT – Relativistic Quantum Field Theory – a combo of both GR and QM. RQFT is a "theory in crisis."
Comment by Joy — September 28, 2005 @ 1:55 pm
September 28th, 2005 at 4:52 pm
Hello Plump-DJ,
I think you've got things pretty well-marked, though I certainly don't think Ken Miller is trying to please everyone, heaven forbid! Naturalistic dominance is a figment of the provocationalists imaginations. Could you possibly believe that the percentage of non-'believers' and heathens (read: anti-spiritualists) in the academy is higher in the social sciences and humanities than in the natural sciences? Well, anyway, I appreciate your comments here.
'Design' is the highjacked (or rather borrowed, repatriated) concept of one particular 'movement' of thinkers in the USA who gathered in California in 1993 to express their disgust against naturalism, materialism, secularism, etc. name your ideological villain. Freud and Marx come to mind (npi), but have already been 'defeated' in the US. Darwin hasn't, if for no other reason than that 'struggle for existence' and 'survival of the fittest' are predominant in American culture and lifestyle/worldview. Phillip Johnson spells this out clearly, by example, as readers well know. Herbert Spencer was more popular in the US than in England, he being the coiner of the the term 'survival of the fittest.' Revd' T. Malthus being the originator of the phrase Darwin used in his long title which begins which 'Origin(s) of Species'. However, don't talk about Malthus or Wallace if you expect no yawning on ID channels; those who would want to go post-Darwinian. This may, however, have nothing to do with TT's here on this list, I don't know their preferences.
IDists make it out to be about evolution vs. design or design vs. chance or Darwin vs. Information Theory or Origins vs. origins or processes vs. Processes or Poof vs. mathematical/specificational/statistical proof. They scathe against, ridicule or ignore theistic evolutionists and evolutionary creationists (but not always, i.e. good to keep dialogue and old friends), since it is inconvenient to acknowledge them, brothers and sisters that they are, no matter how vacuumed ID theology has become. This is partly why/how a voice for Telic Thinkers who function outside the IDM's DI-ID type to promote their cause has come to exist.
'Purely mechanistic forces' – Yes, this is getting to the juice of the matter. But remember, it is IDists who are claiming proof of 'design' exists (i.e. forget the Intelligence when politically incorrect) simply because biologists (who are mechanically inclined) claim to have (philosophically) proved or at least that they believe in 'molecular machines'. It may look like a machine, but it's still organic!! ORGA-MECHA – S. Kubrick, the director of Artifical Intelligence, is still laughing in his grave.
IDists will not tell you the difference between human-made design and non-human-made design. Please ask an IDists and see for yourself. And then they blame K. Miller and throw eggs at him with their voices trying to elevate themselves for a Cause. There are red faces in America in many places these days, not just in ID vs. Evolution (or neo-Darwinism) land.
'Random and undirected' – this certainly couldn't be describing some aspects of the apparently global war on terror, could it?
Wishing for peace in the battles over evolution, creation, ID and dignity rather than arrogance for those extremists who would seek further conflicts,
Arago
Comment by g arago — September 28, 2005 @ 4:52 pm
September 28th, 2005 at 5:11 pm
Because of the details.
Comment by onething — September 28, 2005 @ 5:11 pm
September 28th, 2005 at 5:43 pm
Joy:
Yes, but not in the same way. No one expects that either general relativity or quantum mechanics will be overturned completely with an entirely new paradigm, nor does anyone think that either theory is not supported by evidence. It seems to be the fond hope of the ID community that neodarwinian evolution will be completely overturned as a theory, and that it is not supported by evidence. Actually, the notion of common descent with modification, a central tenet of NDE, is better supported than, say, the current value for the universal gravitational constant.
Comment by ericmurphy — September 28, 2005 @ 5:43 pm
September 28th, 2005 at 6:33 pm
onething:
If there's one thing I've learned dealing with IDists or creationists, it's there is no level of detail that will ever be satisfactory. Given the utter lack of detail in the "theory" of ID, let's just say I'm a little surprised by that.
Comment by ericmurphy — September 28, 2005 @ 6:33 pm
September 28th, 2005 at 9:42 pm
We must be talking of a different kind of detail. From my point of view, Darwinists say things like "What's wrong with the notion of change over time?" There's nothing wrong with it and ID agrees with it, so far as it goes. But what happens when you get up close and personal with molecular biology, is that the details look designed.
Or, at the very least, there are other mechanisms which we do not yet know about, such as when Darwin did not know about genetics, that will greatly improve and expand the picture. RM + NS just doesn't cut it.
Comment by onething — September 28, 2005 @ 9:42 pm
September 28th, 2005 at 10:11 pm
Personally, I don't think it was any accident that Miller was the one on the stand. Besides wanting him to make the scientific case for evolution and against ID, I'd bet the farm that another goal was to showcase someone who was well-known as an evolutionist AND a faithful Christian Catholic. Unfortunately, Miller doesn't represent the teachings of the Church very well, and whenever he delves into theological arguments (the "God wouldn't have done it that way" arguments), he is in way over his head. Laid out as a syllogism, the arguments Miller uses look something like this:
P-1 We observe that many species have gone extinct over the eons
P-2 If God had created the species, none of them would have gone extinct.
Conclusion: Evolution as a blind, purposeless process and NOT God is responsible for the full diversity of life on planet earth.
What's a theological argument doing in what is supposed to be a scientific argument?
Comment by DonaldM — September 28, 2005 @ 10:11 pm
September 28th, 2005 at 11:04 pm
Eric:
How does one do this? Miller doesn't believe that "evolution works without either plan or purpose," yet he erroneously writes this. Miller doesn't believe is a "random and undirected process," yet he erroneously writes this. How does something like that happen?
Well, thousands of school children have probably been misled by this error. In order to learn from the error, we need to know how it happened so we can make sure it doesn't happen again.
Are you suggesting Miller did not intend these words to come into existence: "evolution works without either plan or purpose" and "random and undirected process"? Obviously, the words came into existence through intention. Yet they are now said to be errors. How did such errors occur?
BTW, are you going to reply to DataDoc, who addressed you as follows:
Comment by MikeGene — September 28, 2005 @ 11:04 pm
September 29th, 2005 at 1:26 am
onething:
Yep. That's why there are other mechanisms at work, such as genetic drift. But whether neodarwinian evolution's explanations for the diversity of species cuts it for you just isn't that important to the scientific community. Dawkins calls your argument an "argument from personal incredulity."
If ID has some additional mechanisms it would like to add to the mix to come up with a more complete and robust explanation for life on earth, that would be just great. The scientific community is waiting to hear what they are.
Comment by ericmurphy — September 29, 2005 @ 1:26 am
September 29th, 2005 at 1:39 am
MikeGene:
You're mistaking what Miller believes to what he thinks he can back up, or what he thinks is within the bounds of scientific inquiry. It's entirely possible, isn't it, that Miller believes the first, but doesn't think he can state it with sufficient authority from the evidence to put it in a high school biology textbook?
Have thousands of schoolchildren been "misled" by this "error" Doubtful. For one thing, you're saying it like it's definitely not true that evolution is random and undirected. You don't know that, so to say it's definitely an error is further than you can legitimately go, regardless of what Miller thinks. For another, if you think Miller's statement is even close to the magnitude of the thousands of errors that infest science textbooks in all areas of science, you're kidding yourself. Believe me, there are bigger things to worry about in high school textbooks than one statement by one scientist that for all we know is very likely true anyway.
I"m not suggesting Miller didn't intend these words to come into existence. And again, you're saying these words are "said to be errors," as if they definitely are erroneous. This hasn't even begun to be proven. Do you think this is the first time a scientist has made claims that go beyond the evidence? Do remember Einstein's comment on hearing of Eddington's confirmatory evidence for GTR? If Eddington hadn't come through with the goods, Einstein would have been sorry for god, because his theory was correct.
You're making a mountain range out of an anthill, Mike.
As for replying to DataDoc; I didn't see a need to, because I believe that by and large he is correct. The evidence that evolution is an undirected process, largely (but not entirely) driven by random phenomena has substantial evidence to support it, and none to directly contradict it.
Comment by ericmurphy — September 29, 2005 @ 1:39 am
September 29th, 2005 at 1:57 am
If this isn't a great example of ideological IDists flipping things around, I don't know what is.
Comment by g arago — September 29, 2005 @ 1:57 am
September 29th, 2005 at 2:08 am
Onething:
Really? Does the busted gene for ascorbic acid that humans and chimps have look "designed" to you? Do the thousands of other pseudogenes that used to be functional until a mutation took them out look "designed" to you?
Comment by ericmurphy — September 29, 2005 @ 2:08 am
September 29th, 2005 at 2:15 am
onething:
Or what about the glyceraldehyde-3-phosphate dehydrogenase gene? Humans have one functional copy, and at least 20 busted copies. Does that sound "designed" Same thing with cytochrome c genes; there are more than 20 nonfunctional copies.
Even if the 98% of the human genome that doesn't code for proteins serves some other function, it is a monumentally inefficient use of space, and certainly doesn't look "designed" at all.
Comment by ericmurphy — September 29, 2005 @ 2:15 am
September 29th, 2005 at 6:42 am
Eric M wrote..
How is it inefficent if they serve another required function? My understanding was that non-coding DNA actually does serve a useful function.
Ignoring the apologetics, the link below discusses (briefly) why "Junk DNA" is not so junky!
http://www.reasons.org/resources/connections/2000v2n1/index.shtml#junk_dna
Comment by Plump-DJ — September 29, 2005 @ 6:42 am
September 29th, 2005 at 6:48 am
Eric M wrote..
So you've got personal credulity and they've got personal incredulity. Thats' called "1 All!" Of course this highlights wonderfully the epistemic gaps with "darwinian explanations" and "reality"! (of course this applies equally to ID aswell)
Saying 'it cuts it' because it fits some 'personal explanatory criteria that Dawkins and Co have setup is fine but saying "Yep this is how reality actually is and I can 'demonstrate' this" is another! Remember that quote from Franklin Harold that was floating around the net not so long ago — "No detailed accounts, just wishful speculation!"
Comment by Plump-DJ — September 29, 2005 @ 6:48 am
September 29th, 2005 at 8:23 am
DataDoc:
Since everything we know about mutations leads us to believe that they are random (with regard to fitness) and undirected and since there is NO evidence to the contrary, the real question is why did Eugenie make her mistake.
Not really- Dr. Spetner discussing mutations:
Then we have Barry Hall's experiments as evidence for directed mutations. The experiments Miller uses to try to refute Behe's concept of IC.
Comment by Joe G — September 29, 2005 @ 8:23 am
September 29th, 2005 at 11:46 am
Joe G:
Argument from personal incredulity?
Comment by ericmurphy — September 29, 2005 @ 11:46 am
September 29th, 2005 at 11:51 am
Plump-DJ:
This is the part of the ID argument I've never understood. No evolutionary biologist out there thinks that science knows everything there is to know about how evolution happens. The theory is certainly not a "done deal," nor is any other theory. But neodarwinian evolution has progressed much further than ID has in developing a working description of how organisms evolve. So far, ID has absolutely nothing to say about how organisms evolve at all. Doesn't sound like "1-all" to me…
Comment by ericmurphy — September 29, 2005 @ 11:51 am
September 29th, 2005 at 2:03 pm
"I'm glad that Ken Miller has officially admitted that his science textbook was propagating non-scientific statements about reality.""”Mike Gene
I haven't seen Miller's textbook. But from what's being reported here it appears as if Miller simply "made believe" he hadn't committed an error and only admitted it when forced to do so in court. LOL Maybe Miller hazarded appearing in court w/o legal counsel. Not the "Bright" thing to do. The way our legal system works most people go to court with absolutely no intention or under advisement not to "admit" anything. Call me a starry-eyed idealist, but I don't think science should or is supposed to work that way.
(Also, Miller hasn't "officially admitted" anything. Admitting a factual or conceptual error in court testimony is not the same as scientifically correcting an error in print. Simply excising the statement from subsequent editions is not the way either. Like I said, Miller just "made believe" he hadn't committed an error.)
But since its been questioned that an error was made, what exactly is the error? We are treating this as if it were an isolable misstatement of fact or the inclusion of broad, questionable or disputable, conclusion. It's a lot more than that.
If its an error to include the comment as a statement of fact when it is a questionable conclusion it certainly is widely repeated even though people are certainly aware that it is disputed or questioned. But that doesn't stop them from repeating it. Why? Because the error is in the way we think. Not in how we relate facts and broader conclusions drawn from what we sincerely believe are facts.
Why would anyone believe that it is a positive theoretical statement to describe biological evolution as a "random and undirected process"? It appears as if a positive statement of theory has been misidentified with the natural null hypothesis! It's not such a simple category error however. There is some subtlety to the error"”there must be to an error so often repeated. The reason why Miller (et al) commits this error, misidentifying a positive theoretical statement with the natural null hypothesis, is because he's a priori identified the null hypothesis with the idea that "God did it"! Miller believes that the antithesis of evolutionary theory is not the statement that evolution is a random and undirected process (which it obviously isn't). The null, the antithesis of evolutionary theory, is the idea that "God did it"! In which case, evidence for the null hypothesis ("random and undirected") may actually be interpreted as confirming the (misidentified) theory and as grounds for rejecting the "null" that "God id it"! (LOL Did ya follow that?) But actually the null, "God did it," is unacceptable to science a priori, so there is never a scientific grounds for accepting the null and rejecting the alternative!
Isn't that preposterous?! Why would scientists, otherwise really smart and rational individuals all, put them themselves into such a ridiculous "theoretical" dilemma? My pet-theory is that whenever "theology" (such as it is in this case) enters substantively into scientific thought, the collective IQ immediately drops somewhere between 50-100%. That's my theory.
A theory has been floated that science is self-correcting. I believe. But I also recognize that my belief is a bit of wishful thinking. But the theory suffers from a logical conundrum–It's unfalsifiable. The first step in correcting error is recognizing its existence. The more subtle the error, obviously the more difficult that is.
Isolable factual errors are relatively easy to identify and correct. Science has a real problem in identifying and correcting the doozies. Its more likely that these kinds of errors will be perpetuated, as "textbook orhtodoxy," for generations before they are corrected
Comment by Rock — September 29, 2005 @ 2:03 pm
September 29th, 2005 at 5:32 pm
I find it hard to believe that a process as precise and well controlled as the transposition of genetic elements happens only by chance.
ericmurphy:
Argument from personal incredulity?
Yeah, opposing the argument from credulity- that being the scientists who believe those gentic movements are random because they just don't know any better or just want them to be.
How organisms "evolve" in the ID scheme:
"built-in responses to environmental cues"; genetic algorithms designed to take the available resources and achieve a pre-programmed goal (similar to Dawkins' "weasle" and "Evolving Inventions")
also as Dr Behe states:
Comment by Joe G — September 29, 2005 @ 5:32 pm
September 29th, 2005 at 6:22 pm
Joe G:
Scientists think genetic movements are undirected (which is not the same thing as "random") because they don't see any evidence of design. What they do see is evidence of inadvertant copies, botched copies, obvious transcription errors, and the like. The genotype of most organisms is much too much of a mess to indicate design. If ID adherents want scientists to believe that there's design in the genes, they're going to have to show evidence of it. So far, they've been unable to do so.
What the hell are "built-in responses to environmental cues" How about cosmic rays smashing into genetic material, causing a codon that used to code for one amino acid to now code for a different amino acid (or maybe no amino acid at all)? Sounds like a "built-in response to environmental cues" to me. All I've done is leave out the unnecessary ingredient — a designer who aimed the cosmic ray.
Why do you need a clever genetic algorithm and a pre-programmed goal, when genetic drift and/or natural selection and no goal at all work just as well, and leave out an untestable and undetectable designer?
I've said it before and I'll say it again: Intelligent design does not explain anything that neodarwinian evolution doesn't explain. You can leave out the designer and not lose any explanatory power. Until ID can demonstrate otherwise, it won't get anywhere, the same way it hasn't gotten anywhere so far.
Comment by ericmurphy — September 29, 2005 @ 6:22 pm
September 29th, 2005 at 7:42 pm
And speaking of Mr. Behe (and "Why Is a Fly Not a Horse?") I came across this quote from Behe's review of Sermonti's book:
Hmm. I thought. If the thing about the leaf insects were true, that would be really problematic for NDE. But since I hadn't heard anything about this particular issue, I thought I'd do a little research.
It took me 30 seconds of Internet research ("sermonti leaf insect phasmid") to come across an article that demolishes Sermonti's claim (and, incidentally, Behe's approval of it). Is it any wonder I have doubts about Behe's credibility when it comes to actual biology?
Comment by ericmurphy — September 29, 2005 @ 7:42 pm
September 29th, 2005 at 10:01 pm
Mr M,
Your misrepresent my objection. I never stated that scientists reckon they know everything about Evolution. I also feel this misrepresents even mainstream ID, which to my mind has never claimed that scientsits think they know everything about Evolution. That is the whole point, they don't. So what bits did I object to?
What I did object to is the idea that possible "darwinian explanations" are to be considered reality or even "likely" to be true merely by their existence *and* that there is no good reason to tihnk real design is expressed (at whatever level) in biological systems. People like Dawkins and Co consider undirected Evolution and neo-Darwinism a done deal — *This* is how Evolution proceeded and there is no good evidenece for 'real' design in nature. If there is 'it's all just illusory' because Natural Selection made it happen!" End of discussion.
So i'm not here to tell anyone how it happened, unlike Dawkins and Co. I'm quite happy to remain agnostic until more information becomes available. I'm open to the idea that "real design" is expressed in biology and that there reasons to consider this. I don't doubt Evolution proceeded , i'm merely uncertain the epistemic dots have been connected between so called darwinian scenarios and reality.
Comment by Plump-DJ — September 29, 2005 @ 10:01 pm
September 30th, 2005 at 12:36 am
Yep. That's why there are other mechanisms at work, such as genetic drift.
An irrelevant remark that is probably meant to be cutting. Do I imagine my personal opinions are shaking the scientific community? No. On the other hand, one must be careful about pushing this idea too far. If an interested and reasonably intelligent layperson cannot be justified in having any opinion on this matter, then it should not be taught to them at all. What is odd is that qualified scientists are asking hard and pointed questions of the scientific community, and the answers are quite vague, in those rare instances when they stop calling names long enough to answer at all. Ninety percent of this whole debate is wasted emotional energy in the form of resistance.
Yes, I've read that bit from Dawkins and it is yet another vapid statement from him. He just really is overrated as a thinker. There is not a thing wrong with being incredulous. We should be skeptical and not gullible. If something appears highly unlikely and suspect, and we are unable to convince ourselves of its veracity, is this supposed to be a red flag, not about the theory, but about our thinking process?
I wonder how Dawkins views incredulity about, say, paranormal phenomena?
Comment by onething — September 30, 2005 @ 12:36 am
September 30th, 2005 at 12:48 am
LOL. I'd bet eric found out about the Behe quote from PT.
Comment by MikeGene — September 30, 2005 @ 12:48 am
September 30th, 2005 at 1:48 am
MikeGene:
No, actually I found out the Behe quote from an evolutionnews.org, which I don't think anyone would think was an evolution-friendly site. The quote was actually in an ad for the Sermonti book (I think it's on the jacket of the book), which presumably was Sermonti-friendly as well.
Comment by ericmurphy — September 30, 2005 @ 1:48 am
September 30th, 2005 at 2:05 am
I have not heard the term, busted gene. If mutations take out previously functional genes, I would call that entropy, or Things Fall Apart.
Where did you get that 10>93 number? Isn't that more than all the particles in the universe?
Comment by onething — September 30, 2005 @ 2:05 am
September 30th, 2005 at 11:54 am
Onething:
Sorry about my comment earlier; I try to keep ad hominem statements to a minimum. I think my patience was getting a little frayed.
Anway, obviously "busted" gene isn't a technical term. But "pseudogene" is, and most eukaryotic genotypes are full of them. However, often the same type of mutation that causes a pseudogene actually generates biological novelty. Sometimes the novelty is harmful, most of the time it's neutral, but sometimes it's beneficial (and sometimes it can be both harmful and beneficial, depending on circumstance). My point is, a lot of the time it's just contingent, and shows no sign whatsoever of planning or forethought, which argues against design.
I got the 10^93^ number here. And yes, it is a larger number than all of the particles in the universe. So think about it: what are the chances that humans and chimps would have exactly the same cytochrome c protein? There's no particular reason, not even design, for them to have remotely similar cytochrome c. And, the further you get away from humans in the phylogenetic tree, the more differences you see in cytochrome c. Of course, ID can account for this, but ID could also account for completely dissimilar cytochrome c, which is kind of the problem.
Comment by ericmurphy — September 30, 2005 @ 11:54 am
September 30th, 2005 at 2:02 pm
Originally the topic seemed to be about perpetuating and correcting errors. I think things are far worse than we are imagining.
Eric murphy reminds us that, ""Scientists"¦ don't see any evidence of design." And its good to be reminded because this obvious and pernicious error seems to be spreading and I'm not sure just how hopeful we can be at this point of ever correcting it. Scientists seem to be picking up on this error and repeating it with ever-increasing, and somewhat alarming frequency.
One of the earliest (and apparently more influential)examples of this error I could think of is George C. Williams (1966) "Adaptation and Natural Selection," which I recently reread. I didn't recall just how many nonsensical things he says about "design." What is really amazing is that the book is widely cited as one of the most important works of 20th century evolutionary thought. A formidable defense of Neo-Darwinism! He makes outlandishly plain right from the beginning that he will invoke design arguments, analogies, and terminology, because they are intuitive, clarifying, conventional, appropriate, and authoritatively supported by such theoretical heavyweights as Muller, Simpson, Pittendrigh, and Sommerhoff!
If you've ever met Williams you'd think it was a case of Hollywood typecasting"”he looks and talks just like a Mad Scientist should. But I really have to wonder! Is he mad?! Just a little bit tiched in the head there, aren't ya, George?
Worse, in a later book (1992. Natural Selection.) he compounds the error by further developing this "design" thesis, saying that we know a biological adaptation because it conforms to an a priori expectation for an engineering design specification, then spinning off into biological information as some sort of immaterial Platonic essence, and recommends students of biology study the works of Galen and Paley for insights, even including excerpts of their writings in an appendix!
Yeeow! Something has seriously gone wrong here!
Then there are biologists like Hartwell, Hopfield, Leibler, and Murray (in the widely cited, "From molecular to modular biology," Nature 402: C47-C-52, Dec. 2, 1999.) who make outrageous statements like, "A number of the design principles of biological systems are familiar to engineers," and "Designs such as these are common in biology."
And speaking of "design principles," there is Dr. Michael Savageau (UCDavis), who has asserted for more than thirty years now (virtually unchallenged) that he can abstract predictive design principles from investigations of molecular biological structures and processes. He pointedly (and obviously, erroneously) contrasts these "design principles" with historical contingency and chance ("random and undirected"?).
I thought we should cut-off this sort of nonsense before it goes much further because I've noticed that some researchers are taking Savageau's descriptive and predictive "design principles" seriously as prescriptive and actually attempting to design and redesign life forms using them.
Has the world gone mad?! What could possibly have gone wrong for biologists to veer off so wildly into pseudoscientific and supernaturalistic nonsense like this?!
Something has to be done to stop the spread of this absurd error and I think we are on the right course. We have to go to the source, which is plainly the failure of public education. If we have to go to court to make sure that these errors are not repeated then so be it. Something's gotta be done.
Comment by Rock — September 30, 2005 @ 2:02 pm
September 30th, 2005 at 2:24 pm
Rock:
I've read your post a few times through, and I have to say, I'm mystified as to what position you're taking. Are you saying it's an error to say that there's no evidence for design, or are you saying it's an error to say there is evidence for it? You seem to be criticizing Williams for defending neodarwinian evolution, but at the same time you seem to be criticizing him for positing design.
Everyone keeps saying that a "design" implies a "designer," but I think you can, in fact, talk about one without the other. When a scientist talks about, say, the design of a shark's dorsal fin, I don't think it necessarily means that someone designed the fin. Something could have designed it as well, and by "something" I'm obviously referring to something like selection pressure.
I guess what I'm saying is, what exactly are you saying?
Miller may look a little weird, but he seems to get a lot of respect in the scientific community. Einstein looked a little weird, too.
Comment by ericmurphy — September 30, 2005 @ 2:24 pm
September 30th, 2005 at 5:47 pm
Sorry, eric murphy, would it help clear up the mystification if I said I was being sarcastic? I am a sarcastic SOB, and it gets worse, either as a consequence of the natural ageing process, or possibly from familiarity with the dreary repetitiveness of errors like this: "Scientists think genetic movements are undirected (which is not the same thing as "random") because they don't see any evidence of design."
The language, the logic, the concepts, and theories, the science of design is now, always has been, and always will be an integral and significant element of evolutionary thought and theorizing. And it is true, of course, because scientists do see "evidence of design," which is exactly their object to understand and explain.
People indoctrinated in the bowdlerized version of "Darwinism" taught in the public education system (even all the way through college), or whose sole knowledge of evolutionary theory consists of stock arguments culled from Internet Infidels and Institute of Creation Research websites probably are mystified–and my sarcasm doesn't help much. Sorry about that.
The sarcasm is really a self-defense mechanism. I think some of the questions and problems are particularly intriguing, scientifically. But the discussions, ostensibly "scientific," are almost exclusively about politics and religion, the "politics at God's funeral" (Swinburne?). Being apolitical and irreligious, I feel left out. I respond sarcastically. Sorry.
Comment by Rock — September 30, 2005 @ 5:47 pm
September 30th, 2005 at 6:57 pm
Rock:
No apology necessary. But I don't feel very enlightened (yet) about your position, I guess. So let's see (I'm thinking hard here, and not being sarcastic at all):
Do you believe that neodarwinian evolution (as it is currently constituted, not as it is misperceived by those who simply aren't that familiar with the theory) is adequately supported by the evidence to be a legitimate theory describing the evolution of living organisms? I'm not asking whether or not there are places where the evidence could use some work; clearly there are.
Or do you agree with the the ID position, which seems to be (to the extent IDists can be pinned down to any particular position) that the mechanisms advanced by NDE for the evolution of life are fundamentally inadequate to the task and need to be replaced, presumably by some sort of intelligent design?
Comment by ericmurphy — September 30, 2005 @ 6:57 pm
October 1st, 2005 at 12:34 am
Using a ubiquitous gene such as cytochrome c, there is no reason to assume that two different organisms should have the same protein sequence or even similar protein sequences, unless the two organisms are genealogically related. Dr. Theobald
So if my Escort and my Grand National both use spark plugs does that mean they are related? Or is it due to a common design?
If I were designing (different) organisms would I re-design every protein or DNA sequence? Absolutely not. I would use and re-use at will.
Also the NDE could account for very dis-similar cyto c sequences, and it can also account for them being very similar. Is this kind of a problem for the NDE also?
Comment by Joe G — October 1, 2005 @ 12:34 am
October 1st, 2005 at 3:04 am
Does ID have a hypothesis as to why the more distantly related an organism is from H. sapiens,, the more differences there are in its cytochrome c? Convergent evolution, perhaps? On a target that bears the same relationship to the range of possibilities as an individual electron bears to the universe at large?
No correlation between phylogenetic distance and similarity of cytochrome c (or other proteins) would be a problem for NDE in a way it would not for ID, which is why ID is on shaky ground as an explanation for life on earth. Common descent with modification is of critical importance to NDE. But ID works just as well with common descent with modification as it does with each organism created individually — custom-made, if you will.
Comment by ericmurphy — October 1, 2005 @ 3:04 am
October 1st, 2005 at 8:05 am
There isn't anything in the premise of "common descent with modifictaion" that says that genetic sequences will remain virtually intact so we can follow the lineage.
IF the NDE were indicative of reality we should see all the alleged "pseudo-genes" get removed from a population as they provide no function and come at a reproductive cost.
And yes, ID does say it will follow the evidence where it leads (common descent, special creation or alien colonization). Which to any objective person is more "scientific" than forcing the evidence to fit only one PoV.
BTW did you know that the Dr. Theobald article you linked to has NOT passed peer-review? There is a reason for that…
Comment by Joe G — October 1, 2005 @ 8:05 am
October 1st, 2005 at 12:36 pm
ericmurphy says
You appear either to be assuming Common Descent, not demonstrating it, or you are asking why similar organisms are more similar than dissimilar ones.
What do you see as problematic for ID vis a vis differences in cytochrome c?
Because this issue is one that Miller et al have raised repeatedly against ID, claiming that makes it non-science. It isn't that he was wrong intitially, or later, or what the answer really is. The inconsistency about the issue that many claim drives them, is rather troubling. That Miller, and the gang of 38, and the NABT, all seem to stumble into this "error" on what is supposedly a most crucial point of ID critics, is revealing.
I'm not as concerned as much about what the "real" answer is, is that folks arguing for that position are consistent.
Comment by RogerRabbitt — October 1, 2005 @ 12:36 pm
October 1st, 2005 at 4:15 pm
Since ericmurphy was more than gracious to overlook my snotty attitude, I thought I should respond to his request that I clarify my "position." All I can say, ericmurphy, is that you'll have to trust me that it is not within the realm of material possibility that I ever clarify my position on anything!
After I had typed my way to the end of four pages, in the attempt to meet your request, I thought I should just say something like, There is no convenient label for my position on any of these matters.
But to answer your questions as directly as possible for me, No, I am not "Neo-Darwinist." And, No, I am not an "Intelligent Designer," either.
Mostly, because I don't even know what those labels mean. No one has ever been able to explain to my own satisfaction, and believe me, I've asked, what I have to believe to be a Neo-Darwinist or Intelligent Designer.
That partly explains my feelings of "alienation." I have the strong suspicion that people are arguing, somethimes quite vociferously, over things they feel intensely about, but cannot rationalize.
E.g., if I am required to believe in "gradualism" to be a good Neo-Darwinist. Then I am not any kind of Neo-Darwinist.
You wrote (above) that gradualism is an important explanatory principle, not to be rejected. But I don't think "gradualism" explains anything, and indeed, confuses to quite differnt things–so its the opposite of an explanation. Its a confusion. (Maybe I could be a good Neo-Darwinist and admit I'm confused about gradualism. LOL)
It seems to me a trivial exercise to find exceptions to gradual evolution. Its perfectly conceivable to me that significant evolutionary change can occur over frames characteristic of biochemical reactions, say in milliseconds. I am supposing that wouldn't count as "gradual," but virtually instantaneous by anyone's clock.
A molecular biologist may appreciate the point I'm making, but a population geneticist may dispute that any kind of significant evolutionary change can occur so rapidly. He may define time in terms of rate to fixation, deriving a simple formula for the rate (ratio) as a dimension, a degree of freedom, over the product of the effective population size and the selection coefficient of the numerator. But this allows evolution to occur at any rate, from infinitley fast to infinitely slow, depending upon the values of the terms. (Realistically rapid evolution can occur depending only upon the first two numbers being "small" and the last number, the selection coefficient, being "large.")
I think you can see that theoretically and empirically there is really nothing we can say about the rate of evolution. It may be rapid. It may be gradual.
I think what has happened is that a true statement about the limits of observation has been confused with a (false)positive statement about a process rate. Two differnt things have been confused here.
The classical Darwinian and Neo-Darwinian apology was that we are compelled to assume that the directly observed process, and associated rates, holds for all life and over all time. They understood that this is an example of an observational limit, a sampling or selection effect. Biologists, having evolved themselves so recently, only observe the outcomes of billions of years of evolution. Even on their own theory they should not expect to observe what is characteristic (of the evolutionary process) of all life and over all time! As we just saw, the assumption is not dictated by either theory or observations!
So what explains the assumption they made?
Interesting topic to explore and I've already belabored it, in this context, but it should be further explored.
But it also explains another reason why I'm not a Neo-Darwinists, and it is a fundamental difference in the "philosophy" of science.
I very strongly believe that there are only two assumptions that scientists ever need make: 1) I assume the world exists and 2) I assume I can know a little bit more about it than just that it exists. Seemingly simple, innocous and safe assumptions, but as the philsophers have pointed out ad nauseam these are actually some pretty gigantic assumptions to make. If from the very beginning in science we are going to make such gigantic assumptions, we should do everything we can to eliminate or minimize any further assumptions we make. My rules for making assumptions are that I only make assumptions compelled by the requirement of necessity to proceed. Assumptions that seem necessary to make if I am to go any further in my investigations. And to only make assumptions I have a realistic prosepct of testing. The former rule is difficult. The latter absolutely required.
I am not a Neo-Darwinist because I'm not as willing to assume so much as Neo-Darwinists seem comfortable with. So I really do have a fundamental difference with the Neo-Darwinsits in that respect–and I think its an irreconcilable difference.
So much for my "position." LOL
Comment by Rock — October 1, 2005 @ 4:15 pm
October 1st, 2005 at 6:17 pm
Joe G:
No, but there's definitely something in the premise of "common descent with modification" that more closely related organisms have more similar genotypes, morphologies, anatomical structures, than more distantly-related organisms. Which is why we see, in addition to all the obvious morphological similarities, that chimpanzees are more similar genetically to humans than, say, yeast. And what, again, is ID's explanation? The designer was lazy?
Why does NDE predict that pseudogenes will be removed from the population (BTW, they generally do get removed from bacterial DNA)? There's plenty of suboptimal crap lying around in the DNA of all eukaryotes. Are you saying it's more likely that a designer would leave pseudogenes in the DNA than undirected processes? Would you care to explain why that would be?
Nice try, Joe. It's pretty clear to any objective observer that ID follows its own determination to find design, regardless of where the evidence leads. I've told you a million times why science is skeptical of "design" theories: because a "designer" could have designed any particular structure, and assuming design doesn't explain anything.
Interesting that an ID supporter would start getting all serious about the peer-review process. Are you sure you want to go there, Joe? I don't think anyone's ever claimed that talk.origins is a peer-reviewed journal, but if you look at Theobald's references, I think you'll notice that the vast majority of his sources are, in fact, from peer-reviewed journals.
(Also, not that this proves anything, but I ran the Theobald article past a friend of mine who works for a biotech firm, and a friend of his who is a biologist at Stanford, and they seemed satisfied as to its credibility. Just my own little dude diligence, if you will.)
But since you brought it up, I'd be curious to hear what your interpretation of why Theobald's article is not peer-reviewed. Are you going to claim it's because it doesn't represent the consensus opinion of the scientific community?
Comment by ericmurphy — October 1, 2005 @ 6:17 pm
October 1st, 2005 at 7:17 pm
I'm curious – what is the "reproductive cost" of a pseudogene in a eukaryote? Is this a quantitative concept? If so, what is the range of estimates for this cost?
Comment by Art — October 1, 2005 @ 7:17 pm
October 1st, 2005 at 7:26 pm
Roger Rabbit:
I'm not trying to demonstrate it, but the evidence for it is so utterly overwhelming that I don't think it's necessary for me to do so. My question is, what is ID's hypothesis for the similarity between closely-related organisms.
I'm not asking why similar organisms are more similar than dissimilar ones. I've already stated that the best explanation for the consensus phylogenetic trees based on half a dozen or more lines evidence all converging on the same tree, out of ~10^38^ possbilities, and the even more compelling evidence for nested hierarchies (which phylogenetic trees share with genealogical tables, and for exactly the same reason) is common descent with modification. ID can, of course, accommodate common descent with modification. However, it can just as easily accommodate no relationships at all among taxa, and that's the problem with ID in a nutshell. It can accommodate any set of facts, and thus explains nothing.
Specifically with respect to cytochrome c, there's the same problem. Obviously ID can accommodate the fact that in general more closely related organisms have more similar genetic sequences coding for cytochrome c, but of course ID can also accommodate absolutely no resemblance in cytochrome c proteins from one species to another at all. Hence, the problem.
Comment by ericmurphy — October 1, 2005 @ 7:26 pm
October 1st, 2005 at 7:34 pm
Rock:
Thanks for the gracious reply. I think you make a lot of good points, at least from an epistemological point of view, and I think you made one comment (without, perhaps, meaning it in quite the way I'm going to take it) which goes right to the heart of the issue here:
By that standard, it's surely unnecessary to assume design. The biological sciences have made breathtaking strides, especially in the past few decades, without making any kinds of assumptions about design, one way or another. While it's true that in principle, most biologists probably do assume that life was not designed, it's not clear that that assumption has affected their ability to advance the field of inquiry at all.
Comment by ericmurphy — October 1, 2005 @ 7:34 pm
October 1st, 2005 at 8:09 pm
ericmurphy Says:
And my question, which I apparently was not explicit enough in articulating, is what do you mean by "closely-related organisms"(CRO)? Until that is clarified, one cannot address your question.
If by CRO, you mean to assume common descent, and that is how they are CR, then that assumption colors what explanation we are likely to choose under that assumption. If instead, we are gonna, for the sake of argument, set aside the assumption of CD, then we are back to needing a definition of CRO.
You claim that it isn't just an issue of similarity, so I'm confused about what CRO really means.
Comment by RogerRabbitt — October 1, 2005 @ 8:09 pm
October 1st, 2005 at 8:51 pm
Some people may assume design. I do not. It's not an assumption. It's an inference. And it's not an inference shared only by IDers or creationists. It is shared by biologists (and others). Evolutionary biologists. I think I said that didn't I? (See above.) I said that the object of evolutionary biologists is to explain their shared inference of design. That is to explain what they do not assume. (Since people don't feel it necessary to explain, at least to each other, the assumptions they share.)
Not an assumption… Inference… Good or bad inference… One that requires some 'splainin'.
Comment by Rock — October 1, 2005 @ 8:51 pm
October 1st, 2005 at 9:25 pm
My quote for the day.
Comment by onething — October 1, 2005 @ 9:25 pm
October 1st, 2005 at 10:06 pm
RogerRabbitt:
Here's what I mean by closely-related: all life on earth is organized into "nested hierarchies." In other words, there is no ape that is more closely related to fish than it is to other primates. There is no dog that is more closely related to birds than it is to other mammals. There is no tree that is more closely related to starfish than it is to other plants. But closely related in what sense, you ask? In multiple senses: related by physical structure, related by similar proteins, related by similar chromosomal structure, related by similar pseudogenes, related by similar mutations to functional genes. And the fascinating thing is that no matter which particular criterion you use for establishing relatedness, you get the same nested hierarchies.
This differs from designed objects, like e.g. cars. You can group cars by make, by number of cylinders, by type of fuel used, by color, by presence or absence of power windows/doors/locks, by country of origin, etc. Depending on the criterion, you will get a different hierarchy.
This is not true of life on earth. No matter whether you look at anatomical similarity, genotypical similarity, protein similarity, you always get the same phylogenetic tree. In fact, there is only one true tree. This particular page of the link I sent you earlier will explain in further detail what I mean.
Now, it's not true that biological science has in fact determined the "one true tree." There are many organisms for which where they fit into the phylogenetic tree is controversial. But that doesn't change the fact that, somewhere out there, there really is one true tree. Think of it this way: trace all your ancestors back a thousand generations, in a genealogical tree. There is only "one true tree" of such genealogical relationships. I.e., someone cannot simultaneously be a great grandfather and a third cousin thrice removed to you.
As I said, there is no consensus phylogenetic tree for all the tens of millions of organisms on the planet. For one thing, because the number of possible trees goes up exponentially for the number of organisms, it would be computationally impossible to construct such a tree. But for the 30 major taxa for which there is a consensus phylogenetic tree, the number of possible trees is on the order of 10^38^. Even if science could only get the number down to, say, one of several million trees, that would still have reduced the number of likely trees by, well, 10^38^ trees.
What's important for this debate is that, over the past 145 years, no one has been able to come up with any explanation for the nested hierarchy of life on earth other than common descent with modification. Which brings up another interesting point. In the context of arguing that common descent with modification is "only a conjecture," Defendant's attorney in the Dover trial inadvertently demonstrated that ID is, in fact, unfalsifiable.
Comment by ericmurphy — October 1, 2005 @ 10:06 pm
October 2nd, 2005 at 8:33 am
ericmurphy:
I've told you a million times why science is skeptical of "design" theories
Science isn't. Some or even many scientists are, but that is another story. THose scientists still don't have any evidence that what we observe can come about via unintelligent, blind/ undirected processes. IOW their position seems to be that they will not allow ID because they just can't allow a designer- regardless of the data.
ericmurphy:
because a "designer" could have designed any particular structure, and assuming design doesn't explain anything.
Again reality demonstrates that "assuming" a designer shifts the investigation process. Also if assuming design didn't offer anything then we should be able to rid ourselves of archaeology, SETI and all forensic sciences that detect design.
eric murphy:
It's pretty clear to any objective observer that ID follows its own determination to find design, regardless of where the evidence leads.
Actually the evidence is pretty obvious. That is why most great scientists throughout history were either design theorists or Creationists.
As for Dr. Theobald's article- the original was torn apart by a Creatioist lawyer such that it was re-written.
Comment by Joe G — October 2, 2005 @ 8:33 am
October 2nd, 2005 at 8:39 am
IF the NDE were indicative of reality we should see all the alleged "pseudo-genes" get removed from a population as they provide no function and come at a reproductive cost.
Art:
I'm curious "“ what is the "reproductive cost" of a pseudogene in a eukaryote? Is this a quantitative concept? If so, what is the range of estimates for this cost?
Manufacturing DNA (by the cell) requires energy. The more DNA to be manufactured the more energy required. Therefore it would stand to reason that NS would rid the organism of energy draining waste.
Or perhaps NS is the issue as it only exists when evolutionists want it to- or even does not do what evolutionists want us to believe it does.
We also know of a mechanism that removes "neutral" DNA.
The bottom line here is that "pseudogenes" really aren't and junk DNA really isn't.
Comment by Joe G — October 2, 2005 @ 8:39 am
October 2nd, 2005 at 10:05 am
I asked about the cost of maintaining pseudogenes (or something to that effect – I'm clumsy at the xhtml mark-up and am using a machine that won't preview, so I am not going to try nesting quotes, etc.). JoeG replied:
This is a common misperception – I see if in the students (undergrad and grad) all the time. The fact is that the energy that a eukaryotic cell devotes to DNA replication is a tiny fraction of the overall energy budget of a cell. This means that it is not correct to assume that there is an energetic "selection" to pare unnecessary DNA from a genome.
There is another underlying assumption here that needs to be dispelled – namely, that eukaryotic cells are operating at or near some sort of energetic balance. The truth is that eukaryotic cells are rather energy-rich. This is another reason why genome sizes to not impact the overall energy budget of a cell, at least from a selective standpoint.
Pesudogenes exist – there is no question about that. And "junk DNA" also does. Why do you think the cell devotes so many resources to garbage disposals, JoeG?
Comment by Art — October 2, 2005 @ 10:05 am
October 2nd, 2005 at 10:56 am
Pseudogenes- How do we know they are pseudogenes? Because they look like non-coding representations of genes? Isn't that the same as saying something is designed because it looks designed?
Everyday science is finding that junk DNA really isn't junk. ie it does something (that goes for any alleged 'pseudo' genes). IOW the junk isn't junk and there isn't anything 'pseudo' about the alleged 'pseudo' genes.
It looks like the argument for both is based on ignorance.
Pierre Jerlström, molecular biologist.
Comment by Joe G — October 2, 2005 @ 10:56 am
October 2nd, 2005 at 11:11 am
RUSHING TO JUDGMENT: FUNCTIONALITY IN NONCODING OR "JUNK" DNA
The above article also refutes Art's comment that the energy cost is low.
Comment by Joe G — October 2, 2005 @ 11:11 am
October 2nd, 2005 at 11:44 am
JoeG, an article that is supposed to address the energy costs of "junk DNA" but completely neglects the research in the field of energy cost (such as the 2001 paper by Wieser and Krumschnable in Biochemical Journal – v. 355, pp389-395) isn't of much use to this discussion, I'm afraid.
Again, it's revealing that so many of the resources of the cell are devoted to the "garbage disposal" (something that, collectively, uses a pretty hefty amount of energy). The cell wouldn't need the proteasome and exosome if there wasn't any junk present.
Comment by Art — October 2, 2005 @ 11:44 am
October 2nd, 2005 at 12:06 pm
Joe G:
You've got an entirely wrong idea about how many scientists are enamored of ID. "Some or many" are skeptical of "design" theories? Try something like 99%. The number of actual life scientists who think there's anything to ID probably number in the mid-double digits — and the number isn't going up. I don't see how you can make a distinction between "science" and "scientists" when virtually all scientists dismiss ID.
I've already shown you why this isn't the case. You can't analogyize archaeology, forensics, or even SETI to an inference of an intelligent designer of life. Furthermore, you have yet to present a single example of how the investigation process into the mechanisms for evolution would shift one iota if one infers a designer.
It's also true that most astronomers throughout history, going back thousands of years, thought that the sun revolved around the earth.
God, Joe, have you actually read Ashby Camp's "critique" of Theobald? And Theobald's response? If you seriously think of Camp's criticism as having "torn apart" Theobald, you're delusional.
As for pseudogenes: your claim that they don't exist is wrong. Pseudogenes by definition exist. Pseudogenes are former genes (often it takes a single mutation of a formerly working gene) that no longer code for proteins. If you're going to argue that there are no strands of DNA that don't code for proteins, you're going to be in trouble in no time.
Comment by ericmurphy — October 2, 2005 @ 12:06 pm
October 2nd, 2005 at 12:11 pm
Petrov DA, Hartl DL. 1998. High rate of DNA loss in the Drosophila melanogaster and Drosophila virilis species groups. Molecular Biology and Evolution 15:293-302.
Also bacteria seem to lack junk DNA/ pseudogenes. What happened? Did bacteria retain the mechanism for removing that "junk" (euks lost it) or did bacteria acquire it after the alleged divergence?
Comment by Joe G — October 2, 2005 @ 12:11 pm
October 2nd, 2005 at 12:24 pm
ericmurphy:
You've got an entirely wrong idea about how many scientists are enamored of ID. "Some or many" are skeptical of "design" theories? Try something like 99%. The number of actual life scientists who think there's anything to ID probably number in the mid-double digits"”and the number isn't going up. I don't see how you can make a distinction between "science" and "scientists" when virtually all scientists dismiss ID.
IF what you say is true (I doubt it) I would love to see their reasoning for dismissing ID and also for accepting the anti-ID position. According to one resource there are thousands of scientists who are Creationists in the US alone.
Again reality demonstrates that "assuming" a designer shifts the investigation process. Also if assuming design didn't offer anything then we should be able to rid ourselves of archaeology, SETI and all forensic sciences that detect design.
ericmurphy:
I've already shown you why this isn't the case.
And I have shown you that it is the case.
ericmurphy:
You can't analogyize archaeology, forensics, or even SETI to an inference of an intelligent designer of life.
Perhaps you cannot but don't force your limitations onto others. Either we can or can't make a determination of design. And if biology has some kind of "design wall" I would love to see or read about it.
ericmurphy:
Furthermore, you have yet to present a single example of how the investigation process into the mechanisms for evolution would shift one iota if one infers a designer.
It would shift the same way any other design inference shifts any investigation. For one we would infer that genomes are intelligentlly designed and we should therefore be able to decode them as we would a computer language. Something cobbled togather via random events culled by any selection process wouldn't allow for that.
ericmurphy:
It's also true that most astronomers throughout history, going back thousands of years, thought that the sun revolved around the earth.
Name some of these alleged "most".
As I said with "pseudo" genes- they look like non-coding remnants of coding sequences- which is very similar to saying it looks designed so it must be designed.
Why is it that science is finding that junk DNA and pseudo genes actually do something? IOW the monikers are not warranted.
As for Dr. Theobald's article- why doesn't he submit it for peer-review? Because someone other than a lawyer would get a crack at it…
Comment by Joe G — October 2, 2005 @ 12:24 pm
October 2nd, 2005 at 12:31 pm
JoeG, do you know what the link is between:
1. The fact that, in spite of decades of truly exhaustive mutagenesis work (every base has probably been changed thousands of times) in E. coli, we still have no clue as to the functioning of somewhere between 10-30% of its genome.
2. For every new bacterial genome that is sequenced, as much as 30% the putative genes cannot be assigned a function.
3. This report?
That's right, junk.
And, oh yes, bacteria also have garbage disposals.
A useful concept to help make sense of much of this: the total DNA content of a genome will reflect the rates of "synthesis" (mainly duplications, but HGT may factor in as well in prokaryotes) as well as "loss".
Comment by Art — October 2, 2005 @ 12:31 pm
October 2nd, 2005 at 2:44 pm
Art sez:
JoeG, do you know what the link is between:
1. The fact that, in spite of decades of truly exhaustive mutagenesis work (every base has probably been changed thousands of times) in E. coli, we still have no clue as to the functioning of somewhere between 10-30% of its genome.
2. For every new bacterial genome that is sequenced, as much as 30% the putative genes cannot be assigned a function.
So now ignorance is a reason enough for you?
Function includes much more than just coding for proteins or enzymes. And we are still ignorant as to why a fly is a fly and a horse is a horse. This ignorance is despite many decades of trying to figure that out.
We finally figured out that one gene, one protein is NOT correct. That after how many years of research?
Comment by Joe G — October 2, 2005 @ 2:44 pm
October 2nd, 2005 at 3:30 pm
JoeG, you keep avoiding the issue of the garbage disposals.
Also, in bacteria, for the most part, one gene does equal one protein.
Also, we have a very good idea why a fly is a fly and a horse is a horse. And it boils down to genes and their expression.
One more thing – except for catalytic and small RNAs (which feed things into, um, that's right, the garbage disposal), function in DNA is all about proteins. Directly or indirectly, you cannot escape this.
Now, how about those garbage disposals? Why are they there, if not to dispose of the junk?
Comment by Art — October 2, 2005 @ 3:30 pm
October 2nd, 2005 at 5:09 pm
Art:
Also, in bacteria, for the most part, one gene does equal one protein.
And your point is what? Did today's bacteria "evolve" into this state or was that the way things started out? Because alternative gene splicing sure does look, feel and mimic intelligently designed programs.
Art:
Also, we have a very good idea why a fly is a fly and a horse is a horse. And it boils down to genes and their expression.
I understand the concept. I have heard it many times. I have also heard those arguments refuted. We know what controls embryonic development, however if we substitute a PAX6 gene from a mouse into a fly, the fly doesn't get mouse eyes. IOW the information for "mouse" eyes or "fly" eyes does not reside in the HOX gene(s) cluster(s) that control development. So to say a species is the "sum of its genes" is disingenius at best.
Art:
One more thing "“ except for catalytic and small RNAs (which feed things into, um, that's right, the garbage disposal), function in DNA is all about proteins. Directly or indirectly, you cannot escape this.
Science has already esacped that. Why are you still stuck in the 19th century as far as genetics goes?
Art:
JoeG, you keep avoiding the issue of the garbage disposals.
There is a difference between avoidance and indifference.
Art:
Now, how about those garbage disposals? Why are they there, if not to dispose of the junk?
I am pretty sure I posted that we know of mechanisms that remove 'junk'. So what's your point?
I get it- you are going to be like my wife and take what I post to some absolute extreme, even though my posts contain language that should avoid that. IOW can 'junk' DNA and 'pseudo' genes? I would never catagorically deny the possibility. But to use that as some kind of genetic marker after millions of generations is absolutely absurd given what we do know.
Comment by Joe G — October 2, 2005 @ 5:09 pm
October 2nd, 2005 at 7:49 pm
Joe G:
Is this cite supposed to explain something to me? If so, it would be nice if you could provide a link to it. Or is it an example of a peer-reviewed article by an IDist? (If so, you might want to alert the Discovery Institute; they could use all the help they can get in this department). And if it's the latter, I hope you're not going to try to compete vis a vis the number of peer-reveiwed articles out there. Theobald's article, all by itself, references in excess of 300 peer-reviewed papers.
In any event, I can't make much of the article you cite, unless I can actually read it (or at least a synopsis of it). I've been gracious enough to give you cites for most of the evidence I've referred to; it shouldn't be asking too much for the same in return.
It's true that bacteria don't appear to have junk DNA or pseudogenes. (On the other hand, if chloroplasts really are descended from free-living cyanobacteria, that's another trick bacteria developed that eukaryotes never did.) Your question — did eukaryotes lose the mechanisms for removal, or did bacteria develop them after they diverged from eukaryotes — is certainly a good question, but I don't see how it advances an ID interpretation of evolution no matter what the answer is.
Comment by ericmurphy — October 2, 2005 @ 7:49 pm
October 2nd, 2005 at 8:17 pm
Joe G:
If you think I'm wrong about the relative numbers of biological scientists who believe NDE is a better explanation for biodiversity than ID is, then you're going to have to explain to me why the DI's list of supporters is about 300 (and it's been the same number for years), many of whom are not even scientists, let along biologists, whereas the "Steves Project" has over six hundred names on it, all scientists, all named "Steve" (or some derivative thereof). If you think more than a tiny, tiny fraction of life scientists believe in ID, all I can say is, you're sadly mistaken.
If you think assuming a designer shifts the investigation process, I'd like you to provide an example of a paper of original research, by someone, somewhere, who actually went out discover some new fact about biology, using the assumption that life was designed, which research could not have occurred without such an assumption. If you're right that assuming a designer actually adds something to the body of knowledge about life, this shouldn't be a difficult task.
Joe, you haven't even begun to demonstrate how techniques applicable to archaeology, forensic investigation, or even SETI are in any way applicable to biology. ID has stated again and again that it makes no claims to any kind of knowledge about a "designer," and without that knowledge, it will never make any headway. How far would archaeological research get if we couldn't make any assumptions about the identity of the designers of the artifacts?
There's no "design wall" in biology. But without the slightest hint about the nature of the putative designer, you can't draw any inferences about the design, either.
What do you mean it "would" shift? We've got at least a small number (okay, a tiny number) of scientists, don't we, who already assume design? And it's gotten them exactly nowhere. So if a design assumption does shift the investigation, it seems to shift it in useless directions.
And I'm not sure what you mean when you say an assumption of design would let us "decode genomes." Are you saying we can't already do it? It seems like we're doing a pretty good job of that without any such assumption. We certainly know how the genome works, if we don't always know why it works in a particular way, and in any event, the way genes are either transcribed into proteins or regulate the way other genes are expressed is purely a matter of chemistry, and doesn't require any special knowledge from design.
God, Joe, are you really going to make me come up with a list of pre-copernican astronomers who believed the sun went around the earth? Are we really to the point in this discussion where I have to give exhaustive references for every single assertion I make? Are you really going to take the contrary position, i.e., that before the 15th century, most astronomers believed the earth went around the sun?
No, they look like coding sequences that have suffered mutations that make them non-functional. That has nothing to do with whether pseudogenes were designed or not. Even if pseudogenes resembled something that was designed, that wouldn't be evidence that they themselves were designed. If I see a cloud that looks like a '56 De Soto, does that mean the cloud was designed?
Even if it turns out that "junk DNA" and pseudogenes actually do have a function, that wouldn't in any way falsify NDE. It might be taken as evidence for design, but as I've said before, anything can be taken as evidence for design!
Oh for — Joe, Theobald didn't submit his article for peer review because it's not original research! It's just a synthesis of other peoples' work! You don't submit articles like that for peer review! Are you sure you understand what the peer review process is all about? Articles in Scientific American aren't submitted for peer review, but that doesn't mean the information in Scientific American isn't credible, or is "junk science," or anything. You'll notice, if you read SA, that the authors often cite papers in peer-reviewed journals, but they're just articles. Give me a break.
Comment by ericmurphy — October 2, 2005 @ 8:17 pm
October 3rd, 2005 at 8:44 am
Petrov DA, Hartl DL. 1998. High rate of DNA loss in the Drosophila melanogaster and Drosophila virilis species groups. Molecular Biology and Evolution 15:293-302.
ericmurphy:
Is this cite supposed to explain something to me?
Nope. I posted it for Art's enjoyment.
Comment by Joe G — October 3, 2005 @ 8:44 am
October 3rd, 2005 at 9:06 am
ericmurphy:
If you think more than a tiny, tiny fraction of life scientists believe in ID, all I can say is, you're sadly mistaken.
By now you should realize I don't care what anyone sez. I do care what they can demonstrate.
ericmurphy:
Joe, you haven't even begun to demonstrate how techniques applicable to archaeology, forensic investigation, or even SETI are in any way applicable to biology.
Any endeavor which seeks to determine design from non-design is applicable. One it shows we can do it and two it shows that it does make a difference.
ericmurphy:
ID has stated again and again that it makes no claims to any kind of knowledge about a "designer," and without that knowledge, it will never make any headway.
That is flat-out wrong. First the ONLY way to make any determination about a designer without direct observational evidence or designer input is by studying the design. Second it is obvious that the identity of the designer is not required to do so.
ericmurphy:
How far would archaeological research get if we couldn't make any assumptions about the identity of the designers of the artifacts?
Making assumptions about the designer is not the same as having knowledge about said designer. Do archaeologists know exactly who designed and built Stonehenge? No. Do we know who designed and built the figures on the Nasca plains? No. But in both cases we are getting closer to figuring that out because we are researching the issue by studying the design and the local.
ericmurphy:
But without the slightest hint about the nature of the putative designer, you can't draw any inferences about the design, either.
Perhaps YOU can't but I don't have the same limitations that you do.
ericmurphy:
What do you mean it "would" shift? We've got at least a small number (okay, a tiny number) of scientists, don't we, who already assume design? And it's gotten them exactly nowhere. So if a design assumption does shift the investigation, it seems to shift it in useless directions.
Perhaps they would if they didn't have to first deal with people like you. And as for useless, that explains the NDE in a nutshell- and you have the bulk of the scientists!
And if you want to make assertions about astronomers you had better be able to back them up.
Telescopes didn't become popular until the 17th century.
As I said with "pseudo" genes- they look like non-coding remnants of coding sequences- which is very similar to saying it looks designed so it must be designed.
ericmurphy:
No, they look like coding sequences that have suffered mutations that make them non-functional.
That is what I said. They look like… So if something "looks" designed we can assume it was. Thanks.
ericmurphy:
Even if it turns out that "junk DNA" and pseudogenes actually do have a function, that wouldn't in any way falsify NDE.
It falsifies the scientists who said it was junk- btw the same scientists who belive in the NDE.
ericmurphy:
It might be taken as evidence for design, but as I've said before, anything can be taken as evidence for design!
Not anything can be taken as evidence for design. Not by IDists anyway. More unsubstantiated assertions.
I understand how the peer-review process works. Many articles cite other scientists' work. BTW I am not taking YOUR word for anything. I have yet to get the feeling that you undert=stand the debate or science.
Comment by Joe G — October 3, 2005 @ 9:06 am
October 3rd, 2005 at 11:58 am
The design inference adds "who" and "why" to the scenrario. Both are driving questions to us humans.
Q. "Who designed it?"
A. "We don't know but if we study/ examine/ research it we may be able to come to a reasonable inference."
Q. "Why was it designed?"
A. "We don't know but if we study/ examine/ research it we may be able to come to a reasonable inference."
However it is obvious that those questions will not be answered unless the entire world resources are allowed to ask them without repute.
Right now anyone associated with ID is ostracized by mob mentality…
Comment by Joe G — October 3, 2005 @ 11:58 am
October 3rd, 2005 at 12:18 pm
Joe G:
By now I realize that you won't accept any evidence of evolution short of watching a demonstration of a bacterium evolving into a starfish in front of your eyes. And you'll probably still say, "well, that's all well and good, but where's the evidence that a starfish can evolve into a mammal?"
In other words, your standard for evidence of evolution is impossibly high — "well-nigh irrefragable proof," as they say in government contracts law. On the other hand, you don't seem to need any evidence at all for a design inference.
Joe, we know the people who designed Stonehenge were humans. We know the people who designed the Nazca plains were humans. What can you tell me about the nature of your designer? Is it constrained to follow natural law? You're not even sure about that. So your argument that because archaeologists can detect design, so can biologists, is vacuous.
So I'm the reason IDist can't come up with any original research? I guess I should thank you for the compliment, but it's kind of a comical statement nonetheless. Come on, Joe — who's stopping the forty fellows at the Discovery Institute from making any progress with their researches? I know you've got this image that they're a repressed minority, but that's patently ridiculous. The ID movement has vastly more political power (and money) than the NDE community. The reasons they're not making any progress is because their assumptions are leading them right down a blind alley. If they could come up with some testable predictions of their theory, they might be able to get somewhere. But don't blame me for their hapless flailing about.
Okay, Joe, if you think it's my limitations that are preventing me from drawing inferences about the design of living organisms because of a lack of knowledge about the designer, perhaps you'd like to demonstrate that your lack of such limitations allows you some insight into the nature of evolution denied to us blind men. Got any?
So I guess you don't believe that Galiieo's view that the earth revolved around the sun was a minority opinion at the time? Sorry, Joe, I'm not going to come up with a list of mistaken astronomers from the 15th century and earlier for you. If you want to find out if I'm right, I guess you're just going to have to look. Life's too short for that kind of argument.
No, we don't just "assume" that pseudogenes are busted copies of working genes. When you've got a strand of DNA 2,500 BP long that's identical to another strand of DNA 2,500 BP long except for one altered codon, which makes it non-functional, that's a bit more than just "guessing" what it is. It's lightyears away from saying because something looks designed it must be designed. Remember that face on Mars from a few years back?
So is your point that if scientists draw erroneous conclusions (and later revise their thinking in the light of contrary evidence) we should ignore their work entirely? God, Joe, if there's anyone here who doesn't understand how science works, it's you. "Falsifying scientists"; that's a new one on me.
Oh, really? Show me some biological structure that cannot have been designed. Can you do it? Didn't think so. Therefore, every biological structure can be used as evidence for design.
Joe, you clearly don't understand how the peer review process works, nor what it's used for. No one with such an understanding would be wondering why a purely synthetic synopsis of other researchers' work would be seeking peer review. To even ask the question of Theobald's article reveals your ignorance of the process.
Comment by ericmurphy — October 3, 2005 @ 12:18 pm
October 3rd, 2005 at 1:54 pm
ericmurphy:
By now I realize that you won't accept any evidence of evolution short of watching a demonstration of a bacterium evolving into a starfish in front of your eyes.
All I can say to that is that your inference is incorrect. A bacterium or population of bacteria evolving into something other than a bacterium or population of bacterium would be a start.
Right now we don't even know what makes a species what it is. Evolutionists hope that it is as easy as a species is a sum of its genes and their interactions. However that is not what we finding out.
ericmurphy:
In other words, your standard for evidence of evolution is impossibly high"”"well-nigh irrefragable proof," as they say in government contracts law.
My standards are no higher than yours are for ID.
ericmurphy:
On the other hand, you don't seem to need any evidence at all for a design inference.
Close your eyes, tap your heels together and repeat that over & over. However even that won't make it come true.
Ya see I was a blkindwatchmaker type guy for a long time. Now I am an IDist because of the evidence.
ericmurphy:
Joe, we know the people who designed Stonehenge were humans. We know the people who designed the Nazca plains were humans.
Right because we have studied them. However as I have always said that hasn't helped us to understand the design. IOW seeing that ID is about the detection and understanding of design it is NOT relevant to first identify the designer in order to do so. Both these cases confirm that as "knowing" the designer was human was determined after we first detected and then came to an understanding about each. Also if it turns out that each were actually designed by ET, it would not falsify the design inference.
ericmurphy:
Show me some biological structure that cannot have been designed. Can you do it?
This exposes your utter lack of understanding about science. Which basically means your closing paragraph is meaningless.
However if there wasn't one biological structure, or biological organsim, that didn't fit the criteria laid down by IDists (see Behe, Dembski et al.) we would NOT infer design. IOW we wouldn't have a design inference and there wouldn't be any IDT. However if IDists are right there wouldn't be anyone around to discuss it.
And BTW I don't want to "find out if you are right" I want you to support your assertions or please stop making them. At best anyone from the 15th century and before were stargazers with the only instruments being their eyes. That would make them light years from astronomers.
My point about 'pseudo'genes, if you had bothered to follow along, is that there is a known mechanism for removing junk DNA and therefore to even suggest they can lay around for millions of generations such that they can be used as a genetic marker (what you are doing) is absurd- light years into absurdity. At best the alleged "shared 'pseudo'genes" should be scrambled beyond recognition. That is what real science tells us anyway.
Comment by Joe G — October 3, 2005 @ 1:54 pm
October 3rd, 2005 at 2:18 pm
I'm surprised that the IDers aren't more critical of Joe G's "paradoxical defense." (That's a favorite theme of Mike Gene.)
Let's say I'm a designer (LOL) and I realize that duplicating and then modifying genes is a means-ends strategy that practically recommends itself. Why would I choose not to use this strategy? (What if I think that these arguments against duplication and modification are full of soup?)
What might not recommend this strategy? I might purposefully commit Art's students' error ("I'm curious "“ what is the "reproductive cost" of a pseudogene in a eukaryote? Is this a quantitative concept? If so, what is the range of estimates for this cost?" And, "This is a common misperception "“ I see if in the students (undergrad and grad) all the time. The fact is that the energy that a eukaryotic cell devotes to DNA replication is a tiny fraction of the overall energy budget of a cell. This means that it is not correct to assume that there is an energetic "selection" to pare unnecessary DNA from a genome.") and consider that duplicating a gene does not have any immediate cost/benefit and is, therefore to be rejected as a design strategy because it violates my overarching selection principle; that any changes I make be of immediate benefit, and (erroneously assume) that duplication entails a cost, which I could avoid by not duplicating.
The first thing I might do is modify my selection principle, and accept that some changes I make are not obviously immediately beneficial"”but may prove to be so at some future point in time. (Whoa! Major reconceptualization of my selection principle!"”And my variation principle!) I'm an "intelligent designer." (For the sake of argument.) I'm perfectly capable of anticipating and predicting. That doesn't always work"”but it does seem to work just often enough that I'm not willing to abandon my propensity to anticipate and predict.
If I could assure myself that the immediate cost/benefit ratio is at most marginally different (i.e., makes no immediately selectable difference) compared with the potential advantages, advantages that may not be realized immediately, then I may proceed.
For one immediate cost/benefit analysis see Wagner, A., "Energy Constraints on the Evolution of Gene Expression," Molecular Biology and Evolution 22 (6): 1365-1374 (2005).
http://samba.unm.edu/~wagnera/MBE05_exprcost.pdf
Since I know there are any number of costs associated, both with duplicating and modifying, I might first do the obvious and reduce some of these associated costs, by, e.g., immediately rendering ("mutating") the gene inoperative. (This eliminates one problem Wagner considers.) But I also may consider if maintaining it in operational condition may have some (potential, always looking to the future) advantages, over and above the cost of duplication, such as increasing a dose which may have an advantage. I may opt for maintaining its operational status while modifying it to perform a different operation"”if that is at all possible. Even if in the process of modification the operations are increasingly marginalized until some threshold is reached in which a wholly new function is actualized.
And that, after all, was my original design objective.
I hope (with no real illusions, LOL) that illustrates the problem of confusing the "design argument" with the "anti-evolution argument." A common error in these discussions. Likewise, I hope it illustrates the fallacy of the "evolution argument" being the "anti-design argument."
Not freakin' bloody likely, Rock!
Comment by Rock — October 3, 2005 @ 2:18 pm
October 3rd, 2005 at 7:05 pm
It would be more likely if you communicated more clearly.
Comment by onething — October 3, 2005 @ 7:05 pm
October 3rd, 2005 at 10:28 pm
Joe G:
Dude, you really need to work on your sense of humor.
Anyway, my inference (once you strip out the exaggeration for effect) is that you will not accept any evidence that bacteria can evolve into eukaryotes short of an experiment that actually does evolve bacteria into eukaryotes. Given that it probably took between one and two billion years for this occur naturally, even if you could speed the process up a millionfold, you'd still be waiting around for a thousand years for results. I'm pretty sure I've explained this to you before.
Yes they are. All I need is some reasonably persuasive evidence that ID explains the evolution of life on earth in a way that NDE does not. So far, you haven't given me any evidence, persuasive or not, that ID can do so. Not only can you not give me an example of how ID can explain the evolution of life in a way that NDE cannot, you claim (against all evidence) that life cannot evolve (other than variations within a species), and ID itself states that it makes no attempt to explain how evolution happens at all. I believe I've explained this to you before as well.
On the other hand, as I've pointed out three times in a row, you will accept no evidence for evolution other than actually observing it happen. And you're not even satisfied with evidence of speciation (which is abundant). You want to see evidence of evolution from one taxonomic group to another, a process that takes hundreds of millions to billions of years to happen naturally.
I don't need to do that. All I need to do is scroll back through your messages for a link to an article that gives persuasive evidence for the design inference. You keep saying you follow the evidence wherever it leads, but you've yet to cite any evidence that life is designed at all. A link to your own essay, I'm sorry to say, isn't sufficient.
Are you saying that knowing humans designed Stonehenge hasn't helped us understand the design? Knowing what technologies were available to humans at the time it was built hasn't helped us understand how it was built? Joe, that's just plain silly. if we assumed stonehenge was built by extraterrestrials, we couldn't have excluded any possible building techniques. You're well into the realm of fantasy now.
(I assume you mean my question renders my second-to-last paragraph meaningless, since my final paragraph is about the peer review process, which is another subject entirely) No, actually this exposes the utter unfalsifiability of ID. If it's impossible to falsify the premise that life was "designed" (and it is), then ID is completely lacking in explanatory power. Especially since, as I've said time and again, ID is emphatically not a theory of how a designer intervenes in living organisms in order to drive evolution.
Joe, I hate to be the one to tell you, but in fact there is no known biological structure that cannot, in principle, have evolved through undirected processes. Behe, Dembski, et. al. claim otherwise, but every single one of their examples has been disproved. And since their claim is purely eliminative, this defect is fatal to the ID premise. Again, this doesn't prove that life definitely was not designed, but that's not the sort of thing that can be proven anyway.
I'm not sure what you mean when you say "However if IDists are right there wouldn't be anyone around to discuss it," so I'm not sure how to respond. If you meant to say, "However if anti-IDists are right there wouldn't be anyone around to discuss it," that sounds like you're assuming what you're attempting to prove.
(cont. next msg.)
Comment by ericmurphy — October 3, 2005 @ 10:28 pm
October 3rd, 2005 at 11:07 pm
(cont. prev. msg.)
I've forgotten why the beliefs of 15th-century astronomers are relevant to this debate, but I guess I'll give this one more whirl: I didn't attempt to support my contention that the majority of pre-15th century astronomers believed the sun went around the earth because it's common knowledge, for crying out loud. Are you completely unfamiliar with the ptolemaic heliocentric model that held sway in western cosmology for almost a thousand years? If you claim that all astronomers before the invention of the telescope were "at best…stargazers," I guess that means you think Brahe, Kepler, and Copernicus, three of the most influential astronomers of all time, were mere "stargazers."
And my point about pseudogenes, if you'd bothered to follow along, was that bacteria have a mechanism for removing non-coding DNA from the genotype, eukaryotes don't, and this presents no problem for NDE at all. For one thing, bacteria know plenty of tricks that eukaryotes don't, like photosynthesis (assuming, as the majority of biologists do, that chloroplasts are descended from symbiotic bacteria which have taken up permanent residence in eukaryotic cells), or aerobic metabolism (assuming, as the majority of biologists do, that mitochondria are descended from symbiotic bacteria which have taken up permanent residence in eukaryotic cells). There is absolutely no problem with the idea that bacteria developed the techniques of cleaning up "junk DNA" subsequent to the split between bacteria and eukaryotes. Birds have feathers, no mammals do. Why? Because birds and mammals diverged before ancestral proto-avians developed feathers.
Again, if you want me to believe that all pseudogenes (even the ones that date back a few million years, like the defective gene humans and chimps share for ascorbic acid) should be "scrambled beyond recognition," I'm afraid you're going to have to give me a cite to some article that gives such evidence. And you say this like I'm the only one using pseudogenes as genetic markers. What, you think I made up the idea myself? Try looking here.
Which, I guess, brings me to the final chapter. I think I'm going to have to bail on this conversation, Joe. Looking over our conversation for the last month, I can see that I've started to repeat myself. (Actually, I've been repeating myself for quite a while here). We're going around and around over the same old ground. You state quite flatly that there is no evidence that life can evolve from bacteria to any more complex form of life. You also imply that higher-order taxa (above the species level) cannot have evolved from other taxa (e.g., whales from land mammals). I provide you tens of thousands of words of evidence to support just such a contention, but you continue to deny than any such evidence exists. You don't attempt to refute the evidence I provide; you don't provide contrary evidence; you just deny the existence of the evidence I've given you entirely. This makes for a very frustrating exercise in futility. You remind me of a quote from Nilsson and Pelger regarding David Berlinski's attempted rebuttal of their paper: "It would be much simpler for Berlinski if he went just a tiny step further and denied the existence of our paper altogether."
In the meantime, you have failed to provide evidence that ID can explain anything about the evolution of life. In fact, despite your protestations to the contrary, you effectively deny that evolution can even happen, with your statements that bacteria never have been observed to evolve to anything other than bacteria, that flies never have been observed to evolve into anything other than flies, and that whales cannot have evolved from land mammals. Since bacteria, flies, land mammals, and whales obviously exist, you need to provide some sort of mechanism that explains their existence. You've never come out and said it, but since you effectively deny evolution is possible, you're implying that you believe in special creation.
You've staked out a personal position that is even more extreme than most IDists. Neither Behe nor Dembski deny that evolution happens. "What separates intelligent design from naturalistic evolution is not whether organisms evolved or the extent to which they evolved but what was responsible for their evolution." — Wm. Dembski, The Design Revolution.
Evolution is a fact, Joe. The evidence for macroevolution is staggering, overwhelming. So what remains is an explanation for the mechanisms of evolution, which is where the neodarwinian theory of evolution comes in. I quoted William Dembski weeks ago, stating that ID is not an interventionist theory at all. I.e., it has nothing to say about the mechanisms for evolution.
In any event, this has sort of degenerated into a "yes it is, no it isn't" kind of argument, which gets pretty tiresome after a while. If you think you've presented a compelling argument in favor of ID (and not just a few snipes at the incomplete nature of NDE), I guess all I can say is that I disagree. I'm sure you feel the same way about my arguments, but you can't say I didn't try.
Comment by ericmurphy — October 3, 2005 @ 11:07 pm
October 4th, 2005 at 12:07 am
Why did it take so long for that one step, compared to so many subsequent revolutionary changes?
We do not know who made Stonehenge, Nazca lines or the pyramids. It is false to say we do.
What sort of principles? the ones which sound airy-fairy?
Oh, please. Not even close. If it had been disproved, we would have heard of it.
No logic here. Suppose there was a big theory that the moon was made of cheese, and someone pointed out several good reasons why that could not be so. does that make for a grand theory? No. But does it help the progress of truth if you point out a blind alley? Of course.
Comment by onething — October 4, 2005 @ 12:07 am
October 4th, 2005 at 12:16 am
What I really fantasize about is how amazing it would be to go way back in time and watch a world of living things quite different from the ones we have now. Now, things are pretty well evolved into their niches, and the animals are just so good at being whatever they are and doing what they do. But imagine the hilarity of of the world of many millions of years ago. You could watch a protolion trying to catch a protogazelle. The lion doesn't run very well, but he lives anyway and gets his gazelle, because the gazelle's ears were only at 25% anyway, and he didn't hear the other gazelles start to run. Protobirds get eaten by protofoxes because the protobirds wings are at a clumsy half-stage, but the fox doesn't get all of them because it is about the size of a house cat. Fish have 34% of an eye but their predators noses are in some midway position due to genetic changes. So it all works out, just like it does now.
Comment by onething — October 4, 2005 @ 12:16 am
October 4th, 2005 at 12:54 am
Onething:
I doubt anyone can give a definitive answer to this question, but I'm guessing it's because evolution works more slowly when there's less (i.e., a much smaller genome) to evolve, and that the jump from eubacterial to eukaryotic life may have been the most significant step in evolution short of the invention of sexual reproduction. But in any event, the first evidence for bacterial life is close to 4,000 million years old, and eukayotic life doesn't appear in the fossil record for almost three billion more years. Assuming a billion years of poorly-fossilized remains are missing, we're still talking about a lot of time. I'm wondering what ID's explanation is for the lag-time between the earliest life and the earliest eukaryotic life. God's learning curve? Or was he distracted by working on some other project?
We know they're humans, don't we? Or do you posit, e.g., an extraterrestrial source? Do we assume at least that the Egyptians were lying when they said they built them for their kings?
No. The standard posited theories, e.g., gene duplication, transposition, point mutation, genetic drift, co-option of function, co-adaptation.
If you'd spend some times outside of the ID ghetto on sites like talk.origins.org, pandasthumb.org, and talkreason.org, you would have heard of it.
Logic here.
Let's look at Behe's and Dembski's position with respect to allegedly IC structures. Both say that if a biological structure is IC, according to their definition, then it cannot have evolved through naturalistic mechanisms, and therefore must have been designed. This is, as I stated, a purely eliminative argument, i.e., once all the possible naturalistic explanations have been eliminated, design must necessarily be inferred.
Unfortunately for Behe, Dembski, et. al., biologists have demonstrated that 1) all of the structures Behe has actually identified as IC, such as "the" bacterial flagellum, the mammalian clotting sequence, and the complementary immune system, are in fact not IC (i.e., they can have parts removed and still retain some function, sometimes for the same function, sometimes for different functions). Further, biologists have identified some IC structures, such a bacterial mechanism for metabolizing nylon precursors, that we know have evolved recently, because nylon precursors did not exist in nature prior to about 70 years ago.
I know it will be a slog, onething, but I suggest you wade back through my previous posts, because I have covered most of these issues exhaustively, including citing references, before, and I don't want to waste any more bandwidth going over them again. This is why I'm starting to feel like I'm repeating myself endlessly. I think I've wrung about all the entertainment I can get out of this subject; I think I'm going to take up needlepoint.
Comment by ericmurphy — October 4, 2005 @ 12:54 am
October 4th, 2005 at 1:26 am
Onething:
I agree. I remember looking at some library book (I think I was looking for pictures of a glyptodont), and they had some artist's conceptions of early mammals, some of which resembled, e.g., rabbits, wolves, housecats, etc. And they all had this slightly comical look of prototypes, works in progress, etc. You know, a little clumsy, maybe not all that smart?
Oh, for a time machine. This month's Scientific American has an article about the very early (pre-biotic) earth, and I think it would be fascinating to travel back then. Of course, you wouldn't be able to breathe the atmosphere…
Comment by ericmurphy — October 4, 2005 @ 1:26 am
October 4th, 2005 at 2:24 am
P.S.
(where I said "heliocentric" theory in my response to Joe G above, obviously I meant "geocentric." And I failed, unaccountably, to mention the endlessly entertaining "epicycles.")
Comment by ericmurphy — October 4, 2005 @ 2:24 am
October 4th, 2005 at 8:23 am
ericmurphy:
Anyway, my inference (once you strip out the exaggeration for effect) is that you will not accept any evidence that bacteria can evolve into eukaryotes short of an experiment that actually does evolve bacteria into eukaryotes.
And what evidence, short of watching the designer in action, would you accept for ID?
ericmurphy:
And you're not even satisfied with evidence of speciation …
That is a lie which makes you a liar.
bye-bye.
PS anytime you want to continue this I will but in person. I am not wasting any more of this blog's bandwidth discussing your absurd notions.
Comment by Joe G — October 4, 2005 @ 8:23 am
October 4th, 2005 at 1:30 pm
Well, I tend to think it may be something very like that going on, but it is difficult to see why the learning curve should be so flat there. I assume God is a quick learner. More likely, the reason is that the earliest bacteria were increasing the oxygen level of the planet or some such slow terraforming process.
No, we don't. How can we know that? All we know is that suddenly humans, for example, the Sumerians, came up with about 100 "firsts" for civilization, including knowing long-range astronomical facts, how many planets there were, the color of neptune and uranus (recently proven against predictions). Now, I have not personally checked all these facts but they are certainly intriguing. What Lloyd Pye has to say about the difficulties of creating domesticated plants and animals, for example.
We talk about how the pyramids could have been built, but according to his webiste, creating the pyramids at Giza as the are supposed to have been done would require placing 7 stones per hour, 24/7 for 100 years. the stones are very heavy. There has been no appreciable settling or cracking. And these guys just came out of the stone age and did this. Meanwhile, around the world, all the early great civilizations claimed that there were gods who just came out of the sky and gave this knowledge to humanity. They say this over and over but of course we don't take them seriously. The Bible also uses a plural for the word God, and the word Nephilim means those who came down from the dky. It is a plural.
Of course, the lines of inquiry about ancient civilizaitons and human origins fill whole books, and the only reason I take up the topic is that the ID people have often said, and I think some even seriously consider, that the intelligent designer could have been an alien.
In an era when Dawkins is talking about taking our own evolutin into our hands and when we already modify genetically many life forms, and can clone life forms, and when we talk of whether we can terraform mars, it isn't really necessary to act as if the possibility that this planet's history has something of the sort is totally crackpot.
Of course they built them for their kings. But who were their kings?
What I have read about the flagellum is the Miller essay and Dembski's response. I assume these are the cutting edge. The Miller essay was weak and Dembski hardly broke a sweat. It has not been refuted. I also red Mike Gene's 5-part essay at teleologic, which I found quite impressive. I know you have given a lot of links, and I would be willing to look at them, but are they on this thread or the What If thread?
You claim that the fact ID is eliminative is a fatal flaw. Then you say that the guys are wrong – the structures are not IC. But that is not a flaw due to it being eliminative. What I said is that being eliminative is OK. Whether their inference is correct is a separate question.
I have to ask, Eric, if you have read what I have? Are you likewise avoiding reading the other side? Our writers are better! The Miller-Dembski refutations/counter-refutations are a good read.
Comment by onething — October 4, 2005 @ 1:30 pm
October 4th, 2005 at 2:00 pm
onething:
Interesting ideas regarding the possible non-terrestrial origins of the builders of the pyramids, but I think you'd agree with me that such hypotheses are pretty far out on the fringe, wouldn't you? Most archaeologists seem satisfied that the pyramids were built by human laborers for human kings. And at any rate, that's taking us pretty far afield from the subject at hand.
I guess we'll have to agree to disagree on "the" bacterial flagellum. Another source of disproof of Behe's and Dembski's argument would be Why Intelligent Design Fails, by Matt Young and Tanner Edis. The article in that book comes to the same conclusion as Miller does. I've read Dembski's response to Miller, and I have to respectfully disagree. I think Dembski's response for the most part completely misses Miller's point.
My argument about ID is not that being purely an eliminative argument is a fatal flaw (although it may well be, given how difficult it is to prove a universal negative). My argument is that given that the universal negative it attempts to prove, i.e., IC structures cannot evolve without design, has not in fact been proven (actually, the contrary evidence is substantial), ID's argument is fatally flawed.
In any event, you can find links I've provided in my responses to Joe G and others sprinkled through this thread, the "What If?" thread, and especially at the end of the "Memory Hole" thread.
I doubt if I've read everything you've read, onething, but I have to say the links you have provided have seemed distinctly crank-like, if I can say that without sounding too judgmental (but I guess assessments of credibility always come down to some sort of judgment, don't they?). But I think I've read enough from both sides at this point to make credibility judgments, and frankly I just don't find the ID position particularly compelling.
I'd also have to disagree that ID writers are better. Dembski's prose, just to take one example, is virtually impenetrable. His books take forever to read!
But seriously, onething. Read the links I've provided. Also, spend some time on talkreason and talkorigins. Panda's Thumb is a good resource too. I think they'll give you a better flavor for the consensus opinions of the scientific community on the evolution question.
Comment by ericmurphy — October 4, 2005 @ 2:00 pm
October 5th, 2005 at 2:34 pm
Sticking to the original theme or question, I would like to know if Art (who I know is a skilled scientist and teacher) has revised his opinion. Could it be that your students were right and you were wrong?
I do have some teaching experience. I saved my own sweet ass by saying upfront, first thing, that I will (was and ever will be) wrong in much of what I "instruct."
Your job, as students, is to figure out what I'm wrong about.
Comment by Rock — October 5, 2005 @ 2:34 pm
October 5th, 2005 at 3:02 pm
My comments regarding the energetic "costs" of junk DNA were in the context of DNA that does not encode mRNA and protein. So, Rock, I'm afraid that the paper by Wagner doesn't really change much. (IOW, of course I'm correct
.)
Be that as it may, let's do a bit of exploring. Specifically, let's say that, when it comes to expressed, protein-coding genes, Wagner's calculations are in a reasonable ball-park, and that I'm also correct about the low or nonexistent actual cost of gene duplication. What missing link(s) can help us reconcile these seemingly incongruous statements?
Comment by Art — October 5, 2005 @ 3:02 pm
October 8th, 2005 at 9:51 am
ericmurphy Says:
October 1st, 2005 at 7:26 pm
Well, you're asking how ID explains it.
ericmurphy Says:
October 1st, 2005 at 10:06 pm
IOW, closely-related means those organisms we've put into nested hierarchies based on similarities. I think ID would say they if we put similar organisms together in a classification scheme, that is what we should expect to see when we look at the classification scheme. Your logic is circular.
Now, I understand that you think that the reason the similarities exist is Common Descent, but neither the hierarchies you cite, nor the questions you ask of ID, shed any light upon whether CD is the explanation.
Comment by RogerRabbitt — October 8, 2005 @ 9:51 am