HGT and evolution
by MikeGeneFrom here:
It's a mystery why the speed and complexity of evolution appear to increase with time. For example, the fossil record indicates that single-celled life first appeared about 3.5 billion years ago, and it then took about 2.5 billion more years for multi-cellular life to evolve. That leaves just a billion years or so for the evolution of the diverse menagerie of plants, mammals, insects, birds and other species that populate the earth.
New studies by Rice University scientists suggest a possible answer; the speed of evolution has increased over time because bacteria and viruses constantly exchange transposable chunks of DNA between species, thus making it possible for life forms to evolve faster than they would if they relied only on sexual selection or random genetic mutations.
No, horizontal gene transfer (HGT) has always been present with life from the beginning. The increased "speed and complexity of evolution appear to increase with time," to the extent that it exists, is more likely due to the fact that HGT can exploit a more complex biotic substrate and evolution travels shorter distances.
"Life clearly evolved to store genetic information in a modular form, and to accept useful modules of genetic information from other species," Deem said.
Almost. Life was designed to store genetic information in a modular form, and to accept useful modules of genetic information from other species
January 30th, 2007 at 11:36 am
Wouldn't it be more accurate to say that you think life may have been designed? I understood (perhaps incorrectly) that your position was that this was just a hobby, and you thought it may be interesting to look at biology from a teleological perspective, but that its not science and shouldn't be taught in schools. What have you learned that enables you to definitively state that life was, in fact, designed?
Comment by Aagcobb — January 30, 2007 @ 11:36 am
January 30th, 2007 at 11:47 am
Mike's comment juxtaposed with:
I think Mike is well within the range of credible certainty to state the claim as he did.
Even if you understood correctly, what does this have to do with his article?
Would you be happy if he said:
Life was quite possibly/but not certainly/and certainly not definitely designed to store genetic information in a modular form, and to accept useful modules of genetic information from other species. ?
Comment by Doug — January 30, 2007 @ 11:47 am
January 30th, 2007 at 11:52 am
Aagcobb,
how did the 1st life-form have the foresight to store information in modular form? Did it know that it was probably going to be swapping information from other life-forms? Or that it's descendants would be swapping bits here and there between each other?
Comment by Doug — January 30, 2007 @ 11:52 am
January 30th, 2007 at 11:58 am
Or would he have been happy if METers acknowledged that: since we have no known pathways to life and since we are unable to document or explain the origin of information laden nucleic acids, we must admit that a design perspective is a reasonable alternative to existing theories.
Comment by Bradford — January 30, 2007 @ 11:58 am
January 30th, 2007 at 12:09 pm
Would any ID critic take issue with a statement that: Life was not designed to store genetic information in a modular form, and to accept useful modules of genetic information from other species?
Comment by Bradford — January 30, 2007 @ 12:09 pm
January 30th, 2007 at 12:10 pm
Comment by Doug — January 30, 2007 @ 12:10 pm
January 30th, 2007 at 1:47 pm
Biology's Next Revolution (Nigel Goldenfeld and Carl Woese in Nature).
[ht: Bert]
Comment by Joy — January 30, 2007 @ 1:47 pm
January 30th, 2007 at 5:36 pm
There is further commentary on this:
Doolittle, quite rightly, thinks this is missing the point: if most of the genome came into being through a complicated network of HGT, then we need to start viewing it that way if we're going to actually have all but the most superficial understanding of the history of life on earth.
If this is correct then how can one debunk a design inference unless he has already formulated a consistent theory as to how genomes "came into being through a complicated network of HGT?"
Comment by Bradford — January 30, 2007 @ 5:36 pm
January 30th, 2007 at 6:20 pm
Yes.
Indeed. So I am perplexed as to why you simply tossed away this understanding:
Did I begin with "Science shows"¦" or "Research shows"¦"? Did I end with "therefore, ID is science" or "therefore ID should be taught in schools."? No. And no. I simply played off Deem (as Doug easily figured out).
Deem expresses one perspective and includes the descriptor "clearly" (I dropped that one). What has he learned that enables him to definitively state that life was, in fact, evolved to store genetic information in a modular form? What makes this so clear?
Comment by MikeGene — January 30, 2007 @ 6:20 pm
January 30th, 2007 at 11:55 pm
Hi MikeGene,
Probably the evidence from the last billion years or so of evolutionary development, which, if I understand correctly, you also accept. If all the multicellular diversity is due to evolutionary mechanisms, then in the absence of any evidence of intervention or an intervenor, evolutionary mechanisms are adequate to explain the preceding couple of billion years of biological development.
Comment by Aagcobb — January 30, 2007 @ 11:55 pm
January 31st, 2007 at 12:02 am
Hi Bradford,
A design inference doesn't have to be debunked; it is incumbent on those who wish to infer design to present sufficient evidence to show that design is a more probable explanation than observable evolutionary mechanisms.
Comment by Aagcobb — January 31, 2007 @ 12:02 am
January 31st, 2007 at 12:25 am
Aagcobb:
"Observable" in what way? We don't observe evolution, we infer that it happened (geological evidence) and observe variation and differential death just like Darwin did. That organisms die at different ages and are more or less successful at producing scads of offspring has never been controversial. That variation is present in populations (some more than others) is also uncontroversial.
But all we've got besides variation/differential selection is theory, and dozens of those covering dozens of mechanisms. One of which is apparently HGT. If you want observable mechanisms, they're a dime a dozen. If you want those organized into an explanation for the biodiversity we see, you can take your pick of those as well.
But nobody observes evolution. Even nylon-eating, antibiotic resistant e.coli engineered to produce industrial chemicals in vats is still e.coli.
Comment by Joy — January 31, 2007 @ 12:25 am
January 31st, 2007 at 12:32 am
Hi Joy,
Noone observes anything. The photons striking your eyes may have been designed by Loki to intercede between you and the object you think you are observing. Though I doubt it.
Comment by Aagcobb — January 31, 2007 @ 12:32 am
January 31st, 2007 at 4:30 am
Hi Aagcobb,
You write:
Yes, and it is exactly this acceptance that leads me to this question. We have plenty of evidence about how evolution works among creatures that store genetic information in a modular form. But this is not evidence for how life itself came to store genetic information in a modular form. Science tells us how the architecture has interfaced with the environment for the last billion years. But what about the very origin of the architecture?
That's one plausible hypothesis and it is backed up with a philosophical appeal. But it is not the data that mandate acceptance of this hypothesis. According to the hypothesis that I raise, life was designed and designed to evolve. Thus, pointing out that life has since evolved doesn't exactly help anyone choose your hypothesis over the one I raise.
You need evidence "of intervention or an intervenor." What would that data look like? What would count as such "evidence?"
Comment by MikeGene — January 31, 2007 @ 4:30 am
January 31st, 2007 at 7:29 am
If this is correct then how can one debunk a design inference unless he has already formulated a consistent theory as to how genomes "came into being through a complicated network of HGT?"
Aagcobb: A design inference doesn't have to be debunked; it is incumbent on those who wish to infer design to present sufficient evidence to show that design is a more probable explanation than observable evolutionary mechanisms.
The easiest way to debunk ID is to show the sufficency of a non-ID process. That's why I used the conditional in pointing out that you do not have a coherent alternative theory, if the author is correct. Mindlessly spouting natural selection is not good theory. The author is suggesting a revision of mechanistic concepts. The bottom line is a non-design inference does not have to be debunked in the absence of a plausible accompanying theory.:lol:
Comment by Bradford — January 31, 2007 @ 7:29 am
January 31st, 2007 at 7:44 am
But nobody observes evolution.
Aagcobb: Noone observes anything.
But they do. People actually observe the effects of gravity and accelertation and more. They can measure and compare data with precise predictions based on underlying theory. They can do all this repeatedly. Contrast that with biology's explanation for life's origins and the insistence that unknown and undemonstrable pathways to life equate to a non-telic, non-ID inference.
Comment by Bradford — January 31, 2007 @ 7:44 am
January 31st, 2007 at 4:41 pm
Hi Mike,
Are you talking about abiogenesis. I thought, if I had understood correctly, that you hypothesized that eukaryotes were designed to have added complexity in order to evolve. Now, unless I'm misunderstanding you, you seem to be suggesting that dna was designed in the very beginning. Are you envisioning multiple intervening events, or am I misunderstanding you?
IMO, which is insignificant, anything which makes a design theory at least as, or more probable than, evolutionary theories.
Comment by Aagcobb — January 31, 2007 @ 4:41 pm
January 31st, 2007 at 4:49 pm
Two questions for Mike:
First, in the article it states:
Are they referring to the parts of the immune system that Behe referrences as being IC?
Second, the article seems to suggest that the complexity we see in organisms can be mostly accounted for by HGT in bacteria. If I recall, you seem to favor a view that at least some of the original cells were more complex than bacteria. Could this lead to two inconsistent hypotheses: one where bacteria (and archaea) were the only original cells; and one where something akin to eukaryotic cells were the original cells. Or is there a way to incorporate both views?
Comment by Bilbo — January 31, 2007 @ 4:49 pm
January 31st, 2007 at 5:10 pm
If I design an evolutionary mechanism (and let me assure you, it is a trivial design problem to solve), then the question you asked makes no sense whatsoever. In this case design is the most probable explanation of the evolutionary mechanism. And I should hope so because it is the only correct explanation for an evolutionary mechanism that I have designed.
Or maybe that's "insignificant."
Would that count as an "intervention" (I'm sure somehow, it wouldn't count as "suffcient evidence.") Darwin had an interesting theory about the "intervention" of life forms into the evolutionary process. He devoted most of a book to the subject?
Ever heard of it?
Comment by Rock — January 31, 2007 @ 5:10 pm
January 31st, 2007 at 5:17 pm
Rock, were you talking to Aagcobb or to me?
Comment by Bilbo — January 31, 2007 @ 5:17 pm
January 31st, 2007 at 5:29 pm
Are you the intervenor, Rock?
Comment by Aagcobb — January 31, 2007 @ 5:29 pm
January 31st, 2007 at 5:38 pm
Bilbo:
In general it is believed that different mechanisms for horizontal DNA transfer in bacteria can operate also to eukaryotes with low efficiency and have played an important role in evolution. A couple of enzymes that are involved in antibody production are highly related to transposases so they most probably share a common origin (see works by Nancy L. Craig, for instance Nature. 2004 Transposition of hAT elements links transposable elements and V(D)J recombination. Dec 23;432(7020):995-1001). An alternative hypothesis might be that the transposon arose through escape of a RAG gene rather than vice versa, although there is the difficulty of that they are widespread in insects, whose genomes do not have any RAG genes (AFAIK).
HGT mechanisms themselves are rather interesting, the mechanisms for each process are totally different, and so are the essential components for each of them. For conjugation you need a complex transfer machinery, especially in gram-negative bacteria, involving 15-30 different genes plus cis-acting elements. Transformation is usually mediated by dedicated machineries too, especially in gram-positives, that are unrelated to the conjugative machineries. Transduction is mediated by the ordinary phage
machinery that packs by mistake bacterial DNA in place of its own viral genome.
Sorry for jumping in , this is one of my favorite topics.
Comment by Guts — January 31, 2007 @ 5:38 pm
January 31st, 2007 at 6:17 pm
Sorry, Bilbo, I was responding to Aagcobb, who responded with what I can only presume is a "rhetorical" question.
I am a designer, which means that I intervene in natural processes to control them to obtain my own objectives.
As people say, natural processes do not occur according to a plan, do not have an objective, a goal, a direction, etc.
But guess what?–I, like every other life form, do! I have all of those, none of which is subserved by natural processes (by definition), which is exactly why I intervene in such processes.
How do you explain the existence of a Holstein? It evolved right? LOL
No. I intervened (me personally, LOL) to redirect a naturally occuring evolutionary process to make a cow that produces a lot of milk–my objective. (Actually, I'm, lactose-intolerant and wonder why any adult mammal, which I assume is weaned, would have such an objective–but they do.) Which, btw, falsifies a a direct statement of Darwin's: No creature exists whose "sole purpose" (did he say it that way) is to serve another creature. Sorry, charlie–Holstein.
Serious question? Did you even understand the question? Shall I rephrase? What can I do to help you out here, Aagacobb?
Ya wanna argue about "divine intervention" Is that what you mean?
You don't have an argument with me then. Your argument is with God. LOL
(And good luck winning that argument!)
Comment by Rock — January 31, 2007 @ 6:17 pm
January 31st, 2007 at 6:58 pm
Hi Rock,
I have to disagree there, Rock. From the Holstein's pov, they bred lactose-tolerant humans to feed and shelter them and protect them from predators!
Comment by Aagcobb — January 31, 2007 @ 6:58 pm
February 1st, 2007 at 12:00 am
Hi Aagcobb,
Rather than trying to envision where I am going, it would be better to focus on where I am at. Deem stated, "Life clearly evolved to store genetic information in a modular form, and to accept useful modules of genetic information from other species." It is clear that life stores genetic information in modular form and that this has made life susceptible to HGT (Shapiro calls this "natural genetic engineering"). All I am doing here is noting that any attempt to attribute these two universal features to evolution is simply a non-teleological perspective. A teleological perspective notes the same two observations yet ponders if they are part of a larger design (for that, the President Of The Geological Society Of London would lash out at me and label me an IDiot).
But that is much too vague and doesn't help me. I'm not worried about making a "design theory" more "probable" than "evolutionary theories." That's a long, long way down the road as far as I am concerned. I'm more interested in whether a design perspective can help us better understand life, evolution, and how they interface. Non-teleologists, as usual, are free to ignore me as you won't find me chasing after them in an attempt to get their attention. It's when they start insisting that we are all supposed to adopt their non-teleological perspective that I need to know about the nature of this "evidence" they demand of me. And after over six years of asking, I have been consistently disappointed by the answers.
Comment by MikeGene — February 1, 2007 @ 12:00 am
February 1st, 2007 at 3:46 pm
Hi, Mike
Well, what would you expect? You have to place their responses in context. The last six years was the heyday of the period when creationists were aggressively pushing ID as a valid alternative theory to evolution which ought to be taught in public schools. In that context, the evidenciary bar should be set very high indeed. In the context of a hobby which isn't science and shouldn't be taught in public schools, anything and everything can be considered "evidence" of design.
Comment by Aagcobb — February 1, 2007 @ 3:46 pm
February 1st, 2007 at 4:52 pm
"From the Holstein's pov"¦"
And I truly appreciate the Holstein's sense of humor in these matters and I appreciate the fact that you share the Holstein's perspective, Aagcob, because in this context a lot of people can't maintain their sense of perspective and proportion, which is basically the source of humor. Sometimes these subjects are like arguing about women's fashions with a Wahhabi.
""¦I need to know about the nature of this "evidence" they demand of me. And after over six years of asking, I have been consistently disappointed by the answers.""”Mike Gene
In this context"”It seems natural enough to me to identify "module" with "gene," as Deem seems to do. But there is no basis for such a comparison in the formal theory of Neo-Darwinism. The "genes," Fisher, Wright, and Haldane described are not modules. So when biologists start think of genes as modules they are departing from the neo-classical theory of evolution (not "Darwinism," but MET or Neo-Darwinism, as formally stated) and departing in what direction?
Von Dassow & Munro (1999) argued that the concept of modularity occurs naturally to biologists. And it should. They're right. But the word and the concept itself was borrowed from design science and the biologists (who bother to define the word) define it and use it the same way the engineers do.
Contra Neo-Darwinism where the very concept is alien.
Obviously design science and biology engage in a useful, productive, and theoretically significant exchange of ideas. The Neo-Darwinists did the same!
But not in this case of modularity.
Mike Gene is always asking what his critics require of him, what they require as "evidence." (And I've always advised him and the other IDers to choose their critics like they choose their friends–well. Because some "critics" don't have 'standards.") Which is the same as asking what is required of a theory. Now, if your requirements are pretty lax, then Neo-Darwinian theory should suffice for you. My requirements are different. And they change.
Is this a case of "double-standards"? Do we require more of IDers like Mike Gene then we require of Neo-Darwinists like Fisher, Wright, and Haldane?
But there really is no comparison, as Mike Gene repeats, its not a theory or a science, it's a "hobby." Like collecting stamps, building ships in a bottle, and gardening.
A way to occupy idle time.
To be fair to Mike Gene that explains my continuing interest as well. I am particularly interested, as he is, in how the scientific community reacts to such challenges. Mostly they don't. Even when they do, e.g., http://telicthoughts.com/may-i...
they seem to be intent on nothing else but demonstrating that even scientists can have shit-for-brains.
I am very disappointed in us. (And myself. LOL)
Comment by Rock — February 1, 2007 @ 4:52 pm
February 1st, 2007 at 5:07 pm
"Contra Neo-Darwinism where the very concept is alien."
Uh, "alien," not to be taken literally, Mike Gene. LOL
Comment by Rock — February 1, 2007 @ 5:07 pm