HGT Unseating Darwin

_{Mark

August 4, 2009

Intelligent Design}

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Genes may be freely shared around, but where did they come from is the first place?

Collectivist revolution in evolution Mark Buchanan Nature Physics 5, 531 (2009) doi:10.1038/nphys1352 excerpts

“A coming revolution in biology, may go so far as to unseat Darwinian evolution as the key explanatory process in biology.

The evidence for this radical turnabout has been accruing at an accelerating pace. A fair fraction of most bacterial genomes have been acquired not solely through inheritance from earlier generations, but also through horizontal gene transfer. DNA flows readily between bacterial chromosomes and the external world.

Such gene flow exerts an enormous influence on evolutionary dynamics. This was first suspected when a number of bacteria around the world rapidly gained resistance to multiple antibiotic drugs. Such resistance spread too fast to have been ‘invented’ independently by distinct species, but clearly seemed to have spread from one species to another.

The clear impact of horizontal gene transfer on bacterial evolution has been established only fairly recently.

Horizontal gene exchange may have been the dominant force in an earlier era of evolution. The conjecture is that horizontal gene transfer was indeed required for the present genetic code to take the form it has.

Exploring that point in greater detail will be a task for a new kind of biology, one that breaks with many of the presuppositions of traditional evolutionary thinking.”

Comments

Sal Gal @ 3
Darwin did not make an argument for a “tree of life.” The notion came from Lamarck, and Darwin supposed it true.
Whether someone originated the idea and he supposed it true does not mean he did not argue for it. In Origin of Species, Darwin wrote, "The affinities of all the beings of the same class have sometimes been represented by a great tree. I believe this simile largely speaks the truth. [...] so by generation I believe it has been with the great Tree of Life" - Darwin(1872), pp. 170-171. The Origin of Species. Sixth Edition. Within there ([...]) he seems to be giving a model to support the TOL notion with reasoning based on comparisons he chose to use. I'd classify that as him making an argument for the TOL.JGuy_{August 6, 2009
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jehu:
Perhaps you are unfamiliar with the meaning of the word “plausible.” For something to be plausible it must be at least superficially reasonable. None of the four theories rise to that level.
Your definition and my definition of plausible are pretty much the same. However, you attacked the plausibility of only of the four hypothesees. I admit, the physics of the fission hypothesis also escapes me. However, I am not a physicist. I certainly haven't studied the equations that the presenters of the hypothesis have presented. I bet that a careful look at their numbers would show it to be a realistic possibility. There is some reason why this, the least intuitive of the theories is mentioned first at wikipedia. Likely the reason is that it has some pretty good supporting evidence and calculations. Consider the capture theory -- that an asteroid happened along at the correct angle and speed to be captured in the gravitational pull of the earth. While it would be a "lucky catch", if one could find any case of asteroids being captured in the gravitational pull of planets, which is likely considering all of the rubble floating around out there, the theory's plausibility would go up siginificantly. Again, I am not an astrophysicist, and do not know if such captures have been recorded, but it wouldn't surprise me. This theory seems very plausible to me. The Coformation theory suggests that by the same mechanism that has planets form around stars (which we know happens alot) moons form around planets. We know that there are many moons around the planets in our solar system. The only thing odd about our moon is that there is only one, and its a big one. This theory seems very plausible to me. Lastly, the impact theory. On this theory I happen to have a little more detailed information because I had a chance to dialog with a Ph.D. Physicist about it last summer. The assumption is that at the time of the impact the earth was warmer, more molten, than it is today. The theory accounts for a number of other phenomena, such as the amount of metals that the earth contains. It is not by any means unreasonable from a physicist's perspective. It is, well, a reasonable hypothesis. (That said, recent experiments have put a damper on the theory.)bFast_{August 5, 2009
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Lenoxus
Wow, are you actually deciding the plausibility of fission theory by how you picture it in your mind?
No. I am talking about the physical evidence.
I am assuming — without absolute proof, I admit — that the fission theory has a sufficiently sound Newtonian mathematical basis to be plausible. In part, this is because total non-plausibility would result in its rejection by astronomers from the list of possibilities.
The same wikipedia page that you linked to says that it doesn't have a sound Newtonian mathematical basis because of the angular orbit of the moon and the speed with which the earth would have to spin to throw off a chunk of mantle the size of the moon. Your faith in the scientific establishment is entirely misplaced.Jehu_{August 5, 2009
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Jehu: Wow, are you actually deciding the plausibility of fission theory by how you picture it in your mind? If I went about like that, I would totally deny relativity and quantum mechanics, just for starters. The oft-repeated myth that the Coriolis effect causes bathtub-drain-swirls to differ would make perfect sense to me. I am assuming — without absolute proof, I admit — that the fission theory has a sufficiently sound Newtonian mathematical basis to be plausible. In part, this is because total non-plausibility would result in its rejection by astronomers from the list of possibilities.
Absolutely. They exclude special creation a priori and the field is generally hostile to any suggestion that there is any design in the universe. God is strictly verboten.
Any idea what astronomy might look like, how it might be different, if it incorporated God? Besides perhaps tacking "God must have made this" onto descriptions of newly discovered planets?Lenoxus_{August 5, 2009
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Lenoxus,
Please don’t put thoughts in my head. I have learned that there are several theories, and I believe them plausible; you (as far as I can tell) believe they are not.
Really? You find it plausible that the earth once spun so fast it threw the moon into orbit out of the Pacific Ocean? Simple stating it is plausible as a rhetorical device when all empirical evidence is to the contrary is not very convincing.
Hmm, well, more like “but at least I don’t take God to be an in-and-of-itself explanation for any and all mysteries.
Neither do I or any other theist I know. Only in regards to origins or certain miracles that defy known natural law would I invoke the supernatural.
Indeed, most astronomers have been theists. Why then does modern astronomy not incorporate their theism in its explanations of phenomena? Sheer philosophical bias?
Absolutely. They exclude special creation a priori and the field is generally hostile to any suggestion that there is any design in the universe. God is strictly verboten. "[T]hey became vain in their reasonings and their foolish heart was darkened." Rom. 1:21Jehu_{August 5, 2009
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bFast,
I checked the links that Lenoxus provided. It expressed four naturalistic hypothesees of how the moon came to be. Now, the article made it clear that none of these hypothesees has arisen above the others to unseat the others. However, all four of these hypothesees are “plausible”.
Perhaps you are unfamiliar with the meaning of the word "plausible." For something to be plausible it must be at least superficially reasonable. None of the four theories rise to that level. Let's look at the first one, the fission hypothesis, which states that the Moon broke off from the Earth's crust because of centrifugal forces. Does that sound "plausible" to you bFast? Do you find it even superficially reasonable that the earth once spun so fast that it threw the moon into orbit? If so, how did the earth slow down from that speed? What happened to all of the heat that would have been generated? Why is the moon so chemically different than the earth? Why doesn't the moon orbit in the same plane as the earth's rotation? Clearly, it is not even superficially reasonable. You sound as if, in the case of the moon, "science" has four good picks but hasn't settled on one. In fact, science doesn't have any good picks, any more than it has a good explanation for abiogenesis, the cambrian explosion, or the origin of information in DNA. Finally, the argument that something cannot be the result of natural mechanisms and therefore is the result of intelligence is completely logical. The only people that would disagree are those who have an emotional commitment to the view that the supernatural must be excluded a priori, and those who have been intellectually intimidated by that group.Jehu_{August 5, 2009
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Sal Gal (#11), I haven't received a response to #4, so maybe I am wasting my time. But you said something that should receive a response:
On two or three occasions, I have asked UDers to step forward and acknowledge that ID may one day be falsified. Not a one responded.
I don't remember seeing this question, but admit that I have not read all of the comments on UD, and perhaps I missed it. It will be difficult to falsify ID, and perhaps impossible to falsify it conclusively (which is true for any theory), but for practical purposes ID could be falsified if a significant proportion of the problems that currently plague naturalism could be solved, ID is not like theism, which is compatible with literally any observation. ID postulates not only that intelligence is involved with certain features of the universe, but that at least some of these features are empirically detectable. Thus reasonably demonstrating that several of ID's favorite examples of evidence for intelligence could actually be explained by currently known natural law and reasonable stochastic resources (a fancy way to refer to chance) would basically deflate ID. As a matter of fact, the discovery of a realistic (as opposed to "plausible") scenario for the origin of life without intelligent input, along with a similar solution for the problems of consciousness and the anthropic coincidences, would cause me to change my mind. At that point I would give you the complete efficacy of mechanistic evolution. I have said similar things on this blog, but you may not have read the blog exhaustively either. Suffice it to say that at least for some of us, ID is in fact a falsifiable theory.Paul Giem_{August 5, 2009
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Jehu: "there is no plausible naturalistic theory for the formation of the moon." I checked the links that Lenoxus provided. It expressed four naturalistic hypothesees of how the moon came to be. Now, the article made it clear that none of these hypothesees has arisen above the others to unseat the others. However, all four of these hypothesees are "plausible". Your logic says that just because science has not settled on a particular theory the only logical choice is "god did it". This logic gives ID a bad name.bFast_{August 5, 2009
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Jehu:
But now you have Googled it and learned that there is no plausible naturalistic theory for the formation of the moon.
Please don't put thoughts in my head. I have learned that there are several theories, and I believe them plausible; you (as far as I can tell) believe they are not.
Now you resort to the “well I have no theory but at least I don’t believe in God” gambit.
Hmm, well, more like "but at least I don't take God to be an in-and-of-itself explanation for any and all mysteries." No snark is meant there; I'm just making a point I'm sure you've heard plenty before.
As for “immaterialist astronomy” you might want to check out the work of Galileo, Kepler, and Newton. In fact, it was men who believed in divine creation that formulated and delivered to us the entire scientific process that we now enjoy.
Indeed, most astronomers have been theists. Why then does modern astronomy not incorporate their theism in its explanations of phenomena? Sheer philosophical bias?Lenoxus_{August 5, 2009
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Lenoxus,
Here’s the first hit on Google for the subject, and this section of the relevant Wikipedia article lists the major current hypotheses. I’m sure you’re familiar with them, though, and have a well-made rebuttal for why each of them doesn’t work.
I am disappointed. You sounded like you had a good theory for the formation of the moon. Turns out you were assuming such a theory already existed. But now you have Googled it and learned that there is no plausible naturalistic theory for the formation of the moon.
Meanwhile, I’ll be busy finding something wrong with the non-naturalist hypothesis — oh wait, I can’t. What could I say? “No Designer would be capable of creating spherical satellites! Nuh uh!”? And what could the answer to that be “Uh huh!” Never mind immaterialist biology — how does immaterialist astronomy work?
Now you resort to the "well I have no theory but at least I don't believe in God" gambit. The Apostle Paul once wrote, "since the creation of the world God's invisible qualities--his eternal power and divine nature--have been clearly seen, being understood from what has been made, so that men are without excuse." Rom. 11:20. As for "immaterialist astronomy" you might want to check out the work of Galileo, Kepler, and Newton. In fact, it was men who believed in divine creation that formulated and delivered to us the entire scientific process that we now enjoy.Jehu_{August 5, 2009
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"Lenoxus" (#17) asked: "...how does immaterialist astronomy work?" Isaac Newton (not the first modern scientist, but the last of the magicians) wrote "This most beautiful System of the Sun, Planets, and Comets, could only proceed from the counsel and dominion of an intelligent and powerful Being."PaulBurnett_{August 5, 2009
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Jehu:
Well then, tell me, how did the earth get its moon?
Here's the first hit on Google for the subject, and this section of the relevant Wikipedia article lists the major current hypotheses. I'm sure you're familiar with them, though, and have a well-made rebuttal for why each of them doesn't work. Meanwhile, I'll be busy finding something wrong with the non-naturalist hypothesis — oh wait, I can't. What could I say? "No Designer would be capable of creating spherical satellites! Nuh uh!"? And what could the answer to that be "Uh huh!" Never mind immaterialist biology — how does immaterialist astronomy work?Lenoxus_{August 4, 2009
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bFast,
More importantly, HGT, and the fact that it may make the phylogenic tree undescernable does not falsify UCD.
In terms of single cell organisms, what other evidence is there? According to the current experts we now have three groups of single cell life, archea, procaryote, and eucaryote - which descended from three groups of single cell organisms - which emrged about the same time from an amorphous gene swapping cloud of DNA. There was never a single common ancestor and the organisms didn't descend according to any hierarchical pattern they just kind of gene swapped around in a big web. I am paraphrasing but that is the current thinking. Try formulating a hypothesis that could disprove that version of UCD.Jehu_{August 4, 2009
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Sal Gal, "That there’s a web of life, and not a tree, is very old news." Huh? Textbooks at what level? So Koonin is stupid to be arguing that the TOL is non-existent? Is this like JunkDNA? Make a prediction, then claim you knew all along it was wrong? And have since passed by? LOL. The TOL has been at the center of evolution for more than 150yrs. I learned it in high school, then college, and I doubt it has left textbooks today. I don't have time to confirm. But here is a quick look: "Graphical representations of evolutionary relationships among taxa have a long history in biology. The pervasive effect of two particularly influential representations, the "Chain of Being," rooted in the ideas of Plato and Aristotle, and the "Tree of Life," epitomized by Haeckel's trees of the late 1800s, can still be seen in contemporary representations" TOL still seen in textbooks? 7th-12th grades. The study was done in 2008. http://www.britannica.com/bps/additionalcontent/18/35382784/Seeing-the-Wood-for-the-Trees-An-Analysis-of-Evolutionary-Diagrams-in-Biology-Textbooks So, this is interesting that scientist like Koonin are doing research which shows TOL is dead or dying, yet it has been known for 20 years? I'm curious, does anyone believe his boss would allow research on a 20yr old fact? Doubt it seriously.DATCG_{August 4, 2009
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jehu:
Right, it removes the evidence of UCD and what you are left with is another tautology. You start with UCD, fail to find evidence of it in phylogenetics. Instead of scrapping neo-Darwinism, you decide that HGT and convergent evolution are the reasons and wah-lah you have for yourself yet another Darwinist tautolgy.
The inability to trace the phylogenic tree because of HGT does remove one piece of hopeful supporting evidence, pushing UCD in the direction of tautology. However, the phylogenic tree isn't by any means the only evidence for UCD. More importantly, HGT, and the fact that it may make the phylogenic tree undescernable does not falsify UCD.bFast_{August 4, 2009
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Sal Gal
Horizontal gene transfer and hybrid evolution do not contradict the claim that all organisms we observe today descend from a population of organisms sharing certain characteristics.
Even a young earth creationist would affirm that, as you put it, "all organisms we observe today descend from a population of organisms sharing certain characteristics." So what is your point?Jehu_{August 4, 2009
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Lenoxus
As for “The formation of the earth? The formation of the moon?” all I can say is… wow. You think those came about by non-naturalistic processes? O… kay. I guess I was too early with my putting “geology” on that one-item list.
Well then, tell me, how did the earth get its moon?Jehu_{August 4, 2009
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I am sure then that you will have no problem renouncing the tree of life hypothesis and universal common descent, and will publicly admit that the genetic signals of extant organisms do not provide evidence for hierarchical evolution of species?
Signals? You're begging the question of the existence of a transmitter. Show me. Renounce? Publicly admit? Don't push your religious mode of belief on me. With verbiage like this, why should anyone accept that ID is "all about the science"? All scientific knowledge is tenuous. Some people choose to treat it otherwise in their personal beliefs. I am most definitely not one of them. The biggest problem I have with ID is claims along the line of "we can prove that certain entities are intelligently designed -- no false alarms." If it should happen not only Darwinian evolution is "unseated," but also supplanted by ID, then ID must be susceptible to unseating. On two or three occasions, I have asked UDers to step forward and acknowledge that ID may one day be falsified. Not a one responded. The mainstream evolutionary community was immediately receptive to the notion of the web of life when hard evidence of hybrid evolution came along, twenty years ago. You should consider publicly admitting that your beliefs about the beliefs of evolutionists are based on second-hand, biased, outdated accounts. Horizontal gene transfer and hybrid evolution do not contradict the claim that all organisms we observe today descend from a population of organisms sharing certain characteristics.Sal Gal_{August 4, 2009
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Jehu:
So where do we start? At what point in the movie do we get convincing evidence for a materialist explanation for the origins of anything? The big bang? The laws of nature? The formation of the universe? The formation of the earth? The formation of the moon? The beginning of life? The lack of evidence of UCD or LUCA? The cambrian explosion?
I would like to ask the same-but-inverted question of ID. At what point does non-materialism decide it doesn't "explain" everything? Geology? And why does non-materialism get a free pass in the "explaining things" department? I mean really explaining things, beyond "That was the product of intelligent agency." How the heck does the Cambrian explosion have to do with anything? "Sure, you can get the occasional new species here and there by natural means, but to get that much diverse life over a few million years — that takes Intelligence!" As for "The formation of the earth? The formation of the moon?" all I can say is… wow. You think those came about by non-naturalistic processes? O… kay. I guess I was too early with my putting "geology" on that one-item list. :) much loveLenoxus_{August 4, 2009
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Jehu,
The lack of evidence of UCD
wow, you're still trying to claim that?Khan_{August 4, 2009
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bFast,
HGT does not challenge UCD in any way, nor does it challenge the existance of a phylogenic tree, or neo-Darwinism. The only challenge that HGT offers is that it makes figuring out the phylogenic tree extremely difficult — impossible?
Right, it removes the evidence of UCD and what you are left with is another tautology. You start with UCD, fail to find evidence of it in phylogenetics. Instead of scrapping neo-Darwinism, you decide that HGT and convergent evolution are the reasons and wah-lah you have for yourself yet another Darwinist tautolgy. With Darwinism, it is tautologies all the way down. So where do we start? At what point in the movie do we get convincing evidence for a materialist explanation for the origins of anything? The big bang? The laws of nature? The formation of the universe? The formation of the earth? The formation of the moon? The beginning of life? The lack of evidence of UCD or LUCA? The cambrian explosion?Jehu_{August 4, 2009
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bFast:
When a microorganism devides into two, both sub-organisms can be seen as “children” of the original.
One is the original and the other is a copy. But anyway I agree with most everything else but there does seem to be a conflict. In your opening paragraph you say HGT doesn't challenge the phylogenetic tree (which doesn't exist BTW) and then you say that it makes figuring out that tree difficult/ impossible.Joseph_{August 4, 2009
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HGT does not challenge UCD in any way, nor does it challenge the existance of a phylogenic tree, or neo-Darwinism. The only challenge that HGT offers is that it makes figuring out the phylogenic tree extremely difficult -- impossible? Let me make my case. There are two general models of reproduction -- sexual and asexual. When a microorganism devides into two, both sub-organisms can be seen as "children" of the original. With sexual reproduction, of course, childhood is more obvious. Now, if a microorganism takes on some external dna (HGT), it doesn't somehow change parentage. While the parentage pattern of the original organism is still complete. The DNA that was spliced in doesn't change this in any way. Even if, over many generations, every piece of DNA were to eventually be replaced by DNA that was absorbed via HGT, each organism in the lineage would have a parent. If each organism in the lineage has a parent, then UCD is not challenged. As far as neo-Darwinism being challenged, well, I absolutely don't get that. There are many variations on the single mutational event: point mutation, insertion, deletion, transpostion etc. HGT is just one more available type of mutational event.bFast_{August 4, 2009
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Sal Gal,
Darwin did not make an argument for a “tree of life.” The notion came from Lamarck, and Darwin supposed it true.
I am sure then that you will have no problem renouncing the tree of life hypothesis and universal common descent, and will publicly admit that the genetic signals of extant organisms do not provide evidence for hierarchical evolution of species?Jehu_{August 4, 2009
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Sal Gal, With one-model thinking, you're missing a couple of points. First, idnet.com.au pointed out in his/her first sentence,
Genes may be freely shared around, but where did they come from is the first place?
Simply saying that biologists now recognize "shared genes" doesn't help in accounting where the genes got to one sharing partner in the first place. If a gene shares less than 20% homology with any other gene, one must create over 80% of the gene from scratch, and nobody has shown how one can do this in a step-by-step manner. However, it is quite easy for an intelligent designer to decide he/she wants a given sequence and create it. Secondly, you may remember that one of the arguments that is used against ID is that an intelligent designer, once he/she found a good design, would be to reuse it multiple times. The claim was further made that this reuse of genetic material was absent in nature, suggesting the absence of intelligent design. This claim is psychological if not theological, as Cornelius Hunter would say. But, given those facts, it would be a good argument (there are good theological arguments). The problem with the argument is that given the facts noted in this post, with which I gather you agree, even calling them "very old news", there has been a lot of what is called "horizontal gene transfer". It would be interesting to try to distinguish between unassisted horizontal gene transfer, assisted horizontal gene transfer (which would require design), and simultaneous creation (which would also require design). It certainly looks like what is called "horizontal gene transfer" may be simply an attempt to keep the phenomenon within the paradigm of nature without intelligence, thus denying the ID implications of the phenomenon. Don't forget that humans have in fact made use of assisted horizontal gene transfer, to produce blue roses, insulin-producing yeast, etc. You say,
So where is the contradiction of Darwin’s argument that evolution is a consequence of variety, heredity, and fecundity?
You misunderstand. Nobody is saying that (unassisted) evolution does not happen. What is being said is that this evolution cannot account, by itself, for the production of zebras from archaea. In order to defeat ID, you need to establish not just that evolution happens, but that it can account for all of life. You say,
Darwin did not make an argument for a “tree of life.” The notion came from Lamarck, and Darwin supposed it true.
But is not the absence of gradual branches a major problem? How does one get from algae, and maybe a few edicaran fauna (flora?) and sponges, to trilobites, starfish, mollusks, etc., all at essentially the same time, geologically speaking, and without known intermediates, by step-by-step Darwinian processes? And if not, does this not show that Darwin's theory is inadequate? BTW, since you now claim that a tree of life is not a good metaphor, I suppose that you will now point this out to various Darwinists that visit this blog from time to time and claim that the tree is a good metaphor.Paul Giem_{August 4, 2009
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So where is the contradiction of Darwin's argument that evolution is a consequence of variety, heredity, and fecundity? Darwin did not make an argument for a "tree of life." The notion came from Lamarck, and Darwin supposed it true. That there's a web of life, and not a tree, is very old news. Hybrid evolution in higher species made its way into the literature about twenty years ago, if I recall correctly.Sal Gal_{August 4, 2009
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I have been harping on this for some time. The genetic signals of organisms do not resolve into a tree as predicted by the theory of common descent but rather form a web or a mosaic. In order to salvage some sort of theory of materialist evolution, the twin crutches of convergent evolution and HGT are brought into save the day. This article is at least evidence of the growing awareness that phylogenetics no longer provides evidence of common descent.Jehu_{August 4, 2009
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According to the never linked to copy/paste doesn't work properly on your computer. Here are the missing parts.
[...] some suggest [...] Nearly a decade ago, a review in Nature already surveyed broad evidence showing that the genetic diversity of many bacteria has arisen [...] even in the 1950s, [...] , and that the emergence of life most likely went through a series of stages, with the early stage more Lamarckian in character, and only the latter stages becoming more Darwinian.
How about inviting Dr. Buchanan for a discussion of his paper? You'll just have to tell him which version of his text will be the topic.sparc_{August 4, 2009
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