horizontal gene transfer News

Scientific American: Horizontal gene transfer more common than thought

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And therefore, Darwinism less common, though good luck getting many to draw that out. Here:

There are a few examples of gene swapping between eukaryotes — the domain of life that includes fungi, plants and animals — and even from bacteria to eukaryotes (see ‘Bacterial gene helps coffee beetle get its fix’). But such events, known as horizontal gene transfer, were thought to be rare.

But Daniel Muller, a microbial ecologist at the University of Lyons in France, and his colleagues have cast doubt on that assumption after studying bacteria in the soil around the roots of plants. They found that the bacterial gene acdS, used to promote the growth of plant roots, was also present in several types of fungus. Their work is published today in Proceedings of the Royal Society B.

Muller and his colleagues scanned the genomes of 149 eukaryotes, and found acdS-like genes in 65 of them — 61 in fungi and 4 in parasitic microorganisms called oomycetes, including Phytophthora infestans, the microbe responsible for the Irish potato famine. After analysing the organisms’ genetic family trees, the researchers determined that the most likely explanation was that three different kinds of bacterium had donated the gene to the fungi and oomycetes in a total of 15 different horizontal-gene-transfer events.

Anything HGT does, Darwinian evolution (natural selection acting on random mutation) did not do. If  HGT proves a factor in evolution, it carves a piece out of Darwin’s territory.

See also Horizontal gene transfer from moss to ferns

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75 Replies to “Scientific American: Horizontal gene transfer more common than thought

  1. 1
    JGuy says:

    I’d like to read Walter ReMine’s thoughts on this.

  2. 2
    JoeCoder says:

    I’d like to know what the observed rates of HGT are across microbes, plants and animals, not rates based on the assumption of common descent.

  3. 3
    Acartia_bogart says:

    Anything HGT does, Darwinian evolution (natural selection acting on random mutation) did not do.

    How do you figure that? Natural selection is about the differential survival of adaptive traits. When Darwin proposed this, he had no knowledge of DNA and genetics. And he hadn’t even ruled out the heredity of acquired characteristics as a possibility.

  4. 4
    wd400 says:

    Oh, but AB, this is a News post. There is no requirement (or probability) that it make any sense…

  5. 5
    ppolish says:

    Makes no sense to a Darwinist, Wd400, and I think that is the point of the post.

  6. 6
    wd400 says:

    This claim

    Anything HGT does, Darwinian evolution (natural selection acting on random mutation) did not do

    certainly makes no sense to this evolutionary biologist (and Darwinist in the special version of the term that UD insists on).

    Can anyone explain the logic of it to me?

  7. 7
    PaV says:

    wd400:

    I have a question for you: what effect would HGT have on phylogenetic trees?

  8. 8
    PaV says:

    Can anyone explain the logic of it to me?

    Yes. Think of it in terms of information. Darwinian evolution has to account for the ‘information’ we find in the genome. If HGT takes place, then the ‘information’ found in the genome which receives the information is not due to “natural selection acting on random mutation.”

    If you want to take the silly position that “Of course, HGT itself is a Darwinian process,” then you will have problems with the logic involved.

  9. 9
    Acartia_bogart says:

    Pav:

    I have a question for you: what effect would HGT have on phylogenetic trees?

    Since the HGT would subsequently be inherited in the organisms lineage, I assume that it would simply be a source of new traits in a lineage. In short, it would have little difference.

  10. 10
    wd400 says:

    Pav,

    HGT is one of several processes that makes gene trees differ from species trees. I don’t know how the the “information” in a gene differs when it passed down a tree or ‘jumps’ across branches i that tree.

    (Of course, once a gene is sucked up by some other genome is is subject to normal evolutionary processes and darwinism applies)

  11. 11
    bornagain77 says:

    wd400 states:

    (Of course, once a gene is sucked up by some other genome is is subject to normal evolutionary processes and darwinism applies)

    And yet wd400 cannot provide empirical evidence a single gene/protein that has arisen by unguided Darwinian processes

    “Charles Darwin said (paraphrase), ‘If anyone could find anything that could not be had through a number of slight, successive, modifications, my theory would absolutely break down.’ Well that condition has been met time and time again. Basically every gene, every protein fold. There is nothing of significance that we can show that can be had in a gradualist way. It’s a mirage. None of it happens that way.
    – Doug Axe PhD.
    http://www.metacafe.com/watch/5347797/

    Darwinian Mechanism Proven Unrealistic by Biochemical Evidence
    http://cn.cross.tv/91187

  12. 12
    Acartia_bogart says:

    Ba77

    “There is nothing of significance that we can show that can be had in a gradualist way. It’s a mirage. None of it happens that way.”

    Marfans, Tay Sachs, fragile X and numerous other heritable diseases are caused by a gradualist process. I would call them significant.

    On a side note, how does ID explain the numerous heritable genetic diseases that do not show their nasty little heads until after the person has reproduced and passed along the suffering to his/her offspring. Sounds like one cruel intelligence.

  13. 13
    Joe says:

    Darwinian evolution is about random VARIATION- Darwin didn’t know about mutations. That means Darwinian evolution is OK with HGT as that would be a random variation to Darwinian evolutionists.

    Acartia_bogart:

    On a side note, how does ID explain the numerous heritable genetic diseases that do not show their nasty little heads until after the person has reproduced and passed along the suffering to his/her offspring.

    Darwinian evolution. 😉

  14. 14
    StephenA says:

    On a side note, how does ID explain the numerous heritable genetic diseases that do not show their nasty little heads until after the person has reproduced and passed along the suffering to his/her offspring. Sounds like one cruel intelligence.

    So? That’s only an argument against a benevolent designer. ID doesn’t say whether the designer actually cares about our wellbeing. You have to add extra evidence to find the answer to that.

    We must follow the evidence where it leads. Even if it leads us to believe life was caused by the designs of lovcraftian elder gods.

  15. 15
    Acartia_bogart says:

    StephenA: “We must follow the evidence where it leads. Even if it leads us to believe life was caused by the designs of lovcraftian elder gods.”

    The evil part of my mind would love to see the reaction of the bulk of IDists if it were proven the ID was correct and that the designer was a cruel vindictive little A-hole. Do you really think that they would “follow the evidence where it leads”?

  16. 16
    Joe says:

    Acartia_bogart- If the evidence says the designer was/ is cruel and vindictive, so be it. However the more simple explanation is entropy- ie Darwinian evolution wreaking havoc on a once good design.

    That is what Darwinian is very good at- wreaking havoc.

  17. 17
    ppolish says:

    Yes, a_b, it would he tough on Theists if it turned out Dawkins was the Designer.

    But c’mon, Convergent Evolution is directed, Epigenetics is not random, and HGT isn’t inherited.

    But at least you have your beaks. You’ll always have your beaks. Can’t take that away.

  18. 18
    Acartia_bogart says:

    Joe:

    “Acartia_bogart- If the evidence says the designer was/ is cruel and vindictive, so be it. However the more simple explanation is entropy- ie Darwinian evolution wreaking havoc on a once good design.”

    I love it. What is good about the “designer” (aka, god) is fine with the IDists. What is bad can be blamed on Darwin. How convenient. Heads you win, tails I lose. I believe that has been my argument against ID from day one. Thank you, Joe, for articulating it so well.

  19. 19
    ppolish says:

    a_b, in regards to “designer was a cruel vindictive little A-hole”. Is that your take on the Old Testament? That is a question for Theology, not UD.

  20. 20
    bornagain77 says:

    Acartia_bogart, in case you didn’t notice, when you cited the fact that Darwinian processes are excellent at breaking things, you in fact cited powerful SCIENTIFIC evidence AGAINST Darwinian evolution. You DID NOT cite scientific evidence FOR Darwinian evolution. In fact Behe has written a paper on just how excellent Darwinian processes are at breaking things:

    “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain – Michael Behe – December 2010
    Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain.
    http://behe.uncommondescent.co.....evolution/

    Michael Behe talks about the preceding paper on this podcast:

    Michael Behe: Challenging Darwin, One Peer-Reviewed Paper at a Time – December 2010
    http://intelligentdesign.podom.....3_46-08_00

    The way you framed your argument is a theistic argument not a scientific argument (just like Darwin did in Origin). But why should I care if your theology is all screwed up? I only care if your science pans out!

    In case you are interested, your THEISTIC argument that you have used to try to make your case for Darwinism is properly called the ‘argument from evil’. And that argument is a self refuting argument since in order for evil to exist there must be some ultimate transcendent standard of Good that has been departed from in order for evil to exist in the first place.

  21. 21
    PaV says:

    wd400:

    I don’t know how the the “information” in a gene differs when it passed down a tree or ‘jumps’ across branches i that tree.

    It’s not ‘different,’ but the origin of this information is left unexplained.

  22. 22
    PaV says:

    BA77:

    No, it’s not the “argument from evil”; it’s the “God-of-the-goofs” argument. 😉

  23. 23
    Acartia_bogart says:

    BA77,

    Are you capable of disputing anything using your own thought processes or do you have to rely on Behe and his ilk?

    Please, use your own words, without numerous links to questionable papers. A brain is a terrible thing to waste.

    Just once, I would love to hear you defend a position with your own words. Not Behe’s, or Dumbski’s.

  24. 24
    wd400 says:

    PaV,

    Well, then we have got no further in trying to understand News’ claim:

    Anything HGT does, Darwinian evolution (natural selection acting on random mutation) did not do

    Anyone?

  25. 25
    bornagain77 says:

    AB, In science it is the evidence which has final say. Therefore, since supposedly we are dealing with science and not theology, then I will cite the evidence as many times as I think necessary to defend my position.

    Romans 1:20

  26. 26
    bornagain77 says:

    wd400, it not that we don’t understand, it is that you refuse to understand!

  27. 27
    wd400 says:

    Well, try me. In plain English and without an explosion of links, why is that quoted sentence true?

  28. 28
    Mung says:

    wd400:

    Well, try me. In plain English and without an explosion of links, why is that quoted sentence true?

    That quoted sentence (presumably):

    Anything HGT does, Darwinian evolution (natural selection acting on random mutation) did not do

    That’s true by definition. What’s your problem?

  29. 29
    bornagain77 says:

    “the origin of this information is left unexplained.”
    – PaV

    was that not plain enough for ya?

    i.e. Having highly sophisticated systems sharing information between species is certainly not to be presupposed as ‘random’ Darwinian evolution (just as I don’t presuppose file sharing on computers to be random). And certainly does not explain the origination of information! Yet Darwinists (dishonestly) use this highly sophisticated sharing of information as if it were evidence for ‘random’ Darwinian evolution, all the while the central question of how is the information originating remains completely ignored by Darwinists:,

    Life Is Designed to Fight Darwinism – September 26, 2012
    Excerpt: As expected, the pro-Darwin press release speaks of “evolutionary tricks” and “instant evolution,” but a close reading shows a designed mechanism for surviving under stress:

    “Bacteria may be simple creatures, but unlike “higher” organisms they have a neat evolutionary trick. When the going gets tough, they can simply pick up and incorporate a loose bit of genetic material from their environment. It’s instant evolution, no time-consuming mutations required. This process, known as horizontal gene transfer, is an important reason why nasty bacteria like pneumococci are often able to evade immune system attacks and antibiotic drugs.”

    Needless to say, “evolution” without “time-consuming mutations” is not the neo-Darwinian way. By picking up existing genetic information from the environment through horizontal gene transfer, the bacteria give evidence of design for surviving storms of misfortune:
    http://www.evolutionnews.org/2.....64501.html

    Life is physics – Nigel Goldenfeld and Carl Woese – November 2010
    Excerpt: There is also compelling evidence that not only may mutations be non-random but horizontal gene transfer too need not be random. Enterococcus faecalis, a gut dwelling bacterium, can be resistant to certain antibiotics if it contains the plasmid (an extrachromosmal loop of DNA) pCF10. This plasmid can be horizontally transferred from a donor with the plasmid to a recipient initially without it, through the process of conjugation (bacterial sex). The remarkable feature of this organism, however, is that the transfer is controlled by and initiated by signals sent from the recipient.
    http://arxiv.org/PS_cache/arxi.....4125v1.pdf

    Supplemental note on ‘information sharing’. It is found that cells communicate with biophotonic emissions (i.e. biological laser light)

    Cellular Communication through Light
    Excerpt: Information transfer is a life principle. On a cellular level we generally assume that molecules are carriers of information, yet there is evidence for non-molecular information transfer due to endogenous coherent light. This light is ultra-weak, is emitted by many organisms, including humans and is conventionally described as biophoton emission.
    http://www.plosone.org/article.....ne.0005086

  30. 30
    Joe says:

    Acartia_bogart:

    What is good about the “designer” (aka, god) is fine with the IDists. What is bad can be blamed on Darwin.

    Not Darwin- random mutations. And we have evidence for that in our everyday lives. Go ahead start randomly messing with the electronics of your TV or computer and tell us what happens. Better yet have a child do it so that you know he/ she doesn’t have a clue as to what they are doing.

  31. 31
    Joe says:

    Here’s another one- open your doors and windows during a hurricane and then observe your house when it is over. Next have a professional cleaning crew come in and clean up. Note the difference.

  32. 32
    Acartia_bogart says:

    Joe,

    Does that mean that we also give credit to the designer for inherited diseases?

  33. 33
    Joe says:

    Acartia_bogart- why would it mean that? Doesn’t Darwinian evolution include inheritance? Why, yes, it does.

  34. 34
    Acartia_bogart says:

    Joe:

    Acartia_bogart- why would it mean that? Doesn’t Darwinian evolution include inheritance? Why, yes, it does.

    Hence my argument that ID takes credit for all things that are good and lays all things that are bad on evolution. If ID is correct then the designer must also be responsible for heritable diseases like Huntingtons, haemophilia, Marfans, Tay Sachs, colour blindness, sickle cell, etc.

  35. 35
    wd400 says:

    So that’s a “No” BA, to any of answering the question (why are HGT and “Darwinism” mutually exclussive), using your own words or resisting the link bomb.

    Noted.

  36. 36
    bornagain77 says:

    wd400, since Darwinists refuse to accept anything that might falsify Darwinism, then NOTHING can be ‘mutually exclusive’ to Darwinism (at least in their undisciplined imagination). Even ‘genetic drift’, your favorite smoke and mirrors shell game here on UD, by any reasonable measure, should have dealt a death blow to Darwinism. But, as Berlinski said of the smoke and mirrors of ‘genetic drift’, it is just par for the course for the pseudo-science that is neo-Darwinism:

    Majestic Ascent: Berlinski on Darwin on Trial – David Berlinski – November 2011
    Excerpt: The publication in 1983 of Motoo Kimura’s The Neutral Theory of Molecular Evolution consolidated ideas that Kimura had introduced in the late 1960s. On the molecular level, evolution is entirely stochastic, and if it proceeds at all, it proceeds by drift along a leaves-and-current model. Kimura’s theories left the emergence of complex biological structures an enigma, but they played an important role in the local economy of belief. They allowed biologists to affirm that they welcomed responsible criticism. “A critique of neo-Darwinism,” the Dutch biologist Gert Korthof boasted, “can be incorporated into neo-Darwinism if there is evidence and a good theory, which contributes to the progress of science.”
    By this standard, if the Archangel Gabriel were to accept personal responsibility for the Cambrian explosion, his views would be widely described as neo-Darwinian.
    http://www.evolutionnews.org/2.....53171.html

    ===============

    Active Information in Metabiology – Winston Ewert, William A. Dembski, Robert J. Marks II – 2013
    Except page 9: Chaitin states [3], “For many years I have thought that it is a mathematical scandal that we do not have proof that Darwinian evolution works.” In fact, mathematics has consistently demonstrated that undirected Darwinian evolution does not work.
    http://bio-complexity.org/ojs/.....O-C.2013.4

    Dr. David Berlinski: Head Scratching Mathematicians – video
    http://www.youtube.com/watch?v=hEDYr_fgcP8

    quote from preceding video:

    “John Von Neumann, one of the great mathematicians of the twentieth century, just laughed at Darwinian theory, he hooted at it!”
    Dr. David Berlinski

  37. 37
    Acartia_bogart says:

    BA77:

    wd400, since Darwinists refuse to accept anything that might falsify Darwinism, then NOTHING can be ‘mutually exclusive’ to Darwinism (at least in their undisciplined imagination). Even ‘genetic drift’, your favorite smoke and mirrors shell game here on UD, by any reasonable measure, should have dealt a death blow to Darwinism.

    Why would drift deal a death blow to evolutionary theory? When drift was proposed and extensive evidence supported it, the theory was modified accordingly. That is how science works. Natural selection is still a big part of the theory but we now know that it is not the only way in which traits can become fixed in a population.

    The question I have is, why do creationsists (oops, I mean IDists) continually use the term Darwinism to describe modern evolutionary theory? There are very few biologists today who think that Darwin’s theory explains everything about evolution. How could it? He proposed in over a century ago without any knowledge of genetics and how inheritance works.

  38. 38
    bornagain77 says:

    The ‘modern’ version of Darwin’s theory, the modern synthesis, is false:

    http://www.uncommondescent.com.....ent-502873

    But hey AB, don’t be too sad, you can always take comfort in the fact that quantum mechanics verifies materialism,,,

    http://www.uncommondescent.com.....ent-506157

    OOOPS, scratch that! 🙂

  39. 39
    ppolish says:

    a_b, Wallace recognized Design. And the Creator. Darwin recognized Creator, but downplayed Design. 1850 era ignorance is no defense for Darwin.

  40. 40
    bornagain77 says:

    AB, as to Darwinists refusing to accept anything that might falsify their theory, I remember this exchange with you, an exchange in which you refused to honor the criteria that you yourself laid out for falsification:

    http://www.uncommondescent.com.....ent-502351

  41. 41
    Acartia_bogart says:

    ppolish:

    Wallace recognized Design. And the Creator. Darwin recognized Creator, but downplayed Design. 1850 era ignorance is no defense for Darwin.

    What does this have to do with anything. Both Wallace and Darwin came from an era when belief in god was universal (at least in the western world). And Darwin actually studied to be a pastor.

  42. 42
    ppolish says:

    Belief in God has never been “Universal”. Pre Socratic Atheism all through to today. There were Atheists in Newton’s time. In Galileo’s time. Rarely came up with big scientific breakthroughs, but Atheists always around.

  43. 43
    Acartia_bogart says:

    BA77, sorry, but you can’t state that evolution is falsified because I mentioned something in error (i.e., vertebrate in early cambrian). My intent was simply to state that finding fossils of a more recently evolved organism in a much older geologic stratum (strata?) would falsify the theory.

    With regard to the genetic variation, I was referring to variation within a population, not over time. But ignoring that picking of nits, are you seriously saying that there was no genetic variation between modern and ancient bacteria? I would find that highly unlikely given the variation we see within modern populations of bacteria; even within cultures grown from a single cell.

    Yes, some of the assumptions of the modern synthesis (which isn’t exactly modern any more) have been demonstrated to be wrong (e.g., DNA can only be passed from parent to offspring). But all this does is mean that the source of all genetic variation within a population (an absolute requirement for evolution) is not solely the result of mutations within the population (although, mutations are still the ultimate source of variation). But once these new bits of DNA find there way into the population, the phenotypic expression of this DNA (if there is any) can be acted on by natural selection.

    But the movement of DNA between organisms has been known for a long time in bacteria and plants. Until fairly recently, it was thought that the only natural means of incorporating foreign DNA into the genome of “higher” organisms was through viruses. I have not followed the research on other means of DNA swapping, but it wouldn’t surprise me if it was found to be more common than currently thought. But, again, all this will result in is a tweaking of the evolutionary theory to account for this. In fact, I would think that the IDists would not welcome this type of news as it provides a naturalistic mechanism for more rapid evolution of new traits within a population.

  44. 44
    PaV says:

    wd400:

    So that’s a “No” BA, to any of answering the question (why are HGT and “Darwinism” mutually exclussive), using your own words or resisting the link bomb.

    When, in response to something I posted, you made the distinction between “mutationism” and “Darwinism,” that you view “Darwinism” in some expanded notion, involving all sorts of cellular and genomic mechanisms, and, of course, involving the invaluable neutral drift.

    That’s all fine and good.
    But, let me make two points:
    (1) Behe’s work, his computer simulations and his Edge of Evolution point out to us that with all these “Darwinian” mechanisms at work–this expanded view of yours—-microevolution (let alone, macroevolution) is seriously limited.

    All your theoretical protestations to the one side—we don’t see “evolution” (Darwinism) doing much when ‘push comes to shove.’

    (2) The whole focal point of ID revolves around the notion of “information.” That’s what were most keenly interested in. ( )*** And to say that the ‘information content’ of some stretch of genomic sequences moves from one organism to another is, for us, of very little interest, and of very little consequence.

    And, if truth be known, HGT is all about “adaptation.” It’s not about “macroevolution.”

    I don’t know how to better put it to you.

    This is hard to do because you have this quirk where you insist that everything be phrased in a certain way and be given in its proper context. But, of course, this “phrasing” in a certain way, and this “proper context,” means, of course, just the way that Darwinists would talk about it.

    I’m afraid that won’t happen here. We think outside of the box. We’re not constrained by dogma.

    (***) [Guess what, all those charges of “Creationsim” and “creationism” are no more than drivel. We’re looking here at what organisms can do in a very scientific way. It’s not about “proving God exists.” That is best left to philosophers and theologians. But, of course, if Darwinists were to accept this, then they wouldn’t have their strawman argument to fall back on. That, I’m afraid, is how things really are.]

  45. 45
    PaV says:

    First sentence correction:

    After this section, ” . . . between “mutationism” and “Darwinism, . . . ,” it should read:

    “it became clear . . . ”

    Sorry.

  46. 46
    ppolish says:

    When the debate becomes Naturally Guided Design versus Supernaturally Guided Design, the Science will make more sense. Make better sense.

    The “Appearance of Design” gang are holding back the good Science. The truer Science.

  47. 47
    wd400 says:

    I have no idea what this has to do with the idea that
    Anything HGT does, Darwinian evolution (natural selection acting on random mutation) did not do

    It’s it really this difficult for IDists to admit one of their fellow-travellers is confused?

  48. 48
    wd400 says:

    Just for the sake of absolute clearness. HGT describes the path by which I given gene ended up in a genome. It’s doesn’t preclude that the so-called “information” in the gene arose by natural selection, or that the gene’s being fixed in a population is the result of natural selection (the gene, once itside a genome being just another variant to poentially be selected for or against).

  49. 49
    Acartia_bogart says:

    “When the debate becomes Naturally Guided Design versus Supernaturally Guided Design, the Science will make more sense. Make better sense.

    What? Naturally guided design? What the f— is that? If it’s natural, it’s not designed.

  50. 50
    bornagain77 says:

    Acartia_bogart, nice of you8 to move the goal posts when shown vertebrates are in the early Cambrian. Typical Darwinian response and further proof that Darwinism is unfalsifiable. I could list many more instances where Darwinian predictions have been proven false. But what is the use, you will just ignore them and cling to your atheistic belief because that is what you want to believe no matter what the evidence says to the contrary.

    I’m certainly not ‘picking nits’ to say that modern bacteria have not varied from ancient bacteria.

    The Paradox of the “Ancient” (250 Million Year Old) Bacterium Which Contains “Modern” Protein-Coding Genes:
    “Almost without exception, bacteria isolated from ancient material have proven to closely resemble modern bacteria at both morphological and molecular levels.” Heather Maughan*, C. William Birky Jr., Wayne L. Nicholson, William D. Rosenzweig§ and Russell H. Vreeland ;
    http://mbe.oxfordjournals.org/...../19/9/1637

    “Raul J. Cano and Monica K. Borucki discovered the bacteria preserved within the abdomens of insects encased in pieces of amber. In the last 4 years, they have revived more than 1,000 types of bacteria and microorganisms — some dating back as far as 135 million years ago, during the age of the dinosaurs.,,, In October 2000, another research group used many of the techniques developed by Cano’s lab to revive 250-million-year-old bacteria from spores trapped in salt crystals. With this additional evidence, it now seems that the “impossible” is true.”
    http://www.physicsforums.com/s.....p?t=281961

    Revival and identification of bacterial spores in 25- to 40-million-year-old Dominican amber
    Dr. Cano and his former graduate student Dr. Monica K. Borucki said that they had found slight but significant differences between the DNA of the ancient, 25-40 million year old amber-sealed Bacillus sphaericus and that of its modern counterpart,
    (thus ruling out that it is a modern contaminant, yet at the same time confounding materialists, since the change is not nearly as great as evolution’s ‘genetic drift’ theory requires.) http://www.sciencemag.org/cgi/...../5213/1060

    Static evolution: is pond scum the same now as billions of years ago?
    Excerpt: But what intrigues (paleo-biologist) J. William Schopf most is lack of change. Schopf was struck 30 years ago by the apparent similarities between some 1-billion-year-old fossils of blue-green bacteria and their modern microbial counterparts. “They surprisingly looked exactly like modern species,” Schopf recalls. Now, after comparing data from throughout the world, Schopf and others have concluded that modern pond scum differs little from the ancient blue-greens. “This similarity in morphology is widespread among fossils of [varying] times,” says Schopf. As evidence, he cites the 3,000 such fossils found;
    http://www.thefreelibrary.com/.....a014909330

    Geobiologist Noffke Reports Signs of Life that Are 3.48 Billion Years Old – 11/11/13
    Excerpt: the mats woven of tiny microbes we see today covering tidal flats were also present as life was beginning on Earth. The mats, which are colonies of cyanobacteria, can cause unusual textures and formations in the sand beneath them. Noffke has identified 17 main groups of such textures caused by present-day microbial mats, and has found corresponding structures in geological formations dating back through the ages.
    http://www.odu.edu/about/odu-p...../topstory1

    Scientists find signs of life in Australia dating back 3.48 billion years – Thu November 14, 2013
    Excerpt: “We conclude that the MISS in the Dresser Formation record a complex microbial ecosystem, hitherto unknown, and represent one of the most ancient signs of life on Earth.”… “this MISS displays the same associations that are known from modern as well as fossil” finds. The MISS also shows microbes that act like “modern cyanobacteria,”
    http://www.cnn.com/2013/11/13/.....ient-life/

    You claim that variation of modern bacteria proves that bacteria have far more plasticity than what we witness for ancient bacteria, yet:

    Scant search for the Maker
    Excerpt: But where is the experimental evidence? None exists in the literature claiming that one species has been shown to evolve into another. Bacteria, the simplest form of independent life, are ideal for this kind of study, with generation times of 20 to 30 minutes, and populations achieved after 18 hours. But throughout 150 years of the science of bacteriology, there is no evidence that one species of bacteria has changed into another, in spite of the fact that populations have been exposed to potent chemical and physical mutagens and that, uniquely, bacteria possess extrachromosomal, transmissible plasmids. Since there is no evidence for species changes between the simplest forms of unicellular life, it is not surprising that there is no evidence for evolution from prokaryotic to eukaryotic cells, let alone throughout the whole array of higher multicellular organisms. – Alan H. Linton – emeritus professor of bacteriology, University of Bristol.
    http://www.timeshighereducatio.....ode=159282

    The modern synthesis is falsified mainly because it is now shown that,,,

    “The genome is an ‘organ of the cell’, not its dictator”
    – Denis Nobel – President of the International Union of Physiological Sciences

    ,,, thus directly contradicting the reductive materialistic premise that the modern synthesis is built upon.

    You have no evidence that ‘random’ mutations can generate information. In fact all the evidence we have (Behe) tells us that random mutations degrade information!

    Natural selection, to the extent that it does anything, preserves and reduces information. Natural selection is a eliminative force, not a generative force!

    HGT is very sophisticated information sharing. Information sharing to cope with adaptation to differing environments (and perhaps a few other functions). It is an insult to intelligence to insist they are just randomly swapping information.

    There is no evidence that HGT can solve the insurmountable information problem for Darwinists. For Darwinists to co-opt HGT without addressing the primary question of ‘how does the information originate?’ is disingenuous to put it mildly.

    supplemental note: The ‘simplest’ life on earth, which can’t even be seen with the naked eye is far more complex than Darwin could have dared imagine:

    To Model the Simplest Microbe in the World, You Need 128 Computers – July 2012
    Excerpt: (the parasitic) Mycoplasma genitalium has one of the smallest genomes of any free-living organism in the world, clocking in at a mere 525 genes. That’s a fraction of the size of even another bacterium like E. coli, which has 4,288 genes.,,,
    The bioengineers, led by Stanford’s Markus Covert, succeeded in modeling the bacterium, and published their work last week in the journal Cell. What’s fascinating is how much horsepower they needed to partially simulate this simple organism. It took a cluster of 128 computers running for 9 to 10 hours to actually generate the data on the 25 categories of molecules that are involved in the cell’s lifecycle processes.,,,
    ,,the depth and breadth of cellular complexity has turned out to be nearly unbelievable, and difficult to manage, even given Moore’s Law. The M. genitalium model required 28 subsystems to be individually modeled and integrated, and many critics of the work have been complaining on Twitter that’s only a fraction of what will eventually be required to consider the simulation realistic.,,,
    http://www.theatlantic.com/tec.....rs/260198/

    Music and verse:

    Mandissa – Overcomer
    http://myktis.com/songs/overcomer/

    Isaiah 6:3
    And they were calling to one another: “Holy, holy, holy is the LORD Almighty; the whole earth is full of his glory.”

  51. 51
    ppolish says:

    a_b, if you want a glimpse of the future debate, read Atheist
    philosopher Thomas Nagel’s new book, “Mind and Cosmos: Why the Materialist Neo-Darwinian Conception of Nature Is Almost Certainly False”.

    Natural Design vs “Unnatural” Design is the future debate. Materialist view is simple talking. Won’t be taken seriously sorry.

    Spoiler alert, Mind & Cosmos is a difficult read IMO. It’s no “Darwin’s Doubt”. Stephen Meyers book is a page turner:)

  52. 52
    Acartia_bogart says:

    Ba77:
    “Acartia_bogart, nice of you8 to move the goal posts when shown vertebrates are in the early Cambrian. “
    It is nice to see that when someone admits an error, you ascribe it to something else. I envy the fact that you are infallible. You must be proud (and insufferable).

    “I’m certainly not ‘picking nits’ to say that modern bacteria have not varied from ancient bacteria.”
    Reading comprehension was never your strong suit, was it? I said that I was the one who was picking nits.

    “You claim that variation of modern bacteria proves that bacteria have far more plasticity than what we witness for ancient bacteria, yet:”
    When did I say this? I simply said that the lack of genetic variation in populations would falsify evolution. None of your references suggested that genetic variation within any population, modern or ancient, was not present.

    “The modern synthesis is falsified mainly because it is now shown that,,,
    “The genome is an ‘organ of the cell’, not its dictator”
    – Denis Nobel – President of the International Union of Physiological Sciences”

    It is “NOW” shown? Where have you been for the last 40+ years? It has been well understood for at least half a century that the expression of many genes, and the impact on the whole organism, is greatly affected by environment, both internal and external. I was taught evolutionary theory in the 70s and this is what was taught to me. I remember specifically being told that the genome is not a blueprint, as you imply evolutionary theory states. Hell, anyone who has identical twins, as I do, knows this first hand.

  53. 53
    bornagain77 says:

    Acartia_bogart, you claimed that vertebrates in the early Cambrian would falsify evolution, when shown vertebrates were in the early Cambrian, you suddenly said you made an error. How convenient! That is moving the goal posts whether you admit it or not. How about becoming even more honest and admit nothing will ever falsify Darwinism in your mind because of your philosophical (atheistic) bias? 🙂 Now that would REALLY be an honest admittance of an error!

    ,,,You are shown evidence that bacteria have been the basically the same, both morphologically and molecularly for as far back as we can measure (hundreds of millions of years), and you do not consider that a problem for Darwinism. If you worked for me I would fire you on the spot for stating such an insane statement!

    Neo-Darwinism, the modern synthesis, (which wd400 defends tooth and nail) is dependent on the central dogma being true. Thus finding “The genome is an ‘organ of the cell’, not its dictator” is a direct contradiction to the primary tenet of the modern synthesis. Since you readily admit this view is false, do you now want to ditch wd400 and his defense of the modern synthesis, and leave him on his own, and now join James Shapiro in the ‘natural genetic engineering’ camp? Or perhaps Kaufman in the self organization camp?

    How life changes itself: the Read-Write (RW) genome. – 2013
    Excerpt: Research dating back to the 1930s has shown that genetic change is the result of cell-mediated processes, not simply accidents or damage to the DNA. This cell-active view of genome change applies to all scales of DNA sequence variation, from point mutations to large-scale genome rearrangements and whole genome duplications (WGDs). This conceptual change to active cell inscriptions controlling RW genome functions has profound implications for all areas of the life sciences.
    http://www.ncbi.nlm.nih.gov/pubmed/23876611
    Revisiting the Central Dogma in the 21st Century – James A. Shapiro – 2009
    Excerpt (Page 12): Underlying the central dogma and conventional views of genome evolution was the idea that the genome is a stable structure that changes rarely and accidentally by chemical fluctuations (106) or replication errors. This view has had to change with the realization that maintenance of genome stability is an active cellular function and the discovery of numerous dedicated biochemical systems for restructuring DNA molecules.(107–110) Genetic change is almost always the result of cellular action on the genome. These natural processes are analogous to human genetic engineering,,, (Page 14) Genome change arises as a consequence of natural genetic engineering, not from accidents. Replication errors and DNA damage are subject to cell surveillance and correction. When DNA damage correction does produce novel genetic structures, natural genetic engineering functions, such as mutator polymerases and nonhomologous end-joining complexes, are involved. Realizing that DNA change is a biochemical process means that it is subject to regulation like other cellular activities. Thus, we expect to see genome change occurring in response to different stimuli (Table 1) and operating nonrandomly throughout the genome, guided by various types of intermolecular contacts (Table 1 of Ref. 112). http://shapiro.bsd.uchicago.ed.....0Dogma.pdf

    Also of interest from the preceding paper, on page 22, is a simplified list of the ‘epigentic’ information flow in the cell that directly contradicts what was expected from the central dogma (Genetic Reductionism/modern synthesis model) of neo-Darwinism.

    etc.. etc..

  54. 54
    Mung says:

    wd400:

    It’s it really this difficult for IDists to admit one of their fellow-travellers is confused?

    No. In fact, Salvador Cardoza, who at least claims to be an ID’ist, regularly deletes my posts from his threads.

    But given that you never responded to my post, it’s not at all clear to me that you aren’t the one who is confused.

    Since you seem to have missed it:

    Anything HGT does, Darwinian evolution (natural selection acting on random mutation) did not do

    That’s true by definition. What’s your problem?

  55. 55
    Mung says:

    Acartia_bogart:

    Hence my argument that ID takes credit for all things that are good and lays all things that are bad on evolution. If ID is correct then the designer must also be responsible for heritable diseases like Huntingtons, haemophilia, Marfans, Tay Sachs, colour blindness, sickle cell, etc.

    This is just moronic. ID admits that arguments such as yours can be bad and yet still be the result of intelligent design.

    Of course, since by your own admission your posts cannot reliably be distinguished from nonsensical ramblings, I should certainly not assume that anything I write will be understood by you. But you’re not the only one who reads these posts.

  56. 56
    wd400 says:

    Mung,I read your comment. Twice now. You are mistaken.

  57. 57
    bornagain77 says:

    wd400, I’ve read Mung’s comments and they are not mistaken. I’ve read your comments and you are not only mistaken but intellectually dishonest!

    Moreover, only one person on this thread is getting paid to believe in Darwinism, and it is not Mung!

    Lynn Margulis Criticizes Neo-Darwinism in Discover Magazine (Updated) – Casey Luskin April 12, 2011
    Excerpt: Population geneticist Richard Lewontin gave a talk here at UMass Amherst about six years ago, and he mathemetized all of it–changes in the population, random mutation, sexual selection, cost and benefit. At the end of his talk he said, “You know, we’ve tried to test these ideas in the field and the lab, and there are really no measurements that match the quantities I’ve told you about.” This just appalled me. So I said, “Richard Lewontin, you are a great lecturer to have the courage to say it’s gotten you nowhere. But then why do you continue to do this work?” And he looked around and said, “It’s the only thing I know how to do, and if I don’t do it I won’t get grant money.” –
    Lynn Margulis – biologist
    http://www.evolutionnews.org/2.....45691.html

  58. 58
    Dr JDD says:

    (1) HGT event transfers existing DNA from one organism to another

    (2) The recipient of the DNA may have a new function from this act of HGT

    (3) HGT is only concerned with the transfer of pre-existing DNA

    (4) As a result, in this context new functionality received by this recipient organism is not occurring through mechanisms of gradual change through random mutation of an organism’s existing DNA to produce, through selection, new function.

    (5) Therefore, HGT does not explain addition of new information, but rather borrowed information

    (6) Therefore, this does not fit under Darwinian evolution in the strictest sense as it is not explaining how that functional information arose from non-functionality. It merely explains a transfer.

    Now this does not mean it is not a mechanism that evolution can use, but we are still left with the problem of how the information rose in the first place, which is the main cause and driving force behind what ID asks, hence the criticism of HGT being given so much weight as a mechanism to explain some of evolution (and failing to address the bigger question).

    For example, if you had 2 different computers and they were running many different programs, and you wanted to know who wrote the code for each program on the individual computers. If you found identical programs on each, and knew that one computer was older than the other, you would not answer the question “who wrote this program” by saying “it was transferred over from computer A to computer B.” That is how it got onto that computer, but not who programmed it or how it was programmed.

    As the context of this forum and what we are asking and additionally, what Darwinism seeks to ask (how did functionality arise), it seems fair to say that HGT does not answer that in the slightest. I do not hence understand why there is such “confusion” over this one statement.

    I.e. if a new function in an organism came from borrowed information from another organism then you cannot attribute that specific event to Darwinian mechanisms. You may argue that the original gene in the donating organisms did arise through Darwinian mechanisms but aside from that being an assumption, it is irrelevent when talking about the context of how that organism gained this new function if HGT was involved. It was HGT, not Darwinian evolution.

  59. 59
    PaV says:

    wd400:

    Just for the sake of absolute clearness. HGT describes the path by which a given gene ended up in a genome. It’s doesn’t preclude that the so-called “information” in the gene arose by natural selection, or that the gene’s being fixed in a population is the result of natural selection (the gene, once inside a genome being just another variant to potentially be selected for or against).

    As a favor to us, (I already cleaned it up a bit) when you’re in a hurry, can you check your spelling and grammar errors. Sometimes it’s a bit much. And it looks like you’re hurried. But, . . .

    Having said this,…………….

    You don’t seem to realize that what you suggest is an “assumption” made by Darwinists, yet to be proven.

    IOW, where did the information come from?

    The usual “Get-Out-Of-Jail” card for this question is to simply say: “Oh, but that’s an OOL question.” This, of course, is equivalent to saying: “Well, the question of how “dogs” came about is unknown; but, what we do know is that these ‘breeds’ are the result of artificial selection.”

    This, to me, frames quite well where both sides stand. We want to know where the ‘dogs’ came from. For ‘breeds,’ we have evidence; for the “origin of dogs,” we do not.

  60. 60
    wd400 says:

    OK, I’ll try and catch the typos if y’all try and catch the meaning of what I say.

    Once more, from the top. News thinks that HGT and “Darwinism” are competing explanations on some level “If HGT happened, Darwinism didn’t; if HGT explains some event Darwinism’s domain is reduced). As both PaV and JDD say (while apparently defending News?) this is not the case. To take from JDD, HGT and doesn’t answer questions about the origin of “information” ‘in the slightest’.

    It would be silly to say “that which inheritance explains Darwinism doesn’t”, why isn’t just as silly to say the same for HGT?

  61. 61
    Evolve says:

    wd400,

    Creationists will jump on to anything that breaks the pattern of vertical descent because it provides them a chance to invoke their magician-in-the-sky. So you’ll see them making a lot of noise about HGT, orphan genes and similar phenomena.

    Creationists,
    If HGT happens with one or a few genes, then there are a lot of other genes that are acquired by normal vertical descent. So family trees and inter-species relationships can still be constructed and deciphered using those vertically transmitted genes.
    Phenomena such as HGT, de novo gene synthesis leading to the formation of orphan genes etc are fully expected in a natural setting. They don’t support the presence of your imaginary designer. Now get over it.

  62. 62
    bornagain77 says:

    Evolve, instead of accusing Theists of bad motives, you are welcome to present evidence that information can be generated by unguided material processes and settle the issue once and for all!

    Three subsets of sequence complexity and their relevance to biopolymeric information – Abel, Trevors
    Excerpt: Three qualitative kinds of sequence complexity exist: random (RSC), ordered (OSC), and functional (FSC).,,, Shannon information theory measures the relative degrees of RSC and OSC. Shannon information theory cannot measure FSC. FSC is invariably associated with all forms of complex biofunction, including biochemical pathways, cycles, positive and negative feedback regulation, and homeostatic metabolism. The algorithmic programming of FSC, not merely its aperiodicity, accounts for biological organization. No empirical evidence exists of either RSC of OSC ever having produced a single instance of sophisticated biological organization. Organization invariably manifests FSC rather than successive random events (RSC) or low-informational self-ordering phenomena (OSC).,,,

    Testable hypotheses about FSC

    What testable empirical hypotheses can we make about FSC that might allow us to identify when FSC exists? In any of the following null hypotheses [137], demonstrating a single exception would allow falsification. We invite assistance in the falsification of any of the following null hypotheses:

    Null hypothesis #1
    Stochastic ensembles of physical units cannot program algorithmic/cybernetic function.

    Null hypothesis #2
    Dynamically-ordered sequences of individual physical units (physicality patterned by natural law causation) cannot program algorithmic/cybernetic function.

    Null hypothesis #3
    Statistically weighted means (e.g., increased availability of certain units in the polymerization environment) giving rise to patterned (compressible) sequences of units cannot program algorithmic/cybernetic function.

    Null hypothesis #4
    Computationally successful configurable switches cannot be set by chance, necessity, or any combination of the two, even over large periods of time.

    We repeat that a single incident of nontrivial algorithmic programming success achieved without selection for fitness at the decision-node programming level would falsify any of these null hypotheses. This renders each of these hypotheses scientifically testable. We offer the prediction that none of these four hypotheses will be falsified.
    http://www.tbiomed.com/content/2/1/29

  63. 63
    PaV says:

    wd400:

    ID as we know it wouldn’t, in my opinion, even exist as it does today without our having entered the “information age.” (you know, what Al Gore invented)

    Because of computers and computer code—the digital age—we understand that “machine” languages, like human languages, encode “information.”

    When we look at the “genetic code,” we see ‘coded’ language. And it is only natural to understand the genetic code as containing information. Just as consonants and vowels provide the sounds by which we communicate language, sounds which are then translated into written form, so it is with the biological code, except in this case it is not ‘sounds’ but ‘nucleotides.’

    Now language, quite obviously, cannot exist without there being some kind of delimitation of ‘sound’ itself.

    We know that intelligent agents know how to delimit these sounds, and that the whole gambit of human languages ‘delimit’ the spectrum of sounds to form individual languages. When it comes to the genetic code, that which is ‘delimited’ is, as already state, the sequence of nucleotides. The question then is: what is responsible for this delimitation?

    The neo-Darwinian answer is: chance.

    This is not acceptable. Sir Fred Hoyle, an atheist (are you paying attention “Evolve”?) did a simple calculation with cytochrome C and concluded that its having coming into existence by “chance” was completely unlikely and illogical. The alternative to this is “intelligence,” since we know that intelligent beings have brought into existence so many known and living languages.

    So, for the vast majority of IDists, the only concern we have with neo-Darwinian=Darwinian mechanisms is this: can it help provide an explanation for the kind of delimitation that marks the genetic code.

    So, once again, when it comes to HGT, this manner of sharing information has absolutely no means of explaining the ‘origin’ of the information encoded in the section of sequence that is being transferred.

    Do you see what we’re getting at here?

    We’re defending no one. You have, on the other hand, a proclivity of nit-picking every post here at UD. It’s your not so subtle way of saying: “You don’t know what you’re talking about.” You seem to take some sort of morose delectation in this habit.

    I, on the other hand, find it annoying. However, it is always good to have someone around to keep us honest. We need to be challenged—yet, hopefully, also understood.

  64. 64
    wd400 says:

    So, once again, when it comes to HGT, this manner of sharing information has absolutely no means of explaining the ‘origin’ of the information encoded in the section of sequence that is being transferred.

    So, tell News this.

  65. 65
    Acartia_bogart says:

    A mutation can be vertically inherited. A horizontally acquired piece of DNA can be vertically inherited. So how is this a problem for Darwinian evolution? As far as I can see, it simply broadens the source of variation for natural selection to act on. Since one of IDs arguments with evolution is that the mutation rates in a population aren’t sufficient to explain the rates of change, the presence of HGT only weakens this argument because you must now include the mutation rates in groups that are not part of the population. It’s basic math and probability.

  66. 66
    PaV says:

    wd400:

    Isn’t it true that if HGT is more common than thought, then one of the repercussions will be that our confidence in phylogenetic trees is severely undercut?

    How in the world do you know if you’re dealing with a “gene tree” or a “species tree”? How do you trace such things?

  67. 67
    wd400 says:

    This is irrelevant to the claim News made, but, FWIW:

    We already know that HGT is not so common that it “severely undercuts” out confidence in phylogeny in general. In some specific cases (like the root of the tree of life)HGT is common enough that the species tree will probably nevery be reconstructed (thought the gene trees can be). In other groups, like plants and animals HGT is so rare it’s not a major problem.

    You account for differences between gene trees and species trees (including some which are direct prediction of simple pop. gen. models) but including many gene tress in your analysis.

  68. 68
    arlin says:

    Acartia_bogart, the mistake you are making is that you are letting “Darwinian evolution” include anything that involves differential reproduction. This was not Darwin’s position. “Gradualism” can mean many things, but one of the things it meant for Darwin was that the variations used in evolution are “infinitesimal” or “slight” (his words), and that they blend together, so that change is always smooth. He was led to this position because he believed that organisms are so exquisitely adapted that they can’t have evolved by any process that involved abrupt changes, only by a process that involved continuous shifts. Most scientists in Darwin’s time disagreed with this position. Most scientists today disagree with this position.

    In the theory that Darwin called “natural selection”, the struggle for life shapes organisms in response to conditions by shifting a blending mass of infinitesimal variation. When challenged with the idea that his theory was not a theory of evolution, but only a theory addressing the differential survival of whatever “new births” happen to occur, Darwin literally said that this might be a very good theory but it is “not mine”. When challenged famously by Fleeming Jenkin with the idea that evolution could not occur by blending, but was more likely by discrete inheritance of sports, Darwin chose deliberately to stake his theory on blending.

    What makes the Darwinian position unique is that, once you have assumed abundant random infinitesimal variation, then variation merely becomes a “raw material” and external selection is the only true cause at work– the real explanation for everything. But if this Darwinian position is not correct, then one must look at the internal causes of variation to truly understand creativity and directionality in evolution. Darwinians traditionally dismiss such “internalist” thinking as a form of antiscientific mysticism.

    The application of Darwin’s infinitesimalism to DNA and proteins is obvious. Any sequence can change into any other sequence 1 residue at a time. That is the smallest unit of change, thus it is the Darwinian position.

    This position has been falsified a million times over in molecular evolution. We know that non-gradual changes such as gene duplications and lateral gene transfers are important in evolution.

    So, Acartia_bogart, your position is actually not Darwinism. You are a DiNO, a Darwinian-in-Name-Only. You actually do not believe what Darwin believed, and what was accepted by most of his 20th century followers such as Fisher.

  69. 69
    Acartia_bogart says:

    Arlin, I have never claimed to be a Darwinian. In fact if you read my comments on other posts you will note that I have taken exception to the creationist approach of calling all evolutionary biologists Darwinists. As such, my comment here was only referring to HGT and Darwinian evolution (i.e., natural selection). And as such, HGT is totally consistent with Darwinian evolution because he did not know what the source of variation was. In fact, he had not ruled out the inheritance of acquired characteristics.

    And HGT is not inconsistent with modern evolutionary theory because HGT has been known to be common amongst bacteria for many decades now and the theory has been modified to account for it. We now know that it also occurs in multi-celled organisms, but its affects are minuscule as compared to those seen in bacteria. The HGTs that have been seen in “higher” organisms would still be considered “gradual” variations when the entire phenotype is looked at. Unless you are aware of any HGTs resulting in new senses, changed modes of mobility, larger or smaller brains, etc.

    And once established in an organism’s genome, the HGT can be acted upon by natural selection. So, again, how does this cause a problem for either Darwinian evolution or modern evolutionary theory?

  70. 70
    arlin says:

    Sorry if I mischaracterized your position. But once again, you are equating “Darwinian evolution” with any process that involves differential reproduction, and this is a mistake. I realize that this mistake is very common, but that doesn’t make it any more defensible. When someone like Allen Orr is giving a keynote address and presenting a mathematical model based on a process in which a mutation appears and is then accepted or rejected, and he calls this “Darwinian adaptation”, this is also a mistake. Darwin said that the lucky mutations theory of adaptation was “not mine”, and he said this because he did not believe evolution worked in that way.

    Your statement that “HGT is not inconsistent with modern evolutionary theory because HGT has been known to be common . . . ” is also based on a confusion. The fact that a phenomenon is known by evolutionists does not mean that this phenomenon is consistent with theoretical statements made by teh same evolutionists. For instance, every textbook of evolution says that the role of variation in evolution is that it provides “raw materials” for selection. But a laterally transferred gene is not a raw material. It is a fully formed specific sequence, not a pile of atoms. Therefore, the evolutionary theory presented in textbooks is not consistent with HGT.

    Evolutionary biologists need to work out these inconsistencies. I am confident that they can do so, but one of the first steps is get past the stage of unthinking denial.

  71. 71
    arlin says:

    Sorry if I mischaracterized your position. But once again, you are equating “Darwinian evolution” with any process that involves differential reproduction, and this is a mistake. I realize that this mistake is very common, but that doesn’t make it any more defensible. When someone like Allen Orr is giving a keynote address and presenting a mathematical model based on a process in which a mutation appears and is then accepted or rejected, and he calls this “Darwinian adaptation”, this is also a mistake. Darwin said that the lucky mutations theory of adaptation was “not mine”, and he said this because he did not believe evolution worked in that way.

    Your statement that “HGT is not inconsistent with modern evolutionary theory because HGT has been known to be common . . . ” is also based on a categorical error. The fact that a phenomenon is known by evolutionists does not mean that this phenomenon is consistent with theoretical statements made by the same evolutionists. For instance, every textbook of evolution says that the role of variation in evolution is that it provides “raw materials” for selection. But a laterally transferred gene is not a raw material. It is a fully formed specific sequence, not a pile of atoms. Therefore, the evolutionary theory presented in textbooks is not consistent with HGT.

    Evolutionary biologists need to work out these inconsistencies. I am confident that they can do so, but one of the first steps is get past the stage of unthinking denial and wooly thinking that allows words to shift in meaning in whatever way seems to defend the past statements of authorities.

  72. 72
    Acartia_bogart says:

    Arlin:

    But once again, you are equating “Darwinian evolution” with any process that involves differential reproduction, and this is a mistake.

    I must respectfully disagree. Darwin’s original theory was developed with very little knowledge about what mutations were. The mutations that were known at the time were those that resulted in gross, and almost always deleterious, morphological deviations from the norm. That is the context under which he said that the lucky mutation wasn’t his idea. What Darwin also wasn’t aware of is the process by which certain traits/features could become fixed in a population without them having any known adaptive advantage (i.e., drift). Given this context, it is fair to say that Darwinian evolution really is dominated by differential reproduction.

    For instance, every textbook of evolution says that the role of variation in evolution is that it provides “raw materials” for selection. But a laterally transferred gene is not a raw material. It is a fully formed specific sequence, not a pile of atoms. Therefore, the evolutionary theory presented in textbooks is not consistent with HGT.

    Again, I must disagree. Natural selection acts on the expression of the genes, not the DNA itself. If a functional gene is transferred from another species, and it is adaptive, natural selection may act to result in it becoming ubiquitous amongst the population. Conversely, if it is deleterious, it may be eliminated by natural selection.

    So, whether it is a spot mutation that slightly alters a protein, or the transfer of a fully functional gene that codes for a completely new protein (at least for that population), they both result in an increase in variation in that population and, therefore, are raw material that can be acted on by natural selection.

    But your inference about text books being out of date is a valid one, especially in high schools. All text books, by there nature, can only deal with existing information. And given the length of time it takes to write a text book, the information in them is often many years old by the time it is published. This is made worse by the fact that schools are always dealing with budget issues and they often will use the same text book for many years, even if new versions have been published. Unfortunately, given the speed with which science progresses, I can’t see any solution to this.

  73. 73
    arlin says:

    Acartia_bogart, the words “raw materials” cannot be stretched to mean anything. Try googling images for “raw materials”. What do you see? Iron ore, bauxite, sand, wood pulp, etc. These are all raw (not processed), used in bulk, and transformed in the process of manufacturing. Paper does not look like wood pulp. Nails do not look like iron ore. Computer chips do not look like sand.

    Now, let’s pretend this is an SAT test and you are faced with one of those “analogy” questions. True or false: raw materials are to finished products as variation is to evolution.

    When Dobzhansky said that variation was like the raw material entering a factory, he meant it. When the architects of neo-Darwinism said that mutation provided “raw materials”, they meant to say that the role of variation in evolution is like the role of sand in making a sand-castle (or a computer chip). They believed that the shape of the individual grains of sand didn’t matter, because the sand was used in bulk and transformed.

    For an educated person or a scientist from the previous century, the concept of a “material cause” was familiar. Aristotle said that a thing can have many causes at the same time. He used the analogy of a house. The bricks and beams are the material from which the house is made. They are material causes. A craftsman assembles the bricks and beams into a house. The craftsman is often called the “efficient cause”. Usually when scientists are invoking “forces”, they are referring to efficient causes. But there is also a plan or design from which the house is built. That is the “formal cause” that explains why the house has the shape that it does. And ultimately we could say it is the intention of the designer (the real estate developer) that caused the house to be built. That is the “final” or “ultimate” cause. Darwinians refer to selection as an efficient cause, a formal cause, and even as a final cause. They refer to variation only as a material cause.

    However, a laterally transferred gene is not a raw material. It is not raw, but already evolved. It is not used in bulk (we don’t use 1000 laterally transferred genes to make one new gene). It is not transformed by the process of manufacturing (only tweaked). One cannot say fairly that a laterally transferred gene merely provides substance, without providing form. It provides form as well. The shape of the final gene is very much determined, very specifically determined, by the shape of the laterally transferred gene. In fact, that is precisely how laterally transferred genes are identified, because we can tell where they come from!

    When you say that variation is “raw material”, you mean something completely different than what these words are intended to convey. Your argument does not justify the use of “raw materials”. You say, literally, that because mutations “result in an increase in variation”, they are “raw materials”. That is not the definition of a raw material. A raw material is raw, it is used in bulk, it is transformed unrecognizably, and provides substance only, not form.

    So, the correct answer to the SAT question, is “FALSE”.

    This is not just a problem with old textbooks. Contemporary research papers– even in evo-devo– also invoke “raw materials.” This is because evolutionary biology is in a state of confusion. Reformers have been saying for years that we need to rethink the role of variation in evolution. It hasn’t really happened.

  74. 74
    Acartia_bogart says:

    Arlin, based on your reductionist description of raw material, only the four nucleotides (or the atoms composing them) would be considered raw material. This may be true if all you are doing is defining the raw material for DNA. But that is not what we are talking about. We are talking about the raw material that is acted on by natural selection. Natural selection does not act on DNA directly, or the genes coded within it. It acts on the variation within the phenotypic expression of the DNA within a population. So, in short, it doesn’t matter where that variation comes from. If it comes from mutations causing a change in a protein, natural selection can act on it. If it comes from the inclusion of a fully functional gene through HGT that is expressed in the phenotype, natural selection can act on it. Even if it comes from the inclusion of new genes in a population due to interbreeding between two related species (or population), natural selection can act on it. All of these processes, and probably more, are sources of raw material for natural selection.

  75. 75
    arlin says:

    Acartia_bogart, you have displayed an understanding of basic biology. You seem to know about DNA and phenotypes. That’s great.

    But your response does not address the question. Is it correct to assert that the role of variation in evolution is to supply, not just material, but “raw” material? This question arose because it is a form of the original question, which is whether it is correct to say that evolution by HGT is within the realm of Darwinian evolution.

    I agree that the real issue is not where the variation comes from. This is where people like Ford Doolittle have confused the issues. HGT represents a form of lateral inheritance, and its importance in evolution makes the tree of life more like a net. Darwinians like Ernst Mayr didn’t predict this.

    But neither did anyone else. Biologists didn’t predict lateral inheritance, just like we didn’t predict hydrothermal vent communities living on hydrogen sulfide, and we didn’t predict reverse transcription, and we didn’t predict prions or chemiosmotic coupling or non-canonical genetic codes. All of these things were surprises that contradicted simplifying assumptions made previously. So what?

    We could still have Darwinian evolution if abundant random variation were inserted into organisms from the outside. Furthermore, this variation could include macromutations like the transfer of an entire gene, or the sudden origin of a new gene by duplication. Darwinism doesn’t deny that macromutations happen. However, Darwinism *does* deny that macromutations are the basis of evolutionary change.

    This is the part of Darwinism that is contradicted by HGT. HGT is a challenge to Darwinism, not because the hereditary substances come from outside the organisms, but because, in evolutionary events of HGT, the variations actually incorporated in evolution are macromutations, not “slight” or “infinitesimal” as Darwin demanded in his theory. Their use in evolution violates the doctrine of _natura non facit saltum_. To describe such variations as “raw material” is to abuse the words “raw material”. To say that a fully formed, specific sequence is the “raw material” out of which “natural selection” builds a gene, is to abuse the words “raw material”.

    So far your comments have failed to address this issue.

    The argument that HGT can be included in Darwinism on the grounds that “Darwin couldn’t have known this” would be laughable if it weren’t so sadly common. If Darwinism is a cult, rather than a theory, then defending the founder of the cult personally is the proper response to a challenge to Darwinism. But this kind of argument has no place in science. Good scientific theories are *supposed* to be predictive. They are supposed to fit facts that haven’t been seen yet. They are also supposed to *right*. If they are wrong we reject them, not claim that the original proposer of the theory couldn’t possibly have known that the theory was wrong.

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