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Horizontal gene transfer may be a big factor in evolution, and why it matters

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If we go by this:

It likewise happens to genes that belong to animals, fungi and plants, collectively known as eukaryotes because they boast nuclei in their cells. The ancient communion between ferns and hornworts is the latest in a series of newly discovered examples of horizontal gene transfer: when DNA passes from one organism to another generally unrelated one, rather than moving ‘vertically’ from parent to child.

To whatever extent evolution occurs, we need evidence, not “Anything is possible!” And we’ll get a court order to teach our theory!

Further to: Bacteria use small spear to acquire antibiotic resistant genes, here are some further stories that crossed our screen in 2014, also:

Horizontal gene transfer discovered from bacteria to insects

Horizontal gene transfer: Jumping gene jumped to all three domains of life?

Why horizontal gene transfer is bad news for Darwinism:

[The modern synthesis] is called a synthesis because it is a synthesis between two different mechanisms of evolution. That is what the word synthesis means. The synthesis in this case is: natural selection acting on random mutation (Darwinism) AND horizontal gene transfer (HGT). Darwinism is vertical and HGT is horizontal. So no, HGT is not Darwinism and Darwinism is not HGT. This vid gives the general idea of the difficulty one would face explaining the proposition to one of Darwin’s followers:

The problem HGT creates for Darwinism is that Darwinism has typically functioned as a “must be” explanation for evolution. If genes can be horizontally transferred between bacteria and animals, each and every case of claimed evolution in those animal life forms that have proved capable of it must be tested against HGT. They cannot be simply classed as evidence for Darwinism. Just think of the impact this will eventually have on “Darwinizing the culture.” First, if evolution happens by a variety of means, but mostly not Darwinian – and often just reverses itself – much Darwinism will crumble insofar as it was credited as simply the only “scientific” explanation.

In terms of ending Darwinian neuroencephalopathy (Darwinitis), that may be the most significant news of all. Will Darwin’s followers get a court order forbidding the discussion of non-Darwinian evolution in schools?

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34 Replies to “Horizontal gene transfer may be a big factor in evolution, and why it matters

  1. 1
    goodusername says:

    News,

    [The modern synthesis] is called a synthesis because it is a synthesis between two different mechanisms of evolution. That is what the word synthesis means. The synthesis in this case is: natural selection acting on random mutation (Darwinism) AND horizontal gene transfer (HGT). Darwinism is vertical and HGT is horizontal. So no, HGT is not Darwinism and Darwinism is not HGT.

    By “The modern synthesis” are you referring to the developments in the 1940s?

    Horizontal gene transfer wasn’t even known at that time, and so, obviously, that’s not what the synthesis was about.

  2. 2
    News says:

    The [more] modern synthesis then, the one that must now include HGT.

  3. 3
    ppolish says:

    The mantra of the Current Synthesis is the same as the Modern Synthesis which is the same as Darwinism: “Survival (or else) is unguided and purposeless.”

    What is the mantra of ID? I kind of like “Be the best you can be.”

    “Be the best you can be” is guided and purposeful.

  4. 4
    wd400 says:

    The [more] modern synthesis then, the one that must now include HGT.

    You mean evolutionary biology? We can only know how extensive horizontal gene transfer is as an evolutionary force by using the methods of evolutionary biology (phylogeny, for instance).

    Apart from adding another chance process by which lineages can develop new traits, I’m not sure what else we are meant to take from this. You seem to think HGT is incompatible with and distinct from “Darwinism”, but you haven’t explained why (or indeed which meaning of Darwinism you refer to).

  5. 5
    Mark Frank says:

    I don’t know who wrote this OP but he/she seems to be spectacularly confused. Confused about the modern synthesis, but also confused about Darwin. Darwin proposed that evolution is the result of natural selection operating on unguided variation. HGT is just another form of unguided variation.. As such it poses no problem for Darwin’s principles. It is an example of science advancing and gaining a more detailed understanding of how evolution happens. Something that ID will not touch on principle.

  6. 6
    Mung says:

    Lamarkism is just another form of unguided variation.. As such it poses no problem for Darwin’s principles.

  7. 7
    ppolish says:

    Does the current synthesis posit that HGT is unguided random purposeless?

    If so, then we would expect “good” genes and “bad” genes would transfer. Probably more “bad” genes than “good”.. Is that the case?

  8. 8
    Mapou says:

    The modern synthesis: Incorporate any new discovery that falsifies the previous modern synthesis.

  9. 9
    Mapou says:

    Any intelligent software designer will recognize horizontal gene transfer as an analog of multiple inheritance. This is one of the mainstays of intelligent design aka ID.

  10. 10
    Mapou says:

    MF:

    HGT is just another form of unguided variation.. As such it poses no problem for Darwin’s principles.

    Except when it does. The fact that parrots and other highly vocal birds share the same vocalization genes as humans effectively falsifies common descent. And as we all know, common descent is one of the most cherished of Darwinist doctrines. But no problem. All a Darwinist needs to do to get out of this predicament is to say that HGT is part of evolution and voila. Problem solved.

  11. 11
    Mapou says:

    So how did vocalization genes jump from birds to humans? I hesitate to even think about the possibilities.

    PS. But I’m certain Darwinists already came up with just-so scenario.

  12. 12
    velikovskys says:

    Mapou:
    Any intelligent software designer will recognize horizontal gene transfer as an analog of multiple inheritance. This is one of the mainstays of intelligent design aka ID.

    So if multiple inheritance can not be shown design is falsified?

  13. 13
    wd400 says:

    Mung,

    Check the validity of your first sentence.

    PP,

    Yes. Yes.

    Mapou,

    No one claims parrots and humans share “vocalization genes” by anything other than vertical descent. I guess you are referring to this paper [pdf], which is about expression patterns of genes. i.e., other vertebrates have these genes, just not expressed in the same pattern in the same regions of the brain.

  14. 14
    Box says:

    Mark Frank: HGT is just another form of unguided variation.. As such it poses no problem for Darwin’s principles.

    HGT is a consequence of various complex mechanisms for which evolution has no explanation beyond the usual speculation. Incredible horizontal transfer mechanisms just happened to arise, other than that it poses no problem for Darwin’s principles.

  15. 15
    Mapou says:

    velikovskys:

    Mapou:
    Any intelligent software designer will recognize horizontal gene transfer as an analog of multiple inheritance. This is one of the mainstays of intelligent design aka ID.

    So if multiple inheritance can not be shown design is falsified?

    IMO, yes. Intelligent design over time always uses multiple inheritance.

  16. 16
    awstar says:

    velikovskys at #12

    So if multiple inheritance can not be shown design is falsified?

    Yes, in the same way the big bang is falsified because dark matter can not be shown.

    From wikiPedia.

    Multiple inheritance is a feature of some object-oriented computer programming languages in which an object or class can inherit characteristics and features from more than one parent object or parent class. It is distinct from single inheritance, where an object or class may only inherit from one particular object or class.

    Computer SCIENCE knows all about multiple inheritance and how it originates. Evolutionary Biologists should take heed from other SCIENCE disciplines.

  17. 17
    bornagain77 says:

    Mark Frank at 5 states:

    I don’t know who wrote this OP but he/she seems to be spectacularly confused. Confused about the modern synthesis, but also confused about Darwin. Darwin proposed that evolution is the result of natural selection operating on unguided variation. HGT is just another form of unguided variation.. As such it poses no problem for Darwin’s principles. It is an example of science advancing and gaining a more detailed understanding of how evolution happens. Something that ID will not touch on principle.

    Save of course for when HGT is found to be ‘non-random’

    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

    Box at 14 states:

    HGT is a consequence of various complex mechanisms for which evolution has no explanation beyond the usual speculation

    Just how complex some of these horizontal gene transfer mechanisms are is illustrated by the bacteriophage virus. The “horizontal” gene transfering bacteriophage virus is far more complex than many people have ever imagined, as these following video clearly point out:

    Virus – Assembly Of A Nano-Machine – video
    https://www.youtube.com/watch?v=Ofd_lgEymto

    Bacteriophage T4 DNA Packing
    https://www.youtube.com/watch?v=wNQQz0NGUNQ

    Here is a short video of the Bacteriophage ‘landing’ on a bacterium so as to transfer genetic material:

    Bacteriophage T4 – landing – video
    https://www.youtube.com/watch?v=kdz9VGH8dwY

    The first thought I had when I first saw the bacteriophage virus is that it looks very similar to the lunar lander of the Apollo program. The comparison is not without merit considering some of the relative distances to be traveled and the virus must somehow possess, as of yet unelucidated, orientation, guidance, docking, unloading, loading, etc… mechanisms. And please remember this level of complexity exists in a world that is far too small to be seen with the naked eye.

    As to Mr. Frank’s comment about people being ‘confused about the modern synthesis’, it appears the confusion about the modern synthesis is rampant in that Denis Nobel, President of the International Union of Physiological Sciences, says the modern synthesis is false:

    Modern Synthesis Of Neo-Darwinism Is False – Denis Nobel – video
    https://vimeo.com/115822429

    ,, In the preceding video, Dr Nobel states that around 1900 there was the integration of Mendelian (discrete) inheritance with evolutionary theory, and about the same time Weismann established what was called the Weismann barrier, which is the idea that germ cells and their genetic materials are not in anyway influenced by the organism itself or by the environment. And then about 40 years later, circa 1940, a variety of people, Julian Huxley, R.A. Fisher, J.B.S. Haldane, and Sewell Wright, put things together to call it ‘The Modern Synthesis’. So what exactly is the ‘The Modern Synthesis’? It is sometimes called neo-Darwinism, and it was popularized in the book by Richard Dawkins, ‘The Selfish Gene’ in 1976. It’s main assumptions are, first of all, is that it is a gene centered view of natural selection. The process of evolution can therefore be characterized entirely by what is happening to the genome. It would be a process in which there would be accumulation of random mutations, followed by selection. (Now an important point to make here is that if that process is genuinely random, then there is nothing that physiology, or physiologists, can say about that process. That is a very important point.) The second aspect of neo-Darwinism was the impossibility of acquired characteristics (mis-called “Larmarckism”). And there is a very important distinction in Dawkins’ book ‘The Selfish Gene’ between the replicator, that is the genes, and the vehicle that carries the replicator, that is the organism or phenotype. And of course that idea was not only buttressed and supported by the Weissman barrier idea, but later on by the ‘Central Dogma’ of molecular biology. Then Dr. Nobel pauses to emphasize his point and states “All these rules have been broken!”.

    Physiology is rocking the foundations of evolutionary biology – Denis Noble – 17 MAY 2013
    Excerpt: The ‘Modern Synthesis’ (Neo-Darwinism) is a mid-20th century gene-centric view of evolution, based on random mutations accumulating to produce gradual change through natural selection.,,, We now know that genetic change is far from random and often not gradual.,,,
    http://onlinelibrary.wiley.com.....4/abstract

    “The genome is an ‘organ of the cell’, not its dictator”
    – Denis Nobel – President of the International Union of Physiological Sciences
    http://musicoflife.co.uk/

    Dr. Nobel is hardly alone in his ‘confusion’ about the modern synthesis. At the 10:30 minute mark of the following video, Dr. Trifonov, who has discovered many codes in the genome, states that the concept of the selfish gene has,,,

    ‘inflicted an immense damage to biological sciences’, for over 30 years:

    Second, third, fourth… genetic codes – One spectacular case of code crowding – Edward N. Trifonov – video
    https://vimeo.com/81930637

    And neither is Dr Trifonov alone in his ‘confusion’

    Die, selfish gene, die – The selfish gene is one of the most successful science metaphors ever invented. Unfortunately, it’s wrong – Dec. 2013
    Excerpt: But 15 years after Hamilton and Williams kited [introduced] this idea, it was embraced and polished into gleaming form by one of the best communicators science has ever produced: the biologist Richard Dawkins. In his magnificent book The Selfish Gene (1976), Dawkins gathered all the threads of the modern synthesis — Mendel, Fisher, Haldane, Wright, Watson, Crick, Hamilton, and Williams — into a single shimmering magic carpet (called the selfish gene).
    Unfortunately, say Wray, West-Eberhard and others, it’s wrong.
    http://www.uncommondescent.com.....-heard-of/

  18. 18
    bornagain77 says:

    Dr. Koonin is so ‘confused’ that he actually thinks that ‘the edifice of the Modern Synthesis has crumbled, apparently, beyond repair’:

    The Origin at 150: is a new evolutionary synthesis in sight? – Koonin – Nov. 2009
    Excerpt: The edifice of the modern synthesis has crumbled, apparently, beyond repair.
    http://www.ncbi.nlm.nih.gov/pm.....MC2784144/

    Shoot, the following authors are so confused about the modern synthesis they think the modern sysnthesis is useless as a future framework for evolutionary theory

    The Fate of Darwinism: Evolution After the Modern Synthesis – David J. Depew and Bruce H. Weber – 2011
    Excerpt: We trace the history of the Modern Evolutionary Synthesis, and of genetic Darwinism generally, with a view to showing why, even in its current versions, it can no longer serve as a general framework for evolutionary theory. The main reason is empirical. Genetical Darwinism cannot accommodate the role of development (and of genes in development) in many evolutionary processes.,,,
    http://www.springerlink.com/co.....03g3t7002/

    James Shapiro, who is certainly no slouch in molecular biology, also seems to be ‘confused’ about the ‘unguided’, random, nature of the modern synthesis (i.e. the ‘central dogma’):

    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

    “It is difficult (if not impossible) to find a genome change operator that is truly random in its action within the DNA of the cell where it works’
    James Shapiro – Evolution: A View From The 21st Century – (Page 82)

    James Shapiro is hardly alone in thinking changes to the genome are happening in a ‘non-random’ pattern:

    WHAT SCIENTIFIC IDEA IS READY FOR RETIREMENT? Fully Random Mutations – Kevin Kelly – 2014
    Excerpt: What is commonly called “random mutation” does not in fact occur in a mathematically random pattern. The process of genetic mutation is extremely complex, with multiple pathways, involving more than one system. Current research suggests most spontaneous mutations occur as errors in the repair process for damaged DNA. Neither the damage nor the errors in repair have been shown to be random in where they occur, how they occur, or when they occur. Rather, the idea that mutations are random is simply a widely held assumption by non-specialists and even many teachers of biology. There is no direct evidence for it.
    On the contrary, there’s much evidence that genetic mutation vary in patterns. For instance it is pretty much accepted that mutation rates increase or decrease as stress on the cells increases or decreases. These variable rates of mutation include mutations induced by stress from an organism’s predators and competition, and as well as increased mutations brought on by environmental and epigenetic factors. Mutations have also been shown to have a higher chance of occurring near a place in DNA where mutations have already occurred, creating mutation hotspot clusters—a non-random pattern.
    http://edge.org/response-detail/25264

    Scientists Discover What Makes The Same Type Of Cells Different – Oct. 2009
    Excerpt: Until now, cell variability was simply called “noise”, implying statistical random distribution. However, the results of the study now show that the different reactions are not random, but that certain causes (environmental clues) lead to predictable distribution patterns,,,
    http://www.sciencedaily.com/re.....204217.htm

    Man that is a whole lot of confusion about the modern synthesis. Perhaps we can send Mark Frank and wd400 over to help all these guys out since they ‘just don’t understand evolution’? 🙂

  19. 19
    ppolish says:

    Can HGT increase an organism’s “junk”?

  20. 20
    Mapou says:

    Here’s why WD400 is either out to lunch or grasping at straws:

    “We’ve known for many years that the singing behavior of birds is similar to speech in humans — not identical, but similar — and that the brain circuitry is similar, too,” said Jarvis, an associate professor of neurobiology at the Duke University Medical School and an investigator at the Howard Hughes Medical Institute. “But we didn’t know whether or not those features were the same because the genes were also the same.”
    Now scientists do know, and the answer is yes — birds and humans use essentially the same genes to speak.
    After a massive international effort to sequence and compare the entire genomes of 48 species of birds representing every major order of the bird family tree, Jarvis and his colleagues found that vocal learning evolved twice or maybe three times among songbirds, parrots and hummingbirds.
    Even more striking is that the set of genes involved in each of those song innovations is remarkably similar to the genes involved in human speaking ability.

    Source: Science Daily: Genes tell story of birdsong and human speech

    There are other findings I can point to but this should be enough.

  21. 21
    wd400 says:

    PP,

    Could do. ~5% of your genome is made of dead retroviruses, for instance.

    Mapou,

    Nothing in the quoted section contradicts what I have said.

  22. 22
    Joe says:

    Mark Frank:

    HGT is just another form of unguided variation

    Evidence please.

  23. 23
    Mapou says:

    WD400:

    Mapou,

    Nothing in the quoted section contradicts what I have said.

    Of course it does. They are saying that the vocal LEARNING genes are expressed the same way in certain birds and humans and differently in non-human mammals and non vocal learning birds. What do you think controls or regulates the expression of genes? Answer: non-coding regulatory genes, of course. Some of the regulatory genes must be identical in different species and must have been caused by multiple inheritance.

    Given the above, Darwinists must come up with a mechanism for transferring those genes between distant species. And vocalization genes are just one example. There are others involving plants and animals, bats and dolphins, etc.

  24. 24
    bornagain77 says:

    Refutation Of Endogenous Retrovirus – ERVs – Richard Sternberg, PhD Evolutionary Biology – video
    http://www.youtube.com/watch?v=SrEOe2E0Euc
    Sternberg, R. v. & J. A. Shapiro (2005). How repeated retroelements format genome function. Cytogenet. Genome Res. 110: 108-116.
    Excerpt: Employing an information science model, the “functionalist” perspective on repetitive DNA leads to new ways of thinking about the systemic organization of cellular genomes and provides several novel possibilities involving retroelements in evolutionarily significant genome reorganization.
    http://www.ncbi.nlm.nih.gov/pubmed/16093662

    Shapiro and Sternberg Anticipated the Fall of Junk DNA – Douglas Axe – September 13, 2012
    Excerpt: “In 2005, I published two articles on the functional importance of repetitive DNA with Rick von Sternberg. The major article was entitled “Why repetitive DNA is essential to genome function.”
    These articles with Rick are important to me (and to this blog) for two reasons. The first is that shortly after we submitted them, Rick became a momentary celebrity of the Intelligent Design movement. Critics have taken my co-authorship with Rick as an excuse for “guilt-by-association” claims that I have some ID or Creationist agenda, an allegation with no basis in anything I have written.
    The second reason the two articles with Rick are important is because they were, frankly, prescient, anticipating the recent ENCODE results. Our basic idea was that the genome is a highly sophisticated information storage organelle. Just like electronic data storage devices, the genome must be highly formatted by generic (i.e. repeated) signals that make it possible to access the stored information when and where it will be useful.”
    – James Shapiro
    http://www.evolutionnews.org/2.....64291.html

    Retrovirus in the Human Genome Is Active in Pluripotent Stem Cells – Jan. 23, 2013
    Excerpt: “What we’ve observed is that a group of endogenous retroviruses called HERV-H is extremely busy in human embryonic stem cells,” said Jeremy Luban, MD, the David L. Freelander Memorial Professor in HIV/AIDS Research, professor of molecular medicine and lead author of the study. “In fact, HERV-H is one of the most abundantly expressed genes in pluripotent stem cells and it isn’t found in any other cell types.
    http://www.sciencedaily.com/re.....133930.htm

    Transposable Elements Reveal a Stem Cell Specific Class of Long Noncoding RNAs – (Nov. 26, 2012)
    Excerpt: The study published by Rinn and Kelley finds a striking affinity for a class of hopping genes known as endogenous retroviruses, or ERVs, to land in lincRNAs. The study finds that ERVs are not only enriched in lincRNAs, but also often sit at the start of the gene in an orientation to promote transcription. Perhaps more intriguingly, lincRNAs containing an ERV family known as HERVH correlated with expression in stem cells relative to dozens of other tested tissues and cells. According to Rinn, “This strongly suggests that ERV transposition in the genome may have given rise to stem cell-specific lincRNAs. The observation that HERVHs landed at the start of dozens of lincRNAs was almost chilling; that this appears to impart a stem cell-specific expression pattern was simply stunning!”
    http://www.sciencedaily.com/re.....192838.htm

    Endogenous retroviruses regulate periimplantation placental growth and differentiation – 2006
    http://www.pnas.org/content/103/39/14390.abstract.

  25. 25
    wd400 says:

    Answer: non-coding regulatory genes, of course. Some of the regulatory genes must be identical in different species and must have been caused by multiple inheritance.

    Not identical, there are plenty of ways to skin a cat or pattern a brain. In fact, in the same issue of Science there is a paper that shows convergent evolution (not HGT) in cis-regulatroy sequences associated with vocal learning.

  26. 26
    bornagain77 says:

    the term ‘convergent evolution’, as it is used by neo-Darwinists, is NOT an actual explanation for how any ‘miracle’ might have happened over and over again in widely divergent species but is just a meaningless phrase used to cover up embarrassing findings that disagree with basic assumptions from Darwin’s theory!

    “The reason evolutionary biologists believe in “40 known independent eye evolutions” isn’t because they’ve reconstructed those evolutionary pathways, but because eyes don’t assume a treelike pattern on the famous Darwinian “tree of life.” Darwinists are accordingly forced, again and again, to invoke convergent “independent” evolution of eyes to explain why eyes are distributed in such a non-tree-like fashion.
    This is hardly evidence against ID. In fact the appearance of eyes within widely disparate groups speaks eloquently of common design. Eyes are a problem, all right — for Darwinism.”
    http://www.evolutionnews.org/2.....83441.html

    In fact, Simon Conway Morris has a website documenting hundreds, if not thousands, of examples of ‘convergence’:

    Map Of Life – Simon Conway Morris
    http://www.mapoflife.org/browse/

    Simon Conway Morris: “Fossil evidence demands a radical rewriting of evolution.” – March 2012
    Excerpt: “The idea is this: that convergence – the tendency of very different organisms to evolve similar solutions to biological problems – is not just part of evolution, but a driving force. To say this is an unconventional view would be something of an understatement.”
    http://www.uncommondescent.com.....evolution/

  27. 27
    Mapou says:

    WD400:

    Answer: non-coding regulatory genes, of course. Some of the regulatory genes must be identical in different species and must have been caused by multiple inheritance.

    Not identical, there are plenty of ways to skin a cat or pattern a brain.

    You don’t know that. Given that the regulatory genes that control vocal learning in parrots and humans are much more numerous than the 50 or so coding genes they have in common, I predict that when they are identified, they will prove to have similarities with the analog human genes that will amaze. Prepare to be humiliated. LOL.

  28. 28
    velikovskys says:

    Mapou:

    IMO, yes. Intelligent design over time always uses multiple inheritance.

    How does an non living object inherit ?

  29. 29
    velikovskys says:

    veil:
    So if multiple inheritance can not be shown design is falsified?

    Awstar
    Yes, in the same way the big bang is falsified because dark matter can not be shown.

    I wouldn’t bet against a Jesuit myself, but how does say the structure of the universe as we know it demonstrate multiple inheritance? From whence did it inherit,in multiple?

    Second, inherit connotes a necessity ,one cannot inherit from a non parent after all. Is the designer therefore limited in his range of choices,as evolution is?

  30. 30
    DATCG says:

    Interesting paper in 2007 on failures of Darwinism and Modern Synthesis..

    Is any of this being taught in public schools today. If not, when will it be?

    Darwinist crumbling assumptions and Modern Synthesis Dead Parts…

    However, some of the assumptions at the foundation of The Modern Synthesis started to crumble in the 1970s with the discovery of super-abundant genetic variation that arguably often didn’t evolve under the strict aegis of natural selection. Then cells were found to incorporate genes, mobile genetic elements, and organelles of diverse historical origins. Furthermore, it became apparent in the last decades of the 20th Century that DNA sequences often evolved in ways that reduced the fitness of the organisms that bore them. It is now abundantly clear that living things often attain a degree of genomic complexity far beyond simple models like the “gene library” genome of the Modern Synthesis.

    Dead parts of the Modern Synthesis

    It is important to be clear about common, though not necessarily universal, assumptions of mid-20th Century biology that have been discarded. A partial listing would include at least the following:

    • The genome is always a well-organized library of genes.

    • Genes usually have single functions that have been specifically honed by powerful natural selection.

    • Species are finely adjusted to their ecological circumstances due to efficient adaptive adjustment of biochemical functions.

    • The durable units of evolution are species, and within them the organisms, organs, cells, and molecules, which are characteristic of the species.

    • Given the adaptive nature of each organism and cell, their machinery can be modeled using principles of efficient design.

    This is so juicy. Especially enjoyed reading the reviews and discussions back and forth with Dr. Doolittle and Dr Koonin. Scroll to bottom for their reviews and exchange.

    A sample of feedback about HGT being a major blow from Dr. Koonin who favors pluralism…

    2. Rose and Oakley bring up the newly apparent prevalence of horizontal gene transfer as one of the major blows to the 20th century perspective in biology. This is, certainly, true, but I think the discussion in the paper stops short of really driving the nail down. The real issue is that, when fully conceptualized, extensive HGT undermines the very notion of the Tree of Life (the TOL paradigm) which, certainly, is a big part of the Modern Synthesis (as well as the classical, Darwinian foundation of biology). Simply put, although trees are crucial in depicting certain phases and aspects of life’s history, there is no TOL as such, i.e, evolution of life cannot be presented as a tree, so Darwin’s famous simile fails as an overarching generalization.

    Hahaha….in response to the Koonin’s honest assessment of the Death of Darwin’s TOL Paradigm…

    There is no reason to provide anti-intellectual, anti-evolutionists with quotes like “The Darwinian paradigm is dead”, because this complexity only enhances Darwin’s most profound insight – the universal common ancestry of life.

    Better to insult than be forthright. As they admit, this is the Post-Modern, Post-Darwinian world, yet here they are refusing to adjust themselves to the new reality Post-Darwinian “Pluralism.”

  31. 31
    DATCG says:

    Have no access right now to paper of following abstract. Would be an interesting read…


    Transfer of noncoding DNA drives regulatory rewiring in bacteria

    Here, we show that bacterial genes can rapidly shift between multiple regulatory modes by acquiring functionally divergent nonhomologous promoter regions. Through analysis of 270,000 regulatory regions across 247 genomes, we demonstrate that regulatory “switching” to nonhomologous alternatives is ubiquitous, occurring across the bacterial domain. Using comparative transcriptomics, we show that at least 16% of the expression divergence between Escherichia coli strains can be explained by this regulatory switching. Further, using an oligonucleotide regulatory library, we establish that switching affects bacterial promoter architecture. We provide evidence that regulatory switching can occur through horizontal regulatory transfer, which allows regulatory regions to move across strains, and even genera, independently from the genes they regulate.

    A quote from the paper linked in my post #30 above by authors Rose and Oakley comments back to Dr. Koonin…

    “…this complexity only enhances Darwin’s most profound insight – the universal common ancestry of life.”

    Does it? How? In light of this latest research, evidence shows regulatory regions move across genera even, “independently from the genes they regulate.”

    Koonin’s review commentary to Rose and Oakley…

    (iii) “Species are finely adjusted …”

    -Not just dead but, simply, makes no sense as generalizations because species cannot be objectively defined in prokaryotes and viruses, and however they might be defined arbitrarily, cannot possibly be the fundamental units of anything.

    (iv) “The durable units of evolution are species…”

    -Makes no real sense – see above.

    What is the new “Pluralism?” A Forest of Life? What precisely is this new Post-Darwinian, Post-Modern Synthesis consensus building? Does anyone know?

    It appears scientist agreeing on the death of several antiquated assumptions still cannot leave Darwin behind or agree on all ahead. But it does appear some evolutionary scientist recognize HGT is a “major blow” to the very “notion of the Darwin Tree of Life.”

  32. 32
    Mapou says:

    velikovskys:

    Mapou:

    IMO, yes. Intelligent design over time always uses multiple inheritance.

    How does an non living object inherit ?

    Are you joking or are you being purposely stupid?

  33. 33
    wd400 says:

    Mapou,

    You seem to have backed off from your original claim, that these results were the death of common descent, and are now betting on future results.

    Only the “future” results already exist and you’re wrong, go read the papers I’ve already linked to.

  34. 34
    tjguy says:

    “Horizontal gene transfer may be a big factor in evolution, and why it matters”

    If it is, it ruins any hope of ever putting together a tree of life, although aside from this that is already proving to be a very difficult problem. But creationists question the use of HGT as a “just so story” type of theory saving device.

    This is explained here by creationist Jeffrey Tomkins who wrote a very enlightening article on this entitled “Another Horizontal Gene Transfer Fairy Tale” here:
    http://www.icr.org/article/8673

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