horizontal gene transfer News

Do you ever get tired of filling Darwin’s waste basket?

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If not, this story is not for you. Microbes change genes
Here.

ep. 30, 2013 — Sequestered in Antarctica’s Vestfold Hills, Deep Lake became isolated from the ocean 3,500 years ago by the Antarctic continent rising, resulting in a saltwater ecosystem that remains liquid in extreme cold, and providing researchers a unique niche for studying the evolution of the microbes that now thrive under such conditions. Deep Lake’s microscopic inhabitants are dominated by haloarchaea, microbes that require high salt concentrations to grow and are naturally adapted to conditions — at minus 20̊C — that would prove lethally cold to other organisms. In a detailed analysis published online the week of September 30, 2013 in the journal Proceedings of the National Academy of Sciences (PNAS), researchers have, for the first time, been able to get a complete ecological picture of the Deep Lake microbial community.

What distinguishes this “conversation” is that the haloarchaea of Deep Lake exchange the information of DNA not just between species but among distinct genera, and moreover in huge tranches, some 35,000 letters of code, with not a letter out of place. While it may be slow, that give-and-take is chock full of essential information and the word gets around the community. “The long stretches of highly identical shared sequence between the different lake organisms spurred a strong suspicion of potential cross-contamination at first,” said Tanja Woyke, Microbial Program Lead at the DOE JGI and co-author of the study. “By painstaking validation of the manually finished and curated genomes, however, we were able to exclude any process-introduced artifacts and confirm that this is true inter-genera gene exchange.”

Bye, Darwin.

9 Replies to “Do you ever get tired of filling Darwin’s waste basket?

  1. 1
    Jerad says:

    How cool is that? And all perfectly natural and undirected. Lovely.

  2. 2
    bornagain77 says:

    Jerad sees an extremely sophisticated example of inter-genera gene exchange and reflexively, apparently with no thought, gives this Darwinian response:

    And all perfectly natural and undirected.

    Jerad, such a misinformed statement tells me that you seem to be stuck in the 19th century. To bring you up to date, let me be among the first to welcome you to the ‘directed, non-random’, and very non-Darwinian, 21st century:

    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.

    James Shapiro calls standard Darwinian thinking, such as Jerad exemplified in his statement, to be a “dangerous oversimplification”:

    James Shapiro on “dangerous oversimplifications” about the cell – August 6, 2013
    Excerpt: “Depending upon the energy source and other circumstances, these indescribably complex entities can reproduce themselves with great reliability at times as short as 10-20 minutes. Each reproductive cell cycle involves literally hundreds of millions of biochemical and biomechanical events. We must recognize that cells possess a cybernetic capacity beyond our ability to imitate. Therefore, it should not surprise us when we discover extremely dense and interconnected control architectures at all levels. Simplifying assumptions about cell informatics can be more misleading than helpful in understanding the basic principles of biological function.
    Two dangerous oversimplifications have been (i) to consider the genome as a mere physical carrier of hypothetical units called “genes” that determine particular cell or organismal traits, and (ii) to think of the genome as a digitally encoded Read-Only Turing tape that feeds instructions to the rest of the cell about individual characters [4].”
    http://www.uncommondescent.com.....-the-cell/

  3. 3
    kairosfocus says:

    Now, how did such a community of bacteria come to have an in common mechanism to do such, all by incremental accumulated genetic accidents that all had to confer competitive advantages? How was such an account of the origin of such a mechanism in such a way observationally justified? Or, are we going to see yet another materialist just so story dressed up in a lab coat? KF

  4. 4
    Jerad says:

    Now, how did such a community of bacteria come to have an in common mechanism to do such

    Good question! What’s your answer. With some at least vague answers to how and when would be good.

    Or are you just going to fall back on: some unknown, undefined, undetected designer did it?

    , all by incremental accumulated genetic accidents that all had to confer competitive advantages? How was such an account of the origin of such a mechanism in such a way observationally justified?

    Have you observed your inferred designer in action? Will you specify at least one particular thing it’s done?

    Or, are we going to see yet another materialist just so story dressed up in a lab coat? KF

    Your opinion, not shared by thousands of working biologists who do research and publish their results in peer reviewed journals where they can be studied, criticised and taken apart by others in their field. And then someone will try and duplicate the findings.

    Have you got research and publications to bolster your model? What is your model by the way? Aside from: some unknown, defined and undetected designer did it?

  5. 5
    kairosfocus says:

    Jerad, you continue to show a lack of understanding of design, which is a practice of major professions with known detailed methods — start by looking up TRIZ. We already see nascent molecular nanotech design of cell based life through Venter et al. Tough but doable. Second, you need to refresh the logic of inference on tested, reliable signs, as from tracks to deer, and as we infer to design on seeing the FSCO/I of your post, or as we naturally infer on first seeing some novel instrument. Third, every tub must stand on its own bottom: we know per billions of observed cases that FSCO/I is routinely produced by design, can you show it coming about in our observation by blind chance and mechanical necessity? Until the latter is shown FSCO/I — clearly involved here — is best explained on design. We certainly have no epistemic obligation to abandon inference on a reliable sign in favour of something not shown to have capability to do the required task, on a priori ideological imposition of materialism and proposal of just so stories inspired by that ideology. KF

  6. 6
    kairosfocus says:

    PS: On appeal to authority. The observationally anchored, inductively well warranted case for origin of life through abiogenesis is _________________ . Ditto, for origin of body plans through blind watchmaker chance variations and differential reproductive success leading to incremental descent with unlimited variations is: ______________. Nobel prizes awarded for these demonstrations were ______________ and ______________. (Far too much of origins accounts is tainted by Lewontin_Sagan a priori materialism. And far too much reference is elephant hurling blind appeals to authority.)

  7. 7
    kairosfocus says:

    PPS: Research and pubs — as has been notified to Jerad previously, just willfully ignored as usual.

  8. 8
    Jerad says:

    So, still no attempt at making a commitment as to when design was implemented. Let alone how.

    But we know evolutionary theory is wrong. But we’re not really sure what we are saying except that some undefined, undetected and unmeasurable designer did . . . something . . . at some time.

    I know some of you have started to put together some ideas and I applaud that. But, for the most part, the whole idea of progressing beyond: IT WAS DESIGNED seems an anathema to most ID proponents. Why is that? You’ve had the same data, the same evidence as the evolutionary theorists but . . .

  9. 9
    Mung says:

    Jerad confuses ID with Darwinism. Jerad, it’s Darwinists that engage in historical storytelling. Not sure why you think that’s science, but hey, don’t blame ID for not drinking from that well.

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