Culture Darwinism News

Update on the recent paper on the placenta as a “huge cut-and-paste job” …

Spread the love
File:Placenta.svg
Gray's Anatomy 1918

Here. Cut and pasted from where? Edward Sisson got hold of the study, compared it to the media release, and wrote to say,

Examination of the original paper reveals that it does NOT use the phrase “genomic parasites” or anything like it. Thus it is not appropriate to pick-up that term in any reports on this paper.

No, Edward, but pop science writers sometimes just invent stuff. It’ll get worse.

In brief, the paper reports that a certain class of “hAT-Charlie family DNA transposons” called “MER20s” are vital in the operation of placental pregnancy, due to their effect on endometrial stromal cells (ESCs), and reports that due to various calculations of probabilities, these MER20s must have been “inserted” into “the genome of ancestral placental mammals.” The report uses the word “inserted” several times — but the report makes no statement at all characterizing any mechanism or agent for insertion.

The conclusion will be of interest (I omit the footnote cite references):

“There is broad consensus that many of the changes underlying the evolution of morphology occur by the stepwise modification of individual pre-existing cis-regulatory element modules. However, it is questionable whether the origin of complex novelties — such as the origin of new cell types, which involves the recruitment of hundreds of genes — can be achieved by these small-scale changes. Our findings indicate that the gene regulatory network of ESCs [endometrial stromal cells] was rewired in placental mammals during the evolution of pregnancy, a reorganization partly mediated by the transposable element MER20. … These findings strongly support the existence of transposon-mediated gene regulatory innovation at the network level …. [T]ransposable elements are potent agents of gene regulatory network evolution and add to an increasing body of evidence indicating that the evolution of novel characters involves genetic mechanisms that are distinct from those involved in the modification of existing characters.”

The citations are of interest as well, in that, judging from the titles, they conclude basically the same thing. The papers are in citation footnotes 7, 13, 14, 23, 29 to 35 (11 papers).

If someone read this report and concluded, “Hmmm, something like intelligence must have accomplished the insertions into the DNA,” there is not one word in this report that could be quoted as asserting to the contrary that the mechanism must have been unintelligent & “natural only.” It is the journalists, by applying the “genetic parasites” label, who make that claim.

It’s odd, yes, because pop science writers are usually stronger Darwin fans than anyone. Did they sense that, in this case, something doesn’t quite add up?

Follow UD News at Twitter!

18 Replies to “Update on the recent paper on the placenta as a “huge cut-and-paste job” …

  1. 1
    AussieID says:

    Alex,

    I would love to see what the program would churn out following your suggestion. Does the sonnet merely need to exist or does it need to be able to be published? I would see being published as a requirement/analogy to breeding in the animal family. Has it enough selective advantage to survive?

    Again here is someone who continues not to see the obvious: the programme is working toward a planned endpoint. This is NOT Darwinian evolution … they should know better!

    “Oftentimes excusing of a fault
    Doth make the fault the worse by the excuse.”
    Shakespeare’s King John

  2. 2
    AussieID says:

    Wrong spot!

  3. 3
    tjguy says:

    “There is broad consensus that many of the changes underlying the evolution of morphology occur by the stepwise modification of individual pre-existing cis-regulatory element modules. However, it is questionable whether the origin of complex novelties — such as the origin of new cell types, which involves the recruitment of hundreds of genes — can be achieved by these small-scale changes.”

    Isn’t he admitting here that this is a clear example of irreducible complexity?

  4. 4
    DrREC says:

    Is there a direct link the the quoted material?
    Is Edward Sisson read up on the transposon literature?

    Calling transposons genomic parasites is common and not recent. It also isn’t a spin by science writers.

    “Transposons grow like parasites that have invaded the body, multiplying and taking up space in the genome,” said Vincent J. Lynch, research scientist in EEB and lead author of the paper.”

    Right there in the original press release, titled: “Invasion of genomic parasites triggered modern mammalian pregnancy”
    http://www.physorg.com/news/20.....odern.html

    His second complaint, that “The report uses the word “inserted” several times — but the report makes no statement at all characterizing any mechanism or agent for insertion” merely needs a google search, or maybe a call to the authors.

    The transposons cut, copy and paste themselves (and regulatory elements, or even whole genes captured between them) about the genome. The mechanisms are quite well studied. Wikipedia.

    “Hmmm, something like intelligence must have accomplished the insertions into the DNA,” there is not one word in this report that could be quoted as asserting to the contrary that the mechanism must have been unintelligent & “natural only.”

    I think most scientists would tell you it is impossible to falsify a supernatural (beyond natural only, using the author’s definition) hypothesis. What do you think theistic evolution is?

  5. 5
    News says:

    No direct link. A letter to us. We get ’em all the time.

  6. 6
    rhampton7 says:

    Chemical bonds form by natural, mechanical forces, yet Christians would still attribute the origin of said forces to the Creator? Likewise, if transposon targeting is similarly natural, that does not mean it is an “unintelligent” process.

    Relevant: Testing the palindromic target site model for DNA transposon insertion using the Drosophila melanogaster P-element

  7. 7
    NickMatzke_UD says:

    In brief, the paper reports that a certain class of “hAT-Charlie family DNA transposons” called “MER20s” are vital in the operation of placental pregnancy, due to their effect on endometrial stromal cells (ESCs), and reports that due to various calculations of probabilities, these MER20s must have been “inserted” into “the genome of ancestral placental mammals.” The report uses the word “inserted” several times — but the report makes no statement at all characterizing any mechanism or agent for insertion.

    Uh…someone should tell Edward Sisson that what “transposons” do is “transpose” themselves. Which is the same thing as insertion. Typically a DNA transposon, which I think hAT-type ones are, encodes for a protein that, when produced, goes and finds its gene, snips it out, and pastes it somewhere else, sometimes with some variability at the edges. That’s the “mechanism” he is so desperately seeking. Yet another example of IDists making a God-of-the-Gaps argument based not on a gap in human knowledge, but a gap in their own knowledge.

    Something like 3% or 8% of the human genome is made up of mostly broken copies of DNA transposons IIRC, it’s not revolutionary to say that most of this is parasitic/junk. Rare exceptions — another one is the origin of the RAG system in the vertebrate adaptive immune system — don’t change this overall picture.

  8. 8
    PaV says:

    Nick:

    Would you like to comment on this portion of the author’s summary?

    [T]ransposable elements are potent agents of gene regulatory network evolution and add to an increasing body of evidence indicating that the evolution of novel characters involves genetic mechanisms that are distinct from those involved in the modification of existing characters.”

    This is tantamount to saying that “neo-Darwinism is dead”, or “population genetics is dead.” But, with population genetics/neo-Darwinism dead, what mechanism is there, then, for the increase of actual, physical, real, quantitative information that we see stored in the genome?

    As I told our friend from Cornell, just shifting already present information around is like pressing different letter-number combinations to get a snack out of a machine. Push different buttons, and you get very different snacks. But how did the snacks get there in the first place?

    Darwinism, i.e., RM+NS, is completely helpless to address this.

  9. 9
    PaV says:

    I just found this at PhysOrg.com.

    What emerges is a unified picture whereby previously distinct entities or categories of human diseases, chromosomal syndromes, genomic disorders, Mendelian disease, and multifactorial or complex traits, can now be considered as part of one continuum whereby common and rare variants including de novo (new) mutations in the context of environmental influences result in perturbation of the biological balance of a restricted set of networks activating final common pathways that ultimately cause disease,” the authors wrote in an article that appears in the current issue of the journal Cell.

    Animals are extremely well-tuned machines. This is just another reminder that Sir Fred Hoyle was right when he said that to believe in Darwinism is to believe that a “that a Boeing 747 could be built by a tornado passing through a junkyard.”

    Years ago I predicted that genome-wide studies would be either the death knell of Darwinism or ID. Isn’t it clear whose funeral we’re celebrating?

  10. 10
    DrREC says:

    This is tantamount to saying that “neo-Darwinism is dead”

    Define neo-Darwinism.

    I’m a bit lost how a paper showing a mechanism for wholesale evolutionary re-wiring leading to the placenta is the death of evolutionary biology.

  11. 11
    DrREC says:

    “result in perturbation of the biological balance of a restricted set of networks activating final common pathways that ultimately cause disease,”

    Disease results from perturbation of

    1) A designed system
    2) An evolved system

    Seems like a toss-up to me. Why are the failures of a designed system a win for ID, and the funeral of evolution?

  12. 12
    PaV says:

    Define neo-Darwinism.

    Only a liberal could make such a statement. “It all depends on what the definition of ‘is’ is.”

    Why don’t you look it up in Wikipedia?

    Try thinking this through—and not just relying on politically correct thought.

    It is the “restricted set of networks activating final common pathways” within an organism—NOT mutations, per se—that are critical. This fact completely minimizes the role of mutations in the life of an organism, AND, as usual, demonstrates the deleterious role of certain ‘rare’ mutations ( read, “unfixed”).

  13. 13
    Joseph says:

    There isn’t any evidence that demonstrates transposons are blind, undirected processes. IOW transpsons could very well be a design mechanism.

    Also ID is still not anti-evolution.

  14. 14
    Joseph says:

    A transposon has in it sections of DNA that encode two of the enzymes it needs to carry out its job. The cell itself contributes the other necessary enzymes. The motion of these genetic elements about to produce the above mutations has been found to be a complex process and we probably haven’t yet discovered all the complexity. But because no one knows why they occur, many geneticists have assumed they occur only by chance. I find it hard to believe that a process as precise and as well controlled as the transposition of genetic elements happens only by chance. Some scientists tend to call a mechanism random before we learn what it really does. If the source of variation for evolution were point mutations, we could say the variation is random. But if the source of variation is the complex process of transposition, then there is no justification for saying that evolution is based on random events. Dr Lee Spetner “Not By Chance” page 44

  15. 15
    PaV says:

    DrREC:

    I’m a bit lost how a paper showing a mechanism for wholesale evolutionary re-wiring leading to the placenta is the death of evolutionary biology.

    You see what you want to see. They don’t demonstrate any such “mechanism”. They simply “find” that at 1523 gene locations you can also find transposons that are not present in marsupial mammals.

    In typical Darwinian fashion, you simply assume that there is a “mechanism”, and that it is “Darwinian”. You assume what needs to be “demonstrated”. They demonstrate differences between mammalian lines; they demonstrate that it is transposon driven; and they demonstrate that the positioning is non-random. Anything else is but pure assumption. ID has no need of circular reasoning.

  16. 16
    DrREC says:

    “There isn’t any evidence that demonstrates transposons are blind, undirected processes. IOW transpsons (sic) could very well be a design mechanism.”

    The mechanisms by which transposons operate is well-studied. They conform to thermodynamic and chemical principles. Transposition can be recapitulated using isolated components in a test tube.

    It appears as mechanical as any chemical reaction.

    Could a designer be pulling the strings? I suppose so. Are the laws of chemistry designed? Maybe. Do angels run the electron transport chain? Can I falsify these? No. Are they scientific proposals? No.

    “Also ID is still not anti-evolution.”

    Of course not. It is most often theistic evolution-taking a physical mechanism, and taking on that God may have guided it. You, Joe, can take any thing at all, and tack on “that could be a design mechanism.” Sure could be, in that sense.

    So if you believe in a designer that used genomic parasites to develop the placenta, and then left those genomic parasites around to cause infertility and disease, go for it. Science can’t stop you.

  17. 17
    DrREC says:

    “you simply assume that there is a “mechanism””
    vs
    “they demonstrate that it is transposon driven”

    “and that it is “Darwinian””
    vs
    “They demonstrate differences between mammalian lines;”

    ” ID has no need of circular reasoning.”
    I think that is a perfect statement if you omit circular.

  18. 18
    DrREC says:

    “Only a liberal could make such a statement”

    I’ve never discussed politics here. Is everyone you disagree with a liberal, atheist, darwinist?

    “Why don’t you look it up in Wikipedia?”

    I’m thinking of the modern synthesis. I don’t know what you think of “neo-darwinism”

    Transposons, recombination, gene duplication, even polyploidy are not new discoveries. They are the stuff of random variation that is an input for natural selection. Are you arguing that evolutionary biology only thinks point mutations matter?

Leave a Reply