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From PNAS: What’s wrong with peer review

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From a recent article’s Significance statement:

Our research suggests that evaluative strategies that increase the mean quality of published science may also increase the risk of rejecting unconventional or outstanding work.

You don’t mean stuff that is true but no elite source can afford to admit? Shocka! Abstract

Peer review is the main institution responsible for the evaluation and gestation of scientific research. Although peer review is widely seen as vital to scientific evaluation, anecdotal evidence abounds of gatekeeping mistakes in leading journals, such as rejecting seminal contributions or accepting mediocre submissions. Systematic evidence regarding the effectiveness—or lack thereof—of scientific gatekeeping is scant, largely because access to rejected manuscripts from journals is rarely available. Using a dataset of 1,008 manuscripts submitted to three elite medical journals, we show differences in citation outcomes for articles that received different appraisals from editors and peer reviewers. Among rejected articles, desk-rejected manuscripts, deemed as unworthy of peer review by editors, received fewer citations than those sent for peer review. Among both rejected and accepted articles, manuscripts with lower scores from peer reviewers received relatively fewer citations when they were eventually published. However, hindsight reveals numerous questionable gatekeeping decisions. Of the 808 eventually published articles in our dataset, our three focal journals rejected many highly cited manuscripts, including the 14 most popular; roughly the top 2 percent. Of those 14 articles, 12 were desk-rejected. This finding raises concerns regarding whether peer review is ill-suited to recognize and gestate the most impactful ideas and research. Despite this finding, results show that in our case studies, on the whole, there was value added in peer review. Editors and peer reviewers generally—but not always—made good decisions regarding the identification and promotion of quality in scientific manuscripts. (paywall)

As Retraction Watch explains, “Put another way, peer review rewards mediocrity at the expense of breakthroughs.” Hat tip: Retraction Watch Follow UD News at Twitter!

97 Replies to “From PNAS: What’s wrong with peer review

  1. 1
    bornagain77 says:

    a few notes:

    An Interview with David Noble – Peer Review as Censorship by SUZAN MAZUR – 2010
    Excerpt: SUZAN MAZUR: I’ve been focusing on abuse inside the peer review system in recent articles for CounterPunch. The system seems to have spiraled out of control – to the extent that at the low end we now find virtual death squads on Internet blogs out to destroy scientists who have novel theories. They pretend to be battling creationism but their real job is to censor the free flow of ideas on behalf of the science establishment. The science establishment rewards bloody deeds like these by putting the chief assassin on the cover of The Humanist magazine, for example.
    But you’ve written in “Regression on the Left” that the problem IS the peer review system itself. Why do you think so?
    David Noble: When you say THE problem is the peer review system – the peer review system in my view is doing what it was designed to do — censor. And filter. Peer review is a system of prior censorship, prior review – prior meaning prior to publication. So the idea of abusing the peer review system sort of adds insult to injury, because the peer review system itself is injurious.,,,
    http://www.counterpunch.org/20.....ensorship/

    Interview with Suzan Mazur, the author of “The Altenberg 16: An Exposé of the Evolution Industry” (Corruption of peer-review by big science) – video
    http://www.ustream.tv/recorded/6515194

    Everything we know is wrong, 26 August 2014
    Excerpt: “Every day the newspapers carry stories of new scientific findings. There are 15 million scientists worldwide all trying to get their research published. But a disturbing fact appears if you look closely: as time goes by, many scientific findings seem to become less true than we thought. It’s called the “decline effect” – and some findings even dwindle away to zero.
    A highly influential paper by Dr John Ioannidis at Stanford University called “Why most published research findings are false” argues that fewer than half of scientific papers can be believed,,,,
    He even showed that of the 49 most highly cited medical papers, only 34 had been retested and of them 41 per cent had been convincingly shown to be wrong. And yet they were still being cited.
    Again and again, researchers are finding the same things, whether it’s with observational studies, or even the “gold standard” Randomised Controlled Studies, whether it’s medicine or economics. Nobody bothers to try to replicate most studies, and when they do try, the majority of findings don’t stack up. The awkward truth is that, taken as a whole, the scientific literature is full of falsehoods.”
    http://www.bbc.co.uk/programmes/b04f9r4k

    The Folly of Scientism – Austin L. Hughes – Fall 2012
    Excerpt: the high confidence in funding and peer-review panels should seem misplaced to anyone who has served on these panels and witnessed the extent to which preconceived notions, personal vendettas, and the like can torpedo even the best proposals. Moreover, simplistically defining science by its institutions is complicated by the ample history of scientific institutions that have been notoriously unreliable.
    http://www.thenewatlantis.com/.....-scientism

    Nothing in biology makes sense except in light of theology? – Dilley S. – 2013
    Abstract
    This essay analyzes Theodosius Dobzhansky’s famous article, “Nothing in Biology Makes Sense Except in the Light of Evolution,” in which he presents some of his best arguments for evolution. I contend that all of Dobzhansky’s arguments hinge upon sectarian claims about God’s nature, actions, purposes, or duties. Moreover, Dobzhansky’s theology manifests several tensions, both in the epistemic justification of his theological claims and in their collective coherence. I note that other prominent biologists–such as Mayr, Dawkins, Eldredge, Ayala, de Beer, Futuyma, and Gould–also use theology-laden arguments. I recommend increased analysis of the justification, complexity, and coherence of this theology.
    http://www.ncbi.nlm.nih.gov/pubmed/23890740

    “While the great majority of biologists would probably agree with Theodosius Dobzhansky’s dictum that “Nothing in biology makes sense except in the light of evolution”, most can conduct their work quite happily without particular reference to evolutionary ideas. Evolution would appear to be the indispensable unifying idea and, at the same time, a highly superflous one.”
    A.S. Wilkins, editor of the journal BioEssays, Introduction to “Evolutionary Processes” – (2000).

    “Biologists must constantly keep in mind that what they see was not designed, but rather evolved. It might be thought, therefore, that evolutionary arguments would play a large part in guiding biological research, but this is far from the case. It is difficult enough to study what is happening now. To figure out exactly what happened in evolution is even more difficult. Thus evolutionary achievements can be used as hints to suggest possible lines of research, but it is highly dangerous to trust them too much. It is all too easy to make mistaken inferences unless the process involved is already very well understood.”
    Francis Crick – What Mad Pursuit (1988)

    “In fact, over the last 100 years, almost all of biology has proceeded independent of evolution, except evolutionary biology itself. Molecular biology, biochemistry, and physiology, have not taken evolution into account at all.”
    Marc Kirschner, Boston Globe, Oct. 23, 2005

    “Certainly, my own research with antibiotics during World War II received no guidance from insights provided by Darwinian evolution. Nor did Alexander Fleming’s discovery of bacterial inhibition by penicillin. I recently asked more than 70 eminent researchers if they would have done their work differently if they had thought Darwin’s theory was wrong. The responses were all the same: No.,,, In the peer-reviewed literature, the word “evolution” often occurs as a sort of coda to academic papers in experimental biology. Is the term integral or superfluous to the substance of these papers? To find out, I substituted for “evolution” some other word – “Buddhism,” “Aztec cosmology,” or even “creationism.” I found that the substitution never touched the paper’s core. This did not surprise me. From my conversations with leading researchers it had became clear that modern experimental biology gains its strength from the availability of new instruments and methodologies, not from an immersion in historical biology.”
    Philip S. Skell – (the late) Emeritus Evan Pugh Professor at Pennsylvania State University, and a member of the National Academy of Sciences.

    At the 7:00 minute mark of this following video, Dr. Behe gives an example of how positive evidence is falsely attributed to evolution by using the word ‘evolution’ as a sort of coda in peer-reviewed literature:

    Michael Behe – Life Reeks Of Design – video
    https://www.youtube.com/watch?v=Hdh-YcNYThY

    Biologists Are Getting to Be Less Reticent About Using the Phrase “Design Principles” – November 28, 2014
    Excerpt: The word “design” appears 24 times in the paper. “Selection” appears twice, in the phrase “selective pressure” (one of them is just a repetition from the Abstract). Any form of the word “evolution” appears just once:,,,
    We see, therefore, that “design” references outnumber evolutionary references eight to one. We also find “machine” or “machinery” four times, “coding” or “encoding” 15 times, “information” (in terms of information to be processed) five times, “accurate” (in terms of sensing accuracy) 11 times, “precision” 29 times, “efficient” four times, and “optimal” or “optimum” 28 times. Taken together, these design words outnumber evolution words 40 to 1.
    Do the three passing references to evolution/selection add anything to the paper? One would expect to see it in the final Discussion section, but instead, we find these references to design:,,,
    The paper would lose nothing if its three passing references to evolution/selection were left on the cutting-room floor. All these scientists could do was look at the end product and decide, “Yep, it’s fit. It’s optimal.”
    http://www.evolutionnews.org/2.....91531.html

  2. 2
    Mapou says:

    The biggest problem with peer review is that it is inherently elitist. I don’t think it is needed at all. Great thinkers of the past self-published their works. The entire world should be our peers, not just a minority of know-it-alls. I say, publish your stuff openly. If it is any good, it will survive and thrive. If not, it will disappear.

  3. 3
    Axel says:

    Even as an egregiously unqualified layman, reading that sometimes outstanding work is turned down by a peer-review panel, only for its ideas to be stolen, plagiarized by one of the ‘reviewers’, made my hair stand on end.

  4. 4
    bornagain77 says:

    OT: The Case For Intelligent Design (What does the evidence say?) – Tom Woodward – video
    filmed Nov. 22, 2014
    https://www.youtube.com/watch?v=5egamBlC4lM

  5. 5
    bornagain77 says:

    OT: Biological Information – Purifying Selection 12-20-2014 by Paul Giem – video
    https://www.youtube.com/watch?v=SGJZDsQG4kQ

  6. 6
    Mapou says:

    Peer review promotes intellectual incest which inevitably leads to the birth of intellectual monstrosities. Examples of such monstrosities are: infinite number of parallel universes, time travel, immortality via brain uploading, dirt that can self-assemble into living organisms, conscious machines, intelligent machines that enslave or destroy humanity, legal rights for intelligent machines, etc.

  7. 7
    AVS says:

    Peer review is the best we can do. Yes the system isn’t perfect and certainly may need to be revamped, but it serves its purpose well.

    Don’t worry guys, it isn’t peer review that keeps ID out of credible journals; it’s the lack of science behind ID that does this.

    Merry Christmas! Or happy Channukah, or kwanza or festivus!

  8. 8
    Joe says:

    There is plenty of evidence for ID in peer-review. What is AVS blathering about?

  9. 9
    AVS says:

    In your opinion Joe, what is the best example of scientific evidence behind ID?

  10. 10
    rvb8 says:

    I agree with much that has been posted here so far, and Denyse is right to bring up the growing unease, even within the scientific community, of the lack of voice given to some publishable work.

    There are few world renowned scientific journals, and good original work must be recognised. The Net, as Denyse often points out, is a path that these deserving, yet unacknowledged purveyors of scientific revolution might avail themselves of. The ideas however would actually have to be original, ground breaking, and not the retooling of past efforts; any ideas?

  11. 11
    Joe says:

    AVS:

    In your opinion Joe, what is the best example of scientific evidence behind ID?

    Living organisms, their systems and sub-systems.

  12. 12
    AVS says:

    And you realize that evolution explains these things using a thing called science, right?
    Whereas ID doesn’t use science.
    That is why ID is never found in legitimate journals.

  13. 13
    Mung says:

    Got that Joe?

    Evolution explains the origin of life. AVS sez so.

    It’s not science, but it uses science. Whereas ID doesn’t use science.

  14. 14
    Joe says:

    AVS:

    And you realize that evolution explains these things using a thing called science, right?

    That is the propaganda- well except for the origin of life which evolution doesn’t explain, or so we are told. Unguided evolution can’t even be modeled so it doesn’t explain anything.

    However I would love to see a scientific explanation of how life and its systems and subsystems came to be. I say you are bluffing, as usual

  15. 15
    AVS says:

    Isn’t it joe’s job to be the troll, mungy? Or are you both playing that role now?

  16. 16
    Joe says:

    No AVS, YOU are the troll

  17. 17
    Mapou says:

    AVS:

    And you realize that evolution explains these things using a thing called science, right?

    This is another thing that we can thank peer review for, the in-your-face arrogance of the elite. They think they and only they own science. And while they’re gloating, they and their “science” are sitting on a mountain of crap.

    Paul Feyerabend was right when he wrote in Against Method, “the most stupid procedures and the most laughable result in their domain are surrounded with an aura of excellence. It is time to cut them down to size and to give them a lower position in society.

  18. 18
    mike1962 says:

    AVS: And you realize that evolution explains these things using a thing called science, right?

    Detailed “explanations” of body plans, cell types, organs, tissue types, protein domains, please.

    Thank you

  19. 19
    rvb8 says:

    There are many published evidences for all these areas of study mike1962, and as you have access to the inter-net, they are not even difficult to find. But why is it the responsibility of scientists to dig you up, determine your species of IDer, hold your hand, and lead you through the absolute mountains of evidence? If you have an ounce of curiosity, or rather honest curiosity, the evidence is at your fingertip.

  20. 20
    mike1962 says:

    rvb8,

    Are you new here?

    Don’t be ridiculous

  21. 21
    AVS says:

    I did not say evolution explains the origin of life.

    Evolution is science because it uses science.

    I already told you “modeling evolution” at the level you demand is far out of our reach at the moment.

    We do not have an entire explanation of the evolution of life, we have bits and pieces that we are trying to fit together as we continually discover more of them.

    If you don’t like the arrogance that some of the well-educated scientists throw at you, then educate yourself and talk to us on our level. It’s hilarious when I come on here and watch you guys talk down to commenters who are actually well-versed in biology and think you are actually “winning.” My favorite is probably DNA_Jock. Where has he been? You guys didn’t ban him did you? He was running circles around you guys and you didn’t even know it. The same goes for a couple other commenters on here, you guys think you make sense when arguing your side, but it’s quite obvious to those who speak “biologese” hehe that you guys have no idea what you are talking about.

    You guys piss and moan about the arrogance of the elite, and yet you have no problem reaping the benefits of science.
    Well guess what now science is going in a direction that you don’t like, a direction that shakes your beliefs to the core and really makes you think about life and its meaning, and you don’t like it. That’s just too damn bad. Either up your game, or get left in the dust. Right now ID is doing a pretty good job of being left in the dust.

  22. 22
    AVS says:

    Case in point:

    “rvb8,

    Are you new here?

    Don’t be ridiculous”

    I hope that was sarcasm, or else it’s just a perfect example of the idiocy found here at UD. Everything rvb said is 100% true and yet mike here insists someone else do the work for him. And boy is it a mountain of work.

    Mike, try typing those keywords into pubmed, you’ll get hundreds of thousands of hits, all chock-full of the information you’re looking for.

  23. 23
    Robert Byers says:

    Why should the peers recognize breakthroughs? If its that easy they would of done it! If that easy the curce competence in science would of done it .
    Breakthroughs are just that because of a sharper smarter insight relative to the curve.
    its predictable peers will,sometimes, sincerely miss the breakthrough and be very aggressive in its rejection.
    ID/YEC would fit that without a great hostility needing to be invoked.
    howeverr because ID/YEC touches on christianity by dealing with a creator its predictable that hostility,from that, and the incompetence curve would make it hard to gets papers published and a culture welcoming attempts to get papers published.
    ‘m not sure but perhaps paper rejections are a kick in the gut for thinkers that try to publish papers.

  24. 24
    jazzcat says:

    AVS @9

    “…what is the best example of scientific evidence behind ID.”

    I am currently reading Stephen Meyer’s book, “Signature in the Cell: DNA and the evidence for Intelligent Design.” The book makes a case that the digital information in the genetic code provides strong evidence that the origin of life (in essence the origin of the information necessary to produce the first life) was best explained by an intelligent cause. Meyer bases his argument on a standard method of historical scientific reasoning that can be summarized as follows:

    When attempting to explain events in the remote past we can invoke causes in the present that are known to produce the effect in question. The cause which best explains the event is inferred as the best explanation. From our uniform and repeated experience ONLY intelligence is the cause of new functional digital information. Natural causes such as Chance, Necessity, or some combination of the two are inadequate. We can therefore infer that ID is the best explanation for the origin of DNA, therefore life.

  25. 25
    Axel says:

    AVS @ 21

    ‘Evolution is science because it uses science.’

    I use science, when I use the phone, but it doesn’t make me a scientist, dope. Using science? The hotshots who believed in flogiston used science. Would you say flogiston was a scientific ‘find’?

    Difficult to credit, but in the very next sentence….:

    ‘I already told you “modeling evolution” at the level you demand is far out of our reach at the moment.’

    ‘… FAR OUT OF REACH …. AT THE MOMENT.

    So is finding pink pixies (outside of the atheists’ multiverse, that is.) And you know what? I don’t think time comes into it. Not in a month of Sundays. Do you have a reason for thinking otherwise? Apparently not.

  26. 26
    Zachriel says:

    Robert Byers: its predictable peers will,sometimes, sincerely miss the breakthrough and be very aggressive in its rejection.

    Of course, but it’s your scientific peers that you want to convince.

    In any case, the purpose of peer review isn’t to validate scientific research, but to make a journal manageable by reducing the amount of junk. Higher impact journals tend to publish only the most important research. Publication is just the start of the scientific conversation.

  27. 27
    bornagain77 says:

    Evolution is not a testable/falsifiable science. In fact it is a pseudoscience comparable to tea-leaf reading. (Sorry for offending any tea-leaf readers who think they are doing science) 🙂

    “In so far as a scientific statement speaks about reality, it must be falsifiable; and in so far as it is not falsifiable, it does not speak about reality.”
    Karl Popper – The Two Fundamental Problems of the Theory of Knowledge (2014 edition), Routledge
    http://izquotes.com/quote/147518

    It’s Easier to Falsify Intelligent Design than Darwinian Evolution – Michael Behe, PhD
    https://www.youtube.com/watch?v=_T1v_VLueGk

    Darwinism is a Pseudo-Science:
    The primary reasons why Darwinism is a pseudo-science instead of a proper science are as such:
    1. No Rigid Mathematical Basis (Falsification Criteria)
    2. No Demonstrated Empirical Basis
    3. Random Mutation and Natural Selection Are Both Grossly Inadequate as ‘creative engines’
    4. Information is not reducible to a material basis
    https://docs.google.com/document/d/1oaPcK-KCppBztIJmXUBXTvZTZ5lHV4Qg_pnzmvVL2Qw/edit

    It is also interesting to note that the materialistic/atheistic philosophy also resorts to non-falsifiable pseudoscience when trying to explain the origin and fine tuning of the universe and when trying to explain the enigma of quantum wave collapse in the double slit

    In Nature, Two Cosmologists Chide Other Cosmologists for Lack of Testable Evidence – December 22, 2014
    Excerpt: We have frequently criticized some of the crazy ideas emerging from modern cosmology: notions like the multiverse, inflation, Everett’s “many-worlds” scenario, and other concoctions that try to escape the overwhelming evidence for design in the universe,,. Here’s what George Ellis and Joe Silk say in Nature (“Scientific Method: Defend the Integrity of Physics”):
    “This year, debates in physics circles took a worrying turn. Faced with difficulties in applying fundamental theories to the observed Universe, some researchers called for a change in how theoretical physics is done. They began to argue — explicitly — that if a theory is sufficiently elegant and explanatory, it need not be tested experimentally, breaking with centuries of philosophical tradition of defining scientific knowledge as empirical. We disagree. As the philosopher of science Karl Popper argued: a theory must be falsifiable to be scientific.”
    http://www.evolutionnews.org/2.....92311.html

  28. 28
    Zachriel says:

    bornagain77 (quoting): The primary reasons why Darwinism is a pseudo-science instead of a proper science are as such:

    1. No Rigid Mathematical Basis (Falsification Criteria)
    2. No Demonstrated Empirical Basis
    3. Random Mutation and Natural Selection Are Both Grossly Inadequate as ‘creative engines’
    4. Information is not reducible to a material basis

    1. A mathematical basis is not required in science, though evolution does encompass testable mathematical relationships. Indeed, modern statistical science largely derived from the development of population genetics.

    2. The Theory of Evolution makes many empirically testable claims, including predictions concerning natural selection and branching descent.

    3. “Creative engines” is not a well-defined empirical construct. However, we have significant evidence of the evolution of complex adaptive structures, such as the mammalian middle-ear.

    4. Woo is not relevant to the scientific claims entailed in the theory of evolution. We can show various mechanisms by which adaptation occurs.

  29. 29
    bornagain77 says:

    Zach, not that you ever listen to anybody in your relentless effort to chase your tail around in a circle, but As far as the mathematics of statistics can be applied to Darwinian claims through population genetics, Population genetics falsifies Darwinism:

    Biological Information – Purifying Selection (Mendel’s Accountant) 12-20-2014 by Paul Giem
    https://www.youtube.com/watch?v=SGJZDsQG4kQ

    Using Numerical Simulation to Test the Validity of Neo-Darwinian Theory – 2008
    Abstract: Evolutionary genetic theory has a series of apparent “fatal flaws” which are well known to population geneticists, but which have not been effectively communicated to other scientists or the public. These fatal flaws have been recognized by leaders in the field for many decades—based upon logic and mathematical formulations. However population geneticists have generally been very reluctant to openly acknowledge these theoretical problems, and a cloud of confusion has come to surround each issue.
    Numerical simulation provides a definitive tool for empirically testing the reality of these fatal flaws and can resolve the confusion. The program Mendel’s Accountant (Mendel) was developed for this purpose, and it is the first biologically-realistic forward-time population genetics numerical simulation program. This new program is a powerful research and teaching tool. When any reasonable set of biological parameters are used, Mendel provides overwhelming empirical evidence that all of the “fatal flaws” inherent in evolutionary genetic theory are real. This leaves evolutionary genetic theory effectively falsified—with a degree of certainty which should satisfy any reasonable and open-minded person.
    http://www.icr.org/i/pdf/techn.....Theory.pdf

    Using Numerical Simulation to Better Understand Fixation Rates, and Establishment of a New Principle – “Haldane’s Ratchet” – Christopher L. Rupe and John C. Sanford – 2013
    Excerpt: We then perform large-scale experiments to examine the feasibility of the ape-to-man scenario over a six million year period. We analyze neutral and beneficial fixations separately (realistic rates of deleterious mutations could not be studied in deep time due to extinction). Using realistic parameter settings we only observe a few hundred selection-induced beneficial fixations after 300,000 generations (6 million years). Even when using highly optimal parameter settings (i.e., favorable for fixation of beneficials), we only see a few thousand selection-induced fixations. This is significant because the ape-to-man scenario requires tens of millions of selective nucleotide substitutions in the human lineage.
    Our empirically-determined rates of beneficial fixation are in general agreement with the fixation rate estimates derived by Haldane and ReMine using their mathematical analyses. We have therefore independently demonstrated that the findings of Haldane and ReMine are for the most part correct, and that the fundamental evolutionary problem historically known as “Haldane’s Dilemma” is very real.
    Previous analyses have focused exclusively on beneficial mutations. When deleterious mutations were included in our simulations, using a realistic ratio of beneficial to deleterious mutation rate, deleterious fixations vastly outnumbered beneficial fixations. Because of this, the net effect of mutation fixation should clearly create a ratchet-type mechanism which should cause continuous loss of information and decline in the size of the functional genome. We name this phenomenon “Haldane’s Ratchet”.
    http://media.wix.com/ugd/a704d.....fa9c20.pdf

    Calling all Darwinists, where is your best population genetics simulation? – September 12, 2013
    Excerpt: So Darwinists, what is your software, and what are your results? I’d think if evolutionary theory is so scientific, it shouldn’t be the creationists making these simulations, but evolutionary biologists! So what is your software, what are your figures, and what are your parameters(?) And please don’t cite Nunney, who claims to have solved Haldane’s dilemma but refuses to let his software and assumptions and procedures be scrutinized in the public domain. At least Hey was more forthright, but unfortunately Hey’s software affirmed the results of Mendel’s accountant.
    http://www.uncommondescent.com.....imulation/

    Natural Selection Struggles to Fix Advantageous Traits in Populations – Casey Luskin – October 23, 2014
    Excerpt: Michael Lynch, an evolutionary biologist at Indiana University,, writes that “random genetic drift can impose a strong barrier to the advancement of molecular refinements by adaptive processes.”2 He notes that the effect of drift is “encouraging the fixation of mildly deleterious mutations and discouraging the promotion of beneficial mutations.”3 Likewise, Eugene Koonin, a leading scientist at the National Institutes of Health, explains that genetic drift leads to “random fixation of neutral or even deleterious changes.”4
    http://www.evolutionnews.org/2.....90571.html

    Thou Shalt Not Put Evolutionary Theory to a Test – Douglas Axe – July 18, 2012
    Excerpt: “For example, McBride criticizes me for not mentioning genetic drift in my discussion of human origins, apparently without realizing that the result of Durrett and Schmidt rules drift out. Each and every specific genetic change needed to produce humans from apes would have to have conferred a significant selective advantage in order for humans to have appeared in the available time (i.e. the mutations cannot be ‘neutral’). Any aspect of the transition that requires two or more mutations to act in combination in order to increase fitness would take way too long (greater than 100 million years).
    My challenge to McBride, and everyone else who believes the evolutionary story of human origins, is not to provide the list of mutations that did the trick, but rather a list of mutations that can do it. Otherwise they’re in the position of insisting that something is a scientific fact without having the faintest idea how it even could be.” Doug Axe PhD.
    http://www.evolutionnews.org/2.....62351.html

    2. The fossil record, especially the ‘top down’ Cambrian Explosion, looks nothing like what is predicted in Darwinism. The genetic evidence also looks nothing like what Darwinism predicts:
    3. The mammalian middle-ear ‘just so story’ of Darwinists is a prime example of the pseudo-scientific tea leaf reading of Darwinism that poses as real science.
    4. Calling the fact that ‘information’ is not reducible to a material basis ‘woo’ does not address the fact that information is, in fact, not reducible to a material basis. It merely gave you false comfort in the face of a insurmountable theoretical difficulty for Darwinism. ,,, Epigenetic modes of rapid adapatation are non-Darwinian in their ‘mechanism’ (i.e. saying evolution ‘evolved’ mechanisms to adapt to differing environments invokes teleology, even foresight, within Darwinism’s supposedly unguided processes).

    Zach, I definitely have much better things to do today than waste ANOTHER day watching you chase your tail in a circle, so I will not respond to you any more.

  30. 30
    Joe says:

    AVS:

    I did not say evolution explains the origin of life.

    Yes, you did

    Evolution is science because it uses science.

    No, it doesn’t.

    I already told you “modeling evolution” at the level you demand is far out of our reach at the moment.

    I don’t demand anything. Yours is the position that sez it haz a step-by-step process yet cannot demonstrate such a thing.

    So all AVS haz is bluster and bluffing. How typical is that?

  31. 31
    AVS says:

    Interesting Jazz, but Meyer’s argument breaks down when you look at the structure and function of DNA in a biological context. Characterizing DNA as digital data, works only at a superficial level. It is simply a comparison to help understand the function of DNA. In reality, the inner-workings of the cell at the molecular level are very different from the things IDers compare them to. This poor comparison is then used by Meyer to basically say that because intelligence is the only known cause of digital information, DNA (because it resembles it at a superficial level) also must be intelligently designed.

    It’s like saying the “well the train sitting in the station right now and the train under my Christmas tree look similar, therefore they must have the same designer.”
    That’s not a great example, but it’s pretty close an idea to the attempts at comparing biology to things that aren’t biology-related.

  32. 32
    Joe says:

    AVS- Your position cannot explain the origin of DNA. Your argument breaks down when reality enters.

  33. 33
    Joe says:

    Zacho:

    2. The Theory of Evolution makes many empirically testable claims, including predictions concerning natural selection and branching descent.

    Reference please- that is reference this alleged theory of evolution so we can all see what it predicts. Natural selection has proven to be impotent so what do you think it predicts?

  34. 34
    jazzcat says:

    AVS @31

    Thank you for your reply. It is an interesting counter point. So are you saying that DNA functions as digital information but it in fact isn’t? I would argue that if it functions as digital information it is in fact digital information. It may be other things in addition to digital information but it clearly has at least that function. So to be frank DNA is not digital info on a superficial level, it is digital info in reality.

    Meyer also notes from the structure of DNA it is also clear that DNA is information. Because there are no chemical or physical forces of attraction that sequence the nucleic acids along the backbone this allows DNA to contain a great deal of coding instructions for proteins and for self replication.

  35. 35
    AVS says:

    Once again, Joe, you have resorted to the “evolution hasn’t explained it yet, therefore evolution is wrong” argument.

    Maybe someone should start a set of “ID debating (senseless demands) device” posts.

  36. 36
    AVS says:

    Hmm, I guess DNA could be called digital data jazz, but the problem is that you cannot compare biological molecules and their functions to the non-living things of human design. What’s superficial is this comparison. I’m curious, what do you think is the closest source of digital information that is similar to DNA?

  37. 37
    jazzcat says:

    AVS @36

    I see no reason you cannot compare biological molecules to other things in order to explain their structure/function/origin. Humans design biological molecules all the time.

    “what do you think is the closest source of digital information that is similar to DNA?” I’m not sure I completely understand your question. To answer your question at face value: Humans are the closest source of digital information that is similar to DNA. I’m probably sure that wasn’t the answer you were looking for. Please re-phrase? Thanks!

  38. 38
    jazzcat says:

    AVS

    Would it help if the argument were re-phrased as such?:
    Digital Information as a function ONLY arises from an intelligent source from our uniform and repeated experience. Natural processes such as chance, necessity, or a combination of the two are inadequate and have never been shown to produce the function of digital information. Because DNA functions as information we can logically infer to the best explanation that ID is the origin of the function of Digital Information in DNA.

  39. 39
    AVS says:

    This is the problem, jazz. The molecular world is very different from the macro-scale world that we are much more familiar with. My question was worded poorly, I’m basically asking what is the closest human-designed thing to DNA. I think that if you give your answer to it, I will be able to point out some significant differences between it and DNA.

    Can you give me some examples of molecules designed by humans while your at? Just off the top of your head.

    Thanks

  40. 40
    Joe says:

    AVS:

    Once again, Joe, you have resorted to the “evolution hasn’t explained it yet, therefore evolution is wrong” argument.

    That is your opinion and doesn’t follow from what I have posted. Also ID is not anti-evolution and your ignorance of the debate is still meaningless.

  41. 41
    AVS says:

    It is exactly what you are saying Joe. “Evolution hasn’t explained the existence of ATP synthase,” “evolution hasn’t explained the existence of DNA,” etc. It’s all the same argument, you’re just picking at the current gaps in knowledge and ignoring what is already known.

    Did you take a look at those papers I told you about on the other post that talk about the evolution of ATP synthase by the way?
    I doubt it.
    Ignorance is bliss.

  42. 42
    jazzcat says:

    AVS @39

    “What is the closest human-designed thing to DNA?” blueprints, computer software, hieroglyphic inscriptions, pages of text.

    “Can you give me some examples of molecules designed by humans while you’re at it?” I cannot name the molecular structures off the top of my head but I can name some abstractly: Ribozyme and protein engineering, GMOs, medicines…etc

  43. 43
    jazzcat says:

    I don’t see the relevance in this AVS. You don’t dispute the premise of ID that humans (who are intelligent) have the ability to produce digital information do you?

    Is there a problem with the standard method of historical scientific reasoning you disagree with? We are trying to explain the origin of an event in the remote past: the origin of the information necessary to produce the first living cell.

  44. 44
    Joe says:

    AVS- I am OK with intelligent design EVOLUTION producing DNA and ATP synthase. What cannot be tested nor modeled is unguided evolution doing it. There aren’t any testable hypotheses for such a thing. It cannot be measured, there aren’t any equations, it is all bluff and willful ignorance of your opponents’ positions.

    Did you take a look at those papers I told you about on the other post that talk about the evolution of ATP synthase by the way?

    Yes, nothing that relates to unguided processes and nothing that can be demonstrated scientifically.

  45. 45
    AVS says:

    Do you not see how superficial those comparisons are to DNA and its functions in the cell, jazz? The biggest difference is that the functions of DNA are carried out without the need for a conscious mind. Proteins simply interact with the DNA to copy it, transcribe and express it, correct it, induce mutations, etc. based solely on molecular interactions. Evolution at the molecular level is the alteration of these functions that make small changes in an organism which selection can act on. The basic function of DNA as information storage is comparable to these things, but that is where the similarities end.

    And I think you’re giving a little too much credit to the design of those molecules. They are just slightly modified versions of naturally existing molecules, although this is no small task.

  46. 46
    jazzcat says:

    AVS @45

    You’re mischaracterizing Meyer’s argument. No where does he make the case that the actions DNA carries out are due to a conscious mind. Computers perform software functions without conscious activity. A photo-copier copying the information in a book does not require an intelligent design. What he seeks to explain is the ORIGIN of such information.

    “Evolution at the molecular level is the alteration of these functions that make small changes in an organism which selection can act on.” I agree but this is presuming organisms before the origin of life. There is no natural selection with random variations BEFORE the origin of life which involves selection and variation.

    “The basic function of DNA as information storage is comparable to these things, but that is where the similarities end.” I’ll grant you that statement for the sake of argument. You have admitted that DNA functions as information storage…it stores information. Where did the information come from? It can transmit from organism to organism but the FIRST organism could NOT have the information transmitted to it without first assuming another living organism before that one.

    Where did the information necessary to produce the first life come from? From our uniform and repeated experience only intelligence is the cause. Natural processes have NOT shown the ability to produce new information, they can merely transmit existing information. If my premises are true as you have admitted, then my conclusion would HAVE to be true.

  47. 47
    jazzcat says:

    AVS @45

    “Proteins simply interact with the DNA to copy it, transcribe and express it, correct it, induce mutations, etc. based solely on molecular interactions.” Careful now, it is NOT SOLELY based on molecular interactions it is based on molecular interactions WITH the information contained in the sequencing of the nucleic acids. The sequencing of the nucleic acids are NOT due to any molecular, chemical, or physical interaction.

    You have also highlighted what origin of life researchers call the “DNA enigma.” DNA contains instructions for building proteins, but proteins are required to build DNA strands. It is a chicken & chicken egg dilemma. The mere presence of this closed loop suggests a purposeful arrangement of parts to suit a specific goal.

  48. 48
    Zachriel says:

    jazzcat: Where did the information necessary to produce the first life come from?

    Evolution provides us some clues. The evidence implies branching descent and adaptation through natural selection, adaptation roughly translating into an increase in “information”. As we have a natural mechanism whereby this information can increase, it’s reasonable to suppose that similar mechanisms were involved before the most recent common ancestor. As for the very first life, there are a number of ideas; and while there is no complete theory, there is some tentative evidence supporting abiogenesis, with no evidence of a designer.

    jazzcat: From our uniform and repeated experience only intelligence is the cause.

    That is incorrect. Evolution can result in new information.

  49. 49
    jazzcat says:

    Zachriel @48

    Since we’re talking about the origin of life most of your comment does not apply, however you said this, “As for the very first life, there are a number of ideas; and while there is no complete theory, there is some tentative evidence supporting abiogenesis, with no evidence of a designer.”

    You did not answer my question which where did the information necessary to produce the first life come from?

    “Evolution can result in new information.” Irrelevant to the origin of life. Before life there is NO evolution because there is no biological information transmitted from parent to offspring. There is no mutations in copying DNA because this is BEFORE DNA. Please provide just ONE example of a natural process producing functional digital information?

  50. 50
    Zachriel says:

    jazzcat: Since we’re talking about the origin of life most of your comment does not apply

    Ignoring the evidence doesn’t mean it goes away. Evolution provides information about early life, which helps shed light on its origin.

    Furthermore, you base your position on the false claim that “Natural processes have NOT shown the ability to produce new information, they can merely transmit existing information.” Evolution is the counterexample.

  51. 51
    AVS says:

    Ok, so you want to talk about the origin of information in cells. This is a hot-topic for IDers because of the gaps in origins research. It is extremely difficult to study the earliest forms of life so we have to do our best with what we already know.

    So what do we know?
    We know that nitrogenous bases and sugars can arise from early-earth experiments, minerals bind preferentially to ribose sugars, these minerals were prevalent at the sites of proposed chemical evolution and are capable of catalytic activity, activation of nucleotides has been seen in early-earth experiments, these experiments have produced nucleotide strands up to 100 nucleotides in length even without nucleotide activation, RNA molecules are capable of both information storage and catalyzing a number of chemical reactions, the evolution of ribozymes that join two nucleotides together into a ribozyme that is capable of adding multiple nucleotides has been shown, molecular evolution of ribozymes that catalyze the binding of base to sugar has been demonstrated. This is some of the information behind the RNA world, with the key being that RNA is capable of storing information and catalyzing reactions. The evolution of RNA molecules that were capable of catalyzing chemical reactions conducive to life as we now know it also have the information for their replication stored within them. How exactly these molecules evolved and along with other molecules formed the first cell is certainly a mystery and there is still much we don’t know, but we are piecing the puzzle together.

  52. 52
    jazzcat says:

    Zachriel @50

    Yes Natural processes have NOT shown the ability to produce new information. There is no counter example. This is why the inference to ID works especially at the origin of life, before Darwin’s theory of evolution can “take hold.” Once you provide a counter example of how the information in DNA or RNA in the first life could arise through a wholly natural process, you let us know mmk?

  53. 53
    Zachriel says:

    jazzcat: Natural processes have NOT shown the ability to produce new information. There is no counter example.

    The counterexample is evolution, which is a natural process.

  54. 54
    jazzcat says:

    AVS @51

    We may be getting somewhere. A few points of rebuttal:
    -Prebiotic experiments generally show that some of those required for life can arise but not nearly in sufficient quantities for a prebiotic soup.
    -Random strands of nucleotides would not produce any information therefore function so there could be no selection. It is the specific sequence that is needed.
    -RNA is capable of catalyzing some reactions and capable of storing some information but it is inadequate for producing a living cell.
    -Self replication requires much more information then just an RNA molecule.
    -Furthermore functional RNA contains information which would be the thing we are trying to explain in the first place. Where did the information come from?

  55. 55
    jazzcat says:

    Zachriel @53

    I can see we’re getting nowhere.

    “the counterexample is evolution, which is a natural process.” Really? Then you wouldn’t mind showing me how?

  56. 56
    AVS says:

    Jazz, look into the surface metabolism model. Concentration of the necessary molecules likely occured near or on the hydrothermal vents, providing environments suitable for chemical evolution. Neither of these models are likely to be completely correct but they are small steps toward the generation of the first cell. random strands most certainly can produce function as has been demonstrated in experiments that use millions of random sequences and then select for certain catalytic activity, some of these I just mentioned. And as I said, the sequence of these strands themselves is the information for their replication (similar to DNA) as well as function. The production of the first living cell no doubt also involved other molecules that have been generated in early earth experiments, one of the most important being lipids, which are capable of forming a bilayer on their own. “Self-replication requiring more than RNA” is your opinion, as I said we have already shown the evolution of ribozymes that can add short sequences of template directed nucleotides. The information is inherent to the sequence and resulting shape of the molecule. “Structure begets function.” This is one of the most important ideas of biology. Early ribozymes synthesize random strands of nucleotides, some of these strands will have catalytic activity, this has been demonstrated time and time again. What we have to figure out is which of these catalytic reactions were important for early life and which evolved later.

  57. 57
    jazzcat says:

    AVS @56

    Thank you for your reply. “Signature in the Cell,” has chapters of debunking the current OOL models such as metabolism first, RNA world, clay hypothesis, etc..although I have not gotten that far in the book so I will take a look at your model. Thank you for presenting it.

    Three points we could continue the conversation with:
    1) Water is a poor (thermodynamically unfavored) environment for amino acid synthesis because the reaction releases a water molecule.
    2) Intelligent agents are artifically synthesizing strands and then intelligently selecting them for certain functions. They are also preventing interfering cross reactions that would otherwise not be prevented in a mixture of chemicals.
    3) “structure begets function” does not apply before life. In order for function to arise in the first place the correct sequence must be found. Since there is a vast number of possible sequences theorists must resort to chance, at which odds defy any reasonable chance of happening in the entire universe.

  58. 58
    humbled says:

    Evolution does NOT produce information, not in reality anyway, it only corrupts existing information. Come on folks, this is 101 stuff.

    RM + NS has never produced a new system or body part. Nothing naddah zilch. Since RM + NS cannot do what the Darwin faithful claim it can, but worshipped and defended regardless, Darwinian evolution is exposed as yet another belief system.

  59. 59
    AVS says:

    I’m sure the book has plenty of pseudoscientific nonsense in it, jazz. Anyways,
    1. I assume you’re talking about polypeptide synthesis, not amino acid synthesis. Either way, the presence of ribozymes that catalyze this reaction would overcome this problem. In accordance with this, it’s no surpise to find the ribosome, which is the site of polypeptide synthesis is largely made up of RNA and active site is entirely made up of RNA.
    2. Does it really matter how the experimental strands came about or how they select for them? In the end you are using random sequences and looking for function. This is exactly what would have happened in chemical evolution, it is a model of chemical evolution. Preventing cross reactions is a necessity in experiments like these, variables must be controlled. Who knows, maybe not allowing cross-reactivity is what is keeping us from finding more efficient self-replicators.
    3. “Structure begets function” applies as soon as you have a function. The function is controlled by the structure. You can have many structures many of them will have function to some degree, some will not. Chemical evolution found these structures, likely with low level function, and chemical evolution built upon it. Don’t fall into the trap of think that evolution looks for a single “correct” sequence, it does not.

  60. 60
    jazzcat says:

    AVS @59

    If you are going to presuppose ribozymes catalyzing reactions you would in effect presuppose the presence of biological information, which is what we’re trying to explain the origin of.

    Yes I meant polypeptide synthesis, amino acids linking together, sorry about that.

    It’s funny you don’t see the irony in intelligent agents artifically synthesizing RNA strands and through intelligent selection, selecting those for functions that COULD be a plausible pathway to the first life. Even if some “function” was found, it would be no help to the origin of life, which needs ALL of the proper functions in place at the right time. An RNA that can catalyze one or two reactions does not lead to the synthesis of a protein

    I agree structure begets function as soon as you have function, but a random RNA sequence won’t provide a function. ONly a very very small number of sequences among the VAST combinatorial possibilities provide any function.

    And I don’t appreciate the tone towards Meyer’s book. Have you read it? Critiquing a model is not pseudoscientific.

  61. 61
    Zachriel says:

    jazzcat: -Prebiotic experiments generally show that some of those required for life can arise but not nearly in sufficient quantities for a prebiotic soup.

    Based on what we have discovered so far, but the epoch in question is very ancient, and we have only just begun to explore the history.

    jazzcat: -Random strands of nucleotides would not produce any information therefore function so there could be no selection.

    That’s not necessarily the case. Even simple sequences can have catalytic functions.

    jazzcat: -RNA is capable of catalyzing some reactions and capable of storing some information but it is inadequate for producing a living cell.

    Once you have replication, then you have evolution. A membrane is usually considered essential in order to isolate the replicase, but simple membranes can form spontaneously.

    jazzcat: -Furthermore functional RNA contains information which would be the thing we are trying to explain in the first place. Where did the information come from?

    Random RNA sequences can have function. But you are right. There are many open questions.

    jazzcat: Really? Then you wouldn’t mind showing me how?

    It’s called adaptation. See Darwin 1859.

    jazzcat: Since there is a vast number of possible sequences theorists must resort to chance, at which odds defy any reasonable chance of happening in the entire universe.

    That is your claim, however, there’s no a priori reason for that claim. It’s quite possible that it is inevitable given the appropriate conditions. No one knows at this time.

    humbled: RM + NS has never produced a new system or body part.

    Legs.

    jazzcat: a random RNA sequence won’t provide a function.

    That is incorrect. See Sassanfar & Szostak, An RNA motif that binds ATP, Nature 1993.

  62. 62
    AVS says:

    Yes, as I already said these ribozymes with catalytic activity were generated by the function search carried out by chemical evolution. When the first RNA molecule was able to catalyze a reaction, the sequence became the information for a catalytic molecule. Many RNA molecules are capable of catalytic activity, it was the job of chemical evolution to search for useful molecules and the right combination of useful molecules, of course this was no simple task.
    And look, the protocols of the RNA evolution experiments were specifically designed to mimic the process of natural selection, if you disagree, you should take it up with the scientists themselves or maybe carry out your own experiments. Something tells me you’ve wandered a little too far into the realm of experimental biology to really understand how nonsensical the claims are that you are making.

    “All of the proper functions in the right place at the right time” is a phrase commonly thrown around by IDers despite us not knowing what these functions even are. Who knows how many there are or how many of them are temporally sensitive.
    And no, only one molecule that can catalyze a peptide bond is needed to potentially synthesize a protein.

    And wrong again, a random RNA sequence certainly can provide a function. This was a requirement for the some of the experiments that we have talked about. The investigators started off with random sequences, induced random, mutations, and selected for certain active molecules. These active molecules have developed a function and their sequence is the information for the synthesis of this molecule.

  63. 63
    Andre says:

    Good grief. Lots of twaddle from AVS and Zach but no concrete evidence to back their claims.

    Anything on where the information came from gents?

  64. 64
    Andre says:

    AVS

    the function search?

    So evolution is by your own admission very much guided then?

  65. 65
    AVS says:

    It certainly is hilarious when IDers claim there’s no “concrete evidence” for something.

    And evolution is guided by selection.

  66. 66
    Mung says:

    It certainly is hilarious when people who have been here to UD time and again find it hilarious when IDers claim there’s no “concrete evidence” for something when it’s almost beyond doubt that these people have been asked by the ID’ers here, yes even encouraged, repeatedly, to provide the evidence they claim exists, and consistently fail to do so.

    It certainly is hilarious when IDers claim there’s no “concrete speculation” for something. No, we see that here all the time.

  67. 67
    AVS says:

    Oh Mungy, I gave little Joey a few papers on the evolution of ATP synthase in response to his claims that no one has provided evidence of its evolution. He didn’t read them, and even if he did, I doubt he would understand them. In this conversation, Andre (another genius here at UD), decides to put his two cents in which adds up to pretty much nothing. He has nothing to say that even resembles a scientific thought despite there being plenty of opportunity from the posts I have already made. Instead he asks a question I have already answered numerous times for jazzy and then asks another ridiculous question that shows his complete lack of knowledge on the subject of evolutionary biology.

  68. 68
    Mung says:

    AVS:

    Oh Mungy, I gave little Joey a few papers on the evolution of ATP synthase in response to his claims that no one has provided evidence of its evolution.

    ATP Synthase is an enzyme.

    The evolution of ATP Synthase can easily mean at least two different things.

    1.) An explanation for the existence of ATP Synthase.

    2.) A description of how the ATP Synthase enzyme has changed over time.

  69. 69
    AVS says:

    Oh gotcha mungy, so you choose to ignore the one that we do have evidence for and point to the one that science hasn’t gotten to yet. This is the epitome of the infamous “reading only between the lines of evidence” ID debating device.
    Classic!

  70. 70
    Zachriel says:

    Andre: no concrete evidence to back their claims

    We cited Sassanfar & Szostak.

    Mung: An explanation for the existence of ATP Synthase.

    The evidence suggests ATP synthase evolved when two separate structures combined. See Doering et al., Rotary DNA motors, Biophysical Journal 1995.

  71. 71
    Joe says:

    Zachriel is just another equivocator. We are asking for evidence that unguided evolution produced ATP synthase.

    Grow up already

  72. 72
    Joe says:

    AVS:

    And evolution is guided by selection.

    Pure ignorance. Natural selection eliminates and doesn’t guide anything. How many blind and mindless guides do you know, AVS?

    Oh Mungy, I gave little Joey a few papers on the evolution of ATP synthase in response to his claims that no one has provided evidence of its evolution.

    That wasn’t my claim. Obviously you are just an ignorant troll.

  73. 73
    Joe says:

    Zacho:

    The counterexample is evolution, which is a natural process.

    Intelligent design is a natural process.

  74. 74
    Steve says:

    jazzcat: From our uniform and repeated experience only intelligence is the cause.

    zachriel: That is incorrect. Evolution can result in new information.

    zachriel, that is incorrect.

    All ‘new’ information is derived from previously existing information. In order for non-designed information to arise, darwinian style non-directed, non-purposeful, non-goal oriented information would have to be shown to have taken place at abiogenesis, and continued unabated throughout the history of life.

    But since darwinians say their brand of evolution comes after the first abiogenesis event, logic and reason tell us that darwinian processes can account for a given process ONLY in the context of a designed system.

    So we can see that design stands out as the more logical, reasonable and intellectually desirous explanation as it can account for all of the biological transitions:

    Essential molecules like water, oxygen are designed to form a biosphere.
    Said biosphere designed to sustain life.
    Said life designed in stages, developing in tandem with the developing biosphere.
    Said biosphere designed around oscillating patterns of celestial body movements, resulting in oscillating environmental conditions.
    Said oscillating environmental conditions require organisms have variation designed into them in order to respond to those environmental conditions.
    Said variation creating symbiotic stability within the environment.
    Said stability completing the design.

  75. 75
    Andre says:

    Zachriel

    The evidence “suggests” that you are you have a lesser evolved brain.

  76. 76
    jazzcat says:

    Sorry for the late response guys. Holiday Season got the best of me. I believe Zachriel and AVS persist in a single logical error in this thread. Hopefully this post should correct it.

    Zachriel @61

    “Once you have replication, then you have evolution. A membrane is usually considered essential in order to isolate the replicase, but simple membranes can form spontaneously.”

    What is also considered essential for replication is information bearing molecules. You just admitted that ONCE YOU HAVE replication then you have evolution, but in order to have replication you need information, so you CANNOT explain the origin of information with “evolution” because evolution happens AFTER replication.

    “jazzcat: a random RNA sequence won’t provide a function.
    Z: That is incorrect. See Sassanfar & Szostak, An RNA motif that binds ATP, Nature 1993.”

    Keep in mind what we mean by function. A single nucleotide could chemically interact with “something” but calling it a “function” especially related to the OOL is disingenuous. Either a protein or a gene that codes for a protein would qualify as functionally specific for OOL.

    “jazzcat: Since there is a vast number of possible sequences theorists must resort to chance, at which odds defy any reasonable chance of happening in the entire universe.
    Z: That is your claim, however, there’s no a priori reason for that claim. It’s quite possible that it is inevitable given the appropriate conditions. No one knows at this time.”

    That is not true, we actually DO know that the number of functional sequences among the vast possible combinations of nucleotides with RNA/DNA and amino acids with proteins is vanishingly small. Meyer provides the calculations in his book. From experimental work the number of functional genes/proteins among the vast combinatorial space was about 1 in 10^160 for a modest length gene/protein. Given the probabilistic resources of this universe and given all the time that has past since the beginning of the universe this makes the chance of finding ONE functional gene/protein relevant to OOL implausible by chance. It’s also the reason most OOL researches abandon random searches for function as a plausible model.

    AVS: would you have us believe that random molecules “searched” for the functions it needed without any regard as to how molecules know how to search for what it needs? Searching is a teleological term. Engineers can search because they are forward thinkers and can ask, “which molecules do “I” need in order to generate a living cell.

    @62 “the protocols of the RNA evolution experiments were specifically designed to mimic the process of natural selection.” Again same logical error as Zachriel, natural selection can happen AFTER replication, but replication requires information bearing molecules (in extant cells it requires over 30 proteins in integrated closed loop circuitry). Even in minimal complexity experiments it would require an information molecule, a molecule(s) to transcribe the information, molecule(s) to bind to the new raw materials, an assembly molecule(s) to put them together. These would satisfy “all functions in the right place at the right time.”

    RNA engineers mimic the powers of a designing intelligence in these experiments.

  77. 77
    Zachriel says:

    Steve: All ‘new’ information is derived from previously existing information.

    Depending on your definition of “information”, evolution incorporates information about the environment.

    Steve: In order for non-designed information to arise, darwinian style non-directed, non-purposeful, non-goal oriented information would have to be shown to have taken place at abiogenesis, and continued unabated throughout the history of life.

    It’s easy enough to show that once you have replicators, information can increase in genomes.

    jazzcat: You just admitted that ONCE YOU HAVE replication then you have evolution, but in order to have replication you need information, so you CANNOT explain the origin of information with “evolution” because evolution happens AFTER replication.

    A catalyzing sequence has “information”. Catalysis can occur in random sequences.

    jazzcat: Either a protein or a gene that codes for a protein would qualify as functionally specific for OOL.

    Or a ribozyme.

    jazzcat: we actually DO know that the number of functional sequences among the vast possible combinations of nucleotides with RNA/DNA and amino acids with proteins is vanishingly small.

    That is incorrect. See Sassanfar & Szostak, An RNA motif that binds ATP, Nature 1993.

    jazzcat: Even in minimal complexity experiments it would require an information molecule, a molecule(s) to transcribe the information, molecule(s) to bind to the new raw materials, an assembly molecule(s) to put them together.

    RNA appears capable of acting as both messenger and replicator.

    No one has all the answers concerning the origin of life, but your argument that it is a priori not possible through natural mechanisms is just an argument from ignorance.

  78. 78
    jazzcat says:

    Zachriel @77

    “jazzcat: You just admitted that ONCE YOU HAVE replication then you have evolution, but in order to have replication you need information, so you CANNOT explain the origin of information with “evolution” because evolution happens AFTER replication.
    Z: A catalyzing sequence has “information”. Catalysis can occur in random sequences.”

    Evading the problem eh? Does Catalysis equal replication? What does the sequence catalyze? Does it catalyze amino acids together? Does it catalyze a gene together? The information NECESSARY to produce the first living cell is the information that carries the instructions for building proteins (critical cell functions for survival) and for self replication (critical for continuing survival). An RNA sequence that catalyzes by binding to ATP (Szostack’s paper) does NOT solve this issue.

    My argument is not “impossible” but rather “extremely implausible” for natural mechanisms to produce life. My argument is based on what we know, not from gaps.

  79. 79
    jazzcat says:

    Zachriel

    If I wanted to read beyond the abstract I would have to pay. If you have read the paper can you answer the following questions for me?

    1) How do they synthesize the RNAs in a “random” fashion?
    2) If they are protecting their RNA sequences from degradation from the environment, what would prevent them from degrading WITHOUT their careful experimentation?
    3) The catalyzing sequences that “emerge,” how long are they? (ie # of nucleotides)
    4) If the found function of binding ATP is found, how is this relevant to OOl since they are presupposing other life components.

  80. 80
    Zachriel says:

    jazzcat: Does Catalysis equal replication?

    Replication is a type of catalysis.

    jazzcat: What does the sequence catalyze?

    The substrate, which could be itself (or its mirror).

    jazzcat: Does it catalyze amino acids together? Does it catalyze a gene together?

    The presumption is that replication precedes protein synthesis.

    jazzcat: My argument is not “impossible” but rather “extremely implausible” for natural mechanisms to produce life.

    Then your argument is based on ignorance. You don’t know how it happened, it seems complicated, so there’s no way it did. Does your argument change if we discover catalyzing RNA? Or if we show that contrived RNA can replicate? Or if we show that random RNA sequences can have catalytic function? If not, then what would change your argument?

  81. 81
    jazzcat says:

    Zachriel @80

    “Replication is a type of catalysis.”

    So the answer to the question is NO, they are not the same, replication requires catalysis but calalysis alone cannot cause replication.

    “The presumption is that replication precedes protein synthesis.” Why is this presumed? In extant cells, replication REQUIRES proteins.

    “Your argument is based on ignorance.” No Zachriel, it’s your argument. None of us know how it happened, we weren’t there. You assume that it must be a wholly natural process (a philosophical assertion). I don’t assume an intelligent agent acted, I infer from the presence of biological information which would have been required BEFORE any kind of evolutionary process. Because my argument concludes ID as the best explanation, I am open to new evidence should it come about.

    “Does your argument change if we discover catalyzing RNA? Or if we show that random RNA sequences can have catalytic function?” The experiments you cited are not random and undirected, they are carefully controlled by chemists. RNA is incredibly hard to synthesize but easy to destroy. Nonetheless, my answer is NO because it doesn’t solve the origin of the information necessary to produce the proteins which are critical to cell survival and for self-replication.

    “What would change your argument?” If it could be shown that a blind, undirected process (such as a sea of nucleotides or amino acids) has the capability to produce functionally specific information (genes/proteins). If not random chance then perhaps by necessity. If it could be shown that some sort of physical or chemical law(s) of necessity has the capability to produce functionally specific information. FSCO/I as it is also called. You also have to demonstrate that sufficient prebiotic chemicals existed on the early Earth, enough so that there are sufficient probabilistic resources and time to generate a living cell.

    There are other falsifications to ID theory, but I believe the ones I mentioned pertained to the origin of biological information with regards to the OOL.

    Take Care!

  82. 82
    Zachriel says:

    jazzcat: 1) How do they synthesize the RNAs in a “random” fashion?

    They use a random library and look for the function of interest.

    jazzcat: 2) If they are protecting their RNA sequences from degradation from the environment, what would prevent them from degrading WITHOUT their careful experimentation?

    It’s an experimental setup. It purports only to show that random sequences can have function, consistent with the theory of RNA World. This contradicts your claim above.

    jazzcat: 3) The catalyzing sequences that “emerge,” how long are they? (ie # of nucleotides)

    The library was composed of sequences of length 169. They analyzed the functional ribozymes and experimentally reduced them to length 40.

    jazzcat: 4) If the found function of binding ATP is found, how is this relevant to OOl since they are presupposing other life components.

    jazzcat: What is also considered essential for replication is information bearing molecules.

    jazzcat: So the answer to the question is NO, they are not the same, replication requires catalysis but calalysis alone cannot cause replication.

    See Robertson & Joyce, Highly Efficient Self-Replicating RNA Enzymes, Chemistry & Biology 2014.

    jazzcat: You assume that it must be a wholly natural process (a philosophical assertion).

    The assumption is called a hypothesis, not a philosophical assertion. A hypothesis is a tentative assumption held for the purposes of testing its empirical entailments.

    jazzcat: I infer from the presence of biological information which would have been required BEFORE any kind of evolutionary process.

    Random sequences can have function (information).

    jazzcat: If it could be shown that a blind, undirected process (such as a sea of nucleotides or amino acids) has the capability to produce functionally specific information (genes/proteins).

    Ribozymes from random sequence libraries answer your objection.

  83. 83
    Joe says:

    Z:

    Then your argument is based on ignorance.

    Your projectiuon is duly noted as your entire position is based on ignorance.

  84. 84
    jazzcat says:

    Zachriel @82

    “See Robertson & Joyce, Highly Efficient Self-Replicating RNA Enzymes, Chemistry & Biology 2014.”

    From the highlights: “An optimized self-replicating RNA enzyme was obtained by directed evolution.”

    DIRECTED evolution.

    “Rybozymes from random sequence libraries answers your objection.” NO IT DOES NOT!!! Rybozyme engineers intelligently design rybozymes. They carefully sequence them and protect them from being degraded. They intelligently look for functions that may or may not be necessary for the production of genes/proteins and then say, “This is how random undirected processes produce function.” I say Bull ****

    “The assumption is called a hypothesis, not a philosophical assertion.” Assuming it must be wholly natural is an assumption. If you hypothesize a natural process or processes, describe it/them please? You’ve only described how intelligent chemists look for function out of the chemicals they made.

    Stephen Meyer is proposing a design hypothesis, not an assumption that it MUST be ID because it “looks so complex.”

    What is your explanation for the origin of the genetic information necessary to produce the first life? Even if I grant your case for the sake of argument about ribozymes, a catalytic ribozyme does not contain enough information to produce the necessary genes/proteins to produce a living cell. A catalytic ribozyme doesn’t produce a protein, you still have to sequence the amino acids into a functional protein that will do a critical job in the cell or the cell dies.

  85. 85
  86. 86
    bornagain77 says:

    presupposing naturalism leads to the epistemological failure of science. (Plantinga)

  87. 87
    Zachriel says:

    jazzcat: Rybozyme engineers intelligently design rybozymes.

    The sequences are not designed. They’re random.

    jazzcat: Stephen Meyer is proposing a design hypothesis, not an assumption that it MUST be ID because it “looks so complex.”

    And what are the testable entailments? Consider that the RNA World hypothesis led to the discovery of random RNA sequences with functional characteristics.

    jazzcat: What is your explanation for the origin of the genetic information necessary to produce the first life?

    No one has a complete theory as yet, but one hypothesis is called RNA World. It’s supported by the existence of ribozymes, random-sequence ribozymes, and contrived ribozymes that can replicate themselves.

    jazzcat: A catalytic ribozyme doesn’t produce a protein, you still have to sequence the amino acids into a functional protein that will do a critical job in the cell or the cell dies.

    Don’t think you understand RNA World, which hypothesizes a world before protein synthesis.

  88. 88
    jazzcat says:

    Zachriel @87

    The RNA hypothesis is unsatisfactory, even by today’s scientists, who call for a pre-RNA world.

    From my link @85

    Check out problem 3 and 4.

    “And what are the testable entailments?” Test for functionally specific information, if it meets a certain threshold ID theory infers that the origin of which is design. In the case of biochemistry, test for irreducible complexity by genetic knockout experiements, ID theory infers those structures that meet the test are designed.

    “Don’t think you understand RNA world, which hypothesizes a world before protein synthesis.” No, I do understand it and I asked how is that relevant to the OOL? The RNA hypothesis imagines a world without DNA/Proteins and then hypothesizes NO way to jump to the current system cells use. The RNA molecules have no plausible prebiotic synthesis, no plausible polymer synthesis, no plausible protection from the elements (they break down very easily) and you don’t solve the problem of the origin of genetic information.

  89. 89
    Zachriel says:

    jazzcat: The RNA hypothesis is unsatisfactory

    As we said, there is no complete theory of abiogenesis. There are a lot of unanswered questions.

    jazzcat: Test for functionally specific information, if it meets a certain threshold ID theory infers that the origin of which is design.

    No, ID claims design, but doesn’t provide testable and distinguishing entailments. Furthermore, evolution can increase functional specificity.

    jazzcat: In the case of biochemistry, test for irreducible complexity by genetic knockout experiements, ID theory infers those structures that meet the test are designed.

    No, ID claims design, but doesn’t provide testable and distinguishing entailments. Furthermore, evolution can create irreducible structures.

    jazzcat: The RNA hypothesis imagines a world without DNA/Proteins and then hypothesizes NO way to jump to the current system cells use.

    RNA can not only catalyze RNA, but proteins, as well.

    jazzcat: you don’t solve the problem of the origin of genetic information.

    That’s exactly what it does solve, by acting as genetic memory as well as enzyme.

  90. 90
    Joe says:

    Zachriel:

    No, ID claims design, but doesn’t provide testable and distinguishing entailments.

    Yes, it does and we have told you exactly what those entailments are. OTOH unguided evolution doesn’t provide any testable nor distinguishing entailments. All you can do is equivocate.

    Furthermore, evolution can increase functional specificity.

    Please provide the unequivocal evidence for unguided evolution doing so.

    Furthermore, evolution can create irreducible structures.

    Please provide the unequivocal evidence for unguided evolution doing so.

    Don’t think you understand RNA World, which hypothesizes a world before protein synthesis.

    Don’t think you understand RNA World, which is untestable.

  91. 91
    jazzcat says:

    Zachriel @89

    I’m done. I gave you some testable entailments that lead to a design inference. For some reason you just ignored them and said ID offers no testable or distinguishable entailments.

    I know RNA can catalyze somethings, the problem was there is no evidence it can catalyze EVERYthing necessary for a cell. There is also no confirming evidence that the RNA world existed. It’s all speculation. Does this hypothesis have testable entailments? Falsification criteria?

    “Evolution can increase functional specificity.” “Evolution can create irreducibly complex structures.”

    Don’t make me laugh. Don’t respond to me unless you can show me how. There are no detailed plausible pathways to any irreducibly complex structure in any article or scientific journal. If you ever find one, send it to Michael Behe and he’ll reject his entire theory.

  92. 92
    Zachriel says:

    jazzcat: I gave you some testable entailments that lead to a design inference.

    And as we pointed out, they are not distinguishing entailments. They are entailments of design or of evolution.

    jazzcat: I know RNA can catalyze somethings, the problem was there is no evidence it can catalyze EVERYthing necessary for a cell.

    They don’t have to catalyze everything necessary for a cell, just enough to create replicators. The rest can evolve.

    jazzcat: There is also no confirming evidence that the RNA world existed. It’s all speculation.

    There’s no definitive evidence, no. However, it has led to some interesting confirmations, as pointed out above. A complete theory is still elusive.

    jazzcat: Don’t respond to me unless you can show me how. There are no detailed plausible pathways to any irreducibly complex structure in any article or scientific journal.

    Irreducible complexity was proposed as, not merely possible, but an expected result in evolution a century ago, by Hermann Muller. See Muller, Genetic variability, twin hybrids and constant hybrids, in a case of balanced lethal factors, Genetics 1918.

  93. 93
    Steve says:

    Steve: All ‘new’ information is derived from previously existing information.

    Depending on your definition of “information”, evolution incorporates information about the environment.

    Zachriel, that is incorrect.

    Evolution does not incorporate information about the environment. Organisms do.

    Different animals.

    Steve: In order for non-designed information to arise, darwinian style non-directed, non-purposeful, non-goal oriented information would have to be shown to have taken place at abiogenesis, and continued unabated throughout the history of life.

    It’s easy enough to show that once you have replicators, information can increase in genomes.

    By your omission, you unwittingly concede that evolution is not the cause of the information increase. The replicators are increasing the information.

    Evolution is still going on job interviews.

  94. 94
    Zachriel says:

    Steve: Evolution does not incorporate information about the environment. Organisms do.

    Populations do. When we said evolution, we were referring to the process by which populations change over time, in part due to natural selection.

  95. 95
    Joe says:

    Irreducible complexity was proposed as, not merely possible, but an expected result in evolution a century ago, by Hermann Muller. See Muller, Genetic variability, twin hybrids and constant hybrids, in a case of balanced lethal factors, Genetics 1918.

    LoL! The guy didn’t even know about molecular biology!

  96. 96
    Mung says:

    Zachriel:

    Populations do. When we said evolution, we were referring to the process by which populations change over time, in part due to natural selection.

    And the population changes in the distribution of some trait or traits which are attributes of what, organisms?

  97. 97
    Zachriel says:

    Mung: And the population changes in the distribution of some trait or traits which are attributes of what, organisms?

    That’s right, populations of organisms. Genetic information represents the relationship between the genotype, the phenotype, and the environment. Change the environment, and it can result in a change in the genetic information of the population of organisms.

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