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Casey Luskin on top 10 problems in biological and chemical evolution

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The Top Ten Scientific Problems with Biological and Chemical Evolution

Casey Luskin
More than Myth
February 20, 2015

Here.

[Editor’s Note: The following article is Casey Luskin’s chapter, “The Top Ten Scientific Problems with Biological and Chemical Evolution,” contributed to the volume More than Myth (Chartwell Press, 2014). It has been posted with permission of the book’s editors, Robert Stackpole and Paul Brown. A PDF of this article can be downloaded here.]

Excerpt: Darwin Skeptics Abound

Drs. Axe, Gauger, and Seelke are by no means the only scientists to observe the rarity of amino acid sequences that yield functional proteins. A leading college-level biology textbook states that “even a slight change in primary structure can affect a protein’s conformation and ability to function.”42 Likewise, evolutionary biologist David S. Goodsell writes:

[O]nly a small fraction of the possible combinations of amino acids will fold spontaneously into a stable structure. If you make a protein with a random sequence of amino acids, chances are that it will only form a gooey tangle when placed in water.43

Goodsell goes on to assert that “cells have perfected the sequences of amino acids over many years of evolutionary selection.” But if functional protein sequences are rare, then it is likely that natural selection will be unable to take proteins from one functional genetic sequence to another without getting stuck in some maladaptive or non-beneficial intermediate stage.

The late biologist Lynn Margulis, a well-respected member of the National Academy of Sciences until her death in 2011, once said “new mutations don’t create new species; they create offspring that are impaired.”44 She further explained in a 2011 interview:

[N]eo-Darwinists say that new species emerge when mutations occur and modify an organism. I was taught over and over again that the accumulation of random mutations led to evolutionary change-led to new species. I believed it until I looked for evidence.45

Similarly, past president of the French Academy of Sciences, Pierre-Paul Grasse, contended that “[m]utations have a very limited ‘constructive capacity'” because “[n]o matter how numerous they may be, mutations do not produce any kind of evolution.”46

Many other scientists feel this way. Over 800 Ph.D. scientists have signed a statement agreeing they “are skeptical of claims for the ability of random mutation and natural selection to account for the complexity of life.”47 Indeed, two biologists wrote in Annual Review of Genomics and Human Genetics: “it remains a mystery how the undirected process of mutation, combined with natural selection, has resulted in the creation of thousands of new proteins with extraordinarily diverse and well optimized functions. This problem is particularly acute for tightly integrated molecular systems that consist of many interacting parts…”48 Perhaps it would be less mysterious if the theoretical conceptions could be expanded beyond unguided evolutionary mechanisms like random mutation and natural selection to explain the origin of complex biological features. More.

29 Replies to “Casey Luskin on top 10 problems in biological and chemical evolution

  1. 1
    rvb8 says:

    Perhaps a more worthwhile subject could be, ‘Casey Luskin and the top 10 new fields of study generated by ID.’

  2. 2
    CHartsil says:

    “[O]nly a small fraction of the possible combinations of amino acids will fold spontaneously into a stable structure. If you make a protein with a random sequence of amino acids, chances are that it will only form a gooey tangle when placed in water.”

    >Implying proteins fold by chance and not hydrophobia

    The problem with a list of the top 10 problems with evolutionary theory is that it’s 10 items too long to list them all.

  3. 3
    Joe says:

    No, CH, Casey implies no such thing. The main problem with evolutionary “theory” is there isn’t any theory.

    Heck unguided evolution doesn’t have a mechanism capable of getting beyond populations of prokaryotes GIVEN starting populations of prokaryotes.

  4. 4
    kairosfocus says:

    News,

    I think it will help to enumerate CL’s list of top ten problems for evolutionary materialism, from

    http://www.discovery.org/f/11121

    Problem 1: No Viable Mechanism to Generate a Primordial Soup.

    Problem 2: Unguided Chemical Processes Cannot Explain the Origin of the Genetic Code.

    Problem 3: Random Mutations Cannot Generate the Genetic Information Required for Irreducibly Complex Structures.

    Problem 4: Natural Selection Struggles to Fix Advantageous Traits into Populations.

    Problem 5: Abrupt Appearance of Species in the Fossil Record Does Not Support Darwinian Evolution.

    Problem 6: Molecular Biology has Failed to Yield a Grand “Tree of Life.”

    Problem 7: Convergent Evolution Challenges Darwinism and Destroys the Logic Behind Common Ancestry.

    Problem 8: Differences between Vertebrate Embryos Contradict the Predictions of Common Ancestry.

    Problem 9: Neo-Darwinism Struggles to Explain the Biogeographical Distribution of many Species.

    Problem 10: Neo-Darwinism has a Long History of Inaccurate Darwinian Predictions about Vestigial Organs and “Junk DNA.”

    That is a significant list, and one that speaks to the longstanding UD pro-darwinism essay challenge.

    KF

  5. 5
    Axel says:

    ROFL to the power of n

    ‘As for the “good news,” they still admit: “although we lack many details about exactly how, when, and where the transition occurred from Australopithecus to Homo, we have sufficient data from before and after the transition to make some inferences about the overall nature of key changes that did occur.”95

    In other words, the fossil record provides ape-like australopithecines (“before”), and human-like Homo (“after”), but not fossils documenting a transition between them. In the absence of intermediates, we’re left with “inferences” of a transition based strictly upon the assumption of Darwinian evolution. One commentator proposed the evidence implies a “big bang theory” of the appearance of our genus Homo.96 This does not make for a compelling evolutionary account of human origins.97

  6. 6
    bornagain77 says:

    The Top Ten Scientific Problems with Biological and Chemical Evolution – Casey Luskin – 2015
    Problem 1: No Viable Mechanism to Generate a Primordial Soup.
    http://www.evolutionnews.org/2.....91101.html
    Problem 2: Unguided Chemical Processes Cannot Explain the Origin of the Genetic Code.
    http://www.evolutionnews.org/2.....91111.html
    Problem 3: Random Mutations Cannot Generate the Genetic Information Required for Irreducibly Complex Structures.
    http://www.evolutionnews.org/2.....91121.html
    Problem 4: Natural Selection Struggles to Fix Advantageous Traits into Populations.
    http://www.evolutionnews.org/2.....91131.html
    Problem 5: Abrupt Appearance of Species in the Fossil Record Does Not Support Darwinian Evolution.
    http://www.evolutionnews.org/2.....91141.html

  7. 7
    bornagain77 says:

    Problem 6: Molecular Biology has Failed to Yield a Grand “Tree of Life.”
    http://www.evolutionnews.org/2.....91151.html
    Problem 7: Convergent Evolution Challenges Darwinism and Destroys the Logic Behind Common Ancestry.
    http://www.evolutionnews.org/2.....91161.html
    Problem 8: Differences between Vertebrate Embryos Contradict the Predictions of Common Ancestry.
    http://www.evolutionnews.org/2.....91171.html
    Problem 9: Neo-Darwinism Struggles to Explain the Biogeographical Distribution of many Species.
    http://www.evolutionnews.org/2.....91181.html
    Problem 10: Neo-Darwinism has a Long History of Inaccurate Darwinian Predictions about Vestigial Organs and “Junk DNA.”
    http://www.evolutionnews.org/2.....91191.html

  8. 8
    CHartsil says:

    “Problem 1: No Viable Mechanism to Generate a Primordial Soup.

    See the revisiting of the Miller experiment, and the work by Juan Oro and Szostak

    Problem 2: Unguided Chemical Processes Cannot Explain the Origin of the Genetic Code.

    The past 60 years of organic chemistry has only gotten closer

    Problem 3: Random Mutations Cannot Generate the Genetic Information Required for Irreducibly Complex Structures.

    Lenski and his E. coli have crushed this idea

    Problem 4: Natural Selection Struggles to Fix Advantageous Traits into Populations.

    The smaller the population the more rapidly a trait becomes fixed

    Problem 5: Abrupt Appearance of Species in the Fossil Record Does Not Support Darwinian Evolution.

    By that logic, transitions do support evolution

    Problem 6: Molecular Biology has Failed to Yield a Grand “Tree of Life.”

    Every nested hierarchy in every field lines up with every other nested hierarchy

    Problem 7: Convergent Evolution Challenges Darwinism and Destroys the Logic Behind Common Ancestry.

    The same type of traits evolve, they’re not the same exact traits conferred by the same genes. This is going to happen when certain traits are highly beneficial

    Problem 8: Differences between Vertebrate Embryos Contradict the Predictions of Common Ancestry.

    Going to need a source

    Problem 9: Neo-Darwinism Struggles to Explain the Biogeographical Distribution of many Species.

    Again, source

    Problem 10: Neo-Darwinism has a Long History of Inaccurate Darwinian Predictions about Vestigial Organs and “Junk DNA.””

    Vestigial has always been confused with useless. It doesn’t mean useless, it only means retaining crude or non-original function. As far as junk DNA, transcription does not equal function.

    So it’s really 10 things Casey Luskin needs to go back to high school biology for.

  9. 9
    CHartsil says:

    “No, CH, Casey implies no such thing.”

    >[O]nly a small fraction of the possible combinations of amino acids will fold spontaneously into a stable structure. If you make a protein with a random sequence of amino acids, chances are that it will only form a gooey tangle when placed in water.

    >random sequence

    >chances

  10. 10
    kairosfocus says:

    CH,

    the talking points will doubtless make your fellow ideologues imagine the problems are not real so can be brushed aside. But talking points do not answer to the real issues.

    Let me highlight what happened when two lifelong leaders on the two main approaches to OOL laid out their concerns, leading to mutual ruin — which has not been resolved (starting with the lack of reason to believe the early atmosphere was as M & U suggested):

    ______________

    >> [[Shapiro:] RNA’s building blocks, nucleotides contain a sugar, a phosphate and one of four nitrogen-containing bases as sub-subunits. Thus, each RNA nucleotide contains 9 or 10 carbon atoms, numerous nitrogen and oxygen atoms and the phosphate group, all connected in a precise three-dimensional pattern . . . . [[S]ome writers have presumed that all of life’s building could be formed with ease in Miller-type experiments and were present in meteorites and other extraterrestrial bodies. This is not the case.

    A careful examination of the results of the analysis of several meteorites led the scientists who conducted the work to a different conclusion: inanimate nature has a bias toward the formation of molecules made of fewer rather than greater numbers of carbon atoms, and thus shows no partiality in favor of creating the building blocks of our kind of life . . . .

    To rescue the RNA-first concept from this otherwise lethal defect, its advocates have created a discipline called prebiotic synthesis. They have attempted to show that RNA and its components can be prepared in their laboratories in a sequence of carefully controlled reactions, normally carried out in water at temperatures observed on Earth . . . .

    Unfortunately, neither chemists nor laboratories were present on the early Earth to produce RNA . . .

    [[Orgel:] If complex cycles analogous to metabolic cycles could have operated on the primitive Earth, before the appearance of enzymes or other informational polymers, many of the obstacles to the construction of a plausible scenario for the origin of life would disappear . . . .

    It must be recognized that assessment of the feasibility of any particular proposed prebiotic cycle must depend on arguments about chemical plausibility, rather than on a decision about logical possibility . . . few would believe that any assembly of minerals on the primitive Earth is likely to have promoted these syntheses in significant yield . . . . Why should one believe that an ensemble of minerals that are capable of catalyzing each of the many steps of [[for instance] the reverse citric acid cycle was present anywhere on the primitive Earth [[8], or that the cycle mysteriously organized itself topographically on a metal sulfide surface [[6]? . . . Theories of the origin of life based on metabolic cycles cannot be justified by the inadequacy of competing theories: they must stand on their own . . . .

    The prebiotic syntheses that have been investigated experimentally almost always lead to the formation of complex mixtures. Proposed polymer replication schemes are unlikely to succeed except with reasonably pure input monomers. No solution of the origin-of-life problem will be possible until the gap between the two kinds of chemistry is closed. Simplification of product mixtures through the self-organization of organic reaction sequences, whether cyclic or not, would help enormously, as would the discovery of very simple replicating polymers. However, solutions offered by supporters of geneticist or metabolist scenarios that are dependent on “if pigs could fly” hypothetical chemistry are unlikely to help. >>
    ______________

    And that’s just for starters.

    KF

  11. 11
    kairosfocus says:

    PS: CL, from BA’s links list on problem no 1:

    >>Problem 1: No Viable Mechanism to Generate a Primordial Soup

    According to conventional thinking among origin of life theorists, life arose via unguided chemical reactions on the early Earth some 3 to 4 billion years ago. Most theorists believe that there were many steps involved in the origin of life, but the very first step would have involved the production of a primordial soup — a water-based sea of simple organic molecules — out of which life arose. While the existence of this “soup” has been accepted as unquestioned fact for decades, this first step in most origin-of-life theories faces numerous scientific difficulties.

    In 1953, a graduate student at the University of Chicago named Stanley Miller, along with his faculty advisor Harold Urey, performed experiments hoping to produce the building blocks of life under natural conditions on the early Earth.4 These “Miller-Urey experiments” intended to simulate lightning striking the gasses in the early Earth’s atmosphere. After running the experiments and letting the chemical products sit for a period of time, Miller discovered that amino acids — the building blocks of proteins — had been produced.

    For decades, these experiments have been hailed as a demonstration that the “building blocks” of life could have arisen under natural, realistic Earthlike conditions,5 corroborating the primordial soup hypothesis. However, it has also been known for decades that the Earth’s early atmosphere was fundamentally different from the gasses used by Miller and Urey.

    The atmosphere used in the Miller-Urey experiments was primarily composed of reducing gasses like methane, ammonia, and high levels of hydrogen. Geochemists now believe that the atmosphere of the early Earth did not contain appreciable amounts of these components. (Reducing gasses are those which tend to donate electrons during chemical reactions.) UC Santa Cruz origin-of-life theorist David Deamer explains this in the journal Microbiology & Molecular Biology Reviews:

    This optimistic picture began to change in the late 1970s, when it became increasingly clear that the early atmosphere was probably volcanic in origin and composition, composed largely of carbon dioxide and nitrogen rather than the mixture of reducing gases assumed by the Miller-Urey model. Carbon dioxide does not support the rich array of synthetic pathways leading to possible monomers…6

    Likewise, an article in the journal Science stated: “Miller and Urey relied on a ‘reducing’ atmosphere, a condition in which molecules are fat with hydrogen atoms. As Miller showed later, he could not make organics in an ‘oxidizing’ atmosphere.”7 The article put it bluntly: “the early atmosphere looked nothing like the Miller-Urey situation.”8 Consistent with this, geological studies have not uncovered evidence that a primordial soup once existed.9

    There are good reasons to understand why the Earth’s early atmosphere did not contain high concentrations of methane, ammonia, or other reducing gasses. The earth’s early atmosphere is thought to have been produced by outgassing from volcanoes, and the composition of those volcanic gasses is related to the chemical properties of the Earth’s inner mantle. Geochemical studies have found that the chemical properties of the Earth’s mantle would have been the same in the past as they are today.10 But today, volcanic gasses do not contain methane or ammonia, and are not reducing.

    A paper in Earth and Planetary Science Letters found that the chemical properties of the Earth’s interior have been essentially constant over Earth’s history, leading to the conclusion that “Life may have found its origins in other environments or by other mechanisms.”11 So drastic is the evidence against pre-biotic synthesis of life’s building blocks that in 1990 the Space Studies Board of the National Research Council recommended that origin of life investigators undertake a “reexamination of biological monomer synthesis under primitive Earthlike environments, as revealed in current models of the early Earth.”12

    Because of these difficulties, some leading theorists have abandoned the Miller-Urey experiment and the “primordial soup” theory it is claimed to support. In 2010, University College London biochemist Nick Lane stated the primordial soup theory “doesn’t hold water” and is “past its expiration date.”13 Instead, he proposes that life arose in undersea hydrothermal vents. But both the hydrothermal vent and primordial soup hypotheses face another major problem.

    Chemical Evolution Is Dead in the Water

    Assume for a moment that there was some way to produce simple organic molecules on the early Earth. Perhaps they did form a “primordial soup,” or perhaps these molecules arose near some hydrothermal vent. Either way, origin of life theorists must then explain how amino acids or other key organic molecules linked up to form long chains (polymers) like proteins (or RNA).

    Chemically speaking, however, the last place you’d want to link amino acids into chains would be a vast water-based environment like the “primordial soup” or underwater near a hydrothermal vent. As the National Academy of Sciences acknowledges, “Two amino acids do not spontaneously join in water. Rather, the opposite reaction is thermodynamically favored.”14 In other words, water breaks protein chains back down into amino acids (or other constituents), making it very difficult to produce proteins (or other polymers) in the primordial soup.

    Materialists lack good explanations for these first, simple steps which are necessary to the origin-of-life. Chemical evolution is literally dead in the water.

    References:

    [1.] Eugenie Scott, quoted in Terrence Stutz, “State Board of Education debates evolution curriculum,” Dallas Morning News (January 22, 2009), also requoted in Ed Stoddard, “Evolution gets added boost in Texas schools,” Reuters.com at http://blogs.reuters.com/faith.....s-schools/

    [2.] Karl W. Giberson, Saving Darwin: How to be a Christian and Believe in Evolution, p. 53 (HarperOne, 2008) (“biologists today consider the common ancestry of all life a fact on par with the sphericity of the earth”).

    [3.] In any case, it’s largely a myth that Western Civilization once believed in a flat earth. See Jeffrey Burton Russell, “The Myth of the Flat Earth,” at http://www.veritas-ucsb.org/li.....Earth.html

    [4.] See Stanley L. Miller, “A Production of Amino Acids under Possible Primitive Earth Conditions,” Science, 117: 528-529 (May 15, 1953).

    [5.] See Jonathan Wells, Icons of Evolution: Why Much of What We Teach About Evolution Is Wrong, (Washington D.C.: Regnery, 2000); Casey Luskin, “Not Making the Grade: An Evaluation of 19 Recent Biology Textbooks and Their Use of Selected Icons of Evolution,” Discovery Institute (September 26, 2011), at http://www.evolutionnews.org/D.....Review.pdf

    [6.] David W. Deamer, “The First Living Systems: a Bioenergetic Perspective,” Microbiology & Molecular Biology Reviews, 61:239 (1997).

    [7.] Jon Cohen, “Novel Center Seeks to Add Spark to Origins of Life,” Science, 270: 1925-1926 (December 22, 1995).

    [8.] Ibid.

    [9.] Antonio C. Lasaga, H. D. Holland, and Michael J. Dwyer, “Primordial Oil Slick,” Science, 174: 53-55 (October 1, 1971).

    [10.] Kevin Zahnle, Laura Schaefer, and Bruce Fegley, “Earth’s Earliest Atmospheres,” Cold Spring Harbor Perspectives in Biology, 2(10): a004895 (October, 2010) (“Geochemical evidence in Earth’s oldest igneous rocks indicates that the redox state of the Earth’s mantle has not changed over the past 3.8 Gyr”); Dante Canil, “Vanadian in peridotites, mantle redox and tectonic environments: Archean to present,” Earth and Planetary Science Letters, 195:75-90 (2002).

    [11.] Dante Canil, “Vanadian in peridotites, mantle redox and tectonic environments: Archean to present,” Earth and Planetary Science Letters, 195:75-90 (2002) (internal citations removed).

    [12.] National Research Council Space Studies Board, The Search for Life’s Origins (National Academy Press, 1990).

    [13.] Deborah Kelley, “Is It Time To Throw Out ‘Primordial Soup’ Theory?,” NPR (February 7, 2010).

    [14.] Committee on the Limits of Organic Life in Planetary Systems, Committee on the Origins and Evolution of Life, National Research Council, The Limits of Organic Life in Planetary Systems, p. 60 (Washington D.C.: National Academy Press, 2007). >>

    These and other concerns are not so easily dismissed as CH hopes.

  12. 12
    kairosfocus says:

    PPS: Let’s go on to the notion of creating codes — language! — and algorithms plus linked correct executing machinery by blind chance and necessity at OOL. Again, CL:

    >> Let’s assume that a primordial sea filled with life’s building blocks did exist on the early Earth, and somehow it formed proteins and other complex organic molecules. Theorists believe that the next step in the origin of life is that — entirely by chance — more and more complex molecules formed until some began to self-replicate. From there, they believe Darwinian natural selection took over, favoring those molecules that were better able to make copies of themselves. Eventually, they assume, it was inevitable that these molecules would evolve complex machinery — like that used in today’s genetic code — to survive and reproduce.

    Have modern origin-of-life theorists explained how this crucial bridge from inert nonliving chemicals to self-replicating molecular systems took place? The most prominent hypothesis for the origin of the first life is called the “RNA world.” In living cells, genetic information is carried by DNA, and most cellular functions are carried out by proteins. However, RNA is capable of both carrying genetic information and catalyzing some biochemical reactions. As a result, some theorists postulate the first life might have used RNA alone to fulfill all these functions.

    But there are many problems with this hypothesis.

    For one, the first RNA molecules would have to arise by unguided, non-biological chemical processes. But RNA is not known to assemble without the help of a skilled laboratory chemist intelligently guiding the process. New York University chemist Robert Shapiro critiqued the efforts of those who tried to make RNA in the lab, stating: “The flaw is in the logic — that this experimental control by researchers in a modern laboratory could have been available on the early Earth.”15

    Second, while RNA has been shown to perform many roles in the cell, there is no evidence that it could perform all the necessary cellular functions currently carried out by proteins.16

    Third, the RNA world hypothesis does not explain the origin of genetic information.

    RNA world advocates suggest that if the first self-replicating life was based upon RNA, it would have required a molecule between 200 and 300 nucleotides in length.17 However, there are no known chemical or physical laws that dictate the order of those nucleotides.18 To explain the ordering of nucleotides in the first self-replicating RNA molecule, materialists must rely on sheer chance. But the odds of specifying, say, 250 nucleotides in an RNA molecule by chance is about 1 in 10150 — below the universal probability boundary, or events which are remotely possible to occur within the history of the universe.19 Shapiro puts the problem this way:

    The sudden appearance of a large self-copying molecule such as RNA was exceedingly improbable. … [The probability] is so vanishingly small that its happening even once anywhere in the visible universe would count as a piece of exceptional good luck.20

    Fourth — and most fundamentally — the RNA world hypothesis does not explain the origin of the genetic code itself. In order to evolve into the DNA / protein-based life that exists today, the RNA world would need to evolve the ability to convert genetic information into proteins. However, this process of transcription and translation requires a large suite of proteins and molecular machines — which themselves are encoded by genetic information. This poses a chicken-and-egg problem, where essential enzymes and molecular machines are needed to perform the very task that constructs them.

    The Chicken and the DVD

    To appreciate this problem, consider the origin of the first DVD and DVD player. DVDs are rich in information, but without the machinery of a DVD player to read the disk, process its information, and convert it into a picture and sound, the disk would be useless. But what if the instructions for building the first DVD player were only found encoded on a DVD? You could never play the DVD to learn how to build a DVD player. So how did the first disk and DVD player system arise? The answer is obvious: a goal directed process — intelligent design — is required to produce both the player and the disk at the same time.

    In living cells, information-carrying molecules (e.g. DNA or RNA) are like the DVD, and the cellular machinery which reads that information and converts it into proteins are like the DVD player. Just like the DVD analogy, genetic information can never be converted into proteins without the proper machinery. Yet in cells, the machines required for processing the genetic information in RNA or DNA are encoded by those same genetic molecules — they perform and direct the very task that builds them.

    This system cannot exist unless both the genetic information and transcription / translation machinery are present at the same time, and unless both speak the same language. Biologist Frank Salisbury explained this problem in a paper in American Biology Teacher not long after the workings of the genetic code were first uncovered:

    It’s nice to talk about replicating DNA molecules arising in a soupy sea, but in modern cells this replication requires the presence of suitable enzymes. … [T]he link between DNA and the enzyme is a highly complex one, involving RNA and an enzyme for its synthesis on a DNA template; ribosomes; enzymes to activate the amino acids; and transfer-RNA molecules. … How, in the absence of the final enzyme, could selection act upon DNA and all the mechanisms for replicating it? It’s as though everything must happen at once: the entire system must come into being as one unit, or it is worthless. There may well be ways out of this dilemma, but I don’t see them at the moment.21

    Despite decades of work, origin-of-life theorists are still at a loss to explain how this system arose. In 2007, Harvard chemist George Whitesides was given the Priestley Medal, the highest award of the American Chemical Society. During his acceptance speech, he offered this stark analysis, reprinted in the respected journal, Chemical and Engineering News:

    The Origin of Life. This problem is one of the big ones in science. It begins to place life, and us, in the universe. Most chemists believe, as do I, that life emerged spontaneously from mixtures of molecules in the prebiotic Earth. How? I have no idea.22

    Similarly, the aforementioned article in Cell Biology International concludes: “New approaches to investigating the origin of the genetic code are required. The constraints of historical science are such that the origin of life may never be understood.”23 That is, they may never be understood unless scientists are willing to consider goal-directed scientific explanations like intelligent design.

    But there is a much deeper problem with theories of chemical evolution, as well as biological evolution. This pertains not just to the ability to process genetic information via a genetic code, but the origin of that information itself.

    References:

    [15.] Richard Van Noorden, “RNA world easier to make,” Nature news (May 13, 2009), http://www.nature.com/news/200.....9.471.html

    [16.] See Stephen C. Meyer, Signature in the Cell: DNA and the Evidence for Intelligent Design, p. 304 (New York: HarperOne, 2009).

    [17.] Jack W. Szostak, David P. Bartel, and P. Luigi Luisi, “Synthesizing Life,” Nature, 409: 387-390 (January 18, 2001).

    [18.] Michael Polanyi, “Life’s Irreducible Structure,” Science, 160 (3834): 1308-1312 (June 21, 1968).

    [19.] See William A. Dembski, The Design Inference: Eliminating Chance through Small Probabilities (Cambridge University Press, 1998).

    [20.] Robert Shapiro, “A Simpler Origin for Life,” Scientific American, pp. 46-53 (June, 2007).

    [21.] Frank B. Salisbury, “Doubts about the Modern Synthetic Theory of Evolution,” American Biology Teacher, 33: 335-338 (September, 1971).

    [22.] George M. Whitesides, “Revolutions In Chemistry: Priestley Medalist George M. Whitesides’ Address,” Chemical and Engineering News, 85: 12-17 (March 26, 2007).

    [23.] J.T. Trevors and D.L. Abel, “Chance and necessity do not explain the origin of life,” Cell Biology International, 28: 729-739 (2004). >>

  13. 13
    CHartsil says:

    Try using your own words instead of posting walls of garbage in an effort to stifle conversation.

    Have you noticed that I’ll make my own arguments and cite sources where needed?

  14. 14
    kairosfocus says:

    PPS: I have already summarised an initial response on the confident manner claim about Lenski this morning, providing a clip. Boiling down, the issue was the machinery to do the metabolic work was evidently there but locked off, regulatory mutations in effect turned it on. This has nothing to do with ab initio creating the ability, which is what IC is about.

  15. 15
    kairosfocus says:

    CH, ad hominem, and dismissively unresponsive to substantial evidence; in a context where you had already rudely derided CL so I allowed him to speak for himself in his own voice. Duly noted. KF

  16. 16
    CHartsil says:

    Yeah and I already corrected it. Surprise surprise, all you did there was post excerpts from another blog. This time Behe, talking abut us not being sure that that’s what happened when we had the parent population frozen right behind it. Lol

    It was a system produced by changes in multiple systems, the removal of any of which will cease the function.

    Define IC for us again.

  17. 17
    CHartsil says:

    KF, Gish gallop and unwillingness to have your own ideas. Check

  18. 18
    kairosfocus says:

    PS: If you want me in my own voice, here I am on the underlying FSCO/I issue, which leads me to wonder at your breezy one liners on OOL and origin of prescriptive functionally specific complex info in the context of OOL:

    http://www.uncommondescent.com.....-relevant/

    And, here I am in my own voice on the IC issue (note, what is on p. 2 also):

    http://www.uncommondescent.com.....of-design/

  19. 19
    CHartsil says:

    “here I am on the underlying FSCO/I issue”

    Gap argument, burden shifting. You have to show it’s designed first. Then and only then can you ask anyone to falsify it

  20. 20
    kairosfocus says:

    CH,

    you have been repeatedly corrected on your gap argument one liner, but still press on rhetorically. Which is telling.

    Let’s sum up:

    1 –> Functionally specific complex organisation and associated information, FSCO/I is an observable, recognisable and even quantifiable reality. I have recently used an Abu 6500 C3 reel as a case in point. To measure, a structured list of y/n q’s describing the specifically functional config, will yield an info value in bits. Similar to AutoCAD, wiring diagrams etc.

    2 –> Function emerges from interaction of specifically arranged and coupled parts, where there is some tolerance but beyond 500 – 1,000 bits the tightly constrained sets of functional arrangements will yield deeply isolated islands of function in config spaces so large solar sys or observed cosmos scale resources, per blind chance and mechanical necessity based needle in haystack search, are maximally unlikely to hit on functional clusters.

    3 –> So it is unsurprising that on trillions of observed cases, FSCO/I is reliably the product of intelligently directed configuration. That is FSCO/I is a strong inductive sign of design, one backed up by a needle in haystack search analysis as outlined.

    4 –> So, we have just one known adequate cause that meets the vera causa test for explaining FSCO/I when it appears in traces of the unobservable remote past of origins.

    5 –> Absent ideologically imposed a priori evolutionary materialism, we have here strong positive reason for applying the reliability of FSCO/I as a sign to explain origin of cell based life and of major, complex body plan features across the tree of life.

    6 –> Similarly, this is closely connected to the fine tuning of the complex interacting physics and cosmology that grounds a cosmos that supports C-chemistry, aqueous medium cell based life in galactic and circumstellar habitable zone terrestrial planets.

    7 –> And, the trajectory of findings — contrary to the breezy assertions above — further underscores such, these are not “gaps” being filled in.

    8 –> So, we see good inductive, inference to best explanation reasons to confidently hold intelligently designed configuration as best current empirically grounded explanation of cell based life, body plans and the fine tuned cosmos in which we find such.

    KF

  21. 21
    CHartsil says:

    No, you’ve continually asserted the same gap argument and continually attempted to shift the burden. I just wouldn’t let you.

  22. 22
  23. 23
    CHartsil says:

    >Logic of inference

    Inference never beats out data, especially when it’s as invalid as comparing a living system to a non-living system.

  24. 24
    kairosfocus says:

    CH, inference to best explanation in this case — as you were told but ignored — stands on trillions of data points and is a case of the inductive inference that lies at the heart of science. Indeed, in this very thread in your attempts to object to the point of verging on willful obtuseness on the nature of scientific, inductive reasoning, you inescapably provided several more cases of the consistent pattern that FSCO/I comes from intelligently directed configuration. KF

  25. 25
    humbled says:

    “Gap argument, burden shifting. You have to show it’s designed first. Then and only then can you ask anyone to falsify it”

    Come now CHartsil, design is the default position and the theory that best meets what we understand about nature as well as the reality we experience. Design is also the default position humans tend to be born with. No alternative to design issues any real challenge. All materialistic explanations require the disabling of a persons ability to think critically.

    Since design is the default position all humans experience and recognise in nature, before you materialists get your claws into our school kids and corrupt their fragile minds that is, the burden of proof is on you.

    Demanding as you have done is a downright cheek.

  26. 26
    kairosfocus says:

    H, BTW, the accusation “Gish gallop” is both an uncalled for false and unwarranted accusation of deceit on my part and a smear of the memory of Mr Gish who flat out won several hundred open public debates on origins evidences because the fossil record — as Gould acknowledged — is about stasis, gaps and sudden changes; i.e. it is still the opposite of what Darwin hoped for on wider investigation, after 150 years, 1/4 million fossil species and millions of collected specimens with billions seen in the field. So, as long as a priori materialism is not imposed the evidence does not point where supporters of blind watchmaker evolution wish. Your resort to the rhetoric of false unwarranted accusation whilst failing to address substance and apparently failing to understand that inductive reasoning — the heart of science — is inferential, is duly noted. KF

  27. 27
    kairosfocus says:

    Humbled,

    Pardon but no.

    In the case of the design inference there are actually two defaults.

    First, that relevant aspects of phenomena are explained on lawlike mechanical necessity. This manifests lawlike regularities such as F = m*a. Dropped heavy objects initially fall at 9.8 N/kg near earth’s surface.

    It is defeated by high contingency under closely similar initial conditions, e.g. which face of a die that was dropped will face up after it tumbles and settles.

    This, is defaulted to chance showing stochastic patterns, e.g. a fair die shows a tendency to have any face up 1/6 of the time.

    But under certain special conditions, e.g. seeing a string of 500 coins that we expect to be near 50:50 h-T in no particular pattern showing the ASCII code for the first 72 characters of this post, we see functionally specific complex organisation and associated information, a pattern that is maximally implausible to arise by chance and mechanical necessity — drop and tumble the coins. (A coin is a 2-sided die.)

    There is a known cause of such FSCO/I, intelligently directed configuration.

    So reliable is this that on seeing it, we are entitled to infer design. Even, when we were not in a position to see the actual causal process in action.

    Extending to the world of life, we cannot directly observe the remote origin of cell based life but DNA is a trace of that and it exhibits coded digital, algorithmic information and linked execution machinery.

    Such FSCO/I strongly points to design as its best explanation.

    To overturn that, objectors need to show per observation that such FSCO/I is seen to come about by blind chance and/or mechanical necessity.

    After many attempts — today’s was a resurfacing of some already addressed claims by and about Lenski and his work — consistently such attempts fail.

    That’s why we see the sort of rhetorical tactics the above thread shows.

    KF

  28. 28
    kairosfocus says:

    F/N: More from Behe (2012) on Lenski:

    http://www.evolutionnews.org/2.....66361.html

    _______________

    >> . . . the Lenski lab observed a mutant strain in their experiments that could metabolize citrate in the presence of oxygen, which unmutated E. coli cannot do. (Blount et al. 2008) (Importantly, however, the bacterium can metabolize citrate in the absence of oxygen.) This allowed the mutated bacterium to outcompete its relatives, because the growth medium contained a lot of citrate, as well as oxygen. It was an intriguing result, and was touted as a major innovation, but at the time Lenski’s lab was unable to track down at the DNA level the exact mutations that caused the change.

    Now they have. In a recent publication in Nature (Blount et al. 2012) they report the multiple mutations that confer and increase the ability to transport citrate in an atmosphere containing oxygen. They divide the mutations conceptually into three categories: 1) potentiation; 2) actualization; and 3) refinement. “Actualization” is the name they give to the mutation that first confers a weak ability to transport citrate into the laboratory E. coli. (It turns out that the bacterium is lacking only a protein to transport citrate into the cell in the presence of oxygen; all other enzymes needed to further metabolize citrate are already present.) The gene for the citrate transporter, citT, that works in the absence of oxygen is directly upstream from the genes for two other proteins that have promoters that are active in the presence of oxygen. A duplication of a segment of this region serendipitously placed the citT gene next to one of these promoters, so the citT gene could then be expressed in the presence of oxygen. Gene duplication is a type of mutation that is known to be fairly common, so this result, although requiring a great deal of careful research to pin down, is unsurprising.

    Over time the mutant got better at utilizing citrate, which the authors called “refinement.” Further work showed this was due to multiple duplications of the mutant gene region, up to 3-9 copies. [–> improvement, not a roadblock issue] Again, gene duplication is a fairly common process, so again it is unsurprising. In another experiment Lenski and co-workers showed that increasing the concentration of the citrate transporter gene was sufficient in itself to account for the greater ability of E. coli to grow on citrate. No other mutations were needed.

    A more mysterious part of the whole process is what the group called “potentiation.” It turns out that the original E. coli they began with decades ago could not benefit from the gene duplication that brought together a citT gene with an oxygen-tolerant promoter. Before it could benefit, a preliminary mutation had to occur in the bacterium somewhere other than the region containing the citrate-metabolism genes. Exactly what that mutation was, Lenski and coworkers were not able to determine. However, they examined the bacterium for mutations that may contribute to potentiation, and speculated that “A mutation in arcB, which encodes a histidine kinase, is noteworthy because disabling that gene upregulates the tricarboxylic acid cycle.” (They tried, but were unable to test this hypothesis.) In other words, the “potentiation” may involve degradation of an unrelated gene.

    Lenski’s lab did an immense amount of careful work and deserves much praise. Yet the entirely separate, $64,000 question is, what do the results show about the power of the Darwinian mechanism? The answer is, they do not show it to be capable of anything more than what was already known. For example, in my review of lab evolution experiments I discussed the work of Zinser et al. (2003) where a sequence rearrangement brought a promoter close to a gene that had lacked one. I also discussed experiments such as Licis and van Duin (2006) where multiple sequential mutations increased the ability of a FCT. Despite Lenski’s visually startling result — where a usually clear flask became cloudy with the overgrowth of bacteria on citrate — at the molecular level nothing novel occurred . . . >>

    ______________

    No innovation as such, removal of it looks like two roadblocks then amplification of an existing latent ability blocked for want of promotion, and fixed by gaining that, where the PROMOTOR is not actually a functional part of the actual action of metabolising citrate; looks like the trick was to get the cit into the cell where it could be worked on, in presence of Oxygen. Likely, a functional reversal of an earlier loss of function not necessary in the usual (gut) environment for E coli.

    This shows that exaptation of existing and matched components is possible [we already know about jury-rigging and field mods . . . ], but also reveals that this does not answer to the origin of said abilities and their matching. (Which also underscores the more fundamental significance of FSCO/I, which is what I have always stressed.)

    KF

  29. 29
    kairosfocus says:

    F/N2: Behe continues, responding to Venema:

    ____________

    >> The gene duplication which brought an oxygen-tolerant promoter near to the citT gene did not make any new functional element. Rather, it simply duplicated existing features. The two FCTs comprising the oxygen tolerant citrate transporter locus — the promoter and the gene — were functional before the duplication and functional after. I had written in my review that one type of mutation that could be categorized as a gain-of-FCT was gene duplication with subsequent sequence modification, to allow the gene to specialize in some task. Venema thinks the mutation observed by Lenski is such an event. He has overlooked the fact that there was no subsequent sequence modification; a segment of DNA simply tandemly duplicated, bringing together two pre-existing FCTs. (It is true that the sequence of the protein coded by the duplicated gene includes a fragment from one of the nearby genes, but there is no evidence nor reason to think that the fused fragment is necessary for the activity of the protein.) In my review I classify that as a modification-of-function event. An example of a true gain-of-FCT by duplication cited in my review was the work of Olsthoorn and van Duin (1996) where a 14-nucleotide duplication led to the formation of new functional coded elements (it did not simply repeat pre-existing elements), so it is not just a modification-of-function mutation. The citrate mutation did nothing like that.

    Venema counts the number of mutations needed to get a fully functioning citrate-importing function in Lenski’s work, and arrives at roughly a half-dozen. Unfortunately, several of those are tandem duplications of the weak citT transporter, which clearly are selectable, beneficial mutations. In arriving at the limits to Darwinism, I emphasized that that mechanism would certainly work if gradually-increasing, serial, beneficial mutations could do the job. Thus such mutations do not count in estimating the limit. Only required deleterious and neutral mutations count against the limit to Darwinian evolution. Venema argues that perhaps all of complex functional biology could be reached by gradual, beneficial mutations. Well, bless his optimistic heart, but the data give us no reason to think that, because gradually increasing one protein’s total cellular activity by sequential gene duplication is successively beneficial, all routes to complex systems involving multiple distinct elements will be. Quite the opposite, as I have often argued.

    Professor Venema also counts several “potentiating” mutations as contributing to the system. Unfortunately, whatever those mutations are, they are not part of the citrate metabolic system itself. Rather, they are at most part of the genetic background. If Lenski and co-workers’ speculations are correct (Blount et al. 2012), at least one of the potentiating mutations degrades an unrelated gene, and thus itself counts as a loss-of-FCT mutation. When counting the mutations contributing to the edge of evolution for building a feature, only the ones directly involved in the feature are counted, not ones that indirectly contribute to a receptive genetic background (which are legion). Thus, unlike Venema, I count perhaps three to four mutations — the original duplication placing the oxygen-tolerant promoter near the citT gene, plus several rounds of duplication of that region. All of the mutations are modification-of function ones in the classification system I described. I should add that there is no reason to think that Darwinian processes cannot produce gain-of-FCT mutations, and I reviewed several such events. But they are greatly outnumbered by loss-of-FCT and modification-of-function beneficial mutations.

    In my own view, in retrospect, the most surprising aspect of the oxygen-tolerant citT mutation was that it proved so difficult to achieve. If, before Lenski’s work was done, someone had sketched for me a cartoon of the original duplication that produced the metabolic change, I would have assumed that would be sufficient — that a single step could achieve it. The fact that it was considerably more difficult than that goes to show that even skeptics like myself overestimate the power of the Darwinian mechanism. >>
    _____________

    KF

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