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To dream the impossible dream: the quest for the 50-bit life form

Aleksandr Oparin and John von Neumann. Courtesy of Russavia, Beelaj and Wikipedia.

In two separate comments (see here and here) on a recent post of mine, Intelligent Design critic Dave Mullenix posed a question to ID supporters, which often comes up on this blog:

[W]hy do you ID people insist that the first living thing was complex? 500 to 1000 bits of information? Try 50 to 100. Think of a single polymer whose only capability is reproducing itself, and which is possibly imbedded in the kind of droplets that form naturally…

A simple self replicating molecule isn’t much compared to modern life, but if it self-replicates and allows evolution, it’s all the start we need and a small polymer would do it. Don’t worry about proteins, they come later. Don’t worry about metabolism – that’s also for advanced life. For first life, reproduction with the possibility of Darwinian evolution is all we need and a short polymer will do the trick.

Dave Mullenix confesses to not yet having read Dr. Stephen Meyer’s Signature in the Cell, although he has purchased a Kindle version of the book. I realize that he is a very busy man, and I also realize that other Intelligent Design critics have voiced similar objections previously, so I’ve written this post in order to explain why the scenario Dave Mullenix proposes will not work.

What motivates the quest for a 50-bit life form?

Dave Mullenix is surely well aware of the research of Dr. Douglas Axe, which has shown that the vast majority of 150-amino-acid sequences are non-functional, and that the likelihood of a single protein – that is, any working protein, never mind which one – arising by pure chance on the early earth is astronomically low. Nor can necessity account for the origin of DNA, RNA or proteins. All of these molecules are made up of biological building blocks – nucleotides in the case of DNA and RNA, and amino acids in the case of proteins. Just as the properties of stone building blocks do not determine their arrangements in buildings, so too, the properties of biological building blocks do not determine their arrangements in DNA, RNA and proteins.

If neither chance nor necessity can account for the appearance of fully functional RNA, DNA and proteins, then evolutionists have no choice but to assume that these molecules arose from something even simpler, which was capable of evolving into these molecules. This is the logic which underlies Dave Mullenix’s proposal regarding the origin of life.

Why a 50-bit life form wouldn’t work

Actually, a similar proposal was made by origin-of-life researcher Aleksandr Oparin in the late 1960s. In his original model, put forward in the 1920s and 1930s, Oparin had assumed that chance alone could account for the origin of the proteins which make cellular metabolism possible. However, the discovery of the extreme complexity and specificity of protein molecules, coupled with the inability of his model to explain the origin of the information in DNA, forced him to revise his original proposal for the chemical evolution of life on earth. Dr. Stephen Meyer continues the story in Signature in the Cell (HarperOne, New York, 2009), pages 273-277:

As the complexity of DNA and proteins became apparent, Oparin published a revised version of his theory in 1968 that envisioned a role for natural selection earlier in the process of abiogenesis. The new version of his theory claimed that natural selection acted on unspecified polymers as they formed and changed within his coacervate protocells.[5] Instead of natural selection acting on fully functional proteins in order to maximize the effectiveness of primitive metabolic processes at work within the protocells, Oparin proposed that natural selection might work on less than fully functional polypeptides, which would naturally cause them to increase their specificity and function, eventually making metabolism possible. He envisioned natural selection acting on “primitive proteins” rather than on primitive metabolic processes in which fully functional proteins had already arisen….

[Oparin] proposed that natural selection initially would act on unspecified strings of polypeptides of nucleotides and amino acids. But this created another problem for his scenario. Researchers pointed out that any system of molecules for copying information would be subject to a phenomenon known as “error catastrophe” unless these molecules are specified enough to ensure an error-free transmission of information. An error catastrophe occurs when small errors – deviations from functionally necessary sequences – are amplified in successive replications.[14] Since the evidence of molecular biology shows that unspecified polypeptides will not replicate genetic information accurately, Oparin’s proposed system of initially unspecified polymers would have been highly vulnerable to such an error catastrophe.

Thus, the need to explain the origin of specified information created an intractable dilemma for Oparin. If, on the one hand, Oparin invoked natural selection early in the process of chemical evolution (i.e. before functional specificity in amino acids or nucleotides had arisen), accurate replication would have been impossible. But in the absence of such replication, differential reproduction cannot proceed and the concept of natural selection is incoherent.

On the [other] hand, if Oparin introduced natural selection late in his scenario, he would need to rely on chance alone to produce the sequence-specific molecules necessary for accurate self-replication. But even by the late 1960s, many scientists regarded that as implausible given the complexity and specificity of the molecules in question…

The work of John von Neumann, one of the leading mathematicians of the twentieth century, made this dilemma more acute. In 1966, von Neumann showed that any system capable of self-replication would require sub-systems that were functionally equivalent to the information storage, replicating and processing systems found in extant cells.[16] His calculations established an extremely high threshold of minimal biological function, a conclusion that was confirmed by later experimental work.[17] On the basis of the minimal complexity and related considerations, several scientists during the late 1960s (von Neumann, physicist Eugene Wigner, biophysicist Harold Morowitz) made calculations showing that random fluctuations of molecules were extremely unlikely to produce the minimal complexity required for a primitive replication system.[18]…

As a result, by the late 1960s, many scientists had come to regard the hypothesis of prebiotic natural selection as indistinguishable from the pure chance hypothesis, since random molecular interactions were still needed to generate the initial complement of biological information that would make natural selection possible. Prebiotic natural selection could add nothing to the process of information generation until after vast amounts of functionally specified information had first arisen by chance.

References

[5] Oparin, A. Genesis and Evolutionary Development of Life, New York: Academic, 1968, pp. 146-147.

[14] Joyce, Gerald F. and Leslie Orgel, “Prospects for Understanding the Origin of the RNA World.” In The RNA World, edited by Raymond F. Gesteland and John J. Atkins, I-25. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, 1993. See especially pp. 8-13.

[16] Von Neumann, John. The Theory of Self-Replicating Automata. Completed and edited by A. Burks. Urbana: University of Illinois Press, 1966.

[17] Pennisi, Elizabeth. “Seeking Life’s Bare (Genetic) Necessities”. Science 272(1996): 1098-99.
Mushegian, Arcady, and Eugene Koonin, “A Minimal Gene Set for Cellular Life Derived by Comparison of Complete Bacterial Genomes”. Proceedings of the National Academy of Sciences USA 93 (1996): 10268-10273.

[18] Wigner, Eugene. “The Probability of the Existence of a Self-Reproducing Unit.” In The Logic of Personal Knowledge: Essays Presented to Michael Polyani, edited by Edward Shils, pp. 231-235. London: Routledge and Kegan Paul, 1961. [But see here for a critique by physicist John C. Baez. - VJT]
Morowitz, Harold J. “The Minimum Size of the Cell,”in Energy Flow in Biology: Biological Organization as a Problem in Thermal Physics, New York: Academic, 1968, pp. 10-11.

(Emphases mine – VJT.)

In conclusion: there are good reasons for thinking that a 50-bit life-form would never work. Since it would not be capable of accurate self-replication, it would be unable to evolve into larger molecules such as RNA, DNA and proteins. Intelligent Design critics who attempt to overcome the astronomical odds against these molecules forming naturally by hypothesizing a simpler, 50-bit life-form that generated them are, like the man of La Mancha, dreaming the impossible dream.

Let me finish my essay by quoting the beautiful lyrics of the song, The Impossible Dream. The song was composed by Mitch Leigh, and the lyrics were written by Joe Darion. It was written for the 1965 musical, “Man of La Mancha”:

To dream the impossible dream
To fight the unbeatable foe
To bear with unbearable sorrow
To run where the brave dare not go

To right the unrightable wrong
To love pure and chaste from afar
To try when your arms are too weary
To reach the unreachable star

This is my quest, to follow that star
No matter how hopeless, no matter how far
To fight for the right, without question or pause
To be willing to march into Hell, for a Heavenly cause

And I know if I’ll only be true, to this glorious quest,
That my heart will lie will lie peaceful and calm, when I’m laid to my rest

And the world will be better for this:
That one man, scorned and covered with scars,
Still strove, with his last ounce of courage,
To reach the unreachable star.

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86 Responses to To dream the impossible dream: the quest for the 50-bit life form

  1. If life started naturally, then it probably started as zero-bit. It would not have looked much like life as we know it, so would have been some kind of pre-life or proto-life process.

    Notice that I began that with an “if”.

  2. 2

    Surely any vaguely capable summary of this issue would have to include the possibility of a chemical system in which monomers flow in from the general environment, drying or freezing or some such increases the concentration of monomers leading to polymerization, followed by polymers degrading at a certain rate. Make this system cyclical (day/night or seasonal cycles) and continue for a few million years.

    Then, consider the possibility that some of the polymers catalyze the formation of new polymers that are similar to themselves. This is the beginning of a situation where prebiotic natural selection is *not* a contradiction in terms. The polymerization, monomer inputs, cyclical change in environment, etc., are provided by common natural processes — only much, much later does biology “take over” these functions, at which point they seem “essential” for “self-replication”.

    Now read:

    Martin A. Nowak and Hisashi Ohtsuki (2008). “Prevolutionary dynamics and the origin of evolution.” PNAS September 30, 2008 vol. 105 no. 39 14924-14927

    http://www.pnas.org/content/105/39/14924.full

    Do we know exactly what the chemistry is that could undergo the transition from prevolution to evolution? No.

    But, if someone is going to claim scholarly support for the notion that prebiotic natural selection is impossible, and that there is just no conceivable way to get to a self-replicating sytem, should they be aware of, and cite, major recent work by Harvard biologists that directly contradicts their premise? Heck yes! Did you or Meyer do it? Nope.

    Will scientists ever take ID seriously, when it is the opponents of ID that are forced to do basic literature review work *for* the ID proponents, who can’t be bothered to inform themselves of the actual state of affairs in science, and instead quote decades-old work as if it was definitive? Nope.

  3. You have to just love the belief of the evolutionist.

    All we need is the simplest self-replicating molecule and everything else becomes possible.

    Well, yeah, it would have to include some sort of variation in order for selection to be possible.

    And we’ll ignore the fact that a simple self-replicating molecule that did not vary might well gobble up all the available resources and evolution would never even have a chance.

    Can someone tell my why that would not be the more likely scenario?

    Oh yeah, and not only must it vary, but it must do so in such a way that the variances have a selectable effect.

    So a simple self-replicating molecule isn’t enough.

    Neither is a molecule that simply replicates with variance.

    But even assuming you get a population of self-replicating molecules within which the variations that appear somehow cause a variant to increase in number relative to other variants just what exactly does that get you?

    So consider this as search. At a minimum what does our search have to find? We have at least three targets at a minimum.

    Of all possible chemical combinations that are energetically feasible how many result in what we need to find?

    Is a crystal an example of a self-replicating entity?

  4. Prevolutionary dynamics and the origin of evolution

    Life is that which replicates and evolves. The origin of life is also the origin of evolution.

    Why should we believe this?

  5. 5
    material.infantacy

    If anyone here can speak hand-waving and/or literature bluffing, I’d appreciate a translation of Nick@2.

    Knowing how self-replicating molecules are naturally selected for, and how that correlates/leads directly to natural selection operating at the organismal level would be very valuable indeed.

    If that problem’s been solved, I’d appreciate a reference to the Nobel prize recipient along with references to the correlating empirical results.

    Thanks in advance!

    From the paper:

    “We have proposed a mathematical theory for studying the origin of evolution.”

    So the application of the material in the above linked paper should eventually show us how self-replicators evolved. Put another way, we will then fully understand how evolution evolved.

    “Life is that which replicates and evolves. The origin of life is also the origin of evolution.”

    Stupid creationists.

  6. Some notes as to the profound difference between life and non-life that Nick seems to ‘innocently’ gloss over as if they are not of great concern:;

    Three Subsets of Sequence Complexity and Their Relevance to Biopolymeric Information – David L. Abel and Jack T. Trevors – Theoretical Biology & Medical Modelling, Vol. 2, 11 August 2005, page 8
    “No man-made program comes close to the technical brilliance of even Mycoplasmal genetic algorithms. Mycoplasmas are the simplest known organism with the smallest known genome, to date. How was its genome and other living organisms’ genomes programmed?”
    http://www.biomedcentral.com/c.....2-2-29.pdf

    First-Ever Blueprint of ‘Minimal Cell’ Is More Complex Than Expected – Nov. 2009
    Excerpt: A network of research groups,, approached the bacterium at three different levels. One team of scientists described M. pneumoniae’s transcriptome, identifying all the RNA molecules, or transcripts, produced from its DNA, under various environmental conditions. Another defined all the metabolic reactions that occurred in it, collectively known as its metabolome, under the same conditions. A third team identified every multi-protein complex the bacterium produced, thus characterising its proteome organisation.
    “At all three levels, we found M. pneumoniae was more complex than we expected,”
    http://www.sciencedaily.com/re.....173027.htm

    “The difference between a mixture of simple chemicals and a bacterium, is much more profound than the gulf between a bacterium and an elephant.” (Dr. Robert Shapiro, Professor Emeritus of Chemistry, NYU)

    The Capabilities of Chaos and Complexity – David L. Abel – 2009
    Excerpt: “A monstrous ravine runs through presumed objective reality. It is the great divide between physicality and formalism. On the one side of this Grand Canyon lies everything that can be explained by the chance and necessity of physicodynamics. On the other side lies those phenomena than can only be explained by formal choice contingency and decision theory—the ability to choose with intent what aspects of ontological being will be preferred, pursued, selected, rearranged, integrated, organized, preserved, and used. Physical dynamics includes spontaneous non linear phenomena, but not our formal applied-science called “non linear dynamics”(i.e. language,information).
    http://www.mdpi.com/1422-0067/10/1/247/pdf

    Yet even though there is a ‘universe wide chasm’ between life and non-life the first tiny baby steps on any imagined pathway to life from non-life are are block on each side by impenetrable barriers;

    Nick Lane Takes on the Origin of Life and DNA – Jonathan McLatchie – July 2010
    Excerpt: As Stephen Meyer has comprehensively documented in his book, Signature in the Cell, the RNA-world hypothesis is fraught with problems, quite apart from those pertaining to the origin of information. For example, the formation of the first RNA molecule would have required the prior emergence of smaller constituent molecules, including ribose sugar, phosphate molecules, and the four RNA nucleotide bases. However, it turns out that both synthesizing and maintaining these essential RNA building blocks — especially ribose — and the nucleotide bases is a very difficult task under origin-of-life conditions.
    http://www.evolutionnews.org/2.....36101.html

    Homochirality and Darwin: part 2 – Robert Sheldon – May 2010
    Excerpt: With regard to the deniers who think homochirality is not much of a problem, I only ask whether a solution requiring multiple massive magnetized black-hole supernovae doesn’t imply there is at least a small difficulty to overcome? A difficulty, perhaps, that points to the non-random nature of life in the cosmos?
    http://procrustes.blogtownhall.com/page3

    etc.. etc.. etc..

    ,,, and even IF once you had a ‘simple’ self replicating molecule, the insurmountable ‘information problem’, faced in any materialistic origin of life scenario, certainly does not just magically go away;

    “If complex organisms ever did evolve from simpler ones, the process took place contrary to the laws of nature, and must have involved what may rightly be termed the miraculous.” R.E.D. Clark, Victoria Institute (1943), p. 63.

    The GS (genetic selection) Principle – David L. Abel – 2009
    Excerpt: Stunningly, information has been shown not to increase in the coding regions of DNA with evolution. Mutations do not produce increased information. Mira et al (65) showed that the amount of coding in DNA actually decreases with evolution of bacterial genomes, not increases. This paper parallels Petrov’s papers starting with (66) showing a net DNA loss with Drosophila evolution (67). Konopka (68) found strong evidence against the contention of Subba Rao et al (69, 70) that information increases with mutations. The information content of the coding regions in DNA does not tend to increase with evolution as hypothesized. Konopka also found Shannon complexity not to be a suitable indicator of evolutionary progress over a wide range of evolving genes. Konopka’s work applies Shannon theory to known functional text. Kok et al. (71) also found that information does not increase in DNA with evolution. As with Konopka, this finding is in the context of the change in mere Shannon uncertainty. The latter is a far more forgiving definition of information than that required for prescriptive information (PI) (21, 22, 33, 72). It is all the more significant that mutations do not program increased PI. Prescriptive information either instructs or directly produces formal function. No increase in Shannon or Prescriptive information occurs in duplication. What the above papers show is that not even variation of the duplication produces new information, not even Shannon “information.”
    http://www.bioscience.org/2009.....6/3426.pdf

    Is Antibiotic Resistance evidence for evolution? – ‘The Fitness Test’ – video
    http://www.metacafe.com/watch/3995248

    “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain – Michael Behe – December 2010
    Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain.(that is a net ‘fitness gain’ within a ‘stressed’ environment i.e. remove the stress from the environment and the parent strain is always more ‘fit’)
    http://behe.uncommondescent.co.....evolution/

  7. The work of John von Neumann, one of the leading mathematicians of the twentieth century, made this dilemma more acute. In 1966, von Neumann showed that any system capable of self-replication would require sub-systems that were functionally equivalent to the information storage, replicating and processing systems found in extant cells.

    Why should we believe that von Neumann was wrong?

    http://en.wikipedia.org/wiki/S.....ion#Theory

  8. Life is that which replicates and evolves.

    Taken literally, this claim means that individual organisms aren’t alive, for they do not “evolve” in the way Darwinists use that term.

  9. As to what wiki says:

    Early research by John von Neumann [2] established that replicators have several parts:

    A coded representation of the replicator.
    A mechanism to copy the coded representation.
    A mechanism for effecting universal construction within the host environment of the replicator.

    Exceptions to this pattern are possible. For example, scientists have successfully constructed RNA that copies itself in an “environment” that is a solution of RNA monomers and transcriptase. In this case, the body is the genome, and the specialized copy mechanisms are external.

    It is important to note their ‘exception’ (which was non-referenced);

    Biologic Institute Announces First Self-Replicating Motor Vehicle – Doug Axe -
    Excerpt: “So, advertising this as “self-replication” is a bit like advertising something as “free” when the actual deal is 1 free for every 1,600 purchased. It’s even worse, though, because you need lots of the pre-made precursors in cozy proximity to a finished RNA in order to kick the process off. That makes the real deal more like n free for every 1,600 n purchased, with the caveats that n must be a very large number and that full payment must be made in advance.”
    http://biologicinstitute.org/2.....r-vehicle/

  10. 10

    Yes Nick, let us keep up to date:

    Nick’s 2008 paper suggests the famous “soup” idea:

    A binary soup and the tree of prelife.

    Except what Nick’s fails to mention is that 2010 research has dumped his soup idea in the trash:

    New Research Rejects 80-Year Theory of ‘Primordial Soup’ as the Origin of Life:

    http://www.sciencedaily.com/re.....101245.htm

    There is a major energy problem that Nick pretends is not a problem.

    Maybe thermal vents is the new soup as the article suggests? Then again maybe not:

    Prebiotic chemistry
    points to a low-temperature origin because most biochemicals decompose rather rapidly at temperatures of 100 degrees C (e.g., half-lives are 73 min for ribose, 21 days for cytosine, and 204 days for adenine).

    http://www.ncbi.nlm.nih.gov/pubmed/11539558

    Is it possible the whole entire story is BS and you are blowing smoke up our asses?

  11. 11
    Elizabeth Liddle

    Absolutely right, Mung.

    To enable Darwinian evolution you have to have

    a) a self replicator
    b) that replicates with variance
    c) the variance has to affect efficiency of self-replication.

    Some crystal satisfy the first two but rarely the third.

    And to the third you need to add a fourth:

    d) the possible variance in self-replicatory efficiency has to be multidimensional.

    That’s quite a tall order, but I don’t think it’s much taller than that.

    And organic molecules are pretty special. Personally, I think the stroke of genius on the part of the Designer was:

    Carbon!!!!!

    Just add water, and wait for consciousness :)

  12. 12

    Liz: “Just add water, and wait for consciousness”

    The soup was rejected due to insufficient energy source.

    Despite bioenergetic and thermodynamic failings the 80-year-old concept of primordial soup remains central to mainstream thinking on the origin of life,” said senior author, William Martin, an evolutionary biologist from the Insitute of Botany III in Düsseldorf. “But soup has no capacity for producing the energy vital for life.

    http://www.sciencedaily.com/re.....101245.htm

  13. 13
    Elizabeth Liddle

    It was a little jest :)

    But seriously, I think carbon is the crucial thing. In a carboniferous universe, life may be almost inevitable, given enough planets.

    But maybe not. A SETI signal would be cool :)

  14. The bottom line is that people like Matzke assume that once self-replication appeared, in whatever form and by whatever means, that random errors filtered by natural selection could take care of the rest and produce Mozart and his piano concerti in about 10^17 seconds.

    Any software engineer knows that as the complexity and functional integration of his code increases, the more understanding about how it all works is required, and the less effective trial and error becomes as a developmental strategy.

    This represents the problem of probabilistic resources. There are lots of bacteria, but very few higher life forms in comparison.

    Simple logic dictates that as the complexity of functionally integrated life forms increased, the probabilistic resources must also have increased, in order for the Darwinian mechanism to have had any potential creative power. But the exact opposite is the case. The more sophisticated the system, the fewer the opportunities for Darwinian mechanisms to wave their imaginary magic wands.

    This is why the Darwinian hypothesis is transparently absurd. It is mathematically ludicrous.

  15. Nick Matzke,

    Thank you for your post. Let me make one thing clear up-front: I’m a philosopher. I make no claim to being a biologist, and I therefore welcome criticism from qualified specialists like yourself.

    Having said that, I’d now like to address the criticisms you put forward in your post. You write:

    But, if someone is going to claim scholarly support for the notion that prebiotic natural selection is impossible, and that there is just no conceivable way to get to a self-replicating sytem, should they be aware of, and cite, major recent work by Harvard biologists that directly contradicts their premise? Heck yes! Did you or Meyer do it? Nope.

    The paper you cited by Nowak and Ohtsuki was published on July 14, 2008. Meyer’s book came out shortly afterwards, in 2009. As you are doubtless well aware, preparing a book for publication is a process that takes several months. It is highly likely that Meyer was not aware of Nowak and Ohtsuki’s paper until some time after his book had been sent to his publisher, HarperOne.

    As for myself, all I can say is that I am not a regular reader of PNAS, the journal in which Nowak and Ohtsuki’s paper was published. Perhaps I should be.

    Having said that, I utterly reject your charge that ID proponents “can’t be bothered to inform themselves of the actual state of affairs in science, and instead quote decades-old work as if it was definitive.” My own post refutes this very charge. You want proof? Have a look at the list of references from Meyer that I cited. Go on, take a look! Do you notice something interesting in reference 18?

    [18] Wigner, Eugene. “The Probability of the Existence of a Self-Reproducing Unit.” In The Logic of Personal Knowledge: Essays Presented to Michael Polyani, edited by Edward Shils, pp. 231-235. London: Routledge and Kegan Paul, 1961. [But see here for a critique by physicist John C. Baez. - VJT]

    Yes, there’s a link to a paper entitled, “Is Life Improbable?” by John C. Baez, in Foundations of Physics, Volume 1, No. 1, 1989. Baez attacks the reasoning contained in Eugene Wigner’s argument. I deliberately listed Baez’s critique right next to the reference provided by Meyer, precisely because I wanted to stimulate an open and honest discussion on this thread. You failed to even notice the link I provided. Mullenix would not have made that mistake, I can assure you.

    And now to matters of substance. I had a look at Nowak and Ohtsuki’s paper, and I have to say that I was underwhelmed.

    Why? First, the paper contained absolutely no chemistry. There was only mathematics. Second, the mathematics was not terribly sophisticated. Even I could understand it – and I’m a philosopher who hasn’t studied maths for 30 years. (Full disclosure: I have a B.S. in maths, but that was a long, long time ago.)

    There were no references in the paper to amino acids. There were no references in the paper to nucleotides. There were no references in the paper to polypeptides. There were no references in the paper to polynucleotides. There was one reference in the paper to RNA. There were no references in the paper to DNA.

    You call this a serious origin of life paper? I wouldn’t even call it a science paper. There’s no real world connection here. Where’s the chemistry?

    One sentence illustrates the problem with this paper:

    The theoretical prediction for this threshold, u_c=1?[(d+2a)/r]^(1/n)=0.058, is illustrated by the vertical broken line and is in perfect agreement with the numerical simulation.

    The authors are patting themselves on the back because their theoretical prediction is in perfect agreement with a numerical simulation? Funny. I always thought, with Francis Bacon, that a fundamental criterion for good science was agreement with real-world observations. How silly of me.

    My second substantive criticism of Nowak and Ohtsuki’s paper is that it fails to address Meyer’s “error catastrophe problem” head-on. In his book, Meyer wrote:

    [Oparin] proposed that natural selection initially would act on unspecified strings of polypeptides of nucleotides and amino acids. But this created another problem for his scenario. Researchers pointed out that any system of molecules for copying information would be subject to a phenomenon known as “error catastrophe” unless these molecules are specified enough to ensure an error-free transmission of information. An error catastrophe occurs when small errors – deviations from functionally necessary sequences – are amplified in successive replications.[14] Since the evidence of molecular biology shows that unspecified polypeptides will not replicate genetic information accurately, Oparin’s proposed system of initially unspecified polymers would have been highly vulnerable to such an error catastrophe.

    Notice that in his book, Meyer cites research involving real chemicals: polypeptides. He points out that “the evidence of molecular biology shows that unspecified polypeptides will not replicate genetic information accurately.”

    You refer me to a paper in which the authors make no reference to polypeptides, and hypothesize that for some polymers, the mutation rate is less than a certain critical value:

    There is also competition between life and prelife. Life is selected over prelife only if the replication rate is greater than a certain threshold (Fig. 3). Mutation during replication leads to an error threshold between life and prelife. Life can emerge only if the mutation rate is less than a critical value that is proportional to the inverse of the sequence length (Fig. 4).

    There is no attempt here to rebut Meyer’s observations regarding the error-proneness of polypeptide replication, just a mathematical model that suggests competition can emerge if the error rate is below a certain critical value. Seriously?

    My third and final criticism is that the proposals put forward by Nowak and Ohtsuki fail to account for the specified complexity of life and of proteins. (I’m using the phrase here in the same sense as it was coined by Leslie Orgel.) There is nothing in Nowak and Ohtsuki’s paper that explains how we get to a protein. All it explains is how we get giant polymers in which a “master sequence” is replicated again and again, with a low error rate. That would generate a molecule containing a sequence that was repeated again and again, with slight variations. But that’s not what a protein is like. A protein possesses the property of specified complexity, as does a DNA molecule.

    You may object that a smaller polymer need not possess the property of specified complexity. Fine; but don’t expect me to be impressed when you tell me that a molecule lacking the property of specified complexity can somehow magically explain the emergence of a molecule possessing it.

    And that, as I see it, is what is wrong with your hypothetical scenario, which invokes “the possibility of a chemical system in which monomers flow in from the general environment, drying or freezing or some such increases the concentration of monomers leading to polymerization, followed by polymers degrading at a certain rate. Make this system cyclical (day/night or seasonal cycles) and continue for a few million years.”

    A protein is not a simple repeating polymer, like polyethylene. Unless your fitness landscape is configured in such a way that it favors the production of ever longer non-repeating polymers leading up to the production of the first protein, it is utterly powerless to account for the emergence of specified complexity. But the existence of such a “nice” fitness landscape that allows for the stepwise emergence of proteins and other molecules exhibiting specified complexity would itself be a miracle. Of all possible fitness landscapes that one can imagine, the vast majority will lack this property.

    But hey, I’m not a biologist. Doubtless you can think of 101 flaws in my argument, Dr. Matzke. So let’s hear them.

    And now, over to you.

  16. Looking for a 50-bit lifeform is like looking for a single-line tax form.

  17. Having said that, I utterly reject your charge that ID proponents “can’t be bothered to inform themselves of the actual state of affairs in science, and instead quote decades-old work as if it was definitive.” My own post refutes this very charge. …

    At the same time, it hardly matters even if the accusation were true. For, as we all know, “‘science’ is not about belief and doesn’t require belief” … or, to put it more directly, “‘science’ isn’t about truth and does not necessarily deliver us truth“. And, we can’t use ‘science’ to determine which scientific statements are true and which are not.

    So, when Mr Matzke falsely accuses anti-Darwinists of “not keeping up with the literature”, he’s making an accusation of absolutely no importance, and of very little meaning. He’s accusing: “You haven’t wasted vast amounts of your time poring over the picayune details of this stuff that we who believe it cannot honestly say to be true“.

  18. ‘Science’ is a toy for little boys … men do philosophy. And theology.

  19. Looking for a 50-bit lifeform is like looking for a single-line tax form.

    ————-
    How much did you make?
    Send it …
    ————-

    Yep, even the simplest seems to take two lines.

  20. 20
    material.infantacy

    Hehe,

    1) How much did you make?

    2) How much do you think we should let you keep?

    3) Signature.

    I get three lines, Ilion. xp

  21. llion:

    How much did you make?
    Send it …

    Actually, the first line is redundant, considering the second, so you can condense that to:

    “Send everything”

    which, of course is the same as “how much you made”

    … So maybe life is simple, after all.

  22. vjtorley (#15)

    I am not a biologist either.

    Research into origins seems to be divided roughly into metabolism first and replicator first hypotheses. Your post mostly seems to apply to replicator first hypotheses. Both Nick Matze and I, in the first two comments, were suggesting that metabolism first is an alternative to be considered. As best I can tell, you seem to have answered this with more objections to replicator first hypotheses. It seems to me that you have missed the point being raised.

  23. Neil Rickert,

    You make a very good point. In my own defense, however, I made it quite clear at the beginning of my post, when I was quoting Dave Mullenix, that I was addressing a replicator first hypothesis, because that was the one he proposed when he wrote:

    [W]hy do you ID people insist that the first living thing was complex? 500 to 1000 bits of information? Try 50 to 100. Think of a single polymer whose only capability is reproducing itself, and which is possibly imbedded in the kind of droplets that form naturally…

    A simple self replicating molecule isn’t much compared to modern life, but if it self-replicates and allows evolution, it’s all the start we need and a small polymer would do it. Don’t worry about proteins, they come later. Don’t worry about metabolism – that’s also for advanced life. For first life, reproduction with the possibility of Darwinian evolution is all we need and a short polymer will do the trick. (Italics mine – VJT.)

    I am of course familiar with metabolism-first scenarios for the origin of life. Dr. Stuart Kauffman is a leading proponent of such scenarios, and Meyer devotes a whole chapter of his book (chapter 12) to Kauffman’s proposal, and he carefully explains why he doesn’t think Kauffman’s scenario – or any other metabolism-first scenario – will work. Here are a few highlights from pages 262-264:

    …Kauffman claims that an ensemble of relatively short and “low specificity” catalytic polypeptides and RNA molecules would together be enough to establish a metabolic system. He defends the biochemical plausibility of his scenario on the grounds that some proteins can perform enzymatic functions with low specificity and complexity. To support his claim, he cites a class of proteins known as proteases (including one in particular, called trypsin) that cleave peptide bonds at single amino-acid sites? But is he right?

    Kauffman himself acknowledges that as yet, there is no experimental evidence that such autocatalysis could occur… In fact, Kauffman’s model has at least three significant information-related problems.

    First, it does not follow , nor is it the case biochemically, that just because some enzymes might function with low specificity, that all the catalytic peptides (or enzymes) needed to establish a self-reproducing metabolic cycle could function with relatively low levels of specificity and complexity. Instead, modern biochemistry show that most and usually all of the molecules in a closed interdependent metabolic system of the type that Kauffman envisions require high-complexity and -specificity proteins…

    Second, I discovered that even the allegedly low-specificity molecules (the proteases) that Kauffman cites to illustrate the plausibility of his scenario are actually very complex and highly specific in their sequencing. I also discovered that Kauffman confuses the specificity and complexity of the parts of the polypeptides upon which the proteases act with the specificity and complexity of the proteins (the proteases) that do the enzymatic acting. Though trypsin, for example, acts upon – cleaves – peptide bonds at a relatively simple target, trypsin itself is a highly complex and specifically sequenced molecule. Indeed, trypsin is a non-repeating 247-amino-acid protein that possesses signiicant sequence specificity as a condition of function…

    Third, Kauffman acknowledges that for autocatalysis to occur, the molecules in the chemical minestrone must be held together in a very specific spatial-temporal relationship to one another. In other words, for the direct catalysis of integrated metabolic complexity to occur, a system of catalytic peptide molecules must first achieve a very specific molecular configuration (or what chemists call a “low-configurational energy state”). This requirement is equivalent to saying that the system must start with a large amount of specified information or specified complexity… In short, Kauffman merely transfers the information problem from the molecules into the soup.

    In addition to these problems, Kauffman’s model … does not explain (a) how the proteins in various metabolic pathways came into association with DNA and RNA or any other molecular replicator or (b) how the information in the metabolic system of proteins was transferred from the proteins into the DNA or RNA. And it gives no account of how the sequence specificity of polypeptides arose (given that the bonding affinities that exist among amino acids don’t correlate to actual amino acid sequences in known proteins)…

    Robert Shapiro, a leading chemist at New York University, has recently proposed that origin-of-life researchers begin to investigate metabolism-first models of the kind that Kauffman proposed… Though Shapiro favors these metabolism-first approaches, he acknowledges that researchers have not yet identified what he calls a “driver reaction” that can convert small molecules into products that increase or “mobilize” the organization of the system as a whole. He also notes that researchers on metabolism-first models “have not yet demonstrated the operation of a complete [metabolic] cycle or its ability to sustain itself and undergo further evolution.” In short, these approaches remain speculative and do not yet offer a way to solve the fundamental problem of the origin of biologically relevant organization (or information).

    I submit that the metabolism-first scenario which you and Matzke propose suffers from the same defects as the replicator-first scenario: it utterly fails to account for the origin of biological information. In short, Meyer has done his homework. He makes a very formidable case that Intelligent Design is required to account for the origin of life, and scientists working in the field have yet to answer Meyer’s case. His arguments stand unrefuted.

  24. “Dave Mullenix confesses to not yet having read Dr. Stephen Meyer’s Signature in the Cell, although he has purchased a Kindle version of the book. I realize that he is a very busy man…”

    Hardly a confession. Meyer is a known quantity due to his work with the Discovery Institute and ARN. He seems to see the world through an ID Reality Distortion Field and, judging by his past output, I really don’t expect to ever find anything useful in anything he writes. “Signature” is basically a compilation of things he’s written elsewhere with some added autobiographical passages. Some casual browsing I did right after I downloaded it gave me the distinct impress that he was trying to put one over on the reader.

    I mean really, a Bible believing young man graduates from a conservative religiously affiliated college with a degree in earth science and gets a job as a geologist for an oil company and never thinks it’s worth mentioning that he’s a YEC? I’ve heard that there are YECs working as oil company geologists and I would have been very interested to see how he balanced his belief in a young earth with modern geology, but apparently he’s utterly incurious about how the two mix. At least that’s the impression he tries to give in the book.

    It reminds me very much of Wells writing about his growing suspicion that there’s more to life than Darwinism as he was toiling away in graduate school and then coming across his blog post where Reverand Wells, Moonie pastor and theologian, says that “Father” (Reverend Moon) ordered him to go to graduate school and paid him to attend so that Wells could learn enough to disprove Darwinism.

    And then there’s this gem from page 24: “Even so, like many scientists I had never really thought about where DNA – or the information it contained – came from in the first place. If asked, I would have said it had something to do with evolution, but I couldn’t have explained the process in any detail.” A Young Earth Creationist thinks it might have had something to do with evolution? Tell me another, but make it a little more realistic please.

    And what am I to make of this from page 34? “The Rotary scholarship I had received allowed me to attend any one of five overseas universities, provided I could gain admittance. Several of them offered programs in the history or philosophy of science, but in a pre-Internet era it was difficult to extract detailed information from them about the specializations of their faculties. In the end, I set my hopes on Cambridge, since it had more of a reputation for science than the other universities on my list.” The mind boggles! He couldn’t find information on Cambridge because the Internet wasn’t invented yet? Pull the other one now.

    So it’s not surprising that, “Signature in the Cell” kept getting pushed down on the stack by more useful or at least more interesting books until you brought it up.

    Having now read your quotations from the book plus some surrounding material, I am sorry to say that the main mistake seems to be both Meyer’s and yours. Oparin’s theory called for some pretty elaborate and high information chemicals to be in place before any evolution could start. On pg 272 Meyer mentions amino acids, sugars and other building blocks producing proteins, carbohydrates and other complex polymers and all those chemicals getting trapped in some sort of crude proto-cell membranes and THEN beginning Darwinian evolution. This is way too much information to be assembled randomly.

    This was all published in the 1920s. Frederick Griffith first discovered that there was an inheritance molecule in 1928. Oswald Avery finally figured out that DNA was the molecule in the early 40s. This gave Oparin the additional problem of getting the information needed to reproduce all of the above and somehow putting it into the DNA and he never figured out how to do that.

    But then Meyer assumes that even if he had been able to get the initial information into the DNA somehow, the reproductive machinery would have been too simple to do high fidelity reproduction and the organisms would have been killed off by ever mounting errors, or the “error catastrophe”.

    This doesn’t affect the simple polymer theory of OOL. Assume you have a shortish polymer – a molecule that is a string made of smaller molecules – monomers. Polymers are constantly forming and being torn apart with each new one being different from its predecessors. Finally, one is formed that manages to reproduce itself at least once before it’s torn apart. This would be the first molecule of life.

    Now suppose that before it reproduces itself, it makes several defective copies. Too short, wrong sequence of monomers, folded over on itself, whatever. They don’t reproduce, so they are slowly torn apart like all the other polymers. So long as the original polymer manages to make at least one good copy before it’s destroyed, life goes on.

    Now suppose that the polymer makes a copy of itself that is almost accurate, but contains one or two errors – and that mutated copy also manages to copy itself before it is destroyed. Now we have two, slightly different, polymers reproducing – and Darwinian evolution is off and running. And error catastrophes can’t stop it.

    I notice that you say, “In conclusion: there are good reasons for thinking that a 50-bit life-form would never work. Since it would not be capable of accurate self-replication, it would be unable to evolve into larger molecules such as RNA, DNA and proteins.” Why do you say this? Not because of the error catastrophe. It doesn’t apply. Not because of anything John von Neumann said – the polymer is the information storage and whatever it’s using to reproduce itself – electrostatic attraction bringing in new monomers to add to the polymer under construction or whatever – is the replicating and processing “system”.

    I also noticed Meyer wrote this: 269 “ … I saw no reason to accept this prohibition against considering the design hypothesis. To me, it seemed like an unnecessary restriction on rational thought.” As we’ve been discussing on the “No Good Theology…” thread, any thinking Being is orders of magnitude more complex than anything discussed here and consequently is orders of magnitude less likely to exist.

  25. dmullenix, I noticed after you sneered at the Theistic beliefs of Meyer (you threw sneers at Wells theistic beliefs for good measure), you failed to provide ANY empirical evidence for your atheistic materialistic beliefs themselves. For instance,,, here is ‘your scientific evidence’

    Assume you have a shortish polymer,,,

    ‘Now suppose that before it reproduces itself, it makes several defective copies.’

    Now suppose that the polymer makes a copy of itself that is almost accurate,

    So basically dmullenix you make a extremely bad Theistic argument to support your atheism, as if this refutes Theism, and then you appeal to your imaginary conjectures to support your atheistic beliefs. But this is all just as well for this is precisely the type of argumentation that infuses Darwinian thought ever since Darwin wrote his book, and as this recent peer-reviewed paper pointed out;

    Charles Darwin, Theologian: Major New Article on Darwin’s Use of Theology in the Origin of Species – May 2011
    http://www.evolutionnews.org/2.....46391.html

    From Philosopher to Science Writer: The Dissemination of Evolutionary Thought – May 2011
    Excerpt: The powerful theory of evolution hangs on this framework of thought that mandates naturalism. The science is weak but the metaphysics are strong. This is the key to understanding evolutionary thought. The weak arguments are scientific and the strong arguments, though filled with empirical observation and scientific jargon, are metaphysical. The stronger the argument, the more theological or philosophical.
    http://darwins-god.blogspot.co.....riter.html

    ,,,Moreover dmullenix, science owes absolutely nothing to Darwinian thought,,,

    Materialists like to claim evolution is indispensable to experimental biology and led the way to many breakthroughs in medicine, Yet in a article entitled “Evolutionary theory contributes little to experimental biology”, this expert author begs to differ.

    “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.
    Philip S. Skell – Professor at Pennsylvania State University.
    http://www.discovery.org/a/2816

    Podcasts and Article of Dr. Skell
    http://www.evolutionnews.org/2.....40981.html

    Darwinian Medicine and Proximate and Evolutionary Explanations – Michael Egnor – neurosurgeon – June 2011
    http://www.evolutionnews.org/2.....47701.html

    Science Owes Nothing To Darwinian Evolution – Jonathan Wells – video
    http://www.metacafe.com/watch/4028096

  26. And the kicker dmullenix??? ‘science’ is not even possible within your atheistic/materialistic worldview of neo-Darwinism!!!

    Should You Trust the Monkey Mind?
    Excerpt: Evolutionary naturalism assumes that our noetic equipment developed as it did because it had some survival value or reproductive advantage. Unguided evolution does not select for belief except insofar as the belief improves the chances of survival. The truth of a belief is irrelevant, as long as it produces an evolutionary advantage. This equipment could have developed at least four different kinds of belief that are compatible with evolutionary naturalism, none of which necessarily produce true and trustworthy cognitive faculties.
    http://www.firstthings.com/ont.....onkey-mind

    What is the Evolutionary Argument Against Naturalism? (‘inconsistent identity’ of cause leads to failure of absolute truth claims for materialists) (Alvin Plantinga) – video
    http://www.youtube.com/watch?v=5yNg4MJgTFw

    Can atheists trust their own minds? – William Lane Craig On Alvin Plantinga’s Evolutionary Argument Against Naturalism – video
    http://www.youtube.com/watch?v=byN38dyZb-k

    “But then with me the horrid doubt always arises whether the convictions of man’s mind, which has been developed from the mind of the lower animals, are of any value or at all trustworthy. Would any one trust in the convictions of a monkey’s mind, if there are any convictions in such a mind?” – Charles Darwin – Letter To William Graham – July 3, 1881

    It is also interesting to point out that this ‘inconsistent identity’, pointed out by Plantinga, which leads to the failure of neo-Darwinists to make absolute truth claims for their beliefs, is what also leads to the failure of neo-Darwinists to be able to account for objective morality, in that neo-Darwinists cannot maintain a consistent identity towards a cause for objective morality;

    The Knock-Down Argument Against Atheist Sam Harris – William Lane Craig – video
    http://www.youtube.com/watch?v=tvDyLs_cReE

    “Atheists may do science, but they cannot justify what they do. When they assume the world is rational, approachable, and understandable, they plagiarize Judeo-Christian presuppositions about the nature of reality and the moral need to seek the truth.
    As an exercise, try generating a philosophy of science from hydrogen coming out of the big bang. It cannot be done. It’s impossible even in principle, because philosophy and science presuppose concepts that are not composed of particles and forces. They refer to ideas that must be true, universal, necessary and certain.” – Crevo Headlines

    This following video humorously reveals the bankruptcy that atheists have in trying to ground beliefs within a materialistic worldview;

    John Cleese – The Scientists – humorous video
    http://www.youtube.com/watch?v=-M-vnmejwXo

    ============

    Materialism simply dissolves into absurdity when pushed to extremes and certainly offers no guarantee to us for believing our perceptions and reasoning within science are trustworthy in the first place:

    Dr. Bruce Gordon – The Absurdity Of The Multiverse & Materialism in General – video
    http://www.metacafe.com/watch/5318486/

    This following site is a easy to use, and understand, interactive website that takes the user through what is termed ‘Presuppositional apologetics’. The website clearly shows that our use of the laws of logic, mathematics, science and morality cannot be accounted for unless we believe in a God who guarantees our perceptions and reasoning are trustworthy in the first place.

    Proof That God Exists – easy to use interactive website
    http://www.proofthatgodexists.org/index.php

    THE GOD OF THE MATHEMATICIANS – DAVID P. GOLDMAN – August 2010
    Excerpt: we cannot construct an ontology that makes God dispensable. Secularists can dismiss this as a mere exercise within predefined rules of the game of mathematical logic, but that is sour grapes, for it was the secular side that hoped to substitute logic for God in the first place. Gödel’s critique of the continuum hypothesis has the same implication as his incompleteness theorems: Mathematics never will create the sort of closed system that sorts reality into neat boxes.
    http://www.faqs.org/periodical.....27241.html

    etc.. etc.. etc..

  27. Dave Mullenix (#24),

    I have to say I was rather disappointed by the tone of your last post. You are welcome to disagree vigorously with the claims of Intelligent Design proponents, but misrepresenting them is another matter entirely. You have seriously misrepresented the views of Dr. Stephen Meyer. No doubt your claims were made in all sincerity, but you are badly misinformed.

    You accused Dr. Stephen Meyer of being a young earth creationist (YEC). You wrote:

    I mean really, a Bible believing young man graduates from a conservative religiously affiliated college with a degree in earth science and gets a job as a geologist for an oil company and never thinks it’s worth mentioning that he’s a YEC? I’ve heard that there are YECs working as oil company geologists and I would have been very interested to see how he balanced his belief in a young earth with modern geology, but apparently he’s utterly incurious about how the two mix. At least that’s the impression he tries to give in the book. (Emphases mine – VJT.)

    Where did you get this nonsense? A casual search of Meyer’s own papers utterly refutes your claim. Have a look at The Cambrian Explosion: Biology’s Big Bang (2001 version) and also the 2003 version here: http://www.discovery.org/scrip.....038;id=639 . Allow me to quote a couple of excerpts:

    In this essay, we will test the claims of neo-Darwinism and two other materialistic models of evolutionary theory: punctuated equilibrium and self-organization. We will do so by assessing how well these theories explain the main features of the Cambrian explosion—a term that refers to the geologically sudden appearance of numerous new animal forms (and their distinctive body plans) 530 million years ago…

    The fossils of the Cambrian explosion exhibit several distinctive features. First, as the name implies, the fossils of the Cambrian explosion appear suddenly or abruptly within a very brief period of geologic time. (See Figure 1). As recently as 1992, paleontologists thought the Cambrian period began 570 million years ago (mya) and ended 510 mya, with the Cambrian explosion itself occurring within a 20 to 40 million year window during the lower Cambrian period. In 1993, radiometric dating of zircon crystals from formations just above and just below Cambrian strata in Siberia allowed for a precise recalibration of the age of Cambrian strata. Radiometric analyses of these crystals fixed the start of the Cambrian period at 543 mya and the beginning of the first appearance of the animal phyla (i.e., the Cambrian explosion itself) at 530 mya. (Emphases mine – VJT.)

    Figure 2 in the 2003 version of the article lists the earth’s age as 4600 mya (million years ago). Enough said?

    I’d also like you to have a look at the following article in Discover magazine by Chris Mooney, entitled, Time to refute Stephen Meyer?

    Scroll down to comment number 3 by Intelligent Design advocate Casey Luskin, here:

    http://blogs.discovermagazine......ment-36257 . Luskin writes:

    As an ID proponent myself, I feel it would be great to see some serious critiques of Meyer. I’ll give critics three tips on how not to critique Meyer:

    First, don’t call Meyer a young earth creationist, because he isn’t. (Jerry Coyne tried that tack and had to retract the claim.)

    Second, don’t try to cast Meyer’s argument as a mere negative argument against material causes, as Mooney claims that Meyer “throws up his hands, and says, it’s so improbable, God must have done it.” Meyer arguments for design is unmistakably a positive one, and is not merely a negative argument against evolution…

    Third, don’t attack Meyer’s book before you read it. Anyone who claims or insinuates that Meyer’s argument for design is merely a negative critique of evolutionary mechanisms has clearly skipped a lot of chapters.

    Where, you ask, did Professor Jerry Coyne accuse Dr. Stephen Meyer of being a young earth creationist? The claim (and Professor Coyne’s retraction) can be found in his blog entry for 15 July 2009, entitled, Pro-intelligent-design editorial in Boston Globe. I shall quote a brief extract:

    Stephen Meyer, young-earth creationist and Discovery Institute macher, has published a pro-intelligent-design piece, Jefferson’s Support for Intelligent Design , in today’s Boston Globe. It’s largely an argument from authority, noting that Jefferson imputed the structure of the Universe to design…

    Note: I stand corrected–Stephen Meyer is not a young earth creationist. I was thinking of his Discovery Institute colleague Paul Nelson, whom I debated a while back. My apologies to Mr. Meyer for attributing to him a lunatic idea of his colleague.

    Not a very polite apology, but an apology all the same. Let’s give credit where credit’s due.

    I hope you will be kind enough to retract your assertion that Dr. Stephen Meyer is a young earth creationist. I shall address your other comments in your last post (#24) shortly.

  28. 28
    Barry Arrington

    Dr. Torley, you are a treasure to the ID movement. The élan with which you called Matzke’s literature bluff was beautiful to behold.

  29. No doubt your claims were made in all sincerity…

    No doubt he doesn’t care whether his claim was true or not and a sincere lie (if there can even be such a thing) is still a lie.

    Why do we coddle these people?

    Call what they have said a lie and sit back and watch the moral indignation.

  30. Thanks Barry. I’m glad you enjoyed reading it.

  31. Neil Rickert:

    Research into origins seems to be divided roughly into metabolism first and replicator first hypotheses. Your post mostly seems to apply to replicator first hypotheses. Both Nick Matze and I, in the first two comments, were suggesting that metabolism first is an alternative to be considered.

    So let me explain what is going on here. You (Neil) and Nick were approaching the origin of life as a problem that needs to be solved.

    dmullenix on the other hand had a different problem he was trying to solve.

    So he thinks a simple self-replicator is all that is needed to solve his problem and is satisfied that if he can image one then his problem has in fact been solved.

    So why is it that some people imagine that all they need is a simple self-replicator, and others say whoa there, it’s not that simple?

    I don’t understand why Darwinists [Dave] don’t just say, well, that’s an origin of life issue and leave it at that.

    Instead they feel compelled to assert that ID’ists have failed to consider that all it takes to get to a complex cell with DNA, RNA, proteins, metabolism and cell division (among numerous other things) is a simple first self-replicator and all else follows by some imaginary unspecified unknown and probably unknowable pathways.

    IOW, pure fantasy.

  32. H’mm:

    Let’s put into the listings the recent — c. 2006 — overall summary views of two leading OOL researchers, that I believe on fair comment can be described as mutually destructive and as highly relevant to the state of the case today:

    _________________

    Shapiro, Sci Am: >> RNA’s building blocks, nucleotides, are complex substances as organic molecules go. They each 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. Many alternative ways exist for making those connections, yielding thousands of plausible nucleotides that could readily join in place of the standard ones but that are not represented in RNA. That number is itself dwarfed by the hundreds of thousands to millions of stable organic molecules of similar size that are not nucleotides . . . .

    The RNA nucleotides are familiar to chemists because of their abundance in life and their resulting commercial availability. In a form of molecular vitalism, some scientists have presumed that nature has an innate tendency to produce life’s building blocks preferentially, rather than the hordes of other molecules that can also be derived from the rules of organic chemistry. This idea drew inspiration from . . . Stanley Miller. He applied a spark discharge to a mixture of simple gases that were then thought to represent the atmosphere of the early Earth. ["My" NB: Subsequent research has sharply undercut this idea, a point that is unfortunately not accurately reflected in Sci Am's caption on a picture of the Miller-Urey apparatus, which in part misleadingly reads, over six years after Jonathan Wells' Icons of Evolution was published: The famous Miller-Urey experiment showed how inanimate nature could have produced amino acids in Earth's primordial atmosphere . . .] Two amino acids of the set of 20 used to construct proteins were formed in significant quantities, with others from that set present in small amounts . . . more than 80 different amino acids . . . have been identified as components of the Murchison meteorite, which fell in Australia in 1969 . . . By extrapolation of these results, some 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 . . . I have observed a similar pattern in the results of many spark discharge experiments . . . . no nucleotides of any kind have been reported as products of spark discharge experiments or in studies of meteorites, nor have the smaller units (nucleosides) that contain a sugar and base but lack the phosphate.

    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 . . . .

    The analogy that comes to mind is that of a golfer, who having played a golf ball through an 18-hole course, then assumed that the ball could also play itself around the course in his absence. He had demonstrated the possibility of the event; it was only necessary to presume that some combination of natural forces (earthquakes, winds, tornadoes and floods, for example) could produce the same result, given enough time. No physical law need be broken for spontaneous RNA formation to happen, but the chances against it are so immense, that the suggestion implies that the non-living world had an innate desire to generate RNA. The majority of origin-of-life scientists who still support the RNA-first theory either accept this concept (implicitly, if not explicitly) or feel that the immensely unfavorable odds were simply overcome by good luck. >>

    Orgel (posthumous, 2008, PLOS) >> 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 . . . Could a nonenzymatic “metabolic cycle” have made such compounds available in sufficient purity to facilitate the appearance of a replicating informational polymer?

    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. Each proposed metabolic cycle, therefore, must be evaluated in terms of the efficiencies and specificities that would be required of its hypothetical catalysts in order for the cycle to persist. Then arguments based on experimental evidence or chemical plausibility can be used to assess the likelihood that a family of catalysts that is adequate for maintaining the cycle could have existed on the primitive Earth . . . .

    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]? The lack of a supporting background in chemistry is even more evident in proposals that metabolic cycles can evolve to “life-like” complexity. The most serious challenge to proponents of metabolic cycle theories—the problems presented by the lack of specificity of most nonenzymatic catalysts—has, in general, not been appreciated. If it has, it has been ignored. 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. >>
    ___________________

    It is fair comment to say that OOL studies are in at least as much trouble today as they were a few years ago.

    So, pardon my doubts on failure — since the 1920′s — to credibly identify how a metabolising automaton with the additional feature of a von Neumann self replicator implemented using molecular nanotech, could have plausibly [with our question begging imposition of a priori Lewontinian materialism] arisen by forces of undirected chance and mechanical necessity on the gamut of our observed cosmos across its lifespan to date on the usual cosmological timeline, 13.7 BY.

    GEM of TKI

  33. Dave Mullenix (#24),

    I’d now like to address your scientific comments. I notice that unlike Dr. Robert Shapiro and unlike Dr. Nick Matzke, you favor a replication-first scenario: you hold that organisms acquired the ability to reproduce themselves before they acquired the ability to metabolize anything. That’s fine; but I’d just like to know why you disagree with Shapiro and Matzke on this point.

    You write:

    Assume you have a shortish polymer… that manages to reproduce itself at least once before it’s torn apart. This would be the first molecule of life.

    Now suppose that before it reproduces itself, it makes several defective copies… So long as the original polymer manages to make at least one good copy before it’s destroyed, life goes on.

    Now suppose that the polymer makes a copy of itself that is almost accurate, but contains one or two errors – and that mutated copy also manages to copy itself before it is destroyed. Now we have two, slightly different, polymers reproducing – and Darwinian evolution is off and running. And error catastrophes can’t stop it.

    My answer: That depends on the percentage of errors. If a biopolymer mutates too many times when it replicates, its descendants may lose some of the biological features which have evolved to their advantage, including their ability to reproduce at all. You say that error catastrophes can’t stop Darwinian evolution. Obviously they can, if they prevent an organism from reproducing. Dr. Meyer has argued that the risk of error catastrophe is real, and he claims that the evidence of molecular biology shows that unspecified polypeptides will not replicate genetic information accurately, as these molecules are not specified enough to ensure an error-free (or almost error-free) transmission of information. If I were trying to refute Dr. Meyer, I would be doing some experiments in the lab, with the aim of showing that in fact, polypeptides are capable of reproducing information sufficiently accurately to allow the creation of much larger molecules, without loss of specified complexity.

    The other main problem I have with your scenario is that it fails to account for the origin of specified complexity in the first place. To illustrate this point, imagine a simplified world with 7 amino acids, A, B, C, D, E F and G. How would your polymerization-with-a-few-errors process account for a pattern like the following one?

    GCDEFGCCAFGABCCCFGFEDEFEDCBCDECEDGCDEFGCCAFGABCCCFGFEDEFEDCDEDCBC

    As you can see, while there’s some repetition here, there’s also a lot of interesting novelty too, and as you’ll realize when you recognize where the pattern comes from, it’s highly specific: most changes in the pattern would ruin it, and relatively few would enhance it.

    Instead, what I’d expect to see with your scenario is a pattern exhibiting a high degree of repetition with a few mistakes, more like this:

    ABCDEFGACCDEFGABCGEFGAFCDEFGCDCDEFGABCFEFGABCDEFAABCDECGABCDFFG

    Incidentally, can you guess where I got the first sequence from? I’ll give you a hint: Eisenach. I’ll give you another hint: the sequence would normally start with D. Why did I change it to G?

  34. Hi kairosfocus,

    Thanks for the scientific papers you dug up. They were invaluable.

  35. Here’s Dr. Nick Matzke’s proposed scenario for the origin of life:

    Surely any vaguely capable summary of this issue would have to include the possibility of a chemical system in which monomers flow in from the general environment, drying or freezing or some such increases the concentration of monomers leading to polymerization, followed by polymers degrading at a certain rate. Make this system cyclical (day/night or seasonal cycles) and continue for a few million years.

    And here are Dr. Robert Shapiro’s comments on Matzke’s proposed drying-and-freezing cycle (“A Simpler Origin for Life”, in Scientific American, February 12, 2007) – see here: http://www.scientificamerican......038;page=3

    I will cite one example of prebiotic synthesis, published in 1995 by Nature and featured in the New York Times. The RNA base cytosine was prepared in high yield by heating two purified chemicals in a sealed glass tube at 100 degrees Celsius for about a day. One of the reagents, cyanoacetaldehyde, is a reactive substance capable of combining with a number of common chemicals that may have been present on the early Earth. These competitors were excluded. An extremely high concentration was needed to coax the other participant, urea, to react at a sufficient rate for the reaction to succeed. The product, cytosine, can self-destruct by simple reaction with water. When the urea concentration was lowered, or the reaction allowed to continue too long, any cytosine that was produced was subsequently destroyed. This destructive reaction had been discovered in my laboratory, as part of my continuing research on environmental damage to DNA. Our own cells deal with it by maintaining a suite of enzymes that specialize in DNA repair.

    The exceptionally high urea concentration was rationalized in the Nature paper by invoking a vision of drying lagoons on the early Earth. In a published rebuttal, I calculated that a large lagoon would have to be evaporated to the size of a puddle, without loss of its contents, to achieve that concentration. No such feature exists on Earth today.

    The drying lagoon claim is not unique. In a similar spirit, other prebiotic chemists have invoked freezing glacial lakes, mountainside freshwater ponds, flowing streams, beaches, dry deserts, volcanic aquifers and the entire global ocean (frozen or warm as needed) to support their requirement that the “nucleotide soup” necessary for RNA synthesis would somehow have come into existence on the early Earth.

    On a different topic: some readers have queried Dr. Stephen Meyer’s concerns about “error catastrophe” which I highlighted in my opening post, but Shapiro evidently takes them seriously too:

    Many chemists, confronted with these difficulties, have fled the RNA-first hypothesis as if it were a building on fire. One group, however, still captured by the vision of the self-copying molecule, has opted for an exit that leads to similar hazards. In these revised theories, a simpler replicator arose first and governed life in a “pre-RNA world.” Variations have been proposed in which the bases, the sugar or the entire backbone of RNA have been replaced by simpler substances, more accessible to prebiotic syntheses. Presumably, this first replicator would also have the catalytic capabilities of RNA. Because no trace of this hypothetical primal replicator and catalyst has been recognized so far in modern biology, RNA must have completely taken over all of its functions at some point following its emergence.

    Further, the spontaneous appearance of any such replicator without the assistance of a chemist faces implausibilities that dwarf those involved in the preparation of a mere nucleotide soup. Let us presume that a soup enriched in the building blocks of all of these proposed replicators has somehow been assembled, under conditions that favor their connection into chains. They would be accompanied by hordes of defective building blocks, the inclusion of which would ruin the ability of the chain to act as a replicator. The simplest flawed unit would be a terminator, a component that had only one “arm” available for connection, rather than the two needed to support further growth of the chain.

    There is no reason to presume than an indifferent nature would not combine units at random, producing an immense variety of hybrid short, terminated chains, rather than the much longer one of uniform backbone geometry needed to support replicator and catalytic functions. Probability calculations could be made, but I prefer a variation on a much-used analogy. Picture a gorilla (very long arms are needed) at an immense keyboard connected to a word processor. The keyboard contains not only the symbols used in English and European languages but also a huge excess drawn from every other known language and all of the symbol sets stored in a typical computer. The chances for the spontaneous assembly of a replicator in the pool I described above can be compared to those of the gorilla composing, in English, a coherent recipe for the preparation of chili con carne. With similar considerations in mind Gerald F. Joyce of the Scripps Research Institute and Leslie Orgel of the Salk Institute concluded that the spontaneous appearance of RNA chains on the lifeless Earth “would have been a near miracle.” I would extend this conclusion to all of the proposed RNA substitutes that I mentioned above.

    Shapiro goes on to speak highly of Gunter Wachterhauser’s proposed scenario for the origin of life. Shapiro is honest enough to state that Wachterhauser and his colleagues “have not yet demonstrated the operation of a complete cycle or its ability to sustain itself and undergo further evolution.” However, I would like to say that Wachterhauser has clearly done his homework on the conditions that would need to be satisfied in order for life to originate on Earth, and I greatly respect his detailed, methodical, experiment-oriented approach to the problem.

  36. Barry Arrington: Dr. Torley, you are a treasure to the ID movement. The élan with which you called Matzke’s literature bluff was beautiful to behold.

    Amen to that

  37. Dr. Torley; this may be of interest as to the extreme effort it took to get a ‘tiny’ RNA:

    Origin of Life: Claiming Something for Almost Nothing (RNA)
    Excerpt: Yarus admitted, “the tiny replicator has not been found, and that its existence will be decided by experiments not yet done, perhaps not yet imagined.” But does this (laboratory) work support a naturalistic origin of life? A key question is whether the (tiny RNA) molecule could form under plausible prebiotic conditions. Here’s how the paper described their work in the lab to get this molecule:,,

    RNA was synthesized by Dharmacon. GUGGC = 5’-GUGGC-30 ; GCCU – 5’P-GCCU-3’ ; 5’OH-GCCU = 5’-GCCU-3’ ; GCCU20dU = 5’-GCC-2’-dU; GCC = 5’-GCC-3’ ; dGdCdCrU = 5’-dGdCdCU-3’ . RNA GCC3’dU was prepared by first synthesizing 5’-O-(4,4’- Dimethoxytrityl)3’-deoxyuridine as follows: 3’-deoxyuridine (MP Biomedicals; 991 mg, 0.434 mmol) was dissolved in 5 mL anhydrous pyridine and pyridine was then removed under vacuum while stirring. Solid was then redissolved in 2 mL pyridine. Dimethoxytrityl chloride (170 mg, 0.499 mmol) was dissolved in 12 mL pyridine and slowly added to 3’-deoxyuridine solution. Solution was stirred at room temperature for 4 h. All solutions were sequestered from exposure to air throughout.
    Reaction was then quenched by addition of 5 mL methanol, and solvent was removed by rotary evaporation. Remaining solvent evaporated overnight in a vacuum chamber. Product was then dissolved in 1 mL acetonitrile and purified through a silica column (acetonitrile elution). Final product fractions (confirmed through TLC, 1.1 hexane:acetonitrile) were pooled and rotary evaporated. Yield was 71%. Dimethoxytrityl-protected 30dU was then sent to Dharmacon for immobilization of 30-dU on glass and synthesis of 5’-GCC-3’-dU.
    PheAMP, PheUMP, and MetAMP were synthesized by the method of Berg (25) with modifications and purification as described in ref. 6. Yield was as follows: PheAMP 85%, PheUMP 67%, and MetAMP 36%.

    Even more purification and isolation steps under controlled conditions, using multiple solvents at various temperatures, were needed to prevent cross-reactions. (and the understatement of the year) It is doubtful such complex lab procedures have analogues in nature.
    http://www.creationsafaris.com.....#20100302a

  38. Torley is in a class about which Matzke is unaware.

    Torley thinks, questions, and reasons. Matzke is a hate-filled ideological robot. His purpose is not science; it’s the destruction of his enemies: people who believe that there is more to life than chemistry and chance.

    I am probably the only contributor at UD who understands Matzke, because I was once he, rescued by the Grace of God and equally by a commitment to legitimate scientific rigor, which demands that one follow the evidence wherever it leads.

  39. Wow, sorry I missed this thread earlier. A 50-bit life form? What a hoot!

    “A simple self replicating molecule . . .”

    Gotta love that. The other day I again ran across Dawkins’ faith-based quote about a self-replicating molecule “somehow” coming into existence. I actually laughed out loud when I read it again. Newsflash folks: there is no such thing as a simple self-replicating molecule.

    On a related note, Matzke, like usual, loves to drop literature bomb references, with papers that are either irrelevant, or, in most cases, simply do not support the assertions he makes.

  40. Bornagain77,

    Thanks very much for the link. I loved the comment at the end:

    If Big Science would do its job, the creationists and intelligent design community would not have to be cast in the role of spoil sports, showing why these ideas won’t work. They won’t work anyway, but other insiders, not just the expelled, should be saying so. After all, much of the work was paid for with taxpayer dollars. Where are the watchdogs?

    Where, indeed.

  41. [W]hy do you ID people insist that the first living thing was complex?

    You’ve never heard of a God complex?

    500 to 1000 bits of information? Try 50 to 100.

    Would someone care to demonstrate some things that might be got with only 50-100 bits of information?

    Some examples?

  42. 42
    material.infantacy

    An 10×10 pixel black and white image.

    A 5×5 pixel 4 color image.

    12 ascii characters.

    ~25 morse code characters.

    Lousy encryption.

  43. 43
    material.infantacy

    I retract lousy encryption.

  44. vjtorley at 37 I checked and you’re right, I was wrong. Dr. Meyer has admitted that he believes the earth is 4.6 billion years old. I apologize to him. I found his admission at http://www.antievolution.org/c....._the_earth.

    Again, I was wrong and I apologize.

  45. vjtorley at 33 “My answer: That depends on the percentage of errors.”

    If it manages to reproduce itself at least once before it is destroyed, then the percentage of errors was low enough. (And by implication, it’s duplicate has the same ability.) If one of it’s attempts at reproducing generates an offspring molecule that can’t reproduce, then that molecule is out of the picture. It slowly degrades to become raw materials while the original molecule tries again. Remember, “life” is when the first molecule reproduces itself before it is degraded and that takes into account any failed attempts.

    “The other main problem I have with your scenario is that it fails to account for the origin of specified complexity in the first place.”

    Whoa! Let’s stop and look at that for a moment. What is the specification here? The ability to reproduce itself at least once before it is destroyed. If it reproduces itself, it by definition meets the specification. The exact pattern isn’t important, so long as it meets the specification of reproducing itself before it’s destroyed.

    Google says that Eisenach is the childhood home of Martin Luther and he translated the German Bible while he was hiding in Wartburg Castle in that city. (Some Christians were trying to Expel! him from the earth.) Maybe your pattern is the first letters of a Bible passage in German? Except there are only seven different letters. Wiki also says that Eisenach is the birthplace of Johann Sebastian Bach. Musical notes come in 7 flavors – A through G – so I’m guessing they’re the notes to a musical passage. Jesu joy of men’s desiring? Just a guess. No idea why you switched the initial D to a G.

  46. vjtorley at 34 “Hi kairosfocus,
    Thanks for the scientific papers you dug up. They were invaluable.”

    KF at 33: “Unfortunately, neither chemists nor laboratories were present on the early Earth to produce RNA . . . .

    Of course, plate tectonics were at work even then, dragging millions of tons of sea water under the earth where it then percolated up through geologically active rock formations under conditions of high temperatures and pressure, which greatly speed up all chemical reactions.

    The rocks the water was percolating through provided thousands of different chemicals for the hot water to dissolve and they also provided millions or billions of square kilometers of submicroscopic nooks and crannies to act as catalysts as the hot, chemically laden water flowed by.

    Temperatures also rose and fell sharply as the water percolated past lava channels and then through cooler rocks.

    That’s a lot like a lab except that this natural lab is literally the size of all the continents on ancient earth, down to a depth of several kilometers. The total volume of the microscopic water channels and molecular sized potential catalysts are measured in millions or billions of square kilometers. And this lab was in operation for hundreds of millions of years.

    Note also the third sentence in Shapiro’s title:

    “Energy-driven networks of small molecules afford better odds as the initiators of life.”

    I recommend that everybody read the article, especially pages 5-8 where Dr. Shapiro starts out with:

    “Life With Small Molecules
    Nobel Laureate Christian de Duve has called for “a rejection of improbabilities so incommensurably high that they can only be called miracles, phenomena that fall outside the scope of scientific inquiry.” DNA, RNA, proteins and other elaborate large molecules must then be set aside as participants in the origin of life. Inanimate nature provides us with a variety of mixtures of small molecules, whose behavior is governed by scientific laws, rather than by human intervention.”

    I join vjtorley in thanking you for that citation.

  47. as to:

    ‘Energy-driven networks of small molecules afford better odds as the initiators of life.”

    Refutation Of Hyperthermophile Origin Of Life scenario
    Excerpt: While life, if appropriately designed, can survive under extreme physical and chemical conditions, it cannot originate under those conditions. High temperatures are especially catastrophic for evolutionary models. The higher the temperature climbs, the shorter the half-life for all the crucial building block molecules,
    http://www.reasons.org/LateHea.....iginofLife

    The origin of life–did it occur at high temperatures?
    Excerpt: Prebiotic chemistry points to a low-temperature origin because most biochemicals decompose rather rapidly at temperatures of 100 degrees C (e.g., half-lives are 73 min for ribose, 21 days for cytosine, and 204 days for adenine).
    http://www.ncbi.nlm.nih.gov/pubmed/11539558

    Chance and necessity do not explain the origin of life: Trevors JT, Abel DL.
    Excerpt: Minimal metabolism would be needed for cells to be capable of growth and division. All known metabolism is cybernetic–that is, it is programmatically and algorithmically organized and controlled.
    http://www.ncbi.nlm.nih.gov/pubmed/15563395

    etc.. etc..

    as to;

    ‘That’s a lot (on early earth) like a lab except that this natural lab is literally the size of all the continents on ancient earth, down to a depth of several kilometers.’

    Your right the early earth was a lab set up by God to a place hospitable for advanced life;

    ,,,in conjunction with photosynthetic, and sulfate reducing, bacteria, geological processes helped detoxify the earth of dangerous levels of metal for as far back in time as we can tell:

    The Concentration of Metals for Humanity’s Benefit:
    Excerpt: They demonstrated that hydrothermal fluid flow could enrich the concentration of metals like zinc, lead, and copper by at least a factor of a thousand. They also showed that ore deposits formed by hydrothermal fluid flows at or above these concentration levels exist throughout Earth’s crust. The necessary just-right precipitation conditions needed to yield such high concentrations demand extraordinary fine-tuning. That such ore deposits are common in Earth’s crust strongly suggests supernatural design.
    http://www.reasons.org/TheConc.....tysBenefit

    And on top of the fact that poisonous heavy metals on the primordial earth were brought into ‘life-enabling’ balance by complex biogeochemical processes, there was also an explosion of minerals on earth which were a result of that first life, as well as being a result of each subsequent ‘Big Bang of life’ there afterwards.

    The Creation of Minerals:
    Excerpt: Thanks to the way life was introduced on Earth, the early 250 mineral species have exploded to the present 4,300 known mineral species. And because of this abundance, humans possessed all the necessary mineral resources to easily launch and sustain global, high-technology civilization.
    http://www.reasons.org/The-Creation-of-Minerals

    “Today there are about 4,400 known minerals – more than two-thirds of which came into being only because of the way life changed the planet. Some of them were created exclusively by living organisms” – Bob Hazen – Smithsonian – Oct. 2010, pg. 54

    To put it mildly, this minimization of poisonous elements, and ‘explosion’ of useful minerals, is strong evidence for Intelligently Designed terra-forming of the earth that ‘just so happens’ to be of great benefit to modern man.

    Clearly many, if not all, of these metal ores and minerals laid down by these sulfate-reducing bacteria, as well as laid down by the biogeochemistry of more complex life, as well as laid down by finely-tuned geological conditions throughout the early history of the earth, have many unique properties which are crucial for technologically advanced life, and are thus indispensable to man’s rise above the stone age to the advanced ‘space-age’ technology of modern civilization.

    Metallurgy
    http://en.wikipedia.org/wiki/Metallurgy

    Minerals and Their Uses
    http://www.scienceviews.com/geology/minerals.html

    ==================

    Anthropic Principle: A Precise Plan for Humanity By Hugh Ross
    Excerpt: Brandon Carter, the British mathematician who coined the term “anthropic principle” (1974), noted the strange inequity of a universe that spends about 15 billion years “preparing” for the existence of a creature that has the potential to survive no more than 10 million years (optimistically).,, Carter and (later) astrophysicists John Barrow and Frank Tipler demonstrated that the inequality exists for virtually any conceivable intelligent species under any conceivable life-support conditions. Roughly 15 billion years represents a minimum preparation time for advanced life: 11 billion toward formation of a stable planetary system, one with the right chemical and physical conditions for primitive life, and four billion more years toward preparation of a planet within that system, one richly layered with the biodeposits necessary for civilized intelligent life. Even this long time and convergence of “just right” conditions reflect miraculous efficiency.
    Moreover the physical and biological conditions necessary to support an intelligent civilized species do not last indefinitely. They are subject to continuous change: the Sun continues to brighten, Earth’s rotation period lengthens, Earth’s plate tectonic activity declines, and Earth’s atmospheric composition varies. In just 10 million years or less, Earth will lose its ability to sustain human life. In fact, this estimate of the human habitability time window may be grossly optimistic. In all likelihood, a nearby supernova eruption, a climatic perturbation, a social or environmental upheaval, or the genetic accumulation of negative mutations will doom the species to extinction sometime sooner than twenty thousand years from now.
    http://christiangodblog.blogsp.....chive.html

    One scientist is far more pessimistic about the ‘natural’ future lifespan of the human race than 20,000 years:

    Humans will be extinct in 100 years says eminent scientist – June 2010
    http://www.physorg.com/news196489543.html

  48. as well, plate tectonics is found to be a finely-tuned ‘coincidence’;

    New Definition Could Further Limit Habitable Zones Around Distant Suns: – June 2009
    … liquid water is essential for life, but a planet also must have plate tectonics to pull excess carbon from its atmosphere and confine it in rocks to prevent runaway greenhouse warming. Tectonics, or the movement of the plates that make up a planet’s surface, typically is driven by radioactive decay in the planet’s core, but a star’s gravity can cause tides in the planet, which creates more energy to drive plate tectonics…. Barnes added, “The bottom line is that tidal forcing is an important factor that we are going to have to consider when looking for habitable planets.”
    http://www.sciencedaily.com/re.....124831.htm

    The Life and Death of Oxygen – 2008
    Excerpt: “The balance between burial of organic matter and its oxidation appears to have been tightly controlled over the past 500 million years.” “The presence of O2 in the atmosphere requires an imbalance between oxygenic photosynthesis and aerobic respiration on time scales of millions of years hence, to generate an oxidized atmosphere, more organic matter must be buried (by tectonic activity) than respired.” – Paul Falkowski
    http://www.creationsafaris.com.....#20081024a

  49. dmullenix:

    Remember, “life” is when the first molecule reproduces itself before it is degraded and that takes into account any failed attempts.

    Translation: Life is what I say it is regardless of any evidence to the contrary.

    Is “life” with quote marks different from life without quote marks?

  50. dmullenix @44:

    Steve Meyer didn’t “admit” anything. You make it sound like he finally was backed into a corner and had to admit something he didn’t want to, which is a complete misreading of his position and the record. He, as do many ID proponents, accepts the general view of the age of the earth (currently thought to be around 4.6BY). That the questioner was a complete jerk and that Dr. Meyer had hoped to participate in a fair hearing is clear from the transcript you linked to, but don’t characterize it as some “admission.”

    Your apology is noted, but your characterization of why you were wrong seems a bit off. It wasn’t that Meyer admitted something that you didn’t know he had admitted, but rather that you just didn’t know his position in the first place.

    Sorry to be a bit blunt. Maybe it was just the way you worded the quick comment . . .

  51. Can anyone give us an example of a self-replicating molecule?

  52. 52

    Random responses to various points:

    Shapiro quote:

    And here are Dr. Robert Shapiro’s comments on Matzke’s proposed drying-and-freezing cycle

    That’s a specific response to one specific 1995 experiment, which has definitely been surpassed by the 2009 RNA syntheses. And Shapiro doesn’t deny that freezing, drying, etc. concentration mechanisms would all exist on a prebiotic earth. As long as you have water and ice and volcanoes, concentration mechanisms are a sure thing.

    Re: error catastophe — dmullenix has the basic correct response here:

    But then Meyer assumes that even if he had been able to get the initial information into the DNA somehow, the reproductive machinery would have been too simple to do high fidelity reproduction and the organisms would have been killed off by ever mounting errors, or the “error catastrophe”.

    This doesn’t affect the simple polymer theory of OOL. Assume you have a shortish polymer – a molecule that is a string made of smaller molecules – monomers. Polymers are constantly forming and being torn apart with each new one being different from its predecessors. Finally, one is formed that manages to reproduce itself at least once before it’s torn apart. This would be the first molecule of life.

    Now suppose that before it reproduces itself, it makes several defective copies. Too short, wrong sequence of monomers, folded over on itself, whatever. They don’t reproduce, so they are slowly torn apart like all the other polymers. So long as the original polymer manages to make at least one good copy before it’s destroyed, life goes on.

    Now suppose that the polymer makes a copy of itself that is almost accurate, but contains one or two errors – and that mutated copy also manages to copy itself before it is destroyed. Now we have two, slightly different, polymers reproducing – and Darwinian evolution is off and running. And error catastrophes can’t stop it.

    The only thing I would add is that Nowak’s model explains how you might gradually get above the error catastrophe. Monomers keep flowing in from the general environment, concentration forms polymers, which then degrade. This turnover system creates a population of polymers with a distribution of lengths, and the polymers are continually turning over. But if some of the polymers (or, IMHO even more likely, a combination of even shorter polymers) help catalyze the formation of even approximately self-similar polymers, this will change the equilibrium frequency of such polymers in a positive direction.

    Re: RNA synthesis difficulties — quoting stuff published before 2009, including quotes from Shapiro and Stephen Meyer, is pretty much pointless, since it turned out that making even the “hardest” RNA nucleobase, cytosine, wasn’t so hard. Ironically, what was required was abandonment of the typical chemists’ strategy — first form nucleobases in isolation, then put in phosphate, etc. — and instead have the various ingredients together from the start. This makes the experimental chemist’s life harder when they try to figure out the details of the reactions in the lab, but it is undoubtedly more realistic.

    Published online 13 May 2009 | Nature | doi:10.1038/news.2009.471

    RNA world easier to make

    Ingenious chemistry shows how nucleotides may have formed in the primordial soup.

    Richard Van Noorden
    RNADid life begin with RNA?Wikimedia Commons

    An elegant experiment has quashed a major objection to the theory that life on Earth originated with molecules of RNA.

    John Sutherland and his colleagues from the University of Manchester, UK, created a ribonucleotide, a building block of RNA, from simple chemicals under conditions that might have existed on the early Earth.

    The feat, never performed before, bolsters the ‘RNA world’ hypothesis, which suggests that life began when RNA, a polymer related to DNA that can duplicate itself and catalyse reactions, emerged from a prebiotic soup of chemicals.

    “This is extremely strong evidence for the RNA world. We don’t know if these chemical steps reflect what actually happened, but before this work there were large doubts that it could happen at all,” says Donna Blackmond, a chemist at Imperial College London.
    Molecular choreography

    An RNA polymer is a string of ribonucleotides, each made up of three distinct parts: a ribose sugar, a phosphate group and a base — either cytosine or uracil, known as pyrimidines, or the purines guanine or adenine. Imagining how such a polymer might have formed spontaneously, chemists had thought the subunits would probably assemble themselves first, then join to form a ribonucleotide. But even in the controlled atmosphere of a laboratory, efforts to connect ribose and base together have met with frustrating failure.

    The Manchester researchers have now managed to synthesise both pyrimidine ribonucleotides. Their remedy is to avoid producing separate ribose-sugar and base subunits. Instead, Sutherland’s team makes a molecule whose scaffolding contains a bond that will turn out to be the key ribose-base connection. Further atoms are then added around this skeleton, which unfurls to create the ribonucleotide.

    “We had a suspicion there was something good out there, but it took us 12 years to find it.”

    The final connection is to add a phosphate group. But that phosphate, although only a reactant in the final stages of the sequence, influences the entire synthesis, Sutherland’s team showed. By buffering acidity and acting as a catalyst, it guides small organic molecules into making the right connections.

    “We had a suspicion there was something good out there, but it took us 12 years to find it,” Sutherland says. “What we have ended up with is molecular choreography, where the molecules are unwitting choreographers.” Next, he says, he expects to make purine ribonucleotides using a similar approach.
    The start of something special?

    Although Sutherland has shown that it is possible to build one part of RNA from small molecules, objectors to the RNA-world theory say the RNA molecule as a whole is too complex to be created using early-Earth geochemistry. “The flaw with this kind of research is not in the chemistry. The flaw is in the logic — that this experimental control by researchers in a modern laboratory could have been available on the early Earth,” says Robert Shapiro, a chemist at New York University.

    Sutherland points out that the sequence of steps he uses is consistent with early-Earth scenarios — those involving methods such as heating molecules in water, evaporating them and irradiating them with ultraviolet light. And breaking RNA’s synthesis down into small, laboratory-controlled steps is merely a pragmatic starting point, he says, adding that his team also has results showing that they can string nucleotides together, once they have formed. “My ultimate goal is to get a living system (RNA) emerging from a one-pot experiment. We can pull this off. We just need to know what the constraints on the conditions are first.”

    Shapiro sides with supporters of another theory of life’s origins – that because RNA is too complex to emerge from small molecules, simpler metabolic processes, which eventually catalysed the formation of RNA and DNA, were the first stirrings of life on Earth.

    “They’re perfectly entitled to disagree with us. But having got experimental results, we are on the high ground,” says Sutherland.

    “Ultimately, the challenge of prebiotic chemistry is that there is no way of validating historical hypotheses, however convincing an individual experiment,” points out Steven Benner, who studies origin-of-life chemistry at the Foundation for Applied Molecular Evolution, a non-profit research centre in Gainesville, Florida.

    Sutherland, though, hopes that ingenious organic chemistry might provide an RNA synthesis so convincing that it effectively serves as proof. “We might come up with something so coincidental that one would have to believe it,” he says. “That is the goal of my career.”

    References

    Powner, M. W., Gerland, B. & Sutherland, J. D. Nature 459, 239-242 2009

    What was Stephen Meyer’s main response to this work? Well, said he, it doesn’t explain the origin of information and specified , just the origin of the monomer building blocks.

    But explaining the origin of the information-bearing polymers, given those monomers, is what Nowak’s work is about. VJTorley complained that Nowak’s paper didn’t include any chemistry. Meyer complained that Sutherland’s work didn’t explain information.

    But…shocker, I know…**different papers address different aspects of the issue**!! Not every paper can address every aspect of a huge and complex topic at once. It is decidedly un-scholarly to declare that there is some gaping unsolvable hole in OOL research because one paper doesn’t address every difficulty with the OOL that you can think up over breakfast, when other papers, very well-known in the field if not among armchair critics sitting on blogs, address those issues explicitly.

    To sum up:

    Do we understand everything about the OOL? Obviously not. There are all kinds of puzzles. But are we making progress? Obviously we are. Key difficulties, both conceptual and chemical — including the specific difficulties ID proponents like to raise — are gradually being understood and overcome. If the best difficulties they can think of turn out to evaporate once sufficient knowledge is gained, then we have even less reason to think that the OOL is “impossible” and therefore requires supernatural intervention than we had before.

    What is not convincing at all is to object to the OOL on the basis of either (a) not knowing of obviously relevant work, (b) citing old quotes that have been rendered irrelevant by new work, and (c) failing to consider the obvious point that each paper focuses on a specific question and does not address every issue you might think up while pondering the issue over your cheerios at breakfast.

  53. Can anyone give us an example of a self-replicating molecule?

    http://en.wikipedia.org/wiki/Crystal

  54. “. . . In brief, living organisms are distinguished by their specified complexity. Crystals are usually taken as the prototypes of simple well-specified structures, because they consist of a very large number of identical molecules packed together in a uniform way. Lumps of granite or random mixtures of polymers are examples of structures that are complex but not specified. The crystals fail to qualify as living because they lack complexity; the mixtures of polymers fail to qualify because they lack specificity.” [[Leslie Orgel, The Origins of Life (John Wiley, 1973), p. 189.]

  55. Nick Matzke:

    Re: error catastophe — dmullenix has the basic correct response here:

    The only thing I would add is that Nowak’s model explains how you might gradually get above the error catastrophe.

    If dmullenix has the basic correct response, what need is there of a model explaining how you might gradually get above the error catastrophe?

    Basically Dave did a bunch of hand-waving and asserted without factual basis that there is no “error catastrophe” problem.

    And then you come in and say he’s right but he’s wrong. Go figure.

    Dave asserted that the error catastrophe problem is not relevant to simple enough polymers.

    This doesn’t affect the simple polymer theory of OOL.

    So at what point does it become relevant?

    Well, according to Dave, it never becomes relevant.

    Now we have two, slightly different, polymers reproducing – and Darwinian evolution is off and running. And error catastrophes can’t stop it.

    He just hand-waved away the entire issue.

    You guys are amazing, you really are.

    At some point the length of the genome must increase, and when it does error threshold does in fact become an issue.

    There is no magical Darwinian evolution kicks in and error catastrophes can’t stop it.

  56. >> ‘Organized’ systems are to be carefully distinguished from ‘ordered’ systems. Neither kind of system is ‘random,’ but whereas ordered systems are generated according to simple algorithms [[i.e. “simple” force laws acting on objects starting from arbitrary and common- place initial conditions] and therefore lack complexity, organized systems must be assembled element by element according to an [[originally . . . ] external ‘wiring diagram’ with a high information content . . . Organization, then, is functional complexity and carries information. It is non-random by design or by selection, rather than by the a priori necessity of crystallographic ‘order.’ [[J S Wicken, “The Generation of Complexity in Evolution: A Thermodynamic and Information-Theoretical Discussion,” Journal of Theoretical Biology, 77 (April 1979): p. 353, of pp. 349-65. >>

  57. Mung:There is no magical Darwinian evolution kicks in and error catastrophes can’t stop it.

    There you go again! thinking that ‘science’ can’t have Magick.

  58. The abiotic synthesis of RNA is an ongoing project and progress is being made on several fronts. For published examples see;

    1. Chemoselective Multicomponent One-Pot Assembly of Purine Precursors in Water. J. Am. Chem. Soc (2010)
    2. Phosphate-Mediated Interconversion of Ribo- and Arabino-Configured Prebiotic Nucleotide Intermediates. Angew. Chem. Int. Ed. (2010)
    3. A Stereoelectronic Effect in Prebiotic Nucleotide Synthesis. ACS
    Chem. Biol. (2010)

  59. Mung at 49: Me: “Remember, “life” is when the first molecule reproduces itself before it is degraded and that takes into account any failed attempts.

    Mung: “Translation: Life is what I say it is regardless of any evidence to the contrary.”

    Me: Successful reproduction before death is pretty much the standard definition for first life. I added the part about that taking into account any failed attempts to answer your objection. Life is in quotes because I’m defining it.

    Eric Anderson at 50: Steven Meyer is notoriously coy about giving an age to the earth. That’s the main reason I and many others thought he was a YEC since otherwise why hide his opinion? I used the term “admission” because of his previous reluctance to disclose his opinion and I’m a little surprised the questioner got it out of him. In light of his answer, perhaps his reluctance is because he doesn’t want to jeopardize the Discovery Institute’s funding.

    In what way was the hearing unfair? Were Dr. Meyer and the other witnesses prevented from testifying? Wasn’t that the hearing where the religious conservatives on the Kansas school board were trying to force the Discovery Institute’s “Critical Analysis of Evolution” lesson plan into the science curriculum? Did Dr. Meyer expect the Board to roll over and play dead? Or was it unfair because they ultimately rejected the DI’s plan?

    Mung at 55 “If dmullenix has the basic correct response, what need is there of a model explaining how you might gradually get above the error catastrophe?

    Basically Dave did a bunch of hand-waving and asserted without factual basis that there is no “error catastrophe” problem.

    And then you come in and say he’s right but he’s wrong. Go figure.

    Dave asserted that the error catastrophe problem is not relevant to simple enough polymers.

    This doesn’t affect the simple polymer theory of OOL.

    So at what point does it become relevant?”

    Me: When the organism gets complex enough so the genome has to specify lots of non-genomic material that is essential for reproduction.

    The “simple polymer” is the genome for first life. If it gets clobbered, it’s a small loss and you just try again. If the next try produces a duplicate of the original polymer, the genome lives though another round.

    If it’s slightly different but still reproduces itself and the genome makes an accurate copy of itself on the next try then you’ve got evolution in action.

    But if that genome is specifying a lot of other “finely tuned” molecules that are necessary for more efficient reproduction then small errors in the genome can sabotage their function and you’re into error catastrophe zone.

    “At some point the length of the genome must increase, and when it does error threshold does in fact become an issue.”

    Me: Why? So long as it’s a naked genome, slight errors can be tolerated. In fact, they can lead to evolution.

  60. Hi everyone,

    An interesting paper which claims to resolve the error catastrophe problem has been published recently. Nick Matzke and Dave Mullenix might be interested in this one. I’d like to mention it in all fairness, because although it undercuts arguments I defended in this post relating to the error catastrophe, the paper does represent the latest research in the field. Here it is:

    http://www.plosone.org/article.....ne.0021904

    Saakian DB, Biebricher CK, Hu C-K (2011) “Lethal Mutants and Truncated Selection Together Solve a Paradox of the Origin of Life.” PLoS ONE 6(7): e21904. doi:10.1371/journal.pone.0021904

    Background

    Many attempts have been made to describe the origin of life, one of which is Eigen’s cycle of autocatalytic reactions [Eigen M (1971) Naturwissenschaften 58, 465–523], in which primordial life molecules are replicated with limited accuracy through autocatalytic reactions. For successful evolution, the information carrier (either RNA or DNA or their precursor) must be transmitted to the next generation with a minimal number of misprints. In Eigen’s theory, the maximum chain length that could be maintained is restricted to nucleotides, while for the most primitive genome the length is around . This is the famous error catastrophe paradox. How to solve this puzzle is an interesting and important problem in the theory of the origin of life.

    Methodology/Principal Findings

    We use methods of statistical physics to solve this paradox by carefully analyzing the implications of neutral and lethal mutants, and truncated selection (i.e., when fitness is zero after a certain Hamming distance from the master sequence) for the critical chain length. While neutral mutants play an important role in evolution, they do not provide a solution to the paradox. We have found that lethal mutants and truncated selection together can solve the error catastrophe paradox. There is a principal difference between prebiotic molecule self-replication and proto-cell self-replication stages in the origin of life.

    Conclusions/Significance

    We have applied methods of statistical physics to make an important breakthrough in the molecular theory of the origin of life. Our results will inspire further studies on the molecular theory of the origin of life and biological evolution.

    =================================

    I would invite readers to comment on this paper. Here’s a short comment sent to me by a scientist:

    “This paper is not a model of the origin of a genetic code per se (the term ‘code’ only appears once, and only in reference to Shannon optimal codes and error thresholds). It does give a model of the origin of a fairly long information carrying molecule (DNA, RNA, etc.) despite the Eigen paradox that predicts only short molecules can survive without some kind of error correction. This paper’s solution is that the lack of reproduction for bad sequences saves the day.”

    My own take on the paper is that the error catastrophe paradox should no longer be used as a knock-down argument against the possibility of life starting small. ID advocates would be better advised to focus on the key puzzle surrounding the origin of life: namely, the origin of specified complex information.

    By the way, Dave, if you’re wondering where I got that sequence of letters in post #33 above, try whistling it. Sound familiar? It’s Bach’s Minuet in G major, transposed to the key of C, which is why it starts on G instead of D. You were on the right track.

    Cheers.

  61. Successful reproduction before death is pretty much the standard definition for first life.

    And all you folks out there who have not reproduced yet are not yet alive, and if you don’t reproduce before you die you will never have lived.

  62. dmullenix (#45)

    Thank you for your post. In response to my claim that proposed naturalistic origin-of-life scenarios fail to account for the origin of specified complexity in the first place, you write:

    Whoa! Let’s stop and look at that for a moment. What is the specification here? The ability to reproduce itself at least once before it is destroyed. If it reproduces itself, it by definition meets the specification. The exact pattern isn’t important, so long as it meets the specification of reproducing itself before it’s destroyed.

    You’re right to say that a self-replicating molecule possesses some degree of specificity. However, if the molecule is short and can be reached by an easy chemical pathway, the specified complexity will be low – well below the 500-bit threshold which many ID proponents have claimed that undirected natural processes cannot breach. In Signature in the Cell, on page 496, Dr. Stephen Meyer makes a testable, falsifiable prediction regarding specified complex information:

    No undirected process will demonstrate the capacity to generate 500 bits of new information starting from a nonbiological source.

    To falsify that claim, you need to do one of two things: EITHER show that a nonbiological process can generate that level of specified complexity, OR show that the specified complexity associated with (say) the first living cell is actually much less than 500 bits – i.e. that its origin was far more probable than Dr. Meyer claims it was.

  63. Hi everyone,

    While we’re on the subject of falsifiable predictions, I notice that the paper I cited in #60 above ( http://www.plosone.org/article.....ne.0021904 ) claims that the length of the most primitive possible genome would be about 7,000 to 20,000 nucleotides. That shocked me when I read it, because according to http://users.rcn.com/jkimball......Sizes.html , the smallest genome of any organism yet found is 490,885 base pairs (Nanoarchaeum equitans). The authors defend their low estimate by citing this paper:

    http://www.ncbi.nlm.nih.gov/pm.....ool=pubmed
    Microbiol Mol Biol Rev. 2004 September; 68(3): 518–537.
    doi: 10.1128/MMBR.68.3.518-537.2004
    PMCID: PMC515251
    Copyright 2004, American Society for Microbiology
    “Determination of the Core of a Minimal Bacterial Gene Set”
    Rosario Gil, Francisco J. Silva, Juli Pereto, and Andres Moya.

    Would anyone care to comment? I strongly suspect that it would be impossible to construct a bacterium with a gene set of 7,000 or even 20,000 nucleotides.

  64. Mung @53:

    I realize that some people view a crystal is an example of a self-replicating molecule. Even if it is, it doesn’t teach us anything about the origin of life, of course, but humor me a minute:

    Is a crystal really self-replicating? Do we start with a crystal whose structure is somehow ascertained, copied and replicated in some fashion, or are we simply dealing with what essentially amounts to a dissolved substance precipitating out of a solution? If I let some salt water evaporate in a dish and precipitate out the salt, and then let some more salt water evaporate later, have the original salt crystals “self-replicated” in any meaningful sense of the word? Of course not. They’ve just had new deposits placed upon them, which for chemical reasons may line up to form nice shapes.

    Sorry, but I don’t see crystal formation as even in the same category as the kind of self-replication we’re looking for (not to mention the elephant in the room — CSI).

  65. dmullenix @59:

    I don’t have the impression that Meyer has been hesitant to say what his personal opinion on the age of the Earth is. The age of the Earth is, however, (i) largely irrelevant to ID, and (ii) a hot button for most evolutionists who are trying to making a point or divide and conquer the various viewpoints that are support ID. So, yes, he would be cautious in talking about the age of the Earth in those situations where it is irrelevant or may be construed in an inappropriate fashion.

    I did not say the hearing was unfair. I said Meyer expected the hearing to be fair. I’m not familiar with the entire hearing, nor do I have an overall impression of the hearing as a whole — I’m just looking at the transcript you linked to. A witness has a right to know the purpose of the hearing and why they are there. Also, the witness can ask clarifying questions if needed. Go back and read the transcript — this time not from the viewpoint of gloating about how such an ingenious questioner made Meyer admit something he didn’t want to, but from a standpoint of general tone and human interaction — and I think you will see that, while Meyer was being a bit stubborn because he didn’t want his response to be taken in the wrong context or seen for more than it should be, the questioner was being a real jerk.

  66. Hi everyone,

    Here’s some more feedback on the PLoS paper at http://www.plosone.org/article.....ne.0021904 . As I pointed out above, the authors claimed that the length of the most primitive possible genome would be about 7,000 to 20,000 nucleotides. One of the papers they cited was this one by Gil et al.: http://www.ncbi.nlm.nih.gov/pm.....ool=pubmed

    Microbiol Mol Biol Rev. 2004 September; 68(3): 518–537.
    doi: 10.1128/MMBR.68.3.518-537.2004
    PMCID: PMC515251
    Copyright 2004, American Society for Microbiology
    “Determination of the Core of a Minimal Bacterial Gene Set”

    Someone has kindly drawn my attention to the following passage at the end of the paper:

    At any rate, we should accept that there is no conceptual or experimental support for the existence of one particular form of minimal cell, at least from a metabolic point of view. In this sense, our conclusions must be regarded as provisional. Different approaches, ours among others, should converge in several solutions (35, 49). Finally, one must keep in mind that this kind of research has little relevance for the study of the origin of life, since it is impossible to identify any of the abovementioned diverse solutions with the one adopted by the more primitive cells (63). This is especially true in the cases where a bacterium-centered approach is followed, as described in this paper. Any attempt to universalize the conclusions would necessarily include the comparison with archaeal genomes, more specifically the smallest ones (84). (Emphasis mine – VJT.)

    If one looks at the PLoS paper, it is immediately apparent that L, the length of the genome for the most primitive organism, is critical to the authors’ argument. They assume it is around 10,000. Of the two sources they cite, one (Gil) warns against using his team’s research in connection with the origin of life. The other source (Kun A, Santos M, Szathmary, E .2005. Real ribozymes suggest a relaxed error threshold. Nature Genetics 37: 1008–1011) is not available online, but the abstract contains the following sentence:

    Incidentally, this genome size [7,000 nucleotides] coincides with that estimated for a minimal cell achieved by top-down analysis, omitting the genes dealing with translation. (Emphasis mine – VJT.)

    I for one would like to see some more experimental work on the question of the size of the genome for the first living cell.

  67. 67
    Elizabeth Liddle

    Eric, I have to disagree: the age of the earth is extremely relevant to ID. If the earth is young, or if the biosphere is young (i.e. a few thousand or tens of thousands of years) then Darwinian evolution simply can’t account for the variety of life.

    Some kind of Designer would have to be postulated.

    Darwinian evolution only works for a very old earth scenario. Which of course is the one that many independent sources of data support.

    That doesn’t rule out an ID of course, but it means (IMO) that the Darwinian theory is viable, given an initial self-replicator capable of Darwinian evolution.

  68. Hi Elizabeth,

    I take it from your last post that you would regard Intelligent Design as a scientific theory, regardless of whether it is true or not. You acknowledged that a young Earth would require us to postulate a Designer. In other words, under at least one scenario (one which I don’t happen to accept, I might add), Intelligent Design would be verified! Interesting. Thanks anyway.

    I might add that by the same logic, if it could ever be demonstrated that life on Earth appeared almost immediately after (a) the time when the Earth became capable of sustaining it or (b) the time of the last major cataclysm that could have wiped out all life on Earth (e.g. collision with another large body) then that would also establish the existence of a Designer who created the first living thing (say, four billion years ago).

    ==================================

    UPDATE regarding the PLoS paper:

    Here’s another comment I received on the paper, from a skeptical reader:

    “This doesn’t really strike me as new. Kondrashov and others did lots of work showing that, if you reach a point where any further mutations are lethal, this will (obviously) halt further degeneration, provided the population doesn’t go extinct. This approximates truncation selection. The issue with this is that most mutations are deleterious but low-impact, and thus accumulate. You may still reach an equilibrium point at which any further mutation is lethal, but you certainly can’t have a net information gain.”

    Thoughts, anyone?

  69. Mung @ 61,
    Thank you for sparing me having to make essentially the same comment.

  70. Eric, I have to disagree: the age of the earth is extremely relevant to ID. If the earth is young, or if the biosphere is young (i.e. a few thousand or tens of thousands of years) then Darwinian evolution simply can’t account for the variety of life.

    Some kind of Designer would have to be postulated.

    No, one wouldn’t – not in terms of logical possibility. A particular model of evolution would be knocked down as a result, but other possibilities would remain.

  71. 71
    Elizabeth Liddle

    Good point, Nullasalus. But I can’t think of any.

    Can you?

    Not that there is a lot of point, because the evidence that the earth is about 4 and half billion years old is pretty convincing.

  72. Good point, Nullasalus. But I can’t think of any.

    Can you?

    I can think of plenty.

    Brute facts: These things exist and began to exist, and there is no explanation. Nothing needs to be postulated.

    There are infinite universes and we live in one where various species got Boltzmann’d up by chance.

    There are brute laws that lead to a variety of things coming to exist without fail, and biological forms are among these things.

    The list can go on.

    Likewise, ID does not get falsified simply because the universe is old. In fact, some particular ID scenarios absolutely require an older universe.

  73. “Eric, I have to disagree: the age of the earth is extremely relevant to ID. If the earth is young, or if the biosphere is young (i.e. a few thousand or tens of thousands of years) then Darwinian evolution simply can’t account for the variety of life.

    Some kind of Designer would have to be postulated.

    Darwinian evolution only works for a very old earth scenario. Which of course is the one that many independent sources of data support.”

    Dr. Liddle, thank you for your response. I don’t mean to sound condescending, but this is wrong on multiple accounts.

    1- ID is not a theory that arises only once we decide the time is too short on the Earth for Darwinian evolution to do its job and so we look around for an alternate theory. True, an important implication of ID is that to even mimic minimal crude design you need massive resources and massive amounts of time. In that sense ID contradicts the evolutionary creation story, but not because the earth is 4.6BY old as opposed to 10KY old. I’ll spot you the entire age of the universe — shoot even 100BY — you still won’t find chance and necessity producing anything close to the diversity and complexity of life we see around us today. There is simply no reason to think otherwise, other than wishful thinking. The age of the earth is but a rounding error in the probabilistic calculation.

    2- More important than the negative case against evolution, ID posits that we can draw an inference to design as the best explanation, not based on what we don’t know, but precisely based on what we do know about the cause and effect relationships we regularly observe.

    3- “Darwinian evolution only works for a very old earth scenario.” I agree that the old earth gives Darwinists comfort, because they are easily impressed with all those zeroes. Unfortunately, there is no rational basis to think that even the billions of years could come close to creating what we see around us. Let’s be clear: there is no direct observation of that creative power at play, there is no lab result that gives evidence that such creative power exists. It is only by gazing back at the distant past (vaguely through the mists of time and without running any actual numbers) that we can *imagine* that given all those billions of years Darwinian evolution could do the work of creation.

  74. 74

    vjtorley, what about the energy problem? No one seems to bring it up.
    What role does the Late heavy bombardment have on OOL? Some say life goes back to 4.2bya, others 3.5bya. The earth was smashed at about 4bya. What in your opinion, are the implications?

  75. Mung at 61 All you folks who have not reproduced yet are not alive if you’re the first living thing.

    We’ve got to work on that reading comprehension. You too, Ilion in 69.

    Mung, I read on another board that you’re a lawyer. Is this true?

    vjtorley at 62: “In Signature in the Cell, on page 496, Dr. Stephen Meyer makes a testable, falsifiable prediction regarding specified complex information:

    No undirected process will demonstrate the capacity to generate 500 bits of new information starting from a nonbiological source.

    To falsify that claim, you need to do one of two things: EITHER show that a nonbiological process can generate that level of specified complexity, OR show that the specified complexity associated with (say) the first living cell is actually much less than 500 bits – i.e. that its origin was far more probable than Dr. Meyer claims it was.”

    The first part has been done. Darwinian evolution can add millions of bits of information to a genome. If we have reproducing polymers, they are engaging in Darwinian evolution. We can also use computer GA programs to show gains in information.

    Heck, just reproduction with the new genome getting stuck to the end of the original will double the size of a genome and that second half is ready to evolve out of redundancy and into active information.

    Unless Dr. Meyer is demanding ID style proof ala Thomas Cudworth in the “Why were so many Darwin defenders no shows” thread:

    “By an evolutionary pathway to the flagellum, I mean a step-by-step recipe for building a bacterium with a flagellum, out of a bacterium with no flagellum, not even a partial flagellum. I want to see the flagellum going up in stages before my very eyes, as I can watch a skyscraper going up in stories before my eyes. I want a morphological description of the bacterium for each intermediate stage, an explanation of the selection advantage of each stage, and a list of DNA bases that had to be altered to get to that stage, and what the substitutions were, and the exact locations where all this took place along the bacterial genome. And of course that implies I need a count of the number of necessary stages (10? 20? 100?), and also I need a full discussion of mutation rates and the time-frame that is being hypothesized, so that I can see whether wildly optimistic estimates of favorable mutations are being employed, etc.”

    “A 500-page book, minimum, complete with many diagrams of both DNA sections and morphological changes, would be needed to cover the details I’ve asked for.”

    He calls that “a plausible stepwise pathway” and we’re never going to see anything like that until we invent time travel so we can collect samples, so it’s a safe demand to make.

    The second part is what we’re discussing in this thread, once ID gets over it’s apparently unshakable belief that the first living entity was a complex cell.

    vjtorley at 63: “Would anyone care to comment? I strongly suspect that it would be impossible to construct a bacterium with a gene set of 7,000 or even 20,000 nucleotides.”

    You’re probably right, but any bacterium you see today is a late model honed by billions of years of evolution. 7,000 nucleotides would probably build a much simpler cell that would do pretty well in an early world where it didn’t have to compete with modern bacteria.

    Eric Anderson at 65: “I don’t have the impression that Meyer has been hesitant to say what his personal opinion on the age of the Earth is.”

    Try to find another instance of his giving his opinion on the matter.

    “I did not say the hearing was unfair. I said Meyer expected the hearing to be fair,”

    I think the ID team expected a cake walk. Evolutionary scientists boycotted the meeting and it looked like clear sailing ahead until one attorney showed up and started asking questions.

    You’re right about his tone. The DI was trying to slip one past the Kansas schools with the help of a board that had been captured by fundamentalists and that was not appreciated.

    vjtorley at 66: “the authors claimed that the length of the most primitive possible genome would be about 7,000 to 20,000 nucleotides.”

    While looking up “error threshold” on Wiki, I found this: “Relaxed error threshold (Kun et al., 2005) – Studies of actual ribozymes indicate that the mutation rate can be substantially less than first expected – on the order of 0.001 per base pair per replication. This may allow sequence lengths of the order of 7-8 thousand base pairs, sufficient to incorporate rudimentary error correction enzymes.”

    That article is at http://en.wikipedia.org/wiki/E.....evolution) and the Kun 2005 article (from “Nature Genetis) is at http://www.nature.com/ng/journ.....ng1621.pdf

    “Finally, one must keep in mind that this kind of research has little relevance for the study of the origin of life, since it is impossible to identify any of the abovementioned diverse solutions with the one adopted by the more primitive cells (63). This is especially true in the cases where a bacterium-centered approach is followed, as described in this paper.”

    In other words, we don’t know what the early organisms were like – they were probably very different from modern life. They certainly weren’t bacteria.

    vjtorley at 68: “I take it from your last post that you would regard Intelligent Design as a scientific theory, regardless of whether it is true or not. You acknowledged that a young Earth would require us to postulate a Designer. In other words, under at least one scenario (one which I don’t happen to accept, I might add), Intelligent Design would be verified! Interesting.”

    Such a scenario would rule out Darwinian evolution and when you get right down to it, that IS what ID is about. All of the ID papers (Dembski’s filters and meaningless huge search spaces, Behe’s irreducible complexity, Axe’s proteins – everything I can think of off hand seeks not to establish ID, but to falsify evolution.

    Even Stephen Barr at First Things has noticed this and he’s sympathetic to ID, or at least he’d like to be. http://www.firstthings.com/ont.....ent-design

    And for that matter, even a 6000 year old earth wouldn’t falsify evolution. Many YECs believe that Noah only took a few instances of each group of species on the ark – two wolves, say, and two cattle and then all the various members of the dog family and cattle family somehow evolved from them in just a few thousand years. Evolution on steroids!

    Even if ID somehow did falsify evolution, that wouldn’t automatically prove ID. There could be some other natural process at work. To prove ID, you have to actually investigate it like Darwin investigated evolution and find evidence that actually supports ID, not just falsifies evolution.

    But you’re right, ID could be investigated scientifically, just as the existence of God can be. You have to stick with observable evidence and the evidence would have to support ID but if you do that and you actually found evidence, you could scientifically support ID to the same degree of confidence that science supports evolution. But nobody’s looking that I know of. So far as I know, nobody even has an idea of where to look.

    I see nullasalus has covered a lot of this in #70.

    Nullasalus at 72: None of your examples (brute facts, Boltzmann brains, brute laws) are in any way, “particular models of evolution”.

  76. dmullenix:

    We’ve got to work on that reading comprehension.

    Your failure to put together a coherent argument has nothing to do with my reading comprehension.

    Here’s what you wrote:

    Successful reproduction before death is pretty much the standard definition for first life.

    And all subsequent life is defined differently?

    Then what is your “life” the first of?

  77. 77
    Mission.Impossible

    I don’t mean to impose. I originally composed this for another thread, but It’s no longer accepting comments, so I’m posting it here. It’s intended to show what I belive would be required to demonstrate that a simulation capable of generating CSI had been bootstrapped from simpler elements. I also believe that a reasonable OOL scenario would need to account for the same.

    There were issues with this getting hung up in the moderation queue in the other thread, so I’m hoping this properly goes through.

    THis is a continuation of some thoughts from my post at #244 which explains in more depth why I belive that in order to determine that CSI has been generated by a blind process, either naturally or via simulation, that multiple, interdependent systems need to be represented.

    Do to length I’ll split it up into more than one post. It rambles a bit. In my defense, it would have taken me much longer to clean it up and condense it than it will take anyone to read it.

    Quoting myself from here:

    Ending point: a self-replicating virtual cell, containing at least each of these: an information storage medium, and an information processing system which operates on the medium, into which the systems themselves are encoded. These items are needed because without an abstraction between information storage and functional implementation, we couldn’t do anything but violence to the concept of information, which needs some sort of encryption and decryption protocol between two sets of elements that can have nothing but an abstract link between them — and this protocol must represent a link between an inert symbolic medium and a functional element into which it translates.

    In other words, we need one language which describes the element being operated on, and another language which directly represents the element being operated on. This element must be functional, and the system which does the translating from one to the other must itself be encoded in both languages.

    Let me define how I’m using some terms in case my usage differes some from alternate or more orthodox usage.

    Specified Complexity: the presence of both specification and complexity.

    Specification: a sequence of symbols which conforms to an independently given pattern or function.

    Complexity: a contingent arrangements of matter exceeding 1000 bits. This level of complexity seems to account for every atom in the universe multiplied by every Planck-time quantum state that’s ever occured in its history, squared.

    Information: the presence of specified complexity.

    Chance: randomly contingent but otherwise inexplicable events, such as replication errors.

    Necessity:That which must occur with specific arrangements of matter under a specific set of circumstances.

    Law: That which governs necessity as expressed in the laws of physics and chemistry.

    Protocol: A specification which describes a mapping between two compatible languages, OR an entity which preforms the function of translation between the two.

    continued…

  78. 78
    Mission.Impossible

    …continued…

    For a molecular self-replicator, chance and necessity are demonstrably at work and are sufficient to explain the associated phenomena. For this type of replicator, chance and necessity are known to be operating, and the process can be empirically studied. Chance and necessity are entirely sufficient explanations for what occurs in molecular self-replication.

    Even at 500 or 1000 bits, a molecular self-replicator would be acting out law, sufficiently explained by chance and necessity.

    Why couldn’t we consider the replication process of a self-replicating molecule to be a function, and hence, at a sufficient bit depth, consider it sufficient to fulfill the requirement for specified complexity? Because specifications need to conform to an independently given pattern. One example is the data fed into a program which drives a robotic assembler; a set of blueprints by which an engineer builds a structure is another example. In both cases the specification is independant of the concrete product, and a protocol is required to act upon the specification to produce it. The computer program which drives the robotic assembler represents the protocol, and the ‘thing’ which gets assembled is the product. The engineer that builds the structure is acting as a protocol, and the structure is the product. The product is the result of the specification via the protocol, and not the specification itself.

    So why is a certain type of self-replicator — specifically one with representative DNA, protein sequences, and certain hardware — a requirement for exhibiting the bootstrapping of specified complexity?

    Inside the cell, translating between the DNA and the proteins that it codes for, we have hardware which acts as a protocol between two representative languages, which are entirely compatlibe. The first language, which codes for proteins — the DNA — is merely a set of symbols that provide a data source for an enzyme which translates those symbols into an amino acid chain — a protein — which is an item of another language, a sequence of amino acids which will be folded into a protein.

    The symbol table — the DNA — is data storage; it provides specification for the protein sequence by indicating every amino acid via a codon (a three-letter symbol which corresponds to a specific amino in the chain) and the order in which it appears. This is so that the enzyme can perform not only transcription for a replication event, but translation from the codon into the amino that it codes for. These amino acids, coded for in a given strand of DNA, comprise a protein.

    By chaining these amino acids together, we then have (after folding) a functional protein: something that exhibits high complexity, and exhibits function; but its form is only explicable via the process that created it. The falsification would be an empirical one: that we could observe the process of proteins being sequenced and folded in the wild, such that being machine-assembled wouldn’t be a necessary condition — we could observe the process ocurring via law quite readily.

    Since the sequence of the protein can only be the result of a mechanical process within the cell, we have the requrements of specified complexity: we can trace back the chain of amino acids and arrive at the DNA sequence that specified them and we can determine the necessary role of the protocol. We have an independent pattern acting as a specification, and we have the product that results from the instantiation of the protocol that deciphers it.

    continued…

  79. 79
    Mission.Impossible

    …continued…

    Let’s say we came across a molecule in the wild, and it seemed to exhibit a high degree of complexity in that the permutaitons of the seqence space were significantly large, and we wanted to determine the process that formed the molecule.

    We could easily determine that law was responsible by observing the formation of that molecule via law-like processes, such as with crystal formation. This would provide empirical support for that view; we would have direct experience with a law-like process which assembles that molecule.

    Now suppose we find these molecules all over the place, but we don’t ever observe the formation of them. At that point, we’d have an unknown cause for an observation. Now let’s say later we discover a process which accounts for the molecule. We could then assume that barring the discovery of a dependent process, this one was sufficient. Later, if we did find another process which could assemble the molecule, or other conditions under which it would form, we’d have a complementary process capable of accomplishing the same thing but perhaps via completely different laws or conditions. Until we discovered the second process, we would logically defer to the first as a sufficient cause.

    Given a sequenced folded protein we currently observe one process which accounts for it, one observed phenomenon which results in the finished product, and that’s the intra-cellular processes of storing, translating, sequencing, and folding an amino acid chain into a protein. Whether there was a law-like process outside (or prior to) the cell would always remain a possibility, but we couldn’t posit one until we could observe and document it, that is, demonstrate it empirically. Our explanation for the phenomenon would need to fall squarely on what we’ve observed; we wouldn’t need to put forward as a complementary explanation the notion that it could alternatively be assembed otherwise.

    That said, for the origin of life we need a process that can assemble and fold proteins; and that process, as it’s known, is defined by the machinery in the cell. So the only explanation for what we observe in the cell is the cell itself. We have a paradox. (One way around this is to postulate design. We didn’t observe it being designed, but we know that the process of design, which is an attribute of agency, can solve this problem by lopping off huge sections of the search space via active imagination.)

    It’s all inter-dependant. Even more so if we consider that when we observe the processes in the cell, we observe that the DNA codes for proteins, and some of those proteins actually process the DNA in order to produce other proteins. There’s a paradox (readily acounted for by design); and since the necessary proteins can’t sequence and fold themselves, the only place they can come from, to our knowlege, is inside the cell, via the observed processes which produce them.

    continued…

  80. 80
    Mission.Impossible

    …continued…

    The question that needs to be answered is, where does the information encoded into the DNA come from? Where does the specification come from, the sequence which is read by enzymes and translated into an amino acid chain, or copied into an identical sequence (for replication)? It can’t merely be the result of a self-replicating molecule, unless it could be shown that the molecule could account for the specification and the concrete product simultaneously– that is, the DNA sequences and the protein-based hardware that performs the tasks of translation and transcription, sequencing and folding.

    We need to not only ask how the specification in the DNA came about, but how the concrete product, symbolically embedded into the DNA, came about at the same time, in order to form the functionally integrated whole.

    It’s not just the complexity of what we observe, but the inter-dependent sophistication: that the hardware is dependent on the DNA, and that the DNA is dependant on the hardware (for replication) and that the DNA codes for the harware which operates upon it, along with coding for disparate other functional systems that are required for the cell to function properly.

    So not only do we need to know where the coding information in DNA comes from, but we have a set of necessary conditions for it to be useful in any way, and those include the presence of a set of enzymes which can perform the necessary tasks of translating and transcribing the DNA, and then sequencing and folding the protein. We must also account for how that specification became embedded in the DNA, specifying that which would also need to be present in concrete form at the genesis of this first self-replicating cellular organism. All of it needs to be present at one time, and any proposed OOL theory or CSI simulation will need to account for each together.

    Of note, the specification for any enzyme involved directly in the translation/sequencing/folding process could be considered a sort of meta-data, construing that which is required to use the rest of the data in the strand. The DNA codes for the proteins which comprise the special set of enzymes that are responsible for producing the other proteins in the cell. Even this description of intracellular operations pales in comparison to the integrated functional complexity that is present in even the simplest extant single-celled organism.

    Why is it again that molecular self-replication doesn’t qualify as specified complexity? This is twofold: because a molecular self-replicator can be accounted for via chance and necessity — a sufficient cause, and because specification needs to conform to an independently given pattern. There needs to be a communication of information via a protocol; and the DNA and the harware which processes it, represent the communication from one to the otheer. They are independent of one another, except via a necessary third party, the protocol, which decipheres one and instantiates the other.

    Also, the function of molecular self-replication, even on a 500 or 1000 bit molecule, would likely be readily expressed in a much shorter chain (at a much lower bit depth or sequence length) that would likely fall below the threshhold for determining the presence of CSI; so you would need to judge the complexity of the function with regard to the lowest complexity at which it would operate.

    What it basically comes down to is that any proposed primordial system, the first self-contained self-replicator that would be a candidate for CSI, would need have present the following elements: it would need a storage medium, representative of DNA; it would need the sequence lexicon, which would be the specificaiton for the sequences of proteins which are produced as a result of processing the coded regions of DNA, and it would need hardware which operated on the DNA and translated the DNA codons into the amino acid sequences which would later be folded into proteins. You need all of these things to satisty the requrement for specified complexity and hence for the presence of CSI.

    m.i.

  81. 81
    Mission.Impossible

    You’ll need to forgive the numerous spelling errors, I neglected to spell check.

  82. We’ve got to work on that reading comprehension.

    As someone said recently, “you people are amazing, really!”

  83. dmullenix @75:

    “But you’re right, ID could be investigated scientifically, just as the existence of God can be. You have to stick with observable evidence and the evidence would have to support ID but if you do that and you actually found evidence, you could scientifically support ID to the same degree of confidence that science supports evolution. But nobody’s looking that I know of. So far as I know, nobody even has an idea of where to look.”

    What are you talking about? ID is a very limited concept, namely that intelligent activity sometimes leaves artifacts that can be identified after the fact and that when we see such artifacts in life the inference to the best explanation is that it was designed. It is totally based on observable evidence. People are looking — almost everywhere we look in life we see the kinds of systems/CSI that ID argues is a reliable indicator of intelligent activity.

    Perhaps you are confusing ID with a search for the identiy of the designer?

  84. Mung at 76: Life is surprisingly hard to define. http://en.wikipedia.org/wiki/Life

    “It is still a challenge for scientists and philosophers to define life in unequivocal terms. Defining life is difficult—in part—because life is a process, not a pure substance. Any definition must be sufficiently broad to encompass all life with which we are familiar, and it should be sufficiently general that, with it, scientists would not miss life that may be fundamentally different from life on Earth.”

    The article then lists some of the descriptions of life’s properties:
    Homeostasis, organization, metabolism, growth, adaptation, response to stimuli and reproduction.

    After that, they give some proposed definitions and I like this one: “Life is a self-sustained chemical system capable of undergoing Darwinian evolution.”

    For first life, self reproduction is generally used, but if that definition is applied to all organisms then mules are dead.

    “Then what is your “life” the first of?”

    Life. I’m still wondering if you are a lawyer.

    Eric Anderson at 78: ID is the idea that life was designed. That can be investigated scientifically, but so far as I know the field restricts itself to trying to falsify evolution.

  85. dmullenix @79:

    “ID is the idea that life was designed. That can be investigated scientifically, but so far as I know the field restricts itself to trying to falsify evolution.”

    Not quite. I know this is a nuance, but I think we need to be clear on this. ID is the idea that certain things exhibit the artifacts of intelligent activity. The concept can, and is, applied across a wide spectrum of events, including forensics, archaeology, origin of life, and, yes, the complexity and diversity of life, which is an area where evolution also tries to provide an explanation. To the extent that the two ideas are mutually exclusive (in many senses of the word “evolution” they are not; but to the extent evolution claims to explain all apparent design through unguided processes such as RM+NS, for example, they are) ID does compete with evolution in a negative sense. As does evolution with ID. It is no more valid to say that ID is simply a negative case against evolution than it is to say that evolution is just a negative case against ID. Indeed, given Dawkins’ and others’ comments about the apparent design of life being obvious, evolution really functions as an attempt to challenge the concept of design.

  86. dmullenix and Mung:

    I agree that defining life unequivocally is difficult, and a very interesting question. However, lest we are ever tempted to think that there is some kind of smooth continuium from non-life to life, it is worth keeping in mind that, with only a small number of corner cases, it is typically very easy to distinguish between the two.

    Imagine a Venn diagram with two circles: living things and non-living things. The two circles would be massive, with literally millions of members in each circle. The two circles would also be essentially separate, but if we homed in with a magnifying class on the edges where the circles are closest together we would see that there is a tiny region where the two circles touch, or almost touch, or perhaps overlap, we can’t quite magnify it enough to be sure. At that specific point it is unclear, and teasing out whether there is an overlap, a touch, or a small separation is a very interesting ongoing issue.

    But step back a moment to look at the big picture, and it is very easy to identify 99.99% of the members of each class — so easy that a small child can do it. In fact when my kids were tiny toddlers I used to point to certain objects and ask them: “live or not alive?” For almost all the objects around us in the world, the answer is very obvious, even to a small child.

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