Intelligent Design

RNA, the origin of life and the gullibility of the science media

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Yesterday, “News” brought readers a fascinating story about a report from Science Daily, titled, Reconstructed ancient ocean reveals secrets about the origin of life (25 April 2014), which was also picked up by Linda Geddes, writing for New Scientist. Reading the Science Daily article, I was struck by the extraordinary naivete of mainstream science reporters covering the origin-of-life issue. Consider the following excerpt, taken from the final two paragraphs:

“In the presence of iron and other compounds found in the oceanic sediments, 29 metabolic-like chemical reactions were observed, including those that produce some of the essential chemicals of metabolism, for example precursors of the building blocks of proteins or RNA,” says [Dr. Markus] Ralser, [Group Leader at the Department of Biochemistry at the University of Cambridge and the National Institute for Medical Research]. “These results indicate that the basic architecture of the modern metabolic network could have originated from the chemical and physical constraints that existed on the prebiotic Earth.”

The detection of one of the metabolites, ribose 5-phosphate, in the reaction mixtures is particularly noteworthy. Its availability means that RNA precursors could in theory give rise to RNA molecules that encode information, catalyze chemical reactions and replicate. Whether and how the first enzymes adopted the metal-catalyzed reactions described by the scientists remain to be established.

I wonder how many readers of the article even noticed the two little qualifying words, “in theory.”

The New Scientist report by Linda Geddes also highlighted the detection of ribose 5-phosphate as a metabolic reaction product, suggesting that self-replicating RNA could have formed spontaneously on the primordial Earth:

Detecting the metabolite ribose 5-phosphate is particularly noteworthy, Ralser says. This is because it is a precursor to RNA, which encodes information, catalyses chemical reactions and most importantly of all, can replicate.

Ms. Geddes is to be commended for her balanced reporting: she took care to inform her readers that the experiments performed by Dr. Ralser began with “substances known to be starting points for modern metabolic pathways,” adding that no-one had yet demonstrated that these substances could have formed in the Earth’s oceans, four billion years ago. And as “News” mentioned in her post, Ms. Geddes also pointed out that the reactions observed so far were all degenerative, instead of going from simple molecules to complex ones, they went from complex molecules to simpler ones (e.g. from sugar to pyruvate), prompting origin-of-life scientist Dr. Jack Szostak of Harvard University to remark that on a pessimistic reading of the evidence, “any organics in the ocean would have been totally degraded, rather than forming the basis of modern metabolism.”

While these qualifying remarks are commendable, they hardly even begin to scratch the surface. To see, why, let’s have a look at the chemical structure of ribose 5-phosphate (image courtesy of Wikipedia and Edgar181):

The chemical formula for this compound is C5H11O8P. In other words, one molecule of ribose 5-phosphate contains just 25 atoms. Its molar mass is 230.110 g/mol (or about 230 times that of a hydrogen atom).

Dr. Eugene Koonin: the real problems involved in explaining the origin of life

I’d now like to direct readers’ attention to a review by retired Dutch biologist (and Intelligent Design critic) Dr. Gert Korthof of renowned evolutionary biologist Dr. Eugene Koonin‘s recent book, The Logic of Chance: The Nature and Origin of Biological Evolution, Pearson, FT Press). Actually, Korthof’s review is not a review of Koonin’s entire book, but only of Chapter 12 and Appendix B of the book, which deal with the formidable problems facing any naturalistic origin-of-life scenario (emphases are mine – VJT):

RNA can function both as protein (enzyme) and replicator. However, even under the best-case scenario, the RNA-World hardly has the potential to evolve beyond very simple “organisms” (p. 366). The path from a putative RNA World to a translation system (DNA-protein world) is incredibly steep (p. 376). The hardest problem is that evolution by natural selection can only start after replication with sufficient fidelity is established [2]. Not withstanding all scientific progress, we currently do not have a credible solution to these problems [4].

Why is it so difficult to evolve a DNA-protein world from a RNA-world? Here is Koonin’s specification of the requirements of a coupled replication-translation system (p. 435) (these calculations are the same as in: [3] ):

2 rRNAs with a total of at least: 1,000 nucleotides
10 primitive adaptors of about 30 nucleotides each: 300 nucleotides
at least 1 RNA encoding a replicase: 500 nucleotides

Total (at least 13 RNA molecules): 1,800 nucleotides

The probability of the spontaneous origin of this is: P < 10-1018. The spontaneous origin of 1,800 nucleotides is the Koonin-threshold for the origin of life and evolution. No Origin of Life (OOL) researcher put it more clearly and dramatically than Koonin. Please note 1,800 nucleotides is a minimum. Every OOL researcher that skips over the Koonin threshold makes a serious scientific oversight.

Readers should take note of what Dr. Koonin is saying here. First, the term “RNA” refers to a family of large biological molecules of varying shapes and sizes. When we read scientific articles about an “RNA world,” we need to ask ourselves: what kind of RNA are we speaking of here? How many nucleotides are we talking about? How many science journalists even mention this question, when discussing the plausibility of the RNA world?

Second, let’s consider the 10 primitive adaptors of about 30 nucleotides each, mentioned by Dr. Koonin in the passage quoted above. That’s actually pretty short for an RNA molecule: RNA strands can vary from 20 to 3,354 base pairs in length. Even 20 nucleotides of single-stranded RNA has a molecular weight of 6,569 g/mol, so the molecular weight of a 30-nucleotide primitive adaptor would be 9,853.5 g/mol. That’s nearly 43 times heavier than a molecule of ribose 5-phosphate (pictured above). And if that’s not bad enough, what about the two ribosomal RNAs, with 500 nucleotides each, making them about 700 times heavier than a molecule of ribose 5-phosphate?

Animation of the large subunit of the archaebacterium, Haloarcula marismortui. Proteins are shown in blue and the two RNA strands in orange and yellow. The small patch of green in the center of the subunit is the active site. Image courtesy of Tim Vickers, David Goodsell and Wikipedia.

Third, I’d like to return to Korthof’s remark:

The spontaneous origin of 1,800 nucleotides is the Koonin-threshold for the origin of life and evolution. No Origin of Life (OOL) researcher put it more clearly and dramatically than Koonin. Please note 1,800 nucleotides is a minimum. Every OOL researcher that skips over the Koonin threshold makes a serious scientific oversight.

Let me ask my readers: how many science journalists have you come across who even knew about the Koonin threshold? Be honest, now! None? I thought so.

The probability of the spontaneous origin of these 1,800 nucleotides is less than 10-1018, according to Koonin, whose 2007 article, The cosmological model of eternal inflation and the transition from chance to biological evolution in the history of life (Biology Direct 2007; 2: 15), from which the above calculations were derived, was peer-reviewed by no less than four researchers, including Itai Yanai of Harvard University.

Enter the multiverse

10-1018 is a staggeringly low figure. Dr. Koonin himself concedes that an event of such astronomically low probability would not be expected to happen in the history of the observable universe. So how does he solve the problem? While he acknowledges that someone might (theoretically) come up with an alternative pathway to explain the origins of replication and translation, he prefers to bet on the vast and infinite resources of the multiverse, where anything can happen, given enough time:

All this is not to suggest that OORT [origins of replication and translation] is a problem of “irreducible complexity” and that the systems of replication and translation could not emerge by means of biological evolution. It remains possible that a compelling evolutionary scenario is eventually developed and, perhaps, validated experimentally. However, it is clear that OORT is not just the hardest problem in all of evolutionary biology but one that is qualitatively distinct from the rest. For all other problems, the basis of biological evolution, genome replication, is in place but, in the case of OORT, the emergence of this mechanism itself is the explanandum. Thus, it is of interest to consider radically different scenarios for OORT…

The MWO [“many worlds in one” – VJT] version of the cosmological model of eternal inflation could suggest a way out of this conundrum because, in an infinite multiverse with a finite number of distinct macroscopic histories (each repeated an infinite number of times), emergence of even highly complex systems by chance is not just possible but inevitable.

Why a multiverse doesn’t obviate the need for a Designer

But as I’ve argued in a previous post, the multiverse hypothesis is plagued by two problems: first, as Dr. Robin Collins, an acknowledged authority on fine-tuning, has argued (see section 6 of the linked essay), it merely shifts the fine-tuning problem up one level, as a multiverse capable of generating any life-supporting universes at all would still need to be fine-tuned; and second, as physicist Paul Davies has pointed out, even the multiverse hypothesis implies that a sizable proportion of universes (including perhaps our own) were intelligently designed.

By default, then, Intelligent Design remains the best viable explanation for the origin of replication and translation, and hence of life on Earth. Why? Because it’s the only explanation that posits something already known to be capable of generating life, in order to account for the emergence of life on Earth. That “something” is intelligence.

How many science journalists do you know who realize that in the light of what scientists currently know, the odds of life emerging anywhere in our universe are vanishingly small? What does that tell you about the state of science reporting on the origin of life, at the present time?

Dr. Korthof’s Footnotes

Finally, for the benefit of those readers who are interested, here are the footnotes to Dr. Korthof’s review:

  1. There is a pdf of the book available on the internet with full color illustrations!
  2. Yuri I Wolf and Eugene V Koonin (2007) On the origin of the translation system and the genetic code in the RNA world by means of natural selection, exaptation, and subfunctionalization, Biol Direct. 2007; 2: 14. Free access. Here the authors show that what I call ‘the Koonin threshold’ is based on the Eigen threshold. There is no mentioning of the 1,800 threshold, but there is a qualitative statement: “Indeed, we are unaware of translation being possible without the involvement of ribosomes, the complete sets of tRNA and aminoacyl-tRNA synthetases (aaRS), and (at least, for translation to occur at a reasonable rate and accuracy) several translation factors”. They also discuss ID, irreducible complexity.
  3. Eugene V Koonin (2007) The cosmological model of eternal inflation and the transition from chance to biological evolution in the history of life, Biol Direct. 2007; 2: 15. (This is essentially Appendix B of the book.)
  4. “The origin of life is one of the hardest problems in all of science, but it is also one of the most important. Origin-of-life research has evolved into a lively, interdisciplinary field, but other scientists often view it with skepticism and even derision. This attitude is understandable and, in a sense, perhaps justified, given the “dirty,” rarely mentioned secret: Despite many interesting results to its credit, when judged by the straightforward criterion of reaching (or even approaching) the ultimate goal, the origin of life field is a failure – we still do not have even a plausible coherent model, let alone a validated scenario, for the emergence of life on Earth.” (Koonin, p. 391).
    This text has been quoted by the uncommon descent intelligent design blog (Nov 13, 2011). The fact that the ID community is happy quoting Koonin without specifying a detailed ID alternative, demonstrates they are not interested in science, but only in attacking and ridiculing science. Why don’t IDists want to know how the designer did it?

In answer to Dr. Korthof’s last question, I would personally be delighted to know how the Designer “did it.” However, before we can even address that question, the first thing we need to establish, to the satisfaction of the scientific community, is that an Intelligent Designer is required to account for the origin of life on Earth. Additionally, before we can identify how the Designer acted, we need to be clear about “where” and “when.”

48 Replies to “RNA, the origin of life and the gullibility of the science media

  1. 1
    Dionisio says:

    …the multiverse hypothesis is plagued by two problems: first, as Dr. Robin Collins, an acknowledged authority on fine-tuning, has argued (see section 6 of the linked essay), it merely shifts the fine-tuning problem up one level, as a multiverse capable of generating any life-supporting universes at all would still need to be fine-tuned; and second, as physicist Paul Davies has pointed out, even the multiverse hypothesis implies that a sizable proportion of universes (including perhaps our own) were intelligently designed.

    What about third, even with the multiverse hypothesis, wouldn’t the time from the beginning of this planet to the appearance of the first cell on it, still remain the same? How different would that initial abiogenesis process be for the multiverse case?

    Also, how would the multiverse hypothesis affect the appearance of the complex mechanisms behind the cell fate determination, differentiation and migration, that are observed during the human embryonic development?

    Also, how would the multiverse hypothesis affect the appearance of the elaborate mechanisms behind the genotype-phenotype association?

    Thanks.

    Don’t know if my questions make any sense, though.

  2. 2
    vjtorley says:

    Hi Dionisio,

    Thank you for your post. I suppose Dr. Koonin would reply that from the perspective of the multiverse as a whole, infinite probabilistic resources are available, as there could be an infinite number of universes. In some of these, life would appear quickly, in others slowly, and in others, not at all. Ditto for the mechanisms of the cell.

  3. 3
    Eric Anderson says:

    vjtorley:

    You mentioned two problems with explaining the origin of life by recurring to the multiverse idea.

    There is another, arguably more significant, problem. Namely:

    It doesn’t make any difference whether there are a gazillion other universes out there. We are trying to explain the origin of life in this universe, given this set of physical laws in our universe.

    It makes not one whit of difference whether there are a bunch of other universes out there. Given the existence of our universe, the odds of life originating are 10^-1018 (per Koonin’s number).

    Yes, the multiverse idea pushes the fine-tuning up a level. Yes, it would require a near-infinite number of other universes. Yes, there is precious little evidence for any other universe, and no rational materialistic explanation for what could be producing such universes.

    But more importantly, the existence of other universes is simply irrelevant for explaining how life came about in our universe.

  4. 4
    Eric Anderson says:

    Consider:

    (i) getting a universe with a particular set of physical laws,

    is a separate, independent event from

    (ii) what happens within the parameters of those laws after the universe arises.

    So, we have two factors, independent of each other. Therefore, we in fact have to multiply the factors in order to assess the actual odds.

    In other words, if there are actually multiple universes with different sets of physical laws, then we have to multiply (i) the odds of getting a universe with the right set of laws, times (ii) the odds of life arising within that set of laws.

    So, just to throw out a number, if the odds of getting a universe with the physical laws and constants of our universe is 10^-1018, then the odds of life arising in all of known reality is 10^-1018 (odds of getting the right kind of universe) * 10^-1018 (odds of life arising, given the right kinds of laws).

    So the multiverse argument doesn’t help the odds one bit. Potentially, it even makes things a lot worse.

    The rhetorical value of the multiverse idea to account for life is not so much to increase the mathematical odds, but to function as a perversion of the anthropic principle: “We’re here to observe it, so obviously life arose here.”

    The multiverse doesn’t improve the odds in a mathematical sense, it is just an attempt to argue, in a very vague and unspecified way, that — “Well, lots of things can happen, so we shouldn’t be surprised if something highly unusual happened somewhere sometime. And if it hadn’t happened, we wouldn’t be here talking about it. So, therefore, the unusual must have happened.”

    It is nothing more, not one whit more substantive, than another “just-so” story. It is in the long tradition of the materialist explanation for the universe, life, meaning, everything:

    Stuff Happens.

  5. 5
    Upright BiPed says:

    The appeal to a multi-verse is merely an extension of the materialist narrative; suggesting that some unknown feature of physical law can account for the rise of the translation apparatus. In truth, the organization of the translation apparatus specifically incorporates an independence from determinism because if it were fully dependent on physical determinism it simply could not function. If there was ever a concept were the materialist ideology completely subverts and blinds its adherents, it is most certainly the concept of information.

  6. 6
    Eric Anderson says:

    UB @5:

    In truth, the organization of the translation apparatus specifically incorporates an independence from determinism because if it were fully dependent on physical determinism it simply could not function.

    Exactly.

    Indeed, it isn’t just the case that determinism cannot result in such a system. It is anathema to such a system.

  7. 7
    Dionisio says:

    vjtorley @ 2

    I suppose Dr. Koonin would reply that from the perspective of the multiverse as a whole, infinite probabilistic resources are available, as there could be an infinite number of universes. In some of these, life would appear quickly, in others slowly, and in others, not at all. Ditto for the mechanisms of the cell.

    Dear Dr. Torley,

    Thank you for your comments. I still don’t understand the implications of Dr. Koonin’s ideas for this current universe.

    What Dr. Koonin would reply might sound ok for other hypothetical universes, which we don’t observe yet, but my questions are related to this one we are in now, which hosts abundant and rich life, and science seems to claim (so far) how long ago this life-hosting planet came to be, how long ago it must have been suitable for the kind of life forms it hosts, and how long ago biological life allegedly appeared. Would any of those current scientific claims change as a result of the multiverse hypothesis?

  8. 8
    Charles says:

    fyi link #2 above should be:
    “On the origin of the translation system and the genetic code in the RNA world by means of natural selection, exaptation, and subfunctionalization”
    http://www.ncbi.nlm.nih.gov/pm.....MC1894784/

  9. 9
    Charles says:

    Dionisio @ 7

    For this universe, Koonin put the odds at &lt 10^-1018

    For the next universe, Koonin put the odds at &lt 10^-1018

    For every universe, Koonin put the odds at &lt 10^-1018

    But Koonin put the odds for the *combination* of all 10^1018 universes and more (i.e. an infinite number of parallel “worlds”), that at least one of them will beat those odds, as 10^-1018 x 10^1018 = 1 (i.e. inevitable).

    Some (e.g. Koonin) would argue that our very existance is proof that *if* the “Many Worlds in One” (i.e. Multiverse) theory is true, then our universe is “the one” out of 10^1018 other universes in which those odds were beaten by chance. This works mathematically because it is assumed that “chance” takes a different path in each of the many worlds, and that in one of them “chance” will take a successful shortcut to an RNA world much quicker (the serendipitous accident happens sooner) than the full amount of time required to sequentially, by trial and error, attempt each of the 10^1018 “in vivo” experiments to arrive at a successful reproducing RNA world.

    It’s a tautology, but tautologies can be true, they’re just useless to prove anything, and an untestable tautology that can’t even be tested, scientifically, emprically with observable evidence is even more useless.

    But Koonin’s point is, given the insurmountable low probability for abiogenesis by chance in our universe (because the time required for chance to overcome the low odds &lt 10^-1018) didn’t exist in our universe, then the only alternative to an Intelligent Design solution to the OOL problems is the tautological grasp at straws of the “Many Worlds in One”.

    Koonin’s analysis is essentially a ‘wakeup call’ for evolutionists who reject ID, that the only other game in this world is try to prove that there were/are an infinite number of other worlds such that our world stood a mathematical chance of accidentally producing an RNA world.

  10. 10
    bornagain77 says:

    Dr. Torley, as to the last portion:

    This text has been quoted by the uncommon descent intelligent design blog (Nov 13, 2011). The fact that the ID community is happy quoting Koonin without specifying a detailed ID alternative, demonstrates they are not interested in science, but only in attacking and ridiculing science. Why don’t IDists want to know how the designer did it?

    Actually I am very interested in ‘science’, and I’m very offended that atheistic materialists keep trying to highjack the definition of ‘science’, trying to make science a purely materialistic endeavor, and trying to strip ‘science’ of its necessary Theistic premises. Necessary premises which gave birth to modern science and which continue to be necessary for its continued success:

    Science and Theism: Concord, not Conflict* – Robert C. Koons
    IV. The Dependency of Science Upon Theism (Page 21)
    Excerpt: Far from undermining the credibility of theism, the remarkable success of science in modern times is a remarkable confirmation of the truth of theism. It was from the perspective of Judeo-Christian theism—and from the perspective alone—that it was predictable that science would have succeeded as it has. Without the faith in the rational intelligibility of the world and the divine vocation of human beings to master it, modern science would never have been possible, and, even today, the continued rationality of the enterprise of science depends on convictions that can be reasonably grounded only in theistic metaphysics.
    http://www.robkoons.net/media/.....ffd524.pdf

    “Modern science was conceived, and born, and flourished in the matrix of Christian theism. Only liberal doses of self-deception and double-think, I believe, will permit it to flourish in the context of Darwinian naturalism.”
    ~ Alvin Plantinga

    “Nothing in evolution can account for the soul of man. The difference between man and the other animals is unbridgeable. Mathematics is alone sufficient to prove in man the possession of a faculty unexistent in other creatures. Then you have music and the artistic faculty. No, the soul was a separate creation.”
    Alfred Russell Wallace, New Thoughts on Evolution, 1910

    “Geometry is unique and eternal, a reflection from the mind of God. That mankind shares in it is because man is an image of God.”
    – Johannes Kepler

    Mathematics and Physics – A Happy Coincidence? – William Lane Craig – video
    http://www.metacafe.com/w/9826382

    It is of little wonder to learn that Darwinian evolution, much less the origin of life itself, has no mathematical basis so as to demarcate it from pseudoscience:

    “On the other hand, I disagree that Darwin’s theory is as `solid as any explanation in science.; Disagree? I regard the claim as preposterous. Quantum electrodynamics is accurate to thirteen or so decimal places; so, too, general relativity. A leaf trembling in the wrong way would suffice to shatter either theory. What can Darwinian theory offer in comparison?”
    (Berlinski, D., “A Scientific Scandal?: David Berlinski & Critics,” Commentary, July 8, 2003)

    Oxford University Seeks Mathemagician — May 5th, 2011 by Douglas Axe
    Excerpt: “Grand theories in physics are usually expressed in mathematics. Newton’s mechanics and Einstein’s theory of special relativity are essentially equations. Words are needed only to interpret the terms. Darwin’s theory of evolution by natural selection has obstinately remained in words since 1859.”…
    http://biologicinstitute.org/2.....emagician/

    Active Information in Metabiology – Winston Ewert, William A. Dembski, Robert J. Marks II – 2013
    Except page 9: Chaitin states [3], “For many years I have thought that it is a mathematical scandal that we do not have proof that Darwinian evolution works.” In fact, mathematics has consistently demonstrated that undirected Darwinian evolution does not work.
    http://bio-complexity.org/ojs/.....O-C.2013.4

    “In discussions with biologists I met large difficulties when they apply the concept of ‘natural selection’ in a rather wide field, without being able to estimate the probability of the occurrence in a empirically given time of just those events, which have been important for the biological evolution. Treating the empirical time scale of the evolution theoretically as infinity they have then an easy game, apparently to avoid the concept of purposesiveness. While they pretend to stay in this way completely ‘scientific’ and ‘rational,’ they become actually very irrational, particularly because they use the word ‘chance’, not any longer combined with estimations of a mathematically defined probability, in its application to very rare single events more or less synonymous with the old word ‘miracle.’”
    Wolfgang Pauli –

    “It is our contention that if ‘random’ is given a serious and crucial interpretation from a probabilistic point of view, the randomness postulate is highly implausible and that an adequate scientific theory of evolution must await the discovery and elucidation of new natural laws—physical, physico-chemical, and biological.”
    Murray Eden, “Inadequacies of Neo-Darwinian Evolution as a Scientific Theory,” Mathematical Challenges to the Neo-Darwinian Interpretation of Evolution, editors Paul S. Moorhead and Martin M. Kaplan, June 1967, p. 109.

  11. 11
    Barb says:

    The major problem with the RNA-world theory is its lack of experimental evidence. “Some writers,” says Robert Shapiro, professor emeritus of chemistry at New York University, “have presumed that all life’s building blocks could be formed with ease in Miller-type experiments and were present in meteorites. This is not the case.” Consider the RNA molecule. It is constructed of smaller molecules called nucleotides. A nucleotide is a different molecule from an amino acid and is only slightly more complex. Shapiro says that “no nucleotides of any kind have been reported as products of spark-discharge experiments or in studies of meteorites.” He further states that the probability of a self-replicating RNA molecule randomly assembling from a pool of chemical building blocks “is so vanishingly small that its happening even once anywhere in the visible universe would count as a piece of exceptional good luck.” [Scientific American, “A Simpler Origin for Life,” by Robert Shapiro, June 2007, p. 48.]

    It should be noted that Professor Shapiro does not believe that life was created. He believes that life arose by chance in some fashion not yet fully understood. In 2009, scientists at the University of Manchester, England, reported making some nucleotides in their lab. However, Shapiro states that their recipe “definitely does not meet my criteria for a plausible pathway to the RNA world.”

    The “which came first” problem rears its head when one considers that RNA is required to make proteins, but proteins are involved in the production of RNA. But what if somehow both proteins and RNA molecules did appear by chance in the same place at the same time? Would they then cooperate and form a self-replicating type of life? Hubert Yockey (not a creationist) writes: “It is impossible that the origin of life was ‘proteins first.’” [Information Theory, Evolution, and the Origin of Life, by Hubert P. Yockey, 2005, p. 182.]

    “The probability of this happening by chance (given a random mixture of proteins and RNA) seems astronomically low,” says Dr. Carol Cleland (also not a creationist), a member of the National Aeronautics and Space Administration’s Astrobiology Institute. “Yet,” she continues, “most researchers seem to assume that if they can make sense of the independent production of proteins and RNA under natural primordial conditions, the coordination will somehow take care of itself.” Regarding the current theories of how these building blocks of life could have arisen by chance, she says: “None of them have provided us with a very satisfying story about how this happened.” [NASA’s Astrobiology Magazine, “Life’s Working Definition—Does It Work?” (http://www.nasa.gov/ vision/universe/starsgalaxies/ life’s_working_definition.html)]

  12. 12
    Evolve says:

    This doesn’t sound very convincing. A DNA-Translation system may not have been essential for the first life. Life is just a continuation of non-life; there’s no clear-cut boundary between the two (Viruses are a case in point). As such, the first protocells may have thrived using ribozymes which can function both as a genetic material as well as a catalyst to promote rudimentary metabolism.

    RNA has been shown to be capable of copying itself in the absence of protein enzymes:

    http://www.nature.com/nchem/jo......1086.html
    http://www.sciencemag.org/cont...../1098.full

    RNA can also synthesize ribozymes capable of cleaving and joining other RNA molecules:

    http://www.sciencemag.org/content/332/6026/209

    These processes can generate multiple RNA molecules of varying lengths & sequences which can then serve many functions. So the various RNA species Koonin mentions don’t have to polymerize spontaneously.

  13. 13
    Evolve says:

    Here’s a new study on how protocells could have formed:

    http://www.bristol.ac.uk/news/.....ation.html

  14. 14
    Eric Anderson says:

    Evolve @12:

    Life is just a continuation of non-life;

    No it isn’t. Or at least it has not been shown to be, and there is good reason to think it may not be.

    Why do we not see a gradual continuation from non-life to life all around us? There is a very clear cut boundary, in all but a small handful of corner cases. The fact that we can find a couple of unclear corner cases — among the literally millions of clear-cut cases — does not prove the assertion in question. In fact, the objective conclusion is that it is really the exception that proves the rule.

    Furthermore, I presume you are not asserting that viruses replicate on their own — without the machinery of living cells? Even for your alleged “continuation of non-life” in viruses, they still require a complete, functioning, living cell to replicate.

    Also, the papers you linked to do not show that RNA is capable of self-replication, which is the required step. The researcher-driven, template-guided production of polymers has been discussed several times on this site. None of them have demonstrated self-replication, much less anything that has a chance of working in the real world outside the lab.

  15. 15
    Upright BiPed says:

    (Viruses are a case in point).

    A virus has a translation apparatus and a script of recorded information. A puddle of mud doesn’t.

  16. 16
    chris haynes says:

    Thanks for the fine article.

    Dr Koonin claim about about probabilites in the infinite mutiverse comes from Theoretetical Physicists.

    Dr Alan Guth, an MIT Cosmology Guru, writes: “(In the infinite multiverese), anything that can happen will happen; in fact, it will happen an infinite number of times. Thus, the question of what is possible becomes trivial — anything is possible, unless it violates some absolute conservation law.”

    Koonin’s point about naturalistic abiogenesis going from hopelssly improbable to being certain is exactly what Dr Guth says.
    That is, assuming that the assembly of the required chemistry is sufficient to start life. Whether unknown pheonomona, natural or supernatural, are also needed is unknown.

    Two other things we get from what Dr Guth wrote:
    1) Somewhere in the infinite universe, President Obama and Sarah Palin had a love child. In fact an infinte number of them. That wouldnt violate a conservation law, would it?
    2) Somehwere in the infinite universe, a majority of people think Congress is doing a good job.
    Sorry Dr. Guth, No 2 is ridiculous.

  17. 17
    Mung says:

    Upright BiPed:

    A virus has a translation apparatus and a script of recorded information. A puddle of mud doesn’t.

    You’ve not heard of the mud virus?

  18. 18
    Mung says:

    Evolve:

    Here’s a new study on how protocells could have formed

    From the provided link:

    The most fundamental requirement for the emergence of cells on the early Earth is the existence of a closed compartment, but how this came about remains a mystery.

  19. 19
    Mung says:

    Let’s make a protocell from stuff that cells make!

    The team first prepared membrane-free droplets containing high concentrations of biomolecules such as adenosine triphosphate (ATP), ribonucleic acid (RNA) and a short or long polymer of the natural amino acid lysine, and then added low amounts of a fatty acid.

  20. 20
    Evolve says:

    ///Why do we not see a gradual continuation from non-life to life all around us?///

    Because such precursors will be consumed by existing life forms. The virgin earth, when it formed, had no life forms, which means organic precursors could accumulate and evolve into the first protocells.

    ///Even for your alleged “continuation of non-life” in viruses, they still require a complete, functioning, living cell to replicate.///

    ..which is why I said viruses lie on the borderline

    ///Also, the papers you linked to do not show that RNA is capable of self-replication///

    Oh yes, they do! Read them again. RNA can copy itself without any protein enzymes.

    ///The researcher-driven, template-guided production of polymers has been discussed several times on this site.///

    Template-free synthesis of RNA oligomers have also been reported:

    http://pubs.acs.org/doi/full/10.1021/ja061782k

    http://onlinelibrary.wiley.com.....d7fd978f83

    What do you mean by researcher-driven? Somebody has to test the various hypotheses to find out which model works and which doesn’t. You cannot expect every scenario to exist naturally, especially when you’re dealing with an event (origin of life) that happened 4 billion years ago! The vagaries of nature have long since erased the chemistry of the nascent earth. Those conditions have to be recreated in the laboratory.
    The fact is that under given conditions, RNA has been shown to be capable of copying itself. Now, of course, we don’t understand everything. There’s still a lot of work to be done. But there is progress as one can make out from the papers I quoted.

  21. 21
    Evolve says:

    ///Let’s make a protocell from stuff that cells make!///

    Genius!
    The idea here is to show that biomolecules can self-organize into protocells under certain conditions. In other words, your designer is not required to pack molecules into cells. One job less for the designer!

    By the way you’re saying that nucelotides and amino acids are stuff that cells make? Do you know that adenine, which makes ATP, and other nucleobases have been discovered even in meteorites?! What’s more, they can also be synthesized in non-biological chemical reactions:

    http://www.nasa.gov/topics/sol.....rites.html

    Amino acids have also been detected in space:

    http://www.reuters.com/article.....2I20090818

    http://www.kurzweilai.net/dna-.....llar-space

    Simulated space environments can synthesize dipeptides:

    http://iopscience.iop.org/0004-637X/765/2/111/

  22. 22
    Upright BiPed says:

    Materialists seem pathologically incapable of properly conceptualizing the issues at hand. They are, as a group, completely unable to understand what information is, what it does, and how it does it. Empirical observation simply doesn’t register.

  23. 23
    Evolve says:

    ///A virus has a translation apparatus and a script of recorded information. A puddle of mud doesn’t.///

    No, viruses don’t have any translation apparatus, they rely on the host cell’s apparatus to produce their coat proteins. That’s why viruses have to infect living cells to propagate.

    Your mud is nothing but a collection of molecules. So is life. Your mud has chemistry, so does life. How did inanimate chemistry (found in mud) transform into biochemistry (found in life) is all that needs to be figured out.

    By the way, there are infectious particles called viroids which are just a piece of RNA without any protein coat, but can still infect cells. We also have mobile genetic elements that hop between genes – transposons. Viruses may have originated from such hopping genes.
    In short, nature has a repertoire of molecules somewhere between life and non-life.

  24. 24
    Evolve says:

    ///Materialists seem pathologically incapable of properly conceptualizing the issues at hand. They are, as a group, completely unable to understand what information is, what it does, and how it does it. Empirical observation simply doesn’t register.///

    Creationists are likening biochemistry (which is perceived as information in life) to man-made codes like computer software and language. They, as a group, seem incapable of realizing that computer software and human language lack any chemistry whatsoever!

  25. 25
    Upright BiPed says:

    Hello Evolve. I certainly admit that I misspoke on the virus translation apparatus, but unfortunately at UD there is no edit mechanism after you push play – if you speak too fast, you live with it. The point I was making is that the composition of a virus is constrained by the translation of recorded information. Inanimate matter is not. That point remains entirely valid.

    In any case, my blunder doesn’t alter the complete misconception that materialist such as yourself carry regarding information. It is the most amazing thing.

    The problem I face around here is that materialists generally aren’t even willing to address the issue. No matter what universal observations are brought to bear, the willingness to engage the evidence in earnest is virtually zero.

    Actually I just tried to to have a conversation on this very topic with Gary Hurd following Karl Giberson’s article on The Daily Beast. Hurd seemed like a deer in headlights and literally had nothing of substance to say in return. Apparently he, or Giberson, or the science editors of the Daily Beast felt so strongly about how the whole exchange appeared to onlookers, that they simply removed my posts, leaving Hurd responding to comments that no longer appeared.

    …and so the beat goes on.

  26. 26
    Upright BiPed says:

    They, as a group, seem incapable of realizing that computer software and human language lack any chemistry whatsoever!

    All information is translated by material means (what else would it be?)

    To even suggest that human and machine translation (brains and semi-conductors) are somehow outside of chemistray is just silly.

  27. 27
    Upright BiPed says:

    Evolve,

    If you think that in the human case we have genuine symbollic representations of information and in genetic case we have objects that just act like representations, then by all means, describe your evidence at the material level and point out the distinction between the two.

  28. 28
    Evolve says:

    ///if you speak too fast, you live with it.///

    If you realized your mistake and wanted to correct it all you needed to do was put another post. But you didn’t…

  29. 29
    Evolve says:

    ///To even suggest that human and machine translation (brains and semi-conductors) are somehow outside of chemistray is just silly.///

    Oh my gosh! Semiconductor is a piece of hardware, it doesn’t constitute the computer software. The software is just a script, so is human language.

    In sharp contrast, DNA is a chemical molecule that reacts all the time with other molecules around it (DNA is made up of atoms readily found throughout the universe). It is this chemistry that you are perceiving as the “genetic code”.
    The similarity between DNA and man-made languages ends with the term “code” used to describe both. Otherwise they’re like chalk and cheese.

  30. 30
    Joe says:

    LoL @ Evolve-

    No one likens the translation of nucleotides to amino acids as a code. It is a code. Also no one perceives information in life. It is a fact that living organisms contain and use information.

  31. 31
    Joe says:

    BTW Evolve, the genetic code cannot be reduced to chemistry. The codons do not chemically change to become amino acids. The codons only represent the amino acids. And it is an arbitrary arrangement- no laws apply.

  32. 32
    Upright BiPed says:

    If you realized your mistake and wanted to correct it all you needed to do was put another post. But you didn’t…

    It’s not “if” Evolve … it’s “when”.

    And “when” was not a conducive time for me to do anything about it. As crazy as it sounds, there are occasionally other things more important than UD. Moreover, it doesn’t alter the point being made (and you know it).

  33. 33
    Upright BiPed says:

    Evolve,

    Oh my gosh! Semiconductor is a piece of hardware, it doesn’t constitute the computer software. The software is just a script, so is human language.

    I think you’ve lost your place. Your previous point was that your opponents don’t realize that computer software and human language lack any chemistry. In truth, computer software and human language consist of a set of context-specific relationships, operating in material systems. They quite obviously require the material systems (i.e. chemistry) in order to exist.

    This is certainly no different than the genetic code, which is also a set of context-specific relationships operating in a material system. Your attempt to drive a false distinction is therefore pointless. In each case, the relationships require the objects.

    The objects are chemistry. The relationships are not.

    In sharp contrast, DNA is a chemical molecule that reacts all the time with other molecules around it (DNA is made up of atoms readily found throughout the universe). It is this chemistry that you are perceiving as the “genetic code”.

    No, the opposite is true. The genetic code is a set of physicochemically-arbitrary relationships between the arrangement of nucleotides within codons, and the presentation of specific amino acids at the peptide biding site. And as it is in any other semiotic system, there is a (necessary) physical discontinuity between these, which must be (and is) preserved by the organization of the system.

    This is the whole point Evolve, you simply don’t know what you are talking about with regard to what information is, and what it does, and how it does it.

  34. 34
    Mung says:

    Evolve:

    Do you know that adenine, which makes ATP, and other nucleobases have been discovered even in meteorites?!

    Adenine does not make ATP.

    *sigh*

  35. 35
    Eric Anderson says:

    Evolve @23:

    Your mud is nothing but a collection of molecules. So is life.

    False. Blatantly, patently, utterly false.

    Life is most certainly not “nothing but a collection of molecules.”

    If this is the level of understanding you bring to the table about what constitutes life, then the entire discussion is probably a waste of time.

    Every biochemist and everyone working in origin of life research recognizes that there are special requirements in place, special arrangements needed, information required to get life. Life is most certainly not just another “collection of molecules.”

  36. 36
    Eric Anderson says:

    Wow, I thought the comment @23 was bad. Then as I was scrolling down the thread I ran into this comment:

    Creationists are likening biochemistry (which is perceived as information in life) to man-made codes like computer software and language. They, as a group, seem incapable of realizing that computer software and human language lack any chemistry whatsoever!

    No-one has to pretend that they perceive information in life. It is there. Objectively so. And things like the genetic code were not made up by creationists. It is called a code because it is one.

    As to your last sentence, you are demonstrating that you have virtually no grasp of the issues at hand. The question is not whether chemistry is involved. Everyone knows it is. Everyone (who has any understanding of what they are talking about) also knows that simple “chemistry” on its own explains neither the origin of life nor its ongoing existence. Surely you are not really taking the position that information and coding cannot be placed into biochemical strings because we are dealing with “chemistry”?

  37. 37
    Evolve says:

    ///Adenine does not make ATP.///

    Trying to find loopholes to cover your blunders? The Adenosine in ATP comes from Adenine. That’s what I meant and you know it.

  38. 38
    Evolve says:

    ///False. Blatantly, patently, utterly false.

    Life is most certainly not “nothing but a collection of molecules.///

    Then define life. There’s no precise definition of what a living thing is. All matter – living and non-living are just an arrangement of molecules that undergo physical and chemical transformations. The same atoms and molecules that constitute a living entity are found in inanimate matter throughout the universe. And there exists particles such as viruses which lie on the borderline.

    When it comes to you, all your feelings, sensations and perceptions starts and ends with your brain – with the chemistry that fires neurotransmitters in your brain. To the best of our knowledge, no person or animal has survived beyond his brain.

  39. 39
    Evolve says:

    ///No-one has to pretend that they perceive information in life. It is there. Objectively so. And things like the genetic code were not made up by creationists. It is called a code because it is one.///

    If there’s information in life, then there’s information in dissolving salt in a glass of water! It’s all chemistry, Eric. And chemical reactions happen spontaneously on their own as you witness every second.
    One molecule reacts with another molecule under certain conditions to make a product. Done. That’s it.

    AGCT – so-called DNA code naturally binds to UCGA through hydrogen bonding. And you get RNA. Other molecules (Transcription factors, RNA polymerase etc) speed up this reaction. There are bonds of various sorts that are formed and broken between the atoms of these interacting molecules, all of which are readily explained by chemistry.

    You take these molecules and change physical parameters such as pH or temperature and they will display altered chemical reactions. Their structure changes, their properties change.

    There’s nothing of this sort with computer code and human language. Does English language ever change with outside temperature?!
    By equating DNA with those, all you’re doing is ignoring the reality and doing a disservice to common sense. That’s why your position hasn’t gained a toehold in the scientific community.

    ///As to your last sentence, you are demonstrating that you have virtually no grasp of the issues at hand. The question is not whether chemistry is involved. Everyone knows it is.
    Everyone (who has any understanding of what they are talking about) also knows that simple “chemistry” on its own explains neither the origin of life nor its ongoing existence. Surely you are not really taking the position that information and coding cannot be placed into biochemical strings because we are dealing with “chemistry”?///

    Chemistry DOES explain life processes. Who said it doesn’t? We have this whole branch called Biochemistry that deals with it. Sure, we don’t understand every detail of every process. But that’s why we haven’t shut down our labs and gone home. We’re working on it, not sitting idly like creationists doing nothing other than attacking evolution.

  40. 40
    Evolve says:

    ///In truth, computer software and human language consist of a set of context-specific relationships, operating in material systems. They quite obviously require the material systems (i.e. chemistry) in order to exist.

    This is certainly no different than the genetic code, which is also a set of context-specific relationships operating in a material system. Your attempt to drive a false distinction is therefore pointless. In each case, the relationships require the objects.///

    You’ll go great lengths to fight a lost cause, right?
    Computer code and language may require chemistry to exist (since they are created by humans), but they’re not chemical molecules themselves. Whereas DNA is a chemical. That’s the whole point.

    You’ve got no hope if you can’t get your head around this most fundamental of differences.

  41. 41
    Evolve says:

    ///No one likens the translation of nucleotides to amino acids as a code. It is a code. Also no one perceives information in life. It is a fact that living organisms contain and use information.///

    No one will liken DNA to computer code other than creationists who are desperate to draw parallels between the two.

    A computer code or language is a script that represents something. It has no physical existence or chemistry. You’re taking this traditional idea of a code and applying it to DNA ignoring that DNA is a chemical polymer undergoing natural chemical reactions.

    The “code” in DNA is nothing but chemistry – some molecules bind together favorably under some conditions to give a product. Much like H2O molecules bind to form water.

  42. 42
    Querius says:

    A computer code or language is a script that represents something. It has no physical existence or chemistry.

    LOL, Evolve. You just as clueless as AVS. Here, try this:

    Where is “computer code” stored and how is it retrieved?

    -Q

  43. 43
    Ho-De-Ho says:

    While I respect and endeavour to find the merits in all points of view, I have to admit that I struggle with the “Life is just chemistry” argument. I do not wish to sound combative or sneering as these are ghastly qualities which undermine the dignity of all parties. I shall merely state my reasons.

    While it could be argued in the broadest sense that Life is just chemistry (and no doubt physics too), that broad line of approach could equally describe a bridge or a petrol engine or my sofa. Each of these things is made of chemical properties which are as they are due to the nature of their chemical reactions. If those reactions could never take place then the materials could never in the first place be engineered so as to be assembled into the final product. If one wishes to reduce a bridge down to individual atoms then chemistry is certainly at the heart of it.

    The thing is, that when I behold a bridge I know that something more is involved than just the chemistry and physics. That something is information. I do not say ‘Intelligence’, because the bridge is not actually intelligent of itself, but it is pieced together in an informed way that capitalises on the laws of chemistry and physics. The information does not of itself dwell within the materials and must therefore come from without, which of course we all recognize is some brainy person like Kingdom Brunell.

    Physics, Chemistry and Information make a bridge. Yet if I grind it up and examine it under a microscope it will be ‘Just chemistry.’

    Evolve gave quite a nice definition of code I thought. “A computer code or language is just a script that represents something.”

    That is tidily put, although I fear that I would draw a different conclusion from that definition with regards to DNA. Consider the genes and wotnot on a strand of DNA which are transcribed to make an arm, for instance. The genes are not an arm, but are a representation of said arm. And if we smashed up the DNA so that we just had all of its chemicals, nothing would give us any inclination of an arm at all. In this respect I think Evolve is broadly correct in saying that a code has no physical existence. (Although maybe it is the ‘idea’ that the code produces that doesn’t possess any physicality.)

    Information certainly isn’t a chemical molecule. It can, as has been noted, be impressed upon or use chemical molecules. It is also real. So from whence does it come? Therefore, not all things around us can be accurately summed up as just chemistry.

    In summary then I find this to be the case. DNA is chemistry and abides by the rules of chemistry but it would appear to be an informed use of these laws that make it capable of representing an idea or plan which the cellular machinery develops into a reality. And that is why I think that it is not foolish nor inaccurate for people to refer to it as a code.

    I hope that wasn’t too long a post.

  44. 44
    Upright BiPed says:

    Hello Evolve,

    I’m glad to see you’ve returned to try and make sense of your position. Let’s see what you’ve come up with.

    Computer code and language may require chemistry to exist (since they are created by humans), but they’re not chemical molecules themselves. Whereas DNA is a chemical. That’s the whole point.

    Your first sentence says that computer codes and language may require chemistry because they are made by humans. This is nonsensical to me. Computer codes and languages require matter as a medium to input representations into a system capable of producing a specified effect. This is no different than any other instance of recorded information; whether that information is the product of a human or not has nothing whatsoever to do with it. A representation is an arrangement of matter that evokes an effect within a system, where the arrangement of the medium and the effect it evokes are physicochemically arbitrary. The presence of a representation is one of the four material conditions required to translate recorded information into a material effect. And frankly, its horrible anthropocentric to suggest that only humans create or use representations. Moreover, its completely divorced from reality.

    Your second sentence says that DNA is a chemical, and that’s the whole distinction you’d like to point out. But yet again, this is nonsensical. Firstly, DNA and the genetic code are not the same thing. DNA is the medium by which representations are inputted into a system capable of producing a specified effect. As stated before, the genetic code is the set of physicochemically arbitrary relationships instantiated in the system. They are established by the preservation of the discontinuity between the arrangement of the medium and the effect produced by the system. Once again, this is no different than any other semiotic system even demonstrated to exist. You’ve articulated no distinction.

    Look Evolve, I understand the zero-concession policy you are forced to abide by in the materialists mindset. But there is no sense in you taking positions that are woefully untenable – by anyone’s standards. If you can’t allow yourself to come to an accurate understanding of these issues from a ID proponent, then by all means, turn to a materialist and open your ears. I would suggest the writings of the physicist Howard Pattee as a good place to start. He’s been researching the physics of semiotic control for 50 years.

    cheers…

  45. 45
    Mung says:

    Evolve:

    Do you know that adenine, which makes ATP, and other nucleobases have been discovered even in meteorites?!

    Mung:

    Adenine does not make ATP.

    Evolve:

    Trying to find loopholes to cover your blunders? The Adenosine in ATP comes from Adenine. That’s what I meant and you know it.

    I know no such thing. This is you, right before the bit I quoted:

    The idea here is to show that biomolecules can self-organize into protocells under certain conditions. In other words, your designer is not required to pack molecules into cells. One job less for the designer!

    Then you went on to claim that cells don’t make adenine, that adenine makes ATP.

    So you were wrong, and you mis-spoke, and you failed to correct yourself.

    Hypocrite much?

  46. 46
    Mung says:

    Both adenine and guanine are derived from the nucleotide inosine monophosphate (IMP), which is the first compound in the pathway to have a completely formed purine ring system.

    Purine metabolism

  47. 47
    Querius says:

    Upright Biped,

    Very nicely stated in #44!

    A design in a programming language is an articulated logical concept or relationship that’s typically stored and retrieved from an alloy coating capable of storing magnetic charges, loaded into a semiconductor memory array, and executed by manipulating electrons in a microprocessor.

    The same design using the same programming language could conceivably be stored and retrieved from DNA and executed by manipulating proteins using the nanotechnology available in a cell.

    There’s no fundamental difference except in the means, which is ruled my the laws of chemistry and physics.

    Wow, imagine using a living cell to crack an encryption . . . do this in parallel with many cells that communicate through synapses. To keep the cells alive, implant them somewhere in a human brain (to make the results easily available), or just program the cells in place with a non-replicating virus. The stuff of science fiction (for now). 😉

    -Q

  48. 48
    Upright BiPed says:

    Thank you Q

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