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 . Not withstanding all scientific progress, we currently do not have a credible solution to these problems .
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:  ):
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:
- There is a pdf of the book available on the internet with full color illustrations!
- 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.
- 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.)
- “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.”