Genetics

Researchers: Biology’s optimal ‘molecular alphabet’ may be preordained

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From ScienceDaily:

An international and interdisciplinary team working at the Earth-Life Science Institute (ELSI) at the Tokyo Institute of Technology has modeled the evolution of one of biology’s most fundamental sets of building blocks and found that it may have special properties that helped bootstrap itself into its modern form. …

All life, from bacteria to blue whales to human beings, uses an almost universal set of 20 coded amino acids (CAAs) to construct proteins. This set was likely “canonicalized” or standardized during early evolution; before this, smaller amino acid sets were gradually expanded as organisms developed new synthetic proofreading and coding abilities. The new study, led by Melissa Ilardo, now at the University of Utah, explored how this set evolution might have occurred.

There are millions of possible types of amino acids that could be found on Earth or elsewhere in the Universe, each with its own distinctive chemical properties. Indeed, scientists have found these unique chemical properties are what give biological proteins, the large molecules that do much of life’s catalysis, their own unique capabilities. The team had previously measured how the CAA set compares to random sets of amino acids and found that only about 1 in a billion random sets had chemical properties as unusually distributed as those of the CAAs. …

They found that even hypothetical sets containing only one or a few modern CAAs were especially adaptive. It was difficult to find sets even among a multitude of alternatives that have the unique chemical properties of the modern CAA set. These results suggest that each time a modern CAA was discovered and embedded in biology’s toolkit during evolution, it provided an adaptive value unusual among a huge number of alternatives, and each selective step may have helped bootstrap the developing set to include still more CAAs, ultimately leading to the modern set.

If true, the researchers speculate, it might mean that even given a large variety of starting points for developing coded amino acid sets, biology might end up converging on a similar set. As this model was based on the invariant physical and chemical properties of the amino acids themselves, this could mean that even Life beyond Earth might be very similar to modern Earth life. Co-author Rudrarup Bose, now of the Max Planck Institute of Molecular Cell Biology and Genetics in Dresden, further hypothesizes that “Life may not be just a set of accidental events. Rather, there may be some universal laws governing the evolution of life.” Paper. (open access) – Melissa Ilardo, Rudrarup Bose, Markus Meringer, Bakhtiyor Rasulev, Natalie Grefenstette, James Stephenson, Stephen Freeland, Richard J. Gillams, Christopher J. Butch, H. James Cleaves. Adaptive Properties of the Genetically Encoded Amino Acid Alphabet Are Inherited from Its Subsets. Scientific Reports, 2019; 9 (1) DOI: 10.1038/s41598-019-47574-x More.

It’s worth noting that the origin of the term “bootstrap”:

a loop of leather or cloth sewn at the top rear, or sometimes on each side, of a boot to facilitate pulling it on.

—

Idiom:
pull (oneself) up by (one’s) bootstraps, to help oneself without the aid of others; use one’s resources:
I admire him for pulling himself up by his own bootstraps.

—

It’s not clear that this can really be done, using only naturalistic resources.

It sounds as though these researchers want to quietly abandon Darwinian randomness in favor of a structuralist approach to the unfolding of life but — understandably — do not want to hear from an army of angry Darwinian orcs.

See also: Do genes that jump shake the tree of life? Yes. But what hope is there that textbooks could start teaching reality when even the right to question the Darwinian filler is still a big controversy in many places? Could science writers like Jabr and others agree that it is time to make textbooks about evolution sound like the reality and not like the 1925 Monkey Trial revisited?

9 Replies to “Researchers: Biology’s optimal ‘molecular alphabet’ may be preordained”

  1. 1
    Mimus says:
    September 10, 2019 at 8:55 pm

    It sounds as though these researchers want to quietly abandon Darwinian randomness in favor of a structuralist approach

    The first word in the paper’s title is “adaptive”, so… no.

  2. 2
    martin_r says:
    September 11, 2019 at 12:21 am

    Mimus@1

    From today’s article:
    “… smaller amino acid sets were gradually expanded as organisms developed new synthetic proofreading and coding abilities. ”
    ??????
    “…as organisms developed new synthetic proofreading…” ??????
    organisms DEVELOPED a PROOFREADING ?

    Let me paraphrase R Dawkins:

    It is absolutely safe to say that if you meet somebody who claims that DNA proofreading and repair was not designed, that person is ignorant, stupid or insane (or wicked, but I’d rather not consider that)

  3. 3
    BobRyan says:
    September 11, 2019 at 3:22 am

    Mimus and the other drooling followers of Darwin:
    You’ve never read Darwin’s book. Read his own words. Otherwise, you are merely telling others what you’ve been told by someone else. Darwin has been disproven many times over.

  4. 4
    Mimus says:
    September 11, 2019 at 3:35 am

    What’s wrong with you, BobRyan?

    I’ve read Darwin’s book(s). You repeatedly claim Darwin wrote things that we simply did not. When asked to provide a citation nothing is forthcoming. So I’m not sure if this is some sort of performance-art trolling exercise or you are just very confused?

  5. 5
    BobRyan says:
    September 11, 2019 at 4:26 am

    When Darwin included the 4 races, believing that blacks were not as evolved as the other races, do you agree with that part of his theory? If you actually read Darwin, then you would have to admit that not everything we know today fits nicely into his little bow. Not one Darwinist has actually provided a shred of evidence that macro-evolution exists at all. It has never been viewed and does not hold to valid scientific thought.

  6. 6
    bornagain77 says:
    September 11, 2019 at 4:55 am

    as to:

    There are millions of possible types of amino acids that could be found on Earth or elsewhere in the Universe, each with its own distinctive chemical properties.,,,
    The team had previously measured how the CAA set compares to random sets of amino acids and found that only about 1 in a billion random sets had chemical properties as unusually distributed as those of the CAAs. …
    They found that even hypothetical sets containing only one or a few modern CAAs were especially adaptive. It was difficult to find sets even among a multitude of alternatives that have the unique chemical properties of the modern CAA set.,,,
    There are many possible subsets of the modern CAAs or other presently uncoded amino acids that could have comprised the earlier sets. The team calculated the possible ways of making a set of 3-20 amino acids using a special library of 1913 structurally diverse “virtual” amino acids they computed and found there are 10^48 ways of making sets of 20 amino acids. In contrast, there are only ~ 10^19 grains of sand on Earth, and only ~ 10^24 stars in the entire Universe. “There are just so many possible amino acids, and so many ways to make combinations of them, a computational approach was the only comprehensive way to address this question,” says team member Jim Cleaves of ELSI. “Efficient implementations of algorithms based on appropriate mathematical models allow us to handle even astronomically huge combinatorial spaces,” adds co-author Markus Meringer of the Deutsches Zentrum für Luft- und Raumfahrt.
    As this number is so large, they used statistical methods to compare the adaptive value of the combined physicochemical properties of the modern CAA set with those of billions of random sets of 3-20 amino acids. What they found was that the CAAs may have been selectively kept during evolution due to their unique adaptive chemical properties, which help them to make optimal proteins, in turn helping organisms that could produce those proteins become more fit.

    Oh goody, computer models and statistical methods to compare the adaptive values of the physiochemical properties of amino acids instead of the functionality of proteins themselves. Small problem, there can be no replication to select from without functional proteins in the first place. As Dr. Cornelius Hunter quipped about a similar unrealistic ‘model’, “In other word, for evolution to evolve proteins, they must already exist in the first place.”

    Claim: New Proteins Evolve Very Easily – Cornelius Hunter – April 25, 2017
    Excerpt:  It is now clear that for a given protein, only a few changes to its amino acid sequence can be sustained before the protein function is all but eliminated. Here is how one paper explained it:
    “The accepted paradigm that proteins can tolerate nearly any amino acid substitution has been replaced by the view that the deleterious effects of mutations, and especially their tendency to undermine the thermodynamic and kinetic stability of protein, is a major constraint on protein evolvability—the ability of proteins to acquire changes in sequence and function.”
    In other words, protein function precipitously drops off with only a tiny fraction of its amino acids altered. It is not a gradual fitness landscape. Another paper described the protein fitness landscape as rugged.
    Therefore it is not surprising that various studies on evolving proteins have failed to show a viable mechanism. One study concluded that 10^63 attempts would be required to evolve a relatively short protein. And a similar result (10^65 attempts required) was obtained by comparing protein sequences. Another study found that 10^64 to 10^77 attempts are required, and another study concluded that 10^70 attempts would be required.
    So something like 10^70 attempts are required yet evolutionists estimate that only 10^43 attempts are possible. In other words, there is a shortfall of 27 orders of magnitude.
    But it gets worse. The estimate that 10^43 attempts are possible is utterly unrealistic. For it assumes billions of years are available, and that for that entire time the Earth is covered with bacteria, constantly churning out mutations and new protein experiments. Aside from the fact that these assumptions are entirely unrealistic, the estimate also suffers from the rather inconvenient fact that those bacteria are, err, full of proteins. In other word, for evolution to evolve proteins, they must already exist in the first place.
    This is absurd. And yet, even with these overly optimistic assumptions, evolution falls short by 27 orders of magnitude.
    https://www.evolutionnews.org/2017/04/claim-new-proteins-evolve-very-easily/

    Whereas in the real world of empirical science, the fact of the matter is that, as far as empirical science itself is concerned, (instead of these unrealistic computer models and statistical methods where the unrestrained imaginations of Darwinists are apparently allowed to roam free), functional proteins are exceedingly rare. So rare that a leading researcher stated, “The appearance of early protein families is “something like close to a miracle.” And “In fact, to our knowledge no macromutations … that gave birth to novel proteins have yet been identified.”

    Dan S. Tawfik Group – The New View of Proteins – Tyler Hampton – 2016
    Excerpt: one of the most favorable and liberal estimates is by Jack Szostak: 1 in 10^11. 42 He ascertained this figure by looking to see how random sequences—about eighty amino acids in length, long enough to fold—could cling to the biologically crucial molecule adenosine triphosphate, or ATP.
    At first glance, this is an improvement over Salisbury’s calculations by 489 powers of ten. But while an issue has been addressed, the problem has only been deferred. ,,,
    ,,, nucleotide synthesis, requires several steps. If five enzyme functions were needed (ten are needed in modern adenine synthesis), 43 then the probability would be 1 in (10^11)5, or 1 in 10^55. If all the operations needed for a small autonomous biology were ten functions—this is before evolution can even start to help—the probability is 1 in (10^11)10, or 1 in 10^110. This is more than the number of seconds since the Big Bang, more protons than there are in the universe. In considering a similar figure derived in a different context, Tawfik concedes that if true, this would make “the emergence of sequences with function a highly improbable event, despite considerable redundancy (many sequences giving the same structure and function).”44 In other words, these odds are impossible.,,,
    Tawfik soberly recognizes the problem. The appearance of early protein families, he has remarked, is “something like close to a miracle.”45,,,
    “In fact, to our knowledge,” Tawfik and Tóth-Petróczy write, “no macromutations … that gave birth to novel proteins have yet been identified.”69
    The emerging picture, once luminous, has settled to gray. It is not clear how natural selection can operate in the origin of folds or active site architecture (of proteins). It is equally unclear how either micromutations or macromutations could repeatedly and reliably lead to large evolutionary transitions. What remains is a deep, tantalizing, perhaps immovable mystery.
    http://inference-review.com/ar.....f-proteins

    As to ‘statistical methods’ in general, Ilya Prigogine, an eminent chemist and physicist who received two Nobel Prizes in chemistry, stated,

    “The statistical probability that organic structures and the most precisely harmonized reactions that typify living organisms would be generated by accident, is zero.”
    Ilya Prigogine, Gregoire Nicolis, and Agnes Babloyantz, Physics Today 25, pp. 23-28. (Sourced Quote)

  7. 7
    Fasteddious says:
    September 11, 2019 at 11:35 am

    An imaginative and fascinating Darwinian story:
    Once upon a time, a variety of lifeforms existed with varied sets of amino acids. Thus, these lifeforms already had massive amounts of bio-information to pass on to their progeny. Leave aside for the moment the likelihood that any mutation to that information would be deleterious or fatal; e.g. swapping different random amino acid into pre-proteins is not likely to be a good thing. Somehow these lifeforms came up with other amino acids (randomly collected or somehow produced), which were somehow coded into their bio-information (pre-genome). Since only one in a billion of these sets of amino acids is suitably useful, there must have been a lot of mistakes before zeroing in on the optimum set of 20. Also, somehow the old pre-proteins continued to work despite the changed bio-information and the new amino acid added to the mix, by coincidentally new mechanisms for their selection and bonding.
    Never mind all that, eventually the full set of 20 amino acids was collected and the lifeform continued to live and reproduce. Then somehow, all those older, sub-optimal amino acids (“junk bio-molecules” anyone?), along with their support machinery, were discarded in favour of new ones, via the ever-efficient process of natural selection, all while preserving the lifeform’s viability and reproductive talent at each small step. Then all the other lifeforms did the same things and settled on the same one-in-a-billion set, along with all its support machinery and identical coding hardware. Or perhaps the first one to find the gold ring (AKA optimum set of 20) out-competed everything else so well that the others were left in the dust of common descent, so that all current lifeforms now share the same set of 20 and there are no residues of earlier lifeforms, either living or fossilized, to show that once upon a time there were other variants, notwithstanding that there are examples of lifeforms unchanged in a billion years hiding in ecological niches.
    “Once upon a time” is how fairy tales begin, and this one is similar.

  8. 8
    Mimus says:
    September 11, 2019 at 2:14 pm

    BobRyan,

    In which of his books did Darwin “[include] the 4 races, believing that blacks were not as evolved “? Or are you just making it up?

  9. 9
    aarceng says:
    September 11, 2019 at 9:04 pm

    Before life can start to select for optimal amino acids it must first start with some minimal set as a viable reproducing organism. How did that happen? How small can that minimum set of amino acids be?

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