On variant genetic codes

Craig Venter has achieved celebrity status in Creationist circles for little more than a slightly embarrassed smile. In a discussion involving, among others, Richard Dawkins, Lawrence Krauss and Paul Davies, Venter makes the eyebrow-raising statement that he does not regard Mycoplasma as the same ‘life-form’ as other prokaryotes, or eukaryotes. His reasoning was that they have ‘different genetic codes’. Dawkins reasonably points out that their codes are ‘all but identical’ (they differ in just one position, Trp for STOP). Creationist videos of the exchange tend to fade on the aforementioned smile given in response. The videos are presented, breathlessly, as “Venter denies Common Descent in front of Richard Dawkins!”. However … one difference? Is that really enough to justify a claim of separate origins? This would be like claiming that Norwegian and Swedish had separate origins on the strength of the difference between æ and ä or ø and ö.

When last I looked, there were about 18 known variant codes. More are being discovered all the time. It’s instructive to compare the differences – but first, I’ll run through the basic mechanics of protein coding from DNA.

The code comprises groups of three DNA bases – triplets. With 4 different bases, there are thus 64 different possible triplets. One DNA strand’s sequence is transcribed to ‘messenger RNA’ (mRNA) using base-pairing affinities. A pairs with T (or U in RNA, simply a methylated T) and C with G so the transcript of ACGT is UGCA. This is a physical interaction and not merely an informatic one – ACGT binds most strongly to its complementary sequence (T/U)GCA. Once the mRNA is formed, possibly after some post-transcriptional editing, it is passed to a ribosome for translation into protein. A pool of up to 64 ‘transfer RNA’ (tRNA) molecules is maintained by up to 20 enzymes called aminoacyl tRNA synthetases – aaRSs. The aaRSs are the main Keepers of the Code. Each different aaRS will charge one or more of the different tRNAs with a specific amino acid. The acid is attached to a specific sequence – ACC – at one end of the tRNA. At the other end lies an ‘anticodon’ – a triplet with the same sequence as the original DNA triplet, which has the strongest binding affinity for the complementary sequence present in the transcribed mRNA – the ‘codon’. Charged tRNAs are like paint brushes with a dab of colour on one end and a unique shape on the other. Given a template to line them up and dock the appropriate shapes, dabbing the other ends on a growing string, the same pattern can be produced repeatedly and mechanically.

Translation commences at a ‘Start’ codon – typically, though not universally, corresponding to the amino acid methionine, codon AUG. Given that binding is most strong between a codon and its anticodon, each exposed mRNA triplet has the greatest affinity for just one tRNA. The relevant tRNA docks and the peptide is elongated with the amino acid at its other end. Translation ceases when no tRNA can be found corresponding to a given codon. Such codons – those without tRNAs – are termed STOP codons. Typically, this tends to be more than just a simple passive mechanism – the growing peptide does not merely ‘fall off’ the ribosome for want of an acid, but release factors are triggered, which break the bond between the synthesised peptide chain and the tRNA to which the last acid was attached.

The mechanism described above is universal – all organisms on earth synthesise their proteins in the same way. That alone should cause Venter to hesitate in his dubious assertions regarding ‘life forms’ of separate origin. If everything on earth shares the same system, it really does not indicate that they had separate origins, however much difference in detail. Venter argues elsewhere that sequence data starts to lose sight of a simple tree in deep time, and this is true to some extent, due to such factors as horizontal gene transfer – genes passed among organisms rather than inherited from common ancestors. Yet the very fact that gene transfer is even possible indicates that transfers are between relatives. The kind of things that might more securely indicate separate origins are, for example, L-sugars giving oppositely-coiled DNA, or D-amino acids, or acids other than the canonical 20, or base pairs other than the standard 2. What one would not expect is to be able to pass a ‘well-formed string’ from one organism to another of completely separate origin, yet have an equally well-formed string emerge after processing in a truly foreign system. This is like Jeff Goldblum uploading a virus to the alien computer from an Apple Mac in Independence Day – pure hokum.

Another aspect to consider is the structure of the aaRSs that determine the code. The 20 acids divide neatly between Class l and Class ll, based on their reaction chemistry. Class l enzymes attach the amino acid to the 2′ -OH of the substrate; all but one Class ll enzymes attach to the 3′ -OH. Either way, the acid migrates to the 3′ before the ribosome gets hold of it, so there is no effective difference. Every enzyme in each class bears a sequence relationship to all other enzymes in that class – but there is no such relationship between the classes. It appears from this data that aaRSs arose at least twice, and also that the modern code of 20 acids most likely arose from a much smaller set. All of this activity would have to have preceded LUCA, our last common ancestor, because the various quirks noted above are common to all life. How can that be? OK, one might say ‘design’ – a catch-all that can be invoked to explain all data – but that’s not what Venter thinks, so it’s not clear what explanation he would have for that massive commonality of mechanism and structure, if not genetic common origin.  

But of course – as Dawkins pointed out – it’s not merely the common details of mechanism, but the code itself that speaks loudly of a single surviving origin. The commonest code is termed the ‘standard’ code. This is used in most eukaryotic nuclei, most bacteria and archaea, and plant plastids. On the principle of parsimony, this is most likely the code used by LUCA itself. It has 3 STOP codons – UAA, UAG, UGA – and usually – not always – starts with methionine. In Mycoplasma, UGA codes for tryptophan, which is coded solely by its close neighbour UGG in the ‘standard’ code. This is actually a very common substitution – the codes of nearly all mitochondria do exactly the same at this position, for example. Thus, Venter is effectively saying that our own mitochondria are not the same ‘life-form’ as our nuclei – a perverse notion, since many mitochondrial genes have migrated to the nucleus, and are synthesised there before re-export. He is saying, by implication, that the difficulties we would have synthesising Mycoplasma proteins, or vice versa, preclude gene migration from the mitochondrion, unless that migration preceded the amendment to the mitochondrial code. That’s a strong claim, even if made unknowingly.  

But how can the genetic code change – how could we possibly have common descent of all codes? There are 3 principal possibilities for a code change

  1. Substitution of a STOP by an acid
  2. Acid-for-acid substitution.
  3. Substitution of an acid by a STOP

I have ranked them thus in order of assumed constraint against them.

  • If a STOP is substituted by an acid, it will have the effect of adding a small ‘tail’ to those proteins having that STOP, leaving the core untouched, which is less likely to be damaging.
  • If one acid is substituted by another, this may well affect the core of many proteins, which will have more impact, but the effect is mitigated if the codon is of low usage, or the substitution is for one of similar chemical property.
  • The third is probably rare – it would have the effect of chopping proteins into short segments, depending on the stochastic occurrence of the relevant codon. Nonetheless, in short genomes with biases against certain codons or base pairs, it may occur with some frequency.  

Now, the Mycoplasma/mitochondrial distinction is of the first type – the assumed ancestral code has apparently been amended by addition of UGA to the substrates accessible to  tryptophanyl tRNA synthetase (an aaRS), which is specific to UGG in our nuclei, but UGA/UGG in mitochondria. A and G are both purines, by contrast with the pyrimidines U, C and T. The first are distinguished by a double ring structure, the second are single, and so they present quite different profiles to enzymes, more easily distinguished than the separate bases comprising each class. In this case, it would require a loss of distinction between the purines, rather than a gain of specificity. Nonetheless, it is very common within the code to see a 3rd-position distinction made simply on the basis of whether it is a purine or a pyrimidine, rather than at the level of individual base, so there is nothing exceptional about this particular substitution.

The supposition that filling in of STOP is the likeliest amendment is borne out by analysis of the genetic codes of extant organisms. It appears that the wholesale replacement of one acid by another has hardly occurred at all since the common ancestor; almost all variant sites function as STOP in one or more variant codes. Of 13 codons that vary in one species or another, 7 are a STOP in at least one. If we ignore the 4 codons restricted to yeast mitochondria in which the entire CUx group has seen a substitution of Threonine for Leucine, it becomes 7 out of 9, which is striking. There is a viable mechanistic reason for this, relating to the relatively mild effect of this particular substitution on existing proteins.

This is possibly the means by which the code itself arose – initially only a small amount of the 64-codon matrix was covered by assignments, as suggested by the apparent coalescence of the 2×10 Class l and Class ll aaRS enzymes upon fewer ancestral enzymes. In such a system, consisting of ‘mostly STOPs’, the extra tail added by assignment of a STOP would be quite short – as STOPs become fewer, the length of the average tail will increase, but in early evolution the constraint against this substitution would be less severe. Gradually, as the codon matrix becomes filled in and proteins become more widely used and longer, the code ‘freezes’.

Any acid-for-acid substitutions that divided a codon group, either due to purine/pyrimidine specificity, or individual base distinction, would tend to favour chemically conservative substitutions. This would generate the much-vaunted fault tolerance of the code – translation errors frequently result in a viable product due to chemically related neighbourhoods in the code. On this model, there is no need to use design or positive selection to achieve favourable arrangements; they are a by-product of the constraint on wholesale substitution.

Gradual filling in of STOPs would thus have led to both a richer code, biased towards construction of chemically conservative neighbourhoods, and incidentally to a gradual lengthening of proteins, amending both the v and the n of the assumed v^n ‘search space’ in which some imagine proteins must arise fully formed in a single bound.

And so, having reached more-or-less its present form in the population of which LUCA formed a part, descendants such as Mycoplasma and us sprang forth – with minor variations.

Edit to add – my spreadsheet of the up to date codes table. A code 32 was added just in the last day or so – although, pace J-mac, there are not 32 codes, but around 25, due to mergers. It is not always a straightforward issue to determine whether a code should be considered truly ‘different’ or not. For example, the GUG start codon is occasionally used in our own cells, but comes up as a difference when used in other codes because it is not annotated as part of the ‘standard’ code. And ciliates are just plain bizarre!

The sheet is colour coded to highlight the differences – red for assignment variants from the standard code, and yellow for Start/Stop differences.

110 Replies to “On variant genetic codes”

  1. Mung Mung
    Ignored
    says:

    Is that really enough to justify a claim of separate origins?

    Differences are never a reason to doubt common ancestry. Descent with modification actually predicts that you will have differences. So differences actually confirm the theory.

  2. Mung Mung
    Ignored
    says:

    I’d like to commend you for not once appealing to “natural selection” to explain the origins of the variant codes. Almost makes you wonder why it’s needed at all.

  3. Entropy Entropy
    Ignored
    says:

    Mung:
    I’d like to commend you for not once appealing to “natural selection” to explain the origins of the variant codes. Almost makes you wonder why it’s needed at all.

    There’s natural selection all over it. Only not directly mentioned, and not positive (“Darwinian”) selection. For example, whether the effects of a change in a codon would result in harm is a question about whether there’s going to be negative, aka purifying, selection, with a probability attached to it. For example, the elimination of a stop codon resulting in longer proteins, yet, being at the extremes of the chain not necessarily being harmful (so little to no negative selection), or the fact that genetic code variants happen mostly in organisms with small genomes (or mitochondria, which “happen” to have very small genomes), which is “allowed” because the probability of harm, given a small amount of genes is low (thus selection blind, or, again, little to no negative selection). Etc.

    Sorry. 😁

  4. Allan Miller
    Ignored
    says:

    Mung:
    I’d like to commend you for not once appealing to “natural selection” to explain the origins of the variant codes. Almost makes you wonder why it’s needed at all.

    Well, there is of course a great deal more to life than just variant codes, so one shouldn’t be too quick to dismiss it! And even within those variants, it may have a positive role. For example, Jukes theorises that Mycoplasma‘s filling-in of the UGA Stop relates to its very high (75%) AT content. This can’t be a universal, however, unless mitochondria also have that tendency; I’m more inclined to think it represents weakness of selection against the change.

  5. J-Mac
    Ignored
    says:

    “When last I looked, there were about 18 known variant codes”
    When was that? Right after The Great Debate or The Great Depression?

    There are 31 known variant codes…and counting…

    https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi

    BTW: Many current and former regular contributors have complained about the poor quality of OPs. This is one of them… I just hope the author didn’t bother to check the current number of code variants out of his ignorance and not in the attempt to deliberately deceive the uninformed…

  6. Rumraket Rumraket
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    says:

    J-Mac: There are 31 known variant codes…and counting…

    There’s 24 in that list. They’re not numbered corretly.

  7. Rumraket Rumraket
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    says:

    I always wondered what the heck Craig Venter was getting at. Even for bacteria, with all their HGT, there’s still a detectable central tree-like trend in the histories of individual universally conserved genes. Which makes sense to me as even though HGT is a lot more prevalent among prokaryotes, genes are still primarly passed on vertically many orders of magnitude more frequently than horizontally.

    Puigbò P, Wolf YI, Koonin EV. Seeing the Tree of Life behind the phylogenetic forest. BMC Biol. 2013 Apr 15;11:46. doi: 10.1186/1741-7007-11-46.

    “We set out to address the above question as objectively as possible, first of all dispensing with any pre-selected standard of tree-like evolution. The analyzed FOL consisted of 6,901 maximum likelihood phylogenetic trees that were built for clusters of orthologous genes from a representative set of 100 diverse bacterial and archaeal genomes [1]. The complete matrix of topological distances between these trees was analyzed using the Inconsistency Score, a measure that we defined specifically for this purpose that reflects the average topological (in)consistency of a given tree with the rest of the trees in the FOL (for the details of the methods employed in this analysis, see [21]). Although the FOL includes very few trees with exactly identical topologies, we found that the topologies of the trees were far more congruent than expected by chance. The 102 Nearly Universal Trees (NUTs; that is, the trees for genes that are represented in all or nearly all archaea and bacteria), which include primarily genes for key protein components of the translation and transcription systems, showed particularly high topological similarity to the other trees in the FOL. Although the topologies of the NUTs are not identical, apparently reflecting multiple HGT events, these transfers appeared to be distributed randomly. In other words, there seem to be no prominent ‘highways’ of HGT that would preferentially connect particular groups of archaea and bacteria. Thus, although the NUTs cannot represent the FOL completely, they appear to reflect a significant central trend, an attractor in the tree space that could be equated with the STOL (Figure ​(Figure1).

    Figure 1: The central tree-like trend in the phylogenetic forest of life. The circles show genomes of extant species and the grey tree in the background shows the statistical central trend in the data. For the purpose of illustration, the figure shows an ‘FOL’ made of 16 trees with 20 deviations from the central tree-like pattern.”

  8. Rumraket Rumraket
    Ignored
    says:

    J-Mac: I just hope the author didn’t bother to check the current number of code variants out of his ignorance and not in the attempt to deliberately deceive the uninformed…

    Here’s your chance to go analyze all those genetic codes and see if Allan’s predictions stand up to scrutiny. Is it generally the case, for example, that variant genetic codes are of the type that have replaced stop codons with amino acids, and is it generally the case that more structurally distinct codons are less likely to be substituted?

  9. Allan Miller
    Ignored
    says:

    J-Mac:
    “When last I looked, there were about 18 known variant codes”
    When was that? Right after The Great Debate or The Great Depression?

    There are 31 known variant codes…and counting…

    I literally linked to the wider list in the next sentence! And, as Rumraket said, there aren’t 31. They keep their assigned numbers, but (for example) 8 has been merged with 1. There is no 8.

    I actually spent the afternoon pasting ALL the known codes into Excel, which is where I got my stats on variants from. I put some work in. You?

  10. Allan Miller
    Ignored
    says:

    J-Mac:
    Me: “When last I looked, there were about 18 known variant codes”
    […]
    BTW: Many current and former regular contributors have complained about the poor quality of OPs. This is one of them…

    Wow, thanks. No actual refutation then.

    I just hope the author didn’t bother to check the current number of code variants out of his ignorance and not in the attempt to deliberately deceive the uninformed…

    Skating close to breach of the good faith rule, huh? Follow the link in the very next sentence. I also have edit history, in which an early draft said ‘now there are about 31’ where it now says ‘more are being discovered all the time’. I changed it because I realised it wasn’t actually 31.

    If ‘more are being discovered all the time’ is an attempt to deceive, and suggest the number is limited, it’s a poor one, don’t you think?

    I await your apology.

  11. Allan Miller
    Ignored
    says:

    So, do the additional variants support Venter’s contention? Do they follow the trend I discuss in the OP re: Stops?

    I already know the answer of course, which is where my ‘7 of 9’ stat above comes from. It’s based on analysis of all currently known codes. The additions are mostly exotic mitochondrial codes. Hey, I wonder if that’s significant?

  12. Alan Fox Alan Fox
    Ignored
    says:

    Allan Miller: I put some work in

    And your efforts are much appreciated. Seems like tantalising glimpses of the past are still visible in the present.

  13. RodW
    Ignored
    says:

    Allan
    I really wish you hadn’t written this piece. This topic was always a slam-dunk against the ID position and I would have loved to see it brought up in a recorded debate in front of a live audience. Now Iders will be able to prepare a dishonest rebuttal.
    The way I see it unfolding is:
    Paul Nelson or other brings up the Universal Code as a failed prediction of evolution.
    The counterargument is that biologists had good reasons for thinking the code was universal back in the 70s and 80s. What reason did Creationists/IDers have for the code being universal? All design explanations ultimately fail when you dig a little into them.
    I would then appeal to the audience. Without letting the cat out of the bag you know the code is not universal. Based on either evolution or ID predict (1) what the different code would be and (2) where ( what organisms) we would find this code.
    There are an astronomical number or workable codes, most radically different from the one that exists so its hard to predict what it would be, just that it would probably be very different. As for 2, the obvious candidate for the new code would be humans. With a different code there would be no confusing us for relatives of chimps, plus there would the added benefit of saving millions of lives because viruses from other animals couldnt jump to humans – AIDS, Flu etc.
    Instead what we see is exactly what you’d expect from evolution and natural mechanisms. Its evidence against a designer because one thing we know about designers is that they repair their designs when they accumulate damage. If there was a designer she would have repaired these changes to the code!

    BTW. I used to have posting privileges but let them lapse. Could they be restored?

  14. Mung Mung
    Ignored
    says:

    RodW: This topic was always a slam-dunk against the ID position…

    You seem to hold the mistaken idea that ID requires a rejection of common descent. It doesn’t.

  15. Alan Fox Alan Fox
    Ignored
    says:

    RodW: BTW. I used to have posting privileges but let them lapse. Could they be restored?

    Nothing’s changed. You still have them.

  16. Allan Miller
    Ignored
    says:

    RodW,

    Haha. If Creationists can refute it, let ’em! So far, J-mac (who has been touting this dispute for years) can only come up with the argument that ‘was 18, is growing’ misrepresents the actual number of known variants for deceitful purposes. 😀

  17. Allan Miller
    Ignored
    says:

    Mung: You seem to hold the mistaken idea that ID requires a rejection of common descent. It doesn’t.

    No, I think Rod’s is more about an argument on ‘good design’ than on Common Descent.

  18. RodW
    Ignored
    says:

    Mung: You seem to hold the mistaken idea that ID requires a rejection of common descent. It doesn’t.

    What ID “requires” is irrelevant. Every prominent IDer, save Behe, doubts common descent. That includes newbies such as Gunter Bechly

  19. RodW
    Ignored
    says:

    Allan Miller: No, I think Rod’s is more about an argument on ‘good design’ than on Common Descent.

    I dont know if I’d call it a ‘good design’ argument. I’d say when you look at the big picture here, down to the details, its very clear natural processes have been at work on this most fundamental aspect of all living things, and the notion that God was involved is absurd. Theres just no way to insert God into this picture.

  20. RodW
    Ignored
    says:

    Allan Miller: Haha. If Creationists can refute it, let ’em! So far, J-mac (who has been touting this dispute for years) can only come up with the argument that ‘was 18, is growing’ misrepresents the actual number of known variants for deceitful purposes

    They couldn’t refute it. But they could bog the argument down in irrelevant details and misrepresented facts to confuse the audience.

  21. Alan Fox Alan Fox
    Ignored
    says:

    RodW,

    What do you mean, “could”?

  22. RodW
    Ignored
    says:

    Allan Miller: No, I think Rod’s is more about an argument on ‘good design’ than on Common Descent.

    I haven’t read JMac’s post on good vs bad design. I dont know if I will because I think the debate has moved on. IDers pointed out a long time ago what should have been obvious from the start: all designs have constraints and compromises. – no design can be perfect. The devil is in the details here. Many of the bad designs could have been fixed easily by a designer but not by natural selections. And many fixes seem to be the result of incremental changes not the global big picture solution a designer could implement. The problem is that 1 or 2 or 3 examples of this dont weight the argument heavily in favor of evolution. It takes 100 examples but who is prepared to list 100 examples off the top of their head?

    Theres also the added complication that any bad design will have some silver lining. IDers can always tout that to claim the bad design is really good design.

  23. Allan Miller
    Ignored
    says:

    RodW,

    I haven’t read JMac’s post on good vs bad design.

    No, but we’re confusing two issues here. J-Mac, donning the glove-puppet of Craig Venter, has long tried to argue that variant codes refute common descent, separately from any case on Design.

    My OP is about that ‘descent’ issue, not about design at all.

  24. RodW
    Ignored
    says:

    Alan Fox: Nothing’s changed. You still have them.

    I dont see how. There used to be a box up in the corner to create a post. I dont know how to do it now

  25. Allan Miller
    Ignored
    says:

    RodW: They couldn’t refute it. But they could bog the argument down in irrelevant details and misrepresented facts to confuse the audience.

    Ah, ’tis but one’s daily vexation hereabouts!

  26. Alan Fox Alan Fox
    Ignored
    says:

    RodW,
    I’ll PM you.

  27. Entropy Entropy
    Ignored
    says:

    This was a good OP Allan. Good job.

  28. J-Mac
    Ignored
    says:

    Mung: Differences are never a reason to doubt common ancestry. Descent with modificationactually predicts that you will have differences. So differences actually confirm the theory.

    The universal genetic code was first predicted as evidence for common descent:

    “The genetic code is universal. I regard this as near-conclusive
    proof that all organisms are descended from a single common ancestor.”
    The Blind Watchmaker (1986), Richard Dawkins

    “The genetic code is universal, all but identical across animals, plants, fungi, bacteria, archaea and viruses. The 64-word dictionary, by which three letter DNA words are translated into 20 amino acids and one punctuation mark, which means ‘start reading here’ or ‘stop reading here,’ is the same 64-word dictionary wherever you look in the living kingdoms (with one or two exceptions too minor to undermine the generalization).” -The Greatest Show On Earth -Richard Dawkins

    Now the code variants, 31 of them for now, have been discovered which also have been predicted due to descent with modifications theory…

    The theory of evolution predicts both the universal genetics code and the code variants… Evolution can never be wrong… How could it, if it also predicts contradictions in its predictions?

  29. Allan Miller
    Ignored
    says:

    J-Mac,

    There aren’t 31. It’s not vitally important; the number could be anything for all I care, but it isn’t 31.

    As to your other point, evolution didn’t predict a universal code. It was believed to be universal on empirical grounds. Then variants were discovered – empirically. It wasn’t predicted that there would be variants. That said, the patterns of variation are clearly consistent with evolution, while a design reason for the pattern remains obscure.

    Can you think of a design reason why the strong tendency appears to be the optionality of certain Stop codons?

  30. Allan Miller
    Ignored
    says:

    There are some interesting quirks. Certain ciliates, for example, have no Stop codons – every single codon has a tRNA. Stop is achieved by context dependence – towards the protein ends, release factors compete more strongly and displace the tRNA. Read-through Stops are also quite common.

    Other odd variations relate to alternative Start codons, instead of AUG methionine. We even have some in our own genomes.

    If one subscribes to the view that codes cannot change, one has some explaining to do regarding this baroque variation, often occurring within the same cell.

  31. Allan Miller
    Ignored
    says:

    Entropy:
    This was a good OP Allan. Good job.

    Thanks! J-mac doesn’t like it though. I’m inconsolable. 😀

  32. phoodoo
    Ignored
    says:

    Allan Miller: Can you think of a design reason why the strong tendency appears to be the optionality of certain Stop codons?

    Optionality? I can’t tell if this is one of those times when you are using teleological logic because its convenient, and you actually mean something else?

    Allan Miller: Stop is achieved by context dependence

    Again, are we using convenient language that we really don’t mean? Is there context in the genome?

    I believe evolutionary theory would be so much clearer if writers wrote what they meant, instead of always utilizing some vague analogies.

  33. Alan Fox Alan Fox
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    says:

    phoodoo: Optionality? I can’t tell if this is one of those times when you are using teleological logic because its convenient, and you actually mean something else?

    There’s a choice, you mean, so there must be a chooser. Well, you could say the niche chooses in cases where there is selective pressure.

  34. Alan Fox Alan Fox
    Ignored
    says:

    phoodoo: I believe evolutionary theory would be so much clearer if writers wrote what they meant, instead of always utilizing some vague analogies.

    I don’t see that either understanding by humans or being able to communicate that understanding is guaranteed. Why should we expect phenomena always to be simple enough so that humans can understand? Why should we expect language always to be an adequate tool for communication?

  35. Entropy Entropy
    Ignored
    says:

    phoodoo:
    Optionality?I can’t tell if this is one of those times when you are using teleological logic because its convenient, and you actually mean something else?

    It means exactly what it means: that some stop codons can be aa-codons in other genomes. Nothing teleological about it.

    phoodoo:
    Again, are we using convenient language that we really don’t mean? Is there context in the genome?

    Of course there’s context in the genome. Genomes have dimensions, proteins bind to them. Small molecules bind to them. There’s water all around them, ions, etc. The genome gets transcribed, genes have positions relative to each other in genomes, etc. I don’t understand why you’d be so surprised that there’s context to anything.

    phoodoo:
    I believe evolutionary theory would be so much clearer if writers wrote what they meant, instead of always utilizing some vague analogies.

    It would become very clear to you if you focused on understanding. But all you seem to care about is producing useless angry rants.

  36. phoodoo
    Ignored
    says:

    Entropy: Optionality?I can’t tell if this is one of those times when you are using teleological logic because its convenient, and you actually mean something else?

    It means exactly what it means: that some stop codons can be aa-codons in other genomes. Nothing teleological about it.

    You don’t seem to understand what the word option means. You may be pretending you do, but I am not fooled.

    Who or what is “choosing”?

    Let me help you,

    Option_
    “a thing that is or may be chosen.”

    Alan says it the niche which chooses. Clearly he is using metaphor.

    Do you need me to show you what metaphor means?

  37. Entropy Entropy
    Ignored
    says:

    phoodoo:
    You don’t seem to understand what the word option means.You may be pretending you do, but I am not fooled.

    I’m not pretending and I’m not trying to fool you. Words can have several meanings depending on, ahem, context. Option means that there’s alternatives. The word works all right, as long as the reader is willing to put a bit of effort at understanding.

    phoodoo:
    Who or what is “choosing”?

    Circumstances around the evolution of some organism.

    phoodoo:
    Alan says it the niche which chooses. Clearly he is using metaphor.

    And this is wrong because?

    phoodoo:
    Do you need me to show you what metaphor means?

    You show me? I don’t need help. As I told Nonlin once (the poor gal/guy seems to be a slave of some dictionary, as long as the dependency favours her/his “points” I’d guess), words are our tools, not our masters. It’s up to us to figure out ways to try and convey a message, and it’s up to us to try and understand the message, to try and check the context of the words, and the way the words are being used.

    That’s part and parcel with the beauty, or lack thereof, of literature.

  38. Mung Mung
    Ignored
    says:

    RodW: Every prominent IDer, save Behe, doubts common descent.

    This is false. And as I said, both common descent can be true and ID can be true, so you might want to re-think your position.

  39. Mung Mung
    Ignored
    says:

    Allan Miller: I’m inconsolable.

    You just need a different STOP codon.

  40. phoodoo
    Ignored
    says:

    Mung: You just need a different STOP codon.

    At least the option to choose.

  41. J-Mac
    Ignored
    says:

    Seems obvious to me that the genetic code variants must have evolved and probably continue to evolve, right Allan Miller?

    BTW: There is much, much more to Venter’s denying common descent…
    He also denies Darwinism first and foremost… This phenomena alone deserves a separate OP which should include the great many know scientists who still believe in some kind of evolution and deny common decent not on genetic code variants alone but like Venter, see the evidence of the many different forms of life on the earth that could not have evolved by Darwinian mechanism of mutations and selection…

    https://www.youtube.com/watch?v=c43ckMLN50Q

    that there’s only one life form on this planet.” We have “a lot of different types of metabolism, different organisms,” he said. He turned to Paul Davies and added: “I wouldn’t call you the same life form as the one we have that lives in pH 12 base. That would dissolve your skin if we dropped you in it.” (

  42. Paul A Nelson
    Ignored
    says:

    Allan Miller wrote:

    “As to your other point, evolution didn’t predict a universal code. It was believed to be universal on empirical grounds.”

    The first published prediction of a universal code (Hinegardner & Engelberg, Science 142:1084-5, 1963) was made explicitly in the context of the theory of universal common descent: “Thus, once established, the genetic code will never change…all existing organisms would be descendants of a single organism or species.” In 1985, the late Bernard Davis, at the time at Harvard, expressed the same prediction this way — see the last sentence below:

    “If organisms had arisen independently they could perfectly well have used different codes to connect the 64 trinucleotide codons to the 24 amino acids, but if they arose by common descent any alteration of the code would be lethal, because it would change too many proteins at once. Hence the finding of the same genetic code in microbes, plants and animals…spectacularly confirms a strong evolutionary prediction.” (B. Davis, “Molecular Genetics and the Foundations of Evolution,” Perspectives in Biology and Medicine 28 (1985):251-268; p. 256)

  43. Paul A Nelson
    Ignored
    says:

    About Venter: he has long been skeptical of the theory of universal common descent. See, for instance, his comments in this utterly fascinating roundtable, organized in 2007 by the literary uberagent John Brockman:

    https://www.edge.org/documents/life/Life.pdf

    Actually the whole roundtable is worth a careful read. George Church says sympathetic things about the case for irreducibility of the ribosome, and the late Robert Shapiro (damn I wish he were still alive) is his usual outspoken self about the failures of the naturalistic origin-of-life research program.

  44. Paul A Nelson
    Ignored
    says:

    I think it is entirely possible that observed variant codes derived from a once-universal code by some unknown natural pathways. But that’s not the issue of deepest interest.

    Rather, as J-Mac has observed, the real issue is the evanescent empirical content of universal common descent (UCD). From the early 1960s until the mid-1980s, UCD was seen as powerfully confirmed by — i.e., as predicting — a universal code. When variant codes were discovered, no one (except the maverick theorist Hubert Yockey) said these unexpected findings might challenge UCD. Now UCD predicts the nonsense state of affairs “near-universality” (that young lady is nearly pregnant; 6 is almost 7, and hence for all purposes, nearly odd), or whatever we find.

    The other issue will require me to do some more digging, but right now, AFAIK, every experimental modification of the code has required investigators to “help” the cells over the fitness valley entailed by the coding change. For instance, investigators supply the wild-type tRNA on a plasmid during the transitional period. Otherwise the cells die.

    This is surely significant, in relation to claims made above that the evolution of the code should be easy to accomplish by undirected evolutionary processes.

  45. J-Mac
    Ignored
    says:

    Paul A Nelson:
    About Venter: he has long been skeptical of the theory of universal common descent.See, for instance, his comments in this utterly fascinating roundtable, organized in 2007 by the literary uberagent John Brockman:

    https://www.edge.org/documents/life/Life.pdf

    Actually the whole roundtable is worth a careful read.George Church says sympathetic things about the case for irreducibility of the ribosome, and the late Robert Shapiro (damn I wish he were still alive) is his usual outspoken self about the failures of the naturalistic origin-of-life research program.

    Lol! I was just reading the transcript of this discussion…
    Venter has been skeptical of common descent and Darwinism on many grounds one of them not being able to find the universal genetic code that would work for his cell manipulations…
    “What Freeman was talking about when he said you can separate metabolism from replication is certainly true, and we have at least 20 different modules we could plug in for metabolism. There’s not a universal genetic code that will be an
    operating system — it can be a choice of methane production, or of glucose
    metabolism, or anaerobic metabolism, oxidative metabolism or some other
    approach.
    So the naïve assumption that we could even define an operating system clearly went out the window.”

  46. Gregory Gregory
    Ignored
    says:

    Paul A Nelson,

    Hello again. We met in 2008 at the DI. If you don’t remember me now, a private message would jog your memory.

    You write here about a “naturalistic origin-of-life research program” as well as about “unknown natural pathways.” Why do you call one ‘naturalistic’ & the other ‘natural’? Can you please say why you use an ideology as a mere adjective?

  47. Paul A Nelson
    Ignored
    says:

    Gregory,

    Hi Gregory — of course I remember you.

    “Naturalistic” and “natural” as I’ve used them here mean simply “no intelligence causally implicated.” I take intelligence as a kind of cause to exhibit distinct (or diagnostic) features, such as planning, choice, actualization of abstract entities, etc.

  48. Alan Fox Alan Fox
    Ignored
    says:

    Paul A Nelson:…the late Robert Shapiro (damn I wish he were still alive) is his usual outspoken self about the failures of the naturalistic origin-of-life research program.

    Lovely guy. I had quite a bit of contact with him back in 2005 (mainly to do with his being a reviewer of Behe’s Darwin’s Black Box) during the build-up to the Dover trial. I recall he was sceptical of “RNA World” as a scenario for OOL. He recommended his book Planetary Dreams as a good exposition of his current (2005) views and I still have it. I’ll have a look to remind me. I do recall him mentioning he was agnostic and certainly not a supporter of “Intelligent Design”.

  49. J-Mac
    Ignored
    says:

    Paul A Nelson: Rather, as J-Mac has observed, the real issue is the evanescent empirical content of universal common descent (UCD). From the early 1960s until the mid-1980s, UCD was seen as powerfully confirmed by — i.e., as predicting — a universal code.

    Paul,
    Common descent or uncommon, the variants of the genetic code pale in the comparison of the new discoveries in quantum biology… I know a thing or two about that but there is much more to it…much more…

    Here is just the tip of the iceberg:

    Plants perform molecular maths
    Arithmetic division guides plants’ use of energy at night.

    https://www.nature.com/news/plants-perform-molecular-maths-1.13251

    It is nothing new that photosynthesis is quantum…Darwinists hate the idea but there is no running away from it… No way!

    If I were DI, I would try to get someone on board who understands this issue better than average… someone like Paul Davies…

    If you followed TSZ and PS, you may have seen some of my posts on quantum biology, including J. Wells’s idea of the cell differentiation in embryo development where I think quantum information is a good suspect to explain the math in the category/theory…
    How about the self-assembly of the flagellum? What if it is quantum? What if I can prove it? 😉

  50. J-Mac
    Ignored
    says:

    Paul,
    I just realized you also know a thing or two about the embryo development…as well as Richard Sernberg and obviously, my personal hero, Jonathan Wells 🙂

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