The Genetic Code and Universal Common Ancestry

But more probable on descent

Ok, then some organisms in one part of the ecosystem will never interact with others in a different part. Common biochem not essential. Not essential for the carbon cycle, etc.

This is what happens when people have a winner take all attitude towards evidence. It’s okay to grant a line of evidence to a proposition you think is false (False propositions can have true evidence) instead of just bending over backwards making silly arguments trying to hold onto a poor argument

Let’s assume Common bio chemistry is essential for some cases and not all… while a different bio Chen is not essential…
So it still makes sense to go with the same biochemistry… less work that way.

When I say “who knows what he is?” it’s because he has not made his hypotheses very clear, not that I think he’s lying about anything.

If that’s the objective, wouldn’t it be much easier just to start with multicellular organisms?

So who’s the designer, the one that is concerned with having less work? Not, presumably God. I thought you were going with God as designer.

  1. Why would you want to get away from the ribosome?

  2. Is there an intelligent reason to have stop codons, so that any protein can end with any amino acid residue?

Hmmm… good question. Wouldn’t ending all proteins with polylysine be a good quality control measure?

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On the predictive power of UCA

How does universal common ancestry predict this? Please lay out your logic.

Does universal common ancestry predict that the adoption of proteins by the first replicators could only happen once? Would universal common ancestry have been falsified if the use of proteins - and thereby a genetic code - had been adopted twice independently?

Does universal common ancestry predict that the first organisms to employ a genetic code employed the standard code? Or did life go through several genetic codes before hitting on the standard code? If so, does universal common ancestry predict the fixation of the standard code before LUCA?

No, in my opening post I wrote that universal common ancestry was the best non-teleological explanation for the near-universality of the standard genetic code. You claimed that universal common ancestry predicted it. That’s a different and far stronger claim.

Given the commonalities we see in all life, we can make some inferences about what the last common ancestor of all life was like. It was an organism much more advanced than one still “figuring out” how to get DNA to code for proteins. This means that it was a single species with a single genetic code, even if others may have been around as well.

All our experience with design indicates the need to minimize the risks of error. I don’t know how a supernatural omnipotent being would go about designing things.

Another way of putting that is that using different genetic codes would eliminate a major source of horisontal gene transfer.

Could you please elaborate on this? I’m not sure I’m getting the point you’re making.

The scenario I’m tentatively proposing involves the seeding of Earth with a diverse population of designed cells and viruses, including representatives of bacteria and eukaryota, which then evolved into the present biota. Detecting microbial life in the fossil record is difficult and fraught with conflicting claims (as the criticism of William Schopf’s claims of 3.5 billion years old cyanobacteria shows). But at present the evidence seems to date the first life to at least 3 billion years ago. A single seeding event seems to be the most parsimonious.

Why seeding with diverse bacteria and eukaryotes? Why not a single UCA, for example?

@Ashwin_s

The Atheists and Agnostics on these pages suffer from an extreme trepidation over any thing guided by God.

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And scientists have the same trepidation whether they are Christian or non-Christian. Science can’t answer questions about anything guided by God.

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Really? You can’t figure out that an omnipotent and, need I say, omniscient being would not be concerned with how much work he had to do (zero in all cases) and making mistakes (impossible for an omniscient being)?

No, that’s not another way of putting that. While viruses, specifically retroviruses, can be involved in horizontal gene transfer, that’s not what preventing attack by viruses means.

I was agreeing with you. Just accept the agreement.

Not tenable, considering that the first eukaryote fossils are a couple of billion years after the first bacterial fossils. And genomic studies also show eukaryotes to be much younger than others. There’s also the problem of the incorporation of mitochondria and plastids, which also happened much later than the evolution of the bacteria ancestral to them.

And we have that nested hierarchy to contend with. Your scenario doesn’t work with that unless we propose a long history of evolution to generate that hierarchy, presumably on some other planet, prior to the seeding event. But why postulate that long evolution? In short, what positive evidence do you have for evolution on two planets rather than one?

Are you really willing to propose close to 2 billion years of eukaryote ghost lineages?

Who do you suppose the seeder would be? Are you supposing aliens or gods?

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I didn’t know I was under an obligation to discuss cases brought up by others in an introduction thread in which I repeatedly said I wasn’t going to start an argument.

I have limited time available for these discussions (having a six-month-old tend to have that effect). I’m not trying to “get away” from anything, just trying to prioritize what I focus on.

Yes, I think the use of stop codons in the standard genetic code makes pretty good sense:

Statistical and biochemical studies of the standard genetic code (SGC) have found evidence that the impact of mistranslations is minimized in a way that erroneous codes are either synonymous or code for an amino acid with similar polarity as the originally coded amino acid. It could be quantified that the SGC is optimized to protect this specific chemical property as good as possible. In recent work, it has been speculated that the multilevel optimization of the genetic code stands in the wider context of overlapping codes. This work tries to follow the systematic approach on mistranslations and to extend those analyses to the general effect of frameshift mutations on the polarity conservation of amino acids. We generated one million random codes and compared their average polarity change over all triplets and the whole set of possible frameshift mutations. While the natural code-just as for the point mutations-appears to be competitively robust against frameshift mutations as well, we found that both optimizations appear to be independent of each other. For both, better codes can be found, but it becomes significantly more difficult to find candidates that optimize all of these features-just like the SGC does. We conclude that the SGC [standard genetic code] is not only very efficient in minimizing the consequences of mistranslations, but rather optimized in amino acid polarity conservation for all three effects of code alteration, namely translational errors, point and frameshift mutations. In other words, our result demonstrates that the SGC appears to be much more than just “one in a million”.
Geyer R. & Mamlouk A.M., 2018, “On the Efficiency of the Genetic Code after Frameshift Mutations”, PeerJ 6:e4825

I didn’t claim you were under any obligation, I just asked why.

Why?

Wouldn’t analogous start codons make just as much sense?

This is true for every single theory in science, and for most logically derived arguments. What if we consider the possibility that God plants fingerprints and DNA at crime scenes? Do we throw out forensic science because of this possibility? What if God creates clouds in a way that is indistinguishable from natural processes? What if God creates diseases in a way that is indistinguishable from bacteria and viruses causing disease?

I like the way George Romanes approaches the problem:

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Could you quote from the paper the parts you find relevant? For the record, I find the monopholy of eukaryotes and the bacterial origins of the mitochondria and chloroplast organelles pretty darn convincing. The discussion concerns whether the Tree of Life is polyphyletic at the bacteria-eukaryote split.

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I blogged about this paper here, if you want a simpler summary of the methods and conclusions:

The paper doesn’t discuss any divergences as deep as the prokaryote/eukaryote divide though, the deepest split is between Streptophyta and Chlorophyta.

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Thank you, that was my reading of the paper as well.