The Genetic Code and Universal Common Ancestry

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In my introduction thread the common genetic code was brought up as evidence of the common ancestry of bacteria and eukaryotes (along with the ribosome and the large numbers of proteins and RNAs in common between the two groups). The ribosome is already being discussed in the thread, but I decided to start a new thread for discussing the genetic code.

The genetic code is almost universal; a number of variants have been found, all of which are derived from the standard genetic code (Osawa et al., 1992; Knight, Freeland, & Landweber, 2001).

The near-universality of the genetic code has been cited as evidence for universal common ancestry (Crick, 1968; Hinegardner & Engelberg, 1963). According to geneticist Theodosius Dobzhansky, these biochemical universals are “the most impressive” evidence for the interrelationship of all life (1973, p. 128).

And indeed, from the non-teleological perspective this makes sense: If undirected abiogenesis had occurred several times, it would be an amazing coincidence if in every case the resulting organisms had struck upon the same genetic code. Therefore, universal common ancestry is the best explanation.

This changes the moment we throw teleology into the mix. Rather than having to choose between common descent and convergence, the investigator must now also consider the possibility of common design.

Suppose that the first life on Earth consisted of a diverse population of designed cells. Why would designers employ the same genetic code instead of giving each cell its own code?

Before answering this question, let us ask a counter-question: Why not? What would the point be, from an engineering perspective, of reinventing the wheel? Making multiple codes is extra work and increases the risk of mistakes when genes have to be designed in different languages.

Not only is there no reason for designers to adopt multiple codes, there is good reason to use the same code. If different cell types used different codes, they would be unable to tap into the power of horisontal gene transfer (HGT).

HGT plays an essential role in bacterial evolution, where genetic models indicate that substantial HGT is required for the survival of bacterial populations (Takeuchi, Kaneko, & Koonin, 2014). Though less common in eukaryotes, HGT is not restricted to bacteria. For example, a study found that ferns adapted to shade by horisontal transfer of a gene from the moss-like hornworts from which they diverged 400 million years ago (Li et al., 2014).

In other words, categorizing the standard genetic code as an example of common design is not an ad hoc rationalization; rather, there is a good engineering reason for reusing the code.

References

Crick F.H.C., 1968, “The Origin of the Genetic Code”, Journal of Molecular Biology 38(3):367-379

Dobzhansky T., 1973, “Nothing in Biology Makes Sense except in the Light of Evolution”, The American Biology Teacher 35(3):125-129

Hinegardner R.T. & Engelberg J., 1963, “Rationale for a Universal Genetic Code”, Science 142(3595):1083-1085

Knight R.D., Freeland S.J., & Landweber L.F., 2001, “Rewiring the Keyboard: Evolvability of the Genetic Code”, Nature Reviews Genetics 2(1):49-58

Li F. et al., 2014, “Horizontal Transfer of an Adaptive Chimeric Photoreceptor from Bryophytes to Ferns”, Proceedings of the National Academy of Sciences 111(18): 6672-6677

Osawa S., Jukes T.H., Watanabe K., & Muto A., 1992, “Recent Evidence for Evolution of the Genetic Code”, Microbiological Reviews 56(1):229-264

Takeuchi N., Kaneko K., Koonin E.V., 2014, “Horizontal Gene Transfer Can Rescue Prokaryotes from Muller’s Ratchet: Benefit of DNA from Dead Cells and Population Subdivision”, G3 (Bethesda) 4(2):325-339

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  1. You have given us no reason to think this designing intelligence has even remotely the Psychology as human designers. So all this talk about what designers should and shouldn’t do is irrelevant.

  2. The only plausible option for this designing intelligience is God. An all powerful, all knowing being. So this talk of more work or making mistakes is odd.

  3. Even if common design is a possible explanation and is compatible with a universal code it doesn’t follow that the genetic code isn’t evidence for UCA. UCA predicts it. Design does not. And if you define design as common design then you’re just begging the question. Common Design does not work. When I see people resort to that I know common ancestry has won

Edit: then there are a lot of things common design can’t explain

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If the universality of the genetic code was restricted only and entirely to a shared system of mapping between amino acids and nucleic acids, and if there was no significant levels of hierarchical structure converging on a common ancestral sequence in the components that carry out translation of the code, your argument would have some force.

To elaborate a bit, the shared aspects of the genetic code go beyond merely the mapping of codon triplets to amino acids. It is also the fact that the molecular components that carry out translation are clearly derived from common ancestor molecules that speaks to the genetic code being evidence for common ancestor.
What I mean is that the kind of evidence that testifies to common descent is when ancestral nodes in a phylogenetic tree of a shared similar translation system component increasingly converge on a common sequence as we go further back in time*. You have no reason to expect such a result on common design, except if you mean to say that the “common design” was in fact completely identical if we go far enough back in time, in which case, how is this different from common descent?

If the bacterial and archaeal clades were independently created with an exactly identical translation system and genetic code, down to every single DNA basepair encoding all the shared translation system components, and they each subsequently evolved and diverged from this identical ancestral system, how is this at this present time observationally distinguishable from them having actually shared ancestry once? In such a situation you would seem to have postulated a hypothesis that is indistinguishable from common descent, motivated by nothing else than making a design-hypothesis compatible with the evidence we have.

With respect to your HGT argument, in order to be able to exchange translatable sequences, the different organisms would only need a shared mapping, there wouldn’t need to be any shared components carrying out the translation. It is entirely possible that a significantly different system could implement and translate the code-mapping with which we are familiar.

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I assume, as a working hypothesis, that the designers are of human-like intelligence. Now, I have pointed to engineering reasons for reusing the genetic code - engineering reasons that will face any designer attempting to design life on Earth.

Imagine that NASA’s Pioneer 10 spacecraft was picked up by an extraterrestrial civilization. They might not understand our purpose in sending a drawing of a naked man and woman into space, but they would be able to understand the engineering principles behind Pioneer 10 itself. If one of the extraterrestrial scientists said something to the effect of “Gee, I don’t know why this electricity-producing generator is connected with this electricity-consuming instrument, since we know nothing about the psychology of these unknown designers,” his colleagues would probably look at him funny with their black, almond-shaped eyes.

Please explain your reasoning for arriving at this conclusion.

Please lay out the logic by which universal common ancestry predicts the observed state of affairs. Are any auxiliary hypotheses required for universal common ancestry to predict the observed state of affairs?

More tomorrow, including a reply to @Rumraket.

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I think this is questionable. It is possible that some potential codes and translation systems would be better suited to certain environments, or better suited to facilitating certain adaptive transitions.

Perhaps the genetic code we have is among the set of the best “compromise” codes, having a good overall balance between facilitating adaptation, while minimizing the effects of mutations and mistranslation in a broad category of environments. But there could be codes that are superior in more restrictive conditions.

Some species on the planet seem to have specialized for living near hydrothermal vents even at the earliest stages in the history of life, and to have never abandoned this niche. Is the current genetic code the best option for them, or just the one they got stuck with?

I can certainly imagine reasons for why a multitude of codes could be a superior alternative to the current situation.

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And that’s a huge totally unwarranted assumption

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Different scenario and you seem to be misunderstanding my point. Tell me, what’s my painting style? If I were to paint you something what would you expect to see?

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And I can think of a ton of ways to have different codes and still have HGT in bacteria.

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It’s really quite simple. If UCA is true, then we share an ancestor with a common genetic code. If this code is very hard to alter during the course of evolution (which seems to be the case for many theoretical reasons, not just the observation that there are few exceptions to the universal code), then it follows that most organisms should share the same code. Which is what we see.

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I’m puzzled why he asked me this since he pretty much answered his own question in his OP

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Depends on who the designer is, doesn’t it? If the designer is God, there’s no such thing as extra work; he’s omnipotent. And he doesn’t make mistakes, or so I’m told. What designer are you hypothesizing? Aliens? You need to be clear on your hypothesis, because the expectations differ.

There are also good reasons for not re-using the code: it would prevent attack by viruses. You can explain either situation from an engineering perspective.

But your main point is correct: a universal genetic code is an argument for a single origin of life, not for common descent vs. creation, and it’s the former we were discussing. The evidence for common descent is elsewhere, notably the nested hierarchy. But go on and flesh out your creation scenario. How many separate creation events? What were they? All at the same time or staggered? Ending billions of years ago or continuing?

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Are you a Christian? I am. This one is a hard one to swallow. Do you think God has human like intelligence.

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He said he was agnostic. One presumes he isn’t a Christian. But what is he? That’s the question.

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Hi @Krauze ,

Welcome to Peaceful Science. I have a couple of points (or questions) regarding your proposal about genetic codes. First, you suppose that the designer in your scenario has a human-like intelligence. Given this and the complex nature of the product, I would argue that your model actually predicts, not a single designer, but multiple designers. This is because complicated projects like this are almost always collaborations.

Second, while a single genetic code may make some design sense, I would argue that multiple codes make more teleological sense. This is because I believe one can take advantage of multiple codes to design systems that adapt more rapidly, and economically, to changing environments or developmental cues. For example, suppose that the cell has a fairly common set of mRNAs (rather than the kludgy and varying collection we actually see), perhaps many of which code for more than one protein, depending on the code. It would be fairly easy (and, I emphasize, economical) to switch expression programs by uncharging one set of tRNAs and charging a different set, with the different sets decoding different genetic codes. In this way, it would be possible to connect environment with a small set of tRNA charging enzymes, each of which is specific for a different set of tRNAs. Additional variations of this theme are possible, and collectively they would constitute an elegant and superior alternative to the messy system we see in living cells.

Then there is the fact that, with multiple designers, the possibility of multiple codes makes more sense.

Food for thought, maybe. And, again, welcome.

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Who cares? Why not just take him at his word, and process what he is saying?

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I think your point is wrong here. Often people think about Engineers designing single gadgets.

But the truth is that design works in an eco system.

If an eco system is being designed with organisms interacting with each other, a common bio chemistry becomes essential.

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There are thousands upon thousands of different ecosystems in the world. And many animals in these ecosystems will never interact with others from another ecosystem. They could be on opposite sides of the world. You may point may be valid for an individual ecosystem but there are tons of different ecosystems. So a common biochemistry across the biosphere isn’t essential

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In fact, if the designer was anything like a scientist, they may want to make multiple genetic codes and see how they develop and compare.

I can’t see how a common genetic code would say anything about a designer one way or another. I could see how multiple genetic codes would be difficult for common descent, but in our case (common genetic code), I don’t see how it indicates either way as it’s consistent with both common descent and common designer.

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Not if the objective is to start with single organisms and form multicellular organisms.

The ecosystem I am talking about is the whole earth.

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So common ancestry?