https://www.unz.com/freed/greg-john-razib-and-me/#comment-3500403

Mitchell Porter says:
October 13, 2019 at 7:11 am GMT • 900 Words   ↑
@nokangaroos
I will use this comment to pose my own answers to Fred’s questions. I am not a biologist, but I have spent much time with biologists.

(1) “First, from what simpler coding system did the three-nucleotides-per-codon system arise by gradual and beneficial steps?”

A possible explanation: from an “RNA world” of mutually catalytic RNA sequences (Eigen’s “hypercycles”), which started out having only very weak effects on each other’s probability of replication, but which were selected (i.e. the RNA sequences changed) to make the catalytic relations (whether positive or negative) stronger and more targeted.

Now let me explain the explanation… One needs a primordial environment with two things: nucleotide bases that can assemble into RNA, and protocells – perhaps little more than droplets with a lipid membrane, similar to soap bubbles – containing different populations of RNA molecules.

Thanks to the complementarity of nucleotide bases, a single RNA strand can serve as the substrate on which complementary sequences assemble. RNA strands will also form 3d shapes according to self-interaction, and will attract or repel each other similarly. One RNA may hold another one in place, stabilizing it and making it more suitable as a substrate on which assembly can occur. The strength with which it is held in place, etc, may vary if the RNA sequence is changed even at a single point – this is the RNA analogue of the ‘single nucleotide polymorphisms’ catalogued at SNPedia.

For evolution to occur, the protocells need only ‘reproduce’, something which might initially be driven by natural turbulence, from storms or eruptions on the prebiotic earth. Anything that will break a soap-bubble-like protocell in two. So we have a population of protocells, each containing a different ‘genome’ of RNAs, some of which are ‘inherited’ by the descendant protocells.

Some genomes provide protocells with extra stability, other genomes are more robustly inherited… So I posit a situation of primordial natural selection, which acts upon the RNA genome, and in particular evolves it to be evolvable. This means that if a network of relationships among RNAs arises, which itself facilitates the processes of inheritance and differential selection, then that entire lineage would be favored. The existing system of codons is to be regarded as the product of any number of such network-level genomic evolutionary events.

This may sound vague and unbelievable to skeptics, but it should seem a lot more believable to anyone with knowledge of genetic algorithms.

(2) “male homosexuality seems evolutionarily mysterious”

I consider it a side effect of the way human sexuality works. As far as I can see, acquiring a sexual preference (and I don’t just mean male versus female, but e.g. a preference for Latinas over Nordics) is a matter of conditioning or imprinting, that occurs at crucial moments, such as first orgasms. It may be similar to the way that we acquire a language: we have a natural “language-shaped hole” in our minds, but the language that fills that hole, is the first language that we encounter.

I believe, therefore, that part of Homo sapiens’ “business model” when it comes to sexual selection, is for sexuality to be something that is partly determined by experience. It is set in a direction by the powerful conditioning provided by first sexual experiences, and is reinforced if the same kind of experiences are repeated. That this sometimes results in human individuals acquiring sexual preferences that remove them from the reproductive cycle, is a “sunk cost” of our sexual business model, which is already premised on some males being far more reproductively successful than others.

(3) “flagellum”

All I have to say about this, is that the flagellum seems to be related to the microtubule, a kind of structural element which has many other uses. Evolution at the cellular level consists in part of reusing structures (often beginning with an accidental duplication of the genes coding for the structure, owing to an irregularity in the process of cellular division), the multiple copies of which can then acquire divergent characteristics and potentially divergent functions. Flopping around, and moving in other ways, is something that molecules naturally do; like the RNA hypercycles that are distilled by selection into a tightly knit genetic code, the functionally specialized flagellum can arise from membrane molecules that originally just have a slight bias to their otherwise random thrashing around, but a bias which if adaptive, will be enhanced by selection.

(4) “the mechanism of abiogenesis”

I already talked about one version of this – the RNA world of protocells.

(5) “neutral or deleterious” traits that haven’t been discarded

Some will be like homosexuality, which according to the model I provided before, is a built-in side effect of our sexual model, which relies on a kind of learning (imprinting) which lets us find new sexual characteristics adaptive. Others will be defects or inefficiencies which evolution hasn’t managed to eliminate yet.

(6) Oh, I see RNA World mentioned here, but I don’t actually see an objection, except “no proof yet”. There may be no nanofossils from RNA World, but it is a fact that the specificity and strength with which one RNA acts upon another, does change as the RNA sequence changes.

A final comment. Like Anatoly Karlin, I don’t mind Fred Reed being an evolution skeptic. Maybe the Raelians are right, and we’re the work of design; maybe there’s some force like Sheldrake’s “morphic resonance” which, like Schopenhauer’s life force, just materializes new organisms in one go; maybe we’re living in Neo’s Matrix. But the world as revealed in natural science, and the facts of biology and geology and physics, are all certainly consistent with Darwin’s big idea.

• Agree: nokangaroos