Paul Nelson: Testing for Common Descent (Signal + Noise?)

Design

(Blogging Graduate Student) #140

So what is your source for the “axiom”, if not Crick and the central dogma?


(Paul A Nelson) #141

(Paul A Nelson) #142

I agree, although current theories of codon reassignment are rather messy, and experimental modifications of the code always involve the investigators “helping” the cells across the codon meaning shift (e.g., by supplying the wild-type tRNA on a plasmid during the transition).

What I’m trying to elicit is the theory-based rationale for saying “that could have evolved from LUCA” (majority opinion about extant variant codes) versus “that couldn’t have evolved from LUCA” (counterfactual variant codes that are sufficiently different to indicate separate ancestry). I worry that the threshold is (a) entirely conventional, and follows the data around, rather than being (b) a bona fide prediction grounded in theory.

If the former, (a), UCD isn’t really telling us anything about the world.


(John Mercer) #143

Probably Watson’s version. Does one really need a specific source to cite dogma?

As for the axiom that a prion couldn’t possibly catalyze the folding of its normal counterpart to impart infectivity information, I was training as a virologist when Prusiner first offered the hypothesis. Everyone around me, except for one student considering doing a postdoc with him, thought Prusiner was wrong.

Let’s not lose sight of the subject here: Paul Nelson is arguing that we can’t overcome axioms or dogma, when the reality is that we do so very often. Our resistance is easily broken down by empirical results, not rhetoric.


(John Mercer) #144

Paul, why do you think I included “when” in my challenge?

In what way does something from 1963 contradict what I pointed out?

In 1963, we only knew of the nonsense suppression but not that its mechanism was a partial codon reassignment. Some people said such a mechanism was possible, others said it wasn’t. So what?

Once we had the mechanism of nonsense suppression in hand, which IIRC started to become clear in 1971, it was easy to accept missense codon reassignments.

I disagree vehemently. Here’s a good summary:


Comp Biochem Physiol B. 1993 Nov;106(3):489-94.
Evolutionary changes in the genetic code.
Jukes TH, Osawa S

  1. The genetic code was thought to be identical (“universal”) in all biological systems until 1981, when it was discovered that the coding system in mammalian mitochondria differed from the universal code in the use of codons AUA, UGA, AGA and AGG.

  2. Many other differences have since been discovered, some in mitochondria of various phyla, others in bacteria, ciliated protozoa, algae and yeasts.

  3. The original thesis that the code was universal and “frozen” depended on the precept that any mutational change in the code would be lethal, because it would produce widespread alterations in the amino acid sequences of proteins. Such changes would destroy protein function, and hence would be intolerable.

  4. The objection was “by-passed” by nature. It is possible for a codon to disappear from mRNA molecules, often as a result of directional mutation pressure in DNA: thus all UGA stop codons can be replaced by UAA.

  5. The missing UGA codon can then reappear when some UGG tryptophan codons mutate to UGA. The new UGA codons will be translated as tryptophan, as is the case in non-plant mitochondria and Mycoplasma. Therefore, no changes have taken place in the amino acid sequences of proteins.

  6. Variations of this procedure have occurred, affecting various codons, and discoveries are still being made. The findings illustrate the evolutionary interplay between tRNA, release factors and codon-anticodon pairing.


What aspect of this is so unacceptably messy to you that it renders it impossible or implausible? Keep in mind that there are multiple copies of tRNA genes, so there is ample opportunity for transitional partial reassignments.


(Blogging Graduate Student) #145

Given that there are evidently different “versions”, I think so.

Right, I just don’t think it modifies the central dogma. Maybe I’m confusing your claim that “DNA->RNA->protein->catalysis” was an “axiom” in the 1970s with the central dogma. Rather than saying “the central dogma was modified”, are you making the more obvious claim that “what people thought was the case in the 1970s was modified”? If the latter, then I certainly agree.


(Blogging Graduate Student) #146

I don’t see how it’s a problem that the predictions that flow from UCD depend on other data. Given the angle of a cannon you can’t predict the trajectory of a cannonball - you also have to know the velocity that the cannonball will be shot at. The angle of the cannon tells you what trajectory to expect given the velocity of the cannonball. In the same sort of way, in this example, UCD tells you what pattern of genetic code variants that could exist given the evolvability of genetic code variants.


(John Mercer) #147

Yes, what people thought was the case was the dogma. I thought it was an obvious claim all along. :smiley:


(John Mercer) #148

This is an excellent analogy.

Paul’s concern:

strikes me as entirely inconsistent with how we do science.

It’s not that the threshold “follows the data around,” it is set based on the data we have at the time. That’s why thinking that the code must be invariant in 1963 is not surprising, but once we learn the mechanism of nonsense suppression 10 years later, we easily see a very plausible path to reassigning codons, so it’s no longer the threshold we thought it was in 1963.

This is pointed out in the abstract I quoted above:
The original thesis that the code was universal and “frozen” depended on the precept that any mutational change in the code would be lethal…

Nonsense suppressors are changes in the code. They are not lethal. Therefore the precept (aka dogma or axiom) was wrong.


(Paul A Nelson) #149

Which is another way of saying the UCD/~UCD threshold follows the data around.

I don’t have time today to dig into the details of the Jukes-Osawa scenario, but it’s missing a few steps. For instance, if one consider the variant code present in Tetrahymena (single stop codon UGA, UAA and UAG assigned to glutamine), one finds this:

“The model outlined by Jukes and Osawa…would lead to a potentially awkward intermediate stage where some genes end in [UAA and UAG], but neither [UAA or UAG] recognizing tRNAs nor…release factors exist in the cell. The outcome of this state in eukaryotes is not known, but in eubacteria the cognate tRNA of the penultimate codon remains covalently attached to the carboxyl-terminus of the protein.”

From here (P.J. Keeling exchange with Jukes & Osawa) https://link.springer.com/article/10.1007/PL00022753

“…during the appearance of code deviation, ancient termination codons are acquiring a new sense and new UAA and UAG codons are accumulating in the reading frames. This will generate ambiguity in the length of termination products.”

From here: https://www.ncbi.nlm.nih.gov/pubmed/?term=cohen+adoutte+1995

Of course there’s much more recent work on code evolution that we could dig into, but that’s really a separate thread. The scenarios are messy and assumption-laden. That’s OK – science is messy and assumption-laden. One’s opinion of the plausibility of the existing code evolution stories will depend heavily on the priors one holds. Maybe after I finish with parts 2 and 3 of my reply in this thread, we could start a new discussion of genetic code evolution. Gotta run now, sorry.


(George) #150

@T_aquaticus

THIS is perfectly stated!


(George) #151

@pnelson

I find your amalgamation of positions to be inexplicably confusing.

Is there a thread or posting i can read to understand exactly what your position on Evolution-with-Design is?

Or do you completely reject Evolution-with-Design… and you endorse a long series od special creations?

Sign me ‘Perplexed’


(Paul A Nelson) #152

That’s understandable. I’m confused too. :wink:

A professor (and close friend) once told me, “It’s hard to read your chapter drafts, Paul, because I can’t put you in any familiar position.” I said, well, that’s rough for you, maybe – but it you cannot slot me into one of your customary cubbyholes, then you’ll have to think when you read my work, and not just react reflexively to what you imagine I should be saying.

The origins debate – and this is certainly reflected at this site, despite its many positive features – suffers from a lamentable tendency to dump people into shopworn boxes. “Oh, I don’t have to take him seriously: he’s just another atheistic evolutionist with all the usual prejudices,” or “That guy is obviously a YEC idiot, nothing to see here, move on,” et cetera, ad infinitum.

Valuable insights are lost when we dump our conversation partners into boxes.


(Timothy Horton) #153

They’re also lost when those partners refuse to answer questions about the vagueness in their position, ignore difficult question raised on their claims and instead just repeat those claims.


(Arthur Hunt) #154

Consider, just to turn this particular point on its head, the possibility that termination codons came “later”. Nonstop decay in bacteria may provide an interesting insight into the RNA World that most would never think of.

Not that it’s necessarily correct, but the idea is useful to think of, because it frees us from preconceived notions and constraints.


(George) #155

@pnelson

After 50 times responding to the exact same viewpoint… its easy to build relatively reliable categories.

Based on your comments and the comments of your volunteer editor, it sounds like you confess that you have plenty of sorting to do.

So it really isnt surprising that you have a complaint about being “boxed into” a category. It wkuld seem even your subconscious mind resists categories.

But I think @swamidass is awfully good at handling categories well-established in 2000 years of Christian history.

And since PeacefulScience.Org was founded on its ability to create at least two brand new category “boxes”, (including the “box” of Adam/Eve’s Special Creation with Evolution) I dont think your criticism of this blag makes much sense, let alone being unfair.


(The Honest Skeptic) #156

George, I think that you are reading too much into this. Where an individual is currently on the continuum of understanding about one aspect or another of this debate is often fluid. For you, clearly, it is not. I’ve been reading your posts for months, and you are clearly decided on what happened and how, but many others of us are not. There is plenty of room for new categories, and more will come. Look at the number of ways presented to read Genesis, or the number of ways Adam can be understood. Who would have thought of some of these positions even just decades ago?


(George) #157

@Michael_Callen

The ability to create new and valid boxes is a trademark of @swamidass’ work.

When someone wants to “con” his audience by inventing a box that is logically impossible… this is the place to test it!


(The Honest Skeptic) #158

As you are aware, though, the crux of the matter for so many of these disagreements are that they are theoretical, and not proven in the lab. If we cannot discuss matters that are not concrete, then we, by definition, limit the conversations here. We can’t encourage conversations by discouraging them. That’s also illogical.


(S. Joshua Swamidass) #159

2 posts were split to a new topic: Nelson’s Test of Common Descent Comprehension