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

Design

(Timothy Horton) #85

No, it doesn’t. That claim is just more bog-standard anti-evolution rhetoric.


(Paul A Nelson) #86

Think about the original claim of UCD confirmation, based on the seeming universality of the code.

The code had to be universal, because it could not evolve (i.e., modify codon assignments while simultaneously maintaining cell viability), once the code got up and running. Once the code was established, it was frozen into place.

If one then says, “Well, that original story was mostly true,” one has jettisoned the very assertion one first made. Either she is pregnant, or she is not. There’s no “near” that makes any sense in the context of the frozen accident story.


(Dan Eastwood) #87

I didn’t get in on this last night, but I was going to say I’m pretty sure @pnelson has a card up his sleeve. :wink:


#95

UCD is the red herring. There doesn’t have to be universal common descent in order to determine if two species share a common ancestor. We can determine if chimps and humans share a common ancestor without needing to show that all life shares a common ancestor.

Let’s say for the moment that different genetic codes does indicate separate origins. How many trees do we now have? Maybe two or three? Let’s say that the trees are prokaryotes, archae, and eukaryotes. How does this affect our ability to determine if chimps and humans share a common ancestor? How does this affect our ability to determine if fish and humans share a common ancestor?


(S. Joshua Swamidass) #97

And I got every one of them correct! It is quite easy. They all have the same answer. I won’t spoil the test by saying it yet though.

Really @pnelson? That is a foundational concept in philosophy of science…

Can you tell us more about this summer camp? This student does not seem like an ID supporter. Do you include non-ID students?

I agree. As I’ve said before, UCD is a red herring.

I’m glad someone is making this point in my absence. Thanks @T_aquaticus.


Nelson's Test of Common Descent Comprehension
(S. Joshua Swamidass) #111

A post was merged into an existing topic: Side Comments on Nelson’s Signal + Noise


(S. Joshua Swamidass) #112

8 posts were merged into an existing topic: Side Comments on Nelson’s Signal + Noise


(John Mercer) #120

I agree, just as long as Paul acknowledges the RNA, which he has since done. Ribosomes in which rRNA was replaced by protein would be fascinating, and as you say would call a lot into question.


(Neil Rickert) #121

This is where I would disagree with that student.

I prefer to take UCD as a useful convention. But very little hinges on it.

I see science as primarily pragmatic. I do not see it as seeking absolute metaphysical truth (if there is such a thing).


(S. Joshua Swamidass) #122

One of the first and most helpful things I learned is:

  1. There are rules in biology.
  2. There are exceptions to every rule in biology.
  3. The exceptions are important.

It seems that some are falling prey to the errors that arise from forgetting #2 and #3. The exceptions do not disprove the rule, even if they are important exceptions.


(S. Joshua Swamidass) #123

This is not true for DNA @pnelson.


(Blogging Graduate Student) #124

I disagree. I think a a perfectly universal genetic code would be better evidence of UCD than a near-universal genetic code. Just because X is evidence for hypothesis Y, that doesn’t mean that not-X is evidence against hypothesis Y. Mutually exclusive observations can support a hypothesis to different degrees. The prediction would of course be modified by our understanding of the genetic code and how flexible it might be. If we know that the genetic code is in fact flexible then it might be more surprising if it was perfectly universal, given UCD and evolution.

UCD makes predictions in combination with other evidence, not in isolation. UCD + flexible genetic code makes different predictions to UCD + inflexible genetic code.

So phylogenetic bracketing is no better than hypotheses based on pure chance? Just because something is “logically congruent”, doesn’t mean it should be considered to be equally likely to all other possibilities. Sure, in that sense CD doesn’t make any absolute predictions about character state distributions, but it makes statistical predictions, as @swamidass said, especially in the case of nucleotide characters. This is the basis of phylogenetics. It’s certainly more informative than tossing a coin or rolling a die.


(Dan Eastwood) #125

8 posts were merged into an existing topic: Side Comments on Nelson’s Signal + Noise


(Paul A Nelson) #130

You can read a bit about the seminars here:

https://www.discovery.org/id/summer-seminars/

At least one of the regular readers of this site, whom I will not name (to protect his reputation), attended the seminar, and fits the description of “student” in my dialogue very closely. As Ann Gauger just explained at ENV, ID does not exclude UCD. If it did, I couldn’t have worked fruitfully alongside Mike Behe for 25 years.

ID is a minimal commitment to the detectability of design in nature. At the 2018 natural science seminar, we had agnostic and even atheistic students who nonetheless thought design detection was worth pursuing, for a variety of reasons (and said they would sort out the theological questions later).


(John Mercer) #134

Wow. So much about what people say–even to the point of doing an experiment in which the results are literally what people say–and virtually nothing about what we find when we actually study nature.

OK…

You are sorely mistaken. Who are you alleging made such a claim and when?

Don’t suppressor tRNAs modify codon assignments while simultaneously maintaining cell viability, by literally suppressing lethal mutations?

Wasn’t the amber suppressor discovered in 1960, and the hypothesis that suppressors could be mutations in the anticodon proposed (but not confirmed) in 1962?

Sorry, Paul, but we’ve known that bacteria can tolerate modifications to codon assignments that cause lots of proteins to “run on” for decades. Clearly there’s wiggle room.

This is yet another installment of “Learning biology is better done by learning biology instead of discussing what people actually or allegedly say.”


(Blogging Graduate Student) #135

I think it’s fair to say that the challenges to modifications of the genetic code were used to justify the expectation that the genetic code would be mostly universal from the beginning (early 60s). The authors at the time certainly seem to have left the door open for variations on the standard genetic code though. This was before any were found.

In which case, perhaps it’s a strawman to say “UCD predicted perfect universality of the genetic code”, and more accurate to say “UCD predicted near-perfect universality of the genetic code”, speaking in the context of the 1960s and beyond.

Given what we know today, I think it’s very plausible that all of the variations to the genetic code we know about really are just modifications to the standard code, not indicative of some kind of separate ancestry.
For example, all known variants occur in single-celled organisms (including mitochondria), and I think we could all agree that however modifications to the genetic code might happen, this process would be easier in single-celled organisms. If we had families of mammals walking around with different genetic codes, that would be somewhat harder to explain.
There are also clear biases towards certain variants in different clades, indicative that some of these specific modifications might be selectively advantageous or the result of some underlying susceptibility to change - both cases would increase the evolvability of the variants. If all the variants to the genetic code seemed to be completely random/arbitrary, they might be harder to evolve.


(Dan Eastwood) #136

To everyone: this thread has been moved to the Office Hours category, which changes the rules of participation. Sorry for the switch, but we can make this work.

Please direct questions to the Side Comments thread unless you have relevant expertise. Paul has been very good about addressing most questions so far, so I’m pretty sure he will get to the side comments too.


(S. Joshua Swamidass) #137

There seems to be a common equivocation between axiom and hypothesis in ID literature, especially that which has been directed at me about common descent.


(Blogging Graduate Student) #138

Yes, but since Crick already allowed for it, the discovery of reverse transcription should hardly be considered as a “modification to the axiom”, should it?

Not the kind of information described in the “axiom” through, so again I don’t think it would count as a modification. An addition, perhaps.


(John Mercer) #139

Since I never cited Crick, yes.

Again, I didn’t cite Crick as the source of the axiom. Infectivity clearly is information whether Crick thought of it or not.