Looking for sources on the information argument continued

I disagree with it. The table is not made of DNA nucleotides. It’s made of text. The ‘code’ itself isn’t made of DNA nucleotides either; its physical manifestation is a set of tRNA molecules. The triplets listed in the table are for RNA, not DNA. The DNA ‘information’ is not the ‘code’. As usual, your wording is sloppy and imprecise. You do not seem to understand the process well enough to make meaningful comments.

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That’s not obvious to me. From what I can gather Lynch 2003 does seem to suggest that among all mutations the vast majority are deleterious. I don’t see any reason to dispute that, it makes sense from the standpoint of evolutionary history. Many molecular functions have been evolving under selection for millions of not billions of years, and in such a situtation we would expect the pool of beneficial mutations to diminish over time, partly contributed by the phenomenon of diminishing returns epistasis. As the organism becomes better and better adapted, the distribution is pushed towards more and more deleterious. I made this animation in one of the Genetic Entropy threads we had a while ago:
Animated diminish

I don’t think such a statement supports Bill’s claims though. We’re not talking about the DFE for the genome as a whole. Some parts of the genome are highly optimized by even billions of years of natural selection, so beneficial mutations there would be expected to be both more rare and of smaller effect.

Instead the gene-birth paper deals only with a non-functional non-coding locus of 100 bp picked out of the entire genome.

In a nonfunctional locus the DFE can be effectively anything(most mutations can be beneficial, for example, if most fixed bases have higher metabolic costs), which is modeles in the paper by having the DFE fluctuate over time both in terms of the relative distribution of deleterious to beneficial and by the length of the tails in the distribution. As they say in the paper, even when the DFE is still skewed towards mostly deleterious mutations, such a DFE can still be conducive to gene-birth when the distribution is long-tailed, so that rare large-effect beneficial mutations can still take the locus across the genic threshold.

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[quote=“Michael_Okoko, post:17, topic:14233”]

DNA is not a code? F. Crick thought it was, though!

Hi Rum
Thanks for posting this.

Where it supports my claim is that design is a better explanation for optimization than mutation and natural selection given what we are observing are functional sequences.

How would you model how a functional sequence becomes optimized through mutation and natural selection? How could multicellular organisms sustain life without optimized sequences?

This definition of ID is entirely new to me — now ID is a science for investigating science! Is there no end of questions that ID cannot address? :wink:

However, I will agree in part. ID offers numerous examples that are beyond the limits of science.

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No. Lynch is saying that most de novo mutations which affect fitness are deleterious and are weeded out by purifying selection. From a paper written by Jensen and Lynch:

https://onlinelibrary.wiley.com/doi/10.1111/evo.13650

That’s what I am talking about. A huge portion of our genome is neutrally evolving but in the parts where genes and other functional elements are found, the DFE of new mutations moves toward being deleterious especially if they are highly optimized.

Technically, DNA is not a code. It is a polymer of deoxyribonucleotides connected via phosphodiester linkages. It is a chemical substance and comes in several forms. It can be single-stranded, double-stranded (the form Watson and Crickson found), triple- or quadruple-stranded. The double-stranded, helical form of DNA serves as a repository of genetic information in cells, not the G-quadruplexes or triplex DNA molecules.

Within double-stranded DNA, only certain regions encode useful information for making proteins or RNA while other regions have information for regulating the expression of other sequences. By “information” I mean the specific sequence of nucleotides found in some region of DNA.

The genetic code is simply the table that we draw to help show the mappings between a codon and an amino acid. Pulling up a quote from Francis Collins doesn’t change anything.

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As with everything there are multiple versions of ID. My baseline is Mike Behe’s process of design detection which is best described as a method. ID has a limited scope and that is the biggest issue with it.

All of which are useless.

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I understand this is your very strong opinion. I have stated it is a counter argument to hypothesis such as LUCA. Why do you argue against ID so passionately?

No, it does not support that statement in any way, either. We know of no principle that would mysteriously prevent the evolutionary origin of a functional sequence. That’s just some blind belief creationists have been taught to axiomatize. Nothing, literally nothing in all of of chemistry, physics, or biology, supports it.

You either do that with a DFE and population genetics, or some sort of biophysical model of function combined with the fitness-effects of mutations. For an example of the latter, since you like Lynch so much, here he is a co-author of a paper where they do exactly this just a few years ago:

By inheriting highly functional sequences from their single-celled ancestors. Nobody thinks or suggests multicellular life passed through a stage in which any significant fraction of the “sequences” upon which their life depended had not already been subject to a long history of optimimization by natural selection.

At any given moment of time, any organism would have an overwhelming majority of highly and older functional genes(not necessarily totally optimal, though), and then a tiny minority of relatively and more recently evolved genes still undergoing a considerable degree of positive selection (as opposed to the mostly purifying selection operating on older and better optimized genes). These latter more recent genes would in part consist of diverging duplicates(or recombinations and/or fusions of fragments) of older genes, and de novo genes having evolved from non-coding DNA.

That’s basically how to understand the relevance of gene birth in the history of life.

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I have asked you to provide counterevidence, but you haven’t because there isn’t any. My thoughts aren’t opinion, but pure fact. ID is useless.

I am sorry to disappoint you, but a useless idea like ID does not even come close to competing with the well-supported hypothesis of a LUCA.

Its your indignant refusal to learn that annoys me. You are recalcitrant to evidence that nullifies your claim and refuse to accept corrections of your terrible misunderstanding of really basic concepts. If you can’t get the basics right, there is no way you will understand the more complicated subjects which you want to dabble into.

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Thanks for citing the Lynch paper.

What you need is a model that shows how this works, can be tested biologically and does not have waiting time issues.

The problem here is that highly optimized systems required for sustaining life in multicellular organisms do not exist in single celled organisms. Highly optimized systems in singled celled eukaryotes required to sustain life do not exist in singled celled prokaryotes.

Summarise this design-detection “method”. Provide evidence of its validation (in particular the probability of it incorrectly accepting or rejecting design).

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No, I don’t need a model to “show how this works” to know that you have no reason for thinking there is there is something mysteriously preventing the evolutionary origin of a functional sequence.

But the paper with the population genetic model of gene birth does of course show exactly that.

Systems? What happened to sequences?

They don’t exist there in identical forms, but they do have very similar and already highly optimzed precursors there. Your “problem” is imaginary.

Sure they do, otherwise prokaryotes would not be alive.

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Because we can see through reason and evidence that it is clearly wrong, and that you yourself have been so thoroughly misled by it. Helping to stifle the propagation of bad ideas not supported by any good evidence is definitely a passion of ours, so that’s why we argue against the kind of ID you like. It’s a textbook example of a bad idea not supported by any good evidence.

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There are clear obstacles that you need to assume are not there. How do you validate your assumptions are right? A obvious obstacle is the observation of highly optimized sequences and how they originated.

Not always. The problem is based on real evidence and not imagined evidence.

I am not sure what point you are trying to make.

There are no clear obstacles at all, you need to make them up on your own.

You’re the one with an assumption(that there’s some sort of obstacle) you can’t “validate”. You just believe it’s there without any supporting evidence.

There is no reason to think that’s an obstacle. You’re just asserting that it is.

What evidence is that?

I’m not sure you know what point you are trying to make either.

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More than an assertion Rum its the observation of long sequences. You are dealing with almost infinite mathematical space. How do you mutate through this and find complex function (bacterial flagellum) at all let alone within reasonable waiting times?

If you did not have obstacles we would have a mathematical model that explains how functional sequences arise from non function that could be tested across all biology.

I love how this suddenly turned into a discussion about the origin of multicellularity, or the origin of eukaryotes from prokaryotes.

I thought we were arguing about whether there are good models of de novo gene birth. Which turned into a discussion about the origin of function in a sequence. Which somehow morphed into a discussion of the process of evolutionary optimization in a functional sequence.

No no, those goalposts evaporated and new ones have materialized elsewhere. Now Bill wants us to couple those questions to the origin of eukaryotes, and multicellularity.

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When Crick and @colewd and nearly all biologists say that DNA is a code, they mean that the DNA forming the genes of living beings contain a code made of codons. It is quite pedantic to dispute a term (DNA is a code) representing a useful shorthand that is intended to refer to some quite complex notion.

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