Stern Cardinale: Response to Price, Carter, and Sanford on Genetic Entropy

[RonSewell (RonS)]

@PDPrice

@CrisprCAS9

To what extent is the genome destroyed by a mutation that increases the femur length by 0.01%? If you can’t answer this, genetic entropy is necessarily false.

Can’t be answered. You could ask the same about any one typo in isolation, looking at a whole series of progressively added typos in a computer program. Nonetheless, if you add enough typos to a computer program, eventually it will be completely destroyed. The problem is, fundamentally, that engineering is hard. You don’t get it by randomly throwing changes together.

What puerile nonsense. This from someone who lectures published text authors that they are oversimplifying. A variation in regulation is nothing like a divide by zero crash or overflow or anything to do with a Turing machine.

[thoughtful (Valerie (non-scientist))]

@chris_doesdna2018

@davecarlson

In this case, the term “substitution” is not referring, I think, to any particular type of mutation but to the process of substitution in which a mutation rises from some initial frequency to the point where it is “fixed” (i.e., has a frequency of 1.0 or thereabouts) in the population.

Perhaps! I would simply to refer to that process as fixation rather than substitution, personally. But who knows, populations of haploid lights are strange creatures.

Could we have @Joe_Felsenstein explain his analogy and what his terms meant? Or even if he can say he agrees with you that would be helpful. I would actually like to know how he views this, and I’d like to learn something.

The constant discussion of what terms mean in biology and when they’re used is frustrating.

[PDPrice (Paul Price)]

@swamidass

Was Sanford in agreement with the claim that @Joe_Felsenstein is not an expert in population genetics?

The quote you’re referring to was from Sanford himself. So yes, he agrees with himself. But he never said that Dr Felsenstein was not an expert in “population genetics”.

Yet, they are not experts on the specific topic at hand. They have not spent the last twenty years studying the problem of mutation accumulation.

My sense of Sanford’s meaning here is that these particular scientists being addressed are not known to be experts in the specific niche topic of mutation accumulation, in the way we would think of names such as Kondrashov, Keightley, Lynch, and Eyre-Walker. I don’t believe he meant it as an insult, just a clarifying remark about the nature of their comments.

[Joe_Felsenstein]

I did get myself in trouble the way I used “substitution”. I meant it in the sense of the mutation event followed by the gene frequency changes that get it to fixation. That works in a smallish population. In a bigger one, it may not get all the way to fixation, so things are more complicated.

[dsterncardinale]

@PDPrice

My sense of Sanford’s meaning here is that these particular scientists being addressed are not known to be experts in the specific niche topic of mutation accumulation, in the way we would think of names such as Kondrashov, Keightley, Lynch, and Eyre-Walker. I don’t believe he meant it as an insult, just a clarifying remark about the nature of their comments.

Literally half my thesis. One chapter was even on inducing error catastrophe in ssDNA bacteriophage populations. Take 5 minutes to google me? Apparently not. Easier to just assume I don’t know what I’m talking about, I guess.

[Timothy_Horton]

@PDPrice

My sense of Sanford’s meaning here is that these particular scientists being addressed are not known to be experts in the specific niche topic of mutation accumulation, in the way we would think of names such as Kondrashov, Keightley, Lynch, and Eyre-Walker.

Have you and Carter spent the last the last twenty years studying the problem of mutation accumulation? What research has Sanford done or published on the topic in the last twenty years?

[RonSewell (RonS)]

@PDPrice

My sense of Sanford’s meaning here is that these particular scientists being addressed are not known to be experts in the specific niche topic of mutation accumulation, in the way we would think of names such as Kondrashov, Keightley, Lynch, and Eyre-Walker.

How, exactly, does one become an authority on population genetics and variation without consideration of mutation accumulation?

[Mercer (John Mercer)]

@PDPrice

Do any of the other scientists that we engaged with (e.g. @swamidass , @glipsnort , @Joe_Felsenstein , @Mercer) want to sign their names in agreement with what Stern Cardinale has written here?

Absolutely. I’m also well aware that mutations are produced by chemical reactions, most often transitions caused by keto-enol tautomerizations. Are those not chemical reactions in your expert opinion?

Why would you describe me as a molecular biologist before trying to rebut the points I made about virology, given that my graduate work was in virology?

[PDPrice (Paul Price)]

@Mercer

Are those not chemical reactions in your expert opinion?

Can you remind me what the context of this question is? Where am I supposed to have said something that you’re responding to with this?

@Mercer

Why would you describe me as a molecular biologist before trying to rebut the points I made about virology, given that my graduate work was in virology?

I believe I just defaulted to the description you’ve got here. I don’t know your full history or anything.

[Mercer (John Mercer)]

@PDPrice

Of course it is. We were talking about the speculations of scientists, not nature itself.

We’re also talking about nature itself, in the form of the frequent misrepresentations of data that are true without any interpretation or speculation. The idea that we are interpreting the same data differently is absurd, because you are ignoring most of the data.

@PDPrice

@Mercer

Why would you describe me as a molecular biologist before trying to rebut the points I made about virology, given that my graduate work was in virology?

I believe I just defaulted to the description you’ve got here. I don’t know your full history or anything.

So why are you making grandiose claims about expertise when you can’t be bothered to do a simple PubMed search? And we already clearly established that I was a virologist in a previous conversation. Remember when you tried to claim that none of the data mattered to your claim that H1N1 is extinct, and you were correct because a CDC chart had a little red arrow that you had misinterpreted?

@PDPrice

My sense of Sanford’s meaning here is that these particular scientists being addressed are not known to be experts in the specific niche topic of mutation accumulation…

But Sanford isn’t an expert either. He literally doesn’t know that virologists clone viral isolates. In case you don’t get it, that has a lot to do with mutation accumulation. John Holland, whose paper Sanford cites and misunderstands, was a mentor of mine.

Have you figured out what the “H” and “N” mean in influenza subtype names yet?

Can you explain why Carter’s having done the alignment means that he would therefore be capable of distinguishing changes caused by point mutations from those caused by reassortments? That makes absolutely no sense.

[Roy (34-year veteran)]

@PDPrice

Putting the cart before the horse? “DNA can’t be functional, because otherwise we would all be dead by now from mutational load”. Or… deep time is false. There’s the hidden unquestioned premise.

It’s not hidden, and it’s not unquestioned, it’s simply that the evidence for deep time is overwhelming and includes a lot of data that is completely independent of genetics.

So if GE really does say we’d all be dead by now, then the argument is very simple:

1. If GE is true, then deep time is false.
2. Deep time is true.
3. Therefore GE is false.

QED.

[PDPrice (Paul Price)]

@Mercer

Remember when you tried to claim that none of the data mattered to your claim that H1N1 is extinct, and you were correct because a CDC chart had a little red arrow that you had misinterpreted?

Still repeating blatantly false claims, I see. This really is not worth the time. If you guys want to make a joint response article that deals openly with all the points we made, feel free. I’m done spending time hashing it out here in this forum. I don’t see any further use.

[Roy (34-year veteran)]

@PDPrice

…because you’re imputing your “red and green” analogy to Sanford. But he would never agree with it. Because the genome is information, and encoded information is context-specific. We explained this in our joint article, and you’ve ignored it. Now I’m being forced to rehash. See: HOUSEHOLD v. HOUTNHELDE explanation.

All that means is that the genome is more interlinked and can’t be represented by a set of swtiches directly connected to red/green bulbs. But it can be represented by a set of switches connected to red/green bulbs where each bulb is controlled by a combination of switches. This in no way affects the reasoning the analogy is used to represent, so the point illustrated by the analogy remains valid.

As for your letters analogy, if the initial genome is HOUSEHOLD, then H->M giving MOUSEHOLD and D->E giving HOUSEHOLE would both be detrimental on their own, but having either one of them present makes the other beneficial since together they lead to the alternative adaptive peak MOUSEHOLE. Either mutation will change the ratio of possible detrimental vs beneficial mutations, contrary to the assumptions of GE.

(And comments about MOUSEHOLE being worse than HOUSEHOLD will be ignored due to being based on the assumption that initial genomes were perfect. MOUSEHOLE is just as valid a word as HOUSEHOLD).

[Roy (34-year veteran)]

@PDPrice

Come on now. You’re a genetics professional. I would expect you to respect your own field too much to allow other fields to dictate what “must be the case”. If genetics says the astronomers and geologists are wrong in proclaiming deep time, then let them be wrong. Don’t assume they’re right and then refuse to look for function in the genome on that account.

He’s doing no such thing. If anything, he’s seeing that genetic entropy contradicts astronomy and geology, comparing their respective evidential support, and noting (as we all are) that astronomy and geology are well -supported while genetic entropy is a hodge-podge of fallacies, unjustified assumptions, misunderstandings and falsehoods.

[Michael_Okoko]

@PDPrice

This really is not worth the time.

It has certainly been worth my time.

@PDPrice

If you guys want to make a joint response article that deals openly with all the points we made, feel free.

What’s the point if those points have been thoroughly addressed here and not stood up to scrutiny.

@PDPrice

I’m done spending time hashing it out here in this forum. I don’t see any further use.

I agree. There is no point in rehashing already debunked arguments.

[Roy (34-year veteran)]

@PDPrice

Nonetheless, if you add enough typos to a computer program, eventually it will be completely destroyed. The problem is, fundamentally, that engineering is hard. You don’t get it by randomly throwing changes together.

That completely ignores both reproduction and selection. If you’re going to model evolution as changes to a single organism it’s no wonder you reach faulty conclusions.

And that one is faulty. Programs such as Tierra show that you keep adding typoes to computer programs indefinitely without completely destroying it, and that you can get engineering by randomly throwing changes together.

The human body is vastly more complex and functional than the most complex computer humanity has ever devised.

Paging Edmund Blackadder…

[John_Harshman]

@PDPrice

One field should never take for granted that the speculations of another field must be accurate

Speculation? You keep using that word. I do not think it means what you think it means.

[Rumraket (Mikkel R.)]

@PDPrice

Same old mistake that was directly addressed in the article. The difference in relative fitness is too small to be selectable.

Pure assertion, and empirically demonstrably false. Organisms generally have demonstrably very real fitness-differences between them.

@PDPrice

@Rumraket

@PDPrice

But building up new function from scratch is much harder, not easier than making improvements on existing function.

I’m not convinced this is true, but since already destroyed functions can’t be destroyed even more, further changes to them have become neutral, so don’t contribute to GE, and hence change simply accumulates until functions are gained.

This is your fundamental, fatal problem. You have to be convinced of the obvious.

I’m sorry but you still can’t just declare things to be true by merely repeating the same assertion. And in any case we’re talking about fitness here. Some times reductions in function come with gains in fitness, or the other way around. Your simplistic analogies and metaphors simply won’t do.

This is why I want to talk about real biochemistry and molecular biology, and you totally neglect to actually speak about the examples I give, such as the activity of enzymes, or the relationship between metabolic gains and fitness.

When the enzyme encoded by a gene no longer accelerates a reaction, the locus really does just drift neutrally. Eventually mutations will produce a new function. Random DNA is usually only a few mutations away from gaining a promoter function, for example:

Random sequences rapidly evolve into de novo promoters

And expressed random DNA can frequently exhibit positive fitness effects:

De novo emergence of adaptive membrane proteins from thymine-rich genomic...

@PDPrice

The human body is vastly more complex and functional than the most complex computer humanity has ever devised. So fundamentally, yes

Bzzzt, stop. You can’t begin the second sentence with “so”, because nothing you go on to state follows from the previous sentence. How complex an organism is in relation to a computer (by what measure, by the way?) is simply not relevant to the statement you make.

Disagree? Then where is your equation for change-tolerance where the measure of complexity is a factor?

@PDPrice

we’re talking about inventing computers from scratch, one tiny piece at a time, with no designer at all.

No. This is biology, not cupper wires printed on glass fiber sheets, with little resistors, transistors, and capacitors soldered on to them.

In biology things are usually bendy, stretchy, and soluble in either water or fats, and they grow larger until they divide, or fuse and meld together. Individual cells and most tissues are soft, sludgy mixtures of oily and watery constituents that are mixed together, with many of them more or less freely floating around under diffusion. Contents will loosely associate, attach and transiently stick together, wiggle around under brownian motion, and even some times re-associate if separated, or regrow if damaged. Organisms are governed by the rules of water and oil chemistry and physics, and are more like soap bubbles than sheets of glass fiber.

In computers, nothing exhibits these properties. Stop obsessing about your computer metaphors and learn some real biology please.

[swamidass (S. Joshua Swamidass)]

From Reddit, @PDPrice hails us:

Following our joint article (creation.com/genetic-entropy-defense), the forum chatter has of course continued. Stern Cardinale has posted a “response”, such as it is, in a couple places, and true to form it ignores basically everything that was said and continues to rehash the same arguments as before. As usual, the other antagonists can maintain an illusion of unity by saying as little as possible.

All this endless back-and-forth forum bickering has, I think, outlived its usefulness. I’ve literally been treading the same paths for years on this topic. I am glad we were able to catalogue the responses and tackle them directly.

My proposal for the antagonists is this: if you want to keep up the discussion about GE, don’t just keep sniping from the forums. Get together (like I, Carter and Sanford did) and write a joint response article. Don’t take cheap shots. Don’t bring in unrelated issues to try and “score points”. Just honestly deal with the arguments. Then publish your article online, not in a forum, but on a website. Make it official.

Then, if it is deserving of further comment, perhaps the useful debate can continue. But this endless pot-shot-taking from the forums is enough already. It’s not worth anybody’s time anymore.

https://www.reddit.com/r/Creation/comments/kea7ij/an_invitation_to_a_higher_discourse_on_genetic/

I linked to this thread, and pointed out:

The response was quite cogent, and I am puzzled you did not link to it.

u/PaulDouglasPrice A blog response is a good idea. I’ve also wanted this to be more orderly, and even suggested the same thing to you. Are you, Rob Carter, and John Sanford now ready for a phone call to discuss this? If not, why not?

I personally am not willing to respond much if there is going to be pot shots on our credentials and unwillingness to even take a phone call.

@dsterncardinale this is close to your area of expertise. If you would like to write a blog post / preprint summarizing the critiques of GE, we can (1) manage a peer review of it, (2) publish it on the blog, and (3) typeset it into a PDF and give it a DOI.

At this time, however, I am closing this thread.