"Devolution" and gene loss in evolution

@agauger,

Frankly, you are the only I.D. proponent I know who says she doesn’t use the term.

But even without using the term, I believe you are fairly enthusiastic about referring to “loss of information” as some sort of criticism of Evolutionary theory. Am I wrong in that conclusion?

@agauger

Any change in a population’s gene pool is Evolution.

It’s one’s sense of aesthetics that decides whether it is a good change or not.

If fish lose their fins to become tetrapods, is that a devolved fish?

If mammals lose their legs to become proto-whales… is that a devolved mammal?

If reptiles lose their legs to become snakes… are they devolved reptiles?
Where’s the up-side of not having any legs any more? Devolution, right?

That’s what I thought.

I couldn’t remember, so I googled myself and found these:

so I can’t deny using the term. Fairly enthusiastic? Only two pieces out of many posts. Some sort of criticism of evolution? Yes. Some sorts of losses are effectively permanent, and curtail options for the future. I am thinking in terms of bacteria.

No doubt there are cases where information is lost to the benefit of the organism. Losing the receptor for the HIV virus would be a good example, or losing legs maybe if you’re a snake (though I am not sure of the rationale for that–plenty of other organisms live in similar habitats and keep their legs). Do I think every mutation is a loss of information? Not unless it’s a loss of function, to be consistent with what I’ve said before.
Do I think loss of information is disproof of evolution? No. But no organism can survive a steady loss of genetic information. Consider the effect of mutator strains in LTEE experiments that was recently reported.

When I took my grad school courses a long time ago, it was drummed into me that there was no such thing as the Great Chain of Being, and that there was no up or down to evolution, no goal. Any change, in any direction was simply evolutionary change. That’s why I don’t use devolution (I don’t think I ever have).

I’ve thought about it since then. If the goal is to maximize fitness and you’re under stress in a competitive situation, the quickest, easiest fix is to dump excess weight. That’s what happened in my 2010 paper with Ralph Seelke. That’s a loss of information, but a beneficial mutation. Behe documents others in his paper (Quarterly Review)

E coli is very versatile in its metabolism. It maintains that versatility by regulation of genes, so it doesn’t carry an expression cost beyond the value of its protein products. But if I put it on a starvation diet it will start dumping genes. That’s a permanent loss of information for that strain.
Do I see loss of information as a major driving force in evolution? Probably not. But it’s not innovation or gain of function as a general rule either.

(Here’s where biology is messy. I can think of a possible example where a new beneficial protein is formed by deletion of intervening sequence, resulting in a beneficial, loss of information, gain of function mutation. You’d also have to consider what happened to the original function to know for sure what to call it.)

That’s my first impulse as well. You could use the sequenced human genome and see what percentage of mutations produce putative promoter sites and downstream termination sites in intergenic regions. This would give you an idea of how often ORFan genes might emerge.[quote=“agauger, post:48, topic:36902”]
My husband I did a crude simulation of the rarity of ORFs in different GC content random sequence.
[/quote]

I still think it would be much better to use actual sequenced
genomes since they are now widely available.[quote=“agauger, post:48, topic:36902”]
Thus the only reason this frameshift hypothesis for nylonase is even remotely possible is because the sequence coding for nylonase is most unusual, and contains not one, not two, but three open frames Although frameshift mutations are ordinarily considered to be quite disruptive, at least in this case the putative brand new protein sequence would not terminate early due to stop codons.
[/quote]

This is why I think real genomes would be better since they have features that random sequences will not. In the case of humans, it would be interesting to reconstruct the ancestral sequence using the chimp/gorilla/human triad and see if these ORFan gene reading frames were available in the common ancestor of the triad or if they emerged in either the chimp or human lineages.

I also think that eukaryotic genomes are a much better model if we are talking about human or primate ORFan genes. Obviously, intergenic regions are much more plentiful in the vast majority of eukaryotic genomes.

While I greatly appreciate the work you have done with pseudorandom sequences, I find them to be a bit irrelevant when we are talking about real genomes. While the nyl genes are perhaps and oddity, they are still a reality. You can’t use a bunch of random sequences to argue that they shouldn’t exist. There are also possible sources for regions with multiple reading frames, such as phage DNA that is known to have both sense and antisense genes for the same sequence (if memory serves).

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@agauger

And so?

When a population loses too much information over too much time … the population blinks out of existence.
What exactly is the I.D. justification on the fixation on “loss of information”? Information is gained… information is lost. Sometimes a species loses information at the same time it is gaining information. So what?

You write:

Why do we need to know what to call it? It’s all evolution! Any time someone is trying to keep count of what is lost vs what is gained (if anything), I don’t believe they are on the correct path of understanding Evolution.

Doug Axe
As an ID proponent, I’ve put forward the scientific case for thinking that the thousands of distinct structures that enable protein molecules to perform their specific tasks inside cells cannot have arisen in a Darwinian way. Moreover, the facts of this problem seem to preclude any naturalistic solution, Darwinian or not.

[quote=“agauger, post:72, topic:36902”]
That statement refers to the second phase of our work.[/quote]
That statement refers to the BIG picture of all phases of your work, I think. What are those distinct structures if not folds?

In that paper, the title is
The Case Against a Darwinian Origin of Protein Folds

and he wrote
The aim here will be to decide whether Darwinian mechanisms (broadly construed) can reasonably be credited with this success.

This is silly, because drift is an important part of this success.

You cannot separate them. The two subjects are interlaced and summarized in the quote from Axe at the top.

I also find it interesting that you only quoted the review of Herschlag and described it as just a hypothesis. You did not quote any of the experimental papers of Herschlag.

It seems to me like you are describing him as just a thinker, while you are the doer. Is that the impression you wanted to give to a reader who does not know the research?

But the same fold can have many functions!

[quote=“agauger, post:72, topic:36902”]So i guess I’d say that you have changed the topic from Axe’s 2004 paper to my 2011 paper in order to bring in promiscuity. Moving the goal.
[/quote]I guess I would say that you are making artificial divisions where none exist.

the fact that sequence space vastly exceeds usable protein space, as Doug Axe has made clear in his papers

There the papers are combined and it’s gone from the interpretation of Axe to a fact. Do you agree?

To rub it in, consider that Axe’s calculation of one in 10^74 sequences being functional is way too generous.

Even your own colleagues do not see the seperation you are claiming here! The estimation comes from the 2004 paper you claim is only about folds, and here your colleague says it refers to functions. Have you taken it up with him or her?

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Of course not.

It is interesting that 44 of 66 of the citations in your 2011 paper are from 2004 or before. I have never seen a distribution like that, especially in a field that is growing exponentially. Of the other 22 more modern ones, 3 are yours. For contrast, my just-published paper has more than half of the citations from the past 7 years. My field is not growing as quickly as protein evolution, though.

So I would say that is highly suggesting that you avoided quoting more recent results.

I think the trouble with it comes more from your organisations false claims about what the 2004 paper means.

. The 2004 paper is called Estimating the **Prevalence of Protein Sequences
Adopting Functional Enzyme Folds. You have the wrong paper.

Don’t be ridiculous. We had no such purpose in mind. Now you are looking for anything at all, no matter how strange, to accuse us.

Have you read the paper? Maybe just the title? Prevalence of Protein Sequences
Adopting Functional Enzyme Folds. I know the content of my and Doug’s research. I know the intent of each part of it, what we were trying to demonstrate. You however apparently do not. You make distinctions where there are none, and leave them out when they are there. You even quote the wrong paper. The Case Against a Darwinian Origin of Protein Folds was written in 2010.**

BTW I recommend reading that paper you got wrong.

Since your criticisms no longer involve substance, but only nitpicking, I will stop here. It’s a waste of time.

I agree. So what. I was not the one to insist on the topic of devolution and loss of information.[quote=“gbrooks9, post:86, topic:36902”]

Why do we need to know what to call it? It’s all evolution! Any time someone is trying to keep count of what is lost vs what is gained (if anything), I don’t believe they are on the correct path of understanding Evolution.
[/quote]

See above. I have been badgered in this whole thread about loss of information and whether I thought it was an argument against evolution. Evolutionary change comes in all sorts of ways. That was my point. And your last statement: I don’t know what to call it. A sneer, merely snark, or full scale denigration. Enough already.

@agauger

I am not trying to badger you, I swear. I’m trying to get you to see how the I.D. folks cause their own trouble.

  1. Evolution is evolution whether there is a loss of information, or a combination of “loss of information” and a “gain of information” (and whether the net change “appears” to be a gain or a loss).

  2. Ann, you have distinguished yourself in that you have willingly backed away from most of that rhetoric.

  3. But your I.D. colleagues, for the most part, do not. They lead the charge with a lamental fixation on “loss of information”.

I have summarized these points, using other words, before. It was my attempt to explain why I.D. scientists don’t get much respect.

But you, @agauger, may well merit a higher level of respect, when you understand what it is that separates you from the regular I.D. crowd!

Thanks. I appreciate your response. I actually understood your point about devolution several posts back, and said i would talk to the editor at ENV. I could also post at Uncommon Descent, but i don’t know how much influence i will have there. I have no influence with bloggers in general or Behe.

In many cases the use of the term devolution is rhetorical. I am sorry it annoys you all so, but just remember, there are things you do or say that annoy us.

One of them is to call us dishonest, without firsthand knowledge and based on hearsay. Atheistic blogs are not a reliable source of information.

There is a difference between saying something annoying and using strawman arguments. Devolution is a strawman argument which is why we object to it. If we ever use a strawman argument I hope that you will point it out, and I also hope that we can show the same grace you have shown when responding to those posts.

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Would you say that discussing loss of information is a straw man argument, or is it context dependent?

It could come closest to being context dependent with the problem being that it is often not given a context. Many (not all) ID proponents claim that evolution only results in a loss of information, and then they never define what information is in a scientific manner or describe how it is measured. It’s a bit like saying that ID is false because it can’t produce Marklar, and then never defining what Marklar is. Alternately, a definition is offered but immediately changed once someone presents examples of evolution producing change that fits the original definition. I guess that would be more of a red herring than a strawman.

@agauger

To say that building a valid notion of Evolution is based, in part, on a concept of Devolution, is like saying the validity of Biblical inerrancy is based on the color of the font used to print the Bible in question.

It’s an erroneous premise and throws into question everything else a person might say. I think you are wrong when you opine that “in many cases” the use is rhetorical. We have seen YECs come blasting onto these Boards convinced that the only thing they need to show is that information was lost to disprove that Evolution is valid.

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That doesn’t seem to stop Evolution News & Science Today. One of their most recent articles (written by Cornelius Hunter and NOT Ann Gauger) has this lovely little statement:

“I have often discussed the problem of “early complexity,” and how as we peer back in time — whether in the geographic strata or by phylogenetic reconstruction — things don’t get simpler. This makes no sense in light of evolution and this week’s news of a specimen of a fossil tree from northwest China, revealing and ancient, and highly complex, just makes it worse.”
reference

So lets unpack this. This ~350 million year old fossil of a tree is complex. This is said to be “early complexity”. That seems a bit strange since life first appeared in Earth’s fossil record 4.2 billion years ago. This fossilized tree species existed about 3.8 billion years after evolution started, so I wouldn’t exactly call that “early complexity”.

The EN&ST article also suggests that the theory of evolution requires that complexity should always increase and never decrease (i.e. the idea behind “Devolution”). This is absurd in the extreme. Evolution does not have complexity as a goal. Decreases in complexity is as much evolution as increases in complexity.

So even now there are examples of mistaken ideas where it involves the theory of evolution with respect to the ideas underpinning Devolution.

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