Evolving a new function via gene duplication and divergence

| 92 Comments

Bjørn Østman at Pleiotropy describes new research in Science that shows how duplicated genes can evolve to perform new functions. It presents

… a new model/mechanism by which duplicated genes can retain the selection pressure to not succumb to deleterious mutations. They call it the innovation-amplification-divergene model (IAD).

Basically,

IAD works like this: A gene initially has one function only (A). Then some genetic changes makes it also have a new function, b, which at first is not of too great importance. Then some environmental change favors the gene variants with the minor b-function (the innovation stage). This is then followed by duplication of the gene, such that there are now more than one copy that carries out A and b (the amplification stage). At this stage there is selection for more b, and at some point genetic changes in one of the copies results in a gene that is better at the new function, B. At this point, selection for the genes that do both A and b is relaxed, because the new gene (blue) carries out the new function. The original gene then loses the b function, and we are left with two distinct genes.

Michael Behe, of course, scoffs. Because the researchers did some manipulations that created conditions favorable to the evolution of the new function, Behe claims that

Needless to say, this ain’t how unaided nature works – unless nature is guiding events toward a goal.

Shucks. I guess every experimental manipulation ever performed has been an invalid method of studying some process. But as a PT crew member pointed out on the back channel, “this kind of shit happens all the time in nature.” See, for example, Gene duplication and the adaptive evolution of a classic genetic switch or Escape from adaptive conflict after duplication in an anthocyanin pathway gene.

92 Comments

Well see, you have to do experiments if evolution is going to be science (never mind that they never do a sound test for “design”), but everything’s thrown off if you actually use controls and variables. Because, uh, that’s using your brain–I guess we’d have to hire brainless IDiots to do it all, and since nothing would make sense that way,…

Of course they don’t care about experiments, they’re doing religion. Religion doesn’t need experiments because it’s not in doubt (or they’d be sinning) in their minds.

Glen Davidson

You see, there is always an intelligent designer behind experiments. Therefore, all experiments prove an intelligent designer.

QED.

Cue: incoherent medieval troll appearance and subsequent Wall banishment in 3, 2 …

Funny. Just this morning on the previous thread I was saying that even if Behe’s test of evolution was demonstrated in the laboratory, Behe would dismiss the evidence because it was not natural…and then – BING! – right on cue…

Not only did the new function evolve, but it did so in just three thousand generations. A dramatic demonstration of the power of gene duplication in the evolution of novel traits. And of course, there is absolutely no reason why the same mechanism couldn’t work for more complex traits as well.

It;s almost as if the entire scientific community is conspiring to make Behe look bad. Or maybe he just always chooses the wrong side of every issue.

Not only did the new function evolve, but it did so in just three thousand generations. A dramatic demonstration of the importance of gene duplication in the evolution of novel traits. Of course, the same mechanism would work for more complex traits as well.

It’s almost as if the entire scientific community is conspiring to make Behe look bad. Or maybe he just chooses the wrong side of every issue.

DS said:

Not only did the new function evolve, but it did so in just three thousand generations. A dramatic demonstration of the importance of gene duplication in the evolution of novel traits. Of course, the same mechanism would work for more complex traits as well.

It’s almost as if the entire scientific community is conspiring to make Behe look bad. Or maybe he just chooses the wrong side of every issue.

You can say that again. Oh, you did. :)

Behe appears to have reached the point of quarreling with the fundamental methods of scientific research. I hope that the next time he turns up as an expert witness, he gets skewered with this.

Opposing counsel asks:

Dr Behe, how would you demonstrate that you actually are, rather than merely claim to be, a scientist?

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Moo Moo, I read the entire paper. And I learned that there is a model that explains the origin of new gene function without relaxed selection, which is important to avoid the production of pseudogenes. They also verified the model histidine/tryptophan specialization in using Salmonella. More here.

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parictis said:

Moo Moo, I read the entire paper. And I learned that there is a model that explains the origin of new gene function without relaxed selection, which is important to avoid the production of pseudogenes. They also verified the model histidine/tryptophan specialization in using Salmonella. More here.

In other words, the paper repeatedly proves that Behe is wrong on, many, many, many levels in addition to his laughable dismissal of the paper, and inane remark about nature being goal-oriented.

DS said:

Not only did the new function evolve, but it did so in just three thousand generations. A dramatic demonstration of the power of gene duplication in the evolution of novel traits. And of course, there is absolutely no reason why the same mechanism couldn’t work for more complex traits as well.

It;s almost as if the entire scientific community is conspiring to make Behe look bad. Or maybe he just always chooses the wrong side of every issue.

It doesn’t count unless the experiment produces a bacterial flagellum from scratch. ;-)

I’ve had the “intelligent design” of an experiment discussion with IDiots before. They really don’t have a clue how to do science.

First, if the answer was known by the experimental designer, then there wouldn’t be a lot of point in doing the experiment would there.

Second, even well designed experiments can produce unexpected data. If this wasn’t the case, then every casino game engineer would be a multi-billionaire. They designed the roulette wheel, therefore, they know what every spin will be right?

Third, experiments are designed to reduce the uncertainty and ambiguity of the experiment. Throwing a bunch of random chemicals and adding random amounts of outside influences (water, electricity, heat, etc) may produce something interesting, but how and why? A well designed experiment reduces the uncertain part to one variable that is, in turn, controlled by one independent variable. If you experiment with a pendulum, you don’t vary the length of the string, the mass of the bob, and the height you release it from and then try to figure out the difference in period and or the difference in g in the area. No, you intelligently change on aspect a time, in order to determine that aspect’s influence on one and only one other aspect (length of string and period, for example).

Experiments that are not intelligently designed are useless. However, as shown, this does not mean that all experiments are evidence of intelligent design in the rest of the universe. It is evidence that humans are intelligent and can design a valid experiment that produces useful, unambiguous, and certain results. That’s all.

If one wants to extrapolate this concept to Intelligent Design of the universe and every living thing in it, the one should first find the Intelligence that designed everything and ask that Intelligence why they did such a piss-poor job in designing the experiment that is our universe.

I like pigliucci’s analogy. Experiments are to evolving life as a telescope is to galaxies and stars.

Starbuck said:

I like pigliucci’s analogy. Experiments are to evolving life as a telescope is to galaxies and stars.

Apt analogy. This particular experiment demonstrates the importance of gene duplication in evolution, with or without selective constraints. Duplicated genes allow for neofunctionalization, even when ancestral functions are retained. Darwin would have been fascinated by these types of experiments.

You’ll never hear a creationist say, telescopes are intelligently designed, therefore those galaxies are an artifactual byproduct of the designed telescope!

ogremk5 said:

I’ve had the “intelligent design” of an experiment discussion with IDiots before. They really don’t have a clue how to do science.

First, if the answer was known by the experimental designer, then there wouldn’t be a lot of point in doing the experiment would there.

Second, even well designed experiments can produce unexpected data. If this wasn’t the case, then every casino game engineer would be a multi-billionaire. They designed the roulette wheel, therefore, they know what every spin will be right?

Third, experiments are designed to reduce the uncertainty and ambiguity of the experiment. Throwing a bunch of random chemicals and adding random amounts of outside influences (water, electricity, heat, etc) may produce something interesting, but how and why? A well designed experiment reduces the uncertain part to one variable that is, in turn, controlled by one independent variable. If you experiment with a pendulum, you don’t vary the length of the string, the mass of the bob, and the height you release it from and then try to figure out the difference in period and or the difference in g in the area. No, you intelligently change on aspect a time, in order to determine that aspect’s influence on one and only one other aspect (length of string and period, for example).

Experiments that are not intelligently designed are useless. However, as shown, this does not mean that all experiments are evidence of intelligent design in the rest of the universe. It is evidence that humans are intelligent and can design a valid experiment that produces useful, unambiguous, and certain results. That’s all.

If one wants to extrapolate this concept to Intelligent Design of the universe and every living thing in it, the one should first find the Intelligence that designed everything and ask that Intelligence why they did such a piss-poor job in designing the experiment that is our universe.

The problem with experiments is they could also prove them wrong. Need I remind you of the Wistar Incident? http://pandasthumb.org/archives/200[…]lligent.html

I’ve had the “intelligent design” of an experiment discussion with IDiots before. They really don’t have a clue how to do science.

Science is experimental and observational.

If we never did experiments, we would still be in the stone age.

That might work for creationists but the rest of us have better ways of living.

Behe denying reality some more:

Needless to say, this ain’t how unaided nature works – unless nature is guiding events toward a goal.

Nature is always guiding events toward a goal.

Natural selection, survival of the fittess, differential reproduction, however you want to term it.

Biologically, our goal is to successfully reproduce better than competing genomes.

Moo Moo -

Let’s take it one step at a time.

Can gene duplication occur? Simple yes/no question. Answer this one question.

harold said:

Moo Moo -

Let’s take it one step at a time.

Can gene duplication occur? Simple yes/no question. Answer this one question.

Who wants to go swimming in H2SO?

I was too cryptic; what I meant was a metaphor for what it would be like for people like Moo Moo to take the road you would lead them down.

I may not understand the precise details of the science but, having read the paper, the following things are quite revealing:

To experimentally test the IAD model, we examined a histidine biosynthetic enzyme (HisA),and through continuous selection we created, by duplication and divergence, a new gene that catalyzes a step in tryptophan synthesis.

It seems a bit odd that an experiment that purportedly demonstrates evolution involves the researchers creating a new gene, albeit through mutational means.

In a strain lacking trpF, we selected a spontaneous hisA mutant of Salmonella enterica that maintained its original function (HisA).……We placed this bifunctional parental gene (dup13-15, D10G) under the control of a constitutive promoter that cotranscribed a yellow fluorescent protein ( yfp) gene.

It seems that the researchers directed and guided their experiment towards a goal by selecting various mutants and reconfiguring them to some extent.

The evolved genes fell into three classes: (i) specialized genes with strongly improved HisA activity and loss of TrpF activity, (ii) specialized genes with strongly improved TrpF activity and loss of HisA activity, and (iii) generalist genes whose encoded enzyme showed a moderate increase in both activities

At the end of the day, the “new genes” appear only to display an improved pre-existing chemical activity or even the loss of pre-existing activity that was present in the parental gene.

Moo Moo said:

I may not understand the precise details of the science

Well, there’s your problem right there.

Yet, you don’t let that stop you from criticizing the work of people who do understand the precise details of science.

Are you actually interested in learning this stuff? What would be required (in your opinion) to show you that you are fundamentally mistaken?

In other words, do you plan to learn and understand the “precise details of science” and become an advocate for learning or do you plan to continue spewing forth your arrogant ignorance no matter what anyone else says?

Joe always makes the same mistake. He always thinks that he is more qualified to judge the experimental results than the real scientists who actually performed the research.. He is also obsesses with demanding that everyone read the entire paper, as if reading the abstract was somehow insufficient. At least he isn’t pretending to be a scientist any more. Apparently he has somehow obtained a mail order law certificate and is now calling himself a lawyer. Of course he isn’t any more a lawyer than he is a scientist.

His criticism of the research are of course completely invalid. Once again, the authors, editors and reviewers all disagree with him. But he doesn’t care. He just goes merrily on his way making ignorant claims and trying to denigrate that which he doesn’t understand. At the end of the day all he has is his own incredulity, which is of course completely worthless.

We have known about the importance of gene duplication for forty years now. Some people just can’t seem to get it through their heads. The telescope didn’t make the stars, it simply reveals them to us, just like this experiment.

ogremk5 said:

Moo Moo said:

I may not understand the precise details of the science

Well, there’s your problem right there.

Yet, you don’t let that stop you from criticizing the work of people who do understand the precise details of science.

Are you actually interested in learning this stuff? What would be required (in your opinion) to show you that you are fundamentally mistaken?

In other words, do you plan to learn and understand the “precise details of science” and become an advocate for learning or do you plan to continue spewing forth your arrogant ignorance no matter what anyone else says?

I am qualified to know when someone is trying to put a spin on something. In this case, the experiment was directed by the scientists who selected and reconfigured mutants in order to achieve a modification in two of the pre-existing activities of the original gene. This is an important feat of protein engineering but not really of undirected evolution.

DS said: He is also obsessed with demanding that everyone read the entire paper, as if reading the abstract was somehow insufficient.

I don’t know who are you referring to, but it certainly does help to read a scientific paper, or any paper, beyond the abstract and in its entirety. For those of you who want access to it, but do not subscribe to Science, I have provided a link below:

http://www.umich.edu/~zhanglab/club[…]_02_2012.pdf

Enjoy.

Moo Moo said: This is an important feat of protein engineering but not really of undirected evolution.

Its protein engineering the same way dog breeding is protein engineering. You control the conditions to see what naturally happens under those conditions.

If you think the description of the experiment implies that scientists took teeny tiny tweezers and put together a novel gene - or something equivalent - then your reading comprehension is really poor.

From your earlier post:

At the end of the day, the “new genes” appear only to display an improved pre-existing chemical activity or even the loss of pre-existing activity that was present in the parental gene.

Just so we’re clear, then, you think that a biological system which changes from [gene A performs function 1 and 2], through [gene A duplicates to B, both A and B perform function 1 and 2] to [gene A performs function 1, gene B performs function 2] is not evolving in the sense biologists use the term evolution?

https://me.yahoo.com/a/JxVN0eQFqtmg[…]X_Zhn8#57cad said:

Chris Lawson said: … His entire point was that natural selection and selective breeding were the same process.

Compare teosinte and corn.

The difference is noticeable.

Glen Davidson

Alright, I will compare teosinte to domestic maize strains.

Domestic maize strains are the result of a primate species naturally selecting, in a particular environment, strains of a wild grain, probably teosinte.

The primates probably noticed that some teosinte plants had more or larger seeds, and also noticed that the offspring of those plants also tended to have more and larger seeds. In other words, thousands of years ago, they figured out some key principles of evolution - genetic variation and selection.

There is not a single comment in this thread that says that examples of human breeding cannot be distinguished from other examples of natural selection. It’s rather shocking that you keep implying that someone has said that, and that is what you seem to imply, unless I am misinterpreting.

It is perfectly true that modern teosinte has been acted on by different selective pressures than have modern strains of domestic maize over the years since they diverged.

It’s also perfectly true that sea urchins have been acted on by different selective pressures than oak trees, since their common ancestors diverged.

No-one is saying that all natural selection is homogeneous, or that different types of natural selection cannot be distinguished from one another, or that human agricultural breeding isn’t different in many ways from other types of natural selection.

Glen Davidson -

I should add, I really don’t think we have a dispute here.

I completely agree that the results of human breeding, whether domestic maize or delicate transgenic mice that can only survive in a special human-created environment, tend to be different from the results of other selective forces.

However, I’m sure we both agree that…

1) The process of human deliberate breeding is, among other things, A) natural and B) selection.

2) The fact that humans can “design”, and that we can recognize the “designs” of other humans, including but not limited to products of breeding, does not imply that the bacterial flagellum, Adam and Eve, the first replicating cell on earth, or anything else, had to be “designed” by a deity.

I’m sure you agree with these points, so beyond that, stylistic disputes about the use of the term “artificial selection” have reached an impasse.

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This page contains a single entry by Richard B. Hoppe published on November 12, 2012 5:06 PM.

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