Gauger: Answering Art Hunt on Real Time Evolution

Design

(Ann Gauger) #59

Josh, the whole argument is pointless. I know these enzymes can change functions. They will evolve. It should be stated in my original post. There are naturally occurring bifunctional enzymes, for goodness sake. My original point, and Behe’s original point, is that it is a trivial evolution.

It happens in the wild. Using the lab was a proof of concept experiment, but it didn’t make the earth move, or shatter Behe’s conclusions.You used it as an argument against him, and it has all the force of feathers. Not only that but he saw the article and responded when it first came out.

Maybe you can explain why you think this is so devastating for Behe? It’s not for me, as I already explained.


#60

I think the preferred term is ‘micro-evolution’, to distinguish from change that is impossible without an intelligent agent.


(Faizal Ali) #61

Could you give a specific example of what you would consider to be non-trivial evolution?


#62

I’m missing something. Given that this is the case, why was the distinction between ‘lab’ and ‘natural’ conditions made? What was the point?


(Mikkel R.) #63

It is unclear what you mean specifically by the phrase “they have the same basic chemistry” in a way that makes the evolutionary shift in function from HisA to TrpF any less substantial, than the one you and Axe attempted to carry out for the Kbl -> BioF proteins.

Can you elaborate?


#64

@Agauger

If they modify different R groups then it isn’t the same reaction. Or do you think all hydrolases can evolve to hydrolyze any substrate?

Also, at first glance the activities of BioF2 and Kbl2 look somewhat similar. Both react with CoA, for example:

HisA does not have TrpF activity, so it isn’t a bifunctional enzyme.

It did exist on its own. The mutation to the trascriptional terminator upstream of HisA was a naturally occurring mutation.

You and Axe used the very same experimental setup to test evolutionary pathways. If this is not a legitimate method, then why did you guys use it?

This is a massive about face from our previous conversations. You have said before that you do experiments in the lab to see what is happening in the real world. If this isn’t the case, then why would you do any experiments in the lab? This seems to be a really strange objection.

Again, HisA had no detectable TrpF activity, so this doesn’t apply.


(Mikkel R.) #65

The HisA and TrpF enzyme reactions are both classified under E.C. as 5.3.1.X, and the Kbl and BioF reactions are both classified under 2.3.1.X.

It is not clear to me that the shift in reaction from Kbl -> BioF is substantially more(if at all) chemically extreme, than the shift in reaction from HisA -> TrpF is.

This is the Kbl reaction:


Which was attempted changed into the BioF reaction:

Compare that to the HisA reaction:
HisA%20reaction
Which was evolved into the TrpF reaction:
TrpF%20reaction


(S. Joshua Swamidass) #66

@agauger, where did Behe call it trivial evolution? He did not. That was not his response to us. His response was that it didn’t count because it was an intelligently guided experiment. This remains I strange answer.


#67

@Agauger

It is also worth mentioning that Behe seems to accept lab experiments as acceptable tests for evolution.


(Faizal Ali) #68

So does Ann Gauger. When she’s doing the experiment and it turns out the way she wants, at least.


(S. Joshua Swamidass) #69

Let us start with the fact that his rebuttal ignores the substance of the article to argue that it didn’t count because it was a designed experiment. That is a fallacy.

We can’t make progress when fallacies like this are stubbornly pressed. He asks for experimental evidence, and when evidence is produced it is dismissed as a designed experiment. I’m sure it is seen as clever by some and mendacious by others. Whether intentional or not, this fallacy exposes that Behe’s reasoning is stubbornly self-contradictory.

Even now, both @Agauger and Behe aren’t coming clean about the absurdity of this objection in the first place. I do not trust this. It is not trustworthy.


(Faizal Ali) #70

It seems to me Ann has now backed down from that argument. She’s now claiming the mutations, which she acknowledges occur naturally, are “trivial” and she and Behe knew these could happen all along. Which makes her initial enraged response a bit difficult to understand. But, anyway, the issue now is what constitutes a “trivial” set of beneficial mutations, and what sort of non-trivial adaptations are ID researchers expecting to see in order to confirm evolution.


(Retired Professor & Minister.) #71

@T_aquaticus quoted Behe:

Well, all a scientist has to do to prove me wrong is to take a bacterium without a flagellum, or knock out the genes for the flagellum in a bacterium, go into his lab and grow that bug for a long time and see if it produces anything resembling a flagellum. If that happened, intelligent design, as I understand it, would be knocked out of the water.

Seriously? I’m not a biologist but it is not hard to find several very serious problems with those statements.

I wish I could say that I’m amazed but I’ve seen disturbing patterns in Behe’s arguments for a long time. Even so, this quote from Behe took me aback.

Thanks for posting that excerpt, T_aquaticus.


#72

It’s a pattern we have seen regularly in both the ID and creationist community. We are told that evolution is false because there aren’t any transitional fossils. When transitional fossils are found, we are told that fossils don’t mean anything. We are told that you can’t evolve new enzyme functions in the lab. When those enzyme functions evolve in the lab we are told that lab experiments don’t count. ID/creationism is Lucy, and we are Charlie Brown.


(Blogging Graduate Student) #73

Even worse, we’re now told that creationism actually predicts the existence of transitional fossils.


(Mikkel R.) #74

It is hard not to speculate that if anyone were to run such an experiment, set up the environment in any way to favor the evolution of motility in bacteria with deleted flagellum genes, should such a thing evolve, Behe will declare it an instance of intelligent design that don’t mean anything (the environment was engineered to favor such mutations), and Ann Gauger will call it trivial and say she knew it all along.


(T J Runyon) #75

The no fossil argument is the worst argument against evolution. Not only do you have to take taphnomy into consideration, then finding the exposed rocks before they are eroded away, you also have to hope they are at a location you can access! Things like civil war has caused a lot of problems. People just can’t get to the sites. Local property owners won’t let us on their property to look. Sometimes it’s like anti-evolutionists think we should just be able to go to in the backyard and start digging and then we will find something. Look up the story of Quetzalcoatlus at Big Bend and the lengths paleontologists had to go to uncover it. Anyone who makes such an argument has absolutely no clue about the nature of paleontology


#76

In this case I think a quote from you is appropriate:

“Never infer deceit where incompetence, delusion, confusion, or misunderstanding could explains this just as well. That is a wise rule of thumb.”


(Faizal Ali) #77

Of course, when what someone is saying is demonstrably true, one need only answer “None of the above.” Such is the case with Art’s article. I’ll say no more.


(Ann Gauger) #78

Where did I say that? I think you are misremembering.

In the lab the experimenter sets things up to maximize his success. He puts his gene on an inducible plasmid, for example, then grows the cells carrying his gene, carefully selected to allow him to detect the phenotype, under controlled conditions in a monoculture. Assuming the experimenter is selecting from a random library he has made, he uses conditions he has optimized for the selection to identify the best candidates, then if he is smart he rescreens them in freshly transformed cells. Do you get what I am saying?

Most random newly emerging enzyme activities are weak. They are only useful to the cell, or even detectable, unless strongly overexpressed. The only reason that weak activity is not inactivated by the cell to reduce the cost of expression is because we, the human investigators, apply massive amounts of selection for the function.

Now I have said it is easy to recruit promiscuous enzymes. Harder to recruit from shared reactions but no overlapping promiscuous activity (trpF HisA). They were successful, probably because of their active site location. BioF and Kbl are similar in some ways but one releases CO2 and the other doesn’t. And the active site is constrained. All things I learned as we were going along, BTW. So it didn’t work for Kbl and BioF, even though overexpressed in a very sensitive assay…

The best lab example I know is this: Evolutionary Potential of (!/R)8-Barrels: Functional Promiscuity Produced by Single Substitutions in the Enolase Superfamily†Biochemistry (2003) 42:8387

In this study they found a single mutation that could convert an enzyme from one catalytic activity to a completely new one. One mutation. That’s the goal. For evolution to explain enzyme diversity you need to be able to convert to new functions (get new chemistry) with just a few (two or three max) mutations. The authors of this paper say:

Functional interconversion of homologous enzymes that
catalyze different chemical reactions has been accomplished
in Vitro with as few as four to eight substitutions (13 , 14 ).
However, the natural acquisition of a new reaction with this
number of substitutions is unlikely; during random accumulation
of the required mutations, deleterious mutations
are also expected to occur. In other words, the probability
of evolving a new enzymatic function that requires specific>
multiple mutations is low.

They succeeded in converting both the substrate preference and the reaction chemistry with a single mutation. But it was done on a multicopy plasmid that was overexpressed, so it is not at all clear it would have worked apart from the lab setting. And it was one of the beta barrel enzymes.

If you want to find an evolutionary story that will stump me you will have to go to experiments in the wild. Copley’s papers are a good place to start. But I can tell you that all the ones I have seen are usually a shift in substrate preference with a shared chemistry. Swamidass and friends cited one of them in their review. That is a much better place to argue your case for evolution. Because it really did evolve unaided by human engineering or environmental control.

There are other places where it has worked, usually involving several mutations an

There are other places where it has worked, usually involving several mutations and a