Gauger: Answering Art Hunt on Real Time Evolution

Design

(Ann Gauger) #79

Sorry, Swamidass. David Baker’s lab at the U of Washington makes things nature has never made.


(Ann Gauger) #80

@Rumraket

Take a look at Figure 1 or 2 of the Jürgens paper and notice how they have highlighted the similar chemistry between HisA and TrpF.

So is BioF easier or harder to evolve? This would seem to argue easier> But we didn’t succeed. Why not? Well here. We made another approach.

xhttp://bio-complexity.org/ojs/index.php/main/article/viewFile/BIO-C.2014.4/BIO-C.2014.4

@swamidass
I am sorry you find this untrustworthy. I have laid things out as clearly as I can. My last comment, and we see if your program lets me post. Then I am gone. No one likes to hang around where they are called untrustworthy. No point in explaining if you won’t accept what I say as true.

Look at his original response on Evolution News. I have linked to it in my post if you can’t find it.

A thing can be both intelligently guided (even elegantly) and yield trivial results. Nothing about Nasvall’s results is new or unexpected.

@T_aquaticus

I see I burned through a lot of street cred. I have not said you can’t evolve new enzyme functions in the lab. If you look back you will see that I have repeatedly said you can, just that it may not happen in the wild. Lab experiments count as long as you don’t expand their meaning beyond what they can bear. HisA and TrpF can evolve into one another. Yep. We knew that already. I showed you some of the papers. Subfunctionalization happens. Yep. Knew that already too. Best example I know of comes from yeast, and I think Sean Carroll was an author. The impressive thing was getting all to go together. Like setting up dominos. And if you read what else I posted you can find some pretty dandy examples of what evolution can do.


(Faizal Ali) #81

Here’s the problem: When Ann writes this sort of stuff here, there are lots of experienced and capable scientists to point out her errors and misconceptions. But when she speaks and writes to her creationist followers, vanishingly few of whom have any significant scientific knowledge, she sounds convincing and they will readily accept whatever she has to say.

I’m not sure what can be done about that.


(Arthur Hunt) #82

Prove it. Specifically, prove that the same evolutionary mechanisms that are confirmed in controlled and repeatable lab studies are not operative in the wild.


(S. Joshua Swamidass) #83

I did not say you lied. You have not, as far as I can tell, liked. I did not say you personally were untrustworthy. I mean that the argument you making is difficult to trust, because it seems self-contradictory.

Fair enough. It can be guided and trivial, in your assessment. Let us deal with the first point still. Let us say, for example, that in the studies you and Axe of done, you had succeed in switching function. Would that not have been “guided evolution” too?

You still have not given us an explanation of why it is valid to dismiss the RTE results as an example of ID. Can please give us an explanation or back off of that objection? We can then look at whether or not it is “trivial.”


(Ann Gauger) #84

Maybe there’s a confusion over language here. The experiment was designed. It was planned. It was engineered. That’s what we mean by intelligently designed we don’t mean that God stepped in and made it happen.


(Ann Gauger) #85

You ask whether my experiments with Axe would have constituted guided evolution. Yes. We were asking whether it was possible to convert Kbl into BioF. If we had succeeded in the lab using the techniques we were using the next question would be whether we could get it to go without the amplification on the plasmid, on the chromosome just using simple selection. That would be where I would advocate for anyone who found that they could evolve an enzyme to a new function using high copy plasmids and overexpression and selection. I would say, all right with your gene on the chromosome, one copy, constitutive or inducible expression, see if you can select for a mutation then because that’s the way it happens. In the case of the Naswell experiments they made the gene likely to duplicate by putting it in a construct that was more likely to duplicate than usual. That increased its chances of getting amplification which increased their chances of being able to select for the functions they were looking for.

Most everything we do in the lab is not really a test of evolution. it’s a test of part of the evolutionary story. to put it through the real story requires a great deal more rigor than we ask for.


(Curtis Henderson) #86

Like others have mentioned, I’m also having trouble finding what your true contention is. Of course experiments are designed, they could not be otherwise. What was the point of your 2011 and 2014 papers, if they could simple be dismissed as “they were designed” and therefore “trivial”?


(Ann Gauger) #87

The difference is I didn’t know whether kbl or biof would work or not. They knew trpF and HisA would. All the steps were worked out. They just hadn’t all been run in sequence before.


(S. Joshua Swamidass) #88

@Agauger, this is a shift from what you posted at the beginning of this thread, and in your article.

  1. You wrote the issue was that they did genetic manipulations on the cells. Do you agree now that genetic manipulations are not grounds to dismiss these findings?

  2. You wrote that the issue was that they change the environment of the cells to enable selection. Do you agree now that changing the environment of the cells is not grounds to dismiss these findings?

It seems like your new objections are based on some factual errors:

  1. They placed the gene on a “multicopy plasmid.” (This isn’t true, because it was a low copy plasmid, with only 1 to 2 copies for cells.

  2. That they overexpressed the gene. This also seems false. The cells over expressed it by duplication. If it was already over expressed, they would not have an advantaged to do this.

  3. Earlier you mentioned that it was ain a location with a higher duplication rate. Well, higher compared to what? This might just be high for a plasmid, but low for genomic DNA. More information is needed before we can know if this is a valid objection. Do you have this information?

We have those too. We put them in the paper too. The objection to these is that they are not experimentally demonstrated in the laboratory. (yes, the circularity is obvious).


(Ann Gauger) #89

You have misread what I wrote. I gave a citation to Schmidt et al ( or I thought I did. They are the ones with a multicopy plasmid. I know Nasvall had low copy number… I will go back and read what I wrote before but I have not changed my position. Perhaps my reactions have changed because of the different arguments I was hearing. I will look but not tonight. And my position has not changed.


(S. Joshua Swamidass) #90

The point is very clear. It has been repeated several time. This was the objection:

Let me emphasize: in reviewing a book expressly advocating intelligent design, Lenski et al. can’t seem to distinguish between experiments where investigators keep their hands off and those where investigators actively manipulate a system. Perhaps they can’t see the difference.

We responded:

In addition to @Art’s detailed explanation of several factual errors or misunderstandings in your account, I reduced it down to these two points:

Returning to your experiment with Doug Axe. You also have attempted to test evolutionary mechanisms in the past by altering the environment of the cells and making genetic manipulations. The methodology in this paper is much stronger than yours. It is an open question if, by using their methodology, that the conversions your system failed to make would now become tractable.

Perhaps you can give sensible answers to the bolded questions above. That would be great. Raising new objections is a different issue. These were the key objections you initially raised. If you cannot answer these questions, why should we consider them valid objections? If you can’t answer these questions, and won’t acknowledge these aren’t valid objections, what should infer at that point?

Once that is resolve, there may be reason to go on to all the new objections you’ve raised. Until then, I’m not sure what the point is.


(Mikkel R.) #91

I’d be more interested in an attempt to reconstruct the last common ancestor of all known BioF enzymes, and then the last common ancestor of all known Kbl enzymes. If these two ancestral enzymes are closer in sequence space than their extant descendants, then that is a key prediction of their common descent.

Of course one might have to do the same for a whole host of enzymes from the PLP-dependent transferase superfamily, as it is possible that the actual common ancestor was not measurably active on either substrate, but catalyzed a third reaction from which they both derive.

In fact, I could easily see how that could be the case. It is entirely plausible that they both derive from the 5-aminolevulinate synthase enzyme (HemA), which is in a chemical sense mid-way between them in terms of the type of reaction it calalyzes.

To see what I mean, compare these three reactions. First Kbl:


Then HemA:

Last BioF:

@AGauger why did you not try to convert BioF into HemA, or HemA into Kbl? Why skip over the “middle step”?

It seems rather obvious to me that HemA is a closer chemical reaction to Kbl, than BioF is, and it is more plausble to me that both of them derive from HemA, than it is that Kbl turned directly into BioF.


#92

These three statements are faith based and not part of science.


(Ashwin S) #93

Patrick, whats wrong in saying that Lab experiments are planned/designed?
All experiments are supposed to be designed. Its not a faith based statement. none of the three statements are… the second and third are opinions based on facts. I don’t think they are controversial opinions in themselves.

its debatable whether the “design” involved in the experiment makes it impossible to be replicated in the wild… and that the discussion that’s happening.


(Ann Gauger) #94

We tested all the members of the GABA amino transferase family including an enzyme called ALAS which, as I recall was closer than hemA. And we tested an enzyme that was reported to have bothe kbl and BioF function in vitro. We tested them all by directed evolution. Most wee screened for every possible singl mutation. And soms doubles. Two we screened enough to cover 70% of all possible doubles. The numbers get to be enormous get a library large enough to handle more, all possible 2s for the last 20% or so takes an enormous amount of work. It’s the law of diminishing returns— you have hit most of the doubles now you have only a few specific ones to get…3 mutant combinations are harder still. Reeves et al 2014 Bio-complexity I think I posted a link yesterday,


(Ann Gauger) #95

They are facts.


(Ann Gauger) #96

I do not recognize your restatements or summaries as accurate restatements of my position, especially the wat you condensed them down. So it is clear you have not under stood me yet, and have no right to summarily demand answers to questions framed out of misunderstanding. I will go through my original article article and give you bullet points. Maybe that will help.


#97

@Agauger

I get it. This is also exactly what you and Douglas Axe did in your published paper, and you seemed to indicate that it was a valid test for evolution:

If this was a valid test when you did it. why isn’t it a valid test when others use the same approach?

The larger question is if an experiment on two enzymes can be generalized to all enzymes. I don’t think it can. If it can’t be generalized, then your conclusions about the inaccessibility of new function in evolution is pretty weak. We have also seen that epistatic effects from neutral mutations can play a large role, so it isn’t as simple as changing one amino acid at a time. There could also be a string of overlapping functions that leads an enzyme down a path. If A can go to B, B to C, C to D, and D to E, it would be incorrect to then ask if A can go to E straightaway. There are a lot of problems that I see in the conclusions you and Axe made, but no paper is perfect. This is purely professional criticism, and on the more personal side you both should be commended for putting the work in.

From my reading, it was on a low copy plasmid (~2 copies) under control of the native promoter with the only modification being the removal of the transcription terminator. I will dig a bit deeper and see how it was done.

We already know how that story ends. Anything found in the wild will be chalked up to pre-existing variation.


#98

Speaking for myself, I’m not happy with the established pattern of responses. The generic response has gone reliably like this: “The example is based on experiments, which are run under artificial conditions that human intelligence set up. And even if it shows a feasible aspect of evolutionary development, it’s a trivial change.” That’s why I’m not bothering to chase down papers anymore. For me, the cost/benefit ratio of making that effort is too lopsided.