Changes in gene expression as an explanation for new functions

[Aggie]

I’m currently debating with an “Intelligent Design” proponent at another forum, and I think I need to ask here about one of the arguments he’s using. The thread in question is http://forums.christianity.com/m_3311999/mpage_1/tm.htm , and I’m debating with the member who posts as Jhud.

Jhud believes Michael Behe’s assertion in The Edge of Evolution that the more mutations are required for a certain function to evolve, the more statistically improbable they are to all occur in the same organism, and that nobody has ever observed an example of an entirely new trait evolving as a result of more than two mutations working together. I’ve provided several examples of new functions that appeared to evolve as a result of multiple mutations, but for all of these he’s been able to find evidence that the genetic code for the new trait had already existed in the organism, and the only thing the mutations did was change the expression or non-expression of genes that were already present. Since I’m not particularly familiar with genetics, I don’t know how to answer this.

Can any of the members here provide an example where it’s possible to prove that multiple mutations have led to an entirely new function evolving, rather than just changing the expression of genes that were already present?

 

[sfs]

I will look around. What counts as a trait, though? For example, pyrimethamine resistance in malaria is the result of three coding mutations in the dhfr gene. That makes the enzyme coded by the gene less likely to bind to the drug (if I recall correctly), but does that count as a new trait? It's certainly a new trait for the organism, but generally the goal for the creationist in these exercises is to narrow the definition as much as possible so as to make finding examples harder.

One quick note, on the distinction that jhud is drawing between and "actual mutation" and a regulatory mutation. The technical term for the first kind of mutation is "mutation" and the technical term for the second kind is "mutation". Well, okay, they can also be called coding mutations and regulatory mutations. They're both mutations, however, and both are equally part of evolution. Regulatory changes probably contribute a lot more to the differences between closely related species (like humans and chimpanzees, for example) than do coding mutations.

 

[Aggie]

I will look around. What counts as a trait, though? For example, pyrimethamine resistance in malaria is the result of three coding mutations in the dhfr gene. That makes the enzyme coded by the gene less likely to bind to the drug (if I recall correctly), but does that count as a new trait? It's certainly a new trait for the organism, but generally the goal for the creationist in these exercises is to narrow the definition as much as possible so as to make finding examples harder.

He probably explained this himself better than I can. If you look at his long post a little more than halfway down the first page of the thread I linked to, he gave an explanation there of why he doesn’t consider antibiotic resistance in bacteria to be an entirely new trait. Even if pyrimethamine resistance in malaria doesn’t work exactly the same way, you should still be able to tell from his post whether or not that would qualify in his opinion.

One quick note, on the distinction that jhud is drawing between and "actual mutation" and a regulatory mutation. The technical term for the first kind of mutation is "mutation" and the technical term for the second kind is "mutation". Well, okay, they can also be called coding mutations and regulatory mutations. They're both mutations, however, and both are equally part of evolution. Regulatory changes probably contribute a lot more to the differences between closely related species (like humans and chimpanzees, for example) than do coding mutations.

I think Jhud probably accepts common ancestry, just with a lot of divine genetic tinkering. Behe certainly does, and Jhud’s arguments seem to be based in a large part on what Behe has written. The point Jhud seems to be making is just that in order for evolution to be completely responsible for life’s current diversity, there would need to be examples of new traits arising as a result of multiple coding mutations, and Behe’s claim is that this isn’t possible. It’s a testable prediction: if we can observe an example of a new trait arising in this way, that will falsify Behe’s argument.

 

[shernren]

Har1?

 

[Aggie]

Har1?

What’s Har1? Is that an example of this?

 

[sfs]

Har1?

HAR1 doesn't help here. HAR1 is just a gene (a gene for RNA) that shows an unusually large number of differences in humans even though it is highly conserved between other species. That could easily be the result of intelligent twiddling by the hypothesized Intelligent Twiddler. The goal here is to find mutations occurring and being selected for in real time, so you can be certain that natural processes explain what's happening. (Although I've never really understood this part -- just because you observe the process happening, how does that demonstrate that it's not something supernatural?)

 

[sfs]

Here is one:

AIDS. 1996 Sep;10(11):1205-9. "Selection conditions affect the evolution of specific mutations in the reverse transcriptase gene associated with resistance to DMP 266."
Winslow DL, Garber S, Reid C, Scarnati H, Baker D, Rayner MM, Anton ED.

Selection for drug resistance in HIV resulted in the accumulation of three coding mutations (under one set of experimental conditions). These are not regulatory mutations.

I haven't bothered to read the whole thread over there. Have you asked why regulatory mutations don't count, when they change the characteristics of the organism like any other mutation, and when most biologists think they are responsible for most evolution?

 

[Aggie]

Here is one:

AIDS. 1996 Sep;10(11):1205-9. "Selection conditions affect the evolution of specific mutations in the reverse transcriptase gene associated with resistance to DMP 266."
Winslow DL, Garber S, Reid C, Scarnati H, Baker D, Rayner MM, Anton ED.

Selection for drug resistance in HIV resulted in the accumulation of three coding mutations (under one set of experimental conditions). These are not regulatory mutations.

I haven't bothered to read the whole thread over there. Have you asked why regulatory mutations don't count, when they change the characteristics of the organism like any other mutation, and when most biologists think they are responsible for most evolution?

I think Jhud’s point is that regulatory mutations don’t create coding for any entirely new functions; they just switch functions for which the coding already exists on and off. This seems to be a fairly common “intelligent design” perspective: that every organism has a certain repertoire of potential functions, some of which are active and others of which aren’t, and that organisms can adapt to their environment within the limitations or turning those existing functions on and off. But creating the code for an entirely new function is supposedly something that requires a designer.

Is there any more detailed explanation you can provide about the exact effects of each of the mutations listed there? It might be enough if you can find the full text of that paper online anywhere, but the abstract doesn’t really explain it. And I don’t think Jhud is going to find this convincing unless I can provide a more detailed explanation that shows for certain that these mutations altered the genetic code for the ability itself.

 

[Aggie]

Can't anyone answer my request for a more detailed explanation of this?

 

[sfs]

Can't anyone answer my request for a more detailed explanation of this?

Unfortunately, no -- I'm intensely busy this week. The best place I can think of to go for technical answers and examples would be talk.origins (the usenet group, not the website, although that's good too).

 

[Aggie]

Gluadys recently began participating at the forum I linked to in this thread, so I’m interested in knowing whether there’s anyone else here who’d like to.

It’s one of the only creationism/evolution forums I’ve found where creationists have the majority in terms of numbers, but the moderation isn’t biased in their favor. This can be both a good thing and a bad thing—on one hand, it means that people who debate there to support evolution won’t have quite as easy a time of it, but on the other hand, it means there’s more opportunity to make a difference with some of the people who post there than there is at most forums.

It seems like the sort of place that some of this forum’s theistic evolutionists in particular might want to participate, such as Mallon. Does anyone else want to?

 

[shernren]

I used to post there about a year ago, but was then kicked out and told never to come back again, under any name, without any possibility whatsoever of negotiation or arbitration ... all because I used brainf*ck (with the asterisk!) as an example of an intelligent code that not a single IDer there could identify or quantify the information content of.

I personally think the moderation there is canny: they wait until you make the smallest but clearest violation of the ToS and will then clear you off without a second thought.

 

[Aggie]

I used to post there about a year ago, but was then kicked out and told never to come back again, under any name, without any possibility whatsoever of negotiation or arbitration ... all because I used brainf*ck (with the asterisk!) as an example of an intelligent code that not a single IDer there could identify or quantify the information content of.

I personally think the moderation there is canny: they wait until you make the smallest but clearest violation of the ToS and will then clear you off without a second thought.

You know, if you really wanted to go back there, it isn’t all that difficult to use an IP address and e-mail address that they won’t recognize.

Is your opinion that the moderators there are biased against pro-evolution posters, or do they appear to be this strict with everybody?

 

[shernren]

You know, if you really wanted to go back there, it isn’t all that difficult to use an IP address and e-mail address that they won’t recognize.

Is your opinion that the moderators there are biased against pro-evolution posters, or do they appear to be this strict with everybody?

I was weighing the options and I decided that if they didn't want my company they didn't deserve it. ^^ It's really the same old same old after a while; the usual raging neocreationists, the odd oddball IDer, and the scattered but persistent TEs. Except with less friends because I've been there less.

You'll have to ask USincognito, he's been there for a touch longer than me IIRC and he didn't get kicked off. However, I doubt that it is usual forum policy anywhere to ban a member without possibility whatsoever of discussion based on a single post. With the exception of spambots and trolls, and even then, those don't have good prior posting records. I had never gotten anything close to a warning at any prior time, and my post was an extremely neutral one about the philosophy and mathematics of recognizing information. It is entirely unfair for me to assume that the moderation was biased against me based solely on my case, of course, but I can't help but suspect it.

In any case, they explicitly told me not to come back with different IP / email - and even though I could do it without their detection, I'd rather not. On principled grounds.

Have fun in there. Is Bede still up to his usual cool TE stuff? Ask him about his "supervillain" post.

 

[RecentConvert]

I’m currently debating with an “Intelligent Design” proponent at another forum, and I think I need to ask here about one of the arguments he’s using. The thread in question is http://forums.christianity.com/m_3311999/mpage_1/tm.htm , and I’m debating with the member who posts as Jhud.

Sadly, while I'm looking for a new and more active forum to participate in, this one doesn't qualify. While there are more Creationists to try to speak with, they are totally unreasonable. They are simply immune to logic and reason. What can you say to people like that?

 

[Aggie]

I don’t recall seeing someone named Bede there. Maybe he got unexpectedly banned also.

I don’t think all of the creationists there are so bad, though. There’s one in particular, who posts as “Raptorman”, who’s the most intelligent and reasonable creationist I’ve encountered in several years. The reason I first registered at that forum is because when USincognito first told me about it on AIM, I noticed there was a thread by Raptorman about feathered dinosaurs on the first page of the forum. And—surprise, surprise—the point of the thread wasn’t to propagate some creationist argument about them. The reason Raptorman had posted this thread was to rebuke other creationists who were claiming that all of these fossils were fake, which he considers an obviously faulty argument, and to say that he was e-mailing Answers in Genesis to demand that they correct some such obvious inaccuracies in their articles.

It’s hard for me to resist the opportunity to debate about my favorite topic in evolution (the origin of birds) with a creationist who’s this reasonable. Some of the other people there also seem better than what I’m used to at CF. Jhud, the ID proponent who I mentioned in my OP here, is kind of stubborn but he definitely isn’t stupid. He was a biology major in college, and he knows as much about biology as you’d expect from someone with that level of education about it, which makes him more knowledgeable in this area than almost all of the anti-evolutionists here.

 

[shernren]

Bede used to be infrequent even when I was there (which was probably before last year; ask USincognito, he remembers more about my tenure there than I do ). And I tried looking through the deep archives and couldn't find his supervillain post. Real pity.

Well - hope you enjoy your stay there. It seems like you already are. RecentConvert, don't write the place off, you might just enjoy it. Jhud often makes a little more sense than busterdog even if the logic is still similarly fundamentally a touch off-kilter. You might just like the place!

But me, I'm happy where I am, and if they don't want me back, they don't need me back.

 

[RecentConvert]

shernren, your plea was pursuasive so I tried to read the forum again but... it's just as abominable as I remember. If you were willing to believe that all evidence for evolution was faked by the evil atheistic scientific conspiracy then there's nothing I can say to you and no meaningful discussion can happen...

 

[Tinker Grey]

I'm not sure I understand your comment, RecentConvert. shernren is a TE, not a YEC/OEC.

Now he wasn't always and may not have been on that other board ...

 

[sfs]

Gluadys recently began participating at the forum I linked to in this thread, so I’m interested in knowing whether there’s anyone else here who’d like to.

It seems like the sort of place that some of this forum’s theistic evolutionists in particular might want to participate, such as Mallon. Does anyone else want to?

I was there a couple of years ago. I found the atmosphere unpleasant and the discussions unprofitable, so I didn't stick around. I prefer to keep my blood pressure low.

Random note: I'm typing this while sitting on the auditorium floor at the annual Biology of Genomes conference, listening to a talk about the platypus genome. I just narrowly avoided tripping Francis Collins as he walked by.