Criticisms vs. Attacks: Where's the line?

They once posted a “transcript” of an alleged interview with Barbara Forrest, which was actually a completely fictional parody of her, giving her the name “Dr. Barking Forrest”. So they’re clearly capable of sinking to pretty benthic depths.

Criticisms need to be focused on the science, not on pictures in brochures.

Thanks for the comment. Did you take a look at the second set? These were worse in my opinion, first because it was a gross misrepresentation and second because I was accused of something that is just about the worst thing a scientist can be accused of–hiding or falsifying data that disproved your hypothesis. BTW I never received any email inviting me to respond. I posted in 2012 was because of a public harrassment (I don’t actually know what term to use it was so bad) that occurred at a museum event, when I was repeatedly called a liar and a fraud, even after I explained what had really happened. In my published rebuttal I laid out all the facts (not the misrepresentations of David Brooks). But it has had no effect on any detractors.

When was this?

In 2005, before the Dover Trial. They were subjecting Forrest to public ridicule because they knew she was a witness. They had the fictional interviewer repeatedly get her name wrong, and Barbara attempting to correct it, until she was eventually called “Dr. Barking Forrest” despite all her previous corrections. Originally the article did not contain any advisory that it was an actual parody. Later a note was added saying it was a parody.

In 2005, before the Dover Trial,

Can you give me a little more so I can verify this? If true, such juvenile behavior is inexcusible.

Sure, how about the actual page itself, which is still online?

MW Where talking with Dr. Bark Forrest about intelligent design …

BF That’s Dr. BARBARA Forrest, Marv …

MW Oh, I do apologize. In our studios today is Dr. Barb Forrest –

BF Ph.D.

MW Right, Dr. Barking Forrest Ph.D, and we’re talking about intelligent design. Now let me ask you, Doc, just what’s wrong with intelligent design?

It had no effect on your detractors because what you described was a beneficial mutation. Just because it didn’t produce the activity you were looking for does not exclude it from being a beneficial mutation. Beneficial mutations are permanent changes in DNA sequence that allow the carrier to outcompete others in the population, and that is exactly what appeared to have happened.

A criticism I have (not an attack) is that the definition for “genetic information” or whatever moniker is being used by ID researchers is entirely meaningless. Whenever I see the goal move from “beneficial mutation” to “gain of information” you know something is up. I would strongly suspect that if an ID research tested every mutation that has happened in the lineage leading to humans since the common ancestor of tetrapods that they would define each and every one of them as a loss in information. A gain in information is nothing more than Lucy pulling the football away as Charlie Brown goes to kick it.

2 Likes

New word for me today? Check.

That’s what’s great about this site. Amidst the ivory-tower, professional grade fart banter, you can always build your vocabulary.

Thanks, Jonathan.

8 Likes

I can’t hear the word “benthic” without immediately contrasting it with “limnetic”. Brings back memories of ecology courses, and stickleback evolution (PDF).

Well … kudos to all the forum participants and officials for striving to raise our discourse from the benthic up into the limnetic.

So today was a two-fer for me. My brain may overheat if this keeps up.

3 Likes

Maybe some day, we can follow a verbal Tiktaalik and make it up onto the shore!

1 Like

2 Likes

Ditto. I assumed it was some kind of ancient Greek reference perhaps.

The question I set out to ask was whether the cell could figure out another way to make biotin. The answer was no. What it succeeded in doing was to take up biotin from its dying neighbors. That is a beneficial mutation, yes, in the short term. It does not solve the problem of making biotin. I neither hid, disguised or denied my experimental results. I merely point out that recruitment didn’t work. And that was what we set out to test.[quote=“T_aquaticus, post:27, topic:36875”]
beneficial mutation" to “gain of information” you know something is up.
[/quote]

The term of art is gain of function or loss of function. Those are terms used by geneticists to mean very specific things. A beneficial mutation can be either a gain of function or a loss of function mutation depending on the context. So for example, in a competitive situation where a cell needs to grow rapidly and it is carrying around genes that it does not need, the likely thing that will happen is that one or more genes will be deleted. That’s a loss of function mutation but it’s also beneficial. Gain of function mutations are much harder to come by but they can happen (See my comment about the beneficial mutation I acquired in the lab. It was likely a gain of function mutation that increased transport of biotin.). In Michael Behe’s quarterly review article he discusses both kinds of mutation and describes examples of each.
I wrote a paper with Ralph Seelke in 2010 in which we described a situation where bacteria chose to delete or inactivate genes for making tryptophan rather than take a two step pathway to full function for making tryptophan. The reason ? The genes for making tryptophan they deleted or inactivated were broken and useless to the cell, but they were being expressed and translated. That takes energy, and is costly for the cell when the proteins are nonfunctional. So the cell gained a growth advantage by deleting or inactivating those genes— it was a beneficial mutation. At least in the short term. But by doing so the cell lost the ability to make tryptophan forever. We found that only one out of 10 to the 12th power cells actually took the two—mutation stepwise mutational path to full function. So the takehome message is you can actually get a beneficial mutation by deleting genes. Or by loss of function in other words. And I suppose you might call it loss of information—that’s not the technical term. But bear in mind—beneficial mutations that are loss of function mutations are a one-way street. The function that is lost, if it’s lost by deletion, is gone for good. And it would be fair to say, that there has been a genuine loss of information.

Lenski‘s lab has also shown this. In their long term evolution experiments, they repeatedly see mutator mutations arise. These mutator genes cause an increase in mutation in the genome. In the short term it is a beneficial mutation because it causes in some cases the deletion of genes not being used. That gives the cell a growth advantage. But the continual high rate of mutation eventually causes the self-destruction of the genome due to irrevocable loss of function.

No game playing here.

Juvenile. Yup. mmm now I need characters to make a full comment. My we are up late.

If you agree that it is a beneficial mutation, then you have an example of a beneficial mutation.

Since I wasn’t at the conference nor am I familiar with all of your papers I can’t claim that you deny the existence of beneficial mutations. I don’t know where you stand on that specific issue. However, it appears that we at least have some common ground in appraising these mutations which bodes well.[quote=“agauger, post:34, topic:36875”]
No game playing here.
[/quote]

You listed examples of losses in function, but do you have examples where mutations have given rise to gains in function? I will take a look at Behe’s review article later and see if there is more to comment on.

A recent paper you might be interested in is Starr et al. (2017) from Joseph Thornton’s lab (I think you mentioned you were familiar with his work in another thread). In the paper they showed how mutations in an ancestral estrogen response element gave rise to a steroid response element which included a shift in DNA binding motifs. I would be interested in your comments at some later date as it relates to gain/loss in function. Of course, I hardly expect you to respond to every paper I link to, but I thought it might be of interest.

As others have commented, your grace is uncommon and a model for others to follow. Thanks again for your time and consideration.

2 Likes

Coming back to this claim . . .

In an article written by Axe and Gauger they did say they were trying mimic evolution:

From here on it will become increasingly apparent that each of the problems we describe is compounded by the others. If new enzyme functions can evolve by consecutive adaptive mutations,4 each known to occur spontaneously with reasonable frequency, then Problem 2 would be of no consequence. The difficulty arises from the fact that they typically appear not to be achievable in this way.

As mentioned in the introduction, when we attempted to convert an enzyme to perform a new function, we found it to be surprisingly difficult [2]. The starting point was an enzyme we designated Kbl2 (2-amino-3-ketobutyrate CoA ligase), and the target function was that of BioF2 (8-amino-7-oxononanoate synthase). The structures of Kbl2 and BioF2 are so similar (Fig. 1) that the enzymes are commonly assumed to be close evolutionary relatives. However, after extensive testing of mutations that were carefully chosen for their potential to achieve the desired conversion, we found success to be elusive.
reference

If you are trying to claim that new protein function can not evolve, then perhaps you shouldn’t cite experiments that don’t model evolution. This is a straightforward criticism.[quote=“littledoweknow, post:1, topic:36875”]
So whether or not this was a real-world evolutionary transition is actually irrelevant to their paper or the merits of their findings. The point is that evolutionists believe that functional transitions between two similar enzymes, much like these two, should be a very modest feat for selection and mutation to produe, and the sort of evolutionary change that can happen all the time. They found that such a transition would actually require many mutations before providing some advantage–so many to make it evolutionarily infeasible.
[/quote]

They found no such thing. The evolutionary model uses the ancestral sequence, not the derived sequences found in the two modern species. If you are going to claim that the new protein function could not evolve then you need to start with the protein that evolved, not the derived cousins. Epistasis is a real thing, and it can’t be ignored. Mutations are not an island because they depend on other mutations in the protein. One mutation may negate another, so using the derived proteins is not the same as using the ancestral protein.

1 Like

The great BioLogos experiment of whether it is possible to have a gracious online forum about origins is on shaky ground these days… I’ve just scanned the posts in this thread and have a few observations, and one piece of advice:

  1. There is no strict and formal way of identifying ad hominem attacks. That’s why they’re included in the informal fallacy section of Christy’s rhetoric book, rather than in symbolic logic text books. If I say, “that guy doesn’t know what he’s talking about” is it a statement of fact or an insult or both? It depends on the context. It may be entirely relevant in judging the substance of an argument as to whether that guy knows what he’s talking about. And it’s tough to determine tone in online communication.

  2. Which group is being treated the most unfairly also has to be understood in a particular context. For Christians in general in America, there is no doubt that we who accept evolution are treated far worse than ID people are. Among scientists in general, there is no doubt that ID people are treated far worse than evolutionary creationists. Does anybody really doubt this? The problem is that there are places where those general communities shade into sub-communities. This is one of them. Which leads me to:

  3. This Forum is not intended to be some neutral site. It is maintained by BioLogos, and we have a mission (it’s on the homepage). We’re happy to allow people who do not share our views to come onto the site and interact with others. We hope to understand them better. But there shouldn’t be an expectation that all views here will be found equally plausible. Furthermore, if the Forum doesn’t advance the mission of BioLogos, our leadership should say, “then why are we putting all the time and energy into?” Anyone is free to create their own online message board and invite people there and make up any rules you want. We have our rules here, and we are also the judges of those rules. Our moderators do an incredible job. Yes of course they’re fallible people and have a finite amount of patience and goodwill. But please understand that without them there would be no forum. It’s not their responsibility to make you behave. Which leads me to:

  4. Finally, a piece of (unsolicited) advice: If conversation about origins with people who don’t find your views obvious or plausible makes you angry, go do something else. There are lots of really great things to spend your time on (e.g., it’s October baseball). If commenting on the Forum has become an obsession or an addiction, maybe it’s time to fast from it for awhile. We’d like to keep the Forum going (unlike the other origins organizations), but will only do so if you all can control the level of snarkiness.

Thanks for listening.

7 Likes

@T_aquaticus [quote=“T_aquaticus, post:37, topic:36875”]
They found no such thing. The evolutionary model uses the ancestral sequence, not the derived sequences found in the two modern species. If you are going to claim that the new protein function could not evolve then you need to start with the protein that evolved, not the derived cousins. Epistasis is a real thing, and it can’t be ignored. Mutations are not an island because they depend on other mutations in the protein. One mutation may negate another, so using the derived proteins is not the same as using the ancestral protein.
[/quote]

This will be my last post. I have spent way too much time on this, as valuable and insightful as it has been. I have appreciated our dialog, T_aquaticus, and I hope you have as well.

I am going to take one more stab at explaining the rationale behind our research. When Doug and I were first starting our research I used to argue with him. “No biologist would expect us to be able to convert Kbl into BioF–they are too divergent. There’s too much epistasis!” And he would reply that modern proteins should be no different from ancient ones. If ancient proteins could evolve new functions then, they should be able to now. We had chosen the closest relative we could find to test, and even swapped out nearly the whole active site and binding pocket,but it didn’t work, whether by rational design or directed evolution.

The complaint immediately was, just as I had said, “but you didn’t start with the ancestral form!”

The point of all our research was to demonstrate that only a functional folded protein with some degree of starting activity for the target was amenable to conversion. Furthermore, if the only transitions that can take place are the ones that did take place, then we are extremely lucky to have a functioning metabolism, let alone a mind. Blind evolution has a problem doing this sort of thing. It would appear that epistasis, even at the beginning, constrains the paths that a starting protein can follow, and it continues to do so all along the way.

Are there paths between modern proteins, paths leading to innovation? If there are, they must be constrained as well. We would expect that. Now we get to the problem of cooption, or recruitment. It is our observation that conversion of an enzyme to a new function can work in a reasonable amount of steps, > provided it already has a small amount of activity for the target function (overlap in substrate preference, shared chemistry, etc.) If it has none of the target activity, the enzyme won’t be converted without substantial reworking, more reworking than evolutionary processes could produce. All the papers that claim recruitment to a new function, if you look at them closely, describe proteins with some degree of overlap to start.

It’s a catch-22. According to received wisdom, you have to retrace history, rewind the clock, to be able to interconvert protein function. This suggests evolutionary paths are locked in by epistasis, and there are only one or a few ways to move forward. The fitness landscape may be so rugged that only one or a few paths exist. That’s a very thin needle for unguided evolution to thread, especially if the emerging new function is very weak, and therefore not accessible to selection.

A number of studies have looked at the process from the other end, where the two proteins being compared differ by just a few mutations. The possible pathways from one protein to the other are tested to see if any of them are possible evolutionary trajectories. For beta-lactamase, a 5 mutation difference meant 120 potential pathways but only 18 were evolutionarily feasible. And that’s with the two proteins being nearly identical.

What I’m saying is that evolutionary pathways to new enzyme function appear to be incredibly fine-tuned. We shouldn’t just say “and this thing was coopted to a new function” without testing whether it’s possible. It’s not easy at all. Joe Thornton can tell you about it. So can David Baker and Daniel Weinreich. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4313208/
The title of his paper is > Should evolutionary geneticists worry about higher-order epistasis? The answer is yes.

Believe me or don’t believe me. Just think about it.

And thanks to all my interlocutors.

Ann

P.S. T_aquaticus, I hope you read the whole paper.

Not a criticism, but I find this sort of funny. Back in the early '90s, before the Internet was even a thing, I was the managing editor in charge of five national magazines with a total circulation of about 2 million copies. My constant charge to the editors was “more reader interaction!” We were always racking our brains trying to figure out ways to get readers more involved, more emotionally invested in the product. If your leadership doesn’t understand the value of that …

“Let your conversation be always full of grace, seasoned with salt, so that you may know how to answer everyone.” -Colossians 4:6

This is a place for gracious dialogue about science and faith. Please read our FAQ/Guidelines before posting.