Commentary on the so-called Creation/Evolution/Intelligent Design Debate and Right-Wing nuttery in general - and please ignore the typos (I make lots!)

Friday, February 17, 2006

Latest response to Crevo

Crevo responded to my post on Haldane's dilemma'. My new comments in red.

" As an example of how out of the ballpark your take on Haldane's dilemma is, consider this: Any two humans differ by millions of substitutions. According to your take, no two humans can be related..."No, because our differences are (a) not fixed, and (b) rarely fitness related.

(a) sometimes they are fixed in subpopulations – that is why they can be characterized
(b) rarely is not never
But you miss my point.

There are clear benefits to being human, and while not all of the differences between human and chimps are adaptive, it is reasonable to think that a number of them are (and a number of them have been shown to be). The two that I think are notable and fairly uncontroversial are being obligate bipedals and brain function.

"No, they are not. In fact, they cannot be, for as I mentioned, any two humans differ by some several million nucleotides, therefore, it is impossible to determine how many substitutions, especially neutral ones, are in fact fixed."Well, since, as you said, fixed means 100% of the population, it would be impossible to tell without sequencing the genome of every individual.


However, we can get a general idea without knowing for sure. One often has to make judgment calls. It makes very little difference in the argument if you subtract out a few million on each side to account for variable regions.

Sure. A few million here. A few million there. But boy that 1,667 is the nuts!

"For example, he claims that 1667 fixed beneficial mutations are too few. But he does not know what traits the ancestor had! "

Well, first of all, this is very reasonable considering there was no ancestor.

And you accuse ME of ‘circular reasoning’?

However, we can come to at least some conclusions based on evolutionary theory on what a common ancestor between the two _should_ have. It should have a diminished brain function (probably in relation to _both_ the human and the chimp), and it would be a facultative bipedal animal. These are the traits I will concentrate on. There are probably many other traits one could deduce that such an ancestor should have according to evolutionary theory.

And so what amount of fixed, beneficial mutation is required to get a sapien from this simian? Let’s see…

" Further, in his terrible book, he implies that it would take more than 500,000 such changes if evolution were true.* This is, of course, quite stupid - the human genome only has 25-30-,000 genes!"

It is quite stupid for someone who is a biologist to make such a statement.

Why is that? Please explain it, Mr.Computer-programmer-creationist-with-all-the-answers!

A "change" is not the substitution of an entire gene. _Most_ changes are of single base pairs. Other changes are insertions, deletions, and copies. This is not restricted to the number of genes. Likewise, Haldane's calculations do not require that the change exist in a protein-coding gene. There are many regulatory regions in addition to the genes that the beneficial change could take place in.

It is quite stupid for you to have interpreted what I wrote the way you did. I know that substitutions are not entire genes. However, the point is that if all things averaged out, each gene would require many multiple substitutions. ReMine’s ignorance of development and biology dictate his foolish premise.

As a worshipper of ReMine, I should have thought that Crevo would understand at least HIS claims, but it seems that was asking a bit much. ReMine’s 500,000 claim referred to fixed, beneficial mutation. Such mutations would have to be in genes or regulatory sequence. That is, ReMine’s claim (and your de facto defense of it) implies that each gene (on average) would need to experience ~16 such substitutions, or each gene and some number of regulatory sequences would need to experience some number of such substitutions. That or a smaller number of genes and/or regulatory sequences would necessarily experience multiple fixed, beneficial substitutions

"However, the numbers he was referring to are in fact raw estimates premised on the comparisons of only a few individuals"

If we had the benefit of complete knowledge, such discussions as these would not be needed.
What we have is a reasonable estimate based on known data.

"Even if all of those changes were fixed, the overwhelming majority are in noncoding regions and many that are in genes are neutral or nearly so, and so do not fall into the "dilemma" set forth by Haldane's model."

First of all, I have to wonder at someone who assumes that a change in a non-coding region is neutral. These regions are some of the most important.

I have to wonder at how you deduced that from what I wrote. Here, let’s take a look:

“…the overwhelming majority are in noncoding regions and many that are in genes are neutral or nearly so…”

Is that a bit easier to interpret? Or doesn't correctly presenting your discussion opponant's claims matter to you?

Remember, the claim is that there are fewer than 1,667 beneficial changes separating chimps and humans from their most recent common ancestor.

No, the claim is that 1667 fixed beneficial mutations is too few to account for human evolution from an apelike ancestor according to ReMine. Don't you know your own arguments?

We have evidence of massive numbers of genetic changes, and massive morphological, social, mental, and other differences between chimps and humans. Yet we must have fewer than 1,667 _change events_ separating them.

False. Even ReMine acknowledges 10s of thousands of fixed neutral expressed substitutions. Of course, this all depends on:
1. Haldane’s model being forever and in all circumstances absolutely applicable (it is not)
2. the ancestor not having any traits that require only ‘tweaking’
(also false)
You are assuming what you conclude. Circular reasoning.

And by the way - what are these "massive" changes?

"One of my favorite refutations of this notion is the single point mutation in the FGF3-R gene that causes a form of achondroplasia (dwarfism). One little base pair substitution reduces the number of interphalangeal joints, produces disproportionate alterations in limb length, etc. Now, I am not presenting this as an example of evolution, nor as an example of a beneficial mutation. I am presenting this as evidence - proof even - that phenotypic changes do NOT in fact require large numbers of mutations."

However, the notion itself still stands. If you have a complicated system, minor perterbations in the core components WILL have drastic effects.

Not necessarily. Sure, big phenotypic changes can occur, but such changes are not necessitated by the DNA changes.

The issue is, though, that in order to make a _useful_ change of a core component requires that many genes change in coordination.

Assertion. In fact, my FGFR-3 scenario falsifies the claim.

How many individual changes would it take to turn achondroplasia into a beneficial mutation?

I have no idea what that means. It is not the mutations that are beneficial or not, it is their effect and the interaction of the effect with the environment. If the environment favored achondroplastic individuals, then that phenotype would become predominant. So, in the right environment, it could very well be that single mutation. But so what? I did not present it as a beneficial mutation or a mutation that could be one.

In addition, there are some systems which are made with a switching mechanism, so that a single switch can switch on or off two different pathways. In such cases, both pathways are already designed, you are just switching between them.

Designed? What is the evidence for this? In fact, what is the actual evidence for these ‘single switch can switch on or off two different pathways’ and are they even relevant?

Creating a new pathway, however, requires much adjustment.

Assertion. Please do not assume that biological systems operate just like computer software.

This is the point of my article here. I do not deny that you can get massive body change with a single point mutation. In fact, why stop with that one. There are a huge number of mutations whose effect is so drastic that you die before birth!

Indeed. Those are the ones that are weeded out by selection right away.

The question is not generating a large-scale effect, but generating a large-scale effect that was (a) not already coded in the genome, and (b) beneficial to the organism.

And here comes the strawman. Again, what traits are there that we have but this presumptive ancestor did not have? And I mean traits that were non-existent or are different in kind, not degree? If you cannot address that question, then ReMine’s number is meaningless. Also, phenotype changes need not be beneficial to become fixed in a population.

Just as the achondroplasia example shows, it would take quite a number of changes in coordination to get such changes to be beneficial.

You are making some rather unjustified leaps here. You are merely asserting that there must be additional mutations and coordination. This is most likely because you are unable to divorce what you do know about (computer programming) to what you only barely understand.
What is to say that another single point mutation could not do the job? What is the say that in the appropriate environment that single mutation is sufficient? Nothing. Just empty assertions.

The chances of all of those types of mutations occurring by chance in such a way, and in such sequence as that any of them can be useful is vanishingly small.

How small is “vanishingly small” and how did you figure that out?

"You mentioned 40 million changes in the DNA. Humans and chimps are inferred to have separated from each other about 6 million years ago. That works out to about 7 changes per year, or about 140 per generation (based on a 20 year generation time, which is what ReMine used). 7 a year is astronomical? ~140 per generation is astronomical? In reality, that is very close to the number gleaned from empirical studies."

Nice exercise in circular logic.

Nice way to avoid explaining yourself.

The "empirical studies" are simply calculating the differences between chimp and human genes.

Um, no, they are not. Please do not assume that everyone relies on the same cherry-picked handful of studies that you do.

In order to get that rate one must ASSUME common ancestry, which is precisely what is under consideration. Such calculations are irrelevant in a question of _whether_ there is common ancestry to begin with.

None of this seems to have anything to do with your claims of “astronomical” .

Don't get me wrong, I don't think that the authors of the article were engaged in circular reasoning -- they had a clear separation between their assumptions and their conclusions, and it was a very good paper. The problem is when you use the assumptions to prove the assumption. That's circular reasoning.

You mean like assuming ‘design’ to claim that evolution did not happen? But seriously - if you are dismissing such studies, how can you say anything about the numbers involved?

"The real fact is, you have no idea how many fixed, beneficial mutations would have been required to evolve humans from an apelike ancestor and continuing to claim that 1667 is too few is at best disinformative propaganda and wishful thinking."

It's not _wishful_ thinking, it's _reasoned_ thinking.

It is not even that. No, it is bald-faced assertion.

As someone who creates and modifies codes on a daily basis, I know what kind of interactions are required to get large-scale changes stabilized and working.

So, you alter DNA sequences and see what happens for a living? Or are you making the unwarranted supposition that genes operate just like computer code? Yes – that’s it!
You are not the only one - all creationists with engineering/computer backgrounds seem to think that thei filed of knowledge is universally applicable to biological structures and systems. It is a major fallacy, and one that forces those in such a position to make such silly assumptions.

The two features I said I was focusing on were bipedalism as well as the brain. Here is what Gould says about bipedalism in "Our Greatest Evolutionary Step" (from The Panda's Thumb):"Bipedalism is no easy accomplishment. It requires a fundamental reconstruction of our anatomy, particularly in the foot and pelvis. Moreover, it represents an anatomical reconstruction outside the general pattern of human evolution...[mentions some features that are a consequence of neoteny]...But upright posture is a different phenomenon. It cannot be achieved by the "easy" route of retaining a feature already present in juvenile stages. For a baby's legs are relatively small and weak, while bipedal posture demands enlargement and strengthening of the legs."

These are all changes that are outside the normal range of variation.

And yet other primates – indeed, other vertebrates – have feet and pelvi. And Gould was a paleontologist, not a developmental biologist.

As for the brain, consider the following:From Accelerated evolution of nervous system genes in the origin of Homo sapiens:"...the acceleration of protein evolution is most prominent in the lineage leading from ancestral primates to humans. Thus, the remarkable phenotypic evolution of the human nervous system has a salient molecular correlate, i.e., accelerated evolution of the underlying genes, particularly those linked to nervous system development."

Positive selection on the human genome lists numerous genes which are believed to be beneficially different from chimps. I don't have the data, but I imagine that each of the genes they mention have more than one change event associated with them. The authors conclude:

"Although a fair number of genes have already been identified as targets of positive selection during the evolution of humans and/or primates, these are likely to be the tip of the iceberg. As more genes are added and as alterations in gene sequences are mapped to functional changes, the study of positively selected genes may become a mainstream approach to the dissection of human biology and disease."So, what they have shown is just the tip of the iceberg.

You are not the only creationist to have hawked that article. But like the others I have encountered, you too are gleaning way too much from what is there.

Now, there is a way to salvage the chimp/monkey common ancestor problem with regards to Haldane's dilemma.

You will first have to establish that there IS a dilemma. ReMine was unable to do this, and you have not done so either.
Maybe next time?


crevo said...

For those who want to read my comments by themselves, please see my second post here:

For those who want to compare whether or not my assertions about the difficulty for core functions to handle perterbations, see this paper in the most recent issue of Science (while Davidson may not agree with me on the difficulties of change in this case, he certainly points out that parts of the genome are "more core" than others, and are more constrained against change -- thus, as I said, small changes can lead to dramatic phenotypic results, just not good ones).

Read mine. Read the professor's. Read the cited literature. Decide for yourself!

Doppelganger said...

Yes, please do.

Then read about Haldane's model, and see if ReMine's take on it and Crevo's steadfast defense of it has any merit.

Robert Rapier said...

Crevo: In order to get that rate one must ASSUME common ancestry, which is precisely what is under consideration. Such calculations are irrelevant in a question of _whether_ there is common ancestry to begin with.

Me: That is just flat out false. Mutation rates have been indendently verified. There are many different references for this. Here is a start:

So, if you are so misinformed on this, why exactly do you have any credibility at all when speaking out on biology? The number of Creationst electrical/software/electronics engineers who think that they have some special insight into evolution never ceases to amaze me.


Doppelganger said...

Still no answers to any of the questins I asked. Apparently Crevo, like most creationists, appears to believe that merely making an assertion is sufficient.