Output Stream of Consciousness

The lady who plastered anti-evolution billboards around Minnesota has a website. It is full of, as I would deem it, anti-evolution propaganda, including various quotes mined out of context. Some of them might seem quite damning, like Brian Goodwin's quote:

"Neo-Darwinism has failed as an evolutionary theory that can explain the
origin of species, understood as organisms of distinctive form and behaviour. In other words, it is not an adequate theory of evolution. What is does provide is a partial theory of adaptation, or microevolution (small-scale adaptive changes in organisms)."

You might think that would indicate Brian Goodwin thinks evolution is bunk and/or didn't happen. Well, if you think you might need a little more context, you'd be right:

But far from concentrating on the development of theories of organisms and ecosystems, Neo-Darwinism concentrates on genes as the fundamental entities in biology.

This cannot succeed because it leaves out too much. Organisms are large-scale physical systems that grow and develop, run, fly, produce leaves and flowers, and generate patterns of relationships with each other. Some of them even love and write poetry. Genes do none of these things, and neither do molecules.

Ah, so concentrating on the genes is only part of the picture, in his opinion.

Regardless, the more interesting part of the web site is the forum, where you actually get to see a little bit of debating going on.

I was hoping to keep debating, but the forum has unfortunately gone back to password-protected. The arguments are aggravating but enlightening all the same. One thing I'm mildly pleased at is that they do a little homework over there, which means that some of the arguments go more in depth. That alone is worth it, because it provides some valuable learning material.

In researching some of my answers that I did not yet get to post, I learned more about the alpha helix, including a surprising revelation that in the 3-letter groups of DNA that correspond to proteins, almost a quarter of the possibilities (15 out of 61, or 64 with the stop codes included) give proteins that like to form helices. I was looking up the alpha helix because I finally found a protein picture of an ion channel that shows one of them being made of a significant number of alpha helices.

Anyhow, a short history of the exchange. This was posted to another user as a challenge by the site creator:

Since you seem to understand the evolution of 'hearing,' why don’t you explain in detail the most likely scenario of:
1. The first 3 random mutations of ONE mechanically gated hair cell
2. The first 3 random mutations of the ‘wiring’ for the electrical signals that need to transmit to the brain
3. The first 3 random mutations of the receptors that receive and react to the signals
4. The first 3 mutations needed to connect everything together while you're at it? Unless, everything gets linked together, nothing by itself will produce pressure sensitivity, which is about as basic as you can get in the evolution of hearing.

These links might help you with the mechanics of it all:
http://en.wikipedia.org/wiki/Hair_cell
http://scienceweek.com/2005/sw050318-4.htm
http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=bnchm.box.3378

I replied:

Random mutations from what? All of these would have come from something else.

There's an interesting case of a considerable amount of reuse of one particular ion channel, TRPA1, which is involved in hearing (http://www.thecrimson.com/article.aspx?ref=503849) and expressed in hair cells.

It is also used in other sensory-type situations (http://www.genecards.org/cgi-bin/carddisp.pl?gene=TRPA1) - distinguishing strong smells like cinnamon and mustard, as well as participating in the feeling and detection of cold (http://www.molecularpain.com/content/1/1/16)

There is a considerable amount of reuse of genes, proteins and substances. A number of medications are not to be taken or in some cases handled by pregnant women because the reuse is even for different developmental stages - handling things like hair loss medication that interferes with dihydroxytestosterone can interfere with male fetal development at critical stages, since the testosterone by-products do different things at different stages in the womb.

Distal-less is another pretty fascinating example. It's reused in butterfly development in multiple separate stages from segments to legs to wing spots, and humans have it as well (DLX1-4), performing some similar and some different functions.

You are correct when you say that nothing by itself will produce pressure sensitivity. That ought not compel us to stop finding out why.

My guess is that at least some of the components predate the deuterostome/protostome split, since components of vision go back at least that far (e.g. mouse and human homeobox genes for eye development can cause fly eyes to be expressed in flies)

Remember that mutations are not usually a works/doesn't work scenario. There is duplication in the genetic code (usually, spelling changes in the last of the 3 'letters' doesn't matter), plus the biggest driver in protein shape is the attraction or repulsion to water of the amino acids that make it up, and mutations tend to go between amino acids of similar (but not the same) attraction to water. Many of these mutated proteins simply affect the rates of other reactions (which go on to spur others), and that alone can be better or worse depending on the situation - think metabolism, or mucus production or adrenalin.

This is just what we find when we try to find out how things work. The is no grand moral conspiracy here, and I must say the implication of such is confusing at best.

I know I've used a lot of jargon here, but I'll explain at least the "deuterostome/protostome split". Vertebrates, for example, and insects are developmentally upside-down from one another. You can see it in the larvae or embryos. Up versus down seems a pretty important development, and yet even with some creatures as far removed in time as flies and humans, there is still some commonality, right down to the chemicals used to lay out body plan with instructions for where to put eyes, hearts and legs.

Anyhow, here's the reply by the webmaster that I can't get to reply to just yet. I'll answer between the points:

1. You claim that features arise from “something else” but we’re still waiting for you give us that hypothetical scenario of what that might look like. It should be easy for you as we are giving you the leeway of using fantasy, verses provable facts. If evolutionists can’t even come up with solid hypothetical scenarios on how new features arise from random mutations and natural selection, the theory of evolution is nothing but faith, not science.

They claim coming up with a hypothetical scenario for this is "easy" because we're allowed to use "fantasy" for it?

Can you imagine (okay, pretend you're a molecular biologist for a second) coming up with an answer to this?

"Okay, first, the 150th protein in Cadherin-23 will change from a serine (S) to a proline (P) through a mutation in the triplet codon from UCC to CCC - umm, I guess since proline is hydrophobic, it will push that piece of the protein out... I'll have to go run a simulation to see what that would do"

...and so on for the next two.

Actually, all that jargon there has some basis. Cadherin-23 is involved in gluing cells together, and it's involved in hearing, surprisingly.

Going off to research hearing, I didn't find anything immediately, but when I was around looking at information about ion channels and getting thoroughly overwhelmed, I happened across a reference talking about mechanosensitive channels. Mechanosensitive? That sounded promising.

That led me to this fantastic article on mechanosensitive channels. Go there just for the pretty diagrams. It indicates that there are channels at the cell level that can respond to mechanical stress... not just in animals and animal hearing but in bacteria and all sorts of other critters.

What ended up being even more relevant was an article specifically on hearing. If you look at the picture labelled C, you'll see cdh23, which is Cadherin-23.

Want to be overwhelmed by computer data on Cadherin-23? Look here on GeneCards.

It's a little bit hard to know where to start, so why not find out the protein structure by following the link to here?

You might need an amino acid alphabet chart to sort that out.

There's a list of variants, too. Some of the variants are sequences from broken versions of the genes, like this one that was part of Usher syndrome type 1D, which sounds a bit nasty with deafness and possible later blindness.

Other variants are simply plain old mutations that don't appear to have a negative effect.

(Quite frankly, I would wager that the negative mutations will appear disproportionately often in these lists simply because it's an invaluable tool for disease researchers.)

So now how does the demand for the first three mutations sound? Given that only one of the components of hearing is over 3000 proteins long, which would correspond to over 9000 DNA "letters".

2. You also claim that evolution “reused” a previously evolved ion channel (TRPA1) and that some components “predate the deuterostome/protostome split.” You fail to connect that your weak attempt just pushes the creation of them back to a previous time so you still need to explain how these materials arose originally.

Demanding the "first three mutations" is odd as well because the mutations have to take place in something, so you can keep tracing mutations back and back and back... until the last common ancestor(s) of all surviving life on earth... but even then, we would need to go back much further than that because even the most basic commonalities between life forms on earth are still pretty complex, including DNA and DNA replication. All other cousins to that common ancestral life form went extinct, so we have nothing concrete to compare it to in order to make an educated guess about what even earlier life was like.

So... what first three mutations? Starting where?

3. I have NO idea of what your point is on the medication/pregnant women analogy???

I was just reiterating one of the points that research has found over and over again: many proteins are used in many capacities, not just in different creatures, but in the same creature at different points of its cells' lives.

4. In regard to your comment,
“My guess is that at least some of the components, since components of vision go back at least that far (e.g. mouse and human homeobox genes for eye development can cause fly eyes to be expressed in flies)”

Hox (homeobox) genes again?

“Control genes like homeotic genes may be the target of mutations that would conceivably change phenotypes, but one must remember that, the more central one makes changes in a complex system, the more severe the peripheral consequences become. … Homeotic changes induced in Drosophila genes have led only to monstrosities, and most experimenters do not expect to see a bee arise from their Drosophila constructs.” (Mini Review: Schwabe, C., 1994. Theoretical limitations of molecular phylogenetics and the evolution of relaxins. Comp. Biochem. Physiol. 107B:167–177).
Refer to http://trueorigin.org/homeobox.asp

Evolutionary theory predicts a "use it or lose it" scenario, where if a protein is not important, organisms that have mutations in the DNA that expresses it will survive, and the gene will get riddled with mistakes. Conversely, the more important a protein is, the fewer mistakes in the gene which encodes it will happen. This is not circular reasoning. If you find a protein with very few effective changes between highly unrelated creatures, you can mutate the gene yourself and the organism will die without reproducing, virtually guaranteed.

Their point 4 is actually a very strong pro-evolutionary argument, since Hox genes are quite similar between animals, fungi and plants. The term for this similarity is "highly conserved".

Although I was talking about the Hox genes, they got the wrong impression of what I was talking about. I was not talking about mutating the Hox genes, merely that the Hox genes are so similar between flies and humans that you can substitute a fly Hox gene with a mouse or a human Hox gene, though the human equivalent is not the same.

The monstrosities that result when you move a fly Hox gene somewhere else and grow eyes instead of wings, for example, also happen if you put the equivalent mammal Hox gene there.

Yet mammal Hox genes are more similar to one another than they are to fly Hox genes. You can build a better-than-rough evolutionary diagram using Hox genes alone.

The take-home lesson there is that evolutionary theory would predict that between creatures, if you compare their gene similarity, if two kinds of creatures are more similar in one sample of genes than they are to a third, then you can predict that the similarity will be stronger across the board with other genes.

The only exception, and it's not going to drive your percent similarity down a whole ton, would be selective pressures on some genes - say, for example, the invasion of a venomous predator - but such changes leave their own hallmarks.

5. In regard to your comment,
“You are correct when you say that nothing by itself will produce pressure sensitivity. That ought not compel us to stop finding out why.”

When you figure it out, let us know. But currently, the theory of evolution is still nothing but faith, not science.

I barely scratched the surface in my investigation of mechanosensitive channels. How much would creationists move the goalposts if someone managed to describe the evolution of hearing in sufficient detail? We already have such problems with transitional fossils that fill in "gaps" being either denied by creationists or creating two new "gaps" between them.

Turn this whole problem around, though. "When you figure it out, let us know." What's the creationist explanation of it? Given that the number of ways of making any particular alpha helix or, even more so, ion channel, is exceedingly large, why would the encoding for it be more similar between primates and humans than between mice and humans, than between fish and humans, even when it's got the same darned function?

It would have to be simply and for totally unknown reasons designed that way, but telling us that the patterns we do see that point so strongly to evolution are in fact illusory is rather unbelievable.

It's like saying that rolling two dice can give you any number at all and being told that observing the number never goes below two or above twelve and that seven is the most common number... is an illusion, and that ten thousand is actually possible (and did happen once upon a time!).

It's like saying that manually-copied Bibles or Beowulf or Canterbury Tales that had the same few manuscript errors were actually separately inspired and not copied from each other.

What's their "science"?

6. In regard to your comment,
“Many of these mutated proteins simply affect the rates of other reactions (which go on to spur others), and that alone can be better or worse depending on the situation - think metabolism, or mucus production or adrenalin. “

Think proving they ‘simply’ arose by random mutations and natural selection…

No simple about it, really. Random mutations and natural selection happen now. If we are fools for projecting into the past, why isn't the data saying any different?

"But the data is saying something different." No, we're not talking about quote mining or bad math that presumes the path to current organisms is the only path or that "randomness" is somehow the only force. We're also not talking about long-disproved hoaxes, confusing evolution with the origin of life, or magnifying specific differences of opinion amongst scientists and pretending they cast doubt on the whole edifice.

Why aren't the Discovery Institute or other creationist organizations doing honest-to-goodness research, anyhow? It was supposed to be the Discovery Institute's phase 1, not just to be skipped over in favour of planting their material in schools and going for a full-on PR campaign.

They have a "squirrel to bat" thread. Even by "tipping the scales in evolution's favour", the remaining extremely high odds of getting from A to B are wrong mathematical demonstrations of purported flaws of evolutionary theory. This is precisely like the fact that if I deal you 5 cards, the odds of me dealing you those exact same cards is one in over 310 million... but nevertheless, I dealt you those 5 cards and it was somehow very easy to have done so.

Such are my adventures online when I get into debates. Before I start trying to pick apart anything else, I will bid you a good night :)