Some Ruminations on Natural Selection and Genetics off the film "Evolution's Achilles' Heels."

Watching the film again, Evolution's Achilles' Heels, have a couple of comments I might as well get said.  I've seen just the first two segments, the one on Natural Selection and the next one on Genetics.

Taking down Natural Selection is really pretty easy, although of course it's strongly resisted by believers in evolution.  Remember that Darwin's big discovery was Natural Selection as the supposed engine of evolution, the title of his book being The Origin of Species By Means of Natural Selection.  The obvious simple fact is that Natural Selection works by subtracting or eliminating, not by adding anything, while of course evolution to be true beyond variation within a Kind requires the addition of novel features.  In fact the way natural selection produces new variations is by eliminating other variations.  Natural Selection is one of the ways new variations occur, which are sometimes called "species" if they seem quite different from the parent organism, but the point is that the processes involved are subtractive, and my own observation is that you can only subtract to a certain point when there is no more change possible -- which is my own argument in a nutshell, Evolution Defeats Evolution.  But the film simply makes the point that selection subtracts and that in itself is contrary to what evolution needs in order to be true.

The film doesn't make a distinction between the phenotype or outward form of a creature and its genotype or genetic information, but the changes that are seen in the outward form that is brought about by natural selection occur by the elimination of other forms or phenotypes, and the corresponding elimination of the genetic information that codes for the different forms.   You can have part of the genome being eliminated in one population of a species to produce one new variation, while in a separate population another part of the genome may be eliminated to produce a completely different new variation.  Either way you've got your new variation as a result of subtracting genetic information, and that can never ever produce anything truly new, it can only bring out a new combination of traits already existing in the genome, which makes the whole idea of evolution of species from species impossible.

The next subject is genetics and they cover the amazingly complex workings of DNA replication within a single cell.   They point out that the different parts of the cell couldn't have evolved separately because of their interdependence, one part needing to exist in order to produce another part, that in turn needs to exist for the first part to operate.  They also point out the essential roles of information, communication and language, also interdependent and inseparable, another proof that evolution could not possibly have designed the cell.

Mutation is of course discussed as evolution's only hope of producing anything truly novel, but of course it usually does nothing but destroy things, destroy DNA itself, destroy genes, remove parts of an organism which under certain circumstances can be adaptive, such as wingless beetles on a windy island, sickle cell anemia as the cost of protection from malaria, the loss of the ability to ingest some things protecting against poisons and so on.  All subtractions and eliminations that are sometimes adaptive but not in any sense the Theory of Evolution requires.

They don't discuss the argument I've so frequently encountered, about mutation increasing genetic diversity, which would take too much discussion for this post.  The main answer is that the increase in diversity is usually an increase in disease of one sort or another, that is, ultimately a loss to the organism rather than anything beneficial, let alone of any value toward species evolution.

They present the idea that the term Junk DNA for or the 98% of the genome that does not code for protein, was based on the ideological commitment to the theory of evolution, the interpretation being that it represents former functions in the history of the organism back to the primordial soup, that are no longer of use as the creature has evolved.   Now it is claimed that these noncoding regions of the genome actually do have functions, and many were listed though none of them discussed, so I don't know what science supports them or why there are so many different functions involved. 

I still think that Junk DNA probably IS junk, though not for the evolutionist reasons.  My creationist interpretation is that it represents the result of the Fall, or in other words the operation of death on living things since that event, death not having been part of the original Creation.  Since the Flood wiped out all but eight human beings, and an even higher percentage of animals, a lot of genetic material would eventually have died out in each species as it went on reproducing after the Flood.  So many alleles for a great number of genes would have perished that eventually those genes would themselves die out in the population wherever they were already reduced among the survivors on the ark.  Of course the increase in the destructive effects of mutations in the genome, which the film pointed out are cumulative down the generations, would facilitate the death of genes by destroying alleles to the point that a given gene locus would have no functional alleles left.  What would that be but a "junk" or unfunctional or dead gene?  Thus whatever the junk DNA used to code for is lost to all living things, former functions that would once have supported the enormous longevity that existed before the Flood. 

I like this interpretation because it fits with the Biblical understanding of the Fall.  But again, the idea that noncoding DNA has other functions has to be considered.

Novel features and the evolutionist word-magic flimflam: If you assert it aggressively enough that will make it true.

There's a new thread at EvC about how novel features could have evolved, started by Tangle, who is one of the best posters EvC has ever had. Yes, he's an evolutionist but he's reasonable, he approaches the different subjects carefully, really makes an effort to grasp the best creationist arguments and treats them as rational rather than idiotic, is able to express the arguments articulately, and tries to find good evidence to answer them.

That's what he hopes will come of this new thread, since the last one on the subject degenerated into side issues and what he calls "exotica," or a sort of theoretical neverneverland -- which is usually where I stop reading a thread myself.

Some 17 posts into this new thread my assessment of him is holding up as he's dealing well with the other posts so far and keeping the creationist argument he wants to defeat clearly on the table.

I do want to comment here on JAR's contribution because JAR's arguments for the theory of evolution are mostly irrational and emotional, assuming most of it without evidence and thinking he's produced evidence when all he's done is assert the theory and dumped an observed fact or two into it. That's more or less what they all do but JAR is over the top most of the time. What I quote from Taq in my previous post on genetic information a couple days ago is an example of this kind of thinking, a real salad of assumption, assertion and the occasional fact. And for an example of JAR's inability to distinguish evidence from fantasy see his thread about the mummified man Oetzi from a few years ago.

Anyway, here we have another JAR production. First he asks:

Is this another hunt for the super genome? I thought we put that absurdity to bed long ago?

Tangle does a marvelously clear job of answering this later, the answer being No, a super genome isn't needed, the creationist position is that all the material for variation is in the genome we see now. Again if it weren't for my arthritic bones I'd jump and dance for joy at such clarity.

I used to think some sort of super genome was probably called for to explain the very great genetic variability that would have been needed to support the vigor and longevity of pre-Flood life, both human and animal, but I came to realize that simple heterozygosity for most traits provides an enormous range of variability. And, if junk DNA represents all the genes lost through the bottleneck of the Flood, and killed by mutations down through the generations since then, there would have been a huge range of genetic possibilities available before the Flood, and these two factors alone amount to a "super" genome without having to posit any difference in its structure.

Then JAR gives us this information:

We have come a long way in a fairly short period of time in sequencing various genomes. There are grape and cow and human and ancient human and neanderthal and bee and chimp genome sequencing projects and one factor has become pretty much a universal characteristic and that is that the genomes can be identified.

Send a lab an unknown sample and they send back a short note saying "That's a goat." or "That's a human." or "That's a elm tree".

We have samples from ancient folk and modern folk, from here and from there.

Marvelous! Exactly what a creationist would expect to see! Exactly what exists in reality! Observed facts that confirm creationism. Of course he doesn't notice that he's confirming creationist expectations and assumes instead that he's confirming his evolutionist bias -- or perhaps he thinks that if he announces it aggressively enough it will stop supporting creationism.

But then in a mind-boggling non sequitur he says this:

Novel features evolve over time in populations by changes in the genome that then get filtered by natural selection.

But all he's offered so far is nothing that could support this amazing leap into Evo Fantasyland but in fact supports the creationist view. The fact that solid scientific laboratories can so clearly recognize different Species from a look at their DNA naturally raises the question how one could evolve from another, how novel features could possibly arise. But of course he doesn't know, all he can do is recite the Evolutionist Creed that flatly declares that they DO arise, do "evolve over time in populations by changes in the genome". Uh huh. HOW, Jar? Silence. And he also knows that they "then get filtered by natural selection." Which isn't in dispute.

Then he adds another non-sequitur in another bit of creed:

It all comes down to imperfect copies.

I'm glad Tangle seems to know how to avoid getting entangled as it were in this typical frustrating evolutionist irrationality, and I hope he can continue doing so and get this thread on the track of something useful.

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Then in Post #18 JAR says:

But today we can identify not just individual species from a DNA sample, but often specific populations within a species.

That shows that genomes do change over time.

Again, he says this as if he's saying something that supports evolution, but in fact it supports creationism just as well. It's great to hear that DNA can tell them so much about a species and its varieties, really great. It reflects exactly what a creationist sees in the phenotype, and it's great to see that the DNA reflects it so exactly. The usual variation, the expected variation built into the genome. Microevolution.

Why can't these people at least LEARN what the creationist claims are and stop arguing with their straw men? And this is only one part of the futility of the Evo-Creo debate.

Well, again, I hope Tangle is up to untangling all this.

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5/24 Too bad, apparently Tangle isn't. The thread has degenerated into obscurantist technospeak, more credal announcements peppered with the usual accusations of creationists.

And of course nobody has criticized JAR for posting information as if it was evidence for evolution when it actually confirms creationist expectations just as well, proving again the futility of debate there.

Too bad, started well.

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May 30 follow=up. Tangle again seems to have extricated the question from the oblivion that was threatening:

There have been a couple of further studies by the same people on these mice that add to the evidence. This one shows that natural selection is the mechanism that matches dark mice with dark rocks and light mice with light rocks. (Sadly, I can see only the abstract)

Previous work has demonstrated that two Mc1r alleles, D and d, differ by four amino acids, and are responsible for the color polymorphism: DD and Dd genotypes are melanic whereas dd genotypes are light colored. To determine the frequency of the two Mc1r allelic classes across the dark-colored lava and neighboring light-colored granite, we sequenced the Mc1r gene in 175 individuals from a 35-km transect in the Pinacate lava region. We also sequenced two neutral mtDNA genes, COIII and ND3, in the same individuals. We found a strong correlation between Mc1r allele frequency and habitat color and no correlation between mtDNA markers and habitat color. Using estimates of migration from mtDNA haplotypes between dark- and light-colored sampling sites and Mc1r allele frequencies at each site, we estimated selection coefficients against mismatched Mc1r alleles, assuming a simple model of migration-selection balance. Habitat-dependent selection appears strong but asymmetric: selection is stronger against light mice on dark rock than against melanic mice on light rock. Together these results suggest that natural selection acts to match pocket mouse coat color to substrate color, despite high levels of gene flow between light and melanic populations.

Jun;58(6):1329-41.
http://www.ncbi.nlm.nih.gov/pubmed/15266981 The writers of these papers are very confident that they have identified the genes responsible for coloration in the mice that they have studied (but not other mice in other locations) and say that the difference is 4 amino acids.

How confident can we be that the allele changes are as a result of a mutation of an 'original' gene?

Good question I say. But I'd also say they don't have an answer because that question isn't one they are investigating. Mutation is usually assumed rather than made the subject of scientific inquiry.

Dawkins at UC Berkeley

I'm now listening to a Richard Dawkins talk given at UC Berkeley. It's supposedly built around his book, The God Delusion, but his focus is mostly on evolution.

He's made it clear that to him Natural Selection is the driving force of evolution. In part two [5:19] he's saying that:

Natural Selection is cumulative. It starts from simple beginnings and works up by gradual degrees, incremental degrees, to the prodigious heights of complexity and improbability that we see in the living world.

Here are a couple of examples of the products of natural selection ... On the right is a rose thorn [5:48] an adaptation by roses to avoid being eaten and that thorn has been carved and shaped by natural selection over many generations.

On the left, those are not rose thorns, those are bugs. They too have been carved and shaped by NS into the shape of a rose thorn as protection against their own predators.

Now, obviously he really believes this, and he really seems to have no notion at all that what he's just described is pure fantasy without evidence, entirely an assumption based on the theory. If I were to say the whole scenario is conjured entirely from faith he'd strenuously object and insist that it's based on evidence and fact and is a really elegant example of natural selection in action.

Natural selection is not just an alternative to chance, it's the only ultimate alternative to chance that's ever been suggested. Design is a workable alternative but only in the short term because you still have to explain where the designer came from.

In the interview he did of Wendy Wright, Dawkins expresses frustration that nonscientists feel so free to disagree with scientists, but he quite blithely mischaracterizes matters that philosophers and theologians for centuries have studied all their lives without showing the slightest grasp of anything any of them have said. Christopher Hitchens does the same. They multiply straw man arguments out to absurdity, and unfortunately these arguments appeal to people just as ignorant as they themselves are.

This idea that the Designer must himself have been designed is an old and sophomoric notion and he should have studied enough of the history of religion to know that -- at least if the Designer is considered to be of the order of the Biblical God. Of course, if aliens from outer space seeded our planet they must themselves also have been designed, but this is really getting childish. Not only Biblical theology but philosophy has answered for a God who could have created the entire universe. The philosophical idea of the First Cause is an answer, a cause that itself has no cause. But if you're objecting to Christianity, you need to address what the Bible says, and the Biblical revelation is that God is the Self-Existent One, beginningless and endless, Alpha and Omega, complete in Himself and unchanging. God is not Himself like His creation. Everything in the universe has a cause, but God does not.

God is living spirit and can only be known by living spirit. But Dawkins makes the absurd statement that God's existence should be regarded as a scientific hypothesis. God isn't knowable through science because He is outside the physical universe (unless the obvious inference that design requires a Designer is admitted as science, as truly it should be). If you are going to criticize a religion you should at least know what that religion SAYS (something Pascal pointed out in his Pensees). Of course he's right that God COULD theoretically intervene in a way to convince everyone of His existence even during his lecture, but his ignorance of theology deprives him of any inkling that the sovereign majestic God would choose not to act to dazzle profane unbelievers who would never be brought to a proper respect by such a display.

But I'm getting into nonevolution questions too much now. So back to Natural Selection. It's really amazing how scientists will go on and on about something like that rose thorn example and the bugs that imitate rose thorns, AS IF such examples PROVE evolution. Sometimes such phenomena DO demonstrate natural selection -- I do believe the famous dark and light moths example demonstrates natural selection -- but in the rose thorn case it's hard to know if NS is how the bugs got to looking like rose thorns, or how the rose thorns got there in the first place (I've seen deer eat roses without balking at the thorns in the slightest, which kind of shoots down the idea that the thorns evolved because they succeeded at keeping the roses from being eaten). Wouldn't you have to show that looking like a rose thorn conferred some identifiable protective advantage to the bugs -- but does LOOKING like a thorn accomplish anything at all? These are questions, I don't know, it just seems that too much is being taken for granted here.

But none of this matters anyway because NATURAL SELECTION IS ONE OF THE PROCESSES THAT BRING ABOUT ORDINARY VARIATION OR "MICROEVOLUTION" AND PROVES NOTHING ABOUT THE CLAIM OF EVOLUTIONISTS THAT SPECIES EVOLVE INTO OTHER SPECIES, known as MACROEVOLUTION. In the case of the moths that are less visible against a tree of their same coloring, if they then took up residence on a tree of a different color they'd gradually change to accommodate that new coloring as all the visible types would be eaten. More and more moths with the tree's coloring would come to characterize the population. This isn't evolution, this is just built-in adaptive variation, microevolution, though it is driven by classical natural selection.

This is elementary creationism and it's just amazing that Dawkins completely ignores it.

Besides, I've posted at length here arguing that because of the way selection events (both adaptation-driven and accidental) work on populations, macroevolution cannot ever happen in any case.

[8:00+] He's pursuing the idea that Design is not the only alternative to chance, that the complexity and beauty of nature CAN be explained by Natural Selection.

I'm sure he believes this, but it's typical mystification nevertheless. He cannot prove it but he doesn't need to prove it, he needs only to assert it -- assert it even at the length of an entire book (that carries a lot of persuasive power in itself, however illegitimately) and trot out some homologies that he arranges in a graded series of genetic descent purely mentally, purely imaginatively, without the slightest reference to any actual factual evidence that this relationship has ever occurred in reality. The simple fact that he can come up with such an imaginative sequence is mistaken for evidence in itself. This is delusion. The whole analogy of the blind watchmaker is also nothing but such an imaginative construct about how it all COULD have come about according to natural selection, a mere mental construct also mistaken for evidence, although it exists only in the mind, it utterly defies reason (reason is solidly on the side of design's requiring a designer) and there is no actual evidence for it, but that doesn't stop them from claiming it is so, dogmatically pronouncing that it IS so.

PLEASE, Mr. Dawkins, rethink all this.

7:43 [still Part 2] The logic of creationist arguments is always the same: Some natural phenomenon is too statistically improbable, too complex, too beautiful, too awe-inspiring, to have come into existence by chance. Design is the only alternative to chance that the author can imagine. Therefore, design must have done it. And science's answer to this faulty logic is also always the same; Design is not the only alternative to chance. Natural selection is a better alternative.

Ah heck, we CAN TOO imagine natural selection, same as you can. We can follow out the same Rube-Goldberg sequence of improbable events, acting in a homologically graded series of imaginatively fleshed-out fossils that have never been observed in living reality, to the same preconceived conclusion you come to. Our problem is that we know it flies in the face of probability, reason, logic and any other law of rational inquiry and science that may exist, AND that there is no evidence for it, whereas design OBVIOUSLY implies a designer -- obviously, intuitively, rationally, logically, reasonably and probabilistically -- and I'd add "absolutely" if I could get away with it.

8:18 Notice what rotten logic it is. [This is projected as a numbered list on a screen] [1.] We have Theory A and Theory B.

Ooo, this oughta be good.

[2.] Theory A is supported by loads of evidence.

Well, that sure as heck isn't evolution, as I've been arguing at some length lately. LOADS of what is taken for loads of evidence simply is not evidence but imaginative castle-building -- speculation, hypothesizing, analogizing, computer modeling of mental constructs floating ten feet off the ground, etc.

[3.] Theory B is supported by no evidence at all.

Um, now THAT would be evolution, of course, right? Oh, uh, sorry, yeah, you were going somewhere else with Theory B. But, hm, yoo hoo...

Now here's the key step in the argument: [4.] "I can't understand how Theory A explains phenomenon X. [5.] Therefore Theory B must be right. I bet you don't know how the elbow joint of the lesser spotted weasel frog evolved. You don't? Right then, God did it." This kind of argument is a failure of the imagination. I've described it as the Argument from Personal Incredulity.

Well, I'm not going to claim that all creationist arguments are models of logic, lucidity and fairness, and I'll grant that you've probably been driven crazy by this sort of thing on too many occasions, but really, Mr. Dawkins, this is an awful caricature that ought to be beneath you. I'm sure you must also have seen some doozies offered on behalf of evolution by some similarly confused laymen. (Of course I think you've offered quite a few yourself, though of a more sophisticated kind.)

A metaphor for extreme improbability is a combination lock, a very good high-quality combination lock of the kind they put on bank vaults. A bank robber could theoretically get lucky and hit upon the right combination ... but in practice [such] locks are designed with enough improbability to make this tantamount to impossible, as unlikely as Fred Hoyle's spontaneous coming-into-existence of a Boeing 747.

(what are you working up to, here? That Natural Selection KNOWS the combination perhaps? -- Naaa)

[Part 3/6] But now imagine a badly designed combination lock, one that gives little hints, a bit like the childhood game of hunt-the-slipper where you say "getting warmer, getting warmer, getting cooler, getting warmer, getting warmer." Suppose that each time you turn the dial you get a little bit closer to the correct combination. Suppose that the bank vault door creaks open just a chink and a little bit of money spills out -- The Dribbling Combination Lock ... is a better analogy for Darwinian evolution than the real bank lock which offers only two possibilities, the jackpot or nothing.

Oops, haven't we got a sort of teleological model going here now? Either an all-or-none jackpot-producing system OR a dribbling-bits-of-money system is teleological -- that is, there is a GOAL both are aimed at -- the "CORRECT combination??" But evolution supposedly HAS no goal, right?

And the trouble with creationist arguments is that they all think that Evolution by Natural Selection is a jackpot-or-nothing argument. Nothing could be further from the truth.

You've lost me completely now. Who thinks this? What exactly does it mean, anyway?

But God, the God theory on the other hand, really is a jackpot-or-nothing argument. Because God is postulated as being there from the beginning, before the process of evolution got going. I can imagine god-like beings ... such that if we ever met them, and if they came here, for example, and in order to get here they would have to be god-like, because for sure we couldn't get there -- I mean they'd need to be technological wizards of a sort that we have no comprehension of. We would worship them as gods, but they would not be gods because ultimately they would have evolved by a gradual process. But the God of the Old Testament, the God of the New Testament, the God of the Muslims who's always been there, He is the Ultimate 747.

Wow, WHO suffers from "a failure of imagination?"

This analogy is absolutely crackpot. Only created things fit the model of the Boeing 747 that couldn't be assembled from a junkyard of random parts by chance, but God is uncreated, First Cause, Prime Mover, Beginning and End, Alpha and Omega. If you can't imagine Him, Mr. Dawkins, that's because nobody can exactly literally IMAGINE such a Being who is so utterly outside our normal frame of reference, but we can "intuit" or "sense" Him by these definitions, though no words are adequate here. No PICTURE can even come close. He's not picturable.

You REALLY need to read some theology, this is ridiculous.

2:00 Well, why not teach the controversy?

Okey-doke, I can see we're now in for some more lame straw-man humor and there's no hope in sight at this point that he's going to get around to explaining that odd combination lock thing, but maybe he will eventually. Nevertheless I think I'll take a break here and post what I've got. Sigh. I did hope for something more meaty, a little closer to reality.

But to be as fair as I can be at this point, perhaps he really HAS been driven bonkers by some bad creationist arguments. Unfortunately no evolutionist I've ever run across has ever recognized a GOOD creationist argument and there are plenty of them.

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I thought this was going to be Part 1 of a series of posts but I've listened further and there's no point in continuing. He makes more lame jokes, he doesn't get back to the faulty combination lock so how it relates to natural selection or evolution and why he thinks it matters I still haven't a clue, he carries on and on about people referring to children as "Catholic" or "Muslim" saying we should protest because children can't be either just as they can't be postal workers or philosophers and so on. What's the point? We know it means "child of Catholic parents."

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I have one last thought. "Evolution by Natural Selection" is a near-mantra with Dawkins, a phrase he uses frequently, but it has an old-fashioned ring to my ear, as if evolutionism had moved on to other definitions but he's still stuck back with this oldie. It's a phrase I haven't heard experssed in such a pointed way in a long time.

DOES evolution REALLY proceed by natural selection? Do evolutionists believe that any more? Seems to me it's acknowledged that natural selection is only one of many influences on populations that lead to change in gene (allele) frequency which leads to new phenotypes. Not all changes that stick are adaptive in the strict sense that natural selection requires. They aren't even necessarily driven by reproductive advantage. They may be simply the accidental result of migration or bottleneck. The change may be quite dramatic, adaptable enough too, from such occurrences. It is such accidental factors that are responsible for creating the different subspecies in ring species, not natural selection.

And how is it that when they compare natural selection to domestic selection, as Darwin also did, since domestic selection was his inspiration for natural selection, they manage not to notice that domestic selection always reduces genetic diversity. Isolated populations formed by selection inbreed among fewer genetic possibilities. As in domestic selection, highly inbred types may be especially vulnerable to certain diseases. The reduced genetic diversity can bring about inability to interbreed with other subspecies of the same Species, which is supposedly the definition of macroevolution though it occurs because of this extreme reduction of genetic possibilities which spells dead end for change, and at the extreme an inability to change further at all, none of which bodes well for evolution theory. I guess they just don't think at all, they just toss "mutation" into the mix and ASSUME it all works out to prove evolution.