Tuesday, May 29, 2012

The Genetic Bottleneck challenge to the Flood answered again

On the thread at EvC about how a worldwide flood should have left evidence of severe genetic bottleneck in all living things, it is claimed that there is no such evidence, My answer, which I have given before here, is that they see no evidence for the bottleneck because what they are looking for is what happens to species NOW when there is a bottleneck -- such as the severe homozygosity of the cheetah.

But as I've argued here before, the evidence would simply be a great deal MORE homozygosity after the bottleneck than before, and since we have no way of knowing how much there was before the Flood we can't anticipate how much we should expect to see afterward either. But if there was enormously more heterozygosity before the Flood than there is now, say as much as 75-80% for human beings, as opposed to today's known percentage of 6.7% heterozygosity, then the reduction, the less heterozygosity and greater homozygosity today, wouldn't be noticed, it would be assumed to be normal to the species.

On the usual expectation, Dr. A gives this standard answer to the question how we might determine if there has been a bottleneck in a species:
Well, you look at the size of the population and the amount of genetic diversity within it. In equilibrium (i.e. if the population has been about the same size for a long period of time) the diversity will be proportional to the population size --- there'll be a certain quantity of diversity such that the production of new variants by mutation is just balanced by the elimination of variation by genetic drift.

If there's markedly less diversity than that, this indicates a recent bottleneck.
One clear indicator of reduced diversity is the percentage of homozygosity in the genome: the more homozygosity the less diversity. The problem is that if there was a worldwide Flood, then when you are looking only at today's populations you ARE seeing "markedly less diversity" than would have been the case before the Flood and not recognizing this. Since there is no way to measure the pre-Flood diversity you cannot make this judgment.

HOWEVER, there should be a hint in the fossil record to a much greater pre-Flood diversity, and this does seem to be the case as many species are represented by a huge number of variations. These variations are of course explained by the Theory of Evolution as stages in evolution. But if they were in fact all living populations at the time of the Flood that would in itself demonstrate a very large diversity. There were dozens of different "species" of Trilobites, for instance, and large reptilian sea creatures show an equally great amount of variety, judging from the specimens in the Karoo formation for instance.

The question of the genetics involved, however, seems to me to be most likely answered by the fact I found in Morris and Parker's What Is Creation Science? on page 112, which I quoted in a post on the subject in September of last year, where I quote Parker saying that
human beings are "heterozygous" for 6.7% of their genes, on the average. That means that 6 or 7 times in a 100, the pair of genes for a given trait differ like the genes for brown or blue eyes, or for rolling or not rolling the tongue. Now this may not seem like much. But Ayala calculates a single human couple with just "6.7% variety" could produce 10 to the 2,017 children ...before they would have to produce an identical twin..."
And I go on to comment that
He goes on to say that the whole spectrum of skin color we see today would be easily produced IN ONE GENERATION with just this 6.7% heterozygosity for that trait. Combining that with the same breadth of possibilities for size, hair or fur color, bone type, muscle type, and so on and so forth, would certainly yield an enormous variety of individuals within each created kind or type.

So I figure this 6.7% heterozygosity is what remained on average to all creatures after the Flood, or perhaps it was somewhat more then and has decreased since then. It's still enough to produce enormous variety, everything we see today.

Well, what does a bottleneck do genetically anyway? Doesn't it produce HOMOZYGOSITY for a number of traits? Isn't that what happened to the cheetah -- it has reached the point genetically where most of its genes are fixed and no variety is possible at all. Since the cheetah is of course descended from the cats on the ark, with their already drastically reduced heterozygosity -- perhaps comparable to the 6.7% of human beings -- a later bottleneck would have reduced it even further to the current state of almost 100% fixed loci, so that each individual is almost a clone of all the others, and further variation is as good as impossible.
6.7% heterozygosity as measured today under the assumptions of the ToE would be taken as the norm for human beings, but it could reflect an enormous reduction from a pre-Flood percentage and therefore represents the bottleneck of the Flood itself.

Just another of the many supposedly unanswerable challenges to the Flood and other creationist claims that have been answered quite nicely though the answer is never recognized and the same old challenges keep being repeated.

Friday, May 25, 2012

Creationists who lose their faith

EvC should stick to the evolution-creation debates and leave religion alone, but of course, despite denials, the whole evolutionist framework is just as much against religion as it is about science -- not against ALL religion of course, just TRUE religion. This is why so many young people become atheists when they become convinced of the "science" of evolution.

So here's a rather typical post by Taq that purports to identify a mental deficiency in Christians. The mental deficiency is of course nothing other than the belief itself, and he's oddly quite amazed as if he'd never encountered Christian belief before. That in itself is amazing. Anyway, the accusation of the Christians' "inability to understand" is simply false, so I thought I'd see if I could clarify things for the amazed unbeliever.

Taq is referring to a discussion at another evolution-creation debate board:
Libby Anne recently wrote a "Why I am an atheist" essay over at Pharyngula. In it, she discusses how she argued against evolution but finally conceded that the evidence was on the side of evolution:
[Libby]And then I went to college, where my young earth creationist views were challenged. I responded by fighting back. I argued with both students and professors, sure that I had some sort of truth they were missing. I brought out every argument I had, and went back to my creationist resources for more. As time went by, though, I found my arguments effectively refuted by arguments and information I had never been exposed to before. To my utter shock, it seemed that the evidence actually fell on the side of evolution and against young earth creationism. After nearly a year of fighting, I conceded defeat.
What happened next is fascinating, at least to me. Two creationists felt the need to comment: Dr. Georgia Purdom and Ken Ham from AiG. When I read their responses my jaw just hit the floor. They just don't get it, as Libby Anne was quick to point out. Quite frankly, they would have been better served not saying anything at all. In an attempt to explain why Libby Anne left the faith they have given away the farm, IMHO. Here are just a few excerpts from Dr. Purdom and Mr. Ham:
Libby seems to have things backwards. It’s not that “we know the Bible is true because young earth creationism is true,” but rather because the Bible is true we can believe what God said in Genesis about the time frame in which He created. Although she read AiG resources, attended AiG conferences, and came to the Creation Museum, I have to wonder how much she really understood what she was reading and hearing. The very idea of God creating in six literal days, 6,000 years ago, and the global flood comes from Scripture (and of course the scientific evidence confirms it)!--Georgia Purdom
So the Bible is true because the Bible says it is true, and Libby should have remembered that. Oh, and the evidence backs it up. Why not just say that the Earth is young because that is what the evidence says? I think Dr. Purdom is revealing more than she may want to with this statement.
First I wonder why Taq is so amazed at this response, why his "jaw hit the floor" and how he arrived at the conclusion that Dr. Purdom "just doesn't get it." What does that even mean, she doesn't "get it?" Get what?

Why not just appeal to the evidence for a young earth? Because a Biblical creationist starts from the Bible. Why is this so amazing to Taq? Dr. Purdom is right that it isn't that the Bible is true because creationism is true, and it also isn't true because it says it's true as Taq spins it, it's true because it's God own word and true Christians know this. There shouldn't be a question about this, there shouldn't be anything amazing about this, it's the first principle of Christian belief. Serious Bible believers pursue the creationist debate because God's word tells us the world is not as the evolutionists and Old Earthers say it is, and we expect ultimately to be able to find scientific evidence for the Biblical claims (and as Dr. Purdom says, there is such evidence). What's not to get?
Also, if you read Libby's response it is more than apparent that she did know her stuff, perhaps even better that Dr. Purdom does. It's not that Libby did not understand the arguments, it's that the arguments are WRONG. Creationists just can't understand that.
Well, of course we aren't given the arguments that Libby found so compelling, or what arguments she was using as a creationist, so there is no way to determine the rightness or wrongness of either side of the debates. No matter of course, if it's a creationist argument it's wrong by definition according to Taq, no need to produce specifics so that we could judge for ourselves.

Then Taq quotes Ken Ham:
As we train our children, we need to do much more than just expose them to resources like those produced by AiG; we need to make sure they understand them correctly and are taught to be able to answer questions logically. . .

We can undermine a lot of what we have done if we send our children to the wrong institution (e.g., a compromising Christian college or even a theologically conservative one that does not teach them why they believe what they do—and how to logically defend the Christian faith and so on).

--Ken Ham
Both Dr. Purdom and Ken Ham seem to agree on this point. The solution for creationism failing in the face of criticism is MORE INDOCTRINATION. As Libby Anne puts it:
And the solution Ken Ham and Dr. Purdom make? Double down. That’s pretty much it. Teach the same things, just more. Oh, and isolate yourself and your children from other points of view – oh the dangers of the state college or “compromised” Christian college!
Creationists, is this really the new strategy? When it becomes apparent that creationist arguments can not stand up to criticism is it really the right move to protect creationism from any type of criticism? Is this why creationists are fighting so hard to get evolution out of the classroom?
But it isn't that creationist arguments have failed to stand up against criticism -- or at least there is no way to tell in this case since there isn't enough information either about the creationist arguments Libby used and her understanding of them, or the arguments used against her and whether they could have been handled better.

But nobody has suggested protecting bad arguments from criticism, it is obviously assumed by both Dr. Purdom and Ken Ham that either Libby did not do a good job defending the creationist arguments or she caved in when there was no need to cave in, to evolutionist arguments that could have been answered. In either case, of course the response is that Christian students need better training in dealing with these things.

Taq has no problem with any of it, of course, because he "knows" that the creationist arguments are wrong. Therefore he sees further training as merely indoctrination in wrong arguments. Purdom and Ham know that people who are not solidly grounded in the Bible can be persuaded by the seemingly scientific arguments of evolutionism to give it up. Their answer is to advise better grounding.

It's good to have a good grounding in the science of course if you're going to try to debate evolutionists, but the emphasis should always be on the Bible as God's word and not just on the logic of scientific arguments. That's where a Bible-believing creationist must start, that's where our grounding has to be. The stronger the faith the better will be our scientific arguments too. Some of us don't have the mind to grasp many of the scientific questions anyway, or we can only go so far in that direction, but those who can't grasp the science still need to hold to the Bible even in the face of the kind of ridicule that is constantly coming at us from evolutionists.

The weakest creationist arguments come from those who aren't solidly grounded in the Bible, don't have a real relationship with the Lord, but only give mental assent to the truths they've learned over the years, or abandon parts of the Bible under pressure from the world. Most of the creationist arguments at EvC really aren't very good. And of course those weak in faith capitulate to the supposedly superior science of the evolutionists all too easily.

This is sad because the science that supports evolution is really the flimflam I keep saying it is. It's an illusion. But it SOUNDS scientific, and all genuine science is done in its name as well, without any real justification. The entire disciplines of biological and geological science are given over to it. It's all smoke and mirrors so it's not easily falsified and the fact that it has the allegiance of millions, even though the vast majority of them don't really understand it, exerts a powerful pressure to accept it, especially as it's backed by ridicule of dissenters.

No wonder it's not uncommon for a Christian of weak faith in God and His word to capitulate as Libby apparently did, and others all the time do. Ken Ham is right that you can't just assume that somebody who can repeat all the creationist arguments really has a good grasp on them -- same as it's even possible for someone to think he's a Christian and appear to be a Christian just because he's learned all the basic teachings and does all the accepted things, and yet not really be born again.

If your "faith" is really intellectual learning and tradition it's not really faith and it's easy to lose it. You have to build your learning ON your faith, not the other way around.

What a creationist loses by capitulating isn't just a scientific argument but God Himself. The Bible is either God's word or it isn't. WHOLLY God's word.


NoNukes in Message 8 got it right.
That the Bible is true is a given. So what the Bible says is right. The evidence, when interpreted correctly also supports the Bible, but it is possible to become confused

But Taq still doesn't get it:
Then why even look at the evidence? Why does AiG spend so much time discussing the evidence? If you already believe that you are right and can not be wrong, then why do you need evidence?
Because, knowing that the Bible is the truth we expect science will ultimately confirm it, and we believe it already confirms a great deal of it. It's not science so much as the evolutionist bias that is what we have to overcome, but that requires dealing with the scientific claims.

Wednesday, May 23, 2012

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.

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.


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.

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.
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.

Monday, May 21, 2012

Where Did All the Flood Water Go?

Yahoo! Another question answered.

Been listening to a discussion on Jan Markel's Understanding the Times radio, on the subject The Top Ten Creation/Evolution Issues with Eric Barger sitting in for her. He is interviewing creationist Jay Seegert, who has the website the Creation Education Center, where he addresses the usual problems in the creation-evolution debates with his own emphases. On the program they don't get to all the ten most frequently raised issues, only five of them.

The question that got answered in a way that so captivated me was Where did the water go after the Flood? I've never known how to answer that question and hadn't really given it much thought either, but now that I've heard Jay Seegert's answer I think how obvious it is!

The answer:

There is enough water on the earth right now that if the land areas were all flattened and completely evened out the water would cover it to a depth of 1.7 miles.

Creationists always say there were not such high mountains before the Flood as after, and that the high mountains were raised up after the Flood by plate tectonic movement set in motion as part of the whole Flood scenario, but I haven't seen that made the explanation for what happened to the Flood waters until now.

Of course, the land was rearranged after the Flood, the mountains were raised to spectacular new heights and valleys were formed to new depths, especially on the sea floor where deep trenches now lie. THAT's where all the water went.

Here's an experiment I dreamed up myself to demonstrate this: Make a thick clay type paste out of flour and water (or use modeling clay) and pat it down flat in a container to whatever depth you want, so it has a level surface. Cover it with water to a depth of oh a few inches or whatever. Don't let it stand too long or it will dilute the flour paste. Then pour out the water into a container so you have the same amount. Then gouge out deep valleys in the clay and make high mountains of the gouged-out material, keeping the same amount of clay as before. Pour back the water, the same amount of water as before. You'll have dry land and sea.

Same amount of land, same amount of water.


I would do a dance of joy and celebration if my arthritis didn't hurt so much.

Seegert also said that this mountain-and-valley-building event is referred to in Psalm 104 which made me skeptical at first.

The King James doesn't clearly say that:
KJV - Psa 104:8 - They go up by the mountains; they go down by the valleys unto the place which thou hast founded for them.
"They" refers to the flood waters, but there isn't anything here to suggest the mountains were higher or the valleys deeper than before.

But some of the other translations do say that. One of those few instances where the KJV translation IS inferior to the newer versions.

Some of the other translations say the same as the KJV, but most of them say the mountains rose and the valleys sank:
NKJV - Psa 104:8 - They went up over the mountains; They went down into the valleys, To the place which You founded for them.

NLT - Psa 104:8 - Mountains rose and valleys sank to the levels you decreed.

NIV - Psa 104:8 - they flowed over the mountains, they went down into the valleys, to the place you assigned for them.

ESV - Psa 104:8 - The mountains rose, the valleys sank down to the place that you appointed for them.

RVR - Psa 104:8 - Subieron los montes, descendieron los valles, Al lugar que tĂș les fundaste.

NASB - Psa 104:8 - The mountains rose; the valleys sank down To the place which You established for them.

RSV - Psa 104:8 - The mountains rose, the valleys sank down to the place which thou didst appoint for them.

ASV - Psa 104:8 - (The mountains rose, the valleys sank down) Unto the place which thou hadst founded for them.

YLT - Psa 104:8 - They go up hills -- they go down valleys, Unto a place Thou hast founded for them.

DBY - Psa 104:8 - The mountains rose, the valleys sank, unto the place which thou hadst founded for them; --

WEB - Psa 104:8 - They go up by the mountains; they go down by the valleys to the place which thou hast founded for them.

HNV - Psa 104:8 - The mountains rose, The valleys sank down, To the place which you had assigned to them.
[ May 22 update: After getting a typical rejoinder in my Comments section I have to add that despite all the attempts by creationists to come up with an unanswerable defense of the Flood or any other creationist claim there is always going to be an answer back that purports to be scientific. You can't "bullet proof" your Christian children as Barger and Seegert seem to expect, by having any kind of science-based answer to these things. What is your college student going to do after he's learned all these creationist answers and still someone comes back telling him he's ignorant of physics?

As Seegert points out, this area of science is historical science not the kind of science you can replicate in a laboratory, and historical science can never be proved the way laboratory science can be. So someone like my visitor can always come along and claim that the speed at which the tectonic plates would have had to move since the Flood only 4350 years ago would have generated so much heat that the oceans would have boiled and nothing could have lived afterward. He can't prove that, it's all speculation, but it sure SOUNDS scientific. Perhaps others can make calculations to counter him, but meanwhile your Christian college students are again left without a "scientific" answer.

They have to be fortified primarily with the word of God which tells us Noah and his family and many creatures did survive and go on to repopulate the earth, and, so that they won't be taken by surprise, made familiar with the fact that "science" about events in the prehistoric past cannot be definitively known, and that's the best we can do in the face of all the imaginative but unprovable speculations the other side can always generate against us.

Later yet: HOWEVER, this got me pondering what WOULD be the physics involved and I remembered some of my own speculations and other answers I'd heard in the past, and posted them in the Comments section.]

No novel features, no new information, no evolution

There is another thread at EvC which is basically about the question of whether evolutionary processes can produce new genetic information, but this one is not on the level of the genetics but the phenotype or the traits governed by the genetics. The question is How do "novel" features evolve? I've pretty much lost interest in this question from either angle but thought I'd note this post by Taq which more or less summarizes his view of the whole dispute:
Zaius has once again shown us why creationist claims are useless. They claim that novel features must emerge through evolutionary mechanisms in order to produce the biodiversity we see today. So what would happen if we were able to travel back in time to watch every single generation from the first life to modern life, mapping each and every mutation? At every step the creationist would claim that no novel features evolved, ever.
This pretty much shows that the whole argument is on such a hypothetical level that all the calls for evidence are simply futile -- no evidence could possibly exist for such fanciful guesswork and either side can say anything at all in defense of his position.

So I might as well give my own view of what would happen in the case he describes. If we COULD go back to the beginning of life and map each and every mutation we wouldn't see evolution at all, we'd see exactly what we see today, separated Species or Kinds that vary among themselves and never produce novel features or new genetic information because they never produce anything but their own Kind or Species. From the beginning of life we would see the same Species we see today though perhaps very different varieties of them, plus some Species we don't see today because they've become extinct. On the genetic level at first we wouldn't see many mutations but as the generations succeed one another we would start to see an increase. Mutations alter the genetics of the creature, either producing a genetic disease or not affecting the phenotype in any observable way. Yes, we WOULD claim that no novel features evolved ever because they don't. They never did.
The truth of the matter is that evolution does not need to produce novel features, as defined by creationists, in order to produce the biodiversity we see today. In their attempt to falsify evolution they have moved the goal posts off the field. "Novel feature" is a meaningless term as defined by creationists. "Novel feature" is a hole in the sand where they place their head.
Actually it's not. This particular question really ought to be focused on whether or not mutation is observed to produce new genes, not just new alleles but whole new genes, because that is at a minimum what "new information" implies -- again, at a minimum -- and what is needed if "novel" features could emerge. And novel features must emerge if a Species or Kind could evolve into another Species or Kind.
What does evolution need to produce? Heritable phenotypic change. Does it do that? Yep. Mutations produce changes in phenotype that are heritable, and the frequency of these new alleles is controlled by environmental pressures. Whether anyone names this change "novel" or not is completely irrelevant.
So here we are back at the evolutionist's reiteration of the evolutionist creed: what we observe happening is all that is needed to bring about evolution from one species to another, the great Faith or Fantasy that runs the whole show. They see normal variation within Species and make the mental leap that can never be subjected to evidentiary proof, that evolution is simply normal variation continued without interruption for millions or billions of years.

But let's unpack this statement. He says evolution needs to produce heritable phenotypic change and that it does that. How does he know that EVOLUTION does this? He sees heritable phenotypic change in nature and simply subsumes it under his evolutionist preconception. He assumes evolution and appropriates observable facts of nature to it. That's how it always works. That's the "scientific" procedure of evolutionism right there. Evolution is assumed and whatever is observed is mentally jammed into it. Evidence for any of this is nonexistent, it's all mental gymnastics. But heritable phenotypic change is just as well explained by the creationist assumption instead. Such change is simply the variations that occur within Species, or sometimes known as "microevolution." There is no evidence whatever that such change is open-ended as evolutionists assume, and as I will argue below, as I always do, there is evidence that there is a limit to such changes that confines them to the boundaries of a Species or Kind.
Mutations produce changes in phenotype that are heritable, and the frequency of these new alleles is controlled by environmental pressures. Whether anyone names this change "novel" or not is completely irrelevant
Mutations do produce heritable phenotypic changes, but it is one huge unproven assumption that the mutations create new alleles for viable healthy phenotypic traits; what HAS been proven many many times is that mutations have produced thousands of genetic diseases. It is pure unevidenced theory or assumption that mutations do anything that could further evolution.

The actual cause of NORMAL variation within Species is not mutations but the built-in genetic material that has been there from the beginning, such as genes for the traits that define the Species, plus a variety of alleles for the different genes. Alleles are just different forms of the genes that produce different qualities of a given trait in the phenotype. A gene may govern, say, eye color, and the various alleles for that gene will determine which color the eye will be. Mutations do not produce such viable alleles, they only interfere with these normal genetic variations and often produce distortions that cause diseases in the organism.

Mutations do not create new alleles, this has never been observed, it is something merely assumed by evolutionists, there is no evidence for it. The frequency of existing alleles may of course "be controlled by environmental pressures." Such as natural selection which could wipe out a part of a population, thus reducing the genetic variability and creating a new phenotype from the new gene frequencies thus brought about. Or a simple migration of a portion of a population to a new locale where it becomes isolated from the original population. Again new gene frequencies will be established and a new phenotype emerge. All this occurs from the simple shuffling of the alleles pre-existent in the gene pool. These alleles are pre-existing, built into the Species. There is no need for them to be formed by mutation and there is no evidence that any such thing occurs at all. Again, what there IS evidence for is that mutation is a destructive process; it alters the normal genetic formula, sometimes to the point of destroying its function altogether -- at which point the destroyed gene most likely becomes part of the great genetic graveyard known as Junk DNA. This is an UNhealthy process. Mutations not only do not do anything that could possibly further evolution, they contribute only to the deterioration of a Species.

As for what one CALLS new traits that emerge in new populations as a result of the "environmental pressures," they aren't called "novel" because they AREN'T novel, they are simply selected particular expressions out of the normal range of variation built into the Species. Except for the diseases of course, which ARE novel.

So as usual the best answer to all of this is that in reality what we observe happening IN ORDER to produce heritable phenotypic change is the DECREASE in genetic variability that ultimately leads to inability to vary further at all. Normal variation, or microevolution, has built-in genetic limits. This IS subject to evidentiary proof as I've also many times explained. If I were forty years younger and had a few million dollars I'd set up a scientific project for the purpose.

Normal variation comes about through changes in gene frequencies from population to population, which come about as populations become isolated from other populations, each having their own set of gene frequencies. This produces new phenotypes, especially in the smaller populations. If the new population is appreciably smaller than the original, which is often the case, the phenotypic change can be quite dramatic but the genetic variability of that new population will also be much less.

And so it goes until you can get what is called speciation or the development of a new phenotype that can't interbreed with the others of the same Kind, AND has drastically reduced genetic variability, which is the opposite of what it would need in order to vary further. Meaning: the very processes that bring about evolution lead to a genetic condition in which evolution is ultimately no longer possible at all. That's the end of the trail. Evolution defeats evolution.

Tuesday, May 8, 2012

Why is "new information" so hard to understand?

I don't understand why the concept of genetic information is so difficult and subject to so many odd attempts at defining it. Perhaps I'm the one who doesn't get it, maybe I'm talking about something other than information. But I don't think so.

This confusion comes up on another thread with Wounded King answering a creationist who has quoted an article that seems to be about quantifying information.

Which makes no sense according to my understanding about information, so let me try again to spell out that understanding:

Evolution to be true clearly needs a source of genetic material, something that makes DNA, makes genes etc.

Mutation is usually put forward as that source. Mutation is an accident that occurs during the replication of DNA that can rearrange segments of a gene. Sometimes the rearrangement brings about a change in the function of the gene so that it no longer does what it did before. Sometimes the rearrangement produces no observable change in the function of the gene, that is, it is still able to make the protein it made before and the trait governed by it still appears in the phenotype. Sometimes the rearrangement produces a different protein and this can bring about genetic disease. There are thousands of known genetic diseases as opposed to very few known positive effects from mutation, and those few benefits are gained at the expense of something that's basically destructive to the organism.

The kinds of rearrangements of DNA that mutation can bring about include the inversion of a segment, the exchange of a -- usually short -- segment with the same segment of the opposite paired gene, the duplication of a segment and so on.

I'm sure there are more but my impression is that nothing new is created by these means. That is it is all the rearrangement of given genetic material, and the most common outcome is something damaging to the gene and therefore the organism.

Something new, however, is what is needed if evolution is true. Something new would be a brand new viable gene for a brand new viable trait. A whole new section of the DNA strand as long as a gene that is brand new.

This is necessary because different species have different genes. Even if the majority of genes are common to similar species or even to all species, there are still definitively different genes that characterize the different species. What is needed, clearly, if evolution is true, is a mechanism that can produce such totally new and different genetic material.

As far as I know there isn't the slightest hint of a process that could ever yield such an effect. All that mutations can do is change an existking gene so that it functions differently. Enough mutations to a given gene over generations can kill it too. The very best result of a mutation would be the formation of a viable new allele. But it would still be an allele for an existing gene and an existing trait. And as far as I know even this much has not been observed. Damaged genes have, however, been observed, genes whose function has been damaged or destroyed by the mutation.

The creation of "something new" is what I've understood by "increase in genetic information." Reshufflings of existing genes are not ever going to produce the kind of changes that would lead to a new species.

What are known as new species are formed by the reduction of genetic diversity in a population until the particular alleles of the genes for the traits of the new species are favored and come to reliably characterize this new population or new species. None of this requires mutation or the addition of new information. And the genetic condition of the new species is REDUCED from the original, and every new isolation of a new species is formed the same way, from a genetic reduction.

You can't get evolution beyond the built-in potentials of the Kind because of this natural pattern for the formation of new varieties (which are called new species if they cease to be able to breed with the former population, a condition that can come about simply because of the genetic differences caused by the reduction in genetic variability it takes to form the new species.)

These changes are what is called "microevolution" and they do not require either mutation or new information.

SOMETHING like mutation would be necessary if macroevolution could occur but what mutations actually do doesn't help macroevolution at all.

A mutation that formed a new gene for a new trait, or even a sequence of mutations that could be shown to tend in that direction, is what is needed to generate new "information" which is what is needed for evolution beyond the pattern I've described above.

But even as I say that I realize I'm talking theoretically about something that is only the wishfulness of evolutionists as they deny the pattern I've described above, the fact that new varieties and what are called new species can only come about by reducing or eliminating alleles from the population of the new variety, reducing genetic variability in that population in order to form and preserve a new characteristic or phenotype, and that spells the end to all hopes of macroevolution.

Monday, May 7, 2012

A claim that a big effect from "mutation" makes "new information" irrelevant Pt.2

I have a second response to that thread at EvC I discussed in the previous post. That is, if we assume, as the evolutionists do, that humans did descend from previous life forms -- my main objection in that post was that their holding this assumption amounts to begging the question -- but if we accept their assumption for argument's sake, then perhaps we can entertain the possibility that this is an example of a difference humans have from those ancestors that didn't involve the acquisition of new genetic information.

If I take that as my premise then I have questions: Here is where I really need better description or a picture of what is meant by this "duplicate" gene, how it appears on the DNA strand and so on. My main question would then be, has this sort of change ever been seen within a species? I mean, I've seen many discussions and diagrams of different ways mutations occur and the complete duplication of a gene is not one I've ever seen.

Another question is, of course, that even if this particular human trait did evolve from some animal form, but didn't involve the acquisition of new genetic information, what about all the other differences between humans and animals? We'd need to list them and think about whether it would have been necessary that new genetic information be acquired for each supposedly evolved change to have occurred.

Sunday, May 6, 2012

A claim that a big effect from "mutation" makes "new information" irrelevant is simply definitional hocus pocus

Trixie has started a new thread at EvC titled No "new information" required:
A new paper pubished in Cell has serious implications for IDist arguments of "no new information" and "mutation only breaks things".
Why limit the complaint to IDists? I'm a Young Earth Creationist and I also believe that "mutation only breaks things" in a sense, and does not provide new genetic information.
The researchers have found that a gene responsible for neuron development has been duplicated twice in humans only. One of the copies produces a truncated peptide at high levels which interferes with the original protein. This interference has the result that neurons form more connections and over longer distances.

The duplication etc is seen only in humans. It demonstrates how a duplication of existing information, followed by a "breaking" of the gene can have profound events.
[I'm sure you mean "effects" rather than "events"]. I really can't visualize what this is supposedly describing. Are you saying that human beings happen to have a pair of a gene that occurs only singly in animals? It would help if this were more clearly spelled out, perhaps graphically illustrated. When you say it is "duplicated" do you mean there are two of this gene strung end to end along a strand of DNA or what? What do you mean by "breaking" and how does it relate to "duplication?" Are you saying that the gene that occupies this same position in animals is a continuous line of "code" whereas in humans this "code" isn't the same continuous line or something like that? I'll probably have the same questions as I read the article.

Here is the link she gives to the original article, Scientists Show How a Gene Duplication Helped Our Brains Become 'Human'
A team led by Scripps Research Institute scientists has found evidence that, as humans evolved, an extra copy of a brain-development gene allowed neurons to migrate farther and develop more connections.
(Credit: Photo courtesy of The Scripps Research Institute)ScienceDaily (May 3, 2012) — A team led by scientists at The Scripps Research Institute has shown that an extra copy of a brain-development gene, which appeared in our ancestors' genomes about 2.4 million years ago, allowed maturing neurons to migrate farther and develop more connections.
This is the caption to the photo on the page. 1) Again I need a way to picture what this is referring to. Where does this "extra copy" of this gene show up? Does it just follow an identical copy in marching order along the DNA strand as it were? 2) I must point out that the statement that this "appeared in our ancestors' genomes about 2.4 million years ago" is tendentious and would be better stated as a simple descriptive fact (unless of course the intention is purely to mystify and pre-empt opposing opinions). My attempt at translation would go something like this: Human beings have two copies of a gene that occurs only singly in animals, which allows [maturing?] neurons to migrate farther and develop more connections than occurs in animals. {I put "maturing" in brackets because I really don't know what this means.]
What genetic changes account for the vast behavioral differences between humans and other primates? Researchers so far have catalogued only a few, but now it seems that they can add a big one to the list. A team led by scientists at The Scripps Research Institute has shown that an extra copy of a brain-development gene, which appeared in our ancestors' genomes about 2.4 million years ago, allowed maturing neurons to migrate farther and develop more connections.

Surprisingly, the added copy doesn't augment the function of the original gene, SRGAP2, which makes neurons sprout connections to neighboring cells. Instead it interferes with that original function, effectively giving neurons more time to wire themselves into a bigger brain.
Again we have a tendentious statement, an interpretive statement from the evolutionist point of view, which of course begs the question of interest to a creationist. I assume by "original gene" what is meant is the gene that occurs in animals [all animals? some animals?] at the locus being discussed for humans. If humans were separately designed then there is no "added copy" there is simply a different genetic design at this locus. The statement should read something like: In animals the single gene makes neurons sprout connections to neighboring cells, but in humans the extra gene at this same locus interferes with that function, giving neurons more time etc. I also need to ask exactly-what-neurons-where are governed by this gene or pair of genes? All over the body, in the brain or what?
"This appears to be a major example of a genomic innovation that contributed to human evolution," said Franck Polleux, a professor at The Scripps Research Institute. "The finding that a duplicated gene can interact with the original copy also suggests a new way to think about how evolution occurs and might give us clues to human-specific developmental disorders such as autism and schizophrenia."
The very idea that this is a "duplicated" gene or a "genomic innovation" is tendentious, that is, it is an interpretation based on the assumption of evolution, as is the idea that one of the genes is "original" and the other a "duplication" of it. But of course if human beings did not evolve from some earlier form of life then this genetic difference between humans and animals is in reality a difference in design. In any case, descriptive language is always clearer and less mystifying than interpretive language. How about something like: The finding that two identical genes can interact with each other in such and such a way that is different from what would be expected ...

This is all crucial to the point of this thread. If this is simply a design difference and not a mutation from some previous or "original" gene, which of course the researchers assume in keeping with their evolutionist bias, if it's not a "duplication" of some "original" but simply a way the human genome is different from animal genomes at this particular genetic location, then it's not a mutation in any sense at all and has nothing to do with the question about whether a mutation can bring about new information.

It's nevertheless interesting that the presence of a copy of a gene in humans that occurs singly in animals codes for or governs such a difference in neuronal function or development. This fact can be just as well discussed -- and scientifically investigated -- from this creationist perspective as from the evolutionist perspective.

I could go on demonstrating the tendentious language of this article and attempting to rewrite it in simple descriptive terms, demonstrating that the design paradigm works just as well for the scientific purpose of showing the different function of this genetic formation in humans as compared to that in animals at the same locus. In this paradigm we have simple difference, not the assumed duplication of an assumed original, and there is no "mutation" involved and therefore the whole question of "new information" is irrelevant.

All that is going on here is that the evolutionist bias assumes these things must have occurred. But you can't prove your evolutionist assumptions by simply tendentiously defining away the creationist assumptions. That's called begging the question.

Just one last remark: That there should be big effects from a mutation -- and again, this topic is not an example of a mutation -- does not contradict the creationist position. There can be big effects indeed -- protection from malaria through sickle cell is a pretty big effect, as are all the thousands of other genetic diseases mutations bring about. This is not "new information." A method of generating new genetic information is necessary if evolution is true, "big effects" is not the criterion for new information.