Monday, March 26, 2012

How I Became a Creationist

Somebody started a thread to find out who had known about creationism when so I'll chime in.

I never had a clue about creationism until a couple years after I'd become a Christian in my forties. I was thoroughly indoctrinated in evolution. Of course I knew about the Scopes trial, but I don't think I knew anything about what creationists actually believed and taught. Some idea that they didn't like being descended from apes and that was about it.

I went to church as a child and it was a fairly liberal Presbyterian church though as far as I recall I never heard a word about the age of the earth or how life began or evolved. I did hear the Adam and Eve story but my Sunday School teacher was very open to the question who their children could marry since you aren't supposed to marry a sibling, which already put some doubts about the story in my mind.

I went to live with relatives when I was fifteen and that meant going to a big city school for the first time and there I met people who scorned religion, including a math teacher who spent most of every class performing some kind of antics at the expense of religion. He was considered a great intellect and comedian. My best friend and I worshipped him. Those were the Sputnik years and America was feverishly engaged in promoting science in high schools so we could catch up with Russia. All other areas of study were treated as not worth a bright teenager's time. I wasn't geared to science so I accepted my inferiority, while my best friend went on to get post-graduate degrees in biological science. I did, however, give up whatever I'd acquired of religion to that point, and I first became aware of the theory of evolution in those years, and of course accepted it completely.

Years later I subscribed to Skeptical Inquirer magazine, hoping to find ammunition for my anti-religious and evolutionist beliefs but instead I found that although they covered all the right subjects I couldn't get a grasp of the lines of evidence from what they presented. It left me intellectually suspended. All I could do was take it on faith. Not that I put it in those terms. But the point was that I wanted to be able to muster the evidence for what I believed and it always eluded me.

In my forties I read my way to Christ. I was surrounded by believers in a lot of weird stuff, so it seemed to me, eastern religions, astrology, bizarre cults like Urantia, even pyramid power. I still considered myself to be a rational atheist and it seemed to me the world was coming apart. I thought Western Civilization was the height of human achievement and the political movements that attacked it through the sixties, and the eastern religions and other irrationalisms that rushed in to fill the void, were deeply depressing to me.

A series of events got me looking up something in the New Age bookstore, and some statements by a couple of Hindu gurus I found there got me suddenly believing in God, the God of my childhood though (what little I could remember about all that), not their God. I figured it was all the same. I had no idea who Jesus Christ was or what He had done until much later -- somehow the gospel hadn't really penetrated my head during those years in church. But from then on I read voraciously about religion. I no longer thought all the weird stuff was weird, anything could be true it seemed to me at that point -- and by then I'd had some "supernatural" experiences to help make the case. Occultic or demonic experiences really, through eastern oracles for instance.

It took at least a year to get through the eastern religions to Catholicism, and I thought that's where I was going to stay, but I kept reading and ended up, yes, a Bible-believing Christian. A --*gasp*-- fundamentalist. It wasn't easy with my history to come to that conclusion, not only because of my own ingrained prejudices but those of my acquaintances who were horrified as my reading seemed to be veering in that direction. I was given some books to head me back toward sanity as they saw it, but eventually I overcame all the objections and went thoroughly joyfully "insane." So I lost friends. Well, that's what Jesus said happens when you take up with Him.

And a couple years after that I found some books on creationism, probably in the Christian book store, and began reading in that area. Morris and Whitcomb's Genesis Flood was an eye-opener for me. I laughed when it hit me that the earth really IS only 6000 years old. What an amazing discovery after a lifetime of thinking in terms of billions of years.

Wednesday, March 21, 2012

Yes you DO get loss of genetic diversity with evolution Part 10

Draft to be changed as I can get to it.

[Faith]Consider the dog example while we're at it. Every breed of dog MUST show reduced genetic variability compared to its population of origin because if you want it big you're going to have to eliminate everything that tends to smallness, if you want it good natured you have to eliminate everything that breeds for ferocity, and so on
[Subbie] This is only true if the "first dog" had all possible dog genetic information, and subsequent dogs were created by taking out all the stuff that wasn't necessary for that breed of dog. This idea is ridiculous.
The first dog doesn't usually display a perfect collection of all the desired traits a breeder is seeking, just a tendency. Breeders select animals for the traits they desire. If they want bigness they breed with big dogs, if they want sweet natures they breed the sweetest ones in the litter, trying to IMPROVE the particular trait they are interested in, selecting those individuals from subsequent generations that have the best expression of that trait. They chose the original dog because it had such a trait but its descendants are selected to improve on it. Then they breed it with other dogs with the same trait. You don't need ALL original dog traits, just dogs that have the trait you want. When an unwanted trait shows up they are careful to keep that animal from breeding. Over time the traits they are seeking become established and the ones they don't want get eliminated. This is elementary my dear Watson, no doubt highly oversimplified (you don't usually get a single trait without a company of other traits along with it for instance) but nothing at all ridiculous about it.

Then Taz:
[Faith]A nearly obliterated population such as the seals which were hunted to near extinction, may actually come back in large numbers, but they will come back with much reduced genetic variability compared to their original population. Surely this is obvious?
[Taz] No, it's not obvious, because you are using it in the wrong way. It's like saying each individual atom of my computer is colorless therefore my computer is colorless. There's a fallacy for that. Try to guess what it is. While it is true that the seal population came back with less genetic variation than before, we're talking only a couple generations. You are trying to apply a couple generations of seal as an example of evolution. If I didn't get drawn in by your honest tone, I would have said strawman.

What happened with the seal population you described is called a bottleneck, where an event triggered a loss of many traits and the resulting allele frequency is completely different than the one before. In this particular case with the seal, the event is called over-hunting.

Because we know for a fact that each individual in that population carries at least several mutations compared to its parents, if left undisturbed it is inevitable that genetic variation in that population will increase given enough time. By enough time, I'm talking about at 50 generations or so, not a couple.
And again we are denying the obvious to focus on the nonexistent savior of evolution, (beneficial) mutation, and the unprovable effect of lotsanlotsanlots of TIME. Again, built in alleles are quite enough to produce a huge array of variations in most species, while mutations contribute nothing but death to the mix (yeah, even the "neutral" ones whose effect is simply invisible). And that's all they are contributing to these genetically depleted seals too, not a stepping stone to further evolution but the threat of extinction.

And again, even if mutation did contribute viable new alleles, alleles only vary existing traits, what you need is new traits, new "information" at least whole new genes.
[Taz]As a side note, the rattlesnake population in the southwest are going through a bottleneck event as we speak. People there are hunting down every rattlesnake they could find, which are usually the ones that make a lot of noise. The very trait that helped keep their ancestors from being trampled on are now working against them with humans. There are reports of increasing number of silent rattlesnakes crawling around. Goddamn rednecks...
Yeah, they've selected silent rattlesnakes, what's your point? If they keep it up they'll eventually eliminate ALL the genetic possibilities for noisy rattlesnakes -- which is what ultimately happens with all selection events.
[Taz]I'm sure that one day in the distant future, our children's children will label this period as the great bottleneck era for most species on Earth. Man has been changing and molding population genetics to our liking. I'm sure we'll look back one day and realize the vast changes we've made to wild populations everywhere.
Could be, selection happens by many means and human interference is one of them. What you and others who are in thrall to evolution refuse to consider is that such a bottleneck IS evolution -- big changes in this case, just the stuff of evolution, and it DOES come to a screeching halt because of genetic depletion -- it's just that the whole scenario -- striking new traits plus serious genetic depletion -- happens a lot faster than the usual processes of variation. These normal processes, just like bottleneck, all involve some form of reproductive isolation of a portion of the main population that brings about new gene/allele frequencies. This isolation can occur in many ways, such as migration of a random assortment of individuals, a reproductive preference pattern within a population, natural selection having to do with environmental pressures, and so on. Bottleneck just does it faster.

Friday, March 16, 2012

Yes you DO get loss of genetic diversity with evolution Part 9

And here's Taz on that same thread:
Faith writes:
If you start with twenty alleles in a population for one gene and one of them becomes crucial for a particular environment and therefore gets selected, either rapidly or slowly depending on the selection pressure, you will lose the other nineteen alleles as the one selected comes to determine this particular trait.
But this isn't how evolution works. The other 19 alleles don't just disappear unless there are selective pressures against them.
I clearly defined the situation as having selective pressures. If the selection pressure isn't severe you'll get a reduction rather than a total elimination of the other alleles.
You're still thinking in black and white.

What happens is by some selective pressure, say environmental or predatory, begins to favor one trait out of the 20, we will begin to see a steady increase of that one trait in the population. But the other 19 still remain, perhaps in lower number than before.
For the selected trait to increase, the others have to decrease, it's not a "perhaps" it's a necessity. What do you think "lower number" means anyway? Yes, they may not disappear right away, that would happen only when the new trait has completely dominated the population, but decrease they will when there is selection pressure for that one trait.
Try to think of it like capitalism. Just because Bill Gates began to dominate the silicon valley market doesn't mean all other software companies went belly up. In fact, despite Microsoft's attempts to stamp out their competitions, we still have giant software corporations all over the place. Even in cases of monopolies in the past, no one single commercial entity of a particular market has ever dominated the entire market.
You are determined to put me in the wrong even though what I've said has taken all this into account.
In other words, despite selective pressure favoring one or two or a few traits doesn't mean the overall variation of the gene pool will necessarily decrease.
IF those favored traits come to dominate in the population then the overall genetic variability will tend in the direction of decrease as the other alleles decrease. In many cirdcumstances the other alleles may remain and the original trait distribution could even be regained. But then you don't have evolution, do you? I'm talking about what happens with evolution, with the establishment of new traits or phenotypes, with speciation etc.
Now, if we're talking about the bottleneck effect... that's a different story.
Not really, it's just an extreme and it ought to be taken as an illustration of the formula -- new traits, less genetic variability.

Thursday, March 15, 2012

Yes you DO get loss of genetic diversity with evolution Part 8

NWR on that thread:
Faith writes:
My argument is that natural selection and genetic drift, all the processes that select or isolate a portion of a population, do bring about the change called evolution but also always reduce genetic variability, which is the opposite of what evolution needs.
That's not quite right. Yes, selection reduces variation.
If this is typical and I suspect it is, I've been consistent in saying "genetic variability" but those who argue with me keep wrongly saying "variation" which obscures my point. It's genetic variability that is reduced in the making of a new phenotype, and it's the reduction of genetic variability that eventually brings about the end of a particular line of variation because it runs out of allelic possibilities. Up to that point you can still get further variation of phenotypes by further selection events or just by migration of a small proportion of a population.
As far as I know, genetic drift does not affect variation. And mutation increases variation.
Genetic drift is just one of the ways that a new gene pool is formed and reproductively isolated from a larger gene pool, which develops new phenotypes while reducing genetic variability. And again, I'm talking about GENETIC VARIABILITY OR GENETIC DIVERSITY, not "variation."

And here it comes, the savior of evolution, MUTATION. The ONLY way this inexorable reduction I'm talking about could possibly be prevented -- though only in theory because mutation couldn't succeed at that even if it occurred. Any process that kept putting new alleles into the gene pool would only interfere with the development of the new species that is the predictable result of reproductive isolation of smaller gene pools. You couldn't ever get "speciation" at all, you couldn't get the distinctive variations in the ring species.
You are correct, that if there were only processes that reduce variation, then eventually evolution would run out of variation and would stop. But as long as there are also processes that increase variation, there is no reason to expect evolution to stop.
Actually, this could be taken as a concession of my point and end the discussion with me the winner. At least he does acknowledge that I've got the main process right. "Processes that increase variation" come down to only ONE purely theoretical process, mutation, and as I point out in that thread and here as well, mutation 1) doesn't create viable alleles, and 2) if it did it would prevent the formation of species altogether BECAUSE THE FORMATION OF SPECIES / VARIATIONS DEPENDS ON THE REDUCTION OR ELIMINATION OF ALLELES IN THE POPULATION.
As far as I know, what is mostly noticed is that variation stays fairly constant.
Variation or genetic variability? Phenotypes DO remain fairly constant, the processes that are called evolution that lead to new variations aren't continuously occurring in any observable degree and in that case the genetic variability would also stay constant. But when you DO have evolution, when you are getting new phenotypes, then you are also getting reduced genetic diversity.
A bottle neck, such as caused by isolation of a small population, can result in reduced variation. But the variation is rebuilt during succeeding generations.
A bottleneck is simply the most extreme example of the necessity of reducing genetic variability in order to get a new phenotype. In these cases you usually get complete population-wide homozygosity for most of the new traits. But any new phenotype requires some degree of reduced genetic variability.

And you are wrong that the variation is rebuilt. It has not been rebuilt in the cheetah and shows no signs of ever being rebuilt. And if it were, if that species were to acquire new alleles it would also lose its cheetah character. If you are going to get established species, or speciation, genetic variability must be reduced.
The type of argument you are making could perhaps be used to suggest that the theory overemphasizes selection and underemphasizes the production of new variation. But you won't be able to refute evolution this way, because the empirical evidence shows that variation does build up again if it has been reduced - unless, of course, that particular line goes extinct.
Well, here he's invoked "evidence," but there is no evidence whatever that variation (genetic variability?) builds up again. And there can't be if there is such a thing as a species.

Tuesday, March 13, 2012

Yes you DO get loss of genetic diversity with evolution Part 7

So let's turn to Rahvin for a bit:
Hi Faith. Welcome back.
The problem behind your theory is that it's contradicted by real-world observations. Your predictions are invalidated, because observed evolution has not been reducing genetic capacity for variance.
What are you looking at? If you are looking at the phenotypic variations you may very well see lots of variance. That's microevolution, that's phenotypic microevolution. But if you look at the DNA you should start to see fewer alleles for the selected traits or even population-wide homozygosity for some traits.

The confusing thing is probably that in most cases you don't get any appreciable reduction in genetic diversity. That is, new gene frequencies from a population split just means that you get more of a different kind of allele for a given trait than the other population had, and less of the kind that dominated in the first population, it's mostly a reshuffling. But the fact is that you DO need to reduce or eliminate alleles that produce the "wrong" trait in order for a new trait to become characteristic of the new population, and over a number of selection events and population splits this will show up as a reduction in genetic diversity along with the production and establishment of the new phenotypic trait. IN THE NEW POPULATION. The old population, assuming it's appreciably larger, will no doubt retain the higher proportion of the "wrong" alleles that are lost to the new population because there they aren't "wrong."

It's down any specific line of variation of the phenotype that you are going to encounter this loss of genetic diversity, but since it is down any specific line of variation that you are seeing the production of new traits, that is, evolution, it ought to be clear that the process of production and maintenance of new phenotypic traits, or variation, or evolution, requires this loss of GENETIC diversity.

Even a population split in which the new population is appreciably smaller in number is going to show a lot of phenotypic change along with the genetic reduction, but ANY actual selection of a trait could completely eliminate some alleles and that is where you will REALLY see this formula in operation. Selection definitely reduces genetic variability. Selection is how evolution proceeds. Put two and two together.
Year after year, undergraduate students directly observe evolution in action as they show changes in allele frequency in fruit flies. Other students observe the case of drug resistance spontaneously forming in a population of bacteria.
Are you really looking at the DNA to see the changed allele frequencies or are you inferring them from the "evolution in action" that you are observing, which would of course be the usual microevolution. Drug resistance is the phenotype, what's going on in the DNA?
The process doesn't stop. Variation continues, unimpeded.
And so it may. VARIATION may continue and continue a long time. You are talking about PHENOTYPIC variation here. In some species you can get lots of new variations of the PHENOTYPES, but my claim is that you will eventually reach a point where you can't get any more because the process requires genetic reduction. REQUIRES it. If you are only looking at the phenotypes you aren't necessarily going to be aware of this. But also, since you are dealing with fruit flies and bacteria you may be getting a lot more phenotypic variation for more generations just because they are likely to be genetically more variable than higher animals. Bacteria have a lot less junk DNA for instance than higher animals, which suggests a lot more genetic variability. It's really not a valid comparison with dogs, cats, mice, and humans.
There is no reduction in the possibilities derived from mutation guided by natural selection. At no point to we reach an evolutionary "endpoint" where no more change is possible.
You have apparently not reached it in the laboratory with fruit flies and bacteria (though I suspect you have), but it is reached every day in the wild, with the elephant seals and the North American bison and the cheetah as the most extreme examples. Yes, they are examples of this process, they are not exceptions. Limiting the numbers of a population is what one does to produce a new phenotype, though it doesn't always happen to the extreme of a bottleneck which of course can threaten the survival of the whole species. But even in these cases they seem to be thriving. Nature does this to many degrees all the time, and nearly depleted genetic variability is the result in the case of a bottleneck or founder effect. Again, this is not merely an extreme, it also demonstrates the pattern I'm talking about.

It's based on the well-known observation that you get new species with reproductive isolation and altered gene frequencies. But what is generally overlooked is that altered gene frequencies NEVER means an increase in variability. It may not change the variability much at any given point, but it certainly does not increase it. For that you would need, yes, mutations, but for many reasons that doesn't happen except as an interference, and even if it did happen it wouldn't change anything outside the parameters of the Species, it would only alter the character of the built-in pattern of traits, it isn't going to produce new traits, new genes themselves.

Preserving a breed, preserving a species, requires reduction in genetic possibilities.
And that's just the examples that we directly observe. The fossil record and the other extant life we see today has variety beyond comprehension.
You are talking about PHENOTYPES, and yes you get phenotypic variety "beyond comprehension" -- especially back before the Flood, which is what the fossils are a record of -- but you get it within the Species and you get it only along with reduced genetic variability. Again, the reduction may be quite minimal in a genetically rich species, which is perhaps what you are looking at, and which must describe all species before the Flood, and even many still, but it is still a reduction.
The genetic and morphological evidence for common ancestry of virtually every living thing on the planet is overwhelming,
You are looking at similarities and ignoring the differences and not thinking about what would have to happen genetically in order to produce those differences. You are looking at patterns and imposing your belief that genetic inheritance is the explanation, you do not actually have evidence of that inheritance. Again, look at the differences between one species and another and genetic inheritance isn't going to be the explanation.
to the point that it's better established than the Theory of Gravity. Given that this is the case, and populations continue to diversify into distinct sub-groups before our very eyes,
Yes POPULATIONS continue to diversify, that's the PHENOTYPE. What I'm talking about is something that happens way down the road in most cases, or suddenly when populations are severely reduced. It isn't going to happen in populations that have a great deal of genetic variability and where population splits occur in great numbers -- you'll get some change and you'll get some reduction in genetic variability but it will be negligible in those cases -- it WILL occur, however, just minimally. Many population splits as in ring species, migrations of small numbers -- this is where what I'm talking about will become apparent.

Whenever you get SPECIATION for instance you should see the genetic reduction I'm talking about, certainly NOT the genetic variability that would be necessary if speciation were the springboard to macroevolution you think it is.
it would seem that your premise, that evolution should grind itself to a halt through some sort of genetic entropy, is falsified.
It is happening every day, you are just looking at the wrong end of the phenomena and you are looking where it is occurring least obviously. Conservationists see it every day and so do breeders, it's what they are both working against all the time, trying to prevent it from happening because it is so often accompanied (in this fallen world) by disease -- disease caused by mutations I dare suppose.

Yes you DO get loss of genetic diversity with evolution Part 6

Percy's 6th:
Faith writes:
I’m simply repeating the FACT that selection and isolation, NOT MUTATION, are what bring about the new phenotype that characterizes a whole new population.
Faith, as long you continue to assert that mutation plays no role in speciation there will be no peace for you in this thread. People would not find it outrageous to argue that changing allele frequencies and permutational recombinations of alleles are a more significant factor over mutation in speciation. That would actually be a very interesting discussion. But to just declare that mutations have no role at all is once again to simply deny the real world, and assertions denying what is obviously true tend to draw many responses.
I suppose it could have gone in that direction except that people kept bringing up mutations. But there isn't really much more to say anyway. Changing allele frequences IS the formula for evolution after all, mutations only get stuck in there by debaters. If they are going to define my argument to say that changed allele frequencies are a "more" significant factor than mutatios this is going to keep requiring me to think about those nonexistent mutations anyway. How about just considering the situation without any mutations at all in the mix? They can pretend they are there but only being kept out of the discussion for now if they want.

But even by this point of the thread it's pretty clear my efforts at EvC are all over. And so endeth my last stint at EvC. Oh it limped on for a while but after this there is no point in going back. Ever. And of course they are going to go on ignoring my blog as well, although I'm sure some of them read it from time to time.

I've made the basics of the case: You don't NEED mutations to get new phenotypes, change in gene frequencies does that, and if you kept getting mutations after the breed was established you'd lose the breed. That much ought to be obvious to anyone -- except of course it isn't to evolutionists who are allergic to the implications of it.

But beyond those points, there is simply no such thing as a mutation that can form a healthy allele and they have no evidence for such a thing -- This is, again, merely an article of the faith that's necessary to the idea that phenotypic variation is open-ended, not limited to the Species. Again, all they have is theory, and they treat the theory as fact, without the evidence to justify it. But at least there is an existing stretch of DNA, the gene, for the mutation to work on, which gives them the illusion that it COULD be the source of healthy alleles, but there is nothing at all that can create a gene, the whole sequence of DNA itself that is the basic formula for a given trait.

My whole argument is pretty basic and obvious and would be recognizable IF they didn't keep throwing in the irrelevant baggage of evolutionism.

Breeders should recognize it, conservationists should recognize it. You don't get phenotypic change without a reduction of genetic diversity.

And that spells FINIS to Evolution.

Sunday, March 11, 2012

Yes you DO get loss of genetic diversity with evolution Part 5

This is why there is no point in arguing any of this at EvC. Evolutionists apparently believe what Percy says here:
Every allele in existence today had its origin as a mutation to an already existing allele. Given that all alleles begin as mutations, how can you hope to prove mutations have no role in evolution? Alleles that have been around a while are really just old mutations, but we call them alleles. New mutations are alleles, too, but because they just happened we give them the special name of mutations.
Once things have been so twisted and misdefined where do you start to undo the mess?

Well, let's say this at least: You believe that mutations can create viable functioning alleles but all alleles do is provide interchangeable qualities for a given trait. The gene is for the trait of eye color, the allele makes it the specific color or contributes to the color; the gene is for the trait of ear shape, the allele determines the actual shape or contributes to it. But evolution needs a lot more than variation in traits, evolution needs whole new traits, whole new genes. It's easy enough to see that mutations change the existent sequences of genes, but what makes new genes?

and the next thing to say is: THERE IS NO EVIDENCE THAT MUTATIONS EVER DO ANYTHING BUT INTERFERE WITH A NORMAL FUNCTIONING ALLELE. And I guess I'll have to find some evidence for that somewhere, the Lord willing, and He'll have to help me because most of the stuff out there in Somewhere is corrupted by evolutionist insanity.
[Faith] If you increase the diversity you simply interfere with the development of a new phenotype.
[Percy] Do you understand that this is the same as saying that a new allele, one that isn't the same as any other allele in the newly isolated population or in the original population, hinders the emergence of a new phenotype? If so, you realize this makes no sense, right? You do understand that mutations make the newly isolated population even more different from the original population, right?
Oh brother. What a morass of confusion.

First there ARE no completely brand new unique alleles in the new population, because no such thing ever occurs, this is all a fantasy invention by evolutionists. Mutations do nothing but corrupt, mangle, deform and destroy. Whatever shows up as new in the new population has always been there but the new gene frequencies brought about by the population split have allowed this formerly less expressed or completely repressed allele --or combination of alleles -- to come to greater expression in the new population. THIS allele or combination isn't the thing doing the hindering, this what the new phenotype is based on. What HINDERS is alleles that COMPETE with this new phenotype, such as the alleles that were left behind in the old population and overshadowed it there, and are in much smaller numbers in the new population but if they came to dominate would overshadow it here too. You'd have a different trait or a reversion to the former trait picture rather than a new phenotype. Later on a NEW allele would ALSO interfere with this phenotype. If it's a breed you are trying to keep pure you don't want that to happen; if it's a "species" in the wild then it is simply now something other than that species.

Obviously I misspoke: It's not about the "development" of a phenotype but the maintenance of a phenotype. If you increase the diversity you interfere with the phenotype that is now established. If it is a domestic breed you do not want alien alleles interfering with it. This is all I'm saying.

And no, it is not MUTATIONS that "make the newly isolated population more different from the original population", it's the emergence of formerly suppressed alleles and combinations of alleles that bring about these differences, which is the result of the new gene frequencies. Hey, isn't this change in gene frequencies the very stuff of evolution according to generations of evolutionist teachers? You don't need brand new alleles, just the new frequencies.
[Faith] If mutations or gene flow or any other source of variation kept intruding on this process you would not get these clear established phenotypes.
[Percy] Why not, Faith? You said you were going to prove this. So go ahead and prove it.
Good grief this stuff is so OBVIOUS but there seem to be a dozen ways to twist the meaning of words to make them mean things I don't mean. It's SO simple -- GENE FLOW INTERFERES WITH THE PURE EXPRESSION OF THE VARIETY /BREED /SPECIES. Yikes! The way any species maintains its character or its integrity you might say is by being reproductively isolated from others, this is population genetics 1A. Gene flow interferes with that integrity. How hard can something so simple, and well known for that matter, be made anyway? If mutations DID create alleles, the same problem would keep happening, you could never GET an established identifiable breed or species, because they depend on a stable genetic substrate.

Let me quote Wikipedia on Zygosity again:
True breeding organisms are always homozygous for the traits that are to be held constant.
Are species true breeding organisms or not? (Here I'm using "species" the way evolutionists do)

What a travesty of communication this mess is. I may have botched my presentation enough to contribute to the confusion, but for sure my antagonists were frothing at the mouth to say anything at all against my argument whether they got my point or not -- and Percy obviously didn't -- and say something insulting on top of that.

Yes you DO get loss of genetic diversity with evolution Part 4

And yet another one from Percy:

Hi Faith,
...what I was responding to was that any evolution can only result in reductions in variation. As everyone's been telling you, variation can increase or decrease.
I'd NEVER say "reduction in variation" unless I had a major lapse, I ALWAYS mean "reduction in genetic variability." And evolution DOES only result in reduction in genetic variability. What do you mean by "variation?" If you mean genetic variability or diversity, no it cannot and they have NO evidence that it EVER increases. If you mean variation of the phenotype yes of course you can have more or less of that but I wouldn't talk about it without a modifier to make it clear that's what I'm referring to -- or I hope I wouldn't.


OK, I can see that mutation appears to be the explanation for all change in the minds of evolutionists here...
The reason I mentioned mutation is that the sum total of all alleles in a population is the amount of variation,
This conversation has already gone off the rails in a most frustrating manner. By using the term "variation" the whole meaning of what I'm saying has become muddied. Is he talking about phenotypic variation, which could be said to be the sum total of all the alleles, or is he talking about genetic variability which could also be described the same way. Depends on what you have in mind and I can't tell in this case.
and only mutation can increase the number of alleles.
Absolutely true, that's why evolution needs mutation, it depends on genetic increase, without it there is no evolution beyond the Species. But Creationism does not need mutation, all the necessary genes and alleles for each Species were built in back at the Creation, all quite sufficient for the purposes of huge variation at the level of microevolution.
Natural selection can affect allele frequency, and indeed one way to define evolution is as changing allele frequency over time, but only mutation can increase the number of alleles and thereby increase the amount of variation.
Absolutely true, as I've been saying.
The reason people are bringing up mutations isn't because they think it is the source of all evolutionary change, because obviously it isn't the only source. They're bringing it up because it is the only way to increase variation.
How on earth have I failed to be clear that I know this already? Evolution NEEDS mutations, that's why they've imagined them into existence.
Mixing and remixing the same set of alleles can create unique combinations of alleles that didn't previously exist, but it doesn't change the pool of existing alleles at all.
Well duh.
Almost no reproduction is perfect. Even people have mutations. The average number of mutations per person is usually estimated at between 10 and a hundred. Ignoring mutation might make it easier to claim that variation can never increase, but the real world has spoken.
There is no evidence whatever that normal alleles are created by mutations, this is merely an article of faith to evolutionists. Mutations are mistakes, they only interfere with alleles, change their sequence, sometimes with no observable effect but often so that they don't function as they were meant to, create diseases, and ultimately kill off many of them, which then become junk DNA.

That thread at EvC was a disaster.

Probably my own fault. I wasn't prepared for the aggressive attack, out of practice I guess.

Yes you DO get loss of genetic diversity with evolution Part 3

We continue with Percy's third message:
Faith writes:
This is what must have happened with each of the finch types. A beak type got selected for its usefulness with a particular kind of function, and that got passed on and came to characterize a whole population because the alleles for the other beak types were eliminated from the reproductive pool. The same thing happened with other beak types as each found its peculiar adaptation and became isolated from the other types.
This isn't the way it works. For Darwin's 15 different tanager species there were not 15 different alleles for the shape of beaks, one for each species. Bird beaks are controlled by the expression of the Bmp4 gene. All the different beak shapes are the result of different timing and spatial controls on the expression of the Bmp4 gene. Expression of the Bmp4 gene is under the control of regulator genes with names like Shh and Fgf8.

In other words, beak shape is under the control of more than one gene and more than one type of gene, and bird gene pools of any species possess a great deal of variation. This is why beak expression is so plastic under the influence of changing environmental pressures.
How does this change the FORMULA I'm talking about? It doesn't matter what the specific mechanisms are, you still have to NOT have whatever "expression of the Bmp4 gene" would bring about the wrong kind of beak for the particular variety under discussion.

And I'm aware that some traits are controlled by more than one gene, in fact it has occurred to me that the original "super Genome" that is a necessary assumption of Creationism may have been characterized by more genes per trait among other differences from today's genome, on the idea that junk DNA is genes that were once alive but died down the centuries, probably most of them all at once in the Flood.

But the same principle I'm talking about has to apply no matter how many genes are involved. You still have to SUPPRESS the expression of whatever the underlying genetic formula is for any traits that would compete with the selected trait of the population under discussion. This is a reduction in genetic diversity, and it is NECESSARY in order to get a particular phenotype, and it has to STAY suppressed, OR be eliminated altogether, if that trait is to be preserved.

Yes you DO get loss of genetic diversity with evolution Part 2

Percy again:
Faith writes:
[I'm] constructing an argument to show that selection and isolation single out a particular trait by eliminating all its competition and ultimately make that trait characteristic of a new population that emerges from these processes.
This argument couldn't be more wrong. The alleles for a gene are not involved in a competition where only one is left standing.
Sigh. The main problem seems to be getting it said so that we all at least know what I'm saying. I often use the most extreme example of the point I'm trying to make to indicate the DIRECTION that ALL these processes move in, I'm not trying to hang EVERYTHING on the extreme. Sigh.

It's the PATTERN I'm trying to focus on. Getting a new phenotype, a new variation, a new "species" as evolutionists think of it, REQUIRES that alleles for OTHER (yes, "competing") phenotypes / variations / species be either greatly reduced in the population or eliminated altogether -- the fewer the better for the establishment of the character of the new variation / phenotype / species.
If that were the case then extinction would be an extremely common event because a species ability to survive across changing environmental landscapes is dependent upon variability. Great variability increases the likelihood that at least some subset of a population will survive an environmental change.
Yes, genetic variability IS important for the health of a species, but maintaining genetic variability means NOT EVOLVING. The way you get NEW TRAITS, that is, EVOLUTION, is by isolating the alleles for those traits in their own population and that means ELIMINATING alleles from that population that would bring about different traits. This is how domestic breeding does it and it is also how Nature does it, whether by Natural Selection or Genetic Drift, Bottleneck or a series of population splits over generations with migration and reproductive isolation etc etc etc etc. You won't get a population specifically characterized by green and red striped fur if that population includes individuals that carry alleles for purple and yellow splotched fur.

And such variation does not always threaten extinction although it may at the extremes. However, some animals seem to thrive even with extreme genetic depletion, the elephant seals, even the cheetah does OK considering, etc.
If it were really true that more beneficial alleles eliminate those that are less beneficial or even deleterious then alleles for genetic diseases would have disappeared long ago, and yet genetic diseases like cystic fibrosis persist.
The idea that the alleles must be "beneficial" comes from the Evolution Model. On the contrary, I think accidentally or randomly isolated alleles are probably the more typical foundation for new varieties, they need have no specially "beneficial" properties. They may or may not adapt to a particular niche later. Nature loves variety.

And the alleles that are eliminated still belong to former / other populations /varieties of the same species, it's not as if they died out completely except in some rare extreme cases, it's just that they no longer belong to the population of this new phenotype. The population under discussion may have red and green striped fur while another of the same species has the alleles for purple and yellow blotched fur that would wreck THIS particular variety and vice versa. You don't want Dachshund alleles in the Great Dane breed or vice versa, but alleles for both remain in the dog Species as a whole.
You need to find solutions consistent with both your religious views *and* reality.

Well, I may continue with this attempt to answer objections to my argument here, but just this much dealing with it, even sticking to one antagonist to keep confusion to a minimum, makes it quite clear why I have no interest in being back at EvC. I guess the best construction to put on the problem is that it's a paradigm clash. I'm always talking from my Creationist presuppositions, and although I keep trying to spell those out as I go, the contrary Evolutionist presuppositions are so rigidly held there's little hope of penetrating the fog.

Yes you DO get loss of genetic diversity with evolution Part 1

Getting anyone to accept my claim about reduced genetic diversity, obvious though it is, is the real battle here unfortunately. So let's go back to my last thread on the subject at EvC and see if it's possible to make any headway on it:

Here's Percy's opening gambit on the subject on that thread:
Genetic diversity can go in any direction after reproductive isolation. For example, consider a relatively homogeneous population that becomes divided in two when a river changes course. There are now two populations, both with pretty much the same alleles and allele frequency. Mutations experienced in one population will no longer be shared with the other and the populations will evolve along different paths. If this continues for a sufficient period then they could lose their mutually interfertile quality and become two species.
Let's take it step by step:
Genetic diversity can go in any direction after reproductive isolation.
Of course I am claiming that genetic diversity can NOT go in "any direction" after reproductive isolation. It CAN remain more or less stable for long periods, but otherwise it can ONLY decrease; it can NOT increase. This is of course based on the Creation Model I've spelled out in earlier blog posts, that denies the mutations which are needed by the Evolution Model. Mutations are the ONLY way it could increase.

But to get off the hypothetical and bring this down to a question of evidence and fact, I'm claiming that it DOESN'T increase, and that ought to be provable with the DNA sampling test I've suggested.
For example, consider a relatively homogeneous population that becomes divided in two when a river changes course. There are now two populations, both with pretty much the same alleles and allele frequency.
Of course if you posit a split into two populations that retain the same character as the original I wouldn't expect to see much change either. This is not a scenario that leads to evolution and all I'm talking about is how evolution -- or variation or the production of a new phenotype -- leads to reduced genetic diversity.

This situation would exist if the two new populations are appreciably different in size and/or have appreciably different gene frequencies -- which is in fact more likely to occur in a smaller population. That's when you get the beginnings of the phenomenon I'm talking about. The larger may change too to some degree because its gene frequencies will have changed also, but not to the extent of the smaller one.

But evolution always has to invoke (beneficial) mutations, those imaginary changes in the DNA that fuel the changes the theory requires.
Mutations experienced in one population will no longer be shared with the other and the populations will evolve along different paths. If this continues for a sufficient period then they could lose their mutually interfertile quality and become two species.
Of course there is no evidence that this happens at all. And the Creation Model has no need of them as there are plenty of built-in genes and alleles to bring out all kinds of variations in any Species.

1. Mutation is not needed, the original genetic endowment of each Species fuels all possible variations of that Species.
2. There is no evidence for it, it's purely an article of faith.
3. Where there is evidence of its existence, its effect is either neutral or deleterious, which the Creation Model explains as due to the Fall which brought death, disease and deformity to all living things.
If both populations thrive then diversity could increase in both.
There is no way that GENETIC diversity ever increases after reproductive isolation -- not just "diversity" as PHENOTYPIC diversity is something else, and as my formula has it, phenotypic diversity increases as genetic diversity decreases. I don't know how to prove this as making charts of combinations of genes and alleles quickly gets beyond me, but keeping the Creation Model in mind ought to make it intuitively obvious. One argument I've made is that it ought to be obvious that increases in genetic diversity would prevent ever establishing a domestic breed as its character would always be threatened by the input of new alleles.

As I quote in a post below, from the Wikipedia article on Zygosity:
True breeding organisms are always homozygous for the traits that are to be held constant.
Homozygosity for an entire population is of course the extreme of genetic depletion, also known as "fixed loci" in which there is only one allele in the entire population for the given gene. It's the same situation that Nature has brought about in the cheetah and the elephant seals and the North American bison. It's the FORMULA for getting a new phenotype. It's EVIDENCE that what i'm saying is correct, that you MUST have reduced genetic diversity IF you are to get EVOLUTION.

And again it pertains not just to domestic breeding but also to varieties in the wild -- the beaks of Darwin's finches couldn't be counted on to be stable even if they had been brought about by Natural Selection, they'd always be subject to change that would interfere with their relationship to their environmental niche. In other words an increase in genetic diversity ALWAYS interferes with EVOLUTION. You get evolution or the development of new phenotypes / varieties as you lose alleles for competing traits, which means a decrease in genetic diversity. For a finch population to be characterized by a beak that can crack nuts means it has to NOT have the alleles for beaks that can penetrate small narrow spaces. It could be that an all-purpose beak would work fine and dandy, but the theory says that you get these specialized beaks by natural selection so that they can adapt to their particular ecological niche and since that does appear to be the case they must have alleles FOR their particular adaptation and NOT have the alleles for the other adaptations.

I know I argued this to death on that thread to deaf ears and here I've barely gotten through this one post from Percy. Oh well, might as well keep at it for a while at least.
But if one or both populations suffer some disaster such as flood or famine or an invasive predator or disease that greatly reduces population size, then diversity would be reduced. It all depends upon what happens to the populations.
No, it doesn't ALL depend on that although such events would certainly have an impact. The point I want to keep in mind here is CHANGE IN GENE FREQUENCIES. Many things can bring this about; what brings it about isn't the important thing but simple population splits are usually quite enough for the purpose.

Saturday, March 10, 2012

Speciation + Evolution = LOTS of Trait Diversity with LOSS of Genetic Diversity leading to end of ability to evolve

Another one from RAZD at EvC, Speciation + Evolution = More Diversity
The scene: sitting at computers all over the world ...
"Why don't creationists understand evolution -- it is so simple," the evolutionist wails:

1. Evolution - the change in hereditary traits in populations from generation to generation - is an observed and documented fact, a process that occurs constantly in the natural world around us, and

2. Speciation - the division of parent populations into reproductively isolated daughter populations - is also an observed and documented fact, a process that occurs frequently in the natural world around us.
These two simple processes are sufficient to explain the diversity of life we know, from the world around us, from history, from prehistory and archeology, from geology and physics and paleontology and the fossil record, and from chemistry and the genetic record.
Well, it sounds good on paper, I guess, as theory at least, but unfortunately it fails in reality. Yes, there is an "evolution" by which heritable traits change from generation to generation, but this has never been observed beyond what we call "micro" evolution, or evolution within the genetic limits that define each species, and in fact it can't occur beyond microevolution for the reasons I've given over and over here, which are the same reasons there is no evolution beyond speciation. And yes, speciation is also a documentable fact, but it always occurs with loss of genetic diversity, even to the extreme of fixed loci or total homozygosity for some traits in the population, which makes further evolution beyond speciation purely a pipe dream.

But RAZD just goes on asserting the theory, the pipe dream, as if it were reality, as they all do.
We can even see how evolution causes speciation with Ring Species:

1. the species forms a band made up of several varieties around some barrier to their survival ability,

2. each of the varieties has slightly different hereditary traits from their neighbors,

3. each reproduces with their neighbors in hybrid zones that show a mixing of the hereditary traits of the two neighbors, except that

4. when they meet on the other side of the barrier, the two ends do not mate.

Evolution results in different hereditary traits developing in each of the areas dominated by the different varieties, differences that do not hinder mating until they reach a certain threshold - the difference between the end varieties.

Yes, pretty much but as long as he sticks to the level of traits -- of the phenotypes, of the different observable characteristics between the populations -- he misses the reason what happens happens: The splitting of the populations changes the gene frequencies. When new traits emerge this is because alleles for competing traits have been reduced which can proceed after many population splits to the point that they are completely lost to the new population. After a series of splits the genetic diversity may be quite drastically reduced, and the main reason there is no interbreeding between the first and last populations is the genetic incompatibility that has developed by then.

Again, my prediction is that if you sampled the DNA of the first and last populations (better done in a laboratory where you can sample the first before it too undergoes change), you should find much greater genetic diversity in the first and much reduced diversity in the last, more heterozygosity in the first, more homozygosity in the last, particularly for the traits that are most characteristic of the populations.
Remove any one of the intermediate varieties, so that the band is broken, and you have two distinct species.
We now have more species than before, so life is more diverse. It is so simple:

Evolution + Speciation = Diversity
Way TOO simple, RAZD. Yes you do have more diversity of TRAITS, but you are simultaneously getting REDUCED diversity of GENETIC POSSIBILITIES. This is all just the usual evolutionist daydream based on surface facts completely ignoring what is going on genetically, which is the NECESSARY reduction of genetic diversity, which occurs with EACH splitting off of a portion of the population to form a new population. This is a trend that can keep producing new phenotypes for some time by losing more alleles, but can ultimately arrive at such genetic depletion that no further phenotypic change is possible, a condition like that of the cheetah. Not that this degree of depletion is inevitable, but reduction in that direction certainly is.
This little scenario depicts, I believe, the state of many debates between creationists - people that predominantly use faith to understand the world - and "evolutionists" - people that predominantly use science to understand the world.
What "this little scenario" actually depicts is evolutionist reliance on wishful thinking as they spell out what they THINK happens, because they haven't really faced the GENETIC PICTURE which is working against their all-too-sanguine expectation that change in traits can just go on and on without genetic cost. It really is a daydream, a fantasy. And it's quite the joke that they are constantly claiming to appeal to EVIDENCE and accusing creationists of relying only on faith.

(I skipped his caricature of the creationist response to the above because it is a distraction from what I'm trying to say here.)
Where does "large" change come from? - the change that makes giraffes so different from kangaroos? Simple:

Speciation - the division of parent populations into reproductively isolated daughter populations - is also an observed and documented fact, a process that occurs frequently in the natural world around us, and

Evolution- the change in hereditary traits in populations from generation to generation - is an observed and documented fact, a process that occurs constantly in the natural world around us.
SO simple as long as he just goes on daydreaming about the surface traits and imagining that there are no limits to change.
Speciation + Evolution = More Diversity
After speciation has occurred, the daughter populations no longer share genes through reproduction, and they are free to evolve completely different traits.
Yes, and this lack of sharing of genes means a LOSS OF GENETIC DIVERSITY. Yes, they ARE "free to evolve copletely different traits" but this is ALWAYS made possible by the loss of competing alleles for those traits, which is completely ignored by evolutionists. You can always get new traits BY LOSING competing alleles, but if the population splits that bring this about continue to occur, eventually a point will be reached where you can't get new traits any more because you'll be completely out of alleles. Speciation may not always mean genetic depletion but it certainly means genetic reduction from earlier populations particularly where the main new traits are emerging.
The likelyhood is high that one of them will become quite different, either to inhabit a new ecology that the other is not as well suited to (could have caused the original split), or to make use of the existing ecology in a different way, and this will lessen competition between the two species rather than drive one to extinction.
Lotta sheer conjecture there. It really isn't even necessary to posit environmental or situational reasons for trait changes or even the population splits themselves. Migration will bring about splits and the splits alone will bring about trait changes. The fewer individuals at the start of a new population the bigger the observable trait changes, the ecology is not likely to have much to do with it. It may be that both populations still have sufficient genetic variability even to undergo several further splits if necessary, but since he's completely ignored the whole question of what happens to the genes while focusing on the traits and fantasizing endless change he's going to miss the state of genetic depletion also when it does finally occur after more population splits.
Continued evolution of daughter populations along different ecological paths results in increased diversity - difference - between them over time. That is how the small amount of difference we seen below can become the amount of difference we see between other bird species.
Again, overrated influence from the environment but this is really a side issue, but anyway, the increased diversity is completely the result of the change in gene frequencies brought about by the population split. If the environment contributes an influence that further impacts the population numbers or reproductive isolation and therefore the gene frequencies, then it will contribute to the trait differences between the populations as well, but again, there is no need for this to happen in order for even great differences to come about as the change in gene frequencies alone will do it.
Continued evolution causes more change - in each population, from generation to generation to generation
Along with change in gene frequencies which can rapidly reduce and even eliminate some alleles as the changes continue, to the point that you run out of alleles for enough traits that further change is impossible, probably a very interesting new population with new traits but no more genetic variability.
That should be enough for starters. There is more to discuss about where change occurs, but this is long enough for now. This thread is about evolution after speciation.
A total pipe dream I'm afraid, as speciation is most likely to occur at the very outer edges of the genetic variability of the species, thus preventing further evolution.

Loss of Genetic Diversity same as Loss of Information: Both prevent macroevolution. Evolution Defeats Evolution

[NoNukes says]: A creationist might state that nature cannot create the "information" required to produce novel features and "macroevolution" . Dog breeding includes human intervention which can be viewed as being similar to an ID agent stepping in to add information allowing new features like wiener-dog legs.

I don't really grasp the context of the issue of "novel" characteristics so I'm not sure how to address that, but I can respond to the idea of "information" at least.

Apparently this is easily misunderstood, and I have to agree that the very term "information" is vague or even cryptic in a way. The idea is really pretty simple though, from a creationist point of view anyway. You have a given built-in genetic recipe from the Creation for each species, so the possibility of that species evolving into another would require the addition of whatever is lacking in the first that the second needs. That's the "information" that would have to be added to the genome for it to macroevolve. Perhaps I don't even need to invoke the original Created species for this to make sense. It should be apparent to all that each species does have its own genome, many of which are in the process of being sequenced, and they are being sequenced AS being specific to the particular species they belong to. The DNA for each species has its own characteristics peculiar to that species, genes that aren't found in some other species but only this one, a certain number of chromosomes particular to the species and so on and so forth, with of course occasional exceptions. The genes pertain to the particular trait, perhaps eye color, the alleles define the different qualities of that trait, in this case the color. Wherever there are many alleles for a trait you can get a great variety from the genome as given for that species, you don't need to add alleles. Macroevolution requires getting from these recognizable species to something completely outside the particular genetic recipe, whether you think of them as having evolved to their present identity or been created independently at the Creation. You still have to posit the addition of NEW information that is not already present in the current genome.

New genes at least. New alleles isn't enough. New alleles for extant genes could only give variation to the trait the gene instructs for.

So has anybody ever shown the formation of a new gene? Is there even a theory about how that might come about?

In any case, the whole idea of the need for more information really starts as an observation that the processes of evolution ELIMINATE INFORMATION rather than adding it, and that fact means that evolution is moving in a direction that makes evolution less rather than more possible.

But I think it's clearer to say that evolution reduces genetic diversity. It's really the same observation. Evolution eliminates alleles at the very least and at some extremes may eliminate ALL alleles for a given gene which effectively kills the gene and most probably makes it a corpse in the genetic graveyard known as Junk DNA.

This IS the natural direction of all evolutionary processes. In order to get a new phenotype, especially one that sticks and becomes characteristic of a new population or variation or breed, other alleles for the same traits that give a different character MUST GO. That's LOSS OF INFORMATION, or REDUCED GENETIC DIVERSITY.


Now here comes RAZD answering NoNukes:

Curiously, the mutations that cause short legs are fairly common in many species, including humans - it's called Dwarfism.
So is RAZD saying these mutations are NEW information?

I must ask, how does he know these are mutations? He gives no evidence, he merely CALLS the allele that bring about this trait mutations. Evidence please. I'm willing to consider this a mutation myself just because dwarfism must be thought of as a disease process, which I KNOW mutations produce. But are all shorter legs caused by dwarfism or is it simply possible to get a combination of naturally occurring (built-in) genes/alleles that naturally produce shorter legs? Evidence please.
The difference is between a random mutation occurring and it being spread into the breeding population is selection.
Pure theory, which is all evolution ever has to offer. Is he talking about useful / beneficial mutations, and if so nobody has ever shown that they even occur except in very rare and problematic instances, they are merely ASSUMED to be the source of all change in the genome. But if we are talking about nondeleterious variations the most likely scenario is that a rare normal allele simply comes to expression, and then yes, it will spread in the population if it is selected in the reproductive lottery. If not, it won't. But to call it a mutation is simply to beg the usual questions.
Within the ecological challenges and opportunities imposed by artificial selection, there is a survival and reproductive benefit to having short legs for the dogs being bred that have them, and not having them would be detrimental. This is a rather demanding ecology to survive in, yes?
Could be, depends I suppose. But we still don't know if this is a mutation or simply a normal-occurring healthy allele.
Now the problem with the creationist\IDologist claim about information is that they don't define what the concept means
Well, it's difficult, but I believe I may have succeeded in defining it above. And I vote for substituting the concept of reduction or loss of genetic diversity as being easier to grasp.
or even more importantly, how it can be measured.
As I've proposed, do a DNA sampling of the first and last populations in a ring species, one you find in nature or one you create in the lab. You should find obvious reduced genetic diversity in the last population and probably a progression of reduction in intermediate populations as well. Lots of homozygosity in the last population, a lot more heterozygosity in the first. Go gather a bunch of salamanders from the California ring species, label them and sample their DNA especially the genes for the patterns on their skin.

He goes on to give an irrelevant self-fulfilling chart he claims falsifies the claim about loss of information. He's probably misreading a built-in allelic possibility as new information but it's all just an exercise in proving what he wants to prove.

No, do what I suggest above, see that there really is loss of genetic diversity (same as loss of information) when species evolve. That kills MACROevolution right there.

Evidence for Reduced Genetic Diversity as Necessary Component of Evolution

You want some evidence for the claim that evolutionary processes always involve the reduction of genetic diversity? It's pretty simple, OUGHT to be obvious, and it's all about the reduction of heterozygosity to homozygosity or even less: This is from Wikipedia on Zygosity:
A cell is said to be homozygous for a particular gene when identical alleles of the gene are present on both homologous chromosomes.[2] The cell or organism in question is called a homozygote. True breeding organisms are always homozygous for the traits that are to be held constant.
In nature the same thing applies. Once you get a new variety, a subpopulation that is reproductively isolated from its parent population or other populations of the same species, even the result of a "speciation" event, and especially after it has inbred over some generations, its traits are going to be or become fixed. For a new trait to stick, or continue to characterize the new population, competing alleles for that trait must have been eliminated from that gene pool. THIS IS THE NECESSARY REDUCTION IN GENETIC DIVERSITY THAT ALLOWS A NEW TRAIT TO COME TO CHARACTERIZE A NEW BREED OR POPULATION IN THE WILD, THIS MUST OCCUR FOR A NEW TRAIT TO DEVELOP AND STICK IN A NEW POPULATION.

If they are "true breeding", they will be homozygous for their characteristic traits. This HAS to be true whether the population is the result of natural processes such as natural selection or genetic drift, migration and so on, or domestic breeding decisions.


Take dogs. If you want a Dachshund you have to eliminate all the alleles that specifically produce Great Danes or Golden Retrievers or Chihuahuas etc. If any of those alleles show up in the Dachshund breeding program you'll get a less perfect Dachshund. They make the breed less than what it is supposed to be.

It works the same way in nature, maybe through Natural Selection but probably more often through random events that simply happen to separate a population into two or more subpopulations. A particularly marked salamander emerges because the other markings are genetically decreased by comparison to those for the new marking. The markings of the last species to develop in a ring species of such salamanders should be genetically homozygous. Same with the genetics underlying the last species in the ring of green warblers and so on. You should find decreased genetic variability and probably a lot of homozygosity, just because this is what evolution DOES.

It's NECESSARY to evolution, and if evolutionists weren't always imagining nonexistent mutations into the mix it ought to be obvious even to THEM. The only mutations that are involved are those that contribute diseases to the mix and interfere with the health of the most genetically reduced populations, even to extinction in some cases.

In nature the introduction of disease elements may simply eliminate a new variety, Natural Selection in operation at its most severe, but if the new variety finds a niche it can adapt to it will survive just as a good domestic breed will.

The new variety necessarily comes through a reduction in genetic diversity. That's how evolution WORKS, really, though such an obvious necessity, that must lead to LESS ability to evolve, is simply ignored by believers in evolution who go on spinning evolution out of imaginary mutations.

To repeat the point: If circumstances are such that the populations remain reproductively separate, meaning without gene flow or the sharing of alleles between them, each will develop its own particular characteristics, and as long as there remains no gene flow or reproductive contact between the populations those characteristics will remain. For them to remain means that the alleles for different characteristics have been eliminated. That's what decreased genetic diversity MEANS. This may amount to actual speciation, but at least certainly at the extremes you do get speciation, where the new characteristics are preserved because there is a complete lack of interbreeding with former populations.

Evolutionists regard bottlenecks as events that interfere with the processes of evolution, but they shouldn't. The elephant seal and the cheetah which were produced by severe bottlenecks -- reduction of their former populations to just a few individuals -- that severely reduced their genetic diversity -- really ought to be considered to be examples of speciation, nature doing what domestic breeders do. Bottlenecks are really just one way new varieties or breeds are brought about in nature or in domestic breeding. ALL the processes of evolution tend in the same direction, genetic drift, migration, natural selection, just not as rapidly. Domestic breeding in the past could be described as the artificial creation of genetic bottlenecks for the purpose of developing desired traits for new breeds. You select the desired character and take pains to breed only with others that possess that character. Since a rigid adherence to this formula also usually brings disease problems into the breed, breeders today take care to avoid the most severe bottleneck methods with the most severely decreased genetic variability by mixing with more vigorous but less desirable animals as far as the target trait is concerned, but if it weren't for the threat of disease, these severe methods would be considered the most reliable way of producing the best breeds. SPECIATION.

Yet here we have RAZD at EvC carrying on as if the evolution processes just go on and on producing new phenotypes or varieties or breeds, even past speciation which he treats as the end point of microevolution and beginning of macroevolution, but afterward the same changes continue without a hitch in his scenario.
What separates (micro) evolution from the macro view of evolution (macroevolution) is the process of speciation, as evolution occurs within the breeding population, and nested hierarchies are formed by speciation events, and macroevolution is just a macro view of what occurs over several generations via evolution and speciation.

If we look at the continued effects of evolution over many generations, the accumulation of changes from generation to generation may become sufficient for individuals to develop traits that are observably different from the ancestral parent population. This lineal change within species is sometimes called phyletic change in species. This is also sometimes called arbitrary speciation in that the place to draw the line between linearly evolved geneological populations is subjective and because the definition of species in general is tentative and sometimes arbitrary.
See, he's simply ASSUMING the open-endedness of evolution, the phenotypic changes just go on and on, a neverending ACCUMULATION of changes. He has no evidence for this, though he has charts that give it an aura of authority that are simply meaningless reflections of his false belief. Actually, they are ILLUSTRATIONS of what he believes, they provide nothing in the way of evidence for any of it. And everything he says is also all assumption without evidence. Dawkins does the same thing with his ridiculous computer models of how evolution works, simply programming in his own bias, his assumption of open-ended changes. Sometimes you'll see an evolutionist acknowledging that reduced genetic diversity can sometimes be a problem but they keep that information off in a separate mental compartment, it's something that occurs only with bottlenecks, in extreme scenarios that interfere with evolution, not with evolutionary processes themselves.

Just for the record, here is the most pertinent part of the Wikipedia article on Zygosity:
The words homozygous, heterozygous, and hemizygous are used to describe the genotype of a diploid organism at a single locus on the DNA. Homozygous describes a genotype consisting of two identical alleles at a given locus, heterozygous describes a genotype consisting of two different alleles at a locus, hemizygous describes a genotype consisting of only a single copy of a particular gene in an otherwise diploid organism, and nullizygous refers to an otherwise-diploid organism in which both copies of the gene are missing.

A cell is said to be homozygous for a particular gene when identical alleles of the gene are present on both homologous chromosomes.[2] The cell or organism in question is called a homozygote. True breeding organisms are always homozygous for the traits that are to be held constant.

An individual that is homozygous-dominant for a particular trait carries two copies of the allele that codes for the dominant trait. This allele, often called the "dominant allele", is normally represented by a capital letter (such as "P" for the dominant allele producing purple flowers in pea plants). When an organism is homozygous-dominant for a particular trait, the genotype is represented by a doubling of the symbol for that trait, such as "PP".

An individual that is homozygous-recessive for a particular trait carries two copies of the allele that codes for the recessive trait. This allele, often called the "recessive allele", is usually represented by the lowercase form of the letter used for the corresponding dominant trait (such as, with reference to the example above, "p" for the recessive allele producing white flowers in pea plants). The genotype of an organism that is homozygous-recessive for a particular trait is represented by a doubling of the appropriate letter, such as "pp".

Friday, March 9, 2012

Genetic Evidence of the Bottleneck at Noah's Flood Part 2

The thread continues:

Wounded King Message 4 loves remembering my contributions on this topic at EvC, not that he remembers them lovingLY of course, but here he's claiming there are many possible ways of coming up with a supposed super genome:
(Quoting JAR): First, even if there was some super genome if the Biblical flood stories were true there would still only be at best 14 copies of it to work with and that is still a bottleneck.
(WK): This seems to totally miss the entire point of the 'Supergenome' gambit. It might technically be a bottleneck if we assume that the survivors of the flood were typical of the pre-flood populations but allowing for a 'Supergenome' it is a bottleneck in a population with, by definition, a genetic composition drastically different to what we are used to analysing and the signature of such a bottleneck might be expected to be similarly drastically different.

I can come up with plenty of ad hoc pseudoscientific Supergenome explanations that could account for this. In fact when this topic came up on Faith's The End of Evolution By Means of Natural Selection thread she ended up, with a little help from me, proposing a hypothetical post flood population whose members were all superpolyploid acting as massive reservoirs of genetic variation and this was subsequent to her previous proposal that all of the extra required alleles would have been found in what is now 'junk' DNA.
Yes, that was one of the first things I was playing with as a possible structure for the original genome (and well before WK offered his help on that thread by the way) since of course it MUST have had much more genetic variability than the genome now.

But I found out not too long ago that the original genome really doesn't have to be different structurally from the genome now because it doesn't take much ordinary heterozygosity, or many alleles per gene, to produce all the variations / breeds / races we see today, only 6.7% heterozygosity in the whole population in fact which is the percentage we have now, as I mention in the previous post.

So that does lead to considering that the original genome probably simply had a lot more heterozygosity, and since I'd already figured that junk DNA reflects the death of the original DNA you simply think about the genetic power in those 95% of genes when they were still alive, consider also that there could have been many many genes for any given trait and many many alleles for each, and the possibilitieds of genetic variation become astronomical -- without having to postulate some unusual form for the genome such as polyploidy. Just genes and alleles, the basic stuff of today's genome.

Even two individuals with two alleles each for every gene, that's four different alleles between them -- for EVERY gene in the entire genome including the living versions of today's junk DNA -- are going to produce quite an amazing variety of offspring. It would take many generations for all the possibilities to play out to the point of the genetic reduction of the cheetah.

Then we have Taq in Message 5:
(Quoting WK): In fact when this topic came up on Faith's The End of Evolution By Means of Natural Selection thread she ended up, with a little help from me, proposing a hypothetical post flood population whose members were all superpolyploid acting as massive reservoirs of genetic variation and this was subsequent to her previous proposal that all of the extra required alleles would have been found in what is now 'junk' DNA.
(Taq): It would still require hypermutation to produce so many pseudogenes. The overwhelming majority of pseudogenes are the product of MANY mutations, usually not just one.
No mutations, simply original functional DNA built in at the Creation which has been destroyed over the generations because of the Fall, in fact no doubt a lot of it destroyed BY mutations.


Thursday, March 8, 2012

Genetic Evidence of the Bottleneck at Noah's Flood Part 1

Well, hi de ho, somebody finally decided to try to have a discussion about the claim that the bottleneck of Noah's Flood should have left genetic evidence that it didn't leave. I've many times wondered exactly what evidence they think they would find, so let's hope somebody finally defines it.
In several threads, Jar has brought up the genetic bottleneck argument against the biblical flood and it appears to me to be a slam dunk of an argument. So I thought it was worth expanding on it and teasing out the details.
Sure, go for it.
Perhaps we should start with when creationists think the flood happened (my bold).

When was Noah’s Flood? 1,981 years to AD 0 plus 967 years to the founding of Solomon’s Temple plus 480 years to the end of the Exodus plus 430 years to the promise to Abraham plus 75 years to Abraham’s birth plus 350 years to Shem’s 100th birthday plus 2 years to the Flood. The Biblical data places the Flood at 2304 BC +/- 11 years.

So this is about 4,300 years ago. (Maybe other dates around that time will be claimed but a bottleneck should still be apparent.)
I sometimes round it to 4500 years ago but 4300 is more accurate though a couple hundred years isn't going to change the evidence anyway.
Because all existing species have descended from so few individual so recently, their genomes should be very, very similar to each other - simply because all members of the same species would be close cousins.

Species that we know have undergone a bottleneck, such as the elephant seal and the North American bison - which were hunted to near extinction - and the cheetah, which appears to have also gone through a bottleneck 10,000 years ago, show this genetic fingerprint. In the cheetah's case their genetic variance is so small that their immune systems have so much in common that skin grafts aren't rejected between individuals.
So is this the sort of evidence you'd be looking for? Many fixed loci such as the cheetah's? Is this the "genetic fingerprint" you have in mind?
Jar's argument goes that if all animals and plants on earth (with the possible exception of some fish which may have been able to survive salinity changes) were reduced to either pairs, or sometimes a few more of each species (I don't see how 'kinds' could make a difference) we would see the bottleneck fingerprint in pretty much every plant and animal alive today.
The bottleneck should only be applied to creatures on the ark. Plants were not systematically saved on the ark but had to fend for themselves, same with sea creatures and apparently also insects and microorganisms.
But we don't. And because we don't it's not possible that virtually every species on earth was reduced to two or three individuals only a few thousand years ago.
And this should just about do it for the evolutionist side of the argument. I wonder if any creationists there will be up to answering it.
This is rather a unique situation; the proof does not rely on having witnesses around thousand of years ago, partial archaeological records, 'inferences' or any of the usual escape clauses of indirect evidence, it's repeatable, direct, clear, present and obvious.
I agree, it's a nice set-up for your purposes.
So what's wrong with it?
"What's wrong with it" coming up. Let's see how the thread goes for a bit and then I'll bring on my answers here. I'll post this and then add to it.


JAR has now posted his response in Message 3:
IIRC I first presented that idea back in 2005 or 2006 and the beauty of it is that it begins by assuming only what the Bible stories say is true and asks, "If true, what must we see?"

If someone claims that they shot and hit the target, then we must see a hole in the target. If we look at the target and there is no hole, then the claim that the target was hit is falsified.

The test is also independent of when the flood happened; it does not matter if it was yesterday, 4300 years ago or 200,000 years ago.

Regardless of when the flood happened the genetic bottleneck would have been at the same time for every surviving species. The population would have been reduced to at best 14 critters of a kind and at worst 4 critters of a kind.
Actually it was seven and two of the animals and six human beings -- the three sons of Noah and their wives. Noah and his wife had no more children after the Flood so their genes only count in their sons.

But let's not let this go on too far before giving at least a sketchy answer to it: As JAR goes on to anticipate, the answer is in the "super genome" -- but see my previous post in which I've come around to modifying this notion to mean a more fully functional genome in which what is now junk DNA was then alive and contributing many more genes and alleles to the mix.

I also did a post on this some time back as a matter of fact, answering this same challenge from JAR. There ARE markers of the bottleneck in the genomes of all affected, in reduced genetic diversity which is shown in a reduced percentage of heterozygosity for each species.

JAR is anticipating a much more drastic genetic reduction on the order of the cheetah's and the elephant seal's to near-total HOMOzygosity, but those situations occurred very recently and occurred in gene pools that were already much genetically reduced from the time of the Flood after many generations of population splits. In recent times a severe bottleneck is much more likely to reduce many genes to fixed loci, meaning one allele shared by all the individuals of the bottlenecked population, than would have been the case back at the ark. At that time, assuming the much greater heterozygosity of the far more fully alive genome with very little dead or junk DNA, each individual on the ark would have been heterozygous for enough genes to produce all the variations we see today without the specific markers for reduced genetic variability that JAR is expecting based on TODAY's effects.

As I report in that post I linked above, today's human population has about 6.7% heterozygosity, about which I report one researcher said:
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..."

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.
THEREFORE, at least that much heterozygosity was represented in the passengers on the ark, and since that percentage is standard today there would be no reason to expect to see the usual drastic markers for a bottleneck of the sort that produced the cheetah.

That is, this percentage of heterozygosity we have today IS the marker of the Flood bottleneck. Because of population splits since the Flood that would have reduced it even further, it was no doubt much higher then than it is now, but BEFORE the Flood it would of course have been much much higher. I don't know whether to suppose that ALL genes could have been heterozygous back at the Creation or not, and that would include all the genes that are now in the junk DNA graveyard, but it's not beyond the realm of possibility. For that 100% to have been reduced to 6.7% of the 5% of living DNA still in our genome is a perfectly reasonable expectation of the degree of loss of genetic diversity in the Flood bottleneck.

And THAT's your marker OF the bottleneck. And as I say in that post and imply above as well, so is the great percentage of junk DNA in the genome as well.

There are your markers. But you know what, I know that thread is going to go reeling on without acknowledging this idea. I'm easy to ignore out here in cyber space.

So there really isn't more to say on this subject. However, I'll continue to keep tabs on the thread, including the rest of JAR's post:

But wait, there is more...

one possible way around it has been to invoke some super genome, that the pre-flood genome was somehow different and so allowed for greater variation.

Well, there are two major problems there.

First, even if there was some super genome if the Biblical flood stories were true there would still only be at best 14 copies of it to work with and that is still a bottleneck.
True, but since the mere 6.7% heterozygosity still available in our genome today can account for enormous variety, and AT LEAST that much was represented by the few individuals of each species on the ark, a bottleneck then would have not been reduced to anything like the genetic depletion we expect today. Therefore you are looking for something that fits only your own limited imagination rather than what would really have been the genetic result of such a bottleneck. Just as the early creationist geologists and all of today's geologists persist in looking for evidence of the Flood in all the wrong places.

Second, we have genetic evidence from humans that date to before the 4300 years ago date, from as far back as 30,000 years ago and as far back as 14,000 years ago in the Americas and there is no sign of any super-genome.

I think these two lines of reasoning are pretty solid.
Well, here a creationist simply parts company with the "sciences" that take their mere conjectures about time to be fact. Sorry. The Flood occurred about 4300 years ago and the Creation about 6000 years ago and your age reckonings are nothing but delusion.

And I'm going to skip most of JAR's usual debunkeries of the Bible which usually tend to the blasphemous, and go on to:
In both myths lots of critters get killed, in the myth found in Genesis 6 it seems to be talking about land animals and birds while the myth found in Genesis 7 goes even further and wipes out all living things.

If we play mix and match and take the best scenario from each of the myths we might be able to claim that only the birds and land animals were wiped out based on the passage from the Genesis 6 story and that we have the larger saved population found in Genesis 7.

Based on that mix and match game set we have a situation where all land animals and birds found today will be descended from a population that consisted of at most fourteen critters (seven pairs of clean animals and birds) and at worst case four critters (two pair of unclean animals).
No, take the smallest numbers as I have and only for passengers on the ark, six humans, two unclean animals and seven clean (and remember that most of the clean would have been sacrificed to God by Noah after the ark landed and not have passed on their genes). Sea creatures and plants and others no doubt also perished in great numbers off the ark but we don't have the numbers to calculate in their case.

As for the passengers on the ark, the much greater percentage of heterozygosity in the pre-Flood genome even reduced to a few individuals still accounts for all the variety we see today.
Now that is what I would call a real bottleneck.

We know we can see bottlenecks in the genetic record; a great example is the one in Cheetahs but we even see them in the human genome and most other species.


If the flood actually happened we would see a bottleneck in EVERY species of animal living on the land and EVERY bird and EVERY one of the bottlenecks show up in the SAME historical time period.

Talk about a big RED flag.
Yup you're expecting to see the same situation as in TODAY's bottlenecked populations, the extreme homozygosity even to majority fixed loci, instead of the bottleneck markers that really DO exist, the mere 6.7% heterozygosity and the 95% or more junk DNA.
That bottleneck signature would be something every geneticists in the world would see. It would be like a neon sign, Broadway at midnight on New Years Eve. It would be something even a blind geneticist could see.

So it seems to me to be a very simple test that will support or refute the Flood.

If that genetic marker is there in EVERY species living on land or bird of the air, then there is support for the flood. It does not prove the flood happened but it would be very strong support.

If on the other hand that genetic marker is NOT there, then the Flood is refuted.
Good try but the marker IS there, in fact TWO markers are there, but you miss them because your expectations are wrong.

And for the second argument see the thread Looking for the Super-Genome. -And it ain't found.
Well, now I do have a different idea of what that original genome would have looked like by which I would expect to find a pre-Flood genome with hardly any junk DNA and a majority of heterozygous genes.

The relevant question is whether it's possible to SEE the genome of ANY creature that lived before the Flood or not, and as far as I know they're all fossilized or destroyed and their DNA is not available. JAR's favorite "Oetzi" is most certainly NOT contemporaneous with Adam and Eve but lived after the Flood despite the preposterously dogmatic claims for his age. He was found in the Alps but his DNA shows him to be related to Corsicans, who most certainly did not exist before the Flood. This is all post-Flood terrain that's being described here. The Alps also did not exist before the Flood but like all the high mountains were formed by tectonic forces set in motion along with the other geologic phenomena associated with the Flood event.

In any case the markers for the Flood bottleneck ARE apparent in today's genomes if 100% or near-100% heterozygosity and no junk DNA characterize the original "super" genome.