The Second Law of Thermodynamics contradicts the Theory of Evolution

At EvC they are complaining about creationist arguments concerning the Second Law of Thermodynamics, in a thread titled Infuriating Arguments. This gets into solar energy beyond my abilities.

It seems to me, however, that I've seen creationist arguments about the "closed system" that aren't quite what is being presented here but since I haven't followed them I can't really say anything about them.

But discrediting a particular argument about the Second Law doesn't necessarily discredit the whole creationist claim.

It seems to me to be pretty obvious that the universe IS gradually running down or losing energy or however that should be put. You can always point to factors that demonstrate renewal and growth nevertheless because seeds do sprout and grow to maturity, babies do start from a seed and grow up, the sun does give energy to all life on earth and so on and so forth, and yet, overall, the sun is gradually gradually burning out, living things are subject to disease and death, even extinction of whole species, and that's where we can see the Second Law in operation. Things running down, things running out. Slowly, very slowly. The evidence of the Fall.

The argument of course is that the Theory of Evolution contradicts the Second Law: both can't be true. They solve the problem by tacitly assuming or hallucinating an ever-renewing input of life energy that does not exist.

Oh, and if with much abstruse mathematical conjuring you can "prove" that the Second Law does not describe what I'm describing, then we need another law, that's all, because what I'm talking about IS happening and creationists know it is happening, and anybody with half a brain ought to know it's happening and it doesn't matter one iota whether the Second Law says so to your satisfaction or not.

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Later (Message 17) Trixie says:

Last night someone who was arguing for a 6000 year old earth and a global flood supported their position by linking to information on ice ages dated to 11,000 and 14,700 years ago. Another genius tried to cast doubt on carbon-dating by pointing out problems specific to K/Ar dating then linking to a page which exposed the errors in the usual arguments against carbon-dating, so refuting himself.

I don't know what the argument concerning the ice age(s) was but apparently the creationist failed to make clear that he/she denies the dates assigned by old-earth science, which obviously Trixie accepts as gospel truth. We know there was ONE ice age, but there most likely weren't two, and the one can't be older than the Flood. According to something I read somewhere the ice age was most likely the result of heat released in the Flood period, on the same principle as refrigeration (don't ask, haven't researched this in some time), heat caused probably by tectonic movement.

As for the rest of it, it sounds like the creationist did get confused.

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And in message 46 by Son Goku:

Unfortunately the Second Law of Thermodynamics is a particularly difficult concept to set right to an audience of this kind. This is because a lot of presentations make it appear to be about order and disorder (where as this is only a common, but not universal, consequence of it). Unfortunately an "increase in disorder" fits with all sorts of notions such as the decline of the world after the "fall". I've seen many Creationists using it as scientific proof of their world view, i.e. "Look the world really is decaying!"

I don't think we need the Second Law to know the world "really is decaying," that takes just the minimal knowledge of the fact that the sun IS gradually burning out and life DOES die, and the Second Law seems to reflect this fact. If it doesn't it doesn't, nevertheless the world "really is decaying."

Evolution, racism, conscience-free murder, dehumanization, atheism, all of a piece

This is from Chris Pinto at his Adullam Films site:

Hitler’s concept of the Aryan (exalted or noble) race represented the highest point of the evolutionary pyramid, and all races that fell beneath the Aryan standard were fair game for removal (i.e., extermination). This is why Hitler equated Jews with rats and termites. In fact, the Zyklon-B gas used to murder Jews in the showers of Auschwitz was originally a pesticide developed to kill insects. This is also why the Nazis used Jewish skin, bones and teeth to make lamp shades and brush handles – because killing a Jew was deemed no different than killing a cow, cutting down a tree, or picking cotton from a field – according to Darwinian philosophy. Darwin’s “struggle” for life seems to have been the theme of Hitler’s famous work – Mein Kampf (i.e. My Struggle). His struggle was the preservation of the Aryan race, the favored race according to Hitler.

Some people coming out of Communist countries tell of how the Communists used evolution in schools to remove the consciousness of God from the minds of the people. Evolution removes the authority of God, and makes man his own god – accountable to no one but himself. In Communist countries, Marxist Atheism is the rule and the state is the supreme authority. Yet according to The Black Book of Communism: Crimes, Terror, Repression (first published in 1997), some 94 million people were mass murdered in the 20th century by this atheist form of government. That’s more than all the people killed through the Crusades and the Inquisitions combined. Keep that in mind the next time your atheist friend tells you about the “evils” of religion in government. Also remember that evolution is the cornerstone of both atheism and the occult.

They can deny it all they want, the evolutionists, such as those at EvC forums, and of course they will deny it and muster all kinds of ridiculous notions of "evidence" against it, but it's well known that evolutionism goes hand in hand with dehumanization and atheism.

More evidence for the Flood

This is a unique geological phenomenon known as Danxia landform. These phenomena can be observed in several places in China. This example is located in Zhangye, Province of Gansu.

The color is the result of an accumulation for millions of years of red sandstone and other rocks. layered deposition of wet separated sediments by the Flood of Noah, distorted by tectonic forces set in motion during the same event, now hardened into red sandstone and other rocks.

The messiness (aka bloodiness, harmfulness, ugliness) challenge to creationism answered again

Just a quick comment on that same thread about novel features I posted on below. Tangle has been bringing it back from time to time, Zaius and WK get off into technical neverland occasionally but even they are doing a better job than I would have expected of keeping the main question in mind, which is whether mutations are the source of new alleles / traits, or they are built in from the beginning. So far they are unable to make a definite call. Of course I'm convinced that any actually useful alleles were there from the beginning and that mutations are ONLY destructive accidents that evolutionists have pounced on as their one vain hope for a mechanism of change that could support the theory.

Be that as it may, what I really wanted to comment on was Tangle's off-the-cuff comment in the post linked above:

ABE - as an irrelevant aside, the sheer messiness and complexity of these systems are evidence against design.

Well, it's true that God's original design doesn't account for it, but since what you really mean is that it's evidence against creationism as such, that's not so, Tangle. This is another favorite evolutionist challenge to creationism that has been answered over and over but keeps being thrown out there again anyway.

It can only be answered by a BIBLICAL creationist, however, who accepts Genesis in its entirety and doesn't try to read extra time between the lines or explain away the traditional understanding of the text:

The messiness of genetics is explained not by the Creation -- that is, God's original design -- but by the Fall, which introduced the processes of death and disease into the Creation. Complexity is one thing, expectable in God's Creation -- that rightly should lead to awe and appreciation -- but the kind of complexity that is really unpredictable chaos and confusion that is difficult to interpret must be attributed to the Fall. Mutations must be attributed to the Fall -- until someone can show that their occurrence obeys a law, which so far hasn't happened and doesn't seem at all likely ever to happen. Mutations are accidents, mistakes in the replication of the genetic material, KNOWN to be the cause of thousands of disease processes and NOT known even once to have produced a viable healthy allele.

Design is not challenged by the messiness, the messiness was introduced by disobedience of God, and evidence for this is everywhere in damage to the original creation -- which still shines through in many ways nevertheless.

The Genetic Bottleneck challenge to the Flood answered again

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

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

On the usual expectation, Dr. A gives this standard answer to the question how we might determine if there has been a bottleneck in a species:

Well, you look at the size of the population and the amount of genetic diversity within it. In equilibrium (i.e. if the population has been about the same size for a long period of time) the diversity will be proportional to the population size --- there'll be a certain quantity of diversity such that the production of new variants by mutation is just balanced by the elimination of variation by genetic drift.

If there's markedly less diversity than that, this indicates a recent bottleneck.

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

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

The question of the genetics involved, however, seems to me to be most likely answered by the fact I found in Morris and Parker's What Is Creation Science? on page 112, which I quoted in a post on the subject in September of last year, where I quote Parker saying that

human beings are "heterozygous" for 6.7% of their genes, on the average. That means that 6 or 7 times in a 100, the pair of genes for a given trait differ like the genes for brown or blue eyes, or for rolling or not rolling the tongue. Now this may not seem like much. But Ayala calculates a single human couple with just "6.7% variety" could produce 10 to the 2,017 children ...before they would have to produce an identical twin..."

And I go on to comment that

He goes on to say that the whole spectrum of skin color we see today would be easily produced IN ONE GENERATION with just this 6.7% heterozygosity for that trait. Combining that with the same breadth of possibilities for size, hair or fur color, bone type, muscle type, and so on and so forth, would certainly yield an enormous variety of individuals within each created kind or type.

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

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

6.7% heterozygosity as measured today under the assumptions of the ToE would be taken as the norm for human beings, but it could reflect an enormous reduction from a pre-Flood percentage and therefore represents the bottleneck of the Flood itself.

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

Creationists who lose their faith

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

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

Taq is referring to a discussion at another evolution-creation debate board:

Libby Anne recently wrote a "Why I am an atheist" essay over at Pharyngula. In it, she discusses how she argued against evolution but finally conceded that the evidence was on the side of evolution:

[Libby]And then I went to college, where my young earth creationist views were challenged. I responded by fighting back. I argued with both students and professors, sure that I had some sort of truth they were missing. I brought out every argument I had, and went back to my creationist resources for more. As time went by, though, I found my arguments effectively refuted by arguments and information I had never been exposed to before. To my utter shock, it seemed that the evidence actually fell on the side of evolution and against young earth creationism. After nearly a year of fighting, I conceded defeat.

What happened next is fascinating, at least to me. Two creationists felt the need to comment: Dr. Georgia Purdom and Ken Ham from AiG. When I read their responses my jaw just hit the floor. They just don't get it, as Libby Anne was quick to point out. Quite frankly, they would have been better served not saying anything at all. In an attempt to explain why Libby Anne left the faith they have given away the farm, IMHO. Here are just a few excerpts from Dr. Purdom and Mr. Ham:

Libby seems to have things backwards. It’s not that “we know the Bible is true because young earth creationism is true,” but rather because the Bible is true we can believe what God said in Genesis about the time frame in which He created. Although she read AiG resources, attended AiG conferences, and came to the Creation Museum, I have to wonder how much she really understood what she was reading and hearing. The very idea of God creating in six literal days, 6,000 years ago, and the global flood comes from Scripture (and of course the scientific evidence confirms it)!--Georgia Purdom

So the Bible is true because the Bible says it is true, and Libby should have remembered that. Oh, and the evidence backs it up. Why not just say that the Earth is young because that is what the evidence says? I think Dr. Purdom is revealing more than she may want to with this statement.

First I wonder why Taq is so amazed at this response, why his "jaw hit the floor" and how he arrived at the conclusion that Dr. Purdom "just doesn't get it." What does that even mean, she doesn't "get it?" Get what?

Why not just appeal to the evidence for a young earth? Because a Biblical creationist starts from the Bible. Why is this so amazing to Taq? Dr. Purdom is right that it isn't that the Bible is true because creationism is true, and it also isn't true because it says it's true as Taq spins it, it's true because it's God own word and true Christians know this. There shouldn't be a question about this, there shouldn't be anything amazing about this, it's the first principle of Christian belief. Serious Bible believers pursue the creationist debate because God's word tells us the world is not as the evolutionists and Old Earthers say it is, and we expect ultimately to be able to find scientific evidence for the Biblical claims (and as Dr. Purdom says, there is such evidence). What's not to get?

Also, if you read Libby's response it is more than apparent that she did know her stuff, perhaps even better that Dr. Purdom does. It's not that Libby did not understand the arguments, it's that the arguments are WRONG. Creationists just can't understand that.

Well, of course we aren't given the arguments that Libby found so compelling, or what arguments she was using as a creationist, so there is no way to determine the rightness or wrongness of either side of the debates. No matter of course, if it's a creationist argument it's wrong by definition according to Taq, no need to produce specifics so that we could judge for ourselves.

Then Taq quotes Ken Ham:

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

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

--Ken Ham

Both Dr. Purdom and Ken Ham seem to agree on this point. The solution for creationism failing in the face of criticism is MORE INDOCTRINATION. As Libby Anne puts it:

And the solution Ken Ham and Dr. Purdom make? Double down. That’s pretty much it. Teach the same things, just more. Oh, and isolate yourself and your children from other points of view – oh the dangers of the state college or “compromised” Christian college!

Creationists, is this really the new strategy? When it becomes apparent that creationist arguments can not stand up to criticism is it really the right move to protect creationism from any type of criticism? Is this why creationists are fighting so hard to get evolution out of the classroom?

But it isn't that creationist arguments have failed to stand up against criticism -- or at least there is no way to tell in this case since there isn't enough information either about the creationist arguments Libby used and her understanding of them, or the arguments used against her and whether they could have been handled better.

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

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

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

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

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

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

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

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

====Later:

NoNukes in Message 8 got it right.

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

Exactly.

But Taq still doesn't get it:

Then why even look at the evidence? Why does AiG spend so much time discussing the evidence? If you already believe that you are right and can not be wrong, then why do you need evidence?

Because, knowing that the Bible is the truth we expect science will ultimately confirm it, and we believe it already confirms a great deal of it. It's not science so much as the evolutionist bias that is what we have to overcome, but that requires dealing with the scientific claims.

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

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

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

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

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

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

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

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

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

Then JAR gives us this information:

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

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

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

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

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

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

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

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

It all comes down to imperfect copies.

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

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Then in Post #18 JAR says:

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

That shows that genomes do change over time.

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

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

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

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

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

Too bad, started well.

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

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

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

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

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

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