A barrier to macroevolution & objections to it

During the 1920's and 1930's the population geneticists demonstrated the sufficiency of mutation to provide variation, leading to the Modern Synthesis of Darwinian evolution and genetics, what we today formally call the Synthetic Theory of Evolution, and usually just refer to as the theory of evolution.Meaningful experiments can be conducted in reasonable time periods on organisms with very short reproductive cycles, such as bacteria, and such experiments have demonstrated time and again that favorable mutations quickly spread through populations and act as a source of variation.Your specific example of novel organs fits neatly within an evolutionary context. Duplication produces an extra organ, and then individuation (further mutations causing change in one of the duplicate organs but not the other) causes it to become unique. One example would be multi-legged insects like centipedes, where different yet still very similar species developed from common ancestors by duplication to produce more legs (in some cases) and removal to produce less legs (in other cases).All this evidence means that the role of mutation in evolution is *not* weakly inferred but rather is strongly supported. This is a good summary, and perhaps the best response is, "Yes, of course," but one minor correction is worth mentioning. While there may be scenarios where an essential organ evolves a new and different function, none come to mind right now, and this isn't a scenario anyone from the evolution side is promoting. We've been talking about duplication followed by evolutionary individuation over time through successive generations.What you're probably neglecting to consider is that the low odds of a successful mutation are easily overcome because each reproductive event is a genetic experiment, and there are literally billions of reproductive events every day. Reproduction is imperfect. If the "imperfections" (i.e., genetic differences from parents) produce unfavorable changes in the organism, it competes less successfully with its peers and the "imperfections" tend to become less well represented in the population or even disappear entirely. If the "imperfections" produce favorable changes in the organism, it competes more successfully with its peers and the "imperfections" tend to become increasingly well represented in the population, perhaps even eventually become ubiquitous. I think you meant 4 raised to the power of the number of nucleotides. And it's not as simple as that, either, since the nucleotides are collected into groups of 3 to code for the (I think) 20 amino acids. But the math isn't important to this particular argument, and you go on to say: To the contrary, laboratory studies precisely confirm this, and even genetic algorithms from the field of computer science reinforce the ability of this process to do precisely what you deny is possible. You continue, also incorrectly: Gene duplication during reproduction is a common mutation. So is chromosome duplication (Down's syndrome is a duplication of all or part of the 21st chromosome). Chromosome duplication is extremely common in some plants, and there are some well-known speciation events deriving from this process. Duplicate organs occur all the time as a result of genetic mutations. Since organ duplication is your favored example, let me cite the first study that came up in a Google search: Wnt-5/pipetail functions in vertebrate axis formation as a negative regulator of Wnt/-catenin activity: "Organ duplication was verified in several maternal-zygotic ppt^-/- (mzppt) embryos...".--Percy

Faith wrote:

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The mutations that occur have NOT been SHOWN to bring about this ASSUMED result. WHERE IS YOUR EVIDENCE THAT THEY DO THIS, as opposed to your ASSUMPTION that they do simply because they occur?????

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Faith’s quest for observed evidence here is rational. There should be observed cases that we can point to for discussion.Now Faith, you and I have discussed a great example of this. Have you forgotten it? Remember the paper that WK posted that showed increased genetic diversity in speciating groups of salamanders in California? That seems like the kind of evidence you want. I wish I were an animal biologist with access to the literature on this, because my understanding is that this salamander paper is not unusual, but rather something that is see often. Plus, you have agreed that we have good examples of beneficial mutations.Other examples of increases in genetic diversity due to mutation from bottlenecked species are easy to come up with.1. A big one is bacteria. I know faith doesn’t like bacteria, but bacteria do like Faith, just as they like any other animal. Remember that bacteria don’t have sexual reproduction, so every single bacteria is in many ways an extreme bottleneck, down to one individual that then makes it’s own population (it’s own strain).
Thus the recovery from a bottleneck with increased genetic diversity is happening all over, whenever bacteria fail to die out. I doubt that any of us would go into a hospital and tell them that they don’t have to worry about bacteria, since all of the bacteria are bottlenecks that’ll die out if left alone.
The nylon digesting bacteria and indeed any of the billions of bacteria in your gut are good examples of flourishing bottlenecks.2. Island species. There are thousands of isolated islands on earth, with many species. Many of the species radiated from a few individuals who got there one way or the other, and then flourished and evolved into many species. There have been dozens of papers written documenting that they evolved from a common ancestor on that island, and all of those show a flourishing after a bottleneck. If new mutations didn’t supply new genetic diversity after a bottleneck, then most islands on earth would be barren of both plants and animals, even if one assumes creationism, since those island populations on smaller islands regularly are bottlenecked.3. This may be a special case of the island example, but consider invading foreign species. Examples are common without even much thought. Australia is a great source - cane toads have invaded from people bringing them, and have flourished, showing new mutations as well. When a few rabbits were introduced in Australia the took over the continent and denuded the landscape, and certainly didn’t die out of genetic degradation. Similarly, Cuba, like most islands, has a flourishing population of rats, which were introduced in the past few centuries. We could go on all day with examples of bottlenecked island populations that have flourished, many with new traits.4. humans. Whether one accepts the 60,000 year bottle neck or the creationist extreme bottleneck of a single person just 6,000 years ago, humans have undergone some bottlenecking, and now have all kinds of different alleles that far exceed what could be in one person. Eye color is a great example, as is nearly any other feature like skin color, nose shape, jaw shape, etc. What kind of nose did Adam have? A Roman nose? A ski-slope nose like my sister? A little whitey nose? One with a little ball in the end? A hook nose? A wide Polynesian nose? A “visible nostril” nose like a friend of mine? A long pointy nose? Etc?OK, Faith and others say Adam had a hypergenome with all those alleles and more, and they have since split up and degraded. But in another thread we saw that this idea is testable, and the evidence for it is far outweighed by the evidence against it. Here are some examples from that thread:

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Such a general degradation across genomes, including both human and animal life (not to mention other kingdoms), should be detectable.
The most obvious thing to test are direct samples of ancient vs current DNA. While DNA does generally decay quickly, we do have samples that have survived. Here are some:

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1. Neanderthal DNA. We have some Neanderthal DNA. While a number of dating methods put Neanderthal DNA to between 40,000 and 100,000 years ago (depending on the sample), creationists usually claim that Neanderthals are normal h. sapiens who died in or before the flood. If so, then they are at least 4,500 years old. Using the creationist number, they had only 20 to 1500 years of degradation, compared to 6000 for humans today. Thus their genomes should have only a tiny fraction of psuedogenes and junk DNA. To try some numbers, we need to know how degraded we are today. I don’t know what a creationist would say, but from the claims of people like Faith, I think they would say a high number, since they feel we have degraded a lot since the fall (otherwise it’s a pretty wimpy force of sin and death). So lets say we have only 40% of our good genome left. If that’s the case, then we’ve degraded 60% in 6000 years. If the degradation is linear (again, big guess), then that’s 1% loss every century. So a Neanderthal genome should have around 0 to 15% degradation.

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Such a huge difference would jump out to any geneticist looking at Neanderthal DNA. Since numerous studies have been done on Neanderthal DNA, It must not be there. The researcher couldn’t hide it since other people have seen Neanderthal DNA, and more importantly, they wouldn’t want to, since such a find would gain them instant fame. Even if someone were willing to hide data if it favored creationism, they still wouldn’t hid this since it can be interpreted other ways.

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2. DNA from other ancient animals. We have a huge amount of insects in amber from what creationists would consider pre-flood times. The same math from above applies here, as well as the same logic.

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3. Frequency of disease in the fossil record. Many diseases leave visible signs in bones. Diseases have been shown in fossils across the board, regardless of age. I don’t know that a quantified study of diseased fossil frequency has been done, but since a degradation from the fall until now should show a big difference, such a trend should stick out like a sore thumb, and I’m sure it would have been found if there.

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4. Spina bifida in Neolithic England. The barrows around Stonehenge and similar Neolithic religious monuments are dated to around 2,000 to 5,000 years ago. Thus they should have around half of the degradation we have. Note that creationists generally agree with those dates, since we have roman and other records showing that refer to them as past civilizations. The bodies in the barrows have a high proportion of Spina Bifida (a birth defect). If there has been degradation since the fall, then ancient birth defects should be much lower, not much higher.

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5. Human age at death over the millennia. We have human fossils all over the ancient time frame, and the age of a human fossil can be estimated from bone growth and bone changes. These fossils do not show that ancient people lived to anything near the ages in Genesis. Instead, they show a steady life expectancy, with variation from time to time due to things like food supply. Of course, one could argue that the bone changes that we use to determine age at death simply happened later, which could explain it, but would require that kids lived to, say, 50 years and were still kids, which seems difficult on the parents.

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6. Wooly mammoth frozen bodies. It has been shown that sperm frozen in animals who have been frozen whole is still potent even after a few years. This work has encouraged people to think about using frozen mammoth sperm or eggs to breed or clone a mammoth. The DNA of mammoths has been compared to modern elephants to find differences. If the degradation hypothesis is true, then the mammoths would show little degradation , and the elephants a lot as per the math above. Such a difference would again stand out like a sore thumb. No such difference has been found.

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7. Dendrochronology. Dendrochronolgy, as we know, is the method of counting tree rings to look at their growth in ancient times. Tree ring series go back 10,000 years in some places (I haven’t heard how creationists explain this - maybe a good new thread topic). (Also - what do creationists say about the flying sword mentioned in Genesis 3? Where did it go? Why can’t any skeptic just go and look at it?) Anyway, with better health, trees are known to grow more, giving wider rings. If there has been a general degradation, then it would be easy to see this in the tree ring series, which would show better health in the past, esp 6,000 years ago). They don’t show this however - they show the same amount of health (with variation) today, 100 years ago, 1000 years ago, 3,000 years ago, 6,000 years ago, 9,000 years ago, etc.

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Well, 7 is the holy number according to the numerology soothsayers of the Bible, so I’ll stop there. Just a little thought brings more of them to mind (such as how long kings lived in Chinese records, which go back 4,000 years). In all of these cases, it is possible to test the predictions of the degradation hypothesis, and the predictions don’t match the data. Maybe a good way to explain this is to say that God reached in and altered each piece of this evidence to deceive those he’s already decide to burn in hell, just as “Paul” says he would in 2thes2:11?

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That’s not even mentioning the huge amount of DNA that has been examined from Egyptian mummies that are thousands of years old, or from even more ancient people like the iceman. In all of those cases, the idea of a degradation has been directly tested and found incorrect. Also, thanks archer for pointing me here.Take care-
Equinox Edited by Equinox, : No reason given.

Oh, and as if we needed more examples, I just saw this on one of my old posts-Algae that has been severely bottlenecked by putting it in an aquarium has mutated and is not dying out, but rather has escaped and is taking over in the wild. Please use peek to see how to shorten linksHave a fun evening--EquinoxEdited by AdminJar, : No reason given.

You are giving the same old same old that is not evidence. I am asking for evidence of actual observed documented increase in alleles after actual loss of alleles. As usual you infer and surmise and assume, as I've been saying, you have not proved anything. It was Quetzal who posted the article about the Ensatina and I answered it. What do you think it proves? It shows exactly what I would expect to see in a ring species, developing divergence from randomly selected alleles. Mutation was not shown to have a part in this at all. Mere isolation and new proportions of pre-existing alleles is all it takes to bring about that situation. As I said.To PROVE that mutation has a role you have to prove that new alleles exist that were not in the previous population, and to do that you have to have a THOROUGH allele count of the original population, and if you do find new alleles through mutation you have to prove that they play a role in the divergence of the new species.Typically, as I've been saying, mutation is simply ASSUMED to be the explanation for divergence, without any proof whatever. All the examples you are listing are the very ones I've already discussed and rejected. One-celled creatures simply cannot be used to describe the situation of multi-celled creatures undergoing multiple mutations, most of which do not enhance survival or thriving. Why is it so impossible to construct an experiment to investigate this? I gave an idea for an experiment in the last thread. I'll see if I can locate the link after I post this.{Edit: Here it is.} Again, as I have been saying, you are merely *assuming* that mutations are the explanation. You do not know this, you have not proved this. You have to know the condition of the genome of the original founders in order to say such a thing. For all you know each founder individual had different alleles from each other, or the genome was bigger. You have no idea how many genes were in the founders, so how many alleles are now dispersed in the population simply from that cause. How do you explain that *most* bottlenecks and founder effects lead to a diseased and extinction-vulnerable situation if mutation is such a ready remedy to their plight? Since that situation is certainly as common as the one you are describing, explain how mutations *aren't* the solution there. Great, there are examples where bottlenecks aren't a disaster for the species. So? None of this proves that MUTATION has anything to do with it. Richer genome, more alleles in the founders, whatever, is at least as likely an explanation. And again I'd point out that if mutation were this savior we wouldn't have so many OTHER bottleneck examples where they DON'T thrive. Until you've counted alleles and tracked their effects you know nothing about their source, you are just guessing, simply *assuming* that mutation is the explanation. The human genome was originally very rich. There are LOTS of alleles in the human race, and perhaps genes too, that determine nose form. I answered all that here.Edited by Faith, : To add link.Edited by Faith, : No reason given.

I don’t think anyone would dispute the fact that inbreeding increases the incidence of harmful alleles expressing themselves. Well, that remains to be demonstrated.
200years are for humans a rather short period, given our slow reproductive rate. If we count with a short turnaround in generation 200years mean at most 10generation, i.e. 10 meiotic divisions where new mutations can occur. But if we take the Amish and the Pitcairn populations as examples we should and would expect an increased level of common hereditary traits within those communities compared to the population at large. Some of these traits will be harmful some neutral and others might even be beneficial.But is the situation of any of these two populations so bad that we should label them “endangered species”? When would you predict they will go extinct due to genetic depletion?Now let’s return to Iceland, that started out much like the Pitcairn settlement (but 1100 years ago instead of merely 200), and in the meantime have been decimated by both bubonic plague and natural disasters. It today holds a population around 230 000, it is not heavily afflicted by hereditary disorders but yes, the genetic diversity is less on Iceland than it is on the mainland.
But no one in their right mind would come up with the idea that Icelanders are a dying breed.
So how small and how long can this inbreeding take place? Pitcairn and Amish is still here after 200 years and Icelanders are here after 1100.

I'm not sure what you are trying to prove. Sometimes bottlenecks and founder effects work out fine, sometimes they bring about a condition of such disease-proneness it threatens the survival of the species. I would say that depends on the genomes of the founders. Human beings can always remix with the rest of the human race if necessary so extinction isn't the issue in that case.As I say to Equinox in the above post, you can't explain the success of some populations that are based on bottlenecks on the basis of mutations, which is the whole point of the discussion here, unless you can explain why mutations *haven't* brought about success in the bottlenecked populations that are threatened with extinction because of depleted genetic diversity.

There are any number of explanations. It could be that the weakened population suffers at the hand of a competitor by the time it starts to gain in numbers. Thus it cannot increase in numbers because as it grows in size more and more are killed, limiting their population size and thus making it difficult to increase diversity.Any number of ecosystem changes can reduce the maximum population size of a species which will automatically mean its diversity is stunted. Species which are nomadic by nature are thus doubly hampered because mates might be few and far between and (depending on habit) possibly fairly closely related.Just because genetic diversity can increase after a bottleneck doesn't mean it has to.

I've list case after case that shows what you are looking for. Even like the Apo example where we can show the exact generation the mutation appeared. I can't imagine what more you'd want.
The ones I mentioned you have ignored, as usual, without reason.What about the algae example? There are clear increases in fitness that have arisen after a severe bottleneck.We can both agree that sometimes the genetic loss from a severe bottleneck is too severe to recover from, and that sometimes it is not. However, it's clear that if it survives for a little while, it very often flourishes, while if your degradation idea where right, then it would always die out over time, which we clearly don't see - think about those non-barren small isolated islands for an example.As for Adam's nose, I've responded and we can continue that discussion about the lack of evidence for some kind of degradation.

Could you explain what is meant by indiviuation? As I understand it, individuation referers exactly to the evolution of a new function.Wikipedia defines it this way: Individuation comprises the processes whereby the undifferentiated becomes or develops individual characteristics, or the opposite process by which components of an individual are integrated into a more indivisible whole.Assuming the first sense, individuation is virtually synonymous with the evolution of novel function. I'm curious as to what alternate meaning you have in mind.As far as this claim: I'm sure you are familiar with Dr. Ken Miller and Dr. Douglas Futuyama? This past summer Drs. Miller and Futuyama hosted a massive (over 2 thousand Ph.Ds) evolution symposium.One of the theme of one of the major presentations hosted by Drs. Miller and Futuyama was on that specific topic. The thesis was that the assumption of different functions by an organ is the accurate description of many organs lineage. I won't say claim that this is their description for the lineages of all organs, but they certainly make this claims very strongly. They made this claim in response to Behe's IC. Looking at the bacterial flagellum, they indentified the proteins that they claim belonged to 14 different bacterial organs with various functions that later fused (my word, can't think of a better one right now) into the one organ, the bacterial flagellum. So the concept is at least out there, and I think more highly touted than you realize...

That's right, and to prove that the sun is 150 million kilometers away we have to walk over there and count all the steps on the way because all we have right now are inferences.Edited by fallacycop, : tyo

fallacy cop brings up a good point although I would like to expand upon it.In order to show an increase in diversity it is sufficient to show a situation where there is the mere existance of new alleles where they were known not to occur before. Showing that there was 32 possibile alleles and now there is 33 is not necessary. No counting needed. Faith's requirement is wholly excessive.

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Of course, biblical creationists are committed to belief in God's written Word, the Bible, which forbids bearing false witness; --AIG (lest they forget)

All hypothetical, Mod. My argument is that there is nothing BUT hypotheticals in favor of mutations as the explanation for a supposed gain in numbers of alleles after a bottleneck or any speciation or population splitting event. Of course it can be rationalized. The point is there is no actual evidence.

But I'm not disputing that mutations occur, or the existence of this short list of apparently beneficial ones. But they are no better than hypotheticals in response to this question. That an extremely rare beneficial mutation has occurred somewhere is no evidence that mutations can be counted on to increase alleles in a population that has suffered a population-split reduction. SO few examples, too, Equinox. Hardly the regular occurrence you'd have to be able to demonstrate if you can't show an increase in a particular case. I didn't study the algae example, since it seemed irrelevant after my reply. I haven't ignored these, I've said that the state of the original genome is the most likely explanation for an apparent increase in alleles, and that these very rare examples aren't EVIDENCE, they are just mutations that have happened here and there. I don't know about fitness. Apparently this bottlenecked algae thrived in a new environment? Why isn't the environment the explanation for that? My "degradation" idea isn't this uniform thing you are imagining. The genome in some species and varieties has more diversity than in others. You need something better than 0.03% of the Neanderthal genome.Also, how do you know what degradation should look like in the genome anyway? I've postulated the length of the DNA in relation to the functional DNA. Is that what you have in mind?

If there is no evidence then your own assertion that mutation cannot do so is also dead in the water. Want to explain why a lack of data is a serious problem for people who disagree with you, but doesn't prevent you from calling your own assumptions "fact" ?This thead is for you to argue that there is a barrier. So far it hasn't produced any good reason to suppose that there is. Instead the creationist position is mainly claiming that they haven't been proven wrong. If that's the best you can manage then you don't have a case. Stop trying to shift the burden of proof and try to produce good arguments that there is a barrier - or are you going to concede that the idea is little more than an assumption ?

I'm aware that counting is hard, but without it these claims that mutation explains all changes is just assumption, not evidence. Most studies one reads simply mention mutation as a given. Such and such apparently new allele is simply called a mutation, although there is absolutely no evidence given that it was a mutation. Sometimes you can prove it, but most of the time it's just an assumption. Inference is fine if your theory is not challengeable, but this one is, and you can't rightly treat mutations as fact when they are nothing but suppositions. If you don't count them, how do you know there are new alleles at all? If you assume this from a change in phenotype you CERTAINLY don't know this, since such a change is normally brought about by mere selection of pre-existing alleles, possibly a rare one you didn't know was in the population -- which you didn't know because you didn't do a complete count.Edited by Faith, : No reason given.Edited by Faith, : No reason given.Edited by Faith, : No reason given.