Natural Limitation to Evolutionary Processes (2/14/05)

Only if there's no selection is there a situation of increasing genetic defects in a population, which may be the precise case for homo sapiens. If that's your point, then I agree with you. One of the dangers the human race poses for its own survival is that our ability to develop medical treatments for genetic diseases allows people with genetic defects, who in earlier times would have died young, to produce offspring.One extremem example that comes to mind is cystic fibrosis. Individuals with this genetic defect used to die young, but modern medicine now allows many to live into their 40's. Because cystic fibrosis is an extreme example where every victim is intimately familiar with the consequences of the disease, victims probably rarely pass this gene on. They either choose not to have children, or they use genetic screening to check for the presence of two defective copies of the CFTR gene before birth and terminate the pregnancy.But other less severe genetic defects, like color blindness, are probably passed on all the time. In modern societies the survival cost of color blindness is minimal, but in prehistoric times it was probably much more important. For instance, those with color blindness often have much greater difficulty seeing in the dark.Visual acuity and focussing ability also has a genetic component. Darwin observed in Patagonia that the natives all had far better vision than the Europeans. In a civilization without eyeglasses, the genetic ability to produce good eyesight would be well maintained.So I think you have a good point for homo sapiens, but we're increasing the defects in our gene pool through articial rather than natural means, usually medically related means. We even do the same thing for our pets. For instance, I believe german shepherds have a genetic defect that causes hip problems, but we treat the hip problems and allow the dogs to reproduce. Of course, it was humans who bred german and shepherds and all other dogs from wolves, anyway, so perhaps this is too artificial an example. But you probably get the idea.In the wild, medical means of alleviating the effects of genetic defects are not available, and genetic defects are filtered out, meaning the affected individuals do not survive to produce, or if they do, they produce fewer offspring than unaffected individuals. You say that evolution is impossible, and I grant that your misunderstanding of evolution is impossible. This is representative of too deep a misunderstanding to take the time to correct. I know that's a copout, I'm criticizing without providing the proper counterpoint, but I am pressed for time right now. Please give me a pass on this for now and I'll try to come back to it later. I don't think we should let any formal definitions of "neutral mutations" get in the way of understanding. Whatever those definitions might be, I think your approach makes more sense. Describing as neutral a genetic defect that adversely affects the ability of an organism to produce offspring does not make any sense to us laypeople. Haven't examples of good mutations been provided for you in the past? Anyway, one common type of good mutation is caused by gene duplication. Let's say there's a gene that provides a beneficial protein, say a protein involved in muscle endurance. Now there's a mutation that duplicates this gene, and so muscle cells suddenly start producing twice as much of this muscle endurance protein. That's an example of a beneficial mutation.Any particular gene can experience many different types of mutation, from simple nucleotide replacement to complete inversion to complete removal. While most potential genetic mutations are either harmful or neutral, some mutations are improvements, and the probability that these mutations will happen is not zero. Hence, given time they are inevitable, and to the extent that they provide an advantage they will propagate throughout a population.--Percy

Well, yes, of course, that's why I asked your forbearance. I apologize for poisoning the well, but let me address this issue now.Much of what you're saying takes the form of, "Evolution is wrong because it says such and so," and in many circumstances the actual case is that evolution doesn't say such and so. Anyway, I'll try to be brief.Here's your original paragraph: I'll address it one little bit at a time: I think I'll just leave this one alone. You can't really be serious. Was the context intended to provide a number of qualifiers? In other words, was this intended to be interpreted as saying that there are some limited circumstances where evolution is impossible? This misunderstands speciation, which occurs at the population level. When a population divides into two separate populations that separately evolve so that they are no longer the same species, this does not allow you to reach any conclusions about genetic variability within the two new species (or maybe one new and one old species, if only one of the populations experiences significant evolution). It can happen in ways that either increase or decrease genetic variability.So since your assumption that speciation events reduce genetic variation is incorrect, any conclusions you reach based on this assumption are also likely incorrect.Keep in mind that even in speciation events that do result in reduced genetic variation, the amount of variation can change over time, in either direction.In other words, saying that speciation events can only reduce genetic variation would be like saying that driving can only carry you closer to home, never further. Just as driving can carry you in either direction with regard to position, so can speciation carry you in any direction with regard to genetic variation. The specific circumstances are what govern in each case. The individuals who either experience or inherit the genetic defect are less likely to produce offspring, and any offspring they have that inherit the defect will also be less likely to produce offspring. This means that other members of the population will outproduce them, and it makes it unlikely for unfavorable genes to propagate through a population. Harmful mutations that don't affect reproduction do exist, and they are an interesting story, but they're a side issue.In other words, for the most part it is rather the exact opposite of what you're claiming that in reality happens. Harmful mutations are filtered from a population because they have anti-survival characteristics. That's what selection does, it picks those with the best set of characteristics for survival. What you're describing is the opposite of selection, and is definitely not a part of evolutionary theory.As some have explained, disadvantageous mutations can remain present in a population for long periods of time if they are not too harmful. Think of it like the marine motto: Fatal mutations are eliminated right away, the non-fatal take a little longer (perhaps forever).Addressing this post now... Harmful mutations that don't affect reproduction doesn't seem like a fruitful area for this discussion to explore, but I'm not sure yet before I read on in your message. I'll withhold judgment for now. Crashfrog provided an excellent answer to this already. Rather than seeking to apply specific labels like favorable gene and unfavorable gene or defect, it would be more accurate to create a list of genetic variables, to each of which we would seek some measure of fecundity. Color blindness would be just another variable. It's importance to survival was likely greater in the past than today. Well, maybe it isn't, but are you questioning this because you really doubt that visual acuity provides any survival advantage? Or are you asking this because just in general you doubt that natural selection has any power to affect a population's gene pool, and so you would ask the same question about any example of natural selection.The point I was making was that if there is a difference in visual acuity generally between primitive societies and civilized societies, then it would likely be due to natural selection. I was just giving a clear and easily understood example illustrating the already very well established and understood principle of natural selection. If you don't accept the principle of natural selection then, while mind boggling, that's a whole other conversation.And if it's just that you don't believe visual acuity ever provided any selection advantage for human beings, then we'll talk about hawks instead. Visual acuity is a matter of survival for them, and its why theirs is so much better than ours. I wouldn't phrase it this way myself, but I definitely agree with the sentiments. Once human beings developed the ability to compensate for our weaknesses so successfully as to remove us from true competition with other species, and once we developed the ability to treat diseases and coddle and care for the sick and injured and aged, in other words, once we removed ourselves from the forces of natural selection for so many things, naturally the average robustness of the human world population began to decline. And it will continue to decline. I myself would have died a couple of times before reaching reproductive age were it not for modern medicine. Just one pet peeve first. Have you ever found any evolution site which describes modern evolutionary theory as uniformitarian? It's a big Internet world out there, I suppose it's not impossible, but in general this is not the way evolutionary scientists would characterize evolution. If you really understand evolution so well that you feel justified at resenting implications that you don't understand it, shouldn't you then at least attempt to understand it using the terms that the field of evolution itself employs? Because I'll tell you, to me, as soon as I see the word "uniformitarianism", it's a big red warning flag that some significant misinterpretation of evolutionary theory is about to be presented.That being said, yes, genetic mutations occur, in the aggregate, at a predictable rate. Genetic mutations provide the raw material upon which natural selection operates. And here's where you're taking a wrong turn. How could a "rather sickly bunch" reproduce as effectively as a healthy bunch? They couldn't, right? Therefore, the mutations must be having an effect which interferes with reproduction.In the case of human beings you have to look at the whole picture. If World War III happened tomorrow and sent homo sapiens back to the stone age, I agree that we'd be less successful at surviving than our ancient counterparts. A few generations of no modern medical care would cure this.But if you compare modern human beings *and* civilization with that of the stone age, we are far and away more successful at reproduction. Just the infant mortality rate alone says so.--Percy

I agree, but it isn't because beneficial mutations are rare. Beneficial mutations are ubiquitous. Practically every gene in the human genome (and of all life in general) is the beneficiary of beneficial mutations, tons of them. If that weren't the case we wouldn't have them. Beneficial mutations spread quickly throughout a population. The only time they're overtly visible is in their early stages before they've propagated and before most individuals have them, such as the wisdom tooth mutation Schraf talks about that is uncommon at this point. And if/when the wisdom tooth mutation reaches most of the population, those without it will be considered to have a genetic defect. See how it works?But harmful mutations that reside in that narrow region that permits life but doesn't allow it to flourish are both rare and very noticeable. The human genome has accumulated a number of them, like cystic fibrosis and sickle cell anemia. Harmful mutations that make people very sick generate a lot of attention and are the subject of a great deal of scientific research. Beneficial mutations that just keep people from getting sick or give them slightly greater endurance or strength or intelligence or attractiveness or charm are harder to notice and even when noticed don't rate the same level of scrutiny.--Percy

This is actually just the science of population genetics. It was the work of the population geneticists that revealed the evidence and the mathematical basic for forming the modern synthesis between Darwinian evolution and genetics. Prior to that work there was no evidence that Darwinian evolution and genetics were even consistent and compatible, let alone mutually supportive. I'm not sure what you mean when you conclude your paragraph with this. If this is an argument that mutations can only be harmful, then of course this isn't true, and this has been explained already, both generally by myself, and more specifically by Schraf with her wisdom tooth gene example.Or if it is an argument that only harmful mutations can spread through a population, then this is false, too. Parents pass their genes on to offspring, including mutations harmful or not. Schraf offered the example of her wisdom tooth gene and the HIV gene, and the general example of mutations in bacterial populations where mutations can be studied closely because bacteria provide many generations in a single day.You seem to be just declaring that beneficial mutations either don't exist or aren't really beneficial. I earlier explained how beneficial mutations are inevitable and provided one hypothetical example of a process by which they can happen. And people who don't die from infections caused by wisdom tooth infections produce more offspring than those who do, and people who don't die of HIV a few years after exposure produce more offspring than those who do. These are clearly beneficial mutations with an effect on reproduction. I just explained this in the very message you're replying to: Beneficial mutations that just keep people from getting sick or give them slightly greater endurance or strength or intelligence or attractiveness or charm are harder to notice and even when noticed don't rate the same level of scrutiny. Some have been caught in the act, and you've been provided a couple examples.--Percy

Either this is phrased in a way I'm just not parsing correctly, or you're using a different definition of gene and allele than I am. The definition at Wikipedia says, "An allele is any one of a number of viable DNA codings of the same gene (sometimes the term refers to a non-gene sequence) occupying a given locus (position) on a chromosome," which is pretty much how I think of it. Maybe I'm just not getting your meaning?--Percy

Hi Faith,Before we continue, could we reach an agreement about something important? This is from your previous message to me, but you included it in your opening except: It's really difficult to move the discussion forward if after presentations of evidence you come back with "There's no evidence" or "That's not evidence." If you disagree that what was described was really evidence, or if you don't see how the evidence supports the contention, or if you disagree with the interpretation of the evidence, or if you'd like to offer another interpretation of the evidence, then I think that'd be great. I didn't say there were. You were looking for examples of beneficial mutations, so of course I was talking in the context of mutations. It is much more often the case the beneficial changes are the result of bringing together complementary alleles.But if we go beneath the gene level to the allele level and look at how each individual allele formed, except in those rare cases where the modern gene is very little changed from an ancient common ancestor, such as hox genes, we see that each gene is very different from that of the ancient common ancestor. In many cases the gene didn't exist in the ancient common ancestor, and so the entire gene had to have been constructed out of whole cloth from mutations. The specific sequence of mutations can sometimes be ferreted out by comparisons with sequences from related species that shared common ancestors at points in time in the past. Most of the genes in modern genomes that we take for granted today as "normal" and therefore beneficial to the organism did not always exist. Only mutations can create new genes. Mutations range from simple nucleotide substitutions all the way up to chromosome duplication. True, but we *were* talking about mutations, although now I'm not so sure that you were aware of that. You were expressing doubt about the possibility of beneficial mutations spreading through a population. Uh, no.I don't know if they've established any relative occurrence rates between changes driven by new mutations versus allele frequency changes and recombinations, but they are both significant factors. That we were talking about mutations, i.e., copying mistakes rather than allele remixing during reproduction, does not diminish the importance of allele remixing. Faith, I just despair sometimes of you ever learning what evolution really says. Particularly difficult is that you sometimes think you know things that you don't. Your history of evolutionary theory is wrong. If you want to criticize how evolutionary theory has changed over time then at least learn about it first so you can criticize it for things that have actually happened. I'm not going to bother correcting the above, I've spent too much time on this message already and I'm still on your first paragraph, only 20 more to go. This is false. You complained about this already, and I already explained I wasn't trying to produce an actual example. I was trying to provide an illustration of the principle by using something easily understood, like muscle. If you don't like the explanation of the reason for the illustration then please pick on that next time, but please stop making me repeat the explanation. The most significant indication that it is wrong is the way in which reproductive errors propagate through genomes of populations, population genetics again. It happens now, and analysis of the genes of organisms related at various levels indicates that it was happening in the past. Yes, certainly, God could have just created them the way there were 6000 years ago and then let the process run on from there, but in that case he placed misleading evidence in genomes indicating that the same process was going on for a lot longer than 6000 years. You've misremembered what this was an example of. The Patagonian example was in support of your contention that the human genome is accumulating more and more genetic defects. I agreed with you. I'm tired of repeating myself, if you don't believe me and want the full context then you do the link-clicking and scrolling and searching. I'll bet even you have no idea what you were trying to say in this paragraph. If you don't believe the wisdom tooth example was actually a beneficial mutation, then please address the specifics of my explanation about why it was beneficial. Again, you can do the link-clicking and scrolling and searching yourself. Normally I don't mind repeating explanations, but I'm beginning to believe you're ignoring arguments as a tactic to exhaust the people discussing with you. Please be more specific. This is just an argument from incredulity. What part of the explanation for sickle cell anemia do you have a problem with? This is the identical argument that you made before and that I answered before. Please tell me what problems you had with my answers. Please stop repeating your original arguments as if they had never been addressed. You mean as science? Or as faith? If as science then you couldn't be more wrong. There is no scientific evidence for the creationist viewpoint that God did it. At best we're in the middle of still discussing beneficial mutations. This is just another "There's no evidence" claim that you periodically issue after evidence has been presented. Evidence has been presented, but you can't seem to get beyond repeating your original objections. Please address the arguments that have been made to you.--Percy

I give up.--Percy

No, I'm afraid not, your confounding an explanation from one context with a different context.Mutations are the ultimate origin of all traits, but that little tidbit was provided to you in the context of explaining that all genes that we consider normal were at one time the result of a mutation. I was attempting to provide a broader outlook.New traits can of course be brought about through both new mutations and through allele remixing.Explanations like this are founded upon evidence. It is evidence that enables widespread agreement about the fundamental principles of evolutionary theory and prevents the field from fragmenting into warring schools of thought like psychology and religion. Were it really true that there was no evidence at the core, then evolutionists would not be speaking with one voice as they do here. As long as you persist in employing your various means of denying the evidence you will never understand evolutionary theory to the point where a constructive dialog can take place.--Percy

I haven't looked this up, but I'll go out on a limb and say that most dog evolution has been through selection and emphasis of existing traits using selective breeding, not through mutations causing new traits.--Percy

Faith, I was responding to where you said this: This is fine. But then you concluded with this sentence: I didn't say you were wrong about this. For you to believe I was telling you were wrong requires you to have misinterpreted what I told you in fundamental ways. Your reply is only an attempt to obscure your misunderstanding. I only returned to this discussion because you misrepresented what I had said in an earlier message. I will not be wasting my time submitting any more evidence to your denial machine. I merely ask you to consider that if evolutionary theory were not based upon evidence then there would be as many evolutionary factions as there are religions. Evidence is why evolutionists all have one view and so can argue against a creationist who is alone because few other creationists share their view.--Percy

I think many here would agree with the definition of mutation at Wikipedia. You can read this article, or you can read others that you might find at legitimate science sites, or you can scan back through this thread and see where people have provided less formal definitions, but in any case, I suggest giving yourself a firmer understanding of what a mutation is before discussing it further. Protein is not part of the composition of DNA. Check out the Wikipedia article on DNA. Just be careful of the middle sentence of the first paragraph, because it is grammatically ambiguous. What he means to say is that the amino acid sequences that make up proteins are encoded in DNA by long sequences of nucleotides using a triplet code. There is no protein in DNA.I could continue nitpicking my way through your post, but I'll end here with a question. Sites that have accurate information about the definitions of genes and alleles and mutations and DNA are only a click or two away. Why not use them?A creationist perspective does not require that you remain ignorant of what biology and evolution and genetics really say. Understanding it doesn't require you to become an atheist, but composing meaningful criticisms does require that you understand it. How much sense would it make for someone to criticize Christianity for making a big deal about Jesus seeing his shadow on Groundhog Day? If he didn't believe you when you told him he was mistaken, you'd tell him to study his Bible. And if he didn't believe the Bible, then what?In order for us to have a meaningful discussion we must define terms the same way, but we can't even seem to agree on terms like beneficial, since one of the problems we're having is that one of the reasons you reject the evidence for beneficial mutations is because you can't see how they're beneficial. But you're even disagreeing about terms that have fairly objective definitions, as in this very message where you ask if mutations really aren't random but are instead an inherent part of a genome because they are an inevitable, if stochastic, change.The answer is, "Of course not." It's inevitable that a die will come up 6 on 1/6 of the rolls, but that doesn't make rolling a die a non-random event.I'm now going to mention a detail about mutations that I feel you are bound to misinterpret in some way, but research on some organisms has uncovered many mutational hot spots on DNA strands where mutations are very likely. One of the known causes is stress upon the DNA strand itself, such as at a point where the DNA bends tightly. If the DNA helix is thought of as a rope, a chromosome can be thought of as a tightly coiled and tangled rope of DNA, and the bends can sometimes be very tight.Mutational hot spots means that some places on a genome are more prone to mutation than others, but the precise nature of the mutation and whether it happens at all is still a random event. And copying errors can happen literally anywhere, so since any particular change is possible, it isn't accurate in any meaningful way to say that mutations should be considered part of the original genome. It would be like claiming wood rot on your house is part of the original architectural design.--Percy