The End of Evolution By Means of Natural Selection

Hi Faith,Take it easy on the length, there. I'm only going to respond to the first 10% of what you wrote because you must have misunderstood the example to have given the answer you did.First let us be clear that you believe that allele reduction is the way speciation happens. You think that speciation first begins when a small daughter population becomes separated from the parent population. At this earliest stage they are of course the same species. The daughter population begins with only a subset of the alleles of the parent population, and it may even carry with it all of some alleles leaving the parent population without those alleles. This means that both parent and daughter populations have subsets of the total allele complement of the original parent population. The daughter population, being much smaller, has the smaller subset of alleles.Your scenario continues by saying that over time the daughter population experiences combinations of alleles that never appeared in the parent population, and that it is these unique combinations of alleles that cause speciation.Now that I've set the stage, in more detail this time, I want to once again present my example. We have a parent and a daughter population. The original parent population had 26 genes A through Z and four alleles per gene 1 through 4. The daughter population has over time lost some alleles that it started with and only has two alleles per gene 3 through 4. Here are the chromosomes for Organism P from the parent population and organism D from the daughter population: Even though much time has passed since the separation of the original parent population into a parent and a daughter population, both parent and daughter populations only have alleles from the original parent population. No matter what allele combinations you choose for the daughter population, it will still be a subset from the original parent population, and that makes it genetically a member of the same species as the original parent population.Let me say this another way: you can't create a new species by merely recombining the alleles.In other words, without new alleles, speciation is impossible.Now remember, you believe that creating new alleles is impossible, that the number of alleles in a population can only decline, but I've just shown that without new alleles you cannot get speciation.Therefore your claim that allele reduction can produce new species is proven wrong.Now of course it's possible for allele combinations to produce physical differences that make two populations unfertile with one another, such as might be the case with a size difference or behavioral difference, but genetically you cannot create a new species just by mixing and recombining the original set or a subset of alleles.--Percy

We all know you have other examples, but we're just focusing on one of them right now. I chose the smaller daughter population for the same reason. Your position is that the daughter population with reduced allele diversity begins to experience different allele frequencies and combinations, and that over time this is how the daughter population becomes a new species (I did note the passage of time in both my previous posts). At some point the daughter population becomes a new species, but it's still the daughter population. If it's going to prove a sticking point to you if I continue calling it the daughter population after speciation then I'll say, "the new species that evolved from the daughter population." But whatever name we call it, we're still talking about the same population, just at different points in time. No one disagrees with you that you can get new breeds and races just by changing allele frequencies. You need to keep your focus on where we disagree. We disagree with your claim that reduced allele diversity alone can result in speciation. Actually, yes I have shown it. I won't describe the details again, but here is that example again of the chromosomes from two individuals, one from the parent population and one from the daughter population. I should mention this time that of course sexual species are diploid, meaning that sexual species actually have chromosome pairs rather than single chromosomes. I'm only presenting one chromosome from each population, and we'll assume that they're the haploid chromosomes that reside in sperm and egg: You cannot come up with a set of allele combinations for the daughter chromosome whereby it is not genetically still a member of the original parent population. Therefore, genetically, all members of the daughter population must always be members of the original parent population. Sperm and egg from the two populations will be able to combine because they are genetically compatible.The only way to create a new species that is genetically incompatible is to add genes and/or chromosomes so that the genomes can no longer combine. It is only when the two populations have genes and/or chromosomes that both do not share that genetic incompatibilities arise.The reason that parent and daughter populations remain genetically compatible is that they both have the exact same genes. The parent population has genes A-Z, and the daughter population has genes A-Z. When you put the chromosomes side by side they line up precisely: Look at that, Faith. The A genes line up, the B genes line up, the C genes line up. They all line up from A to Z. These haploid chromosomes will have no trouble combining, and that's exactly what will happen when the sperm and egg come together. That diagram above is precisely what the chromosome pair will look like when the haploid chromosomes, one from the sperm and one from the egg, combine together. The only difference is the allele subset, and any organism with a subset of alleles from the original parent population must be the same species as the original parent population.If you still think that I haven't proven that reduced allele diversity cannot cause speciation then you'll have to be specific about the problems you see in the evidence and rationale I just provided. Just a bald statement that you don't believe I've demonstrated your scenario is impossible leaves me no alternative but to more carefully repeat my evidence and rationale.In case it helps, here's a pair of chromosomes that are genetically incompatible. Note that they both have genes the other does not have, and that they have different numbers of genes. It is these kinds of differences that make species mutually infertile and that are responsible for the separation between species: Again, please examine the above diagram and note how the genes no longer line up. That lack of correspondence of genes between the two haploid chromosomes from sperm and egg is what causes genetic incompatibility. You've misunderstood population genetics. It was the work of population geneticists back in the 1920's that studied the rate of propagation of mutations through populations (among other things, but it's mutations that are relevant to this discussion) and proved that what we observed in nature was compatible with what we learned in the lab about genes, thereby combining Darwinian evolution and genetics into what is today known as the modern synthesis, or also as the modern synthetic theory of evolution. This is Wikipedia's first sentence in it's article on Population Genetics, I've bolded and highlighted the relevant word: Mutation very definitely plays a key role in population genetics, because it is a key element of evolution itself. The central concept of evolution is that genetic copying during reproduction is imperfect, and all else about evolution flows from that.--Percy

Okay, I understand, you're saying that you don't believe new species are ever created, but you go on: When two populations can no longer interbreed with one another then they are different species, but I understand the distinction you're trying to make. Speciation means that two populations gradually over time become genetically distinct, but you believe that two populations can become incapable of interbreeding while remaining genetically compatible.You are correct that this can happen. For example, there's a species of fly that is classified as two species because one variety mates in the early morning while the other variety mates in the early evening. Were members of the two varieties to ever meet they could interbreed, but given their different mating habits this probably doesn't happen very often. The evolutionary expectation is that these two varieties will become more and more genetically distinct until they become two different species in both behaviors and genes.But examples like this are rare. Genetic studies reveal that the vast majority of species are genetically distinct from one another. Closely related species that are still fairly similar genetically can still interbreed with varying degrees of success, while more distantly related species cannot interbreed at all. What we find in nature is a continuum of increasing genetic difference with increasing distance of relatedness, and it comes with an increasing inability to interbreed. Species boundaries are not firm boundaries for closely related species, but they become more and more firm with increasing genetic differences.As I've said several times in this thread, what you're proposing is not impossible, but the bottom line is that examples in nature of the kind of speciation that you claim happens are rather uncommon. They're exceptional enough to deserve mention as oddities.In the cat family some cat species can interbreed at least a little and some cannot interbreed at all, but in general they all have genetic differences. This means that there are differences in which genes they possess. Not all cat species have the same genes. Mutations are how new genes can be created. Mutations can also remove or deactivate genes.So if your position is that mutations cannot produce new genes and chromosomes and so evolution can only rearrange alleles to produce different looking and behaving populations that are genetically compatible, then your proposal does not explain where, for example, all the different cat species came from after the flood. The need for the original kinds saved on the ark to expand into a variety of different species of the same kind is why creationists invoke speciation, but those different species are different genetically. If your position is that changing the underlying genes is impossible, then your scenario explains only the few uncommon cases. The very common cases like the cat family remain unexplained in your scenario.--PercyEdited by Percy, : Minor clarification in last paragraph.

This is probably the most important thing to clear up. You say that speciation represents a "real event," but you "don't believe it's what evolutionists think it is."So what do you think speciation is? Here's a very simple definition that most would agree with from Answers.com: If this is not the definition of speciation you're using then please tell us your definition. Well, yes, but I wouldn't say this the way you did. I think you already have the proper understanding, but because of the way you used the word "replace" without qualification allow me to clarify so just we're sure there's no misunderstanding.So do I expect a mutation to cause one allele to become a new and different allele in that specific individual? Sure! But that mutation to that allele in that one individual does not change that allele in all the other individuals of the population. The population continues to have that allele. What the mutation has actually done is increased the number of alleles for that gene by one. If there were, say, 17 alleles for that gene in the population before that individual experienced that mutation, there are now 18.Lets call the gene X, and let's say that gene X has alleles X1 through X4. During reproduction a mutation changes allele X3 into a new allele that we'll call X5. Let's say that the original allele X3 is possessed by 20% of the individuals in the population, then after that newly born individual experiences a mutation changing their X3 allele into a new X5 allele, the original X3 allele is still possessed by 20% of the individuals in the population. The X3 allele doesn't go away. The X3 allele isn't replaced by the X5 allele, except in the individual that experienced the mutation.So now that we've got the clarification out of the way, let me move on to what you say next about mutations, because that's very important: As far as point mutations and other small mutations changing alleles into new alleles, yet that's correct. But over time as mutations accumulate and selection pressures operate the character of a gene may change. As RAZD pointed out, an allele might begin with alleles X1, X2, X3, X4, but over time the environment changes, causing the selection pressures to change. New alleles in gene X can gradually change the character of the gene so that after a number of generations we no longer have alleles X1, X2, X3, X4 but a completely different set of alleles X17, X42, X51, X63.What is the significance of changes to the character of the gene? Well, if we take the familiar example of the bacterial flagellum, perhaps gene X originally created one of the proteins for a celia, but now the alleles of the modified gene X create a protein that helps the celia twitch a bit, turning the celia into a potential incipient flagellum.But of course mutations do far more than just modify alleles, and one of the most common and important mutation types is gene duplication. Reproduction is a much more dynamic process than is typically imagined, and genes can move positionally around the chromosome. Mistakes can happen that cause genes to be either eliminated or duplicated. Losing a gene can be catastrophic, of course, but gaining a gene that's an identical or near copy of the original gene often has little or no effect.What's important to understand about gene duplication is that one of the genes is free to mutate for other purposes. Research indicates that gene duplication followed by the duplicated gene mutating to acquire a new behavior (e.g., code for a different protein) are extremely common in the genetic history of life.About the cat family example, the reason I introduced that example was because your scenario does not explain where the cat family came from. Not all cat species have the same genes. This could not have happened in your scenario if cats are just one kind because your scenario disallows the creation and deletion of new genes through mutation. But where are the extra polyploid chromosomes where all this extra genetic diversity supposedly resides? We don't see them in the nucleus of most species we look at. Mostly duplicate chromosomes appear in just some species of flowering plants. Since some species have short generation times and some long, species with longer generation times have not had as much time to lose these extra chromosomes, and they should still be there in at least some species, but they're nowhere to be found.If we were to take a completely blank slate approach with no preconceptions then we could say that there are two ways existing species could have arrived at the current genetic composition. One is that they began with huge diversity stored in polyploid chromosomes and have gradually lost that diversity over time. The other is that the have evolved according to evolutionary theory, with selection pruning variation according to the environment and mutation continually adding variation and initiating trial-and-error experiments for selection to play with. What test or experiment or set of observations can you think of that would allow us to choose which scenario is the one that actually happened? What evidence leads you to believe that increased variation results from diminished genetic diversity? Mutations are just reproductive copying errors. What evidence causes you to think they are different in character today than they were in the past? What evidence leads you to believe that mutations have been more deleterious during the last millennium than they were in prior millenniums?--Percy

I'm not so sure you really accept that definition, Faith. It says the species resulting from speciation are usually genetically distinct, but in your scenario of allele reduction it isn't possible for species to become genetically distinct. Going back to my diagram again, these two chromosomes include the only kinds of differences that could emerge under your scenario. Since both chromosomes have the same genes and they both draw upon the same subset of alleles they are, by definition, genetically compatible and are therefore the same species genetically: No matter how you choose and rearrange alleles for Organism D (from the daughter population), you cannot create a chromosome that is genetically incompatible with Organism P (from the parent population). Speciation as defined in places like dictionaries and by people like scientists cannot happen in your scenaro.But standard evolutionary processes that we've observed can produce chromosomes like this that *are* genetically incompatible and therefore *are* different species: So why don't we try to reach agreement on just this one issue for now. Do you agree that speciation resulting in genetic incompatibility is impossible in your scenario? If not then please explain why.--PercyEdited by Percy, : Fix typo.

The [url] dBCode is your friend!

• Luria-Delbruck fluctuation experiment
  
• Replica Plating

--Percy

I think what you meant to say is that you can measure the extent to which resistance to some antibiotic was already present in a population without having come in contact with it.--Percy

Oh, okay. I couldn't see where the selection pressure was coming from, but you're saying that the experimenters are doing the selecting after using the plating to determine where the most resistant bacteria happen to be. This is analogous to what breeders do since people are doing the selecting based upon qualities they're trying to increase in prevalence. But it's very, very hard to believe that "By repeating this process 2-3 times you can end up with a population that is >99% antibiotic resistant," unless the experimenters have an incredibly accurate toothpick. --Percy

Hi Faith,Mutations are random. I'm not aware of any evolutionist here who is so ignorant he thinks mutations are not random. I'm not aware of any evolutionist here who is so ignorant that he would suggest that the necessary mutations are supplied when needed. If you think any evolutionist here is suggesting that mutations aren't random or that they're supplied when needed then you can safely assume you are misunderstanding him.The random mutations that occur in every generation are operated on by selection. Any mutations that provide some advantage in the existing environment will become increasingly prevalent in subsequent generations. It isn't that *the* necessary mutation is provided when needed. There is no known process in evolution that could do such a thing. Rather, it's that every member of each new generation gets a number of random mutations simply because DNA copying during reproduction is imperfect, and inevitably some of them are helpful in the current environment.About your allele question, an allele is a sequence of codons that program for a protein. An allele that experiences a point mutation (substitution of one nucleotide for another) is likely a new allele. For example, say a gene in a population has these four alleles, they differ from one another by a single nucleotide:

[list][*]CATGCCTTACGT
[*]CATGCTTTACGT
[*]CAAGCTTTACGT
[*]CATGCCTTCCGT[/list]

Let's consider one of the organisms in our population that happens to contribute the 1st allele in the list to it's offspring during reproduction, but there's a copying error and one of the nucleotides is copied incorrectly. For example, maybe CATGCCTTACGT becomes CATGCCTTACGA.It is possible that the copying error could transform it into one of the other three alleles, but it is more likely that it would become a brand new allele. If it is a new allele then some of the possible resulting effects are:

• Nothing, because the new codon codes for the same amino acid as the original.
• Nothing, because although the new codon codes for a different amino acid, the slightly different protein with the different amino acid performs the exact same function as the original protein.
• A change in protein function that is deleterious because the altered protein is broken and does nothing, leaving the organism without a possibly important protein.
• A change in protein function that is beneficial because the altered protein does a better job then the original protein

--Percy

You mention speciation as a possibility again, but in the very recent past you denied that speciation was a possibility, saying that you only used the term as a concession to evolutionists and that speciation wasn't really what evolutionists think it is.In my Message 640 I explained why I think speciation is impossible in your scenario, but you didn't respond. It would be very helpful if we could get an answer about whether you think your scenario can produce genetically distinct species, meaning species that are genetically incompatible. When you speak of the lack of evidence for beneficial mutations you should really be saying that you're going to continue to ignore the evidence for beneficial mutations. In another of my messages that you didn't reply to, Message 421, I explain why beneficial mutations are inevitable. Briefly, it points out that unless all genes already have optimal alleles, random change will inevitably create new alleles that are more optimal than existing ones.A more fundamental argument for beneficial mutations is that every allele in every gene in all life everywhere throughout time began as a mutation. The genes of all existing life consist of billions and billions of mutations that proved beneficial. Well I can see how from your perspective there's something very wrong with this picture of the real world, because it doesn't support anything you say. Why don't we break the picture down for you and you can tell us what is wrong with it.

• Because of the complex interplay of many systems in complex organisms, beneficial mutations must of necessity occur in tiny indetectable steps. Beneficial mutations that are easily detectable are necessarily rare. Do you have a problem with this?
  ​
• Because of relatively long generation times, studying the effects of sequences of mutations over a meaningfully large enough number of generations in complex organisms isn't really possible. Do you have a problem with this?
  ​
• Considering only point mutations (single nucleotide substitutions), mutations in bacteria do the same thing as in all other organisms, potentially changing what the protein produced by the gene does. Do you have a problem with this?

Unless you have problems with some of these basic concepts, then simple logic leads to the conclusion that just as a mutation in a bacteria can end up producing a protein that is better than the proteins produced by the existing alleles, so can a mutation in any other organism end up producing a protein that is better than the proteins produced by their existing alleles.While the generation times in complex organisms are too long to observe the complete process in an experiment of any reasonable length, the general principles are the same as in bacteria, and what we see in genomes and what parts of the process we are able to observe in complex organisms is precisely what we would expect to see if mutations are the source of variation.What we never see: polyploid chromosomes in large populations hiding extra variation that isn't expressed.--PercyEdited by Percy, : Improve wording in first point in the bulleted list.

Hi Faith,I'm just going to answer this reply for now, and when we reach agreement on this issue I'll get back to your other replies. This exchange was prompted by my explanation in Message 309 of how beneficial mutations are possible. You accepted that they were possible but expressed doubt that beneficial mutations could ever actually happen, and now you've clarified by explaining that you believe the Law of Probability prevents this from happening.We can use probability to examine the likelihood of a beneficial mutation in bacteria. Let us consider a bacteria population whose genome consists of one million base pairs, and that in one of its genes if an A nucleotide could just change to a G nucleotide then the gene would produce a protein slightly more effective than the current protein. Let's say that the bacteria experience a mutation on average once every 1000 cell divisions, so the probability of a mutation is .001 in every cell division, or, switching to exponential notation which will be more convenient for the numbers we'll be dealing with, 10^-3.With a genome of one million nucleotides the odds of a change in that one particular nucleotide of interest is one in a million or 10^-6, and to get a specific change from A to G would be .333×10^-6. And multiplying this by the 10^-3 likelihood of a mutation we get a final probability of the mutation being A to G in precisely the right place in that gene of .333×10^-9 (that's a probability of less than one out of a billion).The bacteria divide once per hour on average, and there are one billion bacteria in the population. The odds that this mutation will emerge in just one hour, or in other words, after every bacteria has divided just once, are: Which after doing the math turns out to be .283 or 28.3%. There's a 28.3% chance that this beneficial mutation could occur in just a single generation. We can use that figure to calculate the probability that the mutation would occur in just one day: Which comes out to 99.97%. As more time passes the probability becomes higher and higher. These probabilities are so high that you can now see why beneficial mutations are not only possible, they're inevitable.We're only talking about bacteria for now, but let's reach agreement on bacteria before moving on. So let me know if you have any problems or questions about this before we move on.--PercyEdited by Percy, : Fix grammar and typo.

I think what you mean to say is that you don't see how bacteria are relevant to your argument. As others have pointed out, many of the processes we see occurring in bacteria are the same ones we see in all life. Just as physicists work at understanding the complex by first understanding the simple, like Galileo dropping balls of different mass from the tower in Pisa, biologists do the same with bacteria. Much of what we learn about microbiological processes in bacteria apply equally well to all other life.In the case of beneficial mutations, a mutation can result in an improved protein in both bacteria and higher organisms like mammals. The principles are precisely the same, but mammals are much more complicated because all the different mammalian systems like circulation, nervous, digestive, etc, have to continue to play well together. Mammals are also much more difficult to study in real time in evolutionary terms because of generation times that are at least a couple of orders of magnitude longer than bacteria.So if you can let me know if you have any issues or questions about my Message 691 we can continue the discussion.--Percy

No, I never said this. Mutations can be deleterious, neutral or beneficial. If you read through the example I presented in Message 691 you'll see that I present the odds of a specific beneficial mutation as less than one in a billion. That's pretty small odds, and yet with billions of bacteria reproducing every hour or so the odds of that specific mutation occurring approach 1.--Percy

This is addressed to no one in particular.One of the things brought to light by the difference of opinion about the relevance of bacterial studies to sexual organisms is the better way that sexual reproduction takes advantage of mutations. Bacteria accumulate favorable mutations serially while sexual organisms acquire them in parallel. Let me explain.If bacteria A acquires advantageous mutation α while bacteria B acquires advantageous mutation β, it isn't possible for descendants of bacteria A to acquire mutation β. Bacteria do not mate and so there's no sexual sharing of genes between different bacterial lines. Of course descendants of bacteria A can acquire mutation β by experiencing it as a mutation, but not by mating with descendants of bacteria B.But in sexual organisms if organism A acquires advantageous mutation α while organism B acquires advantageous mutation β, descendants of organims A can possibly acquire mutation β when they mate with descendants of organism B. The mutations acquired all at the same time by one generation have the potential to eventually be shared by many organisms generations into the future.Of course bacteria have the ability to share mutations through conjugation, transformation and transduction, but sexual reproduction inherently incorporates this mutation sharing capability, while bacteria can only do it through processes that are peripheral to reproduction.Just posting this because it's sort of related and I found it very interesting.--Percy

Hi Straggler,Given the history I can't be both honest and encouraging, but if you'd like to pursue your idea then I think you should give it a try.--Percy