Evolution Requires Reduction in Genetic Diversity

Hi Faith,I'm trying to maintain a moderator stance in this thread, so I will concentrate on resolving side issues, clarifying ambiguities, and keeping discussion on topic. Necessarily that means there are large portions of your reply that I cannot address because that would force me to cross the boundary from moderation into participation. As you yourself seem to be aware when you say (twice) that you'll have to come back to these issues, you may be drawing conclusions prematurely. You and Denisova should discuss your concerns about bacteria. This is a good statement of your hypothesis, but it must be followed by the evidence supporting it. Only some aspects of this hypothesis are relevant to this thread, so regarding the above for this discussion you only need evidence of:

• "A great deal of vitality in the genome of human beings" prior to around 4500 years ago.
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• "Enormous genetic diversity and vitality compared to now" among animals prior to around 4500 years ago.
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• A decline in diversity and vitality between 6500 and 4500 years ago that is related to "gene death."

Also, you've introduced the term "gene death" but only provided a vague idea of what it means. Back in Message 467 you said: But in this message you've provided this additional information: So it seems that you are defining gene death as occurring in two different ways. One way is when a gene becomes junk DNA, and another way is when a gene is removed from a population. I think you are both overloading and misdefining the term, so I'm ruling that the term "gene death" should no longer be used in this thread and that the discussion should use existing standard terms in this way:

• "Non-coding DNA" will be the term this thread will use to refer to DNA that doesn't code for proteins, what used to be called "junk DNA".
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• "Gene loss" will be the term this thread will use to refer to what happens when a gene is no longer part of a species genome.

In science hypotheses are formed around incomplete evidence and represent the starting point of a scientific process of evidence gathering to support the hypothesis. Creation science differs from science in the way it forms hypotheses, usually basing them upon the Bible instead of upon evidence. Here at EvC Forum forming hypothesis in this way is perfectly acceptable, but it doesn't relieve one of responsibility for the evidence gathering step that must inevitably follow hypothesis formation.You ask where the evidence is going to come from. I can't answer that question for you, but I certainly can't let discussion continue indefinitely with no evidence. No, absolutely not. A scenario consistent with all evidence is a working hypothesis, not evidence. Science is a consensus activity. Theories become accepted because a significant proportion of the relevant scientific community becomes convinced by a body of interwoven evidence. It is perfectly legitimate to offer alternative theories, but if they ignore significant evidence (e.g., radiometric dating) or worse make no sense (e.g., fossil ordering) then their persuasive ability will be fatally handicapped. If you think people are making arguments that are missing evidence then it is your responsibility to call them on it. One person's lack of evidence is not an excuse for everyone else to start pushing ideas without evidence.But you personally don't get to decide what is evidence and what is not, which is the issue I originally responded to. If I let you simply dismiss Denisova's evidence then you could argue that Denisova has no evidence. But I'm ruling that participants don't have the right to decide which evidence they'll accept and which they'll reject. Participants must address all the evidence.You're perfectly within your right to argue that evidence shouldn't be considered because it isn't relevant, which is what you're attempting to do with the Lenski bacterial evidence, but what comes across most in this attempt is that, as you said yourself, you may not have examined the issue closely enough yet. This is something you must establish through evidence, not simply declare. Everyone is in the same boat. Everyone can argue their hypothesis using the evidence supporting it.

Hi Denisova,I understand and share your concerns and am trying to address them.

I know you posted this before I issued my ruling in Message 507, but I just wanted to issue a reminder to everyone since that message was kind of long and it could have been missed.I have ruled against using the term "gene death," and of course that means any related terms are also off limits, such as "dead genes." The term that should be used is "non-coding DNA," and any argument that some thousands of years ago species experienced a process of genes becoming non-coding DNA must be accompanied by evidence.

Dismissing requests for evidence, especially in this way, is very strongly discouraged. Bald declarations void of evidence should be eschewed.

Just to clarify one more time, I'm ruling out use of the the term "gene death" and all derivatives as too ambiguous and conflicted. If you want to refer to pseudogenes that have no function then you could use the phrase "functionless pseudogenes" or any meaningful variation.

AbE: I'm rewriting this first paragraph, which originally included the sentence, "I'm ruling off-topic any discussion about selection." What I meant was that this isn't a thread for discussing whether selection happens. Faith has made some side comments about selection not playing any significant role in evolution, that the resorting of alleles creates the traits, and organisms migrate to new regions where the traits are advantageous. But even Faith has argued for the power of selection when she talks about breeders adding and removing traits, and in any case, that's a discussion for another thread.Also off-topic is whether mutations can be selected against. For this thread it will be assumed that mutations can cause a decrease in fitness that will be selected against.More generally I'd like to request that participants try to move more aggressively toward concentrating on the central topic. I'm going to work hard to eliminate side issues and meaningless challenges.Edited by Admin, : AbE.

Hi Faith,I didn't understand much of your next to last paragraph. I think it likely that others will experience the same difficulty, so I have a couple questions. Would a correct interpretation be that the Flood marked the beginning of gradual process of genes becoming pseudogenes (genes that no longer produce proteins), where pseudogenes are what you mean when you referred to "junk DNA" just above? If not then it would really be helpful if what was meant could be explained, without using the term "gene death" or any related terms.Also, you said the same thing about the Fall, that it caused a gradual process of genes becoming pseudogenes. Since this was already happening when the Flood occurred, how could the flood be said to have caused this process? I'm not sure why you say that new allele combinations lead to fixation, so that point needs clarification.

Both Denisova and PaulK responded to this, but I think they may have arrived at different interpretations, and I'm not sure what you mean either, so some further clarification would be very helpful. Let me describe what you seem to be saying and you can correct as necessary.Assume we have a population of 10 individuals. Every individual has unique and different alleles for a particular gene (i.e., heterozygotic) for a total of 20 different and unique alleles in the population. The genetic diversity for this gene could not be any higher. These alleles produce working proteins in each individual.Now 8 individuals die, leaving just 2 individuals in the population for a total of 4 alleles. How does the absence of the other 16 alleles cause the 4 remaining alleles to stop working (stop producing proteins) to turn the gene into a pseudogene?Of if you meant that the gene would only become a pseudogene in later generations, then when the 2 remaining individuals mate (assuming they're of the opposite sex, and note that they could have mated whether the other 8 individuals were alive or not) why would the alleles of this gene in the offspring no longer produce proteins? Or in any later generation?In other words, how does the removal of alleles from a population cause the remaining alleles to stop working, whether right away or in later generations?

Not now with version 4, but version 5 introduces the ability for members to choose their own theme, which controls colors among other things. There's no release date yet for version 5, but I'm hoping for later this year.The best solution for now for those with vision issues is to use Ctrl-+, or Cmd-+ on a Mac.

Back in Message 480 I noted that you appeared to be using the term "gene death" to refer to two different things:

1. A gene becoming a pseudogene.
2. A gene suddenly being completely "wiped out" from a population's genome, e.g., as a result of the flood.

I can't be sure of this because I'm only inferring the definition from your usage, and I had to guess what you meant by "wiped out," and it's this uncertainty in how you're using the term that was the reason for ruling it out in this discussion. But if you'd like to provide a clear definition, which might be easier to accomplish now that you've withdrawn the claim that the flood caused substantial "gene death," then I'm fine with the term. My guess is that what you really mean by "gene death" is a gene becoming a pseudogene.Just in case anyone's curious, here's a bit of what Jerry Coyne says under the heading "Dead Genes":

quote:

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"Atavisms and vestigial traits show us that when a trait is no longer used, or becomes reduced, the genes that make it don't instantly disappear from the genome: evolution stops their action by inactivating them, not snipping them out of the DNA. From this we can make a prediction. We expect to find, in the genomes of many species, silenced, or "dead," genes: genes that once were useful but are no longer intact or expressed. In other words, there would be vestigial genes. In contrast, the idea that all species were created from scratch predicts that no such genes would exist, since there would be no common ancestors in which those genes were active.
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"And the evolutionary prediction that we'll find pseudogenes has been fulfilled - amply. Virtually every species harbors dead genes, many of them still active in its relatives...Out of about thirty thousand genes, for example, we humans carry more than two thousand pseudogenes. Our genome - and that of other species - are truly well populated graveyards of dead genes."

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I'm having trouble making sense of this, and it's possible others may also be having trouble figuring this out, so I'd like to take a stab at clarifying this. You're saying that genotypic frequencies can change without affecting gene/allele frequencies. This feels possible but unlikely to me.Let me spell out why I feel this way with a specific example. Let's say we have a population with 3 genes (named A, B, C) and 3 alleles for each gene (named A1, A2, A3, B1, etc...), and that they break down like this: But this says nothing about the percentages of the all the possible allele combinations in the population. Let's say the allele permutations in the population break down like this, and I've made these numbers consistent with the first table: Now if over time the frequency of A1-B1-C1 changed from 25% to 1% of the population while at the same time that A3-B3-C3 changed from 1% to 25% of the population, then the gene/allele frequency must also have changed. For example, the proportion of A1 in the population would decline from 78% to 54%, and the proportion of A3 would increase from 9% to 33%.So I think this demonstrates that if the genotypic frequencies change that the gene/allele frequencies will most likely also change. Do I have this right?

Is everyone aware that you're using this very technical and highly specific definition of inbreeding? It's possible that, like me, others are using a definition more along the lines of a small population just breeding with each other. In a population "breeding completely at random," is it reasonable to assume no drift?Also, I think at times that you and Faith are talking about two different things, that sometimes when Faith is talking about the population a short time after the isolating event, you're responding about the population after a lengthy enough period of isolation to result in equilibrium according to Hardy-Weinberg. I only quoted your concluding paragraph, but I read and understood everything that preceded it. I think you've demonstrated what I said, that changing genotypic frequency without affecting allelic frequency is very unlikely. In order to keep allelic frequency constant while changing genotypic frequency you need the highly idealized conditions of no mutation, selection, drift or migration. Do you really require allelic frequency to remain constant, something that seems highly unlikely in the real world, in order to make the point that genotypic frequency has changed but not affected interfertility?Sorry to get this far into the details, but I'm trying to keep this at a level everyone can understand, and I'm sort of using my own comprehension level as a yardstick.

HBD's comments do not warrant this response. Could I suggest that if you have comments about how slavish, sophomoric or brickheaded any other participants are, or about the positive aspects of your own contributions, or about your own emotional state, that you should keep them to yourself.There *is* a moderator on duty here. If you have concerns about conduct in the discussion you should raise them with me rather than trying to deal with them yourself, otherwise the one engaging in misconduct is you.Why don't you try to understand why HBD thinks it's necessary to deal with gene flow in both directions, among other things?

You appear to be attempting the discussion board analog to "suicide by cop" (though of course here it's usually very temporary). There *is* a moderator here.I am, as always, reading the thread in order, responding as I go, and I don't know what comes next. If I decide upon any moderator actions I'll hold off until I finish reading to the end.

Really?I shouldn't need to say any more, but just to be very specific, you should be working toward making your position clear instead of telling others to do your work for you. To everyone else it seems impossible that mere genotypic change in two originally interfertile subpopulations could negatively affect interfertility, because without new alleles or genes any genotypic permutation in either subpopulation could have occurred in the original population. Without new alleles how is a subpopulation to arrive at a genotypic permutation that couldn't have occurred in the original population? People are seeking an explanation from you.I'm not taking a position in the discussion, but being neutral doesn't mean imposing some kind of artificial ignorance or stupidity upon myself. Others have made the genetic considerations very clear. If they're wrong then you have to show how they're wrong.