Rebuttal To Creationists - "Since We Can't Directly Observe Evolution..."

Interesting paper for review. They used brewer's yeast with one group being asexual only and another group having sexual cycles without inbreeding.McDonald MJ, Rice DP, Desai MM. Sex speeds adaptation by altering the dynamics of molecular evolution. Nature. 2016 Mar 10;531(7593):233-6. doi: 10.1038/nature17143. Epub 2016 Feb 24. PMID: 26909573; PMCID: PMC4855304. link

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After ~1000 generations of adaptation, including 11 sexual cycles, we measured the fitness of multiple clones isolated from each population (Methods; note one sexual population ended at generation 900 due to technical failures during evolution). We also measured the fitness of whole-population samples, except in four sexual populations where the spontaneous evolution of frequency-dependent interactions make population fitness undefined (we describe this frequency dependence below). Both clone (Mann-Whitney U, P<0.001) and whole-population (two-sided t-test, P<0.001) fitness data show that sexual populations adapted significantly faster than asexual controls (Figure 1a).

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So first off, in their experimental model they saw faster adaptation in the populations that underwent sexual reproduction.

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To investigate how sex improves the efficiency of selection, we analyzed the dynamics of adaptation. As in earlier studies21,22, asexual populations exhibit signatures of hitchhiking and clonal interference (Figure 2a–d). Groups of functionally unrelated mutations, linked within the same genetic background, change in frequency together as clonal cohorts. The outcomes of evolution are determined by competition between these cohorts. In contrast, sexual populations are not characterized by cohorts of linked mutations (Figure 2e–h). Instead, the dynamics of each mutation is largely independent of other variation in the population. In these populations, mutations that occur on different backgrounds fix independently, while others briefly hitchhike to moderate frequencies where they persist or are eliminated from the population.

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And that is exactly what I have described in this thread. In sexual populations, mutations fix independently without the hitchhiking and clonal interference seen in asexual populations.As a bonus, sexual reproduction is also able to detach beneficial mutations from deleterious mutations:

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As expected, we find that each clonal cohort that fixes in an asexual population contains at least one beneficial mutation. However, we also find that significantly deleterious mutations hitchhike to fixation (Figure 3a,c). Recent theory has argued that the fixation of strongly deleterious mutations can be common in adapting asexual populations25,26. Our results provide the first direct experimental support for this hypothesis. In contrast, recombination decouples hitchhiking mutations from their initial background, and we identify no deleterious mutations that fix in sexual populations (Figure 3b,c). The potential for sex to purge deleterious mutations in non-adapting populations has been extensively studied27 (e.g. in work on Muller’s ratchet). Our experiments show that this effect is important even in adapting populations, confirming recent theory28,29.

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Taq:

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Kleinman writes:

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Lenski would "introduce genetic changes"? It appears you don't understand that mutations occur in the process of DNA replication. DNA replication is an error-prone process.

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Lenski et al. did introduce genetic changes to test the fitness of different mutations:

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To see how genetic context affected citrate metabolism, the relevant module—the citT gene and its newly captured regulatory region—were moved onto a high-copy plasmid, which was then transformed into four clonal backgrounds (Blount et al., 2012). Three of the transformed clones, including the ancestral strain, could grow on citrate in the presence of oxygen, albeit with long delays between the depletion of glucose and the start of growth on citrate and other difficulties (Figure 4a).
Experimental evolution and the dynamics of adaptation and genome evolution in microbial populations | The ISME Journal

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So, are you now going to claim that the reproductive fitness advantage that humans have over chimps is due to a plasmid?

The Kishony experiment used asexual reproduction.You, yourself, stated that mutations move towards fixation together. You said that."After an AB recombination event occurs, there will be an intersection of the A and B subsets. But then the AB variant will be the most fit variant and in the biological competition, will drive all the A only and B only variants to extinction leaving only AB variants."--Kleinman

Can you point to any post where I said any such thing?Are you now arguing that the physical differences between humans and chimps is not due to the DNA sequence differences that exist between our genomes? If so, then why are we talking about mutations at all?Do you agree that the DNA sequence differences between our genomes is the reason for our physical differences and the advantages humans have over chimps in certain environments? Yes or no?

Yes, in asexual organisms. Humans are not asexual organisms. Did you know the Desai team says exactly what I have been saying from the very start?

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Together, our results show that sex increases the rate of adaptation both by combining beneficial mutations into the same background and by separating deleterious mutations from advantageous backgrounds that would otherwise drive them to fixation.
McDonald MJ, Rice DP, Desai MM. Sex speeds adaptation by altering the dynamics of molecular evolution. Nature. 2016 Mar 10;531(7593):233-6. doi: 10.1038/nature17143. Epub 2016 Feb 24. PMID: 26909573; PMCID: PMC4855304.
Sex Speeds Adaptation by Altering the Dynamics of Molecular Evolution - PMC

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I just showed that it does.It's a lot simpler than that. There are three possible mate pairs:
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aaBB : aaBB
AAbb : AAbb
AAbb : aaBB
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Without even doing the math, we can see that a lot of mate pairings will be between AAbb and aaBB. All of their offspring will have both the A and B mutations. There are going to be hundreds of thousands of recombination events (as you describe it) between the A and B mutations.
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So you have about 1 in the bacterial populations and hundreds of thousands in the human population. That seems like a big difference, doesn't it?So says the person who can't tell the difference between 1 and hundreds of thousands, as in the example above. The Lenski experiment doesn't have sexual reproduction, therefore it is not a valid model of human evolution. Again, so says the person who can't tell the difference between 1 and 100,000.

Taq:

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Interesting paper for review. They used brewer's yeast with one group being asexual only and another group having sexual cycles without inbreeding.

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McDonald MJ, Rice DP, Desai MM. Sex speeds adaptation by altering the dynamics of molecular evolution. Nature. 2016 Mar 10;531(7593):233-6. doi: 10.1038/nature17143. Epub 2016 Feb 24. PMID: 26909573; PMCID: PMC4855304.

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link

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After ~1000 generations of adaptation, including 11 sexual cycles, we measured the fitness of multiple clones isolated from each population (Methods; note one sexual population ended at generation 900 due to technical failures during evolution). We also measured the fitness of whole-population samples, except in four sexual populations where the spontaneous evolution of frequency-dependent interactions make population fitness undefined (we describe this frequency dependence below). Both clone (Mann-Whitney U, P<0.001) and whole-population (two-sided t-test, P<0.001) fitness data show that sexual populations adapted significantly faster than asexual controls (Figure 1a).

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So first off, in their experimental model they saw faster adaptation in the populations that underwent sexual reproduction.

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To investigate how sex improves the efficiency of selection, we analyzed the dynamics of adaptation. As in earlier studies21,22, asexual populations exhibit signatures of hitchhiking and clonal interference (Figure 2a–d). Groups of functionally unrelated mutations, linked within the same genetic background, change in frequency together as clonal cohorts. The outcomes of evolution are determined by competition between these cohorts. In contrast, sexual populations are not characterized by cohorts of linked mutations (Figure 2e–h). Instead, the dynamics of each mutation is largely independent of other variation in the population. In these populations, mutations that occur on different backgrounds fix independently, while others briefly hitchhike to moderate frequencies where they persist or are eliminated from the population.

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And that is exactly what I have described in this thread. In sexual populations, mutations fix independently without the hitchhiking and clonal interference seen in asexual populations.

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As a bonus, sexual reproduction is also able to detach beneficial mutations from deleterious mutations:

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As expected, we find that each clonal cohort that fixes in an asexual population contains at least one beneficial mutation. However, we also find that significantly deleterious mutations hitchhike to fixation (Figure 3a,c). Recent theory has argued that the fixation of strongly deleterious mutations can be common in adapting asexual populations25,26. Our results provide the first direct experimental support for this hypothesis. In contrast, recombination decouples hitchhiking mutations from their initial background, and we identify no deleterious mutations that fix in sexual populations (Figure 3b,c). The potential for sex to purge deleterious mutations in non-adapting populations has been extensively studied27 (e.g. in work on Muller’s ratchet). Our experiments show that this effect is important even in adapting populations, confirming recent theory28,29.

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You missed this paragraph from your link:

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We find that sex alters the molecular signatures of adaptation. We observe similar proportions of synonymous, nonsynonymous, and intergenic mutations segregating in sexual and asexual lines (Figure 1b). Consistent with earlier work21, in asexual populations these types of mutations are roughly equally likely to fix, conditional on reaching observable frequency (Figure 1b, Extended Data Table 3). This indicates that natural selection cannot efficiently distinguish between their effects. In contrast, fewer mutations fix in sexual populations, and these mutations are overwhelmingly nonsynonymous. These observations suggest that sex improves the efficiency of selection, so that only beneficial mutations fix.

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I added the red emphasis to help you. And nowhere in your link do they say these fixations are occurring simultaneously. And I've said recombination can increase reproductive fitness such as in the example of Darwin's Finches where the starvation selection sweeps increase the frequencies of particular alleles of surviving members. This is the same effect that is being seen in this experiment you are presenting. What you need to understand but don't is that the alleles must exist in the first place and that requires descent with modification (DNA evolution). So, explain to us how this recombination process gives the reproductive fitness differences between humans and chimps if humans and chimps started from the same gene pool.

Yes it does chief.Here:

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To investigate how sex improves the efficiency of selection, we analyzed the dynamics of adaptation. As in earlier studies21,22, asexual populations exhibit signatures of hitchhiking and clonal interference (Figure 2a–d). Groups of functionally unrelated mutations, linked within the same genetic background, change in frequency together as clonal cohorts. The outcomes of evolution are determined by competition between these cohorts. In contrast, sexual populations are not characterized by cohorts of linked mutations (Figure 2e–h). Instead, the dynamics of each mutation is largely independent of other variation in the population. In these populations, mutations that occur on different backgrounds fix independently, while others briefly hitchhike to moderate frequencies where they persist or are eliminated from the population.

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And here:

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Together, our results show that sex increases the rate of adaptation both by combining beneficial mutations into the same background and by separating deleterious mutations from advantageous backgrounds that would otherwise drive them to fixation. In other words, sex makes natural selection more efficient at sorting beneficial from deleterious mutations. This alters the rate and molecular signatures of adaptation.

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That paragraph just further supports my case. It shows that the beneficial mutations are selected for more efficiently due to sexual reproduction. The beneficial mutations are decoupled from neutral mutations, and those beneficial mutations are put into the same genetic background (i.e. simultaneously increasing in frequency).

Kleinman:

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You don't need fixation for a more fit variant to appear. The Kishony experiment demonstrates this quite nicely.

Taq:

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The Kishony experiment used asexual reproduction.

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Taq is now claiming that sexual replicators can't get adaptive mutations.

Taq:

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You, yourself, stated that mutations move towards fixation together. You said that.
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"After an AB recombination event occurs, there will be an intersection of the A and B subsets. But then the AB variant will be the most fit variant and in the biological competition, will drive all the A only and B only variants to extinction leaving only AB variants."--Kleinman

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When did I say that mutations can move toward fixation together? You are confusing the concept of a variant with multiple adaptive mutations moving toward fixation with multiple variants, each with different adaptive mutations moving toward fixation simultaneously. Are all biologists this confused about the concepts of biological competition and recombination?

Kleinman:

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So, are you now going to claim that the reproductive fitness advantage that humans have over chimps is due to a plasmid?

Taq:

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Can you point to any post where I said any such thing?

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You are the one that brought up the subject of plasmids.

Taq:

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Are you now arguing that the physical differences between humans and chimps is not due to the DNA sequence differences that exist between our genomes? If so, then why are we talking about mutations at all?
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Do you agree that the DNA sequence differences between our genomes is the reason for our physical differences and the advantages humans have over chimps in certain environments? Yes or no?

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Taq, you are the one arguing that humans and chimps have evolved from the same gene pool. You have several mechanisms of genetic transformation, biological competition, descent with modification (DNA evolution), and recombination. Wisely, you admit that plasmids (as did Tany's with his claim of ERVs) didn't do it. Using these mechanisms, how do you account for the reproductive fitness differences between humans and chimps? And why haven't you given the correct explanation of the evolution of antimicrobial drug resistance and why cancer treatments fail? Do you have any mathematical explanation for descent with modification (DNA evolution).

Kleinman:

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I take that line to mean that their experiment largely repeats what Lenski's experiment demonstrates, that of improved fitness over time but each step in improvement becomes smaller as the experiment proceeds. And as you are aware by now from our previous discussions about the Lenski experiment, those improvement in fitness occur one fixation and one mutation at a time.

Taq:

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Yes, in asexual organisms. Humans are not asexual organisms.

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I thought biologists are cloned.

Kleinman:

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Do you think those lines are showing multiple fixations occurring simultaneously? Did you read how the Desai team defines fixation in order to generate those curves?

Taq:

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Did you know the Desai team says exactly what I have been saying from the very start?

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Together, our results show that sex increases the rate of adaptation both by combining beneficial mutations into the same background and by separating deleterious mutations from advantageous backgrounds that would otherwise drive them to fixation.
McDonald MJ, Rice DP, Desai MM. Sex speeds adaptation by altering the dynamics of molecular evolution. Nature. 2016 Mar 10;531(7593):233-6. doi: 10.1038/nature17143. Epub 2016 Feb 24. PMID: 26909573; PMCID: PMC4855304.
Sex Speeds Adaptation by Altering the Dynamics of Molecular Evolution - PMC

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How many times do you want to do the Darwin's Finches example. They are doing selective sweeps to increase the frequency of adaptive alleles which increases the probability of an adaptive recombination event occurring. But the alleles have to exist in the first place.So, take this process of selective sweeps based on your assumption that humans and chimps arose from the same gene pool and explain how recombination gives humans have such a large reproductive fitness advantage over chimpanzees.

I never said any such thing. You are flailing. A and B are two variants. That's multiple variants.You said that when the A and B variants are put into the same genetic background that the combination of the two variants are fittest, so they will be selected for as a combination and outcompete those with just the A or B variant. That's two variants (i.e. multiple variants) moving towards fixation together. That's what you said. You agreed that sexual reproduction combines beneficial variants into the same genetic background and moves them towards fixation. This is exactly what was seen in the Desai group's experiment.Remember the start of this whole conversation? You claimed that only the fittest mutation across the whole genome will move towards fixation, driving the rest of the mutations towards extinction. I told you this wasn't the case for sexual reproduction because multiple beneficial mutations can be combined into the same genome without competing with one another. This is exactly what was seen in the paper I gave. You asked for experiments where this happens, and you now have it. You also asked how this would alter evolution, and I gave you the paper that shows you exactly that.

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Together, our results show that sex increases the rate of adaptation both by combining beneficial mutations into the same background and by separating deleterious mutations from advantageous backgrounds that would otherwise drive them to fixation. In other words, sex makes natural selection more efficient at sorting beneficial from deleterious mutations. This alters the rate and molecular signatures of adaptation.
Sex Speeds Adaptation by Altering the Dynamics of Molecular Evolution - PMC

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Look at the freaking title of the paper:"Sex Speeds Adaptation by Altering the Dynamics of Molecular Evolution"

You are flailing. The paper I gave you is studying de novo mutations. Unless you are trying to claim that mutations don't happen in finches I'm not sure what you are trying to argue. We all agree that natural selection is not mutagenesis. It's the combination of de novo mutations and sexual reproduction that gave rise to the human genome.

Kleinman:

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And nowhere in your link do they say these fixations are occurring simultaneously.

Taq:

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Yes it does chief.
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Here:

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To investigate how sex improves the efficiency of selection, we analyzed the dynamics of adaptation. As in earlier studies21,22, asexual populations exhibit signatures of hitchhiking and clonal interference (Figure 2a–d). Groups of functionally unrelated mutations, linked within the same genetic background, change in frequency together as clonal cohorts. The outcomes of evolution are determined by competition between these cohorts. In contrast, sexual populations are not characterized by cohorts of linked mutations (Figure 2e–h). Instead, the dynamics of each mutation is largely independent of other variation in the population. In these populations, mutations that occur on different backgrounds fix independently, while others briefly hitchhike to moderate frequencies where they persist or are eliminated from the population.

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So you think that the hitchhiking gene is beneficial? Where does it say that?

Taq:

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And here:

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Together, our results show that sex increases the rate of adaptation both by combining beneficial mutations into the same background and by separating deleterious mutations from advantageous backgrounds that would otherwise drive them to fixation. In other words, sex makes natural selection more efficient at sorting beneficial from deleterious mutations. This alters the rate and molecular signatures of adaptation.

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Selective sweeps do increase the frequency of adaptive alleles, that's Darwin's Finches. That's how the probability of an adaptive recombination event improves. But the alleles have to exist in the first place. Show us how humans and chimps could have arisen from the same gene pool by recombination with selective sweeps and humans ended up with greater reproductive fitness than chimps.

I don't think deleterious mutations hitchhiking with beneficial mutations in asexual reproduction is beneficial. The Desai group doesn't think that either. Where did you ever get the impression that this was the case? You are flailing again. Why do you keep going back to "but the alleles have to exist in the first place"? Are you denying that mutations happen in humans or apes or primates? What are you on about? You are flailing again.What I have been showing you is that sexual reproduction reduces or eliminates clonal competition like that seen in asexual organisms. You tried to claim that mutations have to happen one at a time and be selected for one at a time. I am showing you why that is false.If you are asking in general, the answer is natural selection for beneficial mutations. That's why humans can outcompete chimps in many environments.

A little blast from the past: Does evolution in sexual species occur along isolated lineages like it does in the Lenski and Kishony experiments which used asexual organisms?Well Kleinman, does it? Have you learned anything from these posts? Do you see why I kept asking you to learn about sexual reproduction?

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Together, our results show that sex increases the rate of adaptation both by combining beneficial mutations into the same background and by separating deleterious mutations from advantageous backgrounds that would otherwise drive them to fixation. In other words, sex makes natural selection more efficient at sorting beneficial from deleterious mutations. This alters the rate and molecular signatures of adaptation. [emphasis mine]
Sex Speeds Adaptation by Altering the Dynamics of Molecular Evolution - PMC

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