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

Kleinman:

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When you start with the assumption that humans and chimpanzees arose from a common ancestor, you somehow have to account for the reproductive fitness differences between the two replicators. The problem for those that believe this is that you have very few replications to do this accounting problem.

Taq:

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I'm not seeing any population genetics models that demonstrates this. All I am seeing is you referring to big numbers and waving your hands.

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For the number of humans that have ever lived and the number alive today can be found here:
How Many People Have Ever Lived on Earth?
The estimated number of humans before 8000 BC is about 1.2 billion, the number people alive in 2019 was about 7.6 billion and the number of chimpanzees alive can be found here:
Chimpanzee - Wikipedia

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The chimpanzee is listed on the IUCN Red List as an endangered species. Between 170,000 and 300,000 individuals are estimated across its range.

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You don't have a model for this but you have more than enough data. If humans and chimpanzees arose from a common ancestor, what adaptive mutations enabled humans to achieve a population of over 7 billion while chimpanzees have only achieved a population of 300,000?

Kleinman:

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If you assume a mutation rate of 1e-9, you have only on average about 2 mutations at every site in the genome somewhere in that one billion population. You simply don't have sufficient population size to get a lineage that accumulates more than a small number of adaptive mutations.

Taq:

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Let's use a mutation rate of 50 mutations per person in each generation. In a steady population of just 100,000 people that is 5 million mutations per person. With a generation time of 25 years that would be 200,000 generations over 5 million years. This results in 1 trillion mutations over the last 5 million years. We only need about 20 million mutations to produce the differences we see between humans and chimps. Where is the problem?

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The problem is that you are doing a simple-minded neutral evolution calculation. Adaptive mutations must be accumulated on lineages. And it should be clear to you that humans have a reproductive advantage over chimps simply by the population numbers.

JSTOR: Access Check is not a link to Haldane's paper. It's a link to a site that will allow you to access Haldane's paper if you sign up. Here is a link to the actual paper: The Cost of Natural SelectionIs formatting difficult for you? Math seems your central focus but you can't even use subscripts and superscripts? And Latex shouldn't be rocket science for someone so enamored with math.Here's the relevant excerpt from the paper which appears at the bottom of page 14:

The Cost of Selection:

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Let the nth generation, before selection, occur in the frequencies

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And this is not an equation for the cost of selection, just a statement of how he'll be expressing the frequencies. You add: Yes, total frequency of both A and a will always be 1. You're claiming it, you explain it. First provide the specific equation from Haldane's paper that you're referring to, then convert it into units of Joules.
​ You haven't made a point, just a request that others do your explaining for you.--Percy

No, I'm not. I am calculating the number of mutations that would have occurred in the human lineage with with a steady population of just 100,000 humans. That number is 1 trillion. We would only need to keep 1 out of every 50,000 mutations that did occur over that time period in order to get the 20 million mutations we see now. Why is this a problem? How is that a problem? At 2.5 million years ago there would have been 500 billion mutations that had occurred in the human lineage. That's enough for 3 SNP's at every position in the haploid genome 40 times over. Why wouldn't the beneficial mutations during that time reach fixation, and then be passed on to future generations? And?

Kleinman:

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"A" and "a" are different alleles. "A" variants are more fit than the "a" variants.

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It should be clear to you that Haldane's frequency equation is at least a conservation of number equation.
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Percy:

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Yes, total frequency of both A and a will always be 1.

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And as pnA -> 1, qna -> 0. When pnA = 1, fixation (or as Haldane calls it, substitution) has occurred. This is the fundamental equation of biological evolutionary competition. The more fit variants increase in frequency and the less fit variants decrease in frequency when a population is engaged in biological evolutionary competition. The rest of Haldane's paper uses that fundamental equation to compute the number of deaths of less fit variants in that biological evolutionary competition. Those variant going extinct are no longer candidates for adaptive mutations, they are dead. What is important is how many replications the more fit variant are able to do during and after they win the competition because that determines the probability of some member in that subpopulation getting an adaptive mutation.

Kleinman:

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Why is it a conservation of energy equation?

Percy:

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You're claiming it, you explain it. First provide the specific equation from Haldane's paper that you're referring to, then convert it into units of Joules.

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I already have but I'll do it again. It is based on the first law of thermodynamics. It takes energy to replicate, the most efficient user of that energy for survival and reproduction will increase in frequency in the population while the less efficient user of that energy will decrease in frequency in any biological evolutionary competition. This is clearly demonstrated in the Lenski experiment where he energy limits his population. And don't be silly, frequency is dimensionless. It is the total available energy that limits the total population size. If you want to do an energy calculation, you need to know the amount of energy necessary for each replication and the carrying capacity (total amount of usable energy in the environment) and you can compute the population size the environment can support.This frequency equation that Haldane uses is applicable to the Lenski experiment to do the mathematics of biological evolutionary competition and compute the generations to fixation but what happens if you try to apply it to the Kishony experiment? The answer to that is it is not applicable because Kishony's experiment has much greater carrying capacity and significant biological competition is not occurring. Therefore no fixation is occurring.Kishony starts his experiment with bacteria (CFU-colony forming units) that are drug-sensitive. That single drug-sensitive bacterium starting that colony has a frequency of qna = 1 and pnA = 0. The colony grows and qna remains at 1 and pnA remains at 0 until some lucky member gets an adaptive mutation. On average, for a mutation rate of 1e-9, that takes about a billion replications so qna will be (1-1e-9) and pnA will be 1e-9. That is nowhere near fixation. Adaptation does not require fixation and adaptation will be slowed by biological competition as demonstrated by the contrast between the Kishony and Lenski experiments.

Kleinman:

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The problem is that you are doing a simple-minded neutral evolution calculation.

Taq:

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No, I'm not. I am calculating the number of mutations that would have occurred in the human lineage with with a steady population of just 100,000 humans. That number is 1 trillion. We would only need to keep 1 out of every 50,000 mutations that did occur over that time period in order to get the 20 million mutations we see now. Why is this a problem?

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You are doing a neutral evolution calculation. But you can explain to us how 1 out of every 50,000 mutations are kept and which ones humans have kept to give the reproductive advantage over chimps. And tell us what selective advantage each of these 1 out of every 50,000 mutations give and why chimps did get these mutations.

Did you not read my post?The mutation rate is 50 mutations per person per generation. In a population of 100,000 that would be 5 million mutations per generation across the population. Do you agree with this or not? Have you heard of natural selection, neutral drift, and vertical inheritance?Do you agree that the physical differences between chimps and humans are due to the DNA sequence differences between our genomes? Yes or no?

Why compare human population to chip? They are totally separate organisms inhabiting totally separate niches, subject to different evolutionary stresses. The genotypes, phenotypes, and environments are all different between the two. Humans evolved the capacity to walk upright and travel over vast distances where the chimp did not. We also got smart. Chimp evolution did not do that.Seems reasonable that smart mobile humans can inhabit and move between many more niches, and thus generate a larger population across the planet, than chimps who are confined to a few of theirs.Yes, more bodies mean more diversity is accumulated in the larger population. So what? Are you going to compare humans to ants and their 20 trillion sized population? Can you imagine the accumulated diversity in that population?What is the point of this comparison? That humans and chimps evolved in different directions from the common ancestor? That humans are more fit in more disparate niches than chimps? Do you deny that humans, chimps and ants all came from a common ancestor?Or are you saying that humans and chimps must accumulate mutations in lockstep with each other? What is your point?

Kleinman:

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You are doing a neutral evolution calculation.

Taq:

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Did you not read my post?
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The mutation rate is 50 mutations per person per generation. In a population of 100,000 that would be 5 million mutations per generation across the population. Do you agree with this or not?

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So you claim that in the first generation that humans appeared the population size was 100,000?

Kleinman:

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But you can explain to us how 1 out of every 50,000 mutations are kept and which ones humans have kept to give the reproductive advantage over chimps.

Taq:

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Have you heard of natural selection, neutral drift, and vertical inheritance?
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Do you agree that the physical differences between chimps and humans are due to the DNA sequence differences between our genomes? Yes or no?

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So you can't explain how 1 out of every 50,000 mutations are kept and which ones give humans a reproductive advantage over chimps. Chimps have a population of 300,000 today, 3 times greater than your hypothetical example. They should have 15 million mutations per generation. Their reproductive fitness should be increasing 3 times faster because they are getting 3 times more beneficial mutations according to your math. How about 7 billion humans today? According to your math, there are 70,000 times more beneficial mutations occurring in the human population today. Does every newborn child in the world get all those beneficial mutations by vertical inheritance?

Kleinman:

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And it should be clear to you that humans have a reproductive advantage over chimps simply by the population numbers.

AZPaul3:

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Why compare human population to chip? They are totally separate organisms inhabiting totally separate niches, subject to different evolutionary stresses. The genotypes, phenotypes, and environments are all different between the two. Humans evolved the capacity to walk upright and travel over vast distances where the chimp did not. We also got smart. Chimp evolution did not do that.

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You believe that humans and chimps arose from a common ancestor. What mutations allow humans to live and reproduce in all these niches that chimps don't? What mutations did humans get that allow humans to walk upright but chimps didn't get these mutations? What mutations gave us greater intelligence that chimps didn't get? How did all these adaptive mutations accumulate in a lineage of humans but didn't occur and accumulate in a lineage of chimps?

I am saying that in a population of 100,000 and a mutation rate of 50 mutations per person per generation that there will be 5 million new mutations in the next generation. Do you agree with this or not? The explanation is the same explanation as that found in the Kishony and Lenski experiments. It is a combination of selection, drift, and vertical inheritance. You need to learn about fitness landscapes. Each peak is a local maximum for fitness. The problem for many species is that they will ascend a local maximum of fitness, and get stuck there. Why? Negative selection prevents them from reducing their fitness so they can reach a valley and climb up a different local maximum. That's where chimps are.The interaction of mutations, fitness, and environment are not linear things or the same across all species. All the ones that have been fixed in the human population, yes. Do you not know how inheritance works?

Why should a different species with a different genome under different circumstances produce the same genetic anomalies? All those by convergent evolution? That expectation is just stupid.You really do not understand evolution.

Kleinman:

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So you can't explain how 1 out of every 50,000 mutations are kept and which ones give humans a reproductive advantage over chimps.

Taq:

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The explanation is the same explanation as that found in the Kishony and Lenski experiments. It is a combination of selection, drift, and vertical inheritance.

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Well, it's about time. You finally agree that it takes a billion replications for each adaptive mutation in a lineage. I knew you would finally get it.

Kleinman:

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How did all these adaptive mutations accumulate in a lineage of humans but didn't occur and accumulate in a lineage of chimps?

AZPaul3:

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Why should a different species with a different genome under different circumstances produce the same genetic anomalies? All those by convergent evolution? That expectation is just stupid.

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If humans and chimps arose from a common ancestor, didn't they start from the same genome? So what adaptive mutations did humans get that chimps didn't that have enabled humans to achieve a population greater than 7 billion yet chimps have a population of only 300,000?

In the Lenski experiment all of the parallel bacterial populations shared a common ancestor and shared the same genome. However, after growing separately there were different mutations that reached fixation in different cultures. The same for the Kishony experiment.You keep talking about these experiments, but you seem to forget about them. First off, there are more E. coli in your gut than there have been humans who have ever lived. Are E. coli fitter than humans?Second, humans evolved to live in an open savanna. Chimps did not. It seems rather obvious that different mutations would have been beneficial in each population. Mutations that allowed human ancestors to run on two legs would not have been beneficial to chimps who needed to climb trees. Also, epistasis is a real thing. Different neutral mutations potentiate different beneficial mutations because of the interaction between the two mutations. The random rise and fall of neutral mutations in the genetic background can change the evolutionary trajectory of species after they split off from one another.

Agreeing to the same mechanisms in no way means I agree that they occur at the same rate. Your dishonesty is noted.