Why don’t you try to answer those questions. You claim to have modeled evolution, so let’s see it.
Common ancestry.
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You have given an example of a single gene with 17 selective mutations. How does the human lineage accumulate all 17 of these selective mutations?
Can’t you show us the math? You have 17 mutational events and you know the probability of a particular mutation event occurring in a single replication. Now you have 17 selective mutational events. What is the probability of those 17 particular mutations ending up in a single variant? The way a set of selective mutational events end up in a single lineage is demonstrated by the Kishony and Lenski experiment. You say that these examples are asexual replicators and that evolution (descent with modification) works differently for sexual replicators. Explain to us how the human lineage accumulated this set of 17 selective mutations for that gene. Then you can explain how the selective mutations for the 20,000-30,000 other genetic loci can be accumulated as well.
Didn’t you say this as well, “If 1 mutation is already present in 50% of the population, then a second mutation in that same gene will be quite common, as one example”. What if 1 mutation was not present in 50% of the population, but in only 0.5% of the population? What would the probability of that second mutation in the same gene be?
You are the one claiming that humans and chimpanzees descended from a common ancestor and throw out the 50% number and the probability of the next adaptive mutation occurring. When you claim that humans and chimpanzees diverged from the common ancestor, did the human lineage have any of the 17 selective mutations that are measured now?
No, it isn’t T_aquaticus, it is the joint probability of all 18 mutations occurring. That’s why each of the mutations must be amplified (increased in number) in order to increase the probability of each of the individual mutations occurring. That is why descent with modification requires huge populations and high recovery rates as demonstrated by the Kishony and Lenski experiments. Humans and chimpanzees don’t reach a population size sufficient for descent with modification and adaptation to work efficiently for more than a few selective mutations.
This is a common blunder made by those that believe in universal common descent. Neutral evolution is called neutral evolution because there is no change in reproductive fitness. There are about 8 billion humans on earth today and only 300,000 chimpanzees. That is a significant difference in the reproductive fitness of the two species. Neutral evolution does not explain the genetic differences between humans and chimpanzees, the big difference in population size between the two species should make that clear to you. And your example of 17 selective mutations in just one gene should be a wake-up call to you that descent with modification or mutation and inheritance or whatever you want to call it cannot do such a genetic process with the population size that humans have achieved.
No, I haven’t. I’ve given an example of a single gene with differences at 17 bases when comparing the reference chimp and human genome. Nowhere have I said that all 17 are beneficial. More importantly, some of those differences are due to mutations in the chimp lineage.
First, not all 17 need to be in the human lineage. Second, it is because mutations happen. What about this is not sinking in?
I did. Here it is again:
The mutation rate is about 50 to 100 per individual per generation. This means about 50 to 100 neutral mutations reach fixation in the human population per generation. Over 5 million years, that’s about 200,000 generations since sharing common ancestry with chimps which gives us 10 to 20 million mutations that reach fixation in both lineages. This is in line with the approximately 35 million mutations that separate humans and chimps. This is just for neutral mutations. Beneficial mutations would reach fixation even faster. The number of mutations that separate chimps and humans is entirely in line with what we would expect to see.
No, we don’t. We have 17 differences.
Mutation and inheritance.
I never said that.
There aren’t 17 selective mutations. There are 17 differences.
Your math is absolutely wrong. The 17 mutations are already there. The probability of them occurring is 1 in 1, because they happened. Therefore, the probability of a new mutation bringing the total to 18 is just the probability of that 1 mutation.
I already showed you this isn’t true. The number of differences between the chimp and human genomes is consistent with the number expected from neutral drift.
So even without selection for beneficial mutations we would expect the number of differences we see between the chimp and human genomes.
Sorry, but the math doesn’t support your case.
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Read carefully, I wrote selective, not beneficial mutations. And you try to explain this with your terminology “mutation and inheritance” and then you won’t explain the difference between “mutation and inheritance” and descent with modification.
When will it sink in with you that mutations are random occurrences and the joint probability of two or more mutations is computed by the multiplication of the probabilities of each particular mutation occurring? Try computing the joint probability of just 2 of these selective mutations occurring. Perhaps you think you can win two lotteries because somebody wins these lotteries.
So you think that humans and chimpanzees evolved from a common ancestor by neutral evolution? Why do humans have greater reproductive fitness than chimpanzees? And which neutral mutations give humans the reproductive fitness to reach a population size of 8 billion while chimpanzees have achieved a population size of only 300,000?
So, those differences are no longer selective mutations? How did all humans accumulate the same 17 genetic differences?
How did all humans inherit the same 17 selective mutations?
So you don’t believe that humans and chimpanzees descended from a common ancestor? And you said the following in post 136 “If 1 mutation is already present in 50% of the population, then a second mutation in that same gene will be quite common”. Why don’t you tell us the probability of that second mutation occurring if the percentage is 0.5% When are you going to learn that the probability of a second mutation occurring depends on the amplification of the first mutation? The math isn’t that hard.
How did all humans inherit these same 17 genetic differences?
You need to study your probability theory again. This is a conditional probability problem. You can review the concept here:
Conditional Probability
In this case, you have 17 events (with associated probabilities) occurring before the 18th mutation occurs. You have to include the probabilities of all 18 events to compute the joint probability. All 17 of the previous mutations must amplify (increase in number, population size) in order for the joint probability of all random18 events to occur. If any one of the 17 mutations does not amplify, the joint probability will be low for all the events to occur. That is how descent with modification works.
You can believe that if you want but neutral evolution doesn’t explain the huge reproductive fitness difference humans have over chimpanzees. Humans have more than 20,000 times greater population size than chimpanzees. Do you think that neutral evolution does that?
Here’s a reference to help you understand reproductive fitness:
Biology for Dummies
Do you think that neutral evolution gave the ability of humans to reach a population size of 8 billion while chimpanzees only have a population size of 300,000? Please explain to us how neutral evolution gives humans this reproductive fitness advantage.
Sorry, T_aquaticus, this math is intended for someone that understands what conditional probability is. Your math is limited to a neutral evolution calculation even though the human population is about 8 billion and the chimpanzee population is only about 300,000, a huge reproductive fitness advantage.
What’s the difference?
I did explain it. Here it is again:
Descent with modification was coined before genetics was understood. “Mutation and inheritance” is more specific in that it details the actual mechanisms.
Common ancestry. It is the same reason that you and your extended family share the same mutations.
No, I don’t. The probability of an event after it has already occurred is 1 in 1. That’s basic probability.
Each person is born with 50 or so mutations. The odds of any single one of those substitution mutations occurring is 1 in 3x6 billion, the number of possible mutations multiplied by the number alternate bases possible. The odds of all of those 50 mutations happening is 18 billion to the 50th power. I don’t need to tell you this is a rather large number.
And yet, every person is born with 50 mutations despite the complete improbability of those 50 mutations happening. Do you know why?
What I am showing you is that the number of mutations that differ between humans and chimps is well within the range expected from neutral drift alone. Selection for beneficial mutations will fix mutations at an even greater rate. So the number of differences between the genomes is not a problem.
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One cannot compare the biological fitness of two different species because they do not share the same gene pool. This is something one learns in 2nd year population ecology class (at least in my experience). Fitness is calculated as an individual’s contribution to the the gene pool, relative to other individuals also striving to pass along their genes to the gene pool in the next generation. (and humans and chimps don’t interbreed and share a gene pool so one can’t quantitatively calculate the fitness of a chimp compared to a human). But it’s also clear from the definition of biological fitness from Wikipedia if you want to go there:
Fitness (often denoted w 
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Your patience is admirable.
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Actually, none. Do I need to explain your reference to the comparison of human and chimpanzee genes? First, learn what gene polymorphism is, then, you should learn what is meant by a selective mutation and a selective sweep. Then, try to think of any experimental or empirical examples of selective sweeps and why this is evidence that humans and chimpanzees didn’t evolve from a common ancestor.
Explain the mathematical details of “Mutation and inheritance”.
Are you claiming that every human has every mutation that every other human has had overall time?
Have you ever studied probability theory at all? Here is a simple example that shows why you are wrong. Start with a standard playing card deck. What is the probability of selecting two aces out of the deck?
If your selections are independent (you return the first selection to the deck before making the second selection), that probability is (4/52)(4/52)=16/2704, not 1(4/52)
If your selections are dependent (you don’t return the first selection to the deck before making the second selection), that probability is (4/52)(3/51)=12/2652, not 1(3/51)
Just because you selected the first ace does not make its probability equal one. You don’t understand basic probability theory.
You continue to get this wrong. This is not about any mutation occurring, it is about a set of particular mutations occurring. In this case, it is a set of 17 mutations occurring in a single genetic locus.
How many beneficial mutations have the human lineage accumulated to give it the reproductive fitness advantage over chimpanzees?
Are you saying that ecologists don’t measure the reproductive success of different species and compare them? How do ecologists determine the effect that Burmese pythons have on alligators?
This would be a lot easier if T_aquaticus (and perhaps you) would learn some basic probability theory.
Because they were another branch. Why are you asking me such a basic question to which we both know the answer?
Do you mean that chimpanzees haven’t done enough replications for every possible mutation to have occurred but humans have?
Of course ecologists measure effects of species on each other. The interaction you mention between pythons and alligators might be called “predation” for example…
Ecologists also compare demographic parameters of different species, but this is called studying their “life history strategies”. For example, elephants have a “slow life history”—long time to sexual maturation, few offspring produced over the lifetime, and a long lifespan. mice have a “fast life history” -rapid maturity, large litters and numerous offspring, short lifespan. But this is not comparing the fitness of two species, which theoretically impossible because they don’t share a gene pool.
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No. I do not mean either clause of your sentence, nor is it implied.
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So humans and chimpanzees do not and have not ever shared a gene pool? Why is T_aquaticus discussing a comparison of human and chimpanzee genes?
Why can’t chimpanzees (another branch) get every possible mutation at every site in their genome if they do sufficient replications?
The usual roles of selection and drift would apply. Chimpanzees already have genes well adapted to their arboreal lifestyle.
These aren’t relevant to the number of mutations that have occurred. The correct answer is that chimpanzees have also had every possible single-site mutation in the time since they shared a common ancestor with humans.
Chimps and humans do not currently share a gene pool. “genes” and “gene pool” are two different things. If you don’t know these basic concepts, perhaps its time to brush up by reading a first year biology textbook.
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That’s rather rich coming from someone who claimed selective and beneficial mutations were not the same thing.
I already gave that to you.
I also showed you the math.
“The mutation rate is about 50 to 100 per individual per generation. This means about 50 to 100 neutral mutations reach fixation in the human population per generation. Over 5 million years, that’s about 200,000 generations since sharing common ancestry with chimps which gives us 10 to 20 million mutations that reach fixation in both lineages. This is in line with the approximately 35 million mutations that separate humans and chimps. This is just for neutral mutations. Beneficial mutations would reach fixation even faster. The number of mutations that separate chimps and humans is entirely in line with what we would expect to see.”
I am claiming that there are mutations that have fixed across the entire human population, and that is due to common ancestry.
It’s the same as selecting any two specific cards out of the deck. Just the act of drawing two cards guarantees that you will have a highly improbable outcome.
You aren’t predicting which mutations will occur before they happen. Your argument boils down to this:
I deal a 5 card hand from a poker deck. The cards are 3 of hearts, 2 of spades, king of diamonds, jack of diamonds, and 8 of clubs. What is the probability of getting that hand? It is given by the combinations function in math which is :
C ( n , r ) = ( n r ) = n ! ( r ! ( n − r ) ! )The odds of getting that hand are about 1 in 2.6 million. You can plug the numbers in here if you want:
So how is it that I got a hand with a probability of 1 in 2.6 million in the very first try? How is that possible?
Probably much less than the approximately 20 million that accumulated since our lineage split from chimps since most mutations occur in junk DNA. If evenly distributed, 2 million would have occurred in the functional 10% of the human genome, so only they would have a strong chance of being beneficial. Fewer still out of those would need to be beneficial. So only a small fraction would even need to be beneficial.
That seems to be what you are saying. You claim that the 17 differences seen between a human and chimp gene have to all be mutations in the human lineage, as if the chimp lineage never accumulated any mutations.
Our common ancestor was not a chimp and it was not a human. Chimps and humans are separate species who do not share a gene pool. We share a common ancestor. Do you not know what a gene pool is?
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