Register | Sign In


Understanding through Discussion


EvC Forum active members: 49 (9179 total)
0 online now:
Newest Member: Jorge Parker
Post Volume: Total: 918,222 Year: 5,479/9,624 Month: 504/323 Week: 1/143 Day: 1/13 Hour: 0/0


Thread  Details

Email This Thread
Newer Topic | Older Topic
  
Author Topic:   Rebuttal To Creationists - "Since We Can't Directly Observe Evolution..."
Taq
Member
Posts: 10195
Joined: 03-06-2009
Member Rating: 3.2


Message 165 of 2932 (898279)
09-21-2022 6:40 PM
Reply to: Message 164 by Kleinman
09-21-2022 6:20 PM


Re: Apples and oranges
Kleinman writes:
DNA evolution is DNA evolution.
So how does the evolution of DNA in the Kishony and Lenski experiments apply to DNA evolution in human evolution?

This message is a reply to:
 Message 164 by Kleinman, posted 09-21-2022 6:20 PM Kleinman has replied

Replies to this message:
 Message 166 by Kleinman, posted 09-21-2022 7:20 PM Taq has replied

  
Taq
Member
Posts: 10195
Joined: 03-06-2009
Member Rating: 3.2


(2)
Message 178 of 2932 (898316)
09-22-2022 11:44 AM
Reply to: Message 166 by Kleinman
09-21-2022 7:20 PM


Re: Apples and oranges
Kleinman writes:
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.
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.
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.
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?
Under the best of circumstances, Kishony's experiment takes 5 billion replications of a lineage to accumulate 5 adaptive mutations.
The rate at which beneficial mutations are found is dependent on the environment and specific challenges each species faces. It's the same as getting a winning lottery ticket and guessing right on a coin flip.

This message is a reply to:
 Message 166 by Kleinman, posted 09-21-2022 7:20 PM Kleinman has replied

Replies to this message:
 Message 181 by Kleinman, posted 09-22-2022 12:20 PM Taq has replied

  
Taq
Member
Posts: 10195
Joined: 03-06-2009
Member Rating: 3.2


Message 183 of 2932 (898330)
09-22-2022 1:00 PM
Reply to: Message 181 by Kleinman
09-22-2022 12:20 PM


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

This message is a reply to:
 Message 181 by Kleinman, posted 09-22-2022 12:20 PM Kleinman has replied

Replies to this message:
 Message 185 by Kleinman, posted 09-22-2022 2:13 PM Taq has replied

  
Taq
Member
Posts: 10195
Joined: 03-06-2009
Member Rating: 3.2


Message 186 of 2932 (898337)
09-22-2022 2:29 PM
Reply to: Message 185 by Kleinman
09-22-2022 2:13 PM


Re: Apples and oranges
Kleinman writes:
You are doing a neutral evolution calculation.
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?
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.
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?

This message is a reply to:
 Message 185 by Kleinman, posted 09-22-2022 2:13 PM Kleinman has replied

Replies to this message:
 Message 188 by Kleinman, posted 09-22-2022 3:25 PM Taq has replied

  
Taq
Member
Posts: 10195
Joined: 03-06-2009
Member Rating: 3.2


(1)
Message 190 of 2932 (898345)
09-22-2022 3:42 PM
Reply to: Message 188 by Kleinman
09-22-2022 3:25 PM


Re: Apples and oranges
Kleinman writes:
So you claim that in the first generation that humans appeared the population size was 100,000?
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?
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.
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.
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.
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.
Does every newborn child in the world get all those beneficial mutations by vertical inheritance?
All the ones that have been fixed in the human population, yes. Do you not know how inheritance works?

This message is a reply to:
 Message 188 by Kleinman, posted 09-22-2022 3:25 PM Kleinman has replied

Replies to this message:
 Message 192 by Kleinman, posted 09-22-2022 3:55 PM Taq has replied

  
Taq
Member
Posts: 10195
Joined: 03-06-2009
Member Rating: 3.2


(1)
Message 194 of 2932 (898353)
09-22-2022 4:07 PM
Reply to: Message 193 by Kleinman
09-22-2022 4:01 PM


Re: Apples and oranges
Kleinman writes:
If humans and chimps arose from a common ancestor, didn't they start from the same genome?
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.
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?
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.

This message is a reply to:
 Message 193 by Kleinman, posted 09-22-2022 4:01 PM Kleinman has replied

Replies to this message:
 Message 197 by Kleinman, posted 09-22-2022 4:48 PM Taq has replied

  
Taq
Member
Posts: 10195
Joined: 03-06-2009
Member Rating: 3.2


Message 195 of 2932 (898354)
09-22-2022 4:10 PM
Reply to: Message 192 by Kleinman
09-22-2022 3:55 PM


Re: Apples and oranges
Kleinman writes:
You finally agree that it takes a billion replications for each adaptive mutation in a lineage.
Agreeing to the same mechanisms in no way means I agree that they occur at the same rate. Your dishonesty is noted.

This message is a reply to:
 Message 192 by Kleinman, posted 09-22-2022 3:55 PM Kleinman has not replied

  
Taq
Member
Posts: 10195
Joined: 03-06-2009
Member Rating: 3.2


Message 199 of 2932 (898360)
09-22-2022 5:08 PM
Reply to: Message 197 by Kleinman
09-22-2022 4:48 PM


Re: Apples and oranges
Kleinman writes:
That's not right, Lenski's bacteria were not all exact clones in his founders' population.
From the Lenski paper:
quote:
The long-term evolution experiment, or LTEE, is simple both conceptually and practically. Twelve populations were started the same ancestral strain of Escherichia coli in 1988. The ancestral strain has no plasmids or functional prophages, and E. coli is not naturally transformable, so there is no horizontal gene transfer.
Experimental evolution and the dynamics of adaptation and genome evolution in microbial populations | The ISME Journal
What these lineages have in common is that the next adaptive step will take about 1/(mutation rate) replications to have a reasonable probability of the next beneficial mutation occurring.
I already disproved this. In the Lederberg paper the rate of adaptive mutations to streptomycin and phage were different by 3 orders of magnitude:
quote:
The culture is fully sensitive to the phage T-1, as well as to streptomycin, and like most E. coli strains gives rise to resistant mutants at rates of approximately 10^-7 and 10^-10 per division, respectively.
REPLICA PLATING AND INDIRECT SELECTION OF BACTERIAL MUTANTS - PMC
Different adaptations are going to occur at different rates. You can't take the rate of one adaptation and apply it universally to all adaptations.
The math is the same for all evolutionary trajectories.
Then why does streptomycin resistance occur 1,000 times slower than phage resistance?
That is really weird. Are you now claiming that humans and E. Coli share a common ancestor?
All life shares a common ancestor. That's what the evidence shows us.
There are more E. coli in your gut than there ever have been people. Does this mean E. coli are more fit than humans? Yes or no?
Go for it, explain which mutations allow humans to live in open savanna, desert, arctic,... and chimps don't.
It's the mutations we have that chimps do not.
If chimps didn't get those mutations, why not?
They probably did get those mutations, but they were either not selected for because chimps were not in the same environment as humans or those same mutations were not beneficial because of epistatic effects. I have explained this multiple times now.
At what rate does a human lineage accumulate adaptive mutations?
There is no such rate because each beneficial mutation is going to have different levels of fitness increase, and the benefice of a mutation is going to depend on what environment humans are in. The fact you think there should be a set rate means you don't understand how evolution works.

This message is a reply to:
 Message 197 by Kleinman, posted 09-22-2022 4:48 PM Kleinman has replied

Replies to this message:
 Message 201 by Kleinman, posted 09-22-2022 5:54 PM Taq has replied

  
Taq
Member
Posts: 10195
Joined: 03-06-2009
Member Rating: 3.2


(2)
Message 203 of 2932 (898364)
09-22-2022 6:31 PM
Reply to: Message 201 by Kleinman
09-22-2022 5:54 PM


Re: Apples and oranges
Kleinman writes:
Do you think that every bacterium in that strain is an exact clone? Do you think they replicate with a zero mutation rate? Every time a replication occurs there is a possibility of a mutation occurring somewhere in the genome. His populations were diverse to start. The starvation selection condition reduced that diversity by natural selection.
That screeching sound you hear is the goal posts you are dragging behind you.
The strain came from a single colony. That single colony came from a single bacterium. Every bacterium in that experiment descended from the same exact single ancestor.
You tried to imply that humans and chimps should have the same adaptations because we started from the same common ancestor. So why don't we see that in the Lenski experiment?
I don't, the rate of adaptation depends on the mutation rate.
The E. coli in the Lederberg experiment all have the same mutation rate. How do you explain the fact that adaptation to streptomycin occurs 1,000 times slower than phage resistance?
You can't even give a coherent explanation of the Kishony and Lenski experiments.
So says the person who claims that the Lenski experiment did not start with a single ancestor.
Why don't you say that you don't know?
I do know. It is the mutations humans have that chimps do not.

This message is a reply to:
 Message 201 by Kleinman, posted 09-22-2022 5:54 PM Kleinman has replied

Replies to this message:
 Message 206 by Kleinman, posted 09-22-2022 7:18 PM Taq has replied

  
Taq
Member
Posts: 10195
Joined: 03-06-2009
Member Rating: 3.2


Message 213 of 2932 (898390)
09-23-2022 11:18 AM
Reply to: Message 206 by Kleinman
09-22-2022 7:18 PM


Re: Apples and oranges
Kleinman writes:
Even when you start with a single bacterium, when the colony size reaches a billion and the mutation rate is 1e-9, you will have on average, a member in that colony with a mutation at every site in the genome.
A colony only has a few hundred thousand bacteria, but that is beside the point.
You are the one who claimed that the human and chimp lineages should not have evolved differently if they shared a common ancestor. Remember?
Wouldn't that common ancestral population be the same as that colony of bacteria? Wouldn't it also have had genetic variation? The answer is obviously yes. Even with this genetically diverse common ancestral population you claimed that the human and chimp lineages should not diverge through evolution. That's what you claimed.
You are assuming that it only takes a small number of replications and beneficial mutations have a high probability of occurring. You don't understand the mathematical process that is going on in the Kishony and Lenski experiments. The reason why each adaptive step takes a billion replications is that the variant is sampling every possible mutation, beneficial, neutral, and detrimental. The environmental selection conditions determine which category the particular mutation falls into. Try doing the math yourself.
Let's do the math.
Each human is born with about 50 mutations.
quote:
Mutations generate sequence diversity and provide a substrate for selection. The rate of de novo mutations is therefore of major importance to evolution. Here we conduct a study of genome-wide mutation rates by sequencing the entire genomes of 78 Icelandic parent-offspring trios at high coverage. We show that in our samples, with an average father's age of 29.7, the average de novo mutation rate is 1.20 × 10(-8) per nucleotide per generation.
Rate of de novo mutations and the importance of father's age to disease risk - PubMed
If each base in the human genome has a 1 in 120 million chance of mutation then we would get about 50 mutations in a 6 billion base diploid genome. Agreed?
With that mutation rate, in population with a steady 100,000 individuals we would see 5 million new mutations in each generation. Agreed?

This message is a reply to:
 Message 206 by Kleinman, posted 09-22-2022 7:18 PM Kleinman has replied

Replies to this message:
 Message 217 by Kleinman, posted 09-23-2022 11:45 AM Taq has replied

  
Taq
Member
Posts: 10195
Joined: 03-06-2009
Member Rating: 3.2


Message 214 of 2932 (898391)
09-23-2022 11:22 AM
Reply to: Message 212 by Kleinman
09-23-2022 8:08 AM


Re: Apples and oranges
Kleinman writes:
Pardon my error in reading comprehension. And Oh boy! Tanypteryx knows and can list the beneficial mutations that give the reproductive fitness advantage of humans over chimps.
Are the physical differences between chimps and humans due to the sequence differences between their genomes? Yes or no?

This message is a reply to:
 Message 212 by Kleinman, posted 09-23-2022 8:08 AM Kleinman has not replied

  
Taq
Member
Posts: 10195
Joined: 03-06-2009
Member Rating: 3.2


Message 216 of 2932 (898394)
09-23-2022 11:39 AM
Reply to: Message 215 by Tanypteryx
09-23-2022 11:32 AM


Re: Apples and oranges
Tanypteryx writes:
If Taq is a scientist then I assume he knows how to use the scientific method.
He is and he does. He is even a microbiologist, and a molecular biologist (hence the username).

This message is a reply to:
 Message 215 by Tanypteryx, posted 09-23-2022 11:32 AM Tanypteryx has replied

Replies to this message:
 Message 218 by Tanypteryx, posted 09-23-2022 11:48 AM Taq has not replied
 Message 223 by Kleinman, posted 09-23-2022 5:03 PM Taq has replied

  
Taq
Member
Posts: 10195
Joined: 03-06-2009
Member Rating: 3.2


(2)
Message 219 of 2932 (898398)
09-23-2022 11:53 AM
Reply to: Message 217 by Kleinman
09-23-2022 11:45 AM


Re: Apples and oranges
Kleinman writes:
The mistake you are making in your analysis Taq is that adaptive evolution occurs along lineages.
I'm doing the math, as you requested.
If each base in the human genome has a 1 in 120 million chance of mutation then we would get about 50 mutations in a 6 billion base diploid genome. Agreed?

With that mutation rate, in a population with a steady 100,000 individuals we would see 5 million new mutations in each generation. Agreed?
You are lumping all the mutations that are occurring anywhere in the population. You must get all these beneficial mutations into a single lineage.
Please learn how sexual reproduction works.
You need to answer this question for yourself.
The answer is yes. Now, can you answer the question?
Are the physical differences between chimps and humans due to the sequence differences between their genomes? Yes or no?

This message is a reply to:
 Message 217 by Kleinman, posted 09-23-2022 11:45 AM Kleinman has not replied

  
Taq
Member
Posts: 10195
Joined: 03-06-2009
Member Rating: 3.2


(2)
Message 221 of 2932 (898406)
09-23-2022 12:52 PM
Reply to: Message 220 by AZPaul3
09-23-2022 12:09 PM


Re: Apples and oranges
AZPaul3 writes:
We have shown you don't comprehend the subject or the math that you are so enamoured with.
People who comprehend the subject would be able to parse this statement from the Lenski paper Kleinman so often cites:
"When large asexual populations adapt, competition between simultaneously segregating mutations slows the rate of adaptation and restricts the set of mutations that eventually fix."
The word "asexual" means something here. Kleinman just can't seem to understand why that word is so important to understanding the rest of the paper.
"You are lumping all the mutations that are occurring anywhere in the population. You must get all these beneficial mutations into a single lineage."--Kleinman
This is Bio 101. If someone can't comprehend how different mutations can come together in a single individual within a sexually reproducing population . . . words fail me. If Kleinman really did understand the concepts in both the Lenski and Kishony paper he would quickly realize why the competition between bacterial lineages could be overcome in a sexually reproducing species. But alas.

This message is a reply to:
 Message 220 by AZPaul3, posted 09-23-2022 12:09 PM AZPaul3 has not replied

  
Taq
Member
Posts: 10195
Joined: 03-06-2009
Member Rating: 3.2


Message 224 of 2932 (898426)
09-23-2022 5:14 PM
Reply to: Message 223 by Kleinman
09-23-2022 5:03 PM


Re: Apples and oranges
Kleinman writes:
Your model is crude and inaccurate. Try and think about what actually happens physically. Start with the founders of your new lineage. A population size of two is appropriate.
That doesn't happen in nature. Speciation events involve populations, not 2 individuals.
Here is the math again.
If each base in the human genome has a 1 in 120 million chance of mutation then we would get about 50 mutations in a 6 billion base diploid genome. Agreed?

With that mutation rate, in a population with a steady 100,000 individuals we would see 5 million new mutations in each generation. Agreed?
Then use your 50 mutations per genome/generation and try to estimate the number of different lineages on different evolutionary trajectories.
Do you still not understand how sexual reproduction works? Lineages reproduce with each other and mix their mutations together.
Then you have to consider how any one of these lineages can accumulate a set of adaptive mutations. Don't factor in recombination yet until you understand this simpler case.
How can we ignore recombination when it happens for every individual in every generation? The reason that mutations are segregated into lineages in the Lenski and Kishony experiments is because the bacteria in those experiments reproduce asexually. That's why their models only apply to asexual populations. They don't apply to sexually reproducing populations.
BTW, I can think of many mutations that have been identified in humans because they all cause disease. I don't know of any mutations that have been identified as beneficial.
Are the physical differences between chimps and humans caused by the sequence differences in their genomes? Yes or no?

This message is a reply to:
 Message 223 by Kleinman, posted 09-23-2022 5:03 PM Kleinman has replied

Replies to this message:
 Message 225 by Kleinman, posted 09-23-2022 5:52 PM Taq has replied

  
Newer Topic | Older Topic
Jump to:


Copyright 2001-2023 by EvC Forum, All Rights Reserved

™ Version 4.2
Innovative software from Qwixotic © 2024