Understanding through Discussion


Welcome! You are not logged in. [ Login ]
EvC Forum active members: 69 (9101 total)
9 online now:
Newest Member: sensei
Happy Birthday: AlexCaledin
Post Volume: Total: 904,185 Year: 1,066/14,231 Month: 1,066/1,514 Week: 99/234 Day: 32/48 Hour: 2/3


Thread  Details

Email This Thread
Newer Topic | Older Topic
  
Author Topic:   Rebuttal To Creationists - "Since We Can't Directly Observe Evolution..."
Taq
Member
Posts: 9292
Joined: 03-06-2009
Member Rating: 3.2


Message 106 of 2790 (898185)
09-20-2022 11:53 AM
Reply to: Message 94 by Kleinman
09-19-2022 9:30 PM


Re: First
Kleinman writes:
How many beneficial mutations do humans have compared to chimpanzees to account for their population difference?
We can do some back of the envelope calculations. There are about 40 million mutations that separate humans and chimps, so we can split those between the two for 20 million each.
If we go with a high estimate of functional sequence at 10% of the human genome, then that puts us at 2 million mutations in functional sequence. If 10% of those are beneficial, then we are at 200,000 beneficial mutations. This would include indels, both large and small. These numbers exclude genomic arrangements which aren't massive in numbers, but could be important.

This message is a reply to:
 Message 94 by Kleinman, posted 09-19-2022 9:30 PM Kleinman has replied

Replies to this message:
 Message 113 by Kleinman, posted 09-20-2022 12:20 PM Taq has not replied

  
Taq
Member
Posts: 9292
Joined: 03-06-2009
Member Rating: 3.2


Message 108 of 2790 (898187)
09-20-2022 12:01 PM
Reply to: Message 101 by Kleinman
09-20-2022 9:10 AM


Re: Video not available
Kleinman writes:
Try something simpler like applying conservation of energy to the Lenski experiment. What are the energy sources available to the bacteria?
Ultimately, the energy source is the fusion of hydrogen and helium in the Sun. Energetic photons are released by the Sun due to fusion, those energetic particles drive the formation of sugars and higher energy metabolites in plants, and those energy containing molecules (e.g. glucose and citrate) are fed to the bacteria.

This message is a reply to:
 Message 101 by Kleinman, posted 09-20-2022 9:10 AM Kleinman has replied

Replies to this message:
 Message 114 by Kleinman, posted 09-20-2022 12:25 PM Taq has not replied

  
Taq
Member
Posts: 9292
Joined: 03-06-2009
Member Rating: 3.2


Message 109 of 2790 (898188)
09-20-2022 12:04 PM
Reply to: Message 107 by Kleinman
09-20-2022 12:01 PM


Re: Apples and oranges
Kleinman writes:
So you are claiming that there are beneficial mutational differences between humans and chimps.
How else would you explain the physical differences between chimps and humans? If our physical differences are not due to differences in the sequence of our genomes then please tell us what causes those physical differences.
What beneficial mutations give humans the ability to survive and reproduce in the way of life of this species?
They are among the 40 million differences between our genomes.
You assume that humans and chimps come from a common ancestor.
We conclude that humans and chimps share a common ancestor because of mountains of evidence.

This message is a reply to:
 Message 107 by Kleinman, posted 09-20-2022 12:01 PM Kleinman has not replied

  
Taq
Member
Posts: 9292
Joined: 03-06-2009
Member Rating: 3.2


Message 111 of 2790 (898190)
09-20-2022 12:10 PM
Reply to: Message 110 by Kleinman
09-20-2022 12:05 PM


Re: Video not available
Kleinman writes:
I'll give you partial credit for that one. Citrate is also available, and some may argue there is thermal energy available.
‚Äč
Do you believe it takes energy to replicate?
E. coli won't replicate in warm distilled water, or even warm saline.
We all agree that it takes energy to reproduce. What are you on about?

This message is a reply to:
 Message 110 by Kleinman, posted 09-20-2022 12:05 PM Kleinman has replied

Replies to this message:
 Message 115 by Kleinman, posted 09-20-2022 12:30 PM Taq has replied

  
Taq
Member
Posts: 9292
Joined: 03-06-2009
Member Rating: 3.2


(1)
Message 125 of 2790 (898204)
09-20-2022 1:53 PM
Reply to: Message 115 by Kleinman
09-20-2022 12:30 PM


Re: Video not available
Kleinman writes:
Biological evolutionary competition (Darwinian competition) is a conservation of energy (first law of thermodynamics) process.
What physical process isn't?
Is your grand contribution to biology the rather obvious observation that resources are limited? If so, you are a bit late to the game.

This message is a reply to:
 Message 115 by Kleinman, posted 09-20-2022 12:30 PM Kleinman has not replied

  
Taq
Member
Posts: 9292
Joined: 03-06-2009
Member Rating: 3.2


Message 126 of 2790 (898205)
09-20-2022 1:56 PM
Reply to: Message 122 by Kleinman
09-20-2022 1:30 PM


Re: Video not available
Kleinman writes:
You are right, evolution does happen and the mutation rate is not the significant variable in the process.
The mutation rate is significant. Why wouldn't it be?
This is clearly demonstrated by the fact that HIV has a very high mutation rate but still cannot evolve efficiently to 3-drug combination therapy.
What is demonstrated by single drug therapy? Does mutation rate matter?

This message is a reply to:
 Message 122 by Kleinman, posted 09-20-2022 1:30 PM Kleinman has not replied

  
Taq
Member
Posts: 9292
Joined: 03-06-2009
Member Rating: 3.2


Message 127 of 2790 (898206)
09-20-2022 1:58 PM
Reply to: Message 121 by Kleinman
09-20-2022 1:25 PM


Re: Apples and oranges
Kleinman writes:
Do you think that chimps and humans have the same reproductive fitness in the environment where chimps live?
Do you think a polar bear is well adapted to the Arctic? Do you think a polar bear is well adapted to the Sahara desert?

This message is a reply to:
 Message 121 by Kleinman, posted 09-20-2022 1:25 PM Kleinman has replied

Replies to this message:
 Message 129 by Kleinman, posted 09-20-2022 2:44 PM Taq has replied

  
Taq
Member
Posts: 9292
Joined: 03-06-2009
Member Rating: 3.2


Message 132 of 2790 (898211)
09-20-2022 3:08 PM
Reply to: Message 129 by Kleinman
09-20-2022 2:44 PM


Re: Apples and oranges
Kleinman writes:
Didn't you say you could add up microevolution changes to get a macroevolutionary change? I'm asking you what microevolutionary changes occurred to give the reproductive advantage that humans have over chimps.
Compare the human and chimp genomes. Find the differences.
You won't even tell us how many microevolutionary changes have occurred to give the variants that can grow in the high concentration drug region of the Kishony experiment.
Compare the descendants' genomes to the ancestral genomes. Find the differences.
Biological evolutionary modification isn't a first law of thermodynamics process, it is a second law of thermodynamics process. That process is not conservative.
The process of running a refrigerator is a 2LoT process, and yet it moves along just fine. Since there is ample energy available to biology to drive negative entropy it isn't a problem.
Somebody had to explain to Lenski why biological evolutionary competition slows biological evolutionary adaptation. He's limiting his resources. Kishony doesn't limit the resources as much so his populations evolve far more rapidly but it still takes a billion replications for each adaptive mutation. Why don't you show us how the addition rule explains the reason it takes a billion replications for each adaptive mutation?
The error you are making is in assuming every adaptation is as stringent as that seen in either the Lenski or Kishony experiment. There is no reason to think that the number of mutations necessary for an arboreal ape to adapt to a savanna is as few as the number of mutations that can confer antibiotic resistance or aerobic citrate metabolism. Not all adaptations are equal.
What adaptive mutations do humans have in order to survive and reproduce in these environments that chimps don't have?
Compare the human and chimp genomes. Find the differences.

This message is a reply to:
 Message 129 by Kleinman, posted 09-20-2022 2:44 PM Kleinman has replied

Replies to this message:
 Message 133 by Kleinman, posted 09-20-2022 3:23 PM Taq has replied

  
Taq
Member
Posts: 9292
Joined: 03-06-2009
Member Rating: 3.2


Message 134 of 2790 (898213)
09-20-2022 3:40 PM
Reply to: Message 133 by Kleinman
09-20-2022 3:23 PM


Re: Apples and oranges
Kleinman writes:
I'm not the one claiming that humans and chimps arose from a common ancestor.
You don't even have to accept common ancestry in order to stumble on the stupendously obvious answer.
Do you accept that chimps and humans are physically different because the sequence of their genomes are different? If yes, THERE IS YOUR ANSWER.
You still haven't shown how every human alive today has 200,000 beneficial mutations that give the reproductive advantage over chimps.
Are you aware that mutations happen? It's really a thing.
Even more, we have mountains of evidence that the same process that produces mutations in both chimps and humans right now, in the present, is the same process that produced the differences between their genomes through evolution and common ancestry.
Do you understand the difference between transitions and transversions?
Transitions vs transversions
What we observe is that transitions are much more common than transversions due to the fact that transitions occur between bases that are more similar to each other. We can also measure the bias towards transitions in real time. When we compare the rates of transitions and transversions between the human and chimp genomes it is an exact match to the observed rate at which these mutations occur.
Human Genetics Confirms Mutations as the Drivers of Diversity and Evolution – EvoGrad
You have about 100 billion replications, 99% of which have occurred in the last 10,000 years for that kind of genetic transformation. You need a much larger envelope.
The mutation rate is about 50 mutations per person per generation. With a constant population size of 100,000 that would be 5 million mutations per generation. Over 5 million years you would get 200,000 generations with a generation time of 25 years. That would be 1 trillion mutations that happened in the human population with just a population of 100,000 people. We only needed to keep 20 million of those mutations, or 1 out of every 50,000 mutations. I really don't see a problem with that.

This message is a reply to:
 Message 133 by Kleinman, posted 09-20-2022 3:23 PM Kleinman has replied

Replies to this message:
 Message 135 by Kleinman, posted 09-20-2022 4:11 PM Taq has replied

  
Taq
Member
Posts: 9292
Joined: 03-06-2009
Member Rating: 3.2


Message 136 of 2790 (898215)
09-20-2022 4:35 PM
Reply to: Message 135 by Kleinman
09-20-2022 4:11 PM


Re: Apples and oranges
Kleinman writes:
Do you understand that mutations are random events? And that accumulation of beneficial mutations on a lineage is a Markov process where the joint probability of beneficial mutations occurring is governed by the multiplication rule of probabilities.
Yes, I understand it just fine.
Where is the problem?
That's why your back-of-the-envelope calculation of humans having 200,000 beneficial mutations is wrong. You are using a simple neutral evolution calculation and assuming that 10% of the mutations are beneficial based on rank speculation.
Wrong on both accounts. I never assumed that all mutations are neutral nor did I claim that 10% of all mutations are beneficial. First, I said that only 10% of fixed mutations would occur in functional DNA which means only 10% of fixed mutations would have a chance of being beneficial (assuming de novo gene production is rare). Of those fixed mutations I said maybe 10% are beneficial as just a guess. 10% of 10% would be 1% of all fixed mutations could be beneficial. Again, I stress the word fixed.
I am not saying that 10% of even 1% of all mutations are beneficial. We are talking about the fixed mutations. And wouldn't you know it, beneficial mutations have a much higher chance of reaching fixation than neutral ones on a one-to-one basis. If you want, we could say that 0.1% or even 0.0001% of fixed mutations between humans and chimps are beneficial in humans, if you want.
You are also edging closer to the Sharpshooter fallacy where you assume that the genomes we get at the end were the only possible outcome. What you ignore is the many different paths that could have been taken. Epistasis is also a very real thing. Interaction between mutations can have a profound effect on what paths evolution can and does take. A seemingly neutral mutation can actually influence the fitness impact of future mutations, making a future mutation either beneficial or detrimental where it would have been neutral without the preceding mutation. There is more than one road that leads to Rome.
Why don't you learn how the Kishony and Lenski experiments work?
I already know how they work.

This message is a reply to:
 Message 135 by Kleinman, posted 09-20-2022 4:11 PM Kleinman has replied

Replies to this message:
 Message 137 by Kleinman, posted 09-20-2022 4:44 PM Taq has replied

  
Taq
Member
Posts: 9292
Joined: 03-06-2009
Member Rating: 3.2


Message 138 of 2790 (898217)
09-20-2022 4:55 PM
Reply to: Message 137 by Kleinman
09-20-2022 4:44 PM


Re: Apples and oranges
Kleinman writes:
Why does it take a billion replications in each of their lineages to accumulate each of their beneficial mutations?
Because of the stringency of the fitness landscape. There are only 1 or a few mutations that will allow adaptation to the new conditions. In the Lenski experiment it required a very rare recombination event to evolve aerobic citrate metabolism. In the case of antibiotic resistance there can be as few as 1 mutation that confers resistance. Some adaptations are just harder to come by than others.
On top of that, bacteria are asexual. A lack of recombination in each generation limits the mixing of different mutations and different alleles.

This message is a reply to:
 Message 137 by Kleinman, posted 09-20-2022 4:44 PM Kleinman has replied

Replies to this message:
 Message 139 by Kleinman, posted 09-20-2022 5:08 PM Taq has replied

  
Taq
Member
Posts: 9292
Joined: 03-06-2009
Member Rating: 3.2


(2)
Message 140 of 2790 (898219)
09-20-2022 5:17 PM
Reply to: Message 139 by Kleinman
09-20-2022 5:08 PM


Re: Apples and oranges
Why don't you tell Lenski and Kishony how to make their experiments perform more rapidly?
I don't see why the speed of the experiment matters.
Why doesn't recombination defeat combination therapy for the treatment of HIV?
It does.
quote:
Human immunodeficiency virus (HIV) is a diploid virus: each virion carries two complete RNA genomic strands. Homologous recombination can occur when a cell is coinfected with two different but related strains. Naturally occurring recombinant HIV strains have been found in infected patients in regions of the world where multiple genotypic variants cocirculate. One recombinant HIV strain has spread rapidly to millions of persons in Southeast Asia. Recombination is a mechanism whereby high level and multidrug-resistant strains may be generated in individual treated patients. Recombination also poses theoretical problems for the development of a safe HIV vaccine. Certain features of HIV replication, such as syncytium formation and transactivation, may be best understood as components of a sexual reproductive cycle. Recombination may be an important HIV evolutionary strategy.
Recombination in HIV: an important viral evolutionary strategy. - PMC
Why don't you tell us the mathematics which describes random recombination if you can? I'll even give you a hint. You do that math using the trinomial distribution.
Mathematics is meaningless unless you understand the process you are applying it to. From what I can see, you simply don't understand how evolution or biology works.

This message is a reply to:
 Message 139 by Kleinman, posted 09-20-2022 5:08 PM Kleinman has replied

Replies to this message:
 Message 141 by Kleinman, posted 09-20-2022 5:38 PM Taq has replied

  
Taq
Member
Posts: 9292
Joined: 03-06-2009
Member Rating: 3.2


Message 142 of 2790 (898222)
09-20-2022 5:48 PM
Reply to: Message 141 by Kleinman
09-20-2022 5:38 PM


Re: Apples and oranges
Kleinman writes:
You are claiming that the stringent standards of the experiment are what is causing it to take a billion replications for each beneficial mutation.
I am claiming that the beneficial mutations for the adaptation they are studying are rare. That is the stringency I am talking about.
For the Lenski experiment, they had no idea how long it would take which was part of the experiment. It could have taken just a few days, but it didn't. In the case of the Kishony experiment they would have known the rate of adaptation for the conditions they put the bacteria under so that they could get the results they wanted within the experimental design. The same can be said for classical experiments like the Luria-Delbruck fluctuation experiment and the Lederbergs' plate replica experiment.
3 drug combination therapy for the treatment of HIV works successfully despite the fact that the virus does recombination. If you understood the mathematics of random recombination, you would know why.
What does that have to do with human evolution?
To use an analogy, you are pretending that the odds of winning the lottery can be applied to flipping a coin.

This message is a reply to:
 Message 141 by Kleinman, posted 09-20-2022 5:38 PM Kleinman has replied

Replies to this message:
 Message 143 by Kleinman, posted 09-20-2022 6:58 PM Taq has replied

  
Taq
Member
Posts: 9292
Joined: 03-06-2009
Member Rating: 3.2


Message 150 of 2790 (898236)
09-21-2022 10:55 AM
Reply to: Message 143 by Kleinman
09-20-2022 6:58 PM


Re: Apples and oranges
Kleinman writes:
What Lenski found is that it took billions of replications for each beneficial mutation to occur on his most fit lineage and Kishony found that it requires a colony size of a billion for a beneficial mutation to occur. This should not have been a surprise since beneficial (and all) mutations occur at a frequency of about 1/(mutation rate) replications.
You are again assuming all adaptations are the same. They aren't. Let's take a look at a classic paper, the Lederbergs' plate replica paper:
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
That's a thousand fold difference between beneficial mutation rates for different adaptations.
The mathematics of random recombination works the same for all replicators.
The mathematics are different for each species and each fitness landscape. That's what you can't seem to understand. For some adaptations there might only be a handful of beneficial mutations possible. For a different adaptation there may be thousands of possible beneficial mutations.
Added in edit: How many possible evolutionary pathways are there for an arboreal ape to adapt to an open savanna? I would think there are many, many, many possible pathways. Wouldn't you agree?
The difference is that coin tossing is symmetric with a probability of 0.5 for each outcome.
So it would be incorrect to say that the mathematics for calculating a winning lottery ticket does not apply to the odds of flipping heads?
This same thing applies to different adaptations.

Edited by Taq, .


This message is a reply to:
 Message 143 by Kleinman, posted 09-20-2022 6:58 PM Kleinman has replied

Replies to this message:
 Message 156 by Kleinman, posted 09-21-2022 1:21 PM Taq has replied

  
Taq
Member
Posts: 9292
Joined: 03-06-2009
Member Rating: 3.2


Message 163 of 2790 (898276)
09-21-2022 6:11 PM
Reply to: Message 156 by Kleinman
09-21-2022 1:21 PM


Re: Apples and oranges
Kleinman writes:
Not at all, but use whatever reference you want and give us the correct mathematical explanation for the Kishony and Lenski experiments.
What does the Kishony and Lenski experiments have to do with the evolution of an arboreal ape into the the human species we see today?

This message is a reply to:
 Message 156 by Kleinman, posted 09-21-2022 1:21 PM Kleinman has replied

Replies to this message:
 Message 164 by Kleinman, posted 09-21-2022 6:20 PM Taq has replied

  
Newer Topic | Older Topic
Jump to:


Copyright 2001-2022 by EvC Forum, All Rights Reserved

™ Version 4.1
Innovative software from Qwixotic © 2023