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Author | Topic: Rebuttal To Creationists - "Since We Can't Directly Observe Evolution..." | |||||||||||||||||||||||
Kleinman Member (Idle past 335 days) Posts: 2142 From: United States Joined: |
Kleinman:That's correct, the diversification might also be neutral or detrimental. Kleinman:Experimental evidence shows you are incorrect. The probability of an adaptive mutation depends on the number of replication a particular variant is able to do. That is why the Lenski variants evolve more slowly than the Kishony variants. Lenski energy limits his populations which slows the growth of the individual variant populations. Kishony's colonies easily achieve population sizes of a billion or more. That size population gives a reasonable probability that all possible mutations will occur on some member of that colony when a mutation rate is 1e-9.
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Kleinman Member (Idle past 335 days) Posts: 2142 From: United States Joined: |
Kleinman:It is strange that you would think that physics, math, and experimental evidence are bullshit.
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Kleinman Member (Idle past 335 days) Posts: 2142 From: United States Joined: |
Kleinman:It doesn't take much to explain the physics of Darwinian evolution if you have taken and passed a high school-level physics course. Perhaps you don't understand that it takes energy to replicate?
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Kleinman Member (Idle past 335 days) Posts: 2142 From: United States Joined: |
Kleinman:OK, let's start with the math of competition. Haldane's model in his "cost of natural selection" paper is a good starting point. You can find that paper here: JSTOR: Access Check Note that Haldane's model has been proven to be a conservation of energy process. You have to modify his model for the particular case. For example, Lenski's experiment includes bottlenecking so you have to modify Haldane model as shown here: Fixation and Adaptation in the Lenski E. coli Long Term Evolution Experiment There are a couple of ways to model adaptation. You can use the "at least one rule from probability theory as shown here in this paper: The basic science and *********** of random mutation and natural selection Or you can use a Markov chain random walk calculation to compute the probability of an adaptive mutation occurring as show here: The Kishony Mega-Plate Experiment, a Markov Process Note that either means of computing the probability of an adaptive mutation occurring gives the same result. Either formulation work for the Lenski or Kishony experiment because they are both single selection pressure experiments. Percy:Populations compete for the energy available in the given environment. That's because it takes energy to survive and replicate. Overcrowding may be a selection condition but in and of itself, it is food (energy) that biological populations compete over. BTW. is m-thematics now a forbidden word?
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Kleinman Member (Idle past 335 days) Posts: 2142 From: United States Joined: |
Percy:Sorry, I do not know how to format the equation in dBCodes, but let's call it equation [3]. Their problem is that they are assuming that biological evolution obeys an exponential (or exponential-like) distribution function. The correct distribution function for biological evolutionary adaptation is the binomial distribution. The random experiment is a replication and the two possible outcomes are does an adaptive mutation occur or does an adaptive mutation not occur. If you go back and read this paper, The basic science and *********** of random mutation and natural selection I show how to derive the probability equation for at least one occurrence of that adaptive mutation occurring as a function of mutation rate and the number of replications. Simply go back to first principles and consider the stochastic system and the correct probability distribution becomes apparent. The advantage of deriving the governing equation by first principles is that you can easily extend the model to multiple simultaneous selection conditions. What you end up having are nested binomial probability problems. I hope this makes sense to you.
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Kleinman Member (Idle past 335 days) Posts: 2142 From: United States Joined: |
Kleinman:Perhaps I should have include this part of the Lenski's Team statement to put it in better context for you. Kleinman:I added the bold face. Lenski's Team doesn't understand why competition slows adaptation. That's why I wrote the following and you incorrectly responed: Kleinman:The Lenski Team knows that competition slows adaptation, they see that in their experiment, they just don't know why. Do you think that the ability to form larger colony size slows adaptation? Do you think that doubling the population size doubles the probability of an adaptive mutation occurring?
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Kleinman Member (Idle past 335 days) Posts: 2142 From: United States Joined: |
Kleinman:You seem to be good at formatting, I'll leave that to you. You do seem to be having some difficulty with physics and math. For example, you seem to think that populations are competing for space. There is plenty of space in the Sahara desert but very little available energy for populations to use (no food). Kleinman:Percy has posted equation (5) from my paper: The basic science and *********** of random mutation and natural selection And wants to know the difference between that equation and equation [3] from the Lenski team paper. Distribution of fixed beneficial mutations and the rate of adaptation in asexual populations Equation [3] from the Lenski Team paper is a probability distribution equation. Equation (5) from my paper is an "at least one" probability calculation. That is, what is the probability of a particular mutation occurring at least once in a particular population as a function of mutation rate and population size. Perhaps you should try to figure out what the random trial is and what the possible outcomes are for that equation [3]. I hope that helps clarify the math to you.
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Kleinman Member (Idle past 335 days) Posts: 2142 From: United States Joined: |
Kleinman:They address this question but fail to answer it. If you think they do, feel free to post a quote from their paper that gives the correct explanation and law of physics that justifies their answer. You won't because they didn't. Kleinman:Don't be silly. I know the difference between modification and adaptation. Not every genetic modification is an adaptation. Kleinman:Feel free to post the quote from their paper that explains why competition slows adaptation. You won't because they didn't explain. The reason is very simple. Less fit variants are consuming resources that the more fit variants could use to increase their population size. The more fit variant must first drive the less fit variants to extinction in order for their population to increase in size and improve the probability of an adaptive mutation occurring. It is a simple first law of thermodynamics process and an "at least one" probability problem. Kleinman:Post Lenski's explanation. Kleinman:Good! Do you think that a series of microevolutionary changes add up to a macroevolutionary change?
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Kleinman Member (Idle past 335 days) Posts: 2142 From: United States Joined: |
Kleinman:Of course you won't post their explanation because they have none. Kleinman:OF course, adaptation does not require fixation. The Kishony experiment clearly demonstrates that. Kleinman:Do you understand that the beneficial mutation that gives the greatest improve in fitness fixes first, the beneficial mutation that gives the second greatest improvement in fitness fixes second and so on. But each adaptation/fixation cycle requires the most fit variant to drive the less fit variants to extinction before the next beneficial mutation will have a reasonable probability of occurring on that variant. It is all about conservation of energy, the first law of thermodynamics, which apparently obfuscates this process for you. Kleinman:You understood that the addition rule of probabilities does not apply to complementary events (doubling population size does not double the probability of an adaptive mutation occurring). Now you need to learn that the addition rule of probabilities does not apply to the joint probability of random events occurring. What rule of probability theory applies to the computation of the joint probability of two or more random events occurring?
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Kleinman Member (Idle past 335 days) Posts: 2142 From: United States Joined: |
Kleinman:It's really not that complicated. You have a population consisting of a variety of different with different reproductive fitness competing for a limited amount of energy (food). The most effective variant able to reproduce will drive all the rest of the less fit variants to extinction over generations. That's how biological competition works. Kleinman:That's probably true. But the carrying capacity of a given environment for bacteria and other microbes will be many orders of magnitude larger than that for say, humans and chimpanzees. Kleinman:It's what the Lenski Team measured in their experiment. The number of generations to fixation has been increasing ever since the beginning of the experiment. This shouldn't be surprising to you. Why would a less fit variant fix before a more fit variant? This is about relative reproductive fitness. Kleinman:Are you one of those that think that mutations aren't random occurrences? If so, tell us on which member of Kishony's or Lenski's population the next adaptive mutation will occur.
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Kleinman Member (Idle past 335 days) Posts: 2142 From: United States Joined: |
Kleinman:Here's how you do the math for a single fixation/adaptation cycle Fixation and Adaptation in the Lenski E. coli Long Term Evolution Experiment Kleinman:How many fixation/adaptation cycles do you think humans and chimpanzees have done? Kleinman:Do you mean "clonal" not "clinal"? Lenski's experiment operates by the most fit variant with the previous beneficial mutation fixes and as that subset accumulates replications over generations, the probability of the next beneficial mutation occurring on one of its members increases. This occurs in a sequential manner. The probability of two or more adaptive mutations occurring in a non-sequential manner requires many orders larger population than Lenski allows for in his experiment. This is due to the multiplication rule of probabilities. Kleinman:Sure I will. This is best demonstrated by the Kishony experiment. Watch this short video. https://www.youtube.com/watch?v=Irnc6w_Gsas&t=5s&ab_chann... Kishony correctly recognizes that each adaptive mutation requires about a billion replications. Each time some variant gets an adaptive mutation, it must form a new colony which must achieve a population size sufficient for there to be a reasonable probability for the next adaptive mutation to occur on one of its members. This is due to the multiplication rule of probabilities. I published the math that predicted the behavior of his experiment years before the experiment was performed. Here is that paper: The basic science and *********** of random mutation and natural selection Equations (12,13) show how you apply the multiplication rule to compute the joint probability for a lineage to accumulate a set of adaptive mutations. I do not take credit for being the first to understand this fundamental principle of biological evolutionary adaptation. Edward Tatum wrote about this in his 1958 Nobel Laureate Lecture. Edward Tatum wrote this: Edward Tatum – Nobel Lecture - NobelPrize.org Edward Tatum:
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Kleinman Member (Idle past 335 days) Posts: 2142 From: United States Joined: |
Kleinman:What principles of aeronautical engineering did the Wright Brothers get wrong? Do you think Darwin got biological evolutionary competition and descent with modification wrong? If so, show your physics and math. Kleinman:At least you have some idea of what a conservation principle is. Now, only if you could figure out how to apply it to Darwinian Evolution.
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Kleinman Member (Idle past 335 days) Posts: 2142 From: United States Joined: |
Kleinman:It doesn't complicate it as much as you think. You can do the math for recombination using a trinomial distribution. If you do the math correctly, you will understand why recombination does not defeat the use of combination therapy for the treatment of HIV. Kleinman:That's what Lenski's experiment shows. Some member of the most fit variant sub-population gets an adaptive mutation and that new variant ultimately drives the now less fit variants to extinction. The probability that the new variant gets another adaptive mutation depends on the number of replications it does. The probability that any particular variant gets two adaptive mutations before fixation in that experiment is very low because of the low population sizes being used. It's the same math as if two selection conditions are used simultaneously. For example, Kishony's experiment doesn't work when he uses two drugs simultaneously. Some member of the population has to get two adaptive mutations before it can grow in the next higher drug-concentration region. In order to have resonable probabilities for that to happen, Kishony would need a much much larger mega-plate. The colony size would have to reach about a trillion. If you are interested, here's a paper that shows how to do the math:
The mathematics of random mutation and natural selection for multiple simultaneous selection pressures and the evolution of antimicrobial drug resistance Kleinman:It works the same empirically with sexually reproducing organisms. Common empirical examples of this are the use of combination herbicides and combination pesticides when dealing with weeds and insects in agriculture, both of which are sexually reproducing organisms. Likewise, HIV does recombination but it does not defeat the use of combination therapy. You should learn how to do the math of random recombination. If you can't figure it out, I'll show you how to do the math. Only in very specific instances will recombination lead to variants with beneficial alleles recombining to give offspring with multiple adaptive alleles. You still have the multiplication rule when considering biological adaptive evolution in sexually reproducing organisms. Kleinman:These equations give the mathematica! reason why it takes a billion replications for each adaptive transition in a single selection pressure evolutionary process. When the probability of success for an adaptive mutation occurring in a single replication is the beneficial mutation rate, you will need a large number of replications to have a reasonable probability of at least one of those events occurring. Here's a simple analogy to help you understand: Consider if for your family to survive that your family needs to win two lotteries. And the probability of winning one lottery is 1 in a million, and the probability of winning the other lottery is 1 in a million. For you to win both lotteries, that probability is 1 in a million times 1 in a million equals 1 in a trillion, a very low probability indeed. But let's say, you win one of those lotteries. And because of this, you are a very wealthy man and you can raise a very large family. And all your descendants start buying tickets to the second lottery. As soon as you have enough descendants, there will be a high probability that one of your descendants wins that second lottery for your family. The probability of an adaptive mutation occurring on some variant in a population depends on the number of replications that variant does and the mutation rate, nothing else. There are lots of factors that affect that variant from doing the necessary number of replications for the next adaptive mutation. Competition is one of those factors. It is also possible that a single adaptive mutation does not exist for the given selection conditions. But it all comes down to the fact that the number of replications and the mutation rate determine that probability. And adaptive evolutionary events don't add, they are linked by the multiplication rule as are your chances of winning two lotteries are.
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Kleinman Member (Idle past 335 days) Posts: 2142 From: United States Joined: |
Kleinman:dwise1 thinks that the inventors of powered flight knew nothing about aeronautical engineering. When is dwise1 going to give us his explanation of the physics and math of Darwinian evolution? That really won't fly.
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Kleinman Member (Idle past 335 days) Posts: 2142 From: United States Joined: |
Kleinman:HIV does recombination. If you want, I'll provide you with links to papers where they show this. As for recombination reducing cycles, it doesn't when producing adaptive alleles. What I think you are trying to point out that in some population, you will have one parent with a beneficial allele (call that allele A) at one locus and the other parent having a beneficial allele (call that allele B) at a different locus and when those parents breed, they can produce an offspring with both beneficial alleles A and B. Let's put this into the context of a real situation. One farmer uses a herbicide on his field that selects for allele A and a different farmer uses a different herbicide on a different field that selects for allele B. Both farmers are treating the same weed. So, some of the weeds have allele A, other weeds have allele B, and the remaining weeds have neither allele A nor allele B (call those allele C). What is the probability distribution function that describes this problem and compute the probability that you will get an A parent and a B parent giving an AB offspring as a function of population size, and frequencies of A, B, and C members.
Kleinman:Read this paper by Lenski: https://royalsocietypublishing.org/...10.1098/rspb.2015.2292 Lenski: Kleinman:There are no empirical examples that show that a population evolves more rapidly as they are subject to multiple simultaneous selection pressures. Kleinman:The only numbers you need to use are the mutation rate and population size. The reason why microevolutionary events don't add is they random events. You must compute the joint probability of random events occurring using multiplication, not addition.
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