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

Then why did you say this?"Taq doesn't understand that a phage is not an example of descent with modification. His Lederberg example is not an example of descent with modification."--KleinmanHow is the mutation of E. coli genes resulting in phage resistance not an example of a random walk finding phage resistance in a process that can be modelled by a Markov chain?Like I said, descent with modification is whatever you want it to be at any given moment. Not in any meaningful way with respect to thermodynamics.

It's not inserting into the genome. Phage resistance occurs through mutations of E. coli genes, just like with antibiotic resistance. On top of that, insertion of phage DNA is also a mutation and fits in just fine with descent with modification and Markov processes.Again, you define descent with modification differently at different places.

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Here, we demonstrate that the strictly lytic Escherichia phage vB_EcoM-P10 rapidly selected for resistance in the APEC ST95 O1 strain AM621. Whole-genome sequence analysis of 109 spontaneous phage-resistant mutant strains revealed 41 mutants with single-nucleotide polymorphisms (SNPs) in their core genome. In 32 of these, a single SNP was detected while two SNPs were identified in a total of nine strains. In total, 34 unique SNPs were detected. In 42 strains, including 18 strains with SNP(s), gene losses spanning 17 different genes were detected.
Frontiers | Spontaneous Phage Resistance in Avian Pathogenic Escherichia coli

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That is a category error. All bears are mammals. Cows are mammals. Cows are not bears.Just because you consider something disordered does not make it relevant to thermodynamics. The Jukes-Cantor model is not thermodynamics. People use the term "entropy" outside of thermodynamics. One common example is the use of entropy in information theory, which is not thermodynamics.

". . . never attribute to malice that which is adequately explained by stupidity."--Robert J. HanlonKleinman lecturing the rest of us on how we don't understand thermodynamics only increases the force of the facepalm.The semantics get even worse with "descent with modification".Mutations (SNPs, indels) leading to antibiotic resistance = descent with modificationMutations (SNPs, indels) leading to phage resistance != descent with modification

I think it is descent with modification. Show how it is relevant to thermodynamics. No, it isn't. Just because some Markov processes are relevant to thermodynamics does not make all Markov processes relevant to thermodynamics.You have much to learn.

Apparently, we know a lot more than you do because you can't address anything we have posted.You can't even understand how the evolution of phage resistance is descent with modification.

So you are saying that descent with modification in the Lenski and Kishony experiments is proof of UCD? No, you didn't. You simply asserted it. You have no evidence, and zero understanding of how thermodynamics works. Entropy is not a thermodynamic variable when it is used in information theory, as explained already. Those are analogous processes, not homologous.

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What this empirical example demonstrates is that the sequence of mutations must occur in an order ofever increasing fitness in order for the evolutionary process to have a reasonable chance of occurring.

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That is not true for sexual populations. In sexual populations, beneficial alleles fix independently and are moved from separate genetic backgrounds into the same genetic background. Of course, you will never address this.

It's up to you to demonstrate that the Kishony and Lenski experiments prove UCD. That has nothing to do with thermodynamics. You still can't address anything I post.

The very same way that you think the Lenski and Kishony experiment, drug resistance, and cancer drug resistance prove UCD. Category error. Bears are mammals, but not all mammals are bears. Markov processes can relate to thermodynamics in some systems, but not others. Entropy is about the energy available for work in a system, and you aren't addressing that at all.Let's say we start with a handful of DNA molecules of about 3 kbp, some primers specific to the 5' and 3' ends of the DNA molecules, free nucleotides, buffers/salts, and a polymerase. We cycle the temperature up and down between 60 and 95 C about 40 times. What we end up with is far fewer free nucleotides and a whole bunch of 3 kbp DNA molecules.Has entropy gone up or down? How do you measure it? How do the sequences factor in to your calculation?

And you still won't address it.

So you are saying that the Kishony and Lenski experiments support UCD using your own criteria. This is how antibiotic resistance evolves in sexual populations, and you won't address it. The multiple mutations conferring CM resistance independently move towards fixation and are moved into the same genetic background in the sexually reproducing populations.You try to deflect from these findings by talking about constant environments, as if that addresses anything in these experiments or your misapplication of math from asexual populations to sexual populations.Yes, I did. You ignore it every time. For example, I have discussed this paper: Sexual recombination and increased mutation rate expedite evolution of Escherichia coli in varied fitness landscapesYou just flat out refused to discuss it.

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Theoretical impacts of mutation rate and sexual recombination on population structures. a Mutationally limited fitness landscape, where most mutations fix in a single sweep with very little inter-clonal competition. b Increased mutation rate over (a), more competition and faster evolution observed, but some mutations are lost due to inter-clonal competition. c Adding sexual recombination to (a), due to few available beneficial mutations, no strong influence on evolution is observed. d Both sexual recombination and increase in mutation rate from (a), more rapid evolution is observed and fewer beneficial mutations are lost due to clonal interference

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Fitness improvements during ALE. Black: asexual ara− populations. Blue: asexual ara+ populations. Turquoise: genderless ara− populations. Magenta: genderless ara+ populations. a Chloramphenicol resistance vs. generations in G9+CM evolution. b Trimethoprim resistance vs. generations in G9+TM evolution. c Growth rate vs. generations in G9 evolution. The dotted line in a and b represent the chosen threshold antibiotic resistance level

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And you are saying that they prove UCD. This is exactly how you are treating my explanation of the Lederberg experiment. False. And yet we see large swaths of non-random sequence. Your claims don't comport with reality.

Then why don't you use Mendel's math in your calculations. You have failed to do so in every experiment that uses sexual reproduction.

You are the one saying that the Lenski and Kishony experiments prove UCD. Don't look at me. Now you are saying that 3 drug combination therapy and combination selection pressure in weeds proves UCD.

I'm not confused. You are claiming that the Lenski and Kishony experiment are proof of UCD in the very same way you are saying that I am trying to prove UCD with the Lederberg experiment. Now you are saying that we shouldn't use 3 drug treatment programs with HIV. Why?