Additionally, of the 12 parallel evolution paths, the e coli changed in 3 different ways, in the most numerous case the bacteria optimized their glucose uptake speed at the expense of making an acetate waste product, in the second the e coli split into effectively 2 symbiotic subspecies one of which optimized glucose uptake and the other acetate uptake, in the last single case the bacteria optimized for glucose uptake and then acquire the ability to metabolize citrate which was in the solution to supply minerals. This reinforces @T_aquaticus’ point that random mutation rather than a latent ability of the cell caused the change. A second reinforcement is that the last change required two mutations one of which occurred but had no effect until the second happened.
AP Biology is apparently for high school seniors. Since I took general science in 9th grade, biology in 10th grade, chemistry in 11th grade, and this course description states a prerequisite of chemistry, it is safe to say we are not talking freshmen here, nor teachers without biology credentials of some kind: Classes / Homework - Reseda Charter High School
Your problem there is that The College Board writes the curriculum for the class and administers the test for college credit. Neither Discovery nor local politicians can change that fact. Barking up the wrong tree.
I said that observations are consistent with random mutations, including the observation of ongoing mutagenesis in living populations. The pattern of differences between species is also consistent with random mutations, as shown by @glipsnort wonderful essay here on BioLogos:
https://biologos.org/blogs/guest/testing-common-ancestry-its-all-about-the-mutations
Transitions outnumber transversions, and CpG mutations outnumber all other types of mutations. This is what we see in ongoing mutations in the human population. This is also what we see when we compare genomes between divergent species. This is the evidence that the differences between species is due to random mutations.
Also, the reason for the bias towards transitions and CpG mutations comes down to basic chemistry. It doesn’t have anything to do with transition or CpG mutations being more beneficial. That is why mutations are considered to be random with respect to fitness because the benefice of any specific mutation does not affect how often it occurs.
It’s also worth pointing out that there’s no principle that all mutations have to be random, and in fact some of them aren’t. The CRISPR system in bacteria involves bacteria cutting up DNA from invading viruses and incorporating it into their own genomes, where it can serve as a template for recognizing and destroying the same virus in the future. That’s not really random, but we can identify the mechanism by which the mutation occurs. The bulk of mutations, though, show no sign of being anything other than random.
groovimus:Where is it shown that the mutations generating that system were themselves random
A specific question regarding a ‘repair system’ that undoes presumably degrading random mutations. A repair system that does not undo all mutations, somehow has the information necessary to allow beneficial mutations to remain. My specific question is this: where is it proven that such a system was built up by truly random mutations? I don’t need an extrapolation that says [in general] observations are consistent with random mutations because I am wanting specific proof that a system which can discriminate between various mutations and weed out the harmful ones, is not some some sort of information processor that can discriminate between random mutations and J. Cairnes’ “directed mutations” based on his research. In other words I was asking for a specific proof of the advent of this information processing system as a result of “truly random” mutations that somehow ‘knew’ (possessed information) to ignore the home stretch of mutations that built itself? Where is that specific proof?
This is the evidence that the differences between species is due to random mutations.
Apparently this evidence is not on par with what is considered irrefutable proof. The paper I linked above by Barry Hall analysing the work of Cairnes states: In 1988, John Cairns and his collaborators took the first step toward fulfilling that prediction when they showed that some spontaneous mutations are very non-random in that they occur as specific responses to selection pressures (Cairns, Overbaugh & Miller, 1988). They pointed out that the existence of adaptive mutations had not been adequately tested, and they provided some evidence for the occurrence of such mutations in the lacZ gene of E. coli (Cairns, Overbaugh & Miller, 1988). D The link again: Adaptive mutagenesis: a process that generates almost exclusively beneficial mutations | SpringerLink
Hall has not appeared to refute Cairnes over the years; actually his work somewhat is supportive. Another interesting passage from the same paper: Cairns’ most controversial conclusion was that mutations appear to be directed by selective pressures (Cairns, Overbaugh & Miller, 1988). When we say that adaptive mutations are specific to the selection pressure, we mean that the selective conditions are not generally mutagenic and that mutations accumulate only in the genes that are under selection, but not in other genes that are not under selection.
There are plenty of other workers saying things that are not in line with your answer. James Shapiro for one: In combination, cytogenetics and molecular genetics have taught us about many processes that lead to biological novelties “independently of natural selection” — hybridization, genome duplication, symbiogenesis, chromosome restructuring, horizontal DNA transfer, mobile genetic elements, epigenetic switches, and natural genetic engineering (the ability of all cells to cut, splice, copy, and modify their DNA in non-random ways). As previous blogs document and as future blogs will discuss, the genome sequence record tells us that these processes have accompanied rapid changes in all kinds of organisms. We know that many of them are activated by stress under extraordinary circumstances. link: Does Natural Selection Really Explain What Makes Evolution Succeed? | HuffPost Impact
Got that? and modify their DNA in non-random ways. - independently of natural selection Please don’t ridicule that it was said in a popular forum. He is a microbiologist at a world class university, stating his position. And I know that he does not verbally support ID. Everyone knows that his publishing career would be finished in the life sciences if he did.
What I asked for is something that is probably outside the the realm of science which is to prove that the only kind of mutations allowable are only stochastic in nature. How would that be proven beyond any reasonable doubt? With a massive preponderance of evidence?
Can we review some basic points before you get too upset with one of the other participants here:
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At BioLogos, there are many, many supporters who believe that things that appear random are not random in God’s view. So when you get on the “down with randomness” bandwagon, please be careful where you step, because my big feet will probably be on the wagon with you.
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In any sophisticated cell system, “Mutation Repair” operates within the parameters allowed by the cell’s DNA. So, ironically, mutation repair systems evolve, like any other part of a cell’s DNA.
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What is interesting is that there must be natural limits to “Mutation Repair”, right? How do we know?: because mutations continue to occur in branches of life all over the planet.
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This may well be a natural result of evolution. How so? Life forms that developed overly perfect systems of DNA replication would be expected to have less variety in their population genetics. So when there is a broad threat to the population (a new predator, the extinction of a plant or animal species that provides the food for the population, etc.) the one thing that enables the population to survive the stress of the new circumstances is to have a handful (or a few handfuls) of species members that are different enough from the rest of the population (in the correct way), they become the winners of the future generations of reproduction.
In other words, species that too perfectly replicated their genes, all things being equal, were more likely to become extinct - - leaving species to prosper that were only moderately able to accurately replicate their genes.
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So having a Mutation Repair system that repairs most mutations is probably a good compromise.
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You seem to be pretty impressed with this sentence:
"In 1988, John Cairns and his collaborators took the first step toward fulfilling that prediction when they showed that some spontaneous mutations are very non-random in that they occur as specific responses to selection pressures (Cairns, Overbaugh & Miller, 1988). "
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Okay… let’s review:
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Lots of BioLogos supporters believe, like I do, that God specifically arranged every significant mutation experienced by Humans. You can’t get any less non-random than that. And if God controls the environment too… well, that’s just a grand slam!
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Mutations that are controlled by specific non-random epi-genetic factors triggered by the environment can only be important if you think that God is also arranging the environmental conditions, right? Otherwise, you’d have to claim the environment was the Intelligent Designer, rather than God, yes?
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When evolutionary scientists routinely find stunning examples of evolutionary convergence…
… one might read them describing how the environment shapes evolution in rather predictable (i.e. non-random) ways! While epi-genetic factors haven’t received as much press as they should, it doesn’t really trouble scientists if:
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the population’s gene pool changes in unpredictable ways via mutation… or
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a population’s appearance and function responds generally to consistent environmental conditions that are found in various parts of the earth, with various populations that are not related to each other… or
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the population’s gene pool changes in predictable ways because of the evolution of a feedback system that accelerates the population’s coping with environmental changes.
In fact, I think the scientists are generally impressed that such systems have become a recognized part of life’s “tool kit” to survive change!
Terrific summary. Very practical. Thanks.
What the heck is that kind of comeback all about? Exactly who on here has pled the case of serious discussion to the exclusion of disrespect and ridicule and emotional perturbation?
“down with randomness” bandwagon
That does not include yours truly. I don’t know why I have to repeat myself but here goes: back at my post #66 what I asked for is the PROOF for the EXCLUSIVITY of random mutations, and as such a falsification of Caines, Hall, Shapiro and others. This would be the general case. If this proof is beyond empirical science, so be it. That would be a weakness of Darwinian theory, and according to you guys should be inadmissible in a high school classroom discussion because it would be in line with the “strengths and weaknesses” principle of education that got passed in the Louisiana, Tennessee, Kansas, and Texas legislatures with the guidance of DI.
The special case would be as first stated in the first post by yours truly: for a mutation to happen as part of a mutation sequence to generate novel form or function AND be random, it would be statistically independent of all others in the sequence. To be independent, it would be empirically shown to happen with invariant probability regardless of whether any, or preferably all other of the mutations had happened and regardless of the order in which they occurred.
OK you guys have not provided the empirical evidence strictly proving what was asked for. I appreciate the effort going into some long posts like the one I reply to here and the one by Jay describing the calendar/textbook issue. However, the issue is not whether evolution happened. Or whether textbooks will discuss the weaknesses. The issue is whether the core RM/NS principle is exclusive. And I haven’t seen any links on here that point to the proof. And the side issue is whether teachers could be fired for printing out this thread and showing their students that you guys can’t provide the proof on a level with, say, the inverse square law of point charge forces. Assuming you are all life sciences professionals as a didactic condition. In the 4 states mentioned the teachers are protected from such, and as such the legislation was a big win for academic freedom for the teacher, who might also plant the seed that the RM/NS principle is unfalsifiable and because of such so is the entire Darwinian edifice. Then the students may encounter Karl Popper in college and what he had to say regarding that.
Isn’t that just the fundamental difference between theories and laws? You can’t prove any theory with the level of proof of a law because they are two very different concepts in science. Laws describe observed realities via math and physical constants. Theories compile multiple well-established hypotheses into models that have explanatory and predictive power. They can’t be “proven,” they can only be supported or challenged by empirical evidence.
Empirical evidence is what I’m looking for and I have not seen links to that evidence specifically asked for. OK ignore that reference to the point charges, obviously what I ask for would require gargantuan statistical studies.
Proof in general is beyond empirical science. Scientists think in terms of the weight of the evidence and the degree of support for a conclusion, not proof. So you’re starting off on the wrong foot.
Genuine discussion of genuine strengths and weaknesses of any scientific theory should not be inadmissible in high school classrooms. Given the long history of specious attacks on evolution, however, caution is a good idea about any particular claims of its weakness.
That’s a really strange argument. Why should randomness of mutations have anything to do with their statistical independence? Randomness here is a statement about their effect on fitness, which is an orthogonal to statistical dependence. A mutation that damages a particular DNA repair mechanism is not statistically independent of later mutations, for example, but all of the mutations can still be random with respect to fitness.
Why is that the issue? As I noted earlier, I think it’s reasonable to conclude that not all mutations are random. The adaptive mutations you’re talking about may be random (in the biological sense) or not – I think currently the balance of the evidence suggests they are random (e.g. here), but it’s far from certain – but what difference does it make to the dominant role that random mutations have in generating genetic variation?
And this is why this argument is hard to take seriously. Jumping from “a small subset of mutations under very specific conditions may not be random” to “the role of random mutations is unfalsifiable” has no basis at all in logic. The randomness of most mutations can be falsified by showing that they’re not random, something you’re claiming can be done for these mutations.
You mean when Popper said this? “The theory of natural selection may be so formulated that it is far from tautological. In this case it is not only testable, but it turns out to be not strictly universally true. There seem to be exceptions, as with so many biological theories; and considering the random character of the variations on which natural selection operates, the occurrence of exceptions is not surprising.”
Instead of huffing and puffing and stomping on a religious site, why don’t you visit the Pandas Thumb blog? They will have plenty of answers for you.
Why should randomness of mutations have anything to do with their statistical independence? Randomness here is a statement about their effect on fitness, which is an orthogonal to statistical dependence.
If you’re going to put all of the creative power of random mutations on the “random” part, you might want to give a nod to the people in the hard sciences and statistics that random means random, i.e. the outcome of a strictly stochastic process. What is strange about stochastic processes? I don’t come on here telling you guys your ideas are strange.
groovimus: The issue is whether the core RM/NS principle is exclusive.
glip: Why is that the issue? …what difference does it make to the dominant role that random mutations have in generating genetic variation
because the Darwinian canon allows only for stochastic processes as ‘creative’ seed. It makes no allowance for deterministic ones. It seems almost unbelievable that I have to point this out.
And this is why this argument is hard to take seriously. …“the role of random mutations is unfalsifiable” has no basis at all in logic.
Let me clarify with logic that you will certainly label illogical. The way I should have worded it is ‘the absolutely exclusionary role of random mutations is unfalsifiable’. You are going to have to admit that that Darwinian theory is and always has excluded any deterministic causal nexus to the mutations addressed in the theory. You could go around this logical blockade by just keeping on this road of oblique accusation of illogic. I don’t come on here telling you guys you make illogical arguments.
You mean when Popper said this
Again lack of clarity as no clear designation of “that” when as the use of “that” by yours truly was in reference to unfalsifiability generally. People get in a hurry sometimes.
So if you folks admit to deterministic mutations, explain to me how that is allowable in the larger framework of Darwinian theory. Jerry Coyne and the other famous materialists like Dawkins and Myers, have to my knowledge not discussed this, nor dualist Darwin apologists like Ken Miller whose book “Finding Darwin’s God” I read cover to cover. I don’t remember any deterministically caused mutations discussed in that book.
I haven’t been following this thread too much, but this phrase is quite bizarre. Why would you write this phrase at all?
What do you propose a deterministic cause (or deterministic mutations) might look like in a scientific experiment? Who does the ‘determining?’ How does the ‘determiner’ interact with the genome? Will you be the first to actually specify what mechanism the intelligent designer used to sneak in gene duplication events or even whole genome duplications? I look forward to your publication and personally suggest looking to publish in Nature Nanotechnology.
Irrelevant tangent. I assume you intend to attack the concept of random mutations in evolutionary biology. if so, the fact that physicists mean something somewhat different by “random” has no bearing on the subject. What does statistical independence have to do with the concept of random mutations that is actually held by evolutionary biologists?
(Note: there’s also no requirement in the physical sciences that random events be statistically independent, so your argument doesn’t work even in that context.)
What “Darwinian canon”? Strict Darwinism is known to be wrong in all sorts of ways; evolutionary biologists have no qualms about adopting non-Darwinian mechanisms into evolutionary biology. So no, you didn’t answer my question.
Well, maybe, but so what? If that’s true of Darwinian theory and some mutations are deterministic (although you haven’t actually demonstrated that any are), then Darwinian theory will be wrong in those cases. Just as it has been wrong in other cases.
Since I quoted Popper explicitly stating that Darwinian evolution is falsifiable, the quotation still seems apropos.
Let’s assume the CRISPR case I gave earlier qualifies as “deterministic” as you mean it here. A bacterium is invaded by a virus, deterministically incorporates some viral DNA into its genome, and is now able to recognize viruses in the future. Because the mutation is deterministic, it does not contribute to Darwinian evolution. Okay. . . so what? All of the other mutations that are also occurring in this bacterium and its offspring are random (in the biological sense) and are appropriately described by Darwinian evolution.
Where’s the problem?
There is something amiss with your request. You want pro-Theist evolutionists to prove to you that Evolution is random… and yet most of us (or certainly a great many of us) don’t think Evolution is random.
Why do you keep arguing as if these boards are full of atheists?
He wants us to act like Atheists… and then fail to prove that Atheists are correct. It’s all kind of weird, ain’t it?
I haven’t been following this thread too much, but this phrase is quite bizarre. Why would you write this phrase at all?
I don’t come on here and tell you guys your phrasing is bizarre. You know very well that there are people like Jerry Coyne and Richard Dawkins who live by a Darwinian canon. It is their creation story. There is nothing wrong with describing an overarching series of stories that validate a worldview as I just did. Inserting the word “bizarre” in this discussion is superfluous. Maybe you guys don’t see the Darwinian story as part of a materialist canon but it sure is treated as such in academia and by many in the media. I’m not understanding the deprecating language.
What do you propose a deterministic cause (or deterministic mutations) might look like in a scientific experiment?
I haven’t been following this thread too much,
Right because I have introduced quotes from three scientists that maybe you didn’t see, and they all three have proposed “directed mutation” as coined by Cairnes. I would think it would be fair to use the systems theory and mathematical terminology ‘deterministic’ to apply. I am not going to propose anything but except maybe you guys read their papers. Why should I propose the experiments when they have already been done and are being done by Shapiro and others?
(Note: there’s also no requirement in the physical sciences that random events be statistically independent, so your argument doesn’t work even in that context.)
Yes you are right and this is quantified by cross-correlation. However it is quite obvious that my argument works because of the vehement opposition to Shapiro, Cairnes, and Hall based on their allowance for a deterministic nexus in the generation of mutations. If I use the term ‘strictly random’ to mean ‘with no deterministic causal nexus’, then it would be fair to say that this is all the Darwinian canon allows for as is taught in the schools. Maybe there are plenty of workers in the neo-Darwinian camp who openly or not so openly support the three researchers I mention, but Coyne, Myers, and Dawkins seem not to be among them.
If that’s true of Darwinian theory and some mutations are deterministic (although you haven’t actually demonstrated that any are),
Again why me? I have provided 3 researchers words right here and a couple of links to their narratives.
Since I quoted Popper explicitly stating that Darwinian evolution is falsifiable, the quotation still seems apropos.
OK but that’s his opinion. I did not introduce his opinion on Darwinian or neo-Darwinian theory. I introduced him for what hs is famous for and he is not famous for his opinion on evolution.
A bacterium is invaded by a virus, deterministically incorporates some viral DNA into its genome… Where’s the problem?
ID has no problem with this obviously. But some strictly hard core neo-Darwinian workers would maintain that the mechanism for incorporating viral DNA into the genome was itself generated over a long sequence of strictly random mutations (as I used the term above). But I’m speculating as I haven’t actually seen this argument, but would bet on it being said.