Message 361 of 393 (792886) 10-14-2016 6:28 PM

Reply to: Message 360 by Kleinman 10-14-2016 6:17 PM

See post #275.

Where "somehow" involves (a) a mathematical proof (b) common sense (c) a computer simulation (d) empirical evidence.

So if you have some math, involving "nested binomial probability problems" or otherwise, that shows different, now would be a great time to present it.

Message 362 of 393 (792887) 10-14-2016 6:28 PM

Reply to: Message 353 by Dr Adequate 10-14-2016 5:18 PM

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You think starvation is a soft selection pressure?

That depends crucially on whether it's hard or soft.

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All adaption by rmns requires lineages to address nested binomial probability problems.

Well, perhaps you could show us some math.

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And why do you keep ignoring my question whether the intensity of selection alters the evolutionary trajectory to adaptation?

Where did you ask me that?

The answer is obviously yes.

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If the same selection pressure is applied at low intensity, does it require different mutations for adaptation than if the selection pressure occurs at high intensity?

It may.

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Message 363 of 393 (792888) 10-14-2016 6:31 PM

Reply to: Message 355 by Kleinman 10-14-2016 5:33 PM

As I already said

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If the experiments were MORE lethal, then they couldn't be easily compared, we'd need to know population size per generation before being able to estimate

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Basically I don't know because you haven't provided any numbers. Intuitively, if the conditions result in a low maximum population size it is likely to take more generations to find solutions.

However, as I said, if you reduce the starvation as you increase the thermal stress to retain an equilibrium in population size such that it remains comparable in both experiments, then we might expect it would simply take twice as long, counted in generations. This is a simplification, of course, to point out we don't need to worry about the multiplication problem here. With other considerations we might find it takes less.

Again, that depends on HOW LOW. There is a middle ground that exists between TOO LOW and TOO HIGH, we predict that species that are undergoing adaptation exist here. It is useless then to use examples where the selection pressure is obviously too high or too low. The selection pressures acting in combating viruses and bacteria, especially with regard to combination therapy are specifically designed to be to TOO HIGH.

You have to determine the magnitude of the selection pressures facing the dinosaurs to determine whether it was too high for feathers to evolve. You have just examined the conditions of HIV under certain therapies and concluded that HIV's evolution in inhibited in that case. You have tried to say that this demonstrates that multiple selection pressures always inhibit evolution, but you have not addressed the issue of magnitude which invalidates your argument. That's the bit you need to address.

Message 364 of 393 (792889) 10-14-2016 6:31 PM

Reply to: Message 354 by Dr Adequate 10-14-2016 5:19 PM

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So, here are the results of some simulations differing only in the number of selection pressures operating.

Click to enlarge.

As you can see, the rate of adaptation is faster the more selection pressures are operating, in line with (a) my math (b) common sense.

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Message 365 of 393 (792890) 10-14-2016 6:32 PM

Reply to: Message 359 by Kleinman 10-14-2016 6:10 PM

You admitted that conservative selection pressures don't count. Just thought I should remind you.

That's one of the many things you don't know that has prevented you from actually proving anything about dinosaurs.

Message 366 of 393 (792891) 10-14-2016 6:33 PM

Reply to: Message 364 by Kleinman 10-14-2016 6:31 PM

No, that's the result of simulations, as I said in the post to which you are ostensibly replying.

Message 367 of 393 (792892) 10-14-2016 6:40 PM

Reply to: Message 362 by Kleinman 10-14-2016 6:28 PM

Lenski takes a random sample of 1% of the population every day to start a new colony and discards the rest. Insofar as it's meaningful to ask under such circumstances whether the environmental pressures are hard or soft, they're soft.

Well, so far all you've shown us could have been knocked off in five minutes by a bright middle-schooler and comes nowhere close to proving your point, so yeah, some more math would be nice.

Try considering the case where the intensity is 0.

Adaptive evolution is often a tradeoff. If there is more of an upside associated with making a change, then it's more likely to outweigh the potential downside.

Edited by Dr Adequate, : No reason given.

Message 368 of 393 (792893) 10-14-2016 6:46 PM

Reply to: Message 358 by bluegenes 10-14-2016 6:00 PM

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Kleinman writes: As for the Citrate metabolizer (e coli has alway been able to metabolize Citrate because it has a Krebs cycle), appeared at about generation 31500, not at 100 generations.

I said "change the circumstances". I know the Lenski experiment took over 30,000 generations for Cit+. The multi-mutation adaptation can happen in less than 100 generations in other circumstances.

http://jb.asm.org/content/198/7/1022.full

That, ironically, is a paper by creationists who didn't like the idea that the occurrence of Cit+ in Lenski is special, and set out to show that it could happen easily. It can.

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So, where are your calculations? Surely they're not based on the view that an adaptation involving 5 or more mutations in sequence would take ~31,000 generations in a culture of bacteria in any or all environments? How are environments factored in?

You still seem to be assuming that organisms have to be threatened with extinction in order to evolve, as suggested before. They don't. Flying squirrels evolve alongside the non-flying versions they descend from, and both thrive. It's just better to be able to glide in certain environments. Same with dinosaurs. The fliers existed alongside the non-fliers for tens of millions of years. They just fill different niches

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Message 369 of 393 (792895) 10-14-2016 7:07 PM

Reply to: Message 365 by Dr Adequate 10-14-2016 6:32 PM

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I disagree with you. I think combination selection pressures are the rule in nature. Drought, starvation, thermal stress, disease, predation,...

You admitted that conservative selection pressures don't count. Just thought I should remind you.

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How large is that population size for dinosaurs?

That's one of the many things you don't know that has prevented you from actually proving anything about dinosaurs.

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That's not your fixation calculation again?

No, that's the result of simulations, as I said in the post to which you are ostensibly replying.

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Do you think the intensity of selection in the Lenski experiment is hard or soft?

Lenski takes a random sample of 1% of the population every day to start a new colony and discards the rest. Insofar as it's meaningful to ask under such circustances whether the environmental pressures are hard or soft, they're soft.

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Again?

Well, so far all you've shown us could have been knocked off in half an hour by a bright middle schooler and comes nowhere close to proving your point, so yeah, some more math would be nice.

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Now I would like to see some empirical evidence of that, you obviously have that.

Try considering the case where the intensity is 0.

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Why might that happen?

Adaptive evolution is often a tradeoff. If there is more of an upside associated with making a change, then it's more likely to outweigh the potential downside.

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Message 370 of 393 (792896) 10-14-2016 7:27 PM

Reply to: Message 359 by Kleinman 10-14-2016 6:10 PM

And if the population started high rather than built up, that would have increased the probability sooner. So what? How is rmns working 'better'? If we removed the poison and let them grow with very little competition and then poured anti-biotic at 1,000 times the normal required dosage into the mix...do you think that more bacteria would survive it? Is that what you mean by 'better'?

Then you agree with me.

Back to the point, however, you haven't determined the magnitude of the selection pressures faced by the ancestors of feathered dinosaurs. The number of pressures and that they act in concert is irrelevant. There are thousands of selection pressures acting ALL the time everywhere. The question is of magnitude.

Very large.

I am remembering that it's populations.

No it isn't. All the dinosaurs still count. You don't ignore their lottery entries just because one won. That would imply all dinosaurs went extinct. This is not true. A thousand different lineages could independently mutate in the direction of feathers. That you think you can discount these suggests your maths training was poorer than you've been letting on.

Because of sex, it doesn't have to occur in one of its descendants. Did you forget dinosaurs were sexual organisms?

Did he measure all variants to have increased by the same amount in lockstep? His population must have exploded.

The first question is too vague, but I've answered it already where it seems relevant. No, the colonies are not giving the same variants, why do you ask?

Are you certain?
Do they never reach an equilibrium condition when the number that die without reproducing equals the number that reproduce before the sum total food is exhausted? Given that not all food is available to any given bacteria, is there not a certain density at which not all bacteria are able to acquire enough food to reproduce? Where they are basically getting in each others way (deliberately or otherwise)?

Let's suppose that simultaneously, 10 bacteria evolve an anti-biotic resistant mutation. This is best case for your argument, lowering this number hurts you. Let's say there are a billion non-resistant varieties. That means the frequency of resistant types is is 10 in a billion. Each variant is individual and so each variant has a frequency of 1 in a billion.

In order that these variants all amplify while keeping this frequency this is what you say we should expect:

Population of resistant variants 100. Population of non-resistant variants: 10 billion.
Population of RV 1000. Population of nRV: 100 billion.
Pop RV 10,000. Pop nRV: 1 trillion.
RV 100,000. Pop nRV: 10 trillion.

I believe culture density maximums are usually around a million to a billion bacteria per ml. There aren't a lot of ml even on the megaplate, there are less that have no poison.

Given the resistant variety has twice as much food and therefore space, what happens when the non-resistant variant reaches saturation?

RV 1,000,000 (approx 1 ml of volume): Pop nRV: 100 trillion. (100,000 litres required)

Are you seriously telling me that the frequencies stay the same? Because that seems extraordinary when we examine the numbers.

Edited by Modulous, : No reason given.

Message 371 of 393 (792897) 10-14-2016 7:30 PM

Reply to: Message 368 by Kleinman 10-14-2016 6:46 PM

Interesting to you, because it shows the type of multi-mutation adaptation that you seem to think highly improbable happening repeatedly with ease.

I agree with the first sentence, but not with the "information" waffle.

So tell me, can numerous beneficial mutations be facing positive selection in one species at the same time?

Message 372 of 393 (792898) 10-14-2016 7:43 PM

Reply to: Message 369 by Kleinman 10-14-2016 7:07 PM

Often. Unless they're new.

Perhaps you meant something when you wrote that.

No, that's the result of simulations, as I said in the post to which you are ostensibly replying.

What do you mean by "his intensity of selection"?

Good, good. And maybe some time this month we could get on to the interesting bit?

And hence the population will follow a different evolutionary trajectory than if the intensity was not zero. Proving that the intensity matters.

Would these be the "nested binomial probability problems" that you've spent the past week not actually posting about?

Message 373 of 393 (792899) 10-14-2016 8:00 PM

Reply to: Message 369 by Kleinman 10-14-2016 7:07 PM

You have confused theory with application. The details about the dinosaurs is a practical problem we can apply theory to. The theory of evolution is not that dinosaurs evolved into birds. The theory of evolution provides an explanation for how dinosaurs evolved into birds.

The theory of relativity does not say that a planet mercury exists, and that the precession of the perihelion of its orbit should advance in such a way.

It instead can provide an answer as to what the precession should be, given the existence of Mercury.

There are still many unanswered questions about our cosmological history, even in our own solar system. That doesn't mean all the associated theories are not settled, it may be a lack of data that results in unanswered questions. We have a perfectly understandable lack of data about dinosaurs. What we do have is consistent with, indeed highly suggestive of, the notion that some of them evolved into birds.

We do not have the data you require to apply your simple mathematics in order to prove the whole thing a charade. And neither do you.

Message 374 of 393 (792901) 10-14-2016 10:39 PM

Reply to: Message 270 by Kleinman 10-14-2016 11:35 AM

If you don't know then you cannot invalidate evolution with your calculations.

Evolution works by beneficial mutations being selected by natural processes -- success in living and breeding. The probability of a mutation being beneficial would seem to be central to any mathematical approach trying to show that evolution is broken.

Which leaves the door open to later mutations that can build on them.

Yet every individual in every species has several.

For individuals that survive from zygote to born young. All those that die from birth defects are because of less than sufficient fidelity.

This is confused. There is one mutation, it occurs randomly, and that means both location and format\type are part of the same mutation, not two separate problems. The same type in a different location would be a different mutation.

There is no "correct mutation" -- the mutation happens and then selection operates on that mutation, whether it is in location A or location B, whether it is type K or type L. Whether or not it is beneficial is that probability discussed above that you admit you don't know.

This seems to be the root of your problem, trying to make a single mutation event into a two event process.

It also seems from this that you are calculating the probability of a given mutation occurring in a second individual. Certainly when you go to two mutations occurring independently in different individuals the maths would give an extremely low probability for occurrence, but that is not how evolution works.

Yet we know that they all occur every generation of every species. All natural selection needs are some beneficial mutations and a low rate of death/fertility problems (where selection pressure enters the picture).

This too is confused. If I take a coin and toss it 53 times I end up with a pattern of heads and tails, and the probability of my getting that specific pattern is 1.

If I try to match that pattern with another 53 tosses the probabilities are, by the multiplication rule, extremely minute. You only use multiplication when the same steps need to be reproduced. Evolution does not work that way.

Again, we get back to the question of the probability that a mutation will be beneficial, which you admitted you don't know ... certainly then you can't know the probability of a second mutation being beneficial, but that isn't the worst of your problem.

There are actual documented experiments (one involving E. coli) where a neutral mutation occurs in one generation and then in a later generation a second mutation occurs where the combination is beneficial, meaning that the original mutation is now beneficial. Calculating the probability that those two specific mutations would occur (the "correct mutations" at the "correct locations") would result in a very small number, but the probability that it occurred is 1: it happened.

Your model is wrong because there is an assumption of structure to the mutation process being necessary to evolution, and that assumption is false.

Enjoy

Message 375 of 393 (792909) 10-15-2016 8:48 AM

Reply to: Message 340 by Kleinman 10-14-2016 3:53 PM

As I expected, the debate has become very repetitive. One frequently seen pattern is for people to argue that the example of fatal selection pressures on bacteria and viruses cannot be generalized to other levels of selection, and for you to reply that your papers show otherwise. But your papers are not accessible to the people here, so you must stop citing them. Even if they were accessible you must still present your evidence and arguments in the thread, using links only as references. Arguing, in effect, "This link shows I'm right" or "This link shows you're wrong," is strongly discouraged here at EvC Forum.

This is the only equation you've presented:

What you must do is substitute actual values into this equation demonstrating evolution impossible. If I don't see this presentation very soon I will drop this thread into summation mode.

Edited by Admin, : Typo.

Edited by Admin, : Fix equation to eliminate the smilie.