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Author Topic:   Explaining the pro-Evolution position
Modulous
Member (Idle past 329 days)
Posts: 7789
From: Manchester, UK
Joined: 05-01-2005


(3)
Message 275 of 393 (792790)
10-14-2016 11:54 AM
Reply to: Message 242 by Kleinman
10-13-2016 8:38 PM


Numbers are as important as maths
I actually learned about the multiplication rule of probabilities in elementary school.

You aren't special in having been subject to a Western education.

Maybe evolutionists don't want to think about the multiplication rule for stochastic processes.

A theory instantly falsified by reading papers on evolution.

You show me your degrees and I'll show you mine. And I'm pretty sure I've had a lot more training in mathematics and physics than you.

What difference does it make when you are only using elementary school mathematics?

The mathematics of rmns is not dependent on the intensity of selection.

Wrong. You have only been doing rudimentary mathematics of random mutations. You have not done any mathematics of natural selection. Obviously the magnitude of the selection forces is of vital importance.

If I had a population of 100,000 humans and I shot them all in the face, the population will never evolve bullet resistance. The selection pressure is too high. If, on the other hand, I was to regularly fire bullets at a height of six foot at the population - the selection pressure is much lighter. If only about 8% of the population is over 6 foot tall, then the population can retain its size, and maybe we'd find shortness or cautiousness may increase in frequency.

And don't get me wrong, I'm not saying that evolution is impossible, I'm giving you the mathematical rules which govern how evolution by rmns works. It is the theory of evolution which is mathematically irrational based on how rmns works. It is the multiplication rule of probabilities which kills the theory of evolution.

Except you need actual numbers to show this, which you haven't provided. You have obfuscated the magnitude of NATURAL selection by pointing to an example of ARTIFICIAL selection and said that the 'maths is the same' for both. This may be true, but the NUMBERS are different.

If you think I'm cherry picking the data, post a real, measurable and repeatable example of rmns that doesn't obey my mathematics.

The issue is that the numbers involved in viral resistance to combination therapy are enormously different from the evolution of birds. Without examining the numbers related to dinosaurs and birds, how could we say for sure? As has already been pointed out - - we have done the mathematics as it relates to dinosaurs and birds, and the numbers suggest it is entirely feasible.

The theory of evolution doesn't explain anything. It doesn't explain how rmns works

The theory of evolutions explains that the genome and phenome are related, and that genes are the unit of inheritance {I'm simplifying}. It explains that that during replication of the genes during reproduction, errors can occur. These errors are based on stochastic processes related to environmental processes that are chaotic are thus unpredictable, hence sometimes called 'random' or 'chance' mutations. Since the phenome is related to the genome, mutations can sometimes affect the phenome. That might make it more likely the genes replicate, or not.

It's a theory which takes the concept of common descent and says every living thing we see today came from some replicator from the primordial soup.

That's natural history.

The theory of evolution is the theory for how life changes. It is neutral as to history, just as any scientific theory is. Natural historians utilize the theory of evolution, theories of geology, astronomy, geography, climatology etc etc etc, to try to understand the specific history of life on earth. Natural history is a story. A narrative. It is evidence based, it relies entirely on science (as opposed to history that also uses documentation and interpretation of human motivations), but it is not a 'scientific theory', in the same sense that Theory of Evolution is a scientific theory.

Also there is not one 'natural history' The details are constantly being argued and debated. But this isn't the theory of evolution. Not sure where you got your training from to have confused history with science.

It's the same math for all replicators.

Dinosaurs aren't replicators. They are reproducers. Their genes are the only thing that gets replicated.

The calculations for rmns are actually quite simple.

Did it not strike you as odd, that given how simple they are, it took YOU to notice this issue? And that millions of other highly trained people completely missed it? You must think very highly of yourself, and very poorly of others. To a pathological level.

No, what I am saying is that the creation of new alleles by rmns only works efficiently when a single gene is targeted by a single selection pressure.

NATURAL selection CANNOT target. That's its defining feature. You've confused the special case of ARTIFICIAL selection with the general case of NATURAL selection.

In a natural setting, rather than a lab, the environment changes naturally. Usually quite slowly, but with some jitters. Either it changes slowly enough that biological populations have the time and the numbers to find a 'solution' to the new problems and opportunities it presents or it doesn't. One way the population goes extinct (the eventual outcome in most cases), in the other it has evolved.

That's why the NUMBERS are important, not just the mathematics.

PaulK, the reason there is no rational way that feathers can evolve from scales by rmns is there are too many genetic loci which must be transformed simultaneously. Every evolutionary step (beneficial mutation) must amplify in order to improve the probability of another beneficial mutation occurring on some member of the lineage with that particular mutation. rmns only works efficiently when a single selection pressure targets a single gene at a time.

There was no such selection pressure of 'become birds or die', that is comparable to 'evolve resistance to antivirals or die'. Many Jurassic dinosaurs that did not evolve flight or become 'early birds', went on to become Cretaceous dinosaurs and did fine for a long time. So it seems basically obvious that the evidence suggests the situations, and thus those pesky NUMBERS were radically different.

Evolution will have to occur at a rate of much greater than a thousand generations per beneficial mutation if scales are going to be transformed into feathers.

Well let's plug some numbers actually involving feathers shall we?

Let's say the Sauropsida arose 300 million years ago and feathered Sauropsida appeared about 200 million years ago. That gives us 100 million years. Generation time for similar organisms is about 1-4 years, we'll call it 2 years. So 50 million generations, is it enough?

50,000,000 generations / 1000 generations per beneficial mutation = 50,000 beneficial mutations

Sounds sufficient to me.

Edited by Modulous, : No reason given.


This message is a reply to:
 Message 242 by Kleinman, posted 10-13-2016 8:38 PM Kleinman has not yet responded

  
Modulous
Member (Idle past 329 days)
Posts: 7789
From: Manchester, UK
Joined: 05-01-2005


Message 291 of 393 (792806)
10-14-2016 12:33 PM
Reply to: Message 276 by Kleinman
10-14-2016 12:01 PM


the equality of pressure?
On the other hand, rmns is the creation of new alleles in order to adapt.

Yet more evidence I am correct in my assessment of your argument. Random mutations create new alleles. Natural selection does not create new alleles. And NONE OF IT happens 'in order to adapt'.

The new alleles are in competition with the other alleles. If it replicates at a faster rate than they, they will increase in frequency - else they won't. That's natural selection. It doesn't create alleles it's just the phenomena that alleles which are able to replicate more, will be more replicated.

And if the adaptation requires the creation of multiple different new alleles at different genetic loci due to multiple different selection pressures simultaneously, the chances of adaptation are extremely low and the process is extremely slow if it going to happen

If apply pressure to carbon, will I get a diamond? Surely it depends on the magnitude of the pressure. Why do you assume all pressures are equal in biology?


This message is a reply to:
 Message 276 by Kleinman, posted 10-14-2016 12:01 PM Kleinman has responded

Replies to this message:
 Message 313 by Kleinman, posted 10-14-2016 1:54 PM Modulous has responded

  
Modulous
Member (Idle past 329 days)
Posts: 7789
From: Manchester, UK
Joined: 05-01-2005


(1)
Message 317 of 393 (792835)
10-14-2016 2:20 PM
Reply to: Message 313 by Kleinman
10-14-2016 1:54 PM


Re: the equality of pressure?
The first half of the cycle consists of a beneficial mutation occurring

Nope. Any mutation.

the other half of the cycle (natural selection) consists of amplification of that beneficial mutation in order to improve the probability of the next beneficial mutation occurring on some member of that population who has the previous beneficial mutation.

Nope.

Natural selection is one process by which some alleles increase in frequency, others decrease in frequency and others retain their frequency. There is no purpose, reason or intent to change the frequencies. Thus 'beneficial mutations' are not increasing in frequency SO THAT they can accrue more beneficial mutations to their lineage. They increase in frequency because the mutation increases their replicative success SO they increase in frequency by virtue of how numbers work.

There can be competition between different variants if there are limited resources in the environment. rmns works best in environments that are not limited in the resources.

This is nonsense. It is wrong. It is not supported by data. It is falsified by data. As far as it can be said to be a coherent claim. But then 'works best' is scientifically meaningless, so a true assessment is impossible.

Selection pressures kill or impair the ability of some or all members in a population to reproduce. These pressures can vary in intensity.

Exactly. So saying that the selection pressures in one case demonstrates evolution is impossible in other cases is kind of silly isn't it?


This message is a reply to:
 Message 313 by Kleinman, posted 10-14-2016 1:54 PM Kleinman has responded

Replies to this message:
 Message 327 by Kleinman, posted 10-14-2016 3:00 PM Modulous has responded

  
Modulous
Member (Idle past 329 days)
Posts: 7789
From: Manchester, UK
Joined: 05-01-2005


Message 328 of 393 (792848)
10-14-2016 3:12 PM
Reply to: Message 326 by Kleinman
10-14-2016 2:48 PM


Re: Lenski
Lenski's experiment works because he doesn't starve his populations to death.

Yup.

So if you put starvation pressure and thermal stress on the population at the same time, well you figure it out.

All things being equal it would take the same generational time as the starvation experiment plus the generational time of the thermal stress experiment. That is, if the second experiment was as lethal as the first (ie., the number of bacteria that died without reproducing in the starvation experiment is the same the number of bacteria dying w/o reproduction in the starvation + thermal stress test), then it would just be a case of evolving one (which we know how long that takes) then evolving the other (and we know that too).

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. That's a bit like the difference between being a dinosaur in a normal environment and a virus being bombarded with disparate poisons that have been tailored to kill it. One is a little more lethal and the results consequently may differ.


This message is a reply to:
 Message 326 by Kleinman, posted 10-14-2016 2:48 PM Kleinman has responded

Replies to this message:
 Message 338 by Kleinman, posted 10-14-2016 3:48 PM Modulous has responded

  
Modulous
Member (Idle past 329 days)
Posts: 7789
From: Manchester, UK
Joined: 05-01-2005


(1)
Message 333 of 393 (792854)
10-14-2016 3:36 PM
Reply to: Message 327 by Kleinman
10-14-2016 3:00 PM


Re: the equality of pressure?
What do you think happens if the mutation is detrimental?

It tends to decrease in frequency.

rmns is not dependent on the relative frequency of variants in a population.

Obviously.

Natural selection is the name for some of the factors that cause frequency changes in a population.

Random mutation can impact frequencies.

Drift can impact frequencies.

Here's an example where rmns is occurring in an environment where variants are not competing for resources in the environment:
http://www.slate.com/...cteria_evolving_drug_resistance.html

No it isn't. The bacteria are competing for food. The reach a certain population size. In that environment certain mutations help them (make them more efficiently utilize the limited food, or opening up new food sources), others hinder them.

. So saying that the selection pressures in one case demonstrates evolution is impossible in other cases is kind of silly isn't it?
Feel free to quote me if you think I said that.

No problem.

rmns will not transform reptiles into birds.

There is a specific mathematical reason why combination therapy works for the treatment of HIV.

the reason rmns can't do it is the multiplication rule of probabilities.

You seem throughout to be arguing that because HIV combination therapy inhibits evolution, then evolution in contexts such as dinosaur->bird is likewise inhibited to the same kind of degree. This assumes the selection pressures moving dinosaurs towards birds are on a par with the selection pressures applied to HIV during combination therapy. This is silly.

What I have said and will continue to say because it is a mathematical and empirical fact of life is that rmns only works efficiently when a single gene is targeted by a single selection pressure at a time.

Natural history has proven natural selection to be inefficient. Efficiency doesn't provide us any cause to suspect the evolution to birds is impossible. Natural selection does not target. SELECTION may be more efficient this way, but natural selection does not target. Natural selection is MASSIVELY INEFFICIENT. This has long been observed. What does efficiency matter and how does it prevent dinosaur to bird evolution? You have not said.

And this process does not work by changing the relative frequencies of variants in a population but works by amplification of the particular variants.

How do those variants get amplified in nature if not by increasing their frequency in the population?

Edited by Modulous, : No reason given.


This message is a reply to:
 Message 327 by Kleinman, posted 10-14-2016 3:00 PM Kleinman has responded

Replies to this message:
 Message 342 by Kleinman, posted 10-14-2016 4:16 PM Modulous has responded

  
Modulous
Member (Idle past 329 days)
Posts: 7789
From: Manchester, UK
Joined: 05-01-2005


Message 339 of 393 (792860)
10-14-2016 3:51 PM
Reply to: Message 338 by Kleinman
10-14-2016 3:48 PM


Re: Lenski
Lenski's starvation stress slows the doubling time for his population to about every 7 hours.

I was referring to the number of generations, not hours. Thus everything else you said is irrelevant. Unless you think that dinosaur generation time was changed from 2 years to 20 years because they weren't birds?

In fact, if there is too many selection pressures on the population yet the population is not driven to extinction, what you will see is the population will just drift. This is what happens to HIV when subjected to the three drug therapies.

The number of pressures is considerably less important than their magnitude. This is the central problem with your whole thesis. You need to address this.

Edited by Modulous, : No reason given.


This message is a reply to:
 Message 338 by Kleinman, posted 10-14-2016 3:48 PM Kleinman has responded

Replies to this message:
 Message 355 by Kleinman, posted 10-14-2016 5:33 PM Modulous has responded

  
Modulous
Member (Idle past 329 days)
Posts: 7789
From: Manchester, UK
Joined: 05-01-2005


Message 350 of 393 (792872)
10-14-2016 5:11 PM
Reply to: Message 342 by Kleinman
10-14-2016 4:16 PM


Re: the equality of pressure?
It tends to decrease in frequency.

Yup

So we agree that random mutation does not 'consist{s} of a beneficial mutation occurring'. Good. That's all I was saying with this.

rmns is not dependent on the relative frequency of variants in a population.

Obviously.

Natural selection is the name for some of the factors that cause frequency changes in a population.

rmns is not dependent on relative frequencies of variants in the population

Obviously.

Natural selection is the name for some of the factors that cause frequency changes in a population.

Was there some reason you repeated yourself?

They are not competing for food initially because the petri dish is so large

But they don't evolve antibiotic resistance initially. So how does this demonstrate that rmns is working 'better'?

At what point do you say that the probabilities are so low that the particular outcome is impossible.

The point is that you are treating the selection pressures affecting HIV subject to combination therapy (a distinctly unnatural event) as the same as those affecting the dinosaurs and trying to conclude this means the dinosaurs could not have evolved into birds. You are trying to suggest the probabilities are the same, or worse, without providing any evidence of this. You just use the obfuscatory 'the maths is the same' line I have previously criticised as insufficient.

You might say that winning a single lottery is possible and that winning two lotteries is also still possible but not very likely and winning three lotteries, that's getting a little iffy, how about you winning 10 lotteries or a 100 lotteries?

If the odds of winning a lottery is 1 in 10,000,000 and I buy a quadrillion tickets, I expect to win a billion times in one lottery or once in a billion lotteries or any combination between.

However, you have not provided the numbers to answer the question in the case of dinosaurs, you have assumed the lottery or lotteries the dinosaurs entered was the same as the lottery or lotteries HIV enters during therapy. This is an empirically false assumption, hence your incorrect conclusion.

Despite your attempt to distract from this point, it remains the fatal flaw in your argument.

You can have amplification without any change in the relative frequency of the variants in a population by having all variants amplifying simultaneously.

It's possible, but stupendously unlikely, for this to occur in nature. It cannot happen for long.

That's what you are seeing in the video of the bacteria evolving resistance.

No, it isn't.

You see multiple different colonies forming and then you get mutant variants in several of the colonies which can then start growing on the increased concentration antibiotic bands.

But the variants that have not evolved the antibiotic resistance don't amplify. At least there is no evidence that if they do, they do so at exactly the same rate as the bacteria with the new food source. Indeed we can use the work of Lenski already presented to demonstrate adequately that having fewer food sources inhibits amplification compared with having more.


This message is a reply to:
 Message 342 by Kleinman, posted 10-14-2016 4:16 PM Kleinman has responded

Replies to this message:
 Message 359 by Kleinman, posted 10-14-2016 6:10 PM Modulous has responded

  
Modulous
Member (Idle past 329 days)
Posts: 7789
From: Manchester, UK
Joined: 05-01-2005


Message 363 of 393 (792888)
10-14-2016 6:31 PM
Reply to: Message 355 by Kleinman
10-14-2016 5:33 PM


Re: Lenski
So do you think the amplification time (starvation alone=>about 1000 generations per beneficial mutation) would speed up if a small thermal stress was added to his populations or would the number of generations per beneficial mutation increase?

As I already said

quote:
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

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.

Large numbers of low intensity selection pressures do not cause rmns to work, you get drift under these conditions.

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.


This message is a reply to:
 Message 355 by Kleinman, posted 10-14-2016 5:33 PM Kleinman has not yet responded

  
Modulous
Member (Idle past 329 days)
Posts: 7789
From: Manchester, UK
Joined: 05-01-2005


Message 370 of 393 (792896)
10-14-2016 7:27 PM
Reply to: Message 359 by Kleinman
10-14-2016 6:10 PM


Re: the equality of pressure?
But the populations are amplifying improving the probability that the first beneficial mutation will land on some member of a population

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'?

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

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.

How large is that population size for dinosaurs?

Very large.

And remember, or learn, that rmns occurs on lineages, you know, common descent.

I am remembering that it's populations.

And that quadrillion population is now reduced to a new lineage of 1 with that first beneficial mutation.

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.

And until that variant amplifies, the probabilities are very low that the 2nd beneficial mutation will occur on one of its descendants.

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

Well then how did Weinreich measure so many different variants from his one targeted antibiotic selection pressure?

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

What do you think you are seeing in the video. Do you think that all the colonies are giving the same variants?

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?

The non-antibiotic resistant variants amplify until the resources of the plate are exhausted

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.


This message is a reply to:
 Message 359 by Kleinman, posted 10-14-2016 6:10 PM Kleinman has not yet responded

  
Modulous
Member (Idle past 329 days)
Posts: 7789
From: Manchester, UK
Joined: 05-01-2005


Message 373 of 393 (792899)
10-14-2016 8:00 PM
Reply to: Message 369 by Kleinman
10-14-2016 7:07 PM


Re: the equality of pressure?
Yes, one of the many things you do not know {about dinosaurs} I thought the theory of evolution was settled science?

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.


This message is a reply to:
 Message 369 by Kleinman, posted 10-14-2016 7:07 PM Kleinman has responded

Replies to this message:
 Message 381 by Kleinman, posted 10-15-2016 10:11 AM Modulous has acknowledged this reply

  
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