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Author Topic:   Explaining the pro-Evolution position
Kleinman
Member (Idle past 697 days)
Posts: 136
From: United States
Joined: 10-06-2016

 Message 316 of 393 (792834) 10-14-2016 2:14 PM Reply to: Message 299 by PaulK10-14-2016 12:56 PM

Re: Mathematics cannot change reality but when done correctly can predict it
quote:
quote:

You don't think that the multiplication rule of probabilities is a roadblock?

Quite obviously it is not. To anyone with a proper understanding of probability theory. I already explained why it is not.

Do you concede that it is possible to generate sequences of arbitrarily small probability ? Or do you think that there is some limit that can't be passed ? Some minimum probability ?

Well if it isn't the multiplication rule of probabilities which has led to the success of combination therapy for the treatment of HIV, then what is it? What do you think is suppressing the evolution of drug-resistant variants in this circumstance?
 This message is a reply to: Message 299 by PaulK, posted 10-14-2016 12:56 PM PaulK has responded

 Replies to this message: Message 318 by PaulK, posted 10-14-2016 2:22 PM Kleinman has not yet responded

Modulous
Member (Idle past 80 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 Kleinman10-14-2016 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

PaulK
Member
Posts: 14551
Joined: 01-10-2003
Member Rating: 1.6

 Message 318 of 393 (792836) 10-14-2016 2:22 PM Reply to: Message 316 by Kleinman10-14-2016 2:14 PM

Re: Mathematics cannot change reality but when done correctly can predict it
quote:

Well if it isn't the multiplication rule of probabilities which has led to the success of combination therapy for the treatment of HIV, then what is it?

Trying to change the subject is hardly a good argument. I have already explained the problem with your use of probability Message 95

Now perhaps you could start by acknowledging that the multiplication rule for probabilities is in no way a roadblock to generating sequences of arbitrarily low probability. Do you even understand that much ?

Edited by PaulK, : No reason given.

 This message is a reply to: Message 316 by Kleinman, posted 10-14-2016 2:14 PM Kleinman has not yet responded

Kleinman
Member (Idle past 697 days)
Posts: 136
From: United States
Joined: 10-06-2016

 Message 319 of 393 (792837) 10-14-2016 2:23 PM Reply to: Message 300 by ringo10-14-2016 12:56 PM

Re: Mathematics cannot change reality but when done correctly can predict it
quote:
 Kleinman writes:You don't think that the multiplication rule of probabilities is a roadblock?

I asked for a physical roadblock. So far it looks like you've just got the mathematics wrong, so a mathematical roadblock doesn't cut it.

This mathematical theorem is a physical roadblock to the accumulation of beneficial mutations on a lineage. If at any time the lineage does not amplify, the probabilities of another beneficial mutation occurring on that lineage are low.
quote:
 Kleinman writes:I hope your expectations aren't too high when you buy tickets to two different lotteries and think you are going to win both.

Of course there's nothing to prevent that from happening.

There's nothing from preventing you from winning a hundred lotteries, well nothing except the multiplication rule of probabilities.
quote:
 Kleinman writes:And then if you think about the length of the human genome, 3e9, how many tickets do you need to buy to win all those lotteries?

But it isn't a question of winning all of them independently. What if the prize in Lottery A is a million tickets for Lottery B?

Bingo, you just won your second lottery. Just hope that you don't have to win two lotteries at the same time in order to win your prize.
 This message is a reply to: Message 300 by ringo, posted 10-14-2016 12:56 PM ringo has acknowledged this reply

Kleinman
Member (Idle past 697 days)
Posts: 136
From: United States
Joined: 10-06-2016

 Message 320 of 393 (792838) 10-14-2016 2:29 PM Reply to: Message 303 by Taq10-14-2016 1:10 PM

Re: Lenski
quote:
 That's the point, Lenski is using only a single directional selection pressure, starvation. He is selecting for the most efficient energy users. And if Lenski were to add a second simultaneous selection pressure, for example, thermal stress, the amplification of the mutations which increase energy efficiency will be slowed by the thermal stress applied to these populations.

As long as the thermal stress was not lethal, the adaptation for energy efficiency would not be slowed. Bacteria with adaptations to just one of the selection pressures would outcompete bacteria with none of the adaptations.

You are making an assumption that the energy fit variants will not be inhibited from reproducing when held at sub-optimal temperatures. There's a reason laboratories run their incubators at particular temperatures.

And Taq, you still haven't answered my simple question to you. Does doubling population size double the probability of a beneficial mutation occurring?

 This message is a reply to: Message 303 by Taq, posted 10-14-2016 1:10 PM Taq has responded

 Replies to this message: Message 322 by Taq, posted 10-14-2016 2:35 PM Kleinman has responded

Kleinman
Member (Idle past 697 days)
Posts: 136
From: United States
Joined: 10-06-2016

 Message 321 of 393 (792839) 10-14-2016 2:34 PM Reply to: Message 306 by PaulK10-14-2016 1:24 PM

Re: Is it summation time?
quote:
Your problem is not understanding rmns in terms of drug resistance. Your problem is that you refuse to understand that drug resistance is a special case. And you will never understand rmns until you take off those blinkers and consider it in other contexts.

How does evolution of drug resistance differ than evolution by rmns to any other kind of selection pressure? What is the mathematical difference between Lenski's experiment and let's say this experiment:
http://www.slate.com/...cteria_evolving_drug_resistance.html
 This message is a reply to: Message 306 by PaulK, posted 10-14-2016 1:24 PM PaulK has responded

 Replies to this message: Message 323 by Taq, posted 10-14-2016 2:36 PM Kleinman has responded Message 325 by PaulK, posted 10-14-2016 2:40 PM Kleinman has responded Message 337 by Dr Adequate, posted 10-14-2016 3:40 PM Kleinman has responded

Taq
Member
Posts: 7610
Joined: 03-06-2009
Member Rating: 2.7

 Message 322 of 393 (792840) 10-14-2016 2:35 PM Reply to: Message 320 by Kleinman10-14-2016 2:29 PM

Re: Lenski
 Kleinman writes:You are making an assumption that the energy fit variants will not be inhibited from reproducing when held at sub-optimal temperatures.

The effect of thermal stress would be the same for both the energy fit and the less energy fit. This would allow the energy fit to outcompete the less energy fit.

 Does doubling population size double the probability of a beneficial mutation occurring?

It doubles the probability of any mutation occurring at a specific locus.

 This message is a reply to: Message 320 by Kleinman, posted 10-14-2016 2:29 PM Kleinman has responded

 Replies to this message: Message 330 by Kleinman, posted 10-14-2016 3:18 PM Taq has responded

Taq
Member
Posts: 7610
Joined: 03-06-2009
Member Rating: 2.7

 Message 323 of 393 (792841) 10-14-2016 2:36 PM Reply to: Message 321 by Kleinman10-14-2016 2:34 PM

Re: Is it summation time?
 Kleinman writes:How does evolution of drug resistance differ than evolution by rmns to any other kind of selection pressure?

Selection pressures are rarely binary between survival and death. It wasn't as if a species with scales would go extinct in a single generation if it didn't evolve feathers.

 This message is a reply to: Message 321 by Kleinman, posted 10-14-2016 2:34 PM Kleinman has responded

 Replies to this message: Message 331 by Kleinman, posted 10-14-2016 3:23 PM Taq has responded

Taq
Member
Posts: 7610
Joined: 03-06-2009
Member Rating: 2.7

 Message 324 of 393 (792842) 10-14-2016 2:37 PM Reply to: Message 315 by Kleinman10-14-2016 2:09 PM

Re: Mathematics cannot change reality but when done correctly can predict it
 Kleinman writes:Try climbing two different flights of stairs at the same time.

That's exactly what sexual species do.

 You win a lottery, everyone wants to marry you.

 This message is a reply to: Message 315 by Kleinman, posted 10-14-2016 2:09 PM Kleinman has responded

 Replies to this message: Message 332 by Kleinman, posted 10-14-2016 3:32 PM Taq has responded

PaulK
Member
Posts: 14551
Joined: 01-10-2003
Member Rating: 1.6

 Message 325 of 393 (792843) 10-14-2016 2:40 PM Reply to: Message 321 by Kleinman10-14-2016 2:34 PM

Re: Is it summation time?
quote:

How does evolution of drug resistance differ than evolution by rmns to any other kind of selection pressure?

If you had been paying attention you would know. For drug resistance selection pressure comes in the form of an environmental factor which greatly reduces the fitness of all non-resistant members of the population.

What happens in the case of soft selection where the fitness of the "original" strain remains high ? Where the only factor reducing it below 1 is competition with other members of the species who possess a recent mutation (or a mutation recently become advantageous due to environmental change)

 This message is a reply to: Message 321 by Kleinman, posted 10-14-2016 2:34 PM Kleinman has responded

 Replies to this message: Message 334 by Kleinman, posted 10-14-2016 3:38 PM PaulK has responded

Kleinman
Member (Idle past 697 days)
Posts: 136
From: United States
Joined: 10-06-2016

 Message 326 of 393 (792844) 10-14-2016 2:48 PM Reply to: Message 308 by Dr Adequate10-14-2016 1:27 PM

Re: Lenski
quote:
 That's the point, Lenski is using only a single directional selection pressure, starvation.

But this exerts pressure on a whole lot of loci. Why would it make a difference if each locus had the same amount of pressure on it, but from a different underlying environmental cause? How in the world would that show up in the math? By the time you've put it into numbers and put the numbers into the equations, you can't tell if both loci are under pressure from starvation, or if one is under pressure from starvation and the other from fire-breathing dragons. That disappears from the math just like the color of objects disappears from problems in kinetics.

Starvation will deplete the energy from many biochemical pathways. If you are going to try to find the targets for this kind of selection pressure, look at the pathways which require the most energy. Lenski's experiment works because he doesn't starve his populations to death. Lenski also did an experiment with thermal stress and it is well known that the conformation of enzymes is temperature dependent. To find the targets for thermal stress, look for the enzymes whose activities are most affected by temperature. So if you put starvation pressure and thermal stress on the population at the same time, well you figure it out.
quote:
Unless you can show me some math which does take into account the causes of the pressures, and explain to me how and why it does so ...

Why doesn't anything evolve resistance to Iodine? The reason is that Iodine is a very reactive molecule binding to all kinds of biological molecules, denaturing the molecules, far too many targets for rmns to have any chance for a replicator to evolve resistance to this chemical.
 This message is a reply to: Message 308 by Dr Adequate, posted 10-14-2016 1:27 PM Dr Adequate has responded

 Replies to this message: Message 328 by Modulous, posted 10-14-2016 3:12 PM Kleinman has responded Message 329 by Taq, posted 10-14-2016 3:13 PM Kleinman has responded Message 335 by Dr Adequate, posted 10-14-2016 3:38 PM Kleinman has responded

Kleinman
Member (Idle past 697 days)
Posts: 136
From: United States
Joined: 10-06-2016

 Message 327 of 393 (792846) 10-14-2016 3:00 PM Reply to: Message 317 by Modulous10-14-2016 2:20 PM

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

Nope. Any mutation.

What do you think happens if the mutation is detrimental?
quote:
 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.

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

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
The Lenski experiment, on the other hand, has his variants competing for the resources of the environment.
quote:
 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?

Feel free to quote me if you think I said that. 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. And this process does not work by changing the relative frequencies of variants in a population but works by amplification of the particular variants.
 This message is a reply to: Message 317 by Modulous, posted 10-14-2016 2:20 PM Modulous has responded

 Replies to this message: Message 333 by Modulous, posted 10-14-2016 3:36 PM Kleinman has responded

Modulous
Member (Idle past 80 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 Kleinman10-14-2016 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

Taq
Member
Posts: 7610
Joined: 03-06-2009
Member Rating: 2.7

 Message 329 of 393 (792849) 10-14-2016 3:13 PM Reply to: Message 326 by Kleinman10-14-2016 2:48 PM

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

Perhaps you should figure it out.

 Why doesn't anything evolve resistance to Iodine? The reason is that Iodine is a very reactive molecule binding to all kinds of biological molecules, denaturing the molecules, far too many targets for rmns to have any chance for a replicator to evolve resistance to this chemical.

You claim that RMNS can't produce the features we do see. Why don't you focus on the features we do see instead of the features we don't see.

 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 340 by Kleinman, posted 10-14-2016 3:53 PM Taq has responded

Kleinman
Member (Idle past 697 days)
Posts: 136
From: United States
Joined: 10-06-2016

 Message 330 of 393 (792851) 10-14-2016 3:18 PM Reply to: Message 322 by Taq10-14-2016 2:35 PM

Re: Lenski
quote:
 Kleinman writes:You are making an assumption that the energy fit variants will not be inhibited from reproducing when held at sub-optimal temperatures.

The effect of thermal stress would be the same for both the energy fit and the less energy fit. This would allow the energy fit to outcompete the less energy fit.

What you are not seeing is that the thermal stress will be impairing the replication of the energy fit variants when compared to running the experiment at the ideal temperature. The ability to amplify any beneficial mutation for a given selection pressure can and is impaired by other selection pressures.
quote:
 Does doubling population size double the probability of a beneficial mutation occurring?

It doubles the probability of any mutation occurring at a specific locus.

So if the probability of a beneficial mutation occurring for a population size N is let's say 0.6 and you double the population size to 2N, the probability becomes 1.2?

What you've done here (and it is commonly done) is confuse complementary events (does the mutation occur or doesn't it occur) with additive events (like the probability of rolling a 1 or a 2 with a fair die).

Here's a more detailed explanation if you are interested. Let's say you want to compute the probability of rolling at least a single 1 with two rolls of a die. The probability of rolling 1 with a single roll is 1/6. If you roll the die a second time, the probability of rolling the 1 is again 1/6. But you don't add 1/6+1/6=1/3 to compute the probability of getting at least a single 1, the correct value is 11/36. Try and understand why.

 This message is a reply to: Message 322 by Taq, posted 10-14-2016 2:35 PM Taq has responded

 Replies to this message: Message 344 by Taq, posted 10-14-2016 4:45 PM Kleinman has responded

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