Summations Only

quote:

---

Time is not measured in seconds, minutes, hours for rmns, the measure of time for rmns is replications (generations).

Quite: so generation time is also something you'd need to know.

---

Ok, go for it, how much time for a generation for your dinosaur.

quote:

---

The reason I answer I don't know to a question is I don't know.

​

But why did you say you didn't need to know?

---

Because the mutation rate is going to be higher than the beneficial mutation rate.

quote:

---

What you can do with calculations like mine are obtain estimates of the upper limits of the probabilities for rmns. Assume that when the mutation occurs at the particular site, it is always the beneficial mutation, that will raise your probabilities slightly but it will not make the multiplication rule go away when more than a single beneficial mutation must occur on a lineage.

​

Again, the probability of that is 1 --- given enough time.

---

--- given enough time and your population doesn't go extinct.

quote:

---

Kleinman writes:

​

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

No more so than having more than one step in a flight of stairs is a problem. All you do is rinse and repeat the same process.

---

Try climbing two different flights of stairs at the same time.

quote:

---

I hope your expectations aren't too high when you buy tickets to two different lotteries and think you are going to win both.

​

You don't have to win both. The descendants of two winners can meet up and combine their winnings. That is how sexual recombination works.

---

You win a lottery, everyone wants to marry you.

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?

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.

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?

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:
Scientists create video of bacteria evolving drug resistance.

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.

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:
Scientists create video of bacteria evolving drug resistance.
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.

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.

quote:

---

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.

---

So you think that a range animal cannot be subjected to thermal stress, starvation, predation, disease, dehydration,... at the same time?

quote:

---

Kleinman writes:

​

Try climbing two different flights of stairs at the same time.

That's exactly what sexual species do.

---

And then there is always 3 and more different flights of stairs. What happens then?

quote:

---

You win a lottery, everyone wants to marry you.

​

Your tacit admission of defeat is accepted.

---

Not quite yet, you still have quite a few more flights of stairs to climb. We are going to get you cardiac fit and teach you a little probability theory before this is over.

quote:

---

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.

---

You can see this same thing with drug selection pressures, watch this video:
Scientists create video of bacteria evolving drug resistance.

quote:

---

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)

---

You are describing the Lenski experiment which takes more than a thousand generations per beneficial mutation. Do you think his experiment would run faster if Lenski applied a little thermal stress to his population as well?

quote:

---

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.

---

Lenski's starvation stress slows the doubling time for his population to about every 7 hours. Under ideal conditions, bacteria can double every 20 minutes. Stress these bacteria more and it will only slow their generation time which will in turn, slow the amplification time which will in turn slow the evolutionary process even more so. 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.

quote:

---

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.

---

I have figured it out, I published the mathematics of random mutation and natural selection for multiple simultaneous selection pressures. But in order to understand this paper, you need to understand the difference between complementary events and additive events.

quote:

---

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.

---

I have done this, all my mathematics is done based on real, measurable and repeatable examples of rmns.

quote:

---

What do you think happens if the mutation is detrimental?

It tends to decrease in frequency.

---

Yup, and it will also decrease in number and that's why it's very unlikely that you will get a beneficial mutation on a member of this lineage

quote:

---

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.

---

But the mathematical fact of life is that rmns is not dependent on relative frequencies of variants in the population, it is dependent on the ability of a particular lineage to amplify.

quote:

---

Here's an example where rmns is occurring in an environment where variants are not competing for resources in the environment:
You’ve reached a 404 page.

​

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.

---

They are not competing for food initially because the petri dish is so large, if you tried to run this experiment in a standard sized petri dish then competition for resources would start almost immediately and it would be much less likely that you would see the evolution of drug resistance.

quote:

---

. 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.

---

At what point do you say that the probabilities are so low that the particular outcome is impossible. 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 you have enough significant figures on your calculator, you might claim this is still possible but you better have a lot of significant figures on your calculator, otherwise, it will say 0.

quote:

---

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?

---

You can have amplification without any change in the relative frequency of the variants in a population by having all variants amplifying simultaneously. That's what you are seeing in the video of the bacteria evolving resistance. 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. On the other hand, you can have fixation without any amplification. Simply kill off all the variants except the one which is now fixed.