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Author Topic:   Evolving New Information
Dr Adequate
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Message 26 of 458 (509155)
05-19-2009 3:04 AM
Reply to: Message 25 by slevesque
05-19-2009 2:16 AM


Dumb Creationist Strawman
If you want to use the former (descent with modification) to prove the latter (dinosaurs are the ancestors of birds, modern apes and humans have a common ancestor, etc.) ...

No-one does use the former to prove the latter. Descent with modification is the explanation of how the latter occurred. The proof that it occurred would lie in the fossil record, comparative morphology, embryology, molecular phylogeny, et cetera ...


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 Message 28 by slevesque, posted 05-19-2009 3:16 AM Dr Adequate has responded

  
Dr Adequate
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Posts: 16107
Joined: 07-20-2006
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Message 32 of 458 (509175)
05-19-2009 4:12 AM
Reply to: Message 28 by slevesque
05-19-2009 3:16 AM


Sorry, i should have said:

''If you want to use the former (descent with modification) to justify the possibility of the latter (dinosaurs are the ancestors of birds, modern apes and humans have a common ancestor, etc.) you will need much more than that.''

I acknowledge it is not the same thing. But my original idea was this one.

Well, in that case, I would point out that we know of mutations that fuse and split chromosomes, that insert and delete bases, and that change any base to any other base. We know of some other sorts of mutations too, but these alone are sufficient to convert any eukaryote genome to any other eukaryote genome.

Hence, descent with modification is indeed sufficient to achieve the results you specify.


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Dr Adequate
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Posts: 16107
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Message 39 of 458 (509477)
05-22-2009 2:02 AM
Reply to: Message 38 by slevesque
05-22-2009 1:27 AM


And then they arrive with the proofs of the theory of evolution, and I have variation of the color of peppered moth in the population, and the beaks of finches on the galapagos island, plus some story about big and small fishes in amazone rivers, similar to the peppered moth.

Those are examples of natural selection in action.

They are not the proofs of:

... the happening of life in ancient-earth oceans, then about how bacterias evolved into fish, to ampibians, etc. from dinosaurs to birds, from australopithecus to humans, etc.

Please try to distinguish between these two concepts.

There could be an effort done to distinguish the evolution: simple descent with modification and the theory of evolution: from bacteria to bacteriologist.

You have that almost exactly the wrong way round.

We will be discussing these subjects I hope, but in genetics alone, a good read would be ''genetic entropy ...'' by Dr. John Sanford. He gives a couple dozens citations from population geneticists which are extremely revealing of the many problems genetics and mutations pose to the theory of evolution.

A look through the reviews of it suggests that he has a theoretical argument that what we observe can't happen and what we never observe must. It reminds me of the (apocryphal) story of the scientists who claimed to have proved that bees can't fly.

It also appears to be standard creationist rubbish, although maybe I'm doing him a disservice --- maybe they got it from him.

Edited by Dr Adequate, : No reason given.


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Dr Adequate
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Posts: 16107
Joined: 07-20-2006
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(1)
Message 50 of 458 (509580)
05-22-2009 3:18 PM
Reply to: Message 49 by Taq
05-22-2009 2:59 PM


This is similar to my point in Mesage #28.

I think I'll expand on it.

Stevesque, knowing what we do about mutations, we can say with absolute certainty that there is a sequence of mutations from a fish to a newt, or from a reptile to a bird, or from a monkey to a human --- or, for that matter, from a butterfly to an elephant, although that last one hasn't happened.

This is trivially true: it is true in the same way that it is true that by adding, subtracting, and changing enough words one could change A Tale Of Two Cities into Moby Dick.

So when considering a proposed evolutionary transition, there are only two questions we need to ask:

(1) The theoretical question: could there be a sequence of intermediate forms between the start and end of the proposed transition such that each new form is favored or at least tolerated by natural selection? For while the nature of mutations places no restrictions on what can happen, the law of natural selection does.

(2) The evidential question: does the evidence we have confirm or contradict the proposition that the proposed transition did in fact take place?


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Dr Adequate
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Posts: 16107
Joined: 07-20-2006
Member Rating: 7.3


Message 55 of 458 (509606)
05-22-2009 6:58 PM
Reply to: Message 51 by Son
05-22-2009 4:45 PM


I like this explanation, can I quote it for future reference? It will avoid creationists muddling the issue with their "information theory".

I wrote it up for the SkepticWiki here --- you may find the other arguments handy as well.


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Dr Adequate
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Posts: 16107
Joined: 07-20-2006
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Message 60 of 458 (509643)
05-23-2009 4:38 AM
Reply to: Message 56 by slevesque
05-23-2009 3:09 AM


I don't know which review you read, but his argumentation is not solely theoretical. it is based on population genetics, and on the cost of selection.

What he advances is this: mutations are accumulating in the genome, reducing slowly, but steadily, the overall fitness of the population. The vast majority of mutations are deletirious, with again most of them being near-neutral, and so are in Kimura's 'no selection zone' in his graphic of mutation distributions. It has no relevance with 'what we are seeing can't happen', he is right on par with the population geneticists.

Except that the population geneticists think that he's talking rubbish.

Now, I understood his argument. He predicts that species must be "doomed" by the accumulation of genes which are not harmful enough to be rooted out by natural selection, but which cumulatively will cause a species to degenerate so much that it goes extinct. Theoretically, this seems puerile to me, but let's leave aside theory and look at practice.

Consider E. coli. Consider that even if we accepted the minimum YEC age for the Earth, the bacterium E. coli has reproduced through generations in the order of billions. Consider further that as this is a bacterium, it is faced with "Muller's ratchet", which makes it harder for natural selection to eliminate harmful mutations than in "higher" organisms.

Has it gone extinct? No. But we do see that faced with novel environmental challenges, it evolves rapidly to meet them. What he predicts must happen hasn't; what he says can't happen we can see happening.


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 Message 61 by slevesque, posted 05-23-2009 4:53 AM Dr Adequate has responded

  
Dr Adequate
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Posts: 16107
Joined: 07-20-2006
Member Rating: 7.3


Message 62 of 458 (509645)
05-23-2009 4:54 AM
Reply to: Message 58 by slevesque
05-23-2009 3:52 AM


Although I agree there has been revisions of his calculations in the past fifty years, there are no actual numbers that come even close to the fixation rates needed.

But this is not true.

I did the math:

Now, a new neutral variation thrown up by mutation is one of 2N versions (some identical) of the site, where N is the size of the population (the 2, of course, is there because we are dealing with diploid organisms). Because the variation is neutral, this means that it has no better nor worse chance of going on to fixation in the gene pool than the other 2N-1 versions of the site. It follows that when it first arises, its probability of fixation is 1/2N. A more detailed version of the proof will be found here.

Now, let the probability of the mutation in an individual be μ. Then the probability of it arising in a generation will be 2Nμ. So the probability, in any generation, that such a mutation will arise and eventually go on to fixation is 2Nμ/2N; and since we can cancel the 2N on the top and bottom of this fraction this works out to be just equal to μ.

So, let M be the average probability of any mutation arising at any site, expressed in mutations per base pair per individual (i.e. the mutation rate for the population), and let the number of sites be s. Then it follows from the result just given relating the rate of mutation to the rate of fixations that the expected number of fixations per generation is simply given by Ms. Hence if g generations go by, the expected number of fixations is given by gMs.

So, consider what happens when you take a population and divide it into two populations that are unable to interbreed. Each of them will separately undergo different mutations and different fixations: after g generations, each will have undergone gMs fixation events. Therefore, the genetic difference between them since separation is given by gMs + gMs, or, more simply, 2gMs.

[...]

We may therefore draw the following conclusion:

Conclusion : If a population is separated into two non-breeding populations, then to a good degree of approximation the genetic difference between them will be equal to two times the number of generations since separation, times the mutation rate, times the number of sites in the genome.

[...]

Take humans and chimpanzees as an example. Paleontologists claim that the fossil record shows that they diverged about seven million years ago. This leads to a prediction about what we should expect to see if we look at the chimp and human genomes.

Take the average time between generations to be 20 years (not an unreasonable figure, given the documented lifespan and breeding habits of chimpanzees). Hence, in seven million years we would have 350,000 generations.

The rate of single nucleotide substitutions in primates can be found directly by observing the rate at which people exhibit genetic diseases caused by dominant single nucleotide substitutions which are not inherited from their parents, and so represent new mutations: the figure is 1.7 × 10^-8 single nucleotide substitutions per nucleotide per generation (figure from A.S. Kondrashov, Direct estimates of human per nucleotide mutation rates at 20 loci causing Mendelian diseases).

The last figure we need is the size of the genome: approximately three billion sites.

So plugging these figures into the equation derived above, we get a prediction: the divergence (counting only single nucleotide substitutions) between the chimpanzee and human genomes should be approximately 35,000,000 single nucleotide substitutions.

And it is (see Ebersberger et al, Genomewide Comparison of DNA Sequences between Humans and Chimpanzees).

This means you have to fix over 3 mutations per year in the population (considering the divergence 6 millions years ago). Even considering generations of 1 year, this is, at best, unrealistic.

My argument from mathematics and facts trumps your argument from incredulity. The math, by the way, is standard population genetics, I disclaim all originality.

To see that your incredulity is unjustified, consider (a) the mutation rate in humans and (b) the rather lovely mathematical result that the rate of substitution per site per generation in the entire gene pool is equal to the rate of mutation per nucleotide per generation in the individual.

---

To quote the Genetics Society of America:

The GSA supports educating students in genetics and consequently feels it important to express its views on the teaching of evolution in elementary and secondary schools. The GSA strongly endorses such teaching, as genetics and evolution are two very closely interwoven disciplines. In fact, evolution might be summarized as population genetics over time.

Hmm ... I wonder what they know about population genetics that you don't?

Edited by Dr Adequate, : No reason given.


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 Message 85 by slevesque, posted 05-30-2009 3:45 AM Dr Adequate has responded

  
Dr Adequate
Member
Posts: 16107
Joined: 07-20-2006
Member Rating: 7.3


Message 63 of 458 (509646)
05-23-2009 5:06 AM
Reply to: Message 61 by slevesque
05-23-2009 4:53 AM


Prokaryotic genetics is very different then eukaryotic genetic. The no selection zone of mutations is quasi-inexistent ...

That's a good way to wish away inconvenient results. Anything which breeds fast enough to definitively prove you wrong is deemed not to suffer from these magical mutations which cause extinction but aren't selected against. And anything that doesn't, has them ... even though you have no empirical evidence to support this claim.

Since you claim that the dividing line is between prokaryotes and eukaryotes, how do you feel about ... yeast? That's eukaryotic. What's the excuse this time?

... thus why bacteria populations adapt rapidly to new environment, but remain overall static in that they stay the same specie. E.Coli has remained E.Coli from its discovery in 1885 up until now.

(1) The singular of species is species. "Specie" means currency.

(2) What criteria are you using to identify bacterial species?

One key criterion used for identifying E. coli is its inability to feed on citrate ... the very ability that was produced in Lenski's long-term evolution experiment:

In 2008, Lenski and his collaborators reported on a particularly important adaptation that occurred in one of the twelve populations: the bacteria evolved the ability to utilize citrate as a source of energy. Normally, in oxic conditions, E. coli cannot transport citrate from outside the cell to the cell interior (where it could be incorporated into the citric acid cycle); the lack of oxic citrate transport is considered a defining characteristic of the species.

Lenski's first paper on the subject can be found here.

Edited by Dr Adequate, : No reason given.


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 Message 64 by slevesque, posted 05-23-2009 5:53 AM Dr Adequate has responded

  
Dr Adequate
Member
Posts: 16107
Joined: 07-20-2006
Member Rating: 7.3


Message 66 of 458 (509652)
05-23-2009 6:13 AM
Reply to: Message 64 by slevesque
05-23-2009 5:53 AM


How convenient you took away the phrase that would solve the puzzle .

What was it?

I didn't mean a clear line between prokaryotes and eukaryotes.

Ah, backpedalling.

Its about the no selection zone as I mentioned. It is quasi-inexistant due to low noise, and so the phenotype reflects much, much, much more the genotype of the bacteria.

Er ... what? This doesn't appear to mean anything. "Quasi-inexistent due to low noise"?

And what do your statements about bacteria have to do with yeast, which is a eukaryote?

And what evidence do you have for anything you're saying?

As for that second question, let's just say that if the bacteria hasn't changed from its original description at the moment of its discovery (and the further more precise descriptions that came afterwards) then it is still the same species.

But it has changed in such a manner. A defining characteristic of the species has been altered. Anyone who had found something that behaver like Lenski's bacteria in the wild who checked to see if they were E. coli would have found that they weren't and would have announced the discovery of a new bacterial species.

Edited by Dr Adequate, : No reason given.


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Replies to this message:
 Message 69 by slevesque, posted 05-24-2009 2:14 AM Dr Adequate has responded

  
Dr Adequate
Member
Posts: 16107
Joined: 07-20-2006
Member Rating: 7.3


Message 68 of 458 (509704)
05-24-2009 1:43 AM
Reply to: Message 67 by slevesque
05-24-2009 1:36 AM


Ok, well next time I'll use more concrete examples such as dinosaur to bird so that it won't be confusing for anyone.

I don't think that your false statements are confusing anyone but yourself.


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 Message 67 by slevesque, posted 05-24-2009 1:36 AM slevesque has responded

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 Message 70 by slevesque, posted 05-24-2009 2:16 AM Dr Adequate has responded

  
Dr Adequate
Member
Posts: 16107
Joined: 07-20-2006
Member Rating: 7.3


Message 71 of 458 (509708)
05-24-2009 2:44 AM
Reply to: Message 70 by slevesque
05-24-2009 2:16 AM


Is it false to say that birds could become the ancestors of some horse animal in the future ?

Yes. Something that looked kind of horsey, but was descended from birds, would not be a horse, any more than a dolphin is a shark. From a cladistic standpoint, what you're talking about is impossible simply by definition. It is certainly not what onifre was telling you.

But you have more interesting things to be wrong about; I suggest that we focus on those.


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Dr Adequate
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Posts: 16107
Joined: 07-20-2006
Member Rating: 7.3


Message 72 of 458 (509710)
05-24-2009 2:54 AM
Reply to: Message 69 by slevesque
05-24-2009 2:14 AM


The phrase was about the no selection zone.

Then I await its relevance with keen interest.

noise is what determines the range of the 'no-selection zone' in Kimura's mutation distribution. Bacterias have have a very high signal-to-noise ratio because there noise is very, very small.

"Noise"?

So even nearly-neutral deletirious mutations in bacteria have an impact on the phenotypic level on which natural selection can happen.

If you propose that in eukaryotes deleterious mutations have no effect on the phenotype, I should be fascinated to know in what sense they are deleterious.

Likewise, beneficial mutations are rapidly fixed in a population, and the fast accumulation of such mutations makes the optimization of bacteria populations to new conditions very fast (sometimes in a matter of days) Thus, there is no muller's ratchet in those populations.

You might want to look up the term: "Muller's ratchet".

It is, by definition, a mechanism which causes the accumulation of deleterious mutations in asexually reproducing organisms. Such as bacteria.

There is not much difference between the noise in yeast and in bacterias, and so again no muller's ratchet.

Again, you should define "noise", look up Muller's ratchet, and try to provide a shred of a scrap of a scintilla of evidence for anything you're saying.

The difference I could see would be in their mutations rates. Eukaryotic (if I'm not mistaken) have more efficient mutation-correcting mechanisms which would slow down any adaptation compared to bacterias.

And presumably would also "slow down" these hypothetical mutations which cause extinction but are invisible to natural selection.

P.S: YEAST IS A EUKARYOTE. I may have mentioned it once or twice. If your excuse depends on the genetic differences between prokaryotes and eukaryotes, then it does not apply to yeast.

Funny how E.Coli capable of feeding on citrate had already been identified in the past, but were nonetheless recognized as mutant E.Coli

Not at all funny. As with Lenski's experiment, they knew that they were looking at E. coli.

You would not find Lenski's bacteria in the wild if 'the wild' would be in oxygen rich conditions. You have to remember that it was known before Lenski's experiment that E.Coli could ''feed'' on citrate in anaerobic conditions. Lenski put his E.Coli in a very citrate-rich environnment, with very little glucose, keeping them in some sort of starvation mode so that if a mutation could get the citrate inside the cell, it would be beneficial due to a high concentration of citrate.

And they adapted to these conditions. Rather than, for example, going extinct. Biology: 1; Creationist gibberish: 0.

Although the fitness of the bacteria has increased, it has come at a cost:

Of course. All adaptations come at a cost.

If you take Lenski's E.Coli, and give them an abundance of glucose, they will not only regain their ability to feed on it, they will also loose their citrate-feeding capability

Evolution strikes again!

Put them in different environnments, and they will develop different 'new traits' accordingly. But all in all, they will always remain E.Coli.

Apart from not having one of the defining characteristics of E. coli.

Just like, "all in all", humans are still monkeys.

Edited by Dr Adequate, : No reason given.

Edited by Dr Adequate, : No reason given.


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Dr Adequate
Member
Posts: 16107
Joined: 07-20-2006
Member Rating: 7.3


Message 75 of 458 (509741)
05-24-2009 10:16 AM
Reply to: Message 73 by slevesque
05-24-2009 3:29 AM


Phenotypic noise. It is the simple concept that factors other then the genome influence natural selection. Mostly enviromental factors such as nutrition,chance etc.

You mean genetic drift? And you're claiming that bacteria are immune to this? Really?

On what basis, other than that you really want it to be true?

How are bacteria immune to "nutrition, chance, etc"?

Surely nutrition, for example, must affect bacteria in some way. In that they die if they don't get adequate nutrition.

Signal-to-noise ratio is often expressed in terms of heritability. a heritability of 1 means the trait is 100% heritable (such as blood type). As an example, height has a heritability of 0.3

So you mean: "low heritability of the characters affected by the genes under discussion". Fair enough --- you may introduce what terms you like so long as you define them. I still can't see where you're going with this, though.

They are not neutral, they are nearly-neutral (neutral mutations don't exist, see kimura).

That would be Kimura the founder of neutralism and the author of The Neutral Theory of Molecular Evolution, yes? Can you quote him as saying that there are no neutral mutations? (Hint: no.) Can you quote him as saying that all near-neutral mutations are harmful? (Hint: no.) Can you quote him as saying:

Although much progress has been made in biology since Darwin's time, his theory of natural selection still remains as the only scientifically acceptable theory to explain why organisms are so well adapted to their environments.

(Hint: yes.)

Can you quote him as saying:

Our civilization would be pitifully immature without the intellectual revolution led by Darwin.

(Hint: yes.)

It's possible that he understands the implications of his work better than you do.

Maybe a quote from Muller will make it a little more clear:

If that is Muller talking about Muller's ratchet, then he is, by definition of Muller's ratchet, talking about organisms that reproduce asexually. Such as bacteria.

Incidentally, that's H. J. Muller, yes? The guy who described The Origin Of Species as "the greatest book ever written"?

I hope this makes it clearer. For the mutations to accumulate in the population, they most be selectable. In order for them to be selectable, signal-to-noise ratio most be high. So bacterias (and yeast), due to very small noise, have practically no accumulations of deletirious mutations.

So now not only do these extinction-causing mutations have very little effect, but they don't always have all or any of the very little effect that they have. But they can still make a species go extinct.

So bacterias (and yeast), due to very small noise, have practically no accumulations of deletirious mutations.

Do you have any evidence for this claim?

Are you aware that Muller, whom you just quoted with apparent approval, completely disagrees with you? Once more, I urge you to look up the phrase "Muller's ratchet" and find out what it actually means.

I won't come back on the Lenski experiment, as I think my explanation was pretty clear. You say its evolution, fine, as long as your showing it as simple descent with modification, and not as one of the steps of bacteria-to-man evolution.

Descent with modification is all evolution. It's the definition of evolution.

What Lenski's experiment, and countless others, demonstrate, is that we see evolution in which natural selection causes the fixation of adaptive mutations. We see this all the time. We do not see species going extinct as a result of mutations so subtle in their effects as to be invisible to natural selection. Ever.

Edited by Dr Adequate, : No reason given.

Edited by Dr Adequate, : No reason given.


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Dr Adequate
Member
Posts: 16107
Joined: 07-20-2006
Member Rating: 7.3


Message 86 of 458 (510334)
05-30-2009 4:06 AM
Reply to: Message 83 by slevesque
05-30-2009 3:15 AM


Find Kimura's mutation distribution graphic, you will see that 0 (neutrality) is an asymptote.

I'm not sure what you think that means, but I'm fairly sure that you're wrong. What do you mean by "Kimura's mutation distribution graphic"? Is it one of the figures in The Neutral Theory Of Molecular Evolution (yes, that's The Neutral Theory Of Molecular Evolution) and if so, which one? If you will tell me which figure, I shall tell you what it means.

And I am absolutely certain that Kimura, the founder of neutralism, did not deny the existence of neutral mutations.

Also on Muller ratchet, notice that it was never observed to cause the extinction of bacteria species. It was, in fact, very, very, very seldom observed. Remember that at the time Muller thought of this, technology wasn't good enough for him to test it. It is still much more hypothetical than experimental, exactly because of what I was saying earlier.

The only experimental documentation of muller's ratchet I found is this:
- Chao, 1990, Fitness of an RNA virus decreased by Muller's ratchet, Nature 348: 454 - 455

Muller ratchet has not yet been falsified. The vast majority of geneticist agree that it exists. ... Its existence in bacteria populations is not questioned by evolutionist or creationist.

Again, I don't see what you're driving at. I said that the concept of Muller's ratchet only applies to asexually reproducing organisms, such as bacteria, in which I am, of course, right.

Your reply that its existence in bacteria is not questioned does not constitute a rebuttal. I am not questioning its existence in bacteria. I am asserting its existence in bacteria.

It is because of what I have explained (noise, etc.).

Your excuse about there being no "noise" in bacteria, besides being palpable rubbish, was intended as an excuse to allow you to pretend that bacteria are immune from accumulating deleterious mutations, remember? If you are now admitting that bacteria are subject to Muller's ratchet, then you admit that they do in fact do so, and that moreover they do so by a mechanism that does not apply to sexually reproducing organisms.

Ask a geneticist and he will give you aproximately the same answer.

No.

The interpretation creationist do of it is debatable, but for that you'll have to read the book instead of just reading the critics on amazone.com

As he can't explain what he's talking about, and you are at least willing to try, I believe I'll stick to debating with you.


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Dr Adequate
Member
Posts: 16107
Joined: 07-20-2006
Member Rating: 7.3


Message 87 of 458 (510335)
05-30-2009 4:21 AM
Reply to: Message 85 by slevesque
05-30-2009 3:45 AM


Ok, I'll try to follow you here.

According to your calculations, how many mutations would be fixed in a single generation ? Your equation is gMs if I'm not mistaken.

Now 1 generation means g=1. M=1.7 ~ 10^-8 and s=3 000 000 000

So, according to you, there is 510 mutations fixed per generation, am I correct on this ?

I make it 51.

If so, why the part on ƒÊ ?

I don't know how the characters in red display on your browser, but on mine they're the fortissimo symbol followed by a capital E with a circumflex. This makes your question someone opaque.


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