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Author Topic:   Extent of Mutational Capability
Pressie
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Posts: 1714
From: Pretoria, SA
Joined: 06-18-2010
Member Rating: 3.2


Message 181 of 279 (793655)
11-03-2016 5:40 AM
Reply to: Message 171 by CRR
11-02-2016 7:57 PM


Re: The Maths
CRR writes:

It's known as Haldane's Dilemma.

Then you provide a reference to an Electrical Engineer writing something somewhere about mutations. Lots and lots of words and formulaes and nothing else. No maths done.

From there:

Also, this paper focuses on single substitutions (non-overlapping in time). Multiple substitutions (overlapping in time) are an advanced topic to be covered in another paper. Until the basics are covered, we need to leave out genetic complexities, like sexual reproduction and diploidy.
What? He writes a paper only dealing with point mutations in organisms having kids asexually and diploidy? Then goes on about humans and chimps?

Colour me unimpressed. To me ReMine seems to be a bit of a loon. He missed all those other forms of mutations we know of and discovered since 1957.

So, CRR, could you show us the maths? Not a reference. The maths supporting your claims.


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Message 182 of 279 (793657)
11-03-2016 7:12 AM
Reply to: Message 177 by PaulK
11-03-2016 1:40 AM


Re: The Maths
PaulK writes:

You know, citing Walter ReMine is hardly going to prove your case. And I recognise "saintpaulscience" as ReMine's site and the claim of 1667 mutations as his assertion. ReMine's opinions are not accepted science.

I'll make this same point to CRR, that he can argue any position he likes regardless of any current scientific consensus and that he's encouraged to argue Walter ReMine's position here, but that he must bring the arguments into the thread.


--Percy
EvC Forum Director

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Admin
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Message 183 of 279 (793658)
11-03-2016 7:14 AM
Reply to: Message 178 by CRR
11-03-2016 3:32 AM


Re: The Maths
CRR writes:

You say you don't trust my source without looking at it; without evidence

Participants here are encouraged to make their case in their own words and use links only as references. It's actually in the Forum Guidelines:

  1. Bare links with no supporting discussion should be avoided. Make the argument in your own words and use links as supporting references.

--Percy
EvC Forum Director

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RAZD
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From: the other end of the sidewalk
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Message 184 of 279 (793659)
11-03-2016 7:40 AM
Reply to: Message 159 by dwise1
11-02-2016 12:03 AM


Most probability exercises involve a particular series of independent events all happening in a particular sequence. ...

Which, as you say, is not the way evolution works.

But that's not what we are talking about. We are talking about a population and about the probability of at least one of them succeeding. What we want to know is the probability of at least one member of the population succeeding. ...

Now let's assume a larger population size, like 10,000, which in the wild shouldn't be too unreasonable:
Q = q10 000 = 4.517-5
P = 1-Q = 0.99995483
Approaching dead certainty, wouldn't you agree? ...

Thank you for supporting my more bald assertion that "For the purpose of maths we can say that this has a probability of >0.99, so we can use 0.99 and be conservative."

For each generation.

But the question I was addressing was the probability of two successive mutations and whether one was dependent on the other. They aren't. The probability of the second mutation occurring is not reduced because another mutation preceded it. The probability of a mutation is dependent on the whole genome, not any previous mutations.

Of course, my MONKEY, like Dawkins' WEASEL, does not simulate evolution, but rather it compares two different kinds of selection: single-step selection and cumulative selection. The target is the alphabet in alphabetical order. Single-step selection involves trying to put the alphabet together randomly in one attempt and, when that fails, start all over from scratch. I calculated that in order to have one in a million chance of success, you have to run the program on a supercomputer (performing 1,000,000 attempts per second, hence running 1000 or 10000 times faster than the fastest PC) for many several times the 14-billion-year ago of the universe. Yet both MONKEY and WEASEL succeed within seconds (or within a half-hour in the case of the original WEASEL), every time without fail. By using cumulative selection, which is based on evolution. Single-step selection is based on creation out of nothing, creation ex nihilo.

Even though single-step selection has absolutely nothing to do with how evolution works, creationists continually try to saddle us with that loser of theirs.

Precisely. When a mutation happens in one generation then it becomes part of the genome for the next generation, and the probability of a mutation in the next generation is still 0.99, and whether or not it forms a synergy with the previous one is the same as whether or not it forms a synergy with the rest of the genome.

That successive mutations do happen has been observed in experiments ([i]E.coli[i]), but that occurs because the first mutation is built into the genome where the second mutation occurs, not because they are linked into a pattern that must happen.

Enjoy


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RebelAmerican☆Zen☯Deist
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jar
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Posts: 29183
From: Texas!!
Joined: 04-20-2004
Member Rating: 2.7


Message 185 of 279 (793664)
11-03-2016 9:12 AM
Reply to: Message 173 by Coyote
11-02-2016 9:07 PM


Re: The Maths
Coyote writes:

You cite a website titled "saintpaulscience.com" as your source.

I don't trust any religious group or evangelical type who claims to be doing science. If they were to say the sun rises in the east I'd have to check it the next morning to see if their claims were correct. The reason is, so many of their claims have been found to be nonsense. See the Index to Creationist Claims for a refutation of a lot of their claims:

In this case it is a publishing company located in St Paul Minnesota but still just a vanity press it seems with the sole purpose of hawking the authors own books.


My Sister's Website: Rose Hill Studios My Website: My Website

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Dr Adequate
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Posts: 15948
Joined: 07-20-2006
Member Rating: 5.0


Message 186 of 279 (793667)
11-03-2016 9:37 AM
Reply to: Message 178 by CRR
11-03-2016 3:32 AM


Re: The Maths
You say you don't trust my source without looking at it; without evidence

And yet you have seen fit to engage with the only person who did dismiss your nonsense out of hand, rather than with any of the people who carefully pointed out what's wrong with it. Really you should be grateful to Coyote: it seems that without him you'd have had no comeback at all.


This message is a reply to:
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Replies to this message:
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dwise1
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Posts: 2912
Joined: 05-02-2006
Member Rating: 4.4


(3)
Message 187 of 279 (793670)
11-03-2016 10:26 AM
Reply to: Message 179 by Tangle
11-03-2016 3:43 AM


Re: The Maths
From Musgrave's post cited in your quote, Weasels, ReMine, and Haldane's dilemma:

quote:
There has been some discussion on the newsgroups talk.origins and sci.bio.evolution over the last year or so regarding Walter ReMine's claims that a version of Dawkins' "weasel" program, which demonstrates the efficacy of selection, nevertheless demonstrates a serious limitation on the rate of evolution, in agreement with Haldane's Dilemma, a rate so low that Mr. ReMine claims this makes the current accounts of human origins (and other higher vertebrates) implausible

. . .

Fortunately, Will Pratt of the University of Nevada found a copy, and as a result Robert Williams was able to get a copy of David Wise's program MONKEY (see http://www-personal.monash.edu.au/~ianm/whale.htm), which ReMine used. As I also noted earlier, after running it several times, and looking at the code, I couldn't find any hint of Haldane's Dilemma in the program. What was I missing?

The answer is actually blindingly simple, and is an embarrassment to Mr. ReMine.

. . .

Can you see where ReMine has made his error? I actually wasted a couple of hours comparing the effects of mutation rates on different programs before I realized it, but it should have been blindingly obvious (so I'm stupid, okay, but I was expecting something subtle).

Here's the key line: "Then we reduce the reproduction rate to that of the higher vertebrates, say to n=6."

Well, knock me down with a stick of mortadella and call me Jake. Mr. ReMine doesn't know how these programs work! In the vast majority of weasel simulations, including Wise's, the program takes a string, makes x copies of it with single letter mutations in one or more copies of the string, then chooses the best string and makes x copies of that with mutations, then chooses the best string from those copies, and makes x copies ad infinitum until the target string is reached. In many of these programs, the value x is a user entered variable called "number of offspring" or similar wording.

The important thing to note is that in Wise's program, Dawkins' original, Wesley Elsberry's weasel.pl and my WEASEL4.BAS (see sig) the "reproduction rate", i.e. number of offspring, IS ALSO THE POPULATION SIZE! Of course you will see only slow substitution in any of these programs when you only have 5 offspring, as there is only a TOTAL POPULATION of 5 strings at any one time![1]

Of course, in the real world, most organisms have populations of more than 5 individuals :-). Trying to compare the substitution rate in a population of 5 indviduals with the substitution rate in a population of between 10,000 to 100,000 individuals is a pretty big blunder to make, even allowing for the other problems in trying to compare this program with a real population. The information about "offspring" number isn't hidden, it's clear in the description given by Dawkins and in David Wise's documentation.

ReMine's argument totally collapses, without even having to point out the other, obvious problems.


I am that David Wise and MONKEY is my program (http://cre-ev.dwise1.net/monkey.html). Not only do I describe what MONKEY does, but I also analyzed the probabilities involved. I even provide the source code (then written in Pascal, but now also converted to C). What the program does is so easy to understand and information is so freely available, it boggles the mind how creationists like Remine and Royal Truman can get it so wrong. They have to be trying very hard to misunderstand it. They certainly have strong motivation to misunderstand everything: protecting their faulty theology from reality.

Verily it was written: "Everybody's got something to hide, except for me and my MONKEY!"


This message is a reply to:
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Replies to this message:
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jar
Member
Posts: 29183
From: Texas!!
Joined: 04-20-2004
Member Rating: 2.7


(2)
Message 188 of 279 (793671)
11-03-2016 10:48 AM
Reply to: Message 187 by dwise1
11-03-2016 10:26 AM


and verily it was ordained to happen
dwise1 writes:

Verily it was written: "Everybody's got something to hide, except for me and my MONKEY!"

And an obvious proof of Intelligent Design and Control is that I happen to be listening to the White Album right now.


My Sister's Website: Rose Hill Studios My Website: My Website

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Coyote
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Posts: 5937
Joined: 01-12-2008
Member Rating: 3.8


(1)
Message 189 of 279 (793672)
11-03-2016 10:56 AM
Reply to: Message 178 by CRR
11-03-2016 3:32 AM


Re: The Maths
You say you don't trust my source without looking at it; without evidence

Looks like I was right in not trusting your source without looking at it.

From the posts that followed mine it appears that site is Walter ReMine's!

He's the one pushing the "Baraminology" nonsense! I'm familiar with that stuff--what a joke. He's just trying to make "kinds" seem scientific to bolster his religious beliefs. In fact, he's doing the exact opposite of science.


Religious belief does not constitute scientific evidence, nor does it convey scientific knowledge.

Belief gets in the way of learning--Robert A. Heinlein

In the name of diversity, college student demands to be kept in ignorance of the culture that made diversity a value--StultisTheFool

It's not what we don't know that hurts, it's what we know that ain't so--Will Rogers

If I am entitled to something, someone else is obliged to pay--Jerry Pournelle

If a religion's teachings are true, then it should have nothing to fear from science...--dwise1

"Multiculturalism" demands that the US be tolerant of everything except its own past, culture, traditions, and identity.


This message is a reply to:
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Replies to this message:
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Pressie
Member
Posts: 1714
From: Pretoria, SA
Joined: 06-18-2010
Member Rating: 3.2


(1)
Message 190 of 279 (793696)
11-04-2016 9:23 AM
Reply to: Message 189 by Coyote
11-03-2016 10:56 AM


Re: The Maths
Yes, Coyote, for some reason YEC's think that nobody knows about nonsense YEC's write? Even me, as a non-genetisist could pick up that ReMine wrote nonsense.

Hey, CRR, show us the maths.

YEC's really are delusional. What bothers me is that they think that all people are as delusional as they are.

CRR, show us the maths.

Edited by Pressie, : No reason given.

Edited by Pressie, : No reason given.

Edited by Pressie, : No reason given.


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RAZD
Member
Posts: 18861
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 3.6


(1)
Message 191 of 279 (793702)
11-04-2016 3:43 PM
Reply to: Message 190 by Pressie
11-04-2016 9:23 AM


The Maths vs reality
YEC's really are delusional. What bothers me is that they think that all people are as delusional as they are.

I don't think this is accurate. Deluded maybe, but not necessarily (insane) delusional. Being deluded is similar but worse than ignorant, imho, because they are mis-informed not uniformed.

This is like Faux Noise Nutwerk listeners knowing less real facts about current events than people that don't listen to any news.

CRR, show us the maths.

Again, the problem is that mathmatic models cannot change reality, they can only model it, and when the results do not match reality then either the assumptions used or the model itself is wrong, not reality.

Enjoy


we are limited in our ability to understand
by our ability to understand
RebelAmerican☆Zen☯Deist
... to learn ... to think ... to live ... to laugh ...
to share.


Join the effort to solve medical problems, AIDS/HIV, Cancer and more with Team EvC! (click)

This message is a reply to:
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CRR
Member
Posts: 534
From: Australia
Joined: 10-19-2016
Member Rating: 1.3


Message 192 of 279 (793896)
11-07-2016 2:38 AM
Reply to: Message 176 by Dr Adequate
11-02-2016 10:32 PM


Re: The Maths
Actually your (or sfs's) maths is wrong by several orders of magnitude.

By your argument the number of mutations in the human lineage should be 100 x average population size x 350,000. Say an average size of 1 million and you get ~3.5x10^13; which is larger than the size of the genome. If all those actually got fixed it would be error catastrophe!

But they don't all get fixed; only a very small proportion do. Genetic drift is far more likely to eliminate a neutral mutation than to fix it.

A large number of conceptions never even make it to birth if the mutations are lethal within the first 9 months so the a filter has already been applied to the types of mutations that appear in each succeeding generation. This is probably why so many of them appear to be near neutral.

A bit of thought should show you that the calculation is flawed. If we have fixed 18 million mutations in 350,000 generations that comes to 50 mutations being fixed per generation. The human genome is not varying at anything like this sort of rate. There are only a couple of mutations that are currently in the process of being fixed, one of which is adult lactose tolerance. It would also mean that there would be a great deal of variation in the human genome around the world, but it is actually notable for the low variation worldwide.

It appears you and sfs have been seduced by fortuitously good agreement between a wrong calculation and experimental results.


This message is a reply to:
 Message 176 by Dr Adequate, posted 11-02-2016 10:32 PM Dr Adequate has responded

Replies to this message:
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CRR
Member
Posts: 534
From: Australia
Joined: 10-19-2016
Member Rating: 1.3


Message 193 of 279 (793897)
11-07-2016 2:40 AM
Reply to: Message 186 by Dr Adequate
11-03-2016 9:37 AM


Re: The Maths
I have a real life so can't always respond immediately. That happened to be one I could tackle in some down time on the train. I have now responded to you so you don't need to feel left out.
This message is a reply to:
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CRR
Member
Posts: 534
From: Australia
Joined: 10-19-2016
Member Rating: 1.3


Message 194 of 279 (793898)
11-07-2016 2:42 AM
Reply to: Message 190 by Pressie
11-04-2016 9:23 AM


Re: The Maths
Who has refuted ReMine's paper? No one that I know of.
This message is a reply to:
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Replies to this message:
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Dr Adequate
Member
Posts: 15948
Joined: 07-20-2006
Member Rating: 5.0


(3)
Message 195 of 279 (793909)
11-07-2016 3:21 AM
Reply to: Message 192 by CRR
11-07-2016 2:38 AM


Re: The Maths
By your argument the number of mutations in the human lineage should be 100 x average population size x 350,000.

[...]

But they don't all get fixed; only a very small proportion do.

I see what you're missing.

You're not familiar with the math, are you?

It's actually very pretty. Y'see, the chances of a neutral mutation going on to get fixed is inversely proportional to the size of the population (as you say "only a very small proportion"). Whereas (this is what you seem to be getting at with your "100 x average population size" bit), the number of mutations per generation in the population is proportional to the population size.

And so these two things cancel out exactly, leaving us with the lovely result that the rate of fixation of neutral mutations in the population is exactly their rate of occurrence in an individual!

Isn't that nice?

A bit of thought should show you that the calculation is flawed. If we have fixed 18 million mutations in 350,000 generations that comes to 50 mutations being fixed per generation. The human genome is not varying at anything like this sort of rate.

Yes it is. The figures for the mutation rate are taken from observing how much mutation happens.

There are only a couple of mutations that are currently in the process of being fixed

What a strange thing to say.

Why in the world did you say it?

It appears you and sfs have been seduced by fortuitously good agreement between a wrong calculation and experimental results.

It seems that you are being prematurely condescending.

---

ETA: From Wikipedia:

Under conditions of genetic drift alone, every finite set of genes or alleles has a "coalescent point" at which all descendants converge to a single ancestor (i.e. they 'coalesce'). This fact can be used to derive the rate of gene fixation of a neutral allele (that is, one not under any form of selection) for a population of varying size (provided that it is finite and nonzero). Because the effect of natural selection is stipulated to be negligible, the probability at any given time that an allele will ultimately become fixed at its locus is simply its frequency p in the population at that time. For example, if a population includes allele A with frequency equal to 20%, and allele a with frequency equal to 80%, there is an 80% chance that after an infinite number of generations a will be fixed at the locus (assuming genetic drift is the only operating evolutionary force).

For a diploid population of size N and neutral mutation rate μ, the initial frequency of a novel mutation is simply 1/(2N), and the number of new mutations per generation is 2Nμ . Since the fixation rate is the rate of novel neutral mutation multiplied by their probability of fixation, the overall fixation rate is 2Nμ 1/2N = μ.

Edited by Dr Adequate, : No reason given.

Edited by Dr Adequate, : No reason given.


This message is a reply to:
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