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Author Topic:   Extent of Mutational Capability
Dr Adequate
Member (Idle past 285 days)
Posts: 16113
Joined: 07-20-2006


(2)
Message 140 of 279 (793486)
10-30-2016 9:41 AM
Reply to: Message 136 by mike the wiz
10-30-2016 7:03 AM


I've always thought of this question as being the wrong way around. We must go from knowledge and facts firstly. Known facts. It is a known fact that specified complexity, contingency planning, information, etc..comes from intelligent design.
Please present evidence for this claim, and define "specified complexity".
Note that mere assertion is not evidence.
Instead of saying, "is there a limit to evolution", the correct logical question is this; "is there any reason to believe a non-intelligent process can come up with the most marvellous designs on the planet?
To which the answer is, of course, yes. (See this thread, passim.)
Is there any reason to believe that evolution is an omnipotent, omniscient, UNLIMITED, creative force?"
None whatsoever; it is certain that evolution is no such thing, as any scientist would tell you if you ever listened to scientists.
Which is why when we look at living things which were clearly not created by an omnipotent, omniscient, unlimited, creative force, it makes sense to ascribe them to evolution, and it makes no sense to ascribe them to God, who is (by definition) an omnipotent, omniscient, unlimited, creative force.
In the same way, because evolution is supposed to have invented hearts, lungs full bodies with complete moving chassis' (skeletons) and everything else, including all of the correct materials, such as enamel for teeth instead of wood, and bones for hands instead of blubber, then I expect to see a portion of macro-evolution's abilities, by seeing in the lab, it invent an organ or a new anatomy in a fruit fly or a bacteria.
You mean like fruit flies getting an extra pair of wings?
Or the evolution of multicellularity in Chlorella? That sort of thing?
The "little adds up to a lot" argument of micro evolution, is a false argument, and even if you argue it isn't, I remain of the opinion it is false and nobody can convince me otherwise, so I don't care if people disagree because I always know what I am talking about. The fact is adding up a general stasis in the fossil record, doesn't add up to macro.
For example, if we take a jellyfish that is 500 million years old, and compare it to a modern one which is identical, obviously if we add up such micro-evolution, we don't get macro. Nor is there ever any indication of change within the fossil counterpart, beyond superficial change, IMHO. For example we might find a giant platypus or nautiloid or croc, but they are giant, but anatomically not really any different beyond superficiality.
By majority of the evidence, we don't see bats or turtles or bunnies or starfish or apes, evolving, we see them stay the same. (I don't refer to human evolution with apes, but the things which would have had to evolve into apes, quadruped progenitors that are completely absent/fictional).
Are you really claiming that there is no evidence of macroevolution in the fossil record?
Are you feeling quite well?
The true question is; "is there a reason to believe evolution is an unlimited, creative designer with more brains than things with brains despite it having no intelligence
And the answer again is: none whatsoever, as any scientist would tell you if you listened to scientists instead of the crazy crap in your head.
No silly person can convince me that the designs I see in nature, created themselves ...
Has any silly person ever tried? Or have people told you something else which you are deliberately misrepresenting because you find yourself impotent to argue against the stuff that people actually say?
It's obvious, that God created the universe. Obvious.
Yeah, you've just got to look at the Loa loa worm burrowing through the eyeball of an African child to immediately, obviously see the magnificent sublime nature of its creator. Though I would challenge any creationist to go further and infer that the creator must at some point in his career have been outwitted by a talking snake.
Edited by Dr Adequate, : No reason given.
Edited by Dr Adequate, : No reason given.
Edited by Dr Adequate, : No reason given.

This message is a reply to:
 Message 136 by mike the wiz, posted 10-30-2016 7:03 AM mike the wiz has not replied

  
Dr Adequate
Member (Idle past 285 days)
Posts: 16113
Joined: 07-20-2006


Message 151 of 279 (793532)
11-01-2016 10:02 AM
Reply to: Message 148 by CRR
11-01-2016 3:51 AM


Seriously? This is basic stuff.
And yet apparently you can't do it.

This message is a reply to:
 Message 148 by CRR, posted 11-01-2016 3:51 AM CRR has not replied

  
Dr Adequate
Member (Idle past 285 days)
Posts: 16113
Joined: 07-20-2006


Message 152 of 279 (793533)
11-01-2016 10:10 AM


What Is CRR's Argument?
It looks like CRR's argument, if he produced it, would involve playing Texas Sharpshooter with neutral mutations fixed by drift as the retrospectively declared targets, but he's not being very clear about it.

  
Dr Adequate
Member (Idle past 285 days)
Posts: 16113
Joined: 07-20-2006


Message 165 of 279 (793602)
11-02-2016 2:31 PM
Reply to: Message 161 by Gregory Rogers
11-02-2016 8:26 AM


If I could centre in on one of them: the whale example. The evolutionary position here is, I believe, that the whale-ancestor was a land mammal which adapted to sea life and ultimately became the whale of today. The vestigial limb is cited as proof of this.
I would like to ‘unpack’ this a bit: the ID and Creationist response here is to say that the limb is not vestigial, but has a natural function, serving as an attachment point for muscles that both male and female cetaceans need to reproduce.
Well, as you point out, we can compare with other sea creatures. Sharks get by fine without vestigial hips and thighs. Sp if God wanted to make a sea creature that could reproduce, he didn't have to do so in such a way as to supply evidence for evolution.
We can also look back in the fossil record, and see how earlier whales had vestigial legs that were external and had weensy little toes on the ends of them. These were not necessary for the attachment of reproductive muscles. Here's the foot of a Basilosaurus.
Here's a look at Dorudon:
Edited by Dr Adequate, : No reason given.

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Dr Adequate
Member (Idle past 285 days)
Posts: 16113
Joined: 07-20-2006


(6)
Message 166 of 279 (793603)
11-02-2016 2:34 PM


Could I add that the evolutionists are getting unreasonably testy. These are fair questions to which we have perfectly good answers, so why be annoyed at people asking them? This is what we're here for.
Edited by Dr Adequate, : No reason given.

  
Dr Adequate
Member (Idle past 285 days)
Posts: 16113
Joined: 07-20-2006


(1)
Message 167 of 279 (793606)
11-02-2016 2:47 PM
Reply to: Message 161 by Gregory Rogers
11-02-2016 8:26 AM


More About Whales
Some of our most interesting discussions on this forum have been about whales. You can look at them here. Lots of evidence is cited.
EvC Forum: Evidence for Evolution: Whale evolution
EvC Forum: Creationist response to cetacean femur, leg atavism, and limb bud.
EvC Forum: Animals with bad design.

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Dr Adequate
Member (Idle past 285 days)
Posts: 16113
Joined: 07-20-2006


(1)
Message 174 of 279 (793644)
11-02-2016 10:23 PM
Reply to: Message 171 by CRR
11-02-2016 7:57 PM


Re: The Maths
Briefly. Haldane's Dilemma establishes a limit of 1,667 beneficial substitutions (where a substitution is almost always one nucleotide) over the past ten million years of the lineage leading to humans.
Well, obviously it's impossible to be that precise (saying "a limit of 1667" is absurd) but I'd say it would be around that order of magnitude, yes.
Now all you have to do is tell us how many beneficial mutations there actually were on the lineage leading to humans, so that we can compare the two figures.
I'll wait.
The generation time for chimps is similar to humans but even allowing a shorter time there should be no more than 5000 mutation differences separating chimps and humans if the evolutionary scenario is correct.
Wrong, CRR. Because Haldane's dilemma only applies to beneficial mutations. Quite different math applies to the accumulation of neutral mutations. The math shows that we should expect those in the tens of millions.

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Dr Adequate
Member (Idle past 285 days)
Posts: 16113
Joined: 07-20-2006


Message 176 of 279 (793646)
11-02-2016 10:32 PM
Reply to: Message 171 by CRR
11-02-2016 7:57 PM


Re: The Maths
Forum member sfs posted this some time ago. He isn't around, but I am and I've done a very similar calculation; I'm only posting his 'cos I don't have mine with me and I'm lazy. Anyway, my point is that if anyone has any questions about it, they can ask me.
sfs writes:
The scientific question then is this: Do genetic differences between humans and chimpanzees look like they are the result of lots of accumulated mutations? What predictions about the differences can one make, based on the hypothesis that they are all the result of mutation?
For starters, we should be able to predict how different the genomes should be. The seven million years of evolution in each lineage represents about 350,000 generations in each (assuming 20 years per generation). How many mutations happen per generation? Estimating mutation rates is not easy (at least without assuming common descent): it is hard to find a few changed nucleotides out of 3 billion that have not changed. By studying new cases of genetic diseases, individuals whose parents' do not have the disease, however, it is possible to identify and count new mutations, at least in a small number of genes. Using this technique, it has been estimated[1] that the single-base substitution rate for humans is approximately 1.7 x 10^-8 substitutions/nucleotide/generation, that is, 17 changes per billion nucleotides. That translates into ~100 new mutations for every human birth. (17 x 3, for the 3 billion nucleotides in the genome, x 2 for the two genome copies we each carry). At that rate, in 350,000 generations a copy of the human genome should have accumulated about 18 million mutations, while the chimpanzee genome should have accumulated a similar number.
The evolutionary prediction, then, is that there should be roughly 36 million single-base differences between humans and chimpanzees. The actual number could be determined when both the chimpanzee and human genomes had been completely sequenced. When the two genomes were compared[2], thirty-five million substitutions were found, in remarkably good agreement with the evolutionary expectation. Fortuitously good agreement, in fact: the uncertainty on most of the numbers used in the estimate is large enough that it took luck to come that close.
Footnotes:
[1] Kondrashov AS. Direct estimates of human per nucleotide mutation rates at 20 loci causing Mendelian diseases. Human Mutation 21:12-27 (2003).
[2] The Chimpanzee Sequencing and Analysis Consortium. Initial sequencing of the chimpanzee genome and comparison with the human genome. Nature 437:69-87 (2005).

This message is a reply to:
 Message 171 by CRR, posted 11-02-2016 7:57 PM CRR has replied

Replies to this message:
 Message 192 by CRR, posted 11-07-2016 2:38 AM Dr Adequate has replied

  
Dr Adequate
Member (Idle past 285 days)
Posts: 16113
Joined: 07-20-2006


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.

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 Message 178 by CRR, posted 11-03-2016 3:32 AM CRR has replied

Replies to this message:
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Dr Adequate
Member (Idle past 285 days)
Posts: 16113
Joined: 07-20-2006


(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:
 Message 192 by CRR, posted 11-07-2016 2:38 AM CRR has replied

Replies to this message:
 Message 199 by CRR, posted 11-12-2016 1:50 AM Dr Adequate has replied

  
Dr Adequate
Member (Idle past 285 days)
Posts: 16113
Joined: 07-20-2006


Message 196 of 279 (793912)
11-07-2016 3:22 AM
Reply to: Message 194 by CRR
11-07-2016 2:42 AM


Re: The Maths
Who has refuted ReMine's paper?
See this thread, passim.

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 Message 194 by CRR, posted 11-07-2016 2:42 AM CRR has not replied

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Dr Adequate
Member (Idle past 285 days)
Posts: 16113
Joined: 07-20-2006


(1)
Message 202 of 279 (794252)
11-12-2016 11:32 AM
Reply to: Message 199 by CRR
11-12-2016 1:50 AM


Re: The Maths
However there is still a hole in your argument. You calculation relies on the estimated number that would become fixed in infinite time ...
No, what in the world gave you that idea?
As for the rest of your post, I would point out that the figures are not perfectly known, we're just ballparking it here. When we're looking at millions of years, does it matter what might or might not have happened since 1 AD? That would only been important if we were going for a factitiously precise figure. The fact remains, we expect millions of differences between chimps and humans as a result of neutral mutation and drift alone, and so anyone ignoring this has messed up.
ETA: Note that whenever we start the clock on the process, there is already neutral variation in the gene pool. It is true that a neutral mutation that happened yesterday will not have been fixed yet, bit now consider what's going to happen at the other end of the process.
Edited by Dr Adequate, : No reason given.

This message is a reply to:
 Message 199 by CRR, posted 11-12-2016 1:50 AM CRR has replied

Replies to this message:
 Message 206 by CRR, posted 11-13-2016 5:21 PM Dr Adequate has replied

  
Dr Adequate
Member (Idle past 285 days)
Posts: 16113
Joined: 07-20-2006


(1)
Message 203 of 279 (794253)
11-12-2016 1:21 PM
Reply to: Message 199 by CRR
11-12-2016 1:50 AM


Re: The Maths
But if fixation is too confusing, let's think about two individuals, let's say me and this chimpanzee.
I have of course acquired μ mutations of my own. But what did I get from my parents? Well, they each acquired μ mutations of their own. What with diploidly, they each passed on μ mutations to me, and since I have two parents, that makes a grand total of μ. But what did they get from their parents? Well of course the same reasoning applies
So if there have been G generations between now and the chimp-human split, then I have had time to accumulate μG mutations. As similar processes have affected the chimp line, the chimp in the photo has also had time to accumulate μG mutations (ballparking generation time as the same for both species). The difference between me and the chimp should therefore be 2μG mutations. Which is what I said.
(Note that to a very good first approximation, because the genome is so big all the mutations we're talking about will be different; for our ballpark figure we can neglect the occasional coincidence.)
---
As we don't exactly know μ and G, there's no point in striving for a high level of accuracy. What we can say is that the difference between me and the chimp should be of the order of 2μG.
And this is sufficient on its own to undermine ReMine's nonsense about Haldane's dilemma: there is simply no need at all to suppose that all the mutations (or even more than a tiny fraction of them) that separate us from chimps are beneficial mutations fixed by selection; but these are the only mutations to which Haldane's dilemma applies.
Edited by Dr Adequate, : No reason given.
Edited by Dr Adequate, : No reason given.
Edited by Dr Adequate, : No reason given.

This message is a reply to:
 Message 199 by CRR, posted 11-12-2016 1:50 AM CRR has replied

Replies to this message:
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Dr Adequate
Member (Idle past 285 days)
Posts: 16113
Joined: 07-20-2006


Message 207 of 279 (794282)
11-13-2016 8:58 PM
Reply to: Message 206 by CRR
11-13-2016 5:21 PM


Re: The Maths
What in the world gave me that idea? Fixation - Wikipedia(population_genetics)
"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 {\displaystyle p} p in the population at that time. " Note ULTIMATELY.
Note that "ultimately" does not mean "after a infinite amount of time".
After an infinite amount of time all of the neutral mutations would have occurred.
I agree that population figures are not perfectly known, actually they are very rough estimates. However that works both ways since it also limits the precision of your calculations.
That's fine, I'm just establishing plausibility, which I have, it's not me going around claiming to have proved that there's been time for exactly 1,667 mutations.
A very rough estimate assuming an average population of 90,000 is that 1/2 of the first generation neutral mutations would have been fixed (T,mean=4Ne), and less in each succeeding generation so that perhaps 1/4 of potential mutations would have bee fixed in the 350,000 generations available.
No, you can't do that. Kimura's time is from when the mutation arises, when there's only one copy of it. So if it's already been around for some time the probability that at any given time there's still only one copy and that the same math applies is negligible.
Overall I believe you have failed to substantiate your claim that genetic drift alone is sufficient to explain the number of genetic differences between humans and chimps.
But you've been wrong a lot lately.
Any thoughts on message #203?
Edited by Dr Adequate, : No reason given.

This message is a reply to:
 Message 206 by CRR, posted 11-13-2016 5:21 PM CRR has not replied

  
Dr Adequate
Member (Idle past 285 days)
Posts: 16113
Joined: 07-20-2006


Message 211 of 279 (794315)
11-14-2016 2:48 PM
Reply to: Message 209 by Pressie
11-14-2016 5:51 AM


Re: The Maths
I don't believe you at all. You lie.
Please remember that CRR is quoting ReMine on this issue; so if this is false then CRR is not lying, he is being lied to.

This message is a reply to:
 Message 209 by Pressie, posted 11-14-2016 5:51 AM Pressie has replied

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