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Author Topic:   Extent of Mutational Capability
Dr Adequate
Member (Idle past 284 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 284 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.

This message is a reply to:
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New Cat's Eye
Inactive Member


(1)
Message 168 of 279 (793612)
11-02-2016 3:26 PM
Reply to: Message 167 by Dr Adequate
11-02-2016 2:47 PM


Re: More About Whales
So what I'm about to say is super nitpicky, but I thought you might want to be like the cool kids...
In your links, you can see at the end where it says "&t=16094". That's the thread ID. There's a dBCode for linking to those:
[tid=16094] becomes:
Evidence for Evolution: Whale evolution
The other ones are:
Creationist response to cetacean femur, leg atavism, and limb bud.
Animals with bad design.
I dunno, seems better than just posting that ugly address. And more informative too.
And I second your post that some people are unnecessarily being dicks in this thread.

This message is a reply to:
 Message 167 by Dr Adequate, posted 11-02-2016 2:47 PM Dr Adequate has not replied

  
dwise1
Member
Posts: 5930
Joined: 05-02-2006
Member Rating: 5.8


Message 169 of 279 (793617)
11-02-2016 3:46 PM
Reply to: Message 161 by Gregory Rogers
11-02-2016 8:26 AM


Vestigial, Vesmigial!
Closing the topic should be left up to the administrators. When the originator arbitrarily closes a topic it is seen as being very rude, though you could request that an administrator close it before its time. The process involves an administrator first placing the topic into summation mode, wherein anyone who had participated can submit one and only one final message which sums up their thoughts about the topic and how it went. After all the summation messages have been posted, the admin will then close the topic. However, one can later request that the topic be reopened. Of course, if the topic is spinning out of control, an admin can close it much more abruptly. In such cases, it is also not uncommon for an admin to close a topic temporarily in order to encourage the participants to cool down before continuing.
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.
That is an example of creationists lying by shifting the meanings of words. Such "semantic shifting" is very widely used in creationist quote-mining (see Message 158 above). It's an attempt at "word magick", making something go away by redefining its name. Such "word magick" is a dishonest and deceptive practice best left to lawyers {1}.
In this case, there is a very strict definition for "vestigial" to mean that that feature serves absolutely no purpose whatsoever, and the practical definition used by scientists to mean that it no longer serves its original purpose and hardly any other purpose. It's the difference between being of very little use and absolutely no use whatsoever.
Hence the cetacean vestigial pelvis is indeed vestigial because it no longer serves to support the hind legs, which no longer exist (though can occasionally still be expressed {2}). The fact that some muscles still attach to what's left of that atrophied feature does nothing to eliminate the fact that the pelvis is vestigial and tells us something of the whales' evolutionary past, just like the vestigial pelvis in some snakes.
The best way to test this is, I would say, to examine the limb itself: looking at bone structure, basic design, etc., what are the evidences as to its background: are there clear indications, parallels, of limbs of a land-mammal; alternatively, is there clear evidence that it has, and has only ever had, the sole function of an attachment point for reproductive organs.
As Dr Adequate points out in Message 165 and AZPaul3 in Message 164, look at the fossil record which experts have studied extensively. In the much earlier cetacean ancestors you will find better defined pelvises and hind legs which had started to atrophy away. You will clearly see that those earlier pelvises served the function of articulating those hind legs. Clearly, being an attachment point for reproductive organs was never the sole function of the pelvis.
You can research this in the paleontology journals in the periodicals section your local university library, just as Merle Hertzler had done. He was a young-earth creationist I met on CompuServe in 1993-1994. He was the first honest creationist I had encountered since I had started trying to discuss this issue circa 1984. Not only did he do his best to discuss creationist claims (an extremely rare quality in creationists) but he would also research not only his claims but also the responses he got. As happens all too often to honest creationists, he learned that his claims were false and in a year's time he ended up on the other side arguing against creationism. He tells that story on his page, Did We Evolve?. Basically what happened was that an "evolutionist" had referred him to a book in which there was a citation in a paleontology journal, so he went to look that up. And he found more and more evidence that the creationists had always told him did not exist. I seem to recall that the citation had to do with cetacean fossils.
A further angle would be to compare other sea creatures to see if they have a comparable external mechanism.
Do you mean fish? Their reproductive systems are nothing those of mammals -- remember, whales are not fish, but rather mammals and as such have reproductive organs like other mammals and not at all like those of fish who basically do all their egg fertilizing in the open water. Though I'm not familiar with shark reproduction, especially considering that some are viviparous (ie, give live birth).
But still, since fish have no limbs in their evolutionary history, there would be no reason to expect them to have vestigial pelvises. Remember that evolution works by modifying what's already there. Unlike in designing a car, you cannot just completely redesign and replace an entire component in an animal; rather you are stuck with modifying what it already has (eg, in cars we completely changed how the engine is mounted and had to completely redesign how the radiator fan is powered, in cars we replaced the old pneumatically powered intermittant windshield wipers with a completely new electronic design). So as you compare the limbs of amphibians, reptiles, mammals, birds, both modern and fossil, you will see the same bones in the same relative positions over and over again. Their sizes and shapes will vary, but they are the same bones and you can trace them back to certain fossil fish.

Footnote 1:
An excellent example of lawyers redining words is found in the story of the Lintillas in The Hitchhiker's Guide to the Galaxy:
quote:
Lintilla is a rather unfortunate woman who has (as of Fit the Eleventh of the radio series) been cloned 578,000,000,000 times due to an accident at a Brantisvogan escort agency. While creating six clones of a wonderfully talented and attractive woman named Lintilla (at the same time another machine was creating five hundred lonely business executives, in order to keep the laws of supply and demand operating profitably), the machine got stuck in a loop and malfunctioned in such a way that it got halfway through completing each new Lintilla before it had finished the previous one. This meant that it was for a very long while impossible to turn the machine off without committing murder, despite lawyers' best efforts to argue about what murder actually was, including trying to redefine it, repronounce it, and respell it in the hope that no one would notice.
From Fit the Eleventh:
quote:
Arthur Dent: Why are there three of you?
Lintillas: Why is there only one of you?
Arthur Dent: Er ... (He is totally stumped by this)
Footnote 2:
It would be interesting to look at the development of whale embryos. For example, baleen whales have no teeth, but they still have genes for teeth and during embryonic development they start to form teeth which are then reabsorbed. Similarly, chickens have genes for teeth which we can cause to be expressed; in experiments fetal mouse gum tissue was placed on the jaws of chick embryos which caused teeth to start to form.
So my question is whether we see hind legs and the associated pelvis start to form in a whale embryo. I think that we should see that, since some individual whales have been found with vestigial hind legs (ie, not fully formed nor functional).

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dwise1
Member
Posts: 5930
Joined: 05-02-2006
Member Rating: 5.8


Message 170 of 279 (793625)
11-02-2016 5:04 PM
Reply to: Message 161 by Gregory Rogers
11-02-2016 8:26 AM


Vestigiality
Regarding the definition of "vestigial", refer to the Wikipedia article, Vestigiality. In the introductory first section:
quote:
Vestigiality refers to genetically determined structures or attributes that have lost some or all of their ancestral function in a given species, but have been retained during the process of evolution.[1] Assessment of the vestigiality must generally rely on comparison with homologous features in related species. The emergence of vestigiality occurs by normal evolutionary processes, typically by loss of function of a feature that is no longer subject to positive selection pressures when it loses its value in a changing environment. The feature may be selected against more urgently when its function becomes definitively harmful. Typical examples of both types occur in the loss of flying capability in island-dwelling species.
And the first paragraph of the Overview section:
quote:
Vestigial features may take various forms; for example they may be patterns of behavior, anatomical structures, or biochemical processes. Like most other physical features, however functional, vestigial features in a given species may successively appear, develop, and persist or disappear at various stages within the life cycle of the organism, ranging from early embryonic development to late adulthood.
Vestigiality, biologically speaking, refers to organisms retaining organs, which have seemingly lost the entirety of the original function. The issue is controversial and not without dispute; nonetheless, vestigial organs are common, evolutionary knowledge. In addition, the term vestigiality is useful in referring to many genetically determined features, either morphological, behavioral, or physiological; in any such context however, it need not follow that a vestigial feature must be completely useless. A classic example at the level of gross anatomy is the human vermiform appendix though vestigial in the sense of retaining no significant digestive function, the appendix still has immunological roles and is useful in maintaining gut flora.
So the definition of "vestigial" does not require that trait to be absolutely useless, whereas the creationist redefinition does require that. In that way, creationists try to redefine vestigiality out of existence in order to create "evidence" against evolution. They are creating a false claim and a deceptive argument.
Again, the lesson learned is that you need to learn about the science in question so that you can evaluate what both sides say about it. It is not enough to simply collect arguments, but you must also determine the worthiness of those arguments.

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CRR
Member (Idle past 2242 days)
Posts: 579
From: Australia
Joined: 10-19-2016


Message 171 of 279 (793635)
11-02-2016 7:57 PM
Reply to: Message 150 by PaulK
11-01-2016 5:52 AM


The Maths
It's known as Haldane's Dilemma. A clear exposition is given in http://saintpaulscience.com/CostTheory1.pdf .
"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. The origin of all the uniquely human adaptations would have to be explained within that limit." [http://users.minn.net/science/Haldane.htm]
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.

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AZPaul3
Member
Posts: 8513
From: Phoenix
Joined: 11-06-2006
Member Rating: 5.3


(1)
Message 172 of 279 (793638)
11-02-2016 9:03 PM
Reply to: Message 171 by CRR
11-02-2016 7:57 PM


Re: The Maths
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.
And the actual comparison studies show your number off by an order of magnitude then halved yet again. We and our brother chimps really are that closely related.
Haldane's work presents no bar to evolution in any way at any level as the man himself concluded in his book.
quote:
Unless selection is very intense the number of deaths needed to secure the substitution by natural selection, of one gene for another at a locus, is independent of the intensity of selection. It is often about 30 times the number of organisms in a generation. It is suggested that in horoletic evolution, the mean time taken for each gene substitution is about 300 generations. This accords with the observed slowness of evolution.
page 524 Haldane JBS. (1957).
When understood and used properly Haldane's Dilemma really isn't.
source
Edited by AZPaul3, : No reason given.

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Coyote
Member (Idle past 2105 days)
Posts: 6117
Joined: 01-12-2008


(1)
Message 173 of 279 (793639)
11-02-2016 9:07 PM
Reply to: Message 171 by CRR
11-02-2016 7:57 PM


Re: The Maths
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:
An Index to Creationist Claims
There are so many such claims that they even have a name: PRATT--Point Refuted a Thousand Times. But that doesn't stop creationists from repeating these claims endlessly.
In virtually all cases those folks are not doing science, rather they are doing religious apologetics--often fishing through the scientific literature for any perceived support for their religious beliefs, all the while ignoring any evidence that contradicts their religious beliefs. That's the exact opposite of science! We see a lot of that in this website.
So, we have fossil and DNA evidence that supports the theory of evolution. No armchair math-based claims can overturn that theory. To overturn the theory of evolution you need fossils and DNA evidence that contradicts, or can't be explained by, the current theories, and you need dating results that show a young earth.
Are you up to the challenge?

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.

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Dr Adequate
Member (Idle past 284 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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Coyote
Member (Idle past 2105 days)
Posts: 6117
Joined: 01-12-2008


Message 175 of 279 (793645)
11-02-2016 10:29 PM
Reply to: Message 174 by Dr Adequate
11-02-2016 10:23 PM


Re: The Maths
Haldane's dilemma only applies to beneficial mutations. Quite different math applies to the accumulation of neutral mutations.
And what is "beneficial" or "neutral" can change significantly over time as each is measured only in relation to successful reproduction.

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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Dr Adequate
Member (Idle past 284 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).

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PaulK
Member
Posts: 17822
Joined: 01-10-2003
Member Rating: 2.2


Message 177 of 279 (793651)
11-03-2016 1:40 AM
Reply to: Message 171 by CRR
11-02-2016 7:57 PM


Re: The Maths
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.
The first problem is that Haldane's Dilemma assumes hard selection. Soft selection can work in parallel so it does not hit the same limit, so you have not even got a limit on the number of beneficial substitutions.
The second problem is that you don't go anywhere with your number. You don't offer any argument that the number is insufficient, and since your number explicitly leaves out substitutions due to drift the actual differences in the genome are going to be considerably larger.
(As a side note, even the number of changed bases due to selection will be considerably larger - mutations that affect multiple bases are less common than point mutations but not so rare that they can be ignored)

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CRR
Member (Idle past 2242 days)
Posts: 579
From: Australia
Joined: 10-19-2016


Message 178 of 279 (793652)
11-03-2016 3:32 AM
Reply to: Message 173 by Coyote
11-02-2016 9:07 PM


Re: The Maths
You say you don't trust my source without looking at it; without evidence
I on the other hand have read many articles on talkorigins and I don't trust it with good evidence on which to base my opinion.
If you refuse to examine the evidence from one side you will naturally come to a biased opinion.
Edited by CRR, : Typo corrected

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Tangle
Member
Posts: 9489
From: UK
Joined: 10-07-2011
Member Rating: 4.9


Message 179 of 279 (793653)
11-03-2016 3:43 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. A clear exposition is given in http://saintpaulscience.com/CostTheory1.pdf
You can't come here with 60 year old refuted claims and hope to blunder your way through. Please take particular note of the sentence I've highlighted in bold. Only creation 'scientists' continue to use 'facts' that have been shown to be wrong with better evidence.
Why do they do that do you think?
Claim CB121:
J. B. S. Haldane calculated that new genes become fixed only after 300 generations due to the cost of natural selection (Haldane 1957). Since humans and apes differ in 4.8 107 genes, there has not been enough time for difference to accumulate. Only 1,667 nucleotide substitutions in genes could have occurred if their divergence was ten million years ago.
Source:
ReMine, Walter J., 1993. The Biotic Message, St. Paul Science, Inc.
Response:
Haldane's "cost of natural selection" stemmed from an invalid simplifying assumption in his calculations. He divided by a fitness constant in a way that invalidated his assumption of constant population size, and his cost of selection is an artifact of the changed population size. He also assumed that two mutations would take twice as long to reach fixation as one, but because of sexual recombination, the two can be selected simultaneously and both reach fixation sooner. With corrected calculations, the cost disappears (Wallace 1991; Williams n.d.).
Haldane's paper was published in 1957, and Haldane himself said, "I am quite aware that my conclusions will probably need drastic revision" (Haldane 1957, 523). It is irresponsible not to consider the revision that has occurred in the forty years since his paper was published.
ReMine (1993), who promotes the claim, makes several invalid assumptions. His model is contradicted by the following:
The vast majority of differences would probably be due to genetic drift, not selection.
Many genes would have been linked with genes that are selected and thus would have hitchhiked with them to fixation.
Many mutations, such as those due to unequal crossing over, affect more than one codon.
Human and ape genes both would be diverging from the common ancestor, doubling the difference.
ReMine's computer simulation supposedly showing the negative influence of Haldane's dilemma assumed a population size of only six (Musgrave 1999).
Links:
Williams, Robert, n.d. Haldane's dilemma. http://www.gate.net/~rwms/haldane1.html
References:
Haldane, J. B. S., 1957. The cost of natural selection. Journal of Genetics 55: 511-524.
Musgrave, Ian, 1999. Weasels, ReMine, and Haldane's dilemma. The Talk.Origins Archive Post of the Month: September 1999
ReMine, Walter J., 1993. The Biotic Message, St. Paul Science, Inc.
Wallace, Bruce, 1991. Fifty Years of Genetic Load - An Odyssey. Cornell University Press. See particularly Chapters 5, 6, 8, and 9.
Williams. (See above)
CB121: Haldane's Dilemma

Je suis Charlie. Je suis Ahmed. Je suis Juif. Je suis Parisien.
"Life, don't talk to me about life" - Marvin the Paranoid Android
"Science adjusts it's views based on what's observed.
Faith is the denial of observation so that Belief can be preserved."
- Tim Minchin, in his beat poem, Storm.

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PaulK
Member
Posts: 17822
Joined: 01-10-2003
Member Rating: 2.2


Message 180 of 279 (793654)
11-03-2016 5:03 AM
Reply to: Message 178 by CRR
11-03-2016 3:32 AM


Re: The Maths
I very much doubt that you have fairly evaluated the talk origins archive.
If you can come up with valid criticisms then please start a thread. You won't be the first to try, and wouldn't be the first to fail.

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