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Author Topic:   Can the standard "Young Earth Creationist" model be falsified by genetics alone?
mindspawn
Member (Idle past 2661 days)
Posts: 1015
Joined: 10-22-2012


Message 91 of 161 (707245)
09-25-2013 8:51 AM
Reply to: Message 88 by RAZD
09-24-2013 2:12 PM


Re: post flood humans
Let's put this another way: there is no documented\recorded record\evidence of a world wide flood for the entire period covered by human, hominid and ancestral ape fossils.
Agreed, I have been researching the Carboniferous landscape, and if ancient Indian legend matches the most hospitable regions, mankind was living on the island of Siberia as we headed towards the flood (PT boundary). Most of the world was subject to glaciation and periodic extinctions, but the higher latitudes (Island of Siberia) were less susceptible. Then after the flood, humans were isolated on the Arabian plate during this period. While the world was recovering from the hot dry conditions after the flood and before the ark animals reached significant populations, amphibuous reptiles dominated terrestrial habitats. They survived the flood in marine habitats and yet quickly adapted to terrestrial habitits due to the lack of any other terrestrial fauna. This is why they are consistently in the lower triassic/Jurassic layers. Humans and mammals had spread slightly during the end of the cretaceous into Africa and northern regions but generally not into the large dinosaur regions. (large mammals including humans mainly headed north)
(possibly we should discuss this in the flood thread - not biology)
After the K-T extinction, and its ice age, humans and mammals dominated the world.
You can (try anyway to) ignore the age of rock formations in the pursuit of your pet delusional theory, but you cannot ignore the laws of geology that relate to the relative ages of layers, superposition being one: lower layers are older than upper layers.
I agree with relative ages. I also partially agree with radiometric dating to determine relative dates.
All human, hominid and ancestral ape fossils lie above the K-Pg boundary while the P-T boundary is below the K-Pg boundary.
Of note Orthida brachiopods became extinct during the P-T extinction event. Fossils of these brachiopods are found on Mt Everest:
No problem with this.
Edited by mindspawn, : No reason given.
Edited by mindspawn, : No reason given.

This message is a reply to:
 Message 88 by RAZD, posted 09-24-2013 2:12 PM RAZD has replied

Replies to this message:
 Message 161 by RAZD, posted 11-01-2013 6:13 PM mindspawn has not replied

  
NoNukes
Inactive Member


(1)
Message 92 of 161 (707255)
09-25-2013 11:01 AM
Reply to: Message 90 by mindspawn
09-25-2013 8:27 AM


If it is a human, then why can't you find the quote?
The caption under Figure 1 talks about the roles of both the chimpanzee reference and the human reference. I did not find the caption to clearly answer the question, but it does at least provide evidence that there is a human reference involved.
Beyond that, bluegenes explanations for why the reference cannot be the chimpanzee are fairly strong. Why do you keep ducking them?
Also aren't there 36 humans involved? Why are you reducing the count to 34?
So if you claiming the reference sequence is the chimp, then you have a huge problem.
What a strange thing to say. Isn't that your claim?

Under a government which imprisons any unjustly, the true place for a just man is also in prison. Thoreau: Civil Disobedience (1846)
I believe that a scientist looking at nonscientific problems is just as dumb as the next guy.
Richard P. Feynman
If there is no struggle, there is no progress. Those who profess to favor freedom, and deprecate agitation, are men who want crops without plowing up the ground, they want rain without thunder and lightning. Frederick Douglass

This message is a reply to:
 Message 90 by mindspawn, posted 09-25-2013 8:27 AM mindspawn has not replied

  
bluegenes
Member (Idle past 2478 days)
Posts: 3119
From: U.K.
Joined: 01-24-2007


(1)
Message 93 of 161 (707268)
09-25-2013 1:09 PM
Reply to: Message 90 by mindspawn
09-25-2013 8:27 AM


mindspawn writes:
If it is a human, then why can't you find the quote? Your whole argument hinges on that. And exactly which human is involved makes a big difference. If the "A" individual is the reference sequence this is impossible because then there would be no differences, but you are claiming >600 differences. If the reference sequence is one of the 35 then this makes a complete hash of the first 185 so-called differences, because they have to be deduced backwards from differences with the "A" individual.
The human reference sequence is a genome considered to be "typical". You still don't seem to understand that in order to find within human differences, you have to compare humans with each other. Rather than giving you a quote or a link, I want you to understand things like that.
mindspawn writes:
ie if the reference is human and one of the 35, he is more likely to represent Y-Adam because the 35 have a wider representation that the "A" individual. Therefore any differences of the 285 plus 185 between A and the rest are more likely to be mutations of A. It could be 400 with A, and 70 with the others, we do not know.
The first two sentences are incorrect (all individuals are equal distance in time from the Y ancestor, and how similar they are just depends on how many mutations they've had on their lineage). The third sentence is correct, although 400 is extremely unlikely. We can draw the whole chart they've got, and fill in the mutations using "A" as an outgroup until we reach the most recent common "Y" ancestor of the 35. We are then left with 470 SNPs. What I'd do here is estimate so as to give "A" something around 310, with 160 on the other branch.
mindspawn writes:
Then we go further down the generations and get 54 differences between the next split. Who has Y-Adam nucleotides, and who has mutations, we don't know. It could be split 27 each group. But you count the next 54 differences twice even though most likely one of them has Y-Adam mucleotides.
You're still showing that you don't understand the paper or the tree.
We know the mutations because "A" serves as an outgroup. I expect it's going to take me a long time to explain to you why that is, but it would be really nice if you showed that you could figure it out for yourself..
mindspawn writes:
To compare this against the chimp is also a huge assumption considering you have already admitted that the chimp has big differences with a human.
I'm not comparing anything to a chimp. Read my last post. The researchers just use them for the root of the tree. That is, to decide where to place the 470 mutations. But we can estimate that.
mindspawn writes:
Why should the chimp represent the ancestral alleles unless you are an evolutionist, and to argue for evolution using evolutionist techniques is just circular reasoning. They should have eliminated all variations that matched Y-Adam to reduce the number of variants counted, and without Y Adam they were just guessing and underestimating the y-Adam matches with the non-reference sequences (eg individual A).
1) So if you claiming the reference sequence is the chimp, then you have a huge problem.
You are claiming that the reference sequence is the chimp. I'm telling you it's not, and giving you the rather obvious reason why.
mindspawn writes:
2) If you are claiming the reference sequence is a human of the 35, then your figures are way out, and incorrectly calibrated against the chimp.
I'm not, but if it were one of the 35, the figures would be fine. The reference sequence isn't actually necessary.
mindspawn writes:
3) If you are claiming the reference sequence is the A individual, then how do they record 600+ variations between the A and himself?
They might think of comparing him with any one of the other 35 individuals, if they were smart enough. For us, just finding two humans with 600 variants falsifies YEC, as you should know by now.
mindspawn writes:
4) Or maybe its another human, who knows because you wont tell me.
Anyone who understands the paper knows.
mindspawn writes:
ps just to explain the mutation problem, if two individuals vary from eachother, about half should have the ancestral allele, and half the mutation. When comparing the 6662 mutation sites they only found 391 with the chimp's so-called ancestral allele and assumed the rest to be mutations.
No. That just means they couldn't find the sites for 391 (chimps have a lot of deletions on the Y).
mindspawn writes:
They should have found over 3000 in the non reference sequences if they used the correct ancestral allele, which of course is not available (Y-adams DNA is needed). So using the chimp to eliminate non-mutations has a drastic effect on the study whoever the mystery original reference sequence is.
Try to understand SNPs, which is what we're using. Think of them as loci. If you look at any population group, like our 36, or 37 with the reference, the SNPs are loci which are not identical in all of them. It doesn't matter how many individuals differ at this point, we would still only count one SNP.
So, whether you sequence two individuals, or ten, or 37, and match them against each other, or all against one, you can identify all the loci that do not match across the board.
Next, having done this, your computer can also give you the data on all the individuals' alleles on all of the SNP loci. This is where you can start to build the phylogenetic tree. You identify the very close matches and group them together. With these comparisons, it will be easy to identify "A" as the most different from all (and we know that anyway from other phylogenetic trees). We can establish that he doesn't meet up with the others until we hit the common ancestor. So, we put him to one side, and use him as an outgroup. When another pair have differences on a locus, the one that also differs from "A" is the mutant. "A" has none of the mutations of the others. (It's at this point when we've seen the number of differences between Y and any other individual that we've effectively falsified the standard YEC model).
To understand the tree building, for example, look at the 4th and 5th individuals on the the chart (below for easy reference). They differ on 26 loci. "4" differs also from "A" on 15 and 5 on 11, so the mutations are identified.
Working this way, we get the whole tree up to the common ancestor of the 35. No chimps or other animals involved. Which makes the rest of your ramblings about chimps (do start a thread on them if you want to) irrelevant.
All you'd have to do really to falsify YEC is to match an "A" individual against a non-"A", and count the SNPs. It'll always be far too many for a plausible mutation rate to give you a divergence date within the last 10,000 years.
But the chart is interesting. It tells us, among other things, that on your model, there were stone age cultures in Europe about 1500 years ago. I'll explain that (without using scientific dating) in my next post. You'll love it! Also, if you still don't understand that the way to discover within human differences is by comparing humans to humans, I'll show you the exact human reference that they actually used. But I think you should try to understand the reasoning first.
Edited by bluegenes, : typos
Edited by bluegenes, : No reason given.
Edited by bluegenes, : typos and clarification

This message is a reply to:
 Message 90 by mindspawn, posted 09-25-2013 8:27 AM mindspawn has replied

Replies to this message:
 Message 94 by mindspawn, posted 09-26-2013 3:20 AM bluegenes has not replied
 Message 96 by mindspawn, posted 09-26-2013 5:37 AM bluegenes has replied

  
mindspawn
Member (Idle past 2661 days)
Posts: 1015
Joined: 10-22-2012


Message 94 of 161 (707290)
09-26-2013 3:20 AM
Reply to: Message 93 by bluegenes
09-25-2013 1:09 PM


I feel generally this whole thread is irrelevant because of the uncertainty about germline mutation rates:
The German biologist feels that mutation rates are vastly underestimated. The Australian genetist cant make up his mind who is more correct:
://Later Date for Out of Africa | Human Migration | Live Science
"The researchers estimate that in its effort to avoid false positives (mutations that weren't really mutations), the nuclear DNA method missed quite a few real mutations. That would lead to an underestimate of the mutation rate and a longer estimate for when humans left Africa, diverged from Neanderthals, and other things.
Right now, it's not clear which method is most reliable, Peter Visscher, a quantitative geneticist at the University of Queensland, who was not involved in the study, wrote in an email to LiveScience.
"This debate will continue a bit longer, but soon there is likely to be a consensus on what mutation rates are in the present, because there is so much sequencing being done around the world," Visscher wrote."

This message is a reply to:
 Message 93 by bluegenes, posted 09-25-2013 1:09 PM bluegenes has not replied

Replies to this message:
 Message 95 by NoNukes, posted 09-26-2013 4:31 AM mindspawn has replied

  
NoNukes
Inactive Member


(1)
Message 95 of 161 (707295)
09-26-2013 4:31 AM
Reply to: Message 94 by mindspawn
09-26-2013 3:20 AM


Shuckin' and Jiving started...
I feel generally this whole thread is irrelevant because of the uncertainty about germline mutation rates:
....
quote:
"Right now, it's not clear which method is most reliable, Peter Visscher, a quantitative geneticist at the University of Queensland, who was not involved in the study, wrote in an email to LiveScience."
Of course you do. Now that your butt has been totally kicked, you are copping out. How long did you google to find your weak exit point?
Q: Is the purported uncertainty enough to make a difference for you?
A: Nope.
From the first line of the article you cite:
quote:
Our early human ancestors may have left Africa more recently than thought, between 62,000 and 95,000 years ago, suggests a new analysis of genetic material from fossil skeletons.
In other words, not only is the uncertainty in rates only between a factor of 2 or 3, the evidence for mutation rates completely rules out the Young Earth Creationist model including a Flood occurring only 1500 years after the earth was created. This kind of uncertainty would still place Y chromosome Adam at a point well before Noah and the YEC date of creation of the universe.
How can you possibly be debating in good faith here?
You are not. I don't see any way to continue to give you any benefit of the doubt.
Isn't it well place time to start blaming the observed diversity on the Nephilim? That's what you fellow YECers normally do once pressed to this point. Because multiple lines of genetic evidence show that mutation rates are way to low, by a factor of 10 to 30, to have the current diversity arise from the 8 people on the arc; particularly when 3 of them are direct offspring of two of the others.
Bottom line -- the evidence all shows no relevant bottleneck for humans at anything like a relevant time, and you are left with making excuses why that evidence is not enough.

Under a government which imprisons any unjustly, the true place for a just man is also in prison. Thoreau: Civil Disobedience (1846)
I believe that a scientist looking at nonscientific problems is just as dumb as the next guy.
Richard P. Feynman
If there is no struggle, there is no progress. Those who profess to favor freedom, and deprecate agitation, are men who want crops without plowing up the ground, they want rain without thunder and lightning. Frederick Douglass

This message is a reply to:
 Message 94 by mindspawn, posted 09-26-2013 3:20 AM mindspawn has replied

Replies to this message:
 Message 97 by mindspawn, posted 09-26-2013 8:15 AM NoNukes has replied

  
mindspawn
Member (Idle past 2661 days)
Posts: 1015
Joined: 10-22-2012


Message 96 of 161 (707301)
09-26-2013 5:37 AM
Reply to: Message 93 by bluegenes
09-25-2013 1:09 PM


The human reference sequence is a genome considered to be "typical". You still don't seem to understand that in order to find within human differences, you have to compare humans with each other. Rather than giving you a quote or a link, I want you to understand things like that
Where does your link say that they used a "typical" genome? Please quote this.
It wasn't logical to use the chimp's DNA to eliminate ancestral alleles in the study group and yet they did so. Often evolutionists use evolutionary assumptions that are not in fact applicable in discussions "proving" evolution. So your "its only logical" does not cut it. If you cannot find who the reference sequence is, your argument falls apart, because we unable to analyze the data.
The first two sentences are incorrect (all individuals are equal distance in time from the Y ancestor, and how similar they are just depends on how many mutations they've had on their lineage). The third sentence is correct, although 400 is extremely unlikely. We can draw the whole chart they've got, and fill in the mutations using "A" as an outgroup until we reach the most recent common "Y" ancestor of the 35. We are then left with 470 SNPs. What I'd do here is estimate so as to give "A" something around 310, with 160 on the other branch.
Aah so its just a thumbsuck how to split the 285 and 185. They overestimated the mutations in the 35 individuals and underestimated the 1 individual, that is clear. If you were being fair, you would have allocated about 340 mutations to the A individual. But remember LIFESTYLE affects mutation rates and the A individual is from the most migratory hunter gatherer group. It is actually possible that A did have more mutations than the others.
So once again your study is based on guesswork, nothing about your conclusions is based on anything concrete.
We know the mutations because "A" serves as an outgroup. I expect it's going to take me a long time to explain to you why that is, but it would be really nice if you showed that you could figure it out for yourself..
So we have a reference sequence, an outgroup, and also the chimpanzee reference? And you can't tell me who the reference sequence is. Because who-ever the reference sequence is, will ruin your whole point.
We know that FR and DE-E who together make up 34 of the 36 individuals each differ by 54 core variants from eachother. But how do we know who has the ancestral sequence, and who does not. We have no idea. We have to divide by two just to get a vague estimate. So we divide each section of 54 variants by 2, assuming each one represents 27 ancestral nucleotide sequences, and 27 subsequent mutations. And so on all the way down the tree.We have to do this because we only have the irrelevant chimp sequence as an ancestral sequence, and so this leaves us in the dark who actually has the ancestral (non-mutational) sequence.
I'm not comparing anything to a chimp. Read my last post. The researchers just use them for the root of the tree. That is, to decide where to place the 470 mutations. But we can estimate that.
No.
The researchers used the chimp to cut down the number of variations from 6662 to 6271. This is because they assumed the chimp IS the ancestral sequence, which is downright silly. especially since the chimp's Y-chromosome has only a 70% match with a human, as much a match as a chicken. IF they had the actual ancestral sequence , this would affect the number of mutations.
"We extracted the ancestral allele for each position that was variable in humans (assumed to be the allele present in chimpanzee) using the Ensembl-Compara pipeline (Vilella et al. 2009), release 66, and obtained calls for 6271 of the total number of 6662 variable sites (Fig. 1; Supplemental Table S2)."
How did they reduce 6662 to 6271? THE CHIMP You cannot say the chimp had no effect on the study.
You are claiming that the reference sequence is the chimp. I'm telling you it's not, and giving you the rather obvious reason why.
No. You are misunderstanding me.
In ADDITION to the possibility that the reference sequence is the chimp, the chimp was also used to reduce the number of mutations.
They might think of comparing him with any one of the other 35 individuals, if they were smart enough. For us, just finding two humans with 600 variants falsifies YEC, as you should know by now.
If they counted the variants correctly. Unfortunately they used an ape to eliminate the ancestral alleles. And many other assumptions.
Anyone who understands the paper knows.
If you know exactly who the reference individual is, why are you being so secretive. Are you saying its the Haplogroup A individual?
Next, having done this, your computer can also give you the data on all the individuals' alleles on all of the SNP loci. This is where you can start to build the phylogenetic tree. You identify the very close matches and group them together. With these comparisons, it will be easy to identify "A" as the most different from all (and we know that anyway from other phylogenetic trees). We can establish that he doesn't meet up with the others until we hit the common ancestor. So, we put him to one side, and use him as an outgroup. When another pair have differences on a locus, the one that also differs from "A" is the mutant. "A" has none of the mutations of the others. (It's at this point when we've seen the number of differences between Y and any other individual that we've effectively falsified the standard YEC model).
Let me emphasize, these 6662 positions differed from ONE reference sequence, they were not measuring differences from eachother. The split between how many of those 6662 variants were actually original DNA and how many were mutations is a complete unknown. Please show you understand this point.
Your conclusions are based on wild estimates and evolutionary assumptions (they allow the chimp to represent the ancestral allele)
To understand the tree building, for example, look at the 4th and 5th individuals on the the chart (below for easy reference). They differ on 26 loci. "4" differs also from "A" on 15 and 5 on 11, so the mutations are identified.
Working this way, we get the whole tree up to the common ancestor of the 35. No chimps or other animals involved. Which makes the rest of your ramblings about chimps (do start a thread on them if you want to) irrelevant.
All you'd have to do really to falsify YEC is to match an "A" individual against a non-"A", and count the SNPs. It'll always be far too many for a plausible mutation rate to give you a divergence date within the last 10,000 years.
But the chart is interesting. It tells us, among other things, that on your model, there were stone age cultures in Europe about 1500 years ago. I'll explain that (without using scientific dating) in my next post. You'll love it! Also, if you still don't understand that the way to discover within human differences is by comparing humans to humans, I'll show you the exact human reference that they actually used. But I think you should try to understand the reasoning first.
Why do you think they used the chimp to represent the ancestral alleles? Because they have not worked out which alleles are ancestral, and therefore have no real idea how to eliminate "original alleles" from the 6662 variants.
I understand the reasoning. Could you kindly show me the exact human reference.
I feel that so far, you misunderstand the extent to which their use of the chimp to represent the ancestral allele has affected your conclusions. And so far there are just far to many assumptions (one example - how to distribute the variations between A and DR) and too many variables (mutation rates, generations, % chimp that matches humans, division of mutations between DR and A, division of mutations between the 36 and the 1) and too many overestimations (mutation rate, no of mutation being 6271, no. of mutations in "A")
There is a lot of truth in what I am saying even if you are not seeing it.
Edited by mindspawn, : No reason given.
Edited by mindspawn, : No reason given.

This message is a reply to:
 Message 93 by bluegenes, posted 09-25-2013 1:09 PM bluegenes has replied

Replies to this message:
 Message 101 by bluegenes, posted 09-27-2013 2:41 AM mindspawn has replied

  
mindspawn
Member (Idle past 2661 days)
Posts: 1015
Joined: 10-22-2012


Message 97 of 161 (707307)
09-26-2013 8:15 AM
Reply to: Message 95 by NoNukes
09-26-2013 4:31 AM


Re: Shuckin' and Jiving started...
Of course you do. Now that your butt has been totally kicked, you are copping out. How long did you google to find your weak exit point?
Q: Is the purported uncertainty enough to make a difference for you?
A: Nope.
This is a debate, of course I will use science to support my position, and my position has always been that mutation rates are uncertain. Even Bluegene's initial links upon which his whole argument is based admits that. So does bluegenes admit that.
The link about mutation rates has a very significant effect and would actually make a difference. You see the article adjusted its mutation rates through finding a lot of mutations since a carbon dated individual who was DNA sequenced. When comparing an actual dated individual with modern individuals of the same root haplogroup, they found more mutations than previously expected. This is actual science at work, not guesswork.
Then if carbon dating is wrong, this will additionally affect this new actual mutation rate by the same degree that carbon dating is out.
My argument then becomes one of carbon dating.
In other words, not only is the uncertainty in rates only between a factor of 2 or 3, the evidence for mutation rates completely rules out the Young Earth Creationist model including a Flood occurring only 1500 years after the earth was created. This kind of uncertainty would still place Y chromosome Adam at a point well before Noah and the YEC date of creation of the universe.
A factor of 2 or 3 is huge. If carbon dating is out by a large factor as well, this would have an extreme effects on dates.

This message is a reply to:
 Message 95 by NoNukes, posted 09-26-2013 4:31 AM NoNukes has replied

Replies to this message:
 Message 98 by NoNukes, posted 09-26-2013 8:34 AM mindspawn has not replied
 Message 100 by Coyote, posted 09-26-2013 12:42 PM mindspawn has replied
 Message 104 by bluegenes, posted 09-27-2013 5:15 AM mindspawn has not replied

  
NoNukes
Inactive Member


(2)
Message 98 of 161 (707309)
09-26-2013 8:34 AM
Reply to: Message 97 by mindspawn
09-26-2013 8:15 AM


Re: Shuckin' and Jiving started...
A factor of 2 or 3 is huge.
Perhaps it is huge. But would not be large enough to prevent ruling out a YEC model based on genetic evidence alone. I've provided arguments for why not that I note are completely ignored.
If carbon dating is out by a large factor as well, this would have an extreme effects on dates.
Then if carbon dating is wrong, this will additionally affect this new actual mutation rate by the same degree that carbon dating is out.
Red herring. You must think the people you are debating are complete idiots. And the dates expressed in the article are quite obviously not carbon dates because they are greater that 50,000+ years ago.
But Yes; a factor of 2 two three would be huge for carbon dates, but of course we can calibrate carbon dating so we know that it is not so inaccurate. And of course even a factor of two or three does not help you win that debate either. Wouldn't that make those cave paintings in France and Spain only about 20,000 years old? How does that help you?
Edited by NoNukes, : No reason given.
Edited by NoNukes, : No reason given.
Edited by NoNukes, : No reason given.

Under a government which imprisons any unjustly, the true place for a just man is also in prison. Thoreau: Civil Disobedience (1846)
I believe that a scientist looking at nonscientific problems is just as dumb as the next guy.
Richard P. Feynman
If there is no struggle, there is no progress. Those who profess to favor freedom, and deprecate agitation, are men who want crops without plowing up the ground, they want rain without thunder and lightning. Frederick Douglass

This message is a reply to:
 Message 97 by mindspawn, posted 09-26-2013 8:15 AM mindspawn has not replied

  
NoNukes
Inactive Member


Message 99 of 161 (707311)
09-26-2013 8:59 AM
Reply to: Message 82 by bluegenes
09-23-2013 4:36 PM


Once you know the number of variables (Single Neucliotide Polymorphisms) between two individuals, you can divide by two to get the aproximate number of mutations going back down each line to the common Y-ancestor.
This would seem to be okay when comparing people in a single generation, but I don't think that it works when comparing people of disparate generations. How does this affect your calculations?

Under a government which imprisons any unjustly, the true place for a just man is also in prison. Thoreau: Civil Disobedience (1846)
I believe that a scientist looking at nonscientific problems is just as dumb as the next guy.
Richard P. Feynman
If there is no struggle, there is no progress. Those who profess to favor freedom, and deprecate agitation, are men who want crops without plowing up the ground, they want rain without thunder and lightning. Frederick Douglass

This message is a reply to:
 Message 82 by bluegenes, posted 09-23-2013 4:36 PM bluegenes has replied

Replies to this message:
 Message 102 by bluegenes, posted 09-27-2013 4:09 AM NoNukes has replied

  
Coyote
Member (Idle past 2106 days)
Posts: 6117
Joined: 01-12-2008


(1)
Message 100 of 161 (707349)
09-26-2013 12:42 PM
Reply to: Message 97 by mindspawn
09-26-2013 8:15 AM


Re: Shuckin' and Jiving started...
If carbon dating is out by a large factor as well, this would have an extreme effects on dates.
Another useless "what-if" designed to let you hold onto your delusions.
You have been ducking the C14 thread I started for you for well over a month now, but yet you still assume your radical unevidenced position is the correct one.
Isn't it about time you showed us your evidence?

Religious belief does not constitute scientific evidence, nor does it convey scientific knowledge.
Belief gets in the way of learning--Robert A. Heinlein
How can I possibly put a new idea into your heads, if I do not first remove your delusions?--Robert A. Heinlein
It's not what we don't know that hurts, it's what we know that ain't so--Will Rogers

This message is a reply to:
 Message 97 by mindspawn, posted 09-26-2013 8:15 AM mindspawn has replied

Replies to this message:
 Message 103 by mindspawn, posted 09-27-2013 4:43 AM Coyote has not replied

  
bluegenes
Member (Idle past 2478 days)
Posts: 3119
From: U.K.
Joined: 01-24-2007


(1)
Message 101 of 161 (707401)
09-27-2013 2:41 AM
Reply to: Message 96 by mindspawn
09-26-2013 5:37 AM


mindspawn writes:
I feel that so far, you misunderstand the extent to which their use of the chimp to represent the ancestral allele has affected your conclusions. And so far there are just far to many assumptions (one example - how to distribute the variations between A and DR) and too many variables (mutation rates, generations, % chimp that matches humans, division of mutations between DR and A, division of mutations between the 36 and the 1) and too many overestimations (mutation rate, no of mutation being 6271, no. of mutations in "A")
There is a lot of truth in what I am saying even if you are not seeing it.
You can distribute the SNPs on the A and DR line any way you want. 470 for A and 0 for the rest if you like. You've still got a falsification of YEC. All you need to know is that you can find pairs of humans with more than 600 SNPs on 3.2MBp of the "Y", and you're more than 99% sure that the standard YEC model is false.
As for a lot of truth in what you're saying, the problem is that you'll make fundamental mistakes, get an idea in your head (like thinking that they've used the chimp to find the within human variations in the first place, rather than just to determine the ancestral allele after they are found) and then waste lots of time because of those mistakes.
For example, here:
mindspawn writes:
The researchers used the chimp to cut down the number of variations from 6662 to 6271. This is because they assumed the chimp IS the ancestral sequence, which is downright silly. especially since the chimp's Y-chromosome has only a 70% match with a human, as much a match as a chicken. IF they had the actual ancestral sequence , this would affect the number of mutations.
Firstly, they don't exactly "cut down the number of variations". What the bit you've quoted here means
quote:
"We extracted the ancestral allele for each position that was variable in humans (assumed to be the allele present in chimpanzee) using the Ensembl-Compara pipeline (Vilella et al. 2009), release 66, and obtained calls for 6271 of the total number of 6662 variable sites (Fig. 1; Supplemental Table S2)."
is that they found 6271 of the 6662 variable sites in the chimp. The chimps are missing the rest. Overall, the chimps are missing about 30% of our "Y", but on that particular 8.97 Mbp, they have nearly all of it. In the 3.2Mbp chart we're looking at, they've left out the SNPs for which they don't have an ancestral match, which is about 5%. The only effect this has is that it makes the "Y" ancestor seem a bit younger than it actually is, which is to the advantage of YEC. Now, here's an example of something you've picked up on, misunderstood, and therefore started to base lots of mistakes on your misunderstanding.
mindspawn writes:
The researchers used the chimp to cut down the number of variations from 6662 to 6271. This is because they assumed the chimp IS the ancestral sequence, which is downright silly. especially since the chimp's Y-chromosome has only a 70% match with a human, as much a match as a chicken. IF they had the actual ancestral sequence , this would affect the number of mutations.
The chimp-ckicken comparison is about structure, not SNPs. Whole chunks of our "Y" are missing from the chimp, and whole chunks of theirs from ours. Plus there are all kinds of rearrangements. But where humans and chimps share chunks of it (as in most of the 8.97Mbp that the paper is dealing with) the nucleotide identity is 98.3% the same. So, while the chimp is not the ideal outgroup for these 36 individuals (Neanderthal would be better if it was well enough sequenced) it's pretty good.
If you and I differed on a given locus on the "Y" that also existed in the chimp, we could be 98.3% sure that the one who also differed from the chimp was the one carrying the mutation. This would apply just as much if the similarity between us and the chimps was due to common design by a creator as it does with common descent, because we can establish the 98.3% reality regardless.
So, you could put their figures of 285 and 185 along the A and DR lines if you wanted to without assuming common descent, but it doesn't really matter what we put there so far as the falsification is concerned.
I'll get on to the stone age people appearing in medieval Europe in my next post, hopefully, because I find it amusing.
BTW, you'll find what you're looking for in the Method section of the paper.
Meet GRCh37

This message is a reply to:
 Message 96 by mindspawn, posted 09-26-2013 5:37 AM mindspawn has replied

Replies to this message:
 Message 119 by mindspawn, posted 10-08-2013 4:02 AM bluegenes has replied

  
bluegenes
Member (Idle past 2478 days)
Posts: 3119
From: U.K.
Joined: 01-24-2007


Message 102 of 161 (707404)
09-27-2013 4:09 AM
Reply to: Message 99 by NoNukes
09-26-2013 8:59 AM


NoNukes writes:
This would seem to be okay when comparing people in a single generation, but I don't think that it works when comparing people of disparate generations. How does this affect your calculations?
Could you clarify that question please? Do you mean how would we compare living people to people from archaeological sites?

This message is a reply to:
 Message 99 by NoNukes, posted 09-26-2013 8:59 AM NoNukes has replied

Replies to this message:
 Message 106 by NoNukes, posted 09-27-2013 9:08 AM bluegenes has replied

  
mindspawn
Member (Idle past 2661 days)
Posts: 1015
Joined: 10-22-2012


(1)
Message 103 of 161 (707409)
09-27-2013 4:43 AM
Reply to: Message 100 by Coyote
09-26-2013 12:42 PM


Re: Shuckin' and Jiving started...
Another useless "what-if" designed to let you hold onto your delusions.
You have been ducking the C14 thread I started for you for well over a month now, but yet you still assume your radical unevidenced position is the correct one.
Isn't it about time you showed us your evidence?
I'm not ducking anything at all. There are many of you, and only one of me. I find it difficult to keep up with many areas of science all at once, and multiple discussion topics in each area of science. (geology/biology/microbiology/genetics/particle physics/dendrochronology etc). In each area of science there are those who know more than me, and so I have to do a lot of research. This is nearly an impossible task that I am attempting, if you could kindly have patience for my position I would appreciate that.

This message is a reply to:
 Message 100 by Coyote, posted 09-26-2013 12:42 PM Coyote has not replied

  
bluegenes
Member (Idle past 2478 days)
Posts: 3119
From: U.K.
Joined: 01-24-2007


(1)
Message 104 of 161 (707411)
09-27-2013 5:15 AM
Reply to: Message 97 by mindspawn
09-26-2013 8:15 AM


mindspawn writes:
The link about mutation rates has a very significant effect and would actually make a difference. You see the article adjusted its mutation rates through finding a lot of mutations since a carbon dated individual who was DNA sequenced. When comparing an actual dated individual with modern individuals of the same root haplogroup, they found more mutations than previously expected. This is actual science at work, not guesswork.
The link is about some studies that have given exceptionally low mtDNA mutation rates that mismatch other studies (and, in terms of time, Y-studies like the ones I'm using). Check out the "out of Africa" estimates in the paper we're discussing, and you can see that they support the dates given in the article, and start even younger.
I don't know why you brought up those. The uncertainty is the wrong way round for your model. What you need are exceptionally fast Y mutation rates to support your model, and no-one has found those. You need superfast rates!

This message is a reply to:
 Message 97 by mindspawn, posted 09-26-2013 8:15 AM mindspawn has not replied

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 Message 105 by NoNukes, posted 09-27-2013 9:05 AM bluegenes has not replied

  
NoNukes
Inactive Member


Message 105 of 161 (707423)
09-27-2013 9:05 AM
Reply to: Message 104 by bluegenes
09-27-2013 5:15 AM


I don't know why you brought up those. The uncertainty is the wrong way round for your model. What you need are exceptionally fast Y mutation rates to support your model, and no-one has found those. You need superfast rates!
Because he assumed that you were using the counting method yielding low mutation rates. I suppose in a way it shows his respect for your presentation so far.

Under a government which imprisons any unjustly, the true place for a just man is also in prison. Thoreau: Civil Disobedience (1846)
I believe that a scientist looking at nonscientific problems is just as dumb as the next guy.
Richard P. Feynman
If there is no struggle, there is no progress. Those who profess to favor freedom, and deprecate agitation, are men who want crops without plowing up the ground, they want rain without thunder and lightning. Frederick Douglass

This message is a reply to:
 Message 104 by bluegenes, posted 09-27-2013 5:15 AM bluegenes has not replied

  
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