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Ketchum DNA Paper?

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Re: Ketchum DNA Paper?

Post  Woodwose on Sun Feb 17, 2013 12:19 pm

CMcMillan wrote:THIS IS WHAT WE ARE TALKING ABOUT BELOW:
mtDNA is generally passed un-mixed from mothers to children of both sexes, along the maternal line, or matrilineally

I am not claiming that science is wrong. I'm merely explaining how I understand mtDNA to operate. I could very well be mistaken.

I'm aware that mtDNA is passed on unmixed within a species, but we are talking about hybridsation. From what I have read there seems to be some debate about what happens when hybridisation ceases. Some sources claim that subsequent generations will retain unmixed mtDNA from the hybridisation, whilst other indicate that it's possible that over long periods mutations in mtDNA may result in unique sequences.

It seems that hybridisation is very rare and therefore we don't have enough information to fully understand how it works in the long term.

The issue certainly isn't as clear cut as you make it out to be and the presence of human mtDNA is by no means an indication that the DNA results are legitimate. If however they are legitimate then it should be possible to determine when any hybridisation may have occurred.

As I've said before, we should really wait and see what the experts have to say. I wonder is Sykes has read the paper and will look at the DNA.
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Re: Ketchum DNA Paper?

Post  CMcMillan on Sun Feb 17, 2013 12:43 pm

I have never said the Results are legitimate.
You brought up your confusion about the mtDNA that you don't understand why it shows as HUMAN.

I was showing you how scientists were able to pinpoint Mitochondrial Eve via mtDNA which is "100% Human" and how it followed her up the chain to us.
So I was clarifying your Confusion on HOW and Possibly WHY the mtDNA shows as 100% Human.

The issue certainly isn't as clear cut as you make it out to be and the presence of human mtDNA is by no means an indication that the DNA results are legitimate. If however they are legitimate then it should be possible to determine when any hybridisation may have occurred.

Ketchum did draw conclusions when she beleives it may have happened. This is what a lot of people are debating on her conclusion.
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Re: Ketchum DNA Paper?

Post  Woodwose on Sun Feb 17, 2013 1:18 pm

CMcMillan wrote:I was showing you how scientists were able to pinpoint Mitochondrial Eve via mtDNA which is "100% Human" and how it followed her up the chain to us. So I was clarifying your Confusion on HOW and Possibly WHY the mtDNA shows as 100% Human.

I'm still not 100% convinced that it does make sense - especially when you look at the ongoing debate regarding supposed human and Neanderthal hybridisation.

Shouldn't we expect to find BF nDNA or mtDNA in human populations?
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Re: Ketchum DNA Paper?

Post  Squatchmaster G on Sun Feb 17, 2013 1:43 pm

There's one big problem with the mtDNA that hasn't been discussed in the thread yet:
To begin with, the mitochondrial DNA of the samples (when it can be isolated) clusters with that of modern humans. That isn't itself a problem if we assume that those doing the interbreeding were human females, but the DNA sequences come from a variety of different humans—16 in total. And most of these were "European or Middle Eastern in origin" with a few "African and American Indian haplotypes." Given the timing of the interbreeding, we should only be seeing Native American sequences here. The authors speculate that some humans may have walked across the ice through Greenland during the last glaciation, but there's absolutely no evidence for that. The best explanation here is contamination.
Link

There isn't one Homo sapiens sapiens mtDNA sequence, there's a whole bunch that can be traced back from populations all over the world. Apparently the mtDNA from the alleged Bigfoot samples used in Ketchum's study were mostly non-American Indian haplotypes and if the interbreeding happened 15,000 years ago as she's claiming then that just doesn't make any sense.


Ketchum's interbreeding hypothesis is on sketchy ground anyway. It's certainly a possible explanation for the double-stranded appearance of the nuDNA but her paper apparently doesn't investigate this closely enough to be able to draw that conclusion:
As far as the nuclear genome is concerned, the results are a mess. Sometimes the tests picked up human DNA. Other times, they didn't. Sometimes the tests failed entirely. The products of the DNA amplifications performed on the samples look about like what you'd expect when the reaction didn't amplify the intended sequence. And electron micrographs of the DNA isolated from these samples show patches of double- and single-stranded DNA intermixed. This is what you might expect if two distantly related species had their DNA mixed—the protein-coding sequences would hybridize, and the intervening sections wouldn't. All of this suggests modern human DNA intermingled with some other contaminant.

The authors' description of the sequence suggests that it's human DNA interspersed with sequence from some other primate—hence the interbreeding idea. But the best way to analyze this would be to isolate the individual segments of non-human DNA and see what species those best align with. If the authors have done that, they don't say. They also don't mention how long the typical segment of non-human DNA is. Assuming interbreeding took place as the authors surmise, these segments should be quite long, since there hasn't been that much time to recombine. The fact that the authors don't mention this at all is pretty problematic.
Link

(Note that a decent independent peer review of her paper should have highlighted these problems long ago and given her the chance to rewrite the paper and address these issues. This is another reason why the formal peer review process is important.)

As far as anyone can tell so far the very foundations of her conclusions are pretty shakey which is really bad news for anyone hoping that he paper was going to be the definitive proof that we've been waiting for. At this point we can only wait and see what the independent reviewers make of her data.
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Re: Ketchum DNA Paper?

Post  Woodwose on Sun Feb 17, 2013 2:04 pm

Squatchmaster G,

I think that article has been referenced a couple of times on this thread already. It just didn't generate much discussion and was sidelined.
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Re: Ketchum DNA Paper?

Post  Squatchmaster G on Sun Feb 17, 2013 2:20 pm

I'll also add that assigning an official scientific latin name to a new subspecies solely on the basis of molecular phylogenetics without a type specimen was either pretty ballsy or pretty naive, especially when her phylogenetic tree was as wonky as it apparently was. Species and even clades are often reclassified using molecular phylogenetics but that's only used to refine a previously existing taxonomic definition in conjunction with robust DNA barcoding of mulitple known specimens, not create a new one practically from scratch. Claiming that she'd proved the existence of Bigfoot when the samples she used didn't have a clear provenance was poor science.


Woodwose wrote:I think that article has been referenced a couple of times on this thread already. It just didn't generate much discussion and was sidelined.

I just checked and it hasn't been discussed in this thread before I posted it. I'd previously posted a link to it in a different thread.
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Re: Ketchum DNA Paper?

Post  Woodwose on Sun Feb 17, 2013 2:33 pm

It was linked to and quoted by myself back on page 3, but no matter.
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Re: Ketchum DNA Paper?

Post  Squatchmaster G on Sun Feb 17, 2013 2:46 pm

Woodwose wrote:It was linked to and quoted by myself back on page 3, but no matter.

Ah, you used a tinyurl or something, I was looking for the original url. My bad. Embarassed


But anyway, the info it has on the mtDNA from Ketchum's study is definitely relevant to the discussion at hand. It doesn't make sense under the conclusions she draws and she just didn't supply any explanation for it.
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Re: Ketchum DNA Paper?

Post  Woodwose on Sun Feb 17, 2013 3:04 pm

The best case scenario would be that the DNA is genuine but Ketchum is in way over her head, she's made mistakes and just is not interpreting the data properly.

If independent analysis of the DNA verifies that it isn't contaminated, then I imagine someone more qualified will be able to explain how the DNA should be interpreted.

I suppose there is also the possibility that the mtDNA is down to contamination, but the nDNA is from a species new to science. Although, wouldn't that mean that we should also find unknown mtDNA in the samples?
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Re: Ketchum DNA Paper?

Post  DPinkerton on Sun Feb 17, 2013 3:18 pm

Woodwose wrote:I suppose there is also the possibility that the mtDNA is down to contamination, but the nDNA is from a species new to science. Although, wouldn't that mean that we should also find unknown mtDNA in the samples?

I do not believe so...if that were the case...then everyone around today would not have homo sapien mtDNA...we would have mtDNA derived from the interbreeding of sapiens and neanderthal. The whole ability to track the lineage of a species is based on mtDNA staying consistent.

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Re: Ketchum DNA Paper?

Post  CMcMillan on Sun Feb 17, 2013 3:21 pm

DPinkerton wrote:
Woodwose wrote:I suppose there is also the possibility that the mtDNA is down to contamination, but the nDNA is from a species new to science. Although, wouldn't that mean that we should also find unknown mtDNA in the samples?

I do not believe so...if that were the case...then everyone around today would not have homo sapien mtDNA...we would have mtDNA derived from the interbreeding of sapiens and neanderthal. The whole ability to track the lineage of a species is based on mtDNA staying consistent.

Exactly
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Re: Ketchum DNA Paper?

Post  CMcMillan on Sun Feb 17, 2013 3:42 pm

http://www.nytimes.com/2010/05/07/science/07neanderthal.html?_r=0

Scientists say they have recovered 60 percent of the genome so far and hope to complete it. By comparing that genome with those of various present day humans, the team concluded that about 1 percent to 4 percent of the genome of non-Africans today is derived from Neanderthals. But the Neanderthal DNA does not seem to have played a great role in human evolution, they said.



"So, if any hybridisation happened - it's difficult to conclusively prove it never happened - then it would have been minimal and much less than what people are claiming now," Manica says, in a statement.

However, a draft report headed by David Reich of the Harvard Medical School from the team that first reported the Neanderthal genes looks at differing rates of changes in the genes of both modern humans and Neanderthal samples and comes to a different conclusion. Based on their analysis, they estimate interbreeding did occur from 65,000 to 47,000 years ago, about the time that early modern humans are seen as leaving Africa.

http://content.usatoday.com/communities/sciencefair/post/2012/08/neanderthal-mating-debated-in-duelling-studies/1

Really you both argue that science is the end all be all for proof, yet you both Refuse to understand what mtdna is all about. Yet you both Argue over it not understanding it.
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Re: Ketchum DNA Paper?

Post  Woodwose on Sun Feb 17, 2013 3:56 pm

DPinkerton wrote:I do not believe so...if that were the case...then everyone around today would not have homo sapien mtDNA...we would have mtDNA derived from the interbreeding of sapiens and neanderthal. The whole ability to track the lineage of a species is based on mtDNA staying consistent.

My comment was prompted by the fact that our supposed hybridisation with Neanderthals comes from evidence that we share some of our nDNA with Neanderthals. We do not have any Neanderthal mtDNA in our genetic makeup.
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Re: Ketchum DNA Paper?

Post  DPinkerton on Sun Feb 17, 2013 4:07 pm

Woodwose wrote:
DPinkerton wrote:I do not believe so...if that were the case...then everyone around today would not have homo sapien mtDNA...we would have mtDNA derived from the interbreeding of sapiens and neanderthal. The whole ability to track the lineage of a species is based on mtDNA staying consistent.

My comment was prompted by the fact that our supposed hybridisation with Neanderthals comes from evidence that we share some of our nDNA with Neanderthals. We do not have any Neanderthal mtDNA in our genetic makeup.

mtDNA is passed from the mother....there are only two ways this could have happened...

1) The first interspecies mating between sapien and neanderthal was between a female sapien and male neanderthal...the resulting offspring would have human mtDNA.

2) The first interspecies mating between sapien and neanderthal was between a female neanderthal and male sapien...the resulting offspring would have neanderthal mtDNA.

Since there are no current living neanderthals (people with neanderthal mtDNA)...we can scientifically state that ALL cases of number 2 above lead to dead end family lines.

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Re: Ketchum DNA Paper?

Post  CMcMillan on Sun Feb 17, 2013 4:16 pm

Woodwose wrote:
DPinkerton wrote:I do not believe so...if that were the case...then everyone around today would not have homo sapien mtDNA...we would have mtDNA derived from the interbreeding of sapiens and neanderthal. The whole ability to track the lineage of a species is based on mtDNA staying consistent.

My comment was prompted by the fact that our supposed hybridisation with Neanderthals comes from evidence that we share some of our nDNA with Neanderthals. We do not have any Neanderthal mtDNA in our genetic makeup.

So how is it hard to not believe that Bigfoot has human mtDNA and NDA from something else.
Since this is what we have found with Neanderthal Hybridization
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Re: Ketchum DNA Paper?

Post  Woodwose on Sun Feb 17, 2013 4:18 pm

DP,

Yes that's what I understand the case to be.

If there has been hybridisation and the same scenario applies to BF but Ketchum's mtDNA was show to be the product of contamination, then a modern population of BFs could only be related to us paternally. Consequently BF DNA would have to feature a mix of human nDNA, unknown nDNA and unknown mtDNA.

I think that's right?
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Re: Ketchum DNA Paper?

Post  Squatchmaster G on Sun Feb 17, 2013 4:19 pm

CMcMillan wrote:So how is it hard to not believe that Bigfoot has human mtDNA and NDA from something else.
Since this is what we have found with Neanderthal Hybridization

Because of the varied human mtDNA found in the alleged Bigfoot samples, as I posted about recently in the thread.
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Re: Ketchum DNA Paper?

Post  CMcMillan on Sun Feb 17, 2013 4:21 pm

Squatchmaster G wrote:
CMcMillan wrote:So how is it hard to not believe that Bigfoot has human mtDNA and NDA from something else.
Since this is what we have found with Neanderthal Hybridization

Because of the varied human mtDNA found in the alleged Bigfoot samples, as I posted about recently in the thread.

My gawd go read about mt"EVE" and you will learn we didn't all come from EVE that other women were around but they mtdna was not as strong for a direct line that it was with eve.

Seriously BSG dumbed this down for people go watch the ending of BSG or something
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Re: Ketchum DNA Paper?

Post  Woodwose on Mon Feb 18, 2013 10:59 am

I think that the point Squatchmaster G is trying to make is that the human mtDNA seems to come from people who would not have been in the US at the point of hybridisation.

Yes, we are all interrelated and come from mtEve, but as you say mutations allow us to identify which population group someone is related to (and how recently that relatedness came into place). In which case human mtDNA from an hybridisation event that occurred 15,000 years ago in the US should not have a profile which suggests that the human contributors are most closely related to western Europeans.
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This thread is going to be locked if the personal attacks don't stop...

Post  ***** on Mon Feb 18, 2013 11:07 am

I'm locking this thread indefinitely if you guys can't calm down, and stop with the name calling and personal attacks.


Forum Guidelineshttp://bigfoot.forumotion.com/t325-guidelines-for-trollish-behavior

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Re: Ketchum DNA Paper?

Post  CMcMillan on Tue Feb 19, 2013 11:44 am

those questioning contamination of some of her DNA:

The DNA from these three samples was sequenced using the next generation Illumina platform
at the University of Texas, Southwestern in Dallas, TX, a laboratory that sequences human
genomes 75-77. On average, there were 70-110 million total reads for each sample in each lane,
which is well over 90 Gb of raw sequence for each sample comprising greater than 30X
coverage.
The run summary generated by the HiSeq 2000 next generation sequencer provides scores, Q30,
for run quality 78 . Q30 can also be used to determine if there was any contamination (or mixture)
found in the samples sequenced. According to Illumina, a pure, single source sample would
have an Q30 score of 80 or greater with an average of 85. However, if there was contamination
present in the sample sequenced, the divergent sequences would compete against one another
prior to sequencing causing a contaminated sample to have a Q30 score of 40 to 50. The Q30
scores for the three genomes sequenced had Q30 scores of 88.6, 88.4 and 88.7 respectively for
samples 26, 31 and 140. The Q30 is the percent of the reads that have the statistical probability
greater than 1:1000 of being correctly sequenced. Therefore, not only were the sequences from a
single source, but the quality of the sequences were far above the average genome sequenced
using the Illumina next generation sequencing platform.

Melba S. Ketchum

(Corresponding author)
Patrick W. Wojtkiewicz
Aliece B. Watts
David W. Spence
Andreas K. Holzenburg
Douglas G. Toler
Thomas M. Prychitko
Fan Zhang
Sarah Bollinger
Ray Shoulders
Ryan Smith

DNA Diagnostics, Nacogdoches, TX 75965
North Louisiana Criminalistics Laboratory, Shreveport, LA 71101
Integrated Forensic Laboratories, Inc., Euless, TX 76039
Southwestern Institute of Forensic Sciences, Dallas, TX 75207
Texas A&M University, Microscopy & Imaging Center, Department of Biology and
Department of Biochemistry & Biophysics, College Station, TX 77843-2257
Huguley Pathology Consultants, P.A., Ft. Worth, TX 76115
Helix Biological Laboratory, Detroit, Michigan, 48202
UNT Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX 76107


Author Contributions: M.K., P.W., D.S., A.H., S.B., R.S., and R.S. performed experiments.
M.K, and F.Z. analyzed the genetic data. M.K., A.W., and P.W. wrote and edited the manuscript.
A.H. analyzed and wrote the EM portion of the manuscript. D. S. analyzed and wrote the hair
analysis portion of the manuscript. D.T. analyzed and wrote the histopathology portion of the
manuscript. A.W. also researched pertinent additions to the manuscript and helped with data
collection. M.K. distributed samples, collected and combined data from the blind studies.
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Re: Ketchum DNA Paper?

Post  Woodwose on Tue Feb 19, 2013 11:54 am

Whilst that makes contamination less likely, it does not rule it out completely. The samples must be independently tested by various labs.

I appreciate that this has supposedly already been done and that the participating labs would not allow their results or involvement to be published. However independent verification is an absolute must.

Maybe some of the undisclosed labs will now come forward. If they don't then we will just have to wait for others labs to to re-test the samples (assuming Ketchum allows access to them).
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Re: Ketchum DNA Paper?

Post  CMcMillan on Tue Feb 19, 2013 12:48 pm

You can find the prelim of her paper on line for free in PDF format.
If you are interested in more on how she Avoided contamination and checked you can get the prelim paper.

http://www.venomdoc.com/downloads/No...n_Hominins.pdf


Last edited by CMcMillan on Tue Feb 19, 2013 12:58 pm; edited 1 time in total
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Re: Ketchum DNA Paper?

Post  Woodwose on Tue Feb 19, 2013 12:55 pm

Yes, I've read about the measures she has supposed to have taken. We can't just take her word for it though and the results and samples need to be independently verified.

Researchers who have been very meticulous regarding contamination can and do make mistakes, or overlook potential points of contamination.
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Re: Ketchum DNA Paper?

Post  CMcMillan on Tue Feb 19, 2013 1:00 pm

Woodwose wrote:Yes, I've read about the measures she has supposed to have taken. We can't just take her word for it though and the results and samples need to be independently verified.

Researchers who have been very meticulous regarding contamination can and do make mistakes, or overlook potential points of contamination.

The samples were sent to various places. They all got the same results.
So what do you mean by Independently verified.
She sent the samples to different labs "BLIND" they were just to run tests.
If all the labs came with the same results isn't that Verified?

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