The Ketchum Report

[Guest Jodie]

Depending on what it most closely matched, I would suppose you would have to cross reference the mutations across the known variants among the members of that species before you could even suggest what it might be.

[Guest]

I agree Jodie, as I am sure Dr Ketchum does as well, do you think that part of the delays of the study could be the crossing of the t's and the dotting of the i's involved in getting as many samples as possible, to prove a statistical probability? To overkill the science ?

[Guest Jodie]

To me, overkill is repeating the tests over and over to verify that you got the same results, then sending those samples out to others for the same verification process.

Edited February 26, 2012 by Jodie

[Guest]

Dr.Ketchum did a Question an Answer yesterday on the Bigfoot Evidence Blog by Damian Bravo.....obviously general info but interesting none the less.

[Guest Jodie]

To me, overkill is repeating the tests over and over to verify that you got the same results, then sending those samples out to others for the same verification process.

I gave this some more thought. I keep hearing that there is no hypothesis, but in order to get from point A to point B with the conclusion that you have an unidentified hominid running around in the woods you would had to have established multiple hypotheses each step of the way and tested them to the nth degree since one conclusion would be built upon another, I would think.

I'm guessing here, but you would have to start by culling the ones that initially tested negative for some kind of primate ( human most likely), but that would be based on the assumption that bigfoot is a primate.

From the samples that tested human, you would have to find some kind of way to pull out the genetic difference. This would require developing a primer, that primer would have to be tested and retested again to be able to say it was reliable.

Then you would have to do multiple series of runs on the samples to get enough results to rule out the false positives and false negatives. Once that is done, you would have to get others to verify your results.

From there, you would chose the samples you wanted to do complete genomic sequencing. Processing this data would be monumentally time consuming.

Once you had that, I would think you could do the comparison across the most probable species for known mutations. There are many more mutations out there in any species than has been identified so not all would be in a database.

Here is where I get foggy, how do you chose which mutations to isolate and say this a unique species without a definite chain of custody established? I'm hoping Smeja kept his bloody boots from the shooting incident for that one, but one established link to a sample source is not going to be enough to say we have a bigfoot in the woods IMO.

[southernyahoo]

I'm not arguing with you Mulder, just trying to explain why it isn't so cut and dry. There are a lot of limitations to this study that have already been discussed in the thread that I won't bother to rehash, but I chose not to ignore those just to have my belief validated, it doesn't hinge on the study results. In research involving a hypothesis there are only two conclusions you can reach, modus tollens or a confirmed consequence. In modus tollens the data does not support the consequence. In the second, the data does confirm the consequence but you can't be sure that your specific hypothesis was the reason you got your anticipated results. Confirmation is never 100%. The most you can hope for in all of this is that Dr. Ketchum did dot all of her i's and t's. If so, then there is a high probability that there is something unknown out there in the woods, but you can never logically conclude that the unknown would be bigfoot.

You could have a result of this study where the evidence clearly points to a hominid due to it being most closely related to that group, yet is divergent enough in some regions to qualify as a new species or subspecies. Through the deduction that there is no reportedly extant hominid other than what is called bigfoot, it would be a logical fit. You couldn't say it wasn't bigfoot since bigfoot has no offical definition. People could argue from the position that they don't believe this evidence represents bigfoot because they think bigfoot is something other than what the evidence says, but I think that would be bordering denial.

The study could also reveal several variants.

Due to the fact that species Identification can be done with a 648 bp segment of the cytochrome c oxidase I (COI) mitochondrial gene, I do think that a new species of hominid can be proven with DNA alone, particularly with complete mitochondria & nuclear genomes.

http://www.plosbiolo...al.pbio.0020312

Here's some interesting reading. I don't expect that bigfoot would be proven with such short genetic sequences, but do expect such proof to be concordant with what is in this articlce.

Mitochondrial DNA (mtDNA) has been widely employed in phylogenetic studies of animals because it evolves much more rapidly than nuclear DNA, resulting in the accumulation of differences between closely related species (Brown et al. 1979; Moore 1995; Mindell et al. 1997). In fact, the rapid pace of sequence change in mtDNA results in differences between populations that have only been separated for brief periods of time. John Avise was the first to recognize that sequence divergences in mtDNA provide a record of evolutionary history within species, thereby linking population genetics and systematics and establishing the field of phylogeography (Avise et al. 1987). Avise and others also found that sister species usually show pronounced mtDNA divergences, and more generally that “biotic entities registered in mtDNA genealogies…and traditional taxonomic assignments tend to converge†(Avise and Walker 1999). Although many species show phylogeographic subdivisions, these usually coalesce into single lineages “at distances much shorter than the internodal branch lengths of the species tree†(Moore 1995). In other words, sequence divergences are much larger among species than within species, and thus mtDNA genealogies generally capture the biological discontinuities recognized by taxonomists as species. Taking advantage of this fact, taxonomic revisions at the species level now regularly include analysis of mtDNA divergences. For example, many newly recognized species of birds have been defined, in part, on the basis of divergences in their mtDNA

And here...

The general concordance of mtDNA trees with species trees implies that, rather than analyzing DNA from morphologically identified specimens, it could be used the other way around, namely to identify specimens by analyzing their DNA.

Another snip here.....

The diagnosis of species is particularly difficult when they are young. Moreover, hybridization is often common when the ranges of recently arisen species overlap, further complicating identifications. Such newly emerged species are sometimes referred to as superspecies (Mayr and Short 1970), or species complexes, to indicate their close genetic similarity. For example, the white-headed gulls are thought to have diverged very recently, some less than 10,000 years ago (Crochet et al. 2002, 2003), and hybridization is common among many of them. It is thus not surprising that their COI barcodes and other gene loci are very similar. DNA barcodes can help to define the limits of such recently emerged species, but more gene loci need to be surveyed and more work is required to determine which analytical methods can best deduce species boundaries in such cases. The NJ method used here has the advantage of speed, and performs strongly when sequence divergences are low, so it is generally appropriate for recovering intra- and interspecies phylogeny. However, a library of COI barcodes linked to named specimens will provide the large data sets needed to test the efficacy of varied tree-building methods (for review, see Holder and Lewis 2003).

Even between species that diverged long ago, hybridization will lead to shared or very similar sequences at COI and other gene loci. Because mitochondrial DNA is maternally inherited, a COI barcode will assign F₁ hybrids to the species of their female parent. Hybridization leading to the transfer of mtDNA from one species to another can result in a mtDNA tree that is incongruent with the species tree, but it will not necessarily prevent species from being distinguished, unless the mitochondrial transfer is so recent that their sequences have not diverged (Moore 1995). However, recent hybridization will lead species to share COI barcodes, and we expect that more intensive study will reveal such shared sequences in species that are known to hybridize, such as the white-headed gulls (Crochet et al. 2003) and Mallard/Black Ducks (Ankney et al. 1986; Avise et al. 1990).

[bipedalist]

Still the question of "closely" related to human or modern human, OR NOT, should be one of the results of the study it seems.

From there the process would be where in the branches, tree trunks and twigs all of this fits relative to other great apes, primates, etc. if there can be a "good fit" for the "data". In such case, many will consider it to be a worthy project and the accolades will set the table for further study and hopefully, identification of specific candidate species nomenclatures.

This will be worth the hype to me.

edited for crappy formatting by the forum software....... geesh......

So what is Ed Smith so suspicious and "secret squirrel" about in regards to the alleged primer set that is being used?

Edited February 26, 2012 by bipedalist

[Guest]

Mike I would have sited this study and the one where I believe they found human mutations were slower than anticipated.

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0002700;jsessionid=077D0107E5A3BEEEDDA4FF0DBF5B0543

[Guest Jodie]

Well I went over to the GenBank site and typed in a search for COI primate barcodes. All I found were 15 and there was only one 623 bp segment and the rest were 603 bp segments. There were 1,704,203 linear segments for homo. Does anyone know of a study on primates that is similar to what they did for the North American bird species?

I did a search on Ed Smith but all I could find was commentary on JREF regarding his findings that really didn't make any sense. I could never find any specific report to look at. What is he saying about the primers?

Edited February 26, 2012 by Jodie

[Guest slimwitless]

I assume biped is referring to this comment by Ed Smith on Bigfoot Evidence Blog.

I think the real questions should start with the primer set that should be a real hoot.

Honestly I can not wait for that argument and the soft tail answers.

Ed was the source of the recent rumor about legal action (denied by Ketchum) so keep that in mind.

[bipedalist]

Guess he (Ed Smith) would have to answer that.......

Without parameters in his question about his concerns or disagreements and how this is thought to be incongruous somehow..... (or a 'hoot' as he calls it), I guess it is just one of those loose questions meant to 'stimulate' discussion.

[Guest Jodie]

Well , that is where you get into testing for reliability, maybe that's all he meant by it. Everything else is built upon the premise that they worked.

[Guest 11BRAVO]

just shooting for the first post on 100 pages. haha , nope. dammit.

Edited February 26, 2012 by 11BRAVO

[Guest]

I don't understand the issue about primers, they can get the primer by reveres transcribing the mRNA, to the DNA copy, and amplify. You can get a primer without any knowledge of the sequence, its not an obstacle, just a process. You can trial and error it to, if you suspect the primer is human, then try it, it will either work or not, it won't produce ambiguous results, it will simply not work if its incorrect. I hear these are not even expensive methods.

[Guest SquatchinNY]

When is this report coming out?