The Ketchum Report

[Guest Jodie]

Interesting question about primers on there. She answers saying some were targeted and others were universal.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3031029/

Designing these primers for yet unsequenced genes is still a difficult problem, often based on trial and error. One of the first approaches that comes to mind is to derive primers from an available homologous sequence in a phylogenetically proximal species. Alternatively, if more than one homolog is known, primers can be derived from a consensus sequence, based on a multiple sequence alignment of the homologs. However, the nearest-neighbor approach might be substantially biased toward one end in the phylogeny and does not take sequence conservation into account, whereas the multiple-alignment approach usually does not consider the exact phylogenetic position of the target species and a careful selection of the seed sequences is an additional parameter.

In other words you guess the species, if it looks close, then you try to narrow it down further. So if she guessed, then there will be some controversy over whether the bigfoot DNA fits within whatever species she decided it most closely matched. It probably won't matter where anyone thinks it falls this time around, more than likely no one will agree until more studies can be done.

[Guest]

Right Jodie . So in general within any gene are conserved sequences that are conserved across species . Some even are conserved between us and fruitflies for example . They are regions where the amino acid sequence and therefore the gene sequence are so critical that they cannot vary much and still have a functional protein . Among primates you would expect to have a relatively large number of these conserved areas which can be used to your advantage if trying to design primers to amplify a region of a gene from an unknown species . In this case, you would guess primate and look for areas conserved among primates for the proper primer design . Since primers are usually relatively short , and are designed to flank the region you are trying to sequence, once the sequencing reaction is complete you get the entire sequence in between these primer pairs from your unknown species . Then since you now know the sequence of that area , you can use a portion of that for the design of the next forward primer , but will still have to guess for the reverse , this can be done over and over until you get a large stretch . Hope that made a little sense

[Guest]

So basically what this says is that all mammals share a sequence that makes them "mammals" (as opposed to each mammal type having a separate sequence that makes them mammals), and likewise all primates, etc. So you start broad (mammal, insect, fish, etc) then narrow it (canid, primate, ungulate, etc) and then narrow it further (great ape, monkey, etc) then again (orang, gorilla, chimpanzee, hominid, etc) and keep going until you nail it down precisely?

[southernyahoo]

In other words you guess the species, if it looks close, then you try to narrow it down further. So if she guessed, then there will be some controversy over whether the bigfoot DNA fits within whatever species she decided it most closely matched. It probably won't matter where anyone thinks it falls this time around, more than likely no one will agree until more studies can be done.

It would seem to me if you didn't guess correctly on the proximal species, you'd not get much of a sequence. Also, the work on the DNA wouldn't likely change if you had a body, this same thing must be done with any new species, but with perhaps a little better guess work starting off. With a complete sequence, the statistics take over to determine which species is most proximal. This is just how I understand it at this point.

[AaronD]

The "bear hunter's" story is complete b.s., and this guy will never prove that he's killed 1, let alone 2 bigfoots. He also hasn't killed anywhere near 1000 bears...Saskeptic

There is no Bigfoot, no shootings, no bodies and no Bigfoot "slice-of-thigh" or any other body part forthcoming. My sources are irrefutable. There IS no DNA.

There is no (to say the least) convincing Erickson video. Isn't there....... WTB1

People have been crying about real scientists looking at the proof. Now they are, and you want Nestle's instant answers all hot and steaming with marshmellows in it...... HairyGreek

I like your signature post Southernyahoo, well said !

[Guest Cervelo]

SY,

A liitle better guess work with a body!

That would be the understatement of the century and there would be no guess work involved! LOL

[southernyahoo]

Depends on your perceptions of what you were looking at VS reality. As I've made this point before, You would'nt prove some naked hairy hobo was a new species unless the DNA and the rest of the science confirmed it, since 99.9999999% of all sightings are likely some sort of mistake, right?

[Guest Cervelo]

Your scenario fits perfect with the accepted scientific method for such a discovery and recognition of a new whatever it may be.

Specimen is produced DNA identifies it.

We are in complete agreement!

It's just the order of events that we differ on, I guess we will see whenever the study comes out.

[Guest JiggyPotamus]

This question is based on my limited understanding of the process...Could the reason this is taking so much time be because they are comparing across different species, looking for the most similar relationship? Or is the time simply a factor of the sheer number of samples received, combined with the lengthy time period it may take to extract and sequence useful information?

OR, is it a mistake assuming that the project is taking a long time to complete?

Edited March 29, 2012 by JiggyPotamus

[Guest Cervelo]

Jiggy,

I don't know anything about DNA or care to but here's my take on it.

Some human mumbo jumbo DNA that is so "different" but yet similar enough that it must be from the same source (animal).

But the samples have been taken from so many diffrent locations and under squatchy

circumstances it must be Bigfoot.

It's a fundamentaly flawed proposition from the get go IMO but we will see.....someday

[southernyahoo]

It's not fundamentally flawed. Here's why.

Scenario one: Until 2010 we had never heard of denisovans, didn't know we had interbred with them, didn't have any bones to suggest they ever existed, Then we found a tiny finger bone and tooth, extracted DNA, another hominid is recognized, now we know they contributed to our genetic makeup.

We would not have guessed this by looking at each other.

Scenario two: People keep reporting seeing some hairy biped, a great ape of some sort is a good guess. Other people begin to investigate, they know if there is something like that which is not 100% Hss it will leave some sort of sign, shed hairs, leave scat, tracks etc. Samples get collected, eventually a scientists says, hey, send me that stuff and we'll get to the bottom of it. Turns out the scientist wants to publish on it. New species discovered? Mmmmaybe:)

There's nothing wrong with the sequence of events or the reasoning why if the DNA says new species, then thats what we have, otherwise science wouldn't use it like they do in phylogeny.

[Guest]

. . . Samples get collected, eventually a scientists says, hey, send me that stuff and we'll get to the bottom of it. Turns out the scientist wants to publish on it.

Just to clarify, other scientists have said the same thing, analyzed similar samples, and published on them.

[Cotter]

^^ Sas - can you point me in the direction where to find those published findings (or summaries of them)?

Thanks

[Guest]

Here is my list of recently published papers on bigfoot/yeti stuff. The papers that specifically addressed analysis of hair samples are Wu et al. 1993, Milinkovitch et al. 2004, and Coltman and Davis 2006. I'm pretty sure I've attached these papers to an earlier post in this thread.

1. Wu, X., X. Zeng, and H. Yao. 1993. Analysis of a single strand of hair by PIXE, IXX and synchrotron radiation. Nuclear Instruments and Methods in Physics Research B75: 567–570.

2. Milinkovitch, M C., A. Caccone, and G. Amato. 2004. Molecular phylogenetic analyses indicate extensive morphological convergence between the ‘‘yeti’’ and primates. Molecular Phylogenetics and Evolution 31: 1–3.

3. Lozier, J. D., P. Aniello, and M. J. Hickerson. 2009. Predicting the distribution of Sasquatch in western North America: anything goes with ecological niche modelling. Journal of Biogeography 36: 1623–1627.

4. Lockley, M., G. Roberts, and J. Y. Kim. 2008. In the footprints of our ancestors: an overview of the hominid track record. Ichnos 15: 106–125.

5. Kim, J. Y., K. S. Kim., M. G. Lockley, and N. Matthews. 2008. Hominid ichnotaxonomy: an exploration of a neglected discipline. Ichnos 15: 126–139.

6. Coltman, D. and C. Davis 2006. Molecular cryptozoology meets the Sasquatch. TRENDS in Ecology and Evolution 21: 60–61.

[Guest Jodie]

I figured the primate part was a given when developing the primers based on the black and white test she initially did to distinguish the samples as being either animal or human. My understanding is that she chose the human samples to test further.

I don't think the statistics are going to nail it SY, based on what I was reading in that article. If she starts off with a bias for the wrong end of the phylogenetic tree in the primate family from the beginning would that not skew things?

I'm just not convinced they can say definitively what bigfoot is with just one research study only looking at their DNA. I can't imagine how they went about it since you can't just waltz into a research facility and ask for sequencing and commercial labs can't feasibly offer it for financial reasons.

So I have to assume she sequenced these samples the way she does for her animal DNA. There is probably no difference in sequencing animal versus human DNA but how can you know for sure that you have something unique if you aren't used to looking at human, great ape, or extinct hominid DNA? For all we know, she may not have a definitive conclusion of what it is beyond it being a primate, if that.

Edited March 29, 2012 by Jodie