DNA Testing suggestions Options

[Apeman]

Here’s a way to identify sasquatch DNA:...

This is what's always been done but usually on a broader scale to include all apes, or primates, or mammals. Arguably more specific primers might narrow the contamination risks but since many results are coming back as human, which is presumably one of the closest relatives, it doesn't really matter.... unless your going to try consensus primers excluding humans?

And I mostly agree with Bluegenes as usual- (though after hearing it I don't doubt this woman's expertise, just her initiative.) Without even hearing the tape, the director's statement about needing a match is of course true if she's talking about traditional DNA fingerprinting, which is very different than what we are all advocating. But their apparent explanation strikes me as being just plain lazy because if they got clean DNA for a fingerprint, another hours work and $50 would provide the sequence we're talking about and answer the big question of what the hair was actually from.


Apeman

I just listened and it sounds like they had a request but never ran the hair sample....because of the incorrect "no match" argument. Unbelievable.

This post has been edited by Apeman: Oct 2 2007, 11:00 PM

[Sac-squatch]

So Apeman and BlueGenes,
Are you suggesting that there is further action I should be taking?

[Doubleyouex Whyz...]

This is what's always been done but usually on a broader scale to include all apes, or primates, or mammals. Arguably more specific primers might narrow the contamination risks but since many results are coming back as human, which is presumably one of the closest relatives, it doesn't really matter.... unless your going to try consensus primers excluding humans?

So you think to be viable a technique has to be immune from human DNA contamination? You are dreaming.





Edit to fix quote tags..

This post has been edited by JayleeD: Oct 3 2007, 07:15 AM

[Apeman]

So you think to be viable a technique has to be immune from human DNA contamination? You are dreaming.

I don't think you understood what I was saying. No, I'm not dreaming. My point was that any technique removing the possibility of human contamination, which is of course possible, is likely to similarly miss the target DNA unless it's quite distant from humans. You may not be aware that there is a long history of results coming back as "human," which some believe is definitely evidence of contamination, while leading others to start to wonder if these beings might be a LOT closer to humans than most ever suspected. I was kind of thinking out loud and sorry if I wasn't clear or I didn't finish my thought. No need to jump down my throat, thanks. I should have simply said that what you were suggesting is no different than what has been talked about and tried for years. That isn't meant as a slight to you, just an explanation to everyone else who might think you're suggesting something novel that might finally yield fruitful results.

Sac-Squatch,
It's hard to suggest further steps without knowing what they actually did. Did you pay for anything? If they did sequence your sample there isn't much more that could be done, though sequencing other regions might be interesting. But if they only morphologically typed it, or did standard DNA fingerpringitng, then yes, there is more that could be done. Hope that helps.

Apeman

[Doubleyouex Whyz...]

Dear Apeman, so sorry for my vicious attack. I don’t know what came over me. (I am a beast.)

I am aware that results have come back “human.� But I don’t think there are enough such results – that are good – to worry that human and sasquatch DNA may be quite the same.

I think it’s just that there are very few good samples (actual sasquatch and containing a decent amount of DNA), that contamination is a big problem, and that the good samples are pretty much lost – they are mishandled, not analyzed well, or at all. It’s like you all are saying: most DNA experts consulted on the question don’t really understand the issue.

I don’t think you’re right about the approach I outlined being just so been there, tried that. Not at all. Please don’t take offense. I’m just disagreeing with you.

[Apeman]

I don’t think you’re right about the approach I outlined being just so been there, tried that. Not at all. Please don’t take offense. I’m just disagreeing with you.

I'm not offended at all, there is just more information outisde the public realm than most might be aware of. So your opinion is fair enough, but I can't say much more than "take my word for it."

Out of curiosity, what other approach do you think anyone has taken in order to obtain DNA sequences?

Apeman

PS- I assume you were being sarcastic about your "vicious attack" but in case you weren't, it was less vicious than it was snide and arrogant, but we've all been guilty of that. Yet another reminder for us all to be more courteous to each other, me included.

[BlueGenes]

I am now, also, very curious as to how the UC Davis lab analyzed the hair and tissue sample. Any further and specific details would certainly be appreciated! Ok, I guess I did slam the UC Davis lab tech NPR interview a bit hard. I got thinking about it last night and here is what I came up with: The person interviewed is a forensic scientist. As such, she seemed competant and dedicated to her job and field. But, she is not a geneticist. Forensics using alot of genetic tools, but the fields are different. Forensics "steals" techniques from genetics to answer the questions they are interested in, such as "was this person at the scene of the crime?". Forensic scientists don't look for things outside the normal realm of posibilities.......they simply don't have the time and resources and it's NOT their job to do so.

Furthermore, forensic scientists are not phylogeneticists. Like forensic scientists, phylogeneticists "steal" techniques from the geneticists to answer the questions they are interested in, such as "How different is this specimen, population or species from other specimens, populations or species". Since this field is open to "discovering" unknowns and has the tools and knowledge to do so, it's the direction that I, ApeMan and some others have been proposing as BF research's best hope (short of finding an actual body).

Concerning primers: I guess some of you know that universal primers for many classification levels of organisms have been around for a while (species, family, order and even kingdom). Luckily, that's a wheel that will not need to be reinvented. We won't need to line up homologous sequences and design new primers. The sequence for these primers can be found in many publications and the cost of buying them is rather cheap (I paid about $20 for the last pair I ordered).

ApeMan did bring up an interesting point. If BF is VERY closely related to Homo sapien some (even many) sequences might not be able to differentiate between the two species. Even is this is the case, I'm still hopeful. I'm confident that with enough sequence data a clear difference will be apparent. We're at the point were DNA can infer ones ethnic history.....so eventually finding some sequences unique to BF is almost a given. You just have to look.

[hopeful]

I move that BlueGenes should be given a chance to analyze as much suspected Sasquatch DNA as possible. As he has stated, there are newer and better techniques available today, and I am sure that many of us would be extremely interested in learning the results based on these new methods.

I also move that we somehow locate the existing alleged Sasquatch samples and contact whomever is in possession of them.

Who is good at locating?

Who is good at contacting?

Who is good at getting people to give them samples of their BF samples?

I am good at making motions and asking guestions...

(I am also good at audio transcription, bookkeeping, record keeping, internet research, taking care of animals, and teaching algebra. If any of that would be helpful at all to anybody's BF research progress, please let me know. I'll do what I can to help.)

[Lab Lover]

Blue genes:

Thanks so much for taking the time to listen to the podcast and for adding your clarifications. Although all this is way over my head, it sounds like someone like you should speak with this lab director. Why? Because obviously BF samples (one, at least) are being submitted to her in her official capacity where for whatever reason they disappear. Her public (national broadcast no less) treatment of the subject as a joke, when she and only she had the power to duly investigate an extremely rare sample submitted in good faith, evince at best ignorance of the efforts being made by many BF reseachers and at worst elitist arrogance. When I first heard the interview live I was really offended. But that is not the right approach, I know. I hope someone like you can at least get her attention so that if she is not willing to treat the subject fairly, at least pass the samples on to someone willing to perform the tests you guys are discussing here.

LL

[Apeman]

Because obviously BF samples (one, at least) are being submitted to her in her official capacity where for whatever reason they disappear.

Again, it sounded to me like someone inquired, but never submitted anything- because of the director's negative attitude/admission that she couldn't help/lack of imagination and/or lack of scientific approach. I agree that any such sample is potentially worthy of full analysis but for all we know it was analyzed somewhere else Ken Ken Ken Yielding the usual non-result.

I'll take this opportunity to again remind everyone that there have been dozens of samples analyzed by different labs all over the country- none providing the proverbial smoking gun. But that doesn't mean we shouldn't keep trying and it doesn't mean we aren't. Bluegenes offer has only been on the table a few weeks and only to this very limited and generally suspicious community. I'd encourage Sac-squatch to send Bluegenes a hair or two if he can spare them from his samples and I'd reassure everyone that this is an active area of research on many fronts. No need to push the eject buttons yet.

Lab Lover- Are you free for pet sitting so I can get out in the field more when my broken leg heals?

Apeman

This post has been edited by Apeman: Oct 3 2007, 03:16 PM

[Hairy Man]

Broken leg?? What did you do?? Please tell me you did it chasing after a bigfoot in the dark, right???

This post has been edited by Hairy Man: Oct 3 2007, 03:23 PM

[hopeful]

I am absolutely available for pet-sitting, Apeman! What kind of pet do you have? Broken leg!? I'm sorry about that. What did you do?

[Apeman]

What did you do?

Let's just leave it at "something stupid" and keep on with the thread, but thanks for the sympathy. The pet sitting was also a joke. I just let them roam the wilds and fend for themselves when I need to go away....

Apeman

[Doubleyouex Whyz...]

Apeman wrote: "Out of curiosity, what other approach do you think anyone has taken in order to obtain DNA sequences?"


To start very generally, for instance with primers that identify the order of the animal. Then narrow it down with more and more specific primers until you can determine the species. Can you tell me of anyone doing what I described?

[Doubleyouex Whyz...]

If primers are chosen that perfectly recognize human and chimp DNA they will probably recognize sasquatch DNA. (Areas of homology are probably shared between human, chimp, and sasquatch.)

If the DNA between the primers is significantly different between human and chimp, there are probably some significant differences there between human and sasquatch too.

Many areas of the human/chimp mitochondrial genome fit this description – runs of 100 to 400 base pairs with a dozen or two base differences between human and chimp, for which homologous primers can be made to amplify.

If your sample is from a human you’ll get right-sized products on your gel and the sequences will be exactly human. If the sample is from another animal (besides sasquatch) you won’t get products at all. If the sample is sasquatch, you’ll get human sized products with base changes… that aren’t published as SNPs. You’ll keep amplifying these mtDNA human/chimp divergent stretches, seeing more base changes… and then you’ll see if you can use the same approach on nuclear DNA. (At this stage you’ll be bursting, unable to hold your pipetter steady.)

It’s easy.

[BlueGenes]

Not to offend you (really!), but you're a little bit off on your descrption Doub. You have the basic idea and you're almost there...and that's great! I'm glad you have a good grasp of the basics (too many don't). The stuff concerning the primers, gel bands, SNPs and mtDNA versus nuDNA needs some tweeking. It's been a long day and I don't really have the energy to explain it all right now. Perhaps in a later post. Good night and keep thinking.

[WmRoy]

So Apeman and BlueGenes,
Are you suggesting that there is further action I should be taking?

If I were you, I would...........

I would also go back to the area with your dog if you haven't already........... and why do you have a cadaver dog anyways?

[Doubleyouex Whyz...]

Not to offend you (really!), but you're a little bit off on your descrption Doub. You have the basic idea and you're almost there...and that's great! I'm glad you have a good grasp of the basics (too many don't). The stuff concerning the primers, gel bands, SNPs and mtDNA versus nuDNA needs some tweeking. It's been a long day and I don't really have the energy to explain it all right now. Perhaps in a later post. Good night and keep thinking.

Oh, that’s disappointing. I would like to hear your critique and hope you will get around to providing one.

[Apeman]

Can you tell me of anyone doing what I described?

No, I'm not at liberty to specify anyone not already in the public record, but presumably even some of them have done exactly this basic methodology. But I can tell you it has been and is continuing to be done by some of them and others. All you are talking about is different primer specificities so this is really more of a semantic discussion than a technical one.

I don't really understand why you doubt this? Because the results are, so far, unsatisfying? I don't blame you one bit for that reaction because I have it too. This is why we need to keep at if because you're exactly right, it should be this simple.

But you've got to wonder why, so far, it isn't? (There are at least two very obvious answers.)

Apeman

[Doubleyouex Whyz...]

Well, I wasn’t asking for names. And I didn’t just fall off the turnip truck either, and I don’t know anyone doing what I’ve described. There is not a big sasquatch DNA testing industry out there, so your saying that this has been well tried strikes me as wrong. Anyway, nothing has been well tried. As I said in an earlier post, I think the negative results are mainly to do with easy to understand problems that have nothing to do with the analysis approach. Not to say the analysis approach isn’t important.

“All you are talking about is different primer specificities� – What does that mean?

I don’t think it should be simple. I can easily see why it’s difficult. This stuff is not easy to do. It is not a matter of spending a couple hundred bucks. We’re not talking about having nice vials of blood, we’re talking about crappy samples – small, probably contaminated, full of inhibitors, degraded. And most of the samples are not even real. I’ll be surprised if someone ever gets it.

[Apeman]

We seem to be getting nowhere so I suggest we agree to disagree on "well tried." I'm not sure where you think I was suggesting you'd fallen off the turnip truck so if you got that somewhere it wasn't intended. I was only questioning (but not deriding) your disbelief, but we're all entitled to our skepticism here.

There certainly isn't an industry, but there have been and are labs doing work this way from time to time. There really isn't any other way that's obvious to me- which has been the basis of my line of questioning you on this.

My comment about primer specificities was only trying to point out that there really isn't much difference between order level primers and what you were originally talking about- but specificity was perhaps the wrong word so no worries there, my bad. I thought you might be thinking about something else when we were talking about other methods, but it's clear now and not all that important so don't worry about it.

Apeman

[Doubleyouex Whyz...]

By the way, of the two obvious answers only one carries any weight to me; the Bigfoot is not real one. A creature that looks like that and lives like that has to have different DNA. All the other less obvious reasons stacked together are sufficient to explain why identifying the DNA is so tough.

[Apeman]

A creature that looks like that and lives like that has to have different DNA.

1. Looks like what exactly?

2. Sure, in theory....





No, I agree but am just having a little fun and trying to stretch our imagination a little.

Good night,
Apeman

[Sac-squatch]

I would also go back to the area with your dog if you haven't already........... and why do you have a cadaver dog anyways?

I have a cadaver dog because I work for county and federal agencies finding bodies. You can't have a cadaver dog anyother way from my understanding because the cadaver training scent is not legally available to the public. Like I have said before, my dog does find other decomposition besides human remains, i.e. bear, bobcat, mountain lion and pretty much everything else...the only difference is he doesn't signal unless it is human. And yes I went back today, to that same drainage and Roscoe found nothing of relevance to human remains..2538 hrs of training and counting. BF searching is just a fun side hobby that has relevance to his human cadaver training if set up properly

[Doubleyouex Whyz...]

Apeman, those photos are good, make the point well...

[Bitter Monk]

You can't have a cadaver dog anyother way from my understanding because the cadaver training scent is not legally available to the public.

Most cadaver dogs are trained using placentas. I have no idea why it would be illegal to own a placenta.

This post has been edited by Bitter Monk: Oct 4 2007, 04:14 PM

[Robert]

I, well, actually we, owned one for a short time while my wife was pregnant. I had no idea I was running afoul of the law!

This post has been edited by Robert: Oct 4 2007, 04:33 PM

[Sac-squatch]

Most cadaver dogs are trained using placentas. I have no idea why it would be illegal to own a placenta.

That is certainly news to me. It would seem odd to me that a placenta would be used by "most" cadaver dog training since most decomposed human remains do not have a rotting placenta in them, especially once you get into advanced cadaver dog training that deals with disarticulated remains. Perhaps independents use placentas because they can not have the "cadaver scent pads" that I use which can only be provided by county and federal agencies. BTW, do you also train cadaver dogs??? I would be very interested in sharing methods and ideas with you. Yes, I have heard of alternatives to our scent pads, mainly from dentists who are willing to give up tissue. It is my understanding that having actual human tissue if not stored properly (4 degrees fahrenheit or below) can be very hazarous due to legionnaires disease. But I am no doctor and could be wrong about that. Bitter Monk if you have more experience in this field than I do, I would be keenly interested In having a further dialogue about this subject. Alternatively if you have any other questions that I may be able to answer, I will certainly try to do my best. I am no expert on training having only 2500 hrs+ in training with my dog. But I have been very succesful, perhaps because of my dilligence in training and learning from some of the greats.

This post has been edited by Sac-squatch: Oct 4 2007, 06:41 PM

[Bitter Monk]

You've got PM.

[Sac-squatch]

You've got PM.

I hope you got PM back at ya!