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Archiver > GENEALOGY-DNA > 2006-04 > 1145597610


From: "Alfred A. Aburto Jr." <>
Subject: Re: [DNA] ISOGG 2006 tree
Date: Thu, 20 Apr 2006 22:33:30 -0700
References: <4448526C.9050104@comcast.net>
In-Reply-To: <4448526C.9050104@comcast.net>


> Bonnie Schrack wrote:

> This topic has been addressed by everyone else, who made good points
> while I was in class, so now that I'm free, I just have to put my two
> cents in. Sorry if it's long and redundant! :-)
>
> David wrote:
>
>> All of the S markers will appear in publications in due course - this
>> is a lengthy process. However, rigorous testing has been done on each
>> marker or it would not appear in the 2006 chart. New ones are waiting
>> to be added but we have to do more tests to be absolutely certain of
>> what we are seeing.
>
>
> And Al wrote:
>
>> But still Dr. Faux you appear to be by-passing the peer group review
>> process which is a critcal component of scientific research (the
>> scientific method).
>
>
> Why would you say that, Al, when David just stated that the S series
> markers would be published? There is a major difference between
> by-passing something and doing it when it is feasible.
>

The "problem" I had is that there are these "S" SNPs mentioned in the
ISOGG J tree, but they are undefined basically, except for "provided by
private communication to the ISOGG". What value was there in mentioning
S6, S34, S35 at the top of the J tree when no information was provided
regarding them? Since they were at the top of the J tree I thought they
were important, actually very important, else they would have been
mentioned in a footnote. But then when I tried to find information all I
found was "provided by private communication" --- this seemed to me a
side-stepping of what I know as a normal scientific process. I have seen
a number of publications where authors have used references like
"private communication", but it is never anything of importance to the
subject of the report.

> I think you need to consider that the conditions are different in
> different scientific fields. Genetics is a highly competitive and
> commercialized field -- there are others as well, such as
> pharmacology, that I can think of -- in which certain kinds of new
> discoveries are often not published in full right away, because they
> have a commercial value.


The scientific process is no less important when there is commericial
value involved. Perhaps it is even more important instead.

> Although it's regrettable that there should be such a commercial
> necessity, this is the reality of the field, and it is not considered
> to make discoveries less legitimate as science. The only way they
> would be found to be illegitimate would be if independent testing by
> other labs found the discoveries to be fake and unsubstantiated.


But if information is not provided then how is there going to be
independent testing? Don't you see that?

> If anyone at another lab seriously doubted the new SNPs that are being
> announced by EA, they might well try to expose them as fake, but I
> don't think that's what we're seeing here.


But the SNP information is not disclosed so how can anything be proved
one way or the other? This is where the scientific process gets
by-passed. Problems are more likely to occur when cross-checking (a
normal scientific process) is not allowed. The drug companies make
mistakes all the time (there are many medicines that are not properly
tested or where the rules are stretched trying to meet a deadlines or
budgets, many reasons... there are ongoing lawsuits all the time ...
clearly DNA testing is not this critical, but the same process is at
work ... Dr Faux even indicated it was and it is ...

> It's more a matter of, as Lawrence put it, "We only consider SNPs that
> have been peer-reviewed and published, or that we have discovered
> ourselves." There is rivalry, and a degree of distrust that exists
> between rivals, but that doesn't mean anyone is seriously alleging
> fraud on the part of Jim and David.
>
>> While I understand the profit making aspect of this
>> research, I am just uncomfortable when I see these things happen. There
>> are plenty of cases one can cite where things have gone awry when the
>> scientific method has been by-passed.
>
>
> For you to suggest here that the scientific method itself has been
> bypassed is taking things even further. I think that's an unfair and
> inaccurate use of language, when actually you are only making
> reference to whether the details of a discovery have been published in
> a scholarly journal. The scientific method, on the other hand,
> refers to the process of discovery (the following is a definition
> found on the Internet):
>
> 1. Observation and description of a phenomenon or group of phenomena.
>
> 2. Formulation of an hypothesis to explain the phenomena.
>
> 3. Use of the hypothesis to predict the existence of other phenomena,
> or to predict quantitatively the results of new observations.
>
> 4. Performance of experimental tests of the predictions by several
> independent experimenters and properly performed experiments.
>

It is the peer group review process that I didn't see taking place. But
then later Dr Faux did say that the chart was approved by Drs. Hammer
and Underhill and that was good enough for me as I said in a previous
email. I guess you didn't read all my emails yet?
To me that ended the matter then, but here we are ... so I'll continue
too since you have taken the time ...

> -- There's nothing in there at all about *how* you have to *publish*
> it. Yes, results should be reproduceable; eventually it should be
> possible for others to try out the new SNP and make sure they can get
> the same results, but some delay in that won't negate the validity of
> the discovery.


It may take years though and they may never publish. In a project (in my
previous working life) I worked for, the managers decided it was too
expensive to document but the most elementary details and they did not
want to "waste valuable time and money" publishing so they never
published anything of significance. It caused alot of troubles later on
though when they realized the product did not work right.

> As others have said, there is a certain level of trust that people are
> operating in good faith, unless there are very good reasons to think
> otherwise, such as incredibly claims that are at odds with what all
> others in the field have found.
>
Of course there is. I have not lost any trust in EA as I said in another
email. I think overall the ISOGG Y-DNA chart is a very good product.

> I am going to answer the following, *not* as an official spokesperson
> for ISOGG, but from my personal experience and opinions.
>
>>
>> I suppose the ISOGG had to sign a "non-disclosure" agreement with you
>> inorder to mention S6, S34, S35 for the J haplogroup?
>
>
> Why would a non-disclosure agreement be necessary?


I don't know. I thought that was why the information was given "via
private communication", officially saying you couldn't talk about the
SNPs. Seemed reasonable. In my former work I have had to sign such
agreements with other companies.

> We have never signed any kind of special agreement with anyone, and
> the question has had no reason to come up. It's perfectly sufficient
> that these SNPs have been tested in enough cases to be sure they are
> genuine and non-private SNPs. We don't believe that David and Jim
> have lied to us about that.


Why do you even mention that? I never thought there was any fraud or
lying going on. Don't go there. That is wrong. I'm just pointing out a
potential problem.

> The specific kind of technical details that EA is not ready to publish
> -- because they would make it impossible for them to recoup their
> investments -- aren't at all necessary in order to know where a SNP
> fits into the phylogenetic tree. Such a requirement as you would
> impose has never existed in the past.
>

The only requirement I would impose perhaps, but I have no authority to
do anyway, would be to move S6, S34 and S35 down to a footnote like
S51, but at least say something about them that didn't compromise EA's
position. That's would be about all ...

> It isn't like EA has been the only lab that has been unready to
> publish these kinds of details of new SNPs they have discovered. What
> about all the proprietary markers used in the DNAPrint test? Leaving
> aside its accuracy, or lack thereof, the identity of those markers is
> a closely held secret, but no one doubts that they really exist.
>
> It would be nice if pharmaceutical companies, for example, would allow
> generic versions of their new drugs to be marketed by other companies,
> as soon as they invented them, but our marketing and economic system
> is not set up that way. If there were a different system of funding
> for scientific research, then companies would not have to finance
> their research by having the chance to be the only ones selling newly
> discovered products for some time afterward. That is also the basis
> of they copyright system. This system has been overextended in the
> United States, in my opinion, but still, the creator of a new work
> should have some time in which to enjoy the fruits of their labor
> before it goes into the public domain.
>
>> What bothered me
>> most was that these SNP's appeared right up at the top of the definition
>> of the J tree and there was no other information (references) regarding
>> them given except "privately communicated to the ISOGG". I wondered why
>> they were even included as such.
>
>
> Because they are real SNPs, that we know to have been discovered, and
> which were found to belong at that point in the tree.
>
Well then some words should be added to explain them --- instead nothing
is explained --- no references are given --- nothing. How do I know
they are real SNPs? What is their significance. Why include them if, as
I assumed, one can't say anything about them? Can you tell me what S6,
S34, and S35 are? What are they doing at the top of the J chart?

>> Might have just as well left them out.
>
>
> Why leave out new scientific discoveries?


Well Bonnie. Then please tell me the significance of these new
discoveries. What are S6, S34, and S35? Just a few words ... not
"private communication" though.

> Does this mean science shouldn't be something we pay attention to? I
> don't follow your logic at all. In this particular case, the SNPs
> seem to be phylogenetically equivalent to others that already were
> known. But other S-series SNPs have been very important in defining
> other branches of the Y DNA tree, which you seem to see as even more
> objectionable (see below).
>
I'm reading the chart looking at S6, S34 and S35 but no info is provided
on the web page. I searched the internet too but only ran into model
trains and planes and cars and such ...

>> The "S" SNPs appear to be
>> private, not to an individual, but to a company? Can't you publish
>> them, even to the NCBI, and still retain control?
>
>
> No, once the details of exactly how to do the test are known, many
> other labs would no doubt start offering them, and EA would have lost
> the great investment of time, labor and capital they put into
> discovering them.
>
How about patent pendings and copyrights --- legal languge like
Microsoft and so many vendors use ---

> It isn't like there is some medical benefit needed by humanity, that
> they are preventing from being available to all. It is, to my mind,
> like the formula for many kinds of new products which are trade
> secrets. It would be interesting to know how they are made, but
> unless the research is going to be funded by some government or
> non-profit foundation, it has to be financed this way, as far as I can
> see.


Yes it is not critical, I know that. Still is worries me that normal
scientific protocal is suspended (if you will). I don't know the answer,
I just see the makings for problems ...

>
>> Somehow that makes these SNP's highly unofficial. Perhaps they should
>> not be included in the chart until they are "official" and the right
>> information is disclosed. In the mean time there could be unofficial
>> developmental working charts perhaps ...
>
>
> It appears that the only thing that can make a SNPs "official" in your
> view, is having the full information on their primers published in an
> academic journal. But no one has ever set that up as a standard to
> make a SNP "official." You are the only one I have heard of who
> considers that a requirement.
>

No Bonnie, not exactly. In a previous email I said I understood the
requirement to recoup expenses and make some profit. That is perfectly
reasonable. No one can deny that.

>> I just wanted to learn more about those "S" SNP's in the J tree (I
>> asked Ann initially, but there is no information I guess).
>
>
> You can write to David and Jim any time, to ask about any of their
> SNPs that they have discovered, and they will probably be willing to
> tell you quite a bit. The only thing they would not tell you is how
> to do it yourself. I find both of them very accessible, if all you
> really want is to learn more about those SNPs.
>
We were talking on this list. That was perfectly ok wasn't it?

>> Many, but not all, of the other "M" SNP's have plenty of references
>> given, but not the "S" SNP's.
>
>
> Some of the other SNPs have been published in full because the
> discoverers worked at academic labs which could afford to finance the
> research, without having to cover the costs by selling SNP tests.
> That's great, but not all research in the world can be done that way.
> As Ken alluded to in his comments, most academic labs could care less
> about the interests of genetic genealogists, so they have not always
> concentrated on questions that we would really like to see them address.
>
>> What if an entire haplogroup was defined that way?
>
>
> You've already seen Ken's remarks. Many of us are delighted to have
> EA out there on the cutting edge, doing work that's specifically
> directed at problems of concern to genetic genealogists, and actually
> searching for SNPs that will make a difference for us. When they are
> able to define a new sub-clade of R1b or I, it's something a lot of us
> celebrate, and we are perfectly happy to have an entire haplogroup
> defined that way, as long as all the necessary steps are taken, which
> EA has been doing so far. I don't know why you seem to feel the
> output of Jim Wilson's lab is less trustworthy to define a haplogroup
> than Underhill's or Hammer's. There are a few con artists out there
> in the world of science, and certainly in genealogy, but we have not
> seen anything from EA that would lead us to have any such suspicion.
> They are simply functioning in the way private industry does.
> If anyone would like to help organize a non-profit foundation to fund
> research with results that would go right into the public domain, I
> hope they will speak up or get in touch (I've already thought of a
> name! ;-) ), because that would be very beneficial, no doubt, *but*
> our capitalist system is not likely to stop being the way things
> mainly function for the foreseeable future, so I wouldn't expect the
> way EA is developing SNPs to become less common in the coming years.
>

I don't know the answer. I was just raising a flag when I see a
potential problem. I guess I'm not like others, because the first thing
I thought when I saw S6, S34, S35 in the J tree was what are these? What
do they mean? Where can I learn more about them? Looks like I will have
to wait a while for those answers. Perhaps some words can be added to
say at least a little about them? They seemed important to me.
Al

> Bonnie


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