GENEALOGY-DNA-L ArchivesArchiver > GENEALOGY-DNA > 2006-04 > 1145590380
From: Bonnie Schrack <>
Subject: Re: [DNA] ISOGG 2006 tree
Date: Thu, 20 Apr 2006 23:33:00 -0400
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! :-)
> 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.
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. 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. 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. 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.
-- 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. 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.
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? 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.
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.
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.
> Might have just as well left them out.
Why leave out new scientific discoveries? 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).
> 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.
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.
> 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.
> 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.
> 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.
|Re: [DNA] ISOGG 2006 tree by Bonnie Schrack <>|