Archiver > GENEALOGY-DNA > 2010-02 > 1266397487

From: "Lancaster-Boon" <>
Subject: [DNA] "counting mutations" versus "GD from the modal"
Date: Wed, 17 Feb 2010 10:04:47 +0100

Hi Jonathan

I'd like to remark for the record just in order to avoid any
misunderstanding that although the discussion has been frustrating, I do not
think any of the interlocutors see it as an argument. So here is my next
frustration-describing/frustration-causing remark! :) (BTW, attempts to
summarize the position of other people can be very annoying, but it can also
bring results. I hope I only create a reasonable level of annoyance!)

I think we have clarity on the terminology thing. Anatole has some terms
which caused some confusion, but we have gotten past most of it. In the case
of "counting mutations" and "base haplotype" I at least now know exactly
what Anaotle means. BUT the problem with "first order" versus "complex" (or
can we maybe call it simple versus complex) datasets still remains unclearly
defined, whatever words we use.

The discussion has been long but I believe I am right to say that Anatole
has made two general types of definition of what makes "first order" cases.

1. First order cases are the cases where all haplotypes descend directly
from the same common ancestor. But at face value this is an absurd
definition, and by absurd I only mean that the definition has no logical
meaning and can not be parsed or used: Any two haplotypes descend directly
from the same common ancestor. I presume Anatole means something else, but I
can not work out what.

This also seems to be indicated by Anatole's remarks sometimes (as observed
by Sasson) that certain data sets have no common ancestor, which again is
obviously not possible. Anatole certainly has some other intention than we
are understanding.

Of course it is tempting to suggest that when Anatole says people have no
common ancestor, he means that the path back to the common ancestor will
involve sub-branching, and the sub-branching is not clear (i.e. that there
are multiple likely possibilities).

And in the same way it is tempting to suggest that Anatole must mean that in
a first order case, no sub-groups share MORE RECENT common ancestors than
the one they have with the group as a whole, or if they do, these branches
are clear and easy to define in one most likely way, meaning that in effect
the group can be split into two or more groups that can be handled on their

...But my understanding so far, which may be very wrong, is that Anatole
sees such suggestions as a complete misunderstanding. He objects in
particular to any attempt to say that what he is talking has anything to do
with sub-branching.

2. The second IMPLIED definition (this has not been called a definition yet
I think) is that in first order cases Anatole's two methods (linear and
logarithmic) will agree. This definition would be very clear of course, but
the problem it has is that it is endogenous to Anatole's method.

It would be preferable if nature could be described in terms of properties
of nature rather than the effects it has on someone's mathematical modelling
of nature.

I hope the following words are understood by everyone as positive rather
than negative: the situation seems to be that Anatole himself is a
pragmatist in scientist and does not like holding up practice for theory:
What works, works; When it does not yet work, for example when the two
methods disagree, then by definition this is not yet clearly defined, but we
get on with life without a full understanding of why something sometimes
does not work. Indeed, that is how a lot of science does indeed work, and we
would not want our doctors waiting for a full explanation of every cure.

I presume (and again this is just me) that this is why discussion of
confidence intervals, which is by definition more theoretical, less
practical, has been particularly complicated. I do not agree with the
suggestions being implied sometimes, including by Anatole, that this is just
a matter of people who know what they are talking about and ignorant people.

Best Regards

From: Jonathan Day <>
Subject: Re: [DNA] "counting mutations" versus "GD from the modal"
Date: Tue, 16 Feb 2010 19:39:13 -0800 (PST)
In-Reply-To: <>

I hate to get into the middle of arguments, but as I read it, I think the
problem is over the use of "first order". The need for a qualifier implies
that there is something with a different qualifier. Now, I'll agree with you
completely that there isn't anything that is obviously "second order"* in
haplotypes, with the understanding that the term wasn't invented or
exclusively used by genetic scientists and that other orders exist in all
kinds of sciences. You can't just ignore a qualifier simply because some
very specific context would (at that specific level of understanding) allow
you to infer it. It has meaning, so it has to be used.

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