Archiver > GENEALOGY-DNA > 2010-02 > 1266377953

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: <1981F3E9EA0F46BC912027CFFD8DBDD6@anatoldesktop>

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.

However, I would observe that people on the list come from all kinds of backgrounds and that these sorts of things aren't always going to be obvious. I've also seen people debate (sometimes fiercely) over nomenclature that is (to all practical intents and purposes) entirely interchangeable. The primers that would be useful at the level this list works at are either obscure or don't exist.

*I say "obviously" because although nothing has been identified as observed as being "second order", even the mainstream press is routinely bombarded with new discoveries, new observations on old data, etc. I'm not brave enough to say that "second order" hasn't actually been observed, merely that if it has, no-one significant in the field has publicly said that they've made such an observation and recognized it as such, and that there is nothing in the current model that would allow second order reactions.

The science is changing a little too rapidly for me to feel comfortable with statements stronger than declarations of the current model, current observations and the currently-understood underpinnings. However, that reflects my comfort levels rather than accepted terminology, accepted practices or accepted understanding. But since everyone uses language that reflects their perspective, to some extent, I think we really do need something central we can point to that will help reduce confusion. At the very least, I want something that'll reduce =my= confusion, whether or not it helps anyone else! :)

--- On Mon, 2/15/10, Anatole Klyosov <> wrote:

> From: Anatole Klyosov <>
> Subject: [DNA] "counting mutations" versus "GD from the modal"
> To:
> Cc: "Anatole Klyosov" <>
> Date: Monday, February 15, 2010, 3:39 AM
> >From: "Lancaster-Boon" <>
> >If you use the term "first order" (as you do) it
> implies there is a second
> >order (which in your case you blamed me for assuming
> from your words).
> Sure. In physical chemistry (chemical kinetics and related
> disciplines, and
> this includes ways how mutations occur in haplotypes) a
> first-order reaction
> is A-->P. A second-order reaction is A+B -->Q.
> In other words, in first-order reactions (or first-order
> processes) the
> mutation in a haplotype is going - in terms of its
> description by the
> respective mutation rate constants - "by itself". In
> second-order reactions
> a mutation would have been a result of a collision of two
> haplotypes (or two
> different entities, one of them is the haplotype). It would
> have been quite
> different in mechanism, origin, descriptions.
> In first-order reactions accumulation of mutations in a
> haplotype set should
> match the decrease of base haplotypes in the same dataset.
> Therefore, for
> first-order reactions the linear and logarithmic methods
> should produce the
> same results in terms of TMRCA, and we actually see it.
> This is why those
> matches are important for descriptions of haplotype
> datasets.
> There are no "second-order" processes in mutations in
> haplotypes, or at
> least nobody has seen them. You took the term without
> knowing its meaning.
> What was worth, without defining it.
> Branches and other deviations from first-order kinetics are
> described not by
> "second-order" processes, but as a combination of the
> first-order processes.
> Of course, you are free to call them however you want, but
> you should have
> given a clear definition what the "second-order" was in
> your description.
> Regards,
> Anatole Klyosov
> -------------------------------
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