Tuesday, May 31, 2016


As might be surmised from the earlier post on DNA, genetic genealogists have been having a field day. People are finding cousins. D.A.R. has DNA in its process. Some want such tests to be sufficient. Families are doing grand studies about their ancestry. We all can see the entire sweep across time of human trekking. And much more.

Too, though, the former post started collecting links to technical material. A lot of these revolve around computational phylogenetics. That is part of the modern view and will even more so as we go along. Yet, lots of issues remain to be discussed.

So, we want to bring that to fore, for several reasons. For now, it is mainly to get the issues on the table so that reasonable adults do not run amok. For instance, we see lots of attention given to the y-haplogroup's use. It is a great way to match up paternal lines. However, there are lots of things to consider that might be awry, such as (one of many examples) male siblings or cousins not matching. A few of the reasons for this may be (quoting evolutionary biology graduate of Tulane): one of the Y chromosomes mutated independently in a manner that resembles another haplogroup (very slight chance, however); there can be instances of double Y chromosomes (or just remnants) in the genome but that generally results in infertility issues; the female may have inherited a small fragment (slightly more likely) of her father's Y chromosome; a type of chimerism.

In short, we have technical, legal, moral, and a whole slew of other topics to look at. Fortunately, DNA is a subject of interest of late. That is, we are a couple of decades from first use, several troublesome aspects have been seen and handled, things are getting even more complicated, etc.

Let's use a recent article in The Atlantic to gather material: The False Promise of DNA Testing. The article has a forensic focus, after all CSI (et al) has brought the potential uses to everyone's sight, but the lessons apply to genealogy. What we did not see were the mis-uses, that is, not until after the fact (except, perhaps via some probabilistic notion which usually underestimated the potentials for abuse).

So, this collection is an addition to the prior list which will be organized at some point.
    MathWorks () - A little about the algorithm. 
These links pertain to the use of advanced computing in the interpretative area of DNA analysis in an area that can have serious impact on people. Another technical example of this type of approach was in the last list (Classifying Haplogroup from Y data) which applies directly to our interests.

There are many other steps in the DNA process to discuss, as all along there is computational assistance. We expect to lay out a bit of details about these.

Remarks: Modified: 12/18/2016

06/01/2016 -- Note the source of quote on replication issues. 

06/10/2016 -- Genome Research

06/17/2016 -- Notes about review. Starting with Mendel's work, then insights about genes, chromosomes. Then, we get to modern lab processes with instruments that are enabled via computation. Marking and analysis, for example. We have foundational issues related to mathematics. On the interpretation side, there are local views and grand themes. Predictive-ness an issue. And, finally, memes and their analog ought to come into play.

11/23/2016 -- A recent ACM Communications (Sex as algorithm) had an article by a gene specialist (biology) and a computational mathematicians. There is a little remark by the authors that things are not as clear as many seem to think. "Gene: A unit of heredity and a region of the DNA that encodes a functional product. It is thought that humans have more than 20,000 of these. However, now that coding is known to be far more complex than originally thought, it is no longer clear how to define these units and their boundaries."We will look at this further in the upcoming The Gardner Annals.

12/18/2016 -- Article about DNA published in The Gardner Annals, Vol. III, No. 1.

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