A Prayer Request - and Good News!

A dear aunt died last week - please remember her in your prayers.

As strange as it may sound, this has led to something interesting.

At the luncheon after the burial, I met a cousin-of-a-cousin - if I met him before, the memory is gone - but since he is on her side of the family (she was the widow of my father's brother) it is possible we had never met before.

In any case, he is working on his doctorate in physics, and we talked for a little while on tech matters. It was very funny since my work was in "string theory" the theory of "language", a branch of computer science, but his is in "string theory" the inner structure of elementary particles, a branch of physics!

He is still "in the hunt" for a dissertation topic, but was because of this remarkable - er - concurrence of our field-of-interest, he was curious about my own work, so I gave him a summary - the real short form is "I found fingerprints for bacteria" so you can think about that for a while.

He was somewhat surprised that such a cross-over of disciplines was still possible, and I explained that my work (in "string theory") not only helped with molecular biology, but actually began to reveal some odd things in my own field which hitherto had not been studied. "I think there's still some things no one has solved there - I know of at least one..." and he suggested that I resume my work.

So I did.

And so I can announce: this morning (Thanks Be To God!) I solved the extension of a popular algorithm when applied to DNA sequence analysis, known as ...

Well, now that I think about it, I do not think I should say more here in the e-cosmos.

No, indeed, I am not going to publish it here. After all, if no one has solved it yet, I may actually get to publish it in a JOURNAL. Guys with Doctorates do that from time to time. Hee hee.

This is absolutely hilarious, since the connection between us might be said to represent the complexity which defeats the original algorithm. That much I can tell you.

First, an "alphabet" is the set of symbols upon which some aspect of string theory is based. The usual DNA alphabet is {a, c, g, t} representing the four "bases" (adenine, cytosine, guanine, thymine) from which the strings (or "words") of the genetic code are built. (Notice I use small letters here.)

However, the "wild-card" alphabet for DNA has several other letters, representing more than one of the four bases. We still have A, C, G, and T (which are now the capitals!) but we have others like M which stands for either a or c, S which stands for c or g, and N which stands for any of a, c, g, t.

To help deal with these NEW characters, we have a NEW property, called "matches". In the wild-card alphabet, two characters are said to "match" if there is SOME character which they have in common: for example, A matches M, and A matches N.

Now, for the fun.

A matches M, and M matches C.

But!!! A does NOT match C.

Now, for many of the things you know about in math, when
x SOMETHING y
and
y SOMETHING z,
then often it is true that
x SOMETHING z.

(Like when SOMETHING means "equals".) Us math guys call that "transitive".

But there are some things, even in the NON math world, which don't work that way.

For example, "is a cousin of".

(dr-thursday) is a cousin of (child-of-my-aunt-who-died)
and
(child-of-my-aunt-who-died) is a cousin of (phd-student-in-physics)
but
(dr-thursday) is NOT a cousin of (phd-student-in-physics)

So now you know... stay tuned for more on this very exciting development.

And my sincere thanks to... uh ... x, y, and z.

PS: no, this is not some Fermat-like "the margin is too small to contain this marvellous proof". I have it in code, and it works. Next I have to prove a theorem or two, and there's no "back-of-the-book" to check if I get it right! And then maybe see if anyone did it already, and THEN see if there's still some journal that wants tech stuff like this... Hee hee. What a thrill!