Showing posts with label Lior Pachter. Show all posts
Showing posts with label Lior Pachter. Show all posts

Wednesday, August 31, 2016

"Bits of DNA" from Lior Pachter


We live in a scientific culture populated simultaneously, by increasing numbers of specialists who, even in the same general field, can sometimes barely communicate with one another, and, on-the-other-hand, increasing numbers of “polymaths” who cross boundaries and work in multiple fields at once. This latter category has long fascinated me, especially since the most important future knowledge/findings may well come from them (though specialists too have much to contribute).
Lior Pachter is one such multi-disciplined individual. He calls himself “a computational biologist” though his PhD. from MIT is in mathematics, while his work focuses on genomics and crosses the boundaries of statistics, biology, and computer science. One of his longish blog posts is a favorite of mine, relating to the cross-cultures of biology and math (a really rich read):

[...Another of his posts that is a long-time favorite, by the way, is related to Common Core, education, and math problems (again, very rich with ideas):

I often can’t follow the depth and detail of Lior’s biology blogposts, but that doesn’t prevent me from appreciating the range and manner of his thinking.

While he has been at UC Berkeley for many years, he moves to Caltech (one of his alma maters) next year; a great addition to their talented faculty... and what better place to be working on cutting edge science.

The general field of “mathematical biology” has grown substantially in the last decade (not sure it even existed way back when I was in college), but it’s the sort of field requiring great care — like “Big Data” and other algorithmic areas it can be fraught with misunderstanding or misuse… Pachter seems to approach it with the necessary care and critical eye… and, as a bonus, engages in public communication about it (many scientists don't bother).  He is also a strong proponent of 'open access,' and doesn't shy away from controversy either (sometimes called a 'gadfly'), though I won't delve into that.

I’ve written previously of my delight in Jim Propp’s rich math blogposts for general readers; and broadening out, have cited Brian Hayes' blogposts, which, even when not on math, are fun and thought-provoking for math enthusiasts. And then there is Scott Aaronson's "Shtetl-Optimized" I've noted previously as perhaps my favorite math-related (but wider-ranging) blog (and I never know what to expect from Scott!).  So I’ll add Pachter’s blog ("Bits of DNA") to this list (broadening out still further to more biology than math), of blogs that really shouldn’t be missed, even if not your particular field:

[p.s…. I have no personal connection to Dr. Pachter, beyond an admiration for his online presence.]



Tuesday, December 30, 2014

Two Cultures (EXCELLENT read)


Almost two weeks ago I posted about the obituary for Alexander Grothendieck that was rejected by the journal Nature. Many math/science sites covered that little news story, and I sort of assumed by now it was over-and-done-with.  But even in death, as in life, Grothendieck seems to spread ongoing controversy!
Today, launching off that rejected obituary, mathematician/biologist Lior Pachter of UC Berkeley has posted a remarkable, really incredible and rich post I think, about the two "cultures" of mathematics and molecular biology, which he straddles, but finds little common ground on for its participants.
It's a long, and often technical post, but I think all should have a go at reading it (it may well require more than one sitting, and don't expect to follow all parts).  As a layperson myself, I'm more interested in the broad strokes he is painting than many of the technical arguments that I can't grasp. His "list of specific differences" between mathematicians and biologists is especially interesting, and Pachter is pessimistic about the relationship between the "two cultures," writing at one point, "The relationship between biology and mathematics is on the rocks and prospects are grim," and "The extent to which the two cultures have drifted apart is astonishing." As I implied in my original post (linked to above) I'm not so sure we really have a 'two culture' problem anymore (the term, as most know, comes originally from C.P. Snow over fifty years ago), so much as a fiefdom problem, with intense specialization having subsumed pretty much every field of technical study.

Anyway, if you're a working biologist or mathematician (or really, a scientist of any stripe) READ this piece!:

https://liorpachter.wordpress.com/2014/12/30/the-two-cultures-of-mathematics-and-biology/

As I post this, there are 3 comments to Pachter's article; I suspect there will be many more over time.
Agree or disagree with him, there's LOTS to chew on.