2008 July

Hello from Singapore

by Dr. Hsien-Hsien Lei
Posted July 26, 2008 in DNA in General

Yes, I’m still alive but barely. I’ve given birth to a baby girl and moved from London, UK to Singapore all in six weeks. Been keeping one eye on DNA during this time but can’t say my brain was processing much. Hope to be back in the game next month. Meanwhile, keep calm and carry on!

(15 comments)


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What does DNA mean to you? #14

by Dr. Hsien-Hsien Lei
Posted July 16, 2008 in Meaning of DNA

dna dundeeAndrew Yates of Think Gene is feeling blunt today as he tells us what DNA means to him.

Nothing.

My background is computer science, so to me, DNA is the object code of life. Unlike human-designed languages, DNA is entirely unbounded by intelligibility or elegance —only function.

So we are looking for meaning at the wrong level of abstraction. Our understanding of DNA is tainted by an anthropomorphic misunderstanding of how a language “should” work: “genes” are “sequences of letters” positioned by an “index” like words in a book. One word, one meaning[1]. This is a mistake, as supported by the inconsistent success of genome-wide association studies (GWAS) and the disappointing usefulness of today’s genomic testing.

We don’t try to understand object code in software without abstraction, so why do we try to understand DNA directly in life? Here’s why we shouldn’t try to understand DNA directly —even more so than object code:

* DNA is an implementation, not a map of abstractions. That is, units of DNA have no constraint to “mean” anything. Even object code can usually be interpreted as processor instructions and numbers.
* DNA is a template for amino acids and RNA, not a set of instructions (code) or table of facts (data).
* What DNA “describes” is probabilistic, dynamic, highly context-sensitive. It moves. Its parts move. Its environment moves. It’s chemistry. Object code is discrete and static. It’s math.
* DNA is hard to sequence. Object code is trivial to sequence.

Genomics today is like alchemy: we’re tinkering with a system we don’t understand in hopes of some elixir of longevity —except we call it “the cure for cancer.”

Why? Because we are impatient. Because we vastly over-estimate our ability to understand complex systems without simple abstractions. Because we believe what is difficult must be valuable. Because genomic research today is commercial, and gold must be made.

Well, that’s crap.

In software, we abstract object code with higher-level languages. When that system becomes too complex, we make a new, even higher level interface and abstract again. We continue until surface complexity is low enough to be useful.

In genomics, we label genes with some incomprehensible, ontologically-inconsistent name and then strain to make that gene “mean” some attribute or disease.

There is some use for the black-box, top-down genomic testing, but I believe that this approach alone is wrong. I believe that what we should be doing is creating better abstractions, interfaces, by which DNA can be understood. I believe that the future of genomics —the people who will make DNA mean something— will be the language designers who compile to DNA.

Until then, God laughs. There’s a reason why Window’s object code is everywhere, but the source code is top secret. Bill Gates laughs, too.

(4 comments)


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What does DNA mean to you? #13

by Dr. Hsien-Hsien Lei
Posted July 9, 2008 in Meaning of DNA

dna dundeeTrisha at Ideas for Women has DNA straight:

For me, DNA mostly just means deoxyribonucleic acid.

But also it means that we humans are capable of amazing things. I can remember being in the 5th grade and our teacher was telling us about the 4 bases in DNA. I was, and still am, totally amazed at the fact that we have been able to discover and understand all of this. It wasn’t that long ago that our ancestors believed the earth was flat and the center of everything – now we know we’re just a tiny dot in a huge universe, and we even know how we came to exist as a species. The fact that we have a detailed understanding of what makes us, us – and alive – on the molecular level is extraordinarily amazing!

(4 comments)


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What does DNA mean to you? #12

by Dr. Hsien-Hsien Lei
Posted July 2, 2008 in Meaning of DNA

dna dundeeSandra Porter of Discovering Biology in a Digital World shares what DNA means to her:

DNA means opportunity and adventure. Opportunity, in that my livelihood is completely tied up in DNA. I teach about it. I work with DNA sequences. I enjoy playing with DNA structures. And of course, our company (Geospiza) sells software for managing the production and analysis of DNA data. Opportunity is also the key term because of the diseases that we’ll someday be able to prevent and treat because of the things we’ll be able to learn from DNA. As fara as adventure, “adventure” applies to DNA because getting from here to there is certainly an adventure. Along the way, we’ll find things we want to know and things that we’d prefer not to know, but the adventure of discovery and the process of finding out who we are and where we’ve been is most certainly an adventure.

(3 comments)


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