What does DNA mean to you? #14

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

Andrew 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.

(3 comments)

What does DNA mean to you? #13

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

Trisha 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)

What does DNA mean to you? #12

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

Sandra 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.

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Geeky DNA T-Shirt: XX Chromosomes

by Dr. Hsien-Hsien Lei
Posted June 27, 2008 in Geeky DNA T-shirts

Noelle of XENOTEES writes to tell us she has a new tee available with XX chromosomes on the front. Stylin’!

Available at Etsy for $20.

(1 comment)

What does DNA mean to you? #11

by Dr. Hsien-Hsien Lei
Posted June 25, 2008 in Meaning of DNA

Steve Murphy of Gene Sherpas gets a bit snarky on us with his list of what DNA means to him.

1. AG are the initials of my child. That’s 2 of 4 DNA bases

2. DNA is the beginning……Only G-d knows the end

3. DNA means passion

4. DNA repair means health

5. DNA means a spot on Oprah with Dr Oz

6. DNA means mystery

7. DNA means solution

8. DNA means my favorite people minus an E and and A

9. DNA means, vulnerability in need of protection

10. DNA means the solution for recession

11. DNA means more questions than answers

12. DNA means friend in a wonderful network

13. DNA means genetics…..for now……

(>> Start a discussion!)

DNA Excerpt: Bringing Home the Birkin

by Dr. Hsien-Hsien Lei
Posted June 20, 2008 in DNA Quotes and Excerpts

From Bringing Home the Birkin by Michael Tonello:

Pink-and-green flowered tiles accented the mostly white floor, with the same floral design mirrored in the quilt. The pair of overstuffed chairs and couch were all pink to match, and my masculinity was momentarily threatened until I remembered I was gay. My Y chromosome was further comforted by the dark mahogany furniture and ceiling fans, as well as the gender neutral white walls.

Update: For more, see Christina’s book review at eBeautyDaily.

(>> Start a discussion!)

What does DNA mean to you? #10

by Dr. Hsien-Hsien Lei
Posted June 18, 2008 in Meaning of DNA

DNA holds a lot of meaning for the always thorough Blaine Bettinger of The Genetic Genealogist.

When I first received this question, I quickly realized that I could probably spend hours answering it. DNA has had such a profound impact on my life that I barely know where to begin.

I guess I should start with my own DNA. As a genetic genealogist, I have sequenced tiny portions of my DNA and the DNA of relatives to learn about the ancestral sources of those sequences. The results have allowed me to understand more about my most distant paternal ancestor who came to America and fought in the Revolutionary War, as well as my most distant maternal ancestor who lived in Central America and had Native American roots (which I discovered from the DNA testing). Although these pieces of DNA passed through these individuals with perhaps only a few small changes before reaching me, seeing these sequences gives me the first tenable insight into these ancestors aside from their name and the date of their birth and death. These tiny pieces of DNA have created a link between me and ancestors who died nearly 200 years ago.

Perhaps even more importantly, genetic genealogy has given me the first piece of information about the ancestry of a paternal great-grandmother who was adopted upon birth. Although this small piece of circular DNA from my paternal great-grandmother is not part of my own genetics, it was a part of her; and every decision she made ultimately led to me. Additionally, it is likely that I inherited some other part of my great-grandmother’s DNA. Thus, genetic genealogy has given me clues to some of the secrets contained within my genome.

DNA was also the basis of my graduate research. I worked in yeast genetics, a field with a long and rich history. I spent years attempting to unravel some of the mysteries of yeast genetics, and I was proud to be able to contribute (a very small bit of useful information) to the field. Although I’ve left the bench science behind me, I use the skills and the knowledge I gained on a daily basis.

And lastly, through my blog, DNA has given me an outlet to join the global conversation about genetic testing, genetic genealogy, personalized genetics, and genetic ethics. Through this outlet I have met and befriended numerous interesting and intelligent individuals who are interested in many of the same topics, including Hsien, members of The DNA Network, members of The Genealogists, some fantastic genetic genealogists, and many, many others.

Going forward, DNA will undoubtedly have even more of an effect on my life. I hope to continue to contribute to the conversation about genetic genealogy and personalized genetics, to meet new people who are interested in these issues, and to continue to explore and utilize new technologies that will help me explore my genetic past.

(2 comments)

My Newest Genetics Experiment

by Dr. Hsien-Hsien Lei
Posted June 16, 2008 in DNA in General

Megan
Born last Monday
3.78 kg (8.3 lbs)

(18 comments)

DNA Video: DNA Replication by The Backrow

by Dr. Hsien-Hsien Lei
Posted June 14, 2008 in DNA Podcasts and Videos

I’d say these guys earned their 30 extra credit points in science….

(1 comment)

DNA Quote: Sir William Bragg on Science

by Dr. Hsien-Hsien Lei
Posted June 13, 2008 in DNA Quotes and Excerpts

The important thing in science is not so much to obtain new facts as to discover new ways of thinking about them.

~Sir William Bragg, 1862-1942, British physicist and chemist, winner of the 1915 Nobel Prize in Physics

via Quotes of the Day

(1 comment)