Meaning of DNA

What does DNA mean to you?

by Dr. Hsien-Hsien Lei
Posted January 14, 2009 in Meaning of DNA

dna coffee cup cozy Before I went on maternity leave, I asked fellow DNA Network members to share their thoughts on what DNA means to them. Here are a few more that I didn’t get around to posting earlier.

Jonathan Eisen of The Tree of Life:

DNA is something to sequence.

Misha Angrist of Genome Boy:

DNA: the last three digits of my cell phone number

(Bunch of smart alecks!)

Reader Khushi:

To me, DNA means a way to Demystify Nature’s Accuracy and the interdependence of the two to unfold the hidden secrets.

What does DNA mean to you? Please share your thoughts in the comments and you may be featured here at Eye on DNA!

Photo credit: Coffee cup cozy from evilsciencechick

(3 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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What does DNA mean to you? #11

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

dna dundeeSteve 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!)


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What does DNA mean to you? #10

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

dna dundeeDNA 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)


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What does DNA mean to you? #9

by Dr. Hsien-Hsien Lei
Posted June 11, 2008 in Meaning of DNA

dna dundeeToday, Ramunas Janavicius of Cancer Genetics who is a clinical genetics resident doctor (or SPR) from Vilnius University, Lithuania tells us what DNA means to him.

Well, EVERYTHING. Not only being core of life, this is archetypal image of pervasive and inspiring nature. I like it in a hardware (PCR tube), software (sequence in database) and wetware (t-shirt & popular culture) version.

(>> Start a discussion!)


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What does DNA mean to you? #8

by Dr. Hsien-Hsien Lei
Posted June 4, 2008 in Meaning of DNA

dna dundee

Reader Doug tells us what he thinks of DNA:

DNA is our chance to pop open the hood and tinker around a bit. Surgeons get to slice things up and sew them back together a bit but genetic engineers can really mix things up.

Once you’ve got the DNA, you’ve got it all. The trick is figuring out what to do with it.

(3 comments)


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What does DNA mean to you? #7

by Dr. Hsien-Hsien Lei
Posted May 28, 2008 in Meaning of DNA

dna dundeeWhat does DNA mean to you?

Reader and frequent commenter NA says:

DNA, to me, means everything. It’s who I am. DNA is what separates the haves and the have-nots for pure atheletic talent.

I think he’s joking, but I’m not too sure. You can never really tell with NA.

(1 comment)


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What does DNA mean to you? #6

by Dr. Hsien-Hsien Lei
Posted May 21, 2008 in Meaning of DNA

dna dundeeWhat does DNA meant to you?

Thomas of Aminopop tells us:

I’ve always been a technologist, a hacker. For me that inclination has played out mostly in the arena of computers and software, but the larger Hacker Ethos — of using existing technologies in new or unexpected ways, or of combining new and old technologies in surprising ways — keeps leading me towards DNA. And DNA seems like the most hackable substance on the planet at this point. For me, that insight started with an interest in Genetic Algorithms — a programming approach that leverages raw computing power, profligate mutation and fitness selection over traditional software design. Once I started to grok how GAs worked, I started getting this strange, gut feeling for the billion-year, mondo genetic algorithm derby that is Life On Earth. Here’s this linear data stream — the genome, or better yet, all the genomes — written in this foreign language, totally protean in expression, capable of transforming a planet… I mean, infotech is great, but it’s really nothing next to the power of sequenced protein. How can you not be just totally hypnotized by that awesome power? And once people harness it, I think it’s going to make the infotech boom look like a tea-party. And I’ve always been kind of a closet Life Sciences geek, so that suits me fine. So that’s it: to me, DNA represents the Next Great Hack — maybe the Last Great Hack; who knows what the world — what humanity — will look like on the other side of the biotech boom?

As an investor, DNA means opportunity: huge leaps in efficiency, innovation, design and scale of drugs, foods, fuels, manufactured hard goods, even information technology. Hard to even imagine all of it. I don’t think people generally get it, yet. That’s why I’m doing my blog, Aminopop.com — as a regular discipline to try to get a handle on it all. I don’t even feel like I’m very good at it, yet, but not to try seems kind of insane, especially at this moment in history. So I just jump in.

As a humanist, DNA suggests a moment of truth, historically speaking. Wresting our ongoing genetic definition from the mostly cruel forces of natural selection is going to be a profoundly defining moment. What is human? It’s what we say it is — and what we write that it is, when we master the glyphs, grammar and syntax of the genome. It’s the ultimate act of existentialism. (I know, I know; maybe I saw Blade Runner too many times…)

(4 comments)


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