2008 May

DNA Video: History of the Species

by Dr. Hsien-Hsien Lei
Posted May 31, 2008 in DNA Podcasts and Videos, DNA in General

Work by the MRG at Goldsmiths.
Including: William Latham, Stephen Todd, Frederic Fol Leymarie, Miki Shaw, Ben Jefferys, Lawrence Kelley.

At the core of this work is the idea of feeding DNA data sequences into a rich 3D form generator called FormGrow, to generate organic-looking 3D growth structures, creating an equivalence of the DNA mapped into an alternative multi-dimensional space.

via Kevin Kelly

(>> Start a discussion!)


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DNA Quote: Former Surgeon General Dr. Richard H. Carmona

by Dr. Hsien-Hsien Lei
Posted May 30, 2008 in DNA Quotes and Excerpts

surgeon general richard carmonaFrom a Dr. Val Jones interview of Vice Admiral Richard H. Carmona, MD who served as Surgeon General from August 2002 to August 2006:

This tool [U.S. Surgeon General's Family History Initiative] helped people to begin identifying their risks based on a good family history – which busy docs don’t pay enough attention to anymore. When you know your history, genomics becomes valuable. If we can characterize disease, then we can search for potential genetic loci to help explain what’s going on and take a preventive approach to modifying the person’s environment to mitigate risk.

HT: Kevin, MD

(1 comment)


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Breakthrough: Scientists Encode Genome

by Dr. Hsien-Hsien Lei
Posted May 29, 2008 in DNA in General

walking femaleFrom MSNBC:

Scientists encode [sic] first woman’s genome: Project allows scientists to compare DNA of men and women

Wow! They’ve encoded an entire genome! NOT.

Usually, the reference is to a genome being decoded although there is debate surrounding the use of that terminology as well. RPM at evolgen says:

…decoding a genome is a long and tedious (possibly endless) process. To decode a genome, we would have to figure out the function for every gene product and how those gene products interact. And even if we simplify decoding to merely identify genes, there is more to a gene that its protein coding sequence.

<snip>

So, let’s abandon the idea of “decoding a genome” and refer to the process for what it is: sequencing euchromatin and preliminary analysis of protein coding sequences.

Photo credit: Walking female form, Wellcome Images via Creative Commons

(>> Start a discussion!)


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NHGRI Director Francis Collins to Step Down on August 1

by Dr. Hsien-Hsien Lei
Posted May 28, 2008 in Personalities with DNA

francis collinsLast year I wondered why Dr. Francis Collins, director of the National Human Genome Research Institute (NHGRI), seemed to be keeping a low profile. Maybe he was already plotting his exit then.

About an hour ago, I received an email from the man himself announcing his plans to resign from the NHGRI starting August 1, 2008. (For a second I thought I was on some personal mailing list of his until I realized it was distributed via the Genetic Alliance Announcements List. D’oh. Delusions of grandeur….) He is leaving to devote time to “writing, reflection and exploration of other professional opportunities in the public or private sectors.” Alan E. Guttmacher, M.D., will become acting director.

Here’s an excerpt from his email:

Looking back, I’m tremendously proud of our collective work in leading the Human Genome Project (HGP) to its successful conclusion in 2003, and of our wide range of large-scale projects that built upon the foundation laid by the HGP. Collectively, these projects and the priceless data they generated have transformed biomedical research and empowered researchers all around the world. I’m also proud of these projects’ commitments to protecting the privacy of genetic information and addressing the ethical, legal and social implications of genome research.

In addition to his work on the human genome, Dr. Collins has also been known for his controversial religious beliefs. In a 2006 interview I conducted with Dr. PZ Myers of Pharyngula, he said the following of Francis Collins’ book – The Language of God.

Once upon a time, I would have said that my view of genetics/genomics wouldn’t be much different from those who profess a faith — good scientists can sequester their religious beliefs from the practice of science. Unfortunately, I’ve since read Francis Collins’ new book, and that incoherent spewage of irrational lunacy is swaying me the other way, to regard religion as a toxin that corrupts good minds. The Language of God is precisely the kind of example that convinces me of the destructive failures of religious belief.

What memories do you have of Francis Collins?

Update: Sandra Porter at Discovering Biology in a Digital World remembers Dr. Collins singing about DNA with a guitar at a fund-raising dinner.

More: Francis S. Collins to Step Down as Director of National Human Genome Research Institute, NIH News

(1 comment)


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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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DNA Video: DNA Jewelry

by Dr. Hsien-Hsien Lei
Posted May 24, 2008 in DNA Podcasts and Videos

Two young women at UC Davis Picnic Day 2007 make DNA jewelry. This would make a great party activity!

(1 comment)


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Books About DNA: DNA: Promise and Peril

by Dr. Hsien-Hsien Lei
Posted May 23, 2008 in DNA Quotes and Excerpts

dna promise peril mccabeDNA: Promise and Peril by Linda L McCabe and Edward RB McCabe

The genetic revolution has provided incredibly valuable information about our DNA, information that can be used to benefit and inform–but also to judge, discriminate, and abuse. An essential reference for living in today’s world, this book gives the background information critical to understanding how genetics is now affecting our everyday lives. Written in clear, lively language, it gives a comprehensive view of exciting recent discoveries and explores the ethical, legal, and social issues that have arisen with each new development.

Here is Kathy Johnston’s impression of the book as originally posted at GENEALOGY-DNA:

As I am sitting here thumbing through the book, I get the impression that it is well written. It touches on forensics, ethics, race, gender, patents, cloning, reproductive medicine, gene testing, engineering and health insurance policies. However, I think they completely missed the impact that genetic genealogy is having right now and will have in the future as more of us order tests on ourselves.

Dr. Edward McCabe is a co-director for the UCLA Center for Society and Genetics so if anyone should know about the social impact that amateur DNA research is having, he should know. But I think they missed the boat on this one. The authors stressed that recreational DNA research represents “an extremely small part of the genome” but I don’t think they realize how many tests are actually being ordered on extended family members.

These academicians never seem to get it when it comes to understanding pedigree collapse, extended family and surname research projects and how the Internet and globalization will be revolutionizing genealogy through DNA search engines and pedigrees as more and more people are tested. Think of all the retired people who are spending their money on this hobby and helping labs to build branches on the phylogenetic trees that previously only universities could do. In addition, I should think a major university with a huge public policy department like UCLA would be looking at the social and medical impact of genetic genealogy. Well, it may be good thing that we are not on their radar screen right now. We can grow undisturbed.

This is what the McCabes think about genealogy DNA testing:

These laboratory analyses are expensive. Studies indicate that an individual’s knowledge of his or her ancestry is relatively accurate. In medical genetics, we know that one of the least expensive and most powerful genetic tools available to us is a good family history. The decision to carry out DNA testing for ancestry will be up to the individual. A far less expensive and excellent alternative available to many of us is to learn about our ancestry from the elders in our families. In addition, relatives’ stories will have far more cultural meaning than biological measures of ancestry.

I was just surprised that they have not seen the explosion of DNA studies being performed by us so-called amateurs. Genealogy will eventually make its way into the academic circles as the researchers figure out they need better pedigrees to help them figure out the more complicated mechanisms of inheritance especially when they look more at epigenetics.

(>> Start a discussion!)


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Watch Detects Alien DNA

by Dr. Hsien-Hsien Lei
Posted May 22, 2008 in DNA Products

Are you aware of the dangers alien DNA can wreak? Probably not unless you’re wearing the Tokyoflash Biohazard watch.

biohazard watch 2

With the threat of Alien Invasion growing ever closer & the distinct possibility that “they” are already here, it’s about time we had a device to detect the humans from the human-oids. The Biohazard wrist scanner probes the immediate vicinity for Alien DNA & displays the results so that you may assess the threat level.

Available for just $179.29 plus free shipping.

HT: Boing Boing

(2 comments)


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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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Helix Health Genomic Medicine Webcast

by Dr. Hsien-Hsien Lei
Posted May 20, 2008 in DNA and Disease

pretty is what changesWhoa! Almost missed it.

Fellow DNA Network member, Dr. Steven Murphy, and his company, Helix Health, will be hosting a webcast tomorrow, May 21, 2008 at 1:00 pm EDT.

How Genomic Medicine Is Changing the Management of Breast & Ovarian Cancer

Registration is free and will feature Jessica Queller, author of Pretty is What Changes: Impossible Choices, The Breast Cancer Gene and How I Defied My Destiny.

(1 comment)


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