Decoding Watson on PBS

I would like to thank John Kwok for alerting me to this new PBS documentary about James Watson, the controversial co-discoverer of DNA structure. I was tagged in a post about it on Facebook by John who saw Professor Ken Miller of Brown University share a link to the film. I agree wholeheartedly with Dr. Miller's assessment of the documentary. It is unafraid in confronting the racism and sexism of Watson while allowing the story of the discovery of the double helix to shine.

I must add one note. Though the story of discovery is certainly abbreviated, I think it worth mentioning one character who is left out in this telling.  Jerry Donohue, an organic chemist from Wisconsin of whom few have ever heard. Donohue provided a crucial course correction right before Watson put the puzzle together (The Double Helix pg. 120).  Watson had been using cardboard models of the four nitrogenous bases that constitute DNA. He made these flat cut-outs based the structures published in The Biochemistry of Nucleic Acids by J. N. Davidson.  Watson was using the cardboard models to try and conjure how the bases might fit together to form a helix (which he knew must be the structure from Rosalind Franklin's famous photograph 51.) However, these cardboard models were misshapen. Homologous oxygen atoms poking out from the thymine and guanine models were in the enol (O-H) rather than the keto (=O)  form.  Jerry Donohue pointed this out and only then could Watson make the key observation that adenine pairs with thymine just as guanine pairs with cytosine. It was as though Donohue passed him the ball on the one-yard line!

When I read Watson's The Double Helix for the first time last year I was startled to learn about Jerry Donohue and hope he is also remembered for this serendipitous correction!

Frances H. Arnold Nobel Lecture

If you are or know a graduate student, pay particular attention to this starting at around 17:55.

Diatomaceous Art

“The Diatomist” by Matthew Killip

The Diatomist from Matthew Killip on Vimeo.

Urban Garden Projects - Berlin

Speaking Gardens - The Berlin urban gardening movement (TRAILER - english version) from ReneResi on Vimeo

The Copy Co-Op: reworking the "selfish" gene.

The nucleosome. Image generated from the protein data bank file deposited by Luger et al in 1997.  This a representative model of the atomic structure of one nucleosome the basic packaging unit of chromatin. Chromatin is the mixture of DNA and proteins that make up chromosomes, the heritable parts of living things.

Recognize Rosalind Franklin!

Ant Metropolis: superorganism manifest?

Open Access Crusaders: interview with the Eisen Brothers

Vampire Phylogeny

 

"Teeth lengthened by receding gums glow in the shaded valleys of the Carpathian basin. The genetic milieu of the Visigoths, Huns, Carpians, and Slavic peoples have swirled over centuries as granite crags pushed populations into shallow gene pools. A ghoulish thing of legend emerged from Transylvania and has since soaked literature and pop-culture with a reddish froth. Science and medicine have given us reason not to fear for our necks in a story that is truly stranger than fiction... "

Thus begins one of my most successful Blog Posts.  The idea to write up this particular hypothesis on a biochemical etiology of vampires was born on a fall day in 2008. A fellow graduate student at Colorado State - Nicholas Clark and I were talking about "talking about science" to the public.  We decided a useful method to engage the public would be to hook them in with a popular topic and then sneak in some hardcore biochemistry.  So we did it. We planned a "Biochemistry of Halloween" lecture and delivered it the following fall.  There were 60-70 people in attendance and the talk was wildly popular. So popular in fact that Nick and I were invited to present the talk for the Colorado State Alumni association at the Park Hill library in Denver the following year. This time there were more people from the general public and our presentation was met with even greater enthusiasm.  One of the attendees even came up to us afterwards and asked us for all our references as she was particularly interested in the porphyria/vampire hypothesis as her ex had a form of the disease and was now in jail for attempting to slit her throat with a paring knife.

After this experience I have been hesitant to present this talk because I feared it may be taken the wrong way. As if we were saying "people with porphyria are vampires." This is not what we were trying to get across. I have since finished graduate school and moved on to a postdoc at Emory University in Atlanta. Nick is Postdocing at NIST near Washington DC. 

Recently, I took it upon myself to raise the talk from the dead. I presented it at Nerd Nite Atlanta at Manuel's Tavern on October 16th, 2013.  I also amended the talk to include several disclaimers about porphyria patients and attempt to address the stigma that has recently become associated with this very serious genetic disease. I felt much better about the talk this time and it was well-received by an enthralled audience though it was not the same without Nick and his unique knowledge-set on the biochemistry of Zombies and Zombification. 

Hello Dolly

The New York Times RetroReport (which I've featured previously) focuses its light on Dolly the sheep and the implications of animal cloning. Looking at the legacy of Dolly and all the fear pumped into the mainstream by the media makes me think we really need to stop letting all the chicken little attitudes hog the microphones in the aftermath of biotechnology breakthroughs. I'm talking to you Krulwich!

@thorsonofodin Sets Sail for Science Online Oceans

@thorsonofodin

Here I am in Miami for the first ever Science Online Oceans Conference.

Despite the fact that this entire genre of science is way outside my wheelhouse I decided to make the trek down from Atlanta. I am curious to see what I learn and who I meet. If it is even a fraction of the intensity of the flag-ship Science Online Conference I attended last February then I am sure I'll be reeling for months.

Leading up to the conference I put together a blog post about the Dead Zone in the Gulf of Mexico. I've been following the political and ecological implications of the dead zone problem for years and decided to summarize the current status of the dilemma.
You can check out that post at Scientific American. A big deal for me as it is my debut piece for the SciAm Network.

Follow the emerging information from this event on Twitter using #ScioOceans.

Some cool links so far...

OMG I want to build one of these DIY mini-submarines! Mom! I can finally build that submarine I dreamed of as a kid! OpenROV 

Want - a navy blue uglifish t-shirt. Awesome - Uglifish

Some sweet web-sites I came across at #ScioOceans.
COSEE Florida
The Echinoblog
Bittel Me This
Ocean Conservancy
Story Collider
Upwell
Deep Sea News 
Society of Environmental Journalism
Plankton Portal


Look at my twitter feed over on the sidebar until I update here ------>

My Brain in GIF

My name is Kristopher Hite and this is my brain. I present it here on my website as Tom Paine's Ghost was, once upon a time, conceived up there among the folds. The above animation is a series of images captured by MRI on April 27th, 2013 at Harvard University as part of the Personal Genome Project headed by George Church. I made this GIF using Photoshop and 22 DICOM files given to me by the researchers. If you want to donate your living genome to science you too can have your entire genome sequenced by signing up, passing the informed consent test and coming to Boston for the annual Genomes Environments Traits conference that happens each year around DNA-day April 25th to commemorate the discovery of the double helix. If you want to have your genome sequenced but can not make it to Boston you can still get on the list but I think going to the GET conference expedites the process.

What happened to the Flavr Savr Tomato?

Carl Zimmer recently suggested checking out a newish series from the New York Times called Retro Reports. The video series revisits old news stories that have since faded from the headlines. The digital-short-film format makes it readily accessible and I appreciate seeing the faces of the interviewees.

One of Carl's suggestions is a piece on the defunct Flavr Savr tomato, a timely subject for me as I now work in a plant biology lab using genetic engineering to study epigenetic factors at play during development.  Recently we had a departmental conversation about the controversy surrounding genetically modified crops. With that conversation in mind and after watching this clip I have formed an opinion on initiatives to label genetically modified food.



I am for labeling genetically modified food. Promoting transparency may help us embrace things worth embracing and discard those things that may be harmful to our health. George Church has argued that science ought to be more resilient when faced with ethical dilemmas.  I would like to apply this logic to labeling GMOs. The tool of genetic engineering can be equated with a "hammer." A hammer can be used to build a house or clobber someone over the head. The consequence is not the hammer's fault in either case.

The potential good that may come from genetic modification is overshadowed by the profit motives held by companies like Monsanto that now fuel 95% of the genetically modified crops in production throughout the world. There are under-reported cases like Rainbow Papaya in Hawaii, or Golden Rice where genetic modification has been the hero, not the villain.  It may be naive of me to think that the American public is science-savvy enough to decide for themselves whether a genetically modified plant is beneficial or not. However, I think science could exercise resilience in this case by allowing genetically modified foods to be labeled.  If in the long term some of those foods that are genetically modified prove beneficial to society, then the economy will carry them into wider markets, but if some GM crops prove over time a detriment they will be selected against.    

GMO OMG! ~ a new film from the director of "Dive"

Director Jeremy Seifert is hosted by Josh Zepp to discuss and debate the public furor over genetically modified food crops. A public discussion that needs to happen.

Giant Misshappen Phallus Blooms

The sexual organs of the Giant Corpse Flower.

Below is a live-stream from the United States Botanical Garden in Washington, DC. The man-sized flower you see is known as the "corpse flower." Named for the putrefied stank it emits this carrion flower attracts pollinators by mimicking the smell of rotting flesh. The plant has the largest unbranched inflorescence in the world. Its Latin name is Amorphophallus titanum ~ "misshapen phallus." It is worth noting that this titan of the plant kingdom does not have a regular cycle to its bloom. Blooms may be separated by years or decades. 

Live Video app for Facebook by Ustream

Richard Dawkins and the Electric Kool-Aid Acid MEME

Watch the following video all the way through. A metamorphosis of sorts unfolds before our very eyes.

Frans de Waal and Jeff Schloss: a Conversation about Science and God

Lyrebird repertoire includes chainsaw

I know the resolution on this clip is low but it is completely worth watching. The Australian Lyrebird sings a song of irony for the world to hear. A clear feedback loop in the forest and a beauty to behold.

Leo the Lungfish!

My friend Davide takes care of a lungfish named Leonardo. Watch him clean Leo's tank!

We the Genes!

We the Genes of the United Cells, in order to form a more perfect Union, establish equilibrium, insure homeostasis, provide for the common immunity, promote the general Welfare, and secure Liberty to ourselves and our Posterity, do ordain and establish this Constitution for the United Status of Life. 

In the coming month the United States Supreme Court will likely rule on whether a private company can hold a patent on a human gene.  The company in this case (Myriad  Genetics) has spent a substantial amount of money and time figuring out that mutations in the BRCA1 and BRCA2 genes are associated with an increased risk of developing early-onset breast and ovarian cancer.  Because of this investment the company feels entitled to hold a monopoly on testing and reporting this information to patients who ask their doctor to be screened.  Recall Angelina Jolie's double-mastectomy headlines in recent weeks.

The company feels it has the right to be the only one to read a particular page in a book handed down to a woman by her mother and father.  This book of genes is called the genome. The human genome like the genomes of all other living things has been copied, proof-read, edited, re-drafted and copied again and again countless times over earth's rich and chaotic history. The current edition of your genome is without question a product of nature.

PCR happens.

Using a routine process in basic scientific research called the polymerase chain reaction (PCR) the company can isolate the BRCA1 and BRCA2 genes.  Once the genes are isolated from a blood sample they can be read by any of the well established methods for DNA sequencing.  Neither the method for isolating the genes, nor the method for sequencing the genes are at issue in this case. The patents associated with these decades-old processes have long since run out.  No, The object in question in this case are the BRAC1 and BRCA2 genes themselves. 

Can a company own exclusive rights to read your genes?

I say no. We ought to have the right to pursue any path we like to uncover the information we were each born with. Whether that path be through Myriad genetics, the Harvard-based personal genome project, or sending your blood samples to whoever has access to a PCR machine. Trust me, they are pretty darn common. We should have access to the secrets inside our own cells.

I think there is a fundamental misunderstanding among the justices in this case. The misunderstanding is that in cases of genetic testing the "product" is not necessarily any physical thing but rather naturally occurring INFORMATION.

A technical work-around attorneys representing Myriad Genetics are trying to use is that coding, composite, complimentary DNA (cDNA) is not present in nature and can be patented because it is only produced by scientists. cDNA conveys the sequence information of messenger RNA produced by nature. Though the cDNA itself can be construed as product of human tinkering, the information cDNA holds is not. The information therein is an impression of nature, like a plaster-cast of a wolf-print in the mud, or the ink-blot of a small mouthed bass.  The key piece of information the attorneys for Myriad Genetics leave out is that the cDNA is not used directly but only to gather information from nature.

The patient dos not need or care to have the amplified DNA prepared from their blood sample, the patient wants to know some information so they can make an informed decision about how best to proceed with preventive health measures like a mastectomy or hysterectomy.  Genetic information is a product of nature and is therefore off-limits according to a century of court precedent.

What incentives will researchers have to make discoveries?

While listening to the Oral Arguments in the case between the Association for Molecular Pathology v. Myriad Genetics I am struck at what little credit is given to the motivation propelling scientific discovery.  It seemed to me that the Justices kept asking questions with a particular concern for maintaining a clear market incentive for big genetic discoveries.

It was almost as if the justices were under the impression that market forces are the main drivers of scientific discovery.  This may be a matter of opinion but I do not think Charles Darwin, Jonas Salk, or Carl Woese were in it for the money.

The tone of the Justices' questions regarding market-incentives and scientific discovery reminded me of a conversation on the recent Freakonomics podcast in which the hosts Stephen Dubner and Steve Levitt have the following exchange.

DUBNER: Since fighting cancer is big business, what’s the incentive to find a cure?  

LEVITT: So I would say the incentive for a cancer cure is not really a market incentive, it’s a being a hero kind of incentive. That there are so many doctors out there, researchers, medical researchers who if they could be the one who was forever remembered as the one who prevented cancer, who got rid of cancer, they would do anything to do that. So I think there are really strong incentives out there. And they aren’t exactly market incentives, although I think that person would be quite rich anyway...

I think the "being a hero kind of incentive" is the kind of incentive that pushes the world into a progressively safer more peaceful context. A context where human life-span lengthens and justice systems move away from a punitive to a rehabilitative mode. It is my opinion that knowing as much as we can about our bodies and specifically our genes will allow us to attain an unprecedented state of self-awareness, health and social responsibility.