Big Things for Love

Best thing I read today about love:

We have always loved one another. We’re human, its something we’re good at. But up until recently, the radius and half-life of that affection has always been quite limited. With love alone, you can get together a birthday party. Add coordinating tools, and you can write an operating system. In the past, we would do little things for love, but big things, big things required money. Now we can do big things for love.

This was the concluding thought from a recent talk by Clay Shirky:

I hope one of the big things we can do for love, is to make personal genomes useful. Happy Valentine’s Day.

From Trickle Down Genomics to the Virtuous Circle

In the spaces between the scientist’s bench and the patient’s bedside, practitioners of translational medicine concern themselves with the conversion of basic research into real world medical applications.

The field of translational research is evolving from its trickle down, bench-to-bedside roots into something which approaches an ongoing dialog between scientists and clinicians. From the NIH translational research site:

Scientists are increasingly aware that this bench-to-bedside approach to translational research is really a two-way street. Basic scientists provide clinicians with new tools for use in patients [sic] and for assessment of their impact, and clinical researchers make novel observations about the nature and progression of disease that often stimulate basic investigations.

The silent partner in translational research has always been the patient, who is presumably in bed, supine.

The Virtuous Circle
The field of personal genomics is on course to evolve the model of translational research one step further. Trickle down, bench-to-bedside genomics; two-way streets between researchers and clinicians…to finally, the virtuous circle, where individuals, at their desktops, are equal partners in what is bound to be an exhilarating group exploration of science, medicine, and our shared humanity:


An recent editorial in the journal Nature Genetics signifies this mindshift is indeed underway:

Giving individuals their own genotype is not so much premature as truly disruptive. The individual gains a personal stake in the ongoing research effort and a huge incentive to find out more. A personal stake in finding out something that was not previously known is the key to getting students into research and may well be a powerful tool to educate and interest members of the public in the details of their own health and functioning. This boon was anticipated two years ago by George Church…at the launch of the ‘collaborative research endeavor’ called the Personal Genome Projects (…

…It is right to be skeptical of unknowns, but it would be wrong to underestimate the motivational potential inherent in handing people their genomes and asking them to participate in finding out more about their variation and phenotypes…

…In the meantime, individual genomics will have informed thousands participating in one of the most exciting areas of biomedical research, and it may recruit participants in prospective
studies that they will have funded partially from their own pockets. That being said, they are co-investigators, not patients, and the experiment will be conducted on their own terms!

Hurrah! I’m breathless.

Editorial. Positively Disruptive. Nature Genetics. 40(2): 119. February 2008.

Note to readers: The cast of characters in the graphic design above (aren’t they great?), were kindly provided by Ricardo Vidal. I can’t tell you how convenient it is to have a file folder containing a physician, a scientist, and red-headed woman in a blue dress. Thanks Ricardo! BTW, Ricardo is supplementing his grad school tuition with graphic design work for hire!

Polony A Go-Go

Since when are undergraduates accomplished in bioinformatics, hacking hardware, wetlab work, and bioethics, and music? These folks do exist. This summer, I have had the pleasure of working with the multi-talented James Kugler, an intern in the Church Lab.

I was just alerted to the fact that he is something of a budding musician trying to break out in the nascent scene of “genome pop“. His debut track will surely capture the hearts of ligase molecules across the globe. And no ballad on polony sequencing would be complete without fluorophores, and this one has got them in spades.

Listen to Polony A Go-Go, by James Kugler.

UPDATE (12:35AM): James does not sound like a 4-inch tall, helium-huffing chipmunk IRL. This is a WP and Flash player bug. Oh boy, I hope James doesn’t find out about this. I have just totally made a mockery of his big debut. Everyone please try to keep this on the DL until further notice. James, if you’re reading, I’ve sent in the calvary. We’re going to get your voice back back to normal soon, real soon…

UPDATE 2 (12:36AM): Oh yeah, it just occurred to me that if you go directly to the song URL, rather than rely on the embedded flash player (that is, do not click on the little blue icon next to song link), you can listen to the song at the normal sampling rate in your browser and avoid the chipmunk effect. So copy/past the URL below and have a listen:

Lyrics below the jump.

Read more

If it says GTCACGACAGG then you shouldn’t eat shrimp or nuts

This is a lyric from Jonathan Coulton’s humorous song “That Spells DNA” (lyrics, mp3). Try this verse:

“We start the story when Mom met Dad

And they danced all night and he took her home

It might have been all the wine they had

But they rolled the dice and won your genome”

Or this one:

“Guanine met Cytosine, fell in love

And then Thymine got busy with Adenine

They sent the messenger-RNA

To the ribosome to make more protein.”

You really ought to listen to the whole song. You can listen to more of his songs here, of which he has many because in 2005 Coulton tasked himself with the extraordinary challenge of writing, performing, and releasing a new song every week for a year or more.

All this music is released with a Creative Commons license (Attribution-NonCommercial-ShareAlike). Coulton explains why:

“I give away music because I want to make music, and I can’t make music unless I make money, and I won’t make any money unless I get heard, and I won’t get heard unless I give away music. This is all part of the experiment. I believe it can work, but we all need to adjust our thinking about the relationship between artists and fans - the RIAA thinks that music listeners are criminals and that music should be locked up and protected. I disagree. I think there are times when free music and file sharing can greatly benefit an artist. Believe me, I spent many years making music and not sharing it with anyone, and that didn’t get me anywhere.”

“That Spells DNA” may finally end my long search for a karaoke song that is almost as funny as the thought of me performing it.


PopTech live performance of some of his other songs:

Speaking of geeky songs, someone really needs to lay down a track for these lyrics: Lyse, Lyse Baby.

Zeitgeist of New Clinical Trials Database

The pharmaceutical industry has officially launched their new clinical trials portal which tracks clinical trials globally.  I plugged some key genetics terms into the "Ongoing Trials" search feature to get a quick zeitgeist of the world of clinical trials.  Here is what I found:

search term # results
the 45914
***** *****
genetics 2240
genetic 1570
gene 1446
DNA 845
RNA 775
genes 745
"family history" 573
chromosome 339
inherited 266
genome 150
genomic 105
genomics 25
"genome sequences" 21
"susceptibility gene" 15
genomes 5
"whole genome" 4
"genetic map" 2
"whole human genome" 1
"genome sequence" 0
***** *****
P450 155
titration 126
torsades 62
CYP 60
pharmacogenetics 40
pharmacogenomics 28
pharmacogenetic 25
pharmacogenomic 14
2D6 9
***** *****
mutations 504
mutation 376
genotype 342
polymorphism 135
microarray 60
haplotype 59
karyotype 57
polymorphic 40
genotyped 29
SNPs 34
SNP 17
"sequence variation" 7
centimorgan 2
"gene copy number" 2