Laboratory Science: From Penal Colonies to Video Game Arcades

Laboratory science is filled with dull, repetitive tasks. Casting gels, pipetting, streaking plates, and on and on. Did you know adult C. elegan worms have 969 cells? Well they do. We know that because a number of graduate students were locked locked themselves into a room and painstakingly counted, and re-counted all those cells.

It should come as no surprise that laboratories have been compared to penal colonies. Glorified work camps for the technically adept! The root word of laboratory is “labor” after all.

Does the practice of science really need to be this way? Could science and laboratory work be more playful? In Shapiro’s 1991 book, The Human Blueprint, George Church wonders whether the lab could be turned into something more akin to a video game arcade:

“In counter to Sydney Brenner’s comparison of a sequencing laboratory to a penal colony, George Church has offered an analogy to a video game arcade, a place where a basically repetitive operation is so enjoyable that the participants work voluntarily for hours on end and even pay for the privilege. ”

Comparisons of science careers to video games are much more fun than comparisons to labor camps or penal colonies. The quote from George above challenges us to think beyond metaphors. How might the laboratory environment itself be transformed into something more playful, fun, and engaging?

Robert Shapiro, The Human Blueprint. St. Martin’s Press, 1991. [quote from page 252]

Nom de Ome: A pseudonym for your genome

How common will genomic pseudonyms be in 25 years? When might a person choose to use a Nom de Ome?

In some sense, the Human Genome Project’s human genome reference sequence has a nom de ome (which is “human genome reference sequence”). This sequence was generated mostly from a tissue sample donated by an anonymous male from Buffalo, NY. This volunteer was likely solicited from a newspaper article that ran in the Buffalo News on March 23, 1997. Here are the opening words from that article:

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Video Round-up: Esther Dyson on Charlie Rose, Spencer Wells on Colbert, and important video I can’t show you on genetic discrimination

Esther Dyson was interviewed on the Charlie Rose Show this past week. Charlie Rose ends the show by saying to Esther, “I can’t wait to see your genome”. I think this is the first time I’ve ever witnessed this expression being used like this — said with such endearment too! — but I’m sure it won’t be the last. (A google search for this phrase shows zero results at the time this post was written.)

The first twenty minutes of the show are mostly about Esther’s involvement in the Personal Genome Project (PGP) [disclosure: I work for the PGP]. The discussion doesn’t stop at genomes or health; the rest of the show ventures into the future of commercial space travel, the internet, cookie monsters, personalized search, AI and more. Esther never ceases to inform and inspire me, and challenge the way I think. I’m so glad she is among the folks that will be pioneering personal genomics for the rest of us via the PGP. Check it out:

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Slelling, Genetic Avatars, and Mail Order Chewing Gum Impregnated with your DNA

In David Zindell’s space opera Neverness, the term “slel” is introduced to describe the misappropriation of someone else’s DNA. In a review of Zindell’s book, Orson Scott Card gives us the following definition:

Slel: To take DNA from someone against his will, to create avatars of him, or perhaps children.

Last week Hsien documented the recent efforts of UK police to make slelling a standard practice.

I’ve got two riffs on slelling for you: (1) genetic avatars and (2) DNA bubble gum.

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Richter Scale and Your Genomic Portfolio

The field of personal genomics needs a richter scale. This scale would provide a mechanism for giving each new genomic association a score, maybe from 1-10, based on some criteria such as penentrance, actionability, and validity. Existing genetic tests should be scored as well. Commercially available tests might have additional criteria, like whether there is an FDA-approved test or whether the test is reimbursed.

The higher the score the “better” the association or test. A low score might indicate that the association is very likely just “noise” regardless of the fact that it was all over your morning newspaper.

This scale will be very handy once you have a copy of your own genome. Let’s be honest, if you’re sipping on your morning cup of coffee, reading the paper, and see an article about a newly discovered “gene for alzheimer’s” or “snp for sudden stroke”…you’re going to be compelled to run over to your computer to see if your genome possesses that genetic variant. Without a good way to quickly judge the relevance of the news article, journalistic sensationalism may have you running over to your computer several times a day. That doesn’t sound like a very good use of time, does it?

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Can I see some ID?

Should there be a minimum age requirement for personal genome sequencing? If so, what age?

Or maybe that question is irrelevant — or only relevant for the next decade or two. Future generations might get sequenced at birth (or maybe even prior to birth via PGD). That might leave no individual choice about personal sequencing, in which case, maybe there will be regulations about the minimum age for disclosure of personal genomic data to individuals. 13? 18? 21? 30? What age?

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Twittering Toilets and Phenomic Death Wishes

Unlike the first human genome sequence, which (rather mysteriously) we are able to “complete” every few years it seems, we may never be able to achieve a complete human phenome.

The totality of human physical traits, from the molecular to the behavioral levels, contains just too much information. There are many reasons why setting out to collect a complete human phenome is ill-advised, but even shrinking the goal to a much more manageable-sounding level like 0.01% of a human phenome will still face significant challenges, some economic, some technological, some social-ethical-legal-personal-and-everything-else.

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Best Hegel Reference Heard Today, errr ever

as Hegel said… Kant’s requirement to become acquainted with the instrument, in this case the Mind, before one starts to use it, is like a resolution not to venture into water until one has learned to swim

The insight here is that its impossible to learn to swim without first getting wet.  A reference to this critique of Kant by Hegel was casually slipped into a discussion I had today with a friend about different approaches to introducing new technologies into society. (The quote above came this blog, who also cites the original passage.)

Hodosh to lead Archon X-Prize for Genomics

The Archon X Prize for Genomics has appointed Marc Hodosh to lead the $10 million competition. Hodosh is an entrepreneur and tech geek who recently chaired a robotics competition for segway inventor Dean Kamen.The Archon X Prize will be awarded to the first group that can “build a device and use it to sequence 100 human genomes within 10 days or less, with an accuracy of no more than one error in every 100,000 bases sequenced, with sequences accurately covering at least 98% of the genome, and at a recurring cost of no more than $10,000 per genome.” In other words, the winner must be able to sequence 100 human genomes in 10 days for a $1 million.

The X Prize Foundation has published a video describing the competition, check it out:

So far three teams have registered to compete, including VisiGen Biotechnologies, 454 Life Sciences, and the Foundation for Applied Molecular Evolution.Here are the competition guidelines (PDF).Want to compete? Register here (PDF).

Video: Craig Venter on Colbert Report

Hat tip, Pedro and to those who forwarded this to me.

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