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Sequencing Paradoxes

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As the DNA sequencing field heats up again, the GT staff wondered what relevant lessons could be gleaned from historic scientific thought experiments. Here’s what our research uncovered.

— Jennifer Crebs

 

 

Achilles and the Tortoise

(apologies to Zeno of Elea)

Two researchers are racing to sequence the same genome. Professor A. Chilleus is invited to test out the beta version of a sequencing-by-synthesis device, while Professor Dr. Tör Schildkröte is already plodding away using capillary electrophoresis. Given that Chilleus receives his machine a couple of months after Schildkröte begins, and both are working at a constant speed, the paradox holds that Chilleus will never overtake his colleague.

According to legend, Diogenes the Cynic refuted this argument by walking across the room to show Zeno a list of NIH R01 funding priorities.

 

Schrödinger’s cat and Wigner’s friend

(apologies to Erwin Schrödinger)

A cat is placed in a sealed box attached to an apparatus containing radioactively labeled cDNA and a canister of poison gas. As the sequencing reaction occurs, a particular base pair arrangement will trigger the apparatus to open the canister and kill the cat. When the box is opened, the postdoc will either see a dead cat (successful sequence) or living cat (unsuccessful). However, if the postdoc happens to be a friend of physicist Eugene Wigner, the whole experiment should probably be hushed up.

 

Twin paradox

(apologies to Albert Einstein)

Twin sisters grow up and get similar positions in sequencing labs. One works for a university, while the other signs on with a new, private-sector startup. Both use the same automated sequencing machine, but the industry twin is assigned a project to sequence while aboard a high-speed rocket traveling at near light-speed. When the space-sequencer returns to earth, it is observed that she is younger than the Earth-bound twin. The academic isn’t too disturbed by this, but she is resentful that her sister was able to sequence 3 billion bases in an instant. They are still not on speaking terms.

 

Maxwell’s demon

(apologies to James Clerk Maxwell)

Maxwell described “a being whose faculties are so sharpened that he can follow every molecule in its course” placed between four containers containing bases. This ultra-perceptive ‘demon’ is tasked with opening and closing trap doors to corral nucleotides into each appropriate box. If he is a good worker, however, this demon will work up enough sweat to violate the second law of thermodynamics. In 1929, Leó Szilárd noted that the act of demonic sequencing would also infringe on several IP laws to boot.

 

Trolley problem

(apologies to Philippa Foot)

You are given access to a device with two switches: one will enable you to rapidly sequence five unique human genomes at a total cost of $10,000, whereas the other will complete one genome for $100,000. Which do you choose? Keep in mind that one genome ... belongs to your mother.

 

The Scan

Shape of Them All

According to BBC News, researchers have developed a protein structure database that includes much of the human proteome.

For Flu and More

The Wall Street Journal reports that several vaccine developers are working on mRNA-based vaccines for influenza.

To Boost Women

China's Ministry of Science and Technology aims to boost the number of female researchers through a new policy, reports the South China Morning Post.

Science Papers Describe Approach to Predict Chemotherapeutic Response, Role of Transcriptional Noise

In Science this week: neural network to predict chemotherapeutic response in cancer patients, and more.