Genes, Books, Rants, and Science Fiction
A certain 13-year old has been messing with my documents again:
What was previously titled
“CRE-seq RNA and DNA Illumina Preparation Protocol”
has been somehow changed to
“Glimmer and District 10 CRE-seq RNA and DNA Illumina Preparation Protocol.”
I argue at Pacific Standard that gene patents are a bait-and-switch - they conflate valuable sequence information with the much less valuable physical molecule.
Over the years, Penguin has put some very fine covers on classic science fiction. They have a site showing all of their covers, with a brief history of the thinking behind each series of covers. I’m ready to go out and scour some used book store shelves to find more of these.
So says E.O. Wilson. But you need to read the nuance in the piece, not just the headline. What Wilson is mostly saying is, don’t let your fear of math drive you away from science.
More at The Finch and Pea.
Moreover, the word “regulation” has itself degraded through use by genomicists, from designating evolved effects shown or likely to enhance fitness, presumably by efficient control of the use of resources, to more broadly denoting any measurable impact of one element or process on other elements or processes, regardless of fitness consequences. I think this broadening of definition misleads biologists such as Barroso (43) in a passage cited later in this essay. Pacemakers regulate heartbeats and that is their function: tasers and caffeine also affect cardiac rhythm, but we would not (at least in the former case) see this as regulatory function.
Regulation, defined in this loose way, is, for instance, the assumed function of many or most lncRNAs, at least for some authors (6, 7, 44, 45). However, the transcriptional machinery will inevitably make errors: accuracy is expensive, and the selective cost of discriminating against all false promoters will be too great to bear. There will be lncRNAs with promoters that have arisen through drift and exist only as noise (46). Similarly, binding to proteins and other RNAs is something that RNAs do. It is inevitable that some such interactions, initially fortuitous, will come to be genuinely regulatory, either through positive selection or the neutral process described below as constructive neutral evolution (CNE). However, there is no evolutionary force requiring that all or even most do. At another (sociology of science) level, it is inevitable that molecular biologists will search for and discover some of those possibly quite few instances in which function has evolved and argue that the function of lncRNAs as a class of elements has, at last, been discovered. The positivist, verificationist bias of contemporary science and the politics of its funding ensure this outcome.
— Is junk DNA bunk? A critique of ENCODE, WF Doolittle PNAS April 2, 2013 vol. 110 no. 14 5294-5300Why stat mech for biologists
From Rob Phillips’ lab, Garcia, et al, “A First Exposure to Statistical Mechanics for Life Scientists”:
This paper is a reflection of our attempts to find a minimalistic way of introducing statistical mechanics in the biological setting that starts attacking biological problems that students might care about as early as possible. We view this as part of a growing list of examples where quantitative approaches are included in the life sciences curriculum [1, 2, 3, 4, 5, 6]. As will be seen throughout the paper, one of the key components of this approach is to develop cartoons that provide a linkage between familiar biological concepts and their mathematical incarnation. The courses we teach often involve a very diverse mixture of students interested in how quantitative approaches from physics might be useful for thinking about living matter. On the one hand, we have biology students that want to make the investment to learn tools from physics. At the same time, about one third of our students are from that ever-growing category of physics students who are excited about taking what they know and using it to study living organisms. As a result, we face a constant struggle to not lose either the interest or understanding of one of these two constituencies. The challenge is to be interdisciplinary while maintaining strong contact with the core disciplines themselves.
“In historical terms, when adjusted for inflation, these figures put federal R&D investment (in actual spending power) at its lowest point since FY 2002, and more than $25 billion in constant dollars below the all-time peak in 2010. This represents a roughly 17.1% decline in just three years.”
An illustration of why the English translation of Solaris sucks
The only available English version of Stanisław Lem’s Polish science fiction classic Solaris is a translation from a French translation of the original. It is notoriously bad (which hasn’t stopped Solaris from becoming a classic). Copyright issues have prevented any publication of a new English translation.
Since at one time I spoke Polish fluently, I decided to skip the English and read Solaris in the original, and I now have my hands on the Polish edition. And it is only now that I’ve realized just how badly the English version captures Lem’s terse, dissociated style.
I’ve translated the first few paragraphs below, as literally as I could while still making sense in English:
Newcomer [New Arrival]
At 19 o’clock Deck Time I arrived, passing by those standing around the well, by the metal rungs at the interior compartment. Within it was just enough room to lift my elbows. After screwing the end into the duct protruding from the wall the space suit inflated and from then I could no more make the smallest movement. I stood - or rather I hung - in an aerial bed amalgamated in one whole with the metal shell.
Raising my eyes, I saw through the convex pane the wall of the well and, higher, bent over it the face of Moddard. It immediately vanished and darkness fell, because from the top was laid the hard protective cone. I heard the eight-fold repeated whizz of the electric motors, which tightened the screws. After that - the hiss of the incoming air of the shock absorbers. My sight became accustomed to the darkness. I saw now the sea-green outline of the only gauge.
- Ready, Kelvin? - resounded in the headphones.
- Ready, Moddard - I answered.
- Don’t worry about anything. The Station will pick you up - he said. Good-bye!
For comparison, here is the English translation from the French by Joanna Kilmartin and Steve Cox. Note the added verbiage that is not at all in the original:
At 19.00 hours, ship’s time, I made my way to the launching bay. The men around the shaft stood aside to let me pass, and I climbed down into the capsule.
Inside the narrow cockpit, there was scarcely room to move. I attached the hose to the valve on my space suit and it inflated rapidly. From then on, I was incapable of making the smallest movement. There I stood, or rather hung suspended, enveloped in my pneumatic suit and yoke to the metal hull.
I looked up; through the transparent canopy I could see a smooth, polished wall and, far above, Moddard’s head leaning over the top of the shaft. He vanished, and suddenly I was plunged in darkness: the heavy protective cone had been lowered into place. Eight times I heard the hum of the electric motors which turned the screws, followed by the hiss of the shock-absorbers. As my eyes grew accustomed to the dark, I could see the luminous circle of the solitary dial.
A voice echoed in my headphones:
“Ready Kelvin?”
“Ready, Moddard,” I answered.
“Don’t worry about a thing. The Station will pick you up in flight. Have a good trip!”
As I work through the Polish version, I’ll post the most notable differences between the English translation and the original.
Here’s the above passage in Polish:
Przybysz
O dziewiętnastej czasu pokładowego zeszedłem, mijając stojących wokół studni, po metalowych szczeblach do wnętrza zasobnika. Było w nim akurat tyle miejsca, aby unieść łokcie. Po wkręceniu końcówki w przewód wystający ze ściany skafander się wydał i odtąd nie mogłem już wykonać najmniejszego ruchu. Stałem - czy raczej wisiałem - w powietrznym łożu zespolony w jedną całość z metalową skorupą.
Podniósłszy oczy, zobaczyłem przez wypukłą szybę ściany studni i, wyżej, schyloną nad nią twarz Moddarda. Znikła zaraz i zapadła ciemność, bo z góry nałożono ciężki ochronny stożek. Słyszałem ośmiokrotnie powtórzony świst motorów elektrycznych, które dociągały śruby. Potem - syk wpuszczanego do amortyzatorów powietrza. Wzrok przywykał do ciemności. Widziałem już seledynowy kontur jedynego wskaźnika.
- Gotów, Kelvin? - rozległo się w słuchawkach.
- Gotżw, Moddard - odpowiedziałem.
- Nie troszcz się o nic. Stacja cię odbierze - powiedział. - Szczęśliwej drogi!
What’s at stake in gene patents
Daniel Kevles:
The Court of Appeals’s several opinions made explicit that the case pitted the property rights of innovators and investors in gene-based biotechnology against the rights of free access to and use of human DNA by researchers, physicians, and patients. In effect, the absolute control inherent in DNA patents protects—and thus privileges—this sector of the biomedical complex against all others who have reasons to make use of human DNA. The instrument of the privilege is the current strict interpretation of patent law that is guided beyond legal logic by concerns for incentives to innovation and investment.
It is for this reason that patent defenders are going to great lengths to deny the obvious: patent holders have essentially been granted a monopoly on the information in DNA sequence, and not just the physical substance isolated from cells.
What I’ve been listening to: Chris Thile and Michael Daves and pure bluegrass bliss
