Posts Tagged Books

Hacking the software of life

I just came across Marcus Wohlsen‘s book “Biopunk – Kitchen-Counter Scientists Hack the Software of Life“. It’s already been out there for a couple of months, and was discussed at some depth on boingboing by Mark Frauenfelder.

Just added it here for general interest – something to go on my wishlist – and as a soothing reminder that one is not the only crazy geek who sees the convergence of life- and information science 😉

Just ask Bill Gates. If he were a teenager today, he says, he’d be hacking biology. “Creating artificial life with DNA synthesis. That’s sort of the equivalent of machine-language programming,” says Gates, whose work for the Bill & Melinda Gates Foundation has led him to develop his own expertise in disease and immunology. “If you want to change the world in some big way, that’s where you should start — biological molecules.”

(found on wired “Geek Power: Steven Levy Revisits Tech Titans, Hackers, Idealists” By Steven Levy)

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In the bookstore …

During my studies, I made a habit of visiting the Cambridge University Press bookstore at least once a month. As a kind of wishlist, I noted potentially interesting new books – something I might continue in an open format here. Whenever the occasion and funding presented itself, I could draw from that list and get what seems most relevant and helpful. So far, reading on a tablet or screen does not quite have the same sensual appeal as a book for me quite yet – call me hopelessly old-fashioned. But of course, this being the 21st century, the advantage of carrying an entire electronic library with you in a tin-box that weighs less than your average textbook is a point that’s hard to argue about, especially in combination with advanced search and analysis tools. Nevertheless, here are some recent publications available in classical dead-tree format:

Systems Biology: Simulation of Dynamic Network States
Bernhard Ø. Palsson, University of California, San Diego


EMBOSS User’s Guide
Practical Bioinformatics
by Peter M. Rice, European Bioinformatics Institute, Hinxton
Alan J. Bleasby, European Bioinformatics Institute, Hinxton
Jon C. Ison, European Bioinformatics Institute, Hinxton

The Administrator’s Guide and Developer’s Guide are also available (by the very same authors in a different order).

The European Molecular Biology Open Software Suite (EMBOSS) is a well established, high quality package of open source software tools for molecular biology. It includes over 200 applications for molecular sequence analysis and general bioinformatics including sequence alignment, rapid database searching and sequence retrieval, motif identification and pattern analysis and much more.

The entire list of CUP titles in the section “Genomics, bioinformatics and systems biology” is here.

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Last chance to see – Don’t panic and don’t forget your towel!

Today is Towel day to commemorate the inspiring work and life of Douglas Adams.

When I read the “Hitchikers guide to the galaxy“, it had a profound effect on me: The idea to think of life on earth as a program was fun, a bit unsettling and seemed completely spaced-out. However, after several years in close contact with experimental and theoretical aspects in the life sciences the concept of “life as computation” does not seem that farfetched anymore. Just consider the picture of the theoretical basis of all computation, the universal turing machine and compare it to the schematic drawing of one of the most central molecules in life, the ribosome: they do look very much alike! Not only the ribosome but several other central molecular complexes could be described as state-machines, reading input from one “tape” and producing their output on another tape in a different alphabet.

Douglas Adams was most proud of his book “Last chance to see” – although this is not the most popular of his works. After reading this account of his travels with zoologist Mark Carwardine to meet species around the globe which are on the brink of extinction it became my favourite Adams book – it’s not as hillarious as the HHGTTG, but has a more sincere tone to it. After all, we are talking about (human-made) extinction here.

Linked above is a talk he gave at UCSB (recorded shortly before his death) on the book- I’ve watched it numerous times and love every bit of it. So today is a good opportunity to watch it again, enjoy the wonderful storytelling and titillating humor and share it … His wit about computers, life and the universe is thoroughly missed on this planet.

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Free Science, no more cargo-cult

Mr. Feynman

To link to / expand on the line in the previous post: Reflecting on the fact that people are able (and prone?) to worship “form” (in the sense of increasingly meaningless rituals) over function (in the sense of true understanding) I’d like to touch on Feynman’s famous term “cargo cult science“. From his speech at CalTech the text can be found here, and a .pdf is here. It’s also in his (highly recommended) book “Surely You’re Joking, Mr. Feynman! (Adventures of a Curious Character)”. (more on Cargo Cults on Wikipedia)

Not only the music and film-industry, newspapers but also scientific journals have to re-invent themselves in the face of technological advances in the digital domain. And as so much weight is put on evaluating scientists in terms of one-dimensional and ill-suited metrics (born out of a lack of time, a great deal of ignorance and a creepy tendency towards defensive decision processes) for grants and posts based on their publication record, it’s kind of hard to see a way to replace the underlying structure without crashing the entire edifice.

The analogy to cargo cult is fairly obvious: in the olden days, writing papers was the best way of communicating science over large distances. Journals and proceedings served to gather the information and make them available to a wider audience. As Darwin so aptly wrote: “If any man wants to gain a good opinion of his fellow-men, he ought to do what I am doing, pester them with letters.“. That’s why it’s called “letters to nature” and they always start with “Dear Sir,…“. Read the rest of this entry »

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Mathematical Foundations

This book looks like a solid foundation for teaching the underlying mathematics:

So far, no Customer Reviews@amazon -> note to myself: check it out! Hope someone has read/ used it and shares his opinion…

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