Computational modeling of biological systems is becoming increasingly important in efforts to better understand complex biological behaviors. In this review, we distinguish between two types of biological models—mathematical and computational— which differ in their representations of biological phenomena. We call the approach of constructing computational models of biological systems ‘executable biology’, as it focuses on the design of executable computer algorithms that mimic biological phenomena. We survey the main modeling efforts in this direction, emphasize the applicability and benefits of executable models in biological research and highlight some of the challenges that executable biology poses for biology and computer science. We claim that for executable biology to reach its full potential as a mainstream biological technique, formal and algorithmic approaches must be integrated into biological research. This will drive biology toward a more precise engineering discipline.
Click through for the official web site; the video is just a compilation of informal testimonials. I must say that the sight of young children enthusiastically shaking Bacon Salt on their steamed vegetables is more than a little disconcerting. (Buy it online.)
It can run up to six kilometres at a speed of 20 metres per minute for five hours or more without stopping. It lives longer, has more sex, and eats more without gaining weight. Could the science that created this supermouse be applied to humans?
...
It lives longer and enjoys an active sex life well into old age – being capable of breeding at three times the normal maximum age.
"Our animals live longer and eat almost twice as much as ordinary mice – this is a model to study."
Be sure to watch the video. But whatever you do, don't think of these guys.
Freeman Dyson is certainly working hard to get his message out ...
We are suspicious of genetic engineering, but bio-sciences are about to become the new industrial revolution. It’s not just about GM crops: soon we’ll be designing our own pets and tackling global poverty
This article covers the same ground as Our Biotech Future -- you know, things like housewives sharing "recipes" for "canine-based" automatic toilet bowl cleaners, and kids arguing over genetic "cheats" in Pokémon Live (think doping, a la Tour de France, or baseball) -- but for the newspaper audience, he leaves out the pointers to Carl Woese.
David Bolinsky and his team at XVIVO illustrate scientific and medical concepts with high-drama animation.
These animators are true auteurs, carefully scripting and editing the story of cellular processes to show everyone -- expert and amateur alike -- the truth and the beauty of our bodies.
You've never seen the life of a cell quite like this.
The question I am asking is, how long will it take us to grow plants with silicon leaves?
Dyson has been honing this piece for a few years now, and it just keeps getting better. If the US had a Scientist Laureate, it would be Dyson.
Will the domestication of high technology, which we have seen marching from triumph to triumph with the advent of personal computers and GPS receivers and digital cameras, soon be extended from physical technology to biotechnology?
I believe that the answer to this question is yes.
Here I am bold enough to make a definite prediction.
I predict that the domestication of biotechnology will dominate our lives during the next fifty years at least as much as the domestication of computers has dominated our lives during the previous fifty years.
Join the Homebrew Cloner Club, which meets every first Friday in the mall food court next to Chick Fil A. Please, no chimeras over 36 inches, or the mall police will hassle us. Unless, of course, you are the chimera. Also: plants that make loud noises have to be left outside, unless they have a headphone jack or a mute button.
I wait in eager anticipation of Grey Goo Graffiti.
Meanwhile, Dyson plows right into Joyland:
First, can it be stopped? Second, ought it to be stopped? Third, if stopping it is either impossible or undesirable, what are the appropriate limits that our society must impose on it? Fourth, how should the limits be decided? Fifth, how should the limits be enforced, nationally and internationally?
It's time to reinvigorate the hacker ethic:
Whatever Carl Woese writes, even in a speculative vein, needs to be taken seriously. In his "New Biology" article, he is postulating a golden age of pre-Darwinian life, when horizontal gene transfer was universal and separate species did not yet exist. Life was then a community of cells of various kinds, sharing their genetic information so that clever chemical tricks and catalytic processes invented by one creature could be inherited by all of them. Evolution was a communal affair, the whole community advancing in metabolic and reproductive efficiency as the genes of the most efficient cells were shared. Evolution could be rapid, as new chemical devices could be evolved simultaneously by cells of different kinds working in parallel and then reassembled in a single cell by horizontal gene transfer.
"You shared your code, you shared your genes, ..."
The emerging field of metagenomics, where the DNA of entire communities of microbes is studied simultaneously, presents the greatest opportunity -- perhaps since the invention of the microscope -- to revolutionize understanding of the microbial world, says a new report from the National Research Council. The report calls for a new Global Metagenomics Initiative to drive advances in the field in the same way that the Human Genome Project advanced the mapping of our genetic code.
Biotechnology | Roses are blue, violets are red | Economist.com
Topic: Biotechnology
5:10 am EST, Feb 21, 2007
Mere colour is for unsophisticated lovers. A truly harmonious Valentine gift should smell beautiful as well. Sadly, commercial varieties of cut rose lack fragrance. This is because there is a trade-off between the energy that plants spend on making the complex, volatile chemicals that attract women and insects alike, and that available for making and maintaining pretty-coloured petals. So, by artificially selecting big, long-lasting flowers, breeders have all but erased another desirable characteristic.
The author of this article does a great job of making the science accessible to the general reader.
Now, after some three billion years, the Darwinian era is over.
In the post-Darwinian era, biotechnology will be domesticated. There will be do-it-yourself kits for gardeners, who will use gene transfer to breed new varieties of roses and orchids. Also, biotech games for children, played with real eggs and seeds rather than with images on a screen. Genetic engineering, once it gets into the hands of the general public, will give us an explosion of biodiversity. Designing genomes will be a new art form, as creative as painting or sculpture. Few of the new creations will be masterpieces, but all will bring joy to their creators and diversity to our fauna and flora.
This article is older and much shorter than the essay in New Scientist, but there is overlap between them.
