About
Green Goo ¶
This is the web log of two bioinformatics students from Berlin, Germany, and will serve as the dump for our mad ideas and exciting research. And also all the other stuff. You know, crazy talk.
Bioinformatics ¶
The NCBI defines bioinformatics as
the field of science in which biology, computer science, and information technology merge to form a single discipline. The ultimate goal of the field is to enable the discovery of new biological insights as well as to create a global perspective from which unifying principles in biology can be discerned.
So bioinformatics is probably best described as an ancillary science — a tool to make biological research work. Over the last few decades, biologists and chemists have started to accumulate huge amounds of data. — How huge? Exponential growth huge. Every year, the amount more than doubles: This is clearly a case of running as fast as we can just to stay in the same place.
Collecting and storing the data is challenging enough, but making sense of it is even harder. In most domains, we haven’t had more than a glimpse of the truth yet. Computers take us only so far; the most important part is the development of mathematical concepts to grasp the significance of what biologists find in nature.
Both authors of this blog are intimately involved with algorithms in sequence analysis. However, sequence analysis is still only the most basic step. Since the sequencing of the human genome in 2001, a lot has changed in our understanding of life. On the other hand, the early optimism was misplaced: even though we now know the human genome, we still haven’t decoded it nearly ten years later. We can read the letters and even some words but not the message.
Creating life with the power of computers ¶
Today, we live in a truly exciting age. (For now, I’ll withhold judgment of whether this is good or bad.) I’m not sure how credible Kurzweil’s technological singularity really is — but it doesn’t take a genius to see that we’re certainly moving somewhere. Until very recently, much of research has been a lot like poking in mud. And while this is still true, we’ve nonetheless introduced a lot of thrust and purpose in almost all research. We’re finally getting somewhere.
One of the places we’re reaching is the creation of life in the conventional sense of the phrase. In 2008, the J. Craig Venter Institute has published a minimal complete viable artificial genome, calling it Mycoplasma genitalium JCVI 1.0 (notice the version number). However, the manipulation of existing organisms to fulfil new functions is much older. Bacteria such as E. coli are routinely being modified to produce chemicals which are otherwise hard to manufacture, and chicken eggs are used to cultivate flu shot medication.
Until recently, getting an E. coli cell to detect arsenic was a lengthy process. Scientists are now compiling collections of standard parts with biological functions that may be combined much like Lego bricks. Indeed, they are even now working on software to assist that process. Imbuing organisms with specific detection or factory functions may soon be an automatic process.
All this serves us to develop nanorobots from biological systems. Where physics has, until now, failed, biology is fast taking the lead.
Copyright ¶
All original texts and images on this website are published under a Creative Commons Attribution-Noncommercial-Share Alike 3.0 license, if not noted otherwise. All source codes and source code fragments are licensed under the open source BSD License, if not noted otherwise.
Imprint ¶
- Service Providers
- Konrad Ludwig Moritz Rudolph
- Postal Address
- Finnländische Straße 10, 10439 Berlin
- Contact
- konrad_rudolph [at] madrat [dot] net
- Telephone
- +49 0 30 44 71 45 22