So You Want to Know More About Us?
Chin Hoon Lau
Introduction
Biocomputing, like any other science subject, can be approached from different angles. It can be an academic pursuit with technicalities aplenty where questions like "what do we need to consider when we compare a tumour-causing gene from a human with that from a chicken" or "how can we best compare several protein sequences together" are not out of place. That may sound too dry for some.
The premise of this section is that we can obtain a better understanding of biocomputing by looking at the people in this field. Are biocomputing scientists grave academics who are utilising the latest technological tools in researching obscure subjects or are they far from that?
It is always useful to understand what motivates someone doing biocomputing - the peculiar kind of work that requires a person to face the computer screen for the whole day either trying to make a DNA or protein string dance or to communicate to others the latest information vital for the continuing existence of mankind. How much of biocomputing can be found in their blood? Has biocomputing affected their life-style or has it become part of their lifestyle? What would you imagine a biocomputing scientist to be? Are they like the "Absent-minded Professor", or one of the smart-looking bunch taking care of the dinosour hatchery in the movie "Jurassic Park"? Or, do you prefer to take a more cautious approach and say "hey, careful of stereotyping, that is simply not scientific!". Whatever it may be, we'll leave it to you to draw the conclusions.
Three people working in different areas of biocomputing - namely David Steffen, Georg Fuellen and David Atherton - are here to share their stories. Of course, such a small number of profiles cannot fully represent the complex spectrum of human beings working in biocomputing. Nevertheless, through their brief job descriptions and personality sketches, we hope you can obtain some ideas about the nature of a biocomputing scientist. The data have been obtained through their replies to a questionnaire circulated through e-mail.
What motivates them to do biocomputing?
Professor David Steffen is the president of Biomedical Computing, Inc., a company providing powerful, easy-to-use computing solutions to the biomedical research and clinical communities. He teaches database theory and practice at Baylor College of Medicine and works on biomedical and clinical databases. He is the author of the Tumour Gene Database at Baylor. He wrote the Biocomputing Hypertext Coursebook chapter on Networking, and the Introduction.
David entered biocomputing through biology rather than computer science. As he puts it:
"The two major career directions I considered were law and science. The moral ambiguity of law (e.g. feeling obligated to defend a guilty client) were incompatible with my personality, so I chose science. Within science, the problems in biology, specifically biochemistry, more specifically within the newly-emerging field of molecular biology, seemed the most interesting. When I began in biology, computers were too difficult to use and expensive to be available to biologists. It was only years later that the field of biocomputing began." Click here to know more about David Steffen.
Georg Fuellen finds biocomputing an excellent intermediate research area on his way from computer science towards ageing research (and computational support for it). He is the Biocomputing Course co-ordinator and author for the course material on multiple sequence alignment. He is working towards a Ph.D. at the Research Group in Practical Computer Science, Department of Computer Science and Biotechnology, University of Bielefeld, Germany.
Besides biocomputing, being the co-ordinator for the BioComputing course for two years, he is the person to talk to should you need to know how to handle students' and instructors' grievances over the international cable, how to handle massive influx of e-mail, and how to be alive after having to take care of a bunch of biocomputing students at BioMOO at 3 o'clock in the morning.
Why does he do biocomputing?"Actually, I had a keen interest to study biology, but I never was a good lab-worker in school... So I did Computer Science, and hoped to find a way back to biology. In parallel to my studies in computing, I read Lubert Streyer's Biochemistry book, and for my master's thesis, I did some 'artificial evolution' on the computer: I bred good random number generators. (That's a pretty weird thing to do, huh ? :-) During my year at MIT, I followed up on this, looking at the computer-breeding of good nucleotide mutation schemes for drug design, and at the prediction of protein functionality. Then, my advisor didn't get tenure, and I went back to Germany, now researching (nucleotide) sequence similarity and phylogenetic trees, and, well, organizing courses on the Internet... I believe that dealing with technology in a responsible manner requires a lot of knowledge, for which the Internet is an ideal medium of dissemination, even to the poorest countries."
Click here to know more about Georg Fuellen.
Some people entered biocomputing through a journey that may sound very familiar (or nostalgic!). David Atherton is one of them. David is currently at the University of South Florida, USA. He is working in the Pathology Department, College of Medicine, in a laboratory at the Lee Moffitt Cancer Center. Technically, he is a biological scientist working on the genes involved in the female menstrual cycle and their effects on pregnancy. However, he spends most of his time on the computers in the laboratories, keeping them running smoothly. David administrates files for the electronic journal Frontiers in Bioscience , reformatting articles into HTML documents, and updating the main and mirror sites. He talks about his experience:
I never really decided (by all that the word implies), but rather I knew instinctively, or came to know, I had a tendency towards it. Unfortunately for me at the time, such methods of decision are fraught with danger......
In the UK (where I was born and raised), each person is allowed at age 14 to decide on which subject(s) of education they would like to pursue to acquire a qualification in, and the list of subject(s) are submitted to the school headmaster for approval.
English language and mathematics are compulsory, so I also opted to continue studies in physics, biology, chemistry and computer science, as well as english literature and art. Upon submission to the head, this list was rather quickly rejected and my parents called in for discussion. This may appear hard to believe nowadays, but it did happen, albeit back in 1981. It was said that I would be no good at chemistry, so should study German language instead, and (here's the kicker), computer science would be dead within five years , so I should study geography instead! At that age, one's parents tend to accept the headmaster's words rather than the pupil's, and so it was that I did Geography and German. I got ungraded (ie. I was REALLY bad) in the subjects.
Passing from school to college, I thus did not have enough qualifications to study subjects at advanced levels, so had to take one year to study some subject(s) at 'ordinary' level. I chose to beef up my qualifications in physics and maths (my weakest subjects - still can't do maths without a calculator, and even then, I'm dodgy at best), and finally get to do chemistry and computers - got high passes in both the latters, especially computers, as I had taught myself BASIC and Z80 machine code programming on what was then the state-of-the-art home PC, a Sinclair ZX81 - a 7"x3" soft touch keyboard, 1Kb on-board RAM, no harddisk, but a 256 baud I/O to standard cassette tape storage. It only had 4 chips in it, and the RAM was upgradeable to a whole 16K - Wooo!
Suffice it to say, I went on to do physics, chemistry and biology at advanced level, then a degree in Biochemistry, and a Masters in Molecular Genetics. It was about this time that I noticed a need to understand the internet as a whole in order to help in the study of genetics/biology - an opinion which effectively got me booted out of Oxford U. during my PhD. Strange that it is Oxford U that has hosted one of the VSNS MOO courses ;-)......"
Click here to hear more from David Atherton .
The author would like to thank Haw Hann Goh and Md Maruf Hasan for their assistance.