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Why To Go Into Bioinformatics

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Mark Johnson

Posts: 15
Nickname: mj
Registered: Mar, 2003

Why To Go Into Bioinformatics (View in Weblogs)
Posted: Apr 17, 2003 2:23 PM
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Summary
Why be interested in bioinformatics as a career path?
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This post describes why I think bioinformatics is an interesting field to be in. I also go over why I think it's a good strategic career move. But I could be wrong! So please post a followup if anything I say here gets your attention.

Bioinformatics is not the easiest of computer-related careers. To do real bioinformatics work requires some understanding of biology. It also often requires a great deal of math. The math required differs depending on what area you're in (phylogenetics, 3-d modeling or visualization, sequence analysis, image processing, etc.) So you can't just pick up an O'Reilly book, install Linux, hack on the book for two weeks and then go out and pick up a job. It requires some understanding of the domain; that is, "domain knowledge".

I actually see the requirement of domain knowledge as a career benefit. Primarily, biology is the most interesting thing I can imagine to study. But strategically, I think scientific programming jobs will be more difficult to outsource than general-purpose programming work. Anybody can write a program that stuffs data in a database or presents query results. But not everybody has the knowledge of biology to support a research group in its computational needs. This means both a smaller potential job pool (bad), and a better fit to what jobs there are (good).

I think the days of the high-paid programmer are coming to an end. Bill Gates recently dumped $400M into India, investing in software and business development. The Bill and Melinda Gates Foundation has also invested millions to fight malaria, an endemic disease in India. The business investment move has been controversial, even in India. I think Gates know that there's a lot of good, cheap labor to be had in India. If I were a software engineer in Bangalore, I'd think it was great. But if I were a self-trained, garden-variety Perl hacker in Silicon Valley, I'd think otherwise. Indians are damn good programmers and engineers. The speak English, they compete very well technically, and they're much cheaper than Americans.

I've chosen bioinformatics primarily because I think the genomics and biology revolution is going to make the so-called "computer revolution" into an historical footnote. It's the renassiance science of our age, and I can't bear not to be involved. And programmers and science and technology writers (I'm both) need to communicate directly and regularly with scientists, and understand the research as it is happening. So I'm betting that I'll have more job stability in bioinformatics than I would have in a more general software development career.

If you have thoughts on this (especially if you think I'm wrong!) Please follow up and tell me why!


Adam Endicott

Posts: 2
Nickname: adame
Registered: Jan, 2003

Re: Why To Go Into Bioinformatics Posted: Apr 17, 2003 7:40 PM
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> ... I think the
> genomics and biology revolution is going to make the
> so-called "computer revolution" into an historical
> footnote.

This is the second time I've seen you make this statement in your weblog, and I'm sorry, but I think it's simply absurd.

I love biology as much as anyone, and I do a small bit about it (bachelors in Biochemistry and Cell Biology), but I just don't see what you're driving at with that assertion. I remember when I took my first upper division biology class (Structural Biochemistry) I was as excited about Biology as you seem to be, so I think I know a bit where you're coming from on the enthusiasm angle as well. Perhaps you're just over excited about entering a new field?

I just can't come up with any reason to reach the same conclusion as you do about the relative importance of your "genomics and biology revolution" and "computer revolution". I agree that modern biology research is making fantastic advances that are already improving the lives of billions of people. I agree that future advances may dwarf what we have already accomplished in the biological sciences, and that computers will make these future advances possible. I just don't have the slightest clue why you think this would make the "computer revolution" (as you call it) merely a historical footnote. Perhaps you don't have a full appreciation of how deeply computers have embeded themselves into our society, and into other areas of research besides biology.

If you're going to make these bold statements, I think you need to at least attempt to back them up. What future advances do you see coming out of biotechnology that will dwarf everything else computer technology has made possible?

Erick Herring

Posts: 1
Nickname: herring
Registered: Apr, 2003

Re: Why To Go Into Bioinformatics Posted: Apr 18, 2003 3:02 AM
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Adam: I think that you might be interested in reading Bruce Sterling's recent book, Tomorrow Now: Envisioning the Next Fifty Years (ASIN: 0679463224). It's not science, but it's good for some interesting perspective.

I don't want to speak for Mark, but I think that computers have, to date, only allowed us to do VERY QUICKLY what we can accurately and completely describe. Computers have not changed us as organisms. Even the hard-AI crowd has backed off of predicting the day "real soon now" when we'll achieve immortality by downloading ourselves into a computer.

We don't think much about steam engines or cotton gins anymore, even though both are absolutely essential to the functioning of our modern society. There was a time when everyone who owned a car knew how to work on it -- or had access to someone who knew how. To me, that sounds a lot like computers today. Now, though, only specialists work on cars while the rest of us just count on them to function. And if they don't, we take them to the shop and rent another until ours is fixed.

Once we can hack genes (or even better, proteins), hacking computers is going to seem a touch passe. Computers will be like air -- always there, always instantly available, and, of course, deadly when they malfunction -- which, also of course, they almost never will. What they certainly won't be, however, is the stuff of revolutions. That time will be past.

I think that was Mark's point.

Mark Johnson

Posts: 15
Nickname: mj
Registered: Mar, 2003

Re: Why To Go Into Bioinformatics Posted: Apr 18, 2003 2:11 PM
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Wow, Adam, thanks for a great response! It made me realize that I've been saying that without even saying what I meant by it. I'm glad to have this kind of feedback from a knowledgeable person, as well.

Unfortunately, I have a bit to do this afternoon, but I'll
try to take a few minutes later today to explain my
ideas. Maybe you can talk me out of them! :{)

Adam Endicott

Posts: 2
Nickname: adame
Registered: Jan, 2003

Re: Why To Go Into Bioinformatics Posted: Apr 21, 2003 6:38 PM
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Oh man, what a nightmare. I just finished typing out a (probably way too long) response to this, hit "preview", and of course my computer choose that moment to completely lock up. Right now I think I'd be fine if computers (this one in particular) just sailed off into the sunset :). I'll try to recreate the essence of what I said the first time.

Mark,

I'm looking forward to reading your explanations. I'm not trying to talk you out of anything, just saw the opportunity for an interesting discussion :).


Erick,

Before getting into your points, I wanted to say that to some extent I think we may just be arguing semantics here. My main problem was with the implication (and perhaps that implication is just in my mind) that future advances in biotechnology will be so great as to dwarf everything else that has been (or will be) achieved either directly by computer technology, or because of using computer tools. So I'm probably just reading the "the computer revolution will become a footnote" line more strongly than was intended.

And thanks for the book reference, I'll try to check it out.

...I think that computers have, to date, only allowed us to do VERY QUICKLY what we can accurately and completely describe.

I have a problem with that statement. Taken at face value, I guess I would agree with it in the very narrow sense that a computer will only work if you tell it exactly what to do. However, I see the implication (again with the caveat that I might be reading too much into it) that given enough time, we could have achieved everything we've done so far with computers without them. That implication I would strongly disagree with (even putting aside the (very real and important) fact that computers allow us to do things so much more quickly than "by hand" that almost every non-trivial application of computers would be literally impossible without them). There are several applications of computers where the real benefit comes from the emergent properties of the system. (I'm probably using the term "emergent properties" in a technically incorrect way here, but its a term I like, and I think it makes sense here). For example, the "accurate and complete description" of how the Internet works at its fundamental levels is relatively simple. However, when you wire the whole thing up, what emerges is nothing short of amazing. The modern Internet, especially the World Wide Web certainly goes far beyond the expectations of the people who originally put the thing into motion.

For most applications of computers I think the view of "The whole is greater than the sum of its parts" is much more useful than "you can only get out what you put in".

Computers have not changed us as organisms. Even the hard-AI crowd has backed off of predicting the day "real soon now" when we'll achieve immortality by downloading ourselves into a computer.

This is not at all the argument I was making. I haven't been convinced that such as thing is possible (though I am probably closer to believing it than the average person). And even if it were possible, I don't know that all that many people would jump at the chance. A book reference for you, Permutation City, I think the author is Greg Evans (?). It's science fiction, but it's thought provoking, and a fun read.

We don't think much about steam engines or cotton gins anymore, even though both are absolutely essential to the functioning of our modern society.

Very true. However, I would put computers more on the level of the Industrial Revolution than any specific invention such as the steam engine or cotton gin. Computer technology has much more fundamental and wide reaching applications than either of those inventions.

There was a time when everyone who owned a car knew how to work on it -- or had access to someone who knew how. To me, that sounds a lot like computers today. Now, though, only specialists work on cars while the rest of us just count on them to function. And if they don't, we take them to the shop and rent another until ours is fixed.

I also agree with this. Actually I would characterize the current situation with computers as much closer to the current situation with cars than you have. "Everyone" uses a computers on a daily basis, but practically nobody knows how they work. But does the fact that nobody knows how a car (or a computer) works make them any less important to our daily lives?

Computers will be like air -- always there, always instantly available, and, of course, deadly when they malfunction -- which, also of course, they almost never will. What they certainly won't be, however, is the stuff of revolutions. That time will be past.

Yes, the trend is certainly toward computers everywhere. The average computer user will become less and less aware of what the computer is doing, or even of the idea that there is something called a "computer" there doing anything at all. Again, we're already there in many respects. If you ask the average person what a computer is, they'll point to the box on their desk. They almost certainly won't point to their microwave, maybe not even their cell phone, some might not even recognize their PDA as a computer. But does the pervasiveness of computers to the point that we don't think about them make them less important? I would argue that it makes them vastly more important (and more usable, two aspects which are intertwined).

Once we can hack genes (or even better, proteins), hacking computers is going to seem a touch passe.

I'm not sure I see what you're driving at here. I'll go back to my argument that computers are so useful in so many areas of science and engineering that no single application (such as biotechnology) can be considered vastly more "important" than any other. The advances we have already made, and will make in the future are just as jaw dropping in any other area.

Also, the idea of "once we can hack genes"...what do you have in mind? Genetic manipulation has been a fact for centuries, breeding better crops, manipulating the genetics of animals such as horses and dogs through selective breeding. What is really changing aside from the methods used? We may be on the cusp of being able to do many of these things more directly, and possibly more efficiently, but how much benefit do we really expect to see? The natural processes of evolution are extremely powerful. We have harnessed them by using selective breeding of plants and animals in the past to great effect. Recent advances in genetically modified crops have been a great success, but is this leaps and bounds past what has already been done with just selective breeding? Perhaps, and if not, we'll probably get there in the near future.

But again, why should this relegate the "computer revolution" to the appendix of the history books?

Ian Bicking

Posts: 849
Nickname: ianb
Registered: Apr, 2003

Biology vs. Computers Posted: Apr 30, 2003 10:25 PM
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I think computers actually have more potential to change our lives. Computers are the stuff of societies -- tools of organization and communication. Biology is the stuff of life, but humans don't mess with life that much.

What has affected us most in the past? Certainly domestication of plants and animals has had a significant impact on humanity. It's hard really to judge, because so many things together have affected our history.

But even in the vague sense, I think the greatest, most exciting, most dangerous changes in our history have been social.

Certainly, biology could have great effects in the future, but computers seem like a safer bet to me. Even if computers don't do anything more than they do now, the effect on society is great. Biology has a lot of catching up to do ;)

Angsuman Chakraborty

Posts: 19796
Nickname: angsuman
Registered: Dec, 2003

Re: Why To Go Into Bioinformatics Posted: Jan 21, 2004 3:55 PM
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> Indians are damn good programmers and engineers. The speak English, they compete very well technically, and they're much cheaper than Americans.

Thanks. However I must point out that so are American's. I have worked with some damn good programmers in the valley.

I object to the last part personally. I don't provide services cheaply, rather we provide quality & expertise which others find hard to match. Interestingly we too are in bioinformatics and I agree with you that bioinformatics is a challenging field. Personally I find it very rewarding and fulfilling. As my ex-colleague used to say that we are not designing better file folders here. What moves me is when I see that my work is helping in its little way in the process of drug-discovery & searches for cure.

Outsourcing is inevitable in a global economy. Today american jobs are being outsourced. On the other hand we have coke, pepsi, pizza hut, kfc, burger king, macdonald's selling their products in India & elsewhere, thereby ruining several local industries. Either both has to continue or neither should. It cannot be a one way street.
There is a big discrepancy of salaries in usa & other countries like India for similar skill-set. The flow will continue till such point when the total cost of outsourcing is almost equal to insourcing.

What do you think?

Edward Guiness

Posts: 2
Nickname: edwardg
Registered: Jan, 2004

Re: Why To Go Into Bioinformatics Posted: Jan 28, 2004 8:53 AM
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Angsuman,

To say that outsourcing to poorer economies is justified on the basis that it is consistent with previous corporate exploitation is no justification at all. It may be that outsourcing is a natural outcome (of capitalism and globalisation) but this is not a justification in itself.

Since you run an outsourcing business, perhaps you have a view on the following: Do you think that workers in poorer countries should receive the same rights and privileges as workers in richer countries? I'm referring to holidays, pensions, insurance, legal protection, and unions.

Olivier Lefevre

Posts: 2
Nickname: xolotl
Registered: Sep, 2004

Re: Why To Go Into Bioinformatics Posted: Sep 29, 2004 4:21 PM
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I found this post by chance while looking for something
else. Although it is rather late to reply, I have to tell
you that if you expect to find in "bioinformatics" (an
almost meaningless denomination anyway) a haven against
the forces of creative destruction of early 21st century
capitalism, then you are very mistaken. See, e.g.,
http://www.genomicsociety.com/

Vasundhar Boddapati

Posts: 2
Nickname: igoogle
Registered: Apr, 2005

Re: Why To Go Into Bioinformatics Posted: Apr 3, 2005 9:19 AM
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I am rather scared ...

IT Boom ... as people called when people flew from developing countries to the developed ones.but things changed, rather things changed drastically,making it inevitable for those who saw it as a life making move .
Finally all of them returned to homes, few .. pennyless.

Computers, I am sure are among the top k lists of best innovations but I strongly believe, we some how are influenced by the feeling what ever is added to computer is facinating.

bioinformatics is one such field using heavy computing, Computing as a tool to make efficient decisions,

But the media and the Market (business men, profit making Educational institutions included) are trying to make it big to make money ...

which is not a good developement.

Finally what I request and mention is ... if you are not in bioinformatics there is no need really to be a part of that,
people are out there who forgot what they are doing is bioinformatics and happy in their work...

So please dont make bioinformatics another IT Industry ...
there is much more fun in this .... which I dont like to loose in charm

Kondwani Mkandawire

Posts: 530
Nickname: spike
Registered: Aug, 2004

Re: Why To Go Into Bioinformatics Posted: Sep 22, 2010 8:36 AM
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> Outsourcing is inevitable in a global economy. Today
> american jobs are being outsourced. On the other hand we
> have coke, pepsi, pizza hut, kfc, burger king, macdonald's
> selling their products in India & elsewhere, thereby
> ruining several local industries. Either both has to
> continue or neither should. It cannot be a one way
> street.

Excellent point. Though you'll struggle to get it across coz the richer/developed countries are probably under the impression that the world owes them. i.e. Rape the disadvantaged economies and when their general population tries to make a buck from the globalization factor lets bicker about it like a 2 year old - "MINE!"

suresh s

Posts: 1
Nickname: su6esh
Registered: Oct, 2010

Re: Why To Go Into Bioinformatics Posted: Oct 20, 2010 3:20 AM
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by analyzing the sequence we could know the possible of our target. it may be easily done by using software.so that we go into the bio informatics..

su6esh,

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