Forum: Evolution, not Hadoop, is the Biggest Missing Block in Bioinformatics
gravatar for ugly.betty77
3.3 years ago by
United States
ugly.betty771.0k wrote:

Over the last ten years, I played with Hadoop, GPU, FPGA and every kind of computing device to do bioinformatics. I also tried to answer biological questions using those computational tools. In my opinion, the biggest bottleneck of biology/bioinformatics is not larger and more efficient computer programs, but bioinformaticians trying to answer biological questions. Two biggest hurdles -

(i) bioinformaticians focus too much on the genome/transcriptome, which are only the informational blocks of the organisms and not the mechanical components.

(ii) Even those, who look into mechanical components, do not understand evolution and do not take evolution into account. That does not mean bioinformaticians are not developing tools to align sequences from multiple genomes, but that is very narrow perspective of evolution. The question of which sequences to align itself requires knowledge of underlying biological system, whereas those trying to develop tools seem to have the impression that they can build generic all-purpose tools. This is almost analogous to being a generic 'cook' or starting a generic restaurant to sell 'food' and not specific type of food.

I wrote a blog post on evolution vs mechanistic perspective of living organisms vs even narrower genome-focused view. Please feel free to criticize -

evolution forum hadoop • 1.4k views
ADD COMMENTlink modified 3.3 years ago by Siva1.5k • written 3.3 years ago by ugly.betty771.0k

Stated differently, one might say that a strong appreciation for the underlying contingency and messiness of biological processes is a missing block in bioinformatics (i.e., don't forget the "bio" in bioinformatics). It's understanding that that allows one to step back to a broader evolutionary scale view and make interesting insights. At the end of the day, this is a tough thing to train and I suspect most groups will find it most beneficial to just have members with a broad array of backgrounds.

Anyway, I think this is more helpful in the long term than the "hadoop rulz!" sorts of discussions.

ADD REPLYlink written 3.3 years ago by Devon Ryan77k

Not just messiness, but the understanding of evolutionary continuity seems to be missing from many discussions. For example, a few weeks back I was talking to a computational researcher working on human and mouse brains, and I mentioned my interest in electric fish. The other person seemed oblivious to the fact that research in fish could have any relevance to what he is doing. On the other hand, a physicist of old school thinking would first identify the fundamental question being asked (e.g. interest in figuring out how mammalian brain works), then find the simplest organism, where the same problem is present and proceed up from there. The trick to turn other metals into gold did not come from studying gold endlessly, but by studying hydrogen atom, building up the periodic table and checking where gold is. In biology, evolutionary connections play the role of periodic table.

ADD REPLYlink written 3.3 years ago by ugly.betty771.0k

I guess the person wasn't a neuroscientist :) Electric fish (and squid, for that matter) play a rather important roll in the early understanding of ion channel biophysics. Anyway, try not to judge too harshly. It's easy to miss the forest for the trees, as the saying goes.

ADD REPLYlink written 3.3 years ago by Devon Ryan77k

Interesting topic. The link seems to be dead. Could you fix it? Thanks.

ADD REPLYlink written 3.3 years ago by Siva1.5k

The link works, though I recall having issues reaching the website a couple days ago (perhaps they exceeded their data plan). Try it again and report back if you have problems.

ADD REPLYlink written 3.3 years ago by Devon Ryan77k

Our previous hosting place went bonkers and we switched yesterday to a new company. The link should work and please let me know, if you see any problem.

ADD REPLYlink written 3.3 years ago by ugly.betty771.0k

Strange. The link still does not work for me in Safari (Version 8.0) and Firefox (Version 33.1.1) on Mac OS X Yosemite. It does go the site and says

Not Found

Sorry, but you are looking for something that isn't here.

However it does work in Chrome (Version 38).

ADD REPLYlink written 3.3 years ago by Siva1.5k

Works for me on the same OS and Safari.

ADD REPLYlink written 3.3 years ago by Vivek2.1k
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