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Why I do it: Bioinformatics for Quixotics

I'm still mulling the narrow road between the cities of words and numbers, as it were.1 Around about 03:00 earlier this week, dragnflye and I were discussing Asimov's View From A Height, wherein he recaps the journey that took him from a career in biochemistry into writing.

dragnflye, siocled and I discussed neurologist Oliver Sacks' Uncle Tungsten: Memories of A Chemical Boyhood2, wherein Sacks talks about his love of chemistry from its first beginnings: juvenile adventures in experimental chemistry, some astoundingly dangerous and lucky. Dijkstra might have scoffed a little at kids learning to program that way, but I'm not so sure that any of us didn't. Certainly we've all been covered in the soot of core dumps before (well, I have, at least).
His sociable father loved house calls and "was drawn to medicine because its practice was central in human society," while his shy mother "had an intense feeling for structure ... for her [medicine] was part of natural history and biology." For young Oliver, unhappy at the brutal boarding school he was sent to during the war, and afraid that he would become mentally ill like his older brother, chemistry was a refuge in an uncertain world.

I wonder if there's an affinity for chemistry that comes from that stability, that structure. dragnflye mused that she might have been drawn into chemistry for that reason. I recalled that my father is a physical chemist: first trained as a chemical engineer, later put to work as a process engineer after his Ph.D., but his love was always physical and analytical chemistry.

The upshot of all this, was that dragnflye asked me why I'm in "this" line of work - this being computer science with applications to the computational life sciences. Upon introspection, I find that to this day I'm still rather idealistic about high-impact science. For instance, I'm attracted to the mass impact of computational genomics on:

  • human medicine: pharmaceuticals and other therapies for

    • cancer

    • heart diseases

    • the rallying points of medical research fundraisers: cystic fibrosis, multiple sclerosis, muscular dystrophy

    • mental illnesses



  • crop science: food production, e.g., efficency enhancement for major cereal staples

  • environmental and ecological science: sustainable agriculture, water use


Put most simply, it's kind of a "solve the world's problems" kind of topic. Diseases, hunger, depletion (being staved off, if not "cured"). Singularity notwithstanding, I think the natural conclusion to the population growth dilemma of Malthus does tend to be a catastrophe-punctuated series of shifts: diasporas, sea changes in the means of supporting greater populations, or both. (You were wondering where I was going with that diaspora meme?) The problem is, eventually we will run out of sea changes and diasporas. In Cities in Flight, James Blish had the universe conveniently end c. 4000 A.D., long before this issue came to a head. OTOH, he did face up to the issue of the accelerated entropic death of the universe cf. Asimov's "The Last Question", which I suppose could be considered a trump over Malthusian limitations.

So, is it all worth while? Futile? Irrelevant? A secret plot to start the Eugenics Wars?
The lines are open, and operators are standing by.

On a related note: othercriteria, how did you get in this line of work?

1 Edit, 02:45 CDT Mon 27 Sep 2004: zaimoni and sui_degeneris inform me that these are Dictionopolis and Digitopolis of Norton Juster's The Phantom Tollbooth (1960).
2 Edit, 12:45 CDT Mon 27 Sep 2004: A friend and former colleague of my dad's who retired around the time he did has made a habit of sending him books at Christmas. This was one of them, Feynman's Six Easy Pieces: Essentials of Physics another.

--
Banazir

Comments

( 22 comments — Leave a comment )
hempknight
Sep. 27th, 2004 05:18 am (UTC)
A secret plot to start the Eugenics Wars?

Khan? Khan? Khan.

KHAAAAAAAAAAAAAAAAAAAAN!

--
Danger is my middle name
banazir
Sep. 27th, 2004 09:16 am (UTC)
Buried aliiiiiiiiiiiiive...
I do wish to go on hurting you, you know.
In a non-kinky, non-sexual kind of way.

--
Banazir
hempknight
Sep. 27th, 2004 10:29 am (UTC)
Re: Buried aliiiiiiiiiiiiive...
In a non-kinky, non-sexual kind of way.

Oh, you big tease, you. I like you too.

btw, please reply to my e-mail, post haste.

--
Danger is my middle name
banazir
Sep. 27th, 2004 10:44 am (UTC)
:blink:
Oh, you big tease, you. I like you too.
Now, see, that's the way it should work, but now I'm going to tell you that I'm secretly married to a woondchuck. Now how do you feel?

btw, please reply to my e-mail, post haste.
If you sent it to bhsu@cis.ksu.edu, I didn't get it yet. My file server has been upgraded, and wouldn't you know it, IMAP isn't up yet.

--
Banazir
hempknight
Sep. 27th, 2004 03:29 pm (UTC)
Re: :blink:
I'm secretly married to a woondchuck. Now how do you feel?

huhuhuhuhuh...you said...wood!

If you sent it to bhsu@cis.ksu.edu, I didn't get it yet. My file server has been upgraded, and wouldn't you know it, IMAP isn't up yet.

Force of habit (hitting 'reply') did make me send it to bhsu@cis.ksu.edu. However, it was sent to the e-mail of your evil twin as well just a few moments after that.

--
Danger is my middle name
banazir
Sep. 27th, 2004 10:35 pm (UTC)
Got it
huhuhuhuhuh...you said...wood!
If you talk about how fire is goond now, I shall hafta send the FD your way to give you a... fire safety lesson.

Force of habit (hitting 'reply') did make me send it to bhsu@cis.ksu.edu. However, it was sent to the e-mail of your evil twin as well just a few moments after that.
Mail to my CIS address is down ATM due to a server upgrade. The evil twin address (we're knot rilly twins) is flagging your e-maul as spam and toasting it into the Bulk Mail folder.

Anyway, I got it.

--
Banazir
myng_rabbyt
Sep. 27th, 2004 06:55 am (UTC)
I honestly don't think it's futile. It's an uphill battle, to be sure, but that doesn't mean it's no worth it. To me, that spirit of desire to help--"solve the world's problems"--is kept alive and continuing, which hopefully will lead to more people truly subscribing to it and believing in it and ideally getting more done.

On another related note: Oliver Sachs is a brilliant, brilliant man. The Man Who Mistook His Wife for a Deer was a heart-wrenching but fascinating and enlivening read. I'd like to read more of his work. Must keep Uncle Tungsten in mind.
banazir
Sep. 27th, 2004 10:17 pm (UTC)
Thanks for the rec
I honestly don't think it's futile. It's an uphill battle, to be sure, but that doesn't mean it's [not] worth it.
Hi, Myng. I definitely agree.

To me, that spirit of desire to help--"solve the world's problems"--is kept alive and continuing, which hopefully will lead to more people truly subscribing to it and believing in it and ideally getting more done.
Well, my point was that like the Categorical Imperative, the Golden Rule (Jesuitical ideal), and Golden Mean, it might be an ideal to strive toward - one not achievable within finite temporal existence, but still worth seeking. Or it might be a moving target, like macroevolution: a process of adaptation to the environment, or more generally the conditions of the universe. I don't think we know yet, either.

On another related note: Oliver Sachs is a brilliant, brilliant man. The Man Who Mistook His Wife for a Deer was a heart-wrenching but fascinating and enlivening read. I'd like to read more of his work. Must keep Uncle Tungsten in mind.
:nod: I think the former was "Hat", but thanks for the recommendation.

--
Banazir
myng_rabbyt
Sep. 28th, 2004 06:55 am (UTC)
Re: Thanks for the rec
Well, my point was that like the Categorical Imperative, the Golden Rule (Jesuitical ideal), and Golden Mean, it might be an ideal to strive toward - one not achievable within finite temporal existence, but still worth seeking. Or it might be a moving target, like macroevolution: a process of adaptation to the environment, or more generally the conditions of the universe. I don't think we know yet, either.

I'd rather think of it as an ideal to strive toward. Much like many religions--our innate humanity, I think, keeps us from truly attaining those spiritual ideas we aspire to. But that shouldn't keep us from aspiring to them.

:nod: I think the former was "Hat", but thanks for the recommendation.
Yep, you're right. I was thinking of an article I read about sleep disorders that was titled "The Man Who Mistook His Wife for a Deer"--a good read as well--but the Sachs book was great, too. I want to read his book on migraines, but I haven't gotten around to it yet (just started Austen's Persuasion and re-reading Sense and Sensibility). I'd also like to read The Man Who Tasted Shapes by Richard Cytowic. I started it, but didn't get to finish it.
yahvah
Sep. 27th, 2004 08:44 am (UTC)
For humanity who will derive benefits from your work, it's worth it, but is it worth it to you?
banazir
Sep. 27th, 2004 10:39 am (UTC)
Altruism: Yea or Nay?
So, you who like to mull over deep philosophical and theosophical questions: is there such a thing as pure altruism? Regardless, can one have altruistic reasons for pursuing science?

In the large picture I would say that if it's worth while for humanity, and within my very limited abilities, it should generally be worth while for me. Within practical considerations - e.g., I should like to have a roof over my head (well, unless I'm camping).

--
Banazir
myng_rabbyt
Sep. 27th, 2004 11:10 am (UTC)
Re: Altruism: Yea or Nay?
In another post in another entry somewhere in this wide, wide blog, I remarked that I took an Ayn Randian view on altruism, and I still do: while altruism has its place, it cannot and should not be the motive or the philosophy that drives all things.

Is there a such thing as pure altruism? I honestly don't know. I would hope that at the heart of every human being is a selflessness that would inspire the person to do something for the good of humanity, without thought for the sweat, blood, and tears, or the adulation that could result from their work, or the criticism or rejection that cold occur.

I have faith still in the goodness of humankind, but I am not so naive that I forget about the whim of human nature.
yahvah
Sep. 27th, 2004 11:37 am (UTC)
Re: Altruism: Yea or Nay?
I consider Jesus, Mother Theresa and Ghandi to be examples of individuals whose motivations were purely altruistic. I do so from my own perspective, of course.

And yes, you can have altruistic reasons for pursuing science, too. Why not? There may be nay-sayers, but when it comes to a person's motivations, the only way to know for sure is to learn from the person or be omniscient.
banazir
Sep. 27th, 2004 10:10 pm (UTC)
Re: Altruism: Yea or Nay?
I consider Jesus, Mother Theresa and Ghandi to be examples of individuals whose motivations were purely altruistic. I do so from my own perspective, of course.
I would generally agree. Can you give an example of a researcher, a scientist (classical or modern)? From what you know of Hippocrates or Mencius, how altruistic would you say their creeds were?

And yes, you can have altruistic reasons for pursuing science, too. Why not? There may be nay-sayers, but when it comes to a person's motivations, the only way to know for sure is to learn from the person or be omniscient.
Well, coming to the "learn from": Confucius and Mencius had followers who spent their lives studying their teachings and writings, making commentary, and promulgating their philosophies. I would guess that nearly as much has been written about Confucianism as a humanistic religion as about many theistic religions.

--
Banazir
yahvah
Sep. 27th, 2004 10:17 pm (UTC)
Re: Altruism: Yea or Nay?
Can you give an example of a researcher, a scientist (classical or modern)?

Curie? I was thinking of Hubble earlier today. Hubble never won a Nobel prize, but his contributions to astronomy were (ahem) certainly not less than astronomical, eh? ;-) If it weren't for Hubble's work, I bet there might very well be a lot less theists in the world. But since I don't know the man, I can't say he did his work for purely altruistic reasons.

From what you know of Hippocrates or Mencius, how altruistic would you say their creeds were?

Since I know nothing of them, I would say I have no clue. ;-) How about yourself?
myng_rabbyt
Sep. 28th, 2004 06:57 am (UTC)
Re: Altruism: Yea or Nay?
I consider Jesus, Mother Theresa and Ghandi to be examples of individuals whose motivations were purely altruistic. I do so from my own perspective, of course.
I agree with you. But I would say that they are shining exceptions, and by no means examples of one's average person (which is sad). But I believe the average person can do things with purely altruistic reasons. That's what gives me hope.
andrewwyld
Sep. 28th, 2004 05:28 pm (UTC)
Re: Altruism: Yea or Nay?
I am not sure I agree.  All of these people are justly deserving of our highest admiration.  However, I think it is Precisely that admiration which made them so effective.  They didn't just do important things -- they inspired those they met to do so, too.  It was this quality of calling to the altruism in ordinary people which made all they did possible -- and if ordinary people didn't have any altruism (even latent), they couldn't have made any.

As Raymond Smullyan said, for whose benefit should a completely selfish person cease to be completely selfish?

I also think that any of those people would have told you that being a focus for altruism isn't as difficult as it looks, although they might have been wrong in this.

I want to watch Gandhi again, now.  I'm filling up.
andrewwyld
Sep. 28th, 2004 05:21 pm (UTC)
Re: Altruism: Yea or Nay?
What does it look like?

If it looks like something logically impossible, then there isn't any.

If not, then there is.

(So, for example, someone who denies all their own impulses to serve others cannot exist, because no impulse would then be telling them to serve others.  But someone who love to do things which other people genuinely need, even at zero or negative benefit to themselves, undoubtedly do exist.)
digby_tantrum
Sep. 28th, 2004 05:10 am (UTC)
Prossessing stochaistically.
human medicine: pharmaceuticals and other therapies for cancer

Are you familiar with this man?

http://www.maths.dundee.ac.uk/~chaplain/

I'm trying to remember whether to call you Bill or Banazir. It's the former, isn't it? In which case: Mark.

Although it'd probably be better if I called you Dr Hsu, wouldn't it?
andrewwyld
Sep. 28th, 2004 05:17 pm (UTC)
Looking at this from a negative image viewpoint, I remember having a discussion with a friend in which he argued that, since all events, including any in the human brain, are governed by physical laws, we shouldn't be held morally responsible for our actions.

I ought to have replied:

Shouldn't?

Glancing over the automatic reverse hypocrisy of anyone who spends time and effort arguing that you shouldn't do so for anyone else, it seems to me that, yes, ultimately we're all doomed to extinction.  Therefore any good done for society will ultimaterly perish with the universe (or, likely, sooner).

However, I will also die.  Anyone I ever love will die.  Anyone they love will die.  Whether or not you believe in an afterlife (or time-independent equivalent), our years on this globe are numbered.  I don't, however, believe that I might as well fart around for the whole time and not bother to do anything.  Doing things is fun.  Applying this conclusion to humanity as a whole, we can argue that, just as we try and stay fit in order to do more things, we may as well try and make mankind fit in order to help us all do things.

If nothing else, I think doing good makes us better people (C S Lewis's conclusion, actually), and being better people is as good an objective for a life well-lived as any, and probably better than most.
myng_rabbyt
Sep. 29th, 2004 07:22 am (UTC)
However, I will also die. Anyone I ever love will die. Anyone they love will die. Whether or not you believe in an afterlife (or time-independent equivalent), our years on this globe are numbered. I don't, however, believe that I might as well fart around for the whole time and not bother to do anything. Doing things is fun. Applying this conclusion to humanity as a whole, we can argue that, just as we try and stay fit in order to do more things, we may as well try and make mankind fit in order to help us all do things.
I couldn't agree with you more. And by making "mankind fit in order to help us all do things" we also enrich our own experience, which allows us to continue to do things. In a non-selfish way, by helping others, we do help ourselves, in practical ways. And then there is that philosophical way--"doing good things makes us better people." Not better in a superior way to others, but by improving the persons we are.
andrewwyld
Sep. 28th, 2004 05:40 pm (UTC)
The Scientist
I'm not sure how science fulfils the idea of being a truly great person.

I think a lot of scientists want to make human life better, in practical or philosophical terms.  Science is also frequently a holdout of progressive thinkers who nevertheless don't hold to the postmodernist dogma of total subjectivity -- some things may be objectively better, and these should be promoted (I think tolerance is objectively better, for example, and probably so do most postmodernists, even if they don't say so).

However, to take the obvious example, Gandhi was a lawyer, but he didn't make the world better by being a lawyer.  Being a lawyer was a tool to him.  I think a scientist could use science as a tool in making the world better, and could even give people tools to improve their lives, hygiene, whatever.  But, ultimately, I think the only way to make the world better is to go out and do it, using whatever you have.  If science is what you have, then go to it.
( 22 comments — Leave a comment )

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