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Ask HN: Getting started in biology with a software background

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Re: Ask HN: Getting started in biology with a software background

#141

Post by tikej »

perl4ever wrote: post #131
tikej wrote: post #88

Earlier quoted context omitted.

So much this. I think the most difficult thing about transition from hard sciences such as cs/physics/math to wet science such as biology/sociology/psychology is to get used to the fact that sometimes things don't work and behave as expected and it takes enormous amount of work to get it right. Therefore you can't really go and design things form the first principles, since first principles are not really that well k…

"sometimes things don't work and behave as expected" I think it's a great misconception to think that people who work with computers work things out from first principles. Dealing with complex systems that they don't understand, and repeatedly plunging into new areas, is exactly why computer people think they can handle things like biology. It also seems illogical to say "nobody understands biology, therefore you can…

By that I mean that in biology things are quite... Undeterministic. Working with computer is (except some very rare cases) a work when non-deterministic behaviour is most likely a bug. It's more or less the same in other hard sciences.

In biology (and other non-hard sciences) the systems quite often behave in non-deterministic way. To be clear I don't claim that this non-deterministic behaviour is inherent to biological systems (although it is when we take the quantum limit), but rather that they are so complex that untangling this complexity to get nice casuality is virtually impossible. Add the complexity and lack of understanding _on top of that_.

> It also seems illogical to say "nobody understands biology, therefore you cannot hope to".

I didn't mean to imply that "nobody understands biology, therefore you cannot hope to". I rather meant to express that (at the current level of our species and tools we have) "biology cannot be understood the same way computers are". IMO of course. Therefore applying the same methodology that you apply to hard sciences (math, phys, cs [, chem?]) may not yield as good results and often doesn't.

> If nobody understands much, that makes it more likely an outsider can contribute.

I can agree that it's easier for outsider to contribute something to biology than physics, mathematics or CS. However, to contribute meaningfully good grasp of concepts and techniques is necessary. Contrarily to math, theoretical or CS in biology it has to be acquired at the front lines of the battles i.e. in the lab. I agree that bioinformatics has made huge leaps in the recent years, but AFAIK nearly all significant new contributions in biology come from the laboratory work not theoretical considerations.

Re: Ask HN: Getting started in biology with a software background

#142

Post by omar_a1 »

pochekailov wrote: post #137
omar_a1 wrote: post #135

Earlier quoted context omitted.

I was coming into this thread to recommend looking for entry level part time mcb/bio lab work precisely because of point #1. It's a wax on, wax off thing. The repetition gives you a chance to reflect on the rationale for your technique and bigger picture of what you're doing, in addition to getting hands-on experience in the field.

I think a part-time job would be an overkill I have trained many students to do biology, and I can teach anybody, without any education, to perform molecular biology experiments in 2 weeks. I 2 months, they are usually able to generate scientifically valid ideas for research (although, usually not the best ideas). Biology is extremely simple as a field, and a computer scientist will have no problem getting into the f…

I'd say there's no subtitute for hands on experience. In the same way people on here recommend writing your own project to learn a language over simply reading about it, actually doing lab work gives you an understanding that no biology textbook can provide.

I vehemently disagree with the claim that biology is a simple field, and I'm especially surprised to hear this from someone who did work in this field for 11 years. Anyone who has taken an intro biochem class would back me up on this: life is complicated!

Re: Ask HN: Getting started in biology with a software background

#143

Post by pochekailov »

omar_a1 wrote: post #142
pochekailov wrote: post #137

Earlier quoted context omitted.

I think a part-time job would be an overkill I have trained many students to do biology, and I can teach anybody, without any education, to perform molecular biology experiments in 2 weeks. I 2 months, they are usually able to generate scientifically valid ideas for research (although, usually not the best ideas). Biology is extremely simple as a field, and a computer scientist will have no problem getting into the f…

I'd say there's no subtitute for hands on experience. In the same way people on here recommend writing your own project to learn a language over simply reading about it, actually doing lab work gives you an understanding that no biology textbook can provide. I vehemently disagree with the claim that biology is a simple field, and I'm especially surprised to hear this from someone who did work in this field for 11 yea…

I completely agree about hands-on experience: yes, it is extremely useful to practically do a biology engineering project. What I claim, is that about 2 weeks to 2 months of that is enough.

Regarding your second paragraph: I was fortunate to work in 3 fields in my scientific career: organic chemistry, materials science/organic semiconductors and molecular (synthetic) biology. This gave me ability to compare. What I found out, is that biology has the most interesting problems nowadays, and biology day-to-day work is extremely, outrageously, ridiculously stupid. I can not even start describing how amazingly debilitating molecular biology methods are. Right now, in the middle of the night I am stuck in the lab doing a day-and-half long protocol, all consisting on steps like "put liquid in", "pipette liquid out", "incubate for 5 minutes" and "shake for half hour".

Now here I am, after 15 years of school, 5 years of PhD and 11 years after that, doing work which is less intellectual than flipping burgers in McDonalds.

Fortunately, the fact that biology is so simple, gives me hope that it can be automated fairly easily, which I am planning to concentrate on for the next 5 years.

Please don't mix the plain complexity of life, which appears like "too many things to memorize", and complexity of mathematics and computer science, which is "understanding deep layers of abstractions". While I haven't taken intro bio classes, I read books and tons of papers. They are just plainly simple, you don't need brain to read them, you only need to memorize.

Re: Ask HN: Getting started in biology with a software background

#144

Post by delinquentme »

jchallis wrote: post #105
delinquentme wrote: post #101

Earlier quoted context omitted.

contact info?

Email your CV and a paragraph on your interest to: hr at lucencedx.com Bonus points for citing our active jobs page: https://www.lucencedx.com/careers/

Generic HR inbox?

I don't think you're actually concerned about this.

Re: Ask HN: Getting started in biology with a software background

#145

Post by goatlover »

perl4ever wrote: post #133
goatlover wrote: post #89

Earlier quoted context omitted.

The point is that a computer system can be entirely understood from the chips on up. Sure, it gets complex with millions of LOC. But we humans designed computers and wrote the code. Biology is not like that, and there is lack of a completed understanding form the proteins on up. So you get the complexity amplified on all fronts.

What do you mean "can"? Nobody ever does, so I think it is valid to say that it "cannot". Otherwise, you could just as well say that a biological system can be understood from the atoms on up, since quantum theory provides a complete understanding. I think that you and a lot of people in this thread don't understand the impossibility of understanding millions of lines of code. Do you really think "computer geeks" jus…

> Do you really think "computer geeks" just hold them all in their heads, and then assume that since they can do that, it must not be difficult?

No, but I think a group of geeks could. However a group of biologists cannot explain a biological system in full. When I say a computer system can be understood in full, I mean that human knowledge encompasses the working and programming of the machine, not that one person could know every detail. This is not the case for biology, as there's plenty we don't know.

> Otherwise, you could just as well say that a biological system can be understood from the atoms on up, since quantum theory provides a complete understanding.

It really doesn't provide a complete understanding for biology anymore than it does for sociology. It's not possible for humans to reductively explain such fields in terms of physics. No one can even prove this is possible. But it's not a complete understanding for physics either, since there's Relativity and questions about quantum gravity and dark energy.

Re: Ask HN: Getting started in biology with a software background

#146

Post by kharak »

pochekailov wrote: post #143
omar_a1 wrote: post #142

Earlier quoted context omitted.

I'd say there's no subtitute for hands on experience. In the same way people on here recommend writing your own project to learn a language over simply reading about it, actually doing lab work gives you an understanding that no biology textbook can provide. I vehemently disagree with the claim that biology is a simple field, and I'm especially surprised to hear this from someone who did work in this field for 11 yea…

I completely agree about hands-on experience: yes, it is extremely useful to practically do a biology engineering project. What I claim, is that about 2 weeks to 2 months of that is enough. Regarding your second paragraph: I was fortunate to work in 3 fields in my scientific career: organic chemistry, materials science/organic semiconductors and molecular (synthetic) biology. This gave me ability to compare. What I f…

Good luck with the robot. I wonder, if the individual steps are really that simple, why hasn´t it already be automated already?

And if you don´t mind me asking, what´s the best way to start a little home experiment to see if one may actually be interested in biotech?

Re: Ask HN: Getting started in biology with a software background

#147

Post by teekert »

unearthed wrote: post #140
teekert wrote: post #126

Earlier quoted context omitted.

I work from home sometimes, and 1 of our team members is in the US (but still at the same company). We have no people completely isolated that never come into the office.

I know for programmers / coders its a weird question but what about part time?

Why is this a weird question? I work 90% (36 hours) many of my colleagues work 32. In the Netherlands (in my bubble) it seems almost standard for both parents to go to 32 (4x8) and both have one non-weekend day with the kid(s).

Re: Ask HN: Getting started in biology with a software background

#148

Post by pochekailov »

kharak wrote: post #146
pochekailov wrote: post #143

Earlier quoted context omitted.

I completely agree about hands-on experience: yes, it is extremely useful to practically do a biology engineering project. What I claim, is that about 2 weeks to 2 months of that is enough. Regarding your second paragraph: I was fortunate to work in 3 fields in my scientific career: organic chemistry, materials science/organic semiconductors and molecular (synthetic) biology. This gave me ability to compare. What I f…

Good luck with the robot. I wonder, if the individual steps are really that simple, why hasn´t it already be automated already? And if you don´t mind me asking, what´s the best way to start a little home experiment to see if one may actually be interested in biotech?

Thanks! The reason it was not automated yet, is that non-biologists (including CS engineers) don't know that individual steps are that simple; while biologists do not have experience in thinking in abstractions, and so they simply not seeing that they are doing effectively same operations, just with different reagents.

In general, biologists are very busy pipetting faster than their peers, so they can secure scarce professorship positions. They simply have no time taking step back and looking at more general picture.

People who have skills necessary to build a robot and understand biology, have opportunity to work for companies that pay salaries 5 times higher than academia pays, so they don't bother.

I would not recommend doing any home experiments, especially without professional laboratory experience. Most of the experiments contain dangerous, poisonous or potentially explosive chemicals, and as for a newcomer, the risk is too high.

Instead, I would recommend finding a local biotech interest group, join them and go from there. Alternatively, you can find a local biotech lab and volunteer to help a grad student or postdoc with their project. This is more common than anyone may think. This way, there are no obligations, and you can leave if you don't like it; at the same time, you will get exposure to the state of the art biology.

Again, don't be afraid that you will not be able to bring anything good; biology as a science is ridiculously simple, and if you already have CS or electrical engineering background, you will have no trouble catching up within a month or two (that is how long it takes to our grad students who come from non-biology background to start bringing in new valid scientific ideas).

Re: Ask HN: Getting started in biology with a software background

#149

Post by kharak »

pochekailov wrote: post #148
kharak wrote: post #146

Earlier quoted context omitted.

Good luck with the robot. I wonder, if the individual steps are really that simple, why hasn´t it already be automated already? And if you don´t mind me asking, what´s the best way to start a little home experiment to see if one may actually be interested in biotech?

Thanks! The reason it was not automated yet, is that non-biologists (including CS engineers) don't know that individual steps are that simple; while biologists do not have experience in thinking in abstractions, and so they simply not seeing that they are doing effectively same operations, just with different reagents. In general, biologists are very busy pipetting faster than their peers, so they can secure scarce p…

There are no wet lab communities out here (Switzerland), at least I couldn't find any. But asking a postdoc to help out for free sounds promising.

Btw, I work 50 hours a week plus travel, I don't think it's going to be that fast to get up to speed.

Cheers

Re: Ask HN: Getting started in biology with a software background

#150

Post by omar_a1 »

pochekailov wrote: post #143
omar_a1 wrote: post #142

Earlier quoted context omitted.

I'd say there's no subtitute for hands on experience. In the same way people on here recommend writing your own project to learn a language over simply reading about it, actually doing lab work gives you an understanding that no biology textbook can provide. I vehemently disagree with the claim that biology is a simple field, and I'm especially surprised to hear this from someone who did work in this field for 11 yea…

I completely agree about hands-on experience: yes, it is extremely useful to practically do a biology engineering project. What I claim, is that about 2 weeks to 2 months of that is enough. Regarding your second paragraph: I was fortunate to work in 3 fields in my scientific career: organic chemistry, materials science/organic semiconductors and molecular (synthetic) biology. This gave me ability to compare. What I f…

Genetics and evolutionary ecology falls into the category of "layers of abstraction." Mechanisms for up and down-regulation, self-catalysis, epigenetic.

You're convoluting the simplicity of each step of an experiment with the level of complexity of the field itself. Memorization is a crucial component, but if you believe that's all there then you are severely underestimating the study of life. It would be like claiming that since CS can be boiled down to 0's and 1's that it is therefore a simple field of study.

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