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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

#121

I have spent 11 years in molecular biology research. I must warn you about a survivorship bias. All the exciting news you are hearing are the tip of a giant iceberg that rests on the mounts of a most dull and repetitive labor. Here are some realities that nobody tells you: 1. There are only 3 operations done in experimental biology: liquid pipetting, opening/closing tubes and moving tubes between machines. 90% of pro…

Interesting. It seems automation would greatly speed up this field. I wonder if progress is being made on this front.

You are absolutely right.

After those 11 years in molecular biology, I am absolutely convinced that the bottleneck of the field is not some fancy method, but a total lack of automation.

Modern "CRISPR" cool methods are done with essentially the same tools as the research from 50 years ago.

I would claim, that computer scientists are lucky ones: they have skills to create their own tools. To make a better, more automated programming language, you would need same skills as to use that language.

Biologists on the other hands are different. The skills to do biology are totally different from skills needed to automate biology. And so the gap appears: biologists don't even think of automating, and mechanical/electrical/computer engineers are not even aware of the problem

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

#123

Does this seem really incongruous to anyone else? It's like a biologist hears something about Linux, and asks about how he can start writing kernel patches having never coded anything in his life. It seems like there's an underlying assumption that computer science >> all other sciences, as if the abstract logic of computer programming is a substitute for basic domain knowledge in other fields, often built over hundr…

You see this often when programmers comment on physics, neuroscience or even philosophy. Everything is understood in terms of computer science and the successes of the computer industry, because obviously reality is fundamentally what programmers spend most of their time on. Which is something Jaron Lanier pointed out a while back. Of course I only mean some programmers, and I'm sure mathematicians and physicists are…

I think also they see that the gap between bootcamp grads or smart college dropouts and a masters in CS is not necessarily that large, and assume the same is true for other fields when that is pretty rarely the case.

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

#124
post #44

Earlier quoted context omitted.

In biology, the problem space is extremely vast and very hard to understand. I have a PhD in biology and find computer science relatively logical and simple. You can just look things up. Looking things up for a specific topic is not even easy in biology.

> Looking things up for a specific topic is not even easy in biology How do you find info on bio topics right now?

Finding the actual info is not terribly difficult: Google Scholar and Pubmed, maybe with some of the arxivs.

The trick is interpreting it and putting it into context. A paper will report the results of one specific experiment, and it’s very rarely exactly what you want. Understanding how a result will generalize to other conditions is tricky, even for experts: there are tons of weird feedback loops, unusual dynamics, and other traps for the unwary (plus badly designed experiments and the occasional legit Type I error). For example, doubling the amount of a substance almost never doubles its effect, and in some cases, the effects aren’t even monotonic: ~75% alcohol, for example, is a much better disinfectant than 50 or 100%.

With time—-and lots of paper-reading, you do eventually develop a sense for what factors might matter and how you could check.

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

#125
post #25
post #15

Earlier quoted context omitted.

Yeah I'm not sure I agree you need a full-blown PhD just to understand this stuff. Some-hands on work, definitely. I would say that you need a PhD to be taken seriously as a leader on the science-side of a biotech company though.

You don't need a PhD to find market fits for these types of products. They are self aggrandizing.

Market fit isn’t the only thing that matters.

Theranos had an excellent market fit—-people hate having blood drawn—-but the technology did not work and fundamentally could not work. The whole point of being a subject matter expert is to learn about things like that.

It’s true that there are other routes to becoming an expert in something (and proving it). A masters and a stint at a well-known company certainly works for many people; bootstrapping your own company might be an option too, but you’d need to be very successful to establish your bonafides. The advantage of a PhD is that it’s a fairly well-known quantity.

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

#126
post #51

I'm a self-taught bio-informatician (working at large healthcare company, doing Next Generation Sequencing related things). although I am actively seeking to better myself, My code is horrible, we have one "library" (a file really) full of functions and since 2 months a couple of classes that I already feel like completely re-writing. A lot of code is in Jupyter Notebooks somewhere because we just got the hang of Git…

I love git. Literally the only way to be productive when you've got more than 4 people touching code. Do you guys allow remote work?

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.

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

#128
post #48

Earlier quoted context omitted.

RE: "Having a PhD means that you've spent years on a certain subject. You cannot just read a book and be up to speed on biomedical research and CRISPR." Isn't that what books are for? To compile, document and share knowledge some people spent years to figure out?

There is a huge gap between having knowledge from books and being able to do original research, let alone solving a biomedical niche problem using CRISPR. This gap is usually filled with an advanced degree, where you spend years in the lab, keep track of the latest research in the field, try to find your niche and solve the actual problem. I mean, by all means, try it. But life sciences are not computer science. The…

> But life sciences are not computer science

Exact

1) The use of materials is totally different

Computer programming is a stuf that uses reciclable electricity and "eating your own dog food" kind programs, cheap to produce or free to copy, easily available and in many cases free except by the hardware (Hardware that can be hired, "clouded" or increased gradually).

You don't need to pay a dime for using R, C, Perl or Python and you can obtain the four, ready to use in your computer in less than a half hour. If you need a microscope, there is not an equivalent open source stuff replacement available.

In Biology the matherials will be sold to you only in packages of 10 Kg each pigment, with a caducity date, even when you would need to mix just 10 grams of each one. The spendable one-use only stuff is not free and the price for a single kit is incredible. You will pay it in any case because is indispensable for validating your work and you plan to use 500 of those kits the next year so you are a captive client from this company (that could decide to stop selling you if you try a way to lower the price, and will sue you if you try to copy the formula and make the product by yourself).

2) Documentation is not free and obtaining it is time consuming

In computer programming, you dont need to spent weeks to be delivered to you, or plan a travel to Peru to collect samples of a plant virus. You don't need to spend days just to reach the documentation navigating a miriad of closed or pay per viewed journals, at 50 dollars to peek in each paper.

You can expect to learn something and use it for years. Fortran is still there. You can program automatically your computer to make a hundred of safety copies each working day. In biology you can not clone your amazonian beetles collection, is unique and will be atacked and reduced to dust by real bugs from day one if you do not protect it.

3) There is not an obvious, linear path to success

Errors are random events that you can't always control

In biology you will lose eight months of your research because your samples travelling from Swedden to Madrid end somehow stuck in a Lithuanian airport for ten days and now are defrozen and unusable. You needed this research to assure the new funds and keep running, and now you have three months to obtain new samples, redo and fix it.

You can lose years chasing a dead end or be superseeded by a genius in some part of the planet that discovered the same as you first, or a different and better way to do it.

4) You don't just buy a lab and hire a team to create "something" nice.

Unless you are in the bussiness of teaching science you design the lab according of the exact product what you are trying to create. Any machine that you ordered and will not use enough frequently later is a hole in your presupuest. Any timed out kitt that you bought in excess quantity is your money ending in the dumpster bin.

You need to hire somebody familiar with what "hardware" is trendy and works and what machines are outdated since ten years even if you see it in each faculty and in propaganda.

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

#129

I'm curious who all these sarcastic bio "experts" are that are suggesting getting a PhD or hiring one. I'm a former bio major and researcher/scientist that transitioned to software engineering years ago. I've published papers in bio and worked with many PhDs. Many of them were idiots. Being a PhD doesn't mean anything, it's the independent work that you put in yourself (in an academic lab or by yourself) that determi…

Thank your this. I am also very interested in biology and was looking to find a way to buy used equipment. I was reading biotech books and I was blown away by recombinant DNA and how insulin was invented as a medicine.

I was looking to find a way to buy used equipment

"I'm planning to participate in Olympic games against the best athletes of the planet. I plan to buy a few used sneakers of a similar size than my feet and a second hand tennis racket that is not too worned out. I plan to win against people with brand new and tailor-made equipment".

In short. Don't do it unless you know what you are buying. If you know what you are buying, don't do it if you can afford doing otherwise.

In most cases used equipment will be sold because either the lab had been crushed by better equipped competitors, or is obsolete.

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

#130

my background is in biotech and i've worked at a small handful of biotech startups in a scientific capacity. here's my advice: unless you have friends who can set you up with the right VCs and ensure that they will be willing to overlook your lack of experience and IP, don't bother. you're not going to get up to speed working in the lab on your own in any short amount of time. learning the theoretical stuff that you…

Why are Phds so cheap to hire if their skills are so valueable?

> Why are Phds so cheap to hire if their skills are so valuable?

Is a hamster wheel. Your skills are valuable only while you are running. If you stop, your huge time and money investment loses their value gradually, and if you stop for too much time (getting pregnant, suffering an accident or having small kids) you are out of the game. Thus, for many researchers cheap work is better than none.

And there are the stupid artificial constrains, a damocles sword in the shape of a clock. Scientist work is related with Universities schedule. They can expect to be hired mainly at the beginning of the year or in summer, hired for the next year. If you miss the train you will need to wait for another year.

Scientists are expected also by society to produce X discoveries at the interval of age Y and have a limited time for that. This is really idiot. Would be like expecting Leonardo painting the Monna lisa in three years maximum (and exactly between 27 and 29 yo), or stop painting.

And there is also a huge vanity factor. To be associated with an university or big brand even if you just make the coffee there, is good for the ego and help constructing your identity and selling you better later.

None of those have any relationship with what science really is, a method to solve problems, of course

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