- "He agreed to having the Centre named after him when asked by John Sulston, the founding director, but warned, 'It had better be good.'"
- "My father was a committed Quaker and I was brought up as a Quaker, and for them truth is very important. I drifted away from those beliefs - one is obviously looking for truth but one needs some evidence for it. Even if I wanted to believe in God I would find it very difficult. I would need to see proof."
- 'He declined the offer of a knighthood as he did not wish to be addressed as "Sir"'
- "the most self-effacing person you could hope to meet"
I hope someone writes a good biography of him - I wonder if Andrew Hodges (who wrote 'Alan Turing: The Enigma') could be persuaded....
The early pioneers in genetics were all consummate hackers in the truest sense. For much of the work they were doing, the had very little information about the underlying processes to go on. The were, in effect, reverse engineering life.
It's also worth noting that Sanger's sequencing method, or variations on it, were still used decades later to produce the bulk of the human genome sequence. Only very recently have newer, faster, alternative methods been developed. Even so, Sanger sequencing is still used for smaller scale studies, and is simple enough that almost any modern biology lab can do it on their own (all you need is a thermocycler, some eppindorfs, a sequencing gel apparatus, some photographic film, and all the raw chemicals).
> The early pioneers in genetics were all consummate hackers in the truest sense. For much of the work they were doing, the had very little information about the underlying processes to go on.
Exactly! They only had the most basic tools (even primitive by today's standards!) at their disposal and were still able to discover the most profound and fascinating things about life at the molecular level. All that using only a few simple techniques and a pure deductive logic.
It never ceases to amaze me how much hacker spirit these people had.
When I first learned about molecular biology (late 80s, while in high school), I immediately shifted my interest from just computers to computers and biology. I specifically told people at the time: "studying molecular biology is like being put in front of the world's largest and most complicated computer and being told 'we have no manual, and do not know how it even works, could you figure out by playing with it?'
It took many years for me to reconcile my hacker approach to life with the reality of scientific funding and the rate of progress in human diseases.
My story is very similar. After high school I went to study computer science in college. Then, just before I got my bachelor's degree, I decided to apply to a programme in molecular biology instead of further pursuing master's degree in computer science.
Switching gears was the best decision of my life. I've never had so much fun as I had while attending the introductory lectures in cell or molecular biology. So many mind-blowing things I never would've imagine...
Now I'm hoping to get into a PhD programme in genetics. Can't wait to learn about other amazing stuff waiting out there. :)
I'm on the other side. I have a PhD in chemistry, can do molecular biology, biochemistry - the wet parts, and I am on my last breath with science. Since I can write computer software, (not too terribly disciplined, industrial-wise, at this point, but I can learn), if my attempt to launch a nonprofit research institute fails, I'm going to quit and go into the digital world.
Perhaps the grass is always greener, but I have strong words about what is wrong with science, and if you want to know, feel free to contact me.
Well, I have to admit that, after spending the last three years as a basically full-time intern in our lab, I have a bit of an idea how science is quite broken. I've witnessed some of its problems first hand.
But I still want to do this, nevertheless. The area that I'd like to focus on during my PhD (genomics/computational biology) is something I really believe I'll have fun doing. On the other hand, it should still allow me to use much of the stuff I'll learn there outside science (if it ever comes to this).
I'll definitely drop you a line later, I'd like to hear your thoughts about this.
although you're better off doing sanger by contract. Sanger sequencing costs about $3 a run for really reliable sequencing. Contemporary sanger will likely never be obsolete because for short runs ~1kb where you need to be ~100% sure there are no mistakes, the method is really unbeatable.
Seriously, though, my wife used to work with alternative RNA bases. Localizing them to specific sequences required the most massive sequencing gels I've seen (at least 1m tall), and every surface in the lab had to be continually rinsed with dilute acid. It turns out, human skin contains bucket-loads of non-specific RNAses. Not a problem for most people who work with DNA, but can absolutely ruin a week or more's worth of work if you're in an RNA lab.
The best way to think about life is: RNA is one true source of life activity. Everything else: DNA, proteins, carbohydrates and membranes are just things that RNA decorates itself with to minimize degradation by other RNAs, which are trying their best to cut your RNA into little pieces.
That's why you have to be so careful: life tries very hard to keep the wrong RNAs out.
You're taking my use of the term decorating too literally.
In the case of DNA I meant that RNA likely began to delegate the heredity function to DNA since it was much polymers were more stable at room temperature and it was less likely to form complex 3D structures.
For everyone reading this: if you are tired of making websites and iPhone apps for people to share their cat photos, and want to do something more consequential, consider going into computational genomics. Although Sanger sequencing was/still is used sometimes, the "next-gen" sequencing methods that have become centrally important over the last decade generate massive amounts of data that require a lot of computational analysis, something that most scientists in the field could use assistance with.
Those iPhone apps for cat picture sharing are valued at over a billion dollars by the marketplace, so it's kind of hard for developers to ignore. Truthfully, most of us in the field of biomedical informatics would have much more lucrative careers applying our scientific skills to figuring out how to get more people to click on advertisements.
It's unfortunate because as I see it, most scientific software is universally awful. It suffers from poor usability, poor maintainability, poor stability. Whole swaths of software are abandoned because they were someone's PhD thesis and that person has since moved on. Another commenter here is right: version control, bug tracking, testing, etc... are all luxuries that are seldom employed.
Shameless plug: If you're a hacker and interested in this stuff and want to help, we're always looking for contributors for our open source biomedical data discovery framework: http://harvest.research.chop.edu/ We're trying hard to not do all the things I listed above.
Harvest looks very interesting! I'm a computational biologist in the field working on a startup called SolveBio (https://www.solvebio.com/). We're working on making the worlds biomedical data easily accessible to programmers and scientists. You might find it interesting and useful, especially to plug into Harvest.
SolveBio is exactly what I've been looking for for some other work I've been doing. We're using Harvest to build a variant filtering and reporting tool for clinical applications. We want to integrate external resources but we don't want to have to waste time writing parsers and keeping up with that public data stuff. Drop me a note (email is in my profile) if you want to talk more.
That looks really cool. I'm working on tranSMART (
http://www.transmartfoundation.org/site/scientistsclinicians
) - a tool for connecting phenotypical and genetical data, perhaps it would make sense to integrate the two. Drop me a mail on j.hudecek at nki.nl. Oh and if you could find a spot for me in the private beta, that would be sweet.
It is kind of a sad commentary on the state of things when so many of the brightest and creative minds of a generation are squandering the most productive years of their life writing software to enhance marketing and targeted advertising. And that these are efforts valued on the order of hundreds of billions of dollars.
the false assumption is that all effort in the sciences is not similarly squandered. I assure you, most of it is. At least when you're making a better platform for cat pictures, you are presumably giving someone what they want and making their life marignally lighter. So much science is basically just politically connected higher ups getting money thrown at them for pursuits that if you stopped and thought about you would realize they were not.even.worth.it, or, being chased after by the wrong researcher. And in the process, the poor grad student (or postdoc) is having the best years of their life ground down. In 97% of cases, I'd say the cat pictures are of better social benefit.
I'm getting a lot of this feeling these days. This is an interesting post by the OP. I am going to investigate this more, it might up some avenues to explore further.
And yet, by doing so, large piles of rational cash can be allocated to scientific research. See, for example, Gates Foundation, Rockefellar Foundation, Calico, etc.
What we need are tools that have a lot of input from people actually doing the wet work. The basics of how to do assemblies are more or less worked out, what we need are tools that actually fit with our workflow, and don't require us to kitbash pieces from different packages and have to run perl scripts to interconvert file formats.
Exactly. Someone who is only considered mediocre in a software company will be seen as an amazing software engineer if they are working with scientists.
Many of these scientists are not using version control. They don't have proper websites for their software. The codebases are a mess, and the software is very buggy. This is all low-hanging fruit that most software developers will be able to fix (if the scientists whose code it is are amenable to those fixes - many times they are not).
Actually, these days, most scientists who are at the forefront of computational biology have mastered github. They use markdown for README files, and produce md5summed data sets and command lines so you can repro their work. From what I can tell, this started 3-5 years ago when the kids coming into grad school picked up what the open source hackers were doing.
To be clear: none of this is properly incentivized by the funders, so there's not much selection for this behavior.
Fileset checksumming addresses a different concern from the semantic content of the data. It's merely a way to ensure that two people send the exact same input files to a routine. It's a critical control.
It sounds as if http://www.software-carpentry.org might be something to join for most participants in this thread - a non-profit organization that runs bootcamps for scientists to learn proper coding, version control etc. I think they're always looking for more volunteers.
I don't count Linus Pauling in the same company as the other three.
While he was the 20th Century's premier chemist, by being both absolutely brilliant, and getting his Ph.D. at just the right time to be the first to apply the then new and not yet completed quantum mechanics to chemistry, his second was the notoriously political Peace Prize, and he got that for being a prominent politically correct scientist at the right time.
Given that you're a doctor, I think the odds are on the order of around 1/3000 of winning the Nobel for medicine. So maybe that statistic doesn't say much for two-time winners!
Many years after he'd left, I went to the same "high school" as Fred Sanger. Our biology/science building was named after him. He visited the school every so often and was a very modest and entertaining man. You can get a tiny sense of him from this short video:
https://www.bryanston.co.uk/podium/default.aspx?t=52562&a=47...
- "struggled with physics and mathematics" :-)
- "He agreed to having the Centre named after him when asked by John Sulston, the founding director, but warned, 'It had better be good.'"
- "My father was a committed Quaker and I was brought up as a Quaker, and for them truth is very important. I drifted away from those beliefs - one is obviously looking for truth but one needs some evidence for it. Even if I wanted to believe in God I would find it very difficult. I would need to see proof."
- 'He declined the offer of a knighthood as he did not wish to be addressed as "Sir"'
- "the most self-effacing person you could hope to meet"
I hope someone writes a good biography of him - I wonder if Andrew Hodges (who wrote 'Alan Turing: The Enigma') could be persuaded....
http://en.wikipedia.org/wiki/Frederick_Sanger