8 ms·

I don't disagree completely with this, but just want to point out that it's kind of a bad smell to have computational biologists who are - as someone in the art

• kang 6y ago
  https://news.ycombinator.com/item?id=24070913 https://news.ycombinator.com/item?id=24070913
• acidburnNSA 6y ago
  I have a strong feeling that, if people really put an effort into reading and replicating more papers, we would find that a lot of what's being published is simply meaningless. In grad school I had a subletting roommate for a while who was writing code to match some experimental data with a model. He showed me his model. It was quite literally making random combinations of various trigonometric functions, absolute value, logarithms, polynomials, exponents, etc. into equations that were like a whole page long and just wiggling them around. He was convinced that he was on a path to a revolution in understanding the functional form of his (biological) data, and I believe his research PI was onboard. I guess "overfitted" never made it into the curriculum.
  • gameswithgo 6y ago
    isn’t the saying, 80% of everything is garbage?
    • bryanrasmussen 6y ago
      Sturgeon's Law https://en.wikipedia.org/wiki/Sturgeon%27s_law https://en.wikipedia.org/wiki/Sturgeon%27s_law "ninety percent of everything is crap."
    • cproctor 6y ago
      We better work on making more stuff.
      • omgwtfbyobbq 6y ago
        Better stuff?
        • oneplane 6y ago
          If you have more stuff, and 10% is good, than that stuff can be more of the better.
    • goatlover 6y ago
      Yeah, but one would hope that science has a higher standard. 80% garbage results in science sounds catastrophic to our understanding of the world, and in particular when it comes to making policies based on that science.
      • behringer 6y ago
        You do realize we've been at this for a few thousand years, right? Catastrophic is putting it mildly.
      • adamsea 6y ago
        There's the saying "science advances one funeral at at time." '‘A new scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die, and a new generation grows up that is familiar with it.’ This principle was famously laid out by German theoretical physicist Max Planck in 1950 and it turns out that he was right, according to a new study.' https://www.chemistryworld.com/news/science-really-does-advance-one-funeral-at-a-time-study-suggests/3010961.article https://www.chemistryworld.com/news/science-really-does-adva... Also the story of Ignaz Semmelweis who discovered that if doctors washed their hands it reduced deaths during childbirth - but for a variety of reasons his findings were resisted. https://www.npr.org/sections/health-shots/2015/01/12/375663920/the-doctor-who-championed-hand-washing-and-saved-women-s-lives https://www.npr.org/sections/health-shots/2015/01/12/3756639... https://www.npr.org/sections/health-shots/2015/01/12/375663920/the-doctor-who-championed-hand-washing-and-saved-women-s-lives https://www.npr.org/sections/health-shots/2015/01/12/3756639... Point being, as awesome as science is, it's still a human enterprise, and humans are still, well, human.
      • barrenko 6y ago
        Unfortunately - like bs, power law is fractal.
  • fock 6y ago
    I work in computational materials science (where ML brings funding) and a funny paper of this kind is here: https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.114.105503 https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.11... - they are literally trying out 100000s of possible combinations by brute force, to build a "physical model". Then they go on conferences and brag about it, because they have to (otr they know it's bs). Datasets are soso (you can have a look at QM9...) and for more specialized things, people generally don't bother trying to benchmark or compare their results on a common reference. It's just something new... And with all that: even without doing fancy statistical methods without knowing too much about it, your theoretical computations might not make so much sense (at least in the sheer number which is pumped out and published)...
    • jordigh 6y ago
      > (otr they know it's bs). Well, that's a new acronym for me. I wonder where it came from. Apparently it's "on the real". Sounds like AAVE?
      • EsotericAlgo 6y ago
        I thought it was off the record like the old Pidgin plugin or https://en.wikipedia.org/wiki/Off-the-Record_Messaging https://en.wikipedia.org/wiki/Off-the-Record_Messaging.
      • ortusdux 6y ago
        typo for 'or'?
      • nhooyr 6y ago
        It means off the record.
      • fock 6y ago
        off-the-record (not written, not cited, but available in personal discussions).
        • 6y ago
  • throwaway_pdp09 6y ago
    Not my area at all but isn't this genetic algorithm type stuff?
  • zozbot234 6y ago
    > It was quite literally making random combinations of various trigonometric functions, absolute value, logarithms, polynomials, exponents, etc. into equations that were like a whole page long and just wiggling them around. Technically, we call that a "neural network". Or "AI".
    • aaaxyz 6y ago
      It reminds me more of a genetic algorithm
      • damagednoob 6y ago
        Everytime I think I'm getting somewhere with a GA I eventually realise I've just created a guided monte carlo simulation.
    • mjburgess 6y ago
      This answers the question "will we ever have AI as smart as a human?" Yes. It just turns out it's a particular human, whose analysis is very very dumb.
  • hannob 6y ago
    > I have a strong feeling that, if people really put an effort into reading and replicating more papers, we would find that a lot of what's being published is simply meaningless. People have figured that out long ago [1] (I know the author of that paper lately turned somewhat controversial, but that doesn't change his findings). It's not very widely known in the general public. But if you understand some basic issues like p-hacking and publication bias and combine that with the knowledge that most scientific fields don't do anything about these issues, there can hardly be any doubt that a lot of research is rubbish. [1] https://journals.plos.org/plosmedicine/article?id=10.1371/journal.pmed.0020124 https://journals.plos.org/plosmedicine/article?id=10.1371/jo...
• epistasis 6y ago
  It's not usually computational biologists who are using Excel. What if you want to share data with a wetlab biologist who want to explore their favorite list of genes on their own?
  • meow1032 6y ago
    There are lots of great computational biologists, but being a computational biologist doesn't necessitate being good with computers. Plenty of PI's rely pretty much exclusively on grad students and post-docs to run all their analyses. Not that I'm saying using excel is bad either. I use excel plenty to look at data. But scientists need to know how to use the tools that they have.
  • baddox 6y ago
    If people are just looking at the spreadsheets then wouldn’t the cells interpreted as dates not be a problem? It seems like it would only be a problem if you’re doing computation on the cells.
    • benhurmarcel 6y ago
      Excel changes the displayed text when it interprets the text as date. You store "MARCH1", it displays "1-Mar".
• gameswithgo 6y ago
  it would be nice if everyone was expert at everything, but they cant be. it would be nice if they hired experts but money doesn’t grow on trees. we often insist on a degree of excellence we refuse to pay for
  • meow1032 6y ago
    It's not about being an expert at everything or hiring more people. These aren't particularly hard problems, it's not difficult to find biologists who are incredibly adept at using python, R or C. It's about thinking about how science gets funded and how it gets implemented. I've written here before about the difference between "grant work" and "grunt work", and how too computer touching tends to get looked down upon at a certain level. If you're deciding who gets a large-scale computational biology grant, and you're choosing between a senior researcher with 5000 publications with a broad scope, and a more junior researcher with 500 publications and a more compuationally focused scope, most committees choose the senior researcher. However, the senior researcher might not know anything about computers, or they may have been trained in the 70's or 80's where the problems of computing were fundamentally different. So you get someone leading a multi-million dollar project who fundamentally knows nothing about the methods of that project. They don't know how to scope things, how to get past roadblocks, who to hire, etc.
    • kaesar14 6y ago
      What's your source on it not being difficult to find biologists who are adept at using python, R, or C? Most biologists operating in private industry or academia have many years of training in their fields and many have learned their computational tools as they've gone on, meaning they've never received proper training. It seems dubious to claim that there's this neverending source of well trained biologists who are also adept at programming.
      • shpongled 6y ago
        I would say the number of biologists who actually understand programming is extremely small. I've been programming for fun for ~15 years, and I'm about to finish a PhD in chemical biology (e.g. I started programming in C far before I started learning biology). You might occasionally run into someone who is passable - at best - with R or Python. But most of the code they might write is going to be extremely linear, and I doubt they understand software architecture or control flow at all. I don't know any biologists who program for fun like me (currently writing a compiler in Rust).
• dustingetz 6y ago
  you shouldn't. Your own industry is totally dysfunctional, scaled beyond reason, little accountability beyond profits, and morally bankrupt. Why shouldn't every other industry be too?
• Balgair 6y ago
  In grad school I had a friend that was doing olfactory (smell) research on rats with tetrode drives (wires in their brain). He was looking at the neuronal response to smells that they gave the rats and had a few signals to match up. There was the signal from the arduino running the scent gates, the amps that reported the weak neuronal currents, the nose lasers that gated the ardunio, etc. He was having a hard time getting through all the data in his MatLab code and I offered to help for some beer. After the 11th nested 'if' statement, I upped the request to a case of beer. I'm not certain he ever got the code working. To the larger point, scientists are not programmers. They got into their programs to do research. What keeps them going is not the joy of programming, but the thrill of discovery. Programming is nothing but a means to an end. One they will do the bare minimum to get working. Asking hyper stressed out grad students to also become expert coders isn't reasonable. And yes, that means that the code is suspect at best. If you load the code on to another computer, make sure you can defenestrate that computer with ease, do not use your home device.
  • whatisthiseven 6y ago
    I keep seeing this sentiment when it comes to those in the natural sciences, but it makes no sense. I could replace "programming" in your above little bit with "mathematics" and it would be just as weird. Our modern world runs on computers and programs, just as our modern world and modern science built itself on mathematics and required many to use it. So too the new world of science may require everyone to know to program just as they know about the chemical composition of smells, or the particulars of differential equations, etc. And I know your argument isn't "they shouldn't learn programming", but honestly since I keep seeing this same line of reasoning, I can't help but feel that is ultimately the real reasoning being espoused. Science is getting harder, and its requirements to competently "find the exciting things" raises the bar each time. I don't see this as a bad thing. To the contrary, it means we are getting to more and more interesting and in-depth discoveries that require more than one discipline and specialty, which ultimately means more cross-functional science that has larger and deeper impacts.
    • rorykoehler 6y ago
      Tbh I think its a case for multidisciplinary research. You wouldn’t only hire one skill set to run a company, even a tech one, so why should research be any different? That’s probably where the deep insights are.
• deleted 6y ago
  [deleted]
• t34saves 6y ago
  Considering how Perl was chosen as the computational biologists lingua franca in 1990's - 2k's since it was good at text manipulation (since genes are represented by text) I would say they don't have a history of making good choices.
  • s800 6y ago
    Why?
• dekhn 6y ago
  I'm an ex-computation biologist who did most of his work in python but periodically had to interop with excel. THe basic assumption I have is that when I input data into a system, it will not translate things, expecially according to ad-hoc rules from another domain, unless I explicitly ask it to do so. It's not clear what data input sanitization would mean in this case; date support like this in Excel is deeply embedded in the product and nobody reads the documentation of Excel to learn how it works.
• sincerely 6y ago
  Sorry for asking but are you familiar with how MS Excel aggressively converts data to dates? There's no way to "sanitize" it (without resorting to hacky solutions like including extra characters) and even if you fix the data, it will re-change them to dates the next time you open the file.
  • jaywalk 6y ago
    You're simply incorrect. If you set the column format to Text it will never convert data to dates, including when you open the file.
    • zozbot234 6y ago
      Great, how do you set a custom column format in a CSV file?
      • ryukafalz 6y ago
        I'm only familiar with LibreOffice and not Excel myself, but: if you want to be sure a column is treated as text in a CSV file, you have LO quote text fields on save, and have it treat quoted fields as text on import. I assume Excel must have similar options.
      • rini17 6y ago
        LibreOffice, on opening of CSV file, always pops an import dialog where you can do this. To keep the column format permanently, save as ods.
• jhbadger 6y ago
  For the most part we aren't talking about computational biologists but experimentalists using Excel. People at the bench need to collect their data somehow, and using Excel for tabular data and Word for text data is just what they know. Typically they then pass these files over to computational biologists for analysis. Yes, it would be nice if they would use more appropriate tools, but I know from experience that the typical result of trying to teach them better tools is the experimentalists just rolling their eyes and saying that they don't have time to learn some nerdy program because they have experiments to run.
• Myrmornis 6y ago
  It's also my experience of research in biological sciences that it is a widespread belief/fact that in order to get published in a top journal, the analysis methods must be "fancy", for example involving sophisticated statistical techniques. I worked on computational statistical methods so I'm not against that per se, but the problem is that if you have the training to contribute at the research front of an area of biology you rarely have the training to understand the statistics. Some would say that the collaborative publication model is the solution to that, but in many cases the end result isn't what one would hope for. I do think that less emphasis on "fancy" statistics, and more emphasis on simple data visualizations and common sense analyses would be a good thing.
  • FrojoS 6y ago
    Agreed. And to add to that: The more fancy the statistics have to be, the less robust are the results.
• fortran77 6y ago
  Excel is a wonderful tool and a type of programming that is very accessible to many people. I use it all the time.