{"id":49,"date":"2008-03-29T19:58:39","date_gmt":"2008-03-29T17:58:39","guid":{"rendered":"http:\/\/occamstypewriter.org\/boboh\/2008\/03\/29\/scientific_service_industries\/"},"modified":"2008-03-29T19:58:39","modified_gmt":"2008-03-29T17:58:39","slug":"scientific_service_industries","status":"publish","type":"post","link":"https:\/\/occamstypewriter.org\/boboh\/2008\/03\/29\/scientific_service_industries\/","title":{"rendered":"Scientific Service Industries"},"content":{"rendered":"

I was happily writing a reply to Jennifer’s neo-Ludditism<\/a>, and it was becoming a whinge about the awful things biologists do when they aren’t doing their work properly (i.e. the way statisticians work). Then I started writing it as a blog post. I’ve now decided me eulogising Notepad (it even includes Comic Sans MS!) is not what’s required. And anyway, something more interesting came up.<\/p>\n


\nThe discussion over there drifted into the problems of getting support from bioinformaticians. I’m almost a bioinformatician – I’m a biostatistician, which is a bioinformatician who doesn’t have stupid amounts of data. Many of the comments are familiar to me, looking over the fence from the other side (admiring their grass). I’ll make my comments in the context of statistics, but I think most of them will transfer fairly well to bioinformatics. But, as with anything, your mileage may vary.
\nThe frustration from the biologists’ side is nicely summed up by Richard Grant’s comment<\/a>, which is worth quoting in full:<\/p>\n

\nI’m carefully trying to avoid an \u2018us and them’ thing here. I’m not entirely successful, but please keep my intent in mind as you read this \ud83d\ude09\n<\/p><\/blockquote>\n

\nMy experience, having desperately wanted bioinformatical help, is that the bioinformaticians are too interested in proving the fossil record0, or something equally fatuous, to lend their skills to an interesting biological problem. Certain people from the group I’m thinking of have come all the way to Australia to give seminars, and people have walked away saying \u201cWhat was the point of that?\u201d\n<\/p><\/blockquote>\n

\nAnd before you bite me, Neil, that’s because what they were doing was biologically useless, not because we didn’t understand it.\n<\/p><\/blockquote>\n

\nI would love to have bioinformaticians on site, who wanted to collaborate. And I know such beasts exist \u2013 Neil himself has given me useful pointers (he’s 600 miles from me, so a more formal collaboration is not impossible, just more tiresome) and I appreciate that. But my experience is that Neil is unusual in this respect. (Having said that, my DPhil supervisor was a skilled BI and loves turning computers loose on interesting biology, too.)\n<\/p><\/blockquote>\n

\nNow I’m expecting that a lot of bioinformaticians will now crawl out of the silicon-work and say \u201cHey! I want to help you!\u201d and that’s brilliant, really. But many of us more \u2018wet’ biologists (including those of us who can hack a little bit of silico stuff) have been burned by uninterested comp biol people.\n<\/p><\/blockquote>\n

\n0 We know it’s true. What’s the point of saying this group of proteins is related to that group by this much, if there’s no functional information?\n<\/p><\/blockquote>\n

Richard’s view is one I come across a lot, and I think there are a few issues underlying it which are quite common.
\nThe first is an institutional problem. At the places I’ve worked, the quality of statistical support for biologists has been pretty bad. I did my PhD in a large plant biology institute, and when I arrived there as a callow youth with just a Bachelor’s degree, I was the only person there with any statistical qualifications. This is hardly unique.
\nThe unfortunate thing is that I chat to researchers and they say yes, they really need someone in their department to provide statistical support. But this message doesn’t filter up to the higher echelons. But hiring statisticians requires money and a commitment that can only really come from the top.
\nSome places do this better than others. For example, Scotland has BioSS<\/a>, who provide statistical support to the biology community there. But in other places there is nothing except people with a bit of knowledge providing the support on a voluntary basis. The problem with this sort of support is that the people giving the support don’t always have the training themselves, so they rely on their own training they received from biologists, which means you see all sorts of odd pieces of advice (in the UK, professional training is available from the RSS<\/a>, for those who want it).
\nRichard in his comment complains that when he has tried to get advice from bioinformaticians, they haven’t been interested, or they have been more interested in solving abtruse computational problems, rather than the biological problem that Richard is interested in. Again, I’ve seen this, and I have sympathy for both sides. The people he is going to for advice will not be paid to act as consultants (I hope not, anyway!), so for them the incentive comes from working on problems that are interesting to their field. Hence, they have rather different motivations. But this doesn’t help Richard – he might get his name on a paper, but doesn’t get his problem solved. How to get round this? Well, obviously if a collaboration were to continue successfully, both sides would need to find out how to make it work for both of them, and I will leave it to people wiser than me to suggest strategies.
\nThere are a couple of alternatives. One is that Richard has to find somebody else to work with. Finding someone within his university or institution can be difficult for the reasons I’ve outline above. Working with someone who isn’t in the same region is possible, but (as Richard acknowledges) is not the same. Sometimes you just need to sit down together with a cup of coffee and a large pile of paper or a whiteboard and explain things to each other, or thrash out how you are going to deal with a particular problem.
\nThe other alternative for someone having difficulties finding a good collaborator is that they educate themselves to do the work they need. Sometimes this can be done – the skills or knowledge may not be too difficult for a non-specialist to pick up. But it takes time, and wet-lab biologists are meant to be getting themselves wet in the lab. At some point there has to be a trade-off, when a biologists admits that they are a biologist, not a statistician or a computer scientist. A lot of the time they are also not going to understand the material as well as an expert could, and so are not going to do as good a job at solving their problems – a lot of time I’m asked questions that take me a couple of minutes to answer, but the questioner would only solve after a couple of day’s hard work.
\nSo, what is a poor biologist to do? You tell me!<\/p>\n","protected":false},"excerpt":{"rendered":"

I was happily writing a reply to Jennifer’s neo-Ludditism, and it was becoming a whinge about the awful things biologists do when they aren’t doing their work properly (i.e. the way statisticians work). Then I started writing it as a … Continue reading →<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[],"class_list":["post-49","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"_links":{"self":[{"href":"https:\/\/occamstypewriter.org\/boboh\/wp-json\/wp\/v2\/posts\/49","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/occamstypewriter.org\/boboh\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/occamstypewriter.org\/boboh\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/occamstypewriter.org\/boboh\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/occamstypewriter.org\/boboh\/wp-json\/wp\/v2\/comments?post=49"}],"version-history":[{"count":0,"href":"https:\/\/occamstypewriter.org\/boboh\/wp-json\/wp\/v2\/posts\/49\/revisions"}],"wp:attachment":[{"href":"https:\/\/occamstypewriter.org\/boboh\/wp-json\/wp\/v2\/media?parent=49"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/occamstypewriter.org\/boboh\/wp-json\/wp\/v2\/categories?post=49"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/occamstypewriter.org\/boboh\/wp-json\/wp\/v2\/tags?post=49"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}