The Roots of Bioinformatics in Theoretical Biology

By Grant Jacobs 01/04/2011 19


I have previously written about the origins of bioinformatics as a field, starting by reposting an article I wrote in 2002, The Mythology of Bioinformatics, and subsequently introducing the first and second articles in the Roots of Bioinformatics series published in PLoS Computational Biology.

A third article in the series,* The Roots of Bioinformatics in Theoretical Biology, is now available.

I’ve yet to find time to read this slowly–perhaps later this weekend!–but I’d like to invite readers to share their thoughts about Prof. Paulien Hogeweg’s thesis that ’the original meaning of the term is re-emerging’.

Paulien takes as a starting point what she and a colleague wanted to capture in their use of the term ‘bioinformatics’ that they coined in the early 1970s to describe their studies of ’informatic processes in biotic systems’. She then takes us through a personal account of what she has seen taken place since, closing with a brief summary of how she sees things as standing today.

I have to admit I’ve generally used the term ‘computational biology’ to capture work away from the ‘pure’ informatics side of things,** with it’s focus on data management and information theoretic approaches, but I like the notion that work in the field–by whatever name you wish to call it–should pull together many levels and aspects of biology rather stand aside from things founded on biologic concepts. (The ‘biologic concept’ element is one reason I use the term computational biology, with it’s emphasis on biology.)

The Paul Nurse’s lecture that she refers to in closing was part of a series The Great Ideas of Biology, a talk titled Organisms are information networks presented at the Royal Institution, London:

My first thoughts are that the term ‘information’, while useful in computational applications, has always bothered me just a little, as it’s a sort of ‘added on’ concept. Ideally, I prefer to think in terms of physics and chemistry. The thing that bothers me, I guess, is that information as a concept carries with it a danger of–in a sense–anthropomorphising a subject. But maybe this is too philosophical for a Friday night…!

I’d be interested to hear reader’s thoughts on the article and video.

ResearchBlogging.orgReference

Hogeweg, P. (2011). The Roots of Bioinformatics in Theoretical Biology PLoS Computational Biology, 7 (3) DOI: 10.1371/journal.pcbi.1002021

Footnotes

* I’m assuming, of course, that I haven’t missed any!

** Don’t confuse this with thinking that I dislike this aspect! – my own interests span those from quite close to biological to things that are, in essence, pure computer science applied in the arena of bioinformatics.


Other articles in Code for Life:

Russell Doolittle on Life before Bioinformatics

The roots of bioinformatics

Who has the most bioinformatics scientists?

New academic visas for New Zealand

The mythology of bioinformatics

Epigenetics and 3-D gene structure


19 Responses to “The Roots of Bioinformatics in Theoretical Biology”

  • Grant, I agree with the use of computational biology rather than bioinformatics because it emphasizes the nature of the data analytics part of the field. There is computational chemistry, computational physics (although very wide), computational fluid dynamics, computational finance, computational economics, computational linguistics, computational statistics, computational complexity, etc, etc,… They all have commonality in high-end mathematical/statistical analysis & methods being used.

  • Unusual for me to post late on a Friday night. Anyway, cheers Grant, I’ve just finished my tray of Steinlager (2 doz) and my mates have got us a taxi (they’re all standing outside) ready to roll into the viaduct (Auckland) to chat to people in bars about computational biology. Hehe, no, we’re going to enjoy some hip-hop dance, I’m the one who’s gonna show them how to do the Michael Jackson moves.

  • I don’t think I could cope with biology if I wasn’t seeing it as a system of information. On the small scale yes, it’s physics and chemistry but in any system dealing with more than one or two reactions, I think I have to look at it as a system of information. The danger of anthropomorphizing a system would only come, I imagine if you start thinking that the systems are consciously aware of the information they generate.

    I very rarely get the chance to make the distinction between computation biology and informatics, not being employed at the moment. Talking to the general public, 80% of people will cope with biologist. a few more will dig to make the distinction between marine/ecology/micro/molecular and that’s pretty much where it stops. I’d be there forever if I tried to make the distinction between computational bio and informatics.

  • The last point he made that biology is a complex system is absolutely true. Complex system theory, which originated in physics/mathematics have now been adopted in other complex system domains such as biology, climate, economics etc. The whole is more than the sum of the parts, where dynamic properties of the system , such as self-emergence, self-organized critically (SOC), phase transition (eg solid to liquid – melting or liquid to gas – vaporization, etc), scale invariance, spontaneous order, which have all being applied & observed biology.

    “SOC : Self-organized critically”
    http://en.wikipedia.org/wiki/Self-organized_criticality

    Grant I’m aware that “Control System Theory” is now being applied in Systems Biology (feedforward/feedback loops, input-output transfer functions, natural resonance frequency/cycle, etc,…). Just a question, if control system theory is being taught in biology today at any level? Either under/post graduate?

    Earthquake phenomena is claimed to be a SOC phenomena, establishing it as a complex system.

    “Self-Organized Criticality and Earthquakes” by A. Sornette and D. Sornette ,1989 Europhys. Lett. 9 197.

    Anyway here are some application of SOC in biology that I have found on the net and I think there are more.

    “Self-Organized Criticality in Developing Neuronal Networks”
    http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001013

    “Self Organized Criticality in Biology: From Membrane to Neurons and Behavior”
    http://www.cbs.mpg.de/news/events/calendar/128

    Complex system researchers have now apply SOC into economics.

    Last, I think that over time, biology will spread out further and become overlapped (widely) with other fields (mathematics, physics, chemistry, computing, engineering control, signal processing, etc,…)

  • Physicist Joseph L. McCauley from University of Houston has recommended in a paper he published (see below) that physics courses must include a paper in cell biology, since that’s where the interesting place were complex systems can be applied & studied.

    McCauley quoted:
    We meet real complexity in nature in cell biology, also in quantum computation, along with econophysics they’re the fields of the future in physics. Every physics student should be required to take a good, stiff course in cell biology from a text like „Fat Alberts“ [51], as Ivar Giæver calls it.

    “Response to “Worrying Trends in Econophysics””
    http://arxiv.org/ftp/physics/papers/0606/0606002.pdf

  • Continuing on in control & feedback in biology, here is another useful reading, which is cited in the paper I posted above in (The role of Control System Theory in systems biology).

    “Molecular Systems Biology and Control”
    http://www.ecse.rpi.edu/~agung/ese680files/Sontag%20-%20molecular%20systems.pdf

    Some here may ask, why am I posting links to articles on biology even though I’m not a biologist. I’ve worked as a design engineer before in robust control system & signal processing designing, so I’m just posting them here as an interest in their applications in other domains (non-engineering).

  • Grant, I’ve got a comment that’s being help up for moderation

    I think you know by now that if you include many links your comment will get held up – it’ll be the case for most blogs on this forum, if not all of them. (From memory, more than two links will trip the moderation filter; 2 links flagging moderation is a common setting for many blogs in my experience.)

  • Grant said…
    I think you know by now that if you include many links your comment will get held up

    Yes, that’s why I split my last 2 comments into 2 separate ones rather than 1 comment (which was a one post originally), so as to avoid the filter from holding it in the moderation folder.

  • Falafulu Fisi 2 days ago

    Grant said…
    I think you know by now that if you include many links your comment will get held up

    Yes, that’s why I split my last 2 comments into 2 separate ones rather than 1 comment (which was a one post originally), so as to avoid the filter from holding it in the moderation folder.

    ah… the old ‘how to get passed red tape’ trick… where would we be without red tape and bureaucratic rules???

  • It’s there for readers’ benefit, not ‘rules for the sake of rules’. If comments with many links are let through, spam would get through.

  • I’m not sure I can justify this, but I’ve always though of bioinformatics as being more to do with dealing with data, and computational biology more to do with modelling and applying other techniques to biology.

    My university/departnent does actually teach the concept of biology as an information processing system at an undergraduate level (in the context of development, and it doesn’t call it bioinformatics). That course is all the introduction I’ve had to the idea, really, but I do think it’s a powerful one. Thinking of biology in terms of information processing makes the concepts of networks and regulatory modules make a lot more sense, at least. It may also make biology more accessible to non-biologist scientists.

    It does all come down to physics and chemistry in the end, but thinking in terms of information is useful. I haven’t found that it’s led me into thinking in an anthropomorphic way (not any more than I might usually!) – if anything I find it encourages me to think about biology in a much more abstract way.

  • Liz,

    Thanks for popping in and saying something. This place (my blog) is rather quiet lately… Peeking at your blog, I see you use LyX too :-)

    I’m not sure I can justify this, but I’ve always though of bioinformatics as being more to do with dealing with data, and computational biology more to do with modelling and applying other techniques to biology.

    Similar view to mine; I’ve babbled on aimlessly about this in the past, e.g.

    http://sciblogs.co.nz/code-for-life/2010/01/08/more-on-what-is-a-computational-biologist-and-related-disciplines/

    It does all come down to physics and chemistry in the end, but thinking in terms of information is useful.

    I’m not saying using the concept of information is not useful. I am also ever so gently pulling chains a little… :-) (In the hope of encouraging conversation while I’m a bit too busy to write much.)

    I’ve used the concept myself, of course, as everyone does. I’m just saying it carries with it a risk of misrepresenting what is actually taking place (at least at a lower level), of an abstraction that in talking about a system, or a collection of molecules, in one particular way gives them properties they may not really have. In many cases it’d be a philosophical objection, rather than a practical one, but I still think it’s worth bearing in mind as you make models, etc.

    I realise ‘anthropomorphising’ is an awkward choice of words and not quite right, hence why prefixed it with ‘in a sense’. I wish I had time to explain more fully, but I’m flat out!

    if anything I find it encourages me to think about biology in a much more abstract way.

    It can, for sure. Abstraction has it’s issues if not used wisely, as well all know.

  • Grant –
    Yes, I have seen the science cookies! They’re brilliant. I might submit my cake to one of the roundups :)

    I think I do see what you mean about the danger of misrepresenting things by looking at them at a higher level. I think the important thing is remembering, whatever level you’re looking at, that there are molecules involved… I don’t know though, I am finding I’m getting more and more interested in the systems/information processing way of looking at things.

  • I might submit my cake to one of the roundups :)

    You should! – there can’t be too many C. elegans cakes :-)

    I don’t know though, I am finding I’m getting more and more interested in the systems/information processing way of looking at things.

    For what it’s worth I was when I started out, too. Being in a structural biology section for my Ph.D. studies cured me of that – or spoiled me, depending on your point of view! Seriously, there’s room and a need for both as long as you’re aware of the limitations. Personally I think much of the systems-type work will need physical information added to it to help it work well, though, for example spatial/location information. (There’s more but I have to get back to coding…)

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