Ask a bioinformatician?

Admins of the Bioinformatics group at Nature Network received an email from Corie Lok today:

Just wanted to let you know that membership of your bioinformatics group has broken 400, making it by far the biggest group on Nature Network! Congratulations.

With such a large membership, I thought the time is right to do something in the group to stimulate more discussion in the group’s forum. Do you have any thoughts on how we can do that? What kinds of conversations lend themselves to an online forum that would be important for bioinformaticians? Are there any key people in the field, or authors of recent important papers, that the 400 group members would want to talk to in the forum? Perhaps we can invite them to join the forum, say a few words, and then offer to answer people’s questions on a specific topic.

I like this idea. If you have any suggestions or other thoughts on how to stimulate discussion at NN, visit the group, let Corie know or leave a comment here.

5 thoughts on “Ask a bioinformatician?

  1. One good discussion topic might be the issue of increasing time spent on formatting and preparing data you mentioned before.
    Another related topic which comes to mind is standards. Maybe not the most exciting topics to get people together to discuss, but certainly important ones.

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  3. I’d also like to see more discussion of the daily challenges faced by working bioinformaticians: data munging, standards and so on, rather than focusing on the great and glorious. Like you say, making it exciting is the challenge.

    I’d also like to see better features at NN to facilitate discussion; I left a comment on that at Deepak’s blog.

  4. One commandment should be to know these scientists work!

    Peer-reviewed and accepted July 2006
    Physics of Life Reviews

    Self-organization vs. self-ordering events in life-origin models

    by Dr. David Abel and Jack Trevors PhD

    Self-ordering phenomena should not be confused with self-organization. Self-ordering events occur spontaneously according to natural “law” propensities and are purely physicodynamic. Crystallization and the spontaneously forming dissipative structures of Prigogine are examples of self-ordering. Self-ordering phenomena involve no decision nodes, no dynamically-inert configurable switches, no logic gates, no steering toward algorithmic success or “computational halting”.

    Hypercycles, genetic and evolutionary algorithms, neural nets, and cellular automata have not been shown to self-organize spontaneously into nontrivial functions. Laws and fractals are both compression algorithms containing minimal complexity and information. Organization typically contains large quantities of prescriptive information. Prescriptive information either instructs or directly produces nontrivial optimized algorithmic function at its destination. Prescription requires choice contingency rather than chance contingency or necessity. Organization
    requires prescription, and is abstract, conceptual, formal, and algorithmic. Organization utilizes a sign/symbol/token system to represent many configurable switch settings. Physical switch settings allow instantiation of nonphysical selections for function into physicality. Switch settings represent choices at successive decision nodes that integrate circuits and instantiate cooperative management into conceptual physical systems. Switch positions must be freely selectable to function as logic gates. Switches must be set according to rules, not laws. Inanimacy cannot “organize” itself. Inanimacy can only self-order. “Self-organization” is without empirical and prediction-fulfilling support. No falsifiable theory of self-organization exists. “Self-organization” provides no mechanism and offers no detailed verifiable explanatory power. Care should be taken not to use the term “self-organization” erroneously to refer to low-informational, natural-process, self-ordering events, especially when discussing genetic information.

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