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The FANTOM designer

Nature FANTOM studies networks in cells 

“An international consortium has released an analysis of unprecedented detail showing the genes and proteins that guide an immature cell to its final identity.

The models show that a complex network of transcription factors is responsible for a cell’s differentiation, with no one ‘master regulator’ in control. “It’s like a transcription-factor democracy,” says Harmen Bussemaker, a computational biologist at Columbia University in New York. From an evolutionary standpoint, distributing responsibility is a good strategy, he says: “It would not be a good design principle to have an Achilles’ heel.”

(Don’t they mean “From a design standpoint”?)

Piero Carninci of Japan’s Institute of Physical and Chemical Research (RIKEN), in Yokohama found that RNA is produced from retrotransposon sequences in a highly regulated manner that varies among different cell stages and types3 Carninci says studies are under way to determine what function these transposons may have.”

(Yet another bit of junk DNA is found not to be such?)

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13 Responses to The FANTOM designer

  1. (Don’t they mean “From a design standpoint”?)

    That would depend on the purpose of the design.

  2. The lack of an apparent master regulator is evidence not so much of good design as it is an indication of immaterial phenomena as the organizing principle.

    I think we will find in the not too distant future that the concepts of force, momentum, information, and their interactions are in fact responsible for biological life and are themselves living ideas.

    Science will confirm what has been known intuitively from the start.

  3. Oramus:

    Very interesting concepts. I agree, only I would not necessarily use the term “immaterial” (which has heavy and ambiguous philosophical implications), and speak instead of phenomena “not necessarily explained by current scientific models”.

    IOW, if:

    The models show that a complex network of transcription factors is responsible for a cell’s differentiation, with no one ‘master regulator’ in control. “It’s like a transcription-factor democracy,” says Harmen Bussemaker, a computational biologist at Columbia University in New York. From an evolutionary standpoint, distributing responsibility is a good strategy, he says: “It would not be a good design principle to have an Achilles’ heel.”

    then, what is “in control”? Because control is certainly there. The usual assumption that things go well for “sheer luck” will not do. The concept of a “transcription-factor democracy” is intriguing, but will not do just the same. Have we ever known a democracy which works without any “coordination”? Are computer programs a “small procedures democracy”, without any general plan?

    So, the phrase: “no one ‘master regulator’ in control” just means: “we have not found, according to our assumptions, models and methodology, any ‘master regulator’ which may be able to ensure the general coordination according to a pre-existing plan and the relative information content”.

    That’s very different for stating that no “master regulator” exists. Maybe they have to try harder. Maybe they just have to change their assumptions and models. The fact is, the regulation is there. Or is Dawkins or someone else ready to affirm that the new darwinism is about things which appear regulated, but indeed are not? Will that become the “blind controller” theory?

  4. It’s all likely due to the “blind organizational force of the gaps”.

  5. Gpuccio,

    “…and speak instead of phenomena “not necessarily explained by current scientific models”.”

    Applying Allen MacNeils comments in Bleak Conclusions post, his words, “non-natural phenomenon” and insert it as such…

    “…and speak instead of non-natural” phenomenon “not necessarily explained by current scientific models”.”

    Or is that to presumptive or misused considering their talk of design? To account for the programmatic shared responsibilites of rules-based regulation?

    I’m thinking Allen will object to my use of non-natural from his earlier discussion.

    Democratic is a failed analogy.

    Shared regulatory duties can happen under different political systems. Shared regulatory duties and distribution do indicate a highly complex system.

    And is it fair to say, even more irreducibly complex as a network?

  6. Scheeseman,

    LOL, gaps of Orwellian thought minders who let the article thru with the word “design” in it. Where’s NCSE when you need good thought police today? Are they to busy down in Texas chasing dumb cowboys away from re-education camps?

    “From an evolutionary standpoint, distributing responsibility is a good strategy, he says: “It would not be a good design principle to have an Achilles’ heel.”

    (Don’t they mean “From a design standpoint”?)

    Haha… no, it is obvious a subversive IDist infiltrated the Darwinian lair and inserted the word. NCSE will send out evolutionary thought police soon for clearing and cleaing operations. Where is Dembski btw? Has anyone seen him? Hmmmm?

  7. 7

    When I was in college I listened in my science courses for how many times the professors used the word “evolve” and the word “design” or any variations on the root words. Guess which one usually won?

  8. I guess someone forgot to mention metaphors are not actual…

  9. Does anyone think that the following quote supports ID?

    It would not be a good design principle to have an Achilles’ heel.

  10. gpucci,

    Thanks for your comment and point take. DATCG’s non-natural phenomena is a good suggestion.

    If I were to seek an approach on how to discover a master regulator, I would definitely go in the direction of studying our Chi/magnetic field BTW, I have experienced Chi pulsating through my body twice already. I think we in the West would call it our electro-magnetic field. IMO it is not some kind of by-product, but a bodily system in its own right.

    I think its just a huge gold mine of information just waiting to be discovered.

    Regarding a master regulator’s characteristics, I would think its structure to be more in terms of a benevolent oligarchy.

    I say this because three seems to be a prevalent numerical theme in the Universe. Maybe its because three is the most stable of simple combinations; two being too weak, four creating diminishing returns.

    So I propose our Chi as one of the regulators. Now, for those other two.

  11. “So I propose our Chi as one of the regulators. Now, for those other two.”

    I think I know ‘em, and Chi by another name.

  12. It would actually be quite a problem for evolutionary theory if there were a master regulator.

    Perhaps a more apt term than democracy would be, harking to Selfridge, pandemonium.

  13. prhean, you sound like one of those PT posters. Just couldn’t stand it anymore, eh?

    Why would you think our electro-magnetic field has not place at the table? Have you experienced your own magnetic field/Chi after doing Chi Kung?.

    Didn’t think so. As you like to tell creationists, ‘please, do the work, man; do the work. Then come back and tell me if nothing happened.

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