Is There A Systems Biologist In The House?

| 16 Comments

I had an op-ed in the Albuquerque Tribune a couple of weeks ago, on the topics of a rash of creationist bills in the New Mexico Legislature, and the super-sneaky tactics of the New Mexico Science Foundation.

Of course, in this “Tit-for-tat” world of ours, our local Intelligent Design Creationists finagled an op-ed response. Joe Renick, Executive Director of the Intelligent Design Network, is the author of Fear of exposure: The fight against academic freedom is rooted in the worry that Darwinism’s weakness will be revealed. It’s quite a ramble, but this little tidbit is what caused me to have a coffee spit-take:

Joe Renick Wrote:

The greatest threat to the Darwinian dogma today is science itself.

There is a revolution underway in the biological sciences. A whole new field of biology called “Systems Biology” has emerged during the past 10 or 15 years. This revolution is just as profound for the biological sciences today as the transition in physics was from classical physics to quantum physics and relativity in the early part of the 20th century.

In this exciting new field, research is guided not by Darwinian principles but by design principles because design principles are needed to explain design-like features.

Now hold on just a minute! Sure, “Systems Biologists” use words like “design” occasionally, but that doesn’t automatically mean they think “designs” in nature must be “poofed” into existence by an un-named magical being.

I would like to see a few (or even a dozen) letters from bonafide Systems Biologists setting Renick straight in the Albuquerque Tribune. It’ll be a quality Lesson for New Mexico Creationists: completely misrepresent an entire discipline, and you might just get chewed out.

Some comments on “Systems Biology,” along with information on writing the Trib, appear below the fold.

I used two routes to find a representative center for Systems Biology, and they both landed me at the same place. First, I checked out the Links page of the super-sneaky “New Mexico Science Foundation” (a young earth creationist front organization), and found a prominent link to the Institute for Systems Biology. This same outfit comes up #1 in a Google Search for “Systems Biology”.

There’s a nice description of what “Systems Biology” entails on this page:

Systems biology is the study of an organism, viewed as an integrated and interacting network of genes, proteins and biochemical reactions which give rise to life. Instead of analyzing individual components or aspects of the organism, such as sugar metabolism or a cell nucleus, systems biologists focus on all the components and the interactions among them, all as part of one system. … Traditional biology — the kind most of us studied in high school and college, and that many generations of scientists before us have pursued — has focused on identifying individual genes, proteins and cells, and studying their specific functions. But that kind of biology can yield relatively limited insights about the human body.

As an analogy, if you wanted to study an automobile, and focused on identifying the engine, seat belts, and tail lights, and studied their specific functions, you would have no real understanding of how an automobile operates. More important, you would have no understanding of how to effectively service the vehicle when something malfunctions. So too, a traditional approach to studying biology and human health has left us with a limited understanding of how the human body operates, and how we can best predict, prevent, or remedy potential health problems.

When I used Google to search the site for “Design Principles,” I found reference to a paper titled “Evolution of ‘design’ principles in biochemical networks.”(de Atauri P, Orrell D, Ramsey S, Bolouri H., 2004. IEE Proc Sys Biol. 1(1):28-40).

I found a copy of Evolution of “design” principles in biochemical networks, and it isn’t even close to what Renick is claiming in the Trib (Shocked! I’m shocked, I say!):

We believe that evolution does result in recurring, dynamic organizational principles in biochemical pathways. Moreover, we posit that, in spite of its inherent inaccuracies, computer modelling and simulation can be used to identify and study such “evolutionary design principles”. To make specific and illustrate our point, in the rest of this paper, we present a model of the yeast galactose utilization pathway (a metabolic module) built from existing, publicly available data, and highlight several features of the model that embody “design principles” already predicted theoretically, and/o r observed in other biochemical pathways.

A search for “evolution” on the Institute’s website also brought up this little gem:

A third observation that came from the human Book of Life is remarkably gratifying. If we again rifled through the Book of Life for a human, a fish, a fly, and a yeast (a small, single-celled organism that makes beer), what was absolutely amazing was the large number of shared words (although the spellings were somewhat different). Even more important, many fundamental biological systems composed of those genes and proteins were remarkably similar. This underscores the enormous unity that exists in all life. We all descended from a single common ancestor at the beginning of life and subsequently diverged (changed) in very different directions. However, all life is intimately interconnected by this common heritage.

Contrary to Renick, all this does NOTsound like a discipline that has abandoned “Darwinian principles” for “design principles.”

If you are a Systems Biologist, please comment on this egregious abuse of your discipline below, and better yet, send in a brief comment to the Albuquerque Tribune. Here is how to write a letter to the Trib:

Address a letter to the editor in care of Editor, The Albuquerque Tribune P.O. Drawer T Albuquerque, NM 87103

Send us e-mail: editorATabqtrib.com (AT=@). Please note, we do not accept and will not open e-mails that include attachments. See below for details.

You must include your name, address and phone number (for verification). Try to keep the letter within 250 words and please avoid comments that might be deemed slanderous, libelous or in poor taste.

There is more info at the Trib’s Contacts Page.

Let the Flagellations begin!

By the way - if there are any Systems Biologists out there who actually agree with Renick, please let us know here.

General comments on Renick’s op-ed are also invited.

My bottom line: as Daniel Patrick Moynihan said, “Everyone is entitled to his own opinion but not his own facts.”

I think Renick is making up his own facts. This is why we continue to oppose “Intelligent Design” - once you lose the Facts, you’ve lost Science.

16 Comments

darn,

I’m a systematic entomologist. What are “designed principles”? It seems like those are just buzz words to describe shared derived or primitive characteristics. Why can’t they use existing terminology? Systems biology (in part) is a junior synonym of organismal biology and physiology. It’s just that there has been such a large push in molecular and cellular biology that some biologist had forgotten that there are whole organisms and that these organisms are related. Now that some of the molecular jockeys have remembered that they think they have found a whole new field of biology. In truth, they are just returning to the basics.

Bob

I predicted the misuse of SB by creationists last July in a comment over at EvolutionBlog

The next thing to happen is that IDists will cite Systems Biology papers as unwittingly proof of their claims. Such papers will provide them with illustrations much more dynamic compared to the boring ever so often reproduced figure of a bacterial flagellum and lots of mathematics to play around with. Until now they seemingly missed this new field of biology. This will change as soon as an abstract or the MESH terms of such papers contain the term “design”.

I have corrected some spelling mistakes here)

I’m not a systems biologist, but needless to say, the claim is utter rubbish. Systems biologists are very interested in the evolution of protein interaction networks, gene circuits, etc. They’re not interested in ID in the least. Why would they be? It has nothing to offer.

It’ll be a quality Lesson for New Mexico Creationists: completely misrepresent an entire discipline, and you might just get chewed out.

They won’t learn a thing. They’ve been systematically misrepresenting entire disciplines for years now, and they’ve been chewed out aplenty. All they’ve done is flex their persecution complex, claimed that the people chewing them out are “Darwinists” who are being mean, and intimated that the only reason why scientists overwhelmingly disagree with them is because of brainwashing and suppression. There is no amount of evidence that could ever convince such people of their error.

“There is no amount of evidence that could ever convince such people of their error.”

I agree. However, convincing others of their error is still useful.

How dare they misrepresent physiologists … er, systems biologists.

I’m not a “systems biologist” either, but I am a “systems theorist” in the social sciences. My own sense is that systems theory goes back a lot farther in both the natural and social sciences, and it has nothing at all to do with “design theory”.

In the social sciences, especially the area I am most familiar with, “systems theory” has always been synonymous with “evolutionary” approaches to social systems.

I could rant on, but I feel that it is a waste of breath…

Systems theory has nothing to do with design theory and it is no way, size, shape or form inconsistent with basic neo-Darwinian ideas or concepts.

The underlying basic principle of systems theory is that such phenomena as “ecosystems”, “sociocultural systems” or any other entity need to be understood and analysed as integrated wholes. That means developments in one area systematically influence developments in another area. There is some disagreement about how much autonomy can be granted to “subsystems” and from which direction determination comes from.

The only way systems theory runs into any conflicts with “Darwinism” or with “neo-Darwinism” is in the fact that systems theory focuses on emergent properties and higher level analysis than someone who is for example strongly influenced by Richard Dawkins or Daniel Dennett. I might also add that systems theorists might also be more inclined towards the kind of holistic biology suggested by Lynn Margulis.

Beyond the “holism” vs. “reductionism” debate however systems theory is really not anything beyond just standard, conventional science.

Systems theory is completely, totally, entirely naturalistic in conception.

Chip Wrote:

The underlying basic principle of systems theory is that such phenomena as “ecosystems”, “sociocultural systems” or any other entity need to be understood and analysed as integrated wholes.

Another description of the system analysis I have seen is “top-down” as opposed to “bottom-up”. Biology is doing both of course.

Which is actually the point of systems theory: uniting the top down and the bottom up together.

Even so, an underlying assumption of systems theory is that patterns and order emerge at higher levels that cannot be understood solely by simply aggregating the behavior of the individual units. This does not of course preclude analysis of the lower levels.

systems theory: yet another attempt to explain why fossil evidence just dosn’t say natural selection.

levi: Another dimwitted creotroll bandying about words he clearly doesn’t understand.

Or maybe you could expand on your little one-liner and explain precisely what you mean by that.

levi Wrote:

systems theory: yet another attempt to explain why fossil evidence just dosn’t say natural selection.

No-one ever claimed the fossil record said “Natural Selection”. The fossil record says “change over time” and “all these organisms are related to one another”, i.e. the facts of evolution (in the sense of change over time)and common descent.

Natural Selection explains these observations, and has been confirmed by other (independent) observations.

Maybe if you took the trouble to learn something, you could assess it for yourself, instead of parroting someone else’s strawman arguments.

This is the closest anything to do with systems biology comes to supporting ID:

http://genomebiology.com/2006/7/7/322/abstract

I’ve been to a few systems biology conferences, and a sizeable proportion of the talks etc. deal specifically with the evolution of systems. Suggesting that because we treat systems as having some analogies to manmade systems this is evidence for their design always gets a laugh.

Chip Poirot is right in his description of systems theory. I speak as an evolutionary biologist with some familiarity with systems theory as applied to biology. The concept of autopoiesis of Maturana and Varela is a theory of life as a particular kind of self-producing, dynamic system of molecular assemblage and dissasemmblage, that conform borders and are units with a distinct inner and outer environment. This bold proposal removes the need for any vitalist, teleological or teleonomical notions at the origin of life or in life itself, explaining the basic properties of organisms, specially autonomy. That’s better than Jacques Monod’s weird teleonomy as a theory of life, and better than a sloppily defined notion of “information” or “programming”, unfortunately used all over biology. In the end it is peddled at anthropomorfic metaphorical crap value. Precisely the kind of discourse that could mislead someone into thinking some kind of intelligence is missing somewhere. And yes, of course that “selfish genes” controlling lumbering robots do not help much either… all is part of the excessively “gene happy” atmosphere and the general acceptances of the metaphor of genes “·controlling” or “coding” everything in the organism. I think there, in the “code” crappy metaphor, and no better basic theory of life, is the big problem we should strive to correct within the scientific field itself. Greater understanding of systems theory and autopoiesis can help unlock biology from this crippling and misguiding metaphorical language.

Hahahahahaha… this is hilarious.

Systems biology and its cousin disciplines of artificial life, simulation science, and complex systems modeling talk about evolution all the time. The whole focus is on understanding how X evolves or how evolution does Y or how to get a simulated evolutionary system to achieve Z.

I’ve been to a number of conferences in these areas. If you took a drink of beer every time someone said “evolution” you’d be dead of alcohol poisoning within an hour or two.

Silly, silly stuff.

I bet next they’re going to argue that the new field of nanotechnology disproves the germ theory of disease because… well… not we’re talking about small things that aren’t germs… so…

Hilarious!

Adam,

Huh?

Renick makes this bizarre statement towards the end of this farrago: “Thomas Huxley, Darwin’s bulldog, who saw relatively little scientific value in Darwin’s theory but saw great value in its ability to provide the foundation for a new secular religion to replace Christianity…”

Huh? This is a new creationist claim for me. Is it original to Renick?

And while it’s clearly a lie, what sort of statements by Huxley or facts about him is Renick taking out of context to make this claim? I’m assuming he has some mined quote or other to throw at whoever objects to this characterization of Huxley’s attitudes, and I’d be curious to know what it is, if anyone has any ideas.

About this Entry

This page contains a single entry by Dave Thomas published on March 28, 2007 9:30 AM.

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The circus is in town; the creationist calliope is wheezing away again is the next entry in this blog.

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