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Why Do Sequences Think They Are So Special?

The views expressed are those of the author and are not necessarily those of Scientific American.


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Today’s programming on Culturing Science is brought to you by Dennis Waters. He currently serves as the historian of Lawrence Township, New Jersey when he’s not squatting near a tree trunk or gravestone collecting lichens. He founded GenomeWeb.com, a news site and publisher for molecular biologists, in 1997 and still serves as the chairman of their board. He also has the privilege of being my father. Follow him on twitter @dpwaters.

I am here to half-heartedly* promote a new book comprising seventeen of the classic papers of my PhD advisor, Howard Pattee. The book, called Laws, Language and Life, is co-edited by Pattee himself—well into his 80s and as sharp as ever—and by neurolinguist and Pattee scholar Joanna Rączaszek-Leonardi of the University of Warsaw.

But rather than ask you to purchase it, I shall use the totally remarkable occasion of the book’s publication to wholeheartedly urge you to go read some Pattee in whatever form you can find.

Why read Pattee?

Well, we know that the living world depends on sequences of nucleic acids for its existence and ongoing operation. We also know that humans evolved the ability to create, manipulate, and copy acoustic sequences, and later to commit those sequences to the more permanent medium of writing. Finally, we know that our advanced technological civilization is increasingly dependent on storing, moving, and processing bit strings—sequences of zeros and ones.

So what is it with sequences?

This is essentially the question Pattee has been studying for the last 50 years.

Pattee trained as a physicist at Stanford and still writes about biology (and brains) with a demanding precision. The questions that puzzle him concern the physical nature and systemic functions of sequences of symbols. Pattee’s complaint with conventional biological and cognitive science answers to these questions is that we will never understand the high-level use of sequences by the human brain without first understanding their nature and function at a much simpler level.

This is Pattee’s inner physicist speaking: why model a complex system when you can model a simple one? Thus his search for the evolutionary origin of this problem. As he put it in his 1969 paper “How Does a Molecule Become a Message?” (paper #2 in the book):

I am convinced that the problem of the origin of life cannot even be formulated without a better understanding of how molecules can function symbolically, that is, as records, codes, and signals. Or as I imply in my title, to understand origins, we need to know how a molecule becomes a message.

More specifically, as a physicist, I want to know how to distinguish communication between molecules from the normal physical interactions or forces between molecules which we believe account for all their motions. Furthermore, I need to make this distinction at the simplest possible level, since it does not answer the origin question to look at highly evolved organisms in which communication processes are reasonably clear and distinct. Therefore I need to know how messages originated. (Emphasis his)

“Message” implies “sequence,” so his question centers on how everyday physical systems change their behavior when molecules become organized sequentially. If we can come to grips with this problem, then perhaps we have a fighting chance of understanding how other sequence-based systems (like language) function.

Thus the cell becomes his point of departure for understanding sequences at all levels. Here is how he put it in his 1982 paper “Cell Psychology: An Evolutionary Approach to the Symbol-Matter Problem” (#10 in the book):

High level concepts such as intentions, meanings, thoughts, and so on, which we associate only with minds, must have had evolutionary precursors in a more or less gradual sequence. The problem is that we do not have a clear concept of what the simplest “intention,” “meaning,” or “thought” might look like. This is because psychology has traditionally been defined by only highly evolved “mental” activity, so that even though we study brains at the cellular or even molecular levels, there is the tacit belief that no real psychology can exist at a simple level.

Human physiology was also first defined as the study of gross organs and body fluids, but gradually these concepts were generalized and refined by the study of simpler organisms until today we find the foundations of human physiology in cell physiology. This does not mean that cells explain or exhibit all higher level processes. Cells do not have feet or ears, but they have motility and irritability, which are basic functions of feet and ears.…

I suggest that brain-level psychologies are not likely to converge until we have some agreement on the foundations of cell psychology. Obviously I am not suggesting that cells have minds any more than cells have feet, but cells are certainly matter-symbol systems which hopefully can be more clearly understood and modeled.

When Pattee looks for “matter-symbol systems” in the cell, he naturally focuses on the sequences of the genetic code. Can we find a principled way to distinguish between the two complementary roles of nucleic acid sequences? On the one hand, they behave like ordinary molecules, forming bonds and doing all of the lawful things that molecules can do. On the other hand, their function in living systems is to act as a template to “communicate” how to construct amino acid sequences and ultimately the tertiary structure of proteins.

We understand that their ordinary behavior is controlled by the laws of physics. But we also understand that there is no law of physics that says genetic sequences must be exactly the sequences that they are; alternative sequences are easily imagined. In other words, biology may be consistent with universal physical laws but the interesting sequence-based behaviors of living things depend on what Pattee calls specific arbitrary rules. To the untrained eye these rules may look like laws, but they are not. As Pattee explains it in his 1978 paper “The Complementarity Principle in Biological and Social Structures” (#8 in the book, and the first paper of his that I ever read):

The basic distinction between laws and rules can be made by these criteria: laws are (a) inexorable, (b) incorporeal and (c) universal; rules are (a) arbitrary, (b) structure dependent and (c) local. In other words, we can never alter or evade laws of nature; we can always evade or change rules. Laws of nature do not need embodiments or structures to execute them; rules must have a real physical structure or constraint if they are to be executed. Finally, laws hold at all times and all places; rules only exist when and where there are physical structures to execute them. (emphasis his)

As you have doubtless noticed, Pattee is difficult to summarize in a brief essay. He has never stopped asking the “big questions” in biology, so you should not read him expecting easy answers. Instead, you should expect fresh new ways of posing these classic quandaries, with a relentless insistence on explanations that would satisfy a working physicist (though very much not from a reductionist perspective). You will benefit from reading Pattee in direct proportion to your interest in these “big questions”—and in inverse proportion to your level of satisfaction with how they have been answered to date.

With Pattee, the answers elude, but the questions improve.

Pattee’s trail of papers on theoretical biology, cognitive science, artificial life, etc. stretches back to the 1960s The new book’s publication is totally remarkable because—despite producing this large body of work over all of those decades—Pattee has never written anything close to book-length. In 1973 he edited the well-regarded collection Hierarchy Theory, but that’s it. In the 40 years since then, everything else is papers, papers, papers. (Including his latest, published just last month.)

It is a treat to see so many of the good ones finally collected and available, though unfortunately in a package only within budgetary range of institutional libraries. But it can’t hurt to petition your library to get a copy. Please. Meanwhile, go forth and read a little Pattee. A few seconds on Google Scholar will not disappoint you.

I now return you to your regularly scheduled blogger. Thanks, sweetie.

*The reason I say “half-heartedly promote” is that—as happens with too many technical books aimed at narrow markets—the publisher is charging a small fortune for it. So I will not urge you to drop whatever you’re doing and then spend $159 on a book by someone you have probably never heard of.

Image 1: Manuscript page from Copernicus’s De revolutionibus orbium coelestium
Image 2: DNA strand by Michael Ströck

Hannah Waters About the Author: Hannah Waters writes about natural history and the way people think about nature. She lives and works in Philadelphia, PA, but really on the internet. Follow on Twitter @hannahjwaters.

The views expressed are those of the author and are not necessarily those of Scientific American.





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  1. 1. sjfone 10:35 am 05/18/2013

    Game of Genomes. Also Dr. Pattee is heavy-duty, like totally.

    Link to this

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