Rediscovering Life

A thousand-stranded tapestry: how organisms employ their genes

Stephen L. Talbott

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This article is part of “Rediscovering Life”, a news portal for the Biology Worthy of Life Project. Copyright 2013 The Nature Institute. All rights reserved.
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Posted: July 19, 2013   (Article 7)

On the Biology Worthy of Life website I have posted a new document entitled, “How the Organism Decides What to Make of Its Genes". It is perhaps the strangest piece I have ever published, being the only one I would advise you not to try to read. It is also the only one almost guaranteed in advance to contain at least some bits of misleading information. And, most importantly, it may be the one most likely to seriously mess with the heads of practicing biologists, many of whom (I have slowly come to recognize) are so burdened by the demands of their narrow fields of research that they may scarcely be aware of much of the literature even in disciplines rather closely related to their own. The document in question is intended to provide the kind of healthy shock that may come from suddenly gaining a much wider vantage point.

It contains, in outline form, an extensive set of notes drawn from the technical literature on the broad topic of gene regulation. As I have pursued my researches on this topic, I have sporadically, inconsistently, and not always in a well-organized fashion, thrown various observations and quotes from the literature into one large file for future reference. The file grew, and I began to realize what an extraordinary picture this collected information presents, and how little appreciated the picture is, even among molecular biologists.

Despite my reservations about placing a “mere” collection of notes before the public (what ignorance on my part, dating back to the early days of my research, will thus be exposed?), I was finally persuaded by Craig Holdrege, the director of The Nature Institute, of the value of the project. It required that I do some more careful HTML formatting while making at least a minimal stab at imposing a more disciplined organization on the material. But “minimal” remains the operative word.

But I will say no more here about the limitations of the document. I have placed a set of caveats in a separate file referred to at the beginning of the notes.

I said the notes were not intended to be read in any straightforward sense, and were likely to mess with the heads of biologists. Let me explain. All the non-biologist or interested layman really needs to do is slowly scroll down through the (very long) document, noting the boldface headings and reading snippets here and there whenever the urge strikes. As for the biologist, the same strategy is fine, except the urge to read here or there may strike rather more often, and special areas of interest may provoke greater attention.

In any case, the point is this: I believe that few people, lay or professional, have ever taken note of the wide range of processes — all interpenetrating or “cross-talking” — that bear on gene expression. You will doubtless take me to be overstating the matter, but I will nevertheless say it: I believe that the simple act of scrolling down through this document with reasonable awareness of what it is about can prove a game-changer for one’s sense of genes, cells, organisms, and life itself. I have never seen anything remotely approaching this synoptic view of the amazing variety of interconnected processes bearing on gene expression. The picture that emerges is one of an almost incomprehensibly interwoven unity, wherein the whole unavoidably takes precedence over the parts in our understanding.

Against the value of that lesson, the imperfections of the document hardly matter. This is why, against all my natural instincts for self-protection, I have decided to post it online, blemishes and all.

You be the judge. I will welcome corrections and suggestions. I continue to add to the document on a regular basis, and will periodically post updated versions. You can always find the latest version at http://natureinstitute.org/txt/st/org under the title, “How the Organism Decides What to Make of Its Genes”.

To view the document now, here is a direct link

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Bibliographic note. The greatest defect in the document is its lack of a bibliography corresponding to the hundreds of author citations in the text. These citations are keyed to a bibliographic database of my own, which is not in publishable form, and I currently lack time to construct a proper bibliography for public consumption. Nevertheless, the author citations in conjunction with the quotations offered should prove easily traceable through a search engine. If you require a reference you cannot find, please feel free to contact me and ask for it. Incidentally, virtually all citations are taken from mainstream literature — journals such as Science, Nature, Nature Genetics, Nature Reviews Genetics, Cell, Genome Research, and probably something like forty or so more.

Tags: epigenetics; gene regulation; holism; transcription
Further information: The entire “Biology Worthy of Life” website might be considered, in greater part, a readable commentary on the dramatic implications of the notes on gene regulation discussed here.

This document: BiologyWorthyofLife.org/comm/ar/2013/thousand-stranded-tapestry_7.htm

Steve Talbott :: A thousand-stranded tapestry: how organisms employ their genes