NetFuture #188

NETFUTURE
Science, Technology, and Human Responsibility

Editor’s Note

Updates from the “Toward a Biology Worthy of Life” project

What If We Could See Everything Bearing on Gene Expression?

Warning: The attempt may overwhelm you

About this newsletter

Editor’s Note

In the last issue of NetFuture I announced a new feature, available on the “Toward a Biology Worthy of Life” website. It was called “Revolution in the Making? Notes from the Biological Literature”, located here. The page is still there, but I have changed the title to reflect the fact that I will now be using it as a kind of portal opening onto just about everything new that I write. This will continue to include notes on the current literature, but much more as well.

The new title of the page is “Rediscovering Life: From Molecules of Information to the Wisdom of the Organism”. If you wish to follow my work on genetics, epigenetics, molecular biology in general, and evolution, the best thing to do would be to bookmark that page, which will probably be updated every one to three weeks. Or you can subscribe to its contents via an RSS feed (about which, see immediately below).

As for NetFuture: for the time being — and until some new creative urge strikes — I expect it to become something rather more like an email alert service, with, say, quarterly postings containing some links with very brief annotations. Perhaps it will have a few surprises on occasion. Or perhaps I will revisit some of the topics covered in past years. For me personally, a great deal is in flux now, so I will have to wait and see.

You can subscribe to the new content. Regarding the page I just now suggested you might want to bookmark: there is another option. I have added an RSS subscription feature enabling you to receive automatic notice of all new material. This means you can have links to new postings show up automatically in a bookmark folder of your browser, or in a standalone RSS reader. And if you subsequently want to unsubscribe, it can be as easy as deleting a bookmark.

For those of you familiar with RSS “feeds” (as these channels for automatically delivering content are often called), the process of subscribing will be trivial. Unfortunately, if you’re not already familiar with RSS, how it all works can be baffling — and highly dependent on your browser or other web access application. Your best bet is to get someone familiar with RSS feeds to guide you through what will usually be a very brief process, often amounting to just a few clicks of your mouse.

For what it’s worth, there’s a link that should help users of Internet Explorer 7, 8 or 9. If you use Firefox or Safari, you may find that simply clicking on an RSS feed link will lead you through a more or less self-explanatory process — although anyone’s ability to navigate the “self-explanatory” will still depend on a certain amount of prior experience.

Whatever your situation, you can give it a try by going to natureinstitute.org/txt/st/org/comm/news.htm and clicking on the little orange icon near the top right of the page. The main difference between subscribing to the RSS feed and simply bookmarking the page is that, in the latter case, you will not receive automatic notice of new content (via your bookmarks or RSS reader), and the content you’ve previously looked at will not be marked as already read. But, as an aid, I always date-stamp the content items on the page, with the newest placed at the top.

(As an aside: isn’t it amazing how much web content today is undated — and also unattributable to any person with a real name? The omissions seem to illustrate that general detachment from spatio-temporal existence encouraged by our computer assistants.)

What If We Could See Everything Bearing on Gene Expression?

(The text below duplicates the content of the latest posting to the portal page mentioned above. Admittedly, there’s no necessity for the duplication, but this one occasion may serve as a transition to the “new order of things” I’ve just described above.)

On the Toward a 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”.

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.

About This Newsletter

NetFuture, a freely distributed electronic newsletter, is edited and mostly written by Stephen L. Talbott (http://natureinstitute.org/txt/st), author of Devices of the Soul: Battling for Our Selves in the Age of Machines. Copyright 2013 by The Nature Institute. All rights reserved.

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