Mental Indigestion

by Jim Caryl

Month: February, 2009

Writing about reading…

READING about writing has been a pass time for some time, but writing about reading is a first. Those who know me know that I am a passionate reader; I’ll read from an eclectic range of genres, though of course I have my favourites. But I don’t really want to write about what I read, rather, I’d like to write about how I read.

My entire life, well, teenage onwards, I have carried a rucksack or satchel wherever I go. In this bag I always have certain essentials: a notebook, pens, journals, papers and a book (or two). More recently I also carry an iTouch and mactop, and perhaps more bizarrely, a torch and a whole array of iPod, camera and mic adaptor cables. You see, on the one hand I love technology; I am an unashamed technocrat, though perhaps less so than the eminent Stephen Fry. On the other, I lament the loss of handwriting, and very much enjoy putting pen to paper, hence the notebook. One thing I can never be without, however, is some reading material.

I almost always have more reading material than I would ever have time to duly read and digest, but carry it none the less, hoping I may just absorb the material by prolonged contact. This is certainly nothing unusual, most academics and students I know have been guilty of carrying papers around for weeks, without ever actually doing more than skimming them.

Books though, what a slave to them I am, and what guilt they engender by the mere fact that I haven’t read all of them yet! The process of preparing to read a book is described quite nicely in a recent article by Mandy Brown at A List Apart; the article is not exclusively about this subject, being more to do with the process of presenting web writing in an accessible and readable manner, but she none the less echoes any sentiments I could offer:

Think of your first encounter with a book. You look at the cover to get a sense of it, then perhaps flip to the back or the flaps to skim the publisher’s copy. Opening the book, you might glance at the title page, or quickly run your eyes over the table of contents. Maybe you peek into the back to check the page count, or casually assess the weight of the book in your hand. If it’s a hardcover, you might take the dust jacket off, lest it get in the way.

Most readers engage in at least one and usually several of these behaviors—they’re a kind of pre-reading ritual, part of the culture of books. And yet they serve an important purpose as well, in that they ease the transition between looking and reading. They help the reader establish interest, and they serve as an invitation to reading, setting the stage for the act that follows.

I spend a lot of time looking, holding and admiring books. People say, “Don’t judge a book by its cover”; I’m not sure which people, but people say this. Now I don’t think anyone would say that a book is crap based solely on how it looks, but they’ll certainly pass it by. Time is so limited now, so precious. If we’re going to invest our much prized spare time by reading the labour of one author, amongst so many others, then there has to be a draw. In the absence of the Times Literary Supplement, New York Book Review or some other trusted review of current literature, how else do we pick out books if not by them grabbing our eyes?

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Wordle update…

Time for a new Wordle: see at a glance what I’ve been blessaying (blog essaying) about recently.

A dichotomy of research…..


I AM a juggler by profession, but it is not balls that I juggle; instead, I juggle variables.

I currently work on basic technologies research. This does not mean to say that my research is basic, rather it means that the technologies that we are trying to develop are at a fundamental, or grass-roots, level. As such, some might call such research ground-breaking; though I hasten to add that this term is more considered in it’s metaphorical context. If any of you have ever had to dig in a new garden, or have led the way in deep snow on a mountain, then you’ll have some idea of what breaking new ground is all about. It is hard, unrelenting and there is no lateral movement, you either move forward into new ground, or you back-step until you get to base camp and set off in a new direction.

I am working on a biochemical reaction (a reaction involving biomolecules such as proteins and DNA) that has been shown to work in solution, in a tube. Other people have shown this, and I have shown it. However, interesting as this reaction is, we want to go further with it and have it work on a solid gold surface. Why? Well, ultimately we would like to be able to control the reaction by using an electric field, to turn it on or off, or better still control the precise level of its activity.

Having a biological system that works at the flick of a switch seems like a pretty cool idea, right? You’re sitting in a small, dusty village in central Africa or central South America. You’ve taken a load of blood and saliva samples that you intend to test for certain antibodies, or for the presence of current bacterial or viral diseases. It’s hot, there is no power and it took you a week of travel to get there. You are worried that your samples will degrade before you can get into a position to test them, and if you are especially well funded, you will have brought a whole portable lab with you, at great cost, and at great loss if it breaks on route.

What if, instead of the above hassle, you take out the small box you brought with you, in which there are several foil-wrapped packets containing plastic cassettes about the size of your thumb, but considerably flatter. What if you could inject the blood or saliva sample in at one end of the cassette, wait a minute and at the other end one of several LEDs light up. The combination of LEDs will tell you what the cassette has detected. Inside the cassette are small flow-channels that each contain different biomolecules that have all been painstakingly developed to function in this capacity. Simple, potentially very cheap, a laboratory on a chip.

Furthermore, you flick a switch on the cassette, which makes the juice from the small battery alternate from just powering the LEDs to instead put an electric field through the flow-cells; you can now conduct a second set of reactions using biomolecules that had been inactive until that point. TWO labs on a chip! Lab on a chip technology already exists, but there is much further for it to go, and this requires basic technologies research.

Ideally we would have a chip that could perform logic functions, so rather than it just detecting molecule A and it saying “hey man, you’ve got some molecule A here”, or likewise with molecule B; perhaps if molecule A and molecule B are both present, then this indicates something more serious, which is indicated by the presence of molecule C. Rather than you wasting time, and another chip, going back and testing the blood sample again for molecule C, the chip can detect both A AND B in combination, and in doing so will have activated another internal component that is able to then detect C. However, if the chip detects only B, NOT A, then this could indicate something else, so it triggers something that can detect this something else, perhaps molecule D. See? A logical chip.

Well, returning from the realms of near-future science fiction, in order to achieve any of the above in my basic technologies research, there are several variables we (meaning I) need to juggle, and this is where the fun pain starts:
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Writing for all…

Who are the best people to communicate science? Is it the actual scientists producing the science? Is it other scientists who are not directly involved in the science? Is it journalists or science writers? I would argue that it is largely irrelevant; the best people to communicate science are those who are interested in it.

If you would have asked me the same question 10 years ago, I might have answered differently. I might have suggested that it is best that scientists communicate science and that journalists leave well alone, but then these would be the words of a recent graduate, cock-sure and arrogantly entering into their chosen field with the kind of bravado that I still see in every newly minted graduate. In any case, 10 years ago we were dealing with the height of the MMR-autism fallacy that demonstrated precisely the wrong way to go about reporting science. As we get older though, we mellow as we start to see the bigger picture; amusingly it is this attitude that is probably responsible for so many teenage tirades against their parents, the teenager believing that the parents don’t take anything seriously, and the parents, having seen it all before, have the benefit of perspective.

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A question of balance…

Giving equal attention to “all sides” can misrepresent the prevailing scientific consensus.

One of the major issues that is often debated in science journalism is one of balance. It is an issue raised to public awareness by a pamphlet produced by Chris Mooney entitled, ‘Blinded By Science: How ‘Balanced’ Coverage Lets the Scientific Fringe Hijack Reality’ (Columbia Journalism Review, November 2004). In it he asserted:

…the journalistic norm of “balance” has no parallel in the scientific world and, when artificially grafted onto that world, can lead reporters to distort or misrepresent what’s known, to create controversies where none actually exist, or to fall prey to the ploys of interest groups who demand equal treatment for their “scientific” claims.

A journalist may try to find a compromise or objective ‘truth’ by combining numerous sources and affording them equal opportunity to give their opinions, and allow the reader to make up their mind. The question is, how well does this journalistic system of ‘objectivity’ serve a science journalist when reporting on science topics.

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Hox box…


WHAT do hedgehog, merlin and okra have in common with jelly belly, pimples and Genghis Khan? What if I said that hedgehog is not just a cute, spiny mammal? That Merlin is not just the name of a bird and a wizard? That okra is not just a vegetable? Would you be interested to learn that “jelly belly” is crucial for gut muscle development? “Genghis Khan”, far from being a Mongol lord who conquered Asia, is involved in the stimulation of structural components in cells. Oh, and we can look to “Merlin” to restrain cell proliferation.

Confused? Don’t be. They are all names of genes – sequences of DNA that exert influence on a creature by encoding and regulating the production of a protein. These particular genes are found in Drosophila melanogaster, otherwise known as the fruit fly.

Scientists are interested in a region of the fruit fly chromosome called the “homeobox”. The homeobox (“homeo”, from the Greek for “similar”, and “box” as the sequence is in a defined package) contains “Hox genes”. First identified in fruit flies in the early 1980s, they control the different aspects of body development: head, legs, wings or other structures. Interestingly, many other creatures, including humans, possess these genes, where they carry out similar functions. We are all basically running on the same genetic software.

Research in this area is helping us to understand why our head is where it is, why we have two arms joined to our upper body and not to our hips, and why we have feet, rather than hands, at the ends of our legs. More significantly, they are helping to identify the genetic basis of certain human diseases by helping us understand the mechanisms of this genetic control; errors in embryonic development account for a large number of spontaneous abortions in humans.

Hox genes produce simple proteins that govern the activities of other “target” genes, which result in the development of a specific body parts at specific locations; it is those “target” genes that contain the specific information about how and what appendages look like,  and the hox genes control the degree to which those target genes are switched on or off. The arrangement of genes mirror the arrangement of the body parts they control, starting with the head at one end, followed by the mid-sections, and so on. It’s a logical blueprint that works because it represents economy of information.

In the above figure the hox gene clusters of the fruit fly are colour coded for the respective sections of head-bottom development they control, and below are the homologous (performing the same function) genes in a mouse. Whilst we mammals have four clusters of these gene groups, some of which have become redundant or lost due to compensation by one of the other clusters, the startling similarity with the fruit fly hox cluster is unmistakable.

So over the course of millions of years, despite the changes to body form and function (the changes to the specific genes that the above clusters control) in the course of animal evolution, the controlling elements themselves have been conserved. This says something important about the blueprint of animals on Earth; if it works, keep it.
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