The dead zone…

rb2IMAGINE that you’re walking along a path in the middle of a prairie, minding your own business. As you’re walking, you find yourself getting out of breath; you find you’re unable to exert yourself as you can’t seem to breath fast enough. Pretty soon you start becoming slovenly, slow moving, dulled; there’s something wrong with the air, there’s not enough oxygen; you’re in the ‘dead zone‘. You try to move away from where you are, but you don’t know where the bad air started. Before long, it’s too late.

A similar experience may happen to deep ocean fish. They need oxygen too, they just manage to get it from the water, but there’s a problem. A report in the April 17th edition of Science, by Peter Brewer and Edward Peltzer (Monterey Bay Aquarium Research Institute, Moss Landing) describes how ‘Ocean “dead zones” [defined as regions where normal respiration is greatly limited and the expenditure of effort is physiologically constrained], devoid of aerobic life, are likely to grow as carbon dioxide concentrations rise.’ In order to understand what their report is about, we need a little background.

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To whom are they selling…?

IN the past few years I have found myself on the receiving end of some fairly bizarre advertising campaigns from large biotech companies.

First there was MWG Biotech (as they were called at the time), who make short stretches of single-stranded DNA called oligonucleotides, which many of us use in our experiments. They decided to market these using cartoon characters, the chief of whom was ‘Olly Oligo”. This was the first time I asked myself, ‘who the hell are they aiming this at?’

Then we were assaulted with the extremely kitch ‘PCR Song‘ from Bio-Rad. Thanks for this guys, it took weeks to try and forget it.

PCR song
Bio-Rad's PCR Song

Then came Eppendorf’s ‘It’s called epMotion‘ music video for a robotic liquid handling station; a deliberately tongue-in-cheek boy-band styled affair, also available as a ring tone. I wasn’t swayed.

Eppendorf's epMotion boys
Eppendorf's epMotion boys

The most recent shockers, inciting this post, are from the Biotech giant Roche, who are marketing a means of monitoring cell cultures using electrical impedance measurements, xCELLigence. However, they’ve gone for a more obvious tack. They’ve done a rock video.

Roche's exCELLigence rock
Roche's exCELLigence rock

Actually, they loved it so much, they did a second rock video. Why do just one when you can have two videos for twice the price?

I’m actually now speechless.

The great divide…

[ratings]

IN geographic terms, the ‘great divide’ is used to define the point in the USA, roughly following the course of the Rocky Mountains, where on one side a drop of water will run down into the Pacific Ocean, and on the other, it will run down into the Atlantic.

There is however another great divide in the USA, which is between those that have a basic knowledge of the world around them, and those that don’t. The online newszine Science Daily described a recent poll commissioned by the California Academy of Sciences, in which a series of basic questions, designed to assess basic science literacy, were posed to 1,002 adults over a four day period last December. The poll has been ongoing (though in a less rigorous sense) online at the CAS website. The results were as follow:

  • Only 53% of adults know how long it takes for the Earth to revolve around the Sun [a year, 365 days]
  • Only 59% of adults know that the earliest humans and dinosaurs did not live at the same time. [Duh]
  • Only 47% of adults can roughly approximate the percent of the Earth’s surface that is covered with water. [where the answer of 65-75& was taken as approx. correct, though 15% gave the correct response of 70%]
  • Only 21% of adults answered all three questions correctly.[!]
  • Less than 1% of U.S. adults know what percent of the planet’s water is fresh [3%]

Hands up who thinks this is unacceptable?

No, it’s not. So why is the USA finding it has a problem with scientific literacy? Well, please just indulge me. Let’s think about Pakistan, where many (though not all) Madrassas (Islamic schools) are engaging in the indoctrination of a new generation of children into fundamentalist rhetoric; this comes at the cost of education that can raise people out of poverty and morbidity; education that gives them some control over their lives. However, for many, Madrassas are the only source of ‘education’. Yet if you speak to a young professional on the street of moderate urban centres such as Karachi, they are not going to present you with the fundamentalist hard-line; they are the lucky few, to have been born into a better area, perhaps to a richer family whom are well educated.

It is not such a great step to see such a partisanship developing in the USA, with the richer, well educated ‘elite’ being outnumbered by those who are disenfranchised from modern successes, scientific discoveries and societal benefits. Those left behind in progress increasingly turn inward toward timeless stalwarts such as the fundamentalist hard-line, which not only serves to widen the gulf to be crossed by communicators of science, but ultimately results in senators, congressmen and governors becoming willing to bow down to public anti-science opinion, i.e. votes, at a government level, thus jeopardising the future scientific and medical progress.

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A dichotomy of research…..

[ratings]

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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Premature conclusions

Something the media is very good at, and alas some scientists too, is making a conclusion about a scientific investigation before actually performing the investigation.

This is not how science works!

A recent example of this appeared in today’s Daily Mail, the popular gutter-rag that leads the way in pseudo-scientific sensationalism:

Women who drink coffee or tea during pregnancy may increase their baby’s odds of developing cancer, doctors believe.

Experts say caffeine may damage the DNA of babies in the womb, making them more susceptible to leukaemia, the most common cancer in children.

To establish the link, scientists at Leicester University will scrutinise the caffeine intake of hundreds of pregnant women and compare the results with blood samples from their babies after birth.

Researcher Dr Marcus Cooke said there was a ‘good likelihood’ the study would make a connection. Previous research has shown that caffeine damages DNA, cutting cells’ ability to fight off cancer triggers such as radiation.

Changes of this kind have been seen in the blood cells of children with leukaemia. Scientists know they occur in the womb, but do not know why.

‘Although there’s no evidence at all of a link between caffeine and cancer, we’re putting two and two together and saying: caffeine can induce these changes and it has been shown that these changes are elevated in leukaemia patients,’ added Dr Cooke.

So, they’re planning to investigate this link, though Dr Cooke is quoted as (apparently) saying there is a ‘good likelihood of making the connection‘, despite, as he is later quoted, there being ‘no evidence at all of a link between caffeine and cancer’.

Dr Cooke is also quoted as saying that ‘previous research has shown that caffeine damages DNA, cutting cells’ ability to fight off cancer triggers such as radiation‘; now, I am not going to judge Dr Cooke on the basis of such quotes, because I well know how much gutter-rags like to quote out of context, but I can’t help wondering whether this prior research was a case of caffeine being introduced to cells in a dish, rather than to an actual living and breathing mammal. Any number of chemicals can cause physiological disturbance to cell cultures, but these do not necessarily translate to their being harmful to us generally.

So what’s my problem?

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