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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The same, but different…

Epigenetics is a term that is being bandied around quite a bit in the biological literature these days. It is not a new term, but in its current definition the term is used to term heritable changes in gene expression that occur without changes to the DNA.

So what does this actually mean? Well, most people will be familiar with the fact that DNA provides the blue print for how an organism is put together, and that over time mutations in the DNA can change certain properties of what that organism looks like; or they may result in a genetic disease, such as cystic fibrosis or sickle cell anaemia.

However, how do we explain the phenomenon wherein sets of identical Human twins, whom share identical DNA, one twin can develop schizophrenia, pancreatic cancer or diabetes, whilst the other remains unaffected? If we were interpreting their development on the basis of their DNA sequence only, then we have a conundrum.

The answer is that DNA is involved in a dynamic, interpretative process. For example, you may buy a new computer, and in this computer there is a graphics chip that is controlled by a piece of software called “firmware”. This software tries to get the most out of the hardware. Every so often, a new piece of firmware is released, and sometimes it can revolutionise the function of that graphics chip. The chip hasn’t changed, but the software has. This is not a perfect analogy, but what I want to convey is that sometimes the hardware doesn’t need to change; sometimes you can just change the way it’s used.

Thus, the sequence of bases of DNA does not necessarily have to be altered for a new effect to be seen in the resulting organism; some changes can occur by epigenetic processes. There are several different types of epigenetic process, and these differ depending on whether we are speaking about high organisms, such as Humans, or single-celled organisms, such as bacteria.

At the simplest level, one such epigenetic change might be a process call methylation; in this, a chemical group is literally tacked onto the DNA at a certain sequence, which can result in a change of gene expression. If a gene is seen as a piece of DNA that results in a functional product, then we can start to see how changing the level at which this product is produced can have an effect.

One of the recent and interesting findings about such epigenetic changes is that they too can be inherited, leading to questions about the nature of “genetic memory”, the idea that the lifestyle lead by your grandparents can have had a direct effect on the way that your DNA expresses its instructions. In the example of the twins, once identical twin embryos have separated, each cell division can result in the accumulation of an increasing number of these epigenetic changes, adding up to quite a difference over a life-time. Thus even things that are the same can be different.

The perils of positivity….

IN science and medical publishing, everything is positive. Less than 4% of articles deal with negative results. There is a perception that negative results are non-results; only positive results are worth publishing. Why is it that showing that something does something is so much more important that showing that something doesn’t do something?

Obviously, I expect some common sense in this; I don’t very well expect that a paper should be published just because you have demonstrated that drinking water doesn’t cause sunburn, this would be a deeply unsurprising discovery. But what if it is a study that demonstrates that a particular drug doesn’t do what people expected it to do? What if it is a biotechnology that doesn’t work for a whole swathe of biological research?

Online science forums (or fora) are replete with anecdotal evidence describing how time, and time, and time again research scientists make the same mistakes, or encounter the same limitations, in particular techniques. This is because no-one ever publishes such limitations, or at least, not more than 4% of the time.

So what is the problem? Well, science is expensive. Very expensive. It is expensive in material cost, and it is expensive in research hours. To have discovered that you’ve wasted a year doing work that elsewhere in the world someone once wasted a similar amount of time doing, only, 3 years ago, is deeply frustrating.

In coffee breaks around the world, many scientists have discussed the idea of a Journal of Negative Results, a compendium that can be consulted at the outset of a research project to determine whether a technique or approach has already been taken toward a research problem, but has been found not to work. Sometimes such negative results a mentioned, but only in passing, and only after an alternative technique resulted in positive results, which resulted in the subsequent publication. They are rarely keyword searchable and thus inordinately difficult to find.

As I mentioned, science costs a lot of money, far more money than is necessary. This is largely because the money isn’t real, there is poor ownership of it, it is monopoly money. If it were coming out of our own pockets, we simply wouldn’t pay the price we do, we’d demand more competitive prices. Consumable companies are free to charge extortionate prices for items that they are producing by the million. I have tubes in my lab that cost £3.75 each; they can only be used once, and invariably one or two of them can be wasted due to one problem or another. Kits are all the rage in research; pre-fabricated methodologies with all the reagents and instructions one needs to perform a particular experiment. The reagents themselves cost practically nothing in most cases, yet the kits can cost anywhere between £300 – £1500, and in many circumstances, afford you between 5 – 20 experiments.

Now this combination of expensive research is part of what leads to negative results being unwanted. There’s no real money in debunking an idea, it must come along side a positive result if it is to come at all. In the pharmaceutical industry, it is part of the reason why any new drug being produced is just too much of an investment to allow to fail, so the pressure is on to ensure, by hook or by crook, that the drug is licensed. Ben Goldacre writes at length about this in his recent book, and blog of the same name, Bad Science; this is most definitely worth a read!

Expensive research also prevents investment into rarer diseases, or any medications that run the risk of having a short shelf-life. One class of drugs that have fallen foul of this economic equation are antibiotics, and this is a rather long pre-amble into what I wanted to say in this blog essay (or blessay, and Stephen Fry attests to horribly calling it).

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“Two plus two makes five” – Winston Smith, 1984.

IF enough people believe it, or if it is illegal not to believe it, will it be true?

I spend a lot of my time, probably too much, waging a battle of wits and reason with the truly and irredeemably unreasonable. The usual subject is the scientific theory of evolution. I preface the noun “theory” with scientific so as there is no mistaking exactly what we mean by theory.

Whenever I hear the words “Just a theory….” levied at a scientific theory, it sends a shudder down my spine. As I’ve mentioned before, and I will undoubtedly continue to do so, a scientific theory is not speculation or opinion, it is a comprehensive, logical and above all testable model that represents the best means of explaining the evidence. Furthermore it facilitates predictions that can be tested experimentally to continue to verify the reliability of the theory. The theory of evolution is just such a theory:

The theory of evolution explains that variation exists between individuals within a species, it explains how natural selection can act to drive this variation and it shows how, and describes why, some organisms display characteristics that make them better suited, i.e. fitter, for life in the environment in which they live. It explains how these “fitter” organisms are the ones more likely to survive and pass on their characteristics to offspring. It explains how, over time, these characteristics become a trait in all members of a species, and how less favourable characteristics can be lost. Ultimately, the theory of evolution explains how a species, over this long period of time and subject to much genetic change steered by natural selection, can be very different from its ancestors.

Now, the above paragraph is qualitative, and largely non-technical. However, bound up within the above is some impressively complex science. The debates that rage amongst scientists is not about the validity of the above, it’s about the specifics of how they’re achieved. Part of what I aim to do with this blog is not re-write any of the perfectly excellent books on evolution that are available, but to tackle those areas that are taken advantage of by religious fundamentalists. Science is a dynamic subject; by the time it is written up in a book, it is already out of date. As I mentioned before, there is a battle of wits going on out there, between scientists or other such rational free-thinkers, and religious fundamentalists (which for want of a better term, I call “Fundies”).
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On science in society

[ratings]

AT this time, as the Large Hadron collider (LHC) comes online, and we hear tales of the doomsayers (and here) who would stifle curiosity, free enquiry and discovery, I think to my own area of science and the great efforts we have to go to defend the science that gives, and has given, so much to society. The LHC beam line has thus far met all expectations, and when it starts the actual collisions in the next few months there is absolutely nothing to suggest that it will cause the end of the world. Science is under attack like never before; media sensationalisation, poor science education, the barrier between those “in the know” and those not, and the rise of religious fundamentalism are largely to blame.

There comes a point when you really must accept the advice of experts, because you can’t expect to be an expert on everything about which you hold an opinion, this would be an unreasonable and untenable position. You trust that a cardiac surgeon knows how to perform your quadruple by-pass surgery; you trust that aeronautic engineers have really created an aeroplane that will fly; and you trust that if you buy a phone, you are in fact going to be able to call someone with it. So if the LHC scientists say that the comparatively low energy bombardments (yes, large for human experiments, but nothing compared to what the Earth experiences from the Sun) are not going to cause cataclysmic damage to the Earth, then you have to trust that they are sensible, rational, careful and intelligent people who know what they’re about, and believe that what they are doing is good for our society.

Many people go through life imagining worldly attributes into a world that is inherently, and obviously, physical in nature. A world that does not in fact conform to any such imaginings, except in the heads and societies of those who enjoy protection from the crueller and more selective attributes of the physical world; a protection afforded to them by scientists, technologists and engineers, people whom they presume to lecture, deride and slander in the errors of our ways. This is largely because the pursuit of knowledge in the physical world has resulted in knowledge that contradicts the inherited fantasy of some social groups. All I would say is that it is not sensible to hold an opinion in the face of overwhelming evidence to the contrary; wisdom comes from noticing when ones opinions are disproved by evidence.
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Intellectual vandalism….

There is a new fictional film, masquerading as a documentary, currently being aired in the US.  Several of my US friends went to see it (admittedly mourning their monetary contribution to the creationist cause) and have let me know not to waste my life, or money, going to see it. In turn, I encourage similar of anyone reading this. The fiction-doc is called “Expelled: No Intelligence Allowed” and it is yet more anti-science propaganda in favour of Intelligent Design, spewing outlandish, intellectually dishonest rhetoric. In their polemic pursuit of self-righteousness they also managed to demean a host very respected scientists, including Richard Dawkins and PZ Myers.

I’m not fond of commenting on things I haven’t actually seen, but I am of like-mind with my friends, and to be honest, I’m painfully well aware of the nature of such attacks on science; the very discipline that has permitted them the technology of producing a film in the first place. The National Centre for Science Education has produced a website to address the intellectual vandalism the film may do to those lay audience members who may inadvertently take the producer at his word.

The producer, amongst other things, contends that the theory of evolution contributed to the holocaust committed by the Nazis, communism and the rise of atheism. This is of course nothing new, creationists have been peddling this tripe for a long time; it is all part of their belief that atheists are inherently immoral, as if atheism is itself a religion that preaches immorality. Alas, like little children, they cannot believe that anyone can know something that they don’t.

To address one point however, one might suspect that such an arrogant and self-righteous man as Hitler would happily go into depth about how he employed evolutionary theory in his final solution, yet never once does mention evolutionary theory in the whole sorry tirade of Mein Kampf, I know, I’ve read it. Furthermore, he was on a crusade to create an Aryan race, whom he believed to be the created in the highest image of the lord; hardly the comment of a proud atheist or evolutionist.

Religions deal in the manner in which they believe people should live their lives, unfortunately, to those arguing from a platform of ignorance about science, there is a general misunderstanding that science similarly prescribes a way of living. This is not correct. Even if Hitler had been employing the theory of evolution in his reasoning, this does not mean that the theory is any way morally awry. Evolution is a scientific theory, it is neither good, nor evil; science makes no prescriptions on how to live your life. It is not to be confused with Social Darwinism, which is a philosophical construct based upon “survival of the fittest”.

Richard Dawkin’s premise is that by understanding natural selection we can selectively abrogate the rather emotionless and indifferent edge of this process, not become slaves to it.

Spirituality

AMAZEMENT still strikes at our primitive emotions. When we are left in bewildered awe at a spectacle or new insight, it tugs at us in a manner that a reasoned scientific account can do no justice. It is, in many respects, a “religious” experience, but the word “religious” is bandied around in place of a slew of terms that could be used.

Such experiences are spiritual, being of matter (the brain still being a material object), yet insubstantial and deeply emotive. Whether it is some perception of a deity, or a new dimension of worldly understanding provided by science, these experiences are linked in their spiritual nature. In fact, I am with Carl Sagan in my belief that science is a profound source of spirituality.

In talking about spirituality, there is no implication of talking about religion. Spirituality is a sense of meaning (or purpose) and unity, but it does not have to be divinely inspired; it should not be confused with mysticism, which is concerned with magic, the occult and supernatural. The scientific journal Nature defines spirituality it as “An inner sense of something greater than oneself. Recognition of a meaning to existence that transcends one’s immediate circumstances”. It’s a good word, and one that we ought to take back, releasing it from its pre-scientific context.

Nature and the universe certainly put us in our place with the realisation that the atoms that make up your body are billions of years old, they’ve made many other things in their existence, and will continue to do so long after we’re gone; we are simply borrowing them for a while. Scientists, and readers of science, have a lot to be spiritual about. We have a particular impulse to understand the world around us. It is a great injustice to ignore the natural world in favour of an inferior and artificial facsimile in the form of the supernatural. Why ignore what is in front of your eyes, from the sub-atomic to the cosmos, and instead make it up?

Science doesn’t have all the answers, but it has more than any faith can offer me. Science has so many more questions that it will answer, whereas most faiths have said everything they have to say. Fortunately, as a rational human being, and a scientist, I don’t need anyone to agree with me to be comfortable in my reasoning. If a million scientists decided to recant on DNA being the basis of genetic inheritance, unlikely as that is, it would mean nothing. DNA would still continue to be the basis of genetic inheritance unless they had hard evidence to the contrary. It is this facility than enables freethinking, rational people to be truly uninhibited and unprejudiced.

So why is spirituality important? Science can, in a practical sense, only really deal with the material; though this “material” may extend well below the size of an atom, or may be as intangible as love or trust. We still inhabit physiologically stone-age bodies with minds hard-wired for day-to-day problem-solving, strategic planning and interacting with the physical world that our ancestors could see, hear, touch, smell and taste. Yet we managed to arrive at this state in the absence of both writing and mathematics. Most of what we’ve achieved since then has been achieved by co-opting these more primitive thought processes (the original “transferable skill” set) and applying them in a new direction: complex reasoning and abstract theoretical modelling, applied to science and mathematics.

It is no surprise, therefore, that much of what we have learned in science is difficult to process, especially when they are beyond the resolutive power our innate senses; we need things to have defined boundaries and exist at the right scale. We know there is a sense of change; that processes are shaping life, the planet and the universe around us. We are part of something shared, much greater than ourselves, and every time science offers a new awesome insight into this, we find a connection with our spirituality.