Mental Indigestion

by Jim Caryl

Month: November, 2009

The ‘negatome’ – a database of negative information…

Research bloggingWE researchers often joke that no-one ever publishes negative results, but that doesn’t mean to say that negative results aren’t extremely useful. On one level, knowledge of such negative results can prevent you repeating the same mistakes that countless other researchers, in other labs, have undoubtedly made over the years. On the other hand, they can provide a valuable dataset with which to generate new and useful information. One such example is the ‘Negatome Database‘, which has been reported by Smialowski et al.1 in Nucleic Acids Research advance access (November 17, 2009).

The Negatome is a collection of protein and domain (functional units of proteins) pairs that are unlikely to be engaged in direct physical interactions. But why on Earth would we want to know about proteins that don’t interact with each other; in fact, why do we need to know about proteins that interact at all?

Macromolecular machineResearchers recognize that that a cell doesn’t function purely by the action of individual proteins, but instead by large macromolecular complexes mediated by many interacting proteins.  The image to the left indicates an example macromolecular ‘machine’, in this case those involved in signal processing at the neuronal synapses (and which are likely to be working quite hard right now!).

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I WAS in London last weekend (pics) meeting some wonderful people. One topic of conversation that came up late one evening was spirituality. It’s something that I have, in the past, had a lot to speak about. However, often pre-conceived notions of what spirituality really means (and we are well into in the realms of semantics here) hinder some discussion. This wasn’t the case the other day; as cursory as the discussion was, spirituality was not viewed as a skeptically-negative concept, but we were all way too tired, and the safe side of sober, for that discussion to last.

I’m re-posting an old post, written when I had something to say about the matter.


Post, of the same name, re-posted from an earlier incarnation of this blog:

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.

Windshield splatter analysis…

rb1A few years ago I took part in an RSPB survey called the Big Bug Count, which sought to quantitate what had hitherto been anecdotal accounts that the number of insect splats on car windscreens had decreased in recent years. Essentially it was a sticky pad of define area that was placed on the front registration plate of your car. Following a car journey (I drove the 20 miles from from Keswick to Windermere), the number of bugs splats were counted and the results submitted.

Some suggested that the dwindling insect splats may in fact be due to cars being more aerodynamic, and not the tin boxes of previous decades. However, even I had noticed that I was swallowing fewer bugs on my bike rides around Cumbria than my childhood years, but hardly scientifically rigorous data – I do after all scream with glee less now than I used to.

Unfortunately, because the ‘bug splat’ survey, as it became known, was the the first such study by the RSPB, they could draw no conclusions as to whether the insect population was dwindling (despite what some press articles claimed) until subsequent seasonal surveys, over multiple years, were performed.

Of course, what some of you may have noticed is that the RSBP doesn’t seem to have followed up with any further surveys – at least none that I’ve been able to find in 30 mins of googling and scouring their website. Shame, so we had a baseline, of sorts, against which nothing further has been measured.

But assessing species diversity is an important task, as I’m sure anyone can appreciate. Changes in biodiversity act as markers of climate change or pollution, and have knock on effects on the food chain, such as bird life.

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Stand up for research…

I’VE had a bit of an axe to grind recently about the government’s proposed policy on requiring such a large proportion of research funding to be allocated on the basis of economic and social impact. The University & College Union (UCU) is curently hosting a petition, signed against the statement that I’ve copied from their site below.

Sign it if you care to.

From the UCU’s website:

The latest proposal by the higher education funding councils is for 25% of the new Research Excellence Framework (REF) to be assessed according to ‘economic and social impact’. As academics, researchers and higher education professionals we believe that it is counter-productive to make funding for the best research conditional on its perceived economic and social benefits.

The REF proposals are founded on a lack of understanding of how knowledge advances. It is often difficult to predict which research will create the greatest practical impact. History shows us that in many instances it is curiosity-driven research that has led to major scientific and cultural advances. If implemented, these proposals risk undermining support for basic research across all disciplines and may well lead to an academic brain drain to countries such as the United States that continue to value fundamental research.

Universities must continue to be spaces in which the spirit of adventure thrives and where researchers enjoy academic freedom to push back the boundaries of knowledge in their disciplines.

We, therefore, call on the UK funding councils to withdraw the current REF proposals and to work with academics and researchers on creating a funding regime which supports and fosters basic research in our universities and colleges rather than discourages it.

[12,007 signatures at 11:43, 16 Nov 2009]

Sign the petition here.