Food for thought…

FINALLY, some lectures that don’t require a trip to London. Some big names are coming all the way up North, way up to the provinces, to give lectures as part of a celebration of 150 years of On the Origin of Species:

24th November 2009

2pm: Dr Gordon Chancellor
Charles Darwin, his life and his science
Dr Gordon Chancellor is from the UK Data Archive at the University of Essex. He is an Associate Editor of which hosts the largest online resource in the world relating to Charles Darwin.

2.45pm: Professor Steve Jones
Is human evolution over?
Professor Steve Jones is Professor of Genetics at University College London and is one of the best known contemporary popular writers on evolution. He is a television science presenter and writes a science column in the Daily Telegraph.

3.30 – 4pm: Interval

4pm: Professor Sydney Brenner
The Reconstruction of the Past: Reading the Human Genome
Professor Sydney Brenner opened the JIF building in 2007, now known as the Wellcome Trust Brenner building. Sydney was awarded the Nobel Prize for Physiology or Medicine in 2002 for his seminal work on discoveries of organ development and programmed cell death.

4.45pm: Professor Sir Alec Jeffreys
DNA fingerprinting and the turbulent genome
Professor Sir Alec Jeffreys is Royal Society Wolfson Professor at Leicester University. He discovered DNA fingerprinting 25 years ago. Among other important aspects of this method is that it allows identification of people by detecting variations in their genomes and has altered forensic science world wide.

5.30pm: Close

It’s going to be popular. Off to try and get a ticket, otherwise I’ll be sweating it out in a lecture teatre watching a live video feed instead.

Holes in the ice…

Research bloggingCRYOCONITE (‘ice dust’) holes are small pock-like depressions that are strewn over the surface of glaciers, looking much like a pristine snow drift after you’ve thrown a handful of gravel at it. Such melt-holes have been documented on glaciers at both poles, and on other glaciated regions such as Iceland, Greenland, Canada and the Himalayas. According to one account, at least, cryoconite holes  have been a bane to scientists working on the Greenland ice sheet, the holes being typically full of slushy ice, and big enough to step in by accident. However, cryoconite holes have been the subject of much debate in recent years; a debate centring on their role as contributors to glacial melting. Continue reading “Holes in the ice…”

Bug eat bug…

This post was chosen as an Editor's Selection for ResearchBlogging.orgAS if it’s not hard enough at the bottom of the food chain, being cannibalised by your own bottom-dwelling compatriots must add insult to injury. The soil dwelling Gram-positive bacterium Bacillus subtilis is fully equipped to take appropriate action when faced with food shortages; a sub-population of cells initiate a process of dormancy by turning themselves into hardy, robust spores. In this form the bacteria are capable of enduring temporary, or prolonged, harsh environmental conditions.

However, this is not a process entered into without some careful deliberation. Sporulation, the act of forming a spore, is an energy intensive process that results in the formation of the essentially inactive spore, and the death of the ‘mother’ cell producing it. It comes as no surprise, therefore, to discover that B. subtilis has evolved a means of delaying sporulation as long as possible.

In an alternative strategy,  a sub-population have a genetic pre-disposition to become cannibals.

Continue reading “Bug eat bug…”

Risk taking and audacity in science…

Research bloggingIn the October edition of Cell1, Amy Maxmen, a New York based science writer, discusses how tackling long-standing scientific problems (i.e. studies that have been prone to failure), or refuting dogma, are perceived to be a poor strategy for early-career researchers; and contends that perhaps they shouldn’t be.

One of the reasons for this is down to the policies of research grant committees.

A common complaint among researchers is that in order to be funded, they feel they must submit conservative grants filled with so much preliminary data that their predictions aren’t quite predictions any more. As Venter says, “The problem in [grant] study sections is the philosophy of proposals being reviewed as contracts instead of ideas.”

My own thoughts are that sometimes the amount of preliminary data required in a grant submission is so great that you’re half way to addressing the research goals at the first base, but only at the cost of the remnants of the last grant, which were used to finance the preliminary studies for the next. It’s as if the research councils are looking for a sure thing, a guarantee of success.

This is not how science should work.

Continue reading “Risk taking and audacity in science…”

Lateral thinking…

[Promoted from my Posterous ‘Overflow‘ blog…]

LATELY I have been wresting with a particular problem in the lab. I have been trying to put a rather complex DNA molecule down on a gold surface with the aim of having it perform the same chemistry on a surface as it does in solution.

Generally, when putting DNA down on a gold surface, we synthesise our DNA with a particular chemical modification, a thiol, on one end of the DNA strand. A thiol is essentially a sulphur atom, usually together with a hydrogen (-SH), and sulphur forms a strong bond with gold, so this is we want.

Unfortunately, we live in a very oxidizing world (basically, everything rusts), so my thiol gets oxidized to a rather less useful S=O. There are numerous other atoms that can reduce my thiol too, such as other thiols, or metals such as magnesium, zinc, copper etc.

This isn’t generally a problem as an oxidized thiol can be reduced back to -SH, making it ready to react with my gold surface.

Only, it turns out that my DNA adheres to the gold at too great a density. Like a mosh pit at a concert, the poor blighters are unable to move, and this results in them being unable to perform the particular reaction that they normally manage when not constrained.

So I modify my approach and use another layer between the gold and the DNA. This layer can be used to dictate how much of the gold surface is actually available to be bound. The chemistry is quite complicated, with several steps, all of which degrade quite rapidly, so it has me running around to make sure I get all the steps completed in time.

First a layer of long floppy carbon chains go down on the gold, and the ends of these molecules are reacted with another chemical that makes them able to react with yet another chemical, this latter chemical being capable of reacting with a thiol. Phew.

I have spent more time than I care to mention trying to get this approach up and running, all the while having to deal with the fiddly, slow and rather cumbersome thiol-based chemistry, which has a propensity to rust.

Then it occurs to me. The only reason I was using a thiol on my DNA in the first place was to stick my DNA directly to a gold surface. As I’ve already determined that we can’t do this (too dense), I really don’t know why I’ve spent time running around testing numerous crosslinking agents that can link the surface to my thiol-DNA.

Time to ditch the thiol and use something that connects DIRECTLY to the first layer of floppy carbon chains.

Never mind the blue skies…

IN YESTERDAY’S Guardian, Ian Sample highlighted the threat posed to British physics if the government maintains its inexorable stance that science should be aimed at money-making enterprise, at the cost of answering the big questions about life, the universe and everything.

[UPDATE 07/10/2009: Ian  Sample reports again on 7th October describing that the Nobel prize-winning chemist Venkatraman Ramakrishnan, whose animated lecturing I’ve been fortunate enough to witness, ‘has also attacked government plans to divert research from basic science into projects that are expected to have a quick financial pay-off.’ See also David Mitchell’s wonderfully acerbic commentary on the subject.]

[UPDATE 23/10/2009: The Times has run an article describing how “Hundreds of eminent scientists including Professor Richard Dawkins and six Nobel prizewinners are campaigning against plans to put an end to university research that is deemed worthless….More than 200 chemists, physists and medics say the measures will mean universities will lack the cash to fund academics to undertake the kind of “blue-sky thinking” that led to the discovery of DNA, X-rays and penicillin.

Here, I re-post a blog I wrote back in April when I learnt of the impending deficit in basic research funding highlighted in the government’s Budget document.

Basic research

[First published 24th April 2009]

TODAY ‘The Scientist’ reported that the UK government is going to bail out biotech, investing £750 million ($1.1 billion) to bolster this and other ailing commercial science and technology sectors. This isn’t a bad thing, per se, but at what cost?

Continue reading “Never mind the blue skies…”

A shortcut to mushrooms…

Research bloggingI REFER in this case not to one of the opening chapters of the Fellowship of the Rings, but in fact to the September edition of Trends in Microbiology, in which a Dutch research team lead by Luis Lugones describe some interesting work with mushrooms.

Building upon an earlier patent by Lugones, the paper by Elsa Berends1, proposes for the first time the use of mushroom-forming fungi (the basidiomycetes) to produce N-glycosylated therapeutic proteins, an important class of protein-based therapeutic drug that represent a multi-billion dollar market.

‘Glycoproteins’ (proteins that have been processed by attaching a small string of sugars) are often prescribed to plug gaps in the metabolism of patients who for various reasons were born with, or have developed, errors of metabolism; these include insulin for treatment of diabetes, erythropoietin for treatment of anaemia, blood-clotting factors for haemophilia and a further 93 products (as of 2007).

Continue reading “A shortcut to mushrooms…”

The cutting edge…

This post was chosen as an Editor's Selection for ResearchBlogging.orgI HAD barely started reading this week’s edition of Nature when in the Research Highlights1 section a study really piqued my interest.

Surgeons operating to remove malignant tumours often struggle to differentiate such tumours from surrounding healthy tissues. To ensure the complete removal of a tumour, surgeons also need to remove some of the surrounding healthy tissue, which of course isn’t desirable, especially in the brain.

A surgical electrode is a popular means to bisect (cut out) tissues. This makes use of a high-frequency electric current that is focussed into a highly localised ‘blade’ that effectively evaporates biological tissue as it comes into contact: water in the cells rapidly boils, proteins are precipitated and the membranes of the cells disintegrate forming a gaseous cloud of molecular ions of the major tissue components.

An innovative study MSpublished by team of researchers in Budapest, lead by Zoltán Takáts2, makes use of the fact that thermal evaporation of different tissues results in gaseous clouds with potentially different ion signatures. The team coupled a suction tube to a surgical electrode, and when cutting begins the tube draws the ions into an instrument called a mass spectrometer, something with which all CSI fans should be familiar. Using this process Takáts’ team found they could differentiate between healthy and malignant tissues, which provides a great basis for real-time tissue analysis under the knife, so to speak.

Continue reading “The cutting edge…”

The science inside…

Research bloggingA THESIS in the current edition of Nature Nanotechnology addresses the tricky minefield of scientists’ objectivity; the premise being that, on the basis of several lab studies carried out by social scientists, science is more subjective than many scientists realise.

Such lab studies stem from the desire to understand the creation of scientific knowledge from within the scientific community, which is certainly a worthwhile subject of study, but then again, if you were to walk into an operating theatre halfway through a bowel resection, you might think they were actively butchering the poor patient. I would thus err on the side of caution before leaping to conclusions about the validity of science on the basis of such sociological discourses.

There is this rational scientific ideal where, in order to be as objective as possible, we withdraw from our personal identities (nationality, gender, religion), thus diminishing our individuality and, consequently, our subjectivity. This of course sounds like a lab full of robots, and frankly the idea of working in a lab with a bunch of emotionless, predictable automatons makes me shudder. Then again, some of us do, and I’d love to hear how that works out for those people.

The thesis cites two influential pieces of ‘lab studies’ literature, both within high-energy physics: on one side (in Beamtimes and Lifetimes, by Sharon Traweek), it was revealed that scientific culture was replete with subjective cultural values and practices, yet Traweek concluded that,

good science can come from a lab even when various kinds of subjectivity are at work.

On the other side (in Constructing Quarks, by Andrew Pickering), this is contrasted by the conclusion that the scientific culture was so far removed from the ‘ideal of pure objectivity’ that,

the understanding of quarks developed by physicists was not to be believed because the science had been corrupted too much by non-scientific influences.

Fortunately, the thesis continues, most lab studies are closer to Traweek’s than Pickering’s, yet despite the differences in their conclusions, both studies address a mild concern of subjective values and practises.

Continue reading “The science inside…”

Addicted to DNA…

Research bloggingBACTERIA can find themselves in the rather undesirable position of being addicted to parasites. The parasites in question are not of the blood-sucking sort however, but rather of the gene-sucking sort.

In nature there are numerous genetic entities, various forms of DNA, that parasitise bacteria:

  • bacteriophages (viruses that infect only bacteria),
  • plasmids (usually a circular strand of DNA that exists separately to the bacteria’s chromosome),
  • transposons (a unit that consists of a collection of genes that inserts itself into the host’s chromosome, but can cut itself free and reinsert itself elsewhere on the chromosome) and conjugative transposons (also capable of transferring themselves from cell to cell between bacteria),
  • genomic islands (again, a collection of genes that usually encode particular functions – disease-causing factors or antibiotic resistance – that have arrived from another organism and have become fixed in the chromosome).

We also have integrative conjugative elements (ICEs) that, like conjugative transposons, insert themselves into the host’s chromosome where they are replicated along with the host’s DNA, but then periodically (often under stress) cut themselves free and mail a copy off to another host cell.

Transfer of any of the above genetic entities can result in a bacterial cell acquiring new and desirable traits as such as the ability to consume new food sources, or resist antibiotics, or be more invasive. These traits have been picked up via the many occasions that these elements have jumped into and out of bacterial chromosomes, taking bits of those chromosomes with them.

The transfer of new traits by these genetic entities is referred to as Horizontal Gene Transfer (HGT), which is a term that is perhaps easier to understand if we consider that sexual reproduction, the process by which your parents produced you, is a form of vertical gene transfer; so too is the division of a single bacterial cell to produce a copy of itself and a ‘daughter’ cell. By comparison, horizontal gene transfer might be likened to you reaching out to touch your cousin and acquiring his or her ginger hair and freckles.

The thing that unites these genetic elements is that, being parasites, they need the host cell in order to produce more of themselves. Sometimes these elements don’t provide anything useful to the cell, sometimes they’re more of a burden, but some of these genetic parasites have evolved ways to ensure that the cell doesn’t toss them aside.

Continue reading “Addicted to DNA…”