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This blog is currently on hiatus owing to work commitments. Whilst I still keep an eye on the goings on at RiAus, and contribute to the work of the good folks at eLife, little will be added to this blog for the foreseeable future. Simon Says remains open for business, albeit at a reduced capacity. Thanks for stopping by, and I hope the archive of content found here will prove to be of interest.

Monday, 16 December 2013

The Naked Scientists Guide to Genetics

I HAVE had the pleasure over the past two months to work with the Naked Scientists at Cambridge University, culminating in a one-hour live show on BBC Radio Cambridgeshire last night.

As part of my internship, kindly funded by the Genetics Society, I made an audio guide to Genetics, introducing the key terms - DNA, genes, chromosomes, alleles and so on - while meeting fascinating people who work in the field. I come across a strange creature from the depths of the sea bed, and make some furry friends! Plus, humans are 50% banana, yet only 4% Neanderthal. What does that mean?

The guide is available to listen and download here in its entirety or as separate sections.


Feedback is very welcome, as I've never made anything like this before.


Contributors, in order of appearance:
Enrico Coen, President of the Genetics Society
Max Telford, University College London
Mark Thomas, University College London
Eugenio Sanchez-Moran, University of Birmingham
Nelly Brewer, Rothamsted Research

Terms explained:
DNA, Nucleotide, Genes, Chromosomes, Genome, Chromatin, Mutation, Allele (dominant and recessive), Genotype, Phenotype, Heterozygote, Homozygote, Epistasis

Music: Adventure, Darling by Gillicuddy freemusicarchive.org/music/gillicuddy/; Dan-O, at danosongs.com.

Monday, 18 November 2013

Nikolai Vavilov: Forgotten Scientist

CENTENARY celebrations are afoot for the life and legacy of Alfred Russel Wallace, the co-discoverer of evolution by means of natural selection, who died in 1913. Many are familiar with the story of Charles Darwin, but fewer are aware of Wallace's contribution, which triggered the publication of Darwin's seminal work. Wallace is one of many poorly appreciated, and forgotten, scientists.

Another, is Nikolai Ivanovich Vavilov.

A botanist and geneticist who uncovered the geographical origins of widely grown crop plants, whose worked inspired the modern study of Crop Wild Relatives (CWRs), and whose collections were so valuable that they were guarded night and day throughout the two-year World War II Siege of Leningrad, during which at least one of his assistants starved to death; an adventurer once stranded in the Sahara, who led caravans across unmapped Afghan mountains and up the crocodile-infested Nile; a scientist whose work ensured the global population could be fed, Nikolai Vavilov died of starvation in a Soviet gulag, forgotten.

Vavilov's scientific career featured many more adventures than most scientists could dream of. Posted to Iran in 1916 to collect plants on behalf of the Russian Empire, he was arrested before even leaving his own country, charged as a 'German spy' for carrying German textbooks and diaries written in English. He was abandoned by Kyrgyz guides in the Pamir mountains in Central Asia; took a caravan of fourteen guides "and two revolvers" into Eritrea; caught malaria in Syria; caught typhus in Ethiopia; and further visited the United States; Central and South America; China, Taiwan, Japan and Korea, all in the name of collecting plants.

But why?

Sunday, 17 November 2013

Where the Booze is Cheaper

"Queen Victoria, listening to a military band at Windsor, was captivated by a certain tune and sent a messenger to ascertain the title of it. He returned in some embarrassment and said that it was called 'Come Where the Booze is Cheaper'."

They Were Singing by Christopher Pulling,
seen in Encyclopedia of World History, 1999, edited by Professor Jeremy Black

Monday, 16 September 2013

Islands

If I went away
— tropical island, somewhere sunny every day —
but everyone I ever cared about remained
...would I tan or would I fade?
The Cat Empire, In My Pocket

Wednesday, 14 August 2013

Faith

Monday, 1 July 2013

Monday Nostalgia: Women in Science, know your limits (c. 1971)

THE route to my lab at the University of Birmingham has been the same for three years. Walking from the Selly Oak Grange Road entrance, past the School of Mechanical Engineering and up past the Haworth Building, it was only in the final few weeks of lab work, prior to this period of thesis writing, that I noticed a statue nestled in the gardens. Feeling nostalgic as the realisation dawned that I shall be leaving soon, I took a closer look. The artefact, of wrestling bodies entwined, is now surrounded by plant life, much less prominent than it once was. Beneath it, a plaque describes the statue as a present from postgraduate students of the School of Thermodynamics to Professor F. K. Bannister, who founded the school.

The school is now long defunct, and I had never heard of it - so I went online. What I found was a job advert for the school, written in a style long since abandoned. If you are female, thermodynamics was not a world open to you in 1971, since the advert refers only to the candidate throughout as 'he'. While gender bias in science remains an issue, we can at least be proud that it is moving in the right direction, and has come a long way since 1971. Also present on the page were adverts for the University of Zambia, and a media production role at the Loughborough University, seemingly a pioneer of science outreach.


Monday, 24 June 2013

Monday Science: On Carrots, Cake and Sperm

It’s the carrot in front of the mule and the cake in front of the child: individuals are drawn to reward. But surround them by that reward — a mule in a field of carrots, a child in a cake shop — and behaviour switches from unidirectional to hyperactive. The greyhound that focuses on the moving rabbit wins the race: the greyhound that gets distracted by rabbits in the field next door may one day reach the finish line, but not because of the lure.

So it is in biology. Chemotaxis, the process by which cells and bacteria move according to certain chemicals in their surroundings, relies on a gradient of attractive or repulsive cues to cause directed movement. Surround a cell by growth factors and it will grow in all directions, but form a gradient in one direction only and it will grow that way. This is how nerves form complicated networks throughout the body, wrapping around other structures, and it is how good sperm find an egg.

More than 70 million couples globally are affected by infertility, of which at least half are due to the inability of sperm to fertilize the egg. This is because sperm quality per sample is usually highly variable, with many mutated cells and poor swimmers.

Despite technological advances, fertility treatment remains inefficient, with about a 30% success rate. The hurdle of poor sperm quality has not been overcome. Fertility treatment is also expensive and has a deep emotional cost.

Now, researchers at the Universidad de Córdoba in Argentina have developed a method for separating good sperm from poor sperm, offering hope for the improvement of assisted reproductive technology, and it’s all down to that single carrot, dangled before the mule.

Egg cells mature within a cluster of cells called cumulus cells, which are essential for the egg’s development and protection. One of the many jobs of the cumulus cells is to kick out the steroid hormone progesterone. Sperm react positively to gradients of very low amounts of progesterone, but, like the child in a cake shop, go wild if surrounded by too much. It also happens that the cells that respond most efficiently, and less chaotically, to the very lowest concentrations of progesterone are the very best sperm, the ones that would, given the opportunity, competently fertilize an egg. This new study from the laboratory of Prof Laura Giojalas takes advantage of this behaviour.

Their device, called the sperm selection assay (SSA), takes only 20 minutes to operate, using a low concentration progesterone gradient between two small plastic dishes, between which the sperm swim. After this time, the collected sample contained three times as many high quality sperm cells than both normal and poor quality starting samples. In addition, with only a 20 minute run time, the experiment can be repeated to further improve sample quality. Purified sperm from the SSA also had reduced DNA damage.

The SSA was particularly effective when run on extremely poor quality starting samples, where the level of high quality cells could be increased by up to 11 times.

These are still early days — having more good cells per sample still does not guarantee fertilization — but the SSA is a helpful step towards overcoming this hurdle in human fertility treatment.


Gatica, L. V. et al. Picomolar gradients of progesterone select functional human sperm even in subfertile samples. Mol. Hum. Reprod. epub 31 May 2013
doi:10.1093/molehr/gat037

Monday, 17 June 2013

Monday Science: Gangnam Style vs Neuroscience

In our office there is a filing cupboard that cannot be opened. Once, a long time ago, it was closed and locked, and the key has long since disappeared. Nobody knows who closed it. Nobody knows who has the key. But somewhere this key does exist.

In kitchen drawers across the world, there are loose keys, whose keyhole has been lost to human knowledge. Sometimes we try an unknown key in an unopened lock, wiggling it around in the vain hope of finding a match, but ultimately we usually find disappointment.

Our knowledge of biology can be just as mismatched. The ‘lock and key’ analogy is often used to describe biological concepts to describe two molecules that fit together to make something happen. The key molecule fits into the lock molecule, opening the biological door: to use scientific terms, the ligand fits into (or on to) the receptor protein, triggering downstream signalling — think of a free-floating molecule pushing a big red button on a cell, causing the cell to light up. The problem is, we’re aware of many keys and many locks, but all too often we can’t find a match. We call the unassigned receptors ‘orphan receptors’.

One such orphan receptor is called Ptp10D but, because that’s a boring name, I’m going to call it Psy, like the bloke who rides invisible horses. Now a group of scientists led by Professor Kai Zinn at the California Institute of Technology, have worked out what the key is to getting Psy excited, leading to full-on, no holds barred nervous system development.

Zinn's team took as many unknown keys as they could, and tried them in the Psy lock. To do this in biology, specifically at the microscopic level of cell biology, you need to use a few tricks and tools. Enter my good friend the fruit fly, in which a genetic tool called the Gal4/UAS system has been introduced. Don’t worry about the jargon, all you need to know is that it allows you to increase the amount of a protein (in this case the potential keys) in very specific settings. When they increased the amount of one key, which is called Sas, they found that an enzyme-linked form of Psy started to glow, the very signal they were looking for that suggested an interaction.

Monday, 10 June 2013

Monday Science: The Animal Pairs Game


THIS is an activity I made for ThinkTank museum as part of a Meet the Scientist event on the theme of evolution and adaptation. Though my work does have a strong evolutionary angle, I do not specifically work on adaptation or taxonomy, but I wanted to gain experience demonstrating different topics. The activity – a pairs game – required a lot of effort on my part on the day, as I needed to explain constantly facts and concepts in biology (my audience were a mixture of ages, mostly young children); this I did not mind, and it was very rewarding for both myself and my visitor, but is worth warning about should you wish to try a similar activity.

The idea is to match animals based on similarity. That is, can you find two mammals? Two birds? There are traps and there are difficult animals, but the activity can be tailored depending on your audience (instead of two mammals, why not try pairing adaptations, habitats or common features such as spikes), and not all cards need to be used at any one time. I do urge you to read up on the subject of classification – it’s no longer really taught but it underpins so much of what we as biologists do. If we do not know what we are really looking at, and where it fits in the tree of life, how can we truly know the context of our results?

The full cards are below.

Monday, 27 May 2013

Monday Presentation: Using Twitter as a Postgraduate Researcher

I'm moving house, so no time to write a Monday Science post this week. Instead, here's the talk I gave last Friday entitled 'Using Twitter as a Postgraduate Researcher'. If it looks familiar, it should, as I've posted it here before. But this one is NEW! and DIFFERENT! and features fewer TERRIBLE JOKES! It's also better thought through. Comments, as always, welcome.


Monday, 20 May 2013

Monday Science: Brains and Blue Icing

It is said that when a sense is lost, particularly that of sight, remaining senses are heightened. This is true not only in those individuals who could once see — although they do have better spatial awareness — but also in people who were born blind, since these individuals have been shown to have accelerated brain processing ability in the regions responsible for the remaining senses. But how can the brain do this? How can it intrinsically know things it can no longer directly determine in the ways it was built to do?

Fruit flies similarly have the ability to continue to perceive their environment in times of sensory loss. For example, they can determine the nutritional value of food, even when their ability to taste has been impaired. Now, a study in Nature Neuroscience has uncovered details as to how this might be possible.

Flies that are incapable of tasting — by means of genetic mutation in the taste receptors around its mouth and proboscis — actively select easily digested sugars over harder to stomach compounds. After all, they still need to eat well. This ability is particularly strong during times of starvation, so the researchers looked deeper to see if this was to do with sugar levels in the haemolymph, the liquid that circulates around the insects’ body, something akin to blood plasma. They found that starved flies were no longer able to choose between glucose and agar, or different kinds of glucose, if their food was supplemented with a chemical that prevents the passing of glucose from the gut to the haemolymph. Just to check that this wasn’t because the chemical was messing everything up and the flies were just off their food completely (and who can blame them, on a diet of agar and chemicals), they repeated the experiment using agar and fructose, which differs chemically and isn’t prevented from passing into the haemolymph. This time the flies chose the fructose.

On top of this, flies that have had their ability to taste restored, but are still chemically unable to absorb glucose into their haemolymph, actively choose the sweetest foods they can find, even if those sugars are the hardest to digest and therefore the worst nutritional option. They’re like toddlers presented with the option of cake with blue icing, or Ryvita and hummus - sweetest wins, regardless of whether it's any good for them.

Monday, 13 May 2013

Monday Science: The Happy Birthday DNA Show


TWO weeks ago I attended the Communicating Your Science workshop organised by the Genetics Society and held at Chicheley Hall, a country mansion owned by the Royal Society. The workshop focused on storytelling, communication in interdisciplinary research, scientific writing, publishing, business and radio broadcasting. I absolutely loved it. As part of this, we were challenged by The Naked Scientists crew to create a 15 minute radio show, with less than 24 hours notice, to be recorded as live with no interruptions. Above is a link to the show my group created, which just so happened to be recorded on 25th April 2013, the 60th anniversary of the Watson and Crick paper in which the structure of DNA was revealed. We were allowed some pre-recorded segments, which is where I feature along with our vox pops from 'the streets of Milton Keynes' (actually the staff in the venue, hence the tweeting birds in the background). Consequently I had no live vocals so I took on the role of show producer, gesticulating silently to signify timings, panic and relief when it was all over!

Disclaimer: as this was done so quickly, the science in it may not be completely accurate. It was more for the experience of putting a show together than for complete accuracy.

Monday, 22 April 2013

The Universe As It Is


“Peeping through my keyhole I see within the range of only about thirty percent of the light that comes from the sun; the rest is infrared and some little ultraviolet, perfectly apparent to many animals, but invisible to me. A nightmare network of ganglia, charged and firing without my knowledge, cuts and splices what I do see, editing it for my brain. Donald E. Carr points out that the sense impressions of one-celled animals are not edited for the brain: ‘This is philosophically interesting in a rather mournful way, since it means that only the simplest animals perceive the universe as it is.’”

Pilgrim at Tinker Creek by Annie Dillard
(with thanks to Liz Wainwright)

Tuesday, 16 April 2013

#bgrs2013

Click here to read the Storify of the event.
(Biosciences Graduate Research Committee student symposium 2013, University of Birmingham)

Friday, 29 March 2013

RiAus: Defying the laws of nature. Again.

EXCITING news! I am now a blogger for the Royal Institution of Australia (RiAus). My first post, 'Defying the laws of nature. Again.' is now up, and can be accessed here. As it was my first post, I couldn't resist the temptation to bring in a few old friends: the thylacine and the Tasmanian devil. I am looking forward to the many future opportunities this position with RiAus will offer, and the challenges they set me!

Defying the Laws of Nature. Again. by Simon Bishop for RiAus

Monday, 18 March 2013

Monday Science: Look at his happy, happy face

IN THE beginning, there was the mouse. There was also the nematode worm (Caenorhabditis elegans), the African clawed frog (Xenopus laevis), the fruit fly (Drosophila melanogaster), thale cress (Arabidopsis thaliana) and the zebrafish (Danio rerio), and, to a lesser extent, chickens, rabbits, guinea pigs and daphnia. These were the model organisms of science. Now, it seems, there's a new member of the club.

Say hello to this chap:

Source


Doesn't he look happy? He's an axolotl, a curious species of endangered amphibian that lives only in the lakes around Mexico City — lakes that are being threatened by pollution and competition by invasive species. Fully grown axolotls are neotenic salamanders, 'adults' that are stuck with juvenile features because they never went through metamorphosis. Other species of salamander lose their gills and move on to land as they develop, and the happy-go-lucky, flapping external gill form of the axolotl can be induced to do this by the artificial application of thyroid stimulating hormone, but in its natural environment the axolotl is content to stay in a larval state for the duration of its life. Think of it as a tadpole that has grown its legs, but never becomes a frog.

Axolotls are not a new model in science, but a recent push into research in regeneration and injury repair has seen a flurry of articles and interest in using the threatened amphibian. Because of its perpetual larval state, the axolotl is able to regenerate lost limbs, instead of forming a scar. February was a bumper month for axolotl developmental biology papers, so I picked one, and now I’m going to tell you what it said.

Tuesday, 12 March 2013

Exciting Tasmanian Devil News!


REGULAR readers of this blog will know that I am a big fan of the Tasmanian Devil. It is a black and white ball of fur, underneath which is a marsupial carnivore, one so keen on its food that once it starts eating nothing can distract it, and nothing will be left once it is finished (its blood-curdling squeals of delight are the origin of its name 'devil', when heard by early settlers at night). It is also dying.

This from a previous post of mine:
In a phenomenon almost unique to science, the already small population is suffering from a transmissible form of cancer called Devil Facial Tumour Disease (DFTD), with over 70% of the population infected. It is almost completely lethal, causing swelling in the mouth and face, leading to suffocation and starvation. 80% of the population has been wiped out since its discovery in 1996, and it is predicted that the species could be extinct within 25-35 years.
I have previously covered the discovery that the low genetic diversity in the species has existed in the population for at least 100 years and how this has implications on how we decide which species to invest conservation efforts on. I also introduced the disease and explained why low genetic diversity in the species could be a blessing or disaster for its survival, and how, biologically speaking, the cancer is utterly remarkable — it is contagious and makes its own myelin, a protein usually seen only in the nervous system, which the immune system never attacks.

I hurry through these details because there is new news. It is covered very nicely here and here by Ed Yong, but I shall cut to the chase:

Monday, 11 March 2013

Monday Science: There Be Dragons, Says Bloke

IT was the news that I had been waiting for for years. ‘Antarctic Lake Vostok yields 'new bacterial life'’ claimed BBC News Online last Thursday. ‘Unclassified Life Found in Antarctic Lake’ claimed RIA Novosti. ‘‘Unclassified and unidentified’ life found in Antarctic lake’ claimed the Telegraph. My eyes widened, and my heart started to beat a little faster.

Russian scientists have been drilling into Lake Vostok, a lake that has been sealed beneath 2.3 miles of permanent Antarctic ice for between 14 and 25 million years, since 1998. What they might find in the waters it contains piqued the interests of scientists around the world, myself included. Imagination ran wild as the possibilities were considered — if anything lived down there (and early tests suggested it might) it relied on an unknown energy source, since no light can penetrate the glacier above, and it would have been geographically isolated from other life forms for so long that it would likely have diverged on to its own evolutionary path. In short, if anything lived down there, it would be unlike anything we have ever seen.

But drilling was slow progress, held back by the triple whammy of isolation (Vostok Station is extremely isolated, even by Antarctic standards), inhospitality (it is the location of the coldest ever recorded temperature on Earth, a frightening -89⁰C) and concerns over contamination of the lake by the drilling process. Researchers got within 50 metres of the lake surface in 2011, and to the lake surface itself in 2012, but were forced to withdraw before analysis could begin as Antarctic winter drew in.

After 15 years of painstakingly slow work, teasing followers hoping for news, it was therefore a disappointment that a team from the United States beat the Russians to the achievement of being first to drill into an Antarctic lake, accessing Lake Whillans, which is covered by a not insubstantial 800 metres of ice. Furthermore, initial water samples showed that Lake Whillans “definitely harbours life”, according to a researcher on the team. A British team also came very close to accessing Lake Ellesworth, 2.1 miles beneath the ice.

Now, finally, samples from Lake Vostok are now on the research vessel Akademik Fyodorov, which will depart Antarctica for Russia in May. On arrival, water and ice samples will be sent to institutes in St Petersburg and Irkutsk for further analysis, estimated to be published later in the year or early 2014. But herein lies a problem: analysis is not yet complete, nor verified, and yet the news has already been broken to the wider world. It is now established: life has been found in Lake Vostok.

Or has it?

Monday, 4 March 2013

Monday Science: Snake Venom is a Natural GPS Tag

Source: badgerbadgerbadger.com, obviously
IT MUST be difficult being a snake.

Everyone thinks you're ugly, frightening or just plain mean. You have no legs. You have to keep yourself warm. Nobody will talk to you at parties.

But perhaps the most difficult thing about being a snake is finding food. Without limbs you can’t catch, trap or use tools. You’re a funny shape, limiting the places where you can hunt. You’re also surprisingly defenceless – no body armour, save scales; and no appendages to use to fight back against reluctant prey while you’ve got your teeth stuck in.

Given such disadvantages, snakes have had to acquire some of the most efficient hunting techniques in nature. In non-venomous snakes, mechanical constriction and jaw-holding are used to great effect, whereas some venomous snakes are eye-wateringly lethal beasties. Sea snakes are some of the worst. I once had a sea snake thrown at me, an experience I am not keen to repeat.

Two tactics are employed by venomous snakes to ensure that lunch is served. First, there are the strike-and-hold behaviours, like that employed by the cobras, clinging on to the prey while the venom takes effect, but this has inherent risks if the prey itself has sharp claws and a propensity to go down with a fight. Then there are the strike-and-release behaviours of the rattlesnakes and vipers, when prey are left to wander off and suffer their final moments alone. This is safer for the snake, but adds a complicating factor: once the venom has done its job, how does the snake find its prey once more, particularly when there may be trails of other suitable, but very much still alive and feisty, prey nearby?

Thursday, 17 January 2013

But How Do They Know? | Courses of Horsies

EMBERS glow, flames flicker and on go the burgers: patties of prime, premium (and lesser) cow bits squished together in a juicy, fatty disc to be wedged, burnt bits and all, between two pieces of near-stale 'bread', lashings of tomato ketchup and accompanied by a token splodge of potato salad. Ah, the joy of the summer barbecue.

Hold on. You did say 'beef' burger, right?
Retired
Source: me

This week the Food Safety Authority of Ireland (FSAI) published results of tests on beef products on sale in a number of supermarkets in the UK and Republic of Ireland, discovering traces of pork and horse meat in beef burgers and pork in other beef products. In one case, in Tesco Everyday Value Beef Burgers, the product was found to be 29.1% horse meat. The case has proved an embarrassment for the food manufacturers involved and for Tesco, Aldi, Lidl, Iceland and Dunnes Stores, and has ignited a number of debates. Is it ethical to eat horse, ask some? Why did the UK's Food Standards Agency not spot these discrepancies? What failings occurred in quality and supply chain control that allowed this to happen?

I can't answer any of those. But I can answer this: how do they know those burgers contain horse? How can you take a burger, pulverize it and identify the species it is composed of? Welcome to the world of Food Forensics.

Thursday, 3 January 2013

Whimsy

Giant rubber duck at Sydney Festival
Source

"Consider the following: In nature, there are 142 known species of Anseriformes, the order to which ducks, swans and geese belong. Of those species, only one, the white Pekin duck, a domesticated breed of mallard, produces spotless yellow ducklings. Since the invention of plastic, four known species of Anseriforme have gone extinct; several others survive only in sanctuaries created to save them. Meanwhile, by the estimates of an American sociologist of Chinese descent named Charlotte Lee, who owns the largest duckie collection in the world, the makers of novelties and toys have concocted around ten thousand varieties of rubber duck, nearly all of which are yellow, and most of which are not in fact made of rubber, nor like the Floatees from polyethylene, but from plasticized polyvinyl chloride, a derivative of coal. Why has man just these species of things for his neighbours, a latter-day Thoreau might ask; as if nothing but a yellow duck could perch on the rim of a tub?"