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Monday, 15 September 2014

Wondering about water

One day back in the last century (literally) while I was working on my PhD, I went on an expedition into the University’s library archive. I remember it as a dusty cavern with rows of metal shelves creaking under the weight of volumes that smelled of old paper. You had to get a special key to get in, and I remember nervously looking over my shoulder just in case the lights flickered out and my life turned into a cheesy horror movie. I can’t remember what I was actually looking for now, but what I do remember is that I got diverted. In an ancient, dusty volume I found a paper which had been written about a hundred years ago, at the start of the 20th century.

It concerned the structure of water, its bonding and the shape of the molecules. It was a bit of a revelation at the time. I had been drawing the classic ‘Mickey Mouse’ water molecule diagram for years and I’d just never thought about the fact that there was a time when the structure of water was an unknown. Something that people argued over and, indeed, published papers about.

Now, fast forward a few years, and Things We Don’t Know have asked me to write about water clusters, something which is currently at the edges of chemistry. It almost seems meant to be.

Diagram of water molecule H20 showing pairing of electrons, electron sharing between atoms or covalent bonding, and the effective dipole moment of the molecule. Image copyright Things We Don't Know (CC BY 3.0).
Scientists use the "delta" symbol δ to mean “a little bit”. Oxygen is very electronegative, which means it draws the electrons it's sharing with hydrogen (in a covalent bond) towards itself. This leaves the hydrogens slightly positive and the oxygen slightly negative. You might also think it resembles a famous cartoon character, but we couldn't possibly comment. Image ©Things We Don't Know (CC BY 3.0)

Water is important stuff. Without it, life wouldn’t have evolved on this planet. It’s made up of one atom of oxygen and two atoms of hydrogen, joined together with the oxygen in the middle as H-O-H. One of these elements, oxygen, is the second most electronegative element (topped only by its periodic table neighbour fluorine). Electronegativity is a much-abused term in the world of pseudoscience; all it actually means is the ability of an atom to attract electrons in a covalent bond. Hydrogen is far from the least electronegative, but it’s pretty wimpy by comparison. So basically, examine a water molecule and you find that oxygen has greedily dragged the bonding electrons around itself, like a child refusing to share her sweets with the poor, deprived hydrogen atoms.

Thursday, 28 August 2014

The 3QD Science Prize 2014

We're very happy to report that one of our articles - Squid Lady Parts - is one of 85 articles nominated for this year's 3 Quarks Daily Science Prize.

The first round is open to public vote, so please go there and show your support for us! The other 84 articles are really good too, so we heartily recommend reading them all.

For those of our readers who aren't familiar with 3 Quarks Daily it's a selective aggregation service, or in their words a filter blog. In other words, they share content they like from other sites. Six days a week (Tuesday through Sunday) their editors share items from other websites in the areas of science, design, literature, current affairs, art, and anything else they consider to be inherently fascinating. On Mondays, they publish original material written by themselves.

The 20 most popular articles will then go through to the next round, with the winners being determined by Frans B. M. de Waal - a Dutch/American biologist and primatologist known for his work on the behaviour and social intelligence of primates.

Voting is open until 11:59pm on September 1st, NYC time - which is 5am on September 2nd for the UK.

Edit 04 Sep 2014:
We made it through to the semi-finals!

Our article was the 6th most-voted-for entry of the competition! The editors of 3QD will now make a selection of 6 to 9 articles, which will be passed to Dr. de Waal for the final decision.

A big thank you from all of us to everybody that voted for Squid Lady Parts!

Monday, 18 August 2014

Thinking about Things We Don't Know

Things We Don't Know Venn diagram

Since starting in June, I’ve had a lot of fun with Ed and the team here at Things We Don’t Know. I’ve learnt a lot about where research is headed in several different fields, and I’ve spoken to some pretty cool people about what they do in research. I’ve learnt many things from this internship, here are a few of the less science-y (kind of) things:
  1. There are so many things we don’t know!
  2. Seems kind of obvious, what with common sayings such as, “We know more about space than our oceans”. However, I didn’t realise there are things we don’t about almost everything. Birds, ocean currents, the inner workings of our own minds – we are constantly learning more and more about our own surroundings despite them being the most familiar things to us, and working here has made me so much more aware of that fact.

  3. Priority is key
  4. I used to think time-management was a fairly good skill of mine, until I realised I was keeping up with the small things but not necessarily being on top of everything. Sometimes you have to sacrifice smaller jobs for later, to be able to get a big task done on time. Recognising the importance of each task is a little more difficult – sometimes it relies purely on the deadline. Once you’ve nailed that side of things managing your time effectively becomes much more of a doddle.

  5. Be a zombie
  6. I don’t mean walk around slowly dribbling a bit, I’m talking about eating brains! I’ve been working with people who are experts in many different fields. Picking these big brains has been a huge perk of this job, I’ve learnt many useful tips and tricks which I can now take and use in whichever job I end up doing. People don’t generally mind having their brains picked either, everyone here has been more than happy to teach me.

Saturday, 9 August 2014

Autoimmune diseases - the friendly fire of our immune system

Autoimmune diseases affect millions of people, and have become an important focus of scientific research in the past decade due to their apparent increase in prevalence worldwide[1][2] - and yet little is known about their cause. Our body’s immune system is a pathogen-fighting machine, finely adapted to seek and destroy any foreign invaders which might cause damage within our bodies. To do this, it needs to be able to work out what is dangerous foreign material and what isn't, and sometimes it can get confused. Common allergies like hay fever occur when the body treats harmless pollen like a dangerous pathogen, and mounts an immune response. This can be irritating, but the real problem comes when your immune system becomes convinced your own body is a danger, and begins attacking itself. This is what happens in autoimmune diseases

The precise cause of these diseases is unknown but is thought to be a combination of both genetic and environmental factors[3]. It is known that relatives of people with autoimmune diseases are more likely to develop them, yet multiple studies have shown that in a pair of identical twins, with identical sets of genes[4], sometimes only one twin will develop an autoimmune disease.

This suggests that while genetic factors can predispose you to an illness, an environmental factor may be involved in triggering the development of the disease. One type of environmental factor associated with autoimmunity is infection. Exposure to numerous common viruses has been described as a risk factor for developing autoimmunity. A well-known example is the Epstein-Barr virus (EBV) which is the cause of glandular fever (also known as the ‘kissing disease’ or Infectious Mononucleosis). Over 90% of the adult population are latently infected with EBV, meaning the virus is present in their system but does not cause any symptoms.

Electron microscopic image of two Epstein Barr Virus virions
All viruses have the ability to evade the host’s immune system in some way - this ability to hide from the immune system enables viruses to survive. Immune suppressive responses have evolved in viruses over time, and they have even stolen bits of our immune system that are beneficial to them. Image credit: By Liza Gross[8] ©2005 Public Library of Science (CC-BY).

Just like any other virus, the EBV virus is able to evade its host’s immune system. One way it does this is to produce proteins which modulate the host’s immune system. In the majority of people this has no detrimental effect; however in people with genetic susceptibility to autoimmunity an immune response to the body's own tissues is initiated. We have not yet been able to explain why it affects this small proportion of people, but not the many others also infected.

Friday, 1 August 2014

Four Space Science Videos

A few weeks ago we announced that, through our partnership with Sheffield Hallam University, four teams of media and games design students had worked with us to adapt some of our previously published space science articles into animated videos. Since then, we've been releasing the videos through our YouTube channel. All four videos have now been released, so here's a quick round-up of the four.

The first of these was about the NASA space mission "New Horizons" which is currently en route to Pluto, based on Pluto's New Horizons by Peter Ray Allison. The video was created by a team of four students (Ryan Stewart, Jake Samson-Roberts, John Teo and Jason Vickers), who decided to use a similar "live animation" style as our previous video Why do we sleep?



The second group chose to animate Why are the planets so different?, by Adam Stevens. This group consisted of five students (Renny Nascimento, Will Pritchard, Clark O'Connell, Rachel ? and Romy Nelson). Their chosen style was to use stock motion with a 3D overlay which they produced using 3DS Max and Adobe After Effects, producing an 8-minute video with 5 sections.


Thursday, 31 July 2014

Squid Lady Parts

NOAA OKEANOS Explorer Program , 2013 Northeast U. S. Canyons Expedition
This bobtail squid is very surprised at the absence of squid gynaecologists! Image credit: NOAA OKEANOS Explorer Program

I first saw squid pimples in 2006, on a research cruise in the Sea of Cortez. The little bumps around the female’s mouth looked exactly like whiteheads, as if squid could get clogged pores. They even oozed white stuff when you squeezed, but it wasn’t pus.

It was sperm.

I was just beginning as a graduate student, learning to extract eggs and sperm from Humboldt squid in order to study fertilization and development—or, as I glibly described my thesis, “squid sex and babies.” Though technically I wasn’t studying sex, since in squid copulation is separate from fertilization. Females mate and store sperm for weeks or even months before laying eggs.

Picture of a clutch of squid egg (species type unfortunately not specified) cases on display at the Monterery Aquarium. Photographed on April 2, 2007.
We don't know how the female market squid who laid these egg cases selected which sperm was used to fertilize them. Image credit: "SquidEggCases-MontereryAquarium-April2-07" by User:Captmondo. Licensed under CC BY-SA 3.0 via Wikimedia Commons.
Males help out by pre-packaging their sperm into complex needle-like structures called spermatophores. Each spermatophore can ejaculate (yes, independently!) to become a spermatangium, a sticky sperm mass that attaches to the female’s skin. Then sperm from this mass moves into the little pimples I saw, which are called spermathecae. Confused yet? I sure was!

In the ship’s laboratory, we were able to fertilize eggs with sperm from spermatophores, spermatangia, and spermathecae[1]. But I’m pretty sure squid don’t lay their eggs in Petri dishes, so this doesn’t tell us a whole lot about natural reproduction. Which of the three sperm sources do females use to fertilize their eggs? Why bother with all the processing steps? Does it have to do with female selection or sperm competition?

No one knows, which is a bit surprising because spermatophores themselves have been studied quite intensively. Videos of spermatophore ejaculation and attachment can be found online, and I’ve written about more than one exciting new study. But this is the first time I’m writing about spermathecae, and it’s not because of recent research—it’s to popularize the lack of it.

Friday, 25 July 2014

The Quest for Invisibility

Since long before Harry Potter, scientists have been searching for a way which can allow things to pass us by unnoticed. The invisibility cloak which features in J.K. Rowling’s books may seem magical and otherworldly, but in fact devices which have the effect of making objects completely disappear are much more tangible than you’d think. While they may not look like a silky blanket, cloaking devices are very effective at manipulating signals and jamming detectors so as to obscure the truth about their location.

So there it is, we’ve done it. We have successfully created magic and are able to hide enormous ships or helicopters from being spotted by the enemy – haven’t we?

Well, not exactly. The perfect cloaking device is still just a theoretical concept. Camouflage paint is often applied to try and confuse the eye, “stealth” coatings are used to hide from radar, while cooling techniques are employed to reduce the amount of infrared emission coming from the object trying to stay hidden. However, while these techniques are effective at helping to disguise ships and aeroplanes, we can hardly call them invisible. It is hoped the answer lies in the development of metamaterials – materials which possess properties not found in nature.

Image demonstrating variety of wavelengths of the electromagnetic spectrum
The electromagnetic spectrum covers all wavelengths of radiation, from radar to visible light to x-rays and gamma-rays. Until last year we could only hide things from very specific parts of the electromagnetic spectrum, in some cases by making the object more visible in other parts of the spectrum. Image credit: NASA (public domain)
The development of such materials has huge implications for lens and invisibility devices. The idea of cloaking devices is to create a material which can take an incoming signal, say visible light, and then send it on its way without any interruption from the cloaked object. If you could create a material which can do this effectively enough, it will trick any detectors into thinking there is no object to be seen, since there is no radiation signal to be detected. In theory it’s possible, but there are many obstacles blocking the way.

Wednesday, 16 July 2014

How reliable is psychological science?

Things We Don't Know Anymore


TWDK Psychology doodle copyright Giles Meakin / Things We Don't Know CIC
Our psychology editor Malte Elson explores the “replication crisis”, and questions our level of confidence in established psychology. Image credit: Things We Don't Know / Giles Meakin (CC-BY)

The last few years haven’t been easy on psychological science. Don’t get me wrong – the field in itself is flourishing, boasting an ever-increasing number of publications, journals, conferences, faculty positions, and university graduates all over the world. It has gained more and more respect and acceptance, both in academia and society. The case of Harvard evolutionary biologist and primate researcher Marc Hauser’s fraudulent publications was already fading from our minds when in September 2011, the discovery of the scientific misconduct by the Dutch social psychologist Diederik Stapel shattered the grounds of psychological science. In at least 50 cases of scientific fraud that have been discovered by the Levelt Committee, Stapel had doctored, mangled, and completely fabricated datasets to successfully publish in the field’s top-ranked outlets - up to the most prestigious journals like Science. Among Stapel’s highly regarded publications were findings on how untidy environments encourage racist discrimination[1], or how to reduce racist biases in judges' legal decisions on minority defendants[2]. Nullifying the content of these publications constitutes a setback for social psychology, and - to a somewhat lesser extent – society overall.

Although they work in a highly competitive environment, we trust scientists to be committed to finding the truth. And when playing it smart, like Stapel, it is quite easy to abuse this trust for personal gain in the form of a prestigious academic career. Instead of looking for the truth, Stapel was on a quest for aesthetics, for beauty, as he was quoted saying by the New York Times. One might think that it’s not that much of an issue - Stapel got caught after all! Reaching for the stars he committed fraud, but got brought back down to reality when his deeds were unveiled, so the system works. But does it really?