I forgot I had you, little blog

So I’ve been flicking through pages of this blog and it’s a little mind-blowing to realise how much of my life is up here (albeit heavily disguised and hidden in metaphors and haiku). It made me sad to think I haven’t really documented any of this year in the same sneaky way. I guess it’s a mark of growing up, which is not strictly something I want to do.

Here is an adequately vague summary of 2012:

This is a year of acceptances and successes. I had to accept that my academic plan was going to be different to my peers, come to terms with being the odd-one-out, the only person starting honours halfway through the year.

But honours is crazy. I’ve gotten better at things rapidly. Machines that once terrified me are now my loyal and hardworking subjects.

Haha, Mr Centrifuge, you’re making that high-pitched screeching sound again, but rather than running for my life, I will simply stand beside you and glare, knowing that you’ll shut up any second and get on with the job at hand!

When I say these sorts of things out loud, I gain the fearful respect of the centrifuge, but my coworkers think I’m odd.

I’ve had successes with grades, work, haircuts, and crystallography.

I’ve learned more this year than I expected to, in about as many areas as one could prod with a stick.*

I want to use this blog more, I want to have opinions (something I’m scared of because usually I don’t have enough evidence to back up my opinions, so it all just feels weak), and I want to write about science and cool things that are happening, and blogs and comics that I like on the internet, and awesome music like this:

I miss being vague on the internet.

Perhaps expect more from me, dear readers, as I can feel the procrastination creeping up on me.

Love your mothers.

*Do not prod sensitive areas with sticks.

Hippo sweat; the next big thing in cosmetics?

It’s finally summer here in Australia. For those of us not blessed with the ability to tan, sunscreen is becoming a hot topic. Oddly enough, the next big advance in sun-shielding technology might be thanks to sweaty hippos.

Everyone knows that too much sun is bad for you, and there’s growing evidence suggesting that too little sun can be just as dangerous. The kinds of UV (ultraviolet) radiation that affect us the most are separated into two different ranges of frequencies; UVA and UVB. UVB affects the outer layers of skin. It is responsible for sunburn and the occurrence of most skin cancers. UVA, on the other hand, penetrates further and affects the deeper layers of skin. Wrinkles and loss of skin elasticity are both caused by UVA, and some skin cancers have been associated with this range of radiation too. UVA also causes tanning, which is the body’s response to DNA damage.

Neither kind of radiation is ideal for prolonged, unprotected exposure, but hiding indoors for fear of melanoma is neither fun nor sensible. Vitamin D is produced in our skin when we are exposed to UVB radiation. Lack of exposure to sunlight can result in vitamin D deficiency, which is associated with reduced immune system effectiveness, bouts of flu, tiredness, and muscle weakness. Vitamin D deficiency has also been linked to asthma, heart disease, and cancer.

Here in Canberra (where this blogger is currently hanging out), it is suggested that the ideal amount of unprotected sun exposure varies from a few minutes a day in summer to several hours a week in winter. People with fairer skin may need even less than these recommended times, while people with darker skin may need more sunlight to reach healthy vitamin D levels.

After you’ve met your vitamin D requirements, it’s probably a good idea to lather on some sunscreen. Modern sunscreens are fantastic concoctions that typically combine chemical ‘screens’ and physical ‘blocks’ for UV radiation. Chemical components absorb UV before it reaches your skin, while physical ingredients reflect UV away. The higher the listed SPF (sun protection factor), the longer you can be exposed to sun before damage to your skin will occur. SPF 15 will protect you for fifteen times longer than your natural defences, SPF 30 for thirty times longer, and so on.

Unlike humans, who have to cover ourselves with sunscreens, hippos have the amazing ability to sweat out their own sunscreen. Hippos secrete a bizarre red substance that resembles blood, but actually absorbs and reflects harmful UV very effectively. This hippo sweat is also an insect repellent and an antiseptic, so is basically a sticky crimson wonder-substance. Investigations into how to harness this hippo-power are underway. You might be buying hippo-inspired sunscreens in the near future, and given sunscreens are known to be the best anti-aging creams available, your skin will thank you for it.

Higgs Boson Crash Course

It’s a discovery that’s been hard to ignore. Since early July, news websites and science blogs have been buzzing with the announcement that a Higgs boson-like particle has been observed in CERN’s Large Hadron Collider. The scale of this discovery has been compared repeatedly to man landing on the moon, an analogy that is perhaps a bit difficult to swallow until you wade through the hype and understand the significance of the Higgs boson in our current model of physics.

Bosons are a type of fundamental particle, like electrons and the different varieties of quarks and neutrinos. A fundamental particle is one which cannot be broken down into smaller components; they are the indivisible building blocks of all matter and energy in our universe. Bosons are ‘force carriers’; a quantity of energy associated with a type of field. For example, photons are the force carriers of the electromagnetic field. They are essentially packets of energy that describe light. The already-identified W and Z bosons are the force carriers for the ‘weak nuclear force’ (one of the four fundamental forces of nature, the other three being gravity, electromagnetism, and strong nuclear force).

The Higgs boson is the force carrier for the Higgs field. Both field and particle were proposed in 1964 as a way of incorporating mass into the standard model of physics. As it stands, the mathematics of the standard model does not work if mass is used as ‘input’ into the mathematical machinery, but it also doesn’t give mass as an ‘output’, which has left a gaping hole in our understanding of the physical world. We know mass exists, and the Higgs field might be a method of describing it in terms of the other fundamental particles in the standard model.

The proposed Higgs field would create ‘drag’ on different particles. Some things would be affected a lot by the field and held tightly to it (high mass), while some things would be less affected and be free to move more easily across the field (low mass). The best way to verify this theory is to observe the force carrier associated with the Higgs field; the elusive Higgs boson.

If the particle observed at the LHC is the Higgs boson (it might be something else!), then the existence of the Higgs field could be verified, completing the standard model by incorporating mass into it.

It might not be as flashy as the space program, but this discovery could add the finishing touches to the standard model of physics and for that, it is worth the hype.

 

Printing painkillers

If it’s digital, it can be uploaded, downloaded, shared, edited and embellished. With advances in 3D printing technology, internet accessibility may soon apply to physical items too, including over-the-counter drugs.

3D printers have existed since 2003, and are already in mainstream use for the production of industrial and medical components. Similar to a regular inkjet machine, 3D printers follow digital instructions to produce a physical copy of an item. This is done by precise layering of materials such as plaster or plastic to build up a 3D structure. Demonstrations of the technology have seen 3D scans taken of various items (including an Academy Award statuette and some particularly tasteful gargoyle figurines), then replication of those items in various materials.

There’s more to 3D printing than just copying trinkets though. The potential to perform pre-programmed chemical reactions could turn home offices into small-scale laboratories.

Recent work at the University of Glasgow has demonstrated the capacity of relatively affordable 3D printers to act as tools for performing chemistry. Reaction vessels were ‘printed’ in layers of quick-setting bathroom sealant, and the chemicals required for the desired reaction were ‘printed’ into those vessels. By preparing a digital blueprint for, for example, the production of paracetamol tablets, a specialised chemistry set could be printed out, and a choreographed reaction performed with minimal human input required. The end product would be freshly produced painkillers, essentially downloaded from the internet.

The trials of this technology were carried out using a commercially available 3D printer that cost around US$2000. For that sum of money, and the additional cost of buying reaction ‘recipes’, any household could become capable of producing their own non-prescription medication.

Before this use of the technology becomes commercial, issues of user safety need to be addressed. A printed chemistry set would have to be impossible to adapt for illegal uses; it’s not hard to imagine digital recipes for preparing illicit drugs being shared online. The reactions that could be performed would be limited by the availability and safety of the chemical ingredients. Despite these hurdles, 3D printing and desk-top chemistry might be the next advancement in bringing goods and services into homes.

 

Synthetic DNA changes the definition of ‘life’

Researchers in the UK may have just redefined the meaning of life. An international group based at the MRC Laboratory of Molecular Biology in Cambridge has developed synthetic genetic material they have named XNA.

All life contains genetic information in the form of DNA (deoxyribonucleic acid) or RNA (ribonucleic acid). DNA and RNA consist of a molecular backbone structure and a variety of ‘bases’ that code genetic data; adenine, cytosine, guanine, thymine, and uracil. In the case of XNA, these naturally occurring genetic bases have been replaced by different, ‘alien’ bases (the ‘X’ in XNA stands for ‘xeno’, referring to the alien or foreign nature of the bases).

This synthetic genetic material opens some interesting doors in a variety of fields, including the study of evolution, the potential for genetically designed therapeutics, and exobiology; the search for life beyond Earth.

Scientists have successfully created six types of XNA molecules that mimic DNA and RNA structurally and, most interestingly, behaviourally. Genetic information stored in DNA can be accurately translated onto these XNA molecules through the use of a specially designed enzyme. Another enzyme is capable of translating information back from XNA to DNA. In a sense, XNA is like different genetic language, and these enzymes can act as interpreters.

The benefits of this new genetic ‘language’ are numerous. XNA molecules are designed to be difficult to degrade, which gives them broader applications in genetic medications and therapeutics than natural DNA and RNA.  XNA molecules will be less likely to be deconstructed by the body, prolonging their activity and usefulness. The more robust XNA also expands research parameters; scientists working with XNA will be able to run experiments in a wider range of temperatures and acidities, widening the scope of genetic research.

Researchers have also discovered that XNA is capable of replication and random mutation, hence evolution (just like DNA and RNA). This offers intriguing insights into heredity and evolution, suggesting that there is nothing innately ‘special’ about DNA and RNA; that any molecule structured in a similar way can adapt to changing surroundings.

DNA and RNA have been long thought of as indicators or defining factors of ‘living organisms’. The creation of XNA will no doubt reignite discussion about what it truly means to be ‘alive’.

DRACO could cure the common cold (and cancer)

Winter is coming, and the dreaded cold and flu season will shortly follow. Herbal remedies and bucket-loads of tea may soothe the symptoms of winter sniffles, but the common cold virus itself is famously incurable. That might be about to change, however, thanks to new research at MIT.

In a paper published in 2011, a group of researchers at MIT introduced the world to DRACO: double-stranded RNA Activated Caspase Oligomeriser. DRACO is an innovative anti-viral agent that identifies cells infected by viruses, and then induces ‘cell-suicide’, causing infected cells to die and stop the reproduction of the virus.

Viral diseases are common, and can be much more deadly than the common cold. Chickenpox, hepatitis, influenza (including swine flu and bird flu), polio, herpes, and HIV/AIDS are just a few of the diseases caused by viral infection. Some diseases, such as multiple sclerosis, have been linked to viral infections, although may not be directly caused by a specific virus.

Treatments for specific viruses exist, but viruses have the unfortunate tendency to grow resistant to individual treatments. The flu shot is targeted to a different influenza virus every year, because the disease mutates rapidly, limiting the effectiveness of the previous year’s treatment.

DRACO is the first ‘broad-spectrum’ anti-viral agent. It is not tailor-made to a specific virus, but is able to identify a wide range of viruses by spotting viral RNA (genetic data) inside an organism’s cells. So far, research has demonstrated the effectiveness of DRACO in both treating and preventing infections by fifteen different viruses (including rhinovirus; the common cold).

While further research is required before human trials can begin, the potential uses for DRACO are huge. Sniffling and nose-blowing could be eradicated from campus libraries world-wide. Sudden outbreaks of never-before-seen or newly mutated viruses, like SARS in late 2002 or swine-origin H1N1 in 2009, could be treated and contained. Diseases like polio and AIDS could be made a thing of the past. DRACO is not just an awesome acronym; it could potentially save millions of lives.

For more information, the MIT paper on DRACO, Broad-Spectrum Antiviral Theraputics, is available on PLoS ONE (www.plosone.org)

 

Mars Rover Discovers This Guy

If you were lucky enough to be streaming the footage of the NASA control room on the afternoon of the 6^th of August, you would’ve witnessed NASA scientists dancing, hugging, high-fiving, and crying with joy. They had every reason to be over the moon; their US$2.5 billion Mars Science Laboratory rover, Curiosity, survived a deceleration from 21,000 kilometres per hour to sit comfortably stationary in a dusty crater hundreds of millions kilometres away from Earth. Getting to Mars is expensive and labour intensive, but the data Curiosity will send back to Earth could change our understanding of life in the universe.

It’s understandably difficult to get to Mars. The Red Planet is pretty far away, varying from about 50 million to 400 million kilometres from Earth, depending on both planets’ orbits. Since the 1960s, NASA and the former Soviet Union have been launching satellites and landers in the general direction of Mars, and out of 39 launches, only 20 have reached their destination. Of those 20 successes, 7 have been actual landings on the planet’s surface. The other 13 were satellite missions, providing images of the Martian surface from low orbits.

In 1976, NASA’s Viking 1 landed on Mars and sent back the first images from the surface of the planet, in fact, the first images from the surface of any planet other than Earth. NASA launched their second successful mission to Mars in 1996, with Pathfinder and its on-board microwave-oven-sized robot companion Sojourner landing on Mars in 1997. Sojourner was the first wheeled robot on Mars. It rolled around and collected images and data that suggested that Mars was once an ideal location for life to develop; warm and covered in water.

It wasn’t until 2001 that the Mars Odyssey probe discovered ice under Mars’s dusty surface; the first physical evidence of water on another planet. Twin rovers Spirit and Opportunity landed on Mars in 2003, and found further evidence of ancient waterways on Mars, including mineral deposits associated with free-flowing water. In 2008, the Phoenix rover observed snow falling from Martian clouds. Now it’s Curiosity’sturn to find some microbial life in amongst all that Martian water.

Curiosity is about 3 metres long and weighs 900 kilograms, with a top speed of 90 metres per hour. It is equipped with 17 cameras, and an array of instruments for analysing the content of mineral and soil samples. Its objectives include identifying traces of chemicals that could indicate life, determining how soil and rocks were formed, and establishing a time-scale for the development of the Martian atmosphere by measuring levels of carbon dioxide and other gases. Curiosity will be spending two lonely years on Mars, before shutting down. If evidence of life is found, Mars could well be an environment in which humans could survive. It seems like the stuff of science fiction, but manned missions to Mars might not be too far behind Curiosity’s trail-blazing.

You can follow Curiosity on Twitter, @MarsCuriosity, or you can find Curiosity’s abusive alter ego, @MarsCuroisity. Both are worth your time.

Crowd-Sourced Science

Crowd-sourcing is becoming a powerful force. Enlisting hundreds of thousands of people to complete tiny sections of a larger task is so efficient, you might not even know you’re already participating. Every time you fill out a ‘reCAPTCHA’ box to verify that you’re not a spambot, you’re actually helping to digitise books for ever-expanding digital libraries. In just one day, 200 million ‘reCAPTCHA’ boxes are filled out, amounting to over 150,000 hours of work per day. Whenever you’re asked to type the squiggly words ‘basilisk dissuade’ before you can download a document or tell someone on the internet that they’re wrong, you’re completing a fragment of a huge puzzle.

The awesome might of crowd-sourcing has found its way into the world of science in the form of a game called Foldit.

Foldit was developed in 2008 after David Baker, a protein research scientist at the University of Washington, realised that humans are, in fact, better at spotting complex and creative solutions to scientific problems than computers are.

A recurring problem in the world of protein engineering is identifying the best possible structure for protein molecules to fold into. In order to better understand the inner workings of organisms on a molecular level (and learn more about illnesses and their treatments) researchers need to be able to visualise the correct folding patterns of long and complex protein molecules. Sometimes computer modelling alone cannot determine the most efficient folding pattern of a protein.

Baker’s plan was simple; to develop a puzzle game that could be downloaded for free, feed current protein structure problems into the game, and watch as hundreds of thousands of players came up with unique and creative solutions. The Foldit game presents players with a section of a protein molecule that computer modelling has been unable to arrange into the optimum orientation. Players are given instructions to rotate and bend different parts of the protein section to match certain criteria, and then can submit their attempts. These attempts are collated and compared by protein researchers, and the best possible structures are further investigated.

This isn’t just a little puzzle game designed to help students procrastinate; real scientific results have been reached using Foldit players’ suggestions. Most recently, a computer model of an enzyme capable of aiding in a Diels Alder reaction (a common chemical step in the synthesis of various compounds) has been completed thanks to the input of Foldit players. Players who are particularly active or advanced have even been named in published papers as contributors to the research. By approaching the protein-folding problem with an accessible and fun format, scientists have harnessed the power of hundreds of thousands of human minds to tackle big problems, one small step at a time.

 

If you’d like to join the effort to complete protein structures or just learn more about crowd-sourced research, visit www.fold.it

 

Elevator to SPACE

In August of this year, Washington will be hosting an event that will no doubt capture the imaginations of scientists and sci-fi nerds alike; The Annual Space Elevator Conference. Over the course of three days, researchers, designers, and space enthusiasts will meet up to discuss the challenges of constructing a US$8 billion ribbon that will connect Earth and sky.

The current design consists of a tether fastened to the Earth’s equator, extending to a counterweight about 96,000km away (a quarter of the distance to the moon!). Elevator-riders’ destination will be a space terminal sitting at 36,000km above Earth’s surface. To put this distance into perspective, NASA grants astronauts their space travel wings at an altitude of 80km, Virgin Galactic will take you to 110km for the small sum of US$200,000, and Earth’s atmosphere ends at an altitude of about 1000km. The cable, counterweight, and terminal will orbit Earth as the planet rotates, with the terminal itself existing in ‘geosynchronous orbit’; essentially orbiting at precisely the right distance and velocity to ‘keep up’ with Earth’s rotation.

Getting to 36,000km in a space elevator will involve more than just hitting the ‘up’ button and standing awkwardly in a box, desperately avoiding eye contact with fellow lift-users. Travelers will be zipping along the Earth-to-space tether at 200km/h for about a week, contained in a shuttle capable of deflecting potentially fatal radiation.

For the past five years, NASA has been offering a US$2 million prize to groups that successfully develop a tether capable of withstanding the physical demands of space elevator travel. No group has won this NASA Strong Tether Challenge yet, but 2012 might be the year that changes.

Developments in the technology have put carbon nanotubes at the front of the materials-race for space elevator application. Consisting of a ‘mesh’ of carbon atoms rolled into a cylinder of about 1 nanometer diameter, carbon nanotubes are the strongest known material in terms of tensile strength (withstanding stretching or pulling). Carbon nanotube fiber with a cross section of 1 millimeter squared would be capable of holding about 6400kg. That’s like dangling a Hummer from a ukulele string.

Using this super strong material, the ‘ribbon’ space elevator tether design becomes feasible. A 20cm wide, paper-thin ribbon of carbon nanotube fibers would be sufficient to link Earth to the space terminal, before widening to about 1m to join the terminal to the counterweight.

Before the development of the space elevator can commence, a method for seamlessly joining carbon nanotubes together to form a 94,000km ribbon must be perfected. Spinning fibers together like spinning yarn from wool might be an option, but there is no room for shortcuts where a project of this scale is involved.

The Obayashi Corporation in Japan has announced that they will be capable of building a space elevator within the next 40 years, so there’s every chance we will be lucky enough to witness one of the staples of science fiction becoming a reality.

 

Touchscreens become Feelscreens

(Hey guys, I’m just going to start posting science articles I’ve written, just the ones that aren’t horribly out of date by now.)

(As if anyone actually reads this blog.)

* * *

Forget super crisp true-to-life high-definition 3D TV sets. The future lies with our sense of touch.

If you’ve ever used a Rumble Pak for your Nintendo 64 controllers (mid-90s, anyone?), or set your mobile phone to vibrate, you’ve already experienced the concept of ‘haptic feedback’. ‘Haptic’ is derived from the Greek verb ‘to touch’, and the next two years are likely to see a huge increase in the amount of ‘touching’ being incorporated into technology.

Receiving some sort of physical feedback from a device is an old concept. Light aircraft used to have vibrating weights in their controls to warn pilots of various problems. Arcade games and more modern consoles incorporate appropriately timed lurches and rattles so you can feel your spacecraft exploding around you. Smartphones don’t just vibrate when someone calls you, they offer almost unnoticeable buzzes as you navigate menus and scroll through lists. The world of haptic feedback is already alive in our existing technology, but thanks to companies like Senseg and Immersion, the technology is about to reach a whole new level.

Senseg has developed a coating that can be applied to the touchscreen of a phone or tablet that allows users to feel textures, shapes, and ridges. Demonstrations of the technology have seen stunned interviewers stroking a standard iPad screen and claiming they feel a stone wall, velvet, sandpaper, corrugated cardboard, even individual ball bearings that roll around as they’re touched. The effects are almost unbelievable, and the technology is equally incredible.

The coating Senseg has created is ‘piezoelectric’, which means it has the ability to turn electrical energy into physical movement. The vibration of the coating is undetectable to users, (the coating itself moves a maximum of about 1μm, a hundredth of the width of a human hair), but the electrical charge created on the surface interacts with the user’s fingertips, turning the computer-controlled friction into the illusion of texture. Essentially, the screen stays perfectly flat but electrical friction convinces users that they’re running their hands across a raised surface.

The applications of this technology seem limitless at the moment. Integrating this level of haptic feedback into smartphones, tablets and computer screens will open doors for app developers. On-screen keyboards could be designed to feel like physical keyboards, allowing tablet users to touch-type. Angry Birds and Fruit Ninja could become even more addictive if users could feel the squelch of the fruit (or pig) as they played. Your e-reader could have a paper-like texture. There are some less frivolous applications for Senseg’s haptic feedback too; braille on tablets and smartphones for the visually impaired, or fine-tuned physical feedback for surgeons performing keyhole procedures. Japanese researchers are looking into the possibility of combining haptic feedback with holographic projectors, creating a 3-dimensional world that users can physically interact with.

With Senseg’s technology expected on the market within two years, it seems likely that the digital world might eventually become as tactile as the physical world. Another reason to never log off your computer? We’ll have to wait and see.