More pictures after the fold

The project is a satellite of the worldwide Hyperbolic Crochet Coral Reef project created by Margaret and Christine Wertheim of the Institute For Figuring in Los Angeles.

TT

Civilisation
That’s what they call it
We live
In the plains, in the valleys, in the walls
Stigmatised
As disease-causers and bloody anarchists
Innocent life
Almost unnoticed by the self-appointed Empire

Uneasy truce
Between us and this floating isle
A grain of greed
Tempts tumbling, cascading white cells
Itchy fingers
Coiled tightly around taut leashes
Maddened by M.A.D.
We embrace awkwardly amongst sleeping dogs

A crack
as klaxons echo throughout the ranks
Invaders!
Peacekeepers ready their weapons
Refugees flood
Shot and sunk for the company they keep
Pioneers lost
The finest sieve finds no justice

Meanwhile
In geological time, slow as melting glaciers
A resentful kiss
Between lovers, contains more bitterness than it seems

TT

Anyway, this post I’m going to analyse the poem that I wish had won -

Lustful oxygen

Filled-valence prudes tut-tut

An extinguished flame

Aw, yeah, lustful oxygen. (Photo of James Kleinig flicking water on some tealights by Colin Sinclair)

I was taught in high school that all chemistry is electrons. But, of course, it is all eclipsed by things blowing up. Fire is the thing that I most closely relate to chemistry. It is a source of intrinsic passion, of instinctial awe, of heat and danger. And it’s all caused simply oxygen in the air binding to stuff (carbon in the above case). Oxygen is one of the most reactive elements out there, meaning that it has strong desire to bind and couple with other atoms and molecules. When it does so, it relaxes a bit and releases some energy. That energy is the heat.

But if atoms are already bundled up in couples of high affinity, not even oxygen can break that bond (under normal conditions). Nitrogen gas (N2) is an example of atoms that naturally strongly bound together. This bond means that the two nitrogen atoms share electrons (3 from each atom, in this case) and are both satisfied. Satisfaction as atoms are concerned is defined in terms of valency (a complex topic involving periodic tables, electrons and oxidation states). Once an atom’s valence is filled, then it is stable.

Nitrogen gas makes up 70% of the atmosphere. So we blow out mostly nitrogen when we exhale.  What we do when we blow out a candle is basically surround the oxygen with highly stable nitrogen gas. Oxygen can’t bind to the nitrogen and can’t get to the carbon that it can bind to. What happens then is that the flame is extinguished because no heat is being produced.

Woo, science!

TT

July 28^th was World Hepatitis day; the day to raise awareness of hepatitis B and hepatitis C. Both are very important diseases: together they cause >1 million annual cases of liver cancer, one of the most deadly cancers. Hepatitis viruses (A, B, … G) are completely different viruses. The thing that they have in common is that they all infect the liver.

You may have heard of Hepatitis C recently, as an anaesthetist was charged with infecting 54 women with Hepatitis C in a Melbourne hospital a few months ago.

Biohazard cookies! (Cookies by James Kleinig and Gen Sinclair; photo by Thomas Tu)

The cause of Hepatitis C, the Hepatitis C Virus (HCV), was discovered very recently in 1989. But since then, we’ve recognised that 3% of the world’s population have been infected with HCV. Famous patients include Baywatch actress Pamela Anderson, the infamous Mark Brandon “Chopper” Read, and stuntman Evel Kinevel.

HCV infects the liver and uses your liver cells as a factory to produce more virus. Each patient can have up to 100000000000 viruses floating through their blood; this is enough virus to infect everyone in the world.

Hepatitis has a stigma – patients are regularly shunned as unclean or immoral. But people can be infected in quite innocuous ways, a scratch exposed to a fleck of infected blood is enough to infect you. People can be infected in many ways: improper usage of medical equipment; sharing tattooing needles (as Pamela Anderson has claimed she got infected); sharing bloody razors (as Chopper Read); or otherwise exchanging blood. Before we could screen blood donors for HCV, getting a blood transfusion was also a big risk (as Evel Kinevel found after one of his big crashes).

If infected, you might not even know. Some patients will get flu-like symptoms or jaundice, yellowing of the skin and eyes. But many patients can be completely asymptomatic and are none the wiser.

While some patients will clear the virus, the majority of infected people will be permanently infected. These patients find out they have hepatitis C after they get a blood check, or decades later infection when their liver fails from liver scarring or they are diagnosed with liver cancer.

Over the course of infection, your immune system attacks the foreign virus and the cells that are making the virus. This means your liver is continually destroyed over decades. Eventually this can lead to scarring the liver, which stop your liver from working. Or it can lead to mutations that cause liver cancer.

We don’t have a good way to stop HCV infection. We do not have a vaccine against HCV. While antivirals can cure patients with HCV, they are only effective against 50% of patients who can afford the expensive long-term treatment. So, medical research into new therapies is incredibly important for us to stop HCV in its tracks.

TT

Firstly, one of the blog pictures (from here) gets included in the very awesome photoblog “Things Organised Neatly“. As you see here, it was reposted around the place with comments like “I miss using micropipettes @.@“,  “ahh brings me back to my 10th grade genetics class…fuck“, and (for some reason) “Is it odd that this is sexy to me?“

Secondly, I won second place in an open science haiku competition! The Royal Institution (in conjunction with the Friendly Street Poets) organised the second annual Sci-ku competition earlier this year with the themes being International Year of the Forest and Year of Chemistry. I was picked for second place for this:

Frenzied matter zoo

Then, Mendeleev’s table

The world ranked and filed

I’ll explain this poem a little bit. Before the periodic table, elements were all over the place. Their properties, their weights, their valencies (how many electrons they could give or take away) seemed to be picked almost arbitrarily. Chemists and physicists of the day had to memorise it with no guiding framework. In 1869, Professor Dmitri Medeleev saw that if he arrange elements by their increasing molecular weights, then the chemical properties and valencies came up at regular intervals, i.e. they had a period.

After fussing with different designs (one including a spiral design, which apparently was spurred by a dream of a snake eating its own tail), he came up with a table similar to what we now know as the periodic table of elements. What he noticed was that some elements were missing. With this, he predicted that there were elements within a specific weight range with specific chemical properties that were left to discover. Every prediction ended up being beautifully on target with all the 118 elements so far. Indeed, all the chemicals that make up pretty much every material in our world were now truly and beautifully ordered in a simple table. Perhaps it is also a candidate for “Things Organised Neatly”.

Mendeleev ended up getting a Nobel prize for his work and an element named after him (Element 101 – Mendeleevium). Presently, the periodic table of elements is the central tenet of chemistry, just as the theory of evolution is central to biology and the atomic theory to physis.

In the following weeks, I’ll go through my other (losing) entries and give some analysis of those.

Sorry again for the lack of activity on the blog. I am going pretty well on my thesis, thanks for asking.

Anyway, I was drinking with a couple of friends of mine who are doing their PhDs in environmental health and bioremediation the other night. Long story short, I wake up with this on my hand:

At least it wasn't a dick and balls. Picture taken by Thomas Tu

After some greasy food and coffee, I summoned enough courage to look up “shit burgers” on Google. Then it came back to me, we had been talking about a nutty bit of science where a Japanese team had created faux meat from sewage. While I’m not sure that it isn’t a hoax, here’s a video:

So apparently, this guy got contacted by the sewage people saying they’ve got too much sludge around. The scientist extracts the protein out of the sludge (which is mostly held up in bacteria), puts it in an “exploder” (?) and then you have insta-steak.

Now, while we have previously touched on inserting other people’s poop into you as treatment, I do admit that this seems pretty gross. But if you think about it, the atoms of everything you’ve ever eaten has probably passed through several hundred colons before yours. This is simply a shortcut through the circle of life.

I am a bit worried about making the food completely safe though. It’s true that sewage treatment kills pathogenic bacteria and viruses as part of the processing. The treatment can kill more than 99% of the infectious viruses in the water system. But if you’re pooping out 10¹⁰ infectious particles per gram of faeces, there are still going to be plenty of viruses left to infect you. Indeed the literature is full of studies showing viruses do get past sewage-treatment plants and out into the wild (see references). I haven’t found any literature about this team’s steak-making technology to judge whether it’s going to kill all the viruses either (little help, blogosphere?).

Nevertheless, I think I’m starting to feel queasy again and I’m not sure that’s entirely the hangover’s fault. Enjoy your weekend.

TT

References

He, X., Cheng, L., Li, W., Xie, X., Ma, M., & Wang, Z. (2008). Detection and distribution of rotavirus in municipal sewage treatment plants (STPs) and surface water in Beijing Journal of Environmental Science and Health, Part A, 43 (4), 424-429 DOI: 10.1080/10934520701795731
Fong, T., Phanikumar, M., Xagoraraki, I., & Rose, J. (2009). Quantitative Detection of Human Adenoviruses in Wastewater and Combined Sewer Overflows Influencing a Michigan River Applied and Environmental Microbiology, 76 (3), 715-723 DOI: 10.1128/AEM.01316-09

The science of forensics, specifically forensic psychology, is a tool of the legal system. A forensic psychologist works to assess, identify and clarify psychological issues, without prejudice, in order to satisfy the court’s legal understanding of those issues. Forensic psychologists are often called upon to give psychological insight into cases like that of Arizona shooter Jared Lee Loughner, whose behaviors preceding the attempted assassination of U.S. Representative Gabriele Giffordsmirrored those of a schizophrenic. Thus, the primary function of forensic psychology is to tie or untie the knot that binds mental illness to crime.

Evaluating Mental Illness

A forensic investigation may begin with a judge’s request to determine whether an alleged criminal is competent enough to stand trial. A forensic psychologist is then empowered to independently assess an individual’s sanity, as it relates to criminal responsibility. Likewise, a court may simultaneously require a forensics expert to reconstruct the accused’s state of mind at the time of a crime.

In Loughner’s case, a forensics neuropsychologist (someone who specializes in nervous system and brain evidence) might examine the suspect for trauma that may have caused him to act out. In cases where the accused exhibited strange social behaviors or hallucinated, a serious mental illness that would cause reality detachment, such as schizophrenia, would be considered.

Investigative Tools

While a forensic psychologist draws information to determine a person’s present state and what it was at time the crime was committed, an investigator also evaluates a suspect’s past issues with mental illness, including biological or developmental factors. Physical and psychological tests may be conducted, which often involve IQ testing and MRI or PET scans.

Forensics in Court

Once the assessment of an defendant’s total health picture — medical tests, background and police checks, evidence of deception — has been made, a forensic expert is bound by the court to make the information applicable to the law and worthy of courtroom testimony.

Violent Behavior and Schizophrenia

Although many people believe mental illness is a precursor to violent crime, University of Virginia law school psychologist Dr. John Monahan revealed in an interview with Voice of America, that he thinks a schizophrenic is no more likely to commit a violent crime than anyone else, unless the suspect is a substance abuser or discontinues mental health treatment. Indeed, social scientist Jeffrey Swanson added in the same VOA interview that twisted thinking is not directly linked to violence.

Ultimately it is the duty of a forensic psychologist to effectively span both the medical and legal fields and to serve as a conduit for critical evidence. A forensics expert plays no favorites in a courtroom, presenting unbiased and legally-comprehensible factual evidence. Performing duties only at the behest of the court, a forensic psychologist examines and reports upon a defendant’s past, present and sometimes probable future physical and mental state. Acting as an agent of translation for two respected professions, a forensic psychologist is employed to ensure justice remains fair for those accused of and victimized by crime.

A cut of $400M (absolute peanuts with respect to the size of the Austrlian budget of ~$354600M) over 3 years is being slated for the major federal medical science funding body, NHMRC. To put that in perspective, the NHMRC has an annual budget of ~$700M,  and that’s only after scientists had worked hard for 10 years previously to get up to that competitive rate.

It won’t affect everyone equally. Money gets handed out first to those continuing grants. Those really affected are those young researchers going for new grants; researchers who are more likely to up and change jobs. This would leave a gaping hole in continuing line of researchers and disrupt the entire structure of research. Stop/start funding has huge effects.

Not only that, investment into science is investment into your well-being: pennicilin, cochlear implants, cancer treatments, discovery of the cause of stomach ulcers are all things that have been made possible with Australian research. This is all pretty obvious stuff that has been covered in much better detail by others and still others.

It’s time to do something. Rallies around Australia against these cuts have been planned. Get along to them if 1) you value further medical discoveries that will make your life much more comfortable and 2) are not a jerk. Please visit Discovery need dollars for more details and fliers.

MELBOURNE - State Library – Tuesday 12 April @ 12:45-2PM
SYDNEY - Belmore Park – Tuesday 12 April @ 12:45-2PM
ADELAIDE - Steps of Parliament house, North Terrace – Tuesday 12 April @ 12:30PM (Adelaide time)

Click here to get signs in a printable format

TT

This week, I’m putting up a new banner containing work that I’ve actually done in the lab.

Pretty colours in the liver (Immunofluorescence and photo taken by Thomas Tu)

This is a picture of a slice of liver. It has pretty colours because I’ve stained particular cells with different fluorphores: the blue represents the nucleus of all the cells; the red is the hepatitis B virus-infected cells; and the green are the stem cells and connective tissue. What you can see is that hepatitis B virus only infects the main liver cells and not the stem cells and connective tissue.  And it’s pretty!

TT

Anterograde amnesia is an ailment wherein the afflicted individual loses the ability to transfer new information to long-term memory after a brain injury, while long-term memories from before the injury remain intact. This means that a person who sustains a brain injury will likely have the same personality and the same amount of intelligence they did previously, but be unable to recall events from the recent past. Anterograde amnesia is a mysterious condition, as the exact process of storing memories is still largely unknown to scientists. However, to get a good understanding of the disorder, as many on-going studies are constantly producing new information on anterograde amnesia.

There are multiple causes for anterograde amnesia, all involving some drastic alterations to the brain. For instance, there are many drugs that can have an amnesic effect on patients. Likewise, alcoholic intoxication can also cause temporary anterograde amnesia, if large quantities of alcohol are consumed rapidly. Although the effects usually wear off after becoming sober, restoring memory creation, binge drinking or frequent “blackouts” can result in permanent brain damage.

Anterograde amnesia can also be caused when some people undergo brain surgery. For example, sometimes the removal of a tumor eradicates parts of the brain tied to memory circuits, such as the medial temporal lobe. Similarly, brain injuries that result in damage to the hippocampus, fornix or mammillary bodies can also cause this disorder.

Luckily, anterograde amnesia can usually be treated. Yet as health-cares.net explains, treatments vary depending on the original cause of the disorder. There are many cognitive rehabilitation methods that can teach sufferers strategies to cope with their impairment. If alcohol is the cause, then emotional support, proper nutrition and abstaining from alcohol are the best methods to prevent further memory damage. If the amnesia is caused by a concussion or brain injury, rest and sometimes memory exercises can be beneficial to improvement. Finally, therapy is usually the best option for patients suffering anterograde due to emotional trauma. Oftentimes, the brain, being a powerful and miraculous organ, will “remap” itself, resulting in the patient regaining the ability to store memories.

While some individuals with anterograde amnesia will recover on their own or after a bit of treatment, some cases are irreversible. When anterograde amnesia is permanent, all that can be done for the patient and their family and friends is to teach them how to cope with this ailment. It can be very stressful for both the sufferers and their loved ones, and depending on the severity, this might be a lengthy and trying process.

Anterograde amnesia is a very serious affliction that can result in major, permanent life changes for those suffering from the disorder. While it is possible to recover from the damage that results in anterograde amnesia, it is important to seek out proper medical attention to help ensure that the individual suffering from this disorder is cared for properly. Even if full recovery is not possible, it is entirely possible to learn how to cope with anterograde amnesia, and those afflicted can still lead full and happy lives.