#Microtwjc: The Evolution of Virulence

A long time ago, a bacterium noticed the odd behaviour of its cousins. It had noticed that they had formed a group, and were spending a lot of time together. An unsettling amount of time together. The bacterium's friends told it to not worry. It is perfectly fine for related bacteria to stick together, to live in colonies of individuals.

The bacterium told its friends how its cousins behaviour was different. The cousins had forfeited the life of independence, and had reduced themselves to mere parts of a greater whole, a multicellular organism. it was disgusting, it was socialism. It had to be stopped.

Bit by bit, it rallied other bacteria to it's cause, and together they came up with a plan. They would become virulent. They would evolve the resources to fight their multicellular competitors, invade their cells and feast on their nutrients. So they went to Professor Oak, who happened to have just the right thing for them...

The Ten things I can do now I have a PhD

Ten Things I can now do with a PhD

1. I can introduce myself as the "lu-uurve" doctor to members of the opposite gender.
2. I can finally publish a book about the "Lint" diet , and have it fester on bookshelves around the country as its devotees staunchly defend it even as they succumb to rickets, scurvy and starvation.
3. I can start an advice column, in which I couch my advice in impenetrable jargon to conceal its vacuity.
4. I can drop my PhD into conversations, knowing that it makes me knowledgeable on all subjects, as opposed to the one I actually specialised in.
5. I can now end any argument by taking a tally of people in the room with PhDs, and those without, and then cement my victory by blowing raspberry lasting not less than 3 minutes.
6. I can buy a pair of glasses for the sole purpose of peering over them when talking to people. And occasionally ripping them off dramatically to let everyone know that shit just got real.
7. Whenever someone utters the words "Doctor Who?", I can shout my own name really loudly and pointing at myself. Raucous applause will no doubt follow.
8. I can now defuse "Doctor Doctor" jokes by simply saying "Yes, what is it?". This will always be funnier than the actual joke.
9. I can line up the photos from my BSc, MSc and PhD graduations, put attack statistics under them and pretend that I am a extremely rare and esoteric pokemon, and that these were my evolutions.
10. I can don a cape and mask to begin a career in super-villainy. It's the profession with the best hiring prospects in this economy.

The Final Hurdle

I'd pretty much done everything at this point. Through struggle and sweat and 263 pages of thesis, I found myself edging closer to the finish line.
In theory, anyone can write a long thousand page tract on a topic without applying observation, logic, creativity or even basic grammar to it.
The manuscript I wrote needed to be assessed. But herein lies the problem.
A PhD, unlike many other qualifications, is granted based on the synthesis of new knowledge. The problem of this becomes apparent when it comes to examining a PhD. I'll compare it with learning in a school.
The learning that occurs in schools occurs in the classroom, by a teacher who at least know the standardised answers on their test sheets, if not the subject itself. As a result, examining students knowledge of these subjects is the simple task of comparing their answers to the standardised tests.
A PhD is very different. A student does not do most of their learning in lecture rooms regurgitating the knowledge that is fed to them. A student must use the tools, and the advice of experts (including , but not exclusively their supervisor(s)) in order to gain new knowledge or insight about a subject. In the case of the sciences, the teacher is nature. This becomes problematic when examining PhD, because Nature doesn't have a mark scheme. If it did, it would be behind an infinitely expensive paywall.
This is where the Viva Voce comes in. The exact details for the examination differ between countries, but the basic jist is that it requires the thesis to be assessed by a group of experts in that field, who are able to assess the work, and discuss the new findings of the thesis with the candidate.
A number of people in my lab told me that I would be fine, that it would amount to a nice conversation about my thesis by the only people* who would actually read it. I guess I should have found this reassuring. An experienced tight rope walker may tell you that a hundred metre walk on spider silk over hot lava was simple enough when they did it, but does that mean you'll have no trouble on your first go ?
As it turned out, this was pretty much the case. Aside from one moment where we got into a somewhat philosophical argument about the possible detriments of eradicating an infectious disease, a few moments where I talked myself into a corner, it went well.
In the end, I passed !



*not including those involved with its production

Elementary; The Science of the Perfect Murder

It was television that inspired me to devise the perfect murder. Not for the usual reasons relating to scientific inaccuracy. This isn’t about watching a CSI unbalance a centrifuge, contaminate a sample or holding a pippette backwards. Small errors like this just don’t bother me anymore. I long ago accepted that most television shows are set in a science fiction fantasy world, where science only works when the gods of plot convenience allow it. It was in this frame of mind of that I watched a recent episode of Elementary (S1e17 “Possibility Two”).

For those of you who aren’t familiar with it, “Elementary” is a procedural cop drama with the twist that it is also a Sherlock Holmes pastiche. It follows the detective (played by Johnny Lee Miller) and Joan Watson (played by Lucy Liu) as they solve crime in modern day New York. Johnny Lee Millers interpretation of Holmes can be described by shouting “QUIRKY” and doing the jazz hands so hard that they violently detach and fly across the room. This is a show that proudly flies the flag and wears the matching underpants of silliness. The very definition of TV to turn your brain off and enjoy. Unfortunately, my brain’s off switch is always slightly faulty  and against all odds, this episode did make me think. I am going to spend the rest of this post exploring these thoughts, so I should warn you that this article contains major spoilers.

Taking DRACOnian measures against viruses

When Alexander Fleming shamelessly took credit for a drug produced by the penicillium bread mould, our fight against bacteria completely changed. Even now, bacterial diseases are nowhere near the threat they were before that discovery. But today, we are seemingly having to put up with emerging viruses. Every year, we have to put up with entirely new strains of flu. There is nothing we can do about the viruses that cause the common cold. There are various antivirals out there, but they are specific for specific diseases, like flu, or HIV.
Generally, it’s been fairly difficult to make anti-viral drugs. Often, a lot of the problem comes from the way viruses work. When they are outside the cell, they don’t have any active metabolic processes that can be targeted by drugs. And when they are inside the host cells, the metabolic processes they’re mostly using are ours. So it’s very hard to target the viruses without attacking the host. Compared to bacteria, viruses present a very small target. 
Could a paper published in PLOS One called  “Broad Spectrum Anti-viral Therapeutics” represent a penicillin moment for viruses ? A trailblazer that can transform our relationship with viruses ? To work this out, let’s take a good long look at what these anti-viral therapeutics are, and what they do.  To do that, we have to talk about DRACO.

Are we talking about the DRACO from Harry Potter, or the dragon voiced by Sean Connery in Dragonheart ?

Whilst I compliment you on your knowledge of pop culture, you are wrong on both counts. DRACO is a handy acronym that stands for Double-stranded Ribonucleic acid Activated Caspase Oligomizer. DRACO is the drug that is being purported to extinguish all of those nasty viruses. To understand how it works, we need to take a look at how some of our most pernicious viruses work.
You may have heard about DNA, and how it’s genetic code is a blueprint for life. Your genome is encoded in your DNA. The nucleus of your cell holds all of the DNA, and acts like a library for your genetic code. When your cell needs a specific genetic code to make a certain protein, the nucleus makes an RNA copy of the appropriate gene and sends it out into the rest of the cell, where it can be used to construct a protein.
The goal of a virus is to enter a cell, and to hijack this process to make more viruses. Usually at some point, the virus will attempt to substitute it’s own genetic code for that of the host cell, tricking the host cell to make more viruses ^[1].
However, some viruses can store their genetic code using RNA only. Whilst RNA is less stable than the DNA, it means that these viruses can go straight to the cell machinery that translate RNA into protein, and get ahead with making virus based proteins.

End of Hiatus

A couple of months ago, for reasons too irritating to get into, my internet got cut off, which made blogging nearly impossible. But then again, I needed to focus on writing up my thesis.  That didn't go exactly as well as I planned.....

It turns out, wasting time and procrastinating can occur even in the absence of the internet. As you can tell, internet access is no longer a problem, and so once again I can procrastinate by researching and writing posts for this blog ! Expect more posts soon.

#Microtwjc Why FRET about Biosensors ?

The latest paper for #microtwjc focuses on finding a new way to sense metabolites inside of living bacteria.  Bacteria need to regulate their nutrient intake, because like people, they don't want to get too fat or thin. 

If there isn't enough nutrient in the environment, they need to conserve what they have, and if more appears, they need to consume it as efficiently as possible, but if they did that all the time, it could cause them problems.