Thursday, 18 September 2014

Why are kinases called kinases?

Kinases are one of the biggest and most important classes of enzymes (i.e. protein with catalytic activity) in biology. You can always recognise an enzyme because of the suffix “-ase”. What comes before the -ase then indicates the nature of the enzymatic activity.

The major classes of enzyme have names that give a good clue as to the general nature of this activity. Oxidoreductases, for example, catalyse oxidation-reduction (“redox”) reactions. Transferases transfer chemical groups from one molecule to another. Kinases are transferases: they transfer a phosphate group from one organic molecule (usually ATP, the cell’s primary energy carrier) to another (a protein, lipid or carbohydrate). And this is actually the origin of the kin- part of the name: from the Greek kinein “to move”.

For those wondering, there is also such as thing as a Phosphorylase but this does something subtly different; whereas a kinase transfers organic phosphate groups (i.e. phosphates attached to carbon-based biomolecules), a phosphorylase transfers inorganic phosphate groups (i.e. phosphate+hydrogen) to acceptor biomolecules.

But why -ase? This stems from the ending of diastase, the first enzyme ever discovered. According to Wikipedia:

“The name “diastase” comes from the Greek word διάστασις (diastasis) (a parting, a separation) because when beer mash is heated, the enzyme causes the starch in the barley seed to transform quickly into soluble sugars and hence the husk to separate from the rest of the seed.”

So there you have it. A kinase is an early example of an enzyme that moves something from one molecule to another, hence a name that literally means “an enzyme to move”.

Thursday, 7 August 2014

How (not) to apply for a PhD

As with most academics, I get a fair a number of unsolicited enquiries about possible PhD placements. Unfortunately, a number of these appear to be from students who are receiving little or no advice regarding how to go about making an application.

Every now and then, an application stands out from the bunch for being particularly good or bad. A while back, I received one of the latter, which made me so sad that I thought I would turn my response into a post. What made it particularly tragic was that it was from a student who had received government funding to study abroad, and was therefore in a fairly strong position.

The email (name redacted) was as follows:

On [DATE] "XXX baby" <XXX@yahoo.com> wrote:

Subject: Hello doctor

My name is XXX, I finished M.Sc. degree in XXX University in Iraq at (2012), I have obtained a fund from the Iraqi government to study PHD in Microbiology in the Ustralia.

I had opportunity to be a student of Iraq and My interests are about Bacteriology and Immunity in general and I really hope to get your kind acceptance to pursue my PHD under your supervision in University of UNSW.

Kindly find attached my C.V please which I hope it gives detailed overview about me

Thank you very much

The CV was then attached as several JPEGs of scanned pages. Unusual attachments plus a username of “XXX baby” and subject line of “Hello doctor” meant that this one almost went straight in the bin as spam. Given the number of typos and other errors, it might have been better if it had.

I’ve had some others that were almost as bad, including one that started “Hello Sir !” and proceeded to end every sentence with an exclamation mark! Yes! Every sentence! No! That’s not a good idea!

Lest I get misunderstood, I must stress that the point here is not to be mean to these students. The issue is that they are clearly not getting the advice they need, especially given the fact that they are writing in their second (plus) language and applying to academics with a different culture.

Here then, is my advice/guidance for those wanting to make an unsolicited application for a PhD studentship (though most points still apply if a project is being advertised). I get many applications from overseas students. If I am even to consider you as a potential student then you need to impress me. The following impress me:

Professionalism. Send a well structured email, with a sensible subject such as “PhD enquiry” and a CV (if attached) that is provided as a single sensibly named PDF (or docx), i.e. your name and “CV” feature somewhere in there.

Genuine Interest. Personalise your message and provide some indication that you really know who I am. “Dear Sir” indicates a blanket mailshot to all and sundry and is thus destined for the bin. Knowing who I am is not enough, though. I also want an indication that you know and understand at least something of the research that goes on in my lab. Referencing degree subjects or research experience that match neither my background nor research focus indicates poor research/understanding. A PhD is long, hard graft and I need to know that you have genuine interest or everyone’s time will be wasted.

A clear CV. Your CV should have relevant skills and metrics highlighted. If you are from overseas, remember that I probably do not know what your grades mean, so place them in context. What proportion of students get those grades/medals etc.? This is a research post, so describe some of your research projects and your role in them. When it comes to CVs, evidence is the name of the game. Don’t just list skills and positive attributes: provide examples.

Motivation/Enthusiasm. Good grades are not enough and academic ability will only get you so far in a PhD. Motivation and enthusiasm are critical. As well as a CV that stresses relevant achievements, include a personal statement that convinces me that you want to do a PhD (with me) for the right reasons, and are likely to see it through.

Ask questions. This is basically genuine interest + motivation/enthusiasm but worth stating in its own right as intelligent questions are the evidence of those things. It's your PhD and your life - you should care about what you might be doing. The caveat is this: do not ask a question that is answered by ten minutes of reading my lab's webpages and/or paper abstracts.

Good communication skills. If English is not your first language, get your emails proof-read by someone with good English. Exclamation points after every sentence indicates that communication will be tricky, as does failure to appropriately understand/respond to emails. I am not going to think you are not keen if you take a few days to give a measured response. I am going to think that communication may be insurmountably difficult if I get a speedy response that is riddled with errors.

Funding. Unless you are applying for a specific funded project, you will need to secure your own funding. A clear indication of a funding plan is therefore crucial. If you already have funding, this is good. Better still, would be to detail exactly what that funding covers (i.e. duration? fees AND living expenses? any attached conditions?) and to indicate how the funding was won and how competitive it was. Winning a competitive scholarship is one way to impress. Even better, provide evidence in the form of an official notification of funding etc.

References. Ultimately, it is very tricky to assess a student from a CV and covering letter alone. Again, evidence is the name of the game. Provide two or more faculty members or professional scientists who can provide an academic reference. These should have institution email addresses, not personal gmail/yahoo addresses, as anyone can create these and they will carry less weight.

Fail to hit most of these points and your application is in the bin. (I now have a generic response that I send out to generic applications.) This may seem harsh but there is a lot at stake and it is important to get a good fit between student, supervisor and project; a poor student/fit is a net drain on lab productivity.

A PhD is not something to embark upon lightly. It will consume many years of your life and will quite possibly determine the direction of the rest of your professional life. A PhD application should be made with all of the research, care and attention to detail that this implies.

Saturday, 5 July 2014

STAP retractions are both a failing and a triumph of science

It was looking inevitable and this week two high profile Nature articles on “STAP” (stimulus-triggered acquisition of pluripotency) stem cells were finally retracted in Nature:

Several critical errors have been found in our Article and Letter (http://dx.doi.org/10.1038/nature12969), which led to an in-depth investigation by the RIKEN Institute. The RIKEN investigation committee has categorized some of the errors as misconduct (see Supplementary Data 1 and Supplementary Data 2). Additional errors identified by the authors that are not discussed in RIKEN’s report are listed below.

...

We apologize for the mistakes included in the Article and Letter. These multiple errors impair the credibility of the study as a whole and we are unable to say without doubt whether the STAP-SC phenomenon is real. Ongoing studies are investigating this phenomenon afresh, but given the extensive nature of the errors currently found, we consider it appropriate to retract both papers.

Nature cover the retractions in an editorial, “STAP retracted”, which runs with the tagline,

“Two retractions highlight long-standing issues of trust and sloppiness that must be addressed.”

You can get a sense of those issues from the retraction statement and the editorial, which concludes:

“we and the referees could not have detected the problems that fatally undermined the papers. The referees’ rigorous reports quite rightly took on trust what was presented in the papers.”

They also highlight “sloppiness” in science, manifest as a “growth in the number of corrections reported in journals in recent years”. (Something not helped, in my opinion, by high profile journals such as Science and Nature burying so much of the important methods in Supplementary Data, which is rarely reviewed or edited as critically as material in the main text body.)

You can read more about those issues in the editorial and elsewhere, such as the Faculty of 1000 blog. The STAP papers, their initial irreproducibility and eventual retraction highlight potential failings of the current scientific system, which places far too much emphasis on output quantity and impact rather than (true) quality and integrity.

However, they also highlight the tremendous success of the scientific system.

The fact is, the experiments were repeated, the failure to reproduce results was documented, suspicions were raised and investigations made. Science works because, ultimately, you cannot fake it. Whatever data you make up, whatever results you misinterpret, whatever sloppiness leads to “conclusions [that] seem misleadingly robust”, the truth will out eventually. You cannot hoodwink nature.

And that is why science remains far and away the best (probably only) method we have for establishing the truth about reality. The system maybe flawed, it may waste money and it may lead poor unsuspecting suckers chasing wild geese, but eventually it will self-correct. So, whilst I would never put my trust in individual scientists (unless they have earnt it) or results, and I remain skeptical of every new claim, I still emphatically trust science itself.

Saturday, 28 June 2014

A comprehensive overview of chemical-free consumer products

If, like me, you get a bit annoyed by people who decry “chemicals” (and are usually far too trusting of anything “natural” at the same time), you will appreciate an online paper just published at the Nature Chemical Biology blog, “A comprehensive overview of chemical-free consumer products” by Alexander Goldberg and CJ Chemjobber.

I think that the message is so important, I have reproduced the entire abstract main text of the paper:

Manufacturers of consumer products, in particular edibles and cosmetics, have broadly employed the term ‘Chemical free’ in marketing campaigns and on product labels. Such characterization is often incorrectly used to imply — and interpreted to mean — that the product in question is healthy, derived from natural sources, or otherwise free from synthetic components. We have examined and subjected to rudimentary analysis an exhaustive number of such products, including but not limited to lotions and cosmetics, herbal supplements, household cleaners, food items, and beverages. Herein are described all those consumer products, to our knowledge, that are appropriately labelled as ‘Chemical free’.

Exactly.

Friday, 27 June 2014

Don't put plastic bags in recycling bins

Without recycling - especially plastic recycling - we're all doomed. Seriously. But what’s possibly even more tragic than selfish people who don’t bother to recycle when the service is offered, is people who go to the effort of sorting their recycling and then completely nullify their effort by sticking it in a plastic bag.

There’s some good information on why this is so bad at Planet Ark. It’s worth repeating the main points here:

Human health and our natural resources

The first level of sorting at recycling stations is done by hand.

Workers at the recycling station are sorting through tonnes of material an hour and don’t have time to open bags to find out what’s inside. Your plastic bags could be filled with recyclable material like glass or plastic bottles or aluminium cans. Or they could be full of contaminants like food scraps, plastic wrap or unwanted wine glasses. Even worse, they could be full of dirty or dangerous material like dirty nappies or medical equipment.

Since it’s too dangerous and time consuming to open and sort the bags, they have to be removed from the recycling stream and thrown into the rubbish. That means valuable resources will not be reclaimed. Instead they will be wasted in landfill.

Recycling system efficiency

The next issue with plastic bags is that they interfere with the automatic sorting machines.

Conveyor belts feed the recycling into rotating tunnels, onto spinning wheels and past magnets and eddy currents to separate the plastic, glass, paper, aluminium and steel cans. Plastic bags cannot be sorted from other materials by existing machinery. Instead, they get caught in the conveyor belts and jam spinning wheels and can bring the entire sorting station to a halt. The bags then need to be found and removed by hand - a time consuming and often dangerous process that reduces the overall efficiency of the recycling station or materials recovery facility (MRF).

The photo above shows the sign on all of the recycling bins in our building. Despite this, people still keep putting plastic bags in recycling bins! When I dropped down some recycling earlier this week this is what I found:

Being a good citizen (and without any other crap in the bin), I emptied it out and stuck the bag in the regular bin. Usually, I am not so brave.

It left me feeling angry at the laziness and/or ignorance that made someone think that this was acceptable behaviour. If you see someone put plastic bags in recycling, please tell them not to. And if you do… Stop! Put them in the regular bin or, better still, a dedicated plastic bag recycling bin at your local supermarket (if it has one).

Thursday, 26 June 2014

Earthworks 2013 Barossa Valley Shiraz

From (mostly) Aussie beer to Aussie wine. This week's discovery was Earthworks 2013 Barossa Valley Shiraz. It’s a real corker. Except no cork, obviously. (The Aussies were sensible enough to ditch those years ago.)

A good companion for beef and guinness stew. And blogging! The only downside is a very purple tongue.

The best bit… I bought it on buy-one-get-one-free, so we still have another bottle to enjoy!

Wednesday, 25 June 2014

The tragic wonder of life on Earth today

A sad post over at Why Evolution Is True today: “Last chance to see… pretty much everything, including these Dolichopodids”, reporting on the gloomy effects of systemic neonicotinoid insecticide use... plus some pretty insect pictures.

We are lucky to be alive today. It is probably the only moment in Earth’s history and future in which the technology exists to capture images and videos of creatures great and small, whilst those creatures still exist to marvel at.

It is sad to think that the next generation will not be so fortunate. It’s time that politicians paid more attention to scientists and environmentalists, for the sake of everyone and everything.