Happy New Year!

Best Christmas stocking chocolates ever!

Like many - most? - people my age who grew up in the UK (and Ireland, I think), Christmas stockings are synonymous with Cadbury’s chocolate coins. However, this year was destined to be a Christmas without them, for two good reasons:

First, there was the report earlier this year that Cadbury are no longer making them. This had a considerable public backlash, as captured on Buzzfeed. (The author made one error in his post, ending: “However, all hope is not entirely lost, you can still buy different chocolate coins at supermarkets and pound stores around the country.” Sorry, but other chocolate coins suck in comparison.)

Second, Australian Cadbury’s chocolate is rubbish. (Sorry, Aussies, but it is. We’ve done blind taste tests and everything.)

Fortunately, Santa came up with a much better idea this year: spiced chocolate almonds from Haigh’s Chocolates.

These sound pretty amazing but are even better than they sound: an almond, encased in milk chocolate, encased in white chocolate and dusted with spiced dark chocolate powder (cinnamon, cloves, cardamon and star anise.) One to look out for next year!

Edwards Lab: On the hunt for molecular mimicry in viral pathogens

Yesterday’s excellent Australian Pathogen Bioinformatics Symposium 2014 (#APBS2014) reminded me that this post was a bit overdue: originally posted at the UNSW Science Wavelength blog on October 30, 2014. Following APBS2014, we are also looking into how we can identify which other pathogens might be using a similar strategy.

Read more at the Edwards Lab blog…

Increase your mailbox and get a new massage

I just can’t understand the authors of phishing emails. Why go to all that trouble to mimic an Outlook full mailbox message and then not even bother to proof-read the English. Don’t con artists have any standards? It’s just insulting. (A massage would be nice, though.)

Sculpture by the sea is back

We moved to Sydney just over a year ago and one of the first things we discovered was Sculpture by the sea 2013, an annual free public arts event in which one hundred or so artists create sculptures on the eastern coast from Bondi Beach to Tamarama Beach.

Even without the sculptures, the Coogee to Bondi coastal walk is an impressive piece of coastline and we are lucky to have it on our doorstep. The sculptures really add another dimension, especially the ones that make use of the terrain as part of the art. I’ve not yet seen all of the 2014 offerings, but some of my favourites have this element, including a small army of giant ants and some strange tentacled beasts, draped over the rocks.

Another thing I really like is the use of materials by some of the sculptures. The giant tentacular monster, for example, is made from thousands of bottle tops (left). There may well have been an environmental statement here too, about the amount of plastic (and plastic bottles specifically) that wash up on beaches. There were also some fantastic wooden birds made from old bits of furniture etc.

Another material that always seems popular is super shiny metal, which reflects the viewer, landscape and/or bits of the art itself in interesting ways. Last year, for example, there were some invisible dogs on the beach. This year, the sculptures included some shiny metal cylinders that mirrored flat discs into surprisingly three dimensional images.

It was a glorious weekend for the most part and so the coastal walk sections were predictably crammed with people. If you have the opportunity (as we did last year) to go off-peak, it is highly recommended. I’m already looking forward to going back and seeing what I missed the first time around. More photos on Google+.

Do we need a bioinformatics dead links database?

Keith Bradnam on his ACGT blog has recently highlighted the irksome issue of “link rot” - the unfortunate but all-to-common scenario in which a publication points to a URL that ceases to exist after an oft-too-brief time has elapsed. (In severe cases, before the paper is even published!)

Personally, I think that journals need to take a bigger responsibility in maintaining the integrity of their publications. Surely it is not beyond a big publishing house to have a bot that systematically checks their published links once a week and reports and errors? Authors could be notified and/or online manuscripts updated. In severe cases where the URL is critical to the paper, such as databases and webservers, lack of repair could even lead to retraction.

The problem goes beyond publications, however. For (sometimes mysterious) reasons of their own, even established biological resources quite often change their URLs too. For example, Pfam embeds the Wikipedia entry for a domain into their pages. I was browsing the globin page last week and clicked on a link to see the entry in Interpro, only to be greeted with:

Sorry, the requested URL has changed

The requested URL: http://www.ebi.ac.uk/interpro/IEntry/ac=IPR002338

has moved to

/interpro/entry/IPR002338;jsessionid=BB50E35E3DD96F6C83B7AD432B8E2E2A

You will automatically be redirected to the correct URL in a few seconds. Please update your bookmarks.

It redirected OK but I wonder how long it will be before that redirect itself disappears… and how many Wikipedia articles and database cross-references run the risk of breaking.

Perhaps we need a database where bioinformaticians can report, track, update and hopefully fix all these rotten links? In the meantime, if anyone spots any in my own webpages or papers, please let me know!

The perils of having a (soft) cat

Why Evolution is True posted this cartoon from lunarbaboon last week:

It’s never stopped me going to work but I’d be lying if I said that something like this (without the shoes) had not delayed me going to bed once or twice.

Every conference should be like ABiC 2014 (#ABiC14)

Last weekend, I attended the inaugural Australian Bioinformatics Conference (ABiC 2014) in Melbourne. (Twitter tag #ABiC14 so as not to be confused with the ABIC Foundation conference in California.) I’ve been to quite a few conferences in my time, including a fair few bioinformatics conferences. The latter (in my experience) are often quite dull affairs - good for meeting people and “networking” but not so good for interesting science beyond the invited keynote speakers.

Happily, ABiC14 went far beyond expectations. I signed up because it is important for me as a relative newbie to meet more Australian bioinformaticians. This was accomplished but was only the start of the positive experience of this conference. In fact, the conference was so good that I thought it worth posting its successful attributes/decisions as a model for future conferences (and reminder to myself should I organise one).

Here then, in approximate chronological order, are my top take-home quality attributes of ABiC 2014:

Organisation. The conference website was well organised and clear prior to the meeting. The program outline was available in good time, enabling planning, with abstracts etc. available in a single PDF. The only real improvement I can think of would be to have a printed program (just the outline, not full abstracts) provided upon arrival. However, because there were no last minute changes to the program, this turned out to be a moot point.

Coffee. Science in general, and bioinformatics specifically, is fuelled by coffee. The Aussies do coffee well and ABiC 2014 had the genius idea of a sponsored barista who made a decent cup of fresh coffee to order. I took advantage of this on arrival, which really set me up for the morning session and got the whole thing off to a great start.

Venue. The Royal Children’s Hospital was a great venue. Access by public transport was easy. The lecture theatre was comfortable and a good size. Eduroam provided free WiFi access (even if HTTP sites were unavailable for some reason). Coffee breaks, lunch, and poster sessions were near to the lecture theatre and promoted mingling.

Size. I’m not sure what the final number of delegates at ABiC 2014 was but for me it was the perfect number. (I would guess around 180+/-.) There were enough people for some interesting diversity, presentations and posters but not too many to actually get to chat to people and visit all the interesting posters.

Interesting Science! This is clearly one of the most important aspects of a good conference but sadly one that is often not achieved by a bioinformatics meeting (beyond the keynotes). I think there were several contributing factors to this. First, there were not too many talks and no parallel sessions. There were twenty talks in total, in six sessions of 3-4 talks of 10-50 mins each. Each session kicked off with an invited speaker. By keeping the quantity down, the quality of the talks - and stamina of the audience - was maintained at a very high level. I was expecting to “zone out” and struggle to maintain concentration a few times but I found my attention captured by each speaker. Talk quality was further enhanced by…

No published conference proceedings. Because of the large computer science community within bioinformatics, a lot of bioinformatics conferences have the submitted work published as papers in conference proceedings or a journal special issue. Even when the journal is a good one, this massively decreases the likelihood of getting interesting science, which will normally be either (a) published in a higher impact biology or general science journal, or (b) not yet be ready for publication. As a result, talks tend to be more technical and specialist… and boring. ABiC 2104 avoided this trap.

Food. You don’t go to a conference for the food but having tasty snacks at the breaks and at lunch does add to a general vibe of happiness and satisfaction.

Beer. Scientists and computer geeks are not always the most extrovert of individuals, and a little something to grease the wheels of social interaction never goes amiss. The ABiC committee went as far as to establish the beverage categories of choice with a pre-conference questionnaire. They gained extra brownie points from me for the presence of Fat Yak among the offerings.

Posters. This is largely a composite of the above points but the poster session was one of the better ones I have attended. For a start, the posters were up for the entire conference. It really bugs me when conferences do not do this and it all comes down to choice of venue - so well done ABiC for selecting a venue with this capacity. Furthermore, the poster location had great access - being a wide corridor - and was between the auditorium and the morning/afternoon drinks and snacks, maximising quality exposure. Furthermore, restricting the number of talks saved lots of interesting science for the posters!

Conference Dinner. If you are lucky, the conference dinner will be one of the best networking points of a conference, as your table represents a fairly captive audience with whom you have to interact. Nevertheless, conferences are generally charged to grants and researchers are on a budget, so it is frustrating to be forced to spend a load of cash on a meal that rarely lives up to the expectation of the price tag. ABiC 2014 took a pragmatic solution of booking out a restaurant and bar, and everyone paying for their own meal and drinks ordered off a standard single course menu. It worked really well. The food was good (but not excessive) as was the company. There was only one course but you never need more than that when there are morning and afternoon snacks in the breaks.

Timing. As far as I could tell, the talks generally seemed to stick to time, so coffee/lunch breaks were not truncated. Again, by keeping the number of talks (and talks per sessions) low, this was easier to achieve. Nonetheless, it's still something that is not achieved by all conferences. (I remember one conference in which my talk started 5 minutes after it was supposed to finish!)

Twitter. I’m a bit sporadic on Twitter at the best of times and not entirely convinced that live tweeting in a conference is not generally more of a distraction than a benefit - for those present, at least. However, I did enjoy having the #ABiC14 twitter feed open during the meeting and felt that it added to the sense of community. Of course, the aforementioned interest of the talks (and the smallish size of the meeting) limited the distraction.

As of the end of ABiC 2014, there was no plan for an ABiC 2015. I, for one, really hope that there is one - and that the organisers are able to stick to the same model.

Wikipedia joker almost prescient as Rabbitohs win their first NRL Grand Final for over forty years

Congratulations to the South Sydney Rabbitohs, who have just won the Australian National Rugby League Grand Final 2014. The Rabbitohs are our local team, so we watched the game (on TV) - and it was a cracker!

Although I must confess that it was the first NRL game that I’ve watched properly (being more familiar with Union back in the UK & Ireland), I must also admit that I don’t think it will be my last. It's pretty brutal but very exciting.

I decided to do a bit of reading up on the Rabbitoh’s before the match and was surprised to see that Wikipedia already listed a Rabbitohs win! It was taken down at some point but I got a screen grab first (right). The final score was 30-6, so the jokester in question was only a couple of digits out!

The game started with a crunching tackle which broke the cheekbone of Bunnies’ hero and man-of-the-match (Clive Churchill Medal winner) Sam Burgess. Burgess went on to play the entire game with a broken cheekbone, reminiscent of their 1970 victory when the skipper played 70 minutes with a broken jaw! Tough game, tough players!

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”.

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.

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.

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.

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).

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!

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.

A pale ale beer tasting

The Saturday before last, we were with friends watching England experience their first (but least upsetting) sporting defeat of the past couple of weeks: a tight one point Rugby Union loss to the All Blacks. Despite the defeat, it was a good game and made all the more enjoyable by a fine array of beverages.

In fact, the disappointment of the rugby was over-shadowed by the impromptu pale ale beer tasting that accompanied it. The line up is above, and started with Haymaker, an English import from Hook Norton in the Cotswolds. It was quite strong for a pale ale, at 5% alcohol, but packed full of flavour. Yum.

After that it was on to the Aussie beers. We’d brought some Beechworth pale ale from Bridge Road Brewery, which was good and fruity with a quite hoppy taste. Another craft brewery to add to my increasing watchlist and another fine pale ale to add to the existing favourites. One fifty lashes from James Squire is already on that list, being one of the first decent* beers that I discovered in Australia. (*To my taste.)

Only the final beer let the side down: Coopers was by far and away the worst and, after the others, I have nothing good to say about it. If only it could have been replaced with Fat Yak from Matilda Bay, it would have been a first class collection!

XKCD hits the spot again on climate change

A couple of weeks old but no less poignant:

Climate change deniers are quick to point out that there was still life on Earth at predicted future CO₂ levels and global temperatures. This is true. The problem is, that life did not include us, anything like us, or even anything much like most of the things we eat. Oh yes, and most of the world’s major cities being under water. :sigh:

It’s a position summed up frustratingly well by Doonesbury (via WEIT):

You know you live in Australia when...

… the vending machines sell flip-flops*.

(*You know you've become native when you start calling them “thongs”.)

Mary Anning (21 May 1799 – 9 March 1847)

Today’s Google Doodle is one of my favourites, celebrating the life (or 215th birthday) of Mary Anning, a paleontologist who discovered many fossils along the Lyme Regis coast, including the first complete ichthyosaur skeleton (at age 12 after her brother found the skull) and the first plesiosaur.

Lyme Regis is just down the coast from where we used to live in Southampton and it really has a fantastic shoreline, part of the Jurassic Coast. We paid a visit with a friend in 2011 and although we did not find any ichthyosaurs or plesiosaurs, there were plenty of ammonites to be found in the rocks. It is very humbling to look at something that died tens to hundreds of million years ago and has been sitting in a rock since, waiting to be found.

I think that there was a cast of Mary Anning’s ichthyosaur at the Lyme Regis Museum, which is sited on her birthplace (or it might have been Dinosaurland fossil museum, which is in her old church). Well worth a visit if you find yourself near the Devon coast!

Celebrate 267 years of controlled trials with some affirmative action

Today is International Clinical Trials Day, apparently. Perhaps the most interesting thing about this is that the date commemorates the first recorded “controlled trial” (i.e. comparing treatment and control groups) by James Lind in 1747. 1747!

Anyway, it’s a good excuse to visit the AllTrials campaign site and watch their “make clinical trials count” video, if you've not heard of the campaign or still need convincing. Either way, sign up if you’ve not already! Without having all clinical trials published, vast sums of money are wasted and lives potentially put at risk.

May the 4th be with you at the Hayden Orpheum (the right kind of Hayden)

Last Sunday (May the 4th), we went to see the original Star Wars trilogy on the big screen at the Hayden Orhpeum in Cremorne, North Sydney.

It was a lot of fun, as the Orpheum is quite an old cinema and really embraced the whole Star Wars Day thing. The show started with Darth Vader playing music from the Star Wars soundtrack on a Wurlitzer organ and was followed by a competition for the best Star Wars fancy dress before the films themselves.

(The winner was a very cute miniature Boba Fett.)

I must say, it was great watching the old films on the big screen again. They definitely show their age a bit but it was fun watching with an appreciative audience. The good thing about Star Wars fans is that they are perfectly aware that the films are full of cheesy (if charming) moments, and so there was a lot of applause and occasional laughter at some of the hokier lines and innuendo.

Sitting in a classic cinema watching some classic films did make me realise a couple of things, though.

Firstly, modern cinemas are better. They should be, given how much more expensive they are, but seven hours sitting in an old-style cinema seat really made me appreciate modern “stadium style” seating. (Though I’ve never understood why they call it that, given how uncomfortable stadium seats are!)

Secondly, don’t mess with a classic. The most unfortunate thing of the day is that they did not actually screen the original films - instead we got the “Special Edition” versions.

The last time I saw all three films at the cinema was when the Special Editions were released. At that time, the novelty value masked how terrible the changes actually were. This time, it had been quite a few years since I’d last seen the films and the changes - and how bad they were - really stuck out.

At best they were pointless, such as the extra Tatooine CGI sandtroopers on Dewbacks. However, most of the additions actively made the films worse. Slapstick CGI animals and droids in Mos Eisley, during what should have been a tense scene? Bad. CGI addition of “wonderful human being” Jabba the Hutt in Episode IV? Bad. Making Greedo shoot before (or possibly concurrent with) Han Solo? Bad. Bad. Replacing Sebastian Shaw with Hayden Christensen at the end of Return of the Jedi? Bad. Bad. Bad.

In a way, it was actually slightly ironic that we saw the films in the Hayden Orpheum - the Hayden Christensen replacement got the only audience boo of the night. Why, George, why‽‽

The Special Edition nonsense was not a major distraction, though, and I would still recommend the triple bill on a future Star Wars Day. (Although I think I have my fix for a few years!) The final thing it made me realise is that Star Wars is such a cultural phenomenon, enriched by many of the spin-offs (especially those that take the piss), it really is deserving of a day of celebration.

May the Fourth be with you, always.

Lego, Noah and other movies

Today we went to see The Grand Budapest Hotel.

The adventures of Gustave H, a legendary concierge at a famous European hotel between the wars, and Zero Moustafa, the lobby boy who becomes his most trusted friend.

I won’t give any spoilers here but just say that it's thoroughly entertaining, I really enjoyed it and it’s well worth a watch.

There’s quite a lot of competition at the cinema at the moment, with Captain America (also good) and the Lego Movie (which looks good) among others. One, I won’t be watching is Noah - a movie that I don’t really understand why it was made. If you want to save some money and get the "real" Noah myth, you can do far worse than combining it with another current movie and checking out lego Noah over at The Brick Testament!

As well as the animals going in two by two - dinosaurs included, which should keep the Creationists happy - I particularly like the scene with all the animals crammed into the ark. I’m not sure that even cute lego figures make the story any less horrific, though.

The Royal Easter Show

Last week, we went to the Royal Easter Show at Olympic Park in Sydney. I’ve never been to a county fair or such like before and, I must say, it was a lot of fun.

It’s a really well organised affair and despite the large numbers of people, it never really felt over-crowded. Public transport to and from the venue was included in the ticket, which was a nice touch. Extra shuttles were laid on from central station and exiting the train at Olympic Park with the crowd, I felt like I got a glimpse of the excitement and atmosphere that must have been present when arriving for the Olympics itself.

We didn’t really know what to expect, so we didn’t plan our day as such and mostly just mooched about. There were some events in the main arena as well as a couple of other venues within the Olympic Park. We did not see much but did catch some of the wood chopping, which was interesting and rather crazy. These guys have some very shiny axes and sure can chop wood!

Just before lunch we saw part of the “300mm underhand” competition, in which the competitors stand atop the block to be chopped and then hack down into it. A few well-aimed hefty blows chops out one side before the competitors turn around and chop out the other side to split the log. It’s all over in a few seconds.

Good as the wood chopping was, one of the main motivations for attending the Show was the Arts & Crafts section. My wife knits and knew several people with entries in different knit-craft competition categories, including some winners. Not being so into fashion, my favourites were probably the knitted toys and creative knitting, including a Dr Who and Tardis and South Park nativity scene.

The creativity was not limited to knitted items, of course. Lots of other handicrafts were on display. I particularly enjoyed the cake decorating competition entries, which were simply sublime and incredibly imaginative. These alone were probably worth the entry money.

Something else that really impressed me was the breadth and depth of the agricultural displays geared towards children, which were engaging, entertaining and educational in equal measure. These included cow milking, sheep shearing and a small animal barn in which goats and chickens etc. were roaming free and could be fed with hay that was on sale by the cup.

After checking these out, and some of the “best of breed” animal competitions, we visited the Woolworths fresh food dome. Unfortunately, we has already had lunch at this point - if we go again next year then we will definitely look to eat here instead of the many fast food options available.

The Food Dome was also the home of the impressive agricultural district displays:

Climbing up the walls of the Woolworths Fresh Food Dome, the District Exhibits are one of the Show’s iconic displays, featuring creative and artistic installations assembled from outstanding quality grain, wool, fruit and vegetables. Each display consists of more than 10,000 pieces of the best quality fresh produce from five agricultural districts throughout NSW and South East Queensland.

Following the bad bush fires this year, there were a couple of poignant displays, including one that featured an aerial firefighting helicopter and several fire engines. The size of some of the produce was also extremely impressive!

All in all, it was a really fun day and highly recommended, whether you have kids or not. Well worth the $38.50. It’s on until Wednesday, so if you live in/near Sydney, there’s still time!

Two good eggs (and some mighty fine pork belly)

Today we went for Sunday brunch at Two Good Eggs cafe in Surry Hills, central Sydney.

A good Sunday brunch is probably my favourite meal of the week - not that we have brunch every week - and so it was exciting to go to a cafe that specialised in breakfast and brunch. Starting with a very good flat white, complete with little wafer, we were not disappointed.

The Two Good Eggs menu is pretty diverse and manages to hit both the usual favourites, such as pancakes with bacon and maple syrup, or Eggs Benedict, plus a whole bunch of creative dishes too.

I opted for something that I would never make myself at home: Roast pork belly with poached eggs, caramelised onion and sourdough toast. Delicious! The two eggs were indeed good, cooked to perfection and served atop tasty, crispy pork belly and sweet, sticky caramelised onions. The photo did not do it justice but an attempt seemed obligatory for something so good.

I was lucky enough to sample a couple of other dishes too: Eggs Benedict with smoked salmon and avocado, and “Goats on toast”, a vegetarian dish of “Warm Trinity Cellars French goats cheese with drizzled honey and smashed walnuts on sour cherry fruit toast”. Both were very good, although I’m glad I went for the pork belly.

Not quite as cheap or close as the amazing sandwiches at One Six Nine cafe in Randwick, but I am already looking for excuses to go back! Top notch nosh.

Yet another lengthy investigation concludes that homeopathy is useless

Australia’s main body for health and medical research, the National Health and Medical Research Council (NHMRC), has recently conducted an extensive review of the “evidence for homoeopathy in treating 68 clinical conditions”. Predictably, it concludes “there is no reliable evidence that homoeopathy is effective for treating health conditions”.

No surprise there, but hopefully another nail prepared for the coffin of homeopathy, should drug stores develop of conscience and/or people ever stop getting taken in by utter crap.

The figures are scary, though. According to the news.com.au:

Australians spend almost $4 billion a year on complementary therapies like vitamins and herbs and almost $10 million on homeopathic remedies.

That's $10 million wasted. $10 million dollars that could have been spent on actual medicine. And I shudder to think how much of that $4 billion is wasted on complementary therapies with zero benefit, or worse - probably most of it. To put that figure in context, it is over five times the entire NHMRC 2013/14 budget of $771.2 million for health/medical research funding.

Perhaps the most revealing part of the article was the response of the homeopaths themselves:

However, Australian Homeopathic Association spokesman Greg Cope said he was disappointed at the narrow evidence relied on by the NHMRC in its report.

“What they have looked at is systematic trials for named conditions when that is not how homoeopathy works,” he said.

Homoeopathy worked on the principle of improving a person’s overall health and wellness, and research such as a seven-year study conducted in Switzerland was a better measure of its usefulness, he said.

I’m sorry… what‽ Homeopathy is based on the (utterly discredited) 200-year-old notion that “substances that produce symptoms in a healthy person can be used to [effectively] treat similar symptoms in a sick person”. This is not the principle of “improving a person’s overall health and wellness”, this a principle of targeting specific named symptoms with specific substances. Specific substances that are then diluted far beyond the point that any molecules (or “memory” thereof) remains in the solution (which is then often dropped onto a sugar pill), but specific substances that cause specific symptoms nonetheless.

Mr Cope is right about one thing, though: homeopathy does not work by treating named conditions. Homeopathy does not work.

Don't be an April fool - get (your kids) vaccinated

If there’s one thing that irks me as much as Homeopathy, it’s the anti-vaccination crowd. Therefore, I think that posts like the recent “Dear parents, you are being lied to” at Violent metaphors, deserve as much publicity as they can get. It's a well structured piece, heavily laden with links for further reading, with a heartfelt plea:

In only one respect is my message the same as the anti-vaccine activists: Educate yourself. But while they mean “Read all these websites that support our position”, I suggest you should learn what the scientific community says. Learn how the immune system works. Go read about the history of disease before vaccines, and talk to older people who grew up when polio, measles, and other diseases couldn’t be prevented. Go read about how vaccines are developed, and how they work…

As Professor Simon Foote wrote around a year ago, Parents have a moral obligation to children. Make no mistake about it, failing to vaccinate puts both your children and the children of others at risk. (And not just children.) As the Jenny McCarthy body count reports, preventable deaths in the US alone have exceeded 1300 since 2007, with 100 times that number of preventable illnesses. Whilst not the sole cause, anti-vaxxers must take a share of the responsibility for this.

Like Jennifer Raff at Violent metaphors, I’m sure that some of those opposing vaccination and/or advocating “parental choice” are doing so with the best of intentions. However, good intentions are no defence against disease and anti-vaxxers across the spectrum should take a long, hard look at themselves and ask whether their reasons for opposing the overwhelming global medical and scientific consensus are worth endangering even one life.

If you're not sure, I highly recommend reading the whole article. And if that’s too tame for your tastes, there is also the classic “Angry scientist finds an uneducated internet comment and delivers an epic response…”, which has a slightly less nuanced (but also informative) correction of some anti-vaxxer lies.

The Cat & The Ducklings (Animal Odd Couples)

Via WEIT, here is a crazy/cheery "cat suckling ducklings" story that is fit to be an April Fool's joke but isn't!

20% off The Cabbages of Doom

Yesterday was apparently International Waffle Day, which sounds a bit made-up to me but is excuse enough for Lulu.com to have a 20% sale until the 31st of March. Just use WAFFLESSAY20 to get 20% off The Cabbages of Doom (just 80p!) or for some graphic entertainment, I can recommend Jesus ‘n’ Mo.

Is imported bottled water the most environmentally-unfriendly way imaginable to slake your thirst?

Today is UN World Water Day 2014, which aims to raise awareness of the inter-linkages between water and energy and draw attention to the fact that “768 million people lack access to improved water sources”, many of whom presumably have no safe drinking water.

Meanwhile, in the developed world, we take our safe drinking water for granted so much that we are prepared to spend ludicrous amounts of money to ship in bottled water from other countries. Ignoring the environmental cost of the plastic bottles themselves, I shudder to think what the carbon footprint is to fly water to Australia from Europe.

Sydney, happily, is making some moves with Sydney Tap^TM, which is looking to replace bottled water with tap water. There are also lots of drinking fountains around, which is good.

San Francisco recently announced that it was going one further and banning the sale of bottled water below 21 ounces from city property. Hopefully, other cities will follow suit.

Personally, I would go further than this and ban bottled water altogether. Instead, shops should be able to sell empty reusable water bottles and refills of filtered water for a small fee. I'm sure it would take a bit of getting used to but people would soon learn to carry a water bottle with them. It hardly seems like a big sacrifice for the sake of our future and would act as a constant gentle reminder about the need to avoid excessive packaging.

The wet, wacky and wonderful Sydney's Paddy's Day parade

  Today, we went into central Sydney for the St Patrick’s Day parade. Despite living in Dublin for six years, this was actually my first Paddy’s Day parade. (I’ve never been that into parades, to be honest.) It was a lot more fun than I expected!

Things kicked off with an Irish icon, Spongebob Squarepants, warming up the crowd before the parade proper arrived. Unfortunately, the rain had also arrived - including a short Aussie thunderstorm downpour - but it failed to dampen the spirit of the parade. The Irish are used to a bit of rain, after all!

Although it featured some marching bands and the like, the parade had a somewhat charming, home-made feel, including a St Patrick with genuine cotton wool beard!

Highlight of the parade (for me, at least) was the Father Ted complete with cardboard “Careful now” and “Down with this sort of thing” placards.

St Patrick’s Day proper is tomorrow: have a good one!

(A few more pics here.)

Gold star for Merrell customer service!

 I’ve had a few pairs of Merrell shoes (mostly the super-comfy Moab Ventilator) and generally found them to last pretty well, given how much I wear them. Therefore, I was quite disappointed when my (non-Moab) Merrell shoes broke today, whilst putting them back on in a store changing room. They were under five months old and I have worn them a fair amount but not enough to expect one loops holding the laces to just snap. Without that loop, they could not be laced up properly and were essentially useless as a result.

Being in the city, I decided to visit the Merrell shop in Sydney (where I bought the shoes) to see if there was anything that could be done. The lady in the shop looked at the damage and, having not seen such an issue before, swapped them on the spot for a brand new pair! Now, that’s customer service! (And worthy of public acknowledgement, I feel.)

Well done, Merrell. My faith in your shoes is restored!

Blog titles gone squiffy (again)!

It seems that the titles of my blog posts have gone a bit screwy. This happened once before but I can't remember how to fix it - if anyone knows, please comment below!

Prof Bryan Clarke (1932-2014)

I was sad to read a post on the Evolution Directory (Evoldir) by my PhD supervisor, John Brookfield, that Professor Bryan Clarke died last month. Bryan founded the Genetics Department (later Institute and now Centre for Genetics and Genomics) at the University of Nottingham , where I did both my undergrad degree and PhD. He and retired when I was still an undergrad but, as Emeritus Professor, he was still heavily involved in the department for the rest of my time there.

Although I did not know Bryan well, he always had time for students and was an inspirational character - and that was before the Frozen Ark project was launched. I was particularly impressed by the way that he managed to combine ground-breaking basic science with regular visits to Pacific island paradise!

With permission, I have repeated John’s post below:

It is with great sadness that we have to report to the evolution community the death of Professor Bryan Clarke FRS on Thursday, the 27th February 2014.

Bryan Clarke was a leader in our understanding of the process of evolution for more than four decades. He made fundamental contributions, both empirical and theoretical, particularly in elucidating the forces that maintain genetic variation in populations, and in throwing light on the process of speciation.

Bryan was born on the 24th June 1932, and, following service in the Royal Air Force, was educated at Magdalen College Oxford, from where he received both his BA in 1956 and DPhil in 1961. From 1959 to 1971 he worked at the University of Edinburgh, starting as Assistant Lecturer and rising to a Readership. In 1971 he was the Foundation Professor at the new Department of Genetics at the University of Nottingham, and remained until 1997, when he became Professor Emeritus.

The Darwinian theory of evolution by natural selection identifies genetic differences in populations - polymorphisms, as the key to evolutionary change. It is of fundamental interest whether polymorphisms are affected by natural selection, or solely by genetic drift. Bryan’s research focussed on polymorphisms in snails, including members of the genus Cepaea, the shells of which vary greatly in colour and in their banding patterns. While some had naively suggested that this variation might have no effect on the organisms’ fitness, earlier experiments and observations, from Cain and Sheppard in particular, had demonstrated that these variants were indeed subject to natural selection. But, if there is selection operating on this genetic variation, why does the population not come to consist of only a single, best-adapted, type? The answer is that selection can, in some circumstances, maintain variation rather than destroying it. One mechanism for the maintenance of genetic variation is heterozygote advantage, which explains, for example, the high frequency of the allele causing sickle cell anaemia. Bryan knew that the patterns of inheritance of the polymorphisms in Cepaea could not be explained by heterozygote advantage. Rather, he was able to demonstrate that these are maintained by a different mechanism, frequency-dependent selection, in which the fitness of genetic types increases if their frequencies in the population diminish, thereby creating a stable equilibrium in which multiple genetic types are maintained. His studies of frequency-dependent selection were able to demonstrate the near-ubiquity of this phenomenon when visible polymorphisms are studied in wild populations, and also showed the selective agents which brought this about. The frequencies of polymorphic variants in snails can vary greatly in space, without any obvious environmental correlates. An important and influential step in the understanding of such “area effects” came from Bryan’s models of morph-ratio clines in his 1966 American Naturalist paper.

Studies of visible polymorphisms were augmented, from the 1960s, by the study of polymorphisms in the amino acid sequences in proteins, investigated initially through electrophoretic detection of differences in the electric change on enzyme molecules. As with the visual polymorphisms in Cepaea, some assumed that the changes were invisible to natural selection. Bryan Clarke advocated the view that a large proportion of the changes were indeed subject to natural selection and demonstrated experimental support for this view, particularly for variants in the enzyme alcohol dehydrogenase in Drosophila melanogaster. The study of selection acting on polymorphic differences in amino acid sequences is a direct way to obtain evidence about whether the long-term evolution of the amino acid sequences of proteins is shaped by natural selection. Some believe that protein evolution is almost completely dominated by random forces in which the successful variants were so not because of the advantages they gave to their bearers, but as a result of genetic drift. Bryan Clarke was one of the main advocates of the view that a large part of the evolutionary changes in the amino acid sequences of proteins were indeed driven by Darwinian natural selection, a view that results from large-scale DNA sequencing are confirming in many species.

Bryan Clarke also played a large part in developing our understanding of the process through which species form. He carried out a long-term study of species of the land snail Partula on the South Pacific island of Moorea and neighbouring islands. He appreciated that, in the early stages of speciation, matings between members of populations undergoing speciation do not stop instantly- some hybridisation persists. Species stay distinct notwithstanding there being some gene flow between them. Thus, selectively important genetic differences between species, such as those determining form, colour and behaviour, are maintained as distinct and recognisable features, while the low levels of gene flow resulting from hybridisation allow genetic differences which are not selectively important to randomise themselves between the hybridising forms. These phenomena have been documented in Partula, where less important differences have been shown to be shared between species which live in the same geographic location. The ability to study these early events results from the choice of the Partula species, where speciation has been “caught in the act”. Increasingly, similar phenomena are now being documented in patterns of DNA sequence diversity in other species studied at these early stages.

Through these diverse achievements at the cutting-edge of understanding of the process of evolutionary change, Bryan Clarke was a great mentor and role-model for younger scientists in evolutionary genetics, and supervised more than thirty research students, at least six of whom are now professors. He was a co-founder of the very successful Population Genetics Group, a meeting for population geneticists from the UK and Europe that has been running for almost fifty years.

He was co-founder and trustee of the charity “The Frozen Ark”, which preserves, in the form of DNA and cell lines, the genetic material of endangered animals, to allow future scientific study.

Honours and awards for Professor Clarke reflected his outstanding role in modern evolutionary genetics. He was elected a Fellow of the Royal Society in 1982, became an International Member of the American Philosophical Society in 2003, and a Foreign Honorary Member of the American Academy of Arts and Sciences in 2004. Medals and awards include the Linnean Medal for Zoology in 2003, the Darwin-Wallace Medal of the Linnean Society in 2008, and the Royal Society’s Darwin Medal in 2010.

Bryan leaves his wife Ann, his son Peter and daughter Alex.

Picture from Bryan Clark's obituary in The Telegraph.