The Cabbages of Doom

With all the doom and gloom of climate change, over-population and the stresses of "the rat race", it's easy to forget how amazing the modern world is thanks to advances in science and technology. On Sunday, we were in the city for a spot of sales shopping and a visit to the Australian Museum. When we went to leave the shopping centre for the bus, we looked outside to see it tipping down. I'd brought umbrellas but it was a bit windy. Should we risk a soaking, or wait and see if it would blow over?

In the past, this would have been a bit of a gamble, possibly combined with some kind of superstitious activity to try and alter the outcome. Thanks to the wonders of modern technology, I just had a quick look at the Sydney Rain Radar, saw it was blowing over: and we went and got a (very nice) coffee instead. After coffee, another quick check of the radar confirmed that the rain had moved on. Home and dry!

Of course, the rain radar doesn't always tell you what you want...

It’s going to be a wet one!

One of my Christmas presents this year was Jamie Oliver’s new book, Everyday Super Food. As well as having some delicious-looking recipes, it also contains some advice for healthy living. One of the things recommended was the YOU-app for small steps in mindfulness, food and movement for health and happiness.

The basic idea is to make a positive change to your life through “micro-actions”, which are quick and simple to perform, rather than setting big goals that are hard to meet. The actions come in four flavours: mind, food, move and love. So far, I like it, and it’s inspiring me to make 2016 a year of making positive blog posts wherever possible. The first is this: check out the You app. It’s free!

This time next week, I’ll be running the 14km City2Surf fun run.

I’m not going to pretend that I signed up for this “for charity” - it’s a fitness motivator - but, at the same time, I’d love to raise some money for a cause that I care about and will be "running for the panda" to support wildlife conservation.

Before signing up, I’d never run 14km before, and the City2Surf route also includes the notorious 2km “heartbreak hill” in the middle.

Donating to my supporter page will really help me get up that hill!

There’s no real secret to a long and healthy life: eat a balanced diet with plenty of fresh fruit and veg (but eat your fruit, don’t drink it), However, despite the fact that we all know this deep down, knowing it and doing it are two different things.

Unfortunately, most of the messages we get, and tactics used to modify behaviour, focus on getting us to avoid the stuff we are not supposed to do. Cigarette and alcohol is restricted, taxed and comes with warning labels. Tasty unhealthy foods have “traffic lights” telling you how much bad stuff there is in there (sugar, salt, fat) and what it corresponds to as a percentage of your daily recommendation. There is regular talk of whether there should be a sugar tax or a fat tax.

If you are anything like me, these negative messages are only of so much use. I don’t smoke, and never have (and never will), so that one is easy to obey. The other stuff, however, is generally at its most appealing when my will power is also at its lowest. When I eat unhealthy food it is usually because it scores high on combined taste/convenience, not because I have consciously sought it out.

A tax would probably help in this respect, but what would really help would be something to encourage eating of good stuff, which tends to have the double whammy of being expensive and more effort to cook.

Exercise is the same. We all know we should do it but it’s not always easy to find the motivation. One step (no pun intended) is to know how much you are doing, just as one step to a healthy diet is labelling food. But this only goes so far.

For example, I got a FitBit for Christmas, which was great for seeing how much general exercise I was getting. I walk to work and back so thought that I was probably doing OK. However, my daily step counts for January and February paint a different picture:

The good week in February was our holiday in Tasmania, which featured quite a lot of walking. This included, I still did not have a single week where I hit the 10k goal every day. (Although I was better than the 3.5k-5k average.)

Then came March:

The difference? I’d like to say that I just decided to be more active. I have taken up running again more seriously, which is part of the answer - but only a small part. The main difference is this:

That extra incentive was enough to actually cause a change in behaviour. There weren’t actually that many times that I needed to pick up extra steps at the end of the day - about four times I went for a short evening stroll - but I did change my behaviour to make more trips to the shops on foot and things like that and routinely hit the 10,000 step target. It also served as extra motivation for running.

The annoying thing is obviously 28th March when I lost track of time and midnight came before I’d made the target. It was enough to miss out on the $100 (although I should get $10 credit for 10 consecutive days) - and make me rather cross with myself - but not enough to avoid developing the habit. And, at the end of the day, I think it’s really all about building habits. The incentive has run out but I still went for a stroll on Wednesday to get the extra 700 steps before bed. (Today is a very rainy day off work, which will be the real test!)

The best way to avoid the bad stuff is to replace it with good habits. Rather than taxing sugar or fat, I think that it would be much better to subsidise fresh fruit and veg. Or, if you are going to tax sugar and fat, then use the revenue to subsidise the good stuff. Or give out vouchers for it. Anything, really, to give us more carrots (literally!) and fewer sticks.

Our recent holiday in Tasmania was fantastic but did not start entirely well.

I checked us in online, not long after check-in opened. I thought that our allocated seats might have been over the wing, spoiling the view, so I decided to check whether anything better was on offer. There were not many available seats left but there were a couple of window/middle pairs nearer the front of the plane, in row 9 on the left and somewhere nearby on the right. I figured that during the afternoon flight time the sun would be in the west and we would mostly be heading south, so the left side was probably better. This also had a better chance of coastal views, I thought. Seats 9A & 9B selected. Checked in. Job done.

Later, we became interested in what type of plane it was. (I can’t really remember why: it might have been curiosity as to the number of rows and which ones might therefore be over the wing.) Googling the route, I came across the Seat Guru entry for the likely plane (the one flying the route that day) and I took a quick look. And horror!

Seat 9A is an Economy Class seat that is missing a window.

For reasons that still mystify me, the one window seat on the whole fecking plane without a window was the one that I had so carefully selected for my wife. WTF, Virgin‽ (Actually, that should be "WTF, Boeing‽" - Qantas planes are the same.)

I always check seat guru for long haul flights and big planes but it never even occurred to me that there could be such a crappy seat on small plane like a Boeing 737-800. (Fortunately, my wife was very gracious and laughed about, so my grumpiness on discovery did not last too long!) Lesson learnt.

Always check Seat Guru before choosing your seat. (It probably gives a better indication of the wing rows too!)

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.)

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.

… the vending machines sell flip-flops*.

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

  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.)

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.

After 24 hours, not a lot…

When we arrived in Sydney it was the awesome purple Jacaranda trees and screechy fruit bats that gave us daily reminders that we were in a new a foreign land. At this time of year, it’s the cicadas. As reported in a Daily Telegraph article, Cicadas having a blast this year, it is a particularly noisy year for these insect tree huggers.

According to Wikipedia:

“The male cicada has loud noisemakers called “tymbals” on the sides of the abdominal base. Its “singing” is not the stridulation (where one structure is rubbed against another) that characterizes many other familiar sound-producing insects, such as crickets. Rather, the tymbals are regions of the exoskeleton that form a complex membrane with thin, membranous portions and thickened ribs; contracting the internal tymbal muscles produces a clicking sound as the tymbals buckle inwards, and the relaxing of the muscles causes the tymbals to return to their original position, producing another click. The interior of the male abdomen is mostly hollow, which amplifies the sound. A cicada rapidly vibrates these membranes, and enlarged chambers derived from the tracheae make its body serve as a resonance chamber, further amplifying the sound. The cicada modulates the sound by positioning its abdomen toward or away from the substrate.”

These things are crazily loud! On recent drives down the coast and to the Hunter Valley we would be driving along and hear this noise building, as if we were approaching a hissing downpour of rain through the trees. It was, in fact, pockets of cicadas, “singing” so loudly that even at 100 km/h it sounded loud as we passed. (Louder than “an industrial jackhammer, a chainsaw or even a dreaded vuvuzela horn” according to the Telegraph.)

Although we have cicadas outside our apartment that start up around dusk each night, they fortunately shut up before bed time. (And even if they did not, they’d still be more welcome than a Huntsman spider!)

[Picture from Wikipedia article on Cyclochila australasiae a.k.a. the Green Grocer - “one of the loudest insects in the world”.]

Just before dinner this evening, I spotted one of our cats looking inquisitively above the door. I followed his gaze to this awesome chap. A most unwelcome visitor in our home, I must say! Our Aussie friends on Facebook identified it as a “mostly harmless” Huntsman spider.

“They have been known to inflict defensive bites, but are not widely regarded as dangerous to healthy humans.”

Nevertheless, I cannot say that removing it was much fun, as I certainly did not want to be on the receiving end of a defensive bite! Sadly, our attempted catch-and-release operation went a bit wrong a Mr Huntsman is no more. Time to get a spider catcher I think!

Photo © my lovely wife.

Darwin is soon to disappear from the Bank of England £10 note but he’ll be found in British wallets, pockets and purses for some time to come - not just on tenners but also the special release £2 coins from 2009 to mark 200 years since Darwin’s birth. For obvious reasons, it was one of my favourite coins to get in change. Since moving to Australia, the chances of getting a Darwin coin in my change have susbtantially diminished. Instead, however, there is a fair chance of getting one of my favourite animals, the Echidna, which graces the 5c coin.

Echidnas are one of the iconic animals of Australia. Neither a placental mammal nor a marsupial, the Echidna is a monotreme like the playtpus. Monotremes lay eggs like reptiles and produce milk for their young like mammals but have no nipples. Today, we paid another visit to the Australian Museum (for their Tyrannosaurs: Meet the family exhibit), which uses the Echidna for their main logo. As you would expect, they also have a few specimens in the museum. The one below really looks like the one on the coin - I wonder if it was the inspiration!

I have been lucky enough to see an echidna in the wild once. When on holiday in 2004, I was out for a walk in Mission Beach, Queensland, and I chanced upon the guy below who snuffled across my path. One of the highlights of the trip! Hopefully, it won’t be my last wild encounter.

I hope you all have a great festive season (whatever your particular celebration) and get things you like, even if it is only a plastic drinking straw… (Best cat toy ever!)

And if the weather outside turns frightful, then find somewhere warm and snug to see things out.

(Another Google auto-awesome effort!)

I opened my email this morning to the news that Fred Sanger had died. This was not entirely surprising, given that he was 95, but still sad. Although I have never met him, I think it is fair to say that I am one of many scientists whose careers have been shaped and influenced by the work of this great scientist.

I still remember sitting in lectures as an undergraduate and discovering how “Sanger” sequencing worked - like many of the ideas that change the world, it was gloriously simple and yet spectacularly clever. And, I think it is fair to say, it changed the face of biology forever.

Indeed, that was back in 1977, and Sanger sequencing is still used all over the world today, even in the face of stiff competition from “Next Generation” methods. It was the sequencing method (albeit in a much tweaked and automated version) that got us the Human Genome and one of the world’s leading sequencing centres - the Wellcome Trust Sanger Institute at Hinxton, outside Cambridge - still bears his name.

The centre has a press release about the “remarkable man”, which has been written by greater wordsmiths than I:

“Fred Sanger, who died on Tuesday 19 November 2013, aged 95, was the quiet giant of genomics, the father of an area of science that we will explore for decades to come.

His achievements rank alongside those of Francis Crick, James Watson and Rosalind Franklin in discovering the structure of DNA. We are proud that he graciously agreed to allow our Institute to be named after him.

In research marked by two Nobel Prizes, he developed methods that allow us to determine the order of the building blocks of DNA and of proteins. This technique allowed the languages of life to be read.

Because of Fred’s work we have been able to interpret those languages and to use that knowledge for good.”

There is more, including quotes and links out to other resources about his work, at the site.

I remember thinking in those lectures back in Nottingham how I wished that one day I might have an idea as good as Sanger sequencing. I doubt that I ever will; instead, I will just have to settle for trying to do the best I can with all of the amazing sequence data that now exists as a result.

One of the most surprising statistics about Sydney is that it has more annual rainfall (~1200 mm) than Dublin (~700 mm). It’s not really something that one tends to associate with Australia - particularly as we arrived to news of raging wild fires across New South Wales following a particularly dry winter.

The reason, of course, is that Sydney also has more daily sunshine hours on average too (mean 6.8 per day versus 4.0 for Dublin) - the difference is that when it rains in Sydney, it tends to rain hard. (The main difference, at least - Dublin has around 10 fewer rainy days on average, according to Wikipedia.) This past week or so has been testament to that - so much so that I felt the need to buy a new umbrella at the supermarket today for the 5-10 minute walk back to my office. (My previous umbrella finally died on the way to work this morning.)

If you are visiting Sydney, check the forecast - and, if in doubt, pack an umbrella!

One of the hardest thing about selling up and moving 17,000km away was putting our two cats through the trauma of being shipped off to a cattery then flown half-way round the world before spending another 30 days in quarantine at the other end - and, of course, being without them for all this time (barring a couple of visits). Today was the day that we picked them up from quarantine!

We had obviously done our best to prepare for the arrival of our furry friends - complete with comedy placemats from Ikea for their food and water bowls. (I am not sure whether they will appreciate them as much as we do!)

The whole process was also made much easier through the knowledge that they had been well looked-after throughout. This started with their cattery stay and relocation by PetAir, who have been great and clearly care for all the animals they relocate. We picked them up in the PetAir crate that they were shipped over in, and it made me smile to see the stenciled cats on top. The lady at the quarantine station also made us feel that they had received good care as, like the PetAir staff, she reported a bit on their personalities as well as simply their condition.

The most traumatic part of the process (today) was probably the journey out and back, which was largely due to a combined lack of familiarity with the car (a GoGet Hyundai i30 called Lorna), the route and our new Garmin sat nav. (I am not getting on with the latter but I’ll save that for (maybe) another day.) Given that it was only my second drive in Australia, though, it did not go too badly - thanks largely to some human navigation and Google maps on the iPhone.

Arthur is not shaken by much and so, somewhat predictably, it was he that settled in quickest, giving the apartment a bit of a look over before settling down in the “cat condo” to survey things for a bit.

Mia, on the other hand, went and hid in the bath for a while. I can’t say that I blame her - if it had been me then I think I would have wanted a bit of alone-time. The introduction of a bowl of food was well received and she did not stay in there for long.

Unfortunately, I had to go into work for the afternoon but was pleased to receive reports that tummy-tickles were being enjoyed - and a photo of Arthur doing what he does best: sprawled relaxation.

By the time I got home again, it was almost like business as normal - I got a good greeting, Arthur was only interested in food and Mia was soon surveying her new realm from atop the cat condo. That was, at least, until I started showing an interest - this post has been slowed down at times by a purring Mia on my lap! :o)