Sunday, 26 January 2014

A pair of Matilda Bay's finest Aussie beers for Australia Day

It’s Australia Day so it seems appropriate to post a celebration of something Australian: Matilda Bay beer. Australia Day marks the anniversary of the Brits arriving at Sydney Cove, not far from where I type this, in 1788. Almost two centuries later Matilda Bay Brewing Company established “Australia’s original craft brewery” (according to them) in Melbourne.

I must admit that I was a little fearful of the quality of Aussie beer before moving here; I was routinely disappointed by the offerings during a holiday in 2004 and the less said about the stuff that makes it over to the UK the better. I was happy to be proved wrong! The craft beer industry seems to be thriving and there are some really good ones about. Two of my favourites so far are from Matilda Bay: Fat Yak Pale Ale and Minimum Chips Golden Lager.

Minimum Chips is best on a hot, sunny day but Fat Yak is a fine all-rounder that’s good for any occasion. I look forward to sampling some of the other in the range! (James Squires and Mountain Goat have some good ones too.)

Wednesday, 22 January 2014

If in doubt... ask for evidence!

This one passed me by for a while thanks to an over-active junk email filter. Via the British Humanist Association, I just found out about the Ask for Evidence campaign run by Sense About Science:

The British Humanist Association (BHA) has announced its support for the Ask for Evidence campaign, which aims to hold companies, politicians, commentators and public bodies accountable for the claims they make. The campaign has been launched by Sense About Science, the charitable trust that works to enable members of the public to make sense of scientific claims made in public discussion. The campaign encourages ordinary people to write to organisations and public figures which make scientific claims, to ask them for the relevant evidence.

The Ask for Evidence campaign emphasises that you don’t need to be a scientist to take part – anyone can take part. If you see a claim made by a company, public figure, campaign group, media outlet or official body, which does not present any evidence in support of it, you can contact them to ask that they provide the evidence. You can send a request using an Ask for Evidence postcard, or by using the campaign’s online form. You can also let the Ask for Evidence campaign know that you are doing this, so that they can help.

There’s a bunch of interesting examples on the Sense About Science website, which also provides a great insight into some of the bizarre claims that are made. (Of course, not all of these claims are wrong and, on some occasions, the evidence is provided.)

Some of them are real eye-openers to marketing spin. The response to questioning of Pret’s claim “Pret creates handmade natural food avoiding the obscure chemicals, additives and preservatives common to so much of the ‘prepared’ and ‘fast’ food on the market today” included the gem (my emphasis): “What they eventually said was that there were about 300 or so chemical preservatives available but that Pret only used about 50 of them.”

How much difference this will make in the long run, I don’t know, but there are already several success stories on the examples page. (Some of them are quite bizarre, such as “M&S no longer stock ‘MRSA resistant’ pyjamas.”) Anything that raises public awareness of need for evidence-based claims has to be a good thing, though.

Monday, 20 January 2014

The fabulous pom-pom crab!

Every now and then, something comes along that just needs to be re-blogged. I give you, The fabulous pom-pom crab!:

h/t: @JohnRHutchinson via WEIT. (Original source unknown.)

Sunday, 19 January 2014

The $1000 genome is here... Kind of...

I’m not an avid follower of tech news but something that popped up on my radar this week seemed worthy of a blog post. As Bio-IT World reports in What You Need to Know About Illumina’s New Sequencers, Illumina have announced the first sub-$1000 human genome:

Sequencing costs have been coming down steadily and dramatically since the invention of “Next Generation” techniques and the “$1000 genome” - a full human genome for under $1000 - has long been one of the holy grail targets of cheap sequencing. The cost-per-genome that Illumina quote does indeed represent a substantial drop:

This is not for everyone, as you need to buy at least ten machines as a “HighSeq XTM Ten package at $1 million a piece.

According to the Illumina press release:

The HiSeq X Ten is the world’s first platform to deliver full coverage human genomes for less than $1,000, inclusive of typical instrument depreciation, DNA extraction, library preparation, and estimated labor. Purpose-built for population-scale human whole genome sequencing, the HiSeq X Ten is an ideal platform for scientists and institutions focused on the discovery of genotypic variation to enable a deeper understanding of human biology and genetic disease. It can sequence tens of thousands of samples annually with high-quality, high-coverage sequencing, delivering a comprehensive catalog of human variation within and outside coding regions.

The $1000 price tag only applies “when used at this scale” and it doesn’t say anything about computational costs - storing and processing the vast quantities of data coming of the machine. For many sequencing applications, the computational cost now exceeds the sequencing cost, although I suspect that genome re-sequencing is at the cheaper/easier end of the processing spectrum. Which brings me to the other aspect of my “kind of…” qualifier: the HighSeq XTM still only produces 150bp reads, and at 30x coverage. This is ample for certain applications and will enable you to re-sequence (i.e. use an existing genome sequence as a scaffold to map the short reads onto) most of a “normal” human genome. It will probably struggle, however, when looking at repetitive sequences. Sequencing a genome de novo (i.e. without a template for assembly) will not be possible at the sub-$1000 price tag. Likewise, samples with heterogeneity, such as cancer genomes, need much more that 30x coverage.

As a bioinformatician, announcements like this fill me with a mixture of excitement and dread. Don’t get me wrong: being able to generate so much more data is great. The problem is, we need to be able to do something with all that data. Short 150bp read data is, ultimately, quite limiting: you need loads of it to get decent coverage/assembly and you are always going to be stuck where greater lengths are required to discriminate between repeats etc. Processing, quality-controlling, filtering and assembly these short reads remain a bioinformatic headache. This is definitely progress but, personally, I am still waiting for long-read single molecule sequencing before I get too excited.

Thursday, 16 January 2014

Dive into ocean exploration with a University of Southampton MOOC

I am not entirely sure whether MOOCs (Massive Open Online Courses) have any tangible benefits to the participants (or the hosting institution beyond publicity). Nevertheless, there is no denying that they represent excellent value for money (being free!) and are a great opportunity to learn some really interesting things.

If oceans are your thing and you have a bit of spare time in February and March then check out the Exploring our Oceans MOOC being run by Oceanography at the University of Southampton:

In this six week interactive course, you will see how the ocean depths are no longer out of reach and how they are connected to our everyday lives. We will engage you in our most recent expedition findings and share our knowledge on the least touched areas of our oceans.

Together we’ll look at the animals that swim in these dark waters, the creatures that live on the seabed and the makeup of the underwater environment they live in.

Visit the Exploring our Oceans MOOC page for more details - or to sign up!

Tuesday, 14 January 2014

Whales should not be hunted for scientific research

Hunting whales for commercial exploitation was banned in the mid eighties and for good reason: stocks were dwindling and many of the uses for whale parts (oil etc.) are now redundant. Of course, people still eat whales and, not being a vegetarian, it would be pretty hypocritical of me to take issue with that aspect. (At least whales are free range, although I have no idea how humane their actual deaths are.) The problem is that many species of whale are now endangered or vulnerable. With their long generations and slow reproduction, it is clearly not that easy for populations to rebound.

Japan has got round whaling bans by exercising its right to “scientific” whaling. Not everyone is convinced, though, including the Australian government who have recently reported that they will send out a surveillance plane to the Southern Ocean to monitor Japanese whaling ships having previously challenged Japanese whaling at the UN as “commercial whaling in another guise”. The Japanese, of course, deny this.

The thing is, whilst it’s not my field, I cannot think of any good scientific reasons to hunt (and kill) whales at all. An article in the Japan Times last year, “In science terms, Japan has no need at all to kill whales”, agrees:

“Now, it is true that by catching and killing whales, and analyzing their stomach contents, a lot can be learned about cetacean biology. In the past, it was the only real method available to investigate these animals. But for many years now, it has been entirely unnecessary to kill whales in order to get the information that Japan’s Institute for Cetacean Research says it needs. …

Killing whales provides negligible data to science. Less than 1 percent of the papers published on cetacean biology come from studies that required the killing of a whale.”

Ironically, one of the reasons given to the scientific whaling is to get a better handle on their current populations - perhaps not so ironic if the hope is to use that information to remove the whaling ban.

There are some nations, such as Norway, who object to - and have declared themselves exempt from - the International Whaling Commission moratorium. This is bad (although I think they generally target large whale populations) but at least it is honest. I think it is time to ban scientific whaling just as commercial whaling is banned. That way, if a nation wants flout international consensus then at least the genuine motives will be clear.

Monday, 13 January 2014

Singing (but not stridulating) cicadas

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”.]

Sunday, 12 January 2014

Last year, I was mostly listening to...

I am not entirely sure that I trust the following, as my MacBook hard drive died in the summer of 2013 and a Time Machine backup was overdue. As a result, I think I lost a month or so of play counts and the resulting list is a bit biased towards recent acquisitions. Nevertheless, for posterity (and anyone curious), here is what I was listening to most in 2013 (compiled using the same script as last year.

Top 20 Tracks (most plays) of 2013

# Name Artist Album Plays
1 When I Grow Up Matilda the Musical Original Cast Matilda the Musical (Original Cast Recording) 30
2 Buck Rogers Feeder Echo Park 17
3 Walk Foo Fighters Wasting Light 13
= See The World Gomez How We Operate 13
5 The Duel Anna Phoebe Embrace EP 12
= How Far We've Come Matchbox Twenty Exile On Mainstream 12
7 The Farewell Anna Phoebe Rise of the Warrior 11
= Seven Days In The Sun Feeder Echo Park 11
= The Smell of Rebellion Matilda the Musical Original Cast Matilda the Musical (Original Cast Recording) 11
= No More Heroes Slash Apocalyptic Love (Special Edition) 11
11 Gypsy Anna Phoebe Gypsy 10
= Route 149(A) Anna Phoebe Gypsy 10
= Bombay to Beirut Anna Phoebe Gypsy 10
= See Through Blue Beth Orton Sugaring Season 10
= Viva La Vida Coldplay Viva La Vida Or Death And All His Friends 10
= We Can't Rewind Feeder Echo Park 10
= Naughty Matilda the Musical Original Cast Matilda the Musical (Original Cast Recording) 10
= The Hammer Matilda the Musical Original Cast Matilda the Musical (Original Cast Recording) 10
= His Girl The Budos Band The Budos Band II 10

Top 10 Albums (plays per track) of 2013

# Album Album_Artist Plays/Track
1 Embrace EP Anna Phoebe 8.75
2 Matilda the Musical (Original Cast Recording) Matilda the Musical Original Cast 8.05882352941
3 Gypsy Anna Phoebe 7.66666666667
4 Rise of the Warrior Anna Phoebe 7.41666666667
5 Echo Park Feeder 7.16666666667
6 Fossils Aoife ODonovan 6.3
7 Uno Green Day 6.0
8 Dos Green Day 5.84615384615
9 The Budos Band III (Bonus Version) The Budos Band 5.25
10 Hail to the King Avenged Sevenfold 5.1

There’s a few old favourites in there, like Green Day and Avenged Sevenfold, plus some new discoveries. Feeder is somewhat a blast from the past although I never really got into them at the time and mainly knew of them from a couple of tracks on the Gran Turismo soundtrack. The stand-out new artist in the lists is Anna Phoebe, which can best be described as violin rock music!

Anna Phoebe is instrumental, as is The Budos Band, which is good for background when writing or coding at work - hence the surge in plays over recent weeks. Matilda the Musical is just awesome - a Tim Minchin triumph! We went to see it live in London before the big move Down Under and it was so good that I bought the album straight away and it was the favourite in the car for a while. Indeed, if wasn’t for the MacBook death, I’m sure it would have racked up a load more plays. More on that later, I think.

It’s interesting to see some of my all time favourites are still hitting the most played list, as they did last year: Walk (Foo Fighters), See The World (Gomez), How Far We’ve Come (Matchbox Twenty) and No More Heroes (Slash) are all listen-to-before-you-die tracks. (I suspect that they might be there again next year!)

Top 10 Artists (Most listened to) of 2013

# Artist Plays Tracks
1 Feeder 231 63
2 Green Day 222 103
3 Anna Phoebe 193 25
= Avenged Sevenfold 193 57
5 Vitamin String Quartet 142 57
6 Matilda the Musical Original Cast 137 17
7 Jack Johnson 95 33
8 Matchbox Twenty 93 26
9 Foo Fighters 76 60
10 Gomez 64 65

Tuesday, 7 January 2014

Hunter Valley wine tasting with Wine Country Tours

When we moved to Australia, my fabulous sister-in-law gave us a present of voucher for Wine Country Tours to visit the famous Hunter Valley wine region. (Nothing to do with Huntsman spiders!) At the weekend, we went on the tour and it was great!

Hunter Valley is 2-3 hours north of us, so we had a pretty early start, but much of the journey is through National Parks and very pretty. (At least the bits I saw - I must confess to having a bit of a snooze at times en route despite the often bumpy toad. Tip: if mornings are not your thing, bring a travel neck pillow for the journey!)

The tour itself started with morning coffee and baked goods at Peppers Guesthouse, which was very pleasant. As a bonus, we got to see our first wild kangaroo, even if it was quite far away.

Once refreshed, we drove down the road to the main event: a tour and tasting at Tyrrell’s Wines, where we got up close and personal with some of the vines. Tyrrell’s Wines have been making wine (and family run) since 1858. Indeed, thanks to Phylloxera blighting European vineyards, the winery has some of the oldest vines in the world. At the time of our visit, the grapes were close to full colour and would be harvested in a few weeks. (Sooner for the whites.)

We then had a tour of the winery itself. Our guide, Richard Everett, is a trained Oenologist (winemaker) who worked in the wine industry for many years before moving into the wine guide business; he really knows his stuff and was able to give lots of insights into the wine-making process and the challenges it faces. (If you ever have doubts about the reality of climate change, talk to a winemaker!)

After the tour of the cellars, we then got down to the highlight of the day: tasting (15!) delicious Tyrrell’s wines. The tasting concentrated on what Hunter Valley (currently) does best - Semillon, Chardonnay and Shiraz - with several interesting comparisons, including three “vertical” tastings (same wine, different vintage) and several straight comparisons of the same grape from different vines and/or vineyards. (Tyrrell’s have vineyards outside Hunter too, so we were able to taste some of those and compare!) Richard was great and made the tasting highly educational, entertaining and enjoyable.

It’s fair to say that I came away from the tasting a major fan of Tyrrell’s Wines and will be looking out for them in future. It also really struck home how dynamic the whole wine business is - and how hard oenologists have to work year on year to maintain quality in the face of changing weather and climate.

After the tasting, we went for a somewhat pricey but very tasty lunch at Roberts Restaurant before a flying visit to Hungerford Hill Wines for a second (smaller) tasting with glimpse of the future: “cool climate” wines grown at altitude in the Snowy Mountains.

All-in-all, an excellent day out and highly recommended! (There are a few more photos here.)

Monday, 6 January 2014

How to stop Outlook on Mac OSX replacing quotes & apostrophes with superscript numbers

Since switching to a Mac, I have been experiencing an odd issue with Outlook: although in my message editor all would look well, recipients of my messages would often find the apostrophes (’) replaced with a 1 and “” quotes with 3 & 2.

Today, I had had enough and tried to find the reason/solution. The former, it seems, is because Macs have their own version of ISO-8859 encoding, which means that other platforms do not correctly interpret text encoded in this format. The solution is simply force Outlook to use a different "Preferred encoding" in the Composing Preferences - UTF-8 works for me.

Sunday, 5 January 2014

An unwelcome visitor... our first Huntsman spider

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!

Friday, 3 January 2014

Forget brains, we should be throwing all our money at Climate Science

2013 saw some unprecedented levels of funding being directed towards “ambitious” (read “impossible within the budget”) projects to map and simulate the human brain, with $100 million and €1.6 billion been thrown at these challenges, respectively. There is no denying that brains are important but, only a month after the $100m BRAIN Initiative was announced, 2013 also saw atmospheric carbon dioxide levels exceed 400 ppm for the first time in at least 800,000 years.

This is pretty stark as it is when you look at the Mauna Loa data, being such a sharp and large increase that it can barely be discerned:

Or zoomed in to hit home what we have been doing since the Industrial Revolution:

Climate skeptics would have us believe that this is natural and/or doesn’t really matter. After all, they say, it’s not the highest CO2 has ever been and life did all right back in those high-CO2 days. The thing is, though, even if you disagree with essentially every climate scientist in the world that Climate Change is man-made, it really does matter and life may have done all right at such levels but not life as we know it. For humanity - and all the organisms on which humanity relies - we are going into uncharted territory in both atmospheric CO2 and, perhaps more importantly, global temperature as this great infographic from the World Bank hammers home to startling effect:

I was tipped off to this image by a tweet from Alessio Fratticcioli but not yet been able to find the original.

Here is what they say at the World Bank Climate Change site, though:

“Climate change is a fundamental threat to sustainable economic development and the fight against poverty. The World Bank Group is concerned that without bold action now, the warming planet threatens to put prosperity out of reach of millions and roll back decades of development.

The science is unequivocal that humans are the cause of global warming, and major changes are already being observed. Current global mean temperature is about 0.8° Celsius above pre-industrial levels. The 12 years from 2001 to 2012 rank among the warmest since record keeping began 133 years ago. The intensity of extreme weather-related events has also increased.

Recent experience is a stark reminder that no country – rich or poor – is immune from the impacts of climate-related disasters today.

The World Bank Group believes a 4°C warmer world can and must be avoided. Immediate global action is needed to slow the growth in greenhouse gas emissions this decade and help countries prepare for a 2°C warmer world and adapt to changes that are already locked in.”

The picture is pretty bleak unless we do something about it fast and, worse than that, we still do not even really know how bleak it is. The East Antarctic ice sheet, for example, holds enough ice to raise sea levels by over 50m (and basically submerge almost every major city on Earth). We think it is stable (for now) but we don’t really know. (Somewhat counter-intuitively, increases in sea ice in the region could actually be indicative of more melting: freshwater has a higher freezing point than salt water and thus melted land ice can re-freeze when it hits the colder ocean.)

Having been peripherally involved in some Climate Change studies, the thing that really boggles my mind is how little funding is being channeled into what must surely be the most important questions for all humanity: is the world going to become largely uninhabitable in the near future and is there anything we can do about it? However important brains may be, I cannot help but think that such large chunks of money could be put to better use.