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.)

What do you get if you cross a dead cockroach with a bunch of ants?

After 24 hours, not a lot…

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.

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.)

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 X^TM 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 X^TM 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.

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!

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.