Saturday, 30 March 2013

SMBE has a shiny new website

I'll always have a bit of a soft spot for the journal "Molecular Biology and Evolution" (MBE). Not only does it combine two of my favourite things - molecular biology and evolution - but it was also where I published the main paper from my PhD, Transiently beneficial insertions could maintain mobile DNA sequences in variable environments. Although published by Oxford Journals, MBE is a journal of the Society for Molecular Biology & Evolution (SMBE), which also organises a large annual conference of the same name.

SMBE has a nice shiny new website at As well as news on this and blog posts on relevant topics, you can also see the most read papers from MBE and SMBE's other journal, Genome Biology and Evolution (GBE). You can also keep up to date with SMBE via their new Twitter Stream and Facebook page. (The current Secretary and Treasurer of SMBE are both members of VIBE, the Virtual Institute of Bioinformatics & Evolution (formerly the "Virtual Institute of Bioinformatics, Eire"), through which I got my first postdoc, so it must be good! I miss VIBE meetings!)

Thursday, 28 March 2013

Geek Sculpture at Cold Spring Harbor Laboratory

A couple of weeks ago, I attended the 2013 "Systems Biology: Networks" meeting at Cold Spring Harbor Laboratory, New York.

Cold Spring Harbor Laboratory has a beautiful little campus on the north shore of Long Island, about an hour or so east of New York city. One of its charms is the many pieces of sculpture dotted around the place, including "The Waltz of the Polypeptides" by Mara G. Haseltine, which we passed each time we travelled between our cabin dorm and the talks or food.

As the plaque states:
"The Waltz of the Polypeptides" is the artist's impression of the birth of a protein. As five ribosomes travel the length of a messenger RNA, a protein is created.
It's quite cute and the large subunit of the ribosome looks like it wants a hug once it's released from the mRNA, as seen to the right of the above photo.

The protein in question is identified as Beta Lymphocyte Stimulator (a.k.a. BLyS a.k.a. B-cell activating factor (BAFF)), officially called tumor necrosis factor (ligand) superfamily, member 13b (TNFSF13B). A separate sculpture of the protein backbone sits on the other side of the path. I like it!

(I stayed on for some holiday after the conference - hence the lack of posts recently - so expect a few more travel posts soon.)

Tuesday, 12 March 2013

Tiramisu - the ultimate dessert for entertaining?

My parents-in-law are over to visit for a few days and they always feed us well so we wanted to make something a bit special for dinner. My wife made a lovely Jamie Oliver recipe, roasted butterflied leg of lamb with chickpeas, yoghurt and tray-roasted veg (courtesy of my sister-in-law), and I was on dessert duty. This is unusual for me, as my wife is the baker in the household, but I fancied having another bash at the tiramisu recipe I had (successfully) made a few years previously from The Food of Italy: A Journey for Food Lovers.

Tiramisu is pretty easy to make and, useful when entertaining, can be made almost entirely ahead of time - indeed, it actually benefits from a bit of time in the fridge for the flavours to soak and develop. It also doesn't involve any cooking and, being entirely made of yummy ingredients, it's probably quite hard to actually make it taste bad. The Tiramisu I made was slightly modified from the book:
5 eggs (separated)
170g caster sugar
300g mascarpone
250ml cold strong coffee
3 tbsp Amaretto
Enough sponge fingers for two layers (approx. 36)
40-80g dark chocolate
The recipe says "serves 4" but I would say this serves 6-8! It's quite simple. Separate the eggs and beat the yolks with the sugar until it's smooth and then beat in the mascarpone, again until smooth. In another (very clean) bowl, beat the egg whites until they make soft peaks. (The transformation of egg whites during beating has to be one of cooking's wonders - made no less wonderful because we understand the science behind it.) Then fold the egg whites into the yolk/sugar mix.

Then it's time to assemble. Get a square dish (approx. 25cm x 25cm) to make the Tiramisu in and another shallow dish for dunking the sponge fingers, into which mix the coffee and Amaretto. The original recipe uses brandy or sweet Marsala wine and I've had a delicious alcohol-free version (made by an Italian), so there is some flexibility here.

To assemble, take sponge fingers, dunk them in the coffee to soak some up and cover the bottom of the dish in a single layer. You want to plan to soak up about half of the liquid. I was a bit stingy with the first layer. It worked out fine in the end but you can always make more coffe, so it might be worth being bold with your soakage if in doubt. (Just don't soak up enough to risk the integrity of your sponge fingers.) If your dish an awkward size/shape, I would encourage a (literal) dry run, as once you have placed a coffee-soaked sponge finger, you won't be able to move it. Cover the layer of sponge fingers with half of the egg/mascarpone mix. Repeat with another layer of coffee-soaked sponge fingers. If you have too much coffee/booze mix left, you can gently spoon some more over the fingers to let them soak up some more. (I did this as I had quite a bit left. It's impressive how much they can soak up!) Spread the rest of the egg/mascarpone mix on top and smooth.

At this point, you can cover with clingfilm and put in the fridge for a few hours, or overnight (or eat it straight away). When it's time to serve, grate the dark chocolate over the top for a generous covering. The recipe said 80g but this seemed rather excessive for the size of dish that I had. I only used about 40g in the end, which gave a good covering and so I stopped grating due to a combination of laziness and impatience! When dished up, it did look a bit stingy, so I would probably recommend about 60g for next time.


Don't panic!

And if you do, Google can help... (Happy Birthday, Douglas Adams!)

Monday, 11 March 2013

Wonderful wines of the Western Cape

Beyerskloof Pinotage Reserve 2009On Friday, a new star of the wine world was revealed to me. Beyerskloof Pinotage Reserve 2009 has joined Roaring Meg Pinot Noir as a wine worth remembering - and paying full price for! :op Unlike Meg, though, it's a real bargain at under £14!

The discovery was made at a particularly good tasting of the University of Southampton Wine Club, "Cape Wines", which featured eight excellent South African wines. (All available from SA Wines.) The Beyerskloof Pinotage Reserve 2009 was the last wine of the night and the star of the show (for me) but all eight wines were very palatable. Affordable too! (The most expensive one was still under £20 - and actually my least favourite of the night.)

Rustenberg Syrah 2009Simonsig Frans Malan Reserve 2007A couple of the other reds were also worthy of a mention: the Rustenberg Syrah 2009 and Simonsig Frans Malan Reserve 2007. As one might expect, all three were big and bold, just the way I like my red wine, although the Simonsig had a rather disappointing finish.

I had been expecting to enjoy the reds but the whites were also surprisingly good. The Groot Constantia Sauvignon Blanc 2011 was pleasant but unspectacular - a bit disappointing for a New World Sauvignon Blanc fan. The Vergelegen Chardonnay Reserve 2011, on the other hand, was a pleasant surprise: lightly buttery but crisp. I'm not generally one for Chardonnay but I'd happily have this one again.
Vergelegen Chardonnay Reserve 2011Graham Beck Brut NVThe final notable wine of the night was the least spectacular but worth remembering all the same, which was the opener - a Graham Beck Brut NV. I am not a great champagne drinker but this one was very pleasant and at £12.99 definitely one to note for next time I need something bubbly.

All-in-all, a great evening with some great wines - and eight more reasons to go wine tasting in the Western Cape!

Wednesday, 6 March 2013

The joys of intext and other Google search tips

Every now and then I revisit my growing pool of half-written blog posts and see if any are worth salvaging. One such post is some useful Google search tips from John Todesco.

His post from last summer, How to solve impossible problems: Daniel Russell’s awesome Google search techniques, was sent to me by a colleague at work. There are lots of useful tips in the article but a few in particular stood out for me, including a couple of things I knew but a couple more that I had wondered about but never got round to looking up for myself (modified from John Todesco's post):

Use quotes to search for phrases.

  • Typing “San Antonio Spurs” will show you the websites with the phrase “San Antonio Spurs.” If you don’t use the quotes, Google will search for the terms “San,” “Antonio,” and “Spurs” individually and you might miss pages related to the basketball team.

Use OR but not AND.

  • Don’t bother typing AND in your search queries – Google treats it like any other word.
  • OR in all caps actually works. OR is great for finding synonyms and boilerplate language. Typing “Smith denied” OR “Smith claimed” OR “Smith argued” will find more pertinent websites about the controversy involving Smith.

Use minus, not NOT.

  • Avoid using NOT if you want to exclude a search term. Instead, type a minus sign in front of the word. So if you’re visiting San Antonio but don’t want to visit the Alamo, type: “San Antonio” -Alamo.That will search for the phrase “San Antonio” on web pages that don’t have the word “Alamo.” There’s no space between Alamo and the hyphen.

Minus does not equal plus.

  • Although putting a minus sign in front of a word removes it from a search, adding a plus sign in front of the word does not force Google to include it. It simply stops Google from changing the word into a synonym or correcting the spelling, like putting it in quotes. Typing +Alamo is the same as typing “Alamo”. If you want to force Google to include an exact word or phrase in all your search results, use intext:...

Force Google to include search terms.

  • Typing intext:[keyword] might be Google’s least-known search operations, but it’s one of Russell’s favorites. It forces the search term to be in the body of the website. So if you type: intext:”San Antonio” intext:Alamo it forces Google to show results with the phrase “San Antonio” and the word Alamo. You won’t get results that are missing either search term. This also stops Google using an alternative word that it thinks you're searching for.

Find relational search terms.

  • What if you’re curious about search terms that are near each other on a website? [keyword] AROUND(n) [keyword] is incredibly handy for finding related terms such as “Jerry Brown” near “Tea Party.” (“n” is the number of words near the search terms.) Typing “Jerry Brown” AROUND(3) “Tea Party” will show you all the websites where the phrase “Jerry Brown” was mentioned within three words of “Tea Party.”
I've not yet used AROUND successfully but intext: and -unwanted has already helped me out a couple of times.

h/t: Alistair Bailey

Monday, 4 March 2013

Not so much a ‘wake up call’, having pro-homeopathy MP David Tredinnick on the Commons science committee is the stuff of nightmares

Sadly, the recent kerkuffle over the portrayal of homeopathy on the NHS Choices website and the government's flagrant disregard of scientific advice on culling badgers may well just be the tip of an iceberg that the good ship Great Britain is sailing towards, full speed ahead.

Apparently, the Conservatives want to be the Republican Party so much that they have elected science-illiterate MP David Tredinnick to both the Commons Health Committee and Commons Science and Technology Committee. The problem? In the words of Miriam Frankel in her recent piece, ‘Wake up call’: Q&A with pro-homeopathy MP David Tredinnick, this is a man who "thinks the moon influences human behaviour and believes that homeopathy works."

As a scientist, the piece does not make happy reading.
"I’ve come onto this committee as someone who wants to see it take a broader view of science. I don’t believe that science is about defending the status quo: it’s about pushing boundaries. It’s really significant that I got onto this committee and I think it should be a wake-up call to those in the scientific community who don’t want to explore alternatives."
This doesn't sound too bad until you realise what the alternatives are that he wants to consider: homeopathy, acupuncture and herbal medicine.
"I think there are some good, double-blind placebo-controlled trials that have been conducted by the Integrated Healthcare Hospital, formerly the Royal London Homeopathic Hospital. But there’s also an enormous amount of evidence available through the observation of patients, so we shouldn’t ignore that. The other thing is that is very safe and very inexpensive. It should be more widely available on the NHS. And we should be teaching people to use simple homeopathic kits to stop unnecessary visits to doctors’ surgeries."
What?! Have you even read the House of Commons Select Committee (Science and Technology Committee) Evidence Check for Homeopathy? It's "safe and very inexpensive" because it doesn't contain any active ingredients! It has been explored by science. What possible motive do scientists and doctors have for not promoting homeopathic medicine if it actually worked? Not knowing how it works? We don't know how Paracetamol works but we use that.

It gets worse:
"I think that if the sun has an impact on our lives and the moon has an impact on the tides and cycles, it is logical to suggest that it might have an impact on other aspects of our lives as well. It’s accepted that at certain times certain people’s behaviour gets more extreme at the full moon—that’s, I think, scientifically proven. Hormonal reactions to increased positive ions in the air—the full moon effect—can cause hyperactivity, depression, violent behaviour, etc."
No, David, that's unscientific crap. You're right that science is about "pushing boundaries" but the way we push those boundaries is by ruling out the hogwash, like homeopathy and "the lunar effect". It is most certainly not by promoting hearsay and anecdote as a basis for policy or a way to determine efficacy.

Someone made a petition to remove David Tredinnick from the House of Commons Science and Technology Committee but it's been rejected because "E-petitions cannot be used to request action on issues that are outside the responsibility of the government". Hmmm. I'll feel another letter to my MP coming on.

h/t: Rachel Nesbitt at the Society of Biology.

Sunday, 3 March 2013

Chris Packham shows his star quality in defence of the badgers... and farmers

The British Government's Campaign of Stupid is continuing in full force with the recent news, Pilot badger culls in Somerset and Gloucestershire approved. This is after MPs voted to reject plans for the cull last October following massive scientific and public opposition to the cull.

The issue is summed up nicely in a This is Somerset post, BBC Springwatch star Chris Packham: Face the facts, a badger cull won't work. It's well worth a read - well balanced and cutting right to the heart of the matter. This is not just about trying to save badgers - it is about ignoring scientific evidence and plowing ahead with an expensive course of action that is more likely to make things worse than actually help. That money should be going towards trying to find genuine solutions for the TB problem - such as effective vaccination and finding ways to combat the EU ban on products from vaccinated animals. And this is the big problem with politicians ignoring scientists on scientific matters - public money is wasted on solutions that do not work whilst the problems themselves do not get solved.

h/t: Neil Gostling.

Saturday, 2 March 2013

Another small victory in the fight against quackery but the NHS is yet to dilute its shame to Homeopathic concentrations

As blogged recently by Rachel Nesbitt at the Society of Biology, NHS Choices website becomes ‘neutral’ on homeopathy, the NHS Choices website had recently diluted its stance on the inefficacy of homeopathic 'treatments' in response to lobbying.

Happily, in response to a deluge of disgruntled comments, the original text has now been replaced and the site now begins:
"Homeopathy is a 'treatment' based on the use of highly diluted substances, which practitioners claim can cause the body to heal itself.
A 2010 House of Commons Science and Technology Committee report on homeopathy said that homeopathic remedies perform no better than placebos, and that the principles on which homeopathy is based are 'scientifically implausible'. This is also the view of the Chief Medical Officer, Professor Dame Sally Davies."
It's still not all good news, though. As the website explains further down the page:
"It is available on the NHS?
The Department of Health does not maintain a position on any particular complementary or alternative therapy, including homeopathy. It is the responsibility of local NHS organisations to make decisions on the commissioning and funding of any healthcare treatments for NHS patients, such as homeopathy, taking account of issues to do with safety, clinical efficacy and cost-effectiveness and the availability of suitably qualified practitioners.
Homeopathy is not available on the NHS in all areas of the country, but there are several NHS homeopathic hospitals and some GP practices also offer homeopathic treatment."
I'm not sure if this is a deliberate typo - the link at the top of the page reads "is it available..." rather than "it is available..." but, tragically, yes, homeopathy is available on the NHS in some places. With Jeremy Hunt as Health Secretary and pro-Homeopathy Conservative MP Tredinnick on the Commons science committee, I genuinely fear for any future hopes evidence-based science policies in general (badgers beware), and for the NHS in particular.

In case anyone is in anyone doubt as to the driving force behind promoting homeopathy, the final paragraph of the "is it available..." section reads:
"Homeopathy is usually practised privately and homeopathic remedies are available from pharmacies. The price for an initial consultation with a homeopath can vary from around £20 to £80. Homeopathic tablets or other products usually cost around £4 to £10."
That's right. £4 to £10 for some sugar pills. And if you think that homeopathy is harmless, the tell that to anyone duped into giving their child a homeopathic vaccine. (Their opposition to vaccines is particularly ironic, given that the only shred of science that comes even slightly close to homeopathy is that small amounts of a pathogen - an actual vaccine - can potentially give you protection. The mechanism is entirely different, though. (It's real, for one thing.))

If people want to take a placebo, that is their choice - and it might even still work if given explicitly as such - but hiding the fact that a 'treatment' is just a placebo is irresponsible. Promoting it in favour of actual treatments should be criminal. Thanks to the games played by big pharma, the battle for getting decent evidence-based medicine is hard enough. If we can't even stamp out something as obviously nonsense as homeopathy, what hope do we have?