Gull chicks for company at Dublin Marks & Spencer Rooftop Restaurant

Anyone who watched BBC Springwatch this year will know that gulls are increasingly nesting on the roofs of city buildings, which are safe from predators and provide lots of nice, flat nesting spots. Last week, we met a friend for brunch in the Marks & Spencer Rooftop Restaurant on Grafton Street in Dublin. The restaurant features an outside section overlooking Grafton Street and good for enjoying the rare bit of Dublin summer sun. At present, it also features a pair of cute little gull chicks, being reared on the flat roof section just beyond the barrier. The pictures below are a bit rubbish and out of focus but you get the idea.

What do a Lurcher called Zak and a cheetah have in common?

Actually, these animals have lots in common - they are both mammals, carnivores etc. - but I'm thinking of something a bit more esoteric: both have had their locomotive performance measured by a special collar designed by Alan Wilson and the Structure & Motion Laboratory at the Royal Vetinary College in London. (The same technology was also used for the collars that tracked 50 cats from Surrey in the recent BBC Horizon, “The Secret Life of the Cat” programme, which is well worth a watch!)

The team have used the collars to study cheetah hunting behaviour, which was recently published in Nature and featured in the June 13th Nature podcast. The study itself is interesting and demonstrates how raw speed - the big thing the cheetah is famed for - is actually secondary to agility and power (i.e. acceleration and deceleration) when it comes to hunting success. Even so, the wild cheetahs still chalk up bursts of up to 59 mph (93kph) whilst hunting, which is not too far off the 65mph (105kph) top speed recorded in zoos.

The bit that really appealed to me, however, was how the collars were tested prior to being deployed in the field, which I find pleasingly elegant and effective. Prof Wilson’s pet lurcher, Zak, was given a run about on the beach whilst wearing a collar. (Two actually, as the new collar was being compared to older technology as well.) The data from the collar was then used to reconstruct Zak’s movements, which could be compared to the footprints left in the sand!

(The handsome chap in the photo above is not actually Zak but Dexter, my sister-in-law’s lurcher, on Dollymount Strand with a nice view of Howth in the background.)

Find more details of the study in Nature news, the podcast and, of course, the paper itself:

Wilson et al. (2013). Locomotion dynamics of hunting in wild cheetahs. Nature 498, 185–189.

There’s also some coverage on Why Evolution is True that appeared whilst this post was sitting in drafts.

Chic and cheerful at Urbun cafe, Cabinteely village

Continuing the good coffee theme, earlier this week we had lunch at Urbun cafe in Cabinteely, south Dublin. As befitting a cafe that started life as a market stall, the interior is simple but comfortable and, for want of a better word, wholesome. The knives and forks, for example, were brought to the table in a reused jam jar. (I think the decor might "urban chic" but I'm not really sure - I won't let that uncertainty interfere with a blog post title, though!)

The food was very good. I had the special - a tasty sweet potato and bacon frittata - and also got to sample some of my wife's club sandwich. The frittata was good but the sandwiches at Urbun are pretty special, served on thick slices of lovely fresh bread - highly recommended.

After lunch we had a coffee and that was also excellent. Their barista, Vini, had won third prize in the Irish Barista Championship and did not disappoint. Good stuff!

Impressed with Cafe2u Coffee at the Southampton Kite Festival

I thought I should balance out my last post giving out about coffee on the Jonathan Swift by endorsing some surprisingly good coffee on the go. Last Saturday was the Southampton Kite Festival. Our friends, the Flying Fish Kiting Team, were performing so we went down to lend some support. (And a good performance it was too! Sadly, the weather was not quite so good, so no pictures this year.)

As well as the kite skills of Flying Fish (and their four-man team, L-Katz,) one of the impressive highlights of the day was the coffee from the Cafe2u mobile coffee van that was there. (Last year's culinary stand-out, Biggles Donuts, were not there, sadly.) Proper, freshly made coffee, and not ridiculously overpriced. (I also like the smiling running coffee bean on their logo!)

Irish Ferries coffee disaster!

We recently made a trip from Holyhead to Dublin on the Irish Ferries Dublin Swift. We had a couple of breaks on the drive from Southampton but were feeling in need of a good coffee pick-me-up by the time we had embarked. Having settled down in seats near the onboard "Cafe Lafayette", I unthinkingly assumed that (a) all the places serving hot drinks on board would essentially serve the same, and (b) if anywhere had more/better hot drinks, it would be the cafe. Big mistake on both counts!

If you travel on the Jonathan Swift and like your coffee, avoid Cafe Lafayette at all costs. The coffee tasted like burnt dirt. (It actually reminded me a of the odd occasion at work when I have made myself a cup of Senseo coffee and forgotten to put in a new pod!) Not good.

To rub salt into the wound, when disembarking the ferry we noticed that the "Temple Bar" on board was serving Costa coffee. Duly noted for future trips!

The Ehux genome is here and it looks epic!

In addition to my main research on Short Linear Motifs, I have a number of collaborations with environmental scientists looking at how various organisms, such as corals, might be affected by rising CO₂ levels.

One of the more fun collaborations has been with Bethan Jones (now at Oregon State University) and Debora Iglesias-rodriguez (now at UC Santa Barbara), working on the marine phytoplankton Emiliania huxleyi. Along with Paul Skipp at Southampton, I was involved with with proteomic analysis of this small but important organism. This was challenging because, at the time, their was no annotated genome available - hence the need for some bioinformatics help. (The second paper from this came out in April but my planned blog post was postponed after the Boston marathon bombing and is now sitting on my To Do list.)

Happily, the genome is now out! As reported in the KQED blog post, Opening the Gene Box of a Key Ocean Species:

“This week in the journal Nature, a worldwide team of 75 scientists revealed the genetic blueprint of the one-celled alga Emiliania huxleyi, which may be the most important species you’ve never heard of. The genomes of the domestic dog and cat are interesting, but the E. huxleyi genome is a much bigger story. Some day this organism may become another of our partner species, as vital to us as yeast.”

Even more happily, Bethan and Debora are both authors on the paper (as part of the Emiliania huxleyi Annotation Consortium), Pan genome of the phytoplankton Emiliania underpins its global distribution, which reports “sequences from 13 additional isolates” in addition to the genome of the reference strain CCMP1516. Many years in the making, it’s a bit of an epic, and I look forward to learning some more of Ehux’s secrets.

h/t: Bethan. [Picture from KQED] Citation: Read et al. (2013). Nature doi:10.1038/nature12221.

Are "Happy Eggs" really happy? (And are Viva really pro-welfare?)

Like many people, I am concerned by animal welfare but also rely on official organisations like the RCPA and their Freedom Food campaign:

When you see the Freedom Food label you know that animals have been kept to strict RSPCA welfare standards. The standards cover the whole of an animals’ life, not just their time on farm. A stimulating environment and plenty of room to move around are just two of the many benefits.

Freedom Food can also be an affordable ethical choice, as they approve indoor as well as free range and organic farms. So, make one small change to your shopping and one big change to farm animal welfare.

With the horrors of battery farms so well documented, we are especially watchful when it comes to eggs and chicken, and have been buying “Happy Eggs” for some time. In their welfare page, The Happy Egg Co. state:

All our farmers are dedicated to the wellbeing of their hens and every farm has acres of outdoor space for our hens to roam free, plenty of playhouses, trees and foliage for them to explore and rummage around in, as well as indoor space with nest boxes to give them a little bit of privacy when they’re laying.

I was therefore shocked to read a Viva investigation of “Happy Eggs” farms, which is still doing the rounds online, in which they report:

“… a very different story – one of disease, incarceration, mutilation, short lives and electric shocks.”

It makes for some pretty uncomfortable reading and, if true, really is shocking. If it’s true. The thing is, the expose by Viva is not necessarily neutral - Viva is the “Vegetarians International Voice for Animals”:

“Eating meat; fish and dairy causes environmental destruction, damages human health, contributes to global hunger and inflicts immense suffering on billions of animals across the world.

Viva! believes that the solution to all these problems is in our own hands: the best way to stop the destruction and the cruelty is to stop eating animals now – go vegetarian, or better still, vegan.”

I actually agree with a number of their points but not to the point that I think going vegetarian is the answer. We should eat less meat, certainly - not every day - and there is no need for the cheap, budget meat that floods supermarkets. Animal welfare is very important - how an animal lives is more important in many ways than how it dies. (In nature, animal death is rarely pleasant.)

The worrying thing, however, is not that Viva appears to have an agenda to discredit poultry (and other meat) farming but rather than the RSPCA and Freedom Food considered legal action and accused “Viva and Channel Five of reporting out of context and of withholding important information about animal welfare.” The lack of context included one of the farms being “under veterinary supervision for an outbreak of erysipelas” - a disease that “can unfortunately cause high levels of mortality as well as feather loss”, which accounts for some of the unpleasant observations.

That’s not the worst of the counter-accusations, though:

But the RSPCA is seemingly most angered by the fact that Viva had sat on its findings for three months, only releasing them in early October - to conincide with British Egg Week.

“If Viva had footage that demonstrated a problem as far back as July, then it should have been reported immediately so that the appropriate action could have been taken,” said the statement. “It is disturbing that this information was withheld when there was potential for on-going suffering.

“As a result of the issues raised above and the manner in which Channel Five provided evidence, we are seeking legal advice.”

A separate statement from the Happy Egg Co said it regarded the happiness of its hens as its top priority and it had immediately put in place an audit of all its farms.

So, who to believe?

The closest I have found so far to neutral coverage is on the Spud and Spike blog, which (as far as I can gather) is a personal blog by a mum on the adventures of her two kids. In a post from about a year ago (the expose itself is from 2010) - “Our visit to a Happy Egg Co Farm!” - the author reports conditions much more akin to the Happy Eggs & RSCPA point of view.

Indeed, as she points out, Compassion in World Farming awarded a second Good Egg award to Happy Eggs “in recognition of the packer’s commitment to high animal welfare”. According to the CIWF website:

“Compassion in World Farming was founded over 40 years ago in 1967 by a British farmer who became horrified by the development of modern, intensive factory farming.

Today we campaign peacefully to end all cruel factory farming practices. We believe that the biggest cause of cruelty on the planet deserves a focused, specialised approach – so we only work on farm animal welfare.”

I still find the Viva report a bit worrying - some of the welfare breaches (or “non-compliance issues”) reported were confirmed by the RSPCA - as well as some of the other reports that the RSPCA Freedom Food campaign is not really doing what it says in terms of the depth and frequency of welfare checks. That said, when reports seem to be coming from biased and unreliable sources, it is hard to know what is true and what is not.

If Viva really did sit on their footage for two or three months then they should be thoroughly ashamed of themselves. Prolonging unnecessarily animal suffering is bad enough when it is done for food or for profit. If it is being done purely for publicity by an organisation that is nominally pro-welfare, that really would be unforgivable.

For now, I am going to continue eating Happy Egg Co. eggs - and I think I will be getting my future welfare information from Compassion in World Farming.