The Cabbages of Doom

Feel the Force... of taxonomy!

2012-02-13T21:02:00.000Z

Occasionally, I come across some really weird stuff at work. Today, for example, I was updating some lecture slides on sequence databases (how jealous are you of my students?!) when I came across a classic. The release notes for the current version of the UniProt database has a light-hearted and rather interesting look at taxonomy. (It's not very long if you fancy a peek.)

The thing that stood out, however, was the reference to a paper in The International Journal of Systematic and Evolutionary Microbiology (there's a journal for everything!) by Sassera et al. (2006): 'Candidatus Midichloria mitochondrii', an endosymbiont of the tick Ixodes ricinus with a unique intramitochondrial lifestyle.

Ixodes ricinus is the tick transmits Lyme Disease. Here's one engorged on blood. [Picture by Richard Bartz, taken from Wikipedia.] Handsome devil, isn't it?

The interesting discovery was not the tick, though, but rather a tiny endosymbiotic (i.e. living internally) bacterium. Intracelleluar bacteria are quite well known and many are rather interesting, such as the "male killing" species that alter the sex ratio of the host's offspring because they are only transmitted by females. Candidatus Midichloria mitochondrii, however, doesn't just live inside cells but inside the mitchondria in cells, which hadn't been seen before, I think.

My interest today is not the science, though, but something much more childish and silly. The authors named their discovery after Midi-chlorians, the endosymbiotic ~~travesty~~ microbes from the Star Wars prequels that explain the Force and make grown men of a certain age weep. (Why George? Whyyyyyy??!!) And that's the benefit of discovering a species - you can name it after whatever you like! (Except yourself.)

And for those of you who get depressed by the mention of Midi-chlorians, or want to know more about them, watch this video!

Kindling some Darwin love

2012-02-12T15:34:00.000Z

Today is Darwin Day, marking the 203rd anniversary of the birth of Charles Darwin. I had intended to write a blog post about Natural Selection but reviewing duties and lecture preparations mean that I might have to leave that for another day. Instead, I will just point out that you can get a FREE kindle edition of "Origin of Species", if you've not yet read it. (You don't need a kindle to read this eBook - there are many free Kindle reader Apps available.)

The book itself is over 150 years old but is still worth a read to see what all the fuss is about. It's interesting not just from a science perspective but also from a history perspective. They don't really write them like that any more!

Que Syrah, Syrah

2012-02-11T17:04:00.038Z

Last night we had a Syrah/Shiraz wine tasting at the wine club. I had been looking forward to this, as I am rather partial to a Shiraz or Shiraz blend and was expecting to be blown over by some bold, fruity and maybe slightly spicy red wines from the New World.

The format was quite fun and after a couple of "interesting" Aussie Shiraz variants - namely a Rose (OK but I'm not a big Rose fan) and a sparkling Shiraz (Why?!! Yuck!) - we had a series of five Shiraz/Syrah wines tasted blind, with a quiz asking where were they from and how much did they cost. I also rated mine out of ten. I don't normally reveal my tasting notes, such as they are, because my ignorance is great and my wine vocabulary limited. This time, though, I thought I would make an exception:

There are a couple of things to note here. One is that I only got a couple right (the French and Chilean) and this was essentially a pair of lucky guesses based on (1) the fact that I generally don't like French wine and (2) I liked "E" the best and figured that Chile could knock out a decent full-bodied red. The Chilean in question was a 2008 Lapostolle Cuvee Alexandre from Las Kuras Vineyard (right). It wasn't my favourite ever but it was cetainly good stuff, almost black in colour and with chocolately smoothness. I'm not sure I would pay £15.75 for it but it might be worth it.

The second thing to note is the generally low scores out of ten that I gave the five wines - 4/10, 7.5/10, 5/10, 5/10 and 8/10. Most disappointing of all was the Australian Torbreck "Woodcutter's Shiraz" (below left), which I have made a note of in order to remember to avoid in future! It was not what I have grown to love and expect from an Aussie Shiraz.

Somewhat more successful was the fortified Shiraz Australian "port" from d'Arenberg (above right). This tasted a bit of blueberries with a hint of liquorice and would probably be very nice after dinner with some dark chocolate.

The disappointing aspect of the evening was that in the past couple of weeks, I've had three Shiraz/Syrah or Shiraz blends that, quite frankly, blew everything from last night out of the water. In California last month, we had a fantastic Shiraz from Vermeil Wines in Napa Valley (one for a future blog post), I've already posted about the delicious and bargainiferous Kumala Zenith Merlot/Cab Sav/Shiraz blend and on Thursday, to prepare for last night's tasting, we had a very tasty Australian Shiraz from JJ McWilliam (left).

With the exception of Californian winery tasting sessions, I think I might be sticking to my half-price £10 bottle from the supermarket in future!

Cosy

2012-02-11T12:13:00.000Z

Some days, having your own bed is over-rated.

Intelligent Falling

2012-02-09T22:57:00.002Z

My last post reminded me of a classic article from The Onion, Evangelical Scientists Refute Gravity With New 'Intelligent Falling' Theory. (In case it's not obvious, The Onion is satire!)

Gravity - only a theory

2012-02-09T22:22:00.000Z

Combining two of my favourite things - cute cats and combating common errors in thought about evolution - is this great image by bayanimills. The caption reads:

"Just a theory!" - The hallmark of someone who is ignorant of what a "Scientific Theory" is.

I discovered this through the Why Evolution is True website, although now I think that I should find out what "Instagrams" are. I feel like I might be missing out on something! (This image is reproduced without permission, so please give the love to bayanimills if you like it.)

Exam tips II

2012-02-08T20:49:00.000Z

Exam marking is pretty much over for another Semester and once again I have been struck by how many students make the same mistakes in terms of how they approach answering questions. Knowledge and understanding are obviously important but if your exam technique is poor, you will still struggle to get a good mark.

In addition to the big one (that I have previously covered) of Answer the Question, here are some random tips for optimising exam performance, in no particular order:

☑ When using examples, try to be specific. Demonstrate that you know exactly what it is an example of and why it is an example.

☑ When drawing diagrams: (a) make them big; (b) use a ruler; (c) give them clear labels and/or a legend; (d) refer to them in the text.

☑ Never start a sentence "Therefore..." and assume that the link from the previous paragraph is obvious. It may be obvious but we want to see that you know why it's obvious. More often than not, this comes across as:

I know X somehow means Y but I don't know why, so I will tell you what I know about X and then write "Therefore, Y."

☑ If possible, include a short introductory paragraph that explains how you are going to answer the question. This is particularly important if your first paragraphs are background information that does not directly address the question asked, or you are not answering different aspects in the order they were asked.

☑ Being correct is not enough. I want to see that you know why what you write is correct - demonstrate understanding, not just recall.

☑ Use scientific terminology where possible but always explain what the terms mean. Again, it is a matter of understanding vs. recall. (And, in the worst case scenario that you use a scientific term incorrectly, we will still know that you understand the answer.)

☑ Try not to assume that the person who taught you will mark your script when you write your answer, and draw your figures. They probably will be the same person but, this way, you are less likely to make the mistake of too much assumed knowledge. I may know that the boxes in the figure are genes because you are reproducing my figure but if you do not label them, you will not get any credit for understanding. Again, I am not testing your ability to copy stuff. Likewise, I may know that a given disease-causing mutation is in Gene X but if you do not tell me, I cannot assume that you know.

Google Psyche: 'Dinosaurs Are Jesus Ponies' and other fun revelations

2012-02-07T22:03:00.000Z

Thanks to Twitter (and Ed Yong), I just stumbled across "Google Psyche":

Great moments in Autocomplete, courtesy of Google search and collective consciousness

Google Psyche is an exploration of the stories that the world's Internet searches tell. The company's autocomplete algorithm predicts the word a random web searcher is most likely to type next, providing a statistical probe for our collective consciousness.

This week's offering is a search starting "Dinosaurs are...", which features (among other things) "Dinosaurs Are Jesus Ponies" at number 5.

I'm not entirely sure what this this tells us about our collective consciousness - it's just what people search a lot - and I really don't think that I would describe it as a "statistical probe" but it's still kind of interesting and fun. There must be a local factor in the Google search prediction algorithm, though, because the Jesus Ponies search does not appear in the top 5 for me:

I wonder if this says something about Americans! Of course, it could just be due to a famous quote that I am not aware of - according to the comments on the Google Psyche page, "Dinosaurs Were Made Up by the CIA to Discourage Time Travel" is a song by "Math the Band", which might account for number 3.

I tried it for "Cabbages of..." and was pleased to see "Doom" at number 2, although that might be just due to me lazily using the autocomplete to find my own homepage from time to time. I'm not sure what other people would get. Fourth on the list is very disturbing, though. The mind boggles.

Kumala Zenith Merlot/Cab Sav/Shiraz - another bargain red

2012-02-06T19:13:00.000Z

As I may have mentioned before, I have a rather random but effective wine purchasing strategy. I know roughly what I like (fruity dry whites and robust reds) but I don't know enough about my wine to be able to pick a bottle off the shelf and say for sure that it's going to be good.

Instead, I work on the principles that (1) I won't be too upset if I spend a fiver on a bottle and it turns out not to be too great, and (2) bottles on sale for a tenner are rarely unpleasant. When our wine stocks are a bit low, I therefore poke around the wine section of the supermarket for half-price ten(ish) pound bottles of wine of the general kind that I like. Sometimes it goes wrong but more often that not it seems to work out well.

The latest hit with this strategy was the "Zenith" Merlot/Cabernet Sauvignon/Shiraz blend from Kumala winery. A "juicy, smooth full bodied red wine", this one paired very nicely with beef and mushroom stroganoff. Very quaffable and a real bargain at only £5 from Sainsbury's - get some while it's still on offer!

Alex Wild's insect adventures. (Isn't the Internet great?)

2012-02-05T20:54:00.000Z

I feel like I haven't made enough science blogs of late. One reason for this is that there are others out there doing it so much better! So, instead, until I have something interesting to say, I thought I'd do a quick blog about a science blog.

My friend, Joel, who works on ants, first told me about Alex Wild. This guy takes amazing insect photos, one of which can be seen here from his blog Myrmecos. (I did ask first - because his photos are so cool, Alex has had problems in the past with bloggers, and even the media, taking them without permission.)

The beastie in question is a rare Loboscelidia sp. wasp. I'm not a bug man, so to me it's just a crazy-looking critter but this is actually a really unusual find. You can read the story on Alex's blog but it's great tale of the power of the Internet and how Twitter is not (just) a waste of time filled with the inane ramblings of strangers (in 140 characters or less)! Check out the photos on Alex's website too; they're jaw-droppingly good. (And not all ants!)

The joys of Japanese Whisky

2012-02-05T11:12:00.000Z

Each year, one of my colleagues lays on a themed whisky tasting for the University wine club. In recent years, this has been timed at the end of January to coincide (roughly) with Burn's night. This year, it was Japanese whisky.

I can't say that I really knew anything about Japanese whisky prior to the tasting - to be honest, I did not even know that the Japanese made whisky. Any reservations I had, however, we're blown away when we tasted the five offerings selected.

It seems that the Japanese have been making a real effort to learn how to make quality whisky in the Scottish style, and these five could happily sit unnoticed among those north of the border. My favourite was the "Yoichi" single malt from the Nikka distillery. Smooth, warming and packed full of flavour. Unlike with actual Scottish whiskies, my favourites were not at the higher peat end of the spectrum, although that might have been just my mood on the night.

The only real negative of the whiskies was the price - though good, I cannot help but think you could get a better Scottish one for the same price. That said, the opposite might be true in Japan, and I would definitely look out for some of the local stuff if ordering a whisky in Japan.

The final element of the night was a Japanese/Burns fusion of whisky-related haiku. Unfortunately, there is not yet a collection of these but here is my effort for what it's worth:

A wine drinker sips.
Whisky on a Haggis night.
"It's good but... It Burns!"

I'm not sure whether it strictly follows the rules of good Haiku, and it's a bit unfair on the whisky, which did not burn, but hopefully it captures some of essence of the night.

Busted faith healers try to hide behind "religious persecution" smokescreen

2012-02-04T23:40:00.000Z

There's been a bit of a furore over the past couple of days after a brave citizen reported the Bath contingent of the "Healing On The Streets" (or "HOTS") movement to the Advertising Standards Authority (ASA) for making the unsubstantiated claims that God could heal you (on the street) through them. You can read the actual account of the complaints made at the blog of the complainant, Hayley Stevens.

Hayley is an atheist but, more importantly, a skeptic and complained on skeptic grounds that HOTS were misleading people with claims that cannot be supported by evidence and could detrimentally influence the weak and vulnerable away from authentic medical treatment. ASA agreed and have ruled that HOTS have to remove these claims from their advertising material.

Do HOTS respond with tales of clear and unequivocal healings performed by HOTS teams? No. Of course, HOTS had the opportunity to counter the complaint with convincing evidence that supports their claims but they have none. (Their website contains "Hot Stories" of successful healings - presumably their most convincing stories. Judge for yourself how anecdotal they both(!) are. Why is it that God never regrows an amputated limb or anything else unambiguous and unattributable to placebo?) Instead, they try to deceive and grope for support by playing the "religious persecution" card, totally inappropriately, including a news article disingenuously entitled "UK Advertising Standards Authority try and stop HOTS Bath from sharing the Gospel!"

Well, if HOTS cannot - or will not - tell the difference between "sharing the Gospel" and making unsubstantiated claims, then I think that speaks volumes about both the evidence for their Gospel message and their true motivation for "healing" strangers on the street. (I thought the Gospel was about forgiveness from sin, not healing from physical ills. I obviously did not pay enough attention in Sunday School.)

It's not just HOTS, though. Bible Reflections also ran the story, saying that the ASA "would now like us to recant our Christian faith in the Bible". No, they wanted you to agree to "not make claims which state or imply that, by receiving prayer from [HOTS] volunteers, people could be healed of medical conditions." They are welcome to believe it, they are just not allowed to push those beliefs on others without evidence. Like HOTS themselves, BR went for a misleading headline, claiming that ASA were "trying to stop Healing on the Streets". Again, no. It was not trying to stop them entirely, just to stop their unsubstantiated claims.

The complainant - an individual, not a group, as claimed by Bible Reflections - was not complaining on anti-Christian grounds but rather on anti-non-evidence-based medicine grounds. And quite rightly, too. Anecdotes are not evidence. If people wish to seek out faith healing then that is their business. However, accosting the vulnerable in the street and encouraging them share personal matters with strangers in the hope of unproven potential to be healed is a different matter, and wrong. It would be wrong if it were Homeopaths, wrong if it were psychics and wrong if it is faith healers.

But isn't it all harmless, even if it doesn't work? HOTS are not making money or trying to con people, like psychics or homeopaths.

Well, in some ways, I think faith healers are even worse. HOTS may think that faith healing is harmless because they believe it. But who do they believe God heals? Those with faith, presumably. And what is one of the "reasons" that faith healing does not "work" when it fails? Insufficient faith. How do you prove your faith in God's healing? By avoiding conventional treatments. Sure, HOTS may not explicitly encourage this but it would be very naive to believe that it is not a subtext. Almost as bad, what's the other "reason" it doesn't work? "God's will." Given that most people are not healed - either that or their "Hot Stories" editor needs sacking - what HOTS are really doing is going around implying that people are sick either because they lack faith or it's God's will. That's wrong on many levels.

No one is asking you to "recant your faith", HOTS, just to stop meddling and misleading people with your unproven beliefs. I've seen these people before in Winchester and felt annoyed but not had the guts to do anything about. Well done, Hayley Stevens.

In support of TripAdvisor

2012-02-03T18:50:00.000Z

So, it seems that TripAdvisor has been in the news recently for being unregulated and not being able to assert with 100% confidence that reviews are genuine. Furthermore, certain establishments have been caught encouraging fake favourable reviews. (Not just TripAdvisor.)

I have no doubt that both of these are true but, at the same time, I have personally found TripAdvisor to be pretty reliable. Successes include Kali Mirchi in Southampton, The Dandy Lion in Bradford-on-Avon, and Yak Yeti Yak in Bath. I've also contributed a few reviews myself, so I know they're not all falsehoods.

Most things in life are open to abuse by the devious and determined that lack the scruples of better (wo)men but let's not throw the baby out of the bathwater. Long live TripAdvisor and all who sail in her! (You can read their response to the ASA here.)

Kali Mirchi, Shirley a top Indian restaurant

2012-02-02T22:58:00.001Z

Southampton has quite a lot of restaurants and is particularly well-endowed with good Indian restaurants. Fortunately for me as a curry lover, a whole bunch of the best Indian restaurants are within spitting distance of where I live, Shirley, and work. (Well, spitting distance for a bionic camel. And don't call me Shirley.)

Near the University on Burgess Road is Kairali, which is a great South Indian restaurant. (One without a website it seems.) A bit further along the road, on the corner of Hill Lane and Winchester Road, is Jehangir, an Indian and Bangladeshi restaurant and takeaway. Both are well worth a visit and both have their own charms but I am not going to say any more about either right now. Instead, I want to sing the praises of Kali Mirchi in Shirley - partly because it is long overdue, partly because I have just had a delectable Kali Mirchi takeaway for my dinner.

This place first caught my attention when a friend revealed that it was the #1 restaurant in Southampton, or possibly even Hampshire, on TripAdvisor. (It's currently #2 in Southampton, having been knocked off the top spot by another Indian restaurant, which I am yet to visit.) I think that the first time I went was when my brother came over to visit from Dublin in late 2010. I went back twice more in the next couple of weeks. It was that good.

The dish that really blew me away - and still a favourite - was the Chicken Tikka Malaidar. This is a spicy(ish), creamy, spinach dish; something that I don't think I've seen elsewhere and certainly hadn't tried before. (It's the green one in the picture, which is actually a greedy takeaway portion from two or three weeks ago!) The deliciousness of the Malaidar (also great with lamb tikka or paneer!) has sometimes made it hard to order other things but I may have a new favourite with the Tawa Murgh, "shredded chicken breast cooked on a hot plate with bell peppers in a smooth onion and tomato sauce". (It's the one on the other side of the mushroom rice in the picture. Fantastic Peshwari naan on the far left.) I also heartily recommend the Kadhai - with paneer, if you like Indian cheese. Mmmmmm!

I've now eaten in several times, in large groups and small, and got a few takeaways, both collections and deliveries, and it has always been great. The all-you-can-eat buffet lunch isn't bad, either. (Although I don't think you get Malaidar or Kadhai - at least, there was none the one time I have been at lunchtime.)

I do have one caution, however - don't order the Chicken Tikka Masala! At least, don't order it if you like the generic British coconut-rich Chicken Tikka Masala that (understandably) is Britain's favourite dish (allegedly) and is emulated by pubs and supermarkets across the land. Kali Mirchi, for whatever the reason (presumably the speciality region of India of the restaurant, or possibly even the authenticity of the food) is not that kind of curry house. To be honest, though, there are so many interesting and tasty dishes on the menu, it would almost be a crime to order Chicken Tikka Masala! (The same actually applies to Jehangir. If I fancy Chicken Tikka Masala, I tend to get it from somewhere a bit more "generic".)

In addition to not ordering Malaidar today (I went for Tawa Murgh and Lamb Biryani), I also made one other break from tradition today. I don't normally have wine with curry but there was a bottle of McGuigan Bin No. 528 open, so I figured I have some rather than the traditional lager. It was good! I think I will have to experiment more with curry and wine in future.

Translation UK 2012 website now live

2012-02-01T17:11:00.000Z

The website for the Translation UK 2012 conference is now live:

A meeting bringing together researchers in translational control and other aspects of mRNA metabolism.

Tuesday 3rd and Wednesday 4th of April at the University of Southampton

Online booking is not quite ready but the registration deadline is Feb 20th, so start planning your submission now if you want to come!

The Cabbages of Doom: only 99p from iBooks!

2012-01-31T23:21:00.000Z

At some point, I am going to have to get to the bottom of the slightly wayward pricing of the different formats for The Cabbages of Doom. The good news is that it's only 99p from the Apple iBooks store. (Free sample chapter PDF here.)

Students, answer the question! (And other exam tips)

2012-01-31T13:33:00.002Z

Every year when I mark exam scripts, I am surprised by the number of students that fail to recognise the single most important aspect of an exam answer: it should answer the question! Importantly, questions are rarely (if ever) "Write everything you know about subject X". If, therefore, your answer to a question related to X is to write everything you know about X, you are not demonstrating understanding - quite the opposite.

For example:

"Discuss the role of point mutations and duplications in the evolution of a protein family of your choice."

This does not mean:

"Write everything you know about point mutations and duplications and occasionally mention a protein family as an example when you can."

If you are not discussing the evolution of your protein family - or explicitly providing background material - you are not answering the question.

As a marker, I do not enjoy giving out bad marks. It is especially frustrating if the answer is long and most of what was written is right. Marks cannot be given for just being right, though. Otherwise, people could just write about whatever they wanted in an exam, which would defy the point somewhat.

The same advice applies to diagrams/figures. Don't just reproduce a figure from a lecture because it relates in some undefined way to the topic being examined. Draw a figure to illustrate a specific point. Better still, customise a figure from a lecture - or even create a totally new figure yourself - to illustrate a specific point. Then draw attention to that point by citing the figure at the appropriate point in the text. Don't just hope that I, as a marker, will make the right connection. Of course, I know how the figure connects to the topic/question - I set the question! I want to see whether you know! Unfortunately, unless given evidence to the contrary, I will have to assume that you do not.

Finally, please re-read your answer at make sure that, at the very least, sentences make sense. Exams are your opportunity to demonstrate what you know. Returning garbled nonsense is not a good way to do this. (Unless, of course, garbled nonsense is an accurate representation of what you know, in which case you have other problems!)

Science nay-sayers, why the rush?

2012-01-14T19:34:00.001Z

I get annoyed at the repeated premature announcements that scientific breakthrough X or Y has not yielded the benefits it promised. This week's Nature Biotechnology, for example, features an editorial entitled "What happened to personalised medicine?" with the tag line:

"Personalized medicine falls a long way short of the predictive and preventative healthcare paradigm it once promised."

Notice the past tense? "It once promised." Personalised medicine as a concept has failed, apparently.

The article then says:

"In some respects, 2011 was a banner year for personalized medicine. Academic medical centers began to demonstrate the feasibility of routine clinical genotyping as a means of guiding treatment selection in oncology. The US Food and Drug Administration released its companion diagnostics draft guidance. Sanofi, Pfizer and AstraZeneca signed deals with Medco and WellPoint for access to their large databases of patient data. Cancer Research UK's Stratified Medicine Programme was launched to demonstrate how genetic tests can be used to match National Health Service cancer patients to treatments. And two new targeted oncology therapies, Roche/Genentech's Zelboraf and Pfizer's Xalkori, were approved in conjunction with companion diagnostics for BRAFV600E and structural variants of anaplastic lymphoma kinase (ALK), respectively.

All are no doubt important steps, but illustrative of a rather pedestrian form of progress in personalized care rather than a march to the future."

So, it's not that it's failing to deliver anything. It's just happening too slow. The same thing happened with the Human Genome Project (HGP). This was "completed" less than a decade ago but people have already proclaimed that it has failed to deliver because we haven't been overwhelmed with a deluge of new HGP-derived drugs. The average drug development time is 10-15 years, I think, and that's when you already understand a fair amount about the target. So, even if the genome project truly was "complete" then it is still unrealistic and unfair to have expected it to already have yielded dozens of new therapeutics, even if you ignore the fact that novel targets arising from the genome project are, by definition, going to start off with practically nothing known except the sequence.

Annotation is still ongoing but the current state is over three billion nucleotides, approx 21,000 high confidence protein-coding genes plus over 47,000 gene predictions. This is a lot of data to deal with and it is naive beyond belief to think that the "answers" are just going to magically fall out in a few years. Going back to personalised medicine, the current Ensembl release has over 45 million variants and even this is not enough data. To really make sense of the role of genetic variants, we need a lot more genomes from both patient and control populations, and these patient populations need to be sensibly stratified by, e.g. treatment response. Such data is beginning to come but it is still early days, plus we still don't really know how to analyse all this data.

Biology is flaming complicated and the more we learn, the more messy and complicated it gets. Expecting us to unlock the secrets of first "The Human Genome" and then human variability in a few years goes beyond naive or arrogant, it's ridiculous.

I'm a big believer in The Human Genome Project and it really has changed the world already, even if its "promise" in terms of new drugs etc. will take many more years to be realised. (And this realisation will probably come mostly from Academia rather tha pharma.) I'm also a big believer in the concept of personalised medicine - the tailoring of treatment to the individual based on their particular genetic background. The fact is, however, that whilst this is totally the right road to be heading down, it's going to be a very long and windy road, no doubt with a few wrong-turns and dead-ends along the way.

To be fair, the rest of the editorial does then raise some pertinent points about things that need to happen to facilitate our journey down the road towards personalised medicine. These include better incorporation of the human "microbiome" - in sheer numerical terms, we have far more bacterial cells, genes and proteins in our bodies that human ones - and increased incentives for pharma companies to develop diagnostics as well as treatments. I just wish that the whole thing hadn't been given such a negative spin from the outset. It seems that with live in a world where everything needs to be over-hyped initially and then over-criticised when it doesn't live up to the over-hyping. I say, stop that: it's silly.

21st Century Referencing

2012-01-14T13:37:00.001Z

One of the new issues that I am beginning to see in undergraduate project work is uncertainty regarding how to cite various atypical sources. In my day [gets out pipe and smoking jacket], the most tricky source was a book section or occasional website. Now, though, it seems that podcasts and Youtube videos etc. are being added to list of legitimate and useful sources of information and opinion. Fortunately, help is at hand. The library staff at Anglia Ruskin University have made a really useful Harvard System of Referencing Guide [1] containing all manner of source types and the required information for citations thereof. This is the best website of this kind I have seen and well worth bookmarking if you have to deal with this stuff regularly.

1. Anglia Ruskin University, 2011. Harvard System of Referencing Guide. [online] Available at: <http://libweb.anglia.ac.uk/referencing/harvard.htm> [Accessed 14 January 2012].

Damn fine Dalmatian Dingač

2012-01-14T13:12:00.000Z

Yesterday was the first tasting of the Year for the University of Southampton Wine Club. The tasting was "8 Dalmations":

"The 2012 inaugural wine tasting will bring back fond memories of summer warmth and sun-drenched picturesque shores of the south Adriatic Sea – and hopefully this setting can be recreated by tasting the wines typical of that region: Pelješac peninsula and Korčula Island. Already the ancient Greeks grew vine there and after a brief exile in established wine-making regions of the old and new world more and more wine-growers and makers return to Croatia, only to express their newly polished skills in exciting wines.

We will experience 3 white wines from the Korčula vinogorje (typical/registered region), a relatively green island with rolling hills, famous also for being the home of Marco Polo. In contrast, northern Pelješac is characterised by wind swept escarpments and small villages. Grapes barely survive what nature and the gods throws at them, but for the wine-lover the efforts of hard working small wine estates can be very rewarding, and we will taste 5 reds from the Pelješac vinogorje."

This was a great tasting that embodies all that is good about these events: good company, good nibbles and an interesting selection of wines that I would not normally have access to nor think about trying. (Too be honest, I had never heard of any of them!)

The stand-out discovery for me was my enjoyment of the Dingač red wines. We sampled two robust reds (14.3% and 15% vol!) and a dessert variety, and all three were very tasty. My personal favourite was the 2006 Matuško (right) but others favoured the 2004 Skaramuča (centre). They have an interesting flavour, with a lot more cherry versus the berries of the red wines that I normally go for. Sadly, I think they are only really available in Croatia but it is on my holiday destination wishlist, so I will just have to make a mental note and bide my time!

A flowchart for choosing your religion

2012-01-11T21:55:00.003Z

I'm not sure where this originally came from but it's a classic! (I'm not rich and insane.)

A month (or so) with iPlan

2012-01-11T21:37:00.000Z

At the end of November, our iPlan energy kit arrived. With one full month under our belt, I thought it timely to give an update.

Initial experiences were a bit mixed as the website was done for quite a while but, right from the outset, the ability to monitor energy usage was really useful and reminded me to switch off lighs etc. It was also interesting to see how much energy some of our light use. (Not surprisingly (but still disappointing), the worst offenders were the brightest, most useful ones!)

Less useful at this stage is the daily target. This started off at a fairly reasonable 8.0 kWh per day (although I'm not sure how this was determined) but went down dramatically when I switched to our predicted usage from Scottish & Southern Electric (SSE). You can see this on our monthly usage chart for December, below, where the target line drops sharply on the fourth:

This is clearly nonsense, as the only days that we meet are target are those that either or both of us are away and thus (practically) nothing is being used. (The big spikes caused by extra laundry each side of trips is also clearly visible!) Having contacted SSE, I have learnt that this prediction is based on meter readings and because our reading-before-last was a massive over-estimate, our last period's usage was practically nothing. It should, I am told, sort itself out with our next meter reading later this month. Time will tell. (I still think it is a bit silly that you cannot over-ride their estimate and set your own target; you can set it for a percentage under their prediction but not over.)

Fortunately, even though we can't set a sensible target, we can still feel good about ourselves with some of the other comparisons available, such as the "LikeMe" comparison with "similar homes". It's not clear how a "similar home" is defined but I suspect, given how well we appear to be doing, it does not include a comparison of the number of occupants. (Either that, or the average couple out there are big consumers!)

You can also compare your usage with all iPlan users, although I'm not really sure how much this tells you:

Still, it makes electricity billing more interesting!

Just 24 to go until a big round-number milestone

2012-01-06T09:43:00.000Z

I love geeks! Happy cartoon 1111101000, xkcd!

Oar House (inspired) cod, chorizo and potato one-pot

2012-01-05T21:54:00.000Z

In December, I made the fantastic discovery that The Oar House website has a delicious-looking selection of recipes. Tonight, I tried one out - or a variant thereof, at least - and, whilst not up to the standard of the restaurant itself (a chef issue, I fancy), it was indeed delicious. Errors on my part not withstanding, it was also pretty easy.

The recipe selected was Haddock, chorizo and new potatoes, which appealed to me both because I love fish, chorizo and potatoes but also because it is done all in one pot! Due to availability when shopping, I made it with line-caught cod rather than haddock and, for matters of taste, switched the dry sherry for dry Martini. (Next time, I might use wine.)

Cooking this was easy but, at the same time, highlighted some of my failings (or "room for improvement") as a chef; one feature of the Oar House recipe is a certain absence of key instructions that an experienced chef would know, such as pan selection (it's called a sauté pan for a reason, duh!) and temperature.

First, fry the chorizo for a couple of minutes in the oil - use a sauté pan (or frying pan lid) rather than a saucepan (as I did). Add the spuds and 3 tbsp sherry/martini/wine, put the lid on and cook for 10-15 mins. Stir occasionally to prevent burning. (I was a bit late realising and had to replace a few bits of burnt chorizo. My pan selection also added a few extra minutes before the potatoes were tender.

Once the potatoes are tender, add the tomatoes and parsley and lay the fish on top, add another tbsp sherry/martini/wine then cover and cook for 5 mins. Because of my pan selection, this was not long enough, so I ended up flaking in the fish and giving it a couple of extra minutes to heat properly. (That was ultimate the plan for serving, anyway.)

Despite the hiccups along the way, it was delicious. Perhaps best of all, I am pretty sure that I could do it better next time!

Great Fluorescent Proteins

2012-01-05T13:50:00.004Z

One of the benefits of teaching (and its ugly sibling, marking,) is exposure to interesting bits of science that I would normally not have the time and/or inclination to find out more about. One such thing is the most excellent - and Nobel Prize winning - Green Fluorescent Protein (or "GFP").

I am not a structual biologist and often find myself getting a bit bored at the minutiae of structural details that excite biochemists at lunchtime seminars but I must admit that I find the structure of GFP to be a thing of geeky beauty. GFP has what is known as a beta barrel or "can", which is comprised of a number of beta strands (a particular arrangement of protein strands that make a kind of sheet) wrapped into a tube (or barrel). Within this barrel, sits some modified amino acid residues called the "chromophore", which are responsible for the fluorescent aspect of GFP. This is then protected by caps at the top and bottom of the barrel.

I don't feel too bad about liking this - Julian Voss-Andreae liked it enough to make a sculpture!

GFP works by absorbing light of one wavelength and emitting light of another. In the case of the original GFP from jellyfish, UV or blue light is absorbed and green light is emitted, hence GFP. (The blue light itself is generated by another protein (aequorin), which is "chemiluminescent" and emits light in response to a chemical stimulus - in this case, a release of calcium in response to external stimulation. GFP and aequorin were first isolated from "squeezate", which is what you get when you pass jellyfish through some gauze!)

Other colours also exist, both in nature and as a result of tinkering by various scientists over the years. As well as enabling some fun "lab art", such as this "San Diego beach scene" created in the lab of Nobelist Roger Tsien [Artwork by Nathan Shaner, photography by Paul Steinbach] made using eight different fluorescent proteins, including a Red Fluorescent Protein (RFP) from corals that I have done a bit of work on. (I'll save that for another time.) I love the names of some of the colours too: "BFP, mTFP1, Emerald, Citrine, mOrange, mApple, mCherry and mGrape". (Mmmmmm.... Cherry.)

This diversity has led to some amazing research tools that have in turn led to some amazing discoveries, hence the Nobel prize. There are far too many to list here but one such technique that I make indirect use of in my own work is "FRET": "Fluorescent (or Förster) Resonance Energy Transfer", which is used for (among other things) detecting likely protein-protein interactions. It works a bit like the original GFP in jellyfish, using the emission of light from one protein to trigger fluorescence in the other. Unlike the jellyfish, however, FRET uses a GFP-like protein for each step. Each FP is attached to a different protein of interest and light is provided that excites the first protein. If the two proteins get close enough, such as if they interact, the emission from the first protein excites the second protein and the emission spectrum shifts, allowing the interaction (or, more accurately, proximity) to be detected.

Perhaps more fun are some of the recreational uses of the GFP family of proteins, such as these "GloFish", which demonstrate the power of genetically modification in a fun and friendly way. (Take that, Pope!)

These guys are zebrafish (shown to the right in their normal colours) that have been genetically modified to express different FPs, causing them to fluoresce under different light. (White light works but blue light is best, I think.) You can see videos of them swimming about here. The original goal was to create fish that could be used for detecting environmental pollution etc. but, given restrictions on releasing GM animals into the wild, I think that fun fluorescing pets is probaby a more practical (and lucrative) application! Other GFP'd animals (usually for scientific reasons) include mice, monkeys, cats, pigs and, of course, Alba the GFP albino rabbit, although I am always a little wary of colour enhancement for images of such things. I'd still like to have one as a pet, though!

Mirror Lake - yet another cracking Marlborough white

2012-01-02T20:13:00.000Z

Wine this Christmas was a rather delicious New Zealand Sauvignon Blanc from Mirror Lake in the Marlborough region. Another wine that hits all the right notes for me: crisp, fruity and refreshing. Great stuff.

New Year, New Calendar?

2012-01-01T22:17:00.000Z

Last year, I posted about Isaac Asimov's suggestion for a new rational calendar, freed from the idiosyncrasies of the current dominant Gregorian beast.

Since then, I have come across an even better suggestion that does not include the wholesale renaming of everything that was part of Asimov's vision. (Today would be A-1, for example, not January 1st.) This is the Hanke-Henry Permanent Calendar, described in more detail at wired.com.

Rather than getting too het up about revolutions around the Sun, this calendar focuses on being functional and consistent for users. Like the Asimov calendar, it features four equal quarters, each of 13 weeks. In the Hanke-Henry calendar, however, these quarters are subdivided into a repeating three month cycle of 30 days, 30 days and 31 days. In both cases, there is an extra day (and a quarter). Asimov adds an extra "Year Day" each year and evens the rest (I think) with Leap Years as present. The Hanke-Henry solution is, in some ways, more elegant - an "Extra Week" every 5-6 years, which covers both the extra days and the leap years.

The best thing about - and, from what I can gather, the motivation behind - the Hanke-Henry Permanent Calendar is that each day always falls on the same date every year, hence the "Permanent".
As the architects point out, this means that sports schedules and term times etc. only need to be drawn up once and can then be kept from year to year, unless their content actually changes, as opposed to the current situation where these things must be drawn up afresh.

The big question of course, is would it catch on? Would people feel happy to use it? Well. it seems that I am not alone in thinking that this kind of thing is a great idea. Although by no means scientific, the poll on the website suggests that yes, people would use it - approx. 62% of them, at least.

Will it ever happen? I doubt it. Still, a nice idea.

Veg Every Day: Kale & Mushroom Lasagne

2011-12-31T17:00:00.000Z

Due to various trips and things over the past few weeks - not to mention Christmas - we have not been eating the best of late. When I say "best", what I mean is "healthiest" - the food has been largely delicious, just a little to high in meat, fat, sugar and other yummy things. As a result, one of our newish Year's resolutions is to eat more veg.

To kick-start this endeavour, one of my Christmas presents for my wife was the River Cottage veg every day cookbook. This week, we tried one of the dishes: kale and mushroom lasagne.

The recipe itself is really easy: boil some kale for a few minutes; fry some shrooms with butter, garlic & thyme; make some bechemel sauce (milk, flour, butter, bay leaf, peppercorns, onion); layer up with lasagne sheets (bechemel - lasagne - kale+bechemel - lasagne - shrooms - lasagne - bechemel - Parmesan); cook for 30 minutes. Delicious!

The original recipe was for six but we scaled it down a bit for four and increased the shroom:kale ratio a bit too. I'd also be tempted to try it with spinach some time instead of kale, although the crunch of the kale provided great texture. The leftovers were good too!

The Oar House revisited: still fantastic

2011-12-29T22:26:00.000Z

One of the good things about having relatives in Dublin is that I get to go back from time to time for visits. As my in-laws live there, this includes Christmas - approx. every other Christmas, as it happens. (Not through planning, as such, but it just seems to work out this way.)

Christmas away from home seems to feature even more tasty food and drink than Christmas at home. This year, we rounded things off with a lunchtime visit to The Oar House in Howth on the way to the airport. I've posted about The Oar House before, four years ago. It was one of my favourites then and it still is.

The only problem with The Oar House is choosing what to have, as everything is so good! Fortunately, they have a solution for this too: a delicious and versatile tapas menu that can be ordered as a starter, scaled up for a main course or, as we did, shared among a few of us.

In addition to the must-haves - smokies and prawns of some variety (we had Prawns Pil Pil) - we had the calamari and a trio of dishes from the specials menu. Two of these had a decidedly Mexican theme - grilled prawn nachos and salmon tostadas. Tasty! The third was something that I would not normally order but was very glad that we did: crab claws. These were the biggest and most delicious crab claws that I have ever tasted, in yummy garlicky goodness. Amazing stuff.

Perhaps most exciting of all, whilst visiting The Oar House website for images, I discovered that they have a recipes section. Yummy! Watch this space for more on that. (When I feel brave enough to cook fish.)

30% sale at Lulu - today only!

2011-12-26T10:46:00.000Z

That means you can get The Cabbages of Doom for just £1. Bargain!

Santa's reached Germany!

2011-12-24T22:53:00.002Z

Thanks to Google and NORAD teaming up, I have been tracking Santa's progress this year. He's reached Germany now, so time for bed soon, I think!

Update...

Of course, the actual NORAD Santa Tracker website was even better. You can even watch videos of Santa visiting various major cities and landmarks. Good to see some of the US defence budget being spent on stuff for the good of mankind.

Beyond Busted: Charlie Simpson and the fantastic Fightstar

2011-12-22T10:58:00.000Z

My most recent big musical discovery is that of Fightstar Fightstar, a British rock band whose most famous member is probably Charlie Simpson, formerly of Busted.

I must confess that I don't really know a lot about Busted. My one real experience of them is hearing them sound-check, or possibly rehearse, Year 3000 prior to a gig in Dublin. What I heard was not pretty but this may have been more to do with me being outside the stadium (Lansdowne Road, as it was then,) and/or the fact that they hadn't got their sound set up than a reflection on their talent. Either way, the sound-bite combined with my natural distrust of teen "Pop punk", meant that I have avoided them ever since. This makes the discovery of the sublime Fightstar all the more surprising, as the lead member is none other than Charlie Simpson, formerly of Busted.

I can't really compare Fightstar to Busted but I suspect that the sound is very different, as Fightstar kick out proper rock tunes with heavy guitar and the occasional screeching rock scream, in addition to the more melodic singing that dominates. I find it hard to pigeon-hole bands into genres and so I am not really sure to what sub-category of rock Fightstar belong. (Wikipedia editors have opted for "alternative" or "Post-hardcore", whatever that means.) I would probably just say "Rock" or "Modern Rock", for this is no Bon Jovi either.

It was probably a short customer review on EMusic that made me take the step of having a listen. To paraphrase, it said something along the lines of:

if you like Rock music, you will like this.

I would have to agree 100%. I think that wherever you sit on the rock spectrum, Fightstar offer something. If, like me, you sit somewhere in the middle and enjoy music and influences in all directions from Pop/Rock to Metal, you will love them. The two albums that I have are the later One Day Son, This Will All Be Yours (2007) and Be Human (2009) and, if recommending just one, I would be hard-pushed to choose. (Probably "One Day Son, This Will All Be Yours", especially as you pick up a two-disc version for a bargain on Play.com!) They're both currently available from Emusic, if you want a bargain.

The other factor that made me try them, quite surprisingly, was listening to Young Pilgrim, the more recent solo album of Charlie Simpson. This is a very different beast, and is proper singer-songwriter acoustic pop rock along the lines of Jack Johnson. It's good stuff, though, and definitely marks Charlie Simpson out as an accomplished musician and singer. For me, this was important, as I find that I cannot look beyond bad singing, however good the music is. (The Wildhearts are the possible exception but their singing is not too bad and their tunes are very good!)

When snowmen go bad (Christmas graffiti)

2011-12-19T11:46:00.000Z

Our walk to work takes us through Southampton Common, which features a pedestrian underpass that is a popular spot for the local graffiti artists - and many of these guys are artists, not just vandals who want to tag their turf. The fruits of their labours are not always to my taste but this one, snapped a couple of weeks ago but happily not yet sprayed over, is one of my favourites.

The Cabbages of Doom: Kindle Edition out now!

2011-12-18T12:16:00.000Z

My fictional folly is complete (for now) and The Cabbages of Doom is now available in a Kindle Edition too.

I thought it was going to be priced at £1.49 for the UK market but there seems to have been a glitch somewhere. I did find it a bit odd that the cheapest UK price allowed was lower than the USD or EUR prices. Oh well. If the extra 22p puts you off, the PDF and ePub versions are still only £1.44.

Over Christmas, I shall hopefully blog the full e-publishing experience. It's been interesting and I am sure I could do it better next time! (Content aside, that is.)

BBC Planet Earth/Blue Planet - Deep ocean creatures

2011-12-18T12:08:00.000Z

Thanks go to the Why Evolution is True website for highlighting this video. Amazing footage of some weird and wonderful critters. (Planet Earth and Blue Planet are separate series, for those (like Michael at WEIT) wondering.)

The Cabbages of Doom, PDF version and free sample now available!

2011-12-17T17:41:00.000Z

I am happy to report that a PDF edition of The Cabbages of Doom is now available along with a free sample chapter (PDF). Try before you (maybe) buy!

Polar bear dimwits should cut Attenborough (& BBC) some slack

2011-12-14T23:40:00.002Z

Yesterday, I read something in the "i" that made me angry. For anyone who has missed it, presumably by misfortune of not having access to BBC, Frozen Planet is an amazing series, with spectacular footage and Sir David Attenborough at his narrative best. But, it seems, not everything on the show was quite as it appeared. Some of the polar bear footage of mother and newborn cubs was shot in a zoo.

No, this is not what made me angry. It seems that, for some strange reason, this revelation - revealed by the BBC themselves on their website - has cause furores in some circles, with cries of deceit. The Arts Editor of "i", David Lister, sticks in his own oar, saying: "An explanation on the website is simple trickery. The explanation for a television programme must be made within that television programme." The only insight provided here is that David Lister is a man with a very poor sense of perspective. Apparently, "i" stands for "idiocy" or "ignorance".

The show features a "Freeze Frame" section at the end, where they show some of the behind-the-scenes action getting the footage. For anyone paying any attention, it is blindingly obvious that the footage of animals is sometimes used out of context to aid the narrative. It would not be anywhere near as interesting otherwise. But this is not deceit, or "simple trickery", it's just good film-making. Don't tell David Lister, but some of the action used time-lapse photography - the sun didn't really speed up and circle the Earth in a few seconds.

Seriously, folks! Anyone who takes umbrage at this and thinks it should have been somehow made obvious in the program has missed the point of nature documentaries big time and doesn't deserve the genius of Attenborough and the BBC wildlife units. Ridiculous.

PS. More great polar bear stuff from the BBC here.

The Cabbages of Doom has an ISBN!

2011-12-10T18:16:00.000Z

The blogging has been light of late to due excessive busyness. One of the contributing factors to this has been the e-publication of The Cabbages of Doom through Lulu. I think the book itself will take a bit of time to filter through the system but it has an ISBN number now and everything!

I've also worked on a bit of cover art for the new edition. It's not a masterpiece but is certainly better than the previous, blank cover.

The story itself is essentially unchanged, but I have modified the text here and there, both to correct a few typos and remove a few bits that might not go down so well with a more general audience. (Or made me cringe at my ten-years-younger self!) There was also some reformatting for e-Readers to be done. Overall, though, I am happy.

It will be on sale for the princely sum of £1.44, which works out at 16p a chapter (or about 3p per 1000 words). Should you buy it and hate it, let me know and I will donate the portion that goes to me to a charity of your choice. If, on the other hand, you think it's a bargain, please make a donation to Cancer Research UK or the World Wildlife Fund. (I'm not endorsed by either, in case it's not obvious!)

Playmobil goes recursive

2011-12-04T15:25:00.001Z

During a spot of Christmas* shopping, I came across this gem from Playmobil - it's a Playmobil Playmobil delivery truck! My only regret is that the lorry does not come with little boxes of Playmobil Playmobil delivery trucks itself: that would be truly recursive! (A bit of a missed opportunity in my book!)

[*On my iPhone, my big thumbs typed "Christmad" at first. Seems somehow appropriate when town reaches peak busyness!]

Carcassonne: still the best board game in the world

2011-12-03T21:38:00.000Z

Today, we cracked out Carcassonne for the first time this festive season.

For anyone not familiar with Carcassonne, it's a tile-laying strategy game in which you build up roads and cities and score points for having more of your men (or "meeple") associated with them when they are completed. In my opinion, it has the perfect balance of strategy and luck. The tiles are drawn at random, and so a lot can hinge on getting the right one at the right time. At the same time, however, there are clearly strategic moves to be made. Playing with more then two players can even lead to some interesting cooperative behaviour - and occasional back-stabbing - as temporary alliances form over shared goals. You can obviously sabotage other people's strategies too (a favourite move of mine is to hijack other people's cities) but I don't leave a game of Carcassonne feeling as picked on as after a game of "Settler's of Catan". I also think that the length of the game is just right. "Puerto Rico" is another great game by the the same people (I think) but I always end a game feeling like it was over one or two turns too soon.

Today, we had a bit of a rare occurrence: a finished game without any holes in the middle! When you lay tiles, roads have to match road, cities match cities and fields match fields, so clearly if you get a hole where a specific tile needs to go, you will not always come across it. Normally we play with "The River" expansion, whereas today we just used the basic starting tile, so that might have contributed to the tightness of the layout. Anyway, the end result was quite pleasing, if such things please you. (They please me!)

I'm obviously not going to go through the rules here. (See the Carcassonne Wikipedia entry for a summary. In reading this entry, I just learnt that they have changed the rules for farmers and fields, plus there's now an iOS Carcassonne App, which I will have to check out!) Suffice it to say that if you like board games - or someone you know does - and you are short of Christmas present ideas, you can do a lot worse than getting a copy of Carcassone.

If you already have Carcassonne, I can recommend a couple of the expansions, which are particularly good: Inns and Cathedrals and Traders and Builders.

HTML ASCII code

2011-12-03T16:26:00.000Z

For those of you, like me, who have to write posts in HTML from time to time, a good reference of HTML coded for special ASCII characters is invaluable. The best I have found so far, is on the website of Ed Lazor (www.edlazorvfx.com). No frills, no fuss, just lots of useful HTML codes. (Although he did neglect the interrobang, "‽" - ‽.)

Hoorah for NAR!

2011-12-03T14:44:00.000Z

I have a bit of a soft-spot for Nucleic Acids Research. This is partly because one of my colleagues is one of the Senior Executive Editors, and the Editorial Manager is at the desk next to mine. It is also partly because they have been kind enough to publish five of my papers, which is more than any other journal. This week, however, it is mainly because I have just received my "thank you for reviewing" present of The Oxford Book of Modern Science Writing from Oxford University Press, an anthology of extracts from other scientists that Richard Dawkins has chosen, along with a brief introductory spiel to each one by the man himself.

Reviewing for journals is typically a bit of a thankless task and so I really like that NAR reward their reviewers with a small gift voucher for their parent publisher. It's the little things in life that often make the difference, so well done NAR!

As for the book itself... I have only read one extract so far and I enjoyed it. I'll review the book properly once I have read a bit more. Given that, until 2008, Dawkins held the Simonyi Professorship for the Public Understanding of Science at Oxford, I expect that I am in for a treat.

Festive feline folly

2011-11-30T18:41:00.000Z

It's almost December, so it's time to get the Christmas decorations ready. Arthur has kicked things off for us this year. (Not by choice, obviously!)

In the background, you can just see Mia lurking. She really wasn't sure what to make of Arthur's new attire. I'm not sure if it was the look or all the jingly bells. (Later, thanks to my wife's persistence in these matters, she got to try it out for herself.)

iPlan: geeky gadget fun with energy efficiency

2011-11-27T21:53:00.000Z

Some time ago, I signed up to the "iPlan" scheme of Southern Electric. It was not the cheapest tariff available but the idea is that you can monitor - and therefore reduce - your energy usage, and this appealed to me on several levels. Unfortunately, my iPlan energy monitor never turned up, so I emailed them a week or so ago and they sent out a new one, which arrived on Friday. Yesterday, I cracked it open and had a play.

The device itself is an "Onzo smart energy kit" and consists of two parts: a sensor that clamps on to a cable, and a wireless receiver for monitoring usage.

As the instructions implied, it's was dead easy to set up and start monitoring power usage.

Of course, setting everything up when the washing machine and dishwasher are on and consuming nearly 2,500W is probably not the most reassuring way to start energy monitoring!

It needs to collect data for a week or so before the proper assessment kicks in but it's still interesting to see what effect turning stuff on or off makes. The kettle, for example, wacks a couple of kilowatts onto the reading (not surprisingly), though not for too long. The wireless monitor is great and can be stuck in any room, making such things easy - you can pop it next to the device about to be switched on and watch what happens. I love it!

Our baseline at the moment seems to be around 15-40 watts, although there is a lot of fluctuation. I look forward to testing out a few urban myths over the current weeks, such as the old question of how much power does a TV use on standby versus on? I've already had a bit of a shock about the kitchen lights, so I think this could work as an energy saving device - I'm off now to switch off some lights!

Great and Small, Climb and Hide

2011-11-27T17:26:00.001Z

Today, we got the cat's a present of a new scratching post, as the old one was looking a bit ropey. We got them a "climb and hide" post from Great and Small, as it looked fun and they're worth it. I think Arthur likes it! As I was write this, he is now sitting on top and Mia has gone inside instead - as a black cat in a dark hole, however, she's not quite so photogenic.

My favourite thing about this photo, though, is that it looks like Arthur has climbed into some kind of strange suit in the style of Wallace and Gromit's "Wrong Trousers"!

It's a chunky mug day!

2011-11-26T10:04:00.001Z

There are very few things in life that are as consistently pleasing and comforting as a good cup of tea. As the seasons change, the nights begin drawing in and the mornings start feeling more chill, it is time to break out the big guns for tea delivery. One of my favourite mugs is this one, which was a souvenir from skiing in Breckenridge.

Somehow, it feels too chunky during the summer months but now that it's getting darker and colder, the chunkiness is somehow extra comforting. Unfortunately, I cannot read the name on the bottom to give due credit to its maker, but here it is, in case your deciphering skills are better than mine!

Another Marlborough classic

2011-11-25T11:38:00.000Z

Being a wine-drinker of limited knowledge, I have a fairly crude but effective way of sourcing new wines. When I am in the supermarket, I keep an eye out for half-price bottles of a variety I like (usally Rioja, New World Sauvignon Blanc, or some kind of Shiraz/Merlot/Cabernet Sauvignon affair) that usually costs around £10. Experience has told me that this price range seems to match the (lack of) sophistication of my palate plus the lack of extravagance of my wallet. (I'm prepared to risk a fiver on untested wine but not much more!)

Occasionally, this tactic goes a bit wrong and I bring home something rather bland, or too sweet, destined for a risotto or casserole dish of some kind. Sometimes, though, it reaps welcome rewards. One of the latter is the Sauvignon Blanc from Glenridge Point. This is a crisp, zesty and fruity wine with all the new world features that I love from New Zealand Sauvignons. I will happily add it to my exisiting go-to Sauvignon Blanc from Marlborough: Oyster Bay and Villa Maria. If you are a fan of such things... head to Sainsburys whilst it's still on offer!

TimeTreeHD: an App 2.5 billion years in the making

2011-11-22T22:09:00.001Z

I feel that one of of my weaknesses is a poor memory for facts and figures. Although I tend to learn principles and concepts pretty well, I can easily start to doubt arbitrary pieces of information. This is particularly true when the information itself is subject to change; am I thinking of the new number, or the old one?

One such situation is the age of divergence of different species. As a lecturer of evolutionary biology, this can be a bit embarrassing and awkward. Fortunately, this is not something that I need to worry about (too much) any more, thanks to the TimeTreeHD App for my iPad. Want to know when a cat and a squirrel last shared a common ancestor? (And who wouldn't?!) Simple!

It's 95.2 million years ago (Mya), plus or minus. Probably plus - the "expert opinion" is 97.4Mya. At first, it gives you the mean estimate but down the timeline on the left all the different estimates are marked. The estimates themselves come from all pairwise estimates (in the TimeTree database) featuring species from each side of the tree; cat versus squirrel, for example, includes cow (closer to cat) and mouse (closer to squirrel). Tapping for details allows you to drill down further into different age estimates and see the source publications. Sorted! Well done, TimeTree.Org! (NB. The website might be even better!)

Where do new proteins come from?

2011-11-21T22:38:00.002Z

As part of my second year lectures on protein evolution, I cover (albeit far too briefly) the topic of where new proteins come from. The most common answer to this question, is "other proteins". Gene duplication is common and happens at a variety of levels, from individual domains (independent folding units of proteins) to full length proteins, multiple proteins (on larger chromosomal stretches) to whole genome duplication, in which every single gene is duplicated.

Duplication is so important because it generates a copy that can remain essentially unchanged, performing the ancestral function, and a copy that is free to accumulate mutations. Often - usually - these mutations will ultimately disable one of the copies, generating what are known as "pseudogenes", the easily identified relics of past mutational dead ends. Occasionally, however, a new function will arise, such as the binding of a new enzyme substrate, the the reception of a different wavelength of light, and both copies will be retained.

This is fascinating stuff in itself (and I may post more on it later) but it is not what I want to talk about here. Important as they are, duplications rely on something - an existing protein-coding gene - being there to be duplicated. Where do these proteins come from in the first place? Are all modern proteins just duplicated and edited versions of a suite of ancestral proteins? Does this mean that supporters of Intelligent Design community are right and that some kind of intelligent intervention is necessary to increase the repertoire of proteins that are available?

Well, no. Far from being a statistical improbable event unlikely to ever occur, the "de novo" creation of new proteins from non-coding DNA seems to be a reasonably common event. In an article just published in PLoS Genetics, for example, "De Novo Origin of Human Protein-Coding Genes" (PLoS Genet 7(11): e1002379), Wu, Irwin & Zhang describe sixty such proteins that appear to have arisen in the human lineage since we shared a common ancestor with chimps.

This and other work in the area is nicely summarised in the same issue by Guerzoni & McLysaght in a two page article that is well worth the read, "De Novo Origins of Human Genes" (PLoS Genet 7(11): e1002381). The Wu paper itself builds on earlier work from the McLysaght lab, and they include a nice summary of the type of evidence the work looks for (see the paper for details):

It is important to bear in mind that not all of the sixty novel protein-coding genes might be "true positive" results in the strictest sense. As Guerzoni & McLysaght point out:

"The operational definition of a de novo gene used by Wu et al. means that there may be an ORF (and thus potentially a protein-coding gene) in the chimpanzee genome that is up to 80% of the length of the human gene (for about a third of the genes the chimpanzee ORF is at least 50% of the length of the human gene). This is a more lenient criterion than employed by other studies, and this may partly explain the comparatively high number of de novo genes identified. Some of these cases may be human-specific extensions of pre-existing genes, rather than entirely de novo genes—an interesting, but distinct, phenomenon."

Nevertheless, this is still the creation of de novo protein sequence, just not whole genes. Indeed, if one were to relax the criteria, how much more might this happen within proteins? Domains are frequently linked by disordered regions and also have a tendency to be flanked by intron/exon boundaries, making it quite plausible for extra exons to be picked up along their evolutionary journey. In some ways, therefore, this sixty is likely to be an underestimate.

There are other issues with identification process itself that make real estimates difficult. For robustness, authors limit themselves to stretches of DNA that are present in both humans and chimps, to rule out the loss of an ancestral protein, rather than the gain of a human-specific one. Insertions and deletions ("indels") are quite common and actually account for most of the difference (in absolute genetic terms) between humans and chimps:

"It is now common knowledge human and chimpanzee DNA differ by only 1% (more accurately, they differ in 1%of alignable regions of genome, with a further 3% divergence due to lineage- specific indels)."

It is quite possible, therefore, that a few extra protein sequences have arisen in non-coding human-lineage DNA that was deleted in the chimp lineage. The other limiting factor - and probably one that has a greater impact - is that of protein annotation. Discovery relies on proteins that are annotated as such in the human genome. The problem here is that such annotations are normally made using conservation of proteins from other organisms - something that is, by definition, lacking for lineage-specific proteins. This issue is not insurmountable and there are sources of evidence that are used but it is still likely to result in underestimation.

An important caveat remains, however. Although we have some examples of de novo proteins that appear to have function, for the majority of them we have no idea what they do, if indeed they do anything at all. A more interesting question opens up of when do you define translated DNA as a protein? Leaky transcription and translation almost certainly happens (although I have no idea how much) and so we might be detecting stuff that is really there but only rarely. Alternatively, it might be consistently transcribed and translated but have no function whatsoever - a neutral mutation that has drifted randomly to high frequency but may have no long-term future.

These questions and issues are unlikely to be resolved soon. For now, we just know that de novo creation of proteins is more common than we used to think and is likely to be a substantial source of raw material on which natural selection (and random drift) can act to evolve new functions. What the ultimate fate of these proteins tends to be, only time will tell.

It's a Small World (with Nikon)

2011-11-19T16:39:00.001Z

Whilst doing some email house-keeping today, I came across a link I sent to myself over a month ago for an In Focus article (Nikon Small World 2011) about Nikon's Small World Photomicrography Competition. This has some amazing images and is well worth a look.

The reason I think I emailed this link to my work account was probably this photo of a giant waterflea (Leptodora kindtii), which is one of my favourites (kudos, Wim van Egmond!):

I have to lecture on Eyes and Vision next semester, and therefore keep my own eyes out for good looking eye images. I am now wondering whether this particular specimen was the inspiration for
Olympic mascots, Wenlock and Mandeville:

For those interested in such things, Leptodora kindtii looks something like this and actually eats (among other things) the juveniles of the more familiar water flea, Daphnia:

(Picture from http://zoology.fns.uniba.sk/poznavacka/crustacea.htm)

The Relativity of Wrong

2011-11-19T13:19:00.001Z

Isaac Asimov was a polymath and prolific writer. As well as writing and editing over 500 books, he contributed numerous letters and articles to magazines. Although I must admit that I cannot recommend his joke books(!), I can recommend the piece he wrote for The Skeptical Inquirer called The Relativity of Wrong.

Here's a taster:

The young specialist in English Lit, having quoted me, went on to lecture me severely on the fact that in every century people have thought they understood the universe at last, and in every century they were proved to be wrong. It follows that the one thing we can say about our modern "knowledge" is that it is wrong. The young man then quoted with approval what Socrates had said on learning that the Delphic oracle had proclaimed him the wisest man in Greece. "If I am the wisest man," said Socrates, "it is because I alone know that I know nothing." the implication was that I was very foolish because I was under the impression I knew a great deal.

My answer to him was, "John, when people thought the earth was flat, they were wrong. When people thought the earth was spherical, they were wrong. But if you think that thinking the earth is spherical is just as wrong as thinking the earth is flat, then your view is wronger than both of them put together."

Although written in 1989, this is still a great piece and worthy of a read now and again, especially if challenged about trusting current scientific explanations because they are "all wrong". Take evolution, for example. Whilst the details of evolutionary theory - a body of work, not a single theory - are subject to change, we can be as certain as we are of anything that the essence will not. Although conceptually evolution can be disproven by new evidence, the likelihood of such evidence is vanishingly small and diminishes further all the time. We may not have all the details but we can be confident that evolution is not "wrong".

Resident Evil Afterlife versus The Walking Dead: Special Effects can't buy style...

2011-11-19T09:03:00.000Z

...and bad acting alone does not make a villain.

Last night, I sat down to a bit of a zombie marathon, to catch up on a bit of missed TV that isn't quite to the taste of my wife, who is away for the weekend. To be fair, I can't say I blame her, especially where some of the films are concerned.

First up, though, was a couple of episodes of The Walking Dead, series 2. I've never been a fan of the supercharged high speed zombie but the "walkers" are good old school lurchers and shufflers. The more complete specimens can run a bit but nothing superhuman. Well, nothing more superhuman than being walking dead, of course. Furthermore, the non-superhumanity extends to the walking living too. OK, so the police guys and crossbow dude are a little more accurate with their weapons than I suspect is realistic (and their survival begs the question as to why more army marksmen didn't make it) but these are well within the "suspend disbelief" range.

Because the characters are believable, you care about them. Their struggles may be quite small (each episode) but that makes them more real. When a horde (or herd?) of zombies appears, they don't whip out pairs of firearms and fire of multiple head-shots whilst flying through the air or running up walls; they hide, or run away. Because you care about the characters, there is real suspense and after a couple of episodes I felt the need for some light relief, hence my next choice...

This was the latest offering from the Resident Evil series to make it onto the small screen, Resident Evil: Afterlife. Let's compare and contrast this with the Walking Dead, for a moment. The two are loosely based on the same general premise: nasty virus turns the world's population into zombies while a group of survivors try to continue being survivors. The Resident Evil zombies are also mostly lurchers. Mostly. This is where the similarity ends, though.

Whereas Walking Dead is all about placing characters in a series of plausible scenarios (given the implausible backdrop), Resident Evil is all about placing them in increasing ridiculous and hopeless scenarios and watching them leap, somersault and spray their way out with automatic firearms. And with the death of suspension of disbelief comes a death of any tension or caring about the lead characters who, even when supposedly stripped of their superhuman powers, all exhibit superhuman powers and are bound to escape essentially unscathed. Actually, I'm being a bit unfair in what I just wrote. Sometimes they use semi-automatic or even pump-action firearms. (Plus, of course, explosives and shiny, pointy things.)

This is particularly sad, in a way, because the computer games upon which the films were based were themselves all about tension, suspense and the feeling of panicked desperation when a zombie horde was approaching. (That and incredibly frustrating controls - a double irony is the one thing you often couldn't do in the games was move and shoot at the same time!)

Perhaps I am getting old but I am sure that action movies used to at least pretend to have a story worth taking an interest in, or heroes worth caring about. If you had to make someone superhuman, you at least created an excuse, such as making him a cyborg from the future, or a "chosen one" that was able to bend the fabric of the Matrix to his will. (Maybe a bad choice as even The Matrix went The Way of The Special Effect with parts II and III.) Now it's all about ever more ridiculous and extravagant uses of "bullet time", all the time trying to ignore the stupidity of a hero that is able to nail a foot soldier right between the eyes whilst in free fall down a lift shaft but somehow manages to lose all accuracy as soon as the main bad guy becomes the target.

Then there's the bad guys themselves. In certain circumstances, the deadpan emotionless bad guy works really well. Again, think of The Terminator or Agent Smith. Most of the time, however, and certainly the case for RE Afterlife, an emotionless villain just makes a one-dimensional and dull villain. It comes across more as bad acting than bad attitude - more Arnie in Conan than Arnie in The Terminator.

Perhaps the strangest thing of all is that all these effects don't really impress any more. The Matrix, Inception and others have used all these tricks to great effect in the name of the plot. Employing them for the sake of it is not impressive, it's just lazy. Possibly worse, it actually reduces the impressiveness of the stunts. I could forgive the dodgy dialogue and bad acting in a Jackie Chan movie just to see what Jackie Chan was going to do in the next fight and think "wow"! Can anyone honestly say that, when witnessing a random hero/villain dodging a bullet in slow motion while the camera pans round, they think "wow" rather than "Matrix rip-off"? It is certainly not enough to make up for a lack of coherent story or adequate plot/character development - except (sadly) on opening night at the Box Office, perhaps. It most certainly not enough to get me rushing out to watch Resident Evil Retribution when it comes out.

On the other hand, I am looking forward to catching up with a few more episodes of the Walking Dead over the weekend.

Expelled: No Intelligence Allowed - No Integrity either.

2011-11-17T22:40:00.001Z

Some time ago, I had the saw (and blogged) the terrible, terrible film "Expelled: No Intelligence Allowed". At the time, I thought its main failing was simply that it was vacuous crap, with all the intellectual content of the Jeremy Kyle show. The coverage of Intelligent Design - supposedly the focus of the "film" - was woeful and uninformative, for example. Instead, the filmmaker, Ben Stein, decided to spend a lot of time attacking evolutionary theory, and atheistic Darwinism in particular, as naturally leading to such atrocities as Nazi Germany and the holocaust. (A classic Godwin's Law violation, if only he had restricted such crap to an Internet forum.)

Whilst in many ways it really makes no difference whether Hitler was an atheist or not, or subscribed to "social Darwinism" - any idea can be corrupted and abused, after all - the fact is that there is no good evidence to support Stein's position. Worse, if one actually researched the source material - as presumably a reputable and honest journalist surely would? - one would actually find a great deal to support the opposite view.

In a great piece, "Nazi racial ideology was religious, creationist and opposed to Darwinism", Coel Hillier at coelsblog dispels this particular myth in no uncertain terms by doing exactly that and going to the source. With quotes from original sources throughout, the author neatly knocks down the lies that Hitler was an atheist or a Darwinist and, instead, reveals him as a(n albeit twisted) Creationist and Christian.

Does this in itself mean that Christianity or Creationism are bad? Of course not - no more than arguments about Hitler being an atheist or Darwinist would make atheism or Darwinism inherently bad if they were true. Let's face it, it was obviously plausible enough for people to believe it. Nevertheless, this is one myth I would love to see the back of. It would certainly be good to remove this particular attack strategy from the playbook of certain atheist-haters and anti-evolution lie-mongers; even if you don't understand the science well enough to appreciate the lies they tell on that front, this is a clear-cut integrity failure for all to see. (I think Godwin's Law is still safe, though!)

My best status updates of 2011 (so far!)

2011-11-10T20:04:00.001Z

I'm a bit scared of Facebook Apps in general because I don't really trust them to behave but this one seemed worth the risk: My Top Status In 2010(!) I think it did a pretty good job of highlighting my 2011 (so far!) too. (Good to see a few silly ones made it to the Top 10 too.)

Mount Difficulty, Roaring Meg 2009 Pinot Noir

2011-11-07T21:39:00.000Z

A couple of years ago at the University Wine Club barbecue, we had a delicious red wine from Mount Difficulty, called Roaring Meg.

They say:

This wine exhibits a lovely mix of dark red cherry and black berry fruits along with a hint of licorice. Further complexity is gained from oak spice. The wine has a sweet berry entry which displays these same characters in abundance. Lovely ripe textural tannins rise gracefully out of the mid-palate to finish the wine. These are balanced by the wine’s acidity and fruit, to produce a long fruit-driven finish.

A while ago, we invested in a couple of bottles for special occasions. Fortunately, investing in a couple of nice bottles of wine constituted a special occasion! We cracked one of the bottles open and I am happy to report that it was every bit as delicious as we remembered! Now, I'm just looking for an excuse to declare another special occasion.

Are science and religion compatible?

2011-11-07T21:29:00.000Z

There's been a bunch of stuff flying around the net recently following the "debate" between John Haught (Catholic theologian) and Jerry Coyne (Evolutionary biologist & atheist). I am yet to watch the video, although I intend to, but I thought I would add my twopenneth to the discussion. (It will be interesting to see if I feel the same way after watching the video.)

My initial thought was that I felt a little uncomfortable with this topic as a debate - although upon further reading it seems that it wasn't really meant to be a "debate" in the usual sense. Nevertheless, there was a "for" (Haught) and "against" (Coyne) position. This implies that the answer is "yes" (they are compatible) or "no" (they are not). This, I feel, is a mistake. The answer depends on another question: which religion?

From what I have read, Haught seems to pull out some fairly standard arguments about "different types of explanation" (how versus why). This only holds if there really are different levels of explanation for the phenomena being discussed, although this weakness in the argument can be ignored when one is only interested in compatibility. Even assuming that there are different levels of explanation for the Universe (there may be no "why"), however, this only allows compatibility if the religious position stays in its different realm and does not encroach into that of science - the what and how. (Actually, I think science can sometimes also answer the "why?" questions but probably not all of the "why?" questions that religions and philosophy attempt to address.) In other words, this holds true all the time that religion is not interventionist - if god leaves no trace.

Science and religion are compatible in the sense that one can conceptualise a scenario in which a deity exists and science does not know/care. I believe it's called Deism. (One can conceptualise them, yes, but conceptualisation does not make them true.) One can also conceptualise a different scenario in which god is regularly intervening, performing miracles, healing the sick etc. This type of god would leave traces that are in the realm of science to detect - traces that we simply do not see. (As an extreme case, think Young Earth Creationism.) These religions are not compatible with science, without a lot of intellectual gymnastics that raise serious questions (for me) about the nature of such a god.

The important thing is that not ALL religion is compatible with science and, for me at the least, the religions that ARE compatible are largely pointless and/or irrelevant. I'm yet to watch the video (although I will) but it sounds like Haught knows this and is playing the game of talking about a deist-like non-interventionist god, while at the same time trying to imply that is is also true for other religious positions, such as Catholicism. (I don't mean to pick on Catholicism, it's just the one that Haught is associated with.) From what I have read, he gets caught on this in the Q&A and has to reject Catholicism (in essence, if not explcitily) to maintain his position.

It is right to attack his defence of universal compatibility and force him to explicitly recognise that not all religions - including most of the major ones - are compatible with science. On the other hand, I think the atheists need to be careful too. In "The God Delusion", Dawkins defines "God" (and hence religion) in a very particular way - Deist gods are excluded. (Who cares, or can say anything, about a god that does nothing?) This is useful for such a book and enables reference simply to "god" or "religion" but when targeting the wider population with the notion that "religion and science are incompatible", one has to remember that this is only true for some (albeit probably most) religion. Otherwise, one paints oneself into an uncomfortable corner where on has to start attacking legitimate (if, arguably, pointless) positions to maintain an over-zealous statement. (As I say, I have not seen the video yet, so I am not suggesting Coyne does this. I have seen it happen on discussion boards etc. though.)

So, are science and religion compatible? I think they can be but, personally, I would seriously question the value of the religion that was. If other people choose to believe such things then that, of course, is their decision. And here lies another area where I think atheists need to be careful. A lot of religious folks just don't care whether their religion is compatible with science. They don't care if their religion is apparently logically inconsistent. It's all part of the great "mystery" and not meant to be understood. This is not a position that I myself could maintain but they are not me. Furthermore, as long as they are not trying to structure society, impose moral values, or educate children based on these beliefs, I don't care what they want to believe.

Delete cookies?!

2011-11-06T23:41:00.000Z

Sometimes an act of simple genius comes along that just needs to be shared! Well done, Fernandez, whoever you are!

Heron's Nest Cabernet Sauvignon Pinotage

2011-11-05T18:56:00.000Z

I may not know how to write about wine but I know what I like and I like Heron's Nest Cab Sav Pinotage (2009). If you are in Ireland and like your red wine, I thoroughly recommend popping down to your local Dunnes and getting one or two of these boys.

iAnnotate: what the iPad was made for

2011-11-04T20:36:00.001Z

iAnnotate is probably the best App on the iPad, and certainly the best that I have paid for. If you ever need to read PDFs for anything other than pure interest (and even then, to be honest,) iAnnotate is the App for you.

It's great for organising your PDF library but it's the annotation tools that really make it. Notes are easy to add and the highlighter tool is great for flagging bits of interest - or pulling out quotes. You can even draw free-form, if you like. Once you're done, you can email the annotated PDF for printing etc. or just send the notes and, conveniently, the highlighted text. As an academic, this is the perfect tool for reviewing papers.

On top of all this, iAnnotate is probably the least buggy App that I have used. I'm not sure if it has ever crashed on me and it certainly hasn't lost anything I've done if it has. I initially baulked at the price but this App is worth every penny and I look forward to many happy years of iAnnotating my PDFs to come. Top stuff!

My atheism in a nutshell: no evidence, need or desire for a deity

2011-11-02T23:13:00.001Z

In a response to a comment on another post, I stated that I was a atheist because I had neither evidence nor need nor desire for a deity, in that order. Here, I thought I would expand briefly on this statement.

Evidence first, for this is what came first for me. It is also the simplest to express. Quite simply, everything I have ever experienced makes more sense to me in the absence (versus presence) of a deity. Furthermore, everything I know of the world - including religion itself - makes more sense to me in the absence of a deity. Personally, I don't rate "personal revelation" as a particularly reliable or trustworthy source of evidence. (As a scientist, quite the contrary in fact. We wouldn't need statistics otherwise.) When it comes to "evidence" for the divine/supernatural, I have simply never encountered any other kind - and even experiential "evidence" has been limited to that of other people. (And not from lack of trying, I might add.)

The lack of evidence is probably reason enough for me to be an atheist but I think it is important to acknowledge that there are other factors too. I think people often assume that atheism is a very negative and reactionary thing. Whilst I admit that my rejection of Christianity was negative, I see atheism itself as very positive. It is, I believe, embracing the true nature of the universe. There is more than enough beauty and wonder in this reality for many lifetimes of exploration and curiosity. There is power in shaping our own destiny, purpose and meaning. I just have no need to look to ancient texts for these things, although is interesting to see what ancient cultures thought. I feel like I have been there, tried that and life's too short. I prefer to spend my time pondering mysteries that might be solved in my lifetime. If I'm lucky, I might even solve some myself! This is really what I mean when I say that I don't need a deity/religion (although I also mean that I don't feel the need for one to "explain" anything nor to define morality).

It goes beyond just not needing a deity, though. I have no desire for one. And this lack of desire itself goes beyond my personal philosophical position that, if a god exists, it is either mean or insiginifacnt, and I am interested in neither. For me, a deity or supernatural element belittles and diminishes the true wonders of the natural world: the human brain; the way that unseeing, unthinking and uncaring molecules can interact to produce something as amazing as an ant, or a cat, or a person (or a bacterium etc. etc.); the way that unseeing, unthinking and uncaring cells and molecules can ultimately evolve into something as amazing as an ant, or a cat, or a person (or a bacterium etc. etc.); the truly awesome size of the Universe; the enormity of time; the insignificance of Man in the grand scheme of things but the ultimate significance of a man to a select few; true altruism. You get the idea. I know that my religious friends feel sorry for me and think that I am missing out on something but that's OK: I feel the same way about them.

In the same way, it goes beyond just not needing some externally imposed sense of purpose or meaning or, yes, morality. It is actively desirable that these things come from us, from people, explicitly and with all the limitations that comes with. No (sane) person ever claims to be omniscient. We will not get man-made ethics and morality "right" - there is no absolute "right" - but we can do our best and change our best in the light of new findings or situations. In the (hopefully immortal) words of Tim Minchin: "I don't go in for ancient wisdom. I don't believe just because ideas are tenacious it means that they're worthy." I'm proud to apply 21st Century knowledge and reasoning to 21st Century problems and come up with morality and ethics that may be flawed but can be explained and reasoned and changed if necessary.

Location:Southampton,United Kingdom

Goodbye, little dog. (Levi 1996-2011)

2011-11-01T19:00:00.001Z

Today, my dog-in-law was put down due to failing health. (My wife's dog, Levi, who lived with her parents in Dublin.) I'm not entirely sure why I am blogging about it but I just feel like the little guy deserved a mention.

This picture is possibly a little mean, as he is wearing a bow and not looking his most masculine as a result. It reveals something of his character, though, I think: (generally) well behaved and good fun. He certainly always made me feel welcome whenever I invaded his home.

It also catches him when he was a bit younger and more spritely, taken as it was at Christmas 2007. He was already 11 at this point! We're going back to Dublin this Christmas and it will be strange not to have Levi snuffing at the dining room door while we tuck into the delicious feast that my mother-in-law has laid on.

He made it to 15, or 105 in dog years, which is pretty good going but it is still sad to have to say goodbye to a friend, be they human or animal. He will be missed.

Location:Dublin, Ireland

First authorship determined by coin toss!

2011-10-31T22:04:00.002Z

This week's Science features the most complete and robust mammalian phylogeny to date, in the snappily titled: "Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on Mammal Diversification" by Jan Janečka et al.*

Apart from the beautiful figures (see the main phylogeny below), the thing that really caught my eye was the unusual superscripting of "First/Last authorship determined by coin toss." Never seen that one before! I've been on a couple of joint first author papers before but we've never had to resort to a coin toss to determine the "first first" and "second first" author order. Then again, they've not been Science papers, so I guess the stakes weren't so high.

*The listed first author is actually Robert Meredith but I thought I would play "parallel universe" for poor Jan Janečka, who missed out on the first author coin toss. (The last author coin toss is not so bad as papers do not get abbreviated to the last author in the same way as the first authorship; this paper will always be "Meredith et al.")

Zombie pumpkins (but not pumpkin zombies)!

2011-10-31T20:16:00.000Z

Halloween is a time for reanimating the dead, so here are a couple of dead pumpkins from a previous year. First up, the first pumpkin I was involved with. We called him Henry:
The next two don't have names. Mine is the simpler one on the right. (Not sure you can have a zombie ghost!) The fancy one was carved by my wife, the pumpkin expert of our family!

Happy iHalloween

2011-10-31T08:08:00.004Z

This photo is of the pumpkin that my wife carved for Halloween this year:
It was taken on my iPhone, uploaded to Dropbox, downloaded onto my iPad, cropped using PhotoPad and then blogged with BlogPress*. Isn't technology wonderful?

[*I'm actually a bit annoyed with BlogPress at the moment as it is refusing to pull anything down from online. Hopefully, iOS5 will sort that out, once I can persuade my work PC to let me upgrade. (My recent Windows 7 upgrade has done something strange to iTunes.)]

UK science gives great bang for buck!

2011-10-30T22:09:00.000Z

One of the great things about going to International conferences is seeing some of the work that goes on "across The Pond". This can be both inspiring and depressing - the scale of some of the work is fantastic but, at the same time, it's the sort of stuff that can only happen on a generous budget.

In the UK, we typically have a smaller pot to play with but that doesn't mean that we don't do good stuff. Indeed, a recent Science news piece highlights two recent studies that show (1) the UK “"attracts more citations per pound spent in overall research and development than any other country", and (2) the UK now tops the charts when "ranked by average number of citations" (see figure). Above and beyond this, some of my beleaguered colleagues should also take heart that "The Thomson Reuters report says that ... biological sciences are the strongest area of U.K. research".

It's easy to get depressed with all the budget cuts but hopefully this will inspire us to keep "punching above our weight". (Or, better still, encourage more funding for what should be a source of national pride.)

(By the way, this image was grabbed from the PDF using iAnnotate on my iPad - a great App whose praises I must later sing.)

Small but perfectly formed

2011-10-26T20:22:00.001+01:00

After my recent post about bobtail squid, I felt that I should give some airtime (if you're using WiFi) to the little ocean critters that I am actually involved with: the beautiful Emiliania huxleyi. It's not really a "critter" as such at all - it's a tiny marine phytoplankton, so it's more like a plant really.

Emiliania huxleyi (fondly known as "E hux") is a "Coccolithophore"; the funky appearance comes from the armoured "coccolith" plates that cover the outside of these tiny single-celled organisms. Nobody really knows what coccoliths are for but they are one of the primary reasons for the interest in species as the plates are made out of calcium carbonate. This makes E hux and its relatives a potentially potent carbon sink despite their minuscule size. (The scale bar in the image is 2μm, which is 1 million times shorter than Darth Vader.) This is because huge numbers of coccoliths sink to the sea floor and ultimately become the chalk of the future.

Although it would seem to make more sense to make these plates externally, they actually make them internally and then export them whole, as this video (of a different coccolithophore) shows. In the words of the experts:

"The coccoliths are rather large relative to the cell size; if scaled up to human size it would be like a person giving birth to a car wheel or a dustbin lid."

The project that I am involved with is primarily concerned with Ocean Acidification, which is one of the lesser-known aspects of climate change due to rising carbon dioxide (CO₂). Approx a quarter of atmospheric CO₂ is dissolved by the world's oceans. As CO₂ levels continue to rise due human activity, the amount of dissolved CO₂ therefore also increases. This, in turn, lowers the pH of the ocean, which makes calcium carbonate - the stuff of coccoliths, skeletons and shells - dissolve more easily. The prediction, therefore, is that this will be bad for calcifies, making calcification itself more difficult and reducing the effectiveness of the calcium carbonate structures that they make. (Although we don't yet know what E hux uses its coccoliths for, it's a fair bet that their important.)

The good news is that, as Dr Ian Malcolm would say, "Life finds a way" and so there is every expectation that E hux and friends could evolve and adapt to the elevated CO₂ levels. The bad news, though, is that rate of man-made CO₂ increase is so fast that they may not have the time and capacity to adapt before the oceans get too acidic for them. It is therefore important that we understand both how calcification is regulated and what the capacity of E hux for adaptation to high CO₂ is. Until we get a handle on this, we also don't really know how E hux will respond. Will the increased solubility of the calcium carbonate release more carbon into the ocean, making things even worse? Or, will E hux respond by making thicker coccoliths, incorporating more carbon and help to offset some of the effects of human emissions? (At least, that's my understanding of the main questions.)

In a future post, I'll outline a bit of what we are doing. (I say "we" but my contribution is actually pretty small.) For now, though, just marvel at their coccospherical beauty:

CreatureCast: awesome videos of crazy critters

2011-10-23T22:21:00.001+01:00

In an interesting article about the need for evolutionary biology to go viral, I just came across a fascinating website called "CreatureCast", which features videos of crazy and awesome creatures, made by the Dunn Lab at Brown University. I have only watched the jellyfish one so far but it's well worth a watch. Click here or, alternatively, check out this collection on iTunes:

CreatureCast

Dunn Lab

Biology

Quantum Levitation: I don't understand it but I like it!

2011-10-19T19:25:00.000+01:00

This YouTube video shows something called "quantum locking" of a superconductor in a magnetic field, causing it to levitate in a most outstanding fashion. My brain is too tired now to even try to understand the physics behind this (and I am not sure I would understand even if it wasn't) but the video is well worth a watch anyway!

Quantum Levitation video

Hacienda Monasterio, Ribera del Duero - a Spanish red to beat Rioja

2011-10-15T10:54:00.003+01:00

Last night was the first tasting for the university wine club. The theme was "New vs Old Spain" and we "tasted" (drank!) three whites and three reds. When I think of Spanish wine, I always think of a red Rioja, which is probably my favourite type of wine - I certainly don't remember having a bad one.

One of the good things about attending the wine club is that you get to try things that you wouldn't normally. In this case, it was three Spanish whites, including a White Rioja. I can't say that I will be having any of them again (one tasted like sherry (yuk!), one smelt like cat pee, and (the nice) one was only available in Spain) but it was good to try them.

The reds were more to my taste, including a rather nice Rioja from the Muga winery. Wine of the night (for me), however, went to the Ribera del Duero from Hacienda Monasterio. This one was a bit above my usual price range, at about £30 a bottle - one of the other great things about the tastings. Really good, though. It's still above my price range but I'll definitely remember it for special occasions!

Location:Southampton, UK

My new favourite squid

2011-10-13T20:56:00.003+01:00

They say that you learn something new every day. One of the perks of my job is that some days I get to learn several things! One of today's discoveries was this lovely critter (image, courtesy: National Science Foundation) - isn't (s)he cute‽

This is the wonderful Hawaiian Bobtail Squid. And they really are full of wonder. Bobtail squid are one of nature's "bioluminescent" - light emitting - organisms. As if this is not enough, they are also a great example of that most inspiring and uplifting phenomenon of symbiosis; the bioluminescence is provided by a species of bioluminescent bacteria that live in special "light organs". Nature may be red in tooth and claw but sometimes creatures can get along. (Actually, all multicellular animals are really ecosystems of numerous bacteria, some of which are "friendly", but most don't have anything as cool as glow-in-the-dark Vibrio fischeri.)

The presence of the Vibrio allows the squid to alter its brightness to match the ambient light. It does this using an ink sac, which can essentially block out the light to differing extents. Simple but effective. What do the bacteria get? The squid feed them on amino acids and sugars, which are pumped into the light organ.

As with many marine symbioses, the bacteria are spread horizontally - adult squid vent bacteria daily into the ocean, which can then colonise new squid hatchlings. Although fantastic, this can present a headache for evolutionary biologists trying to predict responses to climate change, for example. Not only do you have to account for host adaptation but potential adaptation (or frailty) of the symbiont, and the interaction of the two; indeed, the paper that drew my attention to these guys was looking to do just that. (In it, they use one of my programs, which is nice (and always surprising) - not just for the citation but also because, abeit in a tiny and trivial way, I feel like I am contributing to the understanding of these amazing creatures.)

Location:Hawaii

The "Curry Lover's Cookbook" Lover

2011-10-13T18:32:00.001+01:00

Last night I cooked a couple of dishes from Mridula Baljekar's "Curry Lovers Cookbook". This is a favourite of mine and thoroughly recommended for anyone, as the name of the book suggest, loves curry.
The first dish was an old favourite, of chicken saag. I tone down the heat a little, with a but less curry powder and chilli than asked, but otherwise stick much to the recipe in the book. I won't reproduce it here (buy the book!) but here's the potted version:

Cook the spices and onions, then add the tomatoes.	Blend cooked spinach, garlic and ginger.	Mix together the onion, tomatoes and spinachy goodness.
Stir in the yogurt and simmer.	Add the chicken, cover and simmer until lovely...	...ignoring requests to dish up early!

For the second dish, we were a little more adventerous and went for something new. I've never cooked okra before but my wife is a big fan, so I made the "okra in yogurt". There's actually not much yogurt involved but it's very easy and super-tasty. Best of all, you only need on pot and you can prepare the whole lot while the chicken saag is simmering away!

Wash and chop your okra into chunks.	Fry some onion seeds, chilli and sliced onion.	Add turmeric and dessicated coconut.
Add the okra and stir-fry briskly.	Then stir in some yogurt, tomatoes and coriander before serving.	Finally, make the cat jealous!

As well as yummy recipes, the book starts with great sections on the different regions of India, their cuisine, and lots of great stuff about the different ingredients that you find in curries and how to balance a menu etc. Educational, beautiful and delicious!

A storming beer from bath ales

2011-10-08T19:11:00.001+01:00

After a reasonable amount of procrastination, I decided not to the gym today. After having an uncharacteristic cooked breakfast this morning and coffee & cakes this afternoon, this is not a decision I am entirely proud of. In my defence, I've been twice this week, which is good for me.

Against my defence, I decided to have a beer instead. Back in my defence, it is a very tasty beer! "Barnstormer" by "bath ales" is a dark, rich bitter, perfect for a (slightly) wintery evening.

Here's what they say:

"Rich in fruit with hints of chocolate, this full-bodied dark ale is a complex but deeply satisfying beer."

Sums it up pretty nicely, I think.

Location:Southampton, UK

Cracking coffee (and cakes!) at the Santo Lounge

2011-10-08T17:42:00.001+01:00

Today, we got up at silly o'clock to watch the rugby. What a great decision that turned out to be! Both my adopted (Ireland) and actual (England) teams lost - and deservedly so. It's a shame that France chose this particular game to start trying but what can you do?

To commiserate ourselves, and reward our subsequent efforts in the home cleaning department, we took off to the local cafe bar for coffee and cakes.I love coffee. More precisely, I love good coffee! (There's a bit of a tautology here as I basically define good coffee as that which I love!) The Santo Lounge in Shirley does good coffee. It also does a tasty range of cakes, which work well in the commiseration/reward stakes!

The Santo Lounge is part of the Loungers chain on cafe bars. The first one we went to was The Trago Lounge in Portswood, which is in a former Pizza Hut - a great trade for Portswood in my opinion. This was a brunch visit, which made it a doubly good discovery as we had been looking for a decent brunch place in Southampton for a while. The Trago Lounge nailed it, as did the Santo lounge in subsequent visits. Having such a place so close is as dangerous as it is convenient!

The Trago Lounge also did fantastic coffee (and cakes), like the Santo Lounge. This bodes well for rest of the chain, so if you have a Loungers cafe bar nearby, I thoroughly recommend checking it out. I know some people have problems with chains - especially chains of cafes or bars - but when they're good, it doesn't bother me at all!

Location:Santo Lounge, Shirley, Southampton

What's the atheist equivalent of RIP?

2011-10-06T20:34:00.002+01:00

It's always a little strange when a truly famous person dies, especially one made famous by being so bloody brilliant at their job; even more so when the results of that job genuinely change the lives of millions. There are few people that really change the world - even most world leaders don't really make an awful difference in the grand scheme of things. Steve Jobs undeniably changed the world and I can't help feel that the world is a poorer place today for his loss. (Even with all the monopolising and money-grabbing that makes me moan about the "evil" Apple corporation from time to time.)

I was going to title this post "RIP Steve Jobs" as the general sentiment - a respect for the deceased and their memory - is right. The implied sentiment - that Steve Jobs is still hanging around in the giant Apple Store in the sky - is certainly not right, though. This is a problem I've encountered before: what is the atheist equivalent of "RIP"? I'm yet to find something that carries the same sentiment but without the baggage. (It's funny how, like Apple products, the influence of religion pervades all things even when you are "on the other side". (Traditionally, I'm a PC/Windows man!))

Anyhoo... I love my iPhone. I love my iPad. I wouldn't have either without Steve Jobs. Hopefully his memory will inspire others on to greatness. It may be tough in the modern age but one man can still change the world and make it a better place.

Howling (dumb)bells

2011-09-29T22:55:00.003+01:00

The only problem with going away to a fantastic conference and staying up late each night talking science (and nonsense) is that you're knackered when you get home.

Add to that a few vet visits with a sick cat (now better, thankfully), a pile of stuff that has piled up in my absence, and a touch of old-fashioned laziness, and the result is a shameful lack of gym visits since my return.

After a last minute abort the previous night (so tired!), I finally dragged my lazy arse to the gym last night. It turns out that a week of eating lots of food and drinking lots of beer doesn't make you fitter. Who'd have known?

Fortunately, I'm not here today to dwell on my gym skills but rather my gym music. This time, I was listening exclusively to "Howling Bells". I don't know much about them, to be honest, so I won't attempt a biography or anything here. (That's what Wikipedia's for, right?) In fact, I only discovered them yesterday but so far I like what I hear.

The music is good gym music as it's fairly up-beat but is also at that mid-range pitch that copes quite well with background noise. I think it will do well in the car for the same reason. The vocals remind me of a cross between Kate Bush, Natalie Imbruglia and Lilly Allen; quite varied in style but always good. Well worth a listen, in any case.

My "Howling Bells" experience is also a great endorsement for making tracks available for free download. I discovered them through a freebie track on one of my favourite music sites, 7digital. The track was "The Loudest Engine" from the album of the same name. I liked it so much that I looked them up on another favourite music site, emusic, had a quick preview listen and downloaded a couple of albums ("Howling Bells" and "The Loudest Engine".) If it hadn't been for the free track, I probably would have never even listened to them and they'd be two album sales and one fan-in-the-making down!

(I say "album sales", although "album downloads" might be more accurate. With emusic, you pay a set amount each month and get a set amount of downloads. I assume the downloaded artists still get their cut, though. It generally works out cheaper than downloading tracks or albums from iTunes, play.com or 7digital. They don't have a complete catalogue but I have found some of my favourite musical discoveries through emusic, including Rage, The White Stripes, Slash's Snakepit, The Qemists, Black Country Communion, Gomez and others. If you have eclectic tastes and download buy a fair amount of new music each month, I definitely recommend it. You can even sign up for a free trial, which gives you a bunch of downloads and then cancel before having to pay. If anyone does want to check out emusic, though, let me know and I can invite you. I think I/we get some extra free tracks that way, which is nice.)

Location:Southampton, UK

Bring back the interrobang!

2011-09-27T20:13:00.004+01:00

Why did they ever get rid of such a useful punctuation mark‽

The Origin of Life - interesting but not a problem

2011-09-25T15:23:00.002+01:00

I've just read an article by a Rabbi Moshe Averick attacking Dawkins for focusing on evolution rather than the origin of life and, essentially, having no evidence against "Intelligent Design" as a result. The original ancestor of all extant (evolved) life is itself incredibly unlikely, therefore needs an explanation, for which a deity (an "Intelligent Designer") is the best, or so the argument goes.

Rabbi Averick is entirely right that the issue of the origin of life is different from that of evolution. Dawkins and others argue about evolution because Creationists and IDers attack evolution, though, not because they are trying to create a smoke-screen. Dawkins acknowledges that we do not know how life arose, only that it did. Throw in a few chemists who calculate the probability of self-replicating molecules arising to be vanishingly small and the Rabbi considers his position solid enough to proclaim as if it is some new and revolutionary truth that will have atheists ducking for cover and/or converting to ID in their masses. It isn't and it won't.

We have no scientific explanation for the origin of life. (Yet?) True. This does not make ID right, though. Any derivation of probabilities are hand-waving in the extreme – this is a one-off (as far as we know) event that happened over 3 billion years ago in conditions very different from our own. It may well be that we never know how it happened. Does this mean it could not have happened? No. Does this mean that I need faith to believe that it did happen? No. It is simple extrapolation from current experience. No life that we have encountered needed divine intervention as an explanation. Nothing in the modern world makes more sense with a deity than without. Why should the past be any different?

By the way, the Bayesian probability of life spontaneously arising is 1.0 because we know that life exists, so all scrabble-board arguments are pointless. They only work if you are outside the system. (The fact that we are here taking about it alters the probability that it happened in our Universe/timeline to be a certainty.) Unless you know how many planets, galaxies and universes there are, it is impossible to say that a one-off event is so unlikely that it could not have happened by chance. In fact, as the number of planets and universes tends towards infinity, so does the probability of anything happening.

You also have to ask yourself the question: so what if a deity kicked everything off 4 billion years ago and then watched? This is fundamentally different to a deity-free universe how, exactly? There is no need to invoke such a being in the first place and, if you do, their existence is pointless. (And then there is the boring old chestnut of where did THEY come from and what is the probability of THEM spontaneously arising?) Is an ageless ever-existing deity REALLY more likely than an infinite number of universes? Not to me.

Hopefully, Creationists and IDers will read the Rabbi's article and leave evolution alone. (They won't - Young Earth Creationists need evolution to be wrong too.) Until they do, he cannot expect Dawkins and others to stop writing books about why evolution is a fact, irrespective of life's origins.

Location:Southampton, UK

Atheism: not faith, not religion

2011-09-25T14:21:00.005+01:00

Two common misconceptions I encounter about rational atheism are this:

1. It requires just as much faith to be an atheist as to believe in a god.

2. Atheism is a religion.

Here's why this is not true, at least for me.

Atheism does not require faith. I suspect that some atheism requires faith - not all atheists are atheist for rational reasons. The argument cannot be levelled at atheists such as myself, however, who believe there is no god based on rationality and experience. A bold claim? No. But to see why, we first have to understand where this idea comes from.

The theist believes that their deity created this and that because their religion/priest/deity/scripture told them so. It therefore follows that the atheist believes that no god made this and that because their atheism tells them so. Atheists "have faith" that there is no god and therefore that there is a godless explanation for everything. They ask atheists whether we believe certain things that cannot be proven - such as the spontaneous origin of life without divine intervention - and then cry "Haha! Faith!" when we acknowledge that we do.

This is wrong. It is wrong because they are making the ancient and oft-repeated mistake of confusing correlation with causation. I do not believe that life spontaneously arose without divine intervention because I am an atheist. I belief that life spontaneously arose without divine intervention and I am an atheist for the same reason. Nothing that I have experienced in my life (including my 18+ years as an evangelical fundamentalist Christian) has required a deity to explain it. More than that, nothing I have experienced could be better explained with a deity than without. The rest is simply extrapolation.

I do not need faith to believe that gravity will not switch off during the night and that I am safe not tying myself into my bed; I simply extrapolate from a lifetime of experience. For the same reason, I do not need faith to be an atheist or believe that there is a god-free explanation for life; I simply extrapolate from past experience. Every satisfactory explanation for anything I have ever encountered has come from science, not religion. Only science, in my experience, honestly and openly adapts its position in the light of new data, and rejects assumptions found wanting. Only science produces predictable, testable and demonstrable outputs, including all the modern technology that makes my life convenient and all the modern medicine that makes my life longer. I don't need faith to believe in these things. For me, atheism is simply an extension of that. No faith needed. (Does this mean that additional evidence or experience could lead me to reject atheism? You betcha. Although it would have to be quite spectacular at this stage!)

There is no "Atheist Religion". This is a simpler one. Atheism is not a religion because it has no dogmas, churches, priests or creeds. There is no atheist scripture or Chief Atheist telling us what to believe. There is one unifying idea - the lack of the existence of god - and that's it. It annoys me when forms have "atheism" and "no religion" as two options under religion. Atheism is not a religion, it is a (lack of) belief! You can have atheist buddhists and theists without religion. Humanism is probably the closest to an atheist religion, fulfilling many of the same roles as religion, but even this is not right because you do not have to be atheist to be a humanist nor humanist to be an atheist.

So, criticise my atheism all you like. Take issue with my materialism and unwillingness to accept certain "alternative forms of evidence". But please, don't accuse me of having faith or religion; I have neither.

Location:Southampton, UK

The Cabbages of Doom: one decade on

2011-09-23T21:44:00.002+01:00

As the end of September looms, so does an important (and slightly scary) milestone for me. A week today will be the tenth anniversary of the submission of my PhD thesis. Eek!

To celebrate the event, I have decided that my first ever peer-reviewed publication deserved another airing. Admittedly, the peer in question was my mate Matt, and the manuscript in question was self-published with a very limited print run. Of course, I am referring to The Cabbages of Doom. You can read the PDF here, or if you need more enticing, here's the blurb:

For Cyril the Squirrel it was just another day. His main concern was the location of his nuts and the daily battle to avoid being eaten by something with nasty sharp bits and a taste for rodent. And then came The Cabbages of Doom.

Suddenly, Cyril found himself the key player in a struggle over time and space for his survival and the safety of those around him. Plus, if he's lucky, a bit of lovin' on the side. Take some marauding vegetables, add a menagerie of talking animals, then chuck in an army of chrome-plated midgets for good measure, and you have a story that will keep you amused and entertained* for, well, a few minutes. Maybe more.

*The author accepts no responsbility for readers that are neither amused nor entertained.

Location:Nottingham, UK

Comfort is a cat called Arthur

2011-09-22T21:41:00.002+01:00

If I could get as comfortable as as our cat, Arthur, looks, I would be a comfortable man indeed.

Location:Southampton, UK

A self-promoting blog poster

2011-09-15T17:10:00.001+01:00

I've been a bit quiet on the blogging front for a while. This is largely because I have been busy making a couple of posters for a conference. For those who are interested and where unable to make it to Austria, here is my poster (click for high quality PDF) ->

It's actually the poster for our recent publication in Molecular Biosystems. (When you're self-promoting, go the whole hog, right?) I aim to attempt a proper lay person's summary in the near future but hopefully the poster will suffice for now for a general overview.

It's not the most world-changing paper ever but I am pleased to see it finally out there, being the culmination of about six years' work. (Not a solid six years, obviously, but a lot of work, nonetheless.)

It's the application of methods we developed to identify convergent evolution at the molecular level. (One of the causes of the delay was that we kept improving the methods before finishing the analysis of the application.) if nothing else, it exposes the lie that evolutionary theory has no practical theory. (We actually use signals of both convergent and "traditional" divergent evolution (i.e. conservation) to predict functional sites in proteins.)

As ever, the story is more complicated than we thought/hoped but it certainly seems that convergence evolution has been quite rampant at the molecular level during the evolution of animals. If you want to know what makes me say that... read the paper! :-p (Or wait for a future blog post.) But now, it's time for dinner!

Location:Seefeld, Tirol, Austria

iPad 2: the perfect conference buddy

2011-09-12T22:47:00.001+01:00

Today I gave my iPad it's first proper road test in a work environment. The (work) reason I wanted one was for conferences; I'd seen others with them before and thought they looked handy. Since getting one, however, I have had mixed view on the iPad versus a laptop for such things.

Pros: Excellent battery life; Instant Access; Great web browsing and PDF reading; Discreet;

Cons: Lack of real keyboard*; Lack of "proper" programs for doing stuff.

*I have a wireless keyboard, which I am using now and makes typing long documents much easier, but this is not really practical when sitting in a conference room.

The biggest concern was the lack of a real keyboard. Would I be able to make good notes?

Today, I attended a one day biofilm conference, and the answer is an emphatic yes! All the pros shone - the iPad is light, instantly on, very responsive, and the battery lasted all day and then some, even connected to WiFi for most of the day. None of the cons turned out to be a problem. I wasn't writing essays but I found the "keyboard" adequate for making conference notes (in "Office² HD") that I could then email to myself or upload on Dropbox. At the same time, the "Idea Sketch" App was great for making visual representations of some of the key themes of the day. With WiFi, looking up things from talks online in real time was quicker, easier and more discreet than with the netbook that I previously used.

My verdict for anyone contemplating an iPad in place of a netbook or laptop for conferences and meetings: it's great! (Especially if the venue has WiFi.)

Location:Southampton, UK

Gay Genius

2011-09-09T18:16:00.002+01:00

I stumbled across this little gem from Happy Place, "The Most Hilariously Effective Signs Supporting Gay Marriage", (thanks to a Stephen Fry tweet) and just had to share it! Some other goods ones at the site too.

Go go gadget milk jug!

2011-09-08T19:57:00.000+01:00

Every now and then, I come across an invention so simple and yet effective that I think: "Why didn't I think of that?" (Of course, my history of exactly zero inventions gives some indication.) One such device is the "Jug-It" milk jug.

I'd seen this bad boy in the supermarket but was rather skeptical, thinking that it would involve a lot of rinsing out of jugs and messy refills. How wrong I was!

One day, the regular milk was out and there was a jug-it offer too good to be true (3 for 2 on refills with a free jug, I think) so I took the plunge. Turns out, it's great! Simple too.

You just clip the bag in position, it's pierced automatically as you close the lid, and then it's ready to pour. Once the bag is empty, whip it out and bin it. Only the spout needs cleaning. No mess. No fuss. Great! Added to that, the bags are usually cheaper than regular milk and you cut down on waste by 75%. What more can you want from you milk delivery device?

It's not The Central Dogma, my dear Watson

2011-09-04T14:20:00.000+01:00

Long before James Watson was stirring up controversy for making comments that could be construed as sexist, racist and pro-eugenics, he was creating problems of another kind. Problems that are still haunting molecular biologists to this day. Problems with The Central Dogma of Molecular Biology.

The "Central Dogma" is something that gets attacked on a regular basis. Attacks come both from scientists and Creationists. The former are trying to sex up their science a little in order to catch the eye of an editor from a "high impact" journal, or science news site. The latter get hung up on the term "dogma", under the mis-guided belief that overturning one cherished idea of contemporary biology somehow invalidates the rest, including evolution.

So, what is The Centra Dogma [ominous timpani drum roll]? And why/how does it get attacked so much?

I must confess that I didn't really understand the fuss until I read an old post about it on Larry Moran's blog, Sandwalk. Why do people keep refuting/attacking an idea that is so obviously wrong? Furthermore, why is there still "The Central Dogma" if it is obviously wrong and gets refuted every couple of years? To be frank, I didn't concern myself too much with it because I am much more interested in ideas and mechanisms than the names given to those ideas and mechanisms. Now that I know what the problem is, however, I realise that I have a responsibility to help do something about it - at the very least to make sure that I teach my students the right thing.

The answer, it turns out, is disturbingly simple. When "The Central Dogma" gets refuted every few years, they aren't refuting The Central Dogma. At least, they are not refuting it as originally defined by genius and polymath, Francis Crick. Instead, they are refuting a badly redefined version his once student, James Watson. (I may be a bit harsh on James Watson but it seems very clear to me who the real brains behind the operation was.) Meanwhile, the original "proper" Central Dogma still hangs around because it has never been refuted.

Crick's original is defined thus:

"The Central Dogma. This states that once “information” has passed into protein it cannot get out again. In more detail, the transfer of information from nucleic acid to nucleic acid, or from nucleic acid to protein may be possible, but transfer from protein to protein, or from protein to nucleic acid is impossible. Information means here the precise determination of sequence, either of bases in the nucleic acid or of amino acid residues in the protein."

Crick, F.H.C. (1958) On protein synthesis. Symp. Soc. Exp. Biol. XII:138-163 quoted in Judson, H.F. The Eight Day of Creation, Expanded Edition (1979, 1996) p. 332. (quoted on Sandwalk blog.)

Note that it is explicitly sequence information that cannot get out again. In other words, a protein sequence is never reverse-engineered into the nucleotide sequence that encoded it. In a nutshell, there is no reverse translation. Now, that doesn't seem like a big deal to us now, precisely because it has not been disproven in over sixty years, but it was not such a trivial statement at the time.

The Watson version, which sadly gets repeated in lots of biochemistry textbooks (and I may have even repeated myself in the past), is just the sequential flow of genetic information during transcription and translation, e.g. DNA → RNA → protein, published in his 1965 book [Watson, J.D. (1965) The Molecular Biology of the Gene. W.A. Benjamin. Inc. New York]. This is the version that keeps getting "refuted" by reverse transcription, epigenetic etc. This model is not wrong - it does happen - but it is certainly not the only flow of information. Nucleotides and proteins both pass information to both nucleotides and proteins. But this is old news and certainly does not challenge any of the core principles of modern molecular biology or evolutionary theory. To pretend otherwise, is just dishonest. (Or ignorant.)

Larry Moran ends his blog post by appealing to all teachers of biochemistry and molecular biology to explicitly adopt the "correct" Crick version. After all, (a) he defined it first, and (b) his is right as a universal principle. I am inclined to agree and will be sure to point out the difference to my students in future. And if you come across authors claiming to have refuted "The Central Dogma", ask them: have you really?!

Communing with the Black Country

2011-09-03T23:54:00.001+01:00

Today's washing up music of choice: "2" by "Black Country Communion". Another fine rock outfit that I recently discovered. I can't remember how, now. Either emusic or a 7digital freebie, I suspect. Anyway, another great album with good vocals and rocking guitar work, well worth a listen.

Favourite track: "The Battle for Hadrian's Wall".

Location:Southampton, UK

TE-Thrust: maybe so but it's still junk DNA

2011-09-03T20:45:00.000+01:00

I recently came across this paper in the journal "Mobile DNA": Mobile DNA and the TE-Thrust Hypothesis: Supporting Evidence from the Primates.

In it, Oliver and Greene describe the evidence from primates to support the "TE-Thrust" hypothesis. In summary, this hypothesis states that transposable elements - mobile genetic elements - have been influential in evolution, particularly in large genetic rearrangements and the like. No arguments there. It then goes on to suggest that these are responsible for "macroevolution" (bleurgh) and the changes consistent with observed "punctuated equilibrium" in the fossil record.

I hate the term "macroevolution". It is made up, arbitrary and essentially meaningless. There is evolution. Full stop. Yes, it happens at different rates and evolutionary changes are of different scales but it is a broad continuum. Differentiating micro- and macro- helps no one but Creationists and IDers who want to stir up controversy where there is none. Besides, I don't know of any work where someone has shown that the scale of the genetic change is related to the scale of phenotypic change - you can have some pretty monstrous point mutations and some largely silent chromosomal translocations. Hype.

Macroevolution aside, the suggestion that TE-thrust has played an important role in the evolution of many lineages seems fair enough. They don't seem to want to leave it there, though. It seems that they think it is not just important but almost essential, and organisms with few TEs get stuck in "stasis" or even go extinct due to their lack of evolvability. I don't see why this necessarily follows - TEs are not the only way to have genetic change. We have a long history of analysing point mutations and other non-TE-related insertions/deletions etc. and know that they play at least some role. Furthermore, TEs are not the only repetitive sequences in the genome. Again, I just say: Hype. Why are people so obsessed with "paradigm shifts"? At best you end up looking over-eager, which makes people distrust your work and actually retards the shifting of paradigms. At worst, you end up looking stupid.

Don't get me wrong - I am not against the idea that TEs have contributed positively to the evolution of their hosts, and even that this contribution might have played an important role in their maintenance. Far from it, in fact: in my own PhD I developed a model in which occasional beneficial insertions could maintain an otherwise selfish mobile element in even a clonal population. I just think that caution is needed when assigning cause and effect to observed trends. Beneficial TE-mediated events can sweep TE-containing individuals through the population via hitch-hiking and can help their spread and maintenance. This does not mean that TE-lacking individuals are doomed.

The last thing to point out - and, to be fair the authors (kind of) say this themselves - is that regardless of the extent to which the TE-thrust hypothesis is right, most transposable elements are still "junk DNA". They may be junk that very occasionally do something useful but unless they regularly contribute to the fitness of an organism, they are junk. Worse than junk, even under TE-thrust most affects of transposable elements are still going to be negative because most large-scale mutations are deleterious. They also put an energetic load on the cell by increasing the amount of DNA that needs to be replicated. I am sure that ID/Creationists and other "it's not junk" fans will ignore this fact and jump on this paper as further evidence for their fantasies but it simply isn't true.

If you can get past the hype and hyperbole, though, this is an interesting paper and has some beautiful examples of how some important traits have evolved through traceable TE-mediated rearrangements. Evolution. It works, bitches.

Ode to a Troll (Part 2)

2011-09-03T18:22:00.000+01:00

Following up from this morning's (now slightly revised) Ode to a Troll, here is a second ditty about those who love to knock discussions off-topic by repeatedly posting nonsense as "Anonymous".

An interesting group, the Anonymids,
A paraphyletic sub-group of hominids,
Their identities veiled,
Their coherence de-railed,
They still moan, "I didn't say what you think I did".

(This one was in response to one "Anonymous" poster complaining that someone else was posting as "Anonymous" and confusing the issue by misrepresenting their position.)

Ode to a Troll

2011-09-03T08:09:00.000+01:00

I'm not sure if a limerick can be an ode but mine is anyway. In case it isn't obvious, this is about a (possible) troll who would post comments only as "Anonymous", repeatedly fail to acknowledge the many (correct) responses to his (or her) challenges and fail to respond to the majority of questions. Eventually, all serious attempts at discourse dried up and all that remained were increasingly fantastical posts. It has nothing to do with the civil disobedience group "Anonymous", as far as I know!

There once was a poster, Anonymous,
Whose refusal to listen was ominous,
With the traffic one way,
Only he can say,
Why he stays here and continues boring us.

(Inspired by real events. I won't mention names, except "Anonymous", which doesn't count.)

Leg aches not headaches

2011-09-02T23:20:00.001+01:00

[Warning: boring, self-indulgent gym post]
Last night, I resisted a last minute invite to the pub and went to the gym instead. I can't say it was as fun but I think it's safe to say that it was better for me and I feel better for it now. Due to the fighting off a bit of cold, I hadn't been for about a week and was in danger of losing the habit, and facing an eternity of online shame to remind me.

New equipment used: cycling machine (boring, like this post!)
Distance: 2km (run); 3km (cycle)

Location:LA Fitness, Southampton, UK

The Redbreast: don't read the blurb

2011-09-01T22:41:00.001+01:00

I have just finished reading "The Redbreast" by Jo Nesbo. I liked it, although I don't think it's as good as the Millennium series. (I suspect Jo Nesbo would not be "the next Stieg Larsson" were it not for the Scandinavian connection.)

It's still worth a read, though, and I will check out another one of the Harry Hole series, although I do wish he hadn't called his lead character "Harry Hole". (Why, Jo? Why would you do this.)

I feel I should share a warning about the book, though: don't read the blurb! I made the mistake of reading the back of the book when I was around half way in, figuring that I was safe from spoilers by then. Wrong! I won't repeat the spoiler here but suffice it to say that the blurb makes a very clear reference to something that happens about 320 pages into the book, somewhat killing the suspense. It probably would have been unexpected and shocking. It wasn't. Thanks, blurb.

While I was googling for the cover image, I also discovered that this wasn't the first Harry Hole book, as I had believed, but the third. Its just the first of the ones translated into English, for some reason. So there you go. The Harry Hole series: the mysteries aren't just in the books.

Location:Southampton, UK

Jesus and Mo

2011-09-01T22:28:00.001+01:00

If irreverent, possible fatwah-inducing cartoons are your thing, then you simply must check out Jesus and Mo. Below is a sample and there's plenty more where that came from!

Our cats don't like cat scans

2011-08-30T21:29:00.001+01:00

In addition to interesting titbits about science, Jerry Coyne at the Why Evolution is True website likes to post about cats. (Having two cats, I can appreciate this!) One of the more recent ones was about cat scans (and a contest). In case you've not come across this, there is a whole website dedicated to "cat scanning" - literally putting your kittie on a flatbed scanner and scanning it!

Inspired, we decided to have a go ourselves. It turns our two are not big fans of the cat scanning! Not even a strategic use of cat treats could overcome their suspicion of the moving (and whirring) white line. A couple of spectacular dismounts left me with one bit of advice for would-be cat scanners: put the scanner on the floor!

Oh well. They won't be winning any prizes but here's our offering to the crazy world of the cat scan:

Intelligent Design in a Nutshell

2011-08-28T22:11:00.001+01:00

Pre-Darwin biologist: "I can see that lots of animals (and fossils) are clearly similar to each other, and share anatomical features across even very distant taxa. Life certainly looks like it's evolved. The problem is, I just don't understand how a random process could have led to such exquisite adaptation: there must have been a Designer."

Darwin: "Hang on, I have an idea. If there are more offspring born each generation than survive to reproduce, then there must be a struggle between individuals for survival. And, if there is variation between individuals such that some individuals are inherently better equipped to survive and/or reproduce, then the result of this competition will be (to some extent) non-random and those individuals who are better adapted will have more offspring than those that are not. And, if there is inheritance of characteristics from parent to offspring, the next generation will be better adapted, on average, than the previous generation as a result. Aaaand, if variation is something that enters the population at each generation, this cycle will continue, resulting in more and more adapted individuals. Over many, many generations, exquisite adaptations can evolve."

Post-Darwin biologist: "Competition: check. Variation: check. Inheritance: check. Mutation: check. Genius! Not only is adaptation from random variation explained, it is hard to see how it could not happen! Well done, Darwin - an elegant solution to a tricky problem. All those oddities in nature make so much more sense, now."

Intelligent Design: "The problem is, I just don't understand how a random process could have led to such exquisite adaptation: there must have been a Designer."

Well done guys... Your big "problem" with Darwin is precisely the problem he elegantly solved 150 years ago. Bravo.

Location:Mostly America but other places too (sadly)

Ain't Life Grand with a 12yo Dalmore

2011-08-27T23:45:00.000+01:00

I'm not a big fan of washing up. (Who is?) I am a big fan of (good) whisky and music, however, and sometimes such things can combine in a moment of excellence that even washing up becomes enjoyable. Such a combination happened for me earlier this week, with a very nice 12 year old Dalmore, which is possibly my favourite whisky, and "Ain't Life Grand" by Slash's Snakepit, one of my favourite albums.

With whisky, I generally go for something very peaty, like a Laphroig or Lagavulin. The problem with these, though, is that I really have to be in the right mood to appreciate them. Dalmore, whilst still (to my amateur palate) clearly a Highland whisky, is not as smoky as these guys but is much more approachable as a result.

Like the Dalmore, Slash's Snakepit are also a fairly recent discovery for me - the album "Ain't Life Grand" is only a little younger than the whisky, with a release date of 2000. Personally, I think Guns 'n' Roses peaked with "Appetite for Destruction" but some of my favourite Slash guitar work is post GNR. Snakepit doesn't have the same vocal presence as GNR but "Ain't Life Grand" is packed full of great riffs and solid rock music. It may be a bit Old School but it's good Old School. In terms of individual great tracks, I think "Appetite for Destruction" still has the edge but, as an album, I think I'd have to side with "Ain't Life Grand". A must for Slash fans and lovers of good rock guitar.

Location:Southampton, UK

Rage Against the Running Machine

2011-08-26T23:59:00.000+01:00

This gym session, I was mostly listening to Rage, a Scandinavian rock group. As their album art indicates, these guys are at the heavier end of the spectrum but don't let that put you off. This stuff is far from a wall of noise. The guitar work is particularly good, with every track laden with rocking riffs. I won't deny that a certain amount of fret wanking goes on but it's always perfectly timed and never seems gratuitous.

If I had to pick a weak element, it would be the vocals. There's nothing wrong with them - no out of tone wailing or excessive screaming - but you can very much tell that they're a Scandinavian rock group and it's simply not my favourite voice. It's not hard to imagine a large bearded fellow, singing into a battle axe a la Lordi on Eurovision. For some songs this works particularly well but it is definitely the aspect of their sound that I tire of first.

Nevertheless, Rage are excellent gym music companions. Not only are they loud, and a little bit angry, but a lot of their songs border on frenetic, which is great for the treadmill.

Gym goer or not, if you are a rocker then check out Rage as soon as possible.

Equipment used: treadmill, vertical traction
Distance: 5km
Future goal: get myself a program

Location:LA Fitness, Southampton, UK

Stretching my gym motivation to breaking point

2011-08-24T21:58:00.001+01:00

[Warning: self-indulgent gym post]

Tonight, I went to the gym again, bringing my average gym costs since June down to just £25 per visit. Hooray!

My new plan is to try out a new machine each visit, until I have worked through them all. Having not yet re-booked for a session plan with a fitness guy (or gal), I went for something easy: the rowing machine. I'm also determined not to "travel" under 5km, so I ran 3km and rowed 2km before a cool-down perambulation (if you can perambulate on a treadmill) and a quick spell with the free weights. A very quick spell.

One problem I have in the gym is that I feel exposed and stupid as soon as I step away from the machines. I don't really know what I am doing when it comes to free weight exercises and stretches. Added to that, I'm not exactly Hercules, so I can only really work with pretty weedy weights, especially if I'm already knackered from rowing etc. Combine this with the fact that the free workout area is pretty small and (it seems) never empty, and you have one very uncomfortable and self-conscious exerciser.

I feel that exercise of this nature is a bit like dancing - if you feel uncomfortable and self-conscious, you look uncomfortable self-conscious. I therefore cut my exercise a bit short and saved my stretches for the changing room (and only then because it was almost empty). Perhaps I should sign myself up for one of the classes in an attempt to face (and conquer) my fear of looking stupid and uncomfortable.

Equipment used: treadmill, rowing machine, free weight
Distance: 3.5km (run); 2km (row)
Future goal: stretch in public after exercise

Location:LA Fitness, Southampton, UK

From Selfish Genes to Public Goods

2011-08-23T23:43:00.001+01:00

Most people have heard of "The Selfish Gene" and many will know what it's about. For those that don't... in essence, it is about "genes" as the primary driving force of evolution. A "gene" in this context is a piece of DNA within some form of entity that replicates that DNA. The rules are simple: if that piece of DNA does anything to increase the chance of its future replication and persistence, it will spread. Usually, we perceive this as a "gene" having some positive beneficial effect on the organism to which it "belongs" (or, perhaps more accurately, within which it is carried and replicated). Life, as usual, is more complicated than that, however, and examples exist of "genes" that spread at the cost of their replicator host - viruses and transposable elements being two such examples.

The point is, though, the genes are "in it for themselves". Yes, they often form complex cooperatives - genomes - that build intricate organisms but only because the members of those cooperatives replicate more successfully in this fashion than going it alone. Natural Selection is not about the good of the species, or even the good of the individual, it is the good of The Selfish Gene.

As you can tell, I am a big fan of this gene's-eye view of evolution. It begs the question, though, if the units of evolution are genes, where does this leave organisms? Species? Even genomes? How does this marry with the standard "Tree of Life" (TOL) model of evolution, in which all species are gradually splitting and diverging over time, carrying their genes with them?

In their recent Biology Direct paper, The public goods hypothesis for the evolution of life on Earth, James McInerney et al. summarise the issue quite nicely. "Horizontal Gene Transfer" (HGT) - essentially the passing of genetic material from one organism to another, other than to offspring (and often a different species) - is widespread, especially in bacteria. So widespread, in fact, that the TOL hypothesis just does not hold up. Instead, we should take a economist-style view of genes as "public goods", with the evolution of Life on Earth as the product of sampling (and retention) of different genes over time, rather than a TOL pattern of bifurcation and divergence.

Of course, the story is a lot richer than that and builds on a body of other ideas. It is also not without criticism. I strongly encourage you to read the paper and the interesting discussion with reviewers that can be found at the end of the manuscript. Time will tell whether the Public Goods hypothesis really offers something more than TOL+HGT but it's definitely something worth considering.

So what does this mean for evolution? Does questioning the TOL put evolution in peril? Well, no. It is important to point out that the genes themselves are still evolving in a tree-like fashion. Molecular evolution and molecular phylogenetics is not substantially altered by this idea. What is altered is the way we interpret this molecular data in terms of trying to determine the relationship of "species", especially bacteria. This is nothing new - the "species" concept for bacteria has been dead for a long time, to be honest - but it potentially gives us some new tools and ideas with which to probe the Natural History of prokaryotic life with more clarity and insight than ever before.

And what about all the claims us evolutionary biologists make about the molecular evidence for evolution, and how we get remarkably consistent trees when looking at different genes from a set of animals? Was that all lies? Well, no. It is also important to point out that the problems with the TOL are largely restricted to bacteria, viruses and the like. For eukaryotes - e.g. plants, animals, fungi - the tree picture is still pretty solid. The authors themselves make a nice analogy with mechanics. Quantum Mechanics did not stop previous observations about Newtonian Mechanics being right, it just extended our understanding into realms where our old Newtonian understanding began to break down. I am not sure whether this idea represents such a game-changer but I do know that it's a exciting, if slightly head-wrecking, time to be a microbial geneticist.

It's a workout, Gym, but not as we know it

2011-08-22T20:39:00.001+01:00

Today, I went to the gym for the first time in quite a few weeks. Too many weeks. So many weeks, in fact, I couldn't even remember when I last went to the gym, so I looked it up. It was June 22 - exactly two months ago, almost to the minute.

Last time, I got a free trial session with a personal trainer. It was pretty good but I was literally still hurting a little a week later - part of the plethora of lame-assed excuses that stopped me going back since. Another part was the shame of seeing said personal trainer, having seemed so keen at the time and then failed to turn up again.

So why go now? Well, the time has come to reverse the polarity of the shaming beam. A friend has just signed up at the same gym and went first thing on Sunday morning, of all times. Then, my wife went earlier today. Finally, of course, there is Rule #1: Cardio. It was time to climb back on the horse. Or, more accurately, back on the treadmill. Without a horse: that would be cheating.

This blog is the final cog in the wheel of shame. My wife and friends are too nice to really make me feel shame for my non-attendance. Instead, therefore, I shall here record my triumphs, or acknowledge my lazy lameness, to be forever electronically recorded for posterity. Or, at least, until the inevitable EM pulse from World War III takes out Google.

Machines used: treadmill
Time run: 30 min
Distance: 5km
Rehydration: lucozade sport, raspberry

Location:LA Fitness, Southampton,United Kingdom

McGuigan Bin No. 528... what can I say?

2011-08-21T23:47:00.000+01:00

I like wine. I never used to like wine. Then I discovered that I didn't like cheap wine. This was unfortunate, as all I could afford (or, at least, was prepared to fork out for) as a student.

Now, my palate (and wallet) have improved a touch, my enjoyment of wine has likewise increased. That said, I still like a bargain, and don't know that much, so I like to go for the half price wines, like this one (£5 at Sainsburys):

Sadly, while my palate has improved enough to increase my enjoyment, it has not yet resulted in an ability to describe wine with anything resembling sophistication. This one's nice for drinking, though!

Location:Southampton, UK