Monday, 27 February 2012

The beauty of The Magic of Reality

Poor old Richard Dawkins has been getting a bit of a hard time recently by clueless journalists. More on that when I have the time but I thought I'd do my little bit to counter these bad vibes (not in a woo way) with a brief pro-Dawkins post. (Well, probably more a pro-Dave McKean post but I'll get to that.)

After flicking through a copy in a bookshop whilst on holiday, I recently got myself a copy of The Magic of Reality. I've not read through much of it yet but I've enjoyed the first few chapters (despite not really being the target audience). The thing I have loved most, though, has been the visual impact. Every page is stunningly illustrated and not just in a "here's a few nice relevant photos" kind of way; instead, the text and illustrations weave around each other with a greater-than-the-sum-of-the-parts impact.

Of course, Dawkins has Dave McKean to thank for the amazing illustrations but it is hard to believe that the images and text could work so well together if he has not also had some input.

I've also found out that you can get it for the iPad for £9.99. Even though I have the book, I must admit that I am sorely tempted.

Wednesday, 22 February 2012

Flying squirrel Google Psyche

Following my earlier post on Flying Squid, I thought I'd do a bit of Google Psyche on the subject, just out of curiosity. I'd got as far as "flying squi", however, when I realised that flying squirrels were much more intriguing Google Psyche subjects!

I think "pet" and "facts" speak for them themselves. I had also known about the "flying squirrel suit", although I did not realise that it came in a "cuddly" Halloween variant.

The pizza is probably most disturbing thought but it turns out to be the name of a Seattle pizza restaurant, rather than a particularly avant garde topping. Meanwhile, "flying squirrel wrestling" is also not quite as cruel as it sounds but is instead the name of a wrestling move. What a weird and wonderful place the world is!

Joining flying squirrels and fish... Flying Squid!

Blogging has taken a bit of a hit recently due to teaching prep but here's a quickie that seemed to good to pass over. Fresh from the Nature News desk comes a report that Squid can fly to save energy. I obviously won't repeat it all but here is the photo of said squid, "flying":


The cool bit is that they are using the same "jet propulsion" system that they do underwater - the resolution is not great but I think the streamers coming out the back of the squid in the photo are the jets of water, firing them out of the sea like a rocket. (Quite literally like a water rocket.)

Air resistance is clearly less than water resistance and so it may not come as a surprise to find out that the squid can actually achieve a higher velocity in the air:
"Because they knew the intervals of time between each photo, O'Dor and his colleagues were able to estimate the squid's velocity and acceleration, and compare them with these values for squid in water. They found that the velocity in air while the squid were propelling themselves with the water jet was five times faster than than any measurements O'Dor had made for comparable squid species in water."

There still seems to be a bit of debate regarding the significance of the "flying" behaviour but first author Ronald O'Dor is convinced that it is normal squid behaviour. He even goes as far as to propose that they might be doing it routinely to save energy. Given the acceleration, I think it also fits the standard predator-avoidance explanation for other marine flyers. More research needed, so hopefully lots more flying squid pictures to come!

Tuesday, 14 February 2012

Feel the Force... of taxonomy!

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!

Monday, 13 February 2012

Kindling some Darwin love

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!

Sunday, 12 February 2012

Que Syrah, Syrah

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!

Saturday, 11 February 2012

Friday, 10 February 2012

Intelligent Falling

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

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.)

Thursday, 9 February 2012

Exam tips II

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.

Wednesday, 8 February 2012

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

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.

Tuesday, 7 February 2012

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

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!

Monday, 6 February 2012

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

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!)

Sunday, 5 February 2012

The joys of Japanese Whisky

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

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.

Saturday, 4 February 2012

In support of TripAdvisor

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.)

Friday, 3 February 2012

Kali Mirchi, Shirley a top Indian restaurant

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.

Thursday, 2 February 2012

Translation UK 2012 website now live

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!

Wednesday, 1 February 2012

The Cabbages of Doom: only 99p from iBooks!

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)

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!)