Thursday, 31 May 2012

You don't have to publish papers to be clever (or read)

There's a bit of a spat going on at the moment between Richard Dawkins and Ed Wilson (and their respective followers) about Kin Selection and Group Selection. I will wade in with my own inconsequential opinion at a later date if/when I understand what the current understanding of "Group Selection" really is. (Group Selection to me is something so blatantly wrong that I suspect there is an updated definition since the "for the good of the species" days. Certainly, Dawkins is being accused of not understanding Group Selection whilst giving convincing arguments against what I was taught Group Selection meant. I'll add the links when I get the chance.)

One thing has cropped up, though, that made me cross enough to write a quick post. Apparently, in a video kicking around somewhere, E.O. Wilson dismisses Dawkins as someone who doesn't understand the theory and should be ignored in part because "he does not publish in peer reviewed journals". Ignoring the potential irony that one of Dawkins' criticisms of Wilson is for ignoring the peer-reviewed criticisms with his (Wilson's) peer-reviewed Nature paper, I think this is arrogance in the extreme. (If he said it - I am yet to watch the video myself. If not, I have heard similar remarks in the past and so the point still stands but Wilson is not guilty of it.)

As a published scientist myself, I have no hesitation in saying that not being published in peer-reviewed journals neither makes you intellectually inferior nor unable to read/understand scientific theories. In fact, I might even go as far as to say that if you are not encumbered with the need to actually do science, you probably have a lot more time to read and think about science. Dawkins is not stupid. He is also retired. If he doesn't "get it", it is nothing to do with his lack of peer-reviewed publication. There are plenty of peer-reviewed scientists who agree with him. (Besides, Dawkins has published in peer-reviewed journals - including Science and Nature - just not for some time. How shocking that a Professor for Public Understanding of Science might publish popular science books rather than peer-reviewed papers.)

I still cannot work out whether this particular argument is just semantics and confusion over definitions, or whether there is more substance to it than that. The fact that clearly intelligent people can be found on each side implies that it is either a subtle argument or a misunderstanding fueled by some big personalities (and fans thereof). Whoever turns out to be right, though, it will be down to the strength of their argument, not the length of their publication record.

Wednesday, 30 May 2012

Phylogenetics: Outgroups and Outliers

I am in the throes of marking at present and one mysterious error is cropping up enough to warrant a short blog post: the confusion of the terms "outgroup" and "outlier" when discussing phylogenetic trees. The source seems to be a familiarity (or exposure) to the term "outlier" in statistics, combined with a lack of familarity/awareness of the term "outgroup". So, what is an outgroup?

An outgroup in phylogenetics simply refers to a lineage that is known to be more distantly related to the other species (or DNA/proteins) being studied. In the example shown, the kangaroo is a known outgroup to the other mammals, as marsupials diverged from the common ancestor of placental mammals prior to the subsequent radiation of placental mammals. This knowledge can be used to "root" the tree, as in this example, but more on that in a later post.

What about outliers? "Phylogenetic outliers" are sometimes referred to but, as far as I am aware, there is no standard definition. Instead, it is a term that is used when some form of numerical test (such as evolutionary rates) or statistics have been applied to a phylogenetic tree and there are particular branches that do not fit the norm - they are "outliers". In this tree, the kangaroo is not noticeably an outlier, although it's evolutionary rate depends on a somewhat arbitrary position of the root on the kangaroo branch. The rodents might be outliers (if there were more data) as they tend to evolve quite quickly due to short generation times. In this particular tree, I doubt it though. (This tree is made up, by the way.)

Most important, though, "outlier" is not a synonym for "outgroup" and should be used with great caution.

Sunday, 27 May 2012

Living it up with Uptons burgers

The sun is continuing to flirt with us, which can mean only one thing... BBQ time! Judging by how busy Sainsburys was this morning when I went shopping for burger buns, I think the whole country had the same idea.

Taking advantage of the current predictability of this hot streak, we had invited a few friends round. As well as the sun itself, we had an extra lure... Louisiana burgers from Uptons butchers.

I must admit that I actually buy most of my meat from the supermarket but I do like the produce from a "proper" butcher, especially for a slightly special dinner - or guests. Fortunately, we have one of the best right on our doorstep: Uptons of Bassett.

These guys have award-winning sausages and burgers (great for BBQs!) and a tasty range of pies etc. in addition to the rest of the usual butcher meat products. Their Louisiana burgers are particularly epic. "Jumbo beef and pork burger with hint of spices", these are definite contenders for the ultimate burger. The only potential problem on a day like today is that everyone else would think so too. Indeed, when I went to Uptons this morning, the queue was almost out the door.

Happily, Uptons also have a fantastic website, and so we were able to pre-order (and pre-pay for) our Louisiana burgers yesterday, so all I needed to do today was go in and pick them up. Perhaps not that shocking or amazing in the 21st Century but I just like it when things work well (i.e. as they should) and the Uptons ordering system works well. If, like me, you are the kind of person that worries about shops selling out of the specific thing you want, this kind of thing can really take the edge off of hosting stress. Well done, Uptons. (The burgers were delicious, too!)

Thursday, 24 May 2012

The cream of cream teas


The sun has come out to play. Hooray! To celebrate, we paid another visit to The New Forest. The target: an afternoon stroll around Wilverley Inclosure. The motivation: a highly recommended cream tea!

The weekend before last, we tried out Walk #12 from Jarrold Short Walks in the New Forest National Park around Lepe. This week it was Walk #11. I really like this book. It fits nicely in the pocket and the walks are all well described. (We've not got lost yet, anyway!) They also have a little bit of local knowledge embedded in them including, in this case, a top cream tea recommendation with a detour to The Station House.

For those not familiar with the concept, a cream tea consists of a scone (or two) with cream (usually clotted) and a jam. And tea, of course! (Although you can have coffee if you want - the scone with cream and jam is the star of the show!)

The Station House, it must be said, does a mighty fine cream tea. I opted for the "Porter's tea" - one plain and one fruit scone, with clotted cream and jam, plus a pot of quality tea. Well worth the walk!

The walk itself was a pleasant 4 mile round trip through the trees. Following a few days without rain, the route was not too muddy (unlike last week's in places) with the exception of one point where we had to "ford the Avon Water" - if you are going to do this walk, make sure you have waterproof shoes! (Or a change of socks, I guess.)

Tuesday, 22 May 2012

Bang-on birthday brownies

We generally split the cooking in our house but my wife is definitely the baker. She made me a delicious carrot cake for my birthday a couple of years ago, so I thought I should try to return the favour for her birthday, last weekend.

Not being an experienced baker, I went for something simple. Simple but yummy! The answer was in Sainsburys Magazine, with a great Oreo brownie recipe by Lorraine Pascale.

Great for a starter like me, the recipe is really easy. Basically, you melt 175g butter (Kerrygold recommended) over the stove and then stir in 200g of chopped up dark chocolate (I used Tesco Finest Swiss 72% dark). Whilst the chocolate is melting in to the butter, whip up the eggs (3 full plus 2 yolks and some vanilla essence) until fluffy. Mix in the sugar (175g soft light brown) and buttery chocolate, adding it round the edge and folding in to keep the fluffiness.
Next, mix in 2tbsp plain flour, 2tbsp cocoa powder and 1/3 packet broken Oreo cookies before pouring into a greased and lined tin. Finally, press in the remaining Oreo cookies. (If in doubt, err towards a 50:50 split of the cookies for this bit, as I found myself running out of room on top.)

All that's left now is to bake on the middle shelf at 180°C for 20-25 min. It was here that things went a little bit wrong for me. The numbers have rubbed off our oven temperature dial, so it was probably nearer 200°C and after 20 min it was beginning to catch a bit around the edges and particularly the corners. Fortunately, once it had cooled, cutting it open revealed that it was not over-cooked on the inside. In fact, it was really light and fluffy... and delicious!

Of course, it's hard to imagine mixing butter, sugar and chocolate and it not being delicious but I think that this is a particularly good outcome for this combination. The Oreos add a slightly salty, crunchy finish to the sweet, chocolately brownie and look pretty too, particularly where the white cream filling shows.

The only sad thing is that we just ate the last two pieces.

Monday, 21 May 2012

Mendeley make my day

When a website is down for whatever reason, it is normally cause for something ranging from mild cursing to much wailing and gnashing of teeth. Mendeley have the solution - an error message that almost made me glad it was down!

Friday, 18 May 2012

Finding Nemo's sex-changing father

Although some animals are parthenogenetic, Most animals reproduce sexually and sexual reproducers basically come in two flavours: hermaphrodites have both male and female sex organs, while dimorphic species have male and female forms. In the latter case, although there are always two sexes, there are a number of different ways that those sexes are determined. Some species, notably reptiles, have environmental sex determinism, where temperature-dependent hormone levels ultimately dictate the sex of an individual. Mammals also have hormone-driven sex differentiation but, for us, the original trigger is genetic - you either have a Y chromosome (or, more specifically, a functional SRY gene) and become male, or you don't and you remain female. And this is just two out of many different mechanisms. (The platypus has ten sex chromosomes but I won't go into that here.)

So, what does this have to do with Finding Nemo? Well, despite the domination of sexual reproduction by "male" and "female" sexes, not all species remain the same sex throughout their life. In sequential hermaphroditism, an animal starts out female and later switches to being male (protogyny) or start out male and become female (protandry). One such animal is the clownfish, star of Finding Nemo. At the beginning of the film, Nemo's mum (Coral) gets eaten by a nasty barracuda and so his dad (Marlin) is left to bring up Nemo as a single parent. In reality, Marlin would become Marlene and turn into a female clownfish and the next most dominant male in the group (who was presumably too shy and hiding from the cameras) would step up and fill Marlin's role as The Daddy.

My understanding is that the rest of the film is entirely accurate.

Thursday, 17 May 2012

New Forest alpacas

The New Forest is famous for its ponies but these are not the only ungulates to be found there. In addition to deer, cows and some fat, spotty pigs, there are also some alpacas, including this one that we saw on our recent Lepe walk. I don't really have anything to say about it - I just wanted an alpaca picture for reference next time I get alpacas and llamas mixed up.


The importance of tailoring job applications

I am recruiting again (a two year bioinformatics postdoc in motif detection) and so my mind has once again turned to the stormy seas of job applications.

Happily, I have already had a few interested parties. (The ad only went live a couple of days ago.) Among them, however, I already have a couple of the "generic" applications that make my heart sink. "Dear Sir/Professor..." (you're emailing me, you should know my name) "...I would like to apply for a position in [insert unrelated research area or, at best, a list of broad research areas that by chance overlap the project area..." (you are applying for a specific project, you should be interested - or, at least, feign interest - in the specific area) "...please see my attached CV/resume and unrelated publication" (presumably in the hope that I will spot the relevant connections that they have failed to).

Getting a job is hard because you never know who you are up against. Writing a decent job application is not so hard, though. At least, not if you are actually suitable for the job. There is a wishlist of criteria, so point out how you meet them and how you are really willing/interested/able to learn the skills that you don't yet have. (Like most wishlists, desired criteria are often up for negotiation in reality.) Mention a keyword or two from the project - the name of the project, at least! - to show that you know what job you are applying for. And, if contacting a specific person, show that you know who you are contacting and what they do.

In an ideal world, you will not have to customise your CV much, if at all, because you are genuinely a good fit for the post. If you are not, though, you will have to do some work. If, for example, your background is in a different field, highlight your relevant experience and compress the pages of irrelevant stuff. If the job really interests you, it is worth the effort. If not, don't bother to waste your time and the poor soul short-listing - you won't get short-listed anyway.

Even if your CV doesn't need customising - and ideally it won't because you will be applying to a job that suits your experience - you still need to put a little effort into your covering letter/email. At the very least, I feel that I am worth the time to look up my name, research interests and the think of a sentence or two about what interests you about my work. If you don't feel that I am worth the time, am I really going to want to hire you? If there isn't enough information, then ask. Show you care. It's not hard. If you don't give me the impression that you care about my work/project/job, I am not going to care about your application. It really is as simple as that.

On the other hand, if you show that you (a) know what you are applying for, (b) really want to do it and (c) have the experience to hit some of my wishlist and track record to learn the rest, I will really want to short-list you, even if someone else looks more experienced/qualified on paper. So, if motifs are (or might be) your thing, you know how to program and you're interested in molecular evolution... drop me a line!

Wednesday, 16 May 2012

It's not hard to use an apostrophe in its rightful place

I've just done it. Twice, if you include when not to use one. Which, I do. Just because iPhones seem to think that "its" isn't a word, doesn't mean that it isn't.

It's. It is.

Its. Belonging to it.

</rant>

Monday, 14 May 2012

No sex please, we're parthenogenetic

Tomorrow is my last double lecture of the academic year and it's on Reproductive Strategies and Sex Determination. Although the prep time is a bit greater, the benefit of teaching subjects that I'm not too familiar with is learning new and interesting things. These lectures had quite a few but one of the real highlights was the parthenogenetic whiptail lizards.

Parthenogenesis is a form of asexual reproduction that occurs in a bunch of animals. Most animals reproduce sexually, with a sperm fertilising an egg to form an embryo that then develops into a baby animal that is a genetic 50:50 mix of each parent. A parthenogenetic animal skips the whole fertilisation thing and produce eggs that develop into embryos without the need for sex or sperm. The mother then gives birth to a daughter whose genes are 100% maternal.



I was already aware of some species of aphids (above) reproducing parthenogenetically, producing clonal nymphs. (Not all parthenogenetic animals produce full clones - some divide their diploid genome in two normally during meiosis but then double the resulting haploid genome to produce a "half clone" diploid daughter that contains half the maternal alleles.) Some aphid species "telescope" and the daughter has its own parthenogenetic daughter developing inside it when it is born! This is rather cool and interesting in of itself but is not actually the focus of this post.

Parthenogenetic organisms are ancestrally sexually reproducing and have evolved the capacity to reproduce without the need for fertilisation, which can be quite handy. We know this in part through phylogenetics (i.e. mapping modes of reproduction onto the family tree of the species in question) but even clearer evidence comes from the observation of sexual behaviours in parthenogenetic organisms.

This brings us to the whiptail lizards. Some of these are parthenogenetic, which is pretty rare in vertebrates. The really interesting thing, though, is that they still exhibit girl-on-girl "mating" behaviour, which is needed to stimulate ovulation and the completion of the reproductive cycle. Being all female, they take it in turns to play the male and female role depending on what point in their hormonal cycle they are - "male" (on top) during peak progesterone levels and female (underneath) when estrogen is on the rise. Some animal species go one stage further and sperm is even needed as a trigger for embryo development, albeit without fertilisation, but this is "gynogenesis", not parthenogenesis. Crazy, huh?

Lepe Lighthouse - small but perfectly formed

Today, we went for a little walk near Lepe and one of the landmarks was the Lepe lighthouse. This is not a giant fence or a trick of perspective, the lighthouse really is tiny! Quite pretty, though. The odd thing, it's set back in the trees, so isn't very visible. I thought that maybe the trees had grown up since it was built and it was no longer in use but it was actually only built in 2000. It could be deliberate, though. It was built to help boats get into the narrow entrance to Beaulieu River, so I guess it only needs to be visible from a specific direction.

The Master Builder's masters of fish and chips

The sun finally came out this weekend. Hooray! To celebrate, we went for a walk near Lepe from the book Jarrold Short Walks - The New Forest National Park. It was a lovely stroll (if a bit damp in places) and I can recommend the book if you live in/near Hampshire.

The highlight of the day, though, was lunch. Back in April, we stayed for a night in The Master Builder's at Buckler's Hard, and had a very tasty dinner in their restaurant. In the Yachtsman's bar before dinner, I had spied some impressive portions of fish and chips being served to other patrons and made a mental note.

The last stretch of today's hike was along the beach near Lepe Country Park, which left us very much in the mood for Fish and Chips, so we thought we would find out if the Master Builder's fish and chips tasted as good as they looked. They didn't. They were better.

All four of us had the fish and chips and the general consensus was that the fish was perfect - light, crisp batter and perfectly cooked chunky fillets of fish. Probably the best I have ever had and, growing up in a seaside town, I've had my fair share of fish and chips! The tartare sauce was also spectacularly good. I'm not sure how they made tartare sauce taste so nice but they nailed it. The chips were not quite so spectacular but certainly nothing wrong with them. The only slight let-down was the mushy peas. I love mushy peas and these were a little on the hard end of the spectrum. They weren't the worst I have had, though, and the fish and tartare sauce more than made up for it. Highly recommended. (Service was quick too!)

Friday, 11 May 2012

Biology Conferences, don't publish papers!

When I was young and naive, I thought it was great when a conference published the submitted paper in a journal. Two for the price of one, right?! No. The older and more experienced (i.e. jaded) that I get, the worse an idea I think the whole publication of submitted talks is. I'm on a few review boards for bioinformatics conferences now and I am always slightly dismayed by the quality of the papers I review. Most of them are straight rejections, with a minority that might be worthy of publication if they make some tweaks. Obviously, I only review a handful of papers for each conference and there are good papers in the overall bunch, but I am more and more convinced that the quality of submissions is driven down by the promise of publication. Here's why...

On the face of it, publication seems like a great way to improve quality. After all, you need to have a finished, polished piece of work in order for it to be published, therefore you will only get talks representing finished, polished pieces of work. The problem is, in Biology at least, this is not what conferences are for. If you want to a finished, polished piece of work, read it in a journal. Preferably, read it in a high profile journal with a good reputation, where you know the review process has probably been quite tough and it has been pre-filtered for interest or impact.

And here is problem 1. If I have a good piece of work that I am really excited about, I am going to want to publish it in high impact journal where it will reach as many people as possible. Usually, this is not a conference proceedings journal. I am, therefore, probably never going to submit my most exciting work to a conference that requires and publishes full papers. If I submit anything at all, therefore, it will be something a bit more mundane and mediocre, or something incomplete and rushed at time of publication.

And here is problem 2. Even if I did think that the conference journal was good enough - some of them are special issues of Bioinformatics or something similar - there is a very definite time window for submission and then publication. Either I just have to happen to have something ready in time, or I have to rush it, or I have to sit on it for ages. Again, if it is something big and exciting, I am going to want to (a) do the best job I can (not rush it) and (b) get it out there as soon as possible (not sit on it), so again, I am put off submitting my best work to the conference.

And here is problem 3. I want to talk about my best and most exciting work at a conference, not something mundane and mediocre or rushed. It may or may not be quite finished or published but that is what I want to get out there and get feedback on. Therefore, not only am I not going to submit by best work to the conference, I probably won't go at all because I need to save my cash for a conference where I can submit what I want to talk about. Furthermore, I am unlikely to want to go and hear a load of other people talking about not-very-high-impact stuff. (Except the keynote speakers who, unbound by the shackles of publication, are usually very good.)

And here is problem 4. As far as I can see, there is a general downward spiral, where quality of submissions is low, quality of talks is therefore low, quality of attendance becomes low and numbers of submissions drop. This then creates pressure to accept papers that are not really worthy of publication - nothing is more frustrating as a reviewer than having your major concerns that need rectifying blithely ignored - and thus the quality drops further and the spiral continues.

The problem now is that I am reaching the stage where I am reluctant to consider even attending a conference that publishes talks as papers, as I have serious quality concerns. Some of the bigger conferences probably have the kudos to remain reasonably unaffected but how long that will last, I am not sure. (And I'm not a fan of big conferences for other reasons.) The only real solution that I can see is to stop publishing conference submissions or, at the very least, have a large section of "breaking science" that does not require full paper submission. Otherwise, I just think the spiral will continue. Life's too short for bad coffee and bad conferences.

Thursday, 10 May 2012

Education is the key to impact

This month is a busy one and two activities that were going on side-by-side last week were (1) writing an outline grant proposal to further develop SLiMSuite (servers and programs) and SLiMdb, and (2) dig up possible "impact" for the upcoming REF. Part of this has featured digging into Google Analytics data for both the bioware servers and my homepage.

Sadly, I stupidly neglected to monitor the documentation and download pages for SLiMSuite (now rectified) but I could get visit data from the webservers and the results made fairly happy reading, especially when compared to the citation metrics associated with the relevant papers.

The bioware.ucd.ie front page currently receives around 350 visits a month from across the world, with 4,174 visits in the period 1 May '11 to 30 Apr '12. Ireland is currently the main user, reflecting the fact that the current host of these resources is University College Dublin, although the balance seems to be shifting towards America now. (Given the amount of science being done there, you would expect the US to be number 1.) Germany and the UK complete the top 4 (again not surprising in terms of both science and presence of participating/collaborating labs) but the usual suspects (India, Canada, Israel, China) are all in there too, which is good to see. The servers themselves receive around 500-1000 page views a month, with the top five servers visited in the period 1/5/11-30/4/12 being: 1. SLiMFinder (2,651 views); 2. SLiMPred (1,812 views); 3. SLiMSearch 2.0 (1,721 views); 4. SLiMSearch 1.0 (805 views); 5. CompariMotif (653 views).

This is all well and good - these are published servers - and hopefully will continue to increase over time, particularly if we can get more funding for development. The thing that surprised me, though, was when I looked at the usage stats for the UPGMA walkthrough I made for a Year 2 practical that I run with a colleague. This website got 5,721 visits in the same period (1 May '11 to 30 Apr '12) - 37% more hits than the bioware front page. This number is also on the rise with nearly 1000 hits last month, due in part to the fact that it now appears on the UPGMA wikipedia page.



This perhaps should not be surprising but when you consider that UPGMA is a largely obsolete method used predominantly for teaching (and quick and dirty clustering) and I knocked up the website in an evening or two, while SLiMFinder is a cutting-edge bioinformatics tool that represents years of hard work, it is still a little depressing. I guess I should make more educational web pages...

Wednesday, 9 May 2012

Your Logical Fallacy is...

Due to grant deadlines and other such fun stuff, I've not had much time/energy leftover for blogging this past week or so. I feel the need to break my May duck, though, so here's a quick post on a useful website - as much so that I have it bookmarked as anything else.

It's yourlogicalfallacyis.com and the idea is that it's a one-stop shop for frequently used logical fallacies that are pulled out whenever someone is trying to argue their point from a position of weakness, ignorance and/or sheer bloody-mindedness. It's going to be good to have a flick through from time to time and make sure that I am not falling into any of these myself. It's easy to do when you want quick closure because you "know you are right" but it is always worth remembering that sometimes you will need to go away and regroup/read up before coming back and tackling an opposing position with facts and logic.

Before people get wrongly excited about this site and it's design, which lets you direct people straight to the fallacy their opponent is making, there is one fallacy I think worth pointing out: the fallacy fallacy - just because someone is making a logical fallacy, does not mean they are wrong. (In other words, please use this site to get arguments back on track, not to "win" them by pointing out that someone else's point is invalid.)