Friday, 30 September 2011

Howling (dumb)bells

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, 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

Monday, 26 September 2011

The Origin of Life - interesting but not a problem

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

Sunday, 25 September 2011

Atheism: not faith, not religion

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.

Saturday, 24 September 2011

The Cabbages of Doom: one decade on

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

Friday, 23 September 2011

Comfort is a cat called Arthur

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

Location:Southampton, UK

Friday, 16 September 2011

A self-promoting blog poster

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

Tuesday, 13 September 2011

iPad 2: the perfect conference buddy

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

Saturday, 10 September 2011

Gay Genius

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.

Friday, 9 September 2011

Go go gadget milk jug!

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?

Sunday, 4 September 2011

It's not The Central Dogma, my dear Watson

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 Central 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

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

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)

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.)

Saturday, 3 September 2011

Ode to a Troll

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

[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

Friday, 2 September 2011

The Redbreast: don't read the blurb

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

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!