Monday, 31 December 2012

Experiments with the iPhone Blogger App

My recent revisiting of the iPad BlogPress App has made me curious about the Blogger App for the iPhone. Like BlogPress, I have not used this for a long time - I may have abandoned it when I first discovered BlogPress - but also not deleted it. I therefore thought I'd try a quick post with it to see how it works.

The interface is very clean and uncluttered and might be a good way of editing text for posts on the go. At the moment, I generally email the text (and pictures) when on the go and then tidy and publish later. I also have a bunch of (notes for) part-written posts in various text editors. If the Blogger App proves reliable, it might be a better solution for both.

One weakness does seem to be how pictures are handled. As far as I can tell, you can either upload images full size or as a number of smaller sizes up to 640x480. I'd prefer something in between. I'm also not sure how much control over placement there is. Out of curiosity, therefore, added the two pictures above to this post and just published it straight from the App to see where they will go. The result is visible to the left and it's not that pretty, so I think a bit of online editing is definitely required. I'd also be a bit worried about the resolution of the pictures if they weren't just iPhone screen grabs, as in this example. (The abundance of white in the first image does not help, it is true.)

As well as the image issues, it's also easier to edit the post in order to add links and formatting to the text, although these can be added manually using raw HTML. The final risk is the tagging: Blogger will add tags but does not suggest existing ones like the Blogger website. Overall, though, I am keen to use it a bit more for the basic text content, until it let's me down. (I had one problem uploading a draft this morning but it was fine when I tried it later.)

Sunday, 30 December 2012

Revisiting the BlogPress App for iPad

The BlogPress App fell out of favour with me some time ago around the time that iOS 5 came out. (Yes, that long ago!) BlogPress had ceased accessing my online posts (draft or published) and then, once I updated to iOS5, it has stopped working altogether. I never deleted it, however, as I always retained the hope that it would get sorted out. As 2012 draws to a close and future blogging in 2013 is on my mind, I therefore thought I would try it out again and see.

I'm not entirely sure whether I trust it enough to publish from it directly - although this post is a test in that respect. I am also worried about the pictures disappearing, as seems to have happened with some of my earlier blog posts. Despite this, however, it does have some nice features including common HTML options (including fonts) and could be useful for drafting posts for subsequent tidying and publishing on a proper computer. (It's more of an oPad after all!)

Indeed, having just looked at the preview for this post, I decided that a bit of extra editing was definitely needed. In particular, the pictures are not embedded that well. I have left the basic code alone but was not happy that the resolution of the image shown was almost half the actual size. (The pane width and image width is 568 pixels but the actual image resolution set by the "/sXXX/" part of the src path is only 288 pixels. Why?!) The Preview itself also looks decidedly odd - squished horizontally and missing the flanking parts of the page. Hopefully, following this quick edit in Safari, it will come out fine...

Some fine wine for Christmas Part II

One of the nice things about having family in two different locations is that it provides a good excuse to extend Christmas. And so it was that we flew to Dublin yesterday with a case full of presents for Christmas Part II. (Note to self: next time, buy smaller presents! The Tonka "Big Rigs" dump truck for my nephew was too good to pass over on the basis of size!)

This Christmas had been relatively alcohol-free so far. That is, until we went to Dublin! This is nothing to do with the stereotype of Irish drinking habits - having been a student in the UK and lived in Dublin for six years, I would say the two cultures are on a par in terms of alcohol consumption - but more do to with not driving and being in non-tee-total company. Last night's dinner was therefore accompanied by a couple of very nice wines. (Thanks to the discerning tastes of my in-laws.)

The first was a classic New Zealand Marlborough Sauvignon Blanc, which we've had before: Mirror Lake. Still crisp, fruity and refreshing.

The second was nicer still - a very fine 2007 Domaine Combier Crozes-Hermitage Clos des Grives from Rhone, France. I'm not the biggest fan of French wine but Crozes-Hermitage seems to be an exception. I remember enjoying one at a wine club event a few years ago and really enjoyed the ‘la Matiniere’ Domaine Ferraton Pere et Fil that we had at The Black Rat in Winchester. This one was a very good Syrah - not quite as fruity and in-your-face as a New World Shiraz tends to be but still packed full of flavour. (And much nicer than any from the Syrah/Shiraz wine tasting from early this year.) Highly recommended.



Saturday, 29 December 2012

Dublin Terminal 2 food court - great for food but poor for hot drinks

Blogging (and writing) might be a bit thin on the ground over the next few days, as we're over in Ireland for Christmas Part II. Then again, there always seem to be lots of things to blog about when you go for a trip.

Flights from Southampton fly in to Dublin Terminal 1 - the old one - but our flight arrival time conveniently coincided with the period that a friend (and old lab buddy) of my wife was passing through Terminal 2 on the way back to Paris, so we went there for a drink.

I have long admired Terminal 2 from the outside - sadly, it opened after I had left Dublin and was no longer making regular trips - but aside from a brief walkthrough, this was the first time I had had the opportunity to have a good look.

The Terminal itself, although open for a couple of years now, is still very pretty new-looking. The Food Court was pretty good too and I was impressed to see a Diep Noodle bar and Gourmet Burger Company among the offerings. (Until the lovely meal at my in-laws this evening, I felt slightly sad not to be staying for dinner!) I was not so impressed by the small mug of hot chocolate from a machine for €3, though. €3! And that was despite there being adverts for O'Brien's - I think it was just the sandwich part of the outfit. (The coffee was from a machine too.) Hmmm.
Oh well. At least on the way back through Terminal 1 we can visit Butlers for a proper hot chocolate - and it has a Starbucks too if we need caffeination!

Friday, 28 December 2012

West Quay food court gets a facelift

This morning, we popped into Southampton and decided to go in early to miss the main sales rush. That meant breakfast in town. We decided to check out the new Cafe Rouge Express in West Quay and discovered that the whole food court has been given a facelift. It looks really nice now and with a new Wagamama and Pizza Express in addition to the Cafe Rouge, a welcome addition to Southampton's lunch options. (I do love Wagamama!) There's an "Ed's Diner" coming soon too, which might sort out the Southampton brunch conundrum.

Thursday, 27 December 2012

More genomes than you can shake a bamboo stick at

I remember when the first eukaryotic genome - that of yeast - was sequenced in 1996. I was still an undergraduate student, studying Genetics. At the time, it felt like it was the golden age of genetics, with the excitement of the ongoing Human Genome Project. The original human genome took over 10 years and cost around 3 billion dollars - approximately one dollar per base pair. (Nowadays, it's less than $10k per genome.)

It is sometimes easy to forget how far we have come in the decade or so since the first human genome was finished but in case you need a reminder, you need look no further than the latest issue of Nature Reviews Genetics, which features the sequenced genomes of sweet oranges, mandarins, pummelos, watermelons and 34 giant pandas. (2% of all the wild giant pandas!)

I like the last paragraph of the editorial too:
"We do not have to just believe in the process of evolution by natural selection. We can see mutation and selection produce varieties and species of crop plants. We can see the process at work in the wild and admire the way it creates and shapes species and populations of animals and plants. And, the most wonderful thing of all is that you can test the predictions of the idea with your own experiments, with your own eyes."
Perhaps the craziest things of all is that sequencing technology is still improving and still getting cheaper. As a bioinformatician, this is both exciting and scary, as data storage and analysis struggles to keep up with data generation. In fact, I wonder whether 2013 will be the year when sequencing itself becomes like the intermediate stage of a laboratory experiment and people will stop storing the raw data once it's been processed - it's probably cheaper just to repeat the sequencing than to store and backup the raw data!

Monday, 24 December 2012

Merry Christmas (Eve)!

Today, I awoke to the smell of cinnamon buns and fresh coffee. A fine way to start the day! The weather outside is frightful but, sadly, not in a white Christmas way, just in a wet Christmas way. It's cozy inside, though, and listening to Christmas tunes is helping maintain the Christmas spirit.

If you need a boost to your own Christmas spirit, my recommendations are White Wine in the Sun by Tim Minchin for music (proceeds to the National Autistic Society) and Miracle on 34th Street (1947 version) for movies. I watched the latter for the first time over the weekend and really enjoyed it, which surprised me somewhat, I must admit! (It manages to avoid be over-schmaltzy.)

And if that doesn't work, here's one of our cats (Arthur) wearing a Santa hat:

Sunday, 23 December 2012

Urban Ears Headphones, one year on and still great

Last Christmas, I received a pair of Urban Ears headphones for a present. Now, almost a year on, I thought they were long overdue a review because they are great!

There are loads of features that I like about these headphones. First, as seen in the picture, they pack down nice and small for easy transport. Unlike my JVC noise-cancelling travel headphones, the folding mechanism is really robust. The headphones stay packed down really well and also feel stable when folded out and on my head. (They do not have a centre hinge like my JVC ones, the ear individually fold inside instead.)

Another thing that I really like is the durable, tangle-free cable, which is wrapped in braided fabric. Genius! Wrapping the cable around the headphones when packed down also stops tangles but the worst entropy-induced knotting I have got with these headphones has been a couple of gentle tugs away from tangle-free audio pleasure. The braided fabric also gives the cable a more robust feel and despite being in my bag most days over the past few months there is no sign as yet of the cable damage that has afflicted my Apple inner-ear earphones.

Which brings me nicely to the next feature... I stuck with the Apple earphones that came with my iPhone for a long time because of the "remote control" on the cable, complete with mic and volume control. The urban ears model I have does not have the volume control (although I believe that others do) but it does feature a handsfree mic and remote control button that will start/stop/skip tracks and answer/end calls. It works so well that these headphones are now my Skype headphones of choice. (I tend to Skype on my iPad.)

There's obviously one key trait of headphones that I am yet to mention: the sound quality. Like the build quality, the sound quality is excellent. I am not an audio snob - I am happy with MP3 versus vinyl, for example - but I do like listening to music and I like to hear the full range of sound that my mortal ears can distinguish. The Urban Ears deliver across the board and certainly match the audio quality of my iTunes recordings. Being headphones rather than earphones, they do a good job of cutting out external noise too. This helps a lot, especially when it's a bit windy outside, although it obviously has a slight downside of reducing peripheral awareness when out and about. (I only use them in safe places.) The snugness of fit also means that they can be a bit uncomfortable after a couple of hours. That's about the only bad thing I can really think to say about them, though, and it's probably not that good to be listening to music for that long without a break anyway. (They are also adjustable, so they're comfortable for regular use.)

It's probably a bit late for Christmas presents but if you are looking for something to spend Christmas money on and you need new headphones, I highly recommend them. (The "Plattan" ones I've linked to are slightly different to mine, whose name I forget, and have an additional "ZoundPlug" for a friend to plug in and share the music. Otherwise, they look essentially identical.)

My favourite Mayan "End of the World" advice


The Independent had a great little articles a couple of weeks ago in preparation for the Mayan non-prediction of the End of the World yesterday: How to prepare for the end of the world: Fit a smoke alarm, leave extra time for journeys, and give your pets a cuddle... "British organisations have been issuing tongue in cheek advice on how to prepare for the upcoming Mayan-predicted apocalypse on the 21st December".

As it happens, I gave one of my cats a good cuddle in the morning because I didn't have to get out of bed early, thanks to an extra day off in honour of The University of Southampton's Diamond Jubilee. My favourite advice, though, had to be from a London Fire Brigade spokesman:
"Fit a smoke alarm on each level of your home, then at least you might stand a chance of knowing that the end of the world is nigh ahead of those who don't.

"If you survive the apocalypse you'll be alerted to a fire more quickly should one ever break out."
[BTW, the glyphs in the picture have nothing to do with the "Mayan Apocalypse", they're from my visit to Xunantunich in Belize.]

Saturday, 22 December 2012

Leek risotto with chestnuts - it may not be healthier than a ready meal but it sure is tastier!

Yesterday, we had "Leek risotto with chestnuts" from Hugh Fearnley-Whittingstall's River Cottage Veg Every Day! The picture (below) does not do it justice, more to do with my bad/rushed food photography skills than the dish itself. I've never used chestnuts in a recipe before and they were tasty! Easy too.

Leek risotto is a bit of a deviation from the normal risotto I make, which has shallots or onions as the first ingredient and then something for the flavour later. The leeks take the place of both elements but they require some additional cooking up front.

Once they've been sauteed in butter for 20 mins or so to make them really silky, though, it's pretty much business as usual: chuck in the risotto rice and fry for a bit with the leeks, cook off a glass of dry white wine, then simmer in stock, adding a bit at a time. The chestnuts were simply crumbled, cooked in a bit more butter for a couple of minutes, and then added at the end. Delicious!

It paired very well with the dry white I used for the risotto too, a Clearsprings Sauvignon Blanc from South Africa. (Half price in Sainsbury's at the moment!)

Celebrity chefs have got some bad press recently following a report on some research on the BBC News website - Ready meals 'healthier' than TV chefs' fare:
"In the study, published in the British Medical Journal, they compared 100 main meals from four TV chefs, who had books at the top of the bestseller charts, to 100 supermarket ready meals. These were then compared to nutritional guidelines set by the World Health Organization.

Red light
On average, meals in the chef's books were less healthy and "more likely to achieve red traffic light labels", the researchers said."
And then the damning traffic lights themselves:


There was a fair amount of butter in this recipe, it is true, but I think this account might be a little harsh on the old celeb chef cook books, even ignoring the very valid comment by the chefs themselves that they feature of mix of "normal" and "special occasion" dishes. There is also a lot more to healthy eating than the "traffic light" system. What about the nutritional value of the food?

It is true that the risotto only had three leeks in four portions but the ratatouille we made at the weekend from the same book was packed full of vegetables. Similarly, Jamie Oliver's English Onion soup recipe from Jamie at Home may have been topped with cheese on toast but was crammed full of onions and leeks.

Not only are these recipes packed full of veg, they're packed through of flavour too! Which brings me to my last point: cooking fresh food and making something tastier than any ready meal has to be better even if it gets the odd red light. Cooking tasty recipes increases confidence and leads to cooking with more fresh fruit and veg. Finally, if there is unhealthy stuff in there, you know because you put it in!

Wednesday, 19 December 2012

Piltdown man: hoax but no giant conspiracy

A century ago today, "Piltdown Man" and associated finds were announced at a Geological Society meeting. It subsequently turned out to be one of the biggest scientific hoaxes of all time, though it was not discovered for over 40 years and we still don't know who did it, or why. (Although there are suspects.) I'm not going to recap the details here because the Natural History Museum and recent Nature Podcast Extra do a much better job than I can. (And WEIT!)

It's a good reminder to all of us in science, however, not to get too carried away with novel discoveries until they have been thoroughly verified. It seems pretty clear that a number of the scientists involved in Piltdown were thoroughly duped and tragically so in some cases. I think it is sometimes easy to forget that not everyone has the level of scientific or personal integrity that we hope all scientists aspire too.

It is also a good reminder of something else, though, which is encouraging in this modern age of Bad Pharma, continuing misrepresentations of evolution and relevations of scientific fraud: with science, the truth will generally out in the end. Piltdown Man was a hoax but human evolution is real and it was predominantly further finds and evidence that cast aspersions on Piltdown's authenticity until new technologies finally revealed it as an unequivocal fraud. What's more, despite its importance in the past, this was not hushed up or swept under the carpet. In the modern age, with its pressures for instant press releases and hurried high impact publications, I take great comfort in that.

Despite some claims to the contrary, there is no giant scientific conspiracy for, in the long run, as scientists we have nothing to gain.

Sunday, 16 December 2012

Evolution is a population-level phenomenon

An argument I have been encountering a lot recently is one that goes something along the lines of:
"Natural Selection cannot be the source of novel adaptations because it only works on what it already present. It does not generate anything and therefore a novel trait cannot be the product of Natural Selection."
These claims are then used to support the primacy of mutation as the driving force behind evolution, often coupled with (unsubstantiated) claims that these mutations are not random. In other words, Natural Selection is a myth and goal-directed mutation is responsible for the evolution of adaptations.

On face value, this can seem like a convincing argument. Natural Selection does only act on existing variation. New variants do have to arise by mutation (for a given definition of mutation), which is independent of selection. However, extrapolating that to mean that adaptive evolution occurs through the source of the new variants, mutation, and not selection is a classic case of confusing individual traits with population/species traits. I suspect that this confusion is the source of misunderstanding for many people who champion directed mutation and denigrate the power or potential of Natural Selection.

We have a tendency to draw phylogenetic trees as single lines for the branches. It is important to remember, however, that these branches - representing the evolution of species of gene sequences - are actually representing whole populations of organisms or molecules.

Evolution is a population-level phenomenon: individuals mutate but they do not evolve. It is true that new variants have to arise in an individual, independent of selection. However, we do not say that a trait has "evolved" until it reaches a high frequency or even reached (effective) fixation in the population.

For example, certain mutations cause polydactyly (extra fingers and toes) in humans but we do not say that humans have "evolved six fingers". For humans, a mutation usually has to reach a frequency of 1% before being considered a polymorphism. This is somewhat arbitrary but it needs to be in at least two generations; otherwise, lethal or sterilising mutations would constitute a polymorphism and this would make the concept pretty useless. Likewise, it would be pretty silly to say that something had "evolved sterility" because a single individual had a sterilising mutation.

Evolution does not need Natural Selection. Random processes are sufficient for a neutral (or nearly neutral) trait to "drift" its way through a population to fixation. However, without invoking an external agent, Natural Selection is the only process that drives a trait through (or from) a population, resulting in adaptive evolution.

Population-level change is still change. A population or species acquiring a new trait is still evolution of a new trait. A novel evolved trait can be the product of Selection.

Friday, 14 December 2012

Coral research at Southampton gets a well-deserved boost

It's always nice to bask in the reflected glory of a collaborator. EU grants are hard to get and funding is getting ever tighter due to the global economic situation, so it was great to read of a local success as reported this week in a University of Soutampton press release. The congratulations go to Joerg Wiedenmann, who heads up The Coral Reef Laboratory here in Southampton.

Joerg does lots of interesting work on corals, looking at how they adapt to (or suffer at the hands of) Climate Change, including work on coral bleaching. I've done a little work with him on coral red fluorescent proteins, which are related to the famous Green Fluorescent Protein (GFP). (The massive diversity of fluorescent protein mutants that now exist are a great example of how single amino acid mutations can have quite dramatic phenotypic effects that would certainly be "visible" to Natural Selection.) It's not published yet, though, and it's very much his project, so I won't write about it now.

Corals have also been in the Science news a lot recently following the recent discovery that they recruit gobies to act as "body guards" and clean off toxic seaweed that would otherwise threaten the coral's survival. Pretty cool!

Corals are generally fascinating animals even when they're not recruiting fish body guards. For one thing, they have symbiotic algae, which photosynthesise and can make up a substantial proportion of the material in each polyp. Indeed, it is expelling these algae under stress conditions that leads to the bleaching that Joerg studies. As an evolutionary biologist studying molecular responses to stress, however, this symbiosis can be frustrating as well as fascinating: corals could acclimate through their own regulatory changes or adapt through evolutionary changes, or these changes could happen in the algae, or by swapping algae. Enough options to keep researchers busy for some time!

Wednesday, 12 December 2012

All aboard The Beagle! (Again!)


Back in October, I posted about Darwin tweeting his adventures on the second voyage of HMS Beagle. (His first.) Well, it seems that I was a bit premature as, although scheduled to depart on 24th October 1931, it did not actually leave until December. Well, if you got bored waiting for the departure, and/or find the tweets tantalising but too short, I am happy to report that Darwin's Diary of the whole journey has also been released in blog form and the first entry is today! (Well, it was six years ago today, but if you want to follow it again in "real time", you can start again today.)

Saturday, 8 December 2012

Is The Theory of Evolution in Crisis?

No. The Theory of Evolution is not in crisis and I get a bit tired of reading that it is - and never from evolutionary biologists, it seems. For some reason, a select band of philosophers, engineers and computer scientists seem to believe that the whole edifice is being challenged and about to come crashing down - and they're not even all Creationists. (I'm not going to single any out here.) The fact is, the very statement that "The Theory of Evolution is in crisis" portrays a deeply flawed understanding.

There is no such thing as "The Theory of Evolution" unless you are referring to the observed fact that all extant life we know about evolved from a common ancestor (or ancestral population). Ironically, this is the bit of evolutionary theory that is furthest from crisis - it is an observation that is so well supported that it is seems incredibly unlikely to ever be overturned. Science is sometimes over-turned in the light of new evidence - and that possibility always remains - but we believe the things we do for a reason and, as science progresses, we get less wrong and less likely to have a major "paradigm change" or "crisis".

"The Theory of Evolution" cannot be in crisis because it is not a single entity. Like the Trinity, it is three in one. In addition to the factual observation that evolution has happened (and even most Intelligent Design advocates seem to accept this), there is evolutionary theory, yes, but this is a body of theories explaining the mechanisms of evolution, not one single theory. There are a few core ideas - such as gene-centric evolution and inclusive fitness being key for understanding adaptation, and most evolutionary change at the genetic level being selectively neutral - but many of the subtle details are still being worked out and debated. This is not a crisis, it is science. Lastly, there is the historical aspect of evolution - how and why did the particular observed trajectory of evolution happen. This is the hardest one of all to get a good answer about because, just like human history, we will never really know. We can't go back and see. Also like human history, we know there are random factors and rare chance events at play, which makes conclusive answers harder still. It's still interesting to propose and test ideas - just because we cannot know, we can still have plausible and implausible explanations based on the evidence. (A global flood around 6000 years ago is implausible given the data, for example.)

A few different potential causes for crisis have been raised and dispatched over the years but one example that seems to recur is the old chestnut of epigenetics. Epigenetics is interesting but does not threaten evolution as a whole. It does have an impact on how we understand about adaptation and, in particular, the effect of "nature versus nurture" on phenotype (though not always in the direction people imagine). It certainly makes life complicated when you study responses to environmental change. I am yet to be convinced that epigenetics seriously challenges any of the core understanding of how evolution happened, however, just as learnt behavioural traits and any other environmentally-influenced phenotypes have not.

The point is that epigenetic markers are erased and rewritten on very short time-scales, whereas the epigenetic machinery and DNA code recognised by that machinery is not and thus, in line with other features of organismal biology, it is a system that has evolved like any other. (The environment is not reaching out and directly making a modification - it is triggering an epigenetic response, which is encoded by the genome.) It may shift the target of evolution to variation in an epigenetic response rather than direct genetic variation of the trait itself (or, more likely, a combination of the two) but it is not qualitatively any different.

When challenged, those proclaiming a "crisis" sometimes admit exaggeration but argue that biologists are in danger of being complacent about evolution, so it should be challenged in this OTT style. Well, I disagree with this sentiment too and such statements again reveal a deep lack of understanding of what evolutionary theory is to an evolutionary biologist - a tangled, complex web of ideas to be appreciated, examined and torn apart as necessary, not some kind of creed of rule book to rally around. To call "crisis" an exaggeration is an understatement of staggering proportions. To accuse biologists of being complacent is just wrong.

As a "front-line" evolutionary biologist, trying to keep up with all the data coming through from projects like ENCODE, I can assure you that we are not "complacent" about any aspect of evolutionary theory. (Except, possibly, the fact that evolution happened.) No good scientist is ever complacent. Doubt and criticism are our core over-riding principles. What we are - and rightly so - is cautious. Great claims need great evidence. New ideas also need to fit with all the existing data as well as the exciting new stuff. For this reason, Jerry Coyne is entirely and absolutely right to explain all these things within a gene-centred framework and that framework still works (as long as you understand what is meant by "gene" in that context).

Finally, when a fantastic new discovery is tested, double-tested and validated, it is accepted and becomes part of the joyous "poetry of reality" as Dawkins put it. Even here, there is no crisis. Evolutionary theory moves on but, like all good science, it does so slowly and carefully, not in a series of knee-jerk paradigm shifts that ignore the fact that we have our current understanding for a reason - and that reason is past experiments and past data that still need explaining under any new framework.

Thursday, 6 December 2012

Surprisingly impressed with Siri

This week, after over five years on the same network, I left O2 and switched to Vodafone. This was purely motivated by money - I wanted to upgrade to an iPhone 4S and the Car Phone Warehouse had a ridiculously good online deal. (Essentially a free phone and a lower monthly tariff that my old one. O2 have always been pretty good to me and, a little ironically, the customer service people you deal with when leaving the network are some of the nicest and most helpful people I've ever dealt with!)

I'd pondered going all out and going for an iPhone 5 but figured that if I did that I might as well upgrade from 32Gb to 64Gb and then we're talking £400 for the phone. Plus, of course, all my iPhone 4 adaptors etc. would cease working and I'd have to get a new case and all the rest. So, I opted for the more thrifty choice.

The new phone itself was transferred to my old number yesterday and so far, so good. Apart from being generally faster, I've not yet done enough to really notice the difference yet but I have given Siri a little road test.

Having last played with voice recognition software when at Uni in the 90's, my expectations were very low and I've actually been very impressed. My first task for him was to give me 1/2lb in kg. (I thought one 250g block of butter would be ok but wanted to check.) The request was understood and the right answer provided. Today, I've tried his DJ capabilities: this morning, he correctly interpreted my request for some Avenged Sevenfold and put their albums on shuffle for me. This afternoon, en route to getting our Christmas tree following a work Christmas social, he correctly understood my wife's request for the Christmas playlist.

I still can't decide whether Siri is purely a gimmick (for most people at least) or whether it will prove to be useful (can operate with gloves!) but these early successes mean that I feel more inclined to find out.

Monday, 3 December 2012

Zooming around the Tree of Life


This morning, whilst feeding the cats, I came across the very fun - and educational - OneZoom Tree of Life Explorer, described in a PLoS Blog article, Fractaltastic Evolution. Currently, it only has mammals and amphibians but it will grow. Birds are next and plans are afoot to use Open Tree of Life data to extend it to 2 million species (or maybe more by then).

It has lots of nice features, including different views, threats of extinction from the IUCN Red List and dates of divergence. The latter can be used to run a "Growth Animation" timeline, which is another useful tool for trying to grasp evolutionary timescales. I can feel some OneZoom-inspired MapTime TimeLines coming on when time allows.

h/t: @phylogenomics