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

Friday, 30 November 2012

AHS Southern Conference 2012, this Saturday at The University of Southampton

The National Federation of Atheist, Humanist and Secular Student Societies (AHS) have their Southern Conference 2012 this Saturday, Dec 1st. It's on Highfield Campus at The University of Southampton, hosted by the Student's Union Atheist Society. One of the speakers is The Tippling Philosopher, whose blog I frequent when time allows (and who also reposted one of my posts on ID Creationism). Nice to see that they're heading to The Crown - my favourite pub near the Uni - afterwards for a pint or two and dinner. (Mmmm... Crown Burger!)

Although I am a member of The Rationalist Association, I've never actually attended an atheist or Humanist event since moving to Southampton, so I will try and get along if I can. If you're in the area, why not check it out?

Saturday, 24 November 2012

Differential survival, (inclusive) fitness, selection and evolution

In my last post about Multi-level selection and The Selfish Gene, I neglected probably the most famous and important aspect of the "Group Selection" debate: "inclusive fitness", which (along with its specific form, "kin selection") can potentially give rise to counter-intuitive adaptive behaviours such as altruism and self-sacrifice. To understand inclusive fitness and how/why (a) it works, and (b) it is important, we have to revisit the importance and meaning of heritability in selection.

The key point is that "fitness" and selection are about more than just differential survival. Differential survival is sufficient for evolution - the population will change with time - but without the heritability aspect, this is not selection and there can be no adaptation.

It's easiest to think about this in terms of purely random events. Imagine two populations of beetle (there sure are a lot of beetles!) living in two trees who, by chance founder effects have different frequencies of an allele that causes melanism (a dark colour morph). Now imagine that one of those trees experiences a rare catastrophic event - perhaps a meteor-strike, or it is on a cliff-top and collapses into the sea - that wipes out its entire beetle population. The frequency of melanic colour morphs in the beetle population has changed - there has been differential survival - but because it was totally unrelated to the causal reason for the differential survival, this is not selection.

Evolution without selection happens all the time and can easily lead to certain traits becoming fixed in a population, even if they have no direct (or only a very weak) fitness effect on those with the trait relative to those without. (Fitness is always relative.) Most changes at the molecular level, for example, are neutral changes occurring through random genetic drift. This is still evolution, it is just not selection - it will not give rise to adaptation. (Although a change of environment - and the environment for genes is never static - could render a previously neutral trait as good or bad.)

So where does kin selection and inclusive fitness come in? Well, a key - and sometimes confusing - point about fitness and selection is that the individuals expressing the heritable trait and the individuals benefiting from the heritable trait do not have to be the same individuals. This is critical because it reinforces the special place that genes have in multi-level selection.

In the last post, I wrote:
Yes, selection can potentially act at some of these different levels - the collective properties of the family, tribe, species or ecosystem can affect the fitness of the genes therein - but only the genes make copies of themselves. Only the genetic information is passed on - all of the physical aspects - the DNA, the chromosomes, the cells, the bodies, the tribes, the ecosystems - are transient vehicles for this information. Only if this genetic information gives rise (in an appropriate background) to the trait that influences fitness - whatever the level that fitness is manifest - will that trait be heritable and selection happen.
This is the difference between "replicators" (in Dawkins parlance) and mere reproducers. The crucial thing about genes is that they make copies of themselves, which are then carried by different members of the population. A particular genetic variant will increase in frequency if the sum total of all its effects is to the collective benefit of carriers of that genetic variant, even if some of its effects are detrimental to some of its carriers. Hence altruism can still spread if it has a genetic basis and the net product is increased survival/reproduction of carriers of the altruism "gene(s)".

There are two more important points about inclusive fitness:

1. Kin recognition is not required. Crucially, there does not need to be a conscious awareness by the altruistic individual; it does not need to be able to recognises its kin or fellow gene-carriers. (Although, clearly, if it can then it will be even more successful.)

2. All fitness is inclusive fitness. Inclusive fitness is one of the few unifying principles of biology that, as far as I can tell at least, applies across the board. Whether you are talking about Artificial or Natural Selection, Individual or Group Selection, it all comes down to inclusive fitness. Even when all of the phenotypic effects of gene are limited to its carrier - pure "Individual Selection" - inclusive fitness comes in to play: as long as it benefits more individuals than it impairs, it will still spread. (The same gene can have different effects in different individuals.)

The nice thing about inclusive fitness is that it works irrespective of the nature by which the sum total of its effects benefit its carriers. These effects can occur at any level of biological organisation and may, indeed, have effects at multiple levels; thanks to inclusive fitness, far from being in conflict, multi-level selection and The Selfish Gene are one and the same.

Thursday, 22 November 2012

Multi-level selection and The Selfish Gene

Yesterday, I attended a seminar run by the University's Institute for Complex Systems Simulation by Samir Okasha, a Professor of Philosophy of Science from the University of Bristol and author of the book "Evolution and the Levels of Selection" (among others). The talk was entitled 'Individuals versus Groups in Evolutionary Biology' and Prof. Okasha gave a very interesting presentation about some of the history and issues surrounding the discussions (and sometimes arguments) about "Group Selection" and its modern incarnation, "multi-level" selection.

It looks like an interesting book too and is on my ever-growing reading list. I'd particularly like to ponder some more his thoughts on emergent group properties - something I do not currently have the time, space or philosophical nonce to explore further in this post.

There was one key aspect of the debate that, in the interests of time, was not covered in detail in his talk: the issue of heritability and what that means for "Units of Selection". The more I think about it, the more I think it is a real barrier for people understanding the problem and, in my opinion, leads to all sorts of confusion about how evolution and selection work.

This is a quote from an Amazon review of his book that sums up the key issue quite nicely:
So often we are bombarded with 'scientists' giving us their metaphysical views as if they were 'scientific fact'. It is therefore refreshing to find a philosopher looking at a science and seeking to clarify the various concepts in that science.

Okasha observes that the various life forms are arranged in a hierarchy:

Generally reproduction occurs at the same level in the hierarchy: organisms reproduce to give organisms; chromosomes divide to give chromosomes; colonies divide to give colonies, and so on. According to the logical formulation of the theory of `natural selection' a) variation, b) differential fitness (different rates of survival and reproduction) and c)heritability (parent - offspring correlation) are required to produce evolutionary change. All these may be present at each of the levels in the hierarchy so there is nothing that necessarily restricts selection to any one level, say at the level of the gene. To claim that selection always occurs at the level of the gene is to confuse the result of selection (the proportion of the various genes in the gene pool) with the process of selection (where in the hierarchy the winnowing actually occurs).
[My emphasis]
This is an argument that I have come across a few times on internet forums and like - often by non-biologists. (I'm not sure why the reviewer puts quotes around 'scientists' - perhaps this is an unfair dig at Dawkins. When these arguments appear, they are often accompanied by a barrage of anti-Dawkins nonsense about dogmas and how our old, flawed understanding of evolution is being overthrown etc. At best, this is a gross exaggeration. In my opinion, it is utter hogwash.)

Quite simply, I don't think this argument works because it overlooks something very important. I have highlighted the key phrases in bold. This review has the matter utterly backwards. To say that selection is occurring at a level other than the gene and not the gene (and "gene" in this context must have the correct evolutionary meaning not the biochemical meaning) is to confuse the agent of selection, which can be gene, cell, organism, family, whatever, and the target of selection - the "gene". This is because, for selection to work, there has to be heritability and this heritability is not simply "parent - offspring correlation".

(At this point, I would like to make it clear that I do not think Samir Okasha makes this mistake. I've not read his book yet but in his talk he was very clear to make the distinction between causality in selection - what we call direct and indirection selection, which correspond to causal and correlative changes in gene frequency. He also pointed out that there is no conflict with multi-level selection and "The Selfish Gene".)

For selection to work, there has to be a causal link between the heritable trait and differential fitness. Mere correlation is not enough. It is enough for evolution - there will be a change over time - but it is not enough for natural selection. And this is where genes are special. Yes, selection can potentially act at some of these different levels - the collective properties of the family, tribe, species or ecosystem can affect the fitness of the genes therein - but only the genes make copies of themselves. Only the genetic information is passed on - all of the physical aspects - the DNA, the chromosomes, the cells, the bodies, the tribes, the ecosystems - are transient vehicles for this information. Only if this genetic information gives rise (in an appropriate background) to the trait that influences fitness - whatever the level that fitness is manifest - will that trait be heritable and selection happen. Reproduction in the important sense - heredity - does not occur "at the same level in the hierarchy".

Has anyone actually demonstrated non-genetic inheritance of any higher-level trait? I'm not aware of any and whenever I have raised this in online discussions, I am normally just met with a barrage of anti-Dawkins nonsense or some vague notions about epigenetics, behaviour and "emergent" properties (which I advocate in general, by the way,) without any specific demonstration or model as to how these higher levels reproduce and pass on their traits to the next generation. Crucially, you have to do more that demonstrate that it could work mathematically or in a computer simulation - you have to demonstrate that there is a corresponding biological reality.

Which brings me to another important point. I would also question the notion of "fitness" at some of these higher levels. Ecosystems do not reproduce at all. There can be competition between groups of organisms, certainly, and long-term differential survival, which will result in evolution - just as random events such as floods and meteor strikes can influence long-term evolution through differential survival. But this is not selection. The ecosystem is changing because of individual success or otherwise and individual success is being influenced by the environment - the changing ecosystem - but an ecosystem is not directly spawning a new ecosystem that inherits its properties and goes off into the world to compete with different ecosystems. (It seems to me that there is one higher level entity capable of non-genetic inheritance - something championed by Dawkins himself. The cultural replicator, or "meme". This is not what multi-level selection is about, though, as far as I can tell.)

A final problem for non-genetic multi-level selection is that many of these "levels" don't really exist in a fashion that makes selection possible - they are part of continua rather than discrete entities. An ecosystem, for example, does not really mean anything specific. I am an ecosystem from the perspective of my gut microbes. The whole planet is an ecosystem. It is useful to drawn the boundaries at different points for specific study but we should remember that these distinctions are arbitrary. Even an "individual" is a woolly concept thanks to symbiosis - and we are probably all symbionts at the end of the day.

The only thing that is absolute is that you can break everything down to genes (genetic information) and their environment. The flow of information is one way. Genetic information is modulated - but not created - by the environment. (Even accounting for epigenetics, which modulates the environment but not the genotype, though this is for another post.) The Selfish Gene (and its Extended Phenotype) still wins.

Or does it...?

There is one problem that remains for the "Selfish Gene" and it is the same one that plagues almost all of biology. Just like all the levels above it, a "gene" (in the evolutionary sense) is just a mirage. In many ways, there is no such thing as a gene. There is just genetic information. We like to talk about a "gene for X" but really what we mean is "heritable genetic information that has a causal but environment-dependent tendency to produce X". This is just a problem of conception and language, though, not the underlying mechanism and theory. Selection is still ultimately acting on genetic information, and it is still selection at this level that gives rise to adaptations, but how you package this genetic material up into genes is, again, context-dependent and (thanks to recombination and mutation) can be complicated.

It fascinates me how we love to try and split continua - life, species, development, genes - into discrete packets even when no such packets exist and then tie ourselves up in knots because we can't let go of those arbitrary (and false) divisions we have made. Ultimately, I think the issue of Individual versus Group Selection might just be this problem, taken to another level.

Wednesday, 21 November 2012

#ProjectEvoMap (not "Project EvoMap"!)

Social media and public engagement are increasingly important for scientists in the modern age. Resources like the University of Oxford's 23 Things are springing up to help young (and old!) researchers harness the power of "Web 2.0" activities, such as Blogs, Wikis, Podcasts and Twitter. Although a blogger and occasional Tweeter, I think I should probably do the course myself; I am sure that I could make better use of social media than my current attempts. (As with most activities, though, the biggest obstacle is time and energy!) I think that one has to be careful about getting obsessive about such things (I went through a phase of trying to post every day, which is not always healthy or productive) but anything that helps communicate science to a wider audience is usually a good thing.
One such project that caught my eye a while ago was ProjectEvoMap - A global map of evolutionary biology research groups, started by an English PhD student in Sweden, Robert Griffin (#ProjectEvoMap). I'm not 100% sold on the name - if, like me, you try to find it and insert a space after "Project" you get all sorts of other stuff - but I really like the idea. It's a pretty simple aspiration: to enable people to locate evolutionary biology labs near places of interest and to generally raise awareness of what (and where) evolutionary biology is being done. I've added my lab and if you're an evolutionary biologist reading this, I hope you'll add yours too.

Friday, 16 November 2012

Artificial Selection versus Natural Selection

One of things you will probably encounter quite quickly if you ever discuss evolution with a Young Earth or Intelligent Design Creationist is a deep confusion about Natural Selection. Often this is as simple as claiming that it doesn't exist and explains nothing, which is clearly and demonstrably utter nonsense. Recently, I experiences a more unusual extension of this claim:
"Natural Selection does not exist. It is all Artificial Selection."
This is usually an attempt to discredit experimental evidence for Natural Selection that comes from direct laboratory manipulations, such as the long-term experimental evolution of bacteria in the lab of Richard Lenski and colleagues.

A less extreme position is to claim that lessons learnt from artificial selection, generating different breeds of dogs, for example, are cannot be extrapolated to nature because Natural Selection is fundamentally different. Both variants of the argument are utterly wrong.
[Image credit: Science Museum.]

So, what is the difference between Artificial Selection and Natural Selection?

Philosophically, I think it is the difference between being directed or undirected. This is different to it being a case of directional versus undirectional. All selection is directional - that's the point. Evolution without any direction happens - neutral evolution and Random Genetic Drift - but this does not give rise to adaptations. Selection, on the other hand, imparts directional constraints to the evolutionary trajectory because some variants do better or worse than others.

This is most clear with "Negative" or "Purifying" selection, in which certain directions are closed because carriers of those variants are less competitive. This is what produces a signal of evolutionary conservation. More dramatic are the cases of "Positive" selection, in which particular variants have increased "fitness" compared to the population (i.e. the genetic material for that variant is more likely to be passed on to the next generation than a random bit of DNA in an individual without that variant) and thus it "sweeps" through the population. (Contingent on the strength of the effect and the population size.)

The point is, though, that while Natural Selection has direction it is not directed - it has no goal it is striving towards. The direction is imposed by the environment that a particular variant finds itself in at the time. This environment includes all the other variants in the population: fitness is always relative.

The direction of selection can also change from generation to generation, even within a generation. (Think of adaptations to hot or cold weather and consider climate variability, for example.) This means that populations can evolve themselves into an evolutionary dead-end, or lose a gene/trait that could prove useful in the future. Evolution by Natural Selection reacts to the now, it does not predict the future. The bills of Darwin's finches are specialised for certain foods they have encountered during their radiation - they have not all remained versatile generalists, ready to adapt quickly to changing food availability.

I think this is the real reason that many religious people have a problem with evolution by Natural Selection: there is no goal, no target, so humanity cannot be the goal. We are not the pinnacle that evolution has been working towards, we are just a by-product of past selection and chance events. (There are, of course, ongoing discussions about the predictability of evolution but this is really a question as to whether, if evolution were re-run, something like us (i.e. intelligent life) would inevitably appear. I can't imagine that any evolutionary biologist would seriously entertain the notion that we would re-appear if life were restarted.) The root of the argument against Natural Selection (but accepting Artificial Selection) is born of the belief that all evolution is directly governed and directed by some kind of deity. (Even if this deity is dressed up as an "Intelligent Designer".) Often, this is coupled with claims along the lines of "there is no such thing as random mutation" and other such arguments, which simply do not account for observations of the world around us. (Not unless, for reasons unclear to me, you postulate a deity who is deliberately out to deceive and make things look random and undirected. I'll save this one, and the randomness of mutation, for another post!)

The directed/directional distinction is just one aspect of the difference, however. To really qualify as Artificial Selection, I think that the directing agent has to be directly choosing (selecting) who reproduces and who does not. This is distinct from Natural Selection, in which the differential breeding success is just a consequence of reactions to the environment. This is why claims that experimental evolution in the lab are Artificial Selection are normally wrong. Laboratory evolution is normally directly studying Natural Selection, albeit with a tightly controlled environment. (One of the key approaches in science is to try and remove as much random variability and simplify the system as much as possible.)

In some ways, it is easy to see this by examining the spectrum of selective regimes used in the lab. Some can be quite complex in terms of responses, such as changes in temperature or the addition (or removal) of certain common or key nutrients. Others are much more defined, such as the addition of an antibiotic resistance, in which a very specific trait - resistance - is being sought. This is still Natural Selection: the environment being controlled and the organisms are surviving differentially based on their genotypes in response to this environment.

It could be - and sometimes is - argued that this is actually Artificial Selection and that the specific antibiotic regime is merely the mechanism by which the human is artificially selecting. It could be argued - blurring the boundaries between the two, which I'll get back to - but it shouldn't be argued, for I think it is a wrong (if forgivable) position to take. Even antibiotic resistance experiments are not purely selecting one trait. There will also be more subtle selection pressures due to the choice of media or growth conditions. As well as resistance, there will still be pressure to grow fast. There may even be complex biotic interactions where a subpopulation protects the rest of the population, such as biofilm formation. Even though the desired outcome might be antibiotic resistance, the experimenter is not (normally) actively selecting individuals. (S)he is not manually screening individuals and picking which ones to propagate.

This is quite different to selective breeding in dogs, for example. Here, a breeder is picking a particular trait - such as the ridge in a Rhodesian Ridgeback and selecting specific individuals with that trait to breed from. This is so powerful as a selective force that it can over-ride normal fitness considerations and evolve a trait that is otherwise downright detrimental to the individuals concerned. A number of pedigree dogs have severe health problems, for example.

This distinction of active versus passive selection of individuals with specific traits is certainly one way to view the Artificial Selection versus Natural Selection issue. There is another way, however, which I tend to err towards and makes the statement that there is no Natural Selection and only Artificial Selection even more erroneous: Artificial Selection is actually just a special case of the more general process of Natural Selection: one end of the continuum. Far from there being no Natural Selection, it is all Natural Selection!

The fact is, philosophy aside, there is no real biological difference between the two. Yes, it's easier to spot and define the selection when it's directed and tightly controlled - which is why it is so useful in the lab - but the basic mechanism of differential reproduction of heritable variants holds true for both. Furthermore, there is a direct analogy for Artificial Selection in nature, in which decision-making agents actively choose which individuals get to reproduce based on specific traits - Sexual Selection. (Intersexual selection, specifically, in which mate choice (as opposed to direct intrasexual competition) is a determining factor in reproductive success.) Sexual selection and mate choice abound in nature and can produce some quite absurd phenotypes that, like the products of artificial selection, are not necessarily healthy. From the perspective of the organisms experiencing the selection, a human imposing Artificial Selection is just part of the environment in just the same way as a choosy mate might be.

One possible example of this is the antlers of the (now extinct) Irish Elk. The photo above (from WEIT) shows male (right) and female (left) Irish Elk skeletons from the Museum Building in Trinity College Dublin. The sexual dimorphism - only the males have the monstrous antlers - is a clear sign of sexual selection and the antlers of male Irish Elk are so massive that it is thought they probably contributed to their extinction.

It's not actually the best example, to be honest, because the initial sexual selection on antlers was almost certainly intrasexual selection between fighting males and even though the Irish Elk antlers are too big for such behaviour, their monstrous size could be linked to increases in body size rather than intersexual selection for big antlers. That said, there must have been some force maintaining such impractical ornamentation and female mate choice is a prime contender. I mainly picked it because my brother works in the Museum Building and I used to see these elk quite regularly when I lived in Dublin. There's also an alternative YEC explanation for their extinction (right, also from WEIT; cartoon by Chris Madden)! If you don't like the elk as an example, there is always the peacock. (Whole books have been written about it if you want to know more.)

So, in conclusion: not only do Artificial Selection and directed evolution provide good tools for investigating aspects of Natural Selection, in very real terms they are Natural Selection. Anyone who claims that Natural Selection does not exist and everything is Artificial Selection has got the situation entirely backwards.

Monday, 12 November 2012

The Cabbages of Doom 2.2

A new edition of The Cabbages of Doom is now available on the Kindle for only 99p (or $1.59). Thanks to some editorial advice (thanks, Karen!), a few grammatical errors and typos have been fixed here and there. It also features a new cover. Following some changes at Amazon Kindle Direct Publishing, it can be lent too. (Though only in America, I think.) The iBooks and Lulu versions will be updated when time and energy allows. (Unless I discontinue them and enrol in "KDP Select".)

If you are curious, visit Amazon to download a free sample, read the blurb or view the sample chapter (PDF). If you need more encouragement, here it's one review so far (for the Lulu PDF version, which is yet to be updated):

This exciting and entertaining first novel exceeded all of my expectations. The story itself is a very imaginative chase across the English country side involving inter-dimensional travellers culminating in an entirely unpredictable hilarious and action packed final confrontation. The story had me laughing out loud and genuinely invested in routing for the good guys (okay, cabbage and small animals). Unlike most self-published first novels in this price range this one was very well spell-checked and surprisingly grammatically correct. If you are in the mood for a smile, a fun story and groan or two for some amazing puns and references to classic films, then this is the best 99p you can spend.
Go on. You'll make my day.

Thursday, 8 November 2012

Standing up for Genetic Modification

It's my 300th blog post and so I wanted to try and post about something that captured the essence of the blog, hence the delay! What could be better than to combine food, science and The Cabbages of Doom?

Actually, The Cabbages of Doom is a bit of a red herring for this post. Just in case there is any confusion, The Cabbages of Doom is not a negative reference about Genetically Modified (GM) foods. (It's a surreal science fiction story about some marauding cabbages from another direction invading Swansea. And only 99p! Review here.)

In fact, I could not be much further away from an anti-GM position. For me, the success of the anti-GM lobby in the UK and across Europe in the late nineties represents one of the biggest scientific, political and media disasters of the modern age. A well-organised and probably well-intentioned but horribly misinformed group of scaremongers managed to hijack the public debate over use of one of the most promising technologies ever to be developed in the history of mankind.

Let's make one thing clear from the outset: there is nothing inherently unnatural about Genetically Modified Organisms (GMO). For a start, many GMO just involve targeted mutations within a strain or introduction of genetic variants from related species. These could potentially be achieved by conventional breeding and artificial selection at much greater expense of time and money (and death). The more advanced GMO involve taking DNA from one organism and inserting it in another. Even these GMO are not really unnatural, even if the techniques used to create them are: although it is rare in multicellular plants and animals, "Horizontal Transfer" of genetic material between organisms - including eukaryotes - does occur in nature. (See Keeling & Palmer (2008) Horizontal gene transfer in eukaryotic evolution. Nature Reviews Genetics 9:605-18 for some examples and discussion.)

It is true that the level of modification desired is unlikely to be achieved by natural mechanisms within the lifetimes of the scientists involved. This, though, is one of the key benefits of GM: it greatly speeds up our ability to generate and evaluate possible genetic solutions to environmental problems. We don't need to wait around just trying to get lucky.

Furthermore, far from being inherently dangerous, many GMO are probably safer to the environment than non-GM alternatives. Why? GM is far more precise and targeted than "traditional" methods of creating mutants for screening, which involve chemicals or radiation and produce something much less predictable. The more we understand the nature of the modification, the easier it is to both predict possible risks and also detect or mitigate them. You only have to look at the problems of "invasive species" to realise that entirely "natural" organisms in the wrong place can be an environmental calamity. By eliminating the ability to customise and refine appropriate native organisms through GM, inappropriate introduced species might be used instead. (Often it is not clear what the problems might be until they are released.) The other reason is that, done right, a GMO can permit reductions in uses of chemical fertilisers, pesticides and herbicides.

Food safety is more of a concern but the solution here is not a blanket ban nor even a blanket hysteria, it is adequate food testing and common sense. If a gene has simply been removed from an organism or repressed, as in the "Flavr Savr" tomato, it is no more dangerous than a new hybrid from natural breeding - DNA is digested when we eat food, so if the product itself is not toxic, there is no obvious risk. If, on the other hand, the GMO is producing something like Bt toxin, one obviously needs to be more careful. Even here, though, it is not obviously the case that using chemicals, or even "organic" alternatives (all GMO are organic!) like spraying Bt strains of bacteria, would be any safer. Preferably, all new foods would undergo appropriate toxicity and allergy testing, whether they were the product of conventional breeding or GM. If there is a genuine problem, clearly that specific GM food should be withdrawn, just as one would do with anything containing, or grown with, new bacteria or chemicals.

So, what went wrong? One of the big problems was the old chestnut of "balanced reporting" in the media. All too often, this seems to equate to equal air time for both sides, no matter how uneven the evidence supporting the two sides was. A calm and cautious (and often already pretty balanced) scientist is paired up with a volatile and definitely one-sided activist. Clearly, this is going to end up biased towards the activist even if their position is weaker and founded on misunderstanding and/or misrepresentation of the science. Worse, the journalists chairing the whole thing often fail to interject when one side is just plain wrong about their facts.

The second problem was education. I don't think it would be such a big problem today because DNA and genomics is in the news so much more but, at the time, a scary proportion of the British public did not think that a non-GM tomato had any DNA in it, for example. (At Nottingham, we had a public debate on the issue and a someone had to be removed because they just kept shouting "I don't want to eat DNA!" and would not stop to have it explained that he was eating DNA in all his regular food.)

The final nail was economics. The anti-GM campaign was good enough at scaremongering that public confidence was weakened, despite (inadequate?) attempts by the scientific community to set the record straight. Supermarkets perceived that they would lose enough custom to warrant pulling the plug and so they did. GM has been largely vilified in the public domain ever since, although I think the EU has now relaxed its zero-tolerance stance. After all, if a supermarket is advertising itself as "GM free" as a good thing, GM must be bad. Right? (Obviously, the consumer desires of someone like me, who would rather eat the cheaper, tastier, less wasteful GM tomatoes, are not so important.)

GMO are not universally good and I am sure there have been situations where big corporations have used GM just to make more money or to increase herbicide resistance and thus use more herbicide, which is bad for the environment. Like any technology, the applications need to be considered on a case-by-case basis.

That said, there are some clear situations where GMO can be a force for good, such as the Golden Rice Project, which seeks to use "biofortified rice as a contribution to the alleviation of life-threatening micronutrient deficiencies in developing countries". Drought- and salt-tolerance maize and other such crops could also be important in our changing world.

The sad irony is that, by resisting the development of government-funded GM crops in academic institutions, the anti-GM lobby have actually driven it all into the hands of large corporations that can get round legislation by doing tests overseas and are far more likely to create the kind of GMO that we don't actually want. (Or, even more scary, unregulated amateur biohackers.)

Whether you think it's man-made or not (it is), Climate Change is a big problem and the more we ignore it, the worse it's going to get. This is a problem so big that we need to throw every weapon in our arsenal at tackling it head-on, and that includes taking a chance here and there. There is a reason that food security is one of the major focuses of UK science funding. We have to feed a growing population on dwindling resources. It's not rocket science. (And I haven't even mentioned biofuels.) Genetically modified organisms represent one of the best - possibly the only - chance we have, short of a massive reduction in the global population. (Population crashes and extinction are natural responses to Climate Change - let's make no mistake here, "natural" is not always good.) It's time to let the genie back out of the bottle and let it be a force for good.

Sunday, 4 November 2012

Intelligent Design is Creationism, just not Biblical (or Young Earth) Creationism

In their FAQ, the Discovery Institute write in response to the question "Is intelligent design theory the same as creationism?":
"No. Intelligent design theory is simply an effort to empirically detect whether the "apparent design" in nature acknowledged by virtually all biologists is genuine design (the product of an intelligent cause) or is simply the product of an undirected process such as natural selection acting on random variations. Creationism is focused on defending a literal reading of the Genesis account, usually including the creation of the earth by the Biblical God a few thousand years ago. Unlike creationism, the scientific theory of intelligent design is agnostic regarding the source of design and has no commitment to defending Genesis, the Bible or any other sacred text. Honest critics of intelligent design acknowledge the difference between intelligent design and creationism."
Well, I am an "honest critic" and I will acknowledge the difference between ID and the restrictive definition of Creationism that they choose to use but I will not acknowledge the difference between ID and Creationism in general. Creationism is the belief that some being outside nature (as we know it) created everything, as opposed to everything arising naturally without any causal agent or intervention. This totally encompasses ID.

The fact that they try to make claims that their designer need not be a deity - and, in particular, is not necessarily the god of the Bible - is irrelevant and demonstrates their intellectual paucity and/or dishonesty. The only ultimate conclusion that can be drawn from the ID "hypothesis" is that the Universe was created by a non-physical intelligence. That sounds a lot like a deity (and Creationism) to me. If "aliens did it" then ID also predicts that those aliens must be the product of ID and the problem is moved but not removed.

The only thing that could part ID from Creationism would be if they came out and stated in pure black and white that they are willing to accept that the proposed Designer of this Universe and/or life on Earth was itself the product of purely natural processes and devoid of input from an external Intelligence. In other words, state clearly that their extrapolation of design ONLY applies to the observed Universe. It wouldn't help their "scientific" claims at all but at least they could honestly cut the ties to their clear and documented Creationist ancestry. (I predict that they will not because I think that even they can see that making this statement would be tantamount to admitting that ID is a wholly unnecessary hypothesis - the only thing that keeps it alive is a stubborn refusal to let go of certain key (flawed) assumptions.)

Even should they take this extra step, the DI and their ID friends have a serious problem that cannot be ignored. The reason that so many critics make the link between ID and Creationism is that, when it comes to the scientific observations and interpretations, ID has the same core ideas as certain flavours of "Theistic evolution" Creationism, and thus all the same criticisms and problems apply.

Creationism is a spectrum with Young Earth Creationism at one end and an almost entirely naturalistic Theistic Evolution at the other. In the former, the Designer ("God") did essentially everything. In the latter, the Designer just kicked things off at the start - designing the Universe to be able to support life - and did nothing else. ID, as described, is indeed incompatible and different to both of these. (They do accept evolution - ruling out YEC - but do not accept that it was a purely naturalistic, unguided process - ruling out naturalistic Theistic Evolution.)


There is a whole spectrum of Theistic Evolution Creationism in between that invokes an on-going intervention of the deity to a greater or lesser extent.

Possibilites include:
☛ intervening to start life by making the first replicators (abiogenesis). Note that this (and designing the Universe) is a wholly separate question as to whether evolution could occur by purely natural (unguided) means
☛ intervening for the "major transitions" in evolution. (The first cell, multicellularity, eukaryotes etc.)
☛ intervening at key points throughout to drive the evolution of complexity
☛ intervening to drive all "macroevolutionary" events but staying out of "microevolution". (A false dichotomy in itself but that's one for another post.)
☛ intervening to drive all evolution by directing all mutations

ID sits at some fuzzy point along this spectrum, as do Creationists. The fact that, for a Biblical Creationist, the Designer was God is largely irrelevant - unless they go the whole hog and deny evolution entirely as a Young Earth Creationist. (A much more intellectually honest position than ID but also so demonstrably wrong position that even the DI appears to disown it on their homepage.)

In fact, ID has a bigger problem than Theistic Evolution Creationism - the motives of the Designer. As ID advocates will be free to point out when critics point out the numerous apparent design flaws in nature, one can only really talk about "good" versus "bad" design if one knows what the design is for. Natural Selection provides an inherent discriminator for things that work better than others - that is how Natural Selection is able to facilitate the evolution of complex adaptations. Theists can argue from their holy books that the end-point was mankind (or whatever) and although I suspect they cannot really get a good handle on their Designer's objectives (why, for example, the inordinate fondness for beetles?), they can probably rule some things out. The ID crowd do not even have that.

Instead, ID is just "God of the gaps" rebranded as "Designer of the gaps". They refuse (but not refute, for their rebuttals are all flawed) possible natural explanations for certain observed phenomena - a Universe "fine-tuned" for life, complex macromolecular machines in biology, and life itself - and make an alternative proposal that is based on unproven and erroneous extrapolations combined with a woeful ignorance of information theory and biology - all cloaked in pseudoscientific language. (Another post for another day.) They then try to find examples of where the theoretical natural explanations for specific phenomena (such as a specific protein complex or specific past evolutionary event) have not been demonstrably proven (despite having a sound theoretical explanation) and insert their Designer with no clue as to its motives or rationale for intervening at that particular point in time and space.

That certainly sounds a lot like traditional Creationism to me. (And whatever it is, it sure ain't science.)

[Edit note: although most YEC and ID leaders are clearly at odds, it should be noted that ID does not actually rule out a Young Earth, it just does not promote it. Given the overwhelming scientific evidence for an old Earth and lack of Biblical Flood, the fact that the ID movement does not explicitly reject these is another indication of its utter lack of scientific motivation. Then, of course, there is Of Pandas and People, a Creationist text that similarly neither accepts nor rejects YEC and is famous for doing a find and replace for "Creationism" (and similar words), replacing them with "Intelligent Design". How can you have a coherent view of biological origins if you can't even decide on something of such fundamental importance?]