Scientist Studies

Wow, this is really huge. John S. Wilkins at Evolving Thoughts reports on a paper that would rewrite the rulebook on evolutionary theory. It's not often, or ever, that you get to read about a change in a field so cataclysmic that it completely changes the outlook on a whole field, certainly not one so important or controversial as evolutionary theory.

If true, the theory of Empedoclean Evolution would totally discredit natural selection, in this Darwin anniversary year of all times. Professor Augustus P. Rillful's paper concerning the importance of horizontal transfer of genes (for example by viral and bacterial mechanisms) foreshadows a comprehensive understanding of all sides of speciation.

Looks like a Nobel-prizewinner, doesn't he?

---

Meanwhile, a couple of other interesting links I found in my morning perusal:

A really fascinating post at Genetic Future about the marketing strategy personal genomics company 23andMe are using. I've always really liked that name, incidentally. Their plan is to form a community of users based around their "mommy bloggers" who'll chat about pregnancy and kids. Daniel McArthur suggests mothers-to-be might graduate from comparing weight gains to genotypes, splashing out on DNA testing kits for their loved ones to determine how their offspring might turn out. It really could be a fantastic marketing masterstroke, making this information seem relevant to a big-spending demographic.

It hasn't gone down well with Steve Murphy "The Gene Sherpa," who highlights the effect it could have on the clinical load. Imagine having to somehow convince a pregnant mother that their child will turn out perfectly normal despite that elevated heart disease risk factor.

It occured to me lately quite how fortunate I am. There are a few science columns I read by guys in their 50s that mention that they'll wait a couple more years for the price to drop on personal genome sequencing, and then they're doing it. That is, getting hold of the sequence for a fraction of their genome, the size and price of which is dependent on the package and company they go for. 23andMe's service tests for a number of significant (disease-indicating) variations at 600,000 positions, at the fairly affordable price of $399. A couple of other operators are in the $1,000-2,500 range, testing roughly a million polymorphisms. Each service is aimed at providing estimates of their customer's 'genetic risk.'

Meanwhile, Knome (another really great name, and tagline!) offer a complete personal genome sequence and analysis, for a somewhat-heftier price. This year-old article suggests a figure of $350,000 (wikipedia haggles down to $99,500) , which would include ongoing support by a team of geneticists and bioinformaticians, apparently (career bells start ringing...). And would you believe it, they output on a sparkly new USB key!

But it won't be in the hundreds of thousands forever. Certainly in 20 years we should anticipate it will be affordable for us regulars - indeed this wide availability is a crucial point of all the genetic dystopias we've been busily envisaging since Human Genome Project results started coming through in 2000. Of course, we all expect health insurance premiums to be calculated on the basis of our genetic disease risk. A short step indeed to Gattaca.

I fully anticipate that within my lifetime I'll be able to have a browse through the complete sequence of As, Cs, Ts and Gs that determine so much about me, without breaking the bank. I only hope I'll be savvy enough to understand what some of it means. It's magical really, and represents an comprehension of human biology standing on the brink of the unimaginable. Beyond it lies real sci-fi territory.

---

Are viruses alive? Yes or No? This question is a controversial one at ERV, where there's frustration at a recent review in Nature Reviews: Microbiology (Bear in mind that with an impact factor of ~15, that's a pretty hefty journal to go spitting on virologists in). The notion of excluding viruses from the "Tree of Life" seems a peculiar one to me: they have played such a huge part in the development of life, and continue to have a huge role in living systems, it really doesn't make sense on a practical level. Ultimately the use of having such a tree is to understand the relationships within it between living things, and the history of their development, and given that viruses have such relationships, they should really be in. That would, at least, be my view from a practical standpoint.

There's an interesting question here anyway, about our definition, ever hazy, of life. It can't rest on autonomy, as last time I checked humans, among other species, wouldn't do terribly well left on our own. Nor can we disqualify viruses simply because it's hard to trace their lineages, as unsatisfying as it may be if we are unable to reach the root of the tree. As we scrabble around trying to find the boundary between living and non-living we naturally enter into questions of abiogenesis. It's a pretty fascinating area to think about, and ill-served by artificially imposing living/dead boundaries.

Those who place great emphasis on science are also the first to abuse it

I've criticised Pharyngula before. It's sort of like when you've had a crush on someone, admired little things about them, picked out things you like about the way they wear their long dark hair, their clothes which are cheap and ready but perfectly in place, their ability to write helpfully and clearly about science. A couple of years later, when you've had some separation, you might be over them when you see them heavily cropped, in a designer dress and only ever ranting about the Pope being evil. A walking advert for the ludicrous "Out Campaign.*"

You keep an eye on them and you resent them. It's emotionally exhausting, I don't mind admitting.

Where do I still agree with Myers? Well... Science must be as apolitical as possible. You don't go into scientific exploration knowing the results in advance, much less in order to confirm your current opinions. You're testing hypotheses, you don't know what you'll come up with, and you don't serve up results with a side-order of heaped invective...

Fuck.

Those fears I had that the sclogosphere (trust me, that'll catch on) might not be a good substitute for peer-reviewed journals are further reinforced. I don't know if Myers has read the original paper (I intend to find it when I visit campus later) but he links to a news source. This study has been reinterpreted by a journalist even before it received the Pharyngula treatment!

Contrast with Ed Yong at Not Exactly Rocket Science, who only uses primary research papers, and does his best to fully understand the research first (read his rules). No reinterpreted headlines here. There's a reason this has become my favourite science blog. A soothing balm, and my new crush!

Is Myers' interpretation accurate? Possibly, I can't rule it out. A biased conclusion can be the correct one if you hitch to the right wagon. But it's certainly not proven. Psychological research has shown a large range of effects religious practice can have on believers, some more intuitive than others. It's a complex set of contributing factors and jumping straight for the "fear and ignorance" parameters seems hugely simplistic and convenient.

PZ Myers has a nice choir to preach to by now, a well-rehearsed line in atheism, a total disregard for the philosophical/theological heritage present-day thought (including much of his) comes from, and plenty of bile. He's certainly a pretty skilled writer, I envy him that. I know full well that he and his followers are content in the knowledge that they are the most rational people in the world, and that's fine. I can only hope my views are somewhat less reductive.

A further annoyance: Scientific knowledge, we all understand, has been built up from foundation levels to much more intricate and detailed platforms. I seem to be reading so much right now where scientists stride boldly and rationally into other areas with no foundation whatsoever. I hope I at least have the good grace to be tentative!

---

There's a whole quagmire here that I shouldn't get into, but the very next post he's made, about Catholicism's opposition to condom use in Africa (an area I should agree with him on), also winds me up. There's a glaring clash in his view that you can't deny human nature, when it's juxtaposed with decrying certain human behaviours as pathological. Read Pharyngula for a few weeks (probably more like days) and you'll understand Myers applies this idea of pathology to a wide range of irrational behaviours.

Admittedly, sex is a pretty fundamental drive for human beings. But one has to wonder, if we've been prone to irrational belief throughout recorded history, and show few signs of stopping now, what's the difference? Can sex be described as pathological? Is hardcore rationalism denying human nature? In the latter case, I think the answer is certainly.

---

*So, if I were worried about religion causing evil to come about because it creates factions that hate each other I'm sure as hell the first thing I'd do is create a new faction that aggressively states its difference to all others
Furthermore, I'd want to alienate moderates with my "if you're not with us, you're against us" attitude. Comparing myself to the great liberators and civil-rights campaigners of history would be my choice technique for squaring things off.

---

Capital letters in headings? I really don't know. I used to, religiously, "every word as important as the word that precedes it" and all that. But in the middle of typing out that title it just struck me as a bit ridiculous, more than a little pompous, frankly.
I shall just see which whims take me.

Taking Refuge

So, a rough day is enough to precipitate a retreat. Such a wonderful retreat, however. One of the things I always appreciate about Nottingham (in comparison to Salisbury, which, lovely though it is, is a backwater) is that there are cinemas here that screen films I actually want to see. The other week I finally saw Waltz With Bashir, and it was worth the wait. Tonight I went to see The Wrestler (in fact, I immersed myself in it completely, and came up drenched in sweat and tears).

I'll note my thoughts on it tomorrow (clue: I liked it), when I can gather them. Suffice to say, combined with a stop-off at Lee Rosy's, it was a fairly perfect evening and I felt positively resurrected walking home, my day of dissertation-toil and application-frustration well behind me. But for now I just want to note that the feature was preceded by this trailer, the first time I've seen it in full:

Sure enough, Milk is next in my list of must-sees. I don't even care that it could be a bit of an Oscars love-in, or that it's one of those deliberately serious-accessible films. I care that this is almost as 'important' as a film could conceivably be dubbed, and it is as emphatically pro-equality with regard to sexuality as you could say Malcolm X or Remember The Titans were with regard to race (for some reason I don't award Brokeback Mountain this accolade, maybe unfairly, but in some way I don't feel it made the same point).

So within my (admittedly myopic and goldfish-like) experience, this is sort of a watershed event in cinema, possibly similarly to Milk's real-world impact. Gays are OK, in a slightly schmaltzy way. Maybe I'm just emotional tonight, but I can't wait.

-------------------------------

I know, I know, I'm so melodramatic. But here it is, and it's no big surprise; I'm tired of listening to partisan arguments for the time being, and more tired still of participating. It's a shame because I've often learnt valuable things in such discourse, both about myself and the subjects in hand. But the internet is an uncivil place. Maybe it's the anonymity, the testosterone, or the ease of finding allies in a global network. At any rate this over-abundant aggro taints everything, and it's boring.

While I thought I had a sense of humour, I'm clearly not terribly thick-skinned, and I wouldn't care to be either. It hurts me in some way to see so much hatred, both casual and calculated. I can't find the precise quote (I do need to watch Stalker again soon; I will correct this later) but when man is born he is sensitive to all things and drinks them in, and when he dies he is cold and hard as stone. Anyway, this is all a bit E/N but, like, whatever.

Our Ugly Response to Fundamentalism

Science blogs can be fascinating. At least, that's when they're (mercifully) discussing science. The New Scientist's own blog, Short Sharp Science, is fairly reliable. Investigation of Scienceblogs.com can be both entertaining and rewarding. Its posterchild, Pharyngula, was pretty good, was quite consistently so for at least a few years.

Looking at Pharyngula today, I'm hugely disappointed. There is no science discussion here, no analysis of new findings. You would say that one post on the whole front page makes a scientific point, as opposed to discussing 'Science' as a cultural/political meta-subject. Most of Myer's posts, for a long time, have been about creationists and the political battleground. Of course, it's just the one guy, and his current thoughts. But there's a worrying overall trend.

A quick browse of related columns and channels on Scienceblogs, Blogger, Youtube and all over the web confirms: we spend as much time 'bashing down fundies' as we do discussing mankinds attempts to push forward the frontiers of our knowledge.

It's a pattern as seductive as it is ugly. Seeing our irrational 'enemy' out of their depth, we point, laugh and deride. I've indulged in it many times before and doubtless will again. I'll feel bad about it afterwards, but I still take that amount of pleasure in seeing extreme views dissected.

Additionally, it's entirely unproductive: I hesitate to use the clichéd term 'straw man,' but we mustn't be misled by the ease with which these positions are ridiculed. Religious fundamentalists can't be considered representative of faith, just as I wouldn't welcome the 'Professors' that frequently speak on their behalf.

There are, I suppose, two things I'd like to see. A degree of restraint on our part as scientists; having fun at the expense of other's ignorance is unlikely to reduce the gulf emerging between scientists and the general population. A more considered response is clearly required. And secondly, for scientists to use online resources to rediscover their love of discovery - and display it once in a while, too.

Edit: Just to add some positive to this post, here's the kind of science blogging that I do consider helpful, courtesy of Gene Expression (one of my favourites). In these articles the author tackles a subject that does get people thinking. They're a good example of how clear explanation can explain everyday phenomena that would otherwise be notched up to superstition. Now we just need to equip the population to understand such excellent writing.

Substitute

The concept of Flat Daddies is giving me some pause for thought this evening. Quite simply, I struggle to know how I really feel about it.

It's wonderful that our feeling for parents, and the amount of love we have to give, are so deep that we can have real joy for a cardboard cut-out. If it helps families, then of course it must be tremendous. And it's fantastic that our free market could never leave such a crucial need unserved (albeit at $50 a pop - this is not a charity).

But it's also incredibly sad that a love that seems so real and vital between a child and their flesh-parent (so as not to discriminate against all the photo-parents out there) could seemingly be easily transferred to a thing.

What does this say about our contemporary view of relationships? These aren't posited as some kind of replacement, but still, how might this make a child feel about objects, as opposed to organisms? Might having this presence inhibit an infant's ability to find the attention that they need during their formative years?

Flat Daddies say on their site: "Experts believe the cutouts are a useful psychological device, especially for children, to help cope with the stress of long absences. It helps the family stay connected and is a constant reminder that even though mom or dad is thousands of miles away, they are still a part of their lives." I hope so. Clearly, I don't know what long-term research exists.

I sympathise greatly with the families that feel a Flat Daddy can help them. Kids should have a two parents, and where families have been wrenched apart through necessity (foreign policy notwithstanding) the effort to keep the other parent 'alive' in their child's mind must be a difficult one.

False Advertising

A google search for Marion (I was looking for 'The Matrix' Shawn, not a teensy Iowa town) brings up this page with its rather amusing tagline.

Where should one place stress on "You can go home again," exactly?

Is this a hack-job in a literal or rhetorical sense? That can't surely be deliberate.


P.S. Even if you've never heard of Shawn Marion, the story about his Chinese-language tattoo is worth a repost.

End of the Line

Torrent fiends: get paranoid.

I find this a little off the mark:

"Concerns are myriad at this point, ranging from how authorities can prove their cases using the easily manipulated user data seized during the initial OiNK raid, to why the police are involved at all in what some have suggested is merely a matter that calls for civil action, to, of course, whether the arrests will continue-- and, if so, who will be next."

I can see why you'd be concerned, but c'mon, you use these sites and these systems for sharing music you have no real right to (I'll repeat that - music may be as free as the air and the birds in the trees, but musicians put the effort in and deserve to make a little back) and you always know if it catches up with you you have no real excuse.

Funnier is the concept of DNA samples and fingerprints being taken, I grant you. Although it's pretty egalitarian that some cardigan-clad pop nerd goes in the database alongside the serial rapist.

All I'll say, as someone who downloads a lot of music but equally buys a lot of CDs and goes to a lot of gigs, is it's impossible to get to grips with certain areas of music without delving into torrents and music blogs. Once you get into real experimental/avant territory you'll struggle to find new stuff you like on MTV2.
I know a lot of people who download albums online and some are good for music, others not so good. But that's describing people in general. On the whole it's an essential part of the progression of music as we know it.

Just don't complain when you get nicked.

Second Hand News

Lately I've become a bit obsessed with Google Trends. It sort of combines two fascinations of mine; how huge swathes of traffic move online, and the uncanny way statistics can document history. Of course, they've only been recording search frequencies from 2004, so it's very recent history, but regardless, it can indicate the rise of youtube or give an idea of how the democratic presidential nomination race has emerged so far.

Maybe more fascinating though, is the short-term chart, for the day's "hottest" search terms. This can unearth some really intriguing stories that maybe won't fully break into the mainstream media and won't be going round for more than a couple of days.

Example: at time of writing, the top search term is "dick cheney sunglasses." Seemingly nonsensical, but of course "Trends" grants you links to news stories, that you might make sense of these weird surges.

And sure enough, enlightenment, here, here, here, and hundreds of others besides I don't doubt.

The story: a press photo of Dick Cheney appears to show a nudey lady reflected in his sunglasses. How embarassing. For the sake of it, here's the photo:

Google trends: positively half hours of intrigue.