Sunday, 24 February 2008

UK Pharyngulites unite!

Confirmed! Come one, come all to the London Pharyngula readers' meet-up on Saturday, 15 March, 7pm at the Doric Arch near Euston Station. When you get there, look for the Pharyngula embryo sign, right. Also, I will wear my Beagle Project t-shirt.

PZ Myers noticed something of "a strange phenomenon" (if you can still call social networking on the internet a strange phenomenon...) that began when Pharyngula readers in Boston organised a local pow-wow marked, of course, by squid. He thought (and I think) this is something worth propagating and so suggested we all get into it and start forming satellite Pharyngulite clubs all over the world.

Turns out there are lots of us here in the UK. As of 19:14 GMT on Sunday, the following had identified themselves in PZ's comment thread as habitating here:
  • Mark UK (Edinburgh)
  • Jonathan (Sheffield)
  • Didi (Norwich)
  • Peter Mc (Whitby)
  • mmghosh (Bristol)
  • Don (Tynedale)
  • Miss Prism (London)
  • Marc (London)
  • Maureen (Hebden Bridge)
  • oh, and me, nunatak (London)
  • You?
So, I thought I'd create a post to help us organise ourselves without having to wade through the hundreds of comments over at PZ's place.

If you are in the UK and interested in meeting up please leave a comment here. If people want to spin off and form sub-groups that's fine by me, everyone's welcome to do their own thing of course!

So, I think all that's left to say is: go forth into the Comment thread, all ye UK Pharyngulites, and self-organise!

Wednesday, 20 February 2008

Total lunar eclipse begins in four hours

At 1:43am GMT (8:43pm EST) the Moon will enter the blurry edge of the Earth's shadow, called the Penumbra. Then, at 3:01am GMT (10:01pm EST) the total eclipse (Moon in the darkest part of the Earth's shadow, the Umbra) will begin, and will last for 50 minutes before the Moon begins its slow exit from the Earth's shadow through the Penumbra on the other side.

So put on a pot of Rainforest Alliance Certified coffee and get ready for a lovely reminder of the orbital dance that takes our cold and lonely Moon about our precious Earth about our helium Sun. Me, I'll be reminiscing about my close encounter with Moon rocks back in November.

More info at NASA (naturally) including diagrams like the above for other time zones and an explanation for why the moon is depicted here moving from east to west.

Update 21 Feb.: Stayed up until 2am only to be thwarted by London fog. Damn. Others were more fortunate. My favorite picture at right, the eclipse as seen from Cape Town.

Saturday, 16 February 2008

Curing the disease of human self-importance

Michael Pollan's book The Botany of Desire* changed my life. More specifically, it changed my lazy, conceited assumptions about the primacy of human consciousness.

Sure, I'd known for a long time that the Great Chain of Being (and its counterpart in evolutionary language, the concept of "higher" species the highest being Homo sapiens) is a load of anthropocentric hogwash. And I've known for slightly less time that there are several simple but earth-shaking ways to visualise the specific truth and putridity of said hogwash.

One of these is this simple list of the number of genes in various genomes that have been sequenced:
Thale cress.....25,500
Sea urchin......23,300
Fruit fly........13,700
Baker's yeast....5,800
E. coli...........4,400
Then, for the more visual among us, there's also the lovely evolutionary tree of life, with its teeny tiny "you are here" annotation (high res pdf):

So, then, if we already know that humans are not at the top of some mistakenly conceived evolutionary escalator, what's so special about The Botany of Desire*?

The core concept of the book boils down to this question: what would happen if we looked at agriculture "not as an invention, not as a human technology, but as a co-evolutionary development in which a group of very clever species--mostly edible grasses--had exploited us/figured out how to get us to basically deforest the world" to benefit their genetic legacy?

It's a new way of thinking about agriculture, to be sure. But how is Pollan's idea any different or better than the list of gene numbers (in which the relative positions of rice and humans are already fairly suggestive of some kind of grassy overlordship), or the "you are here" tree of life?

Pollan's hook does go deeper than the list and the tree, by penetrating the skin of human physical form and getting down to the sinew of human intention. But is the botany of desire really anything more than a "literary conceit" as Pollan himself calls it? Does it actually benefit anyone or anything beyond giving us "some entertaining insights"?

In his Ted talk, below, Pollan argues, I think convincingly, that there are real tangible benefits to thinking about ourselves in this new way. For example, he cites its power to "really make us feel the Darwinian idea". It certainly did that for me. I had seen any number of "you are here" diagrams but it didn't really come home until I thought about how I was being expertly manipulated by the edible grasses.

But enough of my trying to explain it, why not hear it straight from the eloquent and impassioned Pollan himself:

H/t to Greg Laden.

*no Amazon link, support your independent bookstore

Friday, 15 February 2008

Vote! the Nature Conservancy 2007 Photo Contest. And while you're there, why not check out some ways you can help them with their noble causes, not least their Rescue the Reef campaign?

Polar Bears, Hinlopen Strait, Svalbard
Steve Price

Storm, Monument Valley, northern Arizona, USA
Sergej Bulychev

Giraffe and Yellow-billed Oxpecker, Ndutu Conservation Area, Tanzania
Billy Dodson

Tuesday, 5 February 2008

"Barcode of plants mapped" identified tested

I just started a draft post (which I fully intend to decorate with ResearchBlogging's recently besmirched icon) on the new paper that my Google alert tells me is coming out on DNA barcoding in plants, my main area of research at the Natural History Museum.

The only thing missing is... well... um... the paper.

The Nature News article reporting the results of the (as yet nonexistent) paper even links to the paper's DOI, which looks promising until you click it and find out it doesn't actually lead anywhere. So, like any good Web 2.0 denizen, I left a comment there: "The DOI for the cited article does not appear to exist, nor can I find anything about this paper on the PNAS website. Any suggestions?" The response I got was, "Please note that PNAS releases the news of its upcoming papers on Mondays at 5pm Eastern time, but the papers themselves may go live at any time during that subsequent week. So this paper will appear eventually... check back on Friday and you should find it."

Well, okay, but then this has a disturbing (if not surprising) implication: none of the 10+ news reports announcing the findings could possibly be the result of a science journalist actually reading and understanding the paper (which is, I note with interest, one of the guidelines for using the ResearchBlogging icon). (The journalists would, in fact, have had a chance to see the paper before they wrote their news items - see koffeekat's very welcome comment below. -KJ 28/7/09)

So, I thought, what better to do while I'm waiting for the paper to be published than to pick apart some bad science writing? Oh, there's the usual assortment of inaccuracy and sensationalism, but my complaints here are going to be more focused on the specific content, that is, DNA barcoding.

Scalpel, please.

Here is my dart-board collage of the offending titles and sentences from a selection of three news pieces reporting the key findings of the mystery DNA barcoding paper. I gave up after three when it became clear they were all just copying and pasting from the same (lame) press release. In bold are the bits that need trouncing, followed immediately by the actual trounce.
"'Barcode' of plants mapped" (title, Mapped? What, with like a road atlas? I don't need to go into detail on why this is just so wrong, simply because Miss Prism has already done it with verve.

"Scientists have identified a 'barcode' gene that can be used to distinguish between the
majority of plant species on Earth.
" ( Well, actually, according to the news release they tested 1600 species of orchids in the study that is (supposedly) going to be published and yet there are nearly 300,000 recognised plant species. Now, unless you're the US Electoral College, 1600/300,000 does not a majority make.

"As such scientists can use the gene to distinguish between different plants,
even closely related species."
( How closely would that be? ...seems like an important question.

"matK Gene Is
A "Barcode" DNA For Plants (title, ScientificBlogging)." These guys can't even get the word order right. It's a DNA barcode not a barcode DNA.

"They found that
when one plant species was closely related to another, differences were usually detected in the matK DNA
. (ScientificBlogging)". Is ScienceBlogging having a secret internal competition on who can be the most vague? "Usually" in this context could mean one of two things for a putative plant DNA barcode: 1) spectacular success, 2) cringe-worthy failure.

The matK gene may not, however, be able to be used to identify every plant species on Earth.
In a few groups of species, additional genetic information may be required for species-level identification because hybridization - where species cross-breed and genetic material is rearranged - may confuse the information provided by matK
. (ScientificBlogging). Okay, where to begin. First of all, hybridization is not just a minor problem in the plant kingdom, it's more the norm. Second, genetic material is rearranged as a normal result of the normal process of normal sexual reproduction, so hybridization doesn't have anything special going for it there. Third, hybridization does not "confuse the information" but rather the information is inadequate to tell when hybridization has occurred.

The team behind the
discovery found that DNA sequences of the gene 'matK' differ among plant species, but are nearly identical in plants of the same species.
(Bio-Medicine). Not so much a discovery as a trial of something that had already been proposed and partially tested.
Needless to say I am looking forward to the paper actually getting published so I can blog it using words a little more informative than "usually", "majority", "a few" and "closely related".