At school with PLOS Biology

[It's 11:15am on the last day of term at PLOS High School. Form 5b are sat in a biology lesson urging for the bell to ring. The teacher, Mr Scientician, is orating to an inattentive audience.....]
Tiny relative, or pathologically small human? Which is it? Hmmm? Hmmm? Come on, we haven't got all day. Powledge! Are you Chewing?
No? Then would you please answer the question! You class mates are waiting. What is the Hobbit?

EDIT: the answer is "dunno".

Big Up Enlightenment Science

If there is one thing that gets me all excited and ranting on like a 10 year old off his mash on sunny-D and Haribo with a book on dinosaurs and a spiderman costume (other than the action of Tgf-beta signaling in mammalian branchial arch development, now *that* is sexy stuff) then it's the enlightenment. I know, I'm a cool dude.

Those enlightenment men in wigs brought us modern science and medicine. They traveled the world, collecting and describing the natural world, and in doing so laid the foundations for Darwin and his chums; crazy geniuses kick started what has become the dark arts of physical science; anatomy, physiology and pathology were studied, bringing about modern medicine and surgery; and they realised that they, human beings, had the ability to manipulate, tinker and generally arse about with the natural world in order to understand it's hidden mechanincs. But the best thing was, many of them were polymaths. It was BRILLIANT! And that is just the science. It can be argued that none of that would have been possible if it wasn't for the philosophy that defines the enlightenment. I love it. Which is why I got all excited when I was told of the e-Enlightenment Project. The Universities of Oxford, Cambridge, Edinburgh, Duke, Wales, Johns Hopkins and Delaware, as well as Norstedts, Meiner, the Virginia Historical Society, the Voltaire Foundation, and now the Oxford University Press have all got together to publish a multitude of enlightenment era writing, right here on the world wide web. God bless 'em.

As you can probably tell from the ranting here, I'm not all that educated in the philosophy and history of the time, so feel free to mock and correct me. I can always learn, and new knowledge can only be a good thing: that's surely a post enlightenment sentiment.

By JOVE!

Everyone loves the internet right? Of course you do. You may have moments when you hate it, but on balance, you think "that internet, 'salright really".

I do, I love the internet. I'm not obsessive about it, and I don't "live" here, as some are want, (in fact I don't "get" MySpace at all), but on balance I think it is ace. For those of us engaged in research the internet is an invaluable tool. I'm just a lowly PhD student, and so don't remember the dark days before Pubmed and the like, but quite how lit searches were done then, I have no idea.

Now, in these post-YouTube days, it was inevitable that JOVE, the Journal of Visualized Experiments, was created as:

an online journal publishing visualized (video-based) biological research studies.

Brilliant! So now (well, in a while, once there has been time for techniques to be submitted and uploaded), when you needs to learn a new techniques, and no one in your institute knows how to do it, you can watch a video of it, then have a go. Obviously this is no substitute for hands of tutoring in a experiment, but it is a great tool for those having a go on their own. Cool.
Here is a video on how to dissect fruit fly ovaries from Paul Schedl and Li Chin Wong of Princeton University:

errrrrm

Errrrrrm,

Humanity may split into two sub-species in 100,000 years' time as predicted by HG Wells, an expert has said.

Errrrm, yeah. ok...

But in the nearer future, humans will evolve in 1,000 years into giants between 6ft and 7ft tall, he predicts, while life-spans will have extended to 120 years, Dr Curry claims.

Physical appearance, driven by indicators of health, youth and fertility, will improve, he says, while men will exhibit symmetrical facial features, look athletic, and have squarer jaws, deeper voices and bigger penises.

Women, on the other hand, will develop lighter, smooth, hairless skin, large clear eyes, pert breasts, glossy hair, and even features, he adds. Racial differences will be ironed out by interbreeding, producing a uniform race of coffee-coloured people.

However, Dr Curry warns, in 10,000 years time humans may have paid a genetic price for relying on technology.

Spoiled by gadgets designed to meet their every need, they could come to resemble domesticated animals.

errrrm, right. Isn't this what Peter Kolosimo said? But didn't he blame the moon being closer to the earth?

Further into the future, sexual selection - being choosy about one's partner - was likely to create more and more genetic inequality, said Dr Curry.
The logical outcome would be two sub-species, "gracile" and "robust" humans similar to the Eloi and Morlocks foretold by HG Wells in his 1895 novel The Time Machine.

"While science and technology have the potential to create an ideal habitat for humanity over the next millennium, there is a possibility of a monumental genetic hangover over the subsequent millennia due to an over-reliance on technology reducing our natural capacity to resist disease, or our evolved ability to get along with each other, said Dr Curry.

?????? I've lost the ability to comment. I'm going to use some random punctuation. (&^@**£??}}}

He carried out the report for men's satellite TV channel Bravo.

Ahh, I see. See here, here, here and here for further discussion.

Pretty animation

Yes, believe it or not, this post isn't about fossils or evolution.
I just got sent this rather pretty animation of some cellular mechanism. Rather nifty, I'm sure you'll agree. Shame the music is really quite wank. Really, I watched it initially whilst listening to Elbow. It was good. I just watched it again to try and list the mechanisms being shown, but I was too distracted by the sub-Playstation style plinky plonky wanna be Future Sounds Of London. Anything else would have been better. Even, and perhaps especially, a song I wrote once about science. It consisted of one word, which was science, sung over and over to the tune of Auld Lang Syne. Yes, that'd be MUCH better.
Oh well, other than that, it's nice. A good for visualising intracellular activity, especially for school kids. I'd make them watch it, and then test them on what they saw. That's if they all don't need to be rushed to hospital with bleeding ears caused by the rubbish soundtrack.

[BBC: Insert archive pictures form "Walking with dinosaurs" here.]

Hej! Scando-Fossils! Giant plesiosaurs! From Svalbard! Home of Panserbjørne!

Dr. Jørn Hurum, Hans Arne Nakrem and their paleoentologist chums from the Norwegian Natural History Museum in Oslo have been up to Svalbard for a short two week field expidition, during which they uncovered 28 new species of plesiosaurs and icthyosaurs. The biggest (and therefore bestest) of which is a 10 meter plesiosaur, with a 2 meter long head. Look at this picture of it in the ground. See how they usfully put a man in it as scale. Look how that bit of dirt to the right is the head.

Yeah, this is why paleoentology gets kids excited. That one massive monster is eating that other one! Look, that's sweet! How much cooler could botany be? The answer is none. None more cooler.











Good shit. Well done Norwegian bone dudes, though it does look a tad chilly, I'll stay in the lab for now.

Not so well done the BBC. Specifically, not so well done the BBC news website. When ever there is anything in the news about dinosaurs, human ancestors or other prehistoric animals, nine times out of ten they will stick some of their pictures from Walking with Dinosaurs/Cavemen/Beasts on their front page. Fair enough, they cost lots of money to make, but this is over kill. Here's todays example:

Back to school/Cavemen on the Rock

Welcome back, I hope you all had a super summer (Ha! "you all", as if. I know we only have one occasional reader, and they lost their job this summer).

For many of us still bumming about universities, this time of year leaves one reeling as your nice, quiet, sun drenched campus suddenly gets flooded with literally millions of identikit happy, confident, fresh undergrads. Today, I'm out of the lab helping register them (for cold hard cash you understand), and frankly, they are making me sick. When I was 19 and just starting uni I wasn't as happy or good looking. My cynical nausea is off set occasionally by periods of trying to be all suave and witty to all the pretty 19 year old girls as I issue them their email addresses. Then I feel like a dirty old man, and the cynicism returns. The Scientician’s Accomplice insists that they are so happy and confident just because they haven’t been broken by life yet, and the thought of them crying themselves to sleep in a few months time makes me feels somewhat better. The little gobshites.

I'm just bitter as I'm finally coming to my final year of formal education. Imagine how the last Neanderthals stuck on Gibraltar, as reported in Nature this week (doi:10.1038/nature05195) felt as all the hot new Modern Humans started invading their space. It was previously thought we had out competed Neanderthals around 35 thousand years ago (kyr), slowly chasing the dim-witted, but artistically bent brutes to the warmer finges of Europe (there is a movement to try and address the perception of Neanderthals as being stupid cavemen, but come on, they couldn't beat us so they must be rubbish). But now fresh radiocarbon dating results suggest that a population survived up until 28kyr in a cave system on the now British colonial oddity that is Gibraltar.

Here is the transcript of a typical conversation from the time...

Guuur: Bloody hell, here come a load of those fresh faces, confident, large society building "modern humans". Can we get no peace [Guuur actually does air punctuation whilst saying "modern humans"].
Ugg: awwww, no. First there are these bloody tailless monkeys that hang out this god forsaken place, next come these idiots.
Guuur: You know they’re just so happy because they haven’t been broken by life yet. They'll be crying them selves to sleep in a few centuries time.
Ugg: Yeah, the little gobshites.


By the way, the picture is of Erik Trinkaus, Ph.D., professor of anthropology at Wahington University, St Louis. He comes up whe you google image search neandertal phd.

Homeopathy & Malaria

Hey, check it out, two posts under a month apart (just).

There has been a little bit of a scandal over some homeopaths pushing their diluted pills as a prophylactic for malaria.
Newsnight, on the BBC, had an undercover reporter go and speak to some homeopaths around London about what the homeopathic options were for anti-malarials.
I had always been led to believe that malaria was caused by a parasitic invasion of Plasmodium in your liver cells, passed on to you by another host of the parasite: a mosquito. However, it seems to be caused by you having a malaria-shaped hole in your energy that the malarial mosquitos can come along and fill.

Ben Goldacre has a video from Newsnight of some woman from some homeopath's club defending it. She has to resort to saying "ooo, but yeah right, homeopathy has been around for aaaaages, so it must work". I may be paraphrasing.

All very scary. "When alternative medicine goes bad", it should be a series on channel 5.

Book Review: Unwin Hyman Dictionary of Biology, 2nd Edition.

To restart Big Up Science with a bang, welcome to our occasional (i.e. this may well be the one and only) series of book reviews.

This book is quite functionally named, "Unwin Hyman Dictionary of Biology, 2nd Edition", and it seems to have a certain empirical beauty in that [1]. However, scratch beneath the surface, and a cold deceit lies at its black, black heart. This book is the same as the Harper Collins Dictionary of Biology, 2nd Edition. What would have happened if I'd bought the Harper Collins Dictionary of Biology, 2nd Edition as well as the Unwin Hyman Dictionary of Biology, 2nd Edition? What then? Hmmm? it doesn't bare thinking about.

Anyway, get on with it I hear you sigh. Ok.

I bought this dictionary in my first year of my undergraduate studies, way back in 1999. I've never really used it, until now that is. Today I forgot which was which out of tendons and ligaments. Stupid, I know, but is has been one of those weeks.

Tendon a bunch of parallel collagen fibres making up a band of connective tissue which serves to attach muscle to bone[2]

Nice, exactly what I needed to know.

Ligament a capsule of elastic connective tissue that joins bone[3]

That has confirmed it. Good work Hale, Margham and Saunders (the editors of the Unwin Hyman Dictionary of Biology, 2nd Edition).

So in summary, the Unwin Hyman Dictionary of Biology, 2nd Edition is an excellent reference source to remind you which is which out of tendons and ligaments.


Post of normal infrequency, which are just as poorly written will resume shortly. Honest. Thanks for your patience.



[1] Empirical, hmmm if only I had some sort of book full of words and their meaning to check to to see if I used that in the right context there...
[2] Entry truncated, you know, just cos i couldn't be bothered to type the rest
[3] see [2]

Did our ancestors shag chimps (ancestors)?

genetics;manpanzee;evolution

So, do you come here often? Can I buy you a drink? What's that? A banana daquori? Sure. How's about you and I go some where quieter, maybe grab some food?I know this great little place just off the High Street, they serve termites there, you like termites right? Of course you do, what with being a chimp and all. Get your... well, you don't wear a coat, but any way, you've pulled.

Above is a made up chat up line that probably never happened. I've started this post with it as a rubbish joke in reference to a paper recently published on Nature.com which suggests that the divergence of the human and chimpanzee lines may not have been the clean break 7 million years ago as previously thought. The new research by Patterson et al, published online ahead of print, uses the principle of the molecular clock and reckons that the two lines may have diverged as recently as 5.3 million years ago, and further analysis indicates that the X chromosomes diverged later which implies the two lines successfully interbred.
The molecular clock is a sweet "trick" used by geneticists to work out when two populations diverged. This uses the principle that the genome, or parts of the genome, accumulates mutations at a fairly constant rate, and so the more differences between the genomes of the two populations (or species) the greater the time since divergence. I'm loathed to do this, but here is a wikipedia enrty on it, better to look at the papers listed here.

Currently, the authors of this research are very careful to point out that the chimp humping part of this research is at present only a hypothesis, though that hasn't stopped people, myself included, getting rather excited by it all. Any good biologist worth their salt (and a few rubbish wannabes like me) will be able to tell you that the accepted definition of species isn't all that good at describing the messy world of real life, and it's good to see we were no different back in the evolutionary day. Can we still interbreed with chimps? There is a likelihood that we can, since lions and tigers can produce offspring, and there has been a bottle nosed dolphin/false orca whale hybrid (a wholphin) that has successfully bred with another bottle nosed dolphin to produce a do-wholphin (I'm proper sorry about the source of the link, makes me doubt the story, anyone got a better one?). I say likelihood, but I have nothing to back this up, such as how related these species are to one another compared to humans vs chimpanzees, or when they diverged. Rubbish I know. Scrap the likelihood bit. That or go and try for yourself. A friend of a friend says there are places in Indonesia where you can fornicate with Orangs, so try and find a similar place but with chimps. You sick, sick man (or woman, don't want to sexist. It's been had enough to write this without using "man" to describe our species).

I am disappointed by the fact that the words Humanzee or Manpanzee feature not once in this paper. If I were the reviewer I'd insist on it.

All change

I've only gone and bloody wrecked the blog. Dang. That'll learn me for trying to make it look nicer.
It does look nicer though doesn't it? Shame I've lost all our links. Oh well, they weren't very good. By the time anyone reads this (i.e. never) I should have put some new links in. I imagie they will be similar to the old ones.

Honey

Today I have mostly been trying to stain some honey so that the pollen can be visualised can the source flower can be id'ed. Did I ever mention that I'm doing me PhD in developmental biology? NOT Palynology. Oh, this is why my project is moribund.


Apparently the flavour of honey is in some part dependent on the flowers the bee collected her nectar from. This being a hard nosed science blog (stop sniggering) I should back this up with some hard data and a couple of peer reviewed papers. However, I've already wasted too much time finding out about pollen stains to be bothered to look it up. That and the fact that as a mammal biologist, I wouldn't have the slightest idea of how to find that sort of stuff out.

Here is a picture of the honey pollen I stained with a fuschin basic jelly (3.5g gelatin dissolved in 20ml water at 50C, add 25ml glycerol and o.2ml phenol. Mix at 50C. Add Fuschin basic dissolved 1% in IMS or Ethanol until a rich pink colour, in case you are interested). A prize goes to the first person to email in with the correct analysis if the pollen.

aarrrgh, my brain hurts.

It's a Saturday, so there is a fair chance that, like me, you are feeling a little delicate from excessive alcohol (in the form of ethanol) intake last night. I bet that you are not a mug and have gone to work though. I am, so I have. Rubbish.


Do you have a hangover remedy you always rely on? In my experience many people need eggs on the morning after, possibly accompanied with some salty pig flesh all covered in brown sauce and in a sandwich. Or you may prefer the "cleaning" effect of some fruit and cold porridge (muesli). You'll probably be wanting a nice cup of tea with that. And water. Lots of water. When I was an undergrad I used to swear by a BLT with chili sauce washed down with Oasis Citrus Punch, or in severe cases Lucazade Sport ("its gets to your thirst, fast"), whereas this morning I had a grilled halloumi cheese sandwich with garlic yoghurt sauce. But that's because I'm a bourgeois get.


Well it seems that all your remedies are no more affctive than the next one, accoring to not so new research published in the BMJ ages ago. Pittler et al conducted a review of 15 papers investigating various hang over cures, seven of which were rejected as they were non-randomised. Although they do list 20 cures they found ion google, including Marmite on toast (hmmmmmm), kidney dialysis (an option not availible to most I feel) and "russia party" (what the hell is this?), the cures included in the trial are all not things I've ever tried, borage for example. They did not include a grilled halloumi cheese sandwich.
Worringly for me, they highlight that more need to be understood of the pathology of the hangover. I'm sure that the average university has enough drunken idiots (I have no idea who these people are).

I have devised the perfect hangover cure, or atleast what i always want to be done to me when hungover: I want to take my brain out or my skull, and put it in a nice cool bowl of clean saline, swish it about about, then put it back in.... bliss.

Flickr

To celebrate the brave new world of web 2.0 and the semantic web, or some thing, I did a search for the tag science on Flickr.
Look what the first image was. Ace, Darwin and some homonids in Lego form. More science should be represented in lego.

The entry for this photo is sweet too. Explains each of the guys. Not sure if this dude, Kaptain Kobold, is a science geek or simply an admirer, but props to him. Truly this is science embiggment.

Original

edit: now I've worked out how to do pics n'all. Watch out New Scientist's Short Sharp Science Blog, just watch out...

Official BUS statement re:Upstart Science Blog

ooo, get you New Scientist, with your new (ish) Short Sharp Science blog.
Think you are better than Big Up Science!, with your well written, up to the minute posts on cutting edge science news?

Well, let me tell you something, when you've been infrequently posting poorly written things about science since 2005, then you can come play ball with the Big Up Science! massive, you dig?

We get the press releases n'all you know. It's just that we choose to ignore them as we know that what we write will be ill informed nonsense and only one of the Scientician's pals will ever read it.

To teach you a lesson, I'm going to put a link to you here and probably read your blog, as you frequently post interesting things that are just the sort of thing I like to read, thus wasting time when I should really be starting an in situ.

edit: and thet've got picture. Show offs.

Fight Night: Evolution vs creationism! (or why evolution is right and creationism is wrong)

So last night your friendly local scientician popped off to the Royal Society in London for a lecture by Prof. Steve Jones of University College London (UCL) titled "Why creationism is wrong, and evolution is right"(availible here as download, as are a number of other interesting lectures).
Combative title, I'm sure you'll agree. Off I went, anticipating a juicy pompous lecture (pompous in a good way you understand) with creationist baiting much like you get in forums such as talk.origins, and a bitter debate at the end with placard waving members of the Evangelical Alliance egging Prof. Jones as he was ushered into a blacked out BMW to escape the lynch mob. But no, with the exception of a couple of cheap but frankly funny shots at G-Dub (to give the president of the USA his proper hip-hop name), the lecture was a concise primer of the facts of dawinian natural selection with the evidence speaking for itself. And very nice it was too. I'm not going to write about this evidence, it seems to me half the internet is full of this argument already. If you have even the slightest capacity for independent thought you'll be able to see that natural selection as described by the original Chuck-D (to give Darwin his proper hip-hop name) is just the way it is, and that creationism is just mythology and “intelligent” design and the rest are just plain balls.
So I left the lecture with a slight disappointment by the lack of blood spilt and the punches pulled, until I read the statement by the Royal Society issued at the lecture (as reported in the Guardian). The whole point of the lecture was for the RS to issue this statement. Christ, I thought, we are at the thin edge of the wedge with ID and creationism if such statement even need to be made. Prof. Jones in part cited the rise of fundamental Islam and Christianity as reasons for the apparent increase in creationism, but was most dispairing of the special place the PM has for faith schools in the education system. It all seems like madness.
But then I thought about the nice beardy man in purple and my faith in humanity was a little restored. But only a bit. Come on Rowan, have a word with our Tony will you? Or at least make sure Gordon is sensible (and the boy Milliband, just in case). Please.

edit: And Dave too. I suppose.

Hynosurgery... Live!!

So, tonight More4 will be screening a live hernia operation on a hypnotized patient, with no anaesthetic. Crazy. I'll be tuning in for the screams, I'm morbid, I know.

The More4 web site has an interview with the surgeon here, he's done a couple of these before, and seems quite positive but not too hysterical about it, saying that it's not going to replace anaesthesia.
I'd write more, but I've not done my research. Watch this space, maybe. Actually, better to watch this space...

Sinister Snails Fox Crabs

Sinister: such a great word, made all the better for being a synonym for left handed. I've never trusted them left handers.

What the devil am I blathering on about? Well mollusc fanciers (or malacologists as I bet they call themselves when trying to impress girls, like saying you're a scientician of any sort helps you pick up chicks (and no, there are no female malacologists, but don't quote me on that)), have discovered that contrary to expectations, back in the Plio-Pleistocene (2.5 MYA to 1.5 MYA) snails with a left handed, or sinistral (we got there eventually) whorl, had a better survival rate than their right handed, or dextral, cousins. The shock of this is that left handed species of cone snails pretty much went extinct 1.8MYA, and whelk dextral and sinistral species have lived side by side, suggesting no advantage and a possible disadvantage to sinistrality. The disadvantage coming about due to sexual selection form the females.

This research (Dietl and Hendricks, Biology Letters, 2006) reads like a forensic investigation, where they studied the number of repaired crab claw scars on paired samples of similar sinistral and dextral shell fossils, with increased scars indicating more survived encounters with hungry crabs. I did similar things back in my osteology/forensic anthropology days, but never on snails. I'm no malacologist. Or osteologist for that matter.
They then watched a crab (a box crab no less) attacking whelks and concluded that it has difficulty opening sinistral snails, although this was in the discussion and they don't present much data to back it up. Maybe they have better things to do?
The analogy of left handed snails and left handed boxers, tennis players and baseballers is then made (baseballers? is that right? hmmm, I'm English so I dunno. They don't mention cricket, but it's true there too, also in Biology Letters, Brooks et al), since the "opponent" knows little about the southpaw. Hmmm, best not take this too far or we'll be likening Matthew Hayden to a whelk soon.
It's an interesting point, but if the advantage of sinistrallity was so much, then why are they so rare? It is an advantage to be sinistral in a right handed world in terms of survival, but sexual selection pulls the other way for the right handers, a point they make, but they also finish the article with "it's not all about sex", nice quip. Malacologists eh? What are they like.
I say however, if everything was sinistral, or if sinistral and dextral were found in equal measures, then the opponent (crab or over hyped British tennis player) would have more experience of cackhandedness, and so the advantage would instantly disappear.
And so ends another overly long, poorly written and ill-informed edition of Big Up Science!

News: Rowan-Williams rejects teaching of creationism

the Archbishop of Canterbury, the most senior cleric in the Church of
England and the de facto leader of the world wide anglican church has
pubiclically rejected the teaching of creationism in an
interview with the Guardian.
Not really science, I know, but of importance in the teaching of
biology. This is already a huge issue in the US, and growing more and
more here, and it will probably get worse with the whole faith schools
nonsense being banded about just now.

Hwang Woo-suk Sacked

Sacked!

Hwang Woo-suk, the disgraced Korean stem cell researcher has been sacked by Seoul National University for the scandal surrounding his faked human embryonic stem cell research. (For background check here)

LOOK! REALLY IMPORTANT SCIENCE!

You know, when there is a scientific discovery that contradicts things that even your nan might know, we’re talking about the sort of thing that actually spurs me to bother writing this, I am amazed that it doesn’t make the headlines on the News at 10. There has been such an event this week.
Think back to your school days for moment will you, back to those science lessons. Think about that nice carbon cycle diagram you were made to copy, learn for the exam, then, with an irony that was probably lost on you, burn down Big Rob’s on the last day of GCSE exams. Picture that diagram in your mind. Is it there? Good. Now, those arrows coming in and out of the crude plants that you drew (or in my case, the box with PLANTS written in it due to lack of artistic bent), what gasses do they represent? The arrow in to the leaf, now if you were paying attention, they should have Carbon dioxide or CO2 written by them, and the arrows going out should be labelled oxygen, or O2, the word or the symbol would have been enough I’m sure. Where was methane? That’s right, methane was being released from the pile of cow shit, the rubbish tip and the industrial complex. Was it is, I ask you, being released by plants? That’s right, it wasn’t.

BUT IT IS! LOOK!

This has been happening right under our noses for eons. Nobody noticed because no one looked. No one looked because no one expected it. And they discovered it by accident!
We are in early days, but it’s published in nature, so the science must be fairly robust, though as recent events show, a Nature or Science publication does not guarantee against fakery. This may have serious consequences for international carbon trading agreements, such as the Kyoto protocol, which allow planting of trees to off set carbon emissions (methane is more potent greenhouse gas than CO2), and unfortunately may act as ammunition for those resistant to tackling climate change.

So here was have a major piece of science that will cause the basic biology taught is schools to be changed, raises questions on serendipity in science and will have consequences on how we tackle global warming. Yeah, that’s all well and good, but will Jodi Marsh be evicted from the Celebrity Big Brother House? That’s what I really want to know.