Cassetteboy has done it again

Normally, the phrase for this kind of thing would be: “It’s funny, because it’s true.” However, being true makes this tragic. (But still funny at the same time.)

Emperor's New Clothes rap | Cassetteboy

Cassetteboy - Emperor's New Clothes rap

Posted by In My Newsfeed on Monday, 21 March 2016

And if you missed it the first time, check out Cassetteboy’s prophetic Cameron’s Conference Rap from 2014:

Where I'm from

Although I was not born there, I grew up in a small seaside town called Bognor Regis. Not surprisingly, the further from Bognor I go - and I can’t get much further! - the fewer people have heard of it, despite it’s infamy.

A friend post this video on Facebook the other day. For those curious, this is what Bognor looks like from the air. Or, more precisely, what Bognor beach looks like from a drone.

Bognor Regis Feb 2015 from Sussex By Air on Vimeo.

It’s no Sydney, but it’s not a bad beach. There’s even some sand when the tide goes out! :op If you get bored (it’s a bit repetitive), skip to 2:10 or 2:50 and you can see my favourite bit: crazy golf by the pier. (There's a good kebab shop, The Sussex Frier, in the background too! If it's not closed down.)

Awesome Octopi

Via the Youtube channel of a friend from (but no longer in!) Dublin, Jonathan Gordon, here are some awesome videos of octopus camouflage. (Yes, I know that “octopuses” or “octopodes” is more correct for the plural but “octopi” is more fun!) I’ve seen this kind of thing on documentaries before but never realised this kind of thing could happen when just “[diving] down to look at a shell”.

The screenshots give the game away, sadly, but even when you know it’s there, the camouflage is still so amazing that the octopus is hard to spot.

And if that’s too scary for you, here is another video from Jon featuring an über-cute baby octopus “walking on the beach”:

The Cat & The Ducklings (Animal Odd Couples)

Via WEIT, here is a crazy/cheery "cat suckling ducklings" story that is fit to be an April Fool's joke but isn't!

A dancing peacock spider for Valentine's Day

If your Valentine's Day needs a bit more romance, or you just need cheering up, here is a peacock spider trying to woo a lady spider.

A couple of black cats for Halloween

And if Halloween is not your thing, the latest Henri video might be for you. This is not a happy time of year for a black cat who does not suffer fools.

(The pumpkins are getting a lot of love from the trick-or-treaters this year, which is gratifying.)

There's nothing scary about the Spice Kittens

It's Biology Week, so what better excuse to spend some quality time watching kittens! Thanks to felid-fancier Jerry Coyne at WEIT, I was alerted today to the presence of the Spice Kittens Live Webcam. Worry not, for though there is a ginger one, this has nothing to do with the Spice Girls:

Rosemary, a stray, gave birth to her kittens October 5th. She is estimated to be two years old. The two orange boys are Basil & Mace. The buff boy is Sage. The B&W girl is Nutmeg.

Cat coat genetics are actually quite complicated but we would know that Rosemary was (almost certainly) a dam (a lady cat) even if she had not given birth to kittens because she is calico. Calico cats are an interesting (and pretty) example of what is known as X-inactivation.

Cats, like all mammals (including us) have genetic sex determination. (Not all animals do. For some it is temperature dependent or they can even change sex during their lives - see "Finding Nemo's sex-changing father", for example.) Genetic sex determination does not necessarily need sex chromosomes (yeast manage with a single mating type locus (gene)) but in cats (and humans) it is determined by a pair of sex chromosomes. (A single pair of sex chromosomes is normal. The platypus has five pairs!) These are the famous "X" and "Y" chromosomes, pictured right. (Human ones but cats are probably quite similar.) As you can see, the Y (right) is a runty little thing compare to the elegant and well-formed X - and this is where X-inactivation comes in.

The problem is that, with the exception of some short regions at each end, the Y chromosome is missing most of the genes that sit on the X chromosome. This means that a female (XX) has two copies of these genes and males (XY) have only one. This in turn would mean that a female cell would produce approximately twice as much of the products of these genes. Gene dosage is often important: rather than the absolute level of something, it is often the ratio between two things that is important. To compensate for having two copies, therefore, the cells of female mammals switch off one of the copies. This is "X-inactivation".

Because it is random which X chromosome gets switched off, this can lead to some interesting chimeric patterns, including that of the calico cat coat. This in turn is because one of the main coat colour genes - the "ginger gene" - is on the X chromosome. The parts of the calico cat that have a functional ginger gene are like a ginger cat and the parts that inactivate this copy but instead have the recessive "black and white" variant are like a black and white cat. (An extra complication is the status of additional genes that determine how much white patterning there is.)

This also explains why two of the male kittens are ginger - they have inherited their Y chromosome from their father (no ginger genes) plus a random X chromosome from their mother - the ginger one in the case of Basil and Mace. I cannot quite work out whether Sage also has the ginger gene but it has been "diluted" by another coat gene, or whether he is a different colour variant. (The girl, Nutmeg, is a more simple black and white.) The other complicating factor with kitties is that different kittens in a litter can actually have different fathers, so the variety of coat colours within a little can exceed all the possible combinations of one tom and one dam. (It also means that I don't think we can use the colours of the Spice litter to work out what colour the fathers were, except that Nutmeg's father was not ginger.)

Anyway, I am pretty sure that watching kittens is good for your mental health (and you can't catch Toxoplasma gondii online) so do have a little look when you have a spare moment and ponder X-inactivation, study animal behaviour, or just admire their kittie cuteness! (I'm not sure how long the live stream will be up but I will try to remember to update this post if it disappears.) [Edit: The girl kitten now seems to be called Pepper.]

h/t WEIT.

Five Minutes with Ben Goldacre

After yesterday's post about an interview with Richard Dawkins, author of two of my favourite books - The Selfish Gene and The God Delusion - it seemed appropriate to post today about an interview with the author of another of my
"must read" books, Bad Science.

A bit shorter than the Dawkins interview, Five Minutes with Ben Goldacre is a quick-fire tour of:

"bad science", dealing with critics, the importance of randomised trials, whether God exists and Twitter.

I particularly liked Ben's description of himself as an "apatheist". Due to my background, I have quite an interest in religion and think quite a lot about my atheism (although I don't quite consider myself as a "New Atheist") but I think it is always useful (for strident atheists and religious types alike) to remember that there are people out there who really don't care and don't consider it to be that important.

Ben's real passion is clearly science and how to do it properly - particularly in relation to medicine - and I really cannot recommend Bad Science highly enough. Although bordering on ranting at times (but always in "righteous anger"!), the early chapters in particular provide an excellent and accessible introduction to why science - and proper use of statistics - is so important. It is the number one book I recommend to my first year tutees studying Biomedical Sciences, as well as A-level students at Open Days.

Ben now goes beyond being a sterling advocate of evidence-based medicine, however, and also has some interesting ideas regarding "evidence-based policy" and how randomised trials can be applied to government policy. My reading list is quite long at the moment (particularly with the recent ENCODE release) but I think I will be adding his Cabinet Office paper: Test, Learn, Adapt: Developing Public Policy with Randomised Controlled Trials.

The whole Five minutes with series is really good and Matthew Stadlen is an excellent interviewer. I am surprised by the breadth of topics they manage to cover in five minutes without it actually feeling superficial. I guess there is often something to be said for "cutting to the chase".

I only recently discovered the series (thanks to my lovely wife) but another notable episode is that with my most recently discovered heroine in Five Minutes with Caitlin Moran. There's a whole host of others, though, and I look forward to working my way through (most of) the list! (Another BBC triumph!)

A great intro to Humanism by the BHA

Continuing this month's celebration of things that make me proud to be British, here is a lovely (and short) video by the British Humanist Association explaining (a) what Humanism is, and (b) why you don't need religion to have morals or to give life meaning.



I particularly like the quote from Richard Dawkins:"Science is the poetry of reality."

Hoping curiosity won't kill the Rover

In less than 36 hours, the Mars Curiosity Rover will touch down on Mars. Hopefully, it will touch down at the planned pace and not crash land. If you still haven't seen the animation of the landing manoeuvre, then do watch NASA's "seven minutes of terror" video. There are a whole bunch of versions of these kicking around from various news agencies etc. but I think the explanations in the original are the best and they really convey why they are calling it "seven minutes of terror"!

This is science that is way cooler than science fiction because it is (hopefully) really going to happen. I really hope it works. It'll be a nervous day in the NASA control room. As they point out in the video, the distance between Earth and Mars is such that when they first receive word that Curiosity has entered the Martian atmosphere, the rover will already have been on the surface - in one state or another - for seven minutes! Space is big - even our little corner of it.

I'd been hoping to embed the video here but it doesn't seem to be working. To be honest, though, you're better off going to the NASA website as there is plenty of other great Curiosity stuff to explore. (You can find out more about the Curiosity Rover in another NASA video, "The Science of Curiosity: Seeking Signs of Past Mars Habitability", for example.)

Happy Paddy's Day!

Or, Happy St Patrick's Day, if you are feeling more formal. Maybe even "St Pat's". But not Happy "St Patty's Day". Never "St Patty's Day"!! (No, I'm not Irish but having lived in Dublin for six years, I am pretty sure about this.) He's not a burger, he was a 5th Century Amazing Maurice (or, more accurately, Keith) of snakes. (You might need to be a Pratchett fan with a cursory knowledge of post-glaciation species distributions to get that one.)

That is almost my last word on the matter, other than to share this rather good and geeky St Patrick's Day YouTube song that is doing the rounds, combining two of my favourite things: beer and science. I like the fact that the singer looks like he's got in the spirit and had a jar or two before the performance. My only real criticism... it's not the black stuff in the glass.

SPOILER ALERT! Here are the lyrics:

In the year of our lord eighteen hundred and eleven
On March the seventeenth day
I will raise up a beer and I'll raise up a cheer
For Saccharomyces cerevisiae
Here's to brewers yeast, that humblest of all beast
Producing carbon gas reducing acetaldehyde
But my friends that isn't all -- it makes ethyl alcohol
That is what the yeast excretes and that's what we imbibe

Anaerobic respiration*
Also known as fermentation
NADH oxidation
Give me a beer

[CHORUS]

My intestinal wall absorbs that ethanol
And soon it passes through my blood-brain barrier
There's a girl in the next seat who I didn't think that sweet
But after a few drinks I want to marry her
I guess it's not surprising, my dopamine is rising
And my glutamate receptors are all shot
I'd surely be bemoaning all the extra serotonin
But my judgement is impaired and my confidence is not

Allosteric modulation
No Long Term Potentiation
Hastens my inebriation
Give me a beer

[CHORUS]

When ethanol is in me, some shows up in my kidneys
And inhibits vasopressin by degrees
A decrease in aquaporins hinders water re-absorption
And pretty soon I really have to pee
Well my liver breaks it down so my body can rebound
By my store of glycogen is soon depleted
And tomorrow when I'm sober I will also be hungover
Cause I flushed electrolytes that my nerves and muscles needed

Diuretic activation
Urination urination
Urination dehydration
Give me a beer

[CHORUS]

I also love the little disclaimer added by the author, cadamole, marked with the asterisk:

*Actually, this isn't true. While both anaerobic respiration and fermentation occur without the use of oxygen, anaerobic respiration utilizes the electron transport chain to generate ATP, while fermentation does not. My bad. I would have remembered that if I wasn't trying so hard to rhyme. A new corrected version is now up on my channel: http://www.youtube.com/watch?v=L6dzUOYTQtQ

Dedication to accuracy such as this should really be rewarded, so go on... click on the link and give this guy some more views/likes. It's what St Patrick would have wanted.

Feel the Force... of taxonomy!

Occasionally, I come across some really weird stuff at work. Today, for example, I was updating some lecture slides on sequence databases (how jealous are you of my students?!) when I came across a classic. The release notes for the current version of the UniProt database has a light-hearted and rather interesting look at taxonomy. (It's not very long if you fancy a peek.)

The thing that stood out, however, was the reference to a paper in The International Journal of Systematic and Evolutionary Microbiology (there's a journal for everything!) by Sassera et al. (2006): 'Candidatus Midichloria mitochondrii', an endosymbiont of the tick Ixodes ricinus with a unique intramitochondrial lifestyle.

Ixodes ricinus is the tick transmits Lyme Disease. Here's one engorged on blood. [Picture by Richard Bartz, taken from Wikipedia.] Handsome devil, isn't it?



The interesting discovery was not the tick, though, but rather a tiny endosymbiotic (i.e. living internally) bacterium. Intracelleluar bacteria are quite well known and many are rather interesting, such as the "male killing" species that alter the sex ratio of the host's offspring because they are only transmitted by females. Candidatus Midichloria mitochondrii, however, doesn't just live inside cells but inside the mitchondria in cells, which hadn't been seen before, I think.

My interest today is not the science, though, but something much more childish and silly. The authors named their discovery after Midi-chlorians, the endosymbiotic travesty microbes from the Star Wars prequels that explain the Force and make grown men of a certain age weep. (Why George? Whyyyyyy??!!) And that's the benefit of discovering a species - you can name it after whatever you like! (Except yourself.)

And for those of you who get depressed by the mention of Midi-chlorians, or want to know more about them, watch this video!

BBC Planet Earth/Blue Planet - Deep ocean creatures

Thanks go to the Why Evolution is True website for highlighting this video. Amazing footage of some weird and wonderful critters. (Planet Earth and Blue Planet are separate series, for those (like Michael at WEIT) wondering.)

CreatureCast: awesome videos of crazy critters

In an interesting article about the need for evolutionary biology to go viral, I just came across a fascinating website called "CreatureCast", which features videos of crazy and awesome creatures, made by the Dunn Lab at Brown University. I have only watched the jellyfish one so far but it's well worth a watch. Click here or, alternatively, check out this collection on iTunes:

CreatureCast Dunn Lab Biology

Quantum Levitation: I don't understand it but I like it!

This YouTube video shows something called "quantum locking" of a superconductor in a magnetic field, causing it to levitate in a most outstanding fashion. My brain is too tired now to even try to understand the physics behind this (and I am not sure I would understand even if it wasn't) but the video is well worth a watch anyway!

Quantum Levitation video