Posts Tagged molecular biology

Astonishing documentary: Secret Life – the Hidden Life of the Cell aimee whitcroft Nov 28


If there’s one thing you watch today (well, other than wall-to-wall coverage of The Hobbit* and perhaps some videos of sorting algorithms explained through folk dance), it needs to be this.

Secret Universe – The Hidden Life Of the Cell from pbbes on Vimeo.

In this astonishing hour-long BBC documentary released just a month ago, David Tennant narrates the story of what happens when our basic components – cells – come under attach from a virus (in this case, a common respiratory disease-causing virus, the adenovirus).

Not only is it brilliantly beautiful, but also educational – we don’t just see various spherical (or not) objects interacting, but the molecular details making them up. And it’s genuinely thrilling – I was more gripped watching this than I have been watching major Hollywood blockbusters. Yes, I’m a giant nerd in some ways (especially about this stuff), but it’s also really that good.

When I was doing my molecular biology degree earlier this century, we had nothing so detailed. We had to rely on diagrams and our imagination to provide an understanding of how everything interacted – I’m glad to say, I appear to have gotten it right. Happy thought :)


* For those of us in New Zealand. I managed to escape the insanity occurring in central Wellington by heading as far south for lunch as I could while remaining on the island, huzzah!

HTML5 + molecular visulations = win aimee whitcroft Aug 16


Today I was looking into HTML5 (as one does), when I came across an incredible site: CANVASMOL.

canvasmol screenshot

(click to enlarge)

HTML5 is the newest incarnation of HTML (the language in which large bits of the web are written*).  What has people extremely excited about it is that one no longer needs to embed things like video players in website if one is writing in HTML5.  Such functionalities are built in.  Which is why Apple devices don’t currently support, for example, (Adobe’s) Flash.  They say.

And I’m going to leave that there, as it’s a very thorny nest of thorns :)  Also, it’s not the point of this post – other people have written much about it, and a simple search should suffice to sate your…well, curiosity :)

_Anyway_.  CANVASMOL!

A very cool site allowing one to have a look at a variety of different molecules.  In different ways (and one can compare a few at a time, too!).  One can also upload new ones, of course, because one never spend too much time getting wiggly happy fingers over such things. To change the view of a molecule, simply play with the letters/acronyms (beginning X Y Z, which control rotation) at the bottom of the square containing said molecule.

The screenshot above shows oxytocin, which is most famously known as being one of the ‘bonding’ neurotransmitters which are responsible for us feeling all loved-up.  In romantic or parental ways, as well as others.  Hell, I’m pretty sure the Ragdoll cats* belonging to friends of mine cause teh production in humans of ridiculous amounts of the stuff (plus their being high on it constantly).

The others are all fun, too.  I always find looking at buckyballs*** and graphene particularly oooohsome, of course.

Love it.  The site, that is.  Stunning use of in-browser stuff. Wish I’d had things like this when I was studying molecular biology :)


* Huge oversimplification

** The first truly domesticated cat, in which all those feral/killer instincts have been replaced with pure Cuddly.  It’s ridiculous.

*** For a pretty cool explanation of a 120-cell, which is basically a 4 dimensional shape made of 120 dodecahedra (a buckyball is a dodecahedron), see this animation.  Oh, also – behold!  A video tutorial on made a buckyball _out of origami_.  Because you know you want to.

Fresh out: extraterrestrial life _not_ discovered! aimee whitcroft Dec 03

You can thank the rampant speculation caused by NASA’s press release for this blog post’s title1.

[UPDATE: There's now a lot of controversy over the paper, which a number of microbiologists says it's not, um, terribly good...]

Very, very tough little bacteria

Very, very tough little bacteria

And the thing is, the discovery in question is a really awesome and important one.  But it’s also a pretty technical one, and I imagine will leave a lot of people saying something along the lines of ‘meh’.

The discovery is, of course, that scientists have found a strain of bacterium2 which is able to use arsenate instead of phosphate in its biological bits and processes.  To understand why this is awesome, some background…

Background (to be skipped by those who know it)

All of the organisms we’ve come across on earth are made up of the ‘big 6′ – hydrogen, oxygen, carbon, nitrogen, sulphur and phosphorus.  Without any of these, an organism loses its fundamental livingness, and is instead simply a great steaming (or not), pile of failed biochemistry.

If I were in front of a periodic table, I should now point at the element Phosphorus.  With a long wooden stick.  Phosphorus is used in cells in a variety of interesting and essential ways: it forms the backbone of DNA, and is also the ‘P’ in ADP/ATP, the molecules which serve as cells’ energy reservoirs/factories.  Oh, and it’s a heap of other important things as well, including stuff like, you know, proteins.

More pointing at the periodic table now!  Another fascinating thing is that this most marvellous table is not some random agglomeration of elements.  Oh no.  Its structure allows us to make some rather interesting inferences.  For example, elements in a column have a lot in common with each other, and can often substitute for each other in biological processes.  Which is why some critters can use tungsten instead of the very-fun-to-say molybdenum.

Or they can use cadmium instead of zinc.

Or copper instead of iron, for the carrying of oxygen (which is why the blood of some mollusks and bug-type things is green).  Interestingly enough, this substitution breaks the ‘same column’ rule – anyone know why?

And, of course, it’s led to much hypothesizing that it may be possible for life to use silicon instead of carbon3, or, possibly, arsenic instead of phosphorus… The most biologically common form of phosphorus is phosphate, which behaves similarly to arsenate in a number of ways.  The thing is, though, that while arsenic can be substituted for phosphorus in the early steps of some biological pathways, it’s just sufficiently different that later arsenic-based metabolites are unstable.  Which is why it’s toxic: it knocks biological processes over.

Kids: do not try eating arsenic at home (or anywhere else, for that matter)

Main story (those who tuned out, feel free to tune back in)

Right, so!  Some scientists, including NASA people, went out to a lake in eastern California, enchantingly called Mono Lake.  Why?  Well, they were on a treasure hunt.  Or, to be more precise, a bacterium hunt.  Mono Lake is far saltier than usual, alkaline (the opposite of acidic), and contains much higher levels of arsenic than usual as well.  A good place to look for arsenic-using beasties.

They took some of the lake’s sediment and, through various mysterious processes known only to microbiologists (and anyone who cares to read the paper)4, they isolated bacteria from said sediment, and set them to growing in two different mediums – one containing arsenate but no (or very little) phosphate, and one containing phosphate but no arsenate (the control).  And they counted how many bacteria grew.

Now, one would expect the bacteria in the control medium to grow just fine.  That’s what they’re there to do.  But, oh joy!  The bacteria in the arsenate-containing medium (now to be called the As+ group) grew too!  Interestingly, they had a far larger intracellular (‘inside the cell’) volume than did their control friends.  This was due to a number of large vacuoles6 inside the cell ,which the authors theorised might be helping the bacteria to stabilise arsenic toxicity.

They then looked at the cells themselves, to seeing whether the As+ group had actually incorporated arsenic into its structures and functions.  And it had!7 There were clear indications that arsenic had been incorporated into DNA – the As+ group had high levels of arsenic and low levels of phosphorus in its DNA fraction, whereas the control group had low levels of arsenic, but high levels of phosphorus.  It also looks like the As+ group had incorporated arsenic into other of its biomolecules, including proteins and small molecular weight metabolites.

To sum up, then: yes, the beasties certainly prefer phosphorus to arsenic, and grow better in it.  But that’s not the point: it’s the first time anything has been shown to be able to grow without phosphorus!

Feeling the urge to say ‘meh’

Of course, this discovery is very exciting to microbiologists, organic chemists and so forth.  But why would the rest of the world care? A couple of reasons, but let’s tackle the obvious, NASA-promoted one.

Currently, the search for extraterrestrial life hinges is predicated on the assumption that such life will be comprised of the ‘big 6′.  This finding suggests that that may not be the case at all, which in turn expands the scope for our search, by increasing the possible ways in which life might be built.

Which is awesome :)

Secondly, it suggests that even life on earth may have come up with some other interesting solutions to the problem of information storage (currently, we’re most familiar with DNA), and we haven’t been looking hard enough for them.  Which is also pretty exciting.

And so there you have it.  The actual science behind all the hoo-ha.  And some pretty fascinating stuff it is, too.  Congratulations to the lake-wading scientists behind it!

Oh yeah, and you can see some excellent comment on the research, from Kiwi scientists, here.

UPDATE: Something of a rant about embargo breakers.  Thanks to The Sun and The Daily Fail for breaking the embargo on this story yesterday.  What you did was spoil the fun, and hard work of everyone else who had been working on this, and were abiding by the rules.  And you wonder why journalism gets knocked for having low integrity…

‘NOTHER UPDATE: photos from the NASA press conference can be seen here.


1 I mean, seriously, what were they thinking?  They must have known this would cause an absolute sh*tstorm of wild theories.  I’m a huge fan, but this seem a little bit pot-stirring of them…

2 GFAJ-1 of the Halomonoadaceae, to be precise

3 Yes.  Silicon-based life.  Crunchy, and potentially sparkly.  Also, of course, we know that computer chips still use silicon /looks around meaningfully

4 I have.  I’m not going to go into the details, as I fear they will induce snoozing in many of my readers.  My descriptions of the methods used are, therefore, something of a simplification.

5 Phosphate is the most commonly occurring form of phosphate.  Arsenate behaves similarly to it in many ways.

6 A ‘cavity’ inside a cell, surrounded by a single membrane, which contains water, food or other compounds (including waste byproducts from metabolism)

7 UPDATED NOTE: on the recommendation of a commenter, I’d like to stipulate that ‘high’ here is a relative term: it’s a matter of proportionality.  For the full nitty-gritties, read the paper.



Felisa Wolfe-Simon, Jodi Switzer Blum, Thomas R. Kulp, Gwyneth W. Gordon, Shelley E. Hoeft, Jennifer Pett-Ridge, John F. Stolz, Samuel M. Webb, Peter K. Weber, Paul C. W. Davies, Ariel D. Anbar, Ronald S. Oremland (2010). A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus Science : 10.1126/science.1197258

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