Life of a Lab Rat

"Are we nearly there yet?"

We've all been there. Either as the driver or adult passenger on a long car journey to a holiday destination, or as the annoying offspring ourselves, where 'long' is anything more than about half a mile. We've managed to turn that into a bit of a joke: on leaving the Black Castle one of us might ask it before the engine's even turned over. The Pawns are getting the message—and when they haven't, I will usually say "No, we've got about six hours left", which is far better for my sanity at least than "Don't start that again". Even if we are only five minutes from the destination.

"I need a wee-wee"

This one takes a bit of training. It's usually uttered from the backseat just after you've left the M4 service station (where you asked, "Does anyone need the toilet?"), successfully merged between two Eddie Stobarts, and have settled into fifth doing eighty-five.

The trick of course is not to ask who needs the toilet, but to inform your brood that they are, fact, going to the toilet now while we're still safely at Leigh Delamere services, because it's still six hours to Cornwall and we're not stopping again.

Having an 'accident' with a toddler in potty-training while in sight of the services but not being able to get there because the Cambridgeshire rozzers^[0]. haven't yet learned how to direct traffic yet is probably inevitable, so your best bet is to be prepared as best you can. Pack plenty of changes of clothes.

"I'm bored"

"If I hear 'The wheels on the bus go round and round' one more time I shall scream." A generation of parents know all the words to all the Tweenies songs, but at least they're better than the alternative. No, seriously: if ever I hear 'toot toot chugga chugga big red car' again I will have to be restrained from choking Jeff with his own blasted guitar.

Can I have an ice cream?

(Subtext: "I'm bored")

"No"

(Subtext: "In the car? When you're likely to throw up at the next corner? You know how much the upholstery stinks—are you out of your tiny little mind?")

"We just passed the services! Why didn't we stop?"

Because, darling child of mine, we've just spent the last four hours in a traffic jam outside Taunton and we need to be there by seven. And your mother's got a headache.
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If any of that seems familiar, spare a thought for Opportunity, NASA's plucky little rover, about to set off on a seven mile journey to a holiday home by the sea a crater. Seven miles may not seem much (although it can seem like a lifetime on the M5), but NASA claim that, if they can crank up the top speed a bit, they're not going to be 'nearly there yet' for two years.

And there are no service stations on Mars. Or ice creams.

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I started writing this because I was concerned about how the writer of the NY Times piece managed to get 110 yards/day for two years to be anywhere near seven miles (and don't even think about the title to that article). 110 x 365 x 2 = 80,300 yards, which is 45.6 miles. Assuming an Earth year of course, which is what the vast majority of people reading the article might reasonably be expected to think. Martian time is complicated.

Opportunity currently has a heady top speed of 0.1 mph. However, she is a sensitive lady and needs to take care not to trip over rocks and boulders and stuff that you don't (usually) get on motorways, which means she'll be travelling quite a bit more slowly. She is also solar powered, so even if she did spend all day travelling those 110 yards, she'd need to take a couple of days in the sun to recharge her batteries.

NASA says

The rover team estimates Opportunity may be able to travel about 110 yards each day it is driven toward the Endeavour crater. Even at that pace, the journey could take two years.

Note those critical words, each day it is driven. It's not going to be a non-stop journey. There will be toilet breaks.

But that's what you get when journalists swallow press releases without chewing.

The basic unit of life as we know it is the cell. Cells are essentially little bags containing DNA, the genetic material. The bag is made from fatty acids (oil) and some other greasy chemicals.

Oil and water do not mix. But fatty acids have two parts: a 'headgroup' that likes water and a greasy 'tail'. Because of this, if you took a drop of olive oil, say, and shook it up with the right amount of water you would get a suspension of little oily bags, or 'vesicles'. The greasy tails stick to each other and the headgroups stick out into the water. If everything is just right, the fatty acids can arrange themselves so that water is also trapped inside the bag. Think of a balloon, with the rubber being the fatty acids, with air (or water) inside and out.

If you added water-soluble chemicals (such as DNA) before shaking you could get some of them trapped inside the oily bags, and this is essentially how we think the first cells formed on the surface of the juvenile and excitable early Earth.

This is a nice little model, but then we run into problems. DNA consists of two strands that bind quite tightly to each other. They need to be separated before they can be decoded or copied (which needs to happen to make more DNA, to make more cells). Today (and for the last couple of billion years) we have specialized proteins that take care of the business of separating the two strands and building new DNA and RNA. But what happened before these proteins evolved?

One theory is that variations in temperature forced the two strands to separate, so that new DNA precursor molecules ('nucleotides') could assemble on them and react to form new DNA strands. When the temperature drops the new DNA double strands bind nice and tightly again.

However, fatty acid vesicles—our oily bags—are pretty sensitive things. They get upset if the pH is wrong, or if the wrong type and amount of other chemicals is present, or their concentration is low; if there are not enough fatty acid molecules in a certain volume the bags simply pop. Which is sub-optimal for the continued existence of our proto-cell. People assumed that the vesicles would also pop if the temperature changed too much, which puts the kibosh on the theory that thermal cycling could have been how DNA copying evolved. People (like me) who have tried to make fatty acid vesicles in the lab know all about these problems.

But two coves at the Howard Hughes Medical Institute in Boston Lincs Mass have actually done some rather interesting experiments (Open Access article). By making the fatty acid tails slightly longer the vesicles turn out to be surprisingly stable. They can be cooked at 100°C and still hold onto their cargo of DNA.

Simple prebiotic model membranes are clearly more robust than previously appreciated, allowing [for the] uptake of critical nutrients without the loss of larger entrapped material such as oligonucleotides

In other words, you can take these simple bags of DNA, heat them up to separate the strands and not lose anything. What's more, if there are nucleotides (our DNA 'building blocks') floating around outside they will slip into the vesicle at these high temperatures and get trapped inside—where they can stick to the separated strands and make new DNA.

Essentially, then, repeated heating and cooling of vesicles containing double-stranded DNA enables strand separation and re-annealing without destroying the vesicle. These vesicles also take up nucleotides at these higher temperatures, providing a potential mechanism for how proto-cells could obtain nutrients before they got around to evolving the transport proteins that exercise membrane biochemists so much today.

And where on the early Earth might we find such temperature variations? Apart from the diurnal day/night schtick we've got going here, hydrothermal vents and hot springs have long been considered to be candidate sites for early evolution. Cell warms up near the vent or spring, is carried away, cools down, drifts back by convection. Rinse, lather, evolve.

Of course, this doesn't mean we know how life did evolve, but it's a pretty convincing theory of how it could have.

This evening I went along to a presentation about iTunes U. I was accompanied by a couple of the more, eh, radical members of the department and we had a good laugh, not to mention free alcohol, rather un-filling canapés and a discussion on why wild pig was on the menu for a certain vegetarian but calamari isn't.

But, besides your correspondent managing to score a rather splendid freebie, the highlight of the evening was a certain member of the department proclaiming in a loud voice,

The number of people doing anything in science (at USyd) is very limited.

Laugh? I had to help myself to more cauliflower soup.

Conversation n the student office between myself and my young apprentice Beta Gal, just now (edited):

BK: I'm the only person in the world who knows what Protein-de-Jour does!
BG: Ooh! What?
BK: <Explanation>
BG: We're the only two people who know!
BK: Four. Four people.
BG: Who else? <Speculation>
BK: <Indicates other students> These two.
BG: If you tell anyone I'll kill you!

It's a cut-throat world, science.

Never mind flying cars or feeding all the starving children in Africa, this is what science in the 21st Century is all about.

The PDB on your iPhone. Is that so totally frelling cool or what?

Those of you not in this business possibly do not realize how outrageously expensive is the actual doing of science. In the same way that medicine is (artificially) expensive, suppliers of chemicals and equipment to scientists are ripping us off. And it's worse in Australia — there is a stupendous markup that is not accounted for by the obvious extra expense of shipping and storage.

The Black Queen last week discovered that by the simple expedient of sourcing certain not uncommon (and certainly not patented!) chemicals directly from a supplier in the US rather than a multinational distributor of exorbitantly-priced gear with a warehouse in Australia (mentioning no names, but think non-amateur times ten to the sixth), we can save about 12,000 dollars over six months to a year. Including shipping. Twelve grand! And we're not exactly a process lab — nor a manufacturing one.

It's good news for the lab, not least because I'm about to blow another 4 grand on these blasted microarrays. I'm also going to a conference in Maine at the end of June, the plane tickets for which — for some unfathomable reason — are going to cost more than the tickets I've just bought for London.

So every penny helps. Swings, roundabouts, etc.

Anyway. I have, he declared grandiloquently, A Plan.

You see, as the globe, because of the internets, keeps getting smaller, the price of actually oil keeps going up, making travel more expensive. Then there's global warming, fossil fuels are running out, omigodwereallgoingtodie etc., which is only going to make conferences and collaborations more difficult, especially stuck out here on the A E of N. So I'm going to do over a bank apply for money to construct a small fleet of tall ships on which there will be ultra modern labs and a helipad for emergency supplies. We'll cruise the world, working hard, collaborating with anyone who has money but a green conscience, immediately and imminently in touch with everyone via our satellite uplink.

Oh, and a couple of these in case PromegaQiagen pirates show up.

Members of Joel Sussman's lab at the the Weizmann Institute have developed Proteopedia (direct link), an online tool for making structural biology clearer for chemists and biologists by linking textual content to 3D structures.

Impressive.

For a born-again structural biologist like myself, this looks like an invaluable research and teaching aid. I shall follow its career with interest.

(via Peter MR, who reminds me what great fun BioMOO was, back in the day)

Today I have been mostly running gels.

I do a lot of this; it is one of the most useful tools in the molecular/cell biologist's garage. It is used primarily as an identification method (on the basis of relative molecular mass, or more colloquially, size) for DNA and proteins, but often also for purification.

As I'm a Pom, I shall add a restrained "hurrah" to this item of news:

Senate passes stem cell Bill

Hurrah!

The thing about the opposable thumb is that you do not notice it until it does not function correctly. You can achieve this effect by breaking a glass pasteur and shoving the jagged end into the end of the opposable thumb, and spending the rest of the day (and the next, so far) with a whopping great field dressing on it.

Have you any idea how difficult it is to wind or use a Gilson with a non-functional dominant thumb? Or how tacky red smears look on a white keyboard? The only good thing is that I had already Hibiscrubbed my hands and sprayed them with 70% ethanol and the hood was sterile, so I should not be too worried about infection.

Great advances in the biological sciences often depend on technological or intellectual innovation.

The microscope enabled us to see that there was a whole world just below our tangible existence, X-ray crystallography allows us to solve protein structures, nuclear magnetic resonance allows us to torment students and the internet allows us to waste our time in ways undreamed of. The major reasons, I believe, that the human genome first draft was published so quickly after the project was started was the competition between the public and private endeavours, and the advances in sequencing technology and contig assembly software.

So when my very good friend Ricardipus says that he is researching 'New DNA Sequencing Technologies', those in the know should sit up and listen.

As soon as he stops photographing hawks and doves and gets rid of his VIC-20, that is.

Wooaah!! I said I wasn't joking:

The moon might be a good place for a massive storehouse of digital information, sort of a Lunar Library of Alexandria (that hopefully won't burn down). That's the idea proposed by NASA scientist David McKay

(from BoingBoing, thanks to Georg).

The New Scientist says
Hollow lava tubes on the Moon could be used as a giant digital library. That's one commercial possibility for the Moon put forth in a white paper by a NASA scientist.

The video I mentioned yesterday reminded me of what I really want to see come out of all this sciencey stuff. There are vast quantities of data coming out of labs around the world, both 'big science' and 'little science'. The trick is to tie it all together, so that it makes some kind of sense. The second trick is to present it.

It is going to take a while, and some serious thinking about interdisciplinary communication, but I hope that within the next twenty five years or so we will have a working in silico cell. A program that models in exquisite detail the complete (OK, maybe 90% — 'first draft') secret life of any given cell type. Computing power will not be a problem, we will in all likelihood have something smaller than a handheld that can cope with it. But imagine, taking a computer model of a leucocyte, giving it some P-selectin and letting the program run. Or changing random proteins to see if they behave as oncogenes. In time we would catalogue all this information but being able to predict cellular behaviour from a rigorous theoretical background would be incredible.

Imagine it as a teaching tool, too. Build — or use holographic technology to project — a 10 metre spheroid, crowded and swarming with life; walk inside it and follow individual pathways and processes. (Take Australia. Scale it down until it fits across the length of your hand. That scale — inverted of course — is the same order of magnitude as your typical animal cell blown up to 10 metres across).

By 2030? Possibly. I'm not making a prediction, I'm trying to inspire. I think we could do it by then, given the phenomenal increases in both biological knowledge and computing power over recent years.

If you're as old as me, you might remember sometime in the early '90s being completely blown away by Tim Springer's wonderful videos of leucocyte extravasation. For some reason I seem to have a lot of non-science types reading these ramblings and I reckon I've probably just lost half my readership, so I'll step back a bit and put things into plain(er) English.

If you happened to pick up, say Jandl's Blood: Pathophysiology, you might find an opening paragraph that reads something like

Blood is a complex suspension in plasma of nondividing differentiated cells which continuously perfuses the vasculature. It contains a mixture of several very different kinds of cells, all of which stem from an oligarchy of progenitors that originate in marrow or lymph follicles.

Which is a rather complicated way of describing the red stuff that leaks out when you get a real bad paper cut. Essentially, blood is made up of red cells, white cells and little bitty things called platelets, all floating round in a kind of white wine sauce. And it gets everywhere. The red cells are the little fellas that carry oxygen and nutrients around, platelets help stop the red stuff leaking out, and white cells, like knights of old on armour'd chargers, fight infection. Depending on the sort of white cell you are, you can throw chemicals or antibodies at nasties, or actually muscle up and eat invading bacteria and other bits and pieces. Yummy.

After commenting on the enthusiastic scientist at CERN, I thought I should bring your attention to this discussion of dark matter, which tells you just a little bit of why the LHC is going to be useful.

I've just watched Beyond Tomorrow on Channel 7 — essentially the Australian version of Tomorrow's World. It's a light, frothy show with the weekly high point being an extract from Mythbusters.

But tonight they interviewed a scientist at CERN, and what was remarkable was the lady's obvious thrill she got from doing science for the sheer fun of it.

When asked if there were any practical benefits that might arise out of smashing protons together at near-lightspeeds, she said basically said no, we just want to see what happens. Mad props.

I do not normally do the 'content-free' link-blogging thing, but this is so damn' cool I just had to share it. Mouse neurons and galaxies. Can you tell the difference?

Via Eastern Blot.

According to Derek, we're likely to have gainful employ for quite some time.

The book hiding within that link is exactly the sort of thing that the meeja is likely to jump all over, and the actual analysis of Kurzweil's futurology is just going to pass them by. I had a cartoon in my head when the first draft of the human genome was published, which had all these guys (and gals) sitting around wondering what to to do now they'd sequenced it. And of course the work was only just beginning. Sequence is not everything, not by a long banana.

When I get to the bottom

I go back to the top of the slide

Where I stop and turn

and I go for a ride

A bit of a frustrating week.

The thermal cycler broke down just before it had completed a crucial experiment (but I think it went far enough to get some useful data), someone put agar plates with no antibiotic into the ampicillin plate bag (screwing up my cloning), a Western blot is tantalizingly inconclusive and a beautiful hypothesis appears to have been brutally slain.

Henry talks about some typical journalistic scare-mongering.

Now I'm not a developmental biologist, so I'm just basing my opinion on what I remember from seminars and distant lectures. Having said that, the article is an an interesting read, especially seeing as the question 'what does it mean to be human?' is closely related to 'what does it mean to be made in God's image?'.

It's dropped off the front page now, so I'd like to bring your attention to Georg's comment, in which she brings my attention to an article written from a journalist's point of view that, to my simple mind at least, is right on the money.

Non-biologists look away for a couple of lines.

For some reason I got distracted by left-handed DNA earlier. It's a bit of a science geek joke, with a serious point.

Okay, you can look back now.

I then wanted to see what else Tom had to say and came across his Errata & Corrigenda page. And he makes the point very nicely that scientific research progresses through the identification of mistakes and falsification of hypotheses. Additionally, most research claims are false and are corrected by further experiment. There is nothing wrong with this; the observation-hypothesis-experiment cycle is how we do science, and some of those hypotheses will be wrong.

I've mentioned before the misconception that scientists deal with facts. There's an interesting debate — rather a scandal — going on over the synthesis of a chemical originally isolated from a Siberian fungus.

In one of my previous lives I pretended to be a crystallographer.

In other words, I would attempt to persuade concentrated protein solutions to get together and form ordered three-dimensional arrays - crystals - so that I could then shoot X-rays at them. The purpose of this was to determine their structure.

One of the things I was taught when I learned crystallography was to be very, very clean. No dust, human hair, bits of glass or other muck were allowed into the experiment. The most frustrating thing about crystallography is that all proteins are different, and will crystallize (if they crystallize) under different conditions, and there doesn't seem to be any pattern to this at all. The lab's insistence on cleanliness was an attempt to factor out one of the variables in the process. But I soon discovered that this may have been counter-productive. As with a lot of things in research, people disagreed with each other and there was a lot of intuition and opinion without a great deal of solid evidence. I realize that this might come as a surprise to some of you, to those who, perhaps, believe that 'scientists deal with facts'. The truth is that at the frontiers of science we don't know what's going on and we're trying to find out - that's why it's called 'research'. If you want facts, look in a text book (and they all contain mistakes, too).

So as I went on and got more experienced, I began to welcome small amounts of crud in my crystallization experiments. In fact, one recalcitrant protein only ever crystallized once, along what looked like an insect leg. I was never able to repeat that experiment; although I did have gothic fantasies about breeding every different sort of insect I could find and using various bodily insect parts as nucleants. A little too Shelley, perhaps.

Hot from Nature, we have Nature Protocols: Recipes for Researchers.

It's in beta, I'm getting a few 404s and the registration/sign in was weird (stealth login, anyone?) but it could be useful. One of those 'wait and see' projects I feel, and probably in direct competition with the protocols section of the OpenWetWare thing I wrote about last week.

What's interesting to me is that these are peer-reviewed methods, with user comments. So it's almost a Wiki-meets-journal type of thing. Hmm.

OpenWetWare is, and I quote, an effort to promote the sharing of information, know-how, and wisdom among researchers and groups who are working in biology & biological engineering.

Essentially, it's a wiki for biological labs to share information. Think about it: An editable database of all your reagents, projects and protocols and all you need is a web browser.

The aims of the project are certainly laudable: OpenWetWare represents an initial effort to decentralize and lower the barriers to information exchange among all researchers, be they professors, students or research scientists.

This could be worthwhile, or it could be a tremendous waste of time. I'm not sure which at the moment, and it boils down to if it would take too much effort to convert everything we have in (e.g.) Filemaker databases and administer the thing.

We were having an interesting discussion at coffee this morning about information, and how bureaucracies like to collect it even if they can't find a use for it. The context was that granting agencies are now asking for the DOIs of published papers. Naturally the topic wandered a little, and someone brought up the idea that all our papers should be engraved on stone tablets because eventually our civilization will progress to the stage that current technology will be lost, and all our research will become inaccessible.

"If the Rosetta Stone had been on floppy we'd never have been able to interpret hieroglyphics" was one memorable argument.