Lab Rat Writing

Having missed a couple of the other deadlines for Science Writing Prizes, I am determined to manage to get something to submit for the John Rose Prize which (in it's own words) gives an award for:

"The best explanation of a scientific principle of general interest"

Anyone have any ideas about what I should write about? At the moment, I'm leaning towards antibiotic resistance because a) it's in my course and b) it's useful.

Or maybe I could write about Biorefineries, and just reuse bits of my essay? Phage therapy? Although that isn't exactly general interest at the moment unfortunately.

At the very least, writing this in my blog should give me enough commitment too it to actually write the damn thing instead of just waving at the deadline as it passes.

On feeling ill...

I suspect having a cold isn't fun whatever job you're in. Coughing and sneezing in public tend to make people look at you oddly, and try to discreetly shuffle away in case they catch it. In a lab however, it's a whole new level of awkward because everyone around you is working with little eppindorfs and petri-dishes and trying their hardest not to get them contaminated.

Contamination is the One Big Evil in microbial biochemistry. And I've essentially turned into a walking contamination spray. I am already worrying for the fate of the plates I poured today, and it's only a matter of time before people start following me around with ethanol'd paper towels and disinfect everything I've touched.

I'm even starting to want to do it. Thankfully most of my work is done under a laminar hood, which is like a large box with a glass pane in the front which separates me from the plates and the bacteria. Which means that if I cough at the ceiling my plates should manage alright.

If they get contaminated I will scream. This is already the third time I've done this procedure. The first time the actual antibiotic we were using was contaminated, so we just grew nice little colonies of black mould. The second time I forgot to dilute the mixture down, so I was pipetting tiny, tiny amounts of liquid out and all the results were screwy. The problem is, is that the bacteria take five days to grow, which means I've already wasted two weeks and have no results.

And I'm ill. Meh. Welcome to science, two steps forward, six steps backward. :(

Where does the disk go?

Part of what my supervisor is doing for her project involves growing bacteria then challenging them by putting little antibiotic disks on the plates and seeing if the bacteria die or not. She can't make it in today, so she asked me yesterday if I could put the disks on the plates for her.

The procedure was fairly simple and wouldn't take long, so I agreed. I came in this morning all bright and early, and suddenly realised I had no idea where on the plates I was supposed to put the disks.

It the middle? At the edge? Where the bacteria are growing?

It's my fault for acting so competent in my first week. It made her form the impression that I know what I'm doing. :(

Lab Rat in its Natural Habitat

I'm back in a lab! More excitingly, a different lab. I moved in today, so I've just about been allocated bench space and shown where the autoclave is. Today's tasks included cleaning said bench (I pretty much just doused it with70% ethanol and waited for the ethanol to evaporate, I do not want anything contaminating the bacteria I'll be working with) and mixing up a load of media so that I can put it above my bench where it can sit and look all pretty.

The Lab equivalent of hoovering and putting up the curtains basically. As soon as the autoclave has finished (the autoclave is basically just a big pressure cooker which sterilizes everything) my bench will have:

• Four durans (large bottles) of Tap Water Media for growing bacteria in
• Four flat-bottomed flasks of LB media for overlaying plates and growing different bacteria on (used to test if the first bacteria are producing antibiotics)
• One small pot of 40% glycerol (our bacteria occasionally produce spores, and these are stored in glycerol)
• Two pots of sterilized toothpicks (for picking out isolated colonies of bacteria)
• Three empty sterilized flat-bottomed flasks, for as yet undisclosed purposes
• One empty measuring cylinder with foil over the top
  
• Two boxes of pipette tips

And I've just remembered that it should probably have double distilled water as well. Bugger. I will ask my supervisor about that, but water is used quite often and it would probably be helpful to have some around. Although my bench is right next to the MiliQue machine (which occasionally produces noises like a drain with a bad stomach and in some mysterious way ionises the water. Way beyond my MEH unfortunately) so I might be able to get away with it.

These will be placed on the shelf above the Lab bench, apart from the pipette tips which will be on the bench itself, along with my Lab Notebook (yes, it does deserve the capital letter), a biro, a marker pen that is running out of ink (for labelling the bottles), a roll of autoclave tape that probably isn't mine, a little rack for holding eppindorf tubes (ooh, that reminds me, I need to get a rack for the bigger tubes) and a bunsen burner stand that I've yet to move onto someone else's bench.

I'm home =D

In case anyone actually reads this...

...I've added an RSS feed. It's right at the bottom of the page :)

Biorefineries

Part of my course this year involves writing a Long Essay (3000 words, not really that long, but longer than most of the other ones we write). We had a choice of three, and luckily one was about bacteria, so I sort of jumped on it.

"To what extent could microbes be used as "biorefineries" that is, in biological processes for producing chemicals, fuels and polymers?"

I've been writing it for a while now, so I've come to know quite a bit about potential biorefineries and how they could work. The basic principle is that you get bacteria that you've engineered in various ways to produce a range of exciting chemicals, stick them in a fermentor, remove the chemicals at the end and sell them.

They're basically meant to work a bit like oil refineries, except using microbes and easily accessible raw materials rather than chemical processes and oil. Currently the most exciting idea at the moment is to use lignocellulose materials, that is all the bits of plants that don't get eaten (corn husks, rice stalks, bits of tree etc) in order to produce ethanol, to be used for fuel.

The closest thing that exists to biorefineries at the moment are the big ethanol refineries in the USA and Brazil. These produce ethanol from sugary substrates, sugar cane lees and maize at the moment. The major disadvantage of these is that they compete with available food stuffs, which is why there is presently the emphasis on using non-edible materials.

Lignocellulose contains two main chemicals; lignin and cellulose (biologists are not that imaginative sometimes). Lignin can't really be broken down by bacteria as yet, although there are some fungi that will do it. Cellulose can be, but needs specialist enzymes. To remove the lignin, and start breaking down the cellulose, some pretreatment is needed, mostly acids and steam.

The ideal microbe to use therefore, would be one that can break down cellulose and withstand the at least a certain degree of pretreatment, in order to reduce the cost of cooling and neutralising everything. The best one so far is Clostridium thermocellum which works best at 60 degrees C and has very efficient cellulose-digesting enzymes all held together in a complex, the cellulosome.

But when you look for current research on C. thermocellum, the very first thing that hits you is that, well, there isn't very much of it. In fact, there's hardly any of it, especially not heavy-duty 'what would this be like in a biorefinery situation' research. There's a couple of token papers about various aspects of it, and then just nothing. A spookily large amount of nothing.

There is, of course, a standard reason for this (and it doesn't involve conspiracy theories). The people who want to potentially build a biorefinery will want to make money out of it. They want to market the technology, or build a biorefinery with their own special bacteria, not tell every other competitor out there what they're doing.

From the point of view of an economist or a businessman it's a perfectly sensible thing to do. From the point of view of a researcher it's all slightly frustrating because it meant that there's a high probability that several people are all doing exactly the same experiments, and not telling each other. *sigh*

Locked in the Ivory Tower

So...something I heard while on holiday. On the radio. On Classic FM to be precise, during the news. After they'd passed all the stuff about Gaza strip and shirtless politicians, they then went onto this enlightening article (paraphrased here, because I can't remember all the words):

"Scientists have discovered that horses are able to recognise each other by their whinny! A group of scientists from [can't remember where] lead horses past each other while playing the sound of other horses whinnies and found the all the horses were very confused..."

etc, etc. Other experiments were done as well, but you get the general gist. And all the while, I was sort of sitting there with this stunned sort of look on my face, which can eloquently be summed up in three letters: wtf.

wtf.

Classic FM very rarely gives news, even rarer do they give science news, but someone somewhere had decided to give what must have been their five precious minutes of Science News Time to this? What about cancer research, going on in thousands of labs, millions of person hours? Research into biofuels, developmental studies, bacteria, phages (heh), neuroscience, so many many useful, wonderful, interesting and relevant things that are being done by scientists the world over.

But no. Instead we get a quick message about horses from the Department of the Bloody Obvious.

That made me think of something erv wrote a while back. When all the people from the 'framing science' gang were talking about how scientists were staying all aloof in their ivory towers and needed to get out and communicate with people and do other things in a dynamic fashion (and incidentally buy their book).

It was in the context of evolution. And as erv pointed out, she was perfectly happy and perfectly willing and perfectly ready to go into the church, or the town hall or whatever and give a talk on evolution. But they wouldn't let her. So wasn't so much sitting in an ivory tower as locked in it.

Which does sum up science pretty well. Lots of science happens, there are plenty of labs and plenty of people. And every now and again the newspapers or the government get interested and then it's Eat Five Fruits A Day or Scientists Clone Stem Cells or something. But not very much of the actual science gets out there. Lots of people know, for example, that Smoking Causes Heart Disease, but how many people know how, or why, or why some people get it when others don't?

Which is where we hit the ivory tower problem. Scientific papers are written by scientists, for scientists. Scientific conferences are attended by scientists. Scientific societies are joined by scientists. Most researchers have 'posters' for their projects which detail on a piece of A1 paper what their doing and what their results so far are. How many people outside of the scientific community have seen a scientific poster?

Look at all those scientists living in their ivory towers!

The thing is though, is Scientists don't so much live in ivory towers as kind of get locked in them. There is simply, at present, no way for cutting edge research to get out into the public. Sure there are science museums and popular books (Bill Bryson springs to mind) but the real edge of research isn't there, those are olds not news. In some cases, even the basic information isn't there, listening to the cafeteria staff talking sometimes is painful when they hit science (I will make a brief disclaimer here that this means no offense to cafeteria staff. I know bugger all about running a cafeteria, no doubt if I tried they would find it similarly difficult to watch).

How does it get out? When I leave uni and start researching, is there any way I can inform The General Public about what's happening in the exciting world of bacteria and bacteriophage? More importantly, will I have the time or the inclination to try and find out how I'm meant to do that? And if I do, will anyone want to know?

One argument that I've heard against letting cutting-edge science news out is that science changes. Accepted paradigms bend and sway in the wind of scientific opinion (rotfl! I need sleep), new discoveries lurch everything sideways, new stuff happens, and ideas change. There is a worry that, if shown this, people will loose faith in scientists in a sort of "Well those scientists don't know what they're talking about, they keep changing their minds" kind of way.

Will they? Opinions about other news changes all the time, no one seems to mind that too much. Horoscopes are wrong almost all the time, and that doesn't put people off believing them. Besides, I think it's much safer for people to be aware that science is a beautiful changing process; rather than just taking everything at face value as if 'this is the true'.

And of course there's the "Would people be interested?" issue. Take me and economics. I don't understand economics. I don't really want to. Economics, in my mind, happens to economists, whom I would happily lock away in an ivory tower and let them get on with it.

What if people think like that about science?

Really, scientists are in a kind of ivory tower. But why we're there, and whose fault it is, and how on earth we get out I am still not sure about. Science is very complex but it can be made understandable, you just need ways to be able to tell people and for people to want to understand.

"We have barred the gates, but cannot hold them for long ... we cannot get out ... we cannot get out ... "

~Tolkein

Lab Rat Working

Holidays are over :(

Image from here

I did not do the drawing, I hasten to add, but I do feel a bit like that. Sitting on top of seemingly impossible problems with a 'help meeee' sort of look.

At the moment I have decided to concentrate on revision because I am too tired (read lazy) to write my long essay. As my lever-arch file that contains the lecture notes is teetering on the brink of exploding, I've brought a book to write the revision notes in. So far I've filled in approximately half a page of it (NOT GOOD) but hopefully as it is a book rather than bits of paper I can do a NaNoWriMo thingy and try to fill up two pages a day.

Rather than, say, looking for pictures of rats on deviantart. heh.

Interesting Fact Of The Day: As there is now a large database of protein structures, many new structures can be determined by just looking at a DNA or protein structure and comparing it to the ones in the database. If you have the protein structure, you can also look at the individual amino-acids (the molecular building blocks that make up proteins) and using the knowledge of what kind of amino-acids they are (attracted to water, attracted to each other, acidic, polar, etc) make a reasonable guess as to the function.

This is one of those wonderful examples where science is very similar to trying to guess what the picture is on a half finished jigsaw puzzle (without looking at the box. In science there is no box). The more different techniques you use, the better you'll have an understanding of what the protein is, and of course some proteins are a lot easier to guess than others. A protein from a rat (say) with the exact same genetic code as a ribosome protein in a silverfish is easy. Another protein might have sections similar to the silverfish, but other bits that are more like bacterial membrane transporters, in whicch case you'll need a whole barrage of other techniques to figure it out.

Although if your DNA code is wrong to start with; due to contamination, procedural error, crossed communication wires or laziness, none of the fancy computer techniques will give any meaningful result. Nor will any of your experimental work, if you're recreated the protein from the genetic code you've been given.

And this does happen. There was a protein that developmental scientists were looking at a while back where (through no fault of the experimenter) the DNA mutated mid way through the growth-and-extraction process, which meant that everyone who was working on it (trying to find out where it migrated to in developing frog eggs) was working on a protein that didn't exist. Only one amino acid had changed, but it meant that this protein didn't migrate anywhere and all the researchers and poor little phD students were tearing their hair out about it.

Until someone finally decided to go back and check the sequence, essentially go through the whole tedious growing-frogs-and-taking-out-their-DNA-and-getting-the-right-bit-out all over again. They found that the bit of DNA they got the second time around was different to the one everyone else was working on. After that I think they did a couple more checks (well ... I hope they did. To be honest I wouldn't be surprised if they didn't) just to make sure they really had the right stuff, and yay! it migrated and some people wrote some papers and were happy about it.

Quick question: How long was the interval between the first attempt to get the correct DNA sequence and the second?

Answer: 20 years.

Oooops :)

To be fair to the scientific establishment though, there is a good reason for that. Science works on funding, and you just don't get funding for something that has Been Done Before. Another thing science works on is papers. The more papers you write, the more likely you are to get more jobs (and more funding) and you wouldn't realistically be able to publish a paper that just confirms someone else's work, not unless the work in question is starting to look very dodgy, and really needs conformation.

To be ever fairer to the scientists (especially as I am one), those twenty years working with the wrong protein were probably not an entire waste of time. They would have generated a lot of new techniques, and probably several people who were really good at tracking proteins by the end of it.

heh. still funny though. 20 years of the wrong thing...








Image from here