My loyal readers may have noticed that Mind the Gap was silent on the topic of Darwin this year. I have nothing against the man, and admire his work as much as the next girl. I suspect, however, that there is some stubborn kernel inside of me that resists the deification of one individual when scientific advancement is so clearly the product of many people working in concert over a long period of time – and the concept of evolution is no exception. I have also traditionally been adverse to bandwagons, and in this country at least, and especially in the blogosphere, the brass section surrounding the Ascent of Charles was getting a little loud. Still, I think about evolution with silent wonder every day in my line of work. And now that the parade has largely passed by, the street cleaners busy sweeping away the colorful remnants of merriment, it’s been more on my mind than ever.
Strange fruit Not so much a Blind Watchman as a gardener with 20/20
As with any endeavor, there are tasks in science that I enjoy and tasks that I don’t; there is also a strong correlation, for me, between enjoying a task and being good at it. I happen to be a whiz at making stable cell lines: coaxing bits of foreign DNA into immortalized cancer cell lines and selecting out a new strain derived from a single mutant cell. In this procedure, which is more like horticulture than molecular biology, I can induce the evolution of practically any trait that is not lethal to a cell by using a particularly nasty form of artificial selection and letting nature take its red-toothed and clawed course.
A few days before my ski holiday, I transfected two different DNA constructs into a single plate of cancer cells, one encoding a histone protein fused to a fluorescent red tag and the other encoding a newly published actin-binding domain I was eager to try out, fused with a green fluorescent tag. The first construct also encoded a gene conferring resistance to the deadly drug puromycin, while the second construct would allow cells to escape the effects of the equally iniquitous chemical G418. One the second day, I diluted the transfected cells across a series of plates so that the modified clones would not be too crowded to isolate once they began to grow. While I was off on the slopes, one of my lovely colleagues obligingly nuked my Petri dish with several doses of the drugs and watched while hundreds of thousands of cells died off, filling the medium with light-refractive clumps of unhappy corpses. When I got back, the carpet-like monolayer of cells I’d left behind had almost completely vanished, but when I held the plates up to the light and examined their undersides, I could see the faintly glowing, pale spots of resistant colonies scattered across the plastic.
Isolation is satisfying: you wash off the medium, pluck up a sterile glass cloning cylinder with a forceps, dip one end in high vacuum grease and press it down around one of the colonies to form a water-tight seal. A tiny amount of the enzyme trypsin will loosen the colony (consisting of anywhere from twenty to a thousand cells) and the cells can be replated into a small-welled vessel to begin the laborious process of nurturing, expansion and validation. I usually take about twelve colonies to ensure that I get at least one cell line that is healthy and that expresses both markers to sufficient levels, but for the next week or so I’ll have my hands full transferring my new babies to increasingly larger vessels, freezing down samples as back-ups and running tests to decide which will be ultimately be chosen — and which will be flushed.
It’s a jungle out there.
I never really got around to using cloning rings, Jenny. I preferred limiting dilution, although that has problems of its own. It’s a lot of work though, whichever method you use, and I must applaud you for taking twelve colonies!
I admire that you’re organized enough to set up an experiment, go skiing, and then come back to some results.
Nothing like work happening when you’re not around, Steffi.
I use cloning rings because they are sweet and geeky and physical. It’s a ritual, autoclaving all the components, setting it up, watching the cells slowly round up under the microscope. I do this in conjunction with limiting dilution (one of my dilutions was down to one colony) but I worry about few-cell colonies that I can’t see, so prefer to isolate them physically as well. I like to give myself the illusion of perfection.
Jenny, this nice post almost – and I say almost – makes me want to do some labby experimenty things again. You’ve made that vacuum grease sound almost poetic.
There is nothing like vacuum grease freshly out of the autoclave, all smooth and glistening. It took me a long time to find anyone who sells the glass Petri dishes and cylinders; I don’t think many people do it this way any more. I was once in a lab that made its own cylinders out of cut yellow and blue tips, but they always leaked distressingly.
I tried to make a stable cell line at one point, and I did kind of like picking them, but they never survived past a week. I did that at the start of my PhD, for a long time, and it was not doing well for me overall. It made my supervisor think I was completely incompetent at everything. Years later we found out the protein just kills the cells after a couple of days. Until then everything had been done in a shorter time frame.
But I still think that it’s me, that I can’t make a stable cell line.
It’s too bad you didn’t have an opportunity to get back on the horse. There is nothing like the feeling of looking down the ’scope at your prospective babies and seeing them glowing green and red in all the right places.
This time around is a bit weird: I’m getting a number of single-positive clones. I think the second vector I was given has LTRs in it, so perhaps there is some untoward recombination going on, the gene looping itself out while keeping the drug resistance genes. But it’s a good thing I picked twelve, and so far there are only three convincing ones.
Why twelve, Jenny? A full dozen?
It was the number of big colonies I had across three full plates. I kept two other plates as a backup.
But I do tend to be a slave to symmetry — and not only in the lab.
Did you keep a polyclonal backup too?
Yes! I am so busted.
Am I the most paranoid scientist who ever lived?
I think paranoia is a good thing for a scientist to cultivate.
I should have saved an extra well for that, then.
badoom – TISH
Hm. If only we paranoid scientists would be as paranoid about other things… like backing computer files up, say.
Not saying why I say this. Oh, no no no.
Hahahah. Methinks you should confess to Uncle Richard. It’s all right, I won’t laugh.
Much.
I am very paranoid about backups. I used to be very happy with my 2 TB box until someone told me that external hard-drives are notoriously unstable. Now I just live in fear.
You mean it’s not all in your head, Jenny? I’m disappointed.
Ptth. Go kill something.
Heh. Most of my backups go onto a sys-admin-tended, parity-infested, network SAN partition that is RAIDed to the hilt.
Slight problem – Wintle needs to remember to put stuff there. Otherwise, works beautifully. Personal files, on the other hand, are on a loosely organized (slightly bending the definition of ‘organized’) collection of USB keys, DVDs, and the like.
I need one of those external 2 TB thingamabobs. And a lession from Uncle RPG, clearly.
I find once you have a parity infestation it is just so hard to get rid of the little buggers.
My USB keys all tend to get haunted after a few months — full of ghost files, impossible to eject, impossible to reformat. Maybe they can smell fear.
I’m wondering why no one has commented on your blasphemy — referring to St Charles, of course.
taking care of experiments truly is similar to taking care of children. When I go skiing I also find someone to watch and feed them
You know, a teeny tiny little voice in the back of my head is agreeing with Jenny’s refusal to jump on the Darwin bandwagon… but I have to admit I kind of enjoyed all the hoopla.
Jenny – a sure way to get all kinds of ghost files on a USB key is to put it in a Mac. They insist on putting silly imaginary files with names like “.trashes” and “.desktop” on for no obvious reason whatsoever.
Cat, pigeons – get acquainted. ;)
Oh yes—and I wrote about that some time ago at my old place. Wintle seems to be familiar with my archive, so perhaps he could tell you where.
And talking of Wintles, when is Windows going to get a decent filesystem?
I can find that, actually. You left the link in a comment on a post I did about the similar situation with pets, which I posted when I went away this summer … [few seconds of clicking] that’s here and your kids/cells things is here
I am so good at internet!
\o/
If anyone agreed with the blasphemy they might not feel comfortable going on record. I suspect I’m the only one who feels that way, though. Might have something to do with my science education — I had four years of amazing biology teachers in high school and their take was that he was standing on the shoulders of giants — and we were given lots of evidence to back that up. This lesson stuck with me. Amazing contribution, yes, but…
Well, I thought I’d gone on record but possibly not in this forum. I was going to say something about it in the long-promised sequel of mine, but things like pigs and rabbits and Pickfords got in the way. I still will.
So no, you’re not the only one. And I’m sure I’ve seen other people associated with NN mutter about hagiography and suchlike.
Amazing contribution, yes, but…
Please expand – or are you fearful that there is a violent fundamentalist Darwinist sect lurking on NN?
I don’t want to bash Darwin or knock his work, Stephen. I just find the deification annoying. That is all. I’ve been most pleased with the Darwin coverage on television and in print that has taken special pains to acknowledge the vast body of non-Darwin-generated knowledge that contributed — a balance that has been lacking in some venues. And as I think I mentioned at Fiction Lab when we discussed ‘This Thing of Darkness’, the aspect of the novel I found most interesting was that the author dared to prick at the sacred bubble of mythology surrounding Darwin. (Obviously it’s difficult to tell what aspects were true and what were fancy in that at times negative account — one of the joys of historical fiction — but I found it quite refreshing, just as a counterpoint to hype.)
vast body of non-Darwin-generated knowledge
Ok, this made me LOL… I’m thinking of the behaviour of slime molds, the existence of subquarks, the taxonomy of Baryonyx, and a million other unrelated things now. :D
Yes Darwin did come across as a bit of a cad in the book. Flawed heroes are so much more interesting – though I’m not sure either how much of that was really accurate. Must re-read the biog…
I’m planning to go to another Cafe Scientifique event next week, with the title “Should Darwin be an ‘ism?”
By Dr. Rosie Redfield
If I make it (possible scheduling conflict), I’ll report back!
Sounds fascinating! Great title.
Stephen, to be honest I doubt the Darwin character was very real – but I enjoyed the distorted lens all the same.
I at the British Library a bit early for TalkScience last night so I had a look at their smallish Darwin exhibition – it closes Sunday so scoot along if you want to see it.
It was a mine of information. I learnt that on HMS Beagle the ship’s library stretched for 50 ft of the ship’s 90 ft length. That’s what I call getting your priorities right.
Darwin’s influences got honorable mentions and I was charmed to discover that Erasmus Darwin had proposed his ideas “in the less-obvious form of epic poetry using copious footnotes”.
Darwin was clearly a persistent chap. He spent 40 years studying worms – “he even tested their hearing by playing them musical instruments”. That surely would qualify for an Ignobel prize these days.
And he was an innovator – his 1872 book The expression of emotions in man and animals was one of the earliest books to use photographs as illustrations.
But he remains unfathomable. The exhibition said that his greatest passions in life were orchids and barnacles. Somehow the juxtaposition of “passion” and “barnacle” doesn’t seem right to me.
I enjoyed reading in his autobiography about how he was a (self-proclaimed) excellent shot, and spent much of his youth killing large quantities of British wildlife [insert spurious comment about Richard Grant here].
He also claims to have been “rather a naughty boy” if I’m remembering the language correctly, and a spendthrift during his Cambridge days. Not quite the “deified” image we’ve all become used to.
Frank, think of barnacles as book-like objects that occasionally move around and reproduce.
(No, it doesn’t work, does it?)
Thanks for the tip on the BL exhibition — that’s lunch-break distance for me!
think of barnacles as book-like objects
I know as a Librarian I’m supposed to have a passion for books, but to my shame I lack such a thing. Books are nice, sure, but I don’t feel passionate about them as objects.
Oh! I’m scandalized!
I’ve just received an email asking for a volunteer science communicator to work with ‘young people’ to “produce
a dramatisation exploring how Darwin’s theory of evolution is relevant to young people today.”
sigh