Life of a Lab Rat

"How about we go upstairs and look at your cell culture?"

My paper was accepted by JMB today. Woohoo!

This is the one about which reviewer #2 said

the work [...] is of premier experimental and conceptual quality and a role model of how to rationally combine structural biology with molecular biology and biochemistry

so I'm just the teeniest bit chuffed.

I tell you the truth, there is more rejoicing over one colony that is positive than over 19 that aren't.

BioPerl is, apparently, distributed under the Perl Artistic License, and not as I read it first, the 'Perl Autistic Licence'.

"How's your protein?"

If anything is worthy of the soundtrack to 2001: A Space Odyssey, it's this video of Earth-rise from moon orbit, captured by KAGUYA (more).

Dum dumm DADUMM! DUMDUMDUMDUMDUM.

Via Eva, a great slideshow on the abuse of PowerPoint (and indeed any presentation software).

This ties in nicely with my previous rants (passim), and Henry's comments are, as usual, spot on.

HUGE shout out to Audra, who is celebrating her birthday today (Wednesday, for those of you behind the dateline). It's generally considered a milestone, which probably means she's old enough to know better.

Go and leave some good wishes.

Update: And it's the same score for Jenny Hotpants, my favourite editor, I realize this morning. But she doesn't have a 'personal' website.

I'm guessing there's going to be a lot of talk on weblogs around the world about the primate cloning news. I forecast a lot of uninformed blather from a lot of people, from all over the moral, religious, political and scientific spectra. The fires will only be fueled further by the news that Ian Wilmut has decided that converting adult cells back to a pluripotent form is 'better' (in a technical, not ethical sense) than using 'cloned' human embryos.

My own concern is not with the status of human embryos, but with the increasing selfishness of our society, its unthinking dash into complete utilitarianism. I'm not going to say what I think about this, because my own ideas are not fully-formed, but I am concerned that all scientists, even those not involved in such obviously 'ethical' areas, think about what they can do, and more importantly what they should.

Coincident with the safety audit, there's been a bit of a discussion over at the Science Advisory Board about ethidium bromide, 'safer' alternatives and other ploys used by unscrupulous marketeers to get you to buy their company's product.

Ethidium bromide (EtBr) is a chemical that is used to 'stain' nucleic acid (DNA, RNA) so that we can actually see it in gels. Because EtBr allegedly comes up as a mutagen when assayed using the Ames Test (and google for it yourself), it's got quite the reputation for being one of the worst things in the mol biol lab. This is an ideal situation for the talentless hacks marketeers, because it means they can play on lab rats' fears to sell over-priced, under-performing crap.

It turns out that the whole argument against EtBr is so much elephant poo anyway. Perhaps the strongest evidence for the continued use of EtBr is that it has been used for years to treat sleeping sickness in African cattle. And if you do the sums, to get the EtBr dose equivalent that is used to treat one cow, you'd need to drink fifty thousand litres of gel staining solution.

Moreover, when a company decided to test their own EtBr substitute for toxicity and mutagenicity against the 'leading brand', they found that yes, their alternative was safer than the competition, but there was no evidence that it was any safer than EtBr itself:

In the graph, notice how SYBR Green — the 'leading brand' — goes up, which is bad, and then goes down, because the test cells are dying, which is very bad. EtBr ('EB') itself seems to be about as dangerous (i.e. not very) as EvaGreen, the company's chemical being tested. Notice that there is no dose-response effect. That is, in general, if something is dangerous, then the more you put into the system the more effect you get. Here, that does not happen for EB (or EvaGreen), which implies that any mutagenicity that is being detected is noise in the system. Indeed, I might suggest that the falling off in 'mutagenicity' in the three right-most EvaGreen columns is itself indicating a cytotoxic effect. Gosh.

And given that these alternatives are generally less sensitive than EtBr, which means you have to use more, EtBr begins to look like a clear winner.

There's been a bit of discussion in the Cage about the bridge-dismantling video. Those who are interested can read all about what's going happening on the University's website.

But in our proud tradition of getting things wrong, we find that the Cage has been renamed:

To which I would like to add a proposal that could only improve the campus:

Not to mention what the byproducts might do for my roses.

In one of those "Fog in Channel: Continent cut off" moments, the bridge linking our bit to the rest of the campus and Sydney was removed a couple of weeks back. You can see it here:

(Direct link)

The important thing is that Azzuri's Coffee is our side of City Road. Aah. . .

That's all very pretty, but this

is a result.

Yay!

I am proud to tell you that CLC bio (www.clcbio.com) and JPR Technologies (www.jprtechnologies.com.au) have teamed up to service you better in Australia!

I, um, can't wait to be serviced.

Ahem.

Eek!

One of the great tragedies of the modern age is that nobody has invented a 'Find' function for my desk.

sigh

Whut?

Your Aspie score: 90 of 200
Your neurotypical (non-autistic) score: 121 of 200
You seem to have both Aspie and neurotypical traits

Which makes me. . . normal? Heaven forbid!

Previously, on Life of a Lab Rat, we've talked about presentations and Powerpoint rather a lot. Ad nauseam, maybe. But it turns out that, maybe, just maybe, the worm is turning. There's an editorial in the current issue of Nature Cell Biology addressing the empty whizzbangingness of Powerpoint-driven talks.

Yes, they say, Powerpoint (and by extension, Keynote) can be fun, but does a visually striking presentation really make your research more accessible or memorable? they ask, obviously inviting the negative.

However, graphics tools ought to be used only when necessary. It is worth reflecting on the frustrating experience of watching a Hollywood movie so overloaded with special effects that it leaves the viewer drained from sensory overload but intellectually and emotionally unsatisfied. Less is more: after a day of back-to-back talks, nothing is more refreshing than a visually clear, logically constructed and well articulated presentation.

The story is told of Daniel A. Haber, who on realizing that he had lost his presentation, gave a fantastic talk completely without slides. Never mind that this smacks of insufficient paranoia (I've been known to travel with 2 sets of glass slides — one for the carry-on luggage, and one for the hold — and a set of overheads), but it demonstrates what all of us should be capable of; giving a talk with no visual aids at all.

The 'lesson', and suggestion,

focus audience attention on the speaker, do not read off the screen and reserve slides to present key data and to summarize a complex body of work. Why not introduce the talk without slides?

resonate with me, and I shall have to experiment next time I give a talk in a more 'formal' setting.