15 November 2007

Trial move

We used to move all the furniture in my flat in Edinburgh around once every 6 months or so. I get itchy when things get stale or staid. And while I've really liked the ease of Blogger, and kind of like splitting my disparate personalities into three separate blogs, it was getting silly. The whole shebang will be maintained on a wordpress version on a trial basis. Since hardly anyone ever comes to this site for anything other than that mysterious "akatsuki enzyme" and some old food posts, no one should notice any change... Expect me to dither about the whole thing and shift back in a few months of non-blogging.

01 November 2007


I'd like to state for the record that Singaporeans reproduce asexually or via IVF. Sex is not condoned in the island republic, even on their aircraft, and should not be undertaken by anybody. Furthermore, sex between two same-sex individuals could cause the economy to collapse.

This is not a laughing matter.

Stop goofing around with tragic mistakes

Sometimes I wonder if there is or should be a standard of how to classify depths of mistakes. I was somewhat shocked to read that the Met was found guilty in shooting goof. A goof? If Charles de Menezes had survived a minor wound, perhaps it would have been a GOOF. This was on the scale of major FUCK-UP. OK? You don't fucking shoot someone without FIRM EVIDENCE that he is who you think he is. Suspicious actions a terrorist does not make. I know there was a great deal of pressure to crack down on potential terrorist threats. But shoot-to-kill MUST have a firmer basis before being ordered. A shooting of an innocent is not a goof. Not in my style book.


Honestly, you lot on the interwebs can't be left alone! I spend some time away from the keyboard and this sort of shit happens. Now, where have I heard that name Nadine Dorris before? Honestly. Is that woman for real? She's definitely NO sister.

And what's her bag with Ben Goldacre? I read both his posts on the science committee's recommendations on amendements to the Abortion Act and the subsequent brooha about "leaked" memos and failed to detect anything out of the ordinary. What a palavar! Only an self-important idiot would think that the select committee's discussions were "closed meetings". Add that to the initial charge of her ridiculous stance on abortion, and she's in my mind: a lying COWard.

30 October 2007

Don't abort the Abortion Act

Finally, a level-headed statement on the abortion act. I sometimes despair of how abortion seems to be a battle-ground sans scientific evidence to back up wide-reaching statements. Admittedly, those who oppose late-stage abortions do so under moral arguments, but there is no reason why a moral argument should not be based on evidence.

A dork replies

I like Stephen Fry. I don't know him personally, but I enjoy his writing, his blethering, his somewhat awkward sense of style. Not being a stalker-fan, I wasn't aware that he was a gadget-freak until his recent outing. Like I said, not a stalker-fan.

That said, I take great umbrage at one sentiment in his latest post about his adoration of all things dorky:

So, believe me, a love of gizmos doesn’t make me averse to paper, leather and wood, old-fashioned Christmases, Preston Sturges films and country walks. Nor does it automatically mean I read Terry Pratchett, breathe only through my mouth and bring my head slightly too close to the bowl when I eat soup.

I was in complete agreement with him apart from that. What exactly is wrong with pTerry's books? And is his loose sentence construction describing Terry Pratchett readers as being mouth-breathers and head-lowerers? I was appalled. Then chastened. It's true. Every word.

Incidentally, probably apart from the lack of Discworld book ownership, Stephen Fry has described the majority of computer users. I'm not talking about those who just use Microsoft Office for work, but those of us who use them to organise our photos, music, movies, lives, work, and perhaps even interact with others socially1. Most of us who couldn't care less which OS you run on what machine built by whom2. And yes, not everyone's on World of Warcraft (although I would if I had the time).

1 Or anti-socially in the case of trolls.
2 Unless you're a jealous and spiteful git. What's with Windows users mocking me on my Mac over here anyway? I was a very early cross-OS user with a MacintoshII in my early childhood (oh SAM...), an IBM running MS-DOS followed by Windows 3.1 in my early teens was the home PC, and I built myself a series of cheap desktops since then running the whole range of Windows OS until XP, when I moved over to experiment with some of the free Linux OS. A power-board death of my last Fedora-running laptop left me stranded in LA without a home computer, hence the purchase of a Powerbook, which incidentally, is very cheap on this side of the pond. I've loved and hated aspects of ALL the systems I've made and bought in my short lifetime. I just like my Powerbook right now. It does the job quite nicely. Rant? Me? No... I just get constantly ridiculed about my Mac. It seems almost personal. Finally, a "PC" way to stigmatise somebody. They can't make fun of my Scottish accent on a Chinese face, but they can mock my choice of OS. And my dog. They mock my ownership of a dog too.
3 Fark. That was a rant, wasn't it? Sorry....

25 October 2007

Are we taking the terror thing too far?

One of the most level-headed things I've read about the shooting of Charles de Menezes by the Met:

However, [Clare Montgomery, QC] told the jury: "If the Metropolitan Police are exposing the people of London to danger because they are not doing what is reasonable and what is practicable, it is surely in the interests of Londoners that you say so."

The case for the defence sounds a bit more like a John le Carré novel.

18 October 2007

Judge's "error" about "errors"

UK scientists defend Gore film following a judge's finding of Gore climate film's 'nine errors'. The background as quoted:

Mr Justice Burton was asked to rule on whether An Inconvenient Truth could be shown in UK schools. He agreed that it could, provided the "one sided" film was accompanied by guidance notes for teachers.
The case was brought by school governor Stewart Dimmock, from Dover, a father of two, and who is a member of the New Party.
Mr Dimmock did not want the movie distributed to schools. He called the Oscar-winner a "shock-umentary" and objected to children being "indoctrinated with this political spin".

I remember vividly reading a National Geographic magazine about greenhouse gases and how increases in said gases have caused global warming1. This was back when I was a very impressionable child, and it spurred me, along with my peers, to action. From then on, we damn well switched lights, computers and TVs off whenever we weren't abusing our gawd-given right to electricity. It didn't make me a tree-hugging eco-warrior, but it made me very aware of humans' actions on their environment. Photos of polar bears will usually do that.

Nonetheless, it started a lifetime of being careful and making the greenest-possible choices with my limited willpower and means. Damn right I was an impressionable child. Who knows how my life would have been different if National Geographic had been more responsible and published guidance notes to temper the one-sidedness of the greenhouse gases->global warming message. I ought to sue! They denied me decades of swanning about in low-MPG SUVs like the Glorious Humvee, sleeping by the glow of my 200-inch TV and banks of computer monitors, commuting by plane every week from Asia to Europe. And it would have saved me countless hours of sorting my glass from plastic from paper from metal waste. Hours I could have spent swanning about in my Glorious Humvee.

Publicity-hungry toe rags like Stewart Dimmock can go take a flying fuck at a rolling doughnut.

1 Incidentally, this is now known to be an overly simplistic view, but the take-home message is still the same.

17 October 2007

Holliday junction resolution resolved to solve cancer problem

Sometimes I wonder where the breakdown in communication between scientists and journalists lies. In this article about a recent study on a DNA damage checkpoint enzyme, the Beeb describes the study as such:

Research into how the human body repairs damaged DNA has been described as a "major breakthrough".
The way that cells protect themselves from diseases like cancer has been the focus of a study by scientists at Dundee and Leeds Universities.

The enzyme studied1 indeed has a crucial role in DNA damage repair, a mechanism that prevents the DNA in cells from getting more and more mangled with every replication cycle. But to conflate a study on structural analysis of a bacteriophage2 enzyme with cancer in humans annoys me a little. It's sexing up the topic beyond its current reach3.

Some of the responsibility for conflation of basic science with translational/clinical applications lies with scientists. We have to justify what we do: to the funding agencies, to our peers, to the editors of journals, and to the public that ultimately funds our research by taxation. So everything we do has to somehow, however tenuously, be tied in to some disease or some way to make human life better4. So every time we publish our findings, we make that link, however thin, to some major health concern: cancer, heart disease, obesity, cancer, diabetes, cancer, auto-immune diseases, cancer, blah blah blah. And the journalists, with their need to write an interesting article, take a lot of our fatuous crap on faith. Don't ask for solutions. I have none. I am guilty of the same damn crime.

1 Sorry, it's not open access. You're unlikely to be able to read the full thing outside of a first world university/college. It's a bugger isn't it? Incidentally, does anyone else get annoyed that they don't link to the studies in PubMed or even list the first author? Then again, if they had, I wouldn't have seen via PubMed that one of the authors, David Lilley, has published in both Nature AND Science in the space of a week. That's rare.
2 Bacteriophages are a type of virus that "infect" bacteria. Yep. Even bacteria get viral infections. Isn't nature amazing?
3 Don't get me wrong. I think this structural analysis of the protein is a great step forward in understanding how DNA damage repair works. The next step may happen yet. I just don't think the next immediate step is preventing cancer.
4 Caveat: I refer here to research funded by the Medical Research Council in the UK or the various National Institutes of Health etc in the US. My world is very narrow.

15 October 2007

Why do research?

What the great one says, with research substituted for writing.

You don't live there always when you write. Mostly it's a long hard walk. Sometimes it's a trudge through fog and you're scared you've lost your way and can't remember why you set out in the first place.
But sometimes you fly, and that pays for everything.
--Neil Gaiman, genius.

True of any creative field, I suspect. Science to outsiders may not seem as creative as, say, painting or writing. But it is an artform in a way. And every day, we have to find creative solutions to problems1. It's a hard, hard slog; sometimes with no end in sight (like right now!). But the occasional insight into the functioning of the universe makes it all worthwhile.

1 Whether hypothetical or simply practical in terms of lab practice

Merciless treatment of Ming

Menzies' leaving is not much of a surprise. The timing was probably not to his own plans though. But hey, if a general election is a year away, the Lib Dems probably want to get their leadership battle out of the way and all the nasty words forgotten by the time voters cast their ballot.

14 October 2007

Black Watch

It was moving. Shocking. Gripping. And emotionally draining.

The National Theatre of Scotland brought their production of Black Watch to Los Angeles this month. 1. There wasn't a chance in hell that I was going to miss it. And I dragged P along so he didn't have to be the only Perthshire accent on campus for once.

Black Watch is a masterfully crafted piece of theatre. You're sucked in instantly: fascinated by the potty-mouthed neddish lads and their casual sexism and sexual harassment. But they soon become more than stereotypical soldier-types. The playwright, Gregory Burke, didn't feel the need to throw in the usual human-interest wife and kids angle to get us to see these guys as fellow human beings. None of the crap that the Sun and its like put out whenever they run those "our lads in Iraq" pieces. There's not much point in putting in some spoiler space here. After all, this is inspired by recent history. There's no need to explain to you that the media interest in the Black Watch started with the poor timing of the announcement of their regiment's disbandment, which coincided with its deployment in Falluja. Poor PR by Her Majesty's government on the one hand, but without which the world would be poorer by an excellent play. If anything, the loss of the Black Watch as an independent regiment has given us the chance to hear the collective voice of the soldiers who were interviewed for this to happen.

Political statements aside, the direction was superb. The choreography was unexpected and the fighting in balletic fashion somehow made it all the more poignant without romanticising the aggression. The physical nature of the acting somehow brought home the realisation that these are people who live their lives through brawn.

Among the reviews posted on the UCLA page and echoed elsewhere on the interwebs, there are opinions that viewing Black Watch should be compulsory. I would add my voice to this. It not only helps you start to understand why some men/women (but mostly men) enlist, but also some of the disillusionment that they must feel. As said several times in different ways, the "Allied" forces in Iraq had already "won" the "war". It's the peacekeeping that's killing everyone now.

Funniest line of the night: [Description of what life in mortar-filled Iraq is like] "It's like Perth Road [in Dundee] on a Saturday night."

Slightly awkward moment in a mainly American audience: [When the squad was ambushed and stranded] "If we were Americans, we'd have been fucking airlifted out by now."

1 And they're taking it to New York after this weekend. Where it joins their production of Wolves in the Walls, which is as opposite a piece of theatre as I can imagine. Not that I wouldn't enjoy it; being based on a Gaiman and McKean collaboration.

11 October 2007

sign what?

Walking the dog a couple of nights ago, we passed a sign1 that made me smile. And I just couldn't resist using it. So there. The damage is done. Tell me if I should undo it.

1 I'd like to credit the corny genius behind the sign-tist chain of sign shops for this.

Gene targeting ruined my life

While we're blathering about science, the recent award of a Nobel prize to Mario Capecchi, Martin Evans and Oliver Smithies made me remember how much I used to curse their blasted brains during the PhD years. You guys deserve a Nobel prize for making 3 years of my nascent scientific life hell. Then again, without your pioneering work, there'd be no work for the skill-less people in the world like me.

Intelligent female scientist seeks solution

I've been thinking about the future1, my place in it, and my place in scientific research. Having bored myself silly with self-centeredness, I looked further afield. Back in July2, Professor Greenfield was deploring the lack of female scientists in the higher echelons of her profession. She makes a few fair points, but, as can only be expected with such a complex problem, has no solutions. I'd only add that many male scientists face the same problems as female scientists3: publish or perish, wave farewell to a life outside the lab, bid your aging reproductive organs good day and goodbye4, watch all peers ascend on the property ladder while you slum it out, suffer from intense self-doubt5, blah, blah, moan, whinge, whine. Oh, we're back to self-centeredness again. Regardless of the problems and lack of solutions, I got a darn good laugh out of this comment to Prof. Greenfield's article:

"Maybe women scientists are that much more intelligent so they realise that as a career, scientific research is a joke?" --WinstonTheChair

So true.

1 And no, it's not orange.
2 When my head was so far down a microscope there was no light input save that of the very expensive laser. And no, it wasn't orange either.
3 I should know; I live with one.
4 Granted, this is more a problem for XX than XY. But without XX, XY in a partnership with a scientist XX can't do much about it.
5 Believe me, even the most arrogant of scientists has moments of self-doubt. There is perhaps, though, a reciprocal relationship between success in science and self-doubt.

10 October 2007

Dawkins in the Doghouse

As a sign of how little I read outside science these days, it's taken a full week for this debacle to reach my consciousness via the sharpener. And without launching into is-he-or-isn't-he 1, the Sharpener article's comment about prevalent mud-flinging attitudes reminded me of a recent Doonesbury comic [clicky the linky; I don't want to break copyright law and reproduce it here]. LOL all you want. It's sad but true that we are headed towards an era of smear2.

1 For what it's worth, I really don't think Dawkins can be accurately named and shamed as an anti-semite. If anything, as a devout atheist, he's just anti-any-religion-you-care-to-name. Call him an anti-religionist if you must. Anti-semite has overtones of picking on a particular racial and religious group that we all know has been very badly treated by the world in general lately. Bad choice of example. But then again, can you choose any example of religious dominance in state-run affairs and not offend anybody? Hell no.

2 And I don't mean PAP smears. No, those are good things. If we were headed into the era of free PAP smears for all women, that would be much better...

08 October 2007

Sober up; bottled Brown ale all round

Curious Hamster is back to posting1, and as usual, I'm nodding my head in agreement with much of his observations on the state of British politics. I've been thinking recently, what with the deification of Boris Johnson. Oh, what's that? He's just running for mayor? Oh that's alright then. Anyway. It got me to thinking about the damage the Blair era of lies2 had done to politics, let alone the state of the nation. And how it needed a shake-up of sorts. A way of focusing on workable policies instead of false promises. Ah ha ha ha. How naive. Cameron's rehearsed speech did nothing for me. Quite like the inquisitive hamster, it had me in stitches instead. But the comparison of Cameron to Blair with the pronouncement of accompanying doom was sobering. There is no alternative to Brown. Whatever the News of the World's poll says, Labour is still pretty much in power and will be at least for another general election. Whenever Brown has the guts to call it. Sobering.

1 He's been back for a while, but I haven't. So it's taking me some time to get through his recent posts.

2 Oops. Sorry. It's this broken keyboard of mine. I meant spin of course.

01 October 2007

Alisher Usmanov vs Bloggers wot dare to tell it like it is

I switch the computer off for a few days1 and this happens. WTH? Did I side-slip into an alternate dimension? Is my interwebs pulling a fast one on me? This type of shit you can expect from countries with dictatorships, not the UK. Oh, hang on...

1 OK, a few weeks.2

2 And it'll be a few weeks more if this type of shit keeps happening to our freedom of speech (bar libel, wot is a tricky area).

30 September 2007

ludo bites, but not too hard


Instead of collating too many holiday snaps of an evening, I joined some foodies for a bite or two.

27 August 2007

Summer in California

D+K again, originally uploaded by framboise.

We poottled up to North California for a week in Sonoma County (north of San Fran for you non-Californians). And spent a week poottling back down the coast. The photos are slowly being uploaded and when the dog has some time, she might contribute a post or two about her holiday.

Update: First attempt to upload a video clip. Apologies for the poor lighting, direction, sound quality etc. And do pay heed to what happens around 15 seconds in. No trick stones or hired stuntpersons were used.

30 July 2007

Armenian spirits1

Imagine an out-of-focus, poorly-lit photo of ants on the Hollywood Bowl stage here. I couldn't be bothered to take yet another one.

The traditional music of Armenia is brill, but you can keep Armenian pop.

1 No, not the famous cognac. If only I could get my hands on some...

21 July 2007

Attention Muggles

Attn muggles, originally uploaded by framboise.

The latest tome took nearly 6 hours (and interruptions) to read, nearly a whole extra hour more than the last1. And while I give out no spoilers2, my succinct review is that if you loved the previous six, you'll not be disappointed with this one. And if you hate the whole shebang, your mind won't be changed either. I say to all the critics of Ms Rowling: nay-say what you will about the custard-lightness of the early three, the darkness of the latter four, and the ever-increasing need for more judicious editing. It's a very life-affirming series.

I would place the entire series in the genre that Enid Blyton wrote so well. Gripping adventures, one after the other. There are many better-written children's fantasy books out there (CS Lewis, Dianna Wynne Jones, JRR Tolkien, Philip Pullman, amongst several others), but this one seems to have captured the hearts of the reading public. Scholars may debate this for years, some perplexed at the simplicity of the writing, the obviousness of the motifs, the sheer weight of the later books. And most will have to secretly admit being spellbound by JK Rowling's tale spinning.

1 I feel for all you parents out there who will be reading this one at bedtime for months yet. I really do. And I hope the audio tape/CD comes out soon. And that you have invested in lozenges and cough syrup.

2 And never will...

18 June 2007

Windy or what? She finds drafts everywhere

Ooer missus. Trawling through unpublished witterings of mine, what do I find but this?


I'm not entirely surprised to read that:

...in North America, where a 2006 survey revealed that atheists rank lower than "Muslims, recent immigrants, gays and lesbians and other minority groups...

There seems to be a great deal of deity invocation here (apart from mere cursing). Churches1 too. One on every corner. But no corner shops2.


Freaky or what?

1 There may be churches galore but all with locked doors. Whatever happened to "Sanctuary. Sanctuary."?

2 Something's up with that. More G.O.D. than M.I.L.K.

12 June 2007


[crawling out from under the rock]

So, Tony Blair has been getting his knickers in a twist, has he? A choice quote:

Opinion and fact should be clearly divisible. The truth is a large part of the media today not merely elides the two but does so now as a matter of course. In other words, this is not exceptional. It is routine.
--Outgoing Prime Minister Tony Blair, taken from the full speech published by the Indy.

A bit rich coming from the man who convinced Parliament to go to war in Iraq based on no evidence whatsoever of weapons of mass destruction1. I am particularly impressed by the way he has a good whinge about the Hutton inquiry then quickly moves on. And singling the Indy out for criticism? Hmph, I think they'd rather like that. As the leading viewspaper in the UK, it must be nice to know that their words have hit the mark. Own goal, Mr PM. You have indeed said what needed to be said, but perhaps you should now sit down and read it through, paying particular attention to how it also applies to you and your time in government.

1 An over-simplification, but you know the back story. Preach. Choir.

10 June 2007

Catching up

Mexican* chocolate and almond cake

On the 5th of May (Cinco de Mayo), a spiced orange chocolate and almond cake was produced. Twas tasty but needs further work on texture and serving technique.

Oatmeal cookies

And the very next day, the cookie monster, not satisfied with the chocolate cake, demanded some plain cookies. I complied.

wa wa washoku

A week of washoku

After a certain amount of dithering, the food page has been resurrected. With the advent of tags on bloggers, it seems so unnecessary now. But it's just sitting there doing nothing. I felt sorry for it.

So it starts up again with some unfussy Japanese food we cooked or bought in the first week of May.

24 May 2007

What's up with the Lib Dems?

Rejection after rejection. Have the Lib Dems lost their way? Or are they forging a new identity for themselves? One that doesn't tar them with the same brush of failure as their last two ineffectual coalitions?

A revolutionary speaks

Your starter question for 10

What should LFC do next?

We must spend big, says Benitez.

Behh! Wrong answer. You should be spending wisely on young talent, who you can later flog off to the highest bidder.

23 May 2007

Reds? What reds? Do we care anymore?

So, I don't really care that much anymore1, but enough to look for some coverage that doesn't involve having to refresh the BBC or Guardian pages every few minutes. Now, we can't get Five Live over the internet (outside the UK) when they have live commentary because of the whole licence fee issue. For previous events, like the Six Nations, we've managed to get round it by listening to the relevant local station (like Radio Scotland, Wales or NI). This time, a quick try of Radio Merseyside was unsuccessful. That loophole has been closed. :(

But without meaning to spoil the field for the future, I've found radio coverage! I'm not telling you where... Keeping shtum.

1 I am still interested. I may not care either way regarding the results, but I still want to follow good fitba.

2 just as well we follow Scotland then, eh?


LFC in Athens? If I cared anymore, I would be excited. But since their ill-advised purchase on the back of a loan, which they will have to service forevermore or collapse, my interest has waned. Once upon a time, I would have downed tools just to watch the game. Then again, the game would have been at a reasonable hour and not in the middle of my work day. And back in the day, LFC's stablemates wouldn't have been a NHL team.

Right now, without a TV and bereft of Five Live, we get all the footie highlights we need from youtube. And I must confess that I really don't miss it all that much. It's gotten stale for me. It's not so exciting when you already know the score1. And the last World Cup really killed it for us. What joy in watching a game where cheats and actors flourish? And apart from the tawdry purchase of LFC, Benitez has turned a team full of potential2 into a collection of talentless oafs who play uninspired football. In fact, they may as well play American football because I just don't care anymore.

I find myself these days spending more time discussing the woes of Gretna Green and their struggle to comply with the SPL mafia than discussing the glorification of Liverpool. P goes through phases of being dejected by Dundee United's lack of spark, but he remains loyal. Is that the mark of a true fan? A local fan? Did I choose my team badly, not having lived in Liverpool? Does it count that they were the first team to inspire my interest in football? What does it all mean when you stop caring about your team, even if they are about to play in their second Champions League final in 2 years? Am I a bad fan? My blades no longer turn for my team.

What do you call an anti-glory seeker? 'Cos that's what I want to be.

1 Which is almost always the case here, always waking up after the weekend games are over.

2 I am, of course, somewhat biased.

22 May 2007

Step right up; predict a promoter and win...

Win what? Well, nothing more than a few months of hard work, hopefully followed by a nice wee paper...

We're in the mood for science on akatsuki talks rot. Perhaps this has come about since I've acknowledged that I will always be a mediocre blogger, but I could become a better science communicator if I practice writing about things I work on more. And all that stuff about the bloody Viagra-jet lag story (and the media coverage of it) made me realise there is a middle-ground for scientists in the know to discuss hot topics without resorting to the extremes of technobabble (which we're used to applying in our daily work) nor the overly condensed data-free reportage by the media.1

I've toyed with the thought of using this blog to practice writing mini-reviews of interesting published scientific studies, but have been to lazy to date. This may continue, or it may not. But given that nobody actually reads this crap, it doesn't matter. (Hi P! You still reading this surreptitiously? I have a site counter, you know...)

At any rate, since my laptops have a tendency to die after a few years, and I'm not very good at backing up non-essential data, here follows an email I spent a good 15-20 minutes on this evening to a colleague. I think I was being Ms Good Postdoc, but I often fear that I don't give good advice. Time will tell.

The premise: a friend of a colleague needed a starting point for a promoter assay s/he is planning.

My reply to the request, slightly edited:

Hi [colleague],
There are several approaches to finding the promoter of a gene. The first would be to do a quick literature search to see if anyone has already determined the components of that gene's promoter.
If not, the second approach would be to retrieve the gene information from a genomic database (like Ensembl or the UCSC genome browser). These two sites are particularly useful because they allow very quick and easy comparisons across species (e.g. human/mouse/rat/fish). Such comparisons often show what sequence is most conserved: usually the exons and any regulatory elements that are essential (like promoter elements). This only works some of the time and will only highlight very conserved regions. There will be species-specific differences in promoter sequence.
The third, slightly more laborious approach, is to take several kilobases of sequence upstream of the first known exon and perform a promoter prediction. This has become relatively easy on the internet. A quick Google search found these possibilities.
Of course, the difficulty is in choosing one. I cannot recommend one over the other because I haven't tested them myself. There is one particular site I know of that is quite easy to use: Promoter 2 prediction. It looks for known promoter motifs based on already studied PolII promoters.
After that, your friend will have to make the decision of how much of the promoter to clone, and how many different construct lengths he/she wants to try. I guess it will also depend on the restriction sites available in the sequence and how big the sequence is.
As for getting the DNA, it can either be cloned by PCR if it's very small (around 10kb), or it can be "cut" out of a BAC (bacterial artificial chromosome) or PAC or cosmid (large-capacity plasmid) that already contains the genomic region (can be bought from places like the BAC/PAC resource or Invitrogen or Roswell depending on species). The restriction digest method is preferred because it will have no additional errors, and it is also easier to change the length of the promoter region by choosing different restriction enzymes. Some people even use the entire BAC and make small deletions to eliminate predicted regulatory elements.
I hope this is will be helpful in getting your friend started. The real difficulty will be making the construct and testing it; I wish your friend the very best of luck with this!

After sending it, I read what I wrote2 and thought: goddamit, it's all too simplistic. They probably already know all this crap and were probably looking for something concrete. Like a real protocol. Unfortunately, for this and quite a lot of the other molecular biology I do, I do it on the hoof. At some point in the last 10 years, I followed somebody else's protocol (usually the postgrad/postdoc/technician I was asking advice from at the time). Then found alternatives, some of which I now use routinely, some of which I was too lazy to follow-up. Then I switched specialities. Twice. Now, I am used as a mol bio repository by my (ex-)lab. They sometimes even think of me as an expert. But a real expert wouldn't feel so fraudulent in giving advice, would she? Self-doubt creeps in... Oh what if I've screwed up somebody's project giving bad advice?

1 I'm in no way implying real media gets it wrong (although some, like the gawd-awful Daily Mail, get it wrong and deliberately so!); just that they make the assumption that folk just want the headlines. Which may be true. But not this particular folk or her ilk.

2 And after writing this post, I read it and thought: WTH? Why can't you stay on topic? I give up. It's time for dinner.

No sex to have babies? We all want some of that!1

While I'm in a mini talk-about-science mode, have a look at the female hammerhead who didn't need a male (Is anyone else bothered by the way these news articles never provide a link to the scientific article being quoted? I've had a cursory look at Biology Letters and can't find it. This bugs me because I can't accept it on the word of a journalist; I need to see the data. And I'll forget by tomorrow to have a look for the published article again.)

Parthenogenesis, the somewhat sci-fi process of asexual reproduction, even in vertebrates doesn't particularly surprise me2. What does surprise me is that they didn't ask DTB for a quote3...

1 Or is it the other way round?

2 But it makes me think again of why we (as in the generic we) evolved to require sexual reproduction, why parthogenesis doesn't happen more often, and what have those "Red Queen" proponents been up?

3 For P's benefit...

Viagra enhances... jet-lag recovery

BBC picks up on the hot jet-lag study of the day: Sildenafil accelerates reentrainment of circadian rhythms after advancing light schedules, PNAS U S A, 2007.

Some initial thoughts:

  • It's not so much that Viagra, saviour of many a marriage, is the new wonder-drug that will eradicate jet-lag a la melatonin, but that it works via a pathway already known to have an effect on jet-lag.
  • Viagra works through the NO/cGMP/PKG signalling pathway (explanations may follow if I can be bothered)
  • At least one component of this pathway, protein kinase G (PKG), has previously been shown to modulate the "speed" of reentrainment1 (aka switch to new timezone). Update: The same group has shown the involvement of the pathway in phase shifts before too, but I was being lazy earlier.
  • Work has probably already been done on this, but this is a nice example of the difference between phase advance (flying east) and phase delay (flying west) mechanisms. (Sildenafil appears to shorten the time it takes to adapt to flying east)
  • Does the media have someone sit by PubMed and trawl through it for interesting stories2?
  • Why can't I think of cool experiments like this?3

Maybe more on this later. While the world gets excited by yet another use of the blue pill, I still have to ask people for money to fund my somewhat less titillating work. Hmm... Maybe I can incorporate this into my grant application. But somehow, I think jumping on the bandwagon will not go down so well. If only I could think of a clever selling ploy to convince reviewers of the importance of my work4.

1 This is just one of many examples; I'm too lazy to dig them all up right now.

2 For interesting, read: involving sex, drugs and rock and roll. Titillation galore!

3 Well, the thought struck me when I read a colleague's paper on our common model and he mentioned how Viagra worked via the same pathway as the molecule we work on. But I didn't act on it because... I am not as inspired as these clever folk down South.

4 It's perhaps not commonly known (or rather, I didn't know this when I was a lot younger and a lot more naive) that scientists also have to be good salespersons. It's obvious once you get to the post-graduate level (or before if you're somewhat less cossetted), but the more I get into this, the more I wonder about whether the amount of bullshitting that is done is actually detrimental to the science (even though it is currently the default; no bullshit, no funding). But this mini-rant deserves a full post at some point. Not now. Not until I've finished prostituting my work.

18 May 2007

Build him up, tear him down

Amongst the acres of hagiography written about our departing Prime Minister a number of glaring inconsistencies leap out...
Blair leaves at a time not of his choosing - an even more detested in Britain than his mentor Margaret Thatcher—officially the most hated prime minister in recent history.
--Gus of 1820.org.uk


16 May 2007

blame your choice of holidays

...on some new religion that he found
they didn't know his faith was earthly bound
--Mika, Billy Brown|Life in Cartoon

is it wrong to really like such a frivolous album? the mood and melodies may seem frivolous, but the lyrics belie the deep wounds the writer must have borne at some time.

i love the vocal acrobatics, the use of many many voices. but honestly, there are only 2-3 songs that make it out of the album and onto the ipod.

Say goodbye to the world you thought you lived in

It's all in the hands of a bitter, bitter man.
--Mika, Life in Cartoon

Pretty much sums up the state of affairs.

Salmond Victorious

Alex Ferguson2 leaves Man Utd

And beats Margo Macdonald by a landslide to secure the job of Presiding Officer.1

1 I know. I'm two days too late. My mind is temporally disengaged anyway. When are those Scottish elections starting?

2 And the names are not even spelled the same. Sorry. Barrel bottom scraped, scoured, scrubbed and white-washed.

I didn't know squirrels could drive cars

Contrary to popular belief, the electric car is not dead. And "tree-huggers" are the new target market for a 40 km/h battery-powered vehicle. According to the makers of Zenn:

"The existing market in the states is predominantly gated communities or master-plan communities in the southern states. So that's typically a 65-year-old plus person who uses this as perhaps their third or fourth vehicle."

Um. Third or fourth vehicle? What are vehicles one, two and maybe three for then? And what's wrong with walking?

Admittedly, the Zenn-man goes on to describe his future market of younger people looking for an occasional car. But I was already outraged by that point. Third or fourth car... I'm already feeling guilty for using one.

14 May 2007

No enzymes here unless you want enzyme-linked immunosorbent assays

Can anyone tell me what the hell an akatsuki enzyme is and why it keeps popping up in my keyword search1? Is this predicting the day that I discover a new enzyme and egotistically name it after myself? Or is it some crappy New Age bullshit treatment2? You will be sorely disappointed if you're here for that. If anything, I should be joining Ben Goldacre in rubbishing these pseudo-science pieces of crap that purport to make people's lives better when all they do is make them poorer.

1 Statwhore admission: once in a while, I look to see if anyone from an interesting country has stumbled onto my insignificant spot on the www. And I was slightly surprised to find a Kiribati ISP in the collection this week. Hello. I hope I wasn't overly offensive with that silly off-the-cuff remark about coconut oil. And how are the Atollettes?

2 For the record, I enjoy the occasional reflexology massage. I don't buy into any of the claims of direct linkage of my big toe to my brain, ok? It's just a damn foot massage. It feels nice when you've spent the whole day standing while doing experiments to go home and massage your foot. Or hire someone to do it for you. There are no other significant health benefits.

Squint to see Johnny Marr's scowl

13 May 2007

Fuel for thought

Two recent reports pour a fair amount of cold water on the biofuels issue. If you recall, I'm not convinced they are the answer to long-term sustainability, but can have some temporary benefits while the search for a solution to the two-fold problem of oil shortage and global warming continues. The first, published by the UN, starts by acknowledging the necessity of ending reliance on oil for energy needs, particularly in developing nations. But a sharp warning on the dangers of monopoly, further environmental damage in the rush to procure more agricultural land, water demands quickly emerges. Rather a dampener on proceedings. The second report was commissioned by the Co-operative insurance society (an online copy of which I've yet to look for) seems to be in general agreement, judging by the BBC article.

They make good points to ruminate on. Perhaps after Manic May is over.

10 May 2007

Coconut Cars

The story on cars fueld by coconut oil on an island in Papua New Guinea sparked a lively conversation in our household about the various alternative fuels on trial all over the world. Coconut oil sounds like the perfect sort of island-based fuel that seems to make environmental sense. Apart from the lower concentration of sulphur dioxides, nitric oxides and general soot, not having diesel delivered to the island by diesel-burning ships also makes sense (apart from the fact that the ships are still necessary for trade and transport). While coconuts are probably not in as plentiful supply on tropical islands as us continental types would like to think, they do have more coconuts than they can use in terms of juice, meat, soap and cooking oil. This begs the question of just how many coconuts one would have to gather to fuel a moderately low mpg vehicle. And just how much energy is expended on processing the coconuts? Can the processing plants be run on coconut oil too? Can electricity generators be adapted to use it? How long does processed coconut oil last (the cooking stuff tends to ming after a while if not properly stored)? What nasty additives have to go into the mix to get it to burn nicely in infernal combustion engines?

And all these questions got me to thinking just how negative we were being. True, as part of our job, we think critically: always looking for flaws in the data or hypotheses, poking around to ensure data is not misinterpreted, second guessing. All without meaning to be cynical. Just careful.

And it also got me thinking of how news of alternative fuel is always met with a few "so what?"s from the commentators. They have a point: there is absolutely no way that the USA could ever grow enough corn to fuel all their cars with ethanol1; no way that every little Pacific island could be completely self-sufficient on coconuts for oil; no way that Asda's recycling of cooking fat in their trucks could inspire every householder in the UK to rob their local chippy. But they also miss the point that every small number of converts means that the trend for increasing oil-driven energy consumption is ever so slightly diminished. Every solar panel installed, every wind turbine that gets past the "Conservative Communities Concerned for Conservation of their Beautiful and Historical Landscape", every wave harvester makes a difference, however small. Slowly, one small appliance2 at a time, we can slow down the growth of energy consumption. It's accurate to point out that demand for energy is still growing. The alternative energy sources will not fix that problem. That is up to individuals and governments to tackle. It may hurt attempts to invest in alternative energy if we keep lumping them together. For it to work, it must be economically viable, even if the early stages are heavily funded by rich governments.

It also seems fairly obvious to a numpty like myself that it is to the interest of growing super-powers to invest heavily in research in this area now. Countries like China and India already have enormous energy demands, which will no doubt increase. Peak oil may be upon us (although it is still heavily debated, but let's not go into that now). Unless China and India (and any other super-power I don't have the precogniscent ability to see) have ever-lasting supplies of coal or oil, or can twist OPEC's arm, they will need to not just use current alternative energy sources, but drive the development of new ones. Which they probably are already doing (apart from nuclear power, that is; but let's not get into that now either).

This didn't start out as a rant, though it has turned fairly incoherent. I guess my point was that it is easy to be a nay-sayer when it comes to the real benefits of alternative energy sources, be they fuel for vehicles or to provide electricity to needy bloggers. But as the hegemon known as Tesco likes to say, every little helps.

Incidentally, this news comes as I've finished reading a recent LA Times Book Festival purchase: The Sex Lives of Cannibals, by J. Maarten Troost3. I wonder if the inhabitants of Kiribati (pronounced Kikibas4, according to Troost) have the technological ability or drive to consider adopting coconut oil as a fuel? Or failing which, export their copra to their Pacific neighbours in exchange for some food that is not fish.

1 Speaking of which, doesn't the harvesting, transport and processing of the corn crop suck up a whole lot of energy in itself? Oh me oh my, how easy it is to be cynical.

2 e.g. the iPod. Oh, we're back on the greenness of Apple again are we? Incidentally, this reminds me that I desperately wanted a Solio before I left for LA because I thought there would be enough sunshine here for it to work. But they were out of stock then. Would it be naughty to buy one now and have it shipped here? Even more naughty than charging the iPod on the mains every other night?

3 And speaking of the book, this gives me an opportunity to have a photo in the post. Haven't you missed my awful photography?

Book haul

4 Typo: should be Ki-ri-bas. Thanks David. My fingers must have had the dog's nickname (kiki) programmed in instead.

Apple is not exactly a Granny Smith

How is Apple so low on the Greenometer with all those hazardous chemicals that Steve Jobs claims they've eliminated or are in the process of phasing out? Based on no research whatsoever on my part, it sounds like Dell is planning to, but has not actually achieved the elimination of PVC and BRF:

Nokia and Dell share the top spot in the ranking. They believe that as producers they should bear individual responsibility for taking back and reusing or recycling their own-brand discarded products. Nokia leads the way on eliminating toxic chemicals, since the end of 2005 all new models of mobiles are free of polyvinyl chloride (PVC) and all new components to be free of brominated flame retardants (BFRs) from the start of 2007. Dell has also set ambitious targets for eliminating these harmful substances from their products.

The specific report on Apple claims that:

For a company that claims to lead on production design, Apple scores badly on almost all criteria. The company fails to embrace the precautionary principle, withholds its full list of regulated substances and provide no timelines for eliminating toxics polyvinyl chloride (PVC) and no commitment to phasing out all uses of brominated flame retardants (BFRs). Apple performs poorly on product take back and recycling, with the exeption of reporting on the amounts of its electronic waste recycled.


Protracted proclamation

New (b)leader, new (b)liar?1 And to christen the beginning of the end, has Guardian Unlimited hired the same website designer as Times Online?2 And does this hint at some editorial change I've missed out on?

1 Contrived, I know. It's been a long day.

2Update: All these fancy pictures on the new website meant I missed the editor's explanation. Meh.

08 May 2007

Mr Moore, kindly crawl out of Uranus

Sir Patrick Moore has his knickers in a twist about women running the BBC.

I would like to see two independent wavelengths - one controlled by women, and one for us, controlled by men."
"I used to watch Doctor Who and Star Trek, but they went PC - making women commanders, that kind of thing. I stopped watching." --Sir Patrick Moore

07 May 2007

Deafened by Bright Eyes

Green up my Mac

Is this merely Apple patting itself on the back or a genuine effort to lessen the environmental impact of their products? Aside from the lower use of toxic materials (which is to be applauded), Steve Jobs claims that Apple recycled 13 million pounds of "ewaste" last year (9.5% of the weight of product sold 7 years ago) and plans to improve on it. It raises the question of what the 13 million pounds refers to: starting weight of the products or actual weight of suitably reused/recycled material? This comparison suggests the 13 million refers to total product weight and not weight of material recycled. (Actually, while I'm wondering out loud about the validity of the comparison, how about making the products last longer so there's less frequent turnover? Ah... It doesn't make business sense, that's why...)

Anyway, it's an effort to be encouraged and not to put down too much. Perhaps this little piece of PR will encourage the other major computer manufacturers to put some of this in practice themselves (unless they already do, but just haven't come out and said so). I wonder if there are smaller manufacturers out there who are already making greener machines but just not shouting loud enough for a deaf person like me to hear (whatever happened to that $100 laptop project, and will they be recycling the end-of-life products too?).

And speaking of recycling, back to Apple's announcement of their greenhood. If you are one of the many people hanging on to a defunct 2G or 3G iPod with a failed battery, perhaps this 10%-off-future-purchase-unless-you've-already-given-up-and-switched-to-a-Zune offer will appeal:

Let me take a moment to talk specifically about iPods, even though they are included in the above data. All of Apple’s U.S. retail stores, which now number more than 150, take back unwanted iPods for environmentally friendly disposal free of charge. As an incentive, we even offer customers a 10% discount on a new iPod when they bring their old iPod to our stores for proper disposal. This summer we’re expanding it to Apple retail stores worldwide, and we’re also extending it to include free shipping from anywhere in the U.S. No product purchases are required for any of our free take back programs. In a few months, we think we’ll have ‘best of breed’ iPod recycling programs in the U.S., and we plan to continue to expand our free iPod recycling programs globally in the future.

Incidentally, over at treehugger.com, they're promoting an energy-saving alternative google search page, which is not green in the sense of the colour spectrum. Unfortunately, going by the stream of comments at the end of the post, it sounds like this is only useful for CRT monitors and will make no perceptible energy savings on LCD screens. I wonder if lower page load times on the more popular sites (like the Beeb's news page) would help save energy. Or browsing via RSS feeds instead. Or blogging less. That last one I can definitely do.

Disclaimer: I currently love Apple products and own a Powerbook, 3 iPods (don't ask... I'm not as green as I'd like to be), 1 AirTunes router and a small smattering of accessories. So I might be considered somewhat biased.

Travail, toi Français!

Presumably, the French ballots were a lot simpler and this autocrat is exactly what France wants. Ah well, there goes my hope of the 35-hour work week spreading globally...

Scottish Presider

Oh, the Scottish Elections have descended into the realms of the farcical. The ramifications of the huge SNP gain, small party losses and Labour/Lib Dem backlash is that the one party that could not get even one seat in the first Holyrood elections may now preside over its proceedings. (via)

More votes for Scots

"Either we re-run the election or the returning officer contacts these 10,000 people who had their ballot treated as spoiled to ascertain their actual preference. "We need to do that, otherwise democracy is in crisis in Scotland." (via)

Sure. And open the process to bribery of said 10,000 people? I think not.

If there was a re-election, perhaps folk will finally cast their TRUE vote. Methinks that in the future, Scotland should hold practice runs.

05 May 2007

I am one monkey in a billion1

I am a self-confessed billion monkey* (via). Even worse, I am a billion monkey who snaps her monkey nuts before she eats them. See the other very crappy results of my billion monkey machine here.

Incidentally, I know a Real PhotographerTM who enjoys a spot of self photo-ing.

1That means there are 6 more of me on this planet; if one of you reads this, get in touch. Starting to feel like I've been spread too thin.

04 May 2007

Gaelic word for the day

Scottish (Muckadidoodah) Elections 2007

What a dickadeedoodah the elections have been this year! I've missed out on all the fun. Followed doctorvee's twittering and subsequent indignation at the mess made by the decision makers:

Some people wonder what the Scotland Office is for these days. Obviously they are looking for stuff to do, so have been busybodying with this e-counting stuff. The e-counting systems might have been desirable for the local councils, but they did not need to be used for the Scottish Parliament elections.

I was feeling a small amount of sympathy for the poor electorate, expected to cope with oh-so-many ballot papers, until I saw a photo of the ballot sheet (or rather a photo of the poster explaining the ballot sheet). Honestly, it's not that difficult.* Maybe they could have hired some expensive design agency to make the parliament ballot a little clearer (maybe some dozy-brains didn't register the split arrow), but that poster is education enough not to screw up.If you've made the effort to go out and vote, surely you're invested enough in the process to make the even smaller effort to read the instructions. I don't think the blame can be laid on the Westminster or Scottish Parliaments (maybe apart from the decision to have both local and Holyrood elections on the same day). More and earlier voter education? Maybe not. A redesign of the ballot sheets? Ach, I hope they're going to have a good look at the spoiled ballots and work out what went wrong or there's no point in suffrage and we'll have to start testing voters for mental competency before elections.** Ha.

*I would be interested to learn how many of those were true protest votes or if anyone scribbled stuff like "anyone but labour" or crap like that. Don't waste your vote, dammit. At least vote for some small crappy party if you don't like the major ones.

**Disclaimer. Joking, OK? Not proposing this or calling the electorate stupid. Maybe a little bit lazy or dozy or confused, but not stupid. I pretty much agree with what was said here.

Mair on the sorry tale. I like this interpretation :

Electoral systems suffer the same problems as bad software - they are dominated by geeks with no understanding that users have to be able to understand the system you are designing and bolt on a shoddy interface as an afterthought - and by marketing departments/politicians who have a very different agenda from the rest of the industry and force bad design decisions from the word go. (via)

The revelation that the Scotland Office were advised not to hold both elections on the same day is no surprise to me. A department controlled by a party that started its first few years in government spinning and managing the media will take any little advantage they can get to stay in power. Another example of disgusting NuLab behaviour.

(Needs), Wants and Desires

Ach, I have to contend with so many other folks' wants and desires everyday, but no one ever asks what I want. Well, right now, if anyone is paying any attention (hint, hint, P; if you don't listen over brekkie, at least read the blog) I am deeply in love with this glorious type-set map of London (via). If they cannot/will not ship the US, perhaps my ever-loving bro will send it to me via Parcelforce (hint, hint, bro; if you don't reply to my emails, at least read the stupid food blog).

03 May 2007

Be afraid. Be very afraid.

The Sith Lord does not entertain interruptions (via, which was via).

Dogs for all

I can sympathise. It is inevitable when you meet a dog that suits you that you will end up adopting it.

Apaprently, I walk too fast and it's bad for me. Since Singapore tops the table, that's not entirely surprising.

29 April 2007

Cream and bastards rise

Going through my RSS feeds in Thunderbird, I realised I read NOTHING in 2006. Yes, the whole of 2006. Not only did I read no blogs, I also read no books*. That may have been the first time in my life I didn't read voraciously, constantly, indiscriminately. What should I do about the RSS feeds? Mark them all read so I can clear up the folder in what is also my main email software? Or laboriously go through the several thousands?

At any rate, I've started reading other blogs again. Starting with the ones that I read before I started my own. Which is how I came to be watching this awesome piece of lib dubbing, and craving me some of that music too. A search on iTunes proved unfruitful, and although myspace hosts a streaming version of Flagpole Sitta, it's not downloadable. What to do without resorting to naughty illegal downloads or warming up the planet by having Amazon deliver it in a huge box? Last resort, the official website for Harvey Danger, where I don't find the song, but instead end up bittorrenting their latest album little by little. For free. Clever ploy. I'm enjoying it, and probably will buy a hard copy.

Clever ploy.

*Soon to be rectified. My dad gave me The Language of God for Christmas, but I haven't gotten round to getting it off the shelf yet. And I bought two Ray Bradbury books at the LA Book Fest today.

A bit annoyed; lost the post because one of the sites I was trying to buy stuff from decided to crash my Firefox. It's one of those damn sites that seems to close after midnight for maintenance or something. Perhaps I should take the hint and stop buying stuff from them.

27 April 2007

Why on earth would anyone object to Where's Waldo (Wally)?, number 88 on the American Library Association's list of 100 most-challenged books (via). It's not exactly controversial, is it? It's a picture book, for crying out loud. And one with rather tame images at that. (Unless there's a Playboy version I've not seen.)

Update: Ah, I understand now. There really is a "Playboy" version. I think I even have the edition in storage at home...

An interesting analysis of the original cause of the Darfur war/conflict/genocide. An excerpt:

More recent computer modelling has suggested that rain patterns over Africa are influenced rather by ocean temperatures, and those in turn reflect global warming, and the rise of greenhouse gases in the atmosphere. In other words, droughts in Africa may be caused less by its hapless inhabitants and more by oversize cars and cheap flights in Europe and the US.

See, Arnie; all the more reason to get rid of your Humvees.

26 April 2007

The Californian State vs The EPA

So, the Governator may sue the EPA over their slowness in allowing California to pass a vehicle emissions law. While I applaud this state's attempts at tackling climate change, I still find it a little ironic that Schwarzenegger is still driving his damn Humvees.

Extracted from the article:
Teased by conference host Michael Milken about his gas-guzzling Hummers, which emit high levels of greenhouse gases, Schwarzenegger said he was having both retrofitted to run on cleaner, renewable fuels.*
But he said making people feel guilty about what they drive was not the answer, and insisted that energy issues and environmental concerns can be addressed with new technology.
"Women who have children like SUVs. We should let them keep their big SUVs and change the technology."

Something is better than nothing. But I think his point about not making people feel guilty about their lifestyle choices is dangerous in the long run. I can plainly see he's trying to please two diverse camps here: the environmentalists and the rich middle-to-upper class (which are sometimes one and the same thing here). Sure, a rich state looking to cut greenhouse gases can push the development of new technology, which benefits us in some ways. But will this be affordable to all? I doubt it. Not in the short term anyway. It also side-steps the issue of simply making those minor changes to the things you do, and how you do them. In particular, his example of the women with children who like SUVs, aside from the patronising tone, is wrong on other fronts. The fact that the SUVs are big means it takes more energy to drive them forward and more materials (often petrochemical in nature) to manufacture. Whatever new technology is used in terms of propulsion or fueling, the fact remains that these vehicles will always require more energy to propel. How about changing the minds and aspirations of people instead? How about setting an example and getting rid of the Humvees altogether to be the role model for a successful have-it-all-but-can-give-it-up-for-the-sake-of-the-planet American instead? (And recycle them responsibly too; maybe the Army could use a donation of what was once theirs.)

*He may be referring to ethanol as the renewable fuel, but even that is fraught with environmental issues. Will you devote the entire surface area of the country to growing corn to fuel the cars?

Frrrog! This* is SO wrong (via).

*You may not want to click on this if you're a die-hard vegetarian/vegan. Or like frogs.

25 April 2007

Do you want to be the Great Grand Overlord of the British Isles?

Feeling bad. Not giving dog enough attention, not taking good care of P, not calling home enough, not IMing the bro for months, not sorting out the BnB website problem, not writing enough manuscripts for the lab, not producing enough data for the great and glorious leader, not doing my part for the environment by incapacitating every Humvee in sight (and that's plenty round here), using too many plastic bags to pick up doggy poo, not keeping abreast of current affairs, not giving our governors hell over climate change and their bloody stupid self-defeating "war on terror", and worst of all, not following the run-up to the upcoming SCOTTISH ELECTIONS.

One small thought on it though: Gordon Brown1 must be pissing his pants. If the Nationalists get their way (unlikely for the foreseeable future, but I'm no Sybill Trelawney), Westminster would have to reciprocate by kicking out the Scots. That would damn well screw his chances of being Great Grand Overlord of the British Isles, wouldn't it? Unless he wanted to be English.

1Am currently fascinated with this Where's Gordon? map.

So, the kryptonite story is old hat now. But the article made me wonder why the makers of Superman Returns used "sodium lithium boron silicate hydroxide" as the chemical formula for kryptonite when we already have an element named krypton (Kr), which they could easily have faked a compound name with. They missed a trick there. (Unless there's some kosher DC Comic reason for it.)

Pizza Pie

I was going to discuss the merits of different pizza styles and toppings, but I got side-tracked by the discovery that in Iran, pizzas are now known as elastic loaves (via).

So, instead of yet another dull "I made this, then ate it" post, we'll keep it to just the photo of my very-elastic loaf today:

Pizza, 2nd attempt

Oh yeah, the beer was decent. A not-too-sweet pale ale with a hint of bitterness in the aftertaste. Slightly malty, slight hoppy. From the cutely named Otter Creek brewery.

Cross posted on akatsukieats.

I suffered in Nintendo Hell as a child, and never felt much satisfaction from playing that stupid Super Mario Brothers platform level game. So this amused me no end (via). Caution: plenty of swearing.

24 April 2007

Ospreys don't like to be cuckolded.

Humans are quite vicious as a species, but at least two-timed men don't practice infanticide. Or so I hope...

22 April 2007

Old people rock!

Rocking grannies and gramps! An excellent cover of The Who's "My Generation". Check out The Zimmers, and watch for their single coming out in late May.

And remind yourself of the craziness of The Who here.

21 April 2007

amuse bouche

This novel form of webvertising amused me for a few minutes (via buyo). Then I realised I really like her sense of humour, and I might even buy the book or see her when she comes to the Hammer. This stuff really works, huh. I wonder if I could try it on reviewers of my manuscripts...

20 April 2007

green chana/chickpeas/garbanzo beans

I can't be much of an Asian. I've never had green chickpeas (garbanzo to the Merkins). But I bought them from Trader Joe's anyway. They've sat in the freezer for the last month. The green peas, broad beans (fava beans to the Merkins) and pre-shelled edamame have all been scoffed, leaving behind these green versions of my favourite pulse/legume. Chana masala, made with the more usual yellow version of chickpeas, is a favourite standby in our kitchen. Whipped up with tinned chickpeas, tinned tomatoes and whatever Asian spices I have in the cupboard, every chana masala is an adventure in itself. Especially when I get the chillies out (poor P... his poorly tummy can't take the heat).

So it was with a certain amount of suspicion that I opened the bag of frozen greenies today. We haven't had much luck with American frozen pulses. The broad beans are already too far gone for our preference of firmness. Which means we've been substituting it with edamame, which retains its bite a little better, for our other standby: beans and bacon. Anyhoo, a interweb search pulls up a rather tasty looking recipe for harbhara chaat. Seeing the chickpeas in a cone of newspaper reminded me of my childhood, buying kacang puteh from the little cart outside the cinema. We'd get to choose one cone each. My mother always went for the chickpeas, my father for the cashews, my brother for the sugar-coated peanuts. I *always* wavered between the fried lentils and the boiled chickpeas. Somehow, even though the chickpeas were the "healthier" option, I usually chose them.

Green chana

Back to those greenies. They were a little over-cooked. I swear I only allowed them to warm up in boiling water for 2 minutes. Still. Beats soaking dried beans overnight and boiling for an hour. Not having the best stocked kitchen around, I substituted the onions with shallots and the green chilli with red jalapeno. Amazingly, there was a very old and wrinkled mango and lemon in the fruit drawer, so in they went. As for the spices, I'd be mortified if I didn't at least have cumin, coriander and ginger, so it wasn't too difficult to cobble together some chaat masala, after this recipe. Of course, without the powdered dried mango, it won't be the same.


Served with our current pseudo-Asian rice fave, fake biryani, consisting of whatever long-grain rice we have (usually Thai, but sometimes basmati), cardamom, random nuts (pumpkin seeds at the moment) and cranberries. (Yes, cranberries. Not a fan of sultanas, me. So I can't even make fake British-Asian biryani.) Don't knock it till you try it: sweet/sour dried fruit in rice works. Ask the Persians, inventors of polo, which inspired biryani, which inspired this:

Biryani-inspired rice

I love pretending I can cook. And at times like these, when everything comes together even though nothing is authentic, I really feel like I can tackle anything. (Don't mention the pizza...)

Cross posted on akatsukieats.

Spag-balls and chips

Eh. Remember that post about the four staple meals in Britain? No? Never mind. Suffice to say, I made my annual allowance of spag bol today. Only it wasn't spag bol out of a Dolmio jar (let alone Loyd Grossman's). While looking for inspiration to cook the only mince I dare buy at Ralph's: ground buffalo, I came across this recipe for buffalo meatballs, which sounded far to easy to pass up. Plus, I was getting sick of buffalo burgers, buffalo black bean stir fry, buffalo burgers... And I was making cookies and onigiri at the same time, so something that was quick and could sit on the stove while I baked and shaped and walked the dog (re: the dog; just the walking, thanks. didn't cook her). And as the final nail in the coffin, the string of comments on my crappy pizza photo, which made me crave spaghetti.

on top of spaghetti

The only thing I changed was the concentrated tomato soup, of which I'm not a fan. On the other hand, I love having tinned tommies in the store cupboard for my puttanesca fix. So, a tin of blitzed plum tomatoes went into making the sauce instead. If I wasn't quite so busy with other things, I might have added some 'erbs or accoutrements like capers. Oh there we go with the puttanesca again... Oh, and I added some paprika too. I'm currently having a love affair with my tin of Spanish paprika. Some nearly went into the cookie dough mixing bowl by mistake. Now, that would have been an interesting choc chip cookie indeed.

how many can i fit in one mouthful?

The cookies were something of an impulse bake. Was decanting a new bag of flour I lugged home on the bus (not a trivial undertaking with laptop in hand and other important groceries like milk to carry too), and drawn in by the "Extraordinary Chocolate Chip Cookies" recipe on the back of the packet. I like back-of-packet recipes. They're usually piss easy for idiots like me. But this particular recipe must have been developed for industry or a very big, multi-child family. It called for 4 cups of flour, 1 1/2 cups of butter, 2 1/2 cups of sugar (half white and half brown), 2 eggs, 2 tsp baking soda and a 24oz bag of choc chips (or 4 cups). FOUR CUPS OF CHOCOLATE CHIPS?!? P would accuse me of trying to induce a clogged artery so he could be replaced by an upgrade. Even when the recipe was halved, we still had difficulty finding enough containers for the surfeit of cookies.

Cross posted on akatsukieats.

16 April 2007

Despair, death and destruction at the Walt Disney Concert Hall. We've been listening to Wagner and spying on friends.

WDCH Garden

13 April 2007

We've been out and about with the doggy in Santa Monica.

Hot trash

09 April 2007

It's not Easter without chocolate

Dibs on the blue ones

Not a personal subscriber to the Christian concept of Easter. Full of admiration for those who can give up chocolate for Lent. So, have joined them in a day of gorging on chocolate for no other reason than my love for it. Happy Chocolate Sunday!

06 April 2007

Hey you guys!

P doesn't remember ever watching The Electric Company, whereas I watched it religiously as a child. It was on par with Sesame Street as far as I was concerned, just sans muppets and not so babyish. I don't know what made me seek it out tonight. I started singing the "C is for Cookie" song by Cookie Monster on Sesame Street, then HAD to show P the original on youtube. From there, it morphed into a search for The Electric Company sketches. And it finally dawned on me that all those years ago, I watched Morgan Freeman deadpan his way through a kids' show and never realised it. Sure I recognised Bill Cosby; he had The Cosby Show which we also watched religiously as a family. But Morgan Freeman never twigged my not-very-alert actor-radar. I want to watch them all again, but somehow, I fear I may be disappointed. What strikes one as a child as the very pinnacle of broadcasting output may seem a little condescending and overly simple now. I might purchase an episode or two from iTunes, or a DVD, or just spend the rest of the night on youtube...

Amendement: After dithering about I finally acquired a YouTube account just so I could bring you this:

05 April 2007

Muffin madness

Multiple copies of the LA Times were strewn across our apartment floors for a couple of weeks. Perhaps it's not in good taste to explain why in a food post. At any rate, the food section has provided some inspiration for baking the last few weeks. I've not had an upside-down cake for ages; not since childhood days of being allowed to make pineapple upside-down cake unsupervised. So it was with great glee that I made a lemon upside-down cake a few weekends ago for my BBQ. It allowed me to get all sorts of things going on the grill and make a cake at the same time. Recipes should always be this easy. Unfortunately, no photos were taken. A usual. You must think I fake these posts... I was going to link to the LA Times recipe, but found it's a pay-per-view article. Well, sod that. I'm not going to reproduce it here, because I've no doubt there's some copyright law on that. So, there goes my stupid plan of using this blog as my recipe archive.

Multi-story muffin

To make up for a lazy Sunday of frozen waffles and blueberries, I got up early to make muffins on Wednesday. (If it was a lazy Sunday, does that make this a working Wednesday?) The recipe, again, was courtesy of the LA Times, so no link. It called for Meyer lemons, but we're swimming in mandarins at the moment, so mandarins it was. I like recipes that don't faff about too much during the prep stage. This one required the citrus to be roughly chopped, then food-processed, which wasn't overly complicated for early morning. The rest of the muffin recipe was the usual simple stir-wet-into-dry-but-not-too-much. I don't think I'll use this recipe again. It called for 1/2 cup of butter, which, compared to that epicurious recipe from before, is 1/2 a cup of butter too much. (Maybe the banana in the previous recipe added enough moisture and good fat to hold the whole thing together.) But I like the idea of using my spare citrus in this manner. Perhaps I could bastardise the two recipes and come up with something edible, yet P-heart-friendly. More experimentation beckons.

Mucho muffins

Cross posted on akatsukieats.