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getting published jaguar's realm Joshua Files nostalgia other books science writing

My New Editing Regime…and Memories of Subcloning


The publisher and I have agreed a deadline for Joshua bk 1 v3.0. I’m deep in the process of writing Jaguar though, and can’t let the momentum go. So I try to work on Jaguar in the morning at my desk, take a two-hour break to refresh and then it’s on with the editing, which seems to require a different skillset as far as I can tell.

Thank goodness for editors. I’ve said it before and I’ll say it again. Mine is probably going to save me from being a laughing stock, if nothing else – hopefully a lot else but you can’t predict these things.

I like to take my manuscript out for little walks. I can’t be bothered going all the way to the Bod this time around – I’m only spending 2 hours a day on it, what with the Jaguar writing taking up all my morning brain activity. So I’ve been going to Summertown.

The above photo is taken of my set-up at the Summertown Wine Cafe, a bijoux little joint on South Parade which makes the best coffee in Summertown (there are many Italian coffee machines in Summertown, but few baristas who have a clue how to use them). Sadly however, they charge a small fortune for savoury food – best to stick to cake, I’m trying to avoid blimpdom so that’s out.

Blah, blah, blah. Nothin of consequence in this entry sadly. I’m just writing something to have to test in a new way to do an RSS feed. If you read this, you’ve just participated in an experiment.

Do you feel used?

I kind of miss doing experiments. Somewhere in the back of my mind is the niggling feeling that a PROPER day’s work is what I used to pull off at the height of my keenness as a graduate student…a long day in the lab which ends with a successfully identified new DNA subclone to use in a lovely biological experiment.

‘Subcloning’ is a way of starting with a widgey little bit of DNA that is no use to anyone and two days later having bucketloads (as much as a milligram!) of the stuff that you can use to do biological experiments in tissue culture cells or even in unsuspecting fluffy creatures. (Some journals are so fussy that you can’t get published unless your results are in a live organism.)

You insert a piece of experimental DNA into a ‘vector’ of usually bacterial or yeast DNA which has the ability massively to replicate it. Then you can grow the ‘bugs’ in a 500ml culture overnight and in the morning extract enough DNA to ‘transfect’ cells which allow you to test the properties of your experimental DNA. The tricky bit is that when you try to stick your experimental DNA to the vector DNA, only a small fraction will combine to give you the subclone. The rest will just be vector DNA that sticks back to itself.

When I were a lass we used to pick at least 24 bacterial colonies in the hope that 2 or 3 would have the subclone. It could take up to a whole day, a day spent ‘doing minipreps’, as we used to call it. Sometimes you had to use radioactivity and horrible, ooky, gloopy, neurotoxic polyacrylamide gel to help identify the subclone.

(Any molecular biologists reading this, bright young things with your PCR, your DNA synthesisers and sequencing machines…it’s all very easy now, I’ll bet.)

But! Throughout most of career as a molecular biologist I noticed that although I was a good little scientist and picked my 24-48 colonies everytime I wanted to find a correctly subclone, more often than not, colony 1 (the first I picked with a sterile toothpick) actually had the subclone. i.e. I didn’t need colonies 2-24 and all the effort in ‘working them up’ was not actually essential.

Other people in my lab noticed this too. It turns out that in maths the number 1 is disproportionately represented (there’s some rule and it’s used as a way to detect fraud), well, in molecular biology this seems true too.

Don’t think we let that observation go to waste, either. Towards the end of my time in the lab, I would often just pick a colony right off, inoculate my 500ml flask and grow up the bugs without testing whether they had the subcloned DNA in them. It saved a whole day! Of course I tested a sample before I used it to transfect my tissue culture cells. Well, duh.

If you didn’t understand a thing I wrote in the last few paras, tell me. R1X did, so I have tried to rewrite it so that it makes sense.

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cuba jaguar's realm other books writing

A Brush with Cuba in Summertown

Miladis Diaz shows paintings by Cuban artist Fuster at The North Wall of South Parade, Summertown, Oxford

A stroll into Summertown today resulted in a surprise Indian lunch at the Spice Lounge (a bargain at £4.95!), a coffee in Costa’s watching Oxford Uni students spilling out of their Prelims in sub-fusc (and pink carnations…we always wore red or white…since when is it pink?) and then a drop-in to an art exhibition on South Parade where one of Cuba’s premier artists, Fuster, is showing his work.

(see The Colours of Life, in Oxford until 24th June)

Miladis and I had a nice chat about Havana and Cuban art. I told her I was writing a book set in Cuba and this morning had written a scene set in a ‘country school’, where high-school students are used as unpaid labour to harvest coffee for the state-owned industry. I admired her name, as exotic as are many Cuban names.

“The truth is, lots of them are made-up,” she said, blushing.
“And they’re the better for it,” I said.
“I’m not so sure. You get all these silly ones, starting with Y… it’s a generational thing,” she said. “People in their twenties and younger. Ynieski, Yulieski, Yolexis, Yoanni, Yumiel, Yadel, Yonelki, Yunior…”
It was my turn to blush. “I used the name Yoannis for one of my characters,” I admitted, “And I know a Yunior…”

Miladis gave me the phone number of her friend in Havana for next time we’re there. Her friend is a biologist who writes children’s books, as coincidence would have it!

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jaguar's realm other books writing

Jaguar – the Midpoint…

Reaching the Midpoint of a story is always deeply satisfying (for me). You’re beyond the part where you feel you’ve broken the back of the manuscript, in terms of wordcount you’re halfway there if not more, the end starts to loom into view.

More than this though, if you’ve constructed the plot properly, this is where things should seeeriously take off. If you have, the Midpoint should include a spine-tingling reveal, (simply delicious to write)and then the pace should ratchet up a notch, stakes increase, excitement factor nudged up a level…all of which makes the story easier to write.

In past manuscripts, when I’ve reached the Midpoint, typically I find that I can painlessly add another 500 words to my daily target.

Well, today I need to write the Midpoint of Project Jaguar. I’m not sure I’m worthy of it. Looking at what the plot calls for, I’m feeling way too fuzzy to write it well. Battling some virus or other…right eye infected, bloodshot and sore…committee meeting to chair later this afternoon.

A Midpoint is to be relished. I think the writer has to enjoy it, before anyone else. If you don’t have fun telling it the story, how can anyone have fun hearing it?

So…gosh. I’ll have to take a break. Get some inspiration. Maybe go to a juice bar in town and buy Haruki Murakami’s new book?

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Joshua Files writing

Rare books mark climactic page in archaeology’s history

This article in the Boston University Bridge caught my eye two years back and inspired a chapter in ‘Todd Garcia, Boy Archaeologist’, a chapter which didn’t make it to the first two drafts of ‘The Joshua Files’.

The article describes how a book collector came across a super-rare copy of a book by the explorer who kicked off the whole field of Mayan archaeology, John Lloyd Stephens. The bookstore didn’t recognise quite what they had in their shop, not having realised that the apparently insignificant inscription in the flyleaf was from the author to President Martin Van Buren.

Only two copies of this book (‘Incidents of Travel in Central America, Chiapas and Yucatan’) would be more valuable and are in fact still missing…the author’s own copy and the one he gave to his friend and collaborator, the artist Frederick Catherwood.

In real life they are still missing. In ‘The Joshua Files’, however, one of these might be hiding, unnoticed in a second-hand bookshop in Jericho, Oxford…

And today, that deleted chapter (rewritten for Joshua) will be making its way into Invisible City version 3.0.

(Provided I don’t get tempted by something else, like an afternoon at the pool. Fingers crossed for rain…)

Categories
raves writing

The Secret

Whilst dining together at a Lebanese restaurant in Andalucia to celebrate her wedding for the third time, my lovely friend Alison turned to me and asked me if I knew of the secret.

Ummmm, no, I said.

“I mean, ‘The Secret’ – a movie, now a book too – it’s a publishing phenomenon.”

I didn’t know anything about it, living as I do in a claustrophobic fog of adventure stories, school governance and salsa dancing.

Well, I’ve been missing out, by the sounds of things.

From Wikipedia:

The Secret, described as a self-help film,[2][3] uses a documentary format to present the “Law of Attraction.” This law is the “secret” that, according to the tagline, “has traveled through centuries to reach you.” The film features short dramatized experiences and interviews of a “dizzying dream team of personal transformation specialists, spiritual messengers, feng shui masters, and moneymaking experts”.[4] As put forth in the film, the “Law of Attraction” principle posits that people’s feelings and thoughts attract real events in the world into their lives; from the workings of the cosmos to interactions among individuals in their physical, emotional, and professional affairs. The film also suggests that there has been a strong tendency by those in positions of power to keep this central principle hidden from the public. The previews or “clues” to the film, show men who “uncovered the Secret…”.

Oh.My.Giddy.Aunt. It’s prayer for the secular! That is too, too wonderful.

There’s so much I could say about this…but I won’t be tempted. I’ll just relate the rest of mine and Alison’s conversation. (We were enjoying the best part of a bottle of vino tinto at the time.)

“So I don’t need to work hard on making my novels exciting…and the publishers don’t need to work hard marketing them…all we need to do is to visualize the book being a big success…?”

Alison nodded. “Visualize your success. Don’t let any negative thoughts interfere at all! Don’t have anything to do with people who cause you to experience negative thoughts or feelings!”

“Visualize my success…?” I repeated. It surely can’t be that simple. But according to Alison, that’s just what The Secret is all about. If you visualize it enough and with enough of the right vibes (and none of the wrong vibe), the universe will align itself with your wishes. Don’t ask how, but I’m sure there’s an underlying pseudo-scientific explanation designed to bamboozle.

“Visualize it…massively,” Alison said. “Look, I’m doing what I can, babe. I’m already visualizing you paying for us all to come here again next year…”

The following day, more sober, Alison pointed out the flaw in The Secret.

“Anyone who’s ever experienced unrequited love knows that it’s a load of hooey. I’ve spent most of my life fantasizing about various women, visualizing and everything…and it never worked!”

I thought about this for a second. “But did you ever consider asking any of these women…?”

Alison’s face fell. “Wha…? No… You think I should have…?”

The Secret. It’s one of those things that only works if you put in the hard work also. As with prayer – God helps those who help themselves.