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Work Talk, or How Biology Ticks

Actually, the fledgling AI wasn’t on the list of trends I wanted to discuss. Talk about the elephant in the room.

It’s probably because hubby and I had a row about his working hours. He must have come close to a hundred a week. I’m not kidding. He summed it up thus, “Last week I clocked up sixty hours of CPU time.”

“So what? I clock up a few myself when Firefox freezes or Jarte goes into a sulk because I type ‘control-t’ for a new tab and it tries to access the online thesaurus instead.” It’s ‘control-n’ for new file. Jeez.

“No, I mean I clocked up sixty hours of meaningful CPU time on an eight core machine. It was processing.”

“Hrmph.” I shrugged.

“You never take any interest in my work!”

Now wait a minute! I thought we had agreed not to talk about work. Every time I—”

He dismissed me with a wave. “I still know more about any of your projects than you care to remember.”

That is true. I don’t have his memory. “Yeah, but compared to computer programming, biology is easy to understand. I need a degree in computer science to follow what you do. Biology’s intuitive. But doing it is another matter.”

And that brings me neatly to the next item on the list.

Biology is so intuitive that computer programmers who don’t know better are attempting to ‘hack genes’ in their back yards.

I have pointed out to people that most of the methods used in molecular biology are ‘open source’. They are widely published, there are online groups like Bionet Methods And reagents which have been around since the dawn of the internet, and database access is thankfully still possible due to early initiatives to keep them in the public domain. It’s the reagents and tools that are expensive and hard to come by (often with good reason!) and there are only so many shortcuts you can take.

Garage research is fine, but it has to be worthwhile. Even if it’s feasible, making yoghurt cultures (which ones?) glow in the presence of melamine isn’t. Making a melamine detection kit might be.

And this is the point. Genetic engineering is gaining wider acceptance through the grassroots efforts of biohackers and initiatives aimed at students such as iGEM. (iGEM isn’t even last year’s news, but I live in Tadley—which may as well be on the moon—and in fairness it’s only now about to take off.) It’s great PR. Power to the People and all that.

But as for the Garage scientists: don’t waste your time. Discovery counts for very little, it’s the applications that matter.

Here is an example. Antibiotic-resistant superbugs and hospital-acquired infections are big news. So why are there still no solutions to the crisis? Not long ago I heard about a kid being lauded for discovering a ‘natural antibiotic’ in a common plant during a school science project. Will such heroes of future science come up with the answer?

No they won’t. The world abounds with antimicrobial compounds. If I cared to look around our garden, I would find them in anything from soil samples (guess where most of our antibiotics originally come from) to various plants and animals, perhaps even the ubiquitous slugs. We know that they are found in insects and earthworms. One of the most potent killers of superbugs could be a by-product of the silk farming industry.

However, most are difficult or expensive to manufacture and apply and the snag is that when you publish, you destroy the appetite of big pharma to invest. Although that isn’t always the case.

Let’s take a look at one candidate compound. Nisin is a lantibiotic originally isolated from lactobacilli (such as you may find in yoghurt 😉 ) which has been used as a food preservative for decades. It turns out that it has powerful antibacterial activity against Clostridium difficile, a naturally antibiotic-resistant bug with a toxic strain that kills thousands of people a year in the UK alone, mainly from hospital infections. It’s a sporeformer, so hand washing doesn’t do much to help.

Despite the compound being known, activity against C. difficile was perceived as sufficiently novel for a company to file a patent for a formulation ready to go into trials. Alas, as with so many start-ups, AMBI Inc was ahead of its time and possibly in difficulties but anyway keen to cash in. It out-licensed its nisin patents to a company that focusses on skin infections and another that markets it for the treatment of mastitis in cows.

The C. difficile work has been quietly burrowed. People continue to die from C. difficile infections. If trials had been initiated back in 1997 and had been successful (that’s a big if!) then perhaps some of the ten-thousand-odd people for whom C. difficile has been identified as the underlying cause of death could have been saved.

But this is past science. I wanted to talk about the future.

Another time.

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