Apr 25th, 2014, 11:51 am
An ages-old question: "Whence came your idea for this (or that) story?" My favorite reply is from my friend, Harlan Ellison, "I buy them as 6-packs from Schenectady."

Less clever but more helpful, perhaps, is the recognition that authors transmute raw ideas into gold (stories) by the sheer prowess of their imagination. But if you still want to know, consider the article below. Its ostensible purpose is investing but for my purposes here it proves a treasure trove of possible story ideas. And not just the obvious. Can you see them (all)...?
ephemeral

Made-to-Order Life Forms Delivered to Your Door?

“We’re here today to announce the first synthetic cell… this is the first self-replicating species that we’ve had on the planet whose parent is a computer.”

Yes, you read that correctly.

If your mind isn’t already blown, consider that the quote above is from 2010. It was delivered by the famous scientist Craig Venter, who, in addition to leading the private effort to sequence the human genome in 2001, also has the not-insignificant distinction of unveiling synthetic life to the world.

Venter is one of the fathers of an emerging science called “synthetic biology,” which is the next step in genetic engineering. It grew out of the old human desire to manipulate living systems and make them do useful things for us, and involves redesigning organisms for new purposes and creating entirely new living things.

Humans have been manipulating nature for thousands of years, really since the dawn of agriculture. But even compared to the genetic-engineering efforts of the past several decades, the emergence of synthetic biology represents a big step forward.

You see, while the field of genetic engineering has been around for some time, there really wasn’t a lot of engineering going on. The work was slow, complex, and messy. And there was a lack of standardized components.

Scientists started writing genetic code back in the 1970s, using what are called recombinant DNA technologies. It was basically just cutting and splicing genetic code. Eventually you could write anything, but it would take a very long time to do it. Microbiologist and geneticist Andrew Hessel compared the process to writing a ransom note.

That’s all changing, thanks to two rapidly advancing technologies: DNA sequencing (the ability to read DNA); and DNA synthesis (the ability to write DNA).

You’ve heard of the Human Genome Project, of course. It took more than 10 years and about $3 billion to sequence the first human genome. This worked out to about $1 for each base pair of genetic code. Today, we can sequence a human genome on a benchtop device in an afternoon for about $1,000. So in terms of DNA sequencing, we’re essentially able to digitize all the biology we want for a very low cost.

But the real driver of synthetic biology is writing or synthesizing DNA. And to get there it helps to treat biology as just another information technology—to think of cells as nothing more than biological computers. Whereas computers understand binary code, living cells understand a different sort of code—the As, Ts, Gs, and Cs of DNA. Chromosomes function like software, and the genome itself is akin to the operating system.

It’s a pretty simple process. After all, DNA is a molecule comprised of just four nucleotides (i.e., a sugar, a phosphate, and a base—either A, T, G, or C). And today, you can go to your favorite chemical store and purchase a bottle of A (adenine), T (thymine), G (guanine), and C (cytosine) in powder form. Mix ’em up and voilà: instant DNA. But even if that’s beyond your capabilities, there are a number of companies that will make the DNA and ship it to you—all you have to do is provide the company with the desired nucleotide sequence.

Dr. Omri Drori, the founder of Genome Compiler—a simplified solution for designing DNA with standardized components—calls this “democratizing creation.” His vision is that we’ll stop destroying species and instead create new ones to solve problems.

This is huge. So why isn’t there a story about synthetic biology on the front page of every newspaper in the world every day? Because it’s still difficult and expensive to write meaningful lengths of DNA.

By 2008, scientists were able to write pieces of DNA that were up to 20,000 base pairs long, which was long enough to incorporate genes for a single metabolic pathway into a bacterium so it could perform specific tasks; but the goal was always to synthesize entire genomes of bacteria and eventually larger, multicellular organisms.

The major breakthrough came in 2010 when Craig Venter and his team synthesized the whole genome of a bacterial cell consisting of a million base pairs of code. They started with the digital code in the computer, then built the chromosome (the entire genome of most bacteria is contained within one circular chromosome) “from four bottles of chemicals, assembling that chromosome in yeast, transplanting it into a recipient bacterial cell and transforming that cell into a new bacterial species.” They did it at a cost of several dollars per base pair.

More recently a team from Johns Hopkins synthesized a yeast chromosome with 2.3 million base pairs. This is important because yeast are eukaryotes like us. They have similar chromosomes, just smaller.

As with much of technology, the cost of synthesizing DNA is coming down, but it’s still prohibitively expensive in many cases. Writing really short simple strands of DNA will run about 25 cents per base pair, while more complex assemblies can still cost as much as $1 per base pair. Companies like Cambrian Genomics are holding out the promise to make DNA synthesis much cheaper, perhaps thousands of times cheaper. It’ll happen someday, but it hasn’t yet.

So why does this all matter? Because there’s a lot of good that can be done with synthetic biology.

[Ed. Note: I’m fully aware that a number of people think this stuff is apocalyptic. And I’m not trying to suggest here that some of the arguments from those folks are not valid—indeed, their concerns need to be considered carefully. The purpose of this article, however, is just to introduce the topic. I’ll leave the ethical debates to people smarter than me.]

In the long run, the potential for synthetic biology applications is practically limitless. New diagnostics, new therapeutics, new sustainable ways of energy production, and pretty much any other biomolecular and chemical manufacturing outputs—these are all areas where the technology could be applied.

Many such applications are showcased every year at the International Genetically Engineered Machine (iGEM) competitions. At one of these recent competitions, a team of undergraduate students from Munich reengineered four strains of yeast so that when they made beer from the yeast, in addition to alcohol the beer would contain four different molecules as well: xanthohumol (an anticancer molecule); limonene (a lemony-smelling molecule); thaumatin (a protein that’s a natural sweetener); and caffeine. Yes, this group brought to the competition the first naturally caffeinated, biologically synthetic brewski.

Another group of students reengineered E. coli to produce different colors under different disease states. So it would produce one color for colitis, one for rotavirus, one for salmonella, one for stomach ulcers, one for worms, and one for colorectal cancer. (They dubbed their creation E. chromi.) The idea is that you eat yogurt or something containing the E. chromi bacterium, then you just go to the bathroom and peer into the bowl. Whatever color you see, that's what you have. It’s a little gross and sort of funny, but it’s also an interesting way to start thinking about diagnostics of the future.

iGEM competitions aren’t the only place we’re seeing advancements in synthetic biology. It’s already helping in the real world. Researchers have recently engineered a strain of baker’s yeast capable of spewing out an anti-malaria drug on an industrial scale. The French big-pharma company Sanofi has backed the effort and plans on generating millions of doses of the drug each year.

[For now] most of the best work in synthetic biology is still tied up in private companies, labs, and universities...
Apr 25th, 2014, 11:51 am