Rewriting the language of life

E. Coli bacteria

The familiar, idyllic scenery outside your door, bucolic in the spring sunshine, is exceedingly weird. And so are you.

What seems ordinary to us, an oak tree, daffodil, blade of grass, or your own body, is made of atoms forged in the furnace of early, distant stars. And these atoms are nearly entirely empty space, vacuum, with only a few protons and neutrons and electrons forming actual matter.

That’s right, your body is more than 99.9999% empty space, and the reason you don’t sink through your chair is that the electrostatic charge of the atoms in the chair repels the atoms of your body.

What’s the point? Only that things are often stranger than they seem.

Take living things, for instance. DNA is often called the blueprint of life. Think of DNA as a construction and operation manual that tells a dandelion how to be a dandelion, a whale a whale, or a you to be human. The instructions in your DNA account for your height, hair color, gender and also control the ongoing operation of your body. This is the miracle of life.

So it was a bit of a surprise earlier this month when synthetic biologists at the Scripps Research Institute announced  they had created bacteria containing artificial DNA. A biochemist not involved in the project, Steven Benner of the Foundation for Applied Molecular Evolution in Gainesville, Florida,  summed up the shocking finding: “Most people thought this wasn’t possible.”

Think of DNA as a kind of computer program. It is information that regulates how amino acids and proteins, the basis of life, are produced. The researchers at Scripps, led by chemical biologist Floyd Romesberg, have found a way to rewrite that program and have created bacteria which live, grow, and reproduce utilizing segments of man-made, artificial DNA. The descendant bacteria also contain the artificial DNA, and pass it on to their successors.

The point of all this is that bacteria can now be programmed to produce a greatly expanded range of amino acids and proteins. Applications range from new cancer drugs to improved vaccines or even anticounterfeiting, improved forensics, and the efficient production of biofuels. The opportunities are mind boggling.

Even before the achievement of artificial DNA, scientists had become quite capable. According to the Wall Street Journal, “With growing mastery, scientists have been tinkering with this natural information-storage system that is found inside every cell. They routinely cut and splice normal DNA to alter plants, bacteria and animals. They have used its ultraminiature storage capacity to encode books, poems and popular music. They even have programmed DNA to perform computer-like calculations.” (Man-Made DNA Opens Doors, 5/8/2014).

But the Scripps accomplishment opens the door to much greater control and specificity. While current gene manipulation relies on repurposing natural DNA, the advent of artificial DNA greatly expands the designer’s pallet. The natural e. coli bacteria used in this experiment can produce 20 amino acids. When augmented with the Scripps artificial DNA, they can create 172 amino acids. Since proteins are built from amino acids, the scope of protein creation is greatly extended.

There are safety concerns. A number of environmental groups had asked that this research be shut down until the safety aspects could be more fully assessed. But a review by the U.S. Presidential Commission for the Study of Bioethical Issues found no reason to call a halt. Their reasoning was that while the technique added some elements to the language of life, it did not fundamentally change the life process. The Scripps researchers did, however, add a safety feature. Their bacteria were designed to grow only in the presence of a specific chemical additive. In the absence of this additive, the bacteria would stop creating artificial DNA, thereby making escape to the wild highly unlikely.

In the end, whenever we think we have a handle on science, it surprises us. This achievement promises great advances in medical science and many other areas. Perhaps even the holy grail, that being the efficient conversion of carbon dioxide directly into biofuel. What a wonderful outcome, should it come to pass.

Math is the Path to the Middle Class

It was great news for Rhode Island recently. General Dynamics Electric Boat has been awarded a $17.6 billion contract to build ten Virginia-class attack submarines and the Quonset Point facility will be adding 450 jobs. Some commuting workers from Massachusetts may benefit as well.

This is consistent with President Obama’s pledge to build the economy from “the middle out.” The wages from these jobs would inject an additional $30 million into the local economy with beneficial ripple effects (the “multiplier”) boosting barbers and bakers and candlestick makers.

But not so fast. Once of the most common positions on the Electric Boat website is a “QP Inside Machinist.” This job is described as follows:

“Set up, program editing and operation of CNC milling and turning centers. Verifying part configuration to plan requirements using various high tolerance precision measuring tools; must be able to work independently and with minimum supervision.”

From the list of qualifying requirements, this one stands out: Strong mathematical skills in geometry & trigonometry preferred.

Oops. How skilled are our recent high school grades in math? Are they ready for the rigors of the workplace? Or, rather, have they succumbed to our cultural aversion to math?

In Hollywood, only geeks and geniuses (e.g., Matt Damon in “Good Will Hunting”) are good at math. The cool kids steer clear. It’s too hard. It’s not cool. It’s the butt of jokes.

But as can be seen, math may be a qualifying requirement for a well-paying middle class job. And as our information-based economy continues to unfold, this will be increasingly true.

Long gone are the days when one can make a good wage based on the sweat of one’s brow. Lifting 50 pound bags of flour is now relegated to pallet jacks, with a single operator displacing dozens of Italian immigrant mothers who had previously been paid to stack tons of goods. We hate technology, but each of us with a smart phone is embracing it. The workplace has changed.

But have our cultural and educational systems changed apace? Has mathematical literacy, numeracy, become increasingly desirable and culturally acceptable? Alas, it has not.

It is shockingly apparent that we have not prepared our kids for the new workplace. They believe math is hard, uncool, geeky, and hence, avoid it. But if the alternative is a minimum wage job as a barista, are we serving them well?

A plethora of studies have shown that high school math skills are correlated to higher earnings later in life. And not just earnings, math ability also eases our way through the increasingly complex thicket of everyday life. A 2013 study done by researchers at Princeton University found that in the financial meltdown of 2008, poor basic math skills correlated strongly with mortgage defaults. Controlling for all other factors (age, ethnicity, education, household income), the researchers studied hundreds of subprime mortgages across New England. Their findings were surprising in that it wasn’t specifically the choice of mortgage contract that led to default, but rather other life behaviors indicating poor overall financial decision making.

How to motivate kids to learn math and teach them more effectively?

One whimsical thought is that if only the media, Hollywood, and sports idols could embrace this cause, things might be different. We have shifted culturally against smoking tobacco and in favor of gay rights, why not a campaign to make math acceptable? It’s too easy to laugh at math geeks, as witnessed by “The Big Bang Theory” whose innumerate character played by Kaley Cuoco wins our affection.

A more serious route being debated by educators is to teach math in context. For instance, high schoolers should be taught basic financial skills and, in the process, exponents and logarithms. That is how interest calculations and amortization tables are made, why not learn how in context and not as part of an abstract course in algebra? This could be amplified by having chemistry and biology teachers, for instance, explaining the math required to understand their subject matters.

After all, math was not invented as an abstract topic. Fractions were an outgrowth of commerce, where early merchants needed to portion out fractional bushels of grain or wheels of cheese. Multiplying 2/3 times 4 was a practical exercise, not something dreamed up to torture a fourth grader.  Likewise, geometry and trigonometry were developed from the building trades and nautical navigation, not as an abstract brain teaser for high schoolers.

This won’t be solved anytime soon, but we must make numeracy a top goal. Those well-paying jobs at Electric Boat are awaiting.