Biology has changed

You may have heard of CRISPR. If not, check out this popular article in the New York Times about banning it for editing the human genome (specifically the germline – the part of the genome passed to the next generation), or an earlier article that nicely summarizes how the technique works. Basically, it is a technique that scientists can use to specifically rewrite the genetic code of an organism.

That is SO COOL.

Okay, we did have some ways for doing this already. But most of the GMOs you hear about are made by chopping DNA out of one organism and shoving it into another (or literally shooting it) and crossing your fingers that it works. With CRISPR, you can just make some RNA, attach it on a Cas9 enzyme, and the enzyme will write it into whatever organism you choose. But I get ahead of myself. What is CRISPR? What is Cas9? Why is there a picture of Dexter at the top? Do you really want to read this whole post? (Yes you do, if you care about science.)

CRISPR is actually an acronym that I will not break down because it doesn’t really help explain anything. What you need to know is that it was discovered as bacteria’s adaptive immune system. Humans have an innate immune system and an adaptive one. The innate is always there and consists of generalized protection like your skin and natural killer cells. The adaptive is the learning, specific immune system. B cells can remember diseases you have gotten before and produce antibodies that fight off that infection quicker the next time you get it. Vaccines work by tricking B cells into preparing for things like measles and the flu. Bacteria were not thought to have any adaptive immune system until very recently. Some Japanese scientists noticed weird chunks of DNA separated by short spacers in bacterial DNA in the late 80s. Some very smart people figured out that the bacteria was actually chopping DNA out of viruses that attacked it and saving it in its own genome so it could remember how to beat that virus the next time.

That. Read that last sentence again. That is the crazy part. It’s like some alien that eats the brains of its victims and learns all of their secrets. These bacteria collect virus DNA like microscopic Dexters (see, the photo makes sense now) and store it as a record of their victims. Now this is useful in itself. You have a nice continuous record of all the viruses this bacteria and its ancestors have faced. But the important part for us it the way it uses those stored DNA segments. When foreign DNA enters the bacteria it needs to decide whether to use it or lose it (bacteria are notorious for stealing any old DNA they pick up). So the bacteria brings a copy of the stored DNA segments to the new DNA using a protein called Cas9. It then compares stored DNA to new DNA. If they match? CHOP. The dangerous virus is gone.

Scientists have figured out how to attach any DNA segment they make to Cas9 and send it into any organism they choose to. It works for bacteria, plants, lab rats, and even humans. But there’s where it gets tricky. Because now all those Gattaca-esque designer baby dystopian futures are a little bit closer to reality. We can edit out portions of the genome that we know cause problems in the next generation, and we can edit in positive traits, like long eyelashes and not entering the subway car before others have gotten off (not sure about that second gene, but New Yorkers would thank you if you found it). This could move quickly for remedying diseases, but scientists hope that everyone will use caution. Our knowledge of how human genetics works has moved rapidly, but is still a long way from complete. Some sections of DNA have multiple effects that we just can not predict yet. But that’s not even the coolest part.

CRISPR

Diagram of the CRISPR system in a bacterium. (1)Foreign DNA is stored in the CRISPR array. (2) DNA is attached to Cas proteins as crRNA. (3) If new DNA matches crRNA, Cas cleaves it.

Since invasive species are my topic of study, I have always thought of ways to improve the way we control them. An effective control of invasive species must 1) completely remove the population of the species, 2) not be excessively expensive, and 3) be very specific to the organism. Pesticides are good at 1 and 2, having people manually kill invasives is good for 3, and biological control is not bad at all if done right. A gene drive could potentially destroy any sexually reproducing population in a few generations. Yes, you read that right. A gene drive is the process of making a gene spread rapidly through a population by ensuring that it is preferentially passed to the next generation. Mosquitoes are the first species in the cross-hairs for this. We can use CRISPR to engineer mosquitoes in the lab that carry a deadly gene. We release them into the wild and they mate with wild mosquitoes. The first generation doesn’t die because the gene is recessive, but due to biased inheritance, it spreads through the population. When the genes start meeting each other, the mosquitoes start dying. Simple as that. Of course, we will need a few more years of testing until we get there, but it’s coming. (In the meantime, check this out)

So, pay attention when you see CRISPR in the news. I expect many of the big breakthroughs in the next few years will come from it. And just hope that no one figures out a way to make a CRISPR specific enough to target a single individual’s DNA. That would make the most specific poison possible. And hope that I don’t get put on any government watchlists with that last comment.

Photo credits: PNA Bio (http://pnabio.com/products/CRISPR_Cas9.htm)
Deviantart user rumonica (https://www.pinterest.com/hayleyqs1116/dexter/)

NIMBY

I’ve been thinking a lot about NIMBY (Not In My Back Yard) recently. For those who are not familiar, it is a term that came into popular usage in the 80s to describe residents who oppose to a public works project (e.g. nuclear power plant, toxic waste dump…) when it is being built near them, even if they acknowledge that the project is necessary. There was a story on NPR about east coasters opposing new offshore drilling and exploration that is a good current example. The idea I’ve been thinking about (that I will try to elucidate for you over the course of this post) is as follows: Conservation is not a means of protecting resources eternally, but a process of storing resources until the economic situation becomes dire enough that public need for economic vitality triumphs over environmental protection.

To me, the quintessential case of this is when a park gets sold when times get tough. One particularly interesting example is that of Oklahoma’s Lake Texoma State Park. It was a small State Park (1,882 acres) along the shores of a large artificial lake on the southern border of Oklahoma. According to StateImpact Oklahoma, it was a popular park, featuring camping, fishing, and water sports. Due to budget cuts, the state agreed to sell the park to private developers for $14.6 million, with the stipulation that the developers would create a park of “equal value” to replace it. Unfortunately, the company that bought the park never replaced it, nor even built the multimillion dollar retreat they had planned, likely a victim of the recession. The state held on to the park until it became a financial burden, then sold it off without putting in the proper safeguards to replace it. Today, it appears that the area is in limbo; some still call it a state park, but it is not on any OK government websites.

A bigger example is that of Virunga National Park in the Congo. It is Africa’s oldest park, but the brutal civil war in the country has meant that oil company SOCO was able to secure permission to enter the park and begin oil exploration. The company assured everyone that their drilling was nowhere near endangered Gorilla habitat, but fears persisted. Currently, SOCO has agreed not to drill for oil without permission from the DRC and UNESCO, but it still maintains a presence within the park, just in case.

We tend to view our conserved lands as inviolable, but the reality is that their protection is maintained by pieces of paper and promises. I started off talking about NIMBY because I think that the most outspoken critics of local environmental offenders tend to be people who are well-off enough to fight them. Environmental degradation has a short-term economical benefit, even if it has long-term losses. The federal government has made the strategic decision that the desire for cheap oil is greater than the American people’s resistance to offshore drilling. What will happen when our desire for cheap oil outstrips our desire to protect the Arctic National Wildlife Refuge? What will happen if, in 50 years, we begin to run out of a rare element like manganese, and happen to discover a reserve in South Dakota’s Black Hills? Will we be resolute enough to bear the economic burden of true conservation?

The other side of NIMBYism is the other backyard. I think this often gets overlooked in environmentalists’ discussions. Essentially, when you protect a certain resource from extraction without addressing the demand for the resource, you are ensuring that the exploitation will just happen in a poorer person’s backyard instead. If we refuse to drill for oil in the Atlantic, drilling will just increase in Texas or Canada or Iraq. The interesting part is that that oil doesn’t go anywhere. As long as demand remains high, developers will return for the oil years down the road when it runs low elsewhere; and they’ll be offering higher prices. As long as demand remains high, NIMBYists are actually acting so that their children will be offered a higher price for their resources. Sadly, I fail to see a future where environmental conservation does not revert to economic realities given a long enough time scale (and continued population growth). Hopefully, if we work hard enough to conserve, our ancestors will at least get a better price for their goods.