Thursday, July 25, 2013

All the Science News That's Hard to Read (part 2)

[Moderator's Note: This being my own post, I need to warn you that some of what follows in this long essay may contain some political or cultural bias and/or snark. I don't mean to offend anyone, but the posts on this blog are intended to exhibit the opinions of the bloggers as well as provide insights. This blog contains my opinions, so please understand that the views expressed below are mine alone and do not reflect the official views of the university.-JH]

In my last post, I talked about how some of the most exciting science of our time is virtually impossible to tell the public about (or to get the public to read about) because the discoveries are in really complex fields, where vital information is so specialized and detailed that ordinary people aren't likely to be interested in tackling the topic. In this post, I'm going to get more personal about this and talk about why, for me, this difficulty goes beyond being a "fact of life," a natural limit to communication, and slides emotionally into being a frustration, a dilema, and a disturbing problem.

A basic premise of science writing is that it is about meeting the audience halfway -- taking the complexities of contemporary scientific research, as performed by highly trained scientists working in highly specialized fields, and reducing the findings down to plain language, simplifying them somewhat, to the point where they are approachable by members of the general public with moderate educational backgrounds. The art of this kind of writing is to make the subject not just understandable, but also interesting or (perhaps) entertaining. However, even the most "fun" science writing assumes that the audience is willing to approach and be interested. What if they are not?
The road to understanding science has its difficulties. Meet me halfway?
I read an article the other day in Slate that got me upset. It was about how Virginia Heffernan, the highly accomplished former New York Times feature writer, social media critic and occasional science writer, had just admitted that she is really a Creationist. While I object to "creation science" because it fails in its claims to "factually" refute mainstream science (the "facts" here don't stand up to serious scrutiny), I certainly don't object to people believing in Creationism, if that is part of their deep personal beliefs -- beliefs which they are certainly as entitled to as I am to mine. However, what was upsetting about Heffernan's "confession" was that she didn't claim that her creationism came out of any personal religious beliefs, but that the biblical story of the Garden of Eden and Adam and Eve was "a more compelling story" than all the world-changing findings modern science -- of modern physics, the evidence-supported theories of cosmology, the detailed and useful information supplied by modern geological science, and the insightful and powerful implications of evolutionary theory, which is the foundation of modern biology and medicine. My short take on what she  means: it's easier to subscribe to the story of Genesis, because it's easy to understand. Modern science is hard, complicated and bo-ring. (To read other science writers take on this, go here .)
Yes, Virgina, we're all media critics.

Heffernan is a bright, talented and well-educated (Ph.D in English from Harvard) writer, yet she rejects one of the main areas of modern learning because it is complicated, intellectually challenging and she is just not that interested in it. Again, the story is too difficult to be "compelling." I'm afraid that I agree with the Slate article in finding her stance "shameful," but I also think that Heffernan is far, far from being alone in contemporary America. Only a small minority in our country "like" science and are interested in learning more about it.

If you're still reading at this point, you are probably one of the few, and I thank you and commend you for that, but now let me get to why this gives me such personal angst.

As a science writer, my personal experience with the subjects I write on is one of wonder. I have no degree in any science discipline (I am a Cornell BA in English and MFA in Creative Writing) but I have been following the fundamental advances in fields from sociology to theoretical physics to bioengineering for over two decades. In that relatively short time, miraculous new things have been revealed to me (I was present for the the announcement of the first sequencing of the human genome, I have been the first human eyes to see some of the images sent back from Mars, I wrote one of the press announcements for the recent Human Microbiome Project announcement, etc., etc.), many paradigms have shifted (some radically, like in genetics and microbiology) and some fields that are now prominent didn't even exist when I first started doing this work (bioinformatics and metabolomics come to mind). I have been around universities all my life, and I will assert to anyone that contemporary university research is engaged in the most exciting intellectual adventure of our time... and probably of all time. I'm overly dramatic, I guess.
Can I interest you in some WONDER?

But how to convey that wonder to the Heffernans of the world when they aren't willing to meet me halfway and find the same excitement that I find all around me in such abundance?

Here's a specific example: This week, I wrote a university press release about an important piece of university research. Because it's an official university research release, it is necessarily somewhat technical, so I would expect most people (outside of science reporters, who are my main audience) to have some trouble understanding it. But here's the thing: even if I could write about this work in plainer language, the subject matter requires absorbing some background understanding that I suspect most people don't want to deal with.They would find that background information bo-ring. Perhaps they would prefer that I were giving them a more compelling story, say like "Keeping Up with the Kardashians." The story, you see, requires you to know a little bit about proteins.
Yes, proteins. I hope you're not home alone.

Like all stories, my research story actually does have a compelling point of interest (what some of us call a "hook"): the researchers have found what is perhaps the fundamental reason for why bacteria are able to rapidly evolve immunity against antibiotics. The what and the why of this story, however,  are all wrapped up in the details of a specific group of proteins, known by the scary, technical name of  "beta-lactamases."

What do most people know about proteins? I've never seen a survey on this, but here's my guess:
1. They come in meat, eggs, beans and cheese
2. They are good for you.
3. They make you strong.

A few people might know:
4. Most genes exist just to make proteins.

But you need to know a little more than this in order to understand my story. What you need to know you were likely taught in a high school biology classroom, but most people (even people with advanced degrees, say doctorates in English or political science) have long ago forgotten these details because the information was complicated, and they were never that interested. Here are the details I'm talking about:

1. Proteins are large, complex molecules, formed by very long molecular chains made up of hundreds or even thousands of amino acid links, chosen from 20 different amino acid molecules, strung in a precise sequence. The genes in our DNA are a code that our cells translate into those precise sequences.

2. Proteins not only have long, complicated and precise sequences, but they each also have a precise structure, a shape that is formed as these enormously long strands fold up, like a bead necklace wadded into a tangle, that takes on a very specific form, determined by the chemical interaction of the specific amino acids in the sequence with each other. This is what scientists call "conformation." The shapes these molecules form often contain a variety of sub-structures (like the rooms, doors, windows, floors and hallways of a house) known as "helices," "sheets," etc. Further, these complex protein structures can also sometimes snap together like puzzle pieces to form even more complicated protein structures, composed of several protein subunits.

3. Proteins do a variety of important things in our cells and bodies, but one of he most important things they do is act as enzymes -- molecules that help transform other molecules, break them apart, put them together, etc. They are really the control machinery for the chemistry of life. The enzyme usually does this by having a structure (think of it as a pocket or a keyhole) on its surface that is precisely configured both in shape and chemistry, to interact with other molecules -- usually very specific kinds of other molecules. This is called the active site.
A representation of the beta-lactamse molecule, showing the major sub-structures.
Of course, the real background is even more complicated than this, but I'm telling you the basics I think you need to know here. I'm not kidding myself: unless you already happen to know/remember all these details, holding all this in your mind is not easy, and I fully under stand that it is probably not something you would want to research on your own and try to understand in order to understand my story.  But really, I think you should. Why? Because this is fundamental to understanding the physical nature of life -- all life -- which is why they taught it to you in high school. You probably didn't know it then, but it really is fundamental, important knowledge. Convinced? Yeah, I know.

Here's why you need to know all this here: UNC Charlotte researchers Dennis R. Livesay, Donald J. Jacobs and Deeptak Verma have been studying the structure of the protein enzyme beta-lactamase because it is well-know as the source of antibiotic resistance in many kinds of bacteria. The enzyme is a kind of molecular machine that is specifically tuned to chop up the anti-bacterial chemical compounds we call antibiotics. Beta-lactamase is especially disturbing because it has been evolving quickly to adapt to new antibiotics, but whether its adaptability is due to the protein's structure or just to the fact that we have been throwing so many drugs at it that we have accelerated its evolution, no one knows. Perhaps both.

This is the problem that Livesay et al set out to study, using tools that they have developed that allow them to rapidly analyze complex protein structures and their potential behaviors. It's not an easy problem, because, though they are only molecules that can't be seen in detail, even by our most powerful microscopes, proteins are actually very complicated machines, with thousands of different atoms in them, various larger structures (think gears, levers, girders, chambers) and a lot of subtly moving and chemically interactive parts.  Analyzing how these work from a sequence of their chemical parts is a daunting problem, not to mention analyzing a bunch of similar but subtly different proteins to see why one works against one antibiotic, while one works against others. Understanding how and why these changes can evolve is an even larger problem. 

What Livesay was hoping to find were differences in the behavior of the physical structures and the chemistry in different variations of the molecule that might be related to why different bacteria were resistant to different antibiotics. By using their tools, they could see how versions found in different bacterial families had developed different behaviors -- for example, how different parts wiggle and different parts are stiff. In the molecules the dynamics of the molecule differed -- the subunits affected other subunits in new ways. They found that evolution kept changing how the rube-goldberg mechanisms inside the protein's blob-like structure worked. Their work provided a fascinating (to me, at least) look on how evolutionary changes to genes could result in changes in an organism through structural changes in a single molecule. (See why one would need to know about amino acids, conformation and enzymes to understand this research?)

What the team did not discover, however, was that the changes that different bacteria had evolved in the mechanics of the whole molecule had any effect on the way the active site (the place where antibiotics are chopped up) worked. In fact, they found that only very simple changes in the active site -- changes that had no effect on the rest of the molecule and thus were not complicated for the bacteria -- were able to make the site attack new antibiotics. The active site is effectively protected from changes in other parts of the enzyme's structure and vice versa.This finding thus explains why new bacteria are able to develop resistance to new antibiotics so rapidly. Though it is fascinating to think that we are seeing on the molecular level how this all works, Livesay found the result "terrifying" -- and I guess he's right.
Scary: rapidly evolving antibiotic resistant bacteria, as far as most of us know.

Are you terrified? If you have read this far, perhaps you are, but the odds say that most people stopped reading when I asked them to try to remember and consider basic protein chemistry. What bothers (perhaps even terrifies) me is that this is really interesting science, and an important, useful finding about why the phenomenon of drug resistant bacteria is accelerating and plaguing us so severely. Most of us already know someone who has been sickened or killed by antibiotic resistant bacteria, and this research tells us that the bugs are likely to get much, much worse. Knowing something new about this crisis might be worth the public audience's effort -- if they were willing to meet the science writer half way. Perhaps more people will start retaining the basic lessons of high school chemistry and reading more about the new science here...  "Dream on," reality is whispering to me, "dream on."

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