Why do I have to sit in Chem Lab? When will I ever use Chemistry???

Well, how about in the kitchen? It’s holiday time, and I’ve done a fair share of baking and cooking this year, as usual. The melding of ingredients, and the smells and textures of batters are making me think of organic chemistry lab. Yes, I’m weird. Isn’t it obvious by now?

Really, I tell anyone who does science for a living that if you can do science, you can cook. And I suspect that the reverse is also true. I’ll wager that if someone is very good in the kitchen, then they’d also be quite good at the lab bench. You just can’t eat your results there.

The precise mixtures of ingredients and heat (and in some cases cold—if you chill cookie dough before baking, for example) meld the ingredients and set in place chemical reactions that result in all sorts of tasty concoctions.

Biochemically speaking, there are three classes of molecules that we use for calories and nutrition: proteins, carbohydrates, and fats. All are organic molecules, meaning that all form their chemical structures based on a backbone made of the element Carbon. We need all three to make up the cellular structure in our bodies.

Now there are more things necessary in cooking than proteins, carbohydrates, and fats, depending on what you’re making. Breads need yeast to biologically convert some of the carbohydrate in the flour into carbon dioxide gas and alcohol to provide lift, structure, and flavor. Not using yeast, soda breads use baking powder and/or baking soda, which create carbon dioxide chemically with the addition of water and heat. (A short experiment—take a small amount of baking powder and mix on a spoon with water, and watch the bubbles form—this is carbon dioxide gas, which provides the lift needed in cakes, cookies, and soda breads).

I made a lot of sweet soda breads for the holiday this year. One was coconut macadamia nut bread. Very tasty. However, the recipe that I have, as it stands, is coconut macadamia nut BANANA bread. Problem: my husband doesn’t like banana, but he’s a huge fan of coconut and macadamia nuts. So, the easy solution is to just leave out the banana, which I did. But think of that for a minute. What does that do to the texture of the dough and the result of the recipe?

The recipe calls for 3 bananas. We don’t like the flavor of banana, but we still want the sweetness and fat that the bananas add to the batter. So, on a very basic level, if I leave out the banana, I should increase the amount of butter and sugar. Which I did. I’ve made this recipe by just leaving out the banana and not compensating at all, and I was left with a non-descript, crumbly mass that vaguely tasted of coconut. I increased the butter and sugar and got a sweet, moist bread full of coconut and macadamia nuts and none of the offending banana.

For more on food and the science behind food, check out my favorite cooking show on the Food Network. It’s called Good Eats, hosted by Alton Brown. It’s funny, and has great recipes. Alton Brown has great visual aids to show you how certain ingredients work, scientifically. Why ingredients have to be added in certain orders, why things must cook for certain lengths of time, etc. He has a great show where he takes the same chocolate chip cookie recipe and with slight variations shows you how to make 3 different types of cookies: flat and crunchy, tall and cakey, and very chewy. All by slight variations of ingredients (butter or shortening), baking powder (less of it means less rising), and temperature of dough (colder dough yields taller cookies because they ultimately have less time at the target temperature, so don’t flatten as much).

Fascinating and tasty chemistry! You do use it in real life!

CORRECTION: I've been caught in a factual error. Bananas contain almost no fat. The USDA gives a fat content for bananas of 0.4 g for a medium (118 g) banana. I just suppose the bread tastes better with all the extra butter.

Open Access Science

An entry on scientific publishing may not be very fascinating, but I'm going to tell you how to get free access to cutting edge science, free access to slightly old science, and free access to science history.

In the U.S., much, if not most, of the science is funded through grants from public agencies. These include the National Institutes of Health, the National Science Foundation, and others. This means that taxpayer dollars go toward funding most of the research done in academic institutions.

Almost all of that science does get published in peer-reviewed scientific journals, and those journals are accessible to the public. However, they’re not free, and they’re definitely not cheap. It costs more to get a subscription to e.g., The Journal of Biological Chemistry (Printed journal is $2,625 per year and Online journal is $2,460 per year) than it does to something like People (a little over $50 a year). You can get individual papers, but you pay between $15-$30 a paper, depending on the journal.

It’s the law of supply and demand. More people are interested in the latest shenanigans of Britney Spears than say, the Mechanism of Transcriptional Activation by the Proto-oncogene Twist1. (yes, it’s a shame—the proto-oncogene is not as sexy, but it’s much more substantial; however, I doubt it can sing). (FYI, an oncogene is a normal gene, or piece of our DNA, that are usually inactive. When they become activated through some environmental cue or a mutation, they can lead to the formation of a cancer. A proto-oncogene is a normal gene that has the capacity to become an oncogene through mutations or something that leads to a very increased expression of that gene)

Most of us scientists don’t even have subscriptions to these journals. We get access because the institutions where we work buy the subscriptions.

About 10 years ago, I first heard of a movement to get access for regular taxpayers to the science they indirectly paid to have done. It makes sense. If the research is taxpayer funded, then don’t the taxpayers have a right to peruse it? At the time it was being debated, there was even short talk about having researchers save every scrap of paper on which they wrote results.

We joked in the lab about it because some people had results scribbled onto paper towels before they wrote them up more formally in their lab notebook. Would we have to save every scrap, and not only save it, but explain it in a format that anyone could understand? We would spend most of our time decipering the lab codes instead of actually doing the science.

Well, thankfully, we didn’t have to save used paper towels. A new trend in scientific publishing happened, however. I think the first to start it was the Public Library of Science (PLoS). This organization is committed to open access publishing that is free to everyone. The cost of publishing the papers are paid for by the researchers who publish in the journals. The concept of a “page charge” is not new. Most journals have them.

PLoS is committed to open distribution of research. They were smart when they started the venture. They knew that the only way such a venture could succeed is if they had great science there. So, a perusal of the Editorial Board shows respected scientists from many of the world’s top institutions. These are people who have published in Science and Nature, two of the most prestigious scientific journals.

At present PLoS publishes seven journals: PLoS Biology, Medicine, Computational Biology, Genetics, Pathogens, ONE, and Neglected Tropical Diseases. The PLoS journals have editorials and features in addition to the hard science articles.

There are other open access journals out there. You can find a directory here at the Directory of open access journals. At this directory you can get access to research in biology, chemistry, physics, health, as well as law and political science.

Additionally, some other journals, while not entirely open access have several articles each issue that are labeled open access. Most notably in this category is the Proceedings of the National Academy of Science of the USA (PNAS), which publishes many different types of science.

Granted, these are hard research articles. They’re not geared toward the lay public. They are written for other scientists. This is the scientific literature. But it’s out there for anyone to read. Think of it as a portal. You may not understand the papers (I don’t understand all the papers), but if parts of it are of interest, you can do more research on your own on the web about the topic.

I just think that everyone should know about this free resource to the knowledge of cutting edge science.

And just a note. While most of the other journals charge for access to their articles, many offer older articles in their journals for free online. For some, in as little as 6 months after publication the articles are available for free download. What's really cool about this is that some of the very old journals are getting all of their issues available digitally. This means you can read old science articles from the 19th century and early 20th century. Some are great fun. Nature hopes to have its entire archive digitized by early 2008. This means that articles from 1869 can be downloaded (but I don't know if access will be free). PNAS has free access back to 1915. So does the Journal of Bacteriology

So, we can read the cutting edge science and the history of science.

The Death Star is Approaching the Planet. The Death Star is ....Ah, just blast through the planet!

From a galaxy far far away….

So, the front page of my newspaper today tells of an article inside with new pictures of a galaxy releasing blasts of radiation energy that are attacking a nearby galaxy. Talk about a bad neighborhood…

But the pictures are fabulous, and the story amazingly cool!

Picture credit: A black hole jet at the center of a galaxy strikes the edge of another galaxy. Image Credit: X-ray: NASA/CXC/ CfA/D.Evans et al.; Optical/UV: NASA/ STScI; Radio: NSF/VLA/CfA/D.Evans et al., STFC/JBO/MERLIN

This study was released Monday by NASA. There are two galaxies in a system of space known as 3C321. The galaxies are 8.2 billion trillion miles from Earth. The system contains two galaxies quite close to each other (20,000 light years apart) that orbit around each other. Both have black holes in their centers. One of the black holes is releasing a jet of energy that is shooting into the other galaxy. One of the study’s authors, Daniel Evans of the Harvard-Smithsonian Center for Astrophysics, is calling it the “Death Star” galaxy. (If you haven’t seen Star Wars, run don’t walk, to the video store).

The jets of energy are composed of high amounts of X-rays and gamma rays, which can be lethal in high quantities. And in this case, we’re talking about super-high quantities emanating from a black hole. The ozone layer of a planet could be obliterated if it came into the path of one of these jets of energy. It could probably sterilize all life on the planet.

One of the goals of astrophysical research is to learn more about these jets in the study of black holes. They are apparently not uncommon. What is uncommon is to have visual evidence of a jet affecting directly another galaxy. (aside: Hmmm, I thought that nothing could escape a black hole, so what is the nature of this type of energy that it can be released from something that can trap light energy? Anyone know? I’ll have to read up on this)

The effect of this jet on the neighbor galaxy is probably huge. In the long term, however (and we’re talking several million years now), the result of this onslaught on the receiver galaxy could be the formation of new stars and planets.

It’s all a cycle, isn’t it? Destroy what’s there, and something else grows to take its place. It’s like an intergalactic version of the Las Vegas Strip.

(Additional information and images are available at:
http://www.nasa.gov/chandra/ and http://chandra.harvard.edu/)

The Launch

So what is "The Science of Things?" Well, it depends on the science, and it depends on the thing.

I'm hoping to use this space to bring up some happenings in the science world that I find of unique interest (i.e., very cool). Also, I hope to bring out issues about science education and literacy for attention.

I think that adults have less attention for science in our fast-paced world. This leads to a society with less aptitude for science, less knowledge of science, and a basic ignorance of science. I think that the general population really does not have a grasp on “how science is done.”

Adults ignore the science pages in their newspaper (if their newspaper still has one), the science section on their internet news sites, and the science story on the evening news. Or science is given as a sound bite: This drug causes cancer, this food is bad for you, this food is good for you, too much coffee is bad, coffee is good, scientists found a treatment for baldness that works in mice.......

What does a mouse have anything to do with me? And why do I have to stop drinking coffee? I really like coffee.

Maybe our general discontent begins in our education system, and how science is taught in schools. Possibly most people think of it as a mass of facts they have to memorize. Granted, there is some of that, but at its most basic, science is the observation of our surrounding world. Observation should be encouraged. A simple hike in the woods can open the door to questions that could fill thousands of Ph.D. theses. All that is required is curiosity—simple questions that start with “Why…” or “How…”

Well, I’m curious. I’m also a scientist. And I don’t think that we communicate very well with non-scientists. We have trouble sharing our own work and interests as well as the scientific process to people who don’t think about it on a daily basis. This separation leads to mistrust, doubt, and allegations of lack of respect for non-scientists.

How do scientists “do science?” It’s a process—a way of thought, deductive reasoning, and observation.

So, this blog. I want to point out some happenings in science that are of interest to me. It is my blog after all. I also want to shed some light on the scientific process. How is science done? What is the process of deduction, and how to design a simple experiment? To use a common phrase, it’s not rocket science. It’s really basic logic. And last but not least in this evolving blog experiment, I want to explore issues of science literacy and science education. After all, the current generation must educate the next. The next generation should be at least as prepared as I was (and frankly, I’m pretty satisfied with my public school education as a whole).

And finally, science is FUN. There is a lot of coolness out there, and a science geek/nerd like me should be able to point some of it out to you. If I simply manage to describe something that makes you go, “Hmmm. Wow…” then my experiment is a success.

Finally, bear with me. I want the audience for this blog to be scientists and non-scientists. I will try to maintain a balance that will be of interest to both.