Wednesday, April 21, 2010

Earth Day #2: Energy & Oil

Ok, so we mentioned that energy concerns, especially peak oil, are very important topics right now.  A fellow blogger, John L. Clark, has written an interesting piece that explains some of the interdependence of oil, population and consumption, and also has some ideas about what the average citizen can do to address these concerns.   

There's also a book that I'd like to recommend that gives a very good overview about sustainable energy.  It's called Sustainable Energy Without the Hot Air, by David MacKay.  I really like this, because it's got a lot of good information.  I'd recommend starting with the 10 page (pdf download) summary  and then go on to the main book, found here.

Don't be thrown off by the website. It's useful, because it helps the online reader navigate sections of the book, which doesn't have to be read sequentially. I'd recommend starting at Chapter 23, "Sustainable Fossil Fuels" because it talks about coal, which is the next consideration after oil.  Also, a Gt is a gigaton (2 billion pounds, or the curb weight of about 400,000 Hummers.)

Windmill, courtesy of Storm Crypt

Monday, April 19, 2010

Earth Day!

April 22, 2010 is Earth Day, and in honor of that, we're going to have some posts about the environment.  This is more of the application and effects of science rather than the research, so hopefully it will be a fun series. 

First, there's the history of Earth Day.  This was started about 40 years ago by Gaylord Nelson, a Senator from Wisconsin who wanted to call attention to environmental issues.  He believed that grass-roots activities like the ones used by Vietnam protesters provided excellent models that he could use. So in the fall of 1969 he announced that there would be a grass-roots demonstration in the upcoming spring.  During the winter, people called, wrote and sent telegrams about their concerns.  (Yes, the telegram, and no snickering. The world wide web was just California and Utah in '69, and email wasn't going to show up for another 2 years.)  It was a big success: the first Earth Day was on April 22, 1970, and was celebrated by about 20 million people in the US.

How do we use the Earth?

Monday, April 12, 2010

Citizen Scientists

There's an article in Nature magazine that talks about the problems with thinking of science education as only a classroom-based activity.  The big issue is that funding and policy initiatives tend to be limited to grade-level specific education.  This is important, but with the rise of the internet, there's a lot of good-quality, easily accessible content, which results in more people being self-taught about science, rather than from formal classroom study.

There are mixed feelings about this. On one hand, self-directed learning eliminates the big complaint about the classroom: in school you can't always learn what interests you, or learn things at the same time you'll need to use them.  So a Google search on how to build skateboard parks tends to be more interesting to people than sitting through an introductory Physics course, even though both involve the classic problems of inclined planes and sliding blocks.  Also, by using informal tools of education, people can learn about a topic at the time they need it, not just during a brief slice of their academic year.

However, one concern is that there's less attention to strengthening the informal learning communities.  While every child is (supposed to be) guaranteed a public education in the classroom, places that reinforce this learning, like museums, libraries, parks and activity centers are losing funding.  This may mean that self-directed learners only find their communities online, instead of with their neighbors.

Also, while there is a lot of content available to people, there are still questions about what is "good" content?  Who is a valid authority?  What makes a reliable study?  How is this information relevant or useful?  An example of this misunderstanding was when the advocacy of high-profile celebrities implicating the MMR vaccine to the rise in autism was influential in fostering negative public opinion towards vaccines in general.  So in spite of the dissent among researchers, and the fact that the original MMR-autism study was discredited, the rates of MMR vaccinations dropped in the past decade, leading to spikes in measles outbreaks and serious policy concerns

The Nature article has an even bigger question for informal learning: "how do people integrate the disparate pieces of knowledge they acquired at different times and places? And how can anyone assess the overall outcome?"  Their suggestions are to create more partnerships between regular people and community resources, or to pair schools with existing science and research centers. 

I think these are great ideas, and I'd also like to see policy initiatives that are actually geared to teach the non-student how to screen and use the huge amount of scientific literature that's so easily available.  We already do this with our diets by using the Food Pyramid, and it works very well. I think a great idea would be an easily-understood, highly-broadcast diagram that would show people the basics of science literacy:  how to read a chart, how to distinguish between sources, what's the math behind scientific studies, or how to read a journal.  What about you?  Where do you learn about science, and how would you improve it if you could?

Photo Credits:  Law_Keven, Flickr.

Friday, April 9, 2010

The Genome - Going from Letters to Words, Part 1

Let's start with a quick review of our earlier discussions on DNA/RNA.   We said that DNA is our master blueprint, and RNA is like a copy of those instructions that goes to the builders.  We briefly distinguished DNA from RNA by how their sugars are different:  DNA uses deoxyribose and RNA uses ribose. We also said that nucleotides are used to make both molecules, and we discussed how in both cases, the nucleotides are arranged in linear strands, like beads on a string.  We compared the DNA structure to a set of line dancers: one line holding hands with the left and right dancers, and standing opposite their partners.  In DNA there are connections between the two strands, which cause the winding and characteristic double helix form.

This is a picture like the last one we saw.  We can see that the A (adenine) always pairs to T (thymine) and the G (guanine) to C (cytosine).  It's like our line dancers are forced to always choose certain partners to dance with.  In DNA, this forced interaction is because of the bonding between facing pairs: these are the light dashes between the nucleotides.  These are hydrogen bonds between the electronegative (electron withdrawing) nitrogens and oxygens, and the hydrogens on their faced partners.  This is a much weaker kind of bonding than what happens between the side-by-side neighbors (about 1/10th the strength) but these bonds are strong enough to stabilize the structure.  Anytime a structure, how it's bent/shaped or it's position to another object is stabilized, it costs energy to have it not be that way. It's like taking the pacifier away from the baby -- there's a price to pay.  In general, Nature spends energy reluctantly: lower energy means something is more likely to occur. 

So now we have our dancers in two lines facing each other, like a bunch of middle-schoolers in 6th period gym.  For the sake of this example, the kids are named after each nucleotide (so we've got a room of kids, but just 4 names among them.)  Their teacher, Mr. Chargaff, puts them in Group 1 and Group 2, and tells each group to stand in line.  Then he tells them they have to pick partners from the opposite group, and the same partners each time.   What does he tell the substitute teacher to worry about?  What can she gloss over?

The Influence of Primary Structure
Chargraff's rules tell us that all we need to worry about is lining up one line of kids. Once we have that figured out, the position of the other children is automatically enforced.   So if the Group 1 kids are lined up as:

A, T, C, C, G, A; then their partners will line themselves up as
T, A, G, G, C, T, and vice versa.

If the Group 1 kids line up as C, T, C, C, A, A;
then their partners line up as  G, A, G, G, T,  T.

So we only need to get one group of kids organized, and the other kids do the work for us.  The genetic code works in a similar fashion: once we know the line up of one strand, the second strand is precisely defined.  RNA exploits this effect -- it's generally single stranded, which is all that's needed to make an accurate copy of the DNA master print.

So we have a line up of nucleotides.  Where does that get us?

How Robots are like Hamburgers

Monday, March 22, 2010

When Charts are More Confusing Than Helpful

Here's an interesting article from Stubborn Mule about why 3-D charts can be misleading. I was going to use one of these charts for the post about making food choices (When Bad Things Make Sense), so I thought this would be interesting.

Here's the chart:
I really liked this chart when I first saw it.  But can you see the problem here?

The Basics of DNA and RNA:

What's DNA?
This gives us all the information on how to make our cells.  It's like a genetic blueprint, used to synthesize proteins and other molecules. 

What's RNA? 
RNA is the copy of the blueprint that goes to the building crew.  DNA isn't directly read to make proteins, so RNA is used as the copy.  The process of making an RNA copy of DNA is called transcription, and the process of making a protein from RNA is called translation.  The RNA uses a protein called a ribosome to actually manufacture the protein. So the DNA is the master design, the RNA is the blueprint copy,  and the ribosome is the work crew that assembles the protein.

What cats can teach us about our genes

Friday, March 19, 2010

Writing and Social Media

It's a romantic image, but things are a bit different now. In the internet age, there's no delay between when something is written and when it's available for the world to see, and there's no knowing who those readers will be. But with so much content available, how do you drive a reader to your site? There are a few common tools out there to make your blog more accessible, and we'll talk about a few today.

Facebook and Twitter
I am probably the last person on the planet to use these applications. When I see people, I see them face to face, and I just yell when I want to talk to my friends long-distance. But writing is a different story: you can't just collar someone in the hallway and make them read your post about the genome. Luckily, there's a trick for any internet slowpokes out there:


This week, we'll be taking a diversion and discussing how genes work. So the topics will include the basics of gene transcription, translation and splicing. There's some interesting work on gene therapies and so we'll develop the vocabulary to discuss these issues.

Tuesday, March 9, 2010

When Bad Things Make Sense

It looks like Philadelphia is taking a very strong stance by proposing legislation to add a soda tax of $0.02/beverage ounce. This appears to be the biggest tax initiative so far, with the rationale that the tax will act as a deterrent, or at least will fund the care needed for health issues related from these foods. On the surface, a sin tax may seem like a good idea, but there are a few huge problems that undercut the usefulness of this legislation.

One is cheap, but the other is good for you.
The first issue is the everyday cost difference between nutritious and junk foods. Junk food is cheap. It's cheap to make, cheap to ship and store. And because junk food also tends to be high in calories, the cost/consumed energy is lower than that of something more healthful.

One reason is due to politics. Industries like dairy, meat, corn, and grain are heavily subsidized, much more so than fruit and vegetable crops. And while all foods incur transportation costs, fresh foods need careful refrigeration, handling and limited storage times to prevent spoilage. Processed foods can avoid these extra costs, which also keeps the prices low. This chart shows the cost difference between foods like fruits and cookies. The healthful foods have gotten more expensive over time, while the cost of bad-choices food drops.

(the data is U.S. Bureau of Labor Statistics, and the chart was made by David Leonhardt of the New York Times, from the May 20, 2009, article "What’s Wrong With This Chart?")

We used the words "bad-choices food", but sometimes the unhealthy option is the best option or "least-bad" decision. This is when the cost just to eat is really difficult to manage. According to Feeding America, the largest domestic hunger-relief charity, there has been a 46% increase in the number of families that have needed food aid within the past 4 years. And the hallmark of junk food is that it's low in nutrients, but high in calories. If you're poor, really poor, and it's hard just to purchase food, then that cheap, but calorie-laden gallon of Sunny-D is a better buy than the half-gallon of orange juice.

What the ghetto and the country have in common.
The second problem is when money isn't the barrier. Depending on where you live, you may not have access to fresh fruits and vegetables, because there aren't grocery stores in your neighborbood. This is called a "food desert" and it occurs when an area has no supermarkets, or easily-accessible public transportation to get to a store. If you're young, healthy, or have access to a car, then the lack of a real store in your area is an inconvenience. But when you're elderly, disabled, or even working a few jobs to stay afloat, then it becomes very difficult to eat a healthful meal from the food at the local convenience store. These stores, especially the franchise ones, tend to stock more processed and canned goods than fresh, which means more added sugars or salts used as preservatives. Also, because of limited shelf space, the fresh food that is there is higher than in the regular store. It's expensive to be poor, and families both in urban and rural areas are affected.

Who benefits?
There's a definite correlation between food choices and health issues like Type II diabetes and obesity. But because income levels also track these problems, increasing food costs needs to be carefully considered. Philadelphia's proposal taxes the bad foods, but only earmarks 1/3 of the revenue for health related issues -- the bulk of the proceeds will go to the city's general funds. Hopefully this will allow the city to address the surrounding issues that drive people's food choices, because it's not always irresponsibility that puts junk food in the pantry.

Saturday, March 6, 2010

The Big Job of the Small Intestine

Previously, we left our hypothetical meal in a semi-digested state, just ready to leave the stomach for the small intestine. That image may seem unappealing to our brains, but to our bodies, this is just perfect.

The intestine is made up of two components: the small intestine, which starts at the stomach, and connects to the large intestine, which ends at the anus. The small intestine is broken up into main sections. The first section is the duodenum, which completes the job of breaking down food by combining the stomach's contents with enzymes secreted by the pancreas and the gallbladder. The second section has two parts: the jejunum and the ilium, and they are used to absorb the nutrients and fats left from food digestion.

Because each section has different roles, they have slightly different makeups. The entire intestine has a sheath of smooth muscle which is lined by a mucosal layer. The mucosal layer is the site of nutrient absorption, so it needs as much surface area as possible. As a result, the interior layer is highly textured, almost like ruffled fabric and the entire surface is covered in tiny projections called villi. The villi act like little toll-booths, bringing the nutrients from the interitor intestinal space into the bloodstream.

Word Nerd fact: the word "duodenum" references it's length. The term comes from the Latin word "duodecim", which means "12" (duo = two, decim = 10). This was used because the breadth of twelve fingers is the approximate length of the duodenum, which is 25 cm. They must have used a big guy for that measurement: I needed 3 extra fingers to get the same length.

A Schematic of Glycolysis

Friday, March 5, 2010

It All Goes Straight to the Hips

With all the talk about sugars and obesity, what's the direct relationship? We know the basics: eat more calories than you burn, and you gain weight. And we know how to burn calories. But how does the food get turned into fuel?

The First Steps
The digestion process begins in the mouth. Saliva breaks down starch into maltose sugars using the enzyme amylase, and the enzyme lipsase breaks down fats into the constituent fatty acids and glycerol. The food travels from the mouth to the stomach, where 4 main gastric enzymes break down the food into smaller molecules.

The first set of gastric enzymes is similar to those found in saliva: these are the lipases and amylases, that break down fats and starches. However, the stomach also contains proteases which break down proteins and gelatins/collagens into amino acids and peptides.

From the Outside to the Inside
Because the digestive tract (mouth, stomach, intestine, anus) is connected by a sphincters, it can be seen as a long pipeline, with an opening at either end. So how do nutrients get to the organs and muscles, and how does the excess get stored as fuel?

The key here is the actual lining of the pipes. The entire digestive canal has an interior membrane, but it has different properties in each organ. In the mouth, and throat, the membranes are for protection, and don't have any digestive properties. They act as a shunt to take the food to the major digestive sites: the stomach and the intestine.

The lining of these organs take a more active role in food digestion. The stomach's epithelial layer contains glands that secrete proteases, bacteria-killing gastric acids, and a thick mucous that protects the stomach from the acids. Underneath this lining is a sheet of smooth muscle, which allows the stomach to churn it's contents, exposing your food to the different enzymes. When the food finally exits the stomach for the intestine, it's been broken down to peptides, amino acids, fatty acids and glycerols.

Later, we'll discuss how the intestine takes these small molecules and uses it for the body's needs.

Image: Wikipedia

The Lunchlady Goes to War

Recently, First Lady Michelle Obama has spoken about the dangers of childhood obesity in her new initiative: Let's Move. This program attempts to improve childhood health by targeting the main staple of childhood meals: the school lunch. Under the new initiative, school lunch programs are asked to reduce sugars, fats and salt within 5 years, and increase both whole grains and produce within 10 years.

The focus on school lunches isn't limited to the White House. Across the pond, celebrity chef Jamie Oliver has also helped reform the school lunch in an attack against childhood obesity. His program "Feed Me Better" in Greenwich, UK public schools replaced the fast-food style lunches with ones more like home cooking. His efforts have brought him here to the US, with a Food Revolution campaign designed to revamp the food in our public schools. So kids and their school lunches

But what is the link between what kids are eating at school and their weights?

The nutritional requirements of children's lunches are given by the USDA, which also provides sample recipes and menus. An average lunch in my school district is straightforward: proteins are fishsticks, beef patties and turkey dogs. Vegetables are potato rounds, corn, carrots and peas. Dessert is some kind of fruit product, either applesauces, fruit cups or gelatin-molds. The beverages are white, chocolate or strawberry milk.

The Benefit of Stale Bread

On the surface, the USDA menus seem kid-friendly (except for the peas) but there is an aspect of these foods that make it less healthful than what it should be. When food is made at home, from scratch, we use things like common, household items that taste good, but don't hold up for long term storage. So when the cookies get stale, we bake more. Commercially produced food has to withstand transportation and longer shelf-lives, so substitutions are made to keep the food fresh. So while Grandpa's burger-bun recipe calls for plain flour, water and yeast, Grandma's Burger-Buns (TM) have corn solids, corn syrups, vegetable oils and extra sugars to keep the food moist and tasty.

Similar additions are made in kid-favorites like ketchup, spaghetti sauces, and in the flavor packets of prepared spice mixes. They also boost the flavors in non-sweet foods like crackers, as well as sweet foods like yogurts and flavored milks. So even when a child is avoiding the classic junk food like chips and candy bars, fats and sugars appear in the diet. By boosting the amount of basic and unrefined foods like whole grains, fruits and vegetables, there's less room in the diet for high-calorie, low nutrient meals.

Starting in the Cafeteria

Because children spend both breakfast and lunchtimes at school, a key way to improve their diets is to focus on the meals taken there, rather than at home. Mrs. Obama's proposal is backed by the Institute of Medicine (IOM), which also wants to address the socioeconomic links between food and obesity by adding more children to federally-funded lunch programs, and increasing the money invested in these programs to improve the overall diet.

Another target is the advertising and accessibility of junk foods in schools. According to a PBS report in 2000, approximately 98% of high schools had vending machines in schools, and of all schools with vending machines, more than 75% sold soft drinks, while only about 55% sold fruit or vegetable juices. Also, because the schools contract to have the machines, snack-food vendors are allowed to advertise in schools, in exchange for the proceeds off of the vending machine sales. This helps create brand loyalty among the students, so they're more likely to choose the processed snack foods and soft drinks instead of regular foods. This puts lower-income schools at a higher risk, because they're more likely to need the additional revenue from the vending machine sales. Kids in these districts are also more likely to be enrolled in the school's lunch program, so poor food availability has a greater effect on them.

Some school districts, like in New York City, have already taken action by replacing high-fat, sugary snacks in vending machines with lower-fat and sugar treats, and by banning regular bake sales. Other schools, like those in the Los Angeles school districts, have taken stronger measures by banning vending machines altogether. Hopefully, the combined approach of eliminating unnecessary foods and providing better alternatives will reduce the trend towards obesity in the schools.

image is from SpecialKRB: / CC BY-ND 2.0

Monday, March 1, 2010

Fructose and Obesity

In the United States, fructose-sweetened products have a lot of commercial advantages over sugar. Unlike sucrose, which comes primarily from sugar cane or beets, fructose comes from a variety of plant sources, like fruit, and sweet vegetables like carrots and corn.

This variety is what gives fructose it's main advantage: it's cheaper to use surplus corn crops instead of importing sugar cane or beets. And because fructose is processed as the plain syrup, it eliminates sugar's additional costs of dissolving and reconstituting into a particular viscosity.

Fructose is also very sweet, with nearly twice the sweetening ability as regular sugar. This also drives down the cost, as it allows the manufacturers to use less fructose by volume than sucrose.

As a result, fuctose is ubiquitous, making up approximately 9% of the American diet.

So what's the problem?

The first concern with fructose over sugar is it's correlation to obesity. Unlike sugar, fructose doesn't need insulin in order to be metabolized by the body. This might be useful, especially for those who are insulin-resistant, but insulin regulates the body's secretion of leptin, a hormone that signals the body into feeling satisfied after eating. With this cue removed, we eat more, even when our bodies have reached their caloric requirements. The result is increased weight gain.


Wednesday, February 17, 2010

Sweet Things!

This month, we’re going to discuss all things sweet and sugary. This week’s topic is high fructose corn syrup.

High fructose corn syrup is the major sweetener used in commercially made food. However, there some controversy about the safety, efficacy, necessity and even taste of this common product. This is the first article in a series that discusses the science behind the metabolism, flavor, and use of this food (by product? That seemed inflammatory.)

First, the actual food itself. Sucrose, which is plain table sugar, is a dual-sugar molecule, a disaccharide, made of one molecule each of fructose and glucose. Fructose is the common sugar found in fruit or pure fruit juices, and glucose is the sugar produced by our bodies. So common sugar has a 50:50 ratio of fructose to glucose. High fructose is a mix of the sugars with a greater percentage of fructose: in a ratio of approximately 55:45.

Increased fructose consumption is linked with increased risks of type 2 diabetes and obesity. This is due to the way that fructose bypasses the body’s need to use insulin to metabolize the ingested sugar. Also, because fructose reduces the amount of leptin produced, the body is less apt to feel satisfied when consuming foods with more fructose than glucose. However, we use sucrose, which combines the two sugars. Does this mean that a foods with the 5% extra fructose are worse for us overall?

Finally, why do we even like sugars? What mechanisms does our body and brain use to determine what tastes sweet and why we enjoy it? How does the presence of sugar, and especially this kind of sugar, change the way we eat and why? We’ll discuss all of these topics over the next few days.

Part 2: Glucose, Fructose and Insulin

Part 3: Leptin, Aldosterone, and Bikini Season

Part 4: The Difference Between Bread and Cake, Bone and Tendon: How Sugars Work in our Bodies.

Saturday, January 9, 2010

About This Blog

The purpose of Coffee Break Science is to increase science literacy, knowledge and interest about various health issues. This blog is not intended to supplant the advice of your health care provider.