Monthly Archives: November 2013

The Scientific Method (Plus Ponies)

I am a bad teacher, everyone. Absolutely terrible. For there is one topic with which I should have covered in my very first post. A topic that is essential for the study of science but has universal applicability. I am referring to the Scientific Method (which I am going to put in capitols cause it is just that important).

Besides providing a framework for research in the hard sciences (biology, physics, chemistry, etc) the Scientific Method is applicable in many other, squishier sciences (psychology, sociology, etc). Furthermore, an understanding of it can help you think critically in everyday life.

First step is asking a question. This can be just about anything. How much blood is in my body? What stressors affect protein formation? Are ponies ticklish? This step is the “get the juices flowing” step. It doesn’t need to be very specific, but it should be asking a question for which you don’t already know the answer.

Now you do some research. Read up on your topic; articles on past experiments, textbooks, anything. Just get a feel for what is already known. This will refine (or possibly change) your topic, narrowing the focus until you have a manageable chunk to work with. It should also lead you to…

…your hypothesis! Any science teacher will start off by explaining that this should be an “if…then…” statement. Not a question, or a suggestion, a STATEMENT. With your background research you should know what you want to do and have an idea of what will happen. “If I tickle the pony, then it will twitch and whinny; displaying ticklishness.” HOWEVER, the statement does not necessarily need to include the words “if” and “then”. But it should be implied. Some hypotheses are also very long statements and can get cumbersome if you’re a stickler about the “if…then…” phrasing. For instance, I could write my pony hypothesis like this: “By rapidly scratching a pony behind the foreleg, I will induce an immediate, impulsive twitch and excited whinny, as a result of the pony’s ticklishness.” Same hypothesis, but different phrasing. It also has a better explanation of what I plan to do next.

That next step is the experiment! This is the good part; it’s where the action is. Your research should have helped you develop an experimental plan and some of it was explained in your hypothesis. You will have independent variables (variables you have control over, such as pony tickling) and dependent variables (variables in response to the independent variables, like pony whinnies). A good experiment should also consider different factors that are potentially influencing your subject (EX. could the pony be reacting to pests or other ponies?) and address them. Compare these factors separately (EX. Observe pony’s response to flies in isolation vs. response to other ponies sans flies) and ALWAYS include a control (Ex. Observe pony in isolation without any stimulus). Every experiment needs a control to show the significance of the response to your independent variable. If I tickle a pony and it twitches and whinnies I can show doesn’t do so in response to any other kinds of stimulus, I do not have good results until I can prove that ponies do not just twitch and whinny spontaneously. Furthermore, I need a large enough sample size to prove this is typical pony behavior. If I just choose one or even five or ten ponies, those samples are too small to be considered representative. They could all just be weird ponies. So pick a sample that’s large enough to represent to population in question, but easy enough to manage experimentally (100 ponies out of a 400 pony herd would be representative and manageable). Deciding on a sample size is difficult, not only should it be as large as possible, but also random (to prevent selection bias). I could pick out 100 ponies to sample, but if I didn’t draw the names out of a hat, or something, someone reading my paper could say I picked ponies based on their ability to confirm my hypothesis.

Now my pony example is great for many experiments in biology, but how does this translate to subjects in which you do not sample clearly individual things? Samples can be a given volume or mass of a substance. An experiment in water quality may use multiples vials (of the same volume) of water and the number of vials would be the sample size. In chemistry, the sample size may be the number of trials you perform (say, distilling samples of a certain chemical multiple times).

Once you’ve sampled enough/repeated the experiment enough times, you can analyze your results. Use appropriate statistical tests to compare the results of from testing each independent variable and the control. Find their significance. Does this support or destroy your hypothesis? Additionally, was there anything that could have affected results? How well were variables controlled? Was there something you only realize now you should have tested? Explain.

Finally you can report your results. Tell the world what you found! But tell them everything. Show your raw data, your statistical test results, photos of your experimental set up, explain your methods, your background research, EVERYTHING. If you leave things out, this weakens the strength of your conclusions. It looks like you’re hiding something. Even explain the weaknesses of the experiment or potential problems with results. Especially if you can explain why you didn’t do this or that thing (EX. did not observe response of ponies to non-fly bugs because none were present around the herd). Maybe explain that you realize there’s an experiment you can do as background research for the topic as a whole. Admitting weaknesses, particularly if you’re going to follow up on them, can only give you more credibility as a scientist. It also allows other researchers to follow your lead, researching related topics with your suggested improvements.

Understanding the Scientific Method helps you understand new research and see how trustworthy it is even if you’re not a scientist.

Here’s a little life example: In 2005, some folks decided to see how reptiles and amphibians react to microgravity. I kid you not, they sent 53 snakes, lizards and frogs into a parabolic flight to see what they’d do during the zero gravity portion of the flight (sorry, no actual herps in space). It sounds hilarious (and looks hilarious, I’ll post the videos if I can find them) but it also answers a very interesting question about how these animals orient themselves in relation to gravity. The analysis was also very thoughtful, regarding explanations for behavior, lifestyles of each species &etc. But these were only 53 animals from 23 different species and there are thousands of reptile species in the world. Also, only random in the sense that they used whatever they could get their hands on for the experiment. Some regard for a balance of snakes vs. lizards vs. amphibians, but they were restricted by what they could access for the experiment. All in all it was a great idea, with great reporting, a good set up, but a weak sample and thus weak results. But even though you can’t trust the results, you can see how to repeat and improve upon this experiment. Future snakes in space!

Of course, you can also use the Scientific Method in everyday life. Reading the news or looking at a new product, you know to consider where assertions or statistics came from and how they were collected. Maybe it’s not necessary for everything you hear or learn, but isn’t it empowering to know HOW to trust what you hear and learn? To be serious for once (I know, HEAVEN FORBID), I think true intelligence is based less on education, than inquisitiveness. Just that. Want to know more and wanting to know what exactly you do not know. Never let anyone tell you you’re dumb for asking a legitimate question. How else will you learn?

And now, because I can’t sustain the serious, a pony in a sweater:

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Sources

Wassersug, Richard J, Lesley Roberts, Jenny Gimian, Elizabeth Hughes, Ryan Sanders, Darren Devison, Jonathan Woodbury and James C O’Reilly. 2005. The behavioral responses of amphibians and reptiles to microgravity on parabolic flights. Zoology 108(2):107-20.

Photo credit McDougall, Rob. 2013. “Shetland Ponies Wearing Fair Isle Cardigans”. Rob McDougall, Photographer and Filmmaker. 22 November, 2013. < http://robmcdougall.com/recentjan2013.html&gt;

Sweet, Sweet Succes(ful Regulation of Blood Glucose)

I hope you all have been good little boys and girls and grown man/woman-children, because as promised I am going to explain blood glucose regulation. Bad children are temporarily banned from learning. Don’t even try to keep reading. You don’t want to know the punishment.

Anyway, first of all, take a look at this cake:

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LOOK AT IT.

 

We shall be considering this masterpiece of sweet, sweet heaven (courtesy of Stephanie Michaelis at Raspberri Cupcakes) for the rest of my post. Additionally, we have two scenarios: eat the cake and gaze longingly at photos of/not eating the cake.

Now, let’s imagine we get to eat some of this colorful, culinary delight. After some digestion, the pancreas recognizes the resulting increase in blood glucose. The pancreas has exocrine (secretes chemicals such as alkaline solution and digestive enzymes via ducts) and endocrine (secretes hormones directly into the bloodstream) tissues. Within the endocrine tissues are beta cells, the most abundant endocrine cell in the mammalian pancreas. Beta cells synthesize and secrete insulin in response to increased blood glucose. Insulin then travels to the liver and signals glycogenesis; the production of glycogen in skeletal muscle as well as the liver. Insulin will also inhibit gluconeogenesis (the production of glucose from molecules such as pyruvate or lactate) and facilitate glucose transport to cells. As a result, blood glucose will decrease to normal levels.

OK, back to reality. We do not get to eat the cake. We get to salivate with intense longing at the computer screen. We lose track of time. We forget to make a sandwich for lunch. Blood glucose drops. The pancreas detects this drop and other cells in its endocrine tissue, the alpha cells, produce and secrete glucagon into the bloodstream. Because the glucose…is GONE. Get it? Get it? Anyway, the liver receives this signal, glycogen production then decreases while glycogenolysis (glycogen break-down) increases along with gluconeogenesis. Blood glucose then increase to a more normal level.

Insulin and glucagon do not act exclusively of one another, with every spike and drop in blood glucose they work together to bring things back to normal. Of course, they can’t act instantly and can only go so far. For instance, Insulin would struggle if you inhaled an ENTIRE cake, while I can personally advise against long fasts if you want to do anything requiring focus like say…navigating Chicago by yourself on your first visit without passing out on the sidewalk on the way to the taxi. Those are bad life choices; spiking your blood glucose too high too often has long-term consequences and passing out on the sidewalk in a strange city has ALL the consequences.

So be street smart, carry snacks.

 

Source

Sherwood, Lauralee, Hillar Klandorf and Paul Yancey. 2005. Animal Physiology: From Genes to Organisms. Thomson Brookes/Cole, Belmont, CA.

 

Photo credit:

Michaelis, Stephanie. 2011. “Purple Ombre Sprinkles Cake.” Raspberri Cupcakes. 19 November, 2013 <http://www.raspberricupcakes.com/2011/11/purple-ombre-sprinkle-cake.html&gt;

Glucose Gets Up In the Club

Rather than go through the motions of profuse apology and promises to write more in future, let’s just say I was kidnapped by anti-science, anti-blog, anti-fun desert pirates and leave it at that? OK? OK.

Let’s say I ate a cookie. After all the business of masticating, saturating and dissolving said cookie, it comes time to absorb its nutrients. The bulk of this occurs in the small intestine, which is not only highly folded, but the inner surface is covered in small, finger-like projected villi), which in turn are covered in even smaller finger-like projections (microvilli). It is through these that I can absorb the various carbs and sugars this digested cookie has to offer. “But how?!” You ask. Well, I can explain! And later you can explain to me how I can hear you over the internet.

Anyway, you have all these nutrients hanging out in the lumen (the open space inside the intestine) of the small intestine that need to get from there to the blood stream. But first they have to get through the epithelial cells of the microvilli. They can’t simply diffuse (see here for a diffusion review), the concentration of nutrients within the epithelial cells is too high to allow diffusion. This is where membrane transport proteins come in handy. These are proteins embedded in the lipid bilayer of the cell that, through various means, transport molecules and ions from one side of the membrane to the other. In the small intestine in particular, there is a class of transporters called sodium-dependent secondary active transporters. These proteins use sodium to power the transport of various molecules such as carbs, sugars and amino acids into the epithelial cells of the microvilli. Although many work in similar ways, I’m going to use the sodium-glucose symporter as an example.

First off, let’s have a few definitions so that I don’t leave all y’all in the dust. Secondary active transport involves moving one molecule into a cell against its gradient by coupling it with another molecule or ion that is moving (into or out of the cell) with its gradient. So say you’re trying to get into a club, but the room is too full, so either a friend of yours leaves so that you can get in, or you have an assertive friend with you that drags you in whether there’s room or not. A protein/bouncer that allows that first example would be an antiporter (2+ molecules moved in opposite directions), while the second would be a symporter (2+ molecules moved in the same direction). In the case of the sodium glucose symporter, two sodium ions act as the pushy friend to get glucose into the hopping club that is the epithelial cell. Inside the cell there is a high concentration, but a low (and carefully maintained) concentration of sodium. Sodium’s movement down its gradient actually provides the energy to power glucose transport (or pay glucose’s cover, if you want to keep going with the club analogy).

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Yep, that is one hoppin’ club.

 

To get into the blood stream, the process is much simpler. Blood glucose concentration is much lower than that of the epithelial cell, so diffusion is very possible. HOWEVER, glucose still needs help. Dissolved in the cytosol of the epithelial cell, it is hydrated; surrounded by a little cage of water molecules that would need to be stripped on in order for the glucose to pass through the hydrophobic lipid bilayer. Not a terribly favorable reaction. As a result, GLUT-2 transport proteins act to facilitate diffusion into the blood stream. They provide a hyodrophilic environment for the glucose to pass through. Many membrane transporters act as catlysts in this way, lowering the “activation energy” of transport for molecule and ions (much like enzymes catalyzing reactions).

Now that the glucose is successfully transported, there’s just a little housekeeping left. A sodium-potassium ATPase antiporter brings in two potassium ions and boots out three sodium ions. Unlike the sodium-glucose symporter, this is an ATP powered pump. Elsewhere, potassium channels allow for diffusion of potassium ions into and out of the cell to maintain concentration gradients.

Tune in next time and maybe I will explain how blood glucose levels are regulated.

But only if you’re all very good.

So watch it.

 

Source

Sholders, Aaron. “Types of Membrane Transport”. Principles of Biochemistry. Great River Technologies. 2013. eBook.

Sholders, Aaron. “Membrane Transport”. Biochemistry. Colorado State University. Fort Collins, CO. Jan 2013. Lecture

 

Photo credit: Sholders, Aaron. “Types of Membrane Transport”. Principles of Biochemistry. Great River Technologies. 2013. eBook.