A Day in the Life of Tom the Carbon Atom

Honors Biology Times

Friday, December 07, 2012

By Stu D’ent

In the dawn of time, there was nothing. Then there was a single carbon atom, alone in the Universe. His name was Tom.

Tom was part of a carbon dioxide molecule floating alone in the atmosphere. But, billions of years later, you’ll find that Tom’s life has become much more exciting. Now he is an integral part of the carbon cycle and the palm of my hand.

We here at Honors Biology Times had the opportunity to meet Tom over coffee.

Honors Biology Times (HBT): Hello, Tom. Do you have a last name?

Tom…something (T): Hi there. And the name is Tom. Just Tom.

HBT: I apologize. Well, can you describe to me just how the Carbon Cycle works?

Tom, just Tom (TJT): I am quite sorry, but I don’t actually know how it works.

HBT: What do you do every day?

TJT: Oh, you know the usual. I wake up in the morn-

HBT: Tell me about what happens once you get to work.

TJT: Oh, okay! It’s actually kind of hard to explain. Would you mind if I just show you an educational documentary on it instead? It was narrated by Morgan Freeman.

HBT: That’s not actually how an interview works. It’s more of a Q&A sort of thing…Maybe another time?

HBT: Why don’t you tell me about the first step of the Carbon Cycle?

TJT: The Carbon Cycle is actually a really difficult and complicated process. That’s why they pay me the big bucks.

HBT: I didn’t realize it was a paid gig. But let’s get back to the topic.

             

TJT: I can tell you about my simplest transfer, how about that?

HBT: Yes, please. That’s why we’re here. Just…you’re wasting my valuable time. Please enlighten me with a description of your simplest transfer.

TJT: It all starts with the sun.

HBT: Doesn’t it always?

TJT: Why, yes, I suppose that is true. There was this one time when-

HBT: The transfer, Tom.

TJT: Right. So the sun shines on a plant and fuels photosynthesis. Then the plant uses the sun’s energy to convert CO₂ into organic material. That’s where I come in.

HBT: Great start. Now, who do you bond with to become carbon dioxide?

TJT: I like to form a carbon dioxide molecule with two of my oxygen buddies. They’re twins, Larry and Gary.

HBT: They sound like fun guys. Tell me about the conversion into an organic material. What’s that like?

TJT: The entire purpose of photosynthesis is to produce glucose, which I happen to be a part of as well. Basically, after Larry, Gary and I get together, we enter the Calvin Cycle. In the Calvin Cycle, we meet up with two other groups of folks we hang out with a lot: ATP and NADPH! They’re so great. Anyways, we all get together and from glucose (C₆H₁₂O₆). It’s pretty much a huge family reunion with the Carbon, Hydrogen and Oxygen clans all together. Got everything so far? You haven’t written anything.

HBT: Yes. It’s an interview, I’m recording it.

TJT: Recording it without paper? What are you, a magician?

HBT: Just keep telling the story.

TJT: The glucose enters glycolysis. Glycolysis is a part of cellular respiration, so we’re in a completely different process now. I hate glycolysis. Do you want to know why?

HBT: I have a feeling that you’ll tell me either way.

TJT: How do you know me so well? We just met?

HBT: They say I can read people.

TJT: I hate glycolysis because that’s when we get eaten. Have you ever seen the episode of The Magic School Bus when Arnold eats the school bus? It’s like that, but gooier.

HBT: Lovely.

TJT: Finally, I move throughout the biotic world as I move up the food chain. Remember how I started out in a plant? Imagine that plant was a blade of grass eaten by a cute, fluffy bunny. Next, I enter the bunny’s body. Bunnies aren’t as soft on the inside as they are on the outside, by the way. Eventually, I’ll reenter the atmosphere either through respiration or decomposition if the bunny dies without being eaten. And that’s a day in my life.

HBT: Wow, it sounds like you’re a pretty busy guy.

TJT: I can handle it.

HBT: I’m so glad you told me about all of this. I learned in Biology class a long time ago, so I’m glad you refreshed my memory.

TJT: I’m glad to have been invited here. I don’t often get invited places, people don’t really like me. And then there’s all of those environmentalists who think I’m killing the ozone and-

HBT: The interview’s over now, Tom.

TJT: Oh, okay.

HBT: Thank you.

TJT: No problem!

As you can see, the conversations I have with myself are quite interesting.

Into the Woods-November Plot Reflection

Yesterday was our November plot visit. Seeing as winter is nearly upon us, the weather was less than pleasant. It was gray and overcast with a steady, albeit light, rain. By the end of our visit, around noon, it was only 41 degrees (Fahrenheit).

Like the October visit, we could hear cars going by. Notably many more cars than the last visit. Also, since we are well into fall, nearly all of the trees are bare. Only a couple of stragglers and the evergreens still had their leaves. Another difference between November and October was the presence of animal sounds. Back in October, you could hear lots of birds chirping and leaves rustling. But yesterday, we heard nothing but the road. The plot was completely devoid of animal activity except for one spider and a squirrel Alexandre claims to have spotted. No one else saw or heard any evidence of a squirrel, so we can't be certain of even that.

Now, since the majority of the leaves are gone, visibility in the woods has grown to be much better. Our group can observe the surrounding land much better now. For instance, I noticed that there is a house about 40ft away from the plot. Also, there are more fallen logs and branches than there were before. They were all covered in various species of moss and lichen.

In addition to that, there were also two different species of shelf mushrooms present. However, they were the only type of mushroom present. Unlike in October there were no stereotypical "cap and stalk"mushrooms to be found beneath the ground cover in our plot. I wonder why that is. Like last time, we visited after a day of rain. It still rained while we were at the plot. Perhaps it is the change in temperature that determines the types of mushrooms we see?

Overall, I think that our group works really well together and we get along. This is shaping up to be a great project.

 

Cells R Us

In class on Tuesday, we constructed a life size model of a cell. Everyone in class created an organelle to make up part of the cell. I created the Golgi apparatus. The Golgi apparatus is where proteins are processed, sorted and delivered. It contains enzymes that make changes to the proteins. Some proteins are stored within the apparatus while others are sent to other organelles or outside of the cell entirely. The approximate real size of the Golgi apparatus is 10 um (micrometer). The magnified size of my model was 40 cm. I'm not sure what type of cell it was, considering that there were some organelles present that  were only found in animals, some only found in plants and some found in both. If I had to make a final guess, however, I'd guess that we built a plant cell, considering that one of the organelle's made was chloroplast. Since chloroplast only helps with photosynthesis, I'll guess that it was a plant cell. The largest organelles were the nucleus and Golgi apparatus, the smallest were the ribosomes and mitochondria. If I looked at a cell under a microscope, I'm certain that I'd be able to see the nucleus and possibly the Golgi apparatus. In order to see the really miniscule organelles, I'd have to use an electron microscope. I was surprised by exactly how small the ribosomes were, and the fact that the average amount of ribosomes in a cell is 15,000. I guess that, considering how small a cell is, I didn't think there would be something so tiny inside of it.

How pH affects Enzyme Activity Lab

We recently finished a lab observing Changes in Enzyme Activity. My group tested the effects of pH levels on enzyme activity. To do so, we cut three 1g slices of potatoes and put them in a test tube filled with 15mm of hydrogen peroxide. Then we poured in acid into one test tube, a base into another and water into yet another test tube. We then watched and measured the enzyme activity which could be observed by bubbles being produced on the potato. 

In the Changes in Enzyme Activity Lab, my lab group tested to see if pH affected enzyme activity. pH is the level of acidity in an object or its environment. We hypothesized that the pH would affect enzyme activity. I believed that a higher pH would increase enzyme activity. However, in our experiment, the test tube containing hydrochloric acid produced no bubbles at all. 

Some errors that our experiment had were that the amounts of water weren’t exactly the same and that the hydrogen peroxide levels weren’t the same on each potato. We sort of did a visual estimate when pouring the acid, base and water into each test tube. In the future, we could measure out each liquid before pouring it in. We could also use pieces of the same potato and make sure they all had the same amount of skin. Besides those somewhat conscious errors, I think everything else was under control.

Our investigation on enzymes could be applied to real life in a situation like acid reflux. Perhaps eating foods with a lower acidity could keep the condition in check. WE can manipulate enzymes in the environmental industry to benefit an ecosystem by creating/finding enzymes that would cancel out pollutant. Or find an enzyme that would make plants grow faster or produce more food when photosynthesizing.

Plot Reflection

In my honors biology class, we have begun a new project. We have been split into groups and have each chosen a plot in the forest to observe over the course of the next year. The groups consist of four or five members and each has a specific job to do. There are four possible roles: leader, photographer, naturalist and arborist. The leader is in charge of the group’s wiki-space page and delegating tasks to the group. The photographer takes a visual documentation of the environmental growth and changes in the plot over the course of the school year. They will photograph and take videos of both the creatures that live in the plot and the group hard at work. Eventually, the video clips and photographs will all be compiled into one film in the spring. It’s the naturalist’s job to record, collect and identify various organisms found in the surrounding area of the plot site. The arborist identifies the trees within the plot and measures the growth of the young trees. I am the leader of group number 4. Our group’s name is set, which means ‘3’ in Korean. The other group members are: Madeleine, the photographer; JB, the naturalist and Alexandre, the arborist.

We have plenty of trees for Alexandre to study. All the orange flags mark the baby trees.

Our plot site is the closest to the road out of all of the groups in our class. However, the road cannot be seen from our plot. What you can see is the gate separating the forest from the road. You can also clearly hear cars and trucks passing by. In our plot, there is a large, rotting, fallen tree. It is covered in moss and shelf mushrooms. A colony of ants lives within the log and eats the mushrooms. The ground is thick with dead leaves and acorns from the surrounding oak trees. The creatures hiding beneath the leaves mostly consist of large spiders and the occasional ant. Within in the center of the plot is a gathering of over 40 baby trees. All of the trees, both young and old, have leaves that have either fallen off or are living their last days. The day we visited the forest and staked out our plot was just after a plentiful rainfall. As we all know, that’s prime condition for mushrooms. We found some fascinating fungi, including a purple mushroom.  

One thing I really appreciate about this project is its longevity. I think that being able to actually watch the plot’s changes from autumn until spring will be incredible to observe. I love that we’ll be making a video at the end of the project that will serve as somewhat of a digital time capsule. Looking forward, I see my group’s biggest obstacles being organization, time and focus. However, if we continue on the path that we started on a couple days ago, this is going to be a great year.

Mushroom Madness

Chicken of the Woods similar to the one that we found.

During the mushroom foray that my group did, we walked around a trail that went past the cemetery. We found four mushrooms, but they were few and far between. I found this to be odd, since the conditions were great. It had rained nonstop for the past two days and wasn't too hot or cold. We found a chicken-of-the-woods mushroom.Chicken-of-the-woods are large, round and orange live shelf-like mushrooms that grow in clusters on dead trees. We also found another shelf-like mushroom growing on a tree. This one was white and soft. It had gills on the underside which, when touched, turned bright yellow. We believed it to be Cantharellus subalbidus (shown below), however it did not have a white spore print.

Cantharellus subalbidus commonly called the white chanterelle.

Something I found interesting about fungi is how useful they are. Fungi are decompose things, which helps clean the environment of dead and dying matter. The penicillin antibiotics are made from penicillin fungi. This is a huge benefit because penicillin can be used to treat pneumonia, scarlet fever, rheumatic fever, inflammatory heart disease and a multitude of other ailments. Mushrooms in particular are edible fungi. Some other examples of fungi are molds and single-celled yeasts. All fungi heterotrophic and have cell walls made of chitin.

When you are foraging for mushrooms and pick one, you aren't hurting the mushroom at all. In actuality, what you've picked is the mushroom's fruiting body, where it stores reproductive cells. The actual mushroom is called mycelium, which is a collection of long strands of hyphae, which are underground. Mushrooms are commonly found in forests. They grow on mosses, grasses, trees and decaying logs. They will often sprout 1-3 days after a good rain. An important note when collecting mushrooms is to make sure that you get the entire mushroom. This means you should bring along a shovel or trowel. That way, you not only collect the fruiting body, but the mycelia as well. Also, bring a basket so that when you walk through the woods, spores from your mushroom(s) will fall to the ground and grow new mushrooms.

Example of a Chicken of the Woods spore print.

When classifying mushrooms, it is important to note the color of the mushroom's spores. You'd do this by taking a spore print. Spore prints are conducted by cutting of a mushroom's stem, placing it gills/pores down on a piece of brown paper and putting a cup over it. In time, the spores will fall and you'll be able to see and identify them. Also, when conducting a mushroom foray, you can collect your spores in a paper bag so that they'll fall straight into the bag. The white shelf-like mushroom that we collected had brown spores and the chicken of the wood had a white spore print (see left). Spore prints are vital in making sure that you are correctly classifying your specimen.

When classifying mushrooms, you use a biological key(online key that we used). They can be found in a multitude of books and online keys. A helpful tip for when using a key of any kind is to read carefully. Make sure that you're not skimming, but reading every word carefully. Otherwise, you may mistake and edible mushroom for a poisonous one. My group had issues with being able to stick to the tedious process. There are hundreds of thousands of mushroom species and identifying them often takes a long time. It is very easy to misread a word or skip a step and classify your mushroom completely wrong.

Some take-away lessons I've learned from this experience are a) always have someone double check your work, fresh eyes can really make a difference and b) mushrooms have a lot more than meets the eye (literally). Don't pass up the opportunity to go on a mushroom foray simply because it doesn't sound like fun. I wasn't looking forward to it, but the experience ended up being very interesting. So, with that said, best wishes and happy mushroom hunting!

Yes, Birds Really Are Dinosaurs

After reading the article ”Are Bird Really Dinosaurs?”, I have come to realize that yes, modern day birds are the dinosaurs of our time. Paleontologists have determined that birds are avian dinosaurs and that birds have technically been categorized as reptiles. Birds are descendants of a maniraptoran dinosaur, much like a dromaeosaur. 

The evidence to this statement is overwhelming. Even as early as the 16^th century, biologists observed the incredible similarities between birds and “traditional” reptiles. In 1860, a fossil of an Archaeopteryx lithographica was found in Germany. The find was later deemed the “London specimen” and is a fantastic example of the evolutionary transition from traditional reptiles to birds. The Archaeopteryx is considered to be the oldest known bird. Ratite birds (kiwis, ostriches and emus) are extremely similar to theropod dinosaurs. In addition to that, the reptilian features of birds are numerous. Birds have scales on their feet and their feathers are produced by tissues similar to those of scales. Also, they lay eggs and have similar internal organs. Other similarities include: large orbits, elongated arms, forelimbs and clawed hands and hollow, thin-walled bones although there are a multitude of others. 

Some biologists disagree with this theory, although it is obvious that the evidence is too strong to properly dispute. Many of them claim that the gap in fossil record between the early Cretaceous and late Jurassic periods is too big to make any assumptions. Also, they note on the differences in anatomy which could all be related back to evolution. However, this does not disprove the idea of common ancestry. Also, there are no other possible avian ancestors to fill this void. Others argue that dinosaurs did not have feathers even though there is no evidence to prove or disprove that statement.

Overall, I am a strong believer in the idea that birds are modern-day dinosaurs. Although natural selection may have caused them to over time to become smaller and perhaps behave differently than their ancestors, there is no way to successfully challenge this explanation. Birds that live today have had over 150 million years to adapt and migrate, it is obvious that natural selection would have occurred. Features that birds have today most likely were not there, or were different 150 million years ago which shows clearly evolution in progress. However, the links between dinosaurs and birds are so numerous and strong that I think it is logical and likely that they share common ancestry.

Is it Alive? Investigation Reflection

In the Is it Alive? Experiment, we used many different types of biology available to biologists. We used microscopes, slides, cover slips, bromothymol blue and methylene blue. They definitely helped answer the question: is it made of cells? Also, they helped identify whether or not the unknown was converting energy. The bromothymol blue changed color which made it known that carbon dioxide was present while the methylene blue made it easier to see the cell walls. One problem that we encountered during our investigation was that we at first didn't think that our unknown was growing in soil, since growth is a long process. So, we had to wait and keep watching in order to see if anything would happen. I would have given us a longer period of time to watch our unknown grow. If we had that opportunity, we would've known it was a flower and possible which type of flower.

The independent variables in our investigation were the environments we tried to grow the unknown in: fresh and salt water, soil and sand. The dependent variables were the amount of growth shown in each environment. Our control for the experiment was the unknown left plainly in a plastic cup with nothing in it and no covers. The stimulus in our experiment was water. Each environment had water and it did cause growth, without it, the unknown may not have grown at all. I would call our conclusion that our unknown was alive, a fact. While it was already known that plants are indeed living organisms, we simply proved it in our experiment. What I've learned from this lab is that making sure that everyone is working and not simply watching can make a huge difference and also not to make any assumptions before conducting your experiment because it is likely that you may be wrong.

Click to View the Is it Alive? Powerpoint