Thursday, November 27, 2008


Last week I took an Ecology Exam and really drilled the concepts because I needed to do well on it. So I remember a lot of interesting examples of the topics we covered, including parasitism. An example Dr. Baines talked about that particularly stuck in my mind was about this parasitic worm like organism, whose name I can’t recall and did not write down. What I found memorable about the organism was (obviously not the name ;-) that it had the ability to dramatically alter the behavior of its intermediate host (that host which will, “harbor developmental stages of [the] parasite”). Once the parasitic worm infected its host (a snail), it caused biochemical reactions to occur within the body of the snail which resulted in the snail changing its normal behavior in dangerous ways. Instead of the snail moving carefully along the ground and keeping itself well concealed by the tall grass blades within its environment, an infected snail will crawl to the top of the blades of grass. This made the snail more visible to its main predator, local birds. The easily seen, infected snail would then be snatched up and consumed by the bird, which conveniently serves as the definitive host (the, “ host in which [the] parasite reaches maturity”) to the parasitic worm. Once the parasite reaches a certain level of maturity the bird will excrete it in its feces often onto a grassy area. There the parasite will produce offspring which may be picked up by the snail and the whole process of parasitic development is repeated.


As the semester has progressed Dr. Baines has hammered the concept of tradeoffs into our brains. So it makes sense that she asked us the following question on a previous exam: “Explain why organisms are not able to adapt to ALL environmental conditions.” Here is my response: “This is due to the concept of tradeoffs and constraints. Some characteristics may allow individual organisms to be optimally equipped to survive in their own unique environments, however if the environment changes, then that individual might be at a disadvantage (in terms of survival and reproduction) because of their characteristic(s) which was or were previously beneficial. Previously advantageous characteristics might be detrimental to an organism in an environment which has changed drastically from the one they were well adapted to.” I have found the concept can be applied to a variety of situations. Specifically, an example which represents how tradeoffs work would be the changing composition of a tree population. The environment in which these trees exist has a varying moisture gradient (moist to dry). Of the three tree types within the environment, the Douglas-fir is the dominant (or numerous) tree type under moist conditions because it is a superior competitor. The next most numerous tree types under the same conditions would be the Port-Oxford Cedar, followed by the Pacific Madrone. However, as the environment becomes increasingly dry, it is the Pacific Madrone that becomes the dominant tree type (again, the most numerous) because it is well adapted to stressful environmental conditions (when water is limiting). During very dry conditions the Port-Oxford Cedar completely drops out of the picture while the Douglas-fir is found in relatively limited numbers. Therefore no single organism is well adapted to all environmental conditions and tradeoffs exist between stress tolerance and competitive aptitude.

Wednesday, November 26, 2008

Aquatic Changes

At the beginning of the semester Dr. Baines gave us an exam in which one of the essay questions required quite a bit of explanation, but it was interesting so I remember it. She asked us to, "discuss how light, temperature and oxygen levels change with depth and season in aquatic environments and describe any interactions among these factors." So I wrote the following: "During the summer, thermocline occurs which may be described as a rapid decrease in the temperature of woater at a particular depth. during Fall turnover the ater on the top is heated, (by solar radiation), so it becomes more dense thn the water below it and sinks to replace the water at the bottom. In this way htere is an exchange of nutrients within the movement of the water. Furthermore, during the winter months decomposing organisms contribute to a decreased amount of oxygen gas diffusion due to the fact that they needconsume oxygen as they perform respiration. At increased depths there is less penentation of light and so the rate of photosynthesis is decreased. In general, at higher temperatures the rate of oxygen gas diffusion into water decreases (the two elements are inversely proportional). It made sense to me this way at the time I took the exam, but then Dr. Baines returned our exams and saw that she wrote in a comment. What she wrote was that in the portion where I said that, "...during the Fall turnover the water on the top is heated," she commented that I should have said the water is cooled instead. That confuses me because then a good chunk of my response doesn't make sense. So I don't understand why she gave me full credit for my answer, but I'm not going to complain. I haven't taken the time to go back and ask her about it or reread the section of the notes that covers aquatic environments so it's still not exactly clear to me. I just need to go visit her and ask for further clarification on the matter.

Saturday, November 22, 2008

An end to Eco Lab :-(

Earlier last week, we conducted our final Ecology Lab experiment. The purpose of the experiment was to observe characteristics of Island Biogeography. We used ping-pong balls to represent our colonizing species and empty egg cartons to simulate the islands to be colonized. First, we used a empty egg carton which was capable of holding one dozen eggs or ping-pong balls, then we used one half of a carton, capable of holding, duh, six ping-pong balls. Using five balls for each trial, Krizia stood about 1 meter from the 'large island' and tried her best to 'colonize' or bounce, each ball into one of the cups of carton. Liz and I counted how many instances of colonization she got for each trial and caught balls as they flew every which way. After each trial of five balls being tossed at the island we rolled a die to determine at which cup within the carton there would be an 'extinction' event (all cups of the carton were previously labled). By extinction event I mean that if we rolled the die and say rolled a two and there was a ping-pong ball in cup two, that ball would be removed and not counted in the final number of colonizations. We then repeated the procedure after having moved the same carton two meters away from Krizia. Then we used the 'smaller island' to carry out the same procedure while Lisa recorded all of the data and made calculations. What we determined from our readings and experiments was that with a larger sized island, there is decreased chance of extinction. With the smaller island there is increased chance of extinction. Also, as the distance from the 'mainland' increases, there are decreased immigration rates.

Thursday, November 20, 2008

Plant adaptations

Three weeks ago I learned about how plants interact with the environment and change their growth patterns according to which resources are most limiting. I think it all makes sense, so this is what I learned: Since the effects of global warming have led to a gradual increase in the minimum temperatures, this causes the relative humidity to decrease. This subsequently causes a drop in water availability within the atmosphere or the plant’s environment; specifically the soil becomes less saturated and there is less water present in the air to be taken up by the plant. Essentially this means that water is a limiting factor in terms of plant growth, therefore the plant will allocate its resources so that a larger root system will develop and thus the respiration rate increases. This increased rate of respiration means that the rate of carbon loss is increased and since the net carbon gain is the difference between the photosynthetic rate and the respiration rate, the end result is that the net carbon gain decreases.

The Acid fast staining procedure

A couple of months ago I had to learn the acid fast method of staining and write about it. So this blog contains what I learned about that topic. “The acid fast stain… is an important diagnostic stain,” (Talaro, 2008) performed so that one may be able to differentiate between those bacteria containing mycolic acid in their cell walls (which therefore may be classified as acid fast staining bacteria) and those which are nonacid-fast staining. This unique structural characteristic of acid fast bacteria renders its cells impervious to most staining agents; however this type of staining procedure allows for adhesion to this specific type of waxy cell wall (using a combination of dyes) and thus, differential identification. The procedure is done by first smearing and then heat fixing a culture of bacteria to a clean slide. The smear is then covered with adsorbent paper and saturated with Carbolfuchsin. The slide is then placed over a beaker filled one quarter of the way with boiling, distilled water (Ziehl-Neelsen Method) for a period of five minutes. This method is used so that the dye may adhere more readily to the acid fast bacterial cells and prevent drying out. The paper is then removed and the smear is then washed carefully by allowing distilled water to run through it. Next, acid-alcohol is made to cover the smear for one minute in order to decolorize those bacteria which are nonacid –fast staining. Then again the smear is washed gently with water. After this, the counterstain, Methylene blue is applied to the stain for one minute so that the non-acid fast bacteria may be dyed and identified during viewing. This is followed by one final washing of the smear with distilled water. Lastly the specimen is blotted dry using Kim Wipes and viewed under oil immersion magnification. It is expected that those bacteria which contain mycolic acid within their cell walls will retain the fuchsia hue of the Carbolfuchsin dye, while the other cells within the smear will stain purple with the counterstain, Methylene blue.

Bees, pollination & parasites

I had to read an article out of my Ecology lecture text and then write about it so I figured I'd just blog about it as well. Mutualism exists between flowering plants and their pollinators-bees. Plants benefit from this relationship in that they greatly increase their chances of reproduction. The chances of having their pollen grains fertilize another flower are much more probable if they rely on a pollinator like the bee who moves among many flowers in a short amount of time, rather than simply relying on the unpredictability of the wind for reproductive purposes. Flowering plants invest a substantial amount of energy in pollen production and so by utilizing bees as a vehicle for carrying out pollination they are increasing their energy efficiency. The bees benefit by extracting nectar from the flower and then internally converting it into honey (“a high quality energy store”). Once the bees inadvertently pick up the pollen grains, they may consume the highly nutritious grains which are rich in proteins and oils.

A host-parasite relationship exists between bees and two mite species: Varroa and Tracheal. The cost to the host (bees) is their mortality and fitness. The Varroa mite benefits from the relationship by deriving sustenance from the internal fluid of the bee. The Tracheal mite derives nutrition from its host’s body, but also uses this medium as a site for reproduction. Due to varying levels of exposure to the parasites, different host species have developed differing levels of resistance. Often, the more time a bee species is exposed to a parasite, the more likely it is able to develop resistance to the pest and survive if attacked.

Coffee is my kryptonite

About a week and a half ago I remember it was pretty chilly outside and so I decided to buy a small cup of coffee to warm myself up. I know because of past experiences that if I drink more than one cup, my body will not react well, but I thought I would be alright if I just had maybe like three fourths of this small cup. Plus, as I walked through the library lobby I saw a bunch of students sitting around chatting happily while sipping on their cups of coffee. They looked warm and happy and that's how I wanted to be, so you know, monkey see, monkey do. I bought a cup and sipped it while I ate a tasty banana nut muffin, not thinking about the effects the caffeine might have on my body. A couple of hours later, the effects seem to hit me all at once: my stomach felt like it had wings and was fluttering about within my abdomen, my mind was racing with the thoughts of the day and I felt like my heart was beating a little fast. Maybe this means that there is something wrong with my body in terms of metabolism or maybe it could be a bigger problem. But maybe I'm just highly sensitive to the effects of caffeine because I try to stay away from it as much as possible (except on days when I want a hot drink- which doesn't happen often). I don't know what it is but I didn't even finish that small cup and look what happened-Geeze! I like having a drink of coffee every once in awhile, but I tend to forget how ugly it makes me feel inside a couple of hours after I consume it. Oh well, next time I'll try to remember the way I felt and opt for another drink instead. Yeah, I know I'm weird, you don't have comment about it.

I Need Analogies!

Just the other day I was sitting there listening to a microbiology lecture and this tiny but significant detail about the process of translation that I had always had trouble understanding finally became a little clearer. I was always a little shaky on my understanding of exactly how the tRNAs move within the ribosome and interact with (among other molecules) each other to form the polypeptide or protein (aspects of the process of translation). He (my professor) said it's like the tRNA in the P-site says to the one in the A-site, "Oh, I've been here awhile, I'm old and tired already, but you are young since you are newly arrived. So here take my load (the strand of amino acids which are attached to the tRNA in the P-site)." Then that 'old' tRNA is ejected from the ribosome. The 'old' tRNA "hands over" his polypeptide to the 'new' tRNA when a peptide bond is formed between its polypeptide chain and the amino acid on the 'new' tRNA. Then the old guy releases its bond to the polypeptide chain and is ejected from the ribosome. Next, the ribosome moves on down to the next codon on the mRNA, the tRNA in the A-site with its attached polypeptide strand moves over to the P-site and the whole process is repeated again and again. In this way more and more amino acids are added to the chain and a protein is synthesized. I know I should have understood this as a senior in my high school Biology class, but sometimes things just don't click until I hear somebody explain it in a particular way. It's like I have to be able to picture it happening in my mind because I'm a very visual learner like that. Maybe I have it all wrong, but right now this process makes sense to me, so I hope I learned it correctly.

Fun w/Ecology lab

A couple of weeks back we carried out an experiment that was supposed to teach us about predator-prey interactions. It was kind of fun since we got to essentially play around in an organized way while we gathered our data (not datum :-) ). The experiment consisted of one person closing their eyes and then using one finger to search for nuts and bolts that were to placed somewhere in the general vicinity of the table directly in front of them. Once they located a bolt (with a nut screwed all the way to the top of the screw), they were supposed to remove the nut and repeat the process with as many screws as possible for a duration of three minutes. We did this in groups using at first five, then ten and then fifteen screws. What I got from the experiment was that as the number of prey (or screws w/nuts) increased it was easier to "catch" (or in my case blindly attain) them, but the trade-off was that handling time (the time it took to undo each nut from the screw) increased. It worked out well because I think I got the point of lab even though my fingertips were a bit sore after it all. I was a pretty good predator too because although at first my capture numbers weren't that high when compared to those of my good friend Liz (who was the other predator in my group), with each group I handled, my numbers improved. Liz was insane though, she could 'consume' an average of like eighteen screws/nuts in three minutes! Madness, pure madness! Her fingers just flew over the 'prey'.

Stream of Consciousness

I don’t like getting 3.5 out of 5 points-I really thought I had earned better. I didn’t half a** it, you know??? Stray letter…how could I have missed that? The proof is not in the pudding, HAH, I knew that didn’t make sense! Slap, you got rejected, so be tenacious. These are some of the thoughts that flow through my mind as I sit there in Biological Writing sometimes. Dr. Baines picture perfect dog is named Dargo…I didn’t hear her explanation of that? I know she said something about Dr. Zen understanding the significance of the dog’s name because he’s ‘nerdy’ too and into some old comic or something like she is. As I’m proofreading this I feel like circling behaviour and writing ‘This looks funny because I’m not Australian, British or Canadian but I know it is right.’ It’s just that I wanted to comment on it to see if I could get a chuckle out of Faulkes. Haha, as I’m typing this out, the computer agrees with me. What happens if I type colour? Haha, denied again! I really hope I didn’t get any Ethidium Bromide on my sandwich…I don’t want to die yet, honestly, I’m still young and spry. L.o.l., I know that’s totally not up to me, whatever. I don’t see any grammatical or spelling errors on this second page-damn!!! And I need to get to lab!!! What’s wrong with my brain today?!? Props to Dr. Zen because I could never care about “digging” so much, really. Some people make vicious comments. I seriously need to blog. I’ve been avoiding that and it’s festered and grown like an ugly fungus in a dark corner of my mind. Rejection is not final…Really? Could this be true even if my writing consistently contains serious structural errors? I could work on that though…but how? I know, I know, I’m venting but that’s life, so it counts as a biological topic.

Trials of Life-3

These are my descriptions and interpretations of again, the "Trials of Life," DVD. This blog entry is most concerned with interesting examples of mimicry and mutualism in nature.An example of mimicry would be when the walking stick imitates the appearance of leaves in order to achieve a camouflaged look and guard against its predators. The Praying Mantas mimicking the flowery color and appearance of the white orchid while it lies in wait for its prey is another example of mimicry in nature.

One example of mutualism would be the relationship between shrimp and the Gobi. The two species live together in a cave excavated by the shrimp. In return to the shrimp, for having provided the home the share, the Gobi, with his excellent eyesight serves as a guide and protector of the blind shrimp. The shrimp stays in contact with the Gobi by constantly touching the fish with his own antennae. Through this connection the Gobi can tell the shrimp when it is safe to wander out of the cave or when to stay within because predators are in the vicinity. This relationship is symbiotic because they need each other in order to survive. A second example of mutualism would be the relationship between deer and monkeys. In this instance, the monkeys forage in trees and in doing so, drop leaves which the deer pick up and eat. When the monkeys wander down to scavenge for food on the ground, the deer act to warn the monkeys if a predator comes near so that the primates may escape safely back up into the tree tops. This represents a non-symbiotic mutualism since both species could survive without each other and so they have a facultative relationship with each other. These relationships are both good examples of co-evolution because they demonstrate adaptations and contribute to the continued survival of each species involved.

Trials of Life-2

This is just a continuation of my notes and interpretations of the material covered on the Trials of Life DVD. This blog entry focuses more on predator-prey interactions though. An example of a prey species defending itself against predators would be when certain trees develop poison within their leaves in order to deter herbivorous spider monkeys. The monkeys have adapted to this defense so that they are capable of ingesting small amounts of the poison while feeding. If they have had enough poison they simply move on to another plant and may continue eating. A similar situation occurs when particular types of plants are consumed by beetles. Again, the plants produce poisons to defend against its predators, but do so in a way where the poison is produced specifically in the center of its leaves. The beetles have adapted and overcome this defense by puncturing the leaf, causing the milky poison to drain out, and then feeding safely on the end of the leaf. These are good examples of co-evolution because in each case, the two species involved in the predator-prey relationship developed mechanisms to preserve their own survivorship.

Trials of Life-1

Last Wednesday I was forced to stay in Ecology lab and watch a DVD called, "The Trials of Life," which because of the length, I found somewhat boring. Some parts of it I did find interesting though. So because its all about adaptations and I took notes while watching the DVD, I think I write a few blogs about it. Here I go. One specific [behavioral] adaptation of a particular type of prey (in the rainforest environment) would be the Trinidad Tree Frog developing an aquatic nursery to keep its embryos safe from predatory fish. The adult frogs house their developing embryos in a small sphere of sticky jelly (on tree branches, above water), which will dissolve away once the offspring reach a mature stage of development. This then allows them to fall into the main body of water below and complete maturation. The point of the behavior is that the frog embryos are kept away from the predatory fish until they have outgrown their vulnerable infancy stage and developed well enough so that they may be able to defend themselves against attackers. A specific example of adaptation involving partners in a mutualism would be how the shape of the Saber Wing Hummingbird beak has developed so that it fits perfectly with its food source, the Columbian flower. The hummingbird derives nectar from the flower and the flower benefits from the relationship by having the hummingbird carry out its pollination.