So, I’m a little stir crazy, and kind of brain fried, and looking for something interesting but non-school-related to do…
My notes and thoughts from Biology 111, for Monday, September 22, 2008. The entire series can be found here.
Before we get to the actual lecture, there’s something I need to address here.
While taking notes, it is often helpful and even necessary to draw little diagrams and pictures, many of which I reproduce in this series by digital means.
This is often simpler, neater, and more helpful than just scanning pages of notes from my notebook.
Until now, it’s really not made much of a difference, but in this lecture we begin drawing diagrams of cell structure, and while it’s not terribly difficult to do digitally, when drawing them in a notebook it is imperative for accuracy to understand the proper method for drawing a cell. It is a skill which requires a great deal of practice.
Chromosomes and various proteins for example, can be very complicated, and drawing them incorrectly can lead to gross misunderstandings and disaster for the student. To help prevent this, I’ve created a digital animation of the proper method for drawing a chromosome inside a prokaryotic cell. The method employed here can be extended and extrapolations to eukaryotic cell diagramming should not be difficult.
The method, along with this lecture, is below the fold.
My notes and thoughts from Biology 111, for Friday, September 19, 2008. The entire series can be found here.
As we took our first exam on Wednesday, September 17, there was no lecture for that day.
We took the first part of class to go over the exam results. I had left the exam feeling very good, figuring I was unsure about and may have missed two or three questions. Turns out, I missed eight.
Out of 64 students in 3 sections, the highest score was a 91, the lowest a 29, and the median 67. I scored an 88.
Doc said not to sweat it too much, as the first exam is the one everyone does a little less well on, unfamiliar territory, etc., and he drops the lowest exam score.
I was rather surprised at about 5 of my 8 incorrect answers, thinking to myself, “What the hell were you thinking???? You know better than that!!!” I really pulled some dumb answers from out of my butt to very simple answers.
One of my incorrect answers though, was the molecular formula of maltose (two glucose molecules bonded together). Now, without thinking, I simply answered with double the formula of glucose, stupidly forgetting to subtract the water molecule from the hydrolysis synthesis that is required to form maltose from two glucose molecules (or any disaccharide from two monosaccharides).
Hence the unforgettable graphic I made subsequently. After making that animation, I will never repeat that mistake.
After going over the exam, we moved on to Chapter 6 – A Tour of the Cell.
Notes for that brief lecture are below the fold.
My notes and thoughts from Biology 111 Lab, for Monday, September 15, 2008. The entire series can be found here.
In this lab, we learned to use reagents to test for the presence of proteins, starch, and sugars, using distilled water as a negative control.
Since distilled water should be straight H2O and nothing else, each time we did a test, we could see what the reagent did in solution without the presence of whatever it was we were testing for.
We worked in groups, and our group consisted of four students.
A. In the first experiment, we tested for the presence of proteins with Biuret reagent, a highly corrosive blue/purply substance. Our Lab Manual and Doc each warned us about its potential hazards, safety precautions, and what to do if we got it on our skin.
We marked four test tubes at the 1 cm level.
1) Test tube 1 we filled to the mark with distilled water. We then added about 5 drops of Biuret reagent. The water turned light blue. This was our negative control to which we could compare the other tubes when the Biuret reagent was added.
Lab continues, below the fold.
A dozen of your favorite New York City sex bloggers and sex educators are joining together to support Sex Work Awareness, a non-profit whose mission statement says it all:
We believe that all sex workers have a right to self-determination; to choose how we make a living and what we do with our bodies.
We aim to empower our diverse community by building the capacity of sex worker-serving and sex worker member-based institutions as well as the skills and resources of sex workers themselves.
We also conduct research about sex workers and the sex industry in order to better understand it, develop public education initiatives, and advocate for the rights of sex workers.
The theme is burlesque. The poses will be sexy. And who will be posing? Take a look, below the fold!
Hoy en la clase español, aprendemos los verbos regulars y las conjuagcións.
One of my classmates needs some notes she missed.
You can just click the images, which will take you to a larger version of them that is easier to read, OK? If those are still too small, you can click “all sizes” (just above the images there), and it will give you a great big honking sized image.
There are 8 pages.
If you have any questions, leave a comment or email me.
Do well on the quiz tonight!
(The scans of my notes are below the fold)
My notes and thoughts from Biology 111, for Monday, September 15, 2008. The entire series can be found here.
The class started with a reminder that the next class period (Wednesday the 17th) would be our first exam.
Then there was a short review of Hydrocarbons generally, and carbohydrates specifically, just to get us back to the place where we had left off.
We picked up this lecture with our discussion of Lipids.
Triglycerides —> Fats & Oils
Glycerol + 3 Fatty Acids
When a glycerol molecule, C3H5(OH)3 (the vertical part on the left of the image), picks up three fatty acids (the long strings of C and H on the right), they combine to form a triglyceride.
Triglycerides are fats and oils. If the long fatty acid chains all remain straight, each carbon bonding with two Hydrogen atoms and its two neighbor Carbon atoms, the triglyceride can pack densely, and thus becomes a solid at room temperature. This is a saturated fat.
If one or more of the long fatty acids develops a “kink”, ie two Carbons double bond and dump a Hydrogen, the stack can not pack as densely, and thus becomes a liquid at room temperature. This is an unsaturated oil. If there is one kink, it’s a monounsaturated oil, and if more than one, it’s a polyunsaturated oil.
Ta-da. It was kind of cool to suddenly understand the difference between them after having heard the terms for so long in reference to food labels.
We can measure energy in units called calories.
Because of fat’s high percentage of hydrocarbons (all along those fatty acid chains), it has a high caloric content. For comparison, a gram of fat contains 9 calories, while a gram of carbohydrates contains 4 calories. Remember that those Hydrogen – Carbon bonds are high energy content because of the non-polar covalent bond.
(Lecture continues below the fold)
I got my second essay back this morning in English Class. I missed one comma, but managed an A+. I’m pretty happy about that as I was concerned about length as well as flow. I didn’t think it flowed as well as it could have.
Mr. Beverage disagreed, apparently.
When I showed him the title, he got a great big grin, and gave me specific permission to break the “No Slang” rule.
The prompt was a definition using illustration.
The essay, in its uncorrected form, lies below the fold.
My notes and thoughts from Biology 111, for Friday, September 12, 2008. The entire series can be found here.
There are four main classes of organic compounds in living things that Bio 111 is going to cover.
* Carbohydrates, Proteins, and Nucleic Acids are Macromolecules, meaning “really honkin’ big”.
1. Carbohydrates – Sugars – all “ose” endings mean “sugar”.
They have a C:H:O ratio of 1:2:1, so the basic carbohydrate formula would be CH2O
a) monosaccharides –> “one sugar” – these are the simple sugars, and contain between 3 – 7 C atoms in them.
(Lecture continues below the fold)
My notes and thoughts from Biology 111, for Wednesday, September 10, 2008. The entire series can be found here.
In the last lecture, we had left off with a discussion of pH and [H+]. We started this lecture by finishing up with pH.
Remember that pH is a negative log scale, so as [H+] goes up, pH goes down.
We came to definitions right off the bat.
Acid –> Any substance that increases [H+] of a solution. This is accomplished by donation of H+ ions (p+, since a Hydrogen without an e– is just a p+)
HCl —> H+ + Cl–
Hydrochloric acid will break down in solution into its constituent parts, thus directly increasing the [H+] and lowering the pH of the solution.
Base –> Any substance that decreases [H+] of a solution. This can be accomplished in one of two ways:
Donation of OH– to combine with H+ already in the solution
NaOH —> Na+ + OH– —> OH– + H+ —> H2O
Oven or drain cleaner, Sodium Hydroxide, will break down in solution into its constituent parts, one of which is a hydroxide ion. The hydroxide ion combines with H+ in the solution to make water, thus lowering [H+] and raising the pH of the solution.
Sucking up of H+
NH3 + H+ —> NH4+
Ammonia, NH3, will pick up an H+ and become NH4+, thus directly decreasing [H+], and raising the pH of the solution.
Then we moved on to Chapter 4: Carbon and the Molecular Diversity of Life
(The rest of the lecture is below the fold)
My notes and thoughts from Biology 111 Lab, for Monday, September 8, 2008. The entire series can be found here.
In this lab we mostly talked about metric system measurements, then went about taking measurements of various things. Honestly, it was pretty mundane stuff for the most part, and I didn’t enjoy this lab nearly as much as the first two, though I understand the necessity of it.
We used rulers, calipers, and a scale to take measurements of wooden blocks, then calculated their volume and surface area.
We measured the room temperature and the temperature of cold tap water and ice water, and water on a boiling plate, as well as skin temperature.
Then, in the most interesting part of the lab, we measured each other’s tibias, and then each other’s heights (as well as a real dead guy’s tibia). We recorded the tibia length and height of everyone in the lab, and for homework we created scatter plots and trend lines with those numbers.
It was pretty straightforward stuff, really, and well… kinda boring except for the dead guy’s bone that Squicky Britches refused to touch. That was a source of mild humor.
From whence came the art:
The first image is of our textbook, Biology, Eighth Edition, by Campbell & Reese et al.
Other images by me and are licensed under the Creative Commons Attribution- NonCommercial- Share Alike 3.0 License.
So today I attended my first Science Club event. The club keeps a little garden out back of the science building, and it needed weeding.
I stopped by after English class to find Doc all alone, weeding. He pointed out what needed done, what to yank up and what not to, and I set to work. We had the department head pop in and out to lend her hands, and someone who I think is another instructor helped for a while.
It actually turned out to be a nice bit of relaxing time, just chit chatting with Doc about science, the exam, the class, the lab, that sort of thing. We talked about the Thumb and After the Bar Closes, Randi and Dr. PZ, Dover and Brunswick County, Barbara Forrest and Michael Behe, Gould and Dawkins, and Dionaea muscipula, Spanish class and English class, my history with Dr. Bob and my flirtation with L. Ron Hubbard.
It was a great day for it, just the perfect temperature with a perfect breeze, and I was having a good day regarding my neck. I’m kinda glad no one else showed up, in an odd way.
From whence came the art:
That image is titled Nice catch! by Davers, and is licensed by the artist under the Creative Commons Attribution-Noncommercial-No Derivative Works 2.0 license.
My notes and thoughts from Biology 111, for Monday, September 8, 2008. The entire series can be found here.
We left off on Friday discussing the second important emergent property of water, the property of temperature moderation.
On Friday, we began with the third emergent property of water that is critical to biology.
3. Solid form of water is less dense than the liquid form
In other words, ice floats. First we took a quick look at what generally defines each state of matter at room temperatures (we didn’t delve into plasmas etc)
|States of Matter|
|Constant Shape, Constant Volume||Constant Volume, Changing Shape||Changing Volume, Changing Shape|
So we can say that generally speaking, the state of matter is dependent on its density and the fixity of its bonding. Ordinarily, the solid state of matter is more dense than the liquid state, and this unusual property of water has a very important consequence for life.
(More of this lecture, below the fold)
My notes and thoughts from Biology 111, for Friday, September 5, 2008. The entire series can be found here.
On this day, Tropical Storm Hannah was expected to hit, so the college closed at 1 PM. Although that was well after the end of our scheduled lecture, Doc (if I recall correctly) cut the class a bit short to give folks headed home a little extra time.
So in the previous lecture, we had left off discussing Cohesion and Adhesion, the first of the emergent properties of water on the table for discussion. With this lecture, we picked up with the next emergent property on the list.
2. Moderation of Temperature
Water has a relatively high specific heat, which means that water can absorb and release large amounts of heat with little change in temperature.
To discuss this topic, it helps to first have an understanding of the difference between heat and temperature.
(Lecture Continues Below the Fold)
This morning I got back my first English essay, which was turned in on Monday. It was a five paragraph illustration essay on a topic of our choice. English is the last class for which I haven’t gotten something akin to a formal grade letting me know how I’m doing. I did alright, making a few punctuation errors. I have a nasty habit of placing punctuation outside a closing quote mark. I know that’s wrong, I learned it in grade school, but somewhere along the line my brain just decided that’s not the way it’s supposed to go.
There were a couple other places where I inserted or failed to insert a comma where I should not or should have, and I didn’t capitalize “Founding Fathers.” I know exactly what that issue is about. It’s an overreaction to the habit I picked up in German class (back in 1984/85) of capitalizing all nouns. I really have to pay attention to commas and capitalization.
I used the faux-words “Endarkenment” (contrasting with the Enlightenment) and “ignorati” in the essay, and I was a little nervous about whether they would fly. Although Endarkenment survived without comment, Mr. Beverage (his name used with his prior consent) commented next to ignorati: “Nice! I like the contrast to Illuminati!” I breathed a sigh of relief when I read that.
His comment and grade at the end of the paper, as depicted in the image, really made me feel vindicated about my choice of topics and my writing style. His going out of his way to speak to me after class to reiterate his appreciation for my writing reinforced my confidence exponentially.
I’m doing well, and damn it, I belong there.
The essay is below the fold in its uncorrected form.
My notes and thoughts from Biology 111, for Wednesday, September 3, 2008. The entire series can be found here.
We left off before the Labor Day break with polarity and the ability to form hydrogen bonds.
The polarity of the water molecule, having an oxygen to one side and the two hydrogen atoms to the other, gives the molecules a slight attraction to charged molecules, since the oxygen end is going to have a slight negative charge and the hydrogen end is going to have a slight positive charge. This is caused by the unequal sharing of valence e- between the oxygen and the two hydrogens. Because the oxygen pulls harder on the shared e-, they are going to spend more time toward the oxygen, increasing its negative charge a little, and away from the hydrogens, increasing their positive charge a little (actually decreasing their negative charge a little, to be accurate).
That little bit of polarity will cause the oxygen end of one water molecule to be attracted to the hydrogen end of another water molecule (or any other positively charged molecule), and though the effect is small in one pair of molecules, it adds up with millions of molecules.
(More below the fold)