On the Composition of Charles

Swarmed, by LouFCD on Flickr

Swarmed, by LouFCD on Flickr

In my spare time (haha) I’m again reading Darwin’s Origin of Species. It’s an incredibly insightful work for its day or any other, and even modern biology writers, with all the updated information available at our fingertips, are hard pressed to match its beauty.

In reading it again with my own now more advanced understanding of biology, I’m struck by two things in particular within the first several chapters. The first that stands out to me is Darwin’s mastery of the turn-of-phrase. In World Lit II last semester, the pieces we read were exemplars of their time period. The early and mid-nineteenth century works were chosen specifically to highlight the Romantics’ “rejection” of Enlightenment ideals. The systematic logic and naturalistic view of the universe was traded in for adornment, symbolism, and emotion. Yet even then I noted in an essay on my midterm that Darwin was an outstanding exception to this rule.

Romantics viewed the world around them as a natural extension of their emotions. Emotion and Nature are inextricably intertwined, the one often used as a symbol for the other. This was a rejection of Enlightenment ideals of the logic and order of Nature. They valued this emotion and its connection to the natural world almost to the exclusion of reason. (Charles Darwin was a notable exception, whose seminal 1859 treatise on evolution, “On the Origin of Species &etc” being a work replete with both the reason valued by the Enlightenment and the powerful emotive awe treasured by the Romantics.)

(I may transcribe my entire response as a separate post, just for fun – I was pretty happy with the way it came out, under pressure and unedited, and in response to a perfect prompt for taking modern Creationists to the woodshed – you know I took that bait with reckless abandon.)

I stand by that comment, and this latest read reinforces my opinion that Darwin exemplifies the best of both Enlightenment and Romantic writing. His synthesis is unparalleled among the writers of his day.

An oft-quoted example of his beautiful mastery of emotive language is found in the final passage of Origin:

There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.

The other glaring feature of the first several chapters is my own recurring frustration. On nearly every single page I read, I want to just scream backwards through time words of encouragement to get this greatest of minds to take that one last little step that in retrospect is so very very tiny. Darwin was one thought away from picking up the revolutionary idea of Gregor Mendel. He dances all around it, a ballerina doing elegant pirouettes without ever quite stepping on that one spot in the center – particulate theory of inheritance. (Genes, we call them.)

Thus it is, as I believe, that when the males and females of any animal have the same general habits of life, but differ in structure, colour, or ornament, such differences have been mainly caused by sexual selection; that is, individual males have had, in successive generations, some slight advantage over other males, in their weapons, means of defense, or charms; and have transmitted these advantages to their male offspring.

I have to sigh, and be resigned to the facts of history, else I might scream. Particles, Charles, particles.

From whence came the art:

That image is titled Swarmed, by me, and is © 2009.

Loggerhead Sea Turtle Nest Sitting

Turtle Nest, by LouFCD on Flickr

Turtle Nest, by LouFCD on Flickr

I’ve been in the field a few times in the last several weeks. Though my classwork has me about buried, I really enjoy these little stress relievers where I can just enjoy the surroundings and take a few pictures. It started around Labor Day weekend, when I spent several nights sitting a nest of Loggerhead Sea Turtles down on North Topsail Beach. The turtles were due to hatch about any day, so I was very excited. Alas, they never did hatch out while I was there, but it was a relaxing time for the most part anyway.

In fact the Sea Turtle Hospital has no record of a hatch to date (nest 55). There are several possible reasons for that. They may have hatched during a storm while no one was looking, with the storm erasing every trace of their leaving the nest. That happens sometimes. The turtles could have been drowned by a storm as they were hatching, too. Also, while the possibility exists that this was a false nest, the Sea Turtle Hospital folks were pretty sure this was a real nest.

So it was a bit frustrating, sad, and disappointing, but I got some photos of other things that I thought I’d share here anyway. They are below the fold.

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Blogging My Zoology Class 20090904

Our textbook, Animal Diversity, by Hickman, et al

Our textbook, Animal Diversity, by Hickman, et al

I’m going to get back to the Blogging My Biology Class series, finish out 111, do up 112, and tack on my Zoology class as well. It’s going to be a bit jumpy, though, but on the main series page they’ll all wind up in order by date of the class, rather than date of posting.

For now, my classmate Kristy needs notes from a particular day, so that’s up first.

We started out with a few announcements, a reminder that anyone wanting to do 20 hours of service learning would receive 4 points on their final grade, but that forms were due in to the Student Services office by Friday, 11 September. It’s more than half a letter grade in our 7 point grading system, so it’s worth the price of admission.

Next up was Loggerhead Sea Turtle Nest Sitting down on Topsail Island. There are several nests ready to hatch out any day, and anyone wanting to see this was welcome to head down and hang out. I wound up sitting at a nest on Friday, Saturday, and Sunday nights, several hours each night, but no turtles thus far. I may or may not be able to make it tonight. It’s pouring down the rain, I’ve developed a head cold, and I have an 8 AM English class tomorrow. Of course, if I don’t make it, they’ll hatch tonight just to spite me. Little bastards.

Wary Gull, by LouFCD @ Flickr

Wary Gull, by LouFCD @ Flickr

I took a bunch of pictures of other stuff while waiting, and I’ll be posting them here on the blog for your viewing pleasure.

With that, we got back to where we had left off on Wednesday, with the Tissue Level of Organization.

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There Is No Such Thing As Alternative Medicine

Witch Doctor by Felix42 contra la censura @ Flickr

Witch Doctor by Felix42 contra la censura @ Flickr

There is no such thing as alternative medicine. Test it against a placebo. If it works better than the placebo, it’s not alternative – if it doesn’t, it’s not medicine.

At its most basic, the heart of the matter really is that simple.

Think your herb tea cures your cold?

Test it against a placebo. If it works better than the placebo, it’s not alternative – if it doesn’t, it’s not medicine.

The United States federal government has spent $2.5 billion testing alternative medicines.

Ginko biloba helps your memory?

There is no such thing as alternative medicine. Test it against a placebo. If it works better than the placebo, it’s not alternative – if it doesn’t, it’s not medicine.

“Echinacea for colds. Ginkgo biloba for memory. Glucosamine and chondroitin for arthritis. Black cohosh for menopausal hot flashes. Saw palmetto for prostate problems. Shark cartilage for cancer. All proved no better than dummy pills in big studies funded by the National Center for Complementary and Alternative Medicine. The lone exception: ginger capsules may help chemotherapy nausea.”

Shark cartilage cures cancer?

There is no such thing as alternative medicine. Test it against a placebo. If it works better than the placebo, it’s not alternative – if it doesn’t, it’s not medicine.

The board in charge of the testing was artificially loaded with proponents of “alternative medicine”, and still FAILed to find any evidence that these treatments worked any better than placebo.

“The bottom line is that NCCAM is an ideological, not a scientific organization. It exists to validate CAM, not to test whether it works or not. And when it doesn’t produce the results its boosters in the legislature, like Tom Harkin, want to see, there’s serious trouble.”

Guess what? There is no such thing as alternative medicine. Test it against a placebo. If it works better than the placebo, it’s not alternative – if it doesn’t, it’s not medicine.

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Summer Update

Turkey Vulture in the Clouds

Turkey Vulture in the Clouds

So the semester is over and summer is officially here for me, solstice be damned. I’ll probably be able to blog a bit more, and vent some of the accumulated thoughts jumbled up in my brain.

For now, a few bits of updates.

I’ll be reading and reviewing The Unlikely Disciple, by Kevin Roose, for Carnal Nation. I’ll post a link for you when it’s up.

I’ll be hosting the next Carnival of the Liberals here on May 20th. I’ve been receiving submissions and should be getting to those by tomorrow. To this point, they’ve been shunted into a folder in my mailbox just because they started coming in during the lead up to finals week.

Speaking of finals, I think our team project for English 113 (our final was a presentation on one of Hamlet’s soliloquys) went OK, and I expect an A on that and in the class.

I bumped into my Bio 112 prof in a store here in town a few hours after the Bio final. He stopped to say hello and told me I got an A on the final, and complimented my answer regarding The Tragedy of the Commons. I don’t think I did well on the previous exam, so I’m thinking I’m in A/B borderland. Hopefully the final will pull me above the line.

I’ve been doing a lot of photography, uploading pics to my Facebook albums and to Twitpic. Kay is prepping to graduate high school next month, and since the ceremony will be in the football stadium, we needed a decent camera. I had been scrounging to find some cash for summer tuition, but we diverted those funds (and then a little) into getting a Canon EOS Rebel xs a few days ago since I won’t be going to school this summer anyway, and I’ve been using the heck out of it and trying to figure out all those knobs and buttons.

And that’s a bit of a story, too. UNCW Center for Marine Science gives two paid internships per year to Coastal Biology students, and I was nominated by the department for one of them. That was awesome and I was very excited. But then Dub emailed The Chair to tell her that the economy tanked those two internships. That was not awesome and I was bummed. Then Dub emailed The Chair again, and offered one internship on a volunteer basis, and I was offered that. So I guess now I’m quasi-excited. I said from the beginning that I would have done it for free, and in fact assumed it was volunteer at first and was happy to do it, but then I found out I was going to be paid, and now that I’m not going to be paid… well, y’know. I’m excited, but feel a bit like a kid teased with a lolipop. Oh well, I’m looking forward to it. Dub is where I intend to finish my bachelors degree and they have a ton of interesting research projects going, so it’s still a great opportunity. I’m really proud of being nominated for that one slot.

Easy Cool

Easy Cool

And JP. James tried pole vaulting this year for the first time. It’s interesting in that he had no idea that my Pop was a pole vaulter in high school. He seems to love it, finished fifth in the conference, and even went to Regionals. He lettered, and he’s got three more years of vaulting ahead of him. How freaking cool is that?

Oh, and he’s fifteen today. Happy Birthday, son.

From whence came the art:

I took both of those images with my new Canon EOS Rebel xs, and they are each licensed by me under the Creative Commons Attribution- NonCommercial- Share Alike 3.0 License.

Name that Flu

Vote early, vote often! Or write in your own answer!

A Brief History of Moonbats

Lou FCD

Lou FCD headshot by Ben Zvan

Last Thursday evening was a pleasant one. It was mild and welcoming, a good night for a drive to Wilmington. I had been by the University of North Carolina campus there, but hadn’t yet been to visit. I’ve been meaning to head down there to look around for a while now, as that’s where I intend to finish my Bachelor’s degree in Biology. The reason for this trip was mildly ironic given my intentions, as my son James and I were headed there to hear an anti-science advocate speak.

Dr. Michael Behe is a biochemist at Lehigh University in Pennsylvania. He’s also a senior fellow at the Discovery Institute, a well known creationist think tank whose purpose is to disguise religious doctrine as science in order to avoid the Constitutional ban on promoting religion in public schools. It was Behe that we were heading down to see.

Along the hour and a half drive, I gave my son the highlights of the full history of the Intelligent Design Creationism Hoax, parts of which he’s heard before. (Bear in mind here that I was driving, and not working from notes. I’ll be filling in details as I go that he didn’t get during our conversation.) I began with some background on the history of scientific discoveries in biology since Linnaeus. Carolus Linnaeus was Swedish doctor, a botanist, and a zoologist, who set about categorizing life’s varied forms in his long-evolving work, “Systema Naturae”, first published in 1735.

I touched on William Paley’s rehashing of Cicero’s water clock, and the the obvious logical flaw contained therein. In On the Nature of the Gods, Cicero’s character Balbus, a fictional follower of Plato, posited that because a sundial or a water clock has an obvious purpose, we can then infer that it was designed by some intelligence. Balbus went on to argue that because of the complexity of nature, we can therefore infer that the universe is also designed by some intelligence. Balbus concluded that the universe itself was divine, or possibly that the universe had a divine spirit, a sort of mono/pantheism (Collins 187 – 193). Paley bastardized the assertion in 1802, altering the water clock to a watch, and the deity in question to the Christian god (Paley 5 – 13). He failed however to remove the glaring logical flaw that we only perceive complexity in contrast to simplicity, the watch on the background of the heath. One cannot then use the complexity of the watch to argue for the complexity of the heath without undermining the original argument that the watch is itself complex and inherently different from the heath. This was important for what was to come, and I was later quite glad I had taken the time (we had plenty on the ride) to discuss it with James.

(continue reading below the fold)

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Monster Tales from the 112 Lab

Hydra - Feeding Extension by ravenofdreams

Hydra - Feeding Extension by ravenofdreams

So today we did a bunch of cool stuff in our Biology 112 lab. We started out by prepping and inoculating some petri dishes with a couple different kinds of fungi.

Into our first four petri dishes, we inoculated some Arthrobotrys. Arthrobotrys is a genus of predacious fungus. We’ll give them a week to grow, and then next week we’re going to feed some nematodes to them. That’s pretty neat.

Two more dishes got one culture of wild Sordaria and one tan Sordaria for a cross. Two more got one wild and one gray.

Then the really monstrous critter stuff started.

We got a watchglass and a dissection microscope and put a little Hydra in it. We observed its behavior for a while, and then added a few Daphnia. Hydra feed on Daphnia. When the Daphnia comes close, the Hydra‘s tentacles grab it, and then sting it to death while it struggles. It was very cool to watch.

After that, we moved on to some pond water. We’d put a few drops of pond water onto a slide and check it out under the regular scope, and draw anything we saw moving around. I found some neat stuff, including a good size flatworm on one slidefull, and a few Urocetra (centrums?) on a few slides, a Diatom or two, a Ciliate that closely resembled a Paramecium (Doc II identified it as a Plagiopyla minuta or something close)…

It was all very small stuff, and I was busy chasing a Ciliate around the slide to try and get a good view of his cilia. They’re fast little buggers, and since the table mover knobs are on the right side of the scope, and I’m right handed, I was swapping between moving the table and making quick, partial sketches of what I saw. Everything was going along quietly when all of a sudden…

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Buh Bye, Fluff Fluff

Mark Dybul, the man the Bush administration has relied on to spread its fundamentalist sectarian dogma of disinformation and ignorance, has been unceremoniously dismissed.

Sworn in as Secretary of State just yesterday, Hillary Clinton wasted no time cleaning house at the vast department she runs. Today, we have heard, Mark Dybul was asked to submit his resignation as US Global AIDS Coordinator, head of the office in charge of the President’s Emergency Plan for AIDS Relief.

This is a huge first step to ensuring the health and rights of all people at risk of HIV and AIDS: Dybul oversaw the last several years of abstinence-only programs funded by PEPFAR, hob-knobbed a bit too closely with the far right, and never saw a law or policy restriction he could not make even more restrictive. Curious for a self-identified Democrat? Not so curious, I guess, if your career is dependent on pleasing the far right, and if your desire to be Global AIDS Coordinator outweighs your desire to stand up for what is right.

Given the fact that this kind of propaganda is known to have led to the deaths of untold numbers of people, I only wonder why there were no handcuffs involved.

h/t Elizabeth Wood

The Evolution of Classification

File this under, “Just Cool Science”.

From Not Exactly Rocket Science:

Whalefishes, bignoses and tapetails – these three groups of deep-sea fishes couldn’t look more different. The whalefishes (Cetomimidae) have whale-shaped bodies with disproportionately large mouths, tiny eyes, no scales and furrowed lateral lines – narrow organs on a fish’s flanks that allow it to sense water pressure.

The tapetails (Mirapinnidae) are very different – they also lack scales but they have no lateral lines. They have sharply angled mouths that give them a comical overbite and long tail streamers that extend to nine times the length of their bodies.

The bignoses (Megalommycteridae) are very different still – unlike the other two groups, they have scales, their mouths are small and their noses (as their name suggests) are very large.

Based on these distinct bodies, scientists have classified these fishes into three distinct families. Now, it seems they are wrong. Amazingly enough, the three groups are all just one single family – the tapetails are the larvae, the bignoses are the males and the whalefishes are the females. The entire classification scheme for these fishes needs to be reworked, as many distinct “species” are actually different sexes or life-stages of the same animal.

Biology rocks.

I’ve mentioned before that we live on a planet that is 70% water by area. Doc pointed out that it’s about 99% of the biosphere by volume and we’ve explored about 5% of that. That’s a lot of planet we humans have never even visited. I expect there’s plenty more weirdness to be discovered at the bottom of the ocean.

It is an amazing, wonderful, and surprising world we live in, and Ed’s got the pictures to prove it.

h/t Greg Laden

Blogging My Biology Class 20080924

Biology, Eighth Edition, by Campbell & Reece, et al.

Biology, Eighth Edition, by Campbell & Reece, et al.

My notes and thoughts from Biology 111, for Wednesday, September 24, 2008. The entire series can be found here.

Forgive the delay in this, the next installment of the series. At about this point in the semester, the workload and involvement in school just took off, and I needed to devote as much time as possible to homework and studying.

When last we left off, we had just begun a quick tour of the eukaryotic cell and its structures. We’d gone over the Nucleus and the Ribosomes, and some of the membrane-bound organelles like the Endoplasmic Reticulum (or ER), the Golgi Apparatus (or GA), and the Lysosomes.

We’ll pick it up here with number 7, the Mitochondria (another membrane-bound organelle), and we’ll go into more depth when we get to Chapter 9.

The mitochondria are sites of aerobic respiration. Recall that C:H bonds have a high potential energy because of the maximum distance of electrons from the nuclei of the Carbon and Hydrogen atoms. In other words, the electrons they share equally are midway between the C and the H.

(The lecture notes continue below the fold.)

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I Think I’ll PASS

Studying Hard by Kyle Kesselring

Studying Hard by Kyle Kesselring

Ok, I suppose the cat can be released at this point.

There are somewhere about 10 students left in my Bio 111 lecture, about the same in my lab. Considering we started out with well over double that, this is disappointing.

Coastal recognizes this is a persistent problem in particular classes and has a plan to address this high drop/fail rate in these classes. Building on a model from U Missouri KC, they are considering instituting what will be known as the PASS program (Peer Assisted Study Sessions). They will be taking a student that has done well in the class in a previous semester and having that student lead a voluntary group study session a few times a week, so that the student who did well in the past can give students currently taking the class some help.

It’s a paid position (not much, but some), and the peer group leader has to keep separate office hours in addition to the group study sessions, to be available for individual assistance.

Additionally, the peer group leader repeats the class (for free and not for a grade) to keep current with the various sections.

Doc asked me a few weeks ago if I’d do this next semester (assuming the college follows through – it’s not 100% commitment yet), and at the time said I was the first one he thought of. I was pretty chuffed about that, regardless of whether I got the position.

He gave me a letter of recommendation, and I turned that in with my application for employment, and the interview went well, I think.

(More below the fold)

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Evolved and Rational has Tangled Bank 115

Tangled BankThe latest edition of Tangled Bank is up over at Evolved and Rational.

Good stuff, including one of my Blogging My Biology Class posts. Check it out.

For those of you not familiar, the Tangled Bank is a bi-weekly blog carnival. Every couple of weeks, bloggers submit posts about the life sciences to the carnival, and one blogger puts them all in one place round-robin style. The carnival was named after Charles Darwin’s eloquent description of life around us, and how it came to be the way it is.

It is interesting to contemplate a tangled bank, clothed with many plants of many kinds, with birds singing on the bushes, with various insects flitting about, and with worms crawling through the damp earth, and to reflect that these elaborately constructed forms, so different from each other, and dependent upon each other in so complex a manner, have all been produced by laws acting around us. These laws, taken in the largest sense, being Growth with Reproduction; Inheritance which is almost implied by reproduction; Variability from the indirect and direct action of the conditions of life and from use and disuse: a Ratio of Increase so high as to lead to a Struggle for Life, and as a consequence to Natural Selection, entailing Divergence of Character and the Extinction of less-improved forms.

—Charles Darwin

Blogging My Biology Class 20080922

Biology, Eighth Edition, by Campbell & Reece, et al.

Biology, Eighth Edition, by Campbell & Reece, et al.

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.

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Blogging My Biology Class 20080919

Biology, Eighth Edition, by Campbell & Reece, et al.

Biology, Eighth Edition, by Campbell & Reece, et al.

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.

Damn.

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.

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Blogging My Biology Class 20080915 Lab

Biology, Eighth Edition, by Campbell & Reece, et al.

Biology, Eighth Edition, by Campbell & Reece, et al.

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.

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Blogging My Biology Class 20080915

Biology, Eighth Edition, by Campbell & Reece, et al.

Biology, Eighth Edition, by Campbell & Reece, et al.

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.

2. Lipids

Triglycerides —> Fats & Oils

glycerol on the left with three fatty acids

Saturated Fat: glycerol on the left with three fatty acids

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.

Glycerol on the left with three fatty acids. Note the kink in one fatty acid.

Unsaturated Oil: Glycerol on the left with three fatty acids. Note the kink in one fatty acid.

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)

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Blogging My Biology Class 20080912

Biology, Eighth Edition, by Campbell & Reece, et al.

Biology, Eighth Edition, by Campbell & Reece, et al.

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* —> C, H, O
  • Lipids —> C, H, O (sometimes N & P)
  • Proteins* —> C, H, O, N, S
  • Nucleic Acids* —> C, H, O, N, P

* Carbohydrates, Proteins, and Nucleic Acids are Macromolecules, meaning “really honkin’ big”.

1. Carbohydrates – Sugars – all “ose” endings mean “sugar”.

“Carbon Water”

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.

A Few Simple Sugars
C Atoms Molecular Formula Group Name
3 C3H6O3 triose
5 C5H10O5 pentose
6 C6H12O6 hexose

(Lecture continues below the fold)

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Blogging My Biology Class 20080910

Biology, Eighth Edition, by Campbell & Reece, et al.

Biology, Eighth Edition, by Campbell & Reece, et al.

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)

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Blogging My Biology Class 20080908 Lab

Biology, Eighth Edition, by Campbell & Reece, et al.

Biology, Eighth Edition, by Campbell & Reece, et al.

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.