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Been awhile…

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Ok, I know it’s been a long time since my last update. Like… almost a year. It’s fine. I get into this mindset where everything is really difficult, especially if it involves perfecting my word choices and making pictures in MS Paint. Because, you know, Paint is very complicated. I could say that I’ve been really busy (I am a grad student, after all, so I can get away with saying stuff like that) — but really, I am very distractable and also do a bad job keeping up with things. Soooo…

Sorry guys :[

Anyway.

A post is in the works if you feel like hanging in there for a few more days. I promise I’ll finish it!

Thanks for sticking around!

Filed under Uncategorized
March 4, 2012

Thoughts on Sugar

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I’ve been seeing this article on news sites and Facebook lately, and since I’m in the middle of reviewing metabolism, I thought I’d watch that 99-minute video referenced in it. The video is a presentation by Robert Lustig, MD, of the University of California – San Francisco, during which he discusses the trends of adding sucrose and fructose to our diet, and how it has affected us decades later. He also goes into metabolism of three kinds of carbohydrates (glucose, ethanol, and fructose) and compares them to make the point that fructose is a major cause of “metabolic syndrome,” which groups diseases such as diabetes, hypertension, coronary heart disease, and obesity (to name a few).

When I first read the article, I’ll admit that my first response was something along the lines of “Great, another obnoxious scare article that doesn’t really say anything we didn’t already know and just makes everyone freak out about nothing.” I will also admit that I didn’t read the article in its entirety. But I did watch the lecture, and it was actually much better than I expected. So I’ve been thinking about it, and here’s what I have to say.

First, of course, are some definitions –

Carbohydrates are a type of macromolecule made up of carbon, oxygen, and hydrogen in a ring formation. These rings can exist singularly (monosaccharide), in pairs (disaccharide), in short chains (oligosaccharide), or in long chains (polysaccharide). These are broken down in the body to extract energy via various metabolic pathways.

Sugar usually refers to any mono- or disaccharide that can form a crystal and that tastes sweet. These usually end with -ose. Examples are glucose (also known as dextrose), fructose (fruit sugar), sucrose (table sugar or cane sugar), lactose (milk sugar), and maltose (from plant starch).

Ok, so here are the three sugars being discussed:

Glucose is the preferred source of energy in our cells. It can be broken down entirely to yield ATP (adenosine triphosphate; the thing that actually powers cellular processes), water, and carbon dioxide when conditions are good. It’s a monosaccharide and looks sort of like this:

Fructose shares the chemical composition of glucose but differs structurally. It’s still a monosaccharide, but it forms a four-carbon ring with the other two carbons kind of hanging off the side. It also tastes sweeter than glucose, probably due to the structural difference, but this means it also takes an alternate metabolic route. It looks a little like this:

Or at least that’s what it wants you to think…

 

No, I jest. Hey now, put away that tin-foil hat! You can put it back on at the end of the post if you want, but for now just hear me out.

Right, so moving on…

Sucrose is a disaccharide formed by the union of glucose and fructose, like so:

High fructose corn syrup is a syrup composed of both glucose and fructose, though they are not necessarily bound together. The unbound fructose causes the syrup to taste sweeter than sucrose, which is actually less sweet than fructose alone despite the fact that it is a combination of two sugars.

High fructose corn syrup is pretty cheap to produce (partially due to how much corn we grow), and you can use less of it to get the same amount of sweetness as sucrose, though the two are metabolized the same.

 

So hopefully that will make things a little clearer throughout the post.

In the video, Dr. Lustig begins talking about the “fat-free” movement, which is what he (and others) attribute to the increase in sugar in our diet.  Sugar was used to compensate for the corresponding decrease in deliciousness when foods became fat free (because fat is delicious, let’s just be honest with ourselves). I can totally believe that. The problem is the logic that “fat consumed = fat that sticks around; therefore, no fat consumed = no fat that sticks around” is inherently flawed. Fat is how your body stores excess energy, saving it for times when food is scarce. Since fat is not the only source of energy that we eat, of course it is not going to be the only source from which we can generate it either.

Eating fat isn’t the only way to acquire body fat. Just about everything you eat can be stored as fat if you eat too much of it — carbohydrates, protein, and fat can all just equal fat if you don’t use the energy shortly after eating.

The primary form of energy storage is glycogen, which takes glucose molecules and links them into long, branched chains during glycogenesis. Glycogen storage is temporary (usually only up to 12 hours), as it is very quick and easy to break back down into glucose. Glycogen synthesis is the first way in which your food is stored. But once your glycogen stores are completely replenished, if you have any extra metabolites in your system, it will be stored in a more long-term fashion, which is good if food is scarce (and is probably why evolution favored it so) but bad if it is not (as is the case for many people in developed countries).

You depend on a metabolic pathway known as the citrate cycle, which takes place in your mitochondria and requires oxygen, to get as much energy as possible from what you eat. Carbohydrates, amino acids, and fatty acids can all enter this cycle, depending on what’s available. These metabolites are converted to acetyl-CoA (acetylated coenzyme-A, which is essentially a 2-carbon molecule attached to a derivative of vitamin B5) before they can enter the citrate cycle.

However, if the citrate cycle gets backed up (if there is more acetyl-CoA than it can handle, often caused by eating too much) , acetyl-CoA accumulates and must be handled some other way. The body’s method of dealing with too much acetyl-CoA is to send it off to lipogenesis, or the synthesis of fatty acids, which can store 8 (or more) acetyl-CoA molecules per chain.

Lipogenesis occurs in the liver, and the resulting fatty acid products are transported to adipose (fat) cells. In order to get there, the fatty acids get bound to glycerol molecules in sets of three (which is where the term “triglyceride” comes from) to be deemed safe for transport through the blood. When you get blood tests and see your triglyceride levels, it refers to the amount of these fatty acids currently in your blood — after a large (or a fatty) meal, this will probably be pretty high; after fasting, it should be pretty low.

Ok, so excess energy results in the synthesis of fat for long-term storage. But that’s true for eating too much of anything, so why is fructose specifically being targeted as a bad thing? Part of this is due to where glucose and fructose can be utilized.

Glucose can be transported to and broken down in any type of cell.

Fructose can only be metabolized in the liver.

If you are eating a lot of sucrose or high fructose corn syrup in your diet, your liver is going to be overwhelmed with all that extra fructose the rest of your cells can’t do anything with. A lot of this fructose is going to be converted into fat, which you really don’t want hanging around. Not only is it a bad thing to transport through your blood all the time, but it is difficult to break down once you’ve stored it, and too much can damage your tissues because they weren’t meant to have a bunch of fat sticking to them. But it gets better! If there is still an excess of fructose before it is broken down into acetyl-CoA for lipogenesis, it can form some other not-so-great products as well (leading to production of reactive oxygen species, inflammation, and hypertension). Dr. Lustig goes into the biochemistry of fructose metabolism at around 40 minutes into his talk, but I won’t go into it here — animal hormone signaling isn’t really my thing, and I feel like the fructose-to-fat issue is one of the biggest problems with our increased consumption of sugar, with a lot of those other byproducts being secondary to that.

Ok, so finally, I want to mention that “natural” does not always equal “good” or “safe.” People were originally sold on the idea of fructose because it is fruit sugar, and fruit is good for you! Therefore fruit sugar must also be good for you!

Not so.

In nature, fruit does contain fructose… but it also contains a lot of other important things, such as assorted vitamins and fiber. And fiber can actually help you with the fructose that comes along in the package, since fiber adjusts the environment in your intestine to slow absorption of sugar (in addition to making you feel full sooner, so you won’t eat as much as you might otherwise). So fructose in fruit = good, at least in moderation. Eating nothing but apples all day is still probably not such a good idea. But fructose on its own is even worse, as fructose alone has nothing else beneficial to you.

Balance is a tricky thing to obtain, but it’s important.

So next time you’re debating whether or not to buy fat-free food, check to see if it is excessively sweetened with sucrose or high fructose corn syrup. If it is, remember that a high sugar diet is also a high fat diet, and as in all things, moderation is key.

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April 24, 2011

Why I hate Lysol

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I hate Lysol. A lot. Every time I hear or see one of their ads, I find myself getting angry all over again.

Are you worried about having a clean, healthy home? Do you have any of those “breeding grounds for bacteria” that you keep hearing about, like your bathroom or your dishwasher or your dirty socks? Does your soap dispenser frighten you because you have to touch it both before and after washing your hands?

Well, here’s a big secret:

Stop freaking out so damn much.

Seriously.

Right now, right at this moment and right where you are sitting as you read this, you are existing in a sea of microbes. They’re in the air you breathe and the water you drink, they’re in your hair and on your skin, and they’re even living inside you. And you know what? That’s ok. Unless you have a debilitating immune deficiency or disease, you really don’t have to be so completely paranoid about it.

I’m not saying that it’s a good idea to go out and roll around in a pile of trash. But this whole “germs are so scary!” business is getting really obnoxious and, even worse, is actually more detrimental than helpful.

So let’s start first by defining “germ.” Germs usually refer to microorganisms (bacteria, fungi, archaea, protists, and viruses) that are pathogenic, meaning they can cause illness. Well, to be completely correct, viruses aren’t technically “alive” by most people’s standards and thus cannot be classified an organism, but they are often lumped into this group anyway. So yes, it’s best to avoid germs if you can. But humans have been living with germs for as long as they’ve been on the planet, and so the human body knows a thing or two about keeping itself safe.

 

First of all, you have skin. This is a pretty important barrier to germs, since it’s difficult for them to penetrate this layer without finding a cut or break to get them through. Your skin cells are also being constantly regenerated, so even if you have a microbe stuck to you, it will probably get cast away along with the aging layer of cells and just become dust in no time. And not only that, your skin secretes several types of antimicrobial peptides (chains of just a few amino acids, not full-length proteins) and has a slightly acidic property to it, which is quite unfavorable to most germs. Your sweat is full of salts too, which will disrupt certain types of bonds that hold some germs together.

So really, take care of your skin. It does a good job of not making you a pile of germs.

The leaves of plants have a similar layer of protective stuff. In addition to just having “skin” (they still have an epidermal layer), they have a waxy cuticle which prevents both dehydration and penetration of pathogens.

 

You also have several mucous membranes throughout your body. I’ll talk about the nose and lungs, but mucous membranes are part of certain nether regions as well.

Your nose is full of hairs and mucous. It’s ok, you don’t have to be ashamed of it, everybody has them — and it’s a good thing too! When you inhale through your nose, you inevitably also breathe in a bunch of germs. Some of these will get caught on your nose hairs or in your mucous, which will get swept up and swept away towards the back of your nasal passage where it can be swallowed. Very, very few germs can survive the extremely acidic environment of your stomach, and thus you have been saved from those microbes that mean you harm. Alternatively, those germs will get stuck in your mucous until they are blown out onto a tissue, in which case they are still powerless and you are free and clear of them anyway.

Your lungs have a similar sweeping mechanism. All around the epithelium of your lung, you have mucus and what are known as cilia, which are the actual sweepers here. They’re sort of like little hairs that move in a wave-like motion, pushing mucous (and whatever is stuck inside it) up and out of your lungs, towards your pharynx where it can also be swallowed (or coughed out). Again, anything that is swallowed will likely not be able to survive your stomach, and thus you have been saved once again.

Should any of your personal physical barriers fail, you also have an immensely complex immune system. If a germ enters your body somehow, it is likely to be eaten by cells constantly wandering through your blood and lymph (which essentially go everywhere). And if it still manages to survive that, it will eventually trigger an adaptive immune response, in which case the infected cell (and everything in it) will be toast before the infection can get too out of hand. The number of times you actually get sick are very, very low compared to the number of times that germs get into you.

 

But anyway. All that aside, there is one more simple, external method to combat germs that I’ll get to here, and that is soap.

No, not antibacterial soap. Just soap. Soap, simply by being soap, is actually quite good at getting rid of germs.

If you took some soap and zoomed way in on it, this is sort of what it might look like:

Soap is made of a polar (water-soluble) “head” region and a non-polar (water-insoluble) fatty “tail” region. When you put a bunch of these individual molecules together and add water, the water will interact with the polar head groups and force all the fatty tails together (fatty solidarity!). That way, both regions of the soap molecule are happy. In this way, you can get normally water-insoluble substances (like grease, which is also extremely hydrophobic) to wash away with the dirty dishwater.

Germs are really not so different. One way or another, soap will stick to them and allow them to be washed away just like anything else. This is why the soap doesn’t necessarily need to be antibacterial — the bacteria (or any germ) will go away because soap is soap. If it’s antibacterial soap, maybe the germ will be inactivated a little faster, but the end result is the same:

Ok, so now that you hopefully have a greater appreciation for the simpler antimicrobial strategies you have at your disposal, let’s talk about how buying antibacterial products does not actually make you any safer. If anything, it’s more likely that using these products as frequently as we do is only exerting more selective pressure on whatever germs we’re worried about, causing them to evolve new methods to get around our “safe” chemicals.

This applies to antibiotics too, which are exceedingly over-prescribed and, thanks to their mis-use, we now have “superbugs” like the flesh-eating methicillin-resistant Staphylococcus aureus (or MRSA). Staphylococcus aureus used to be killed off easily by penicillin, which prevented the bacteria from forming a cell wall until it developed an enzyme to destroy penicillin. Then it used to be easily killed by methicillin (similar to penicillin, but S. aureus does not recognize it as such), until S. aureus said “You know what? Screw this” and came up with an entirely new, second enzyme to form its cell wall — one that is not inhibited by any antibiotic yet discovered.

Every time you wash your hands or spray your counters with antibacterial or antimicrobial substances, just think about that. Take care of your skin. Take care of your mucous membranes. Wash things with soap and water, or even alcoholic or acidic substances like isopropanol (rubbing alcohol), vinegar, or lemon juice. But don’t immediately assume that just because something “kills 99.9% of germs” that it is better or safer. Using Lysol does not make you safe, and they are only deluding you out of your money by telling you otherwise.

Filed under Basic Biology, Rants, Things That Are Wrong
April 11, 2011

Why You Can’t Be a Monkey’s Uncle

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Just as a disclaimer, I would like to state that I don’t want this to be one of those blogs where scientists complain about creationists/God/politics/whatever. If you want one of those, I’m sure you have many other options. Of course, that being said, here is a post about evolution, which always sparks a lot of anger between those who believe in evolution and those who believe in intelligent design or whatever it’s being called these days. It’s sort of a shame, really, because evolution is quite beautiful and the more you know about it, the more you can appreciate it.

But I really don’t care what you believe. My issue is that since such a huge part of the creationist rhetoric is teaching critical thinking by presenting alternative ideas and letting people decide for themselves what is right, I feel like what is presented as evolution should at least be accurate. Also it seems that if you have a science blog, posting about evolution at least once is somewhat obligatory. And this makes sense. Evolution has tied so much of biology together that it’s really pretty hard to avoid.

So anyway, I’ve been thinking about this a lot today because one argument against evolution keeps coming up over and over again, which is essentially…

“Why do we still have apes if we came from them?”

This is a recent quote from a Florida politician, but this video (poor quality, sorry) shows similar misunderstandings from not only Christine O’Donnell, but another guest and even the host himself. If this is the way most people believe evolution works, it is not acceptable.

So first I will try to clarify this one point, and then hopefully I can explain evolution in a new way so that it makes some more sense.

 

You did not come from a monkey, and whoever told you so was lying.

For whatever reason, humans seem to be awfully full of themselves in believing that monkeys somehow have this “goal” of achieving the status of human being. Either that or our attention spans are too short to consider the fact that the Earth is older than we can truly comprehend, and so instead we focus on amounts of time that we can understand (i.e. hundreds or thousands of years). The accumulation of changes necessary for the monkey/human divergence took millions of years, so maybe it’s just that people don’t think about looking that far back.

But if you did, this is essentially what evolution is describing:

So no, we did not come from monkeys. But we do share a common ancestor with them. This divergence occurred millions of years ago. Monkeys are not “behind” humans in evolution, and they are not “evolving towards” us. They are just monkeys, evolving in their own direction. And we are just humans, evolving in our own direction.

 

There are probably thousands upon thousands of websites out there with the purpose of clarifying some common misconceptions about evolution. Originally I intended to make this post one of those “this is what people say, and here’s how it’s wrong!” but those are boring and, frankly, overdone. So instead, I will try to explain some general concepts of evolution using a metaphor I think most people can appreciate.

 

So let’s say you have survived a zombie apocalypse. Congratulations! Your brains are not someone’s breakfast, and that’s an impressive accomplishment. But zombies have a pretty sizable appetite, and soon they will be coming for you. So what do you do?

Well, you have a few options. First, you can hide. Maybe you found a nice abandoned warehouse with tons of vitamin-fortified cereal or something and you decide to just stay put. Zombies probably hate cereal (no one makes brain-fortified cereal anyway), and if you’re really quiet and sneaky when you absolutely have to leave your warehouse, you might just live a pretty decent life. This is a respectable choice. I love cereal personally, so this is probably what I would do.

But maybe that’s not your style, so you say to yourself, “Self, are you just going to let a little zombie problem control your life? No, I didn’t think so.” And what do you do? You go out expecting a fight. And you go well armed. This is a little more proactive than sitting and hiding, though it comes with its own risks as well. Let’s follow this choice for the rest of the post, mostly because it’s a little more exciting.

There is also a third choice, however. This would be the bad choice. Valid, but bad. This would be the choice you make when you decide that you just can’t bring yourself to leave your home because you have been there for so many years and put so much time into it that you just can’t possibly leave and… well. Unless you live in a fortress, you probably present very little challenge to a zombie. Zombies love to break doors and windows to stick their hands in and grab you. They’d be quite pleased with your decision, but the same can’t be said for you. I’m sure you would make a tasty zombie snack in no time.

In this example, zombies are exerting what is known as selective pressure on you (and the rest of humanity).

After your initial flee of terror, let’s take the second route — the one where you arm yourself because you do not appreciate being chased off by zombies. But it’s the day after the apocalypse and you have no guns or anything else to speak of. What do you do?

Well, first you meet up with two other survivors by chance. This is almost required for experiencing a proper zombie apocalypse.

So the three of you decide to search for weapons together, and eventually you stumble upon a little stash tucked away in an abandoned shed. For the sake of argument, you can only choose one weapon, and once you do, you cannot put it down or choose another one. And it’s dark. So you each pick one up at random. The first person picks a revolver, but it’s unloaded and there is no ammo for it in the shed. The second person picks up a flamethrower, fully fueled, with no idea how to use it. You pick up a pistol and stumble over tons of ammo for it. Victory! The three of you are now armed, though not equally.

These weapons represent random mutations that may occur once an organism is exposed to selective pressure, and each mutation may be varying degrees of helpfulness against said selective pressure. I just want to emphasize the random part here. An organism cannot decide to mutate — it just does. Some regions of DNA have higher chances of being mutated, while others have lower chances of being mutated. I can discuss this in another post maybe. But for now, we’ll stick with this. Silent mutations effectively do nothing. This is a mutation which does not change the genetic code in any way due to redundancy built into the central dogma (each amino acid may have anywhere from 2-4 codons that encode it). Harmful mutations change a gene in such a way that it may become detrimental or even lethal to the organism. These usually do not make it to future generations. The last type, beneficial mutations, will change a gene in such a way that the organism receives some benefit from the change.

Or, to summarize:

 

So the three of you, now armed, continue on your way to find some shelter or maybe food. You encounter several zombies on the way to wherever you go. The person with the flamethrower, having no idea what he is doing, promptly sets himself on fire and burns to a crisp. You must leave him behind. The person with the unloaded gun has no specific advantage, but maybe he is a fast runner, so you two manage to escape most of the zombies just fine.

But then, just as you are about to reach your destination, you encounter a whole bunch of zombies at once! There are at least thirty of them, backing you up into a corner and trying to bite you! With nowhere to run and no means of defense, the person with the unloaded gun cannot rely on his speed any longer, and he is quickly devoured by the frenzied mob. And then it is only you. You, your gun, and your ammo. In a rush of adrenaline, you are able to kill or maim all the zombies, run to safety, and live another day. Good for you!

The zombies have forced you to change yourself by trying to hunt and eat you. To change yourself, you decided to become armed. Your weapon was chosen at random, but fortunately for you, it turned out to be a beneficial weapon. With this new weapon that the zombies could not overcome, you were able to escape. You have won the game.

In nature, it works somewhat similarly. I mean, obviously there are some issues with this metaphor, as there will be with any metaphor. But essentially, it is the same track. An organism is disturbed by a change of some factor in its environment (predation, pathogen, chemical, temperature), and it needs to adapt in order to continue to survive. Mutations (occurring at random) may affect the organism’s ability to deal with these types of stress. Those individuals who undergo beneficial mutations will have an advantage over those with harmful (or even silent) mutations, and thus they will be more likely to thrive in their changing environment.

When these small changes in an organism add up over years and years of adapting to its surrounding environment, that organism may have accumulated enough mutations so it is different from what it was before all those changes occurred. And maybe another member of the same kind of organism took another route — maybe it decided to hide instead of becoming armed, and now it is successful in its own and different way. This is known as speciation. Each new organism, derived from the original species, has taken alternate routes to continue to survive. Neither is necessarily better than the other. They’re just different.

Now the really interesting part in our little example is if a zombie starts to get smart. I know this probably wouldn’t happen because zombies have little to no cognitive function, but for the sake of argument…

Yeah. Now what are you going to do? There are armed zombies. And they are coming for you right as you thought you might be able to get comfortable.

This is known as the evolutionary arms race, or the Red Queen Hypothesis. You’re just going to have to keep running faster and faster in order to stay in the same place and avoid becoming zombie chow. Doesn’t seem fair, does it?

But hey, that’s life.

Filed under Basic Biology, Evolution, Things That Are Wrong
March 31, 2011

The Central Dogma

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It is difficult to understand many aspects of biology without first understanding what has been termed “The Central Dogma,” which essentially describes the flow of information from code (gene) to function (protein). I think it technically only deals with proteins being an irreversible “end product” to genes, but now it has sort of encompassed the entire process of genetic flow. In K-12 biology, and even in many basic undergraduate biology courses, there’s only one pathway presented. But life is amazing and there is really much, much more to it than most people ever hear about.

But basics come first.

In your cells, you have a nucleus. Unless you are a prokaryote, in which case you have sort of a nucleoid region, but if you were a prokaryote, I doubt that you would have any idea what I’m saying right now because you would be a single-celled organism. So anyway, in your nucleus, you have tons of DNA. You have some other stuff in there too, but nuclei are famous for their storage of DNA so we’ll focus on that for now.

DNA, which stands for deoxyribonucleic acid, is composed of a sugar (ribose) “backbone,” bound via phosphodiesterase (phosphate and oxygen) linkages on one side and an aromatic (ring) on the opposing side. These rings are known as bases and are denoted adenine (A), thymine (T), cytosine (C), and guanine (G), which can interact with each other (known as base pairing) to form A-T or C-G pairs and, ultimately, a double-stranded DNA molecule. These base pairs are fundamental to how information in DNA is stored, which I’ll get to in a bit. However, DNA is also confined to the nucleus, so how does it get this information to the rest of the cell?

This brings us to the second type of nucleic acid, termed RNA for ribonucleic acid. It’s also composed of a ribose “backbone,” but with slightly different structure than DNA. Due to this slight difference, it does not normally form double-stranded molecules, and it is also much easier to break apart. RNA also replaces the base thymine (T) with uracil (U), which is a less stable version. Why these differences? If RNA is what’s supposed to be transferring information from nucleus to cytoplasm, why would it be more fragile? Well, if you think about it, this makes sense. DNA is replicated during mitosis and transferred from mother cells to daughter cells. It’s replicated during meiosis to be passed onto offspring. If there’s a mistake in DNA, it could have potentially serious effects for the current cell, its daughter cells, or even the organism’s future offspring. DNA is long-term. RNA, on the other hand, is usually synthesized for very short periods of time, and once it has fulfilled its purpose, it needs to be degraded. If it were too stable, this could result in some equally disastrous problems. For example, if you had a protein that repressed some aspect of metabolism, making it impossible for you to extract energy from your food, would you really want a lot of it hanging out in your cell all the time? Probably not.

Anyway. Inside your nuclei, DNA can be “unzipped” from its double-stranded form to expose the base pairs present on an individual strand. From this template, a molecule of single-stranded messenger RNA (mRNA) can be synthesized complementary to the original, individual DNA strand. In other words, if the DNA sequence reads GCTCAATGC, the mRNA sequence will read CGAGUUACG in order to maintain the rules of base pairing. Once it reaches the end of a gene, it will dissociate from the DNA (which re-zips), be processed for sufficient stability, and will get exported from the nucleus.

Upon exit, mRNA will interact with ribosomes (also composed partially of RNA, though this is termed ribosomal RNA, or rRNA). Once ribosomes bind to specific sites on the mRNA, a third type of RNA (named transfer RNA, or tRNA), will recognize the mRNA sequences in sets of three. Each set of three bases in mRNA is termed a codon, which corresponds to a complementary codon in the tRNA. tRNAs have two main domains — one that recognizes mRNA sequence, and the other that binds to amino acids, which are the building blocks of proteins. Using the same example as above, if the mRNA reads CGAGUUACG, the tRNAs will recognize this message as GCU CAA UGC, which corresponds to the amino acids Alanine, Glutamine, and Cysteine, respectively. Each amino acid has certain properties that will eventually lead to a whole, functional protein.

 

Ok, that was a lot of letters, so here is a slightly simpler diagram!

Hopefully that helps?

 

Right. So.

This protein that forms from successive tRNAs bringing their respective amino acids into close proximity is the end result of the genetic code. Once translated from mRNA, the protein cannot return to its nucleic acid form. This is the essence of The Central Dogma. The mRNA can be translated several times before it is degraded, but ultimately it will be degraded in order to prevent too many proteins from accumulating in the cell.

 

Now, for a long time, this was all that was really understood, and it seems to be what is primarily taught in schools. But to say that this is the only way genetic information operates (that is, DNA is transcribed into RNA, which is translated into protein) would be only a partial truth, so here’s an interesting thing –

Viruses can have either type of nucleic acid to carry their genetic information around, and it can come in different forms. There are families of virus that can have single-stranded DNA, or some will have double-stranded DNA. Other types will have single-stranded RNA, and even more interesting are those that have double-stranded RNA (which is rarely seen in nature except as a temporary intermediate). But those that have single-stranded RNA have devised a clever method to transcribe their RNA into DNA, making their genetic information not only more stable, but also able to integrate into their host’s own genome. Kind of spooky if you think about it. To be fair, DNA viruses can do this too, but the concept of being able to go from RNA to DNA was previously unheard of, which is part of why everyone makes a huge deal about Retroviridae (the other part being the fact that HIV belongs to this family, so there’s that too).

Considering the structure of DNA was only discovered half a century ago, we’ve made some pretty impressive progress in understanding it and how it really works. And we’re not even close to being done. It wasn’t until the 1980s that we really figured out that histones (proteins that associate with and pack DNA into its compact form) can be modified to alter gene expression. This has also wildly changed our view of how genetic information flows, and we will surely be toying with and discovering the intricacies for years and years to come.

 

So there is some very fundamental information about how genes work. Nothing too crazy, right? Now if only I could get the people who do movies to read this so they can stop making it sound like there’s so much voodoo when it comes to genetics, I’d be pleased as punch.

Filed under Basic Biology
March 28, 2011

Knowing What You’re Dealing With

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As mentioned in the previous post, this whole re-make thing was partially inspired by one guy who obviously had no idea what he was dealing with in terms of biology.

To reiterate his claim here, it was essentially that life on Earth is binary — that is, it comes in mutually exclusive and opposing pairs, such as plant/animal or male/female.

Let me start at the most fundamental level, which is simply that it is very, very rare you will find anything that is exclusively one or the other when it comes to life in general. Actually, when it comes to just about anything in general. Viewing the world in terms of black and white will rarely do you any good.

Now that that’s out of the way, what’s this business about the plant/animal classification? In elementary school, you may have noticed that many forms of life fall into the category of plant (the grasses and trees and flowers you see most places, as well as the fruits and vegetables you eat) or animal (most importantly you, maybe your dog or cat, and probably the birds that chirp outside every morning). Maybe even in school you learned about plants and animals and all the different species that occupy different habitats, so on and so forth. That’s all well and good. These things are important.

But also of great importance are the things you don’t see every day.

 

Long, long ago, plants and animals were the only two kingdoms of life. As we invented microscopes and started exploring the world more, we realized, holy crap, there’s a lot of other stuff out there! Thus the “tree of life” started sprouting more and more branches until, lo and behold, we have the following modern-day mostly-accepted tree of life:

Domain Bacteria — composed of the kingdom Bacteria, which is pretty much just what it sounds like. Bacteria includes various pathogenic species such as Yersinia pestis (the Black Plague), Neisseria gonorrhoeae (gonorrhea), Ralstonia solanacearum (various wilts of plants), and… you get the idea. Bacteria also LIVE INSIDE YOU (oooooo), not because you are icky, but because they are part of your natural flora and actually help you digest your food and keep your intestines working properly.

Domain Archaea — composed of the kingdom Archaea, which are prokaryotic (lacking a true nucleus) single-celled organisms that usually live in really weird places. This kingdom used to be lumped in with the bacteria, but they’re so different in terms of metabolism that they recently got their own kingdom and domain instead. Archaea live in unusual, sometimes extreme environments. These are what you will find subsisting off alternative carbon sources (such as methane); in high acidity, salinity, or alkalinity; or in extreme heat or cold. Archaea can also be found in the guts of cows termites and are actually what allow them to extract energy from the cellulose of the grass or wood they eat.

Domain Eukarya — composed of six kingdoms which I won’t name because it starts to get tedious. But these include protozoa, amoebas (spanning two kingdoms), algae (which also span two kingdoms), plants, fungi, and animals. I would like to point out here that no, fungi are not plants. Fungi actually share a kingdom with animals, which I think most people don’t realize. The more you know!

 

These are, of course, always subject to debate. The tree of life has been reorganized so many times since the 1700s that I expect this will change (assuming it hasn’t already, which wouldn’t surprise me). But you can see that plants and animals actually occupy a very, very tiny fraction of all life on Earth. In terms of biomass, maybe they’re on the map somewhere, but in terms of diversity and species… not so much.

Not only that, plants and animals are not opposing sides of biology at all, and although plants are not animals and animals are not plants, they actually have more in common than you might think. If someone tried to compare, for example, a human to Ferroglobus (a member of Archaea found near hydrothermal vents at the bottom of the ocean), then we might have a little more to talk about, but even then I’m sure we have more in common than you might expect.

 

So that brings me to my next point, which is shorter, I promise. This whole “male/female” business is really very silly. Separating members of a species into male and female can lead to one form of reproduction (sexual) to produce the next generation. And that’s fine. Sexual reproduction can be a great way to diversify the genetic pool of a species, but it is certainly not the only way that species can do it.

Let’s break it up into the two fundamental methods of reproduction — sexual vs. asexual. I’m sure by now most people are pretty familiar with how sexual reproduction works, in that it is a joining of two separate sets of genetic information from two members of the species. But this is not always done by splitting a species into two sexes per individual. Plants are a great example of this, where male and female can co-exist in the same flower and can either be cross-pollinated (sexual reproduction) or self-pollinated (asexual reproduction, in which the offspring are genetically identical to the parent). The plant does have male and female gametes in separate organs, but because those gametes may still combine to form a seed, it is not guaranteed that the plant will undergo sexual reproduction each time. This may differ from season to season or even from seed to seed. There are also hermaphroditic animals, namely invertebrates such as snails, slugs, and worms, that have male and female organs but are able to self-fertilize.

Another asexual method utilized by some species is that of budding, which is essentially that a “child” will start to grow out of the “parent” organism and eventually separate to become its own individual organism. This is the preferred method of sponges and most types of yeast, which is probably for the best because I don’t want to imagine what, say, a giraffe starting to bud a baby giraffe would look like.

Even more basic than this is simple division (or mitosis), in which an organism divides and voila! now you have two organisms! Obviously only single-celled things, such as bacteria and protozoa, can get away with this, but it’s still a valid form of asexual reproduction.

Ok, one more thing that I just want to mention about bacteria specifically — while they do undergo mitosis to further their species, they are not without methods of varying their genetic pool. Bacteria are able to take up free DNA from the environment when subjected to stress (like sudden high heat), and individuals can exchange genetic information via pili (singular: pilus). These pili essentially allow the two individuals to fuse briefly, and one bacterium will “donate” a copy of DNA to the recipient bacterium. It’s not technically sexual reproduction, but it’s not completely asexual either. The term used for this is “conjugation.”

So once again, we’ve reached my point. Sure there is male/female, but there’s also both or neither or something sort of in between. The two are not exactly opposing, and they certainly aren’t mutually exclusive. Life will exist where and how it can, and if that means undergoing sexual reproduction, self-fertilization, budding, or just simple mitosis, that’s what it’s going to do.

 

And that pretty much sums up why this guy at the workshop was so off-base. I’m sure he was trying to illustrate a point to further discussion and prompt generation of new and unique ideas, but come on. Let’s be real about this. If you want to talk about strange forms of life and how they might exist, you really have all the inspiration you could ever want right here on your own planet.

Filed under Basic Biology
March 15, 2011

Materials and Methods Gets a Makeover

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Ok, I don’t think this is working out quite like I wanted to. I admit that I’m not completely surprised because I knew that going to grad school would mean less time for crafty stuff, but it’s difficult to really understand what that means until you’re in the middle of it. So really, I haven’t had time to bake or sew or knit or crochet (though I’ve been trying to learn how to do the latter, just with not much success). What I have had time for, since it’s the thing I’m supposed to be doing anyway, is science. And the more science I do, the more I want to talk about it.

How convenient, then, that I have a science-y named blog right here, not getting hardly any use.

Thus, with Kai’s reassurance that people do this all the time, I am reinventing Materials and Methods to something I can really talk about more. And hopefully this place will get a little more exciting. Science really is quite exciting, I promise!

 

I have to admit what really spurred this desire to change, though. I’d been sort of playing with the idea for a couple months (since I haven’t updated since late December — eek!), but this weekend was finally what really sealed it for me. You see, Tucson has an annual Festival of Books, which is pretty much exactly what it sounds like. People gather in droves to the university to look at books or e-readers, learn about literacy and educational programs in the community, squee about their favorite genre, meet their local authors (and get their new books signed!), and go to workshops. This whole thing lasts two full days and is pretty epic, let me tell you. It’s great to see so many people interested in books!

But the workshops are what I really want to bring up. There was one about world-building that I absolutely HAD to go to because I always end up writing alternate-universe-type fantasy for November’s National Novel Writing Month (NaNoWriMo). I was stoked! Maybe I could finally get some help with my 2D worlds and learn how to make them more realistic! Maybe I could get a few new ideas to toy with! There might be so many things I had never thought of, and I would be inspired for my next NaNo story!

The room was crowded, with no vacant seats and people standing near the door or in the corners, waiting for the workshop to start. I thought about turning away because there just wasn’t any room, but there was still a perfectly good spot on the floor, so I sat there instead. Finally, the speaker stood up and introduced himself, and the workshop began….

It was ok at first, if a bit basic. He talked for a few minutes about adding little twists to other worlds while still being inspired by Earth, which is usually kind of how it works anyway, but that’s fine. People were getting into it, so I could appreciate that.

But then came the next point of comparison between Earth and whatever hypothetical world you wanted to create — Biology. The point essentially stated that Earth’s biology was formed in binaries (plant/animal, male/female), and wouldn’t it be just so interesting if your world’s biology was made up of threes or fours instead?!

At this point, I could no longer pay attention. Part of me was irritated at this simplistic presentation of the world, and another part of me was depressed that this might really be the way people think of it.

 

So I am here to tell you that the Earth is a pretty damn weird place, and there is way more to life than most people realize. I am constantly being stunned at how funky things can be on this planet, and that’s part of why I love it so much.

Therefore, next post will be an introduction to life and how this guy is totally missing out on his world view.

Filed under Basic Biology, Things That Are Wrong, Uncategorized
March 14, 2011

A Conglomeration of Links

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I’ll be getting on a plane for Atlanta pretty soon, but I wanted to share these because 1. they’re pretty cool, and 2. if I don’t, I might lose them.  I am awful when it comes to opening new tabs in my browser and then forgetting about them, or about bookmarking things and then never looking at them again.  So maybe if I put them here, they won’t be lost forever in my non-system of keeping links.

Homemade Gifts in a Jar

Domo Cookies

Teacup Pincushions or anything by Betz White

Cute little coin purses

Christmas tree ornament mobile + how-to

Filed under Uncategorized
December 23, 2010

Experiment: Gingerbread Cupcakes

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Oh my gosh, I have been so bad about updating :(  I’ve been doing some crafty things on and off but not really enough to take pictures or write about.  Too much labwork, too much homework, not enough energy.

But (!) I did finally get around to making something yesterday — gingerbread cupcakes.  With cinnamon frosting.  And little gingerbread men.  Oh yes.  Gingerbread tastes and smells delicious, yet for some reason I have not made it in years and years.  So when I found this recipe from Sweet Pea’s Kitchen, I couldn’t help myself.  Too cute!  Also I am apparently unable to make anything besides cupcakes (they’re just so easy and so nicely portioned…).  Anyway.  Kai also has a particular fondness for gingerbread, and since she’s had kind of a rough week at work, it seemed like a good time to try these out.  There is no medicine quite like copious amounts of butter, sugar, and spices.  But I digress.

On to the cupcakes!

Kai’s mom gave me a whole bunch of decorative cupcake papers for my birthday, and when I decided to make these, I knew the red-and-green ones would add a nice bit of festivity.  She also gave me my very first frosting bag + tips, so finally I have some frosting that doesn’t look like it was just plopped onto the top of the poor things.  I guess the gingerbread man hides the frosting a bit anyway, but they just look so much nicer with pretty frosting!

See what I mean?  Big improvement since the fall cupcakes!!

I did make a couple of modifications to the recipe itself because I think there was too much butter in the cake and not enough in the frosting.  I learned my lesson about not-thick-enough frosting last month, so when I saw that mine wasn’t holding its shape very well, I didn’t just say “ehh, I’m sure it’s fine!” like I probably would have otherwise…

So, the recipes (again, from Sweet Pea‘s Kitchen):

Gingerbread Cookies

3 cups flour

3/4 cup brown sugar

3/4 tsp baking soda

1 Tbsp ground cinnamon

1 Tbsp ground ginger

1/2 tsp ground cloves

1/2 tsp salt

1 1/2 sticks (12 Tbsp) unsalted butter, room temperature

3/4 cup molasses

2 Tbsp milk

Combine flour, sugar, cinnamon, ginger, cloves, salt, and baking soda.  Add butter and mix with electric mixer until butter is well incorporated.  Add molasses and milk, mixing until the dough is evenly moistened.

Divide and roll dough into 1/4 inch (or slightly less) thickness between two pieces of parchment paper.  Place in freezer for 15-20 minutes until the dough is firm.

Preheat the oven to 350 degrees and line cookie sheet(s) with parchment paper (or use one of the sheets from the dough once it comes out of the freezer if you like).  Using a small gingerbread-man cookie cutter, cut out shapes from the dough and place on the sheets, spaced about an inch apart.  Bake approximately 11-15 minutes, or until pressure from a finger is met with resistance.

Allow cookies to cool on the sheet for a few minutes, then transfer to a wire rack.  Combine scraps of the dough, re-roll, re-freeze, and repeat.

I recommend making these first so they’ve had plenty of time to cool by the time you’re ready to decorate.

Gingerbread Cupcakes

1 1/2 cups flour

2 Tbsp ground ginger

2 tsp ground cinnamon

1/4 tsp ground cloves

1/4 tsp ground nutmeg

2 sticks (16 Tbsp) unsalted butter, room temperature

1 1/2 cups sugar

3 Tbsp molasses

4 eggs

1 tsp vanilla extract

24 small gingerbread men

Preheat oven to 350 degrees and line a muffin pan with baking cups.

In a medium bowl, combine flour, ginger, cinnamon, cloves, and nutmeg.  Set aside.

In a large bowl, cream together the butter and sugar, then add the molasses and combine well.  Beat in the eggs one at a time, followed by the vanilla.  Add the flour mixture slowly, until fully incorporated.

Fill the cupcake papers about 3/4 full and bake about 30 minutes, or until a toothpick comes clean.  Let cupcakes cool completely before frosting.

Cinnamon Cream Cheese Frosting

8 oz cream cheese

2-3 cups powdered sugar

4 Tbsp unsalted butter, room temperature

2 tsp vanilla extract

2 tsp cinnamon

Combine cream cheese and a portion of the powdered sugar until smooth.  Add the butter, vanilla, and cinnamon until well combined.  Continue adding powdered sugar as needed until frosting becomes thick and does not run or drip.

Spoon the frosting into a decorator bag fitted with the tip of choice (I used closed star for mine) and add frosting in a spiral around the top of the cake.  Top with a gingerbread man.

Makes about 24 cupcakes and a small army of gingerbread men.

Om nom nom!

Filed under Uncategorized
December 20, 2010

Experiment: Fall Leaves

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Oh dear.  I should have written this post about, oh, a month ago.  I have no excuses.  :(

Anyway, I love fall.  By now I think you know this.  But since Tucson doesn’t really experience the lovely color changes of deciduous trees, I decided to improvise — with felt leaves on the wall!

I found this template over at Creating Cupcakes and liked the relative simplicity (seriously, some people obviously have way more patience than I do) and variety of leaves.  So Kai and I hunted down some red, orange, and brown felt for the cause.

Note the festive shirt too :D

Maple leaves are some of my favorites, so I made sure we had enough!

We traced the leaves with fabric pens so we could just wash away the ink with a damp cloth later.  We didn’t really get all of it off, but it sort of added a more worn look (especially to the orange ones) that fit the theme well enough.  Still, next time I might try a different one…

Once all the leaves were cut, it was time to sew the veins on!  I will note here again that I have no patience, especially not for detailed hand-sewing (which is probably why you see this one half done…).  I managed to hand-sew two leaves before giving it up and letting my sewing machine have a go instead.  As long as the thread is contrasty enough, it looks fine.  So if you’re short on time (or lazy like me), let me assure you that it’s ok.

The best part came last — sticking them onto the wall!  We used Scotch tape originally because we are cheap like that, but this did not end so well (i.e. leaves were falling down every few hours — realistic maybe, but not really what was intended).  Painter’s tape is definitely a better choice.

And voila!!  Instant fall-ness in the home!  I have been wanting to try felt wall art for awhile, and this was a lot of fun.  I will definitely be looking for related projects in the future.

Filed under Uncategorized
November 5, 2010

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