Category Archives: Science

Reading Your Blueprint: Karyotyping

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DNA is  what makes us who we are. It identifies us. The government uses it to control us. Well, that last one isn’t quite true…yet. Still most of us, even those of us who should know better, treat DNA as if it were magical fairy dust that wizards in lab coats use to answer questions. But the only difference between the wizards and you is some knowledge and equipment. This blog will help with the knowledge part.

There are three main ways to use DNA to tell something about an individual: Karyotyping, DNA fingerprinting, and Genome sequencing. I’ll go over Karyotyping in this post and tackle the other methods later.  Karyotyping is basically looking at the chromosomes of a cell as it’s dividing. Cells divide to make new cells, but in order to make sure each new cell has everything it needs, everything has to be copied, including the genetic information. Unless the cell is a bacterium (or an archeum), it will keep its genetic information in a sort of ball of denser material called a nucleus. Most of the time this ball is all we see of the cell’s DNA, but if we add a dye and watch the cell divide, we can see several strange, threadlike structures, or bodies, that are colored by the dye. These “colored bodies” are the chromosomes, named after the Greek “chromo” for colored and “soma” for body. A chromosome is actually DNA wound up around proteins and then wound up again and again until it becomes a tight tangled mess, similar to what happens if you twist a coiled telephone cord.

As you look at  chromosomes under a microscope, in other words, you are actually looking almost directly at DNA.  Normally the chromosomes are haphazardly arranged around the nucleus of the cell, but after taking a picture of them, you can rearrange them so that they’re aligned the same way and in order from largest to smallest. This is a Karyotype.

Usually a lab worker who wants to karyotype a person’s blood, will look at some white blood cells, which are easier to work with for a variety of reasons, and wait for themto start dividing. Then, he or she will use a drug such as colchicine or vinblastin to stop the cell from dividing completely. This allows the technician to look at all the chromosomes under the microscope and analyze them using dyes that bind to different genes. The lab worker or another scientist or technician can then compare the karyotype of one individual to another to see what differences they are in where the dye shows up.

The drugs used to stop the cells from dividing have interesting histories. Colchicine started out as the active ingredient in an herbal remedy extracted from autumn crocuses to treat gout and inflammatory arthritis. Crocus extract was used as such as far back as 1500 BCE though it was only isolated from crocus extract in the late 1800’s. Colchicine is still used to treat severe cases of gout today, however, the difference between an effective dose and a toxic one is rather small, so takers of the drug have to be careful.

Chromosomes of a cell. Vinblastin or colchicine used to keep them from separating.

Vinblastin also comes from a plant extract, this time from the madagascar periwinkle plant. The plant was originally crushed into a tea, and researchers noted that people who drank the tea had a lower white blood cell count, leading researchers to look into the active ingredient as a possible treatment for diseases that affect white blood cells.

White blood cells are primarily responsible for the body’s immune response, which causes inflammation, the primary complaint of gout and arthritis sufferers. These cells also  affect a number of diseases, including cancer. White blood cells use microtubules to initiate movement, and all cells use microtubules to separate chromosomes as they divide. Cochicine and vinblastin both inhibit the production of microtubules, which is why the drugs are useful in karyotyping as well as a number of other diseases.

The easiest thing you can do with karyotyping, after determining species, is determining sex. A normal human being has 23 pairs of chromosomes and sex is determined from the 23rd pair. Genetic females have two longer chromosomes, called “X” chromosomes here, while for genetic males one of the chromosomes is shorter and called a “Y” chromosome. Sometimes a person might have two or more X chromosomes along with a Y chromosome in a condition called Klinefelter’s syndrome. There are also a number of other possibilities, such as XXX or even XXXY. All these scenarios usually result in learning disabilities, and regardless of how many X chromosomes there are, if there is a Y chromosome the person will be physically male. These situations where there are more than two sex chromosomes are examples of aneuploidy.

Karyotype of a normal male. From biology.iupui.edu

The word “aneuploid” comes from four Greek words mashed together: “an-” for not, “eu” for good,”ploos” for fold, and “oidis,” which means form or type. So all together you have “not good fold type,” a set of chromosomes that is not correctly paired. This sort of situation can occur in other chromosomes as well, such as in the case of Down syndrome, the second most common inherited  form of mental retardation, where there is an extra copy of chromosome 21.

In biological terms, “-ploid” refers to how many complete sets of chromosomes there are. The normal number of copies for a set of chromosomes is two, so most cells are called diploid. Sperm and eggs only have half the normal amount of chromosomes, so they are haploid. Plants and some other organisms can have more than two sets of chromosomes, making them polyploid. While polyploidy can occur in human fetuses, it never results in birth. In fact no vertebrate animal can be polyploid.

A normal x chromosome on left, fragile x on right.

Fragile X is the most common inherited form of mental retardation, and while it is not a aneuploidy disorder, diagnosticians can also identify it using a karyotype. In fragile X one of the x chromosomes looks thinner in an area that has a long string of the same DNA sequence. Because of this repeated sequence, a protein required for normal development can’t be produced properly and the neurons of the brain cannot form the proper connections as a result.

Diagnosticians can tell that someone has Fragile X from the way a certain area of a chromosome is affected naturally, however they can also tell other genetic attributes by how the chromosome is affected by the dye they use. Giemsa, the most common dye used for karyotyping, will concentrate in different bands on the chromosome, which you can see in the picture of the normal male karyotype above. By comparing where these bands show up between different karyotypes, researchers can begin to find abnormalities and differences that may have something to do with how a person looks, acts, or feels.

Other labeling techniques have also been used to get more information from chromosomes. Especially exciting is the work done on telomeres, which can be labeled using a protein attached to a fluorescent marker. These are the ends of the chromosomes, which are made up of repeating patterns of DNA that act like the aglets of shoelaces, keeping the chromosome from shortening prematurely. Telomeres have been found to be  linked with the aging process. Although the telomeres will shorten and lengthen throughout life, various stresses can cause them to shorten more than usual. It seems the older we are, the shorter our telomeres get. If we can figure out how to lessen the shortening process, we may find a cure for aging itself.

TELOMERES cap the ends of chromosomes. Image: WIKIMEDIA COMMONS/NATIONAL HUMAN GENOME RESEARCH (user GIAC38)

Suggestions? Corrections? Questions? Observations? I’m trying to cover a lot of ground here without letting things get too complicated, so I’m bound to make some mistakes. Please feel free to comment on this post or email me at zorknot (at) gmail.com about what I’ve written.

A Story of Glowing Maps

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The Japanese didn’t have GPS during World War II, at least not in the form that we’re familiar with today.  If ground troops in the Pacific wanted to look at a map, they had to shine a light on it, and that was rather detrimental to their survival prospects if they needed to know where they were while conducting a secret night time operation.

Luckily for the Japanese soldiers, one thing the Japanese knew a good deal about was ocean life. In particular, a crustacean they call an umi hotaru or “sea firefly”  has the unique property that if you prod it, it glows. If you crush a bunch of these little guys up, and pour water on them, you can create a glowing sludge that you can put on your hands. A glow that is dim enough to not be noticed in the field, but bright enough to read a map by.

When the atomic bombs fell on Hiroshima and Nagasaki, it effectively ended the Japanese soldiers’ need for glowing maps. But a young man who had been working at a factory only 15 miles away from Nagasaki when the bombs dropped, would ensure the sea firefly retained its place in human history. A decade and a lustrum after the war, this man, Osamu Shimomura, was studying at Nagoya University when his mentor,  Yoshimasa Hirata, gave him the task of figuring out how the sea firefly glowed.

Sea fireflies. Image from http://mytechnologyworld9.blogspot.com/2010/11/sea-creatures-used-as-light-for-reading.html

Sea fireflies, similarly to the fireflies we’re more used to, glow, in part, because of a protein named luciferin.  When oxygen binds to luciferin in the presence of another protein, an enzyme called luciferase, the molecule glows. Even though the sea firefly had been studied for a number of years, no one had been able to purify its luciferin because it was so unstable. If you’ve ever had a firefly splat on your windshield, you’ve observed this instability first hand. The firefly guts glow, but they quickly fade to nothing. When the firefly splats, its luciferin binds with oxygen in the air, causing it to glow as it degrades, but it’s used up after only a few moments. In order to purify the luciferin from the sea fireflies, Shimomura had to take powder from the crushed creatures and distill it using a complicated apparatus (pictured at right), then get it to crystallize in a special solvent, all before too much of it degraded into uselessness. It was tough work, but Shimomura finally did it, and published his results in a scientific journal that got the attention of Frank Johnson, a professor at Princeton University in the U.S.

At Princeton, Johnson and Shimomura worked on figuring out how jellyfish glowed. At the time, the popular theory was that every living thing that glowed used some form of luciferin and luciferase, but try as they might to purify luciferin  from the jellyfish, they weren’t able to do it. The problem was that the jellyfish they were looking at didn’t use luciferin at all, but a completely different protein.

Jellyfish glowing mechanism. Image from http://www.conncoll.edu/ccacad/zimmer/GFP-ww/shimomura.html

Shimomura suspected this might be the case and looked into the possibility on his own even while Johnson obsessively pursued the luciferin angle. After a tense period of disagreement, Shimomura discovered that the glowing was actually caused by two different proteins: one, which Shimomura and Johnson named after the jellyfish they were studying, (aequorin) and another, present only in trace amounts, which they called simply “Green protein,” because it glowed green when placed under an ultraviolet light.

Thing was, although the green protein was present in only trace amounts, it had a dramatic effect on the bioluminescence of the jelly fish. Aequorin, the more numerous protein, glows blue in the presence of calcium ions, but instead of glowing blue, as one might expect, the jellyfish glow green.  What is happening here is that the blue glow from the aequorin was making the green protein fluoresce green. This was a very interesting property for a lot of researchers and so the green protein was studied in several other labs, and was soon officially renamed “Green Fluorescent Protein” or GFP.

Shimomura and his colleagues spent many years gathering enough of the protein from the jellyfish near Princeton to properly analyze GFP, isolating  the part of the protein (the peptide) that was responsible for its fluorescence. Such fluorescent peptides are called chromophores.

GFP is unique among fluorescent proteins in that its chromophore is within the actual protein, as opposed to being in a compound attached to the protein. This means that if you can copy the DNA that’s responsible for making the protein, you can recreate the protein in all its glowing glory in just about any animal you care to genetically modify , and indeed,  Douglas Prashar and his colleagues  managed to do  just this in 1985, “cloning” the protein so that other, animals could produce the protein. This allowed research on GFP to continue, even as  the jellyfish it originally came from became much harder to work with due to decreased populations.

The nematode worm C. Elegans

In 1989, a marine biologist who spent many of his summers studying at the same research facility that Shimomura worked at, was giving a lecture on fluorescent proteins and bioluminescence when one of the scientists in attendance, Martin Chalfie, had the idea that he could maybe use GFP in his research on nematode worms.

Nematodes have bristles on their bodies, which normally make them very touch sensitive. The system that allows them to feel touch is governed by a very fast molecular motor, operating at least ten times faster than the molecules responsible for vision in humans and other animals. Chalfie was studying how this touch system worked by comparing normal worms with worm mutants that lacked the gene that produced the molecular motor. The problem was that the only way to distinguish between the mutant worms and the regular worms was to either kill them, which would make it impossible to check their touch sensitivity, or to tickle them with a hair, which kind of defeated the purpose.  He wanted to know which worms were touch sensitive, not just that some were and some weren’t.

One thing that nematodes have going for them is that they are transparent. Chalfie realized that if he could get a fluorescent protein to show up wherever the molecular motor was produced, he could easily distinguish between the mutants and the normal worms without having to kill them, because the worms that had the fluorescent protein would glow.

In 1992  when Chalfie and a graduate student of his found out that Prasher had been successful in cloning the gene for GFP,  they contacted him and worked out how to express the GFP gene in bacteria. To their delight, GFP didn’t require any other molecules to get it to glow after it was produced from the gene. All Chalfie had to do was insert the gene into the bacteria, and it made the bacteria fluorescent. That meant that GFP could be used in other organisms easily.

Chalfie’s wife, Tulle Hazelrigg, gave the next contribution to the study of GFP by showing that fusing the molecule to another protein causes that other protein to be fluorescent as well. This meant that rather than simply labeling mutants versus normal animals, researchers could see exactly where the proteins showed up in the animals they studied.

Finally, Roger Y. Tsien, a Chinese-American biochemist working at Berkeley, California improved the GFP molecule by mutating the gene so that the GFP that was produced was brighter and could be seen with the fluorescent scopes that were already widely available in many different labs. He also was able to make GFP mutants that glowed red or yellow instead of green, allowing several different proteins to be viewed at the same time. This gives scientists a glowing map of where all the proteins they want to look at are showing up in their samples.

One of the most remarkable uses of this technology is in the Brainbow technique, developed by Jean Livet, Joshua R. Sanes, and Jeff W. Lichtman, which labels each neuron in the brain of a research animal individually with a separate color formed by a combination of fluorescence molecules.

An image of a rodent brain using the brainbow technique

So we’ve gone from glowing maps of battle grounds, to glowing maps of the brain all in the span of some sixty years.

Osamu Shimomura, Martin Chalfie, and Roger Y. Tsien all received the Nobel prize in chemistry in 2008 for their work on GFP. Shimomura has retired to emeritus status, but Chalfie still works on worms, and Tsien still works on sub-microscopic molecules. They have all changed the world.

My information for Osamu Shimomura came primarily from his 2008 Nobel Prize lecture.I got Martin Chalfie’s story from an interview conducted with him on the podcast Futures in Biotech. I left quite a bit out for simplicity’s sake, so I suggest giving these sources a look if you’re interested.All other sources are available through the hyperlinks I have provided in text.

Immunohistochemistry

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Diagram of how an atomic force microscope works

So there’s this amazing protein you want to study, and it might very well change the world, but you have a problem: how do you study the protein when its too small for even a microscope to see?

There have been a number of solutions to this problem over the years, many of which are still being used. You could, for instance, study the protein’s effects by adding controlled amounts of it to a sample, or you could keep an organism from producing the protein  through surgery, drugs, or geneticsand see what what happens when it isn’t there. More directly, the obvious solution is to get a better microscope. What do I mean by a “better” microscope? Well, although there are some drawbacks, there are some microscopes that can give much higher resolution and/or provide added information about what you’re looking at.

One example of this is an atomic force microscope. How this works is that a small needle on a cantilever connected to a computer is dragged across what you want to look at. The computer then measures all the bumps that the needle encounters and gives a visual representation on the screen. As you might suspect this method has a number of drawbacks, (the cantilever is fragile, samples have to be specially prepared, etc) but it is possible to identify single atoms using this method.

Another type of microscope that can help you find a protein is an electron microscope. The idea here is to use electrons instead of photons to look at a sample. There are a number of drawbacks to this idea as well, for one thing, samples usually have to be “fixed” with a chemical such as Osmium tetroxide  and this can sometimes change the way things in a sample look. However, here the drawback can also be a good thing. What “fixed” means in this case, is that the molecules are attached to the things around them, and so aren’t going to move around all over the place like they would normally. If you want to see stuff moving around, you’re out of luck, but often you want to see where something is at a particular time and you don’t really want it to be free to wander.

There is another benefit to using electron microscopes. Parts of a sample will be darker depending on how electron dense they are after they’ve been fixed.  the electrons that the microscope uses to scan the sample will bounce off of that part of the sample, causing there to be a dark region. It isn’t always easy to tell which molecules will be more electron dense than others, but there are ways of making it easier. For one thing, if you have a molecule that you know is electron dense that you also know will form a bond with the protein you are looking for, you can add that to your sample and then you can compare the dark regions in the treated sample to how an untreated sample looks. The dark regions that appear in the treated sample but not in the untreated will most likely be your protein.

How confocal microscopy works

This trick also works with fluorescent and confocal microscopes. These microscopes shoot  beams of light at a constant, controlled frequency on the sample, causing some molecules to fluoresce, emitting light at a slightly different frequency. Confocal microscopes have the added benefit of being able to control where exactly the lasers focus so that it can show not only where something is in terms of up, down, left, and right, but also where it is in terms of depth. Once again, if you know a molecule is fluorescent and that it binds to the protein you’re looking for, you can add it to your sample and then check it out in the fluorescent microscope to find your protein. That’s great, but how do you find a fluorescent molecule to bind to your protein?

Diagram of antibody production

Well, your body has a ready-made system for finding molecules that will bind to proteins that has been tested over millions of years of trial and error. The immune system. If a virus or a bacterium enters your body and starts causing problems, your immune cells will start producing antibodies for the proteins that are present on the surface of the intruder, so that if it shows up again, it will be dealt with before it can cause any damage. Antibodies are large (by protein standards), y-shaped molecules produced by white blood cells. There are binding sites at the ends of the smaller arms of the y that bind to specific parts of a molecule. The binding sites act as a sort of lock, where the key is the part of the molecule the antibody binds to. There are a huge number of different binding sites that are available due to the genetic information encoding the antibodies getting shuffled and mutated all the time. When a cell in the body gets stressed, it sends out a signal that a white blood cell(a macrophage to be specific ) can respond to. This white blood cell then invites another cell (a T-cell) to take a look.  This T-cell will then go out and talk to another cell (a B-cell), which has a catalog of antibodies available for production that the T-cell can peruse by seeing if the peptide, or protein part, that’s in the stuff the macrophage ate, is also in the B-cell. If any antibodies from the B-cell  bind to something in the T-cell saw in the macrophage, then the B-cell knows to produce more of that kind of antibody. After that, wherever an antibody encounters its target, it triggers a response from other white blood cells.

Sometimes a cell might be stressed, but the antibodies will bind to something that isn’t the cause. Molecules, from peanuts, pet hair, pollen or just about anything might happen to be present in greater quantities than the thing that’s really causing the problem. This is how allergies happen.

That’s the bad news. The good news is that because antibodies can be found for almost any kind of molecule around, scientist can used lab animals to produce antibodies to the proteins they want to study. Furthermore, by manipulating the genetics of the animal, they can cause each antibody to be attached to a fluorescent molecule. The antibodies can be stored in a vial in a freezer and transported cold to labs all over the world. All a scientist needs to do then, is bathe whatever he or she is studying in a dilution of the antibodies, and then look at the sample with a fluorescent microscope. Wherever the sample fluoresces, that’s where the protein is.

This process is called immunohistochemistry. Immuno- because it deals with antibodies from an immune response, histo- from the Greek for tissue, and chemistry because it deals with the binding of molecules.

Antibody production diagram is from A Positron Named Priscilla: Scientific Discovery at the Frontier (1994) National Academy of Sciences (NAS) ( http://www.nap.edu/openbook.php?record_id=2110&page=69 ) all other images from wikipedia.

Molecular motors

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At this very moment, inside every cell of your body, there are thousands, even millions of machines, so small that they can’t even be seen with a conventional microscope, performing tasks in mere fractions of a second without any direct supervision. There are tiny molecular robots working together inside us to accomplish goals that scientists are only beginning to understand, every moment, of every day, through out each of our lifetimes. And it’s not just in our bodies. In the bodies of every living thing these things are active. They are, in fact, required for the basic prerequisites of life, yet individually, they are nothing but dumb molecules, practically inert unless the molecules they interact with are present. These things are called molecular motors.

There are a bunch of examples of these and every time I think about them I’m amazed. I just have enough space to talk about maybe two of them, but really almost all molecular motors rely on three things: energy, tubes, and molecular components.

Chemical structure of ATP

The usual form of energy for molecular motors, the twenty dollar bill in the economics of proteins, is ATP. ATP stands for Adenosine triphosphate, and its called that because it is a molecule made up of adenosine attached to three phosphorus atoms (called phosphates while they’re still bonded to a certain number of oxygen atoms) arranged in a line. If proteins need energy for a reaction, they get the energy by lopping off one of the phosphates of an ATP. ATP then turns into ADP (adenosine diphosphate) and the energy that was stored in the bond between the phosphate and the rest of the molecule goes into whatever is needed by the molecular motor or by the reaction that’s going on. When a molecule snaps off a phosphate, the phosphate is bound to that molecule for a while and the molecule is said to be phosphorylated.

This might be a little boring in itself, but the cool thing is that so many different reactions inside a cell depend on the same ATP molecule. Almost every reaction between proteins involves a phosphorylation or a de-phosphorylation. When you eat food, what you’re really doing is supplying your body with ATP.

Adenosine is actually one example of a class of proteins called nucleotides. They can all carry phosphates, though adenesine and guanine are the ones typically used for energy. The reason nucleotides are called nucleotides though, is that they are all present in DNA, which is found in the nucleus of a cell. There are the four typical nucleotides you might remember from high school biology (Adenosine, Guanine, Thymine, and Cytosine) and then there is another that is only present in RNA, uracil. DNA forms a double helix, or a twisted ladder, with each nucleotide forming a rung in the ladder by binding with a partner nucleotide. As a general rule, adenosine binds with taurine, and cysteine binds with guanine. A goes to T and C goes to G. This is important because, by keeping to this rule, a cell can use single stranded DNA as a sort of photo negative, and use it to make the opposite strand over and over again as many times as it’s needed.

The other “tubes” come in two flavors: microtubules and actin fibers. Microtubules are the scaffolding and road system of an animal cell, keeping thing in place and providing a network of connections to every organelle. Actin fibers are similar to microtubules, except they are more temporary. They are used a lot in things like amoebas to form psuedopods and move around.

Finally there are the actual proteins that make up the molecular motor. Kinesins and myosins are perhaps the neatest looking proteins. They look like thin cartoon characters with really large feet. What they do is they carry or pull things along a tube (a microtubule for kinesins and actin fibers for myosins)by “walking” along it. You can see movies of this like the one below. The feet start out latched to a tube. Then one “foot” will release and latch on again a little ahead of where it was before. Then the other foot will to the same and so on so that the molecule is walking along the tube while carrying some cargo.

DNA polymerase is another molecular motor, though it’s often classified as an enzyme. It latches on to a single strand of DNA, takes phosphates of nearby nucleotides and then uses the energy from the phosphates to attach the nucleotide to its partner on the DNA. If the nucleotide is the wrong match, it gets thrown out. DNA polymerase is basically like a factory worker on an assembly line.

But it’s just a protein.

We’re talking atoms bound together, people. And yet they’re doing these sophisticated things. Perhaps its time we recognized our protein overlords.

Incidentally, if you are interested in this, you might want check out this blog as well: http://informedworship.blogspot.com/

Flagella and Philosophy

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Most bacteria, including E. Coli bacteria, which cause food poisoning, move around by using flagella. Under the microscope, flagella look like kinked up hairs sticking out of the cell and undulating rapidly. If you remember high school biology you might already know, or think you know all about flagella. They’re those hairl-like  things that cells whip back and forth to move forward right?

Not exactly. There are basically two kinds of flagella, the ones that bacteria have, and the ones that eukaryotic cells have. The eukaryotic ones do in fact whip back and forth. The bacterial ones, however, actually propel the cells they’re attached to by corkscrewing through the fluid. As I went over in a previous post, the situation bacteria are presented with isn’t the same as a submarine in a ocean. It’s more like a submarine in a large silo filled with vibrating pebbles. Drag is a huge deal. Bacteria need a powerful technique to move around and a corkscrew type action works rather well.

When you use a corkscrew on a wine bottle you basically turn it around in a circle as it progresses into the cork. So here’s a question: how does a bacterium do that? The flagellum has to be attached to the cell with a buttload of strength to pull the cell along, but at the same time it has to be able spin around like a drill bit. If you look at all the different components of the flagellum (pictured below) you can see that the structure is pretty complicated. WTF? Aren’t bacteria supposed to be primitive organisms?

Well, yes and no. You see, the thing that’s easy to forget about evolution is that every thing that’s around has been evolving for just as long as everything else. It’s just that while our cells were busy trying to figure out how to differentiate and work together to get to places where there was better food and water and such, bacteria were hunkering down and learning to live in the environments they found themselves in. They’re just as good at being bacteria as our cells are at being part of a larger organism. Still, the flagellum is so mind-bogglingly complicated and yet robust in its implementation, that it has from time to time been used to prove or disprove the non-existence of God.

The argument runs something like this: “We and the organisms of Earth have to have been created by a God,” say creationists, “because the bacterial flagella is so complicated that it could not possibly have been formed by chance, any more than a hurricane could blow through a ship yard and create an aircraft carrier.”

“But,” say non-creationists, “each protein that makes up the structure of a flagellum looks similar to proteins used in other, less complicated bacterial structures. Furthermore the flagellum of E. coli is only one variant of many, indicating that one Doesn’t it make sense that flagella might have come from mutations that put the proteins together in ways that were somewhat beneficial? If even one bacterium survived a trying situation better than its neighbors, it would quickly begin to dominate. And evolution of bacteria has been directly observed in nature and in the lab. At the very least that seems more plausible than everything getting poofed into existence through some unknown process by a magical man in the sky.”

You can probably tell which side I favor.

Something that you start to notice if you study biology is how complicated and diverse proteins are. Proteins aren’t just little specks that bump into each other in random ways. Each protein has a different shape and different areas that have different properties that interact with other proteins in different ways depending on environmental factors. It’s an imperfect analogy, but you could almost say proteins have personalities. Almost like people, proteins will work together, compete with each other, and even find things in their environment and use them to accomplish a “goal.” A protein may be stuck in a bad position, for example, and it may come into contact with another protein that likes to pry things apart, and then they will help each other out.

So it’s not exactly the same situation as a hurricane picking up a bunch of aircraft carrier parts and arranging them into a complete aircraft carrier. Its more like a bunch of people who don’t know how to make an aircraft carrier getting a steady supply of parts and enough time and resources to try things out. Eventually, given enough time, people in that situation will eventually make something like an aircraft carrier. Though they’d probably start out making houses, cars, and a number of other things out of the parts before hand. In fact you could look at the current real-life production of an aircraft carrier as an example of evolution. Evolution is simply the effect of variation subjected to some environmental pressure. There were many different types of ship before the aircraft carrier came about. For one thing, there had to be aircrafts in order for there to be any use for one. Humans wanted a place to put planes on the ocean and the aircraft carrier fulfilled that purpose

In a similar way, proteins just want to be in equilibrium, and so they will often use things like enzymes to make equilibrium easier to achieve.

If you are doubtful of any of this, you need only see a video of how a flagellum is formed in a bacteria. The formation of a flagellum is a marvelous and awe-inspiring dance and it happens hundreds of times a second in a single organism ALL THE TIME. You don’t need religion for miracles. You just have to look around.

Size is Everything

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Innerspace is a Steven Spielberg movie that came out in 1987 starring Dennis Quaid, Martin Short, and Meg Ryan. It’s a sort of remake/homage/rip off of a movie that came out in the sixties called Fantastic Voyage, which Isaac Asimov wrote a novelization for. Both movies center on the idea of shrinking people to microscopic sizes and then injecting them into other people to go through the body and fix diseases. This is a really neat idea, and there are some scientists who are finding ways to use microscopic robots to take the place of the humans in the movies and accomplish some of the same things. However, there are two reasons why the scientists are using robots and not Dennis Quaid. First, shrinking people is probably impossible, and second, even if it were possible people wouldn’t be able to do anything once shrunken.

I can show the how true the first point is with common sense for the most part. If humans are made up of cells, how could it be possible to shrink a human to a size smaller than a cell?

Now you could come back with “well, the cells just get smaller!” But cells have to be the size they are. Otherwise they wouldn’t be large enough to hold all the organelles that keep the cell alive and functioning the way it needs to. The organelles themselves are made up of proteins that are in specialized arrangements. A cell has to constantly maintain the numbers of ions it has inside it for example. The cell can use an organelle called an ion channel to do this, but the channel has to be a specific shape. If it is too large it will let all sorts of ions in or out and the cell won’t be able to maintain the right mix of ions. Too small and the channel won’t let anything in, and it might as well not be there. If these channels were shrunk by even five percent, they would no longer function the way they need to. If ion channels don’t work for cells, they die. If all of a person’s cells die, they die too. If a shrink ray shrinks everything equally, a person shrunk even a foot smaller would most likely die within a few moments.

And of course there’s the problem of how it could happen in the first place. In the movie Honey I Shrunk the Kids, the Rick Moranis character says that we are made up of mostly empty space and his shrink ray gets rid of that empty space. First off this idea is based off of the Bohr model of the atom, which has an electron whizzing around a nucleus like a planet orbits around a sun. This isn’t how things are. There isn’t any empty space as such. The more current electron cloud model fits better. The exact location/momentum of an electron cannot be precisely determined and so we can think of it as a sort of cloud around the nucleus. Okay but at any moment we can still say that the atom is mostly empty right? And if we could take out this empty part you could maybe shrink something?  To be fair, there is a real world situation in which this does happen. It’s called the Sun. It’s a lot more bright and ‘splody than what we see in the movie.

To be more precise, and less smart alecky, the reason why the electron is so far away from the nucleus of an atom, is due to its energy. In order to get closer to the nucleus, an electron has to lose energy. When an electron loses energy, it releases a photon. The more energy an electron loses the more energetic the photon is. Photons with a lot of energy, such as X-rays or Gamma rays, are a form of harmful radiation. Never mind that this hypothetical magic device would most likely rip someone apart rather than truly shrink them, the energy released from “removing the space” in all the atoms would be huge, and would likely kill quite a few people.

The second reason why we’ll never have a manned mission to someone’s colon is something called the Rydberg constant. The Rydberg constant is a number you get when you divide inertial forces (momentum, or how long you keep going after you stop trying to move in a direction) by drag forces (friction and viscosity, or how hard you have work to move forward in the first place). The higher the Rydberg constant, the more you are concerned about momentum and the lower, the more drag forces dominate. Generally speaking, the larger you are, higher your Rydberg constant.

We live in a world with a pretty high Rydberg constant.  We can roller skate and ride a bike, coasting almost half the time. When we swim, we pull the water back with our hands and we’re carried forward enough that we can get our hands back into position for another stroke without moving back to our previous position.  These are all situations where the Rydberg constant is high.

We can create low Rydberg constant situations for ourselves if we want though. Imagine a swimming pull full of Jello. If you try to swim in that, you are going to have some problems. For small animals though, they live in this low Rydberg constant situation all the time. An ant that wants to get a drink of water has to be very careful not to get stuck in it.

Even something as large as a cat, experiences a lower Rydberg constant. A cat can fall from many stories up and still suffer only a few broken legs due to the drag forces that act on it as it falls. The cat, being small, has a larger surface area in relation to its mass, and so drag forces come into play more quickly.

For a bacterium, or a hypothetical impossibly shrunken human, the Rydberg constant would be so low, it would be like that swimming pool full of Jello, only worse. You might imagine a vat of gravel that’s shaken up continuously while you’re inside it. Bacteria typically have some sort of flagellum that corkscrews through the stuff they’re in so they can move forward. Why don’t they just use turbines like a submarine would? Well one reason might be that they never developed such a structure in their evolutionary history. The more applicable reason is that in order to combat the drag from the surroundings, a turbine on a bacteria-sized machine would have to be so large, that the drag of the turbine itself would affect the machine’s movement. Imagine trying to use a submarine in a vat of gravel. Or even more ridiculous, an airplane. It’s just not going to work. So you’d have to have a differently shaped vehicle than in the movies. And you can just forget about leaving the vehicle.  You wouldn’t be able to swim around any more than a feather can dictate economic policy.

It often seems like size is just an arbitrary attribute. There are so many stories about shrinking and growing larger because on some level it seems possible. There are a lot of complications hidden under the surface however. An elephant is a very large animal, but it’s bones are thicker in proportion to its size to make up for that. If you shrunk an elephant down to the size of a cat, it wouldn’t be able to move it’s limbs around. If you blew up a cat to the size of an elephant, it would suffocate under its own weight.  Every time you decrease or increase size by a factor of ten, you enter a different world.

Size is everything.

Myxobacteria are Awesome

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Swarming myxobacteria
Image pulled from http://bit.ly/m51q1q

I am writing this post because myxobacteria are awesome, and I think more people should know about them.

You could go through your entire life without ever hearing about myxobacteria. Pretty much everything you need to know about microorganisms in general is that there are things moving around that are so small you can’t see them, sometimes they can help with things like digestion and pollution cleanup, and sometimes they can cause diseases such as salmonella, so you should really make sure to wash your hands, cook your food and  pasteurize things.

Everything beyond that is a detail that you can probably overlook without any serious repercussions.

But what’s the fun in that?

As with just about any facet of science, if you look into microbiology you soon find yourself falling through a magnificent and intimidating rabbit hole of information. It helps to have a specific thing to latch on to to make sense of everything.

Myxococcus fulvus fruiting body
image pulled from http://myxobacteria.ahc.umn.edu/whataremyxos2.html

Even focusing on myxobacteria gives you a lot to take in though. The picture above shows how they move around in swarms or wolf packs. The colors indicate the direction each cell is moving in. For instance, all the cells that are colored orange are traveling to the right. Why do they do this? How do they do this? They don’t have any flagella or cilia (not in the classic sense anyway) They release slime,( myxobacteria comes from the greek myxo for slime after all), but how does that help? I’ll say more about myxo movement in a later post, but there’s more.When food is scarce, myxobacteria start lumping together in visible fruiting bodies, about a millimeter tall,  like in the picture on the right. These fruiting bodies will eventually release bacterial cells with thicker cell walls that act as spores, eventually budding and making more myxobacteria, which then repeat the process.

Well, okay, that’s your basic fungus, right? But the weird thing here is that these are all still bacteria. They don’t even have nuclei! How do they show such complicated behavior?   How do they know enough to organize themselves into a heap to release spores? How is it that the spore cells look so different from the other cells?

Scientists know the answers to many of these questions, but others are still still a mystery. As you go through some of the explanations, you start to notice these strange correlations between how bacteria sense things and how social networks and mobs of people form and behave. You start to wonder about how some professions get more specialized and whether businesses and franchises are fruiting bodies. It’s eerie. And if these dumb bacteria act this way, is it possible that we act in similar ways because we’re in a similar environment? What can we take from that? Are we too much like bacteria, or not enough? What does this say about free will?

Deep, huh?

Like I said, Myxobacteria are awesome.

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