Tag Archives: bacteria

Germ Cultivation

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I recently came upon an article in the New York Times about how people with skin disorders such as acne or eczema could be helped by a sort of topical probiotic treatment. In other words if we take bacteria from the skin of healthy people and spread them on the skin of diseased people, evidence suggests that the good bacteria will fight off the bad bacteria and the skin condition may go away.

This idea of probiotics, (using good bacteria to fight off bad bacteria) has been around for a while now, but it’s been steadily gaining popularity.

I find the whole thing fascinating for a number of reasons. I like the counter-intuitive aspect of it. I like how it looks at the problem of infection from more of a systems perspective, rather than seeing it as a single cause requiring a single remedy. And finally I like how it flies in the face of all the do-gooders who were telling us all how to live our lives in the 80’s and 90’s when I was growing up.

BactRanch

Bacteria husbandry?

It turns out (to a certain extent) it’s better to have children go out and be dirty for a bit. Visiting a farm and interacting with animals, for instance, reduces the risk of asthma. It turns out we shouldn’t take antibiotics every time we get a stomachache since it kills off our gut microbiota and could cause even nastier diseases to run rampant. And now it turns out that if you’re worried about getting a disgusting skin condition, perhaps what you should do is shake hands with as many (healthy) people as possible.

Of course it’s important not to get too carried away. A little dirt outside is okay, but living in filth is not. Just because antibiotics aren’t always the best choice doesn’t mean you should stop using them when you need them. And obviously you should wash your hands often and thoroughly to prevent the spread of diseases like MRSA and the flu.

What the researchers did in this study was put healthy bacteria into a lotion and put this on the forearms of people with eczema. There seemed to be a reduction in the disease, but there are still questions of whether the treatment will continue to work over time, or what might happen if there’s an open wound.

My personal prediction would be that a small open wound like a scratch or abrasion wouldn’t be much of a problem in this case. The bacteria used in the study (Staphylococcus hominis and Staphylococcus epidermidis) are so common that most people’s immune systems will quickly recognize the bacteria in the blood stream and destroy them before they can cause any harm. That “most people” would not include immunocompromised people like the elderly, people preparing for transplant surgery, or AIDS sufferers, however. And if someone has a skin condition, there’s a good chance that something might be off about their immune system.

Ultimately, like many science stories out there, this is cause for some cautious optimism. IF someone has a bacteria-related skin problem, and IF they don’t have some other complicating condition, then they MAY be helped by this therapy IN THE FUTURE (probably 5 years or so I would guess), ASSUMING there aren’t some unforeseen side effects.

As for most of us living outside of laboratories and going about our day to day existences, what I would say this means is that we shouldn’t worry so much about germs. Or more precisely, don’t worry so much about getting rid of them. It’s not good to douse our bodies with antibacterial soaps at every opportunity. It’s also still not a good idea to live in squalor either. Chances are, if you wash your hands regularly and don’t stink, you are clean enough.

Beyond that common sense assessment, if you want to improve your health, you might try finding someone who has healthier skin than you, and shake their hand. Or ask them to rub some lotion on you. Or maybe do none of these things. That way they won’t think you’re a creep and you may benefit from their simple proximity. Yes, it may be that if you want to be prettier, you need to hang around pretty people, which will be easier if you are already pretty. Perhaps yet another astounding example of the Matthew Effect.

How to Achieve Your Dreams

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sky-clouds-above-clouds-wallpaperThe following is a response to a question on Quora. I didn’t quite read the question correctly, but I like what I came up with as an answer. I have no definite expertise on any of this, but I have learned a few things that may be useful for somebody.

dmaicIf you’re serious about accomplishing your dreams, there are some tools that have been developed in the business world that can help. I’ve been involved with some Six Sigma projects, and I like the model of DMAIC for the most part. That is Define, Measure, Analyze, Improve, and Control. These sound boring, but they’re really not. Let’s go through them.

Define
The first step of accomplishing your dreams is to have realistic dreams. This isn’t giving up, this is building up. If you want to fly, great. I’m not going to say you can’t fly. But what exactly do you mean by flying? Is flying an airplane going to work for you? No? How about skydiving, that’s kind of like flying, or hang gliding? Do you actually want to be like a bird, or do you want to be superman?

Already, while we started off with something that seems unattainable, we now have several options that are much more attainable. One of the things that keeps you back in this step is fear. Your dream of flight is nice, but what if you don’t like it? What if it’s dangerous? What if it seems less beautiful? These what-ifs can hold you back, but they shouldn’t be ignored either. Make a list of these fears along with any other risks, because its entirely possible that you actually don’t want to accomplish this particular dream. Next to these risks, you want to list the benefits of accomplishing your dream. What will you gain from it. Why do you want to accomplish it? It could be that while your dream involves flight, what you really want is a feeling of freedom, and there might be better ways of doing this. If you think of some, great, make another list of risks and benefits for this new dream. Does it look better than what you had before? You keep at this until you have something that matches your desires and yet still fits with what can occur in reality.

If, at this point, you still don’t see how you can accomplish your dream, then look for ways to get closer to accomplishing it. If you want to be Superman, maybe look into jet packs, physical fitness, rescue work, or space travel. Depending on what it is about Superman that you most want to be, learning about these subjects might not get you there, but it will get you closer. The idea here is to bring your dream closer to reality by bringing reality closer to your dream.

Measure
weight-scale-400x400-300x300How close are you to your dream today? The easiest example of this is weight loss. If you want to lose 30 pounds before next Thanksgiving, you need to monitor how you’re doing to know if the diet you are on is working or not. Even if it’s something you dread, you have to get on the scale and check, otherwise there is no point in dieting. You can get more sophisticated in this step for more benefit. You can make a graph of your progress for example and a list of all the foods you ate each day and any exercise you did. This way if there is a large dip or a peak, you can see what might have caused it. Weight loss is nicely quantitative, so measuring is easy to do.

The picture to the left links to a blog about not letting scales control your life. This is a common sentiment, and I can understand where it comes from. I think it’s a completely wrong way of thinking about things, but I understand it. If you aren’t having too much success accomplishing your dreams it can be disheartening to measure how far you’ve fallen. This is because humans aren’t robots. If you aren’t doing well in your progress, you need to either move on to the next steps (analyze and improve) or reconsider the previous step. Is loosing weight really what’s important to you? Could it be that you’re really worried about your fitness? Weight may not be the best way to measure that. If you stress eat, you might measure progress by recording times of stress and how you coped. Or maybe whatever is causing you stress is the problem. Putting serious effort into fixing that might be the best bet. You are never going to be able to levitate yourself. That’s depressing. But being able to do a pull up is close. Even Superman started with tall buildings. But whatever you’re goal you HAVE to measure your progress toward it somehow if you’re serious about accomplishing it.

For your more qualitative goals, like flying or perhaps owning your own business, you might need to make a journal dedicated to the goal. You can probably come up with many little goals and you can note your successes and your set backs in a journal as you experience them. The point is to have a record of what works and what doesn’t so you have some guidance in the next step.

Analyze and Improve
If your diet isn’t working out, change it. If you feel like you’re not getting anywhere, move. You do NOT want to be consistent if you are unhappy. A foolish consistency, as Emerson said, is the hobgoblin of little minds. Although you want to make changes that are likely to work and that aren’t too dangerous, remember it’s okay to make mistakes. You are, in fact, required to make mistakes in order to know what does not work for you. There are different kinds of writers, different kinds of digestive systems, you may, in fact, be from the planet Krypton. You can’t just follow someone else’s plan.

It is very important, however, to continue to measure your progress. You might think it’s a good idea to eat nothing but soy products in your diet, but you might find out that you actually gain weight (because, surprise, soy can be fattening!) Give it some time so you can be sure of how things changed, but if things are going worse, change your system back to how it was before if possible, or make another adjustment if its not.

houseflyI’m going to digress here for a moment to talk about house flies. If you watch a fly fly, you might notice how randomly it moves. It buzzes around your sandwich quite a bit yes, but then it takes a trip to the window and the to the lamp shade and back to your sandwich again. The actual motivations and causes for the complicated behavior of a fly is complicated, but one possible way of explaining it is as a modified random walk. A random (or drunkard’s) walk is one in which a moving object moves in a random direction for a random amount of time. The fly does just about the same thing, except it has memory, sight and smell, signals that make it prefer certain directions over others. As long as the good signals are getting stronger, the fly will keep going in the same direction, pretty much, but if there’s a bad signal that’s getting stronger or the good signals are getting weaker, it sort of tumbles in the air and flies in a new, but still mostly random direction. This is rather inefficient, but it works. If you are near a sandwich, and you get further away from it, the signal goes down. You then go in a different direction and maybe this is also leading away from the sandwich so you change directions again, and now you are going toward the sandwich again so you keep going. I should say that the fly is a bit (a LOT) more sophisticated than I’ve described here, and, while a fly does act this way somewhat, this behavior is more like how bacteria move (Howard C. Berg has written a lot of interesting work in “random walks”). The point is, that it doesn’t matter so much what you adjust, or in what way you adjust it; what does matter is how often you adjust it and how closely you monitor your situation.

If things are progressing well, don’t mess with them! But if things aren’t going anywhere, some kind of change is in order. If things are getting worse, than a change is not only a good idea, but an urgent one. Don’t let fear keep you from a better life. You might be in a situation where you don’t have a lot of options, but even if you only have two paths you can go on as Led Zeppelin says, “in the long run, there’s still time to change the road you’re on.”

Control
ControlThis step has two phases. While you’re still attaining your dream and making adjustments, you will probably find it helpful to establish some rules and guidelines. For example, jumping off a building is not an acceptable means of learning to fly. In weight loss, you might find that day to day, your weight varies by about a pound or so there’s no reason to stress about an increase unless its more than that (stress->despair->ice cream so limiting stress is also important). You may also have some go-to adjustments for when things go wrong, such as doing more exercise or taking a quiet moment to watch the birds when you’re feeling down. These guidelines that you develop on your way to your goal are the first phase of control.

The second phase of control occurs after you’ve attained your dream. So you’re successful. Now what? Well, the answer to that question is usually that you want to make sure you stay successful. A lot of the guidelines you came up with in the first phase will work in this second phase, but there may be a few things you need to do differently. If you get a job as a pilot, for example, you need to review all the safety procedures even though day-to-day you may not need to know them. You also need to keep an eye out for new technologies and if necessary train yourself on them so you don’t become obsolete. Once you lose the weight, you have to stay vigilant to keep it off, and you may have to employ different strategies as you age or go through other life changes.

As you may have noticed, all these “steps” overlap, and turn back on themselves like eddies in a river. You could in fact just as easily start with Control, and then notice somethings out of whack and move to Analyze and Improve and then Measure, and then find out what exactly the problem was at the end of the whole process (Define). That’s more or less what happens when police make an arrest. Perhaps it would be better to call these phases or even aspects of goal setting, but I think if you’re looking for a way to start accomplishing your dream, defining your dream is a good place to start. If you’ve got your dream well-defined, measuring your progress is the next thing to try. Then adjusting things as needed, and finally controlling them once you have things pretty well established. They build on each other nicely that way, and besides, that’s how the business world groups them.

Note: This post used pictures from the following websites. Please visit them and consider purchasing any products they’re selling.

http://www.jeesukkim.net/velocity/

http://www.sixsigmadaily.com/what-is-dmaic/

http://blogcritics.org/how-heavy-does-your-scale-weigh-on-you/

http://www.qpm.ca/Pests/House-Fly-How-to-Kill-Exterminate-Get-Rid-Eliminate-Pest-Control.html

http://www.mwultd.co.uk/services/part-exchange/control/

How to Make a Mutant: Transgenesis

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(this creature does not exist)

Even though at some level, we’ve been making mutants for hundreds, even thousands of years through selective breeding and agriculture, these aren’t the kind of mutants we think of. We usually expect something bizarre and alarming that happens almost immediately. Like the Incredible Hulk turning green, or turtles becoming sentient, bipedal, and proficient in martial arts. We get a little closer to that sort of thing with environment sensitive genes.

Biologists usually first learn about these genes in bacteria, with the lac-operon system. The lac-operon system is an arrangement of proteins and DNA that essentially lets bacteria adapt to their environment. Bacteria like to eat sugar, and they survive the best on glucose, the simplest of the sugars. If glucose isn’t available, they can eat other sugars, like galactose or lactose, but that requires more machinery and the bacteria don’t want to rev up those machines until they know they have to. How the lac-operon transcription system works involves the use of two proteins, one that blocks the expression of the lactose-eating gene lac-x and one that amps up the expression. When lactose is present, the blocker protein can’t work, and the amp-up protein only binds if there isn’t any glucose. So with this system, a bacterium can shift to eating different sugars like a car shift gears.  This is something of a simplification of the process, but the upshot is that while the bacterium’s DNA remains the same, it’s expression is altered significantly by the environment.

Similar situations occur in more complex animals. Researchers often make use of temperature sensitive genes in fruitflies to create flies that are genetically identical to a control group, but have a protein that works differently due to being exposed to higher temperatures while forming inside the egg. In nature, this happens with many cold blooded animals whose sex is determined by the temperature where their eggs are kept.

These environmental affects control the expression of genes, and not necessarily the genes themselves, still, this isn’t as trivial as it may seem. The well-known statistic that our genes are 96% similar to chimpanzees’ is only true when we don’t count the so-called junk DNA that doesn’t seem to directly code for anything. But while this DNA doesn’t seem to make anything, recent evidence has shown that it may have an effect on how things are made or when they’re made. In other words the obvious difference between us and other animals may have more to do with how our genes are expressed rather than what genes we have in the first place.

”]Scientists can also insert known genes into the genomes of animals to create transgenic creatures. For example the gene that produces the fluorescent protein GFP in jelly fish can be inserted into the DNA of bacteria using electroporation, a technique where a electric field is used to create pores in the cell membrane of bacteria, which allows foreign DNA to enter. This can also be done through abruptly increasing the temperature, which forces the bacteria to open pores in their membranes to adapt to the situation.

Bacteria will incorporate DNA into their genome, and as long as the new DNA doesn’t interfere with their ability to survive and reproduce, the bacteria will quickly grow in number, providing a way of naturally increasing the amount of foreign DNA available. Scientists can then use  enzymes to cut out the gene that they want from the bacteria and insert it into the genome of a more complicated organism through several methods

Lab workers can insert DNA directly into the nucleus of a stem cell, for example, or simply allow the cell to take in the DNA on its own. Alternatively, scientist might use a virus that has had all its DNA replaced with the foreign DNA so that it can be injected into the cell without direct human supervision.

Optogenetics Experiment in Mouse (Source: MIT)

One of the most dramatic examples of transgenic research involves the use of a protein called channel rhodopsin. This protein is related to the protein that detects light in the cells of our eyes. When the gene that produces the protein is introduced into the neurons of a mouse, and a light of a certain color is show on the neuron through LEDs or  fiberoptic cable implanted in the mouse’s skull, it can cause the neurons to fire, directly affecting the behavior of the mouse. Not only that, but the channel rhodopsin can be altered to respond differently to different types of light so that blue light might cause a neuron to fire, while orange light might cause it to stop firing. This system has opened up an entirely new field of biology called optogenetics and researchers are currently finding ways to use the techniques to help sufferers of all sorts of brain diseases from Parkinson’s to Alzheimer’s.

So real mutants might not fly or shoot laser beams out of their eyes, but in many ways they’re even cooler than that.

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.