Category Archives: Science

Germ Cultivation

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.


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 Study Using PowerPoint

If you’re studying biology, chemistry, art, a pictographic language or any visual subject, you may have to memorize not only words and definitions but also pictures, diagrams, and symbols. Depending on how good you are at drawing, you may be able to use index cards here, but this is time consuming and can be frustrating. We live in a modern age though, and there is a better way.

Everyone has different backgrounds. I was amazed to discover that many  university students I’ve run into haven’t learned how to do this stuff, but isn’t always taught as early as it should be, possibly never in some schools, and besides I’m not sure where exactly I picked it up.  So I’ll start with a very basic introduction to PowerPoint for those who haven’t  used it before.  Then I’ll explain how you can use the program to study complex pictures  in the second section. This might be too complicated for some, too simple for others, but I’m hoping this helps somebody.

Disclaimers: I should note that I use the 2007  version of Microsoft PowerPoint, but I learned these techniques on earlier versions of the software and so you should be able to find the same options on whatever version you have if you hunt for them. There are other presentation software programs out there, but Powerpoint is the one I'm most familiar with and probably the most popular. I'm not going to use the little copyright symbols next to every instance of the word Powerpoint, because that would be annoying, but PowerPoint is the copyright of Microsoft Corporation and that should be understood throughout this post. I believe I am operating under fair use here, but I will take down the page if I get any official looking cease and desist letter. 


On most modern PC and mac computers, there is a program called PowerPoint. If you’ve taken a class anywhere in the last decade, you’re probably encountered it . You might even hate it. It certainly has its critics, but you don’t need to worry about any of that. Basically PowerPoint makes slide shows. The reason why it’s useful is that it combines word processing, image editing, and even a little movie making into one lovable Frankenstein program.

Basically you start out with a screen like this:



You can type in words or copy pictures into the slide and view your finished product by clicking the slideshow symbol (on the bottom to the left of the 52% in the picture). Once you’ve made one slide you can create new ones until you have an entire sequence of slides that you can use for a presentation at a meeting, or for your own benefit. Even if all you do is type text into the various slides, Powerpoint is helpful in a meeting to keep you on track, or as a way of outlining a narrative for a story or talk.

Studying with PowerPoint

You might already see one way to use PowerPoint to study. In the first slide, you might type a word, say, and then in the second slide you can have both the word and the definition. Instant flash card! And its not as difficult to keep from cheating. You could also use a word that describes a diagram that you have to learn to draw, and in the next slide you could have the diagram, which lets you check yourself against somethings that’s probably a little larger, more accurate, and more readable than what you can hurriedly scratch out on an index card.

This does the job in some cases, but in many cases what you have to study is just too complicated for a single slide. Take this picture for example:



If you had to memorize the names and locations of all those organs, it would take a whole stack of index cards . But there’s a trick you can do in Powerpoint that makes studying this stuff a hundred times easier.

First copy-paste or insert the picture into the Powerpoint file (right-click on picture->copy->right click on powerpoint-> paste or Insert->picture symbol-> browse-> enter filename)  Once you do this you can move the picture around if you click on the center of the picture and drag, and you can resize the picture by clicking on one of the dots in the corner and dragging out or in.

So far so boring. Okay, now on the top of the screen there’s the word “home”. If you click on this, it should look something like this:appres2

There should be an area that says “Shapes.” If you click on this button, you’ll get a selection of various shapes you can use. It’s easiest just to use rectangles so just click on the rectangle shape, which should be near the top of the popup menu.appres3


Once you click on the rectangle you can click anywhere on the slide and drag out to create a box however big you want it, and move it over one of the terms you need to know.



Okay. Now you can’t see the word. That doesn’t do you much good on its own. You want to be able to remove the block on command. Go to “Animations” and click on “custom animation.” This will create a panel on the right side of the screen which will let you assign animations to the rectangle.



You want to have the box disappear when you left click. To do this, in the custom animation pane, click on “Add Effect,” then select “exit.” You are given a list of options, but it doesn’t really matter which one you select, they will all cause the box to disappear when you left-click your mouse or hit a cursor key in slide show mode.



Once you select one of the options, powerpoint will show you what the animation will look like. and then an entry will show up in the box toward the center of the pane. This box lists all the different things that have animations in your slide, as well as some options for the animations. You don’t have to worry about those now, but you can play with them to create different effects.

What we’ve done so far is create a box that goes away when you click a button. You can go into slide show mode and confirm that this works. But we could do this by making a new slide without a box in it. So what’s the point? Well, remember copying and pasting? You can do that to the rectangle you’ve just made, duplicating it as many times as you want. And each time you duplicate it, you duplicate the animation as well.



Now, when you go into slide show mode, each time you click your mouse, a block will disappear, allowing you to study not only the names of the organs, but also their locations.

This is incredibly useful for subjects like anatomy and physiology, but it works for anything large and complicated that you need to learn all the elements to. And of course you can use simpler methods for the simpler things you need to know, making powerpoint an excellent tool for review.

Author Attribution

In a scientific paper, the area under the title where the authors are listed is more important than you might think. Obviously, each person listed as an author has (probably) contributed to the paper in some way. There are also often asterisks and other symbols leading to footnotes at the bottom of the first page that tell you which university each author is from. That much you could probably figure out on your own. But there’s a whole snarl of politics involved in how the authors arrange their names. The first name on the paper is usually the person who did the most work on it. This person is typically a graduate student or a post doc (short for post-doctoral, a post doc is someone who has gotten their PhD, but is not yet in charge of a lab).

The first author is not always the most important author in the list, however. By this I mean that if you google their name, (or use a service that lets you search through scientific journals, such as Pubmed)  you might not find much. The head honcho working on the paper is actually more likely to be the last author listed. Google the last author’s name, and you can probably find the website of the lab that worked on the paper fairly quickly.

The head of a lab is often called a PI for principal investigator. You might think of them as a boss, but it might be more accurate to think of a PI as a manager or agent who has his or her fingers in everything, trying to get it to work. A PI can have a lot of power, depending on how much money his or her lab can generate, but they rarely have the power of a CEO. Even in the case of labs that work in the private sector, CEOs don’t have the time to write scientific papers and PIs don’t have the time to take care of high level corporate decisions.

A PI has to keep track of all the scientists he or she is in charge of and find resources to ensure that the lab can continue operating.  Finding resources means writing innumerable grant proposals and promoting research by submitting posters and giving talks at conventions. PIs don’t generally get to do the actual experiments much at all, but they have to know everything that’s going on, and the work couldn’t be done without them. So to make a gardening analogy, the last name is usually the one responsible for providing the soil and seed for the paper, while the first name is the one who waters it and makes sure it’s healthy.

The other names in the author area may be of varying importance. In papers written by an extensive team of scientists there may be hundreds of names in the author area, some of which might not even have had anything to do with the work published. This is because by being part of a team the scientists agree amongst themselves to share credit for any discoveries that the team makes. Which sounds nice, but it is important not to make the mistake of thinking that everyone listed agrees 100% with what’s in the article.

You might also have people listed as authors who might not have even met the other authors. This can happen in situations where someone gathers data, but leaves the organization before anything can be done with it.

There is also sometimes space in a paper for people who have helped, but may not have done enough to warrant being a full author.  Unfortunately because of the large egos involved in science, sometimes someone who really deserves to be a full author gets shoved into this space. You might imagine a beleaguered graduate student, passionate for his subject, yet perhaps socially inept, toiling away at his experiments until he finally has enough data to reach a conclusion. He writes the paper, following all the guidelines and diligently proofreading for grammar mistakes. He gives his paper, his baby, to his PI, thinking now, finally, he will get the recognition he deserves. Only instead of being the first author, the PI puts his friend in as the first author, puts his name as the last author and gives the grad student an honorable mention. The movie Dark Matter is a chilling depiction of this scenario.

There are several organizations, including the Office of Research Integrity (ORI started in June 1992), that are in charge of confronting false author attribution as well as several other forms of misconduct. This is good, but on the downside the very fact such organizations are necessary speaks to how prevalent the problem is. A survey conducted by Eastwood, S et al (referenced here) , where postdocs and new PIs were asked to self-report their conduct showed that 41% said they would list someone as an author for being a friend or for funding them in the future. And the ORI reports that the number of reported cases of general misconduct (of which author mis-attribution is a part)  has been rising, albeit with several large peaks and valleys from 159 in 1996 to 286 in 2010.

Does this mean that all scientists are crooks? No. Does this mean science can’t be trusted? Well, to an extent, yes. But science shouldn’t be trusted. Any information a paper relates should be tested and retested independently not just because sometimes scientists misbehave, but because the information may be incomplete or inaccurate.

If popular media could understand this a little better, I think there would be a lot less confusion about the various studies that come out. Next time you see a news report that reads “Scientists say…” you should ask “Which scientists?”

Tracking Down Scientific Sources

You may have encountered this problem yourself if you’ve ever tried to track down the source of some study from a blog or a piece in a popular magazine. You go through an exhaustive google search until you finally find the article you’re looking for. You click on the link for it, anticipation mounting as you wait for the page to load up. And then, instead of seeing the full article, you see the abstract (or summary) of the article and a little box that says that you can look at the full article if you purchase it for $30 to $40. “Screw that!” you say, “I could buy ten whole magazines for that much!” And unless you have a great deal of patience, that’s where your search ends. And even with patience you might not ever find what you’re looking for without shelling out cash.

Journals are aware of this problem and are finding ways of making it easier to get access to articles. Several journals, such as PLoS One, post all of their articles free online. Others such as Nature and Science, still keep most of their content as pay only, but offer a few articles online. But here are a few tips to get past the pay wall next time you see it.

 (1) Pay the money. Just for completeness, I’m putting this here. If you think of it as a donation for science, paying the fee for the article might not be such a bad idea.

 (2) Become affiliated with a university library and use their journal access. You might be able to use your public library for this as well. Nearly all libraries have stores of journal articles in them, but public libraries tend to focus on popular and literary magazines, while university libraries are more likely to have the more obscure scientific journals. University libraries also usually have a site through which you can access almost  any scientific journal you want to find.  The “almost” is stressed though, because the way that a library gets access to a journal is by paying for it, and if a journal is small or in a strange niche, your library may not have deemed it that important.

 (3) Copy the title of the article and search for it online. This is where you start to be sneaky. Google throws a lot of links at you that you have to cull, but you can narrow your search by copying the exact title of the article and putting it between quotation marks. Often, even though a journal won’t let you see an article, the scientists who helped write it are more than happy to let you see it, and so they might post it on their website. Or it might show up on someone else’s website. Another way you can narrow the search is by using “filetype:pdf” in the search box. If you do this, google will find only pdf files for you, and most scientific articles are in .pdf form.

 (4) Search the name of the last author of the paper. It may seem strange, but the last author of a scientific article is often the most important person involved with it. If you search their name online, you can probably find the website for their lab. The website for the lab usually has a list of publications. You might get lucky and find a link for the article you’re looking for.  Even if you don’t, you might find an article that’s extremely similar to the one you’re looking for that is more available. Such an article might be even more helpful than the one you were trying to find. This can happen because often the information published in smaller articles amounts to an addendum or a further confirmation on research the lab posted earlier.

Along these lines, if the thing you’re looking for relates in any way to human health, you might go to the site PubMed, and seach for it there. There’s a small chance you might find a way to view it from doing this, but more than that, it’s much easier to find articles from the same authors or in similar subjects there. Even without you asking it to, Pubmed will list articles similar to the ones you search for, and again, they might actually give you more or better information than what you were looking for in the first place.

 (5) Look up the contact information for one of the authors and ask them for a copy of the paper. Usually the contact information is written right on the abstract for the article. At most you’ll have to do some googling to get it. Most the time, scientists will probably be happy to give you a copy through an email, though they might be curious as to what you hope to do with it. So if you’re very keen on reading an article without paying the amount you’d pay for a DVD for it, or if you found an article that you can’t even pay for, just asking one of the people who wrote it for a copy nicely cuts the Gordian knot.

Hopefully, these strategies can get you past the pay wall, and let you read the article you’re looking for.


You might think that gels are just things you put in your shoes or in your hair. You might just think of Jello when you hear the word. But gels can do a surprising number of things and can be used in a lot of interesting ways.

First off, what exactly is a gel? The part you know is that a gel is basically a material that’s somewhere between a liquid and a solid. It holds its shape like a solid, but jiggles and deforms as if it were a liquid. What you probably don’t know is that this strange state is caused by a battle between several different forces, some of which try to pull a gel apart, while others keep it together.

Most gels are made up of long stranded proteins or sugars that have a strong negative charge in environment of neutral pH, a situation similar to what  molecules of DNA experience. However, unlike DNA, gel molecules can cross link to one another if they are heated and then cooled. Because of these crosslinks, as much as it would normally take a lot of force to bring the negatively charged molecules together, the crosslinks hold them so they can’t disperse. It’s like a small crowd of people that decide to hold one another’s hands. If they then try to get as far apart from one another as possible, they will form a fairly stable circle. The spaces between the molecules in a gel are usually filled with water or some other liquid medium, giving them their liquid-like properties.

Because gels have these spaces, they can be used as nicely uniform filters as in polyacrylamide and agar gels used in electrophoresis. You can also make aerogels or xerogels by quickly evaporating the liquid inside a gel without allowing the gel structure to change. The resulting materials are light weight (because they are mostly air) and have incredibly large surface areas. : A picture of the structure of a dried hydrogel (or xerogel)

To illustrate this last quality, imagine a solid centimeter-wide cube. The surface area of the cube would be the area of one face of the cube times 6, or 6 square centimeters. Now imagine the cube is broken up into eight cubes each a half a centimeter wide. The surface area of this arrangement is going the six times the area of all the faces on all the cubes, or 6 times 8 times ¼ square centimeters, or 12 square centimeters. That’s twice as much surface area as before, even though the combined volume of the cubes hasn’t changed. If you imagine this happening several more times, you can begin to see what a staggering amount of surface area an aerogel can have.

Why is surface area important? If something has a large surface area, dust and other materials have more opportunities to land on it. This is why if you look at air filters they’re made up of dense meshes of stringy material. Air filters are, in some ways, a primitive form of aerogel.

Another neat thing that we can do with gels is use them as sensors. Because the space in between the molecules of gels can be filled with many different solutions, and the molecules themselves can be engineered to have different properties, gels can be made to drastically change their properties with temperature, in the presence of different chemicals, or when the pH changes. Gels that do this are sometimes called smart gels. Gels can also be made from protein fragments to provide a scaffold for specialized cells, allowing them to be used for a variety of applications in medicine.

Probably the most amazing gels however are living cells and tissue. If you think about it, almost every tissue in your body is made up of a network of molecules connected together and filled with liquid. You are essentially a conglomeration of gels.

How to Make a Mutant: Transgenesis

(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.

How to Make a Mutant: Mutagens

The term “mutant” gets bandied about quite a bit in popular culture. It can mean some freakishly deformed animal or person, or, more recently someone with magical, almost god-like powers (if you think that the X-men stories are completely scientifically accurate, then you have a disturbingly unrealistic understanding of the universe). But the reality is that mutants are all around us. The word comes from the Latin mutantem which means to change. In some sense, then, we are all mutants, as our genes are naturally a mix between the genes of our parents and therefore are always changing. Usually though, by “mutant” we mean some organism that has had their DNA altered by artificial means. Even this more focused definition still applies to an astounding number of the things we look at every day.

There are basically two ways of making a mutant: using a mutagen, or specifically targeting  an organism’s genome. We’ll talk about mutagens first. A mutagen can be anything from nuclear radiation to insecticide. Anything that’s a labeled carcinogen is also mutagen, as cancer is perhaps the most common form of mutation. Since cancer happens naturally, it’s perhaps a little  incorrect to put  it under the heading of “mutation,” but as some unfortunate people are intimately aware, cancer can be caused by man made materials, so it does fit.

Before we get too ahead of ourselves, we should first go over how a mutagen might make a mutant. The way it works is this: every living thing starts out as a single cell. How this cell behaves is determined by the genetic information in the DNA of the cell. This behavior includes how it divides, what structures it makes, whether it moves around, how it connects to other cells, you name it. If this cell is exposed to a mutagen, then this DNA might be altered. For instance, if the cell is subjected to ionizing radiation,  subatomic particles will scour through all the material of the cell including DNA, knocking electrons and possibly even whole atoms off the molecules that make up each material. If the intensity of the radiation is low enough, most cells can repair this damage, but some damage might be too severe to repair, or might be missed by the repairing processes, and if this happens to DNA, a mutant can result.

Ionizing radiation, as you might imagine, is a rather ruthless mutagen. It’s a bit like trying to hit the bull’s-eye of a target with a shotgun. You might get lucky and hit the area you want, but even in the best case scenario you’re going to have collateral damage. So while this type of mutagen is the most commonly found in nature, it isn’t something you want to use to find a beneficial mutation.

A slightly more nuanced approach is to inject material that looks like a section of DNA into the originating cell while it’s dividing. This approach only affects the DNA, and so you don’t have to worry about killing the cell outright, but it’s still random and so it could cause changes that an organism won’t be able to survive. There is a more sophisticated version of this involving actual foreign DNA, but we’ll get to that in the next post.

One of the mutagens most commonly used in labs is a chemical called EMS (Ethyl MethaneSulfonate). This chemical will affect the DNA of a cell by affecting  only a single nucleotide base pair. This allows much more of the mutants to divide and develop fully into adult organisms.

All these methods will produce mutants, and this is far from a complete list, but scientists usually have a specific mutant in mind. For example, a scientist might be interested in muscle growth and wants to find an animal mutant that will mimic a known human disease.

The first step for this is to find the right animal model. Animal models are used in many kinds of research genetic and otherwise. A human model wears fashions or tries different products so that we can see how they supposed look or work in an idealized environment. In a similar way, an animal model is given different ailments so that scientists can see how the animal responds to different treatments and other situations, with the hope that a human might have the same result. Humans are not all that different from other animals, as even Aristotle was aware, (We should venture on the study of every kind of animal without distaste; for each and all will reveal to us something natural and something beautiful. -Parts of Animals I.645a21)  but certain animals are better for studying different systems. If you want to study the higher functions of the brain, for instance, you probably want to work with mice, or chimpanzees. If you are interested in the steps involved with development from a single cell to an embryo, however, you might use zebrafish, as zebrafish embryos are transparent, allowing you to see many processes hidden in other animals.

One thing that is common for most animal models is that they tend to have faster life cycles, and produce more young. If you are a graduate student hoping to get your PhD in two years, you don’t want to have to wait ten months for an animal to get born, just to find out it doesn’t have the right genetic make up and you have to start all over again. In lectures, scientists often talk about how expensive each animal is. In other words, how much grant money goes into studying each individual animal. If a study is supposed to follow the entire lifespan of a rat, then it’s going to take four to seven years, and so that rat is going to be very expensive. If a scientist does a similar study with a fly, on the other hand, it will only take a few months and therefore be only a fraction of the cost. Also, while there maybe eight to twelve rats born from a mother, which is a good number in comparison to a chimpanzee, there still may not be enough chances for the pups (baby rats) to have the right genetic make up. If one of the pups needed for the study dies, it can be devastating, while if a fruit fly dies, there might be forty other flies to take its place. This is one reason why fruit flies are used often in genetic studies.

Two fruitflies contributing to research -

Let’s look into how to make a fruit fly mutant. The procedure is typically to subject fertile, male flies to a mutagen (EMS for example) for a period of time, and then allow them to reproduce with normal female flies. Some degree of care must be taken to ensure that the female flies are virgins, so that there isn’t any chance of another fly’s genetic material getting involved. Thankfully virgin females are paler and a black dot is visible on their abdomens. They are therefore distinguishable from older females, which don’t have the black dot, and males, which have darker coloring and a reddish structure at the ends of their abdomens. To examine these features, a researcher can take flies and subject them to CO2 gas, which knocks them out. They can then manipulate them using tweezers and a low magnification microscope. The virgin female flies are sequestered in a separate vial with a mutagen-treated male and allowed to mate. The female will lay mutant eggs, which will eventually become mutant larvae, and then mutant flies. Depending on what trait a researcher is looking for, they will analyze either the larvae or the flies for altered behavior or health.

Wild banana -

This method  of producing mutants has been around for decades. You might think that they are science fiction things, but if you walk into any sophisticated biology lab and talk to somebody there, you’ll find that mutants are not only studied a lot, but they are almost taken for granted.  Furthermore if you take away the use of mutagen, this kind of directed evolution has been around for ages.Without human intervention bananas are, fat, green, cumbersome things that are difficult to work with. By cultivating the trees that produced the tastiest, easiest to eat fruits, however, humans managed to breed the trees to produce the banana we know and love today, a fruit that fits so nicely in the hand, and opens so easily it seems like it was designed for us. It seems that way because we designed it.

This also has happened with animals. Geneticist Dmitri Belyaev managed to domesticate foxes, by breeding the ones that were the most tame. The breeding program was successful, but oddly the tame foxes began to look an awful lot like dogs.  Belyaev’s research suggests that many of the same genes that control physical attributes, also control behavioral ones. Just as he domesticated foxes within his life time, wolves must have at one time been domesticated by early humans. In other words, when you look at a dog, you’re probably looking at a mutant wolf.

Reading your Blueprint: Genome Sequencing

Logo of the human genome project

In this post I’ll go over the third and most recent method of identifying people through DNA:  looking at their genome. A genome is the sum total of all of the genetic information of an individual organism. If using electrophoresis and PCR is DNA fingerprinting, determining someone’s Genome is writing their DNA biography. It took some ten years for the human genome project to be successful in producing the genome of a human,  a testament to just how much information the genome contains.  Nowadays, of course, scientists and technicians can determine someone’s genome in much less time (about 4 weeks with one machine in 2009), due to the incredible advances in technology we’ve enjoyed, but how did we even get started?  DNA fingerprinting is great if you already know what you’re looking for, or if you want to compare samples of something to something else, but how do you get from that to figuring out every piece of genetic information about that thing?

Well the place it starts is with DNA sequencing. DNA is made up of nucleotides that code for various proteins. About the best thing we could hope for then is to know the sequence of these nucleotides on a sample of DNA so we can know which proteins it will code for. DNA sequencing is the process of determining this sequence.

You might recall that with DNA fingerprinting, restriction enzymes cut up DNA into fragments at specific nucleotide patterns. Those fragments split and replicate again and again through PCR, then a researcher will push them through a gel by electrophoresis, which forms bands on the gel at different levels. The closer the band is to the other end of the gel, the smaller the fragments of DNA are inside that band, and you can compare different samples by seeing where the bands show up when you subject them to the same restriction enzymes.

DNA sequencing takes this a step further. The nucleotides that make up DNA can be in two forms, deoxynucletide-tri-phosphate (dNTP) which is the usual version, and DIdeoxynucleotide-tri-phosphate (ddNTP) which has an extra hydrogen on it that keeps any more peptide bonds from forming. This means that if a DNA strand is elongating, and a ddNTP attaches, instead of a dNTP, the DNA can’t elongate any more. It’s done, terminated, its story is over.

Okay, so what? How does this get us to DNA sequencing? The way we get the sequence of a piece of DNA is  by labeling the DNA fragments by attaching a fluorescent or radioactive marker to either the ddNTP, the primer (which starts the elongation of a piece of DNA) or the dNTPs that make up the rest of the DNA.  Then you can separate each sample into four separate containers, and in each container you add in a different kind of ddNTP. Remember there are four nucleotides found in DNA, Adenine (A), Cytosine (C), Guanine (G), and Thymine (T). Each of these has a terminating, ddNTP form that we can add to a sample. So now you have four samples and each one has a different terminating nucleotide added to it. What this means is that wherever that nucleotide normally appears in the DNA sequence, the DNA well stop elongating there. So for example, lets say we have a piece of DNA with the sequence


In the first sample we add the adenine ddNTP so in that sample we’ll have DNA fragments that look like this:




Because the ddNTP will attach at different points as the DNA elongates during PCR and each possible fragment size will be amplified equally, all of these fragment sizes will be available in the amplified sample that is put through electrophoresis. These different fragment sizes will then form different bands based on how large they are.

If you put all the ddNTP additions together on a gel , the example above would look something like this:













Looking at this result, a technician can tell the exact sequence of the DNA by simply putting the nucleotide where it’s base shows up in the sequence: 1:C,2:A,3:C… and so on.

This is pretty nifty, but this example only deals with a DNA fragment ten NTPs in length. A human genome has DNA that is billions of NTPs long. How in the world can a genome get sequenced in any reasonable amount of time?

The answer comes in three parts. The first trick is to automate the process, so that a researcher doesn’t have to guide each process along by hand. The next trick, related to the first, is to conduct sequencing experiments in parallel. In other words, you want to have several sequencing experiments going on at the same time. The reason why this second technique is related to the first is that the way to do this is to have an array of wells with samples and the required chemicals inside them, then have a machine which deposits a controlled amount of required enzymes or other materials to each sample at the same time. The machine can then heat each well and allow it to cool as needed for PCR.  The final trick is to break apart a long strand of DNA into much smaller fragments and then sequence those fragments randomly, rather than try to do fragments in the order they appear naturally this technique is called shotgun sequencing.

You might wonder how, after all these random fragments are sequenced, can researcher’s put them back together in the proper order. The way this works is similar to a jigsaw puzzle. In a puzzle you may have several pieces that are obviously part of the sky, say and other pieces that are part of other separate areas. If you have several sequences, some of which overlap each other, you can put them together by recognizing that some of them are part of a recognizable pattern. You can put the sequences from fragments with the same pattern together and proceed through the whole genome that way. Obviously, if you were to try to do this by eye, it might be very time consuming, but with the help of computers the situation becomes manageable. So much so that the newest forms of genome sequencing use much smaller fragments that are only few base pairs long, allowing them to sequence all of them in parallel very quickly. A computer can then use statistics to predict where each fragment would show up. This method produces more errors, but makes up for it by the amount of usable information it gives, similar to how Wikipedia makes more errors than an encyclopedia, but makes up for it by being so convenient and covering such a vast array of topics.

Reading your Blueprint: DNA Fingerprinting

Who are you? That’s the question asked repeatedly in the song by The Who that CSI uses as it’s theme song. The answer, it seems, is found in the various pieces of evidence the Crime Scene Investigators find. Sometimes it’s pieces of fiber or pollen that eventually lead to the answer, but by far the most common method of determining identity is analyzing DNA evidence. What you see in the show is attractive people in lab coats taking samples of tissue, sticking them into some machine and then looking at a bunch of bars on a lit screen and saying things about what they mean. How is this any different from the old methods of reading patterns in tea leaves or goat entrails?

First off, I should probably point out that tv shows don’t always get things right. It usually takes much longer to get a result from a DNA sample, and if you recall the Casey Anthony trial and the OJ Simpson trial, DNA evidence does not always lead to a sure result. Well, what good is it, then? It’s not that DNA evidence isn’t useful, it’s just that there are circumstances where it isn’t available or isn’t clear. Similar to fingerprints.

So how do they analyze the samples they gather? They can’t use karyotyping usually, because they need living cells in order to do that. Thankfully, technicians don’t need to have DNA in chromosomes in order to be able to analyze it. As long as all they are looking for is straight DNA, they can get it from almost anything biological. Hair, skin, saliva, blood, and other fluids all contain viable DNA.  You still have to get it out of the sample first.

Close up of polymer gel structure. Water and small molecules can pass through spaces in the mesh. Image adapted from

One way to do this is to crush and dissolve the sample using proteases. Proteases are enzymes that eat up proteins. They are present in a lot of different cells and even in some of the food we eat. If you’ve ever eaten a lot of pineapple and found your mouth sore afterwards, the reason is because of the proteases in the pineapple. This is also the reason why it is very difficult to make pineapple jello. Jello is a type of gel, a substance made up of proteins that form a mesh that traps water inside. If there is too much protease present, that mesh can’t form, and the Jello mix stays syrupy. The materials that keep your body’s cells from moving all over the place are also a mesh of proteins, and so if there is enough protease, some of this mesh will be dissolved. This is why pineapple can make your mouth sore. It is also why a strong protease can eat away the proteins that surround a DNA sample. Hair samples, in particular, have a lot of protein surrounding the DNA, so there needs to be a lot of protease to get to it.

Another way to get at the DNA is by using a detergent. Laundry detergents clean clothes by breaking up the oily materials that trap stains in the fabric. The membranes of cells are also made of oily material, so by using a detergent, we can wash away the cell membranes and get to the DNA inside.

Often both a protease and a detergent is used just to be sure the DNA is accessible. After this, the sample is put through a centrifuge to remove the lighter, non DNA molecules from the heavier DNA. Once the DNA is free, chemicals or heat is used to separate the two strands of DNA into single strands. This allows the restriction enzymes to work on the DNA. Restriction enzymes cut the DNA at specific areas that a technician can determine ahead of time. DNA is formed of four different bases: Adenine, Guanine, Cytosine, and Thymine, Each enzyme attaches to a certain sequence of these bases and cuts the DNA where ever that pattern shows up. DNA from different individuals will have different lengths between each recognized pattern and so will be cut up into differently sized sections after the restriction enzymes do their work.

Image from

The cut up DNA is then poured into a gel, usually made out of agarose or polyacrylamide. Just like Jello, these gels are made of long molecules connected together to form a mesh that partially traps water. The DNA fragments can travel through the spaces in the mesh, but not very easily. Lab workers apply an electric field to the gel using a tray with exposed electrodes that holds the gel immersed in a bath of mostly water mixed with some chemicals to help pass the electricity to the sample.  DNA is made of sugar molecules, and like most things made of sugar, it becomes negatively charged very easily.  In fact, unless DNA is in a solution with a high pH, it will have a slight negative charge, and so the electric field made by the tray device  pushes DNA down the gel toward the positive electrode in a process called electrophoresis.

The larger the piece of DNA, the harder it is for it to pass through the mesh of the gel. Smaller strands will therefore travel farther along the gel in a given period of time.Fragments of DNA that are the same size will be in the same area of the gel after they’ve been pulled through it, forming bands in those areas. These bands are still not visible, however, until the lab worker applies some kind of label to the DNA. This could be a chemical dye that binds to DNA, or DNA fragments with radioactive isotopes attached. The most common chemical dye is ethidium bromide, which is only visible under a black light. The lab worker can place a gel stained with ethidium bromide on a scanner attached to a black light to record the bands in the gel. In the case of radioactive isotopes, a film sensitive to x-rays can be placed on the gel which will turn dark where ever the radioactivity is.

Gels fall apart very easily, so many lab workers will transfer the DNA from the gel to a sheet of filter paper by pressing the paper to the gel and passing a current through it for some time. Then they can apply a label as before to see the bands of DNA.  These bands are what you usually see on tv shows where they compare DNA. By looking at where the bands from different samples show up, a lab worker can tell which samples are from the same source and which ones aren’t.

Debbie Knight at biologyze gives an excellent  detailed accounting of the process of gel electrophoresis here if you’re interested. She uses it to analyze proteins, but the idea is very similar.

Sometimes there isn’t enough DNA in a sample to get visible bands, in fact, this is usually the case. For these situations, there is PCR. PCR stands for Polymerase Chain Reaction. Polymerase is an enzyme that replicates DNA, but it’s more complicated than that. In order for the DNA to be replicated, it has has to be separated into single strands from its usual two stranded arrangement. This is called denaturing the DNA. In nature, this task is performed by proteins called helicases, however in the lab, heat or other chemicals can do the job.  Chemicals are somewhat difficult to work with, because they have to be washed out of a sample every time they are used. Heat is a much better denaturing agent, but most polymerase molecules can’t stand the heat needed to separated the DNA.

Thankfully scientists found the molecule Taq, a DNA polymerase found in bacteria that can withstand the heat.  So what happens during PCR is that after Taq is added, the samples are first heated to a temperature high enough for the DNA to denature. Then the temperatures lowers, letting initiating sections of DNA called primers to attach or anneal to the fragments. Then the temperature raises again to a temperature that is ideal for Taq to replicate the DNA. Finally the samples are heated once more, so that the new DNA fragments separate again with twice as many fragments as before. This reaction is performed again and again, so that first two new strands are made, then four, then eight and so on, the amount of DNA increasing exponentially with every cycle. This way even with a miniscule amount of DNA you can have enough of a sample to work with.


Reading Your Blueprint: Karyotyping

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

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.


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) about what I’ve written.

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