The Science of Things

Swine Flu thoughts (H1N1)

2009-04-29T12:24:00.001-07:00

My first thought on hearing of the swine flu outbreak was that society continues to go 1970's retro. Last I heard of it was around 1976.

So what is the H1N1 or swine flu? Good question. It's a flu virus that started in pigs, but has mutated enough so that it can now infect humans. Flu viruses have chemical markers on their outer surface. It is these adhesins that allow for the binding of the flu virus to cell surfaces before they infiltrate and infect them. The "H1N1" moniker refers to these markers on the virus surface.

These adhesins give the flu virus specificity for hosts. This is why dog viruses don't infect humans and vice versa. That is, until they do. Viruses can have a high mutation rate. Part of the reason for this is some don't really have a lot of mechanisms to make sure that their DNA is copied correctly. This is where mutations arise. This is especially true of viruses such as the flu virus where their genetic information is carried in RNA instead of DNA. And the flu virus is an RNA virus.

See, viruses have to get inside of intact cells in order to reproduce and manufacture more virus particles. They're stripped down life forms that carry genetic information and not much else. They use the host cell for energy and for expressing their genetic information and manufacturing virus proteins--guided by the virus genetic information. They storm the cell and take over, kind of like an invading army. It's an efficient way of life unless your genetic information is contained as RNA. The host doesn't have the enzymes to copy RNA like that. The virus usually has to carry the information for making it, and frankly RNA replication doesn't have as robust as a proof-reading mechanism as DNA replication does.

And viruses are simple organisms to begin with. They only have a few genes as opposed to thousands for bacteria and multiples of thousand for humans.

For the flu virus this means that the adhesin genes change, which lead to the adhesin proteins change. This ultimately results in different adhesin proteins on the surface of flu viruses which can, if the right combination of mutations occur, change a virus that would normally infect pigs now infect humans. (same with birds to humans). Physiologically and biochemically, it turns out that pigs are quite similar to humans.

For more information on the outbreak, check out the CDC website for swine flu. For more information on the life cycle of the flu virus itself check out this site.

Cuteness Alert

2009-03-30T10:17:00.000-07:00

The National Zoo is celebrating the arrival of 2 clouded leopard cubs. All of a half pound each, the cats were born on March 24. This is the first birth of clouded leopards at the National Zoo for 16 years. The species is endangered. Full story and VERY cute pictures here.

Science Solves 20th Century Historical Mystery

2009-03-16T10:58:00.000-07:00

DNA analysis almost 100 years after the crime solves the mystery.

In 1917, after the Bolshevik Revolution in Russia, the members of the Romanov family, the ruling family for several hundred years, were captured. Most of the members were executed and buried in a mass grave. However, the two youngest children were not buried with the rest of their families.

History told of a separate burial for these two children, Alexei and one of his sisters.

However, rumors persisted well into the 20th century that one or both of these children escaped and lived the remainder of their lives in hiding. One "famous" woman, Anna Anderson, a Polish claimed that she was Anastasia Romanov. She wasn't the only one. During the 20th century over 200 people claimed to be one of the missing Romanov's.

In 1991 the missing grave was discovered and most of the Romanov's identified by DNA analysis; however, the last two children were not in the grave.
PLoS ONE. Coble et al. report on the finding of a 2nd grave in 2007 and the identification of the 2 skeletons contained therein as the remains of Alexei Romanov and one of his sisters. It can't be confirmed whether the female was Maria or Anastasia.

So, how do they identify the remains and determine lines of inheritance? They do DNA testing from several different loci in the genome, but one of the most common methods for determining line of ancestry is sequencing of mitochondrial DNA.

Mitochondria are the energy producers in our own cells. Most of the chemical reactions that result in the burning of compounds to create our own energy takes place inside these small organelles located within each of our cells.

Evolutionarily speaking, mitochondria are very old, and evolved from the earliest merging of cells together--one to house the genome, and one to house the energy machinery. An historical artifact of this merger is that mitochondria actually contain their own DNA, and their own ribosomes for making protein from it. A mitochondrial genome (mtDNA) is much smaller in size than the human genome, but is important for cellular function. the mtDNA encodes proteins needed for energy production, and there are genetic diseases ascribed to mutations in mtDNA.

The mitochondrion have many similarities to bacterial cells, even though they cannot survive outside of host cells.

So, with that background of mitochondria is the explanation that sequences of mtDNA will allow you to determine maternal lines of descent. While each of our genomes is an amalgam of the genomes of both our father and mother, the genome contained within each of our mitochondria is only from our mother. The mother contributes the egg, which along with its DNA component contains all the other organelles to allow cells to grow and divide. The sperm provided by the male only provides the second half of the genetic code--and that gets delivered to the nucleus, not to the mitochondrion.

So, the sequence of mtDNA, which is present in all of us, can determine our maternal line of descent. This was one of the powerful tools used to identify the remains of the Romanov children and determine they were the children of Tsarina Alexandra Romanov.

Irrational Rationality--Let's Celebrate!

2009-03-11T08:20:00.000-07:00

I always think of math as this rigid subject. 2+2=4, etc. Can't change that. That's why I absolutely love the term "irrational number."

What a beautiful term!

What's an irrational number? It's a number that basically goes on never-ending. It's a fraction that actually can't be written as a simple fraction because it can't be solved to the final decimal place, and there's no rational pattern to the numbers.

The best example is "π" or Pi. When we write π out or use it in math, we write it out as 3.14. However, π goes on forever--with no pattern to its numbers. It goes on: 3.1415926535897932384626433832795.... never ending. I love the old Star Trek episode where the ship's computer has been taken over by some evil force, and Mr. Spock gets the computer occupied by asking it to put all systems on the problem of solving to the last decimal place the value of Pi. The "entity" inside the computer screams "Noooooooo." It's an impossible task. People have calculated it to over 1 million decimal places, and there's no end in sight and there's no pattern to the numbers.

Even the fraction sometimes used to represent Pi, 22/7, isn't right. It comes close, but it's not identical.

Pi is the ratio of the circumference of a circle to its diameter, so the number has a basis in descriptions of the real world. And it's irrational. (again, I love that term)

So, why the thoughts on Pi? This upcoming Saturday, March 14 is "Pi Day." 3-14. Celebrations will be had throughout geekdom. The San Francisco Exploratorium will have a celebration for it. Coincidentally, it's also Albert Einstein's birthday. The SF Chronicle has an article about Pi Day celebrations here. So, this Saturday will be an "irrational day!" Celebrate well!

With Spring comes Baseball!

2009-03-03T07:59:00.000-08:00

The turning of the calendar leads us to the first whiff of spring, and in my book spring means BASEBALL!

Now, you ask. What does baseball have to do with science???

Now, come on! Everything has something to do with science, and if Isaac Newton were alive today he’d be a HUGE fantasy baseball guy! Why, you ask? Physics, my friend. Simple Newtonian physics. (Well, maybe not entirely simple, but quite elegant).

Several years ago I took a trip to Cooperstown, NY to the Baseball Hall of Fame. It's a wonderful place to visit, even if you're not really a baseball fan. It's a beautiful town, and there's lots to see in the Hall. But I went to a seminar there for everyday folk about the science behind baseball. A couple of years ago the Baseball All Star Game was in San Francisco, where I live, so I went to All Star Fan Fest and went to yet another seminar, Q & A session on the science behind baseball.

Anytime you deal with the movement of objects, you're talking about physics. And when the objects are of the sizes of baseballs and bats, and include wind speeds and curve balls, you're talking Newtonian physics. How do pitchers affect baseballs in such to way to make the balls curve or slide? How does a spit ball work (illegal in the game but still a reasonable question)? What makes a good swing? All of these things have to do with motion, leverage, torque, momentum. If you have a good understanding of these concepts in physics, baseball is a good demonstration of them.

Similarly if you love baseball, that is an "in" to studying physics. It's a real world application.

You can find several sites that give a good low down on the science of baseball, but the Exploratorium has a good one here. They also talk about the biology behind baseball and how your muscles have to work and the reaction time to hit a 95 mile an hour fast ball and the split microsecond decisions your mind and muscles have to make on when to start the swing and process the information your eyes tell you about the location, velocity, and arc of the pitch. You can also find a lot more information at the Baseball Hall of Fame website and others about the same subject.

There's a lot of playing sports that is instinct, but with practice we also become good judges of movement. So in a way, without knowing the theory, we are amateur physicists. The same holds true for all sports: football, basketball, hockey, golf, pool, swimming, etc. Baseball lends itself to this example because of so many great examples of movement: not only the arc of the ball on a pitch, but the arc of a ball after a hit, base running, throwing, types of pitches, the logistics of batting, judging balls and strikes, reflexes and muscle response, hand-eye coordination, velocity, humidity, etc. It's a physicist's and baseball statistician's dream!

And as long as you have a good one, there is no bad time to throw a change-up!

Go Giants!

Cutting Edge techniques to do Ancient Science

2008-11-19T12:25:00.000-08:00

Now they've sequenced the woolly mammoth! How awesome is that?! Not only have they sequenced about 80% of its genome, but they've discerned that they're very closely related to modern elephants (already suspected, of course), and they may have an idea as to why they went extinct!

Just amazing stuff you can tell from a DNA sequence. They were able to get a sample of mammoth DNA from hair of the mammoth. There are some amazingly preserved specimens of the mammoth discovered over the years. Some specimens were so well preserved in ice that the meat is still edible (no word on if it tastes like chicken).

But an analysis of the DNA sequence led by Stephan Schuster lab at Penn State University with Webb Miller as primary author and published in Nature showed that elephants and mammoths are very closely related at a genetic level with a difference of 0.6%, half that of humans and chimpanzees. Furthermore, at an estimated 4.7 billion base pairs, it's 1.4 times the size of the human genome.

They sequenced genomes from several specimens of woolly mammoth and discovered that there was indication of inbreeding among mammoth populations, and not a great deal of genetic diversity. For a species, this is bad news. It means that the entire population is susceptible to being wiped out by disease or climate changes. It could indicate why the mammoth went extinct--simply because there wasn't enough to choose from in the pool of genes within the mammoth population to create individuals who could combat environmental or health stresses.

Nature will charge for access to the article, but you can read a description about it here

The Sounds of Space

2008-11-17T14:20:00.001-08:00

I've been too busy to post much lately, if anyone has noticed. But I heard this story recently on NPR that was just so cool that I had to share it.

Here's the link to the audio of the story.

Two scientists, one from Britain and one from Romania, asked the question, what do things sound like in space? We know what outer space looks like, but do things sound differently out there than here. This is a valid question because lots of atmospheric factors influence acoustics and sound--humidity and carbon dioxide concentration are examples. So, they put various parameters into a computer to try to simulate the atmospheres on Mars, Venus, and on Titan, one of the moons of Saturn. All three of these contain atmospheres. Then they played a Bach organ piece in each of those environments.

They sound different in each one! Not hugely different, but different enough to tell. Then they put each on top of each other and played a solar system symphony with contributions from Earth, Mars, Venus, and Titan. Wow was it dissonant!

So, while there is music in the spheres, it's not always harmonious.

The Ancient Redwoods in the Pouring Rain

2008-11-03T15:46:00.000-08:00

I went to Muir Woods this weekend to walk among the ancient growth redwoods in the pouring rain. There weren’t many people there braving the elements (or actually just one element to brave here—the water), so we had the place pretty much to ourselves. It was mid-afternoon, but dark as the clouds and the tree canopy stole much of the available light. The colors were intense, as the ground cover ferns soaked up their first substantial water in months. The small stream that runs through Muir Woods, practically dry 2 months ago when I was last there was running fast over the rocks and ledges and providing a place for the fish that live there to grow and thrive.

This place is old growth redwoods. It’s been a National Park since the early 1900’s, and the trees that grow there vary in age, with the oldest being close to 1000 years. I like to walk through there and think of the world when those trees were seedlings and how much things have changed in the interim---and how much they’ve stayed the same.

Nature and science exist all the time. We just discover it along the way.

The Lush Sahara

2008-08-15T08:18:00.000-07:00

I've always been fascinated by the fact that the Earth is dynamic. It's always changing. There are the cyclic changes of the seasons, obviously, and the growing crops and gardens. And of recent there is the great melting of the ice shelfs in the Arctic, and how that is affecting not just the local area, but has ramifications for the entire planet.

Sometimes, however, these changes are so incremental that we can't see them. But they happen over geologic time nonetheless.

The Sahara used to be a lush land with lakes and plant life and people. That fact was brought to my attention again this morning as I read my morning paper. Anthropologists hunting for dinosaurs in the Sahara in Niger when they inadvertently stumbled upon a human cemetery dating about 10,000 years ago. This was long before the first pyramids were built in Egypt.

The picture in my paper had three skeletons--a female with 2 children, and the positioning of the bodies, with arms outstretched toward each other suggest that it's a mother and her 2 children. And pollen underneath the bodies indicates that they were buried on top of a bed of flowers. The children were wearing ornamental jewelry (a bracelet made of tusk material).

These people were part of a society of hunters and gatherers and fishermen who lived in this area. Others in the cemetery were quite tall--over 6 feet. This indicates they were healthy and well fed, and quite strong.

It's just interesting to try to imagine what life was like for these people in this lush area that has become desert. And it's a reminder that the Earth does change--sometimes quickly sometimes slowly. In this case, Earth's rotation was slightly altered, which changed the angle at which the Sahara region sees the sun. The result is what you see today.

Today however, we are not experiencing a rotation shift.

The scientific article for the find is here, and the article from my local paper is here.

Everybody In The Pool!!!

2008-08-01T15:18:00.000-07:00

They found water on Mars!

Well, maybe the pool party is a bit premature. But in order to find any type of life with which we're in any way familiar, there has to be water, and it's there.

If there is or ever was life on the red planet, chances are it was/is microbial in nature.

Here's the story

Quanta, Strings, and James Bond.

2008-07-27T16:38:00.000-07:00

I’ll put the disclaimer up front. I’m not a physicist, and I don’t pretend to understand these theories in anything but the smallest, atomic degree; however, that doesn’t mean I’m not fascinated by them.

I was reading a popular magazine the other day, and it said that the newest James Bond movie that would be coming out sometime in the Fall of 2008 is called Quantum of Solace. What a bizarre name, I thought. I’m not the only one because in the article I was reading, the author was complaining about how obtuse the name was. It’s somewhat weird, but I think it’s elegant. It got me thinking about the word “quantum.”

“Quantum” can be a noun or an adjective. It’s an interesting word because it can mean diametrically opposite things. A quantum leap is a massive step, as in—understanding the structure of DNA was a quantum leap in the field of molecular genetics as it helped explain the science of heredity. On the other hand, quantum can also mean extremely miniscule, as in—the size of a quantum of energy can be measured in a billionth of a billionth of a billionth of a unit—in other words, it’s unbelievably tiny.

The field of quantum mechanics is the physics of atomic particles. In other words, it’s the study of the motion of atoms and the particles that make up atoms.

Isaac Newton is one of history's greatest scientists, and he studied many fields including motion, optics, astronomy, theology, and mathematics. He's credited with inventing calculus in order to solve his physics and astronomy questions. The story of popular legend is that Newton first recognized "gravity" when he was sitting under and apple tree, and an apple fell on his head. He's one of the fathers of physics, as his theories described both the motion of everyday objects and stars in mathematical terms.

Now Newton's equations were amazingly accurate, and were enough for modern day scientists and engineers to navigate Earth astronauts to the moon. However, in the 20th century Albert Einstein described that Newton's laws did not fully explain the character and motion of light and space-time. Einstein described space-time as malleable and light existing as particles or quanta of energy. His theory of special relativity posits that space-time is flexible, and that our perception of it can change with the speed we're traveling (the old story of the astronaut who travels for a year at the speed of light and when he returns to Earth, even though he's aged a year, the Earth has aged hundred of years--or something like that).

But even Newton and Einstein didn't explain the whole of physics--the motion of everything in the universe. Why? Well, if you use the equations of Newton and Einstein, they explain very well the motion of everyday objects (cars, apples, birds) and celestial objects (planets, stars, comets), but they cannot explain the motion of atoms and the particles that make up atoms. The laws of physics simply break down when it comes to the very small, or the quantum world.

The quantum world is an extremely bizarre one. It's a world of probability that doesn't seem to make any sense from our view of things. When explaining the motion of a particle (such as an atom or an electron or a quark or muon--there are many of these things, and I don't even pretend to know them all), you can't predict exactly where these things will be in a given moment. It's not like--2 quarks leave the train station going at the speed of light, and how long does it take to reach Pluto, to paraphrase a common physics word problem. You can't say with any surety where the particle is going to be at any one time. All you can do it PREDICT where it will be. And here's the bizarre part--it can be in 2 places at once.

I'm not making this up. The physical laws of our visible world are twisted in the quantum world (and I should point out that we're made up of the quantum world--all the molecules in our body are made up of atoms which are made up of electrons, protons, neutrons, quarks, muons, .......).

Newton's and Einstein's equations just fall apart when trying to describe the motion of these small particles. The field of quantum mechanics was developed to explain the motion of the very tiny. However, the math behind quantum mechanics doesn't do diddly to explain the motion of everyday objects or stars. We don't exist in 2 places at once. I'm sitting in front of my computer now, and no equation is going to predict the probability of me existing both here and in my kitchen at the same time.

So, there is a paradox. If the universe is ordered, how can we there be 2 fields of physics to describe the very small and the very big? There should be some universal theory to explain the motion of everything that would take into account both the big and the small.

Well, there's not an answer, but there is, of course, a theory. (There's always a theory).

A very sexy theory taking physics by storm now is called "string theory." For more on this you can read Brian Greene's great, but somewhat technical book called The Elegant Universe. PBS also made a documentary of it, which is out on DVD, and it's great!

I don't understand the math. But the explanation is that if we describe all the atoms, electrons, neutrons, protons, quarks, muons, etc. as existing not as discrete particles but as strings of energy, then both the motion of big and small can be explained. Think of the strings as violin strings. The identity of the string (be it a electron or proton, etc) is determined by the frequency of how that string vibrates. On a violin, the different strings sound different because they are of different thickness, and so when they are plucked they vibrate on a different frequency. The result is a different sound. Similar to the strings that make up subatomic particles. Their identity is determined by the frequency at which they vibrate.

It's complicated, and I don't understand much more than that, but I still think it's fascinating. There's one problem with the theory in my scientists eye. It's just a theory, and it hasn't been tested. The theory does make predictions that can be tested by experimentation, but the field doesn't have the technology to do those experiments yet. Maybe in the near future, but not now. At the moment, there are lots of physicists doing some extremely complicated math to explain this theory, which is elegant in its simplicity. But until someone can do some experimentation to define it, it's just a theory.

Hurray for Coffee and 2 X Chromosomes

2008-06-17T09:41:00.000-07:00

Today's news has the results of this story showing that coffee drinkers have slightly lower death rates than non-coffee drinkers. Moreover, women drinking 2-3 cups of coffee a day had a 25% lower rate of heart disease. And it didn't matter if the coffee was caffeinated or not.

The study was done with a survey of over 120,000 middle aged men and women. The editors of the journal caution that this does not mean that coffee decreases the chance of dying sooner rather than later. Something else about coffee drinkers might be protecting them. And there may be errors in measurement.

But this reminds me of another study I heard of a few months ago. In that one, they said that coffee has more antioxidant compounds than anything else in our normal diet. Could the antioxidants play a role? Hmmm.

Regardless, I don't have to feel guilt about enjoying that second cup of coffee.

Monkeys Learn to Fish

2008-06-17T07:52:00.000-07:00

I read this news in my local paper last week. Long tailed macaques have a reputation for being highly skilled at finding food. Their food sources are usually fruit, insects, and foraging for crabs near water. No one had ever seen them fish before.

However, in Indonesia, silver haired monkeys were observed doing just that. Not just an isolated incident, but several times over the last 10 years, biologists observed the behavior in these long tailed macaques.

It's exciting to see new behavior in a species long observed. One of the authors of the study, Erik Meijaard with the Nature Conservancy, said "It's exciting that after such a long time, you see new behavior. "It's an indication of how little we know about the species. They are a survivor species, which has the knowledge to cope with difficult conditions. This behavior potentially symbolizes that ecological flexibility."

It shows an ability to adapt to the changing environment and shifting food sources.

They probably fish better than I ever did.

Here's the article.

My Meeting Experience

2008-06-11T07:54:00.000-07:00

I was in Boston last week at the 108th Annual Meeting of the American Society for Microbiology. This is a huge meeting that I've been to several times in the past. I liken it to a buffet of microbiology. All things microbial are there. Thousands of scientists, students, and interested bystanders converge and converse on the great things that are small.

The meeting can be a bit overwhelming because there are so many people and topics. Often there are 2 or more talks going on at the same time that are of interest. But what I like about it is it gives the chance to survey what's new and hot in the field. Also it's a chance to revisit old friends--both microbial and human.

It's not so strange. Trust me. When you've done research on a particular organism, your interest in it doesn't wane simply because you've switched jobs. You always keep an eye on the latest news in what you've worked on before. After all, I dedicated a lot of effort into learning about and understanding a particular organism--it's quirks and traits, and just because I don't work on it anymore doesn't mean that I still don't find it interesting and cool.

But at the ASM meeting there's always something going on. If you find yourself bored by a particular talk, just look in the program: Oh there's a session on photosynthetic bacteria, and I haven't heard anything about photosynthetics in a few years--let's see what's new. The added and unmeasurable benefit of seeing talks outside of your immediate field is that it gives you a fresh perspective on what you DO do on a daily basis. You hear someone talk about studies they do in a completely different bacterium, and you think that maybe such a thing could work for you--either in an ongoing project or a new one for the future--in your system.

The ASM General meeting doesn't have a specific theme; however, themes tend to arise. This year was the year of metagenomics and the question of what is natural human microbiota. In English you ask? Read on:

We can only culture in the laboratory about 10% of the bacteria that are out there. Their diversity is vast, and nutritional and growth requirements unknown or difficult to reproduce in the lab, and we simply can't grow them. Either the temperature, pressure, nutrients are wrong, or they can't grow by themselves. Some only grow in the presence of other bacteria. Nonetheless, they are out there and affecting the environment and ecosystem. Recently, however, scientists have begun extracting DNA from these environments, and simply looking for bacterial signatures in that DNA. With those sequences they can predict bacteria that are in that environment. Some known--many unknown. A very famous study is Craig Venter's Sargasso Sea Project. Venter was a major player in sequencing the human genome. He took his boat to the Sargasso Sea and sampled the water and looked at the microbes that were there and documented the vast unculturable diversity.

This practice of sampling the DNA from an environment to assess the life that is there is Metagenomics.

Lots of metagenomics talks at ASM. And using metagenomics, various scientists are tackling the question of what is normal human microbiota. I wrote about this earlier when I mentioned skin microbes recently. I saw some of that work at this meeting, but scientists are also determining what is normal gut-associated bacteria, oral bacteria.

We're not sterile folks, and these resident microbes do a lot of good for us. And we can't culture them all. But metagenomics is starting to give us an idea of what lives in and on us. Once again, if we can determine what is normal and then see what is abnormal in various diseases, maybe the microbes can be manipulated???

Such probiotic treatment is fodder for the future, but it's nice that technology has provided us with a way to do basic microbiology in a very non-basic way to study the ecology of the microbial world.

Intimate Strangers

2008-05-23T08:01:00.000-07:00

I'm scanning the science news this morning, and come up with 2 similar stories in Science and the New York Times. There's an effort out to identify the majority of the bacteria that live on human skin.

Ewwww, you might say, but not so fast.

These are, for the most part, commensal bacteria. Meaning, they live on and in us with no bad effects. In fact, we WANT them there. They physically block "bad" bacteria from hooking on for a ride. Or they can make the environment a less acceptable place for the disease causers to establish a place.

We peacefully co-exist with our bacteria. There are 10 times as many bacterial cells on and in each of us than there are human cells that make us up. We're talking trillions of bacteria. Each of us is an ecosystem unto ourselves. We are made up of multiple trillions of cells of many different varieties and biological kingdoms. The vast majority of the microbes in the world are beneficial or neutral. They break down waste products, provide us with vitamins, and make the world a much more habitable place.

But scientists are trying to understand what types of bacteria colonize human skin naturally. Scientists at the U.S. National Institutes of Health (NIH) are sampling different areas of the body to find out what average, healthy people carry. Strangely enough, they've discovered that the space between your toes is a barren wasteland for bacteria--they just don't go there. However, elbows, Some of them have been known, such as Staphylococcus aureus, which can be a disease causer, but not all the time. The NIH study has found that 90% of the bacteria they're finding belong to the genus Pseudomonas which is a common soil bacterium, but not known to inhabit skin before.

Moreover, the types of bacteria that are on us differ depending on where on the body you sample. So, the bacteria are picky as to what areas they inhabit. The bacteria on the inner elbow, for example, are of different species from the ones a few inches away on the forearm.

Now, why do they want to know which bacteria inhabit the skin? Well, beyond the fact of it's just good to know what you're dealing with, it might be good to find out at some point if the microbial content differs in people with skin conditions (such as eczema). If there is a difference, perhaps that information could be used for better treatments for those skin conditions.

For more information on this work, here's the link to the NY Times article on it. More links to follow if you're not registered on the Times site.

Bacterial Promiscuity

2008-05-16T10:33:00.000-07:00

Promiscuous behavior abounds in the microbial world! Unknown to the world at large, bacteria regularly "have sex" and transfer DNA. We can get them to do it in the lab too (they're not too picky about mood and music).

You can see photos and movies (G-rated) here.

Basically, the bacteria make an appendage on their surface called a "pilus." It's a long hollow tube, and it can attach to adjacent bacteria. When that happens, DNA can transfer from one cell to the other. This is called conjugation. In basic microbiology labs we do conjugation experiments. You basically grow up 2 different strains of E. coli (usually we use a non-infectious E. coli for these experiments), mix them together in a tube, and let it incubate for various times--usually up to 30 minutes.

You can determine that conjugation has occurred because the recipient strain will have acquired a new trait that is easily tested for--such as antibiotic resistance.

In nature, conjugation and other forms of DNA uptake occur all the time. This is one major reason for the great increase in antibiotic-resistant bacteria. If bacteria are exposed to a sub-lethal dose they can develop resistance. This happens quite often actually--we can demonstrate it in the laboratory. Sometimes this resistance can be transferred to other bacteria.

And after a long time of this happening, you get things like MRSA Staphylococcus aureus that is resistant to many commonly used antibiotics. MRSA is the bacterium getting a lot of press recently--wrestling teams coming down with skin infections, schools becoming infested with it. It's a S. aureus that has acquired some new tools to manage to resist medical onslaughts that attempt to kill it. You can treat it with the right stuff.

This phenomenon of resistance is a major health issue. The bacteria are just doing what comes naturally. They're wonderful at adaptation, and to them they are just adapting to chemical onslaughts and sharing the information. It's only a problem when the bacterium doing the adjusting also happens to be a human (or plant) pathogen.

What's New and What's Cool?!?

2008-05-01T20:21:00.000-07:00

I've been away for a bit. Busy doing writing of a different sort. But I've tried to keep up on things.

So, what have I seen that I thought was interesting?

I watched a Nova episode from 2006 on PBS last night on the exploration of Saturn and its moon Titan by Cassini and the Huygens space probes. Fascinating stuff. Titan is one of only 4 known bodies in our solar system that is rocky and has an atmosphere. The other three being Earth, Venus, and Mars. Venus is way too hot to have any organic molecules present (lead will melt on its surface), and Mars is far too dry. Titan is incredibly cold, but interesting in that it might give insights on what it was like on a very primitive Earth.

Pictures taken by the Huygens probe on Titan showed an alien yet somehow familiar surface. Structures looked like mountains, lake beds, and even volcanoes. However, the rivers are made of liquid methane. It's so cold there that what is gaseous methane on Earth is liquid there. And the volcanoes are actually cryo-volcanoes. When they erupt, they don't erupt lava, but they erupt a mixture of supercooled water mixed with ammonia. The temperature of this is about -100 degrees Celsius!

Methane is an organic molecule made up of carbon and hydrogen. Ammonia is made up of nitrogen and hydrogen. And water is present. These could potentially be building blocks of amino acids (chemicals that make up proteins). It's so darn cold there though, that any chemical activity takes a long time to happen.

So, who knows. Maybe deep down under Titan's surface where it's a bit warmer there are actually microbes down there. Here on Earth we have bacteria that release methane as a byproduct of their metabolism. Could something similar be going on there, deep under the surface of Titan? Could interstellar methanogens be present on one of Saturn's moons? Could those methanogens be responsible for a good portion of the methane on Titan? I'll probably never know in my lifetime, but it's fun to contemplate.

Back when I was in graduate school, taking my general exam, we were asked to think about this question. If there were life on another planet, it would probably be microbial. So for our test question we had to design a microbial ecosystem for this hypothetical planet. It's kind of fun to look at pictures of Titan taken by the Huygens probe, and think that my general exam might actually be playing out in real time somewhere out there.

They've Sequenced James Watson, and They Did it in 4 Months!

2008-04-16T12:20:00.000-07:00

With the plethora of genome sequences from lots of different organisms now being generated, it's almost an afterthought on the news when a new genome arrives. The dog has been sequenced! The horse has been sequenced! Campylobacter jejuni has been sequenced!

See here for my blog on DNA and genomes if you need a ... primer.

A few years ago they finally sequenced the human genome. It was a vast undertaking of many different labs that took 13 years (1990 - 2003) to sequence the 3 billion nucleotide base pairs in our 46 chromosomes. To put it bluntly, the technology that existed in 1990 was not up to that task. To give an example of what needed to happen to achieve this goal, let's compare it to putting a person on the moon.

When John F. Kennedy in 1961 swore to put a man on the moon by the end of that decade, huge resources went into research and development to make it happen. Rockets were designed, space ships were made air tight, and oxygen delivery systems were built. Dehydrated food and drink was made. What happened was an era of huge technological breakthroughs that culminated in Apollo 11 landing on the moon in July of 1969.

More recently, in the late 1980's-early 1990's, scientists started talking about sequencing the human genome. You have to understand what it was like to sequence DNA at this point in history. It was a very long, painstaking procedure. I sequenced DNA by those methods. You got sequence, but you worked hard for not very much. You can't get 3 billion nucleotides of sequence when you have to read sequence by the naked eye and can only achieve, if your lucky, a couple thousand nucleotides a day. (Some pictures of old-style sequence gels here)

Similar to what happened in the moon race, DNA sequencing technology changed dramatically during the drive to sequence the human genome. Dedicated machines designed solely to generate sequence data that is read by computers changed the field (see picture at the top for an example of a computer generated sequence trace). Along the way, the genomes of many other organisms (said dogs, horses, Campylobacter jejuni, for example) were completed as well. And more continue to be completed every month.

And the technology continues to evolve.

Today I open the table of contents to the new issue of Nature, and I see that they've sequenced the genome of James Watson, a Nobel Prize winner who had a hand in discovering the sequence of DNA back in 1953. And they did it in 4 months! From 13 years to 4 months! Yup, the next generation of sequencing technology can do it in a fraction of the time at 1% of the cost of the previous technology.

I could have used that sequencing technology when I was in grad school!

But like any good scientific achievement, the ability to sequence a genome results in a lot of answers, but opens up an enormous amount of questions. Ok, so you know the sequence of the genes. How do they work? Some fascinating work going on in that department that I hope to address in future entries.

Frogs Without Lungs!

2008-04-10T09:37:00.000-07:00

But it's true! Here's the link to the story in the San Francisco Chronicle. It has no lungs, and breathes through its skin. They also say it kind of resembles a small version of Jabba the Hut from Star Wars. But it's well adapted to the streams it lives in, which is cold, rapidly moving streams that are rich in oxygen.

Maybe the lack of lungs keeps it less buoyant so that it isn't swept away in the current.

Evolutionarily it is related to other frogs that DO have lungs, and the biologists think that this may be an example of extreme evolutionary change in response to an environment.

Girls DO like science and math.

2008-03-07T14:23:00.000-08:00

Had this study pointed out to me today. Seems that girls in elementary school liked science better than language arts and social studies. As they got older, they lost some interest in science, but lost interest in the other subjects as well.

Check out the article here.

Order in Nature

2008-02-23T13:32:00.000-08:00

I wonder how many people I’ll lose after the next sentence. The second law of thermodynamics states that the entropy of a system will increase over time. Don’t stop reading! I promise you—I’ll explain my point.

There is an awful lot of complicated math that goes into proving the 2nd law to explain that unless work (i.e. energy) is put into a system, it will inevitably become disordered.

What does this mean? Well, in everyday speak, it’s like cleaning your house. You clean your house, and over time it becomes progressively more cluttered and dusty. It will continue to do so until you put work (i.e. energy) into fixing it up again.

The 2nd law has more to it than just that entropy is inevitable, but that’s the part I’m thinking of now. While the 2nd law is a fundamental part of physics, it has relevance to all science. (Aside: as may become obvious as I continue to blog, physics is the root of it all.)

As a biologist, I realize that to create order, whether that is the manufacture of a complex molecule such as a protein, a highly organized single cell, or an entire multicellular organism (such as a person) requires a huge amount of energy (hence the fact that we must eat to maintain our system).

So, it is because the nature of nature is to become disordered that I find elegance in things that ARE ordered—especially in nature. The fixed number of petals found on flowers, the regular pattern of shapes on a shell, the periodic table.

The periodic table???!!!

Yup, the symbol of a science geek, mostly attributed to a Russian chemist by the name of Mendeleev in 1869. Think about it. The table represents all of the elements found in our universe. And the elements are constructed such that their atomic numbers can be placed in order, based on the number of protons in the nucleus of their atoms.

Hydrogen (H) has 1 proton, Helium (He) has 2, Lithium (Li) 3, and so on.

In other words, the elements are ordered. The building blocks of nature are ordered. There is elegance in that. And a lot of force goes in to maintaining the structure of the atom. The strong and weak nuclear forces are needed to maintain the atomic structure and keep the atom, with its oppositely charged protons and electrons, together. There is a lot of work involved in maintaining order.

It’s Not Just for Camouflage; It’s to Impress the Ladies!

2008-02-13T17:36:00.000-08:00

Remember how you learn about camouflage in nature as a kid? Every teacher brings up chameleons as a perfect example of altering their appearance to blend in a avoid predators that might want to eat the little guys.

Turns out it’s not entirely true!

I just read this article in PLoS Biology by Devi Stuart-Fox and Adnan Moussalli and the accompanying descriptive article for it by Kira E. O'Day. Stuart-Fox and Moussalli studied South African dwarf chameleons (not the type in the picture) in a natural habitat to see what triggered the color changes. It turned out that male chameleons displayed their brightest, most obtrusive color when dealing with other males in the interest of finding a mate.

They still change color to match in with the background when confronted by a predator.

But sure enough the guys are donning their brightest clothes to impress the ladies. And the loser in the chameleon posing promptly dons drab colors and retreats.

The scientists analyzed the variety of background colors the chameleons live with as well as the large capacity of colors both visible and not visible (such as in the UV range that humans can’t see), and they’ve concluded that the evolution of color change in chameleons was actually driven by social signals. In other words, while the chameleons reap the benefit of their color change because of how it can help them hide from predators, what may have actually driven the evolution of the capacity to change color is their social life.

So, guys, think of that the next time you try to decide what to wear when you’re going out clubbing.

It's a Matter of Perspective

2008-02-13T11:55:00.000-08:00

Science is all about seeing relationships between things or patterns of behavior. Sometimes living systems that are vastly different can have great similarities if you look at them in the right way. And really, that is all that is needed to see the similarities—a change of perspective.

For example, what are the similarities between a human and a mouse? Well, on the surface, you may say not a whole lot, but let’s look deeper.

1. They’re both mammals who give birth to live young (meaning they don’t lay eggs).
2. They’re both vertebrates.
3. They both contain about 30,000 genes in their DNA.
4. On a precise basis, their DNA sequences (the letter sequences ACGT of DNA) are 85% identical.

So, all that’s needed to see the similarity is perspective.

The genetic and biochemical similarity between humans and mice is one reason that physiological studies done on mice hold some relevance for humans. It’s not a perfect fit, but if something works or holds true in mice, then there is precedent for thinking it might work in humans as well. Hence all the studies done in mice (well, there are other reasons too).

Sometimes I look at a set of data in several different ways to see if there is a pattern. It’s helpful just to look at the SHAPES of curves or trend lines. They can tell you a lot. And seeing numbers in a visual fashion, such as plotting them on a graph, is a great way to discern trends and differences. Therefore, I look at data in many different ways—visually, as numbers in a table, in graph form (bar graphs, line graphs, pie charts)—all to look for the trend that may not be obvious.

Of course, sometimes there is no trend or similarities and you’re actually comparing apples and oranges. Or rodents and hominids.

Life at the Bottom of the Earth

2008-01-29T17:15:00.000-08:00

I just found this article about scientific research on Lake Ellsworth in Antarctica. Really cool stuff (no pun intended). Contrary to popular opinion, the region is not dead or devoid of life. There is a lot of life beyond what you can see. And while the microbial life happens very slowly there, it still happens. The microbes just have to deal with some extreme stress issues (and bacteria, in general, are very good at doing that). Extreme cold, UV exposure, drying.

Many years ago I met a microbiologist by the name of Robie Vestal who spent some time there doing some microbiology research.

I’ve always loved the idea of the ecosystem he described living a few millimeters WITHIN rocks. Yup—actually inside sandstone. I couldn’t find a picture of the actual Antarctic rocks, but go to this site, scroll down to the third picture, and look at a similar rock found in Yellowstone National Park to get an idea of what such a layer would look like. When they cut into the rocks, there was this thin layer 1 – 10 millimeters inside it. When they looked at it in detail, they found a group of microorganisms inside there. It was a lichen—similar to those that you find on tree bark, or on rock surfaces, but this one lives inside Antarctic rocks.

Lichens are interesting because they are an example of mutualism in action. A lichen is 2 different organisms (sometimes more) living together in a mutually beneficial fashion. One component is a fungus, and the other is an alga or a bacterium. The alga or the bacterium within the lichen is photosynthetic, which means it gathers its energy from sunlight (just like green plants), and provides the primary energy in the system. The fungus lives off of the chemicals (metabolic products) made by the bacterium or alga. The fungus can soak up water better, providing that for the photosynthetic part of the lichen. The bacteria or algae cells live intertwined within the hyphae (hair like structures) made by the fungi.

The lichen takes up residence inside the Antarctic rocks probably because it’s just a little warmer and less dry than living on the surface of the rock. It grows VERY slowly, but it’s there and metabolically active.

NASA is very interested in biological research in Antarctica because it’s one of the few places on Earth that may hold relevance for finding life off of Earth. This is a field of research known as Exobiology. The idea is that if we can understand how microbes withstand extreme environments on our own world, then we may understand what sites to look at on other planets for life or the remnants of extinct life. And the water in the underground Lake Ellsworth is certainly an example of extreme stress. Futhermore, by studying life in extreme situations, we may get a better understanding of how life survived on the early Earth, when the conditions weren't as favorable as they are today.

Genes, DNA, Chromosomes, Genome: The Heredity Bunch!

2008-01-28T18:43:00.001-08:00

So, what’s a gene? Inside each of our cells (except red blood cells, which is another story), we have deoxyribonucleic acid (DNA) molecules. Genes are pieces of DNA that serve as the units of heredity. In cells the DNA is organized into chromosomes, and the entire chromosome complement of a cell is called its genome. Genes contain the code for proteins.

In fact, every living cell, be it a human cell, animal cell, plant cell, yeast cell, fungus cell, protozoan cell, or a bacterial cell has DNA in it. It’s the blueprint of life. It’s what guides every aspect of life development. Our DNA is the guidebook that told our cells to develop as human. My dog’s DNA has many similarities to mine, but enough differences so that she’s not human, she’s a dog (although sometimes it’s uncanny how “human” she can act—also, another story).

DNA guides the chemistry of life. Each gene codes for something—mostly proteins. Another molecule, RNA (ribonucleic acid) is the immediate result of the biochemical reading of DNA. RNA is the carrier of the message to the workhorse of the cell, the ribosome. The ribosome reads the RNA, and a protein is made from the messenger RNA (mRNA).

It’s those proteins that do the work that keeps everything going. They keep the cells burning energy, determine your eye color, determine your development and growth, determine if your earlobes are attached or not, and build the machinery that is your body. All things mundane and fabulous.

DNA is an organic molecule (there’s that word again), meaning that the molecule is constructed on a backbone of Carbon molecules. The molecule is a very long chain that consists of 2 strands organized into a double helix structure. The two strands are bound together along their length. The long DNA chains are made up of nucleotides along a backbone made up of sugars (dexoyribose) and phosphate molecules. Attached to these sugar molecules are organic bases. There are 4 bases in DNA: Adenine (A), Guanine (G), Cytosine (T), and Thymine (T). See the pictures at the top for cartoons of DNA structure and the chemical structure of a C-T base pair.

RNA is a single helix made up of nucleotides along a backbone made up of the sugar ribose with phosphate molecules. Three of the bases in RNA are the same as those in DNA: Adenine (A), Guanine (G), and Cytosine (C); however, there is no thymine in RNA. It is replaced with another base named Uracil (U).

One analogy for DNA is that it’s an alphabet. However, this alphabet only has 4 letters: AGCT. All the variability in life on Earth is derived from different combinations of AGCT.

The two helices of the DNA molecule are connected to each other through bonds between the base molecules on each strand. However, A’s only pair up with T’s, and C’s only pair up with G’s. In that way, the 2 strands complement each other.

Length in DNA is measured in bases. A gene can be hundreds to thousands (kilobases) of bases long, so those 4 bases can combine into countless unique combinations. Hence the genetic variability of life on Earth. Each cell that contains a genome is like a hard drive on a computer. All the information necessary to run all of the functions is contained there. That’s a lot of information! So, there’s a lot of DNA in each cell. How much? If the contents of one human cell’s genome was arranged in a straight line, it would be over 6 feet long! And there are anywhere between 10 and 100 trillion cells in our bodies! (60 – 600 trillion feet of DNA/person! -- 113 billion miles or 182 billion kilometers!)

DNA is the molecule (and an elegant one at that). Genes are pieces of DNA that code for proteins (mostly). The genes and DNA are organized into chromosomes (humans have 23 pairs of chromosomes). All of the genetic information in the nucleus is the genome. So, when they say that they’ve sequenced the human genome, that means they’ve determined the DNA sequence (the combination of AGCT) for each chromosome. In a human male, that’s 3 billion DNA nucleotide pairs!

I'm a Cloner! Wouldn't you like to be a cloner too?

2008-01-11T18:23:00.000-08:00

It’s funny how words take on meanings in the cultural consciousness that are different from what they actually mean. I can think of several examples of words used in various fields of science that have taken on new or slightly different meanings when used in a broad context, such as in the public as a whole. One that comes to mind is the word clone (or cloning).

I am a cloner. I have cloned things. Many things. There. I’ve said it. And I’m proud of it.

No, I have not cloned a sheep, a cat, a cow, or even a horse. I have cloned genes.

The word “clone” can be a noun or a verb. As a verb, it is the act of making a copy of something. The noun “clone” means to be genetically identical to something else. So, the genes I have cloned are clones of the genes they were originally cloned from.

Seriously though, it just means duplicates or copies. Exact copies. There are other meanings that have made their way into common speech (PC computers used to be called IBM clones, for example).

Many scientists clone. Very few clone animals. Those that do clone, clone genes.

And cloning genes, doing molecular biology, while it can be frustrating is actually kind of fun. It’s like doing a logic puzzle. DNA, while a complex molecule, is quite elegant. You can make maps of DNA molecules. At the top of this entry is a map of a plasmid (a small, circular piece of DNA--this one is 2686 base pairs long). We use maps often. And on these maps are markers—road signs in a way. These are called restriction sites.

Restriction enzymes (the real term is restriction endonuclease) cut DNA molecules at very specific sequences in the DNA. So, you can use these restriction enzymes to cut the DNA in a predictable manner, and take a piece of DNA from one strand by cutting it with a particular restriction enzyme and insert it into another strand of DNA that has been cut with that same restriction enzyme. The ends will be compatible. In its most basic form, this is cloning.

In the plasmid map at the top, the restriction sites are the ones labeled all along the outside of the circle. They have names like SspI, NdeI, BsaXI, etc. Each of the enzymes listed have a different DNA recognition sequence (a specific sequence of the ACGT molecules that make up DNA).

And when you have a bunch of pieces of DNA you have to put together in a map—it really is a logic puzzle.

If you like crossword puzzles, you may have an aptitude for molecular biology.

Note: It was far too long and confusing to explain cloning, DNA structure, and genes all in one blog entry. In the next couple of days I'll post a basic explanation of genes, DNA, and chromosomes.

Musings on Science and Women and Science and Kids

2008-01-04T11:28:00.000-08:00

I heard a statistic while listening to NPR recently that girls start to ignore or doubt their aptitude in math before they’re 10 years old. I read the statistics, and I see the op-ed’s in newspapers about how girls are not going into math and science careers. And while I don’t doubt that it is at least partially true, I have to say that in my own experience, I know a lot of women who have chosen math and science careers.

Maybe that’s because I’m in the biological sciences, which does seem to attract more women than, for example, physical sciences or chemistry. But when I was in graduate school, I would say that the majority of my colleagues there were women. In fact, at one point, the lab I was training in had about 6 or 7 females and only 1 man.

After I got my Ph.D. and went on to do post-doctoral training (as is usual for bio-science doctorates), I would say that the ratio of men:women was about 1:1. The generation ahead of me, however, was not so equitable.

Most of my professors were men. Many of them were quite enlightened about having women in their lab. I would have to say that I’ve been really lucky. I can only really think of one case where I felt that I was treated unfairly in a situation, and that it possibly may have been because I was a woman. While a big deal for me at the time, I did make it through the task just fine, and I haven’t really noticed anything like that since. I have been lucky to have wonderful mentors, and to live in a generation that promoted women’s ambitions.

I have heard horror stories from the women who paved the way in the generation before. The stories they told were of male professors who would pass them over in favor of male students for spots in labs because they figured the women weren’t actually serious about their careers. If you’re in graduate school, you’re serious about your field. There were male professors who failed to help women graduate students when it came time to graduate and move on to post-doctoral work, simply because they couldn’t imagine why a woman would want to do it. Well, it’s what you do after you get the degree—move on to the next step in your training. Then there was the real need for these women to not only do well when they finally got faculty positions (which was incredibly difficult for them in the 1960’s), but to excel so much more than their male colleagues just to show that they should be taken seriously.

I am grateful for the women who blazed the trail before me. I think their hard work was reflected in the number of wonderful women scientists I’ve encountered as colleagues along my way.

So, when I hear about girls losing interest in math and science at young ages, it distresses me. I recognize that everyone has different interests, and the technical fields are not for everyone. I’m thinking of people now who do have the aptitude, but lose interest because of some sort of outside pressure. Where and when does the shift in a girl’s mind happen when she thinks she can’t handle math and science anymore?

Here’s a Washington Post article that suggests it’s social pressure, and that it can be overcome. I actually know some wonderful elementary and middle school math and science teachers who are doing great jobs with their kids. I’ve visited a couple of their classrooms and have been impressed with their dedication and enthusiasm. I judge regularly in local science fairs, and see some great questions and great method being used by kids as young as 7th grade.

Here’s the interesting thing though—while the most detailed studies in these science fairs are done by kids in 11th and 12th grades, the more fun projects, and the greatest number of projects, are being done by kids in 7th and 8th grades. It’s a blast to read and judge the 7th and 8th grade projects! I actually learn a lot from them (and get ashamed by the amount of stuff I’ve forgotten over the years).

So, I ask, does science stop being fun after that? Puberty hits with a vengeance, kids start thinking about other things, social pressure.

I may be a bit rambling in this post, but I’m kind of thinking out loud. Any ideas?

Why do I have to sit in Chem Lab? When will I ever use Chemistry???

2007-12-29T13:55:00.000-08:00

Well, how about in the kitchen? It’s holiday time, and I’ve done a fair share of baking and cooking this year, as usual. The melding of ingredients, and the smells and textures of batters are making me think of organic chemistry lab. Yes, I’m weird. Isn’t it obvious by now?

Really, I tell anyone who does science for a living that if you can do science, you can cook. And I suspect that the reverse is also true. I’ll wager that if someone is very good in the kitchen, then they’d also be quite good at the lab bench. You just can’t eat your results there.

The precise mixtures of ingredients and heat (and in some cases cold—if you chill cookie dough before baking, for example) meld the ingredients and set in place chemical reactions that result in all sorts of tasty concoctions.

Biochemically speaking, there are three classes of molecules that we use for calories and nutrition: proteins, carbohydrates, and fats. All are organic molecules, meaning that all form their chemical structures based on a backbone made of the element Carbon. We need all three to make up the cellular structure in our bodies.

Now there are more things necessary in cooking than proteins, carbohydrates, and fats, depending on what you’re making. Breads need yeast to biologically convert some of the carbohydrate in the flour into carbon dioxide gas and alcohol to provide lift, structure, and flavor. Not using yeast, soda breads use baking powder and/or baking soda, which create carbon dioxide chemically with the addition of water and heat. (A short experiment—take a small amount of baking powder and mix on a spoon with water, and watch the bubbles form—this is carbon dioxide gas, which provides the lift needed in cakes, cookies, and soda breads).

I made a lot of sweet soda breads for the holiday this year. One was coconut macadamia nut bread. Very tasty. However, the recipe that I have, as it stands, is coconut macadamia nut BANANA bread. Problem: my husband doesn’t like banana, but he’s a huge fan of coconut and macadamia nuts. So, the easy solution is to just leave out the banana, which I did. But think of that for a minute. What does that do to the texture of the dough and the result of the recipe?

The recipe calls for 3 bananas. We don’t like the flavor of banana, but we still want the sweetness and fat that the bananas add to the batter. So, on a very basic level, if I leave out the banana, I should increase the amount of butter and sugar. Which I did. I’ve made this recipe by just leaving out the banana and not compensating at all, and I was left with a non-descript, crumbly mass that vaguely tasted of coconut. I increased the butter and sugar and got a sweet, moist bread full of coconut and macadamia nuts and none of the offending banana.

For more on food and the science behind food, check out my favorite cooking show on the Food Network. It’s called Good Eats, hosted by Alton Brown. It’s funny, and has great recipes. Alton Brown has great visual aids to show you how certain ingredients work, scientifically. Why ingredients have to be added in certain orders, why things must cook for certain lengths of time, etc. He has a great show where he takes the same chocolate chip cookie recipe and with slight variations shows you how to make 3 different types of cookies: flat and crunchy, tall and cakey, and very chewy. All by slight variations of ingredients (butter or shortening), baking powder (less of it means less rising), and temperature of dough (colder dough yields taller cookies because they ultimately have less time at the target temperature, so don’t flatten as much).

Fascinating and tasty chemistry! You do use it in real life!

CORRECTION: I've been caught in a factual error. Bananas contain almost no fat. The USDA gives a fat content for bananas of 0.4 g for a medium (118 g) banana. I just suppose the bread tastes better with all the extra butter.

Open Access Science

2007-12-26T15:27:00.000-08:00

An entry on scientific publishing may not be very fascinating, but I'm going to tell you how to get free access to cutting edge science, free access to slightly old science, and free access to science history.

In the U.S., much, if not most, of the science is funded through grants from public agencies. These include the National Institutes of Health, the National Science Foundation, and others. This means that taxpayer dollars go toward funding most of the research done in academic institutions.

Almost all of that science does get published in peer-reviewed scientific journals, and those journals are accessible to the public. However, they’re not free, and they’re definitely not cheap. It costs more to get a subscription to e.g., The Journal of Biological Chemistry (Printed journal is $2,625 per year and Online journal is $2,460 per year) than it does to something like People (a little over $50 a year). You can get individual papers, but you pay between $15-$30 a paper, depending on the journal.

It’s the law of supply and demand. More people are interested in the latest shenanigans of Britney Spears than say, the Mechanism of Transcriptional Activation by the Proto-oncogene Twist1. (yes, it’s a shame—the proto-oncogene is not as sexy, but it’s much more substantial; however, I doubt it can sing). (FYI, an oncogene is a normal gene, or piece of our DNA, that are usually inactive. When they become activated through some environmental cue or a mutation, they can lead to the formation of a cancer. A proto-oncogene is a normal gene that has the capacity to become an oncogene through mutations or something that leads to a very increased expression of that gene)

Most of us scientists don’t even have subscriptions to these journals. We get access because the institutions where we work buy the subscriptions.

About 10 years ago, I first heard of a movement to get access for regular taxpayers to the science they indirectly paid to have done. It makes sense. If the research is taxpayer funded, then don’t the taxpayers have a right to peruse it? At the time it was being debated, there was even short talk about having researchers save every scrap of paper on which they wrote results.

We joked in the lab about it because some people had results scribbled onto paper towels before they wrote them up more formally in their lab notebook. Would we have to save every scrap, and not only save it, but explain it in a format that anyone could understand? We would spend most of our time decipering the lab codes instead of actually doing the science.

Well, thankfully, we didn’t have to save used paper towels. A new trend in scientific publishing happened, however. I think the first to start it was the Public Library of Science (PLoS). This organization is committed to open access publishing that is free to everyone. The cost of publishing the papers are paid for by the researchers who publish in the journals. The concept of a “page charge” is not new. Most journals have them.

PLoS is committed to open distribution of research. They were smart when they started the venture. They knew that the only way such a venture could succeed is if they had great science there. So, a perusal of the Editorial Board shows respected scientists from many of the world’s top institutions. These are people who have published in Science and Nature, two of the most prestigious scientific journals.

At present PLoS publishes seven journals: PLoS Biology, Medicine, Computational Biology, Genetics, Pathogens, ONE, and Neglected Tropical Diseases. The PLoS journals have editorials and features in addition to the hard science articles.

There are other open access journals out there. You can find a directory here at the Directory of open access journals. At this directory you can get access to research in biology, chemistry, physics, health, as well as law and political science.

Additionally, some other journals, while not entirely open access have several articles each issue that are labeled open access. Most notably in this category is the Proceedings of the National Academy of Science of the USA (PNAS), which publishes many different types of science.

Granted, these are hard research articles. They’re not geared toward the lay public. They are written for other scientists. This is the scientific literature. But it’s out there for anyone to read. Think of it as a portal. You may not understand the papers (I don’t understand all the papers), but if parts of it are of interest, you can do more research on your own on the web about the topic.

I just think that everyone should know about this free resource to the knowledge of cutting edge science.

And just a note. While most of the other journals charge for access to their articles, many offer older articles in their journals for free online. For some, in as little as 6 months after publication the articles are available for free download. What's really cool about this is that some of the very old journals are getting all of their issues available digitally. This means you can read old science articles from the 19th century and early 20th century. Some are great fun. Nature hopes to have its entire archive digitized by early 2008. This means that articles from 1869 can be downloaded (but I don't know if access will be free). PNAS has free access back to 1915. So does the Journal of Bacteriology

So, we can read the cutting edge science and the history of science.

The Death Star is Approaching the Planet. The Death Star is ....Ah, just blast through the planet!

2007-12-18T16:00:00.000-08:00

From a galaxy far far away….

So, the front page of my newspaper today tells of an article inside with new pictures of a galaxy releasing blasts of radiation energy that are attacking a nearby galaxy. Talk about a bad neighborhood…

But the pictures are fabulous, and the story amazingly cool!

Picture credit: A black hole jet at the center of a galaxy strikes the edge of another galaxy. Image Credit: X-ray: NASA/CXC/ CfA/D.Evans et al.; Optical/UV: NASA/ STScI; Radio: NSF/VLA/CfA/D.Evans et al., STFC/JBO/MERLIN

This study was released Monday by NASA. There are two galaxies in a system of space known as 3C321. The galaxies are 8.2 billion trillion miles from Earth. The system contains two galaxies quite close to each other (20,000 light years apart) that orbit around each other. Both have black holes in their centers. One of the black holes is releasing a jet of energy that is shooting into the other galaxy. One of the study’s authors, Daniel Evans of the Harvard-Smithsonian Center for Astrophysics, is calling it the “Death Star” galaxy. (If you haven’t seen Star Wars, run don’t walk, to the video store).

The jets of energy are composed of high amounts of X-rays and gamma rays, which can be lethal in high quantities. And in this case, we’re talking about super-high quantities emanating from a black hole. The ozone layer of a planet could be obliterated if it came into the path of one of these jets of energy. It could probably sterilize all life on the planet.

One of the goals of astrophysical research is to learn more about these jets in the study of black holes. They are apparently not uncommon. What is uncommon is to have visual evidence of a jet affecting directly another galaxy. (aside: Hmmm, I thought that nothing could escape a black hole, so what is the nature of this type of energy that it can be released from something that can trap light energy? Anyone know? I’ll have to read up on this)

The effect of this jet on the neighbor galaxy is probably huge. In the long term, however (and we’re talking several million years now), the result of this onslaught on the receiver galaxy could be the formation of new stars and planets.

It’s all a cycle, isn’t it? Destroy what’s there, and something else grows to take its place. It’s like an intergalactic version of the Las Vegas Strip.

(Additional information and images are available at:
http://www.nasa.gov/chandra/ and http://chandra.harvard.edu/)

The Launch

2007-12-18T11:33:00.000-08:00

So what is "The Science of Things?" Well, it depends on the science, and it depends on the thing.

I'm hoping to use this space to bring up some happenings in the science world that I find of unique interest (i.e., very cool). Also, I hope to bring out issues about science education and literacy for attention.

I think that adults have less attention for science in our fast-paced world. This leads to a society with less aptitude for science, less knowledge of science, and a basic ignorance of science. I think that the general population really does not have a grasp on “how science is done.”

Adults ignore the science pages in their newspaper (if their newspaper still has one), the science section on their internet news sites, and the science story on the evening news. Or science is given as a sound bite: This drug causes cancer, this food is bad for you, this food is good for you, too much coffee is bad, coffee is good, scientists found a treatment for baldness that works in mice.......

What does a mouse have anything to do with me? And why do I have to stop drinking coffee? I really like coffee.

Maybe our general discontent begins in our education system, and how science is taught in schools. Possibly most people think of it as a mass of facts they have to memorize. Granted, there is some of that, but at its most basic, science is the observation of our surrounding world. Observation should be encouraged. A simple hike in the woods can open the door to questions that could fill thousands of Ph.D. theses. All that is required is curiosity—simple questions that start with “Why…” or “How…”

Well, I’m curious. I’m also a scientist. And I don’t think that we communicate very well with non-scientists. We have trouble sharing our own work and interests as well as the scientific process to people who don’t think about it on a daily basis. This separation leads to mistrust, doubt, and allegations of lack of respect for non-scientists.

How do scientists “do science?” It’s a process—a way of thought, deductive reasoning, and observation.

So, this blog. I want to point out some happenings in science that are of interest to me. It is my blog after all. I also want to shed some light on the scientific process. How is science done? What is the process of deduction, and how to design a simple experiment? To use a common phrase, it’s not rocket science. It’s really basic logic. And last but not least in this evolving blog experiment, I want to explore issues of science literacy and science education. After all, the current generation must educate the next. The next generation should be at least as prepared as I was (and frankly, I’m pretty satisfied with my public school education as a whole).

And finally, science is FUN. There is a lot of coolness out there, and a science geek/nerd like me should be able to point some of it out to you. If I simply manage to describe something that makes you go, “Hmmm. Wow…” then my experiment is a success.

Finally, bear with me. I want the audience for this blog to be scientists and non-scientists. I will try to maintain a balance that will be of interest to both.