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.
Wednesday, April 29, 2009
Monday, March 30, 2009
Cuteness Alert
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.
Monday, March 16, 2009
Science Solves 20th Century Historical Mystery
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.
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.
Wednesday, March 11, 2009
Irrational Rationality--Let's Celebrate!
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!
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!
Tuesday, March 3, 2009
With Spring comes Baseball!
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
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!
Wednesday, November 19, 2008
Cutting Edge techniques to do Ancient Science
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
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
Monday, November 17, 2008
The Sounds of Space
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.
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.
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