Because of the idea that recreational drugs are 'bad', we've had almost no advancement in the 'science' of recreational drugs. A few new substances have slipped through the cracks. Much of the interesting work has been done by a lone chemist, Alexander Shulgin. But every new drug, if at all effective in being 'recreational', is made illegal. The result? Rather than banning all recreational drugs, we insist that people stick to the two well-known drugs that cause by far the most damage to society: alcohol and tobacco.
The same thing has happened with nuclear power. Since Three Mile Island, no new reactors have come online in the United States. Opponents of nuclear power have succeeded in stopping all improvements in safety, cost, and efficiency. The result? 40+ year old plants are continually relicensed even though there are much safer designs available. Fears of proliferation have stopped fuel reprocessing, creating the problem of where to store spent fuel. NIMBY activism has stopped the use of the Yucca Mountain storage facility, forcing on-site storage of spent fuel.
We should be building modern, passive-safe plants. We should be investigating inherently-safe alternatives like thorium-fueled molten salt reactors. The best way to get rid of these old power stations is to make them obsolete.
Of course the anti-nuclear activists don't want the old plants to continue to run. They want them shut down, forcing society to retreat to even older and more toxic drugs: coal and oil.
Tuesday, March 15, 2011
Wednesday, January 5, 2011
netflix, level3, comcast & 'network neutrality'
This Gizmodo story captures perfectly all of my issues with network neutrality. It starts out with the usual hysteria, claiming that there's some giant threat to the Internet from Evil Corporations. (Hey, remember the days of "OMG they are gonna tax our emails!").
After some time to ponder the issue, however, Gizmodo groks the situation:
Even if Netflix realizes that this is bad for their business, they are not allowed to voluntarily give Comcast money to help defray the cost.
In an unregulated environment, Netflix helps defray Comcast's costs, and the users that actually gobble up all that bandwidth help to pay for it.
So which situation is preferable:
1) network neutrality: netflix is not a viable business model, because the bandwidth to support it is not there.
2) network neutrality: netflix still works, but all of Comcast's customers are forced to subsidize those customers that use it.
3) unregulated: netflix works and grows, and comcast grows. Everybody wins.
Notice that I haven't yet mentioned the fact that bittorrent traffic probably consumes even more bandwidth. Once again, all of the ISP's customers are forced to subsidize the minority that are saturating the network with (mostly pirated) bittorrent content. This is actually an interesting problem, because although bittorrent itself is relatively easy to block, its successors will not be. Newer protocols will almost certainly involve some kind of cloaking/encryption, which will be deliberately indistinguishable from legitimate encrypted content.
Services like Netflix and iTunes represent legitimate high-bandwidth services, the kind that will eventually make pirating less attractive. So we are in the midst of a shift of traffic from bittorrent to netflix/hulu/itunes/etc, and I think most people will agree that is a Good Thing. But network neutrality regulations may well stifle this transformation. I don't know about you, but I don't like paying $100+/month to subsidize johnny-down-the-block's massive porn collection.
But oops, you have no choice. Because network neutrality means that Comcast isn't allowed to filter out bittorrent, even if it consumes 80% of their bandwidth. So $80/month goes to johnny-down-the-block, and $20 goes to your own connection. Yea! The Internet is Saved!
After some time to ponder the issue, however, Gizmodo groks the situation:
Indeed, recent reports suggest that Netflix is responsible for a fairly absurd amount of bandwidth, and as Wired points out, the contracts that dictate who is responsible for carrying what traffic are largely left undisclosed to the public. Comcast's statements (unsurprisingly) shift the debate from one of net neutrality to the esoteric and largely uninteresting business of service providers negotiations.But let me 'cast' this situation in a slightly different light. Let's imagine that 20% of Comcast's bandwith is being gobbled up by Netflix users. Now, the infrastructure that Comcast has to build out is expensive stuff. Under 'network neutrality' regulations, Comcast is no longer allowed to pass on any of this cost to Netflix. What happens? Does Netflix's business continue to grow? No. Does Comcast build out additional network to support services like Netflix? No. At least not as quickly as they might have. And if they do, who pays for it? Well, all of Comcast's customers pay for that buildout. Including the ones that don't use Netflix.
Even if Netflix realizes that this is bad for their business, they are not allowed to voluntarily give Comcast money to help defray the cost.
In an unregulated environment, Netflix helps defray Comcast's costs, and the users that actually gobble up all that bandwidth help to pay for it.
So which situation is preferable:
1) network neutrality: netflix is not a viable business model, because the bandwidth to support it is not there.
2) network neutrality: netflix still works, but all of Comcast's customers are forced to subsidize those customers that use it.
3) unregulated: netflix works and grows, and comcast grows. Everybody wins.
Notice that I haven't yet mentioned the fact that bittorrent traffic probably consumes even more bandwidth. Once again, all of the ISP's customers are forced to subsidize the minority that are saturating the network with (mostly pirated) bittorrent content. This is actually an interesting problem, because although bittorrent itself is relatively easy to block, its successors will not be. Newer protocols will almost certainly involve some kind of cloaking/encryption, which will be deliberately indistinguishable from legitimate encrypted content.
Services like Netflix and iTunes represent legitimate high-bandwidth services, the kind that will eventually make pirating less attractive. So we are in the midst of a shift of traffic from bittorrent to netflix/hulu/itunes/etc, and I think most people will agree that is a Good Thing. But network neutrality regulations may well stifle this transformation. I don't know about you, but I don't like paying $100+/month to subsidize johnny-down-the-block's massive porn collection.
But oops, you have no choice. Because network neutrality means that Comcast isn't allowed to filter out bittorrent, even if it consumes 80% of their bandwidth. So $80/month goes to johnny-down-the-block, and $20 goes to your own connection. Yea! The Internet is Saved!
Thursday, December 2, 2010
Truly Alien Aliens
With today's news from NASA about arsenic-substituted microbes from Yellowstone, I've decided to vent about an issue that has bothered me for many years. Nearly everyone that talks about alien life commits horrible acts of anthro-bias. The most annoying canard is the assumption that life will require water. Astronomers focus their hunt for planets in the 'goldilocks zone', not because it might harbor nice planets for humans to live on, but because it is somehow more likely to support any kind of life.
I don't see any strong reason to assume that alien life will resemble life on Earth. Perhaps Star Trek polluted everyone's mind with visions of bipedal blue-skinned aliens that just happen to be the same size as us?
There are two huge anthro-biases of scale: size and time. A single example can explain both: imagine a life form in a gas giant (like Jupiter), where each individual's diameter is measured in kilometers. For obvious reasons this lifeform will 'run' at a slower pace than something that is our size... it may take hundreds of seconds for a signal to move from one part of its body to the other. The organism, were it intelligent, might experience time at a far slower pace than we do. The time between stimulus and action, e.g., a decision to move away from a threat, might be measured in minutes. Such an organism might seem horribly impractical to you, but from the point of view of the organism - that's just the way time moves. It might view humans as outrageously frenetic; an exaggeration of the way we look at hummingbirds.
A contrasting example comes from Robert Forward's book "Dragon's Egg", where a nano-scale lifeform evolves in a matter of weeks on the surface of a neutron star. Most likely it was this book that originally opened my mind to the idea of truly 'alien' life.
Other biases are easy to spot now: assumptions about gravity, density, temperature, etc. I believe life will arise any place where a certain threshold of complexity is met. In Earth's case, the huge oceans, freely mixed, with an abundance of heavier elements are probably what made the difference. Carbon chemistry has definitely been a big win, but is it really impossible to imagine other kinds of 'organic' chemistry, like Silicon?
I don't see any strong reason to assume that alien life will resemble life on Earth. Perhaps Star Trek polluted everyone's mind with visions of bipedal blue-skinned aliens that just happen to be the same size as us?
There are two huge anthro-biases of scale: size and time. A single example can explain both: imagine a life form in a gas giant (like Jupiter), where each individual's diameter is measured in kilometers. For obvious reasons this lifeform will 'run' at a slower pace than something that is our size... it may take hundreds of seconds for a signal to move from one part of its body to the other. The organism, were it intelligent, might experience time at a far slower pace than we do. The time between stimulus and action, e.g., a decision to move away from a threat, might be measured in minutes. Such an organism might seem horribly impractical to you, but from the point of view of the organism - that's just the way time moves. It might view humans as outrageously frenetic; an exaggeration of the way we look at hummingbirds.
A contrasting example comes from Robert Forward's book "Dragon's Egg", where a nano-scale lifeform evolves in a matter of weeks on the surface of a neutron star. Most likely it was this book that originally opened my mind to the idea of truly 'alien' life.
Other biases are easy to spot now: assumptions about gravity, density, temperature, etc. I believe life will arise any place where a certain threshold of complexity is met. In Earth's case, the huge oceans, freely mixed, with an abundance of heavier elements are probably what made the difference. Carbon chemistry has definitely been a big win, but is it really impossible to imagine other kinds of 'organic' chemistry, like Silicon?
Thursday, November 4, 2010
How government broke the auto industry, an alternate history.
How broken is health care? Very.
Trying to explain how broken our current health care system is a difficult task, because it's nearly impossible to imagine an 'unbroken' system. It's a counterfactual. The system has been broken since the 1950's. The fact that it just keeps getting worse makes us long for the days of our youth, when it was only 'mostly dead'.
So I'm going to try an analogy tack.
What is it that is broken about health care? Well, the prices are out of control. The costs of health care spiral year after year, always outpacing inflation. This is an unsustainable situation. But how did this happen?
Imagine if the government stepped in and mandated that employers pay for your auto insurance. Actually, that's not quite right, the original sin is more subtle. The government provides a *tax break* to employers who pay for your auto insurance. Now let's follow this exercise through, and see some of the follow-on effects.
First, you quit really shopping for your auto insurance. It comes as a perk with the job. The best jobs will offer you outrageous auto insurance plans, where you can basically plow through a flock of BMW's in a parking lot with your Bentley and walk away unscathed.
You're not the only person taking advantage of this perk. Lots of people are. The end result is a rise in the accident rate. Also, the subtle market pressure that would have made people want to buy cars that 'break' less is gone. So cars become flamboyant and fragile.
Now, let's imagine what happens to the auto repair business. Well, you take your car down to the shop to get it tuned up. They replace some fluids and belts, and check the air in your tires. Then they tear down the engine to replace all the gaskets and o-rings. What? Well, it's the only way to be sure, sir. Can't risk having the engine blow out, that would be dangerous!
When they're done with your car they don't give you a bill. Instead, you just file a claim with your insurance, and they take care of it. You don't notice that it cost over $2000 to get your car 'tuned up'. But even if you did notice, you wouldn't really care. Because you're not paying for it.
And cars are no longer built to last. The design of cars actually changes over the years, to one that favors cheaper manufacture, but requires regular maintenance. Some cheap cars are essentially rebuilt every 12 months.
After decades of this broken system, the cost of auto insurance begins to dominate the cost of an employee. Companies are in trouble, and they want to back down on these insurance plans. Some companies try to get by without providing auto insurance to their employees, but they are demonized by the public. Some try to offer scaled-back plans, but this is no better... the cost of auto insurance has risen to ridiculous levels, and few could afford it without employer subsidy. The government has a plan where the elderly and the poor get assistance with their auto insurance, but many people are still unable to drive. Or they decide to drive without insurance. That's right: we get the elderly and the poor driving these fragile, unreliable vehicles out on the roads with no insurance.
Now, how will you fix this broken system?
Trying to explain how broken our current health care system is a difficult task, because it's nearly impossible to imagine an 'unbroken' system. It's a counterfactual. The system has been broken since the 1950's. The fact that it just keeps getting worse makes us long for the days of our youth, when it was only 'mostly dead'.
So I'm going to try an analogy tack.
What is it that is broken about health care? Well, the prices are out of control. The costs of health care spiral year after year, always outpacing inflation. This is an unsustainable situation. But how did this happen?
Imagine if the government stepped in and mandated that employers pay for your auto insurance. Actually, that's not quite right, the original sin is more subtle. The government provides a *tax break* to employers who pay for your auto insurance. Now let's follow this exercise through, and see some of the follow-on effects.
First, you quit really shopping for your auto insurance. It comes as a perk with the job. The best jobs will offer you outrageous auto insurance plans, where you can basically plow through a flock of BMW's in a parking lot with your Bentley and walk away unscathed.
You're not the only person taking advantage of this perk. Lots of people are. The end result is a rise in the accident rate. Also, the subtle market pressure that would have made people want to buy cars that 'break' less is gone. So cars become flamboyant and fragile.
Now, let's imagine what happens to the auto repair business. Well, you take your car down to the shop to get it tuned up. They replace some fluids and belts, and check the air in your tires. Then they tear down the engine to replace all the gaskets and o-rings. What? Well, it's the only way to be sure, sir. Can't risk having the engine blow out, that would be dangerous!
When they're done with your car they don't give you a bill. Instead, you just file a claim with your insurance, and they take care of it. You don't notice that it cost over $2000 to get your car 'tuned up'. But even if you did notice, you wouldn't really care. Because you're not paying for it.
And cars are no longer built to last. The design of cars actually changes over the years, to one that favors cheaper manufacture, but requires regular maintenance. Some cheap cars are essentially rebuilt every 12 months.
After decades of this broken system, the cost of auto insurance begins to dominate the cost of an employee. Companies are in trouble, and they want to back down on these insurance plans. Some companies try to get by without providing auto insurance to their employees, but they are demonized by the public. Some try to offer scaled-back plans, but this is no better... the cost of auto insurance has risen to ridiculous levels, and few could afford it without employer subsidy. The government has a plan where the elderly and the poor get assistance with their auto insurance, but many people are still unable to drive. Or they decide to drive without insurance. That's right: we get the elderly and the poor driving these fragile, unreliable vehicles out on the roads with no insurance.
Now, how will you fix this broken system?
Saturday, October 30, 2010
can exaggerate how much the U.S. sucks
This is a response to a self-hating paragraph in a Thomas Friedman column. I typed this in a hurry, and it's woefully incomplete.
The original article is here: Can't Keep a Bad Idea Down
Although it mostly talks about how the Tea Party sucks and the Republicans are dragging us into hell, this paragraph pissed me off:
"Here is a little dose of reality about where we actually rank today," says Vest: sixth in global innovation-based competitiveness, but 40th in rate of change over the last decade;"
This is not bad, considering we are competing with relatively small countries like Norway and Hong Kong. And of course when you're already near the top your rate of change is likely to be small compared to places like China, who have nowhere to go but up.
11th among industrialized nations in the fraction of 25- to 34-year-olds who have graduated from high school
Again, probably not as shocking as it sounds. We're a big, diverse country, and it's harder for us to compete with a country like Germany that has a low birth rate.
16th in college completion rate
This tells me nothing. Perhaps we throw more people into college than we should? Maybe we have state-subsidized college education that encourages the children of the wealthy to party for a couple of years before giving up?
22nd in broadband Internet access
Fiber-to-the-burbs! So grandma and grandpa Kim in South Korea have gigabit fiber to their apartment? Why?
24th in life expectancy at birth
Don't have a quick answer for this one. Get back with me.
27th among developed nations in the proportion of college students receiving degrees in science or engineering
And yet we have a higher education system that is the envy of the world. Why do students from all over the planet come here to study science and engineering?
48th in quality of K-12 math and science education
Again, difficult to believe. How is this measured?
29th in the number of mobile phones per 100 people.
That's because we still cling to land lines. This is totally disingenuous. There are many poor areas of the planet that have leap-frogged over landline technology directly to cell phones, this should be something to celebrate, not used as some kind of criticism of the U.S.
The original article is here: Can't Keep a Bad Idea Down
Although it mostly talks about how the Tea Party sucks and the Republicans are dragging us into hell, this paragraph pissed me off:
"Here is a little dose of reality about where we actually rank today," says Vest: sixth in global innovation-based competitiveness, but 40th in rate of change over the last decade;"
This is not bad, considering we are competing with relatively small countries like Norway and Hong Kong. And of course when you're already near the top your rate of change is likely to be small compared to places like China, who have nowhere to go but up.
11th among industrialized nations in the fraction of 25- to 34-year-olds who have graduated from high school
Again, probably not as shocking as it sounds. We're a big, diverse country, and it's harder for us to compete with a country like Germany that has a low birth rate.
16th in college completion rate
This tells me nothing. Perhaps we throw more people into college than we should? Maybe we have state-subsidized college education that encourages the children of the wealthy to party for a couple of years before giving up?
22nd in broadband Internet access
Fiber-to-the-burbs! So grandma and grandpa Kim in South Korea have gigabit fiber to their apartment? Why?
24th in life expectancy at birth
Don't have a quick answer for this one. Get back with me.
27th among developed nations in the proportion of college students receiving degrees in science or engineering
And yet we have a higher education system that is the envy of the world. Why do students from all over the planet come here to study science and engineering?
48th in quality of K-12 math and science education
Again, difficult to believe. How is this measured?
29th in the number of mobile phones per 100 people.
That's because we still cling to land lines. This is totally disingenuous. There are many poor areas of the planet that have leap-frogged over landline technology directly to cell phones, this should be something to celebrate, not used as some kind of criticism of the U.S.
Saturday, June 5, 2010
Hammers and Operating Systems
When the only tool you have is a hammer, everything looks like a nail.
I've had the good fortune to play around with Windows Vista a little over the past couple of weeks. I've been considering the upgrade to Windows 7, so I've read up a little on the newer features in Windows.
As a security-conscious developer, all the new security features in Windows sound very impressive. You've got your DEP (data execution prevention), your ASLR (address space layout randomization), your stack canaries, stack-smashing protection, sandboxing, virtualization, etc...
When I first saw all these 'technologies' described in one place, an image leaped into my mind.
Picture a guy holding a hammer. He's wearing special metal gloves to stop from smashing his fingers. He's got a sophisticated helmet and face shield to keep from bouncing the hammer back into his own head. He's got a safety harness on, and there's a 10-ft exclusion zone around him to make sure nobody else gets hurt. It takes him about 5 minutes to hammer a nail in.
Of course, the guy is a developer, and the hammer is C. (a more apt metaphor might be a hand-made black powder rifle, but stay with me here...). Instead of fixing the inferior tool that's used to build things, they try to mitigate the damage it causes. Every one of these 'technologies' is needed because the C language is inherently unsafe. Even a highly skilled programmer with decades of experience can still make the kind of mistakes that lead to your system getting pwned by the Russian Mafia, and it's all because of this antiquated, unstable-land-mine of a language.
There's no good excuse for writing critical infrastructure like operating systems (or applications) in a language like C. There are plenty of bad excuses. For example, "it's difficult to hire people to write code in better languages, there aren't enough of them". That's like complaining that everybody's trained to use a hammer, and it's too hard to train people to use a nail gun.
It's not like the technology isn't here. Microsoft themselves have been working on an entire suite of tools to replace C (C#,F#,.NET, Singularity, etc...), but they haven't been able to pull the trigger yet. Why is that? It's true that the development timeline for a huge project like a new operating system could easily span 10-15 years. But let's not make perfect the enemy of good. They could start by rewriting IE in C#. They have the talent, they have the tools, the ability. That one simple step would make Windows far more secure.
You'll notice that I haven't mentioned either Apple or Linux yet. That's because they're nowhere near as far along as Microsoft is on this front. Yup, I said that.
The Great Divide
One big reason for the foot-dragging (or should I say knuckle-dragging) are systems programmers. These guys are true Luddites, and they cling, snarling, to their 40-year old tools. They want nothing to do with the highly mathematical, cryptic, and slow-as-molasses-in-January high-level languages like ML. The thought of garbage collection gives them that sinking feeling of lost control you get just after the plane takes off and throttles back a little. These two camps - the systems programmers and the high-level language guys - don't interact at all. And the high-level language guys are just as much to blame. They're often ignorant of the needs of systems programmers, and even when they are aware of them they dismiss them. Their languages are too hard to use, too hard to read, and too hard to write, and one reason is that they still live mostly in academia, where the motivations are all twisted the wrong way.
I've spent some time in both camps, and would dearly love to bridge them, if for no other reason than this: until it happens there will be no secure operating system, and no secure applications. Also, it's a little lonely being one of the few guys that knows how to use the nail gun.
I know of only one project that's trying to bridge the gap, and that's BitC. If you're interested in both sides of the bridge, you should read The Origins of the BitC Programming Language.
I've had the good fortune to play around with Windows Vista a little over the past couple of weeks. I've been considering the upgrade to Windows 7, so I've read up a little on the newer features in Windows.
As a security-conscious developer, all the new security features in Windows sound very impressive. You've got your DEP (data execution prevention), your ASLR (address space layout randomization), your stack canaries, stack-smashing protection, sandboxing, virtualization, etc...
When I first saw all these 'technologies' described in one place, an image leaped into my mind.
Picture a guy holding a hammer. He's wearing special metal gloves to stop from smashing his fingers. He's got a sophisticated helmet and face shield to keep from bouncing the hammer back into his own head. He's got a safety harness on, and there's a 10-ft exclusion zone around him to make sure nobody else gets hurt. It takes him about 5 minutes to hammer a nail in.
Of course, the guy is a developer, and the hammer is C. (a more apt metaphor might be a hand-made black powder rifle, but stay with me here...). Instead of fixing the inferior tool that's used to build things, they try to mitigate the damage it causes. Every one of these 'technologies' is needed because the C language is inherently unsafe. Even a highly skilled programmer with decades of experience can still make the kind of mistakes that lead to your system getting pwned by the Russian Mafia, and it's all because of this antiquated, unstable-land-mine of a language.
There's no good excuse for writing critical infrastructure like operating systems (or applications) in a language like C. There are plenty of bad excuses. For example, "it's difficult to hire people to write code in better languages, there aren't enough of them". That's like complaining that everybody's trained to use a hammer, and it's too hard to train people to use a nail gun.
It's not like the technology isn't here. Microsoft themselves have been working on an entire suite of tools to replace C (C#,F#,.NET, Singularity, etc...), but they haven't been able to pull the trigger yet. Why is that? It's true that the development timeline for a huge project like a new operating system could easily span 10-15 years. But let's not make perfect the enemy of good. They could start by rewriting IE in C#. They have the talent, they have the tools, the ability. That one simple step would make Windows far more secure.
You'll notice that I haven't mentioned either Apple or Linux yet. That's because they're nowhere near as far along as Microsoft is on this front. Yup, I said that.
The Great Divide
One big reason for the foot-dragging (or should I say knuckle-dragging) are systems programmers. These guys are true Luddites, and they cling, snarling, to their 40-year old tools. They want nothing to do with the highly mathematical, cryptic, and slow-as-molasses-in-January high-level languages like ML. The thought of garbage collection gives them that sinking feeling of lost control you get just after the plane takes off and throttles back a little. These two camps - the systems programmers and the high-level language guys - don't interact at all. And the high-level language guys are just as much to blame. They're often ignorant of the needs of systems programmers, and even when they are aware of them they dismiss them. Their languages are too hard to use, too hard to read, and too hard to write, and one reason is that they still live mostly in academia, where the motivations are all twisted the wrong way.
I've spent some time in both camps, and would dearly love to bridge them, if for no other reason than this: until it happens there will be no secure operating system, and no secure applications. Also, it's a little lonely being one of the few guys that knows how to use the nail gun.
I know of only one project that's trying to bridge the gap, and that's BitC. If you're interested in both sides of the bridge, you should read The Origins of the BitC Programming Language.
Thursday, May 27, 2010
The Ultimate Database
I've been digging around in my genome, using the data collected by 23andme. They collected about a half million SNPs, or "single-nucleotide polymorphisms". Each SNP is a single-letter change in DNA that researchers have teased out by comparing genomes between humans, and even between humans and other animals. You could say that our SNPs are what make us each unique individuals.
For example, the SNP rs12913832 has been found to have a very high likelihood for predicting blue eyes. I have "GG" in that location, which is spot on. But wouldn't it be cool to look at that bit of DNA?
That's where the UCSC Genome Browser comes in. This has got to be the coolest database browsing tool I've ever used. Yeah, it's a little clunky, but when you think about what you're looking at, you are gobsmacked.
Here is the zoomed-in view of the SNP for blue eyes.
In the center of the image lined up with the SNP you will see a series of A's. This shows that in all of those animals, that portion of the HERC2 gene has an A there. In other words, it's a "highly conserved" allele. The graph in the center portion shows how conserved that area of the gene is within the animal kingdom. The HERC2 gene encodes an enzyme that controls the OCA2 (oculocutaneous albinism) gene. Stuffing a G into that location causes blue eyes. (yes, I'm simplifying a bit).
Ok, now to explain a bit more of what's going on in the browser. Above the main image is a smaller image. That's a picture of the actual chromosome, in this case Chromosome 15.
You can navigate through the chromosome by hitting the left and right arrow buttons, and zoom in and out. The image changes radically depending on the level of zoom, showing different levels of detail. The number of SNPs gets very dense as you zoom out.
Here's another interesting gene, TTN. This encodes a muscle protein Titin, and is the largest gene, encoding the largest protein known to man, with the chemical formula C132,983H211,861N36,149O40,883S693. It's just one springy piece of the complex mechanism that muscles are made of.
Looking at the section in the middle you can see that the TTN gene is highly conserved, forming that dark band down the middle of the image. Even the stickleback has a very similar TTN gene.
The dense graph on the bottom are the SNPs in this region of the chromosome. Each of those SNPs is a potential area for research. It's staggering how much is known already, but even more amazing is the sheer size of this project, the database, and animal genomes.
If you scoot over a couple of pages to the left from TTN, you'll find the Homeobox D (or HOXD) genes. These affect things like limb development. If you type 'HOXD13' in the gene box and hit 'jump', you'll zoom in on that single gene. Somewhere in that gene I have a mutation that gives me strange thumbs, just like Megan Fox.
For example, the SNP rs12913832 has been found to have a very high likelihood for predicting blue eyes. I have "GG" in that location, which is spot on. But wouldn't it be cool to look at that bit of DNA?
That's where the UCSC Genome Browser comes in. This has got to be the coolest database browsing tool I've ever used. Yeah, it's a little clunky, but when you think about what you're looking at, you are gobsmacked.
Here is the zoomed-in view of the SNP for blue eyes.
In the center of the image lined up with the SNP you will see a series of A's. This shows that in all of those animals, that portion of the HERC2 gene has an A there. In other words, it's a "highly conserved" allele. The graph in the center portion shows how conserved that area of the gene is within the animal kingdom. The HERC2 gene encodes an enzyme that controls the OCA2 (oculocutaneous albinism) gene. Stuffing a G into that location causes blue eyes. (yes, I'm simplifying a bit).
Ok, now to explain a bit more of what's going on in the browser. Above the main image is a smaller image. That's a picture of the actual chromosome, in this case Chromosome 15.
You can navigate through the chromosome by hitting the left and right arrow buttons, and zoom in and out. The image changes radically depending on the level of zoom, showing different levels of detail. The number of SNPs gets very dense as you zoom out.
Here's another interesting gene, TTN. This encodes a muscle protein Titin, and is the largest gene, encoding the largest protein known to man, with the chemical formula C132,983H211,861N36,149O40,883S693. It's just one springy piece of the complex mechanism that muscles are made of.
Looking at the section in the middle you can see that the TTN gene is highly conserved, forming that dark band down the middle of the image. Even the stickleback has a very similar TTN gene.
The dense graph on the bottom are the SNPs in this region of the chromosome. Each of those SNPs is a potential area for research. It's staggering how much is known already, but even more amazing is the sheer size of this project, the database, and animal genomes.
If you scoot over a couple of pages to the left from TTN, you'll find the Homeobox D (or HOXD) genes. These affect things like limb development. If you type 'HOXD13' in the gene box and hit 'jump', you'll zoom in on that single gene. Somewhere in that gene I have a mutation that gives me strange thumbs, just like Megan Fox.
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