Christmas is still three weeks away but Black Friday, the second most important shopping day in the United States, has already passed. I decided to buy myself another Christmas present, after the DNA kit. This one is more conventional, the G1 from HTC, the first cellphone using Android, the Google operating system based on Linux. For those of you that have seen an iPhone (there are about 15 millions around the world, chances are that you have), the G1 is the first serious competitor. Since the moment I have heard about Android I have been waiting to see one. Since the G1 came out on the market I had seen a lot of videos of how cool the phone is and I really felt like I wanted one. Problem was that it was only sold locked to the T-mobile network that works only in big cities, and Dartmouth is way far from big cities. But recently some people have figured it out how to unlock it and after spending half afternoon reading on forums about people successfully unlocking it and playing around with it I decided to take my chance too.
I got a used one on eBay yesterday and I bought right away an unlocking code and this morning I got a friend SIM to perform the activation, since without it the phone is little more than a brick. Once all these technicalities have been solved I started playing. I do not even have a SIM card but the amount of Internet applications you can play with is so diversified that it is worth it the money just as a PDA. I think of it, for now, as an iPod touch with microphone and gps and a keyboard. Now, let me explain you why Android is so much better than the iPhone. It is not just because it runs Linux, although the open source philosophy has a lot to do with it.
First of all, the phone has a better processor, more memory and a keyboard which, if it might not look aesthetically beautiful when open, it does make it way more functional when browsing. This in turn gives more flexibility to the applications that you can run.
One of the features I like the best is the ability to synchronize with the Internet your contacts, your calendar and your email. This basically puts an end to having to organize your private information more than once ever again. Just one problem less to think about in your life. As the developers put it, if you lose your phone you just buy another one, login into your account, and you are ready to go with no further configuration.
The applications you can install are absolutely innovative. The most surprising is the barcode scanner. You can scan anything with a barcode and in a few seconds you are redirected to a website with a list of online shops with prices for that product. Basically the best deal is now always two clicks away. Merchants will have to deal with this at some point because customers are about to get a lot smarter. Another very cool application is the one that recognizes the name of a song after listening to it for a few seconds. It is not fail proof but it works fairly well. This one exists also on the iPhone actually, as it should be. Applications should not be tied to a given operating system. Another great application to show off the features of the G1 is the one to look at the stars in the sky. Using the accelerometer and the compass built in the phone, it is enough to point it to the sky and the correct region of the sky is displayed on the screen. So easy that I almost cry at all the time spent trying to recognize the stars in the sky equipped with different maps and books. Now it is just about to become much easier.
Overall the idea of the phone is simple. Making the information on the Internet as easily accessible as possible. To this extent, probably the best application is the browser. There is not much to say about it. It works great, as much as the one on the iPhone, since both browser are based on Webkit. If you ever used a browser on a different phone do not get it wrong. The experience on the G1 and the iPhone is completely different and it will not make you regret too much not being in front of the computer.
Someone once said that since the beginning of the 80s little has changed in the PC world, other than the little chord that connects it to the Internet. I can see the point but this new generation of cellphones is adding something new to the PC experience. Maybe 20 years from now we will all have connections deep in our brain that will allow us to connect to the Internet straight with our thought and cellphones will seem something from the past. But, nevertheless, the G1 is about to make history and I am not missing the excitement.
I cannot way to get back home for Christmas to show it off.
Tuesday, December 2, 2008
Thursday, November 6, 2008
My DNA
The day after Halloween, after more than five weeks waiting, the company 23andme finally returned me the results of my DNA test. I was so excited I could barely wait to see. The first impression I had was that there were so many things to look at I did not know where to start. I will start with what was the most fun.
By virtue of being a male, 23andme genotyped both my mitochondrial DNA and my Y chromosome. These two are very special pieces of DNA since they cannot go under recombination. This means that they are passed generation after generation without mixing or changing, other than for mutations. But mutations are rare so they change little even in a 1000 year span. You get the first one from your mom and the second from your dad, if you are a male.
It turned out that my mitochondrial DNA belongs to haplotype H13a1, a rare group that is mainly common around the Caspian sea. According to the history, it was brought to Southern Italy and Southern Spain during the last ice age, something like 20000 years ago. My Y chromosome belongs instead to haplogroup J2, a kind that seems to be very common in Southern Europe, Northern Africa and the Middle East. Again, according to the history, it seems to have migrated multiple times from the Fertile Crescent to Europe and in particular to Italy where it is overall pretty common.
If you are curios about your ancestry you might find this very interesting. Although it only relates to your maternal line and your paternal line. So, for example, it does not witness the fact that I am 25% Greek. Something else surely does though. If you are interested in your ancestry then this might be a first step but you might want to look at ancestry.com. It seems that this company now teamed up with 23andme. Their service works as follows: you try to give them as much information as you can about your pedigree and if you far back enough you end up connecting with the archives that they built that could go back up to the 1600. They only did this for America and Europe but they claim to have already collected more than a billion entries, together with the people that subscribe to their services. My understanding is that 23andme and ancestry.com will do for the world what the company deCODEme did for all the Icelanders. Something we probably all thought impossible 10 years ago will be something normal in an even shorter time.
It might be fun to look at this kind of information, although we do not need to know our ancestry to know how our DNA affects us. It would be enough to understand its language. The real information that determines us is in the rest of the chromosomes. There are almost 100 associations described, as I write, that can be accessed through the 23andme website. These are divided in four categories, associations that put you at a more elevated risk, associations that put you at a decreased risk, associations that put you at a typical risk, and finally associations with traits that are not considered diseases. For example I could confirm the fact that I am an heterozygous for eye color, that is, my eyes are not blue but I can have a child with blue eyes. I seem to be lactose intolerant. This does not mean that I cannot drink milk but only that my ability to digest it decreases faster as years go by. This comes as no surprise since the mutation that prevents that is common only in Northern Europeans.
I also am not a carrier for three severe recessive diseases like cystic fibrosis and others for which the genetic reason has been identified. Not that my life is going to change much because of this, at least not any soon, but it is cool to know. There are so many more things to say that I will stop with a last one. Going bald is something that is usually inherited from your mom, in the meaning that your father has little to do with it. The reason is that a variant of a gene on chromosome X, inherited only from the mom for males, prevents you from going bald (to be precise you have 11 times less chances, but this is a very strong association). It turns out that I do have that variant. This was very cool, also because it is one of the few variations for which I know who I inherited it from.
My next goal now is to convince other people to do it as well. Why is that? Because I believe that what I paid for now is only the tip of the iceberg. The more people will be genotyped the more people will know about the way genes affect people lives. This service gives you at the same time the ability to know more about yourself and help other people know more about themselves. As 23andme puts it, in the same way you help research by giving some money to participate in a race, you can also do it by giving your DNA available for research. Your single contribution will not make the difference but if many people do it, their overall contributions will.
It costs only $399 and that means that everybody in the civilized world can afford it. Now it is only a matter of making people understand why it so important. I believe that in the next 10 years it will change the way we look at what we are and, furthermore, it will give a new insight of what directed evolution to shape us the way we are. How could you not be curios about that?
By virtue of being a male, 23andme genotyped both my mitochondrial DNA and my Y chromosome. These two are very special pieces of DNA since they cannot go under recombination. This means that they are passed generation after generation without mixing or changing, other than for mutations. But mutations are rare so they change little even in a 1000 year span. You get the first one from your mom and the second from your dad, if you are a male.
It turned out that my mitochondrial DNA belongs to haplotype H13a1, a rare group that is mainly common around the Caspian sea. According to the history, it was brought to Southern Italy and Southern Spain during the last ice age, something like 20000 years ago. My Y chromosome belongs instead to haplogroup J2, a kind that seems to be very common in Southern Europe, Northern Africa and the Middle East. Again, according to the history, it seems to have migrated multiple times from the Fertile Crescent to Europe and in particular to Italy where it is overall pretty common.
If you are curios about your ancestry you might find this very interesting. Although it only relates to your maternal line and your paternal line. So, for example, it does not witness the fact that I am 25% Greek. Something else surely does though. If you are interested in your ancestry then this might be a first step but you might want to look at ancestry.com. It seems that this company now teamed up with 23andme. Their service works as follows: you try to give them as much information as you can about your pedigree and if you far back enough you end up connecting with the archives that they built that could go back up to the 1600. They only did this for America and Europe but they claim to have already collected more than a billion entries, together with the people that subscribe to their services. My understanding is that 23andme and ancestry.com will do for the world what the company deCODEme did for all the Icelanders. Something we probably all thought impossible 10 years ago will be something normal in an even shorter time.
It might be fun to look at this kind of information, although we do not need to know our ancestry to know how our DNA affects us. It would be enough to understand its language. The real information that determines us is in the rest of the chromosomes. There are almost 100 associations described, as I write, that can be accessed through the 23andme website. These are divided in four categories, associations that put you at a more elevated risk, associations that put you at a decreased risk, associations that put you at a typical risk, and finally associations with traits that are not considered diseases. For example I could confirm the fact that I am an heterozygous for eye color, that is, my eyes are not blue but I can have a child with blue eyes. I seem to be lactose intolerant. This does not mean that I cannot drink milk but only that my ability to digest it decreases faster as years go by. This comes as no surprise since the mutation that prevents that is common only in Northern Europeans.
I also am not a carrier for three severe recessive diseases like cystic fibrosis and others for which the genetic reason has been identified. Not that my life is going to change much because of this, at least not any soon, but it is cool to know. There are so many more things to say that I will stop with a last one. Going bald is something that is usually inherited from your mom, in the meaning that your father has little to do with it. The reason is that a variant of a gene on chromosome X, inherited only from the mom for males, prevents you from going bald (to be precise you have 11 times less chances, but this is a very strong association). It turns out that I do have that variant. This was very cool, also because it is one of the few variations for which I know who I inherited it from.
My next goal now is to convince other people to do it as well. Why is that? Because I believe that what I paid for now is only the tip of the iceberg. The more people will be genotyped the more people will know about the way genes affect people lives. This service gives you at the same time the ability to know more about yourself and help other people know more about themselves. As 23andme puts it, in the same way you help research by giving some money to participate in a race, you can also do it by giving your DNA available for research. Your single contribution will not make the difference but if many people do it, their overall contributions will.
It costs only $399 and that means that everybody in the civilized world can afford it. Now it is only a matter of making people understand why it so important. I believe that in the next 10 years it will change the way we look at what we are and, furthermore, it will give a new insight of what directed evolution to shape us the way we are. How could you not be curios about that?
Sunday, October 5, 2008
Vermont Corn Maze
Yesterday I went to what is known as the Vermont Corn Maze. The name already explains much of what the place is, that is, a maze inside a field of corn. Have you ever been inside a field of corn? Starting from the summer the corn is so high that it is not much different from a wall. But what is the maze? I had no idea until I actually got inside there.
Together in a group of seven people I went to this touristic location north in Vermont. Upon arrival I entered this big field of corn with the simple belief of how hard could it be to get through a a big field of corn? It is going to be very easy even if the designer was trying to make it as hard as possible. It turned out that I was right only about one of the previous statements. You can imagine which one.
The main problem is that the simple two-dimensional structure was complicated by a couple of bridges going on top of multiple corn paths and after wondering around for a while you could actually get the feeling that no matter how hard you tried you were not going to easily succeed at going through the paths going under the bridge. And this really kept building up your frustration.
While you are inside a corn field everything looks the same. Even on top of the bridges, from where you can see the whole field, you cannot see where the paths go and about twenty meters from you every starts looking like a gigantic field of corn. The sun can help you orientate but it is still very hard to measure how far you went in one direction. I confess that after a while I gave up trying to outsmart the designer and I started to turn left at every fork. It took a long time and my brain gave up trying to build up a map but it eventually worked. I could feel it when I finally ended up under the bridge I tried to go under for so long.
When I finally came out, more than two hours after I entered, the sun was almost sunsetting. I felt defeated and when I looked at the aerial photographs I actually could feel that the designer really managed to outsmart me and all of my friends. It was a good feeling.
After sunset and a long dinner with my group, I returned to the corn field for an adventure night in the corn. A different corn field was set up for groups of people to go through at night while props dressed with horror faces would try to scare you. It was actually not so scary after all but it was so dark that you could not see the props jumping out of the crops. The design was impressive. Imagine yourself going through a narrow path inside a corn field with red candle lights scattered around and corpse like some of which were faked and some of which were real people. Moreover, you could also feel the constant screaming of people in front of you and behind you, mainly girls who seem more easily impressed. And finally the sky on top of the field was full of stars and so clear that you could see the whole milky way.
It might have not been exactly like you could imagine an horror movie but it is probably the as good as you can get experience possible. I will never look at a corn field the same way. Did you know, by the way, that corn was imported to Europe from the Americas? Yes, you probably did. But did you know that corn is that big because it was domesticated by farmers in the Mesoamerica trying to reuse only the plants yielding the most? If not, then check on the internet to see what a wild type corn looks like. If this still doesn't make you feel the magic of corn then go to the Vermont corn maze. Farmers have not run out of ideas on how to play with corn.
Together in a group of seven people I went to this touristic location north in Vermont. Upon arrival I entered this big field of corn with the simple belief of how hard could it be to get through a a big field of corn? It is going to be very easy even if the designer was trying to make it as hard as possible. It turned out that I was right only about one of the previous statements. You can imagine which one.
The main problem is that the simple two-dimensional structure was complicated by a couple of bridges going on top of multiple corn paths and after wondering around for a while you could actually get the feeling that no matter how hard you tried you were not going to easily succeed at going through the paths going under the bridge. And this really kept building up your frustration.
While you are inside a corn field everything looks the same. Even on top of the bridges, from where you can see the whole field, you cannot see where the paths go and about twenty meters from you every starts looking like a gigantic field of corn. The sun can help you orientate but it is still very hard to measure how far you went in one direction. I confess that after a while I gave up trying to outsmart the designer and I started to turn left at every fork. It took a long time and my brain gave up trying to build up a map but it eventually worked. I could feel it when I finally ended up under the bridge I tried to go under for so long.
When I finally came out, more than two hours after I entered, the sun was almost sunsetting. I felt defeated and when I looked at the aerial photographs I actually could feel that the designer really managed to outsmart me and all of my friends. It was a good feeling.
After sunset and a long dinner with my group, I returned to the corn field for an adventure night in the corn. A different corn field was set up for groups of people to go through at night while props dressed with horror faces would try to scare you. It was actually not so scary after all but it was so dark that you could not see the props jumping out of the crops. The design was impressive. Imagine yourself going through a narrow path inside a corn field with red candle lights scattered around and corpse like some of which were faked and some of which were real people. Moreover, you could also feel the constant screaming of people in front of you and behind you, mainly girls who seem more easily impressed. And finally the sky on top of the field was full of stars and so clear that you could see the whole milky way.
It might have not been exactly like you could imagine an horror movie but it is probably the as good as you can get experience possible. I will never look at a corn field the same way. Did you know, by the way, that corn was imported to Europe from the Americas? Yes, you probably did. But did you know that corn is that big because it was domesticated by farmers in the Mesoamerica trying to reuse only the plants yielding the most? If not, then check on the internet to see what a wild type corn looks like. If this still doesn't make you feel the magic of corn then go to the Vermont corn maze. Farmers have not run out of ideas on how to play with corn.
Saturday, September 27, 2008
Bartending
Another Saturday is gone as every weekend that goes by. But this one was pretty different and deserving some talking. The day started with the Computer Science
Symposium on campus. My main reason to be there was to present a poster about my own work. The first part of the symposium was a lot of fun and then I was really glad a couple of people got interested about my work and genuinely spent time listening about what I was saying. It is usually hard to find people that like exactly what you like but I felt like I got their attention even if just for a while. It made my day.
After dinner I went to this party where I was supposed to bartend. I never did it before and that made me feel that no matter how it turned it was going to be
fun. And I was right. I spent four hours straight serving wine and beer for people with little pauses. There were always people in line. What is fun is to end up interacting with all this different people that otherwise would have little interest to come to talk to you. This way instead they basically have no other
choice other than to come. And some are really interesting. Some look at you with fun expressions and since they are either drunk or going to be, it is ok to
make a little bit fun of them. They don't mind. During the day it might be inappropriate but in this case it is totally cool.
As the party went on I started noticing the same people returning over and over again to get more beer and wine. There was actually nothing else to serve. Everybody looks different. There is the guy that is very friendly and will actually start dance for me when I ask it as a price for getting served, there is the guy that looks completely depressed and I wonder if it is the right thing to do to serve him more alcohol. I do it nevertheless.
Among the interesting people that I met there was one of my ex students and my ex instructor of climbing that seemed interested in coming to dance salsa after I promised that I would teach her some moves. My neighbors were there too. Somehow they get to know about all the parties in town.
Overall I am really glad I agreed to bartend for the party. I am usually the kind of guy that eventually gets bored at parties. This way I actually got to have some fun and it made me feel good to serve so many people in a single day. I got served many times so this was my first way to return the favor. Well, almost, since I was paid well.
If I had the chance, I would definitely do it again.
Symposium on campus. My main reason to be there was to present a poster about my own work. The first part of the symposium was a lot of fun and then I was really glad a couple of people got interested about my work and genuinely spent time listening about what I was saying. It is usually hard to find people that like exactly what you like but I felt like I got their attention even if just for a while. It made my day.
After dinner I went to this party where I was supposed to bartend. I never did it before and that made me feel that no matter how it turned it was going to be
fun. And I was right. I spent four hours straight serving wine and beer for people with little pauses. There were always people in line. What is fun is to end up interacting with all this different people that otherwise would have little interest to come to talk to you. This way instead they basically have no other
choice other than to come. And some are really interesting. Some look at you with fun expressions and since they are either drunk or going to be, it is ok to
make a little bit fun of them. They don't mind. During the day it might be inappropriate but in this case it is totally cool.
As the party went on I started noticing the same people returning over and over again to get more beer and wine. There was actually nothing else to serve. Everybody looks different. There is the guy that is very friendly and will actually start dance for me when I ask it as a price for getting served, there is the guy that looks completely depressed and I wonder if it is the right thing to do to serve him more alcohol. I do it nevertheless.
Among the interesting people that I met there was one of my ex students and my ex instructor of climbing that seemed interested in coming to dance salsa after I promised that I would teach her some moves. My neighbors were there too. Somehow they get to know about all the parties in town.
Overall I am really glad I agreed to bartend for the party. I am usually the kind of guy that eventually gets bored at parties. This way I actually got to have some fun and it made me feel good to serve so many people in a single day. I got served many times so this was my first way to return the favor. Well, almost, since I was paid well.
If I had the chance, I would definitely do it again.
Wednesday, September 17, 2008
23andMe
When we look at each other we are all human beings. We can do things that no other animals can do. At the same time each one of us can do just a few of the things that people can do. We are all the the same but we are also so different. For many reasons, of course, but a good chunk of that reason relies on what variations are written on our DNA. Most of those variations, and from a mathematical entropy point of view I really mean a large percentage, can actually be read nowadays. What is even more true is that from this month, actually since last week, it has become extremely cheap, just $399.
Well, I confess, I could not resist. Maybe just to see the contempt on the faces of the people that will wonder how I could have taken such a despicable choice. Right now I am really looking forward to that. But the main reason is definitely pure curiosity. This means entering a new level of consciousness of ourselves. Even if so far most of what we can read we also cannot understand, the small parts that we do understand are already telling a lot. What am I talking about?
First of all, I know that a fourth of me is Greek but for the rest I only know that I am Italian. What does that mean? Not much, since Italian people are actually a messy mix. Is there anything in my DNA that will tell me more about that? Maybe not, but that is already an answer. This overall is already worth it a lot to me. But the real fun is around what each individual SNP being read in my DNA is going to tell. If you like Wikipedia then get ready for the new internet hit, that is, SNPedia. It is already there and it is growing. It aims at organizing all information that can be extracted from SNP data. Right now there are a lot of fun ones, from the SNP that increases your chances to get Alzeheimer to the one that apparently boosts your intelligence.
Many will say, and 23andMe will warn you, that some of what you can read might be knowledge that you would have never wanted and there will be no turning back. The Alzeheimer SNP is the best example. Who would want to know that his brain will slowly die?
I guess I am taking a risk since my paternal grandmother did suffer of a severe brain degeneration and if that was transmitted to my dad or not I guess I will never know unless I found out that I am affected as well. Overall I have only 25% chances. But would that make me really worried? I guess I would still live most of my life with the hope there will be some kind of solution.
Also, my belief is that if there is something that really will make my life a nightmare then it is my duty to make sure I will not transmit that. So if I ever decide to have children then I would never want them to feel the same. Therefore I would need to know that piece of information nevertheless, no matter how painful that could be.
But my belief is that there is nothing too scary written in my DNA and knowing that my mothernal grandparents are both healthy and they have both surpassed the average expected life makes even a little bit more comfortable.
Going back to what really makes me curios I can name a few things. Well, first of all, why am I so skinny and why do I seem to be unable to build up any fat whatsoever? I am sure one gene will not answer the question but a bit of truth would be appreciated. Why have I never developed any cavities even if I have never cleaned my teeth more than once a day? Am I eventually going to get completely bald? Am I resistant to HIV? What do the SNPs say about the fiber composition of my muscles? Why do I have no need for eyeglasses at all? Am I more susceptible than the average to develop lung cancer? And so much more.
It is hard to tell how many things will be known next year because a lot of studies are being developed right now. The more people will be statistically analyzed the more will be known. The only limit will be achieved when everybody on this planet will be genotyped.
Yes, everybody, and with me that means one less to go. Because once I send my sample of saliva I will enter the statistics pool, so if I have a trait I am curios about and nothing is known about it so far, then by giving my data I am providing my own little piece of evidence. Wait a minute. So maybe I should be paid to get my DNA analyzed. Well, this might be stretching it a little bit too much but it is indeed a do ut des thing to do. And knowing that 23andMe is owned in part by Google makes me feel even better about where my money go. That is, the right place.
I want to finish giving my personal opinion. I like to think that our brain and our body are two very distinct things that need each other to exist. Since our brain starts interacting with the world, it starts a journey that is an evolution of its own that stops only with our death. Our body, on the contrary, evolves really little. Natural selection shaped it for a long time, but its journey is about over now. We all need our body in our journey and it would be nice if we could keep it functional. I think this is a new effective way to do that. I really would not want to miss it.
Well, I confess, I could not resist. Maybe just to see the contempt on the faces of the people that will wonder how I could have taken such a despicable choice. Right now I am really looking forward to that. But the main reason is definitely pure curiosity. This means entering a new level of consciousness of ourselves. Even if so far most of what we can read we also cannot understand, the small parts that we do understand are already telling a lot. What am I talking about?
First of all, I know that a fourth of me is Greek but for the rest I only know that I am Italian. What does that mean? Not much, since Italian people are actually a messy mix. Is there anything in my DNA that will tell me more about that? Maybe not, but that is already an answer. This overall is already worth it a lot to me. But the real fun is around what each individual SNP being read in my DNA is going to tell. If you like Wikipedia then get ready for the new internet hit, that is, SNPedia. It is already there and it is growing. It aims at organizing all information that can be extracted from SNP data. Right now there are a lot of fun ones, from the SNP that increases your chances to get Alzeheimer to the one that apparently boosts your intelligence.
Many will say, and 23andMe will warn you, that some of what you can read might be knowledge that you would have never wanted and there will be no turning back. The Alzeheimer SNP is the best example. Who would want to know that his brain will slowly die?
I guess I am taking a risk since my paternal grandmother did suffer of a severe brain degeneration and if that was transmitted to my dad or not I guess I will never know unless I found out that I am affected as well. Overall I have only 25% chances. But would that make me really worried? I guess I would still live most of my life with the hope there will be some kind of solution.
Also, my belief is that if there is something that really will make my life a nightmare then it is my duty to make sure I will not transmit that. So if I ever decide to have children then I would never want them to feel the same. Therefore I would need to know that piece of information nevertheless, no matter how painful that could be.
But my belief is that there is nothing too scary written in my DNA and knowing that my mothernal grandparents are both healthy and they have both surpassed the average expected life makes even a little bit more comfortable.
Going back to what really makes me curios I can name a few things. Well, first of all, why am I so skinny and why do I seem to be unable to build up any fat whatsoever? I am sure one gene will not answer the question but a bit of truth would be appreciated. Why have I never developed any cavities even if I have never cleaned my teeth more than once a day? Am I eventually going to get completely bald? Am I resistant to HIV? What do the SNPs say about the fiber composition of my muscles? Why do I have no need for eyeglasses at all? Am I more susceptible than the average to develop lung cancer? And so much more.
It is hard to tell how many things will be known next year because a lot of studies are being developed right now. The more people will be statistically analyzed the more will be known. The only limit will be achieved when everybody on this planet will be genotyped.
Yes, everybody, and with me that means one less to go. Because once I send my sample of saliva I will enter the statistics pool, so if I have a trait I am curios about and nothing is known about it so far, then by giving my data I am providing my own little piece of evidence. Wait a minute. So maybe I should be paid to get my DNA analyzed. Well, this might be stretching it a little bit too much but it is indeed a do ut des thing to do. And knowing that 23andMe is owned in part by Google makes me feel even better about where my money go. That is, the right place.
I want to finish giving my personal opinion. I like to think that our brain and our body are two very distinct things that need each other to exist. Since our brain starts interacting with the world, it starts a journey that is an evolution of its own that stops only with our death. Our body, on the contrary, evolves really little. Natural selection shaped it for a long time, but its journey is about over now. We all need our body in our journey and it would be nice if we could keep it functional. I think this is a new effective way to do that. I really would not want to miss it.
Saturday, September 13, 2008
Where do great ideas come from?
As a mathematician, most of what constitutes my work is having new ideas and then formalize them and write them down so that they can be shared among other people. An idea per se is a very abstract object. Sometimes it can be a very simple concept but the details to talk about it might make it look very complicated.
When we do recognize great ideas, maybe from a book, from a paper or from talking to someone, we feel that spark of genius in it. The question comes often. Where do great ideas come from? Well, I wished more of that was taught in class. We attend tens of classes in college and graduate school but the only thing we learn is about other people ideas and not about the process that lead them to develop them. Learning this might be a very painful process.
In general, the person that is supposed to teach you that should be your advisor. Although your advisor might not be good at that or simple might not realize the importance of teaching that. Or maybe for every person is different and it is just not something that can be taught. To some extent, you have to find your own way.
My advisor told me that his way to come up with something interesting. When he was in graduate school he was at looking at data and examples and trying to figure out what you could do or might want to do with it. Many papers he wrote came out of this process. So he decided to do the same with me. Mainly, he gave me large datasets and told me to go and play.
Yes, to play, because playing is were ideas come out from. And playing also means to have fun because if you are not having fun then you are not playing.
And indeed I have been playing recently with this massive dataset of genotype data from nine related individuals and this week I feel I really nailed down a cool idea. Now it will take at least two weeks to shape an algorithm to make it work and probably at least a month to write a paper about it and hopefully convince other people about how cool it is.
I spent today a lot of time trying to find out papers through Google scholar that might relate to what just came to my mind but I couldn't find any, yet. That makes me really excited since it motivates me even more to pursue this 100%. But ultimately, in my case, where this idea came from and why has nobody thought about it before?
I have spent many weeks now looking at the data over and over again, seeing what information was lying there, testing algorithms, seeing how they run and why they don't run well sometimes. Confusion added up to confusion until I realized that there was a simple solution lying ahead. Well, simple as compared to the level of mess that had been building up in my head recently. Now my goal is to share with other people and I guess they will judge how simple it is. All ideas look simple to the person that first thinks of them.
Now I have got to go. I feel like I have found my little gold mine and there is a lot of work to do. In this case it also means that there is a lot of fun to go through. I haven't been so excited since the days when I realized that my polynomial factoring algorithm was factoring some special kind of polynomials faster than any other algorithm ever devised for that purpose. I am feeling that my office is the place where the most exciting stuff is going on, even if there is just me there. With my little dream that I might put down something interesting and there might be smart people willing to listen to me because I have something smart to say.
I have known myself for a quite awhile now. That, basically, is really all that I want.
When we do recognize great ideas, maybe from a book, from a paper or from talking to someone, we feel that spark of genius in it. The question comes often. Where do great ideas come from? Well, I wished more of that was taught in class. We attend tens of classes in college and graduate school but the only thing we learn is about other people ideas and not about the process that lead them to develop them. Learning this might be a very painful process.
In general, the person that is supposed to teach you that should be your advisor. Although your advisor might not be good at that or simple might not realize the importance of teaching that. Or maybe for every person is different and it is just not something that can be taught. To some extent, you have to find your own way.
My advisor told me that his way to come up with something interesting. When he was in graduate school he was at looking at data and examples and trying to figure out what you could do or might want to do with it. Many papers he wrote came out of this process. So he decided to do the same with me. Mainly, he gave me large datasets and told me to go and play.
Yes, to play, because playing is were ideas come out from. And playing also means to have fun because if you are not having fun then you are not playing.
And indeed I have been playing recently with this massive dataset of genotype data from nine related individuals and this week I feel I really nailed down a cool idea. Now it will take at least two weeks to shape an algorithm to make it work and probably at least a month to write a paper about it and hopefully convince other people about how cool it is.
I spent today a lot of time trying to find out papers through Google scholar that might relate to what just came to my mind but I couldn't find any, yet. That makes me really excited since it motivates me even more to pursue this 100%. But ultimately, in my case, where this idea came from and why has nobody thought about it before?
I have spent many weeks now looking at the data over and over again, seeing what information was lying there, testing algorithms, seeing how they run and why they don't run well sometimes. Confusion added up to confusion until I realized that there was a simple solution lying ahead. Well, simple as compared to the level of mess that had been building up in my head recently. Now my goal is to share with other people and I guess they will judge how simple it is. All ideas look simple to the person that first thinks of them.
Now I have got to go. I feel like I have found my little gold mine and there is a lot of work to do. In this case it also means that there is a lot of fun to go through. I haven't been so excited since the days when I realized that my polynomial factoring algorithm was factoring some special kind of polynomials faster than any other algorithm ever devised for that purpose. I am feeling that my office is the place where the most exciting stuff is going on, even if there is just me there. With my little dream that I might put down something interesting and there might be smart people willing to listen to me because I have something smart to say.
I have known myself for a quite awhile now. That, basically, is really all that I want.
Saturday, August 16, 2008
Nvidia shame
It is finally time for a little rant. Again, it is about unnecessary inefficiencies. Recently I have been using matlab a lot for my work. Matlab is an amazing program. The main reason I love it is because it is so easy to learn how to do new things. The all software industry should really draw on for how a lot of other things should get done.
Anyway, I recently switched my desktop environment to KDE4.1, probably the best user graphical interface ever devised. One of those gems that once you know how to use will make you feel handicapped when using anything else. Only problem, I started to feel that a lot of applications have become more sluggish when moving the windows around and switching windows. How could that be? How can developers make such a good job on one side and on the other side make me feel like my machine is slower at some tasks than Windows 95 used to be? One thing I was sure: I needed to know.
So I started a Google search and I rapidly concluded the following:
1) KDE4.1 is based on Qt4.4 and this makes large use of a 2D extension called XRender.
2) The XRender extension has been poorly implemented by the Nvidia drivers for at least the past five years.
3) My computer has an Nvidia graphic card.
That was easy to find out. The internet is actually full of forum posts from people outraged by how slow KDE4.1 is on their Nvidia cards despite how much they paid for their bleeding edge graphic cards. Well, at least I didn't pay that much.
Although, why is all of this happening to begin with? The main question is this: why hasn't this problem already been fixed during the past five years? Why do the Ati open source drivers work an order of magnitude better?
Well, I guess the reason relies in this little but wise piece of truth: "the only way to fix the problem is to not fix it". In the past five years linux graphical user interfaces have avoided using XRender because it wasn't well implemented by all of the majors graphic card vendors. But waiting didn't actually help. What is going to help is now the ranting of people against Nvidia about the fact that their drivers work so poorly.
My bet is that if the drivers were open source some KDE4 developers would have put thier good will to fix the problem himself but that is not an option because the drivers were proprietary.
This is 2008. How many more years does the world need to understand that proprietary drivers will always keep giving people headaches? As one of the Google founders said in an interview, developers should multiply the time the user loses because of thier poor implementations by the number of the users they hava and get an idea of how many people lives they have killed. So, how many more lifetimes have to be wasted?
As for doing my part in finding a solution, I will never buy a Nvidia card until Nvidia releases their drivers open source. Will other people understand this and do the same?
Anyway, I recently switched my desktop environment to KDE4.1, probably the best user graphical interface ever devised. One of those gems that once you know how to use will make you feel handicapped when using anything else. Only problem, I started to feel that a lot of applications have become more sluggish when moving the windows around and switching windows. How could that be? How can developers make such a good job on one side and on the other side make me feel like my machine is slower at some tasks than Windows 95 used to be? One thing I was sure: I needed to know.
So I started a Google search and I rapidly concluded the following:
1) KDE4.1 is based on Qt4.4 and this makes large use of a 2D extension called XRender.
2) The XRender extension has been poorly implemented by the Nvidia drivers for at least the past five years.
3) My computer has an Nvidia graphic card.
That was easy to find out. The internet is actually full of forum posts from people outraged by how slow KDE4.1 is on their Nvidia cards despite how much they paid for their bleeding edge graphic cards. Well, at least I didn't pay that much.
Although, why is all of this happening to begin with? The main question is this: why hasn't this problem already been fixed during the past five years? Why do the Ati open source drivers work an order of magnitude better?
Well, I guess the reason relies in this little but wise piece of truth: "the only way to fix the problem is to not fix it". In the past five years linux graphical user interfaces have avoided using XRender because it wasn't well implemented by all of the majors graphic card vendors. But waiting didn't actually help. What is going to help is now the ranting of people against Nvidia about the fact that their drivers work so poorly.
My bet is that if the drivers were open source some KDE4 developers would have put thier good will to fix the problem himself but that is not an option because the drivers were proprietary.
This is 2008. How many more years does the world need to understand that proprietary drivers will always keep giving people headaches? As one of the Google founders said in an interview, developers should multiply the time the user loses because of thier poor implementations by the number of the users they hava and get an idea of how many people lives they have killed. So, how many more lifetimes have to be wasted?
As for doing my part in finding a solution, I will never buy a Nvidia card until Nvidia releases their drivers open source. Will other people understand this and do the same?
Sunday, July 13, 2008
Prouty 2008
Yesterday I participated in the Prouty, a 100 miles ride that takes place near the Connecticut river, in New Hampshire and Vermont. It was a great event with tens of people participating. This year Enrique was riding with me and I was kind of happy I was going to ride with a good friend. It was also his birthday. I never biked that long in the States even if I have experienced longer rides during my fourth year of college.
Things did not go quite right. After about 20 miles I realized that I wanted to go my own pace that was not Enrique's pace. The climax of the ride was the Mt. Cube climb. Despite not being an unmatched climb, I wanted to try my best. After all it was not a race but when you ride your bike it is still nice to race against yourself and this was really a nice occasion to do it. So I left Enrique, despite it was his birthday. I hope he will be able to forgive me. I kind of understand now better why my college friend Valentino always left me behind and teased me about my slowness.
After the climb I started drafting behind different groups. It is a perfect way to keep you motivated and concentrated. Although, every time a steep uphill would show up, I could not sustain the pace of the group and so I would have to wait for a new one to come and give me a lift. Overall it was a lot of fun. I stopped at five of the food stands set up for the event and I ate tons of bananas. I also met a math professor at the third stand I stopped in. We had a nice conversation about biking.
In the end I started dragging a lot. It always comes the moment when the forces abandon you and the muscles give up. You can still bike but every small effort becomes a titanic one and what before looked liked a moderate climb now looks like a wall. It was comforting to see other people dragging too. After all, in the end it does not matter how long it takes.
When I arrived at the last stand I took some time to rest, eat and stretch. I really wanted to be done with it but I knew there were still 10 miles left. I smiled at the idea that it was almost over. But I wanted those 10 last miles to be the best. I thought back about how good it was to be there and why, to begin with, my passion for biking started. And then I thought at the people biking with me that last stretch. I wandered what their motivation was, where their energy comes from.
The whole purpose of the event was to raise money for the research against cancer. More than $2 millions have been raised this year. I also made my little contribution. I confess, I was mainly biking for the fun of it. Some people were riding with a yellow ribbon. To honor those that of cancer have died and those that are fighting against it.
It is weird because I admit that I do not believe the fight against cancer makes a lot of sense. Because cancer is a way to die, and death is a natural part of life that cannot be avoided. But somehow, I felt like there is something very noble in it and I felt like I wanted to honor those that believed in the fight. For them is this day most than any other. And that, to my surprise, gave me the motivation to bike those last miles at my best. Light as a leaf in the wind. To honor those that have fought and are fighting.
Things did not go quite right. After about 20 miles I realized that I wanted to go my own pace that was not Enrique's pace. The climax of the ride was the Mt. Cube climb. Despite not being an unmatched climb, I wanted to try my best. After all it was not a race but when you ride your bike it is still nice to race against yourself and this was really a nice occasion to do it. So I left Enrique, despite it was his birthday. I hope he will be able to forgive me. I kind of understand now better why my college friend Valentino always left me behind and teased me about my slowness.
After the climb I started drafting behind different groups. It is a perfect way to keep you motivated and concentrated. Although, every time a steep uphill would show up, I could not sustain the pace of the group and so I would have to wait for a new one to come and give me a lift. Overall it was a lot of fun. I stopped at five of the food stands set up for the event and I ate tons of bananas. I also met a math professor at the third stand I stopped in. We had a nice conversation about biking.
In the end I started dragging a lot. It always comes the moment when the forces abandon you and the muscles give up. You can still bike but every small effort becomes a titanic one and what before looked liked a moderate climb now looks like a wall. It was comforting to see other people dragging too. After all, in the end it does not matter how long it takes.
When I arrived at the last stand I took some time to rest, eat and stretch. I really wanted to be done with it but I knew there were still 10 miles left. I smiled at the idea that it was almost over. But I wanted those 10 last miles to be the best. I thought back about how good it was to be there and why, to begin with, my passion for biking started. And then I thought at the people biking with me that last stretch. I wandered what their motivation was, where their energy comes from.
The whole purpose of the event was to raise money for the research against cancer. More than $2 millions have been raised this year. I also made my little contribution. I confess, I was mainly biking for the fun of it. Some people were riding with a yellow ribbon. To honor those that of cancer have died and those that are fighting against it.
It is weird because I admit that I do not believe the fight against cancer makes a lot of sense. Because cancer is a way to die, and death is a natural part of life that cannot be avoided. But somehow, I felt like there is something very noble in it and I felt like I wanted to honor those that believed in the fight. For them is this day most than any other. And that, to my surprise, gave me the motivation to bike those last miles at my best. Light as a leaf in the wind. To honor those that have fought and are fighting.
Thursday, July 10, 2008
Thursday Night Salsa
As almost every Thursday I went to dance salsa in Collis. I like it a lot, both for the dancing part and the social aspect. Sometimes it is boring, sometimes it is fun. And sometimes you get to know completely new interesting people, something I have not been used to before coming to Dartmouth.
This time I got to know Catie, a girl from the local area. She struck me since she introduced herself as a nerd. Well, it is not common to find girls that are nerds and it is even less common to find nerds that dance salsa. But then again, that is exactly what is cool about Thursday Night Salsa. You always get surprised.
While dancing we talked a little bit. I usually ask many more questions than answers I give. I discovered that she is a biochemist and that after college she went to work for a startup company in the area around Dartmouth. This company is planning to produce cheap antibodies hacking the yeast using a new secret method that has not been patented yet and that therefore she could not tell me about. I could feel the excitement. The company is hoping to get the job done and then get sold to a big pharmaceutical company and that's good since she is being paid with stock options.
You get to read on books that these things happen. Maybe one day when I will go to buy antibodies at the local pharmacy I might be able to tell that I met one of the people that helped inventing them. You get to really understand what makes the United States the country that changes the whole world. Efficiency and entrepreneurship. The country where ideas get transformed into reality because people are more willing to take risks.
It is just such a different feeling to see it with your own eyes.
This time I got to know Catie, a girl from the local area. She struck me since she introduced herself as a nerd. Well, it is not common to find girls that are nerds and it is even less common to find nerds that dance salsa. But then again, that is exactly what is cool about Thursday Night Salsa. You always get surprised.
While dancing we talked a little bit. I usually ask many more questions than answers I give. I discovered that she is a biochemist and that after college she went to work for a startup company in the area around Dartmouth. This company is planning to produce cheap antibodies hacking the yeast using a new secret method that has not been patented yet and that therefore she could not tell me about. I could feel the excitement. The company is hoping to get the job done and then get sold to a big pharmaceutical company and that's good since she is being paid with stock options.
You get to read on books that these things happen. Maybe one day when I will go to buy antibodies at the local pharmacy I might be able to tell that I met one of the people that helped inventing them. You get to really understand what makes the United States the country that changes the whole world. Efficiency and entrepreneurship. The country where ideas get transformed into reality because people are more willing to take risks.
It is just such a different feeling to see it with your own eyes.
Saturday, July 5, 2008
A tale of two queues
Yesterday, 4th of July, independence day for the American people, I finally flied back to the States. My flight was leaving from Rome. Nice and comfortable since my maternal grandparents live in the eternal city. Although you still need to get to the airport and the only feasible option is to get the train.
My grandpa is always willing to get me to Roma Ostiense, one of the train stations where the train stops. As usual, I head for the vending machines for tickets as I always do since I am allergic to lines. In my opinions lines are the extreme symbol of inefficiency and lack of organization. Although, again, the vending machines are both broken. The information age has been around quite a while. Even in the subway there are plenty of machines to buy tickets but at the Roma Ostiense train station there are only two. And they don't work.
Ok, there is no need to panic, I will buy a ticket as people used to back in the pre-information-age era. The line at the ticket office is not even that long. Only three people. It's 8:24am and the next train leaves at 8:33am so I should manage to get it. But the guy is taking his time. Actually the ticket officer is taking his time too and there is only one. It's 8:28am, 8:31am. I finally decide to drop the idea of buying a ticket and leave for the train but it's too late. Well, no reason to overreact since there is a train every 15 minutes. Too bad the next one is 25 minutes late. I go back to the ticket office and the same guy is still talking while now there are at least 12 people in line, most of them coming from the ticket vending machine. He finally leaves at 8:48am while people behind started to get nervous. I contemplate that I had time to lose another train if it wasn't for the fact that it was late.
I finally get into the 9:03am train, which is pretty full and gets to the airport with some delay. During the trip I am thinking how it is possible that we spend billions of euros to build high speed railroads to save half an hour while the same amount of time can be lost because of technology repeatedly not working in the train stations. I arrive at the airport about 80 minutes earlier than my departure instead of the canonical two hours suggested for international flights. I hurry up and I manage still to get to the gate ten minutes before they start boarding. Although I get placed in seat 39F, the very last one. That means that you can't tilt the seat and that you are going to be the very last to get out of the plane, a critical feature if the plane lands late and you need to make a connection.
After a long flight, during which I ended up watching four movies, 10000 BC, Natural Treasure 2, Hercules and PS I Love You, I land in Philadelphia where I board a smaller flight to Boston. This time my seat is 6C, the second one after the first class seat. That's very good news since getting out first will give me better chances to catch the bus for Hanover, my final destination.
During the flight the captain is happy to inform us that, thanks to tail wind, we are going to land 25 minutes earlier. After that happens and the plane parks in front of the gate and everybody stands up, anxious to get out. But the door doesn't open. The captain first informs us that they are having difficulties with the connecting bridge, then that they are still having mechanical difficulties and that a mobile stair is on her way in case the problems could not be solved. We impatiently wait, seeing that freedom is just a few steps away. Sadly, jumping out of the plane is not an option. Finally, 25 minutes after parking, the captain informs us that the mobile stair arrived but it is going to connect at the back of the plane. It is 6:48pm and the bus starts going around the terminals at 6:55pm. Running would be an option if it wasn't that you have to wait for all of the people in front of you, that means all of them, again, to get out of the plane. The best ones are those that wait until is their turn to start organizing their luggages. Electrocution should be the only outcome for their behavior. After a short run, I manage to collect my luggage and step out of the airport at 6:56pm. The bus arrives just about 5 minutes later making me draw a sigh of relief. Only sad point, they are showing Natural Treasure 2 aboard, again.
Long story short, even here in the United States, the land of efficiency, they manage to have dozens of people lose their time for the most stupid reasons. Maybe my grandpa was right when he said that it was better during the Fascism when trains were never late. Too bad the world is not like Wikipedia, where if something is wrong you can actually fix it instead of cursing the people who are guilty of it. For everything else, I guess the only option is to have a little patience.
My grandpa is always willing to get me to Roma Ostiense, one of the train stations where the train stops. As usual, I head for the vending machines for tickets as I always do since I am allergic to lines. In my opinions lines are the extreme symbol of inefficiency and lack of organization. Although, again, the vending machines are both broken. The information age has been around quite a while. Even in the subway there are plenty of machines to buy tickets but at the Roma Ostiense train station there are only two. And they don't work.
Ok, there is no need to panic, I will buy a ticket as people used to back in the pre-information-age era. The line at the ticket office is not even that long. Only three people. It's 8:24am and the next train leaves at 8:33am so I should manage to get it. But the guy is taking his time. Actually the ticket officer is taking his time too and there is only one. It's 8:28am, 8:31am. I finally decide to drop the idea of buying a ticket and leave for the train but it's too late. Well, no reason to overreact since there is a train every 15 minutes. Too bad the next one is 25 minutes late. I go back to the ticket office and the same guy is still talking while now there are at least 12 people in line, most of them coming from the ticket vending machine. He finally leaves at 8:48am while people behind started to get nervous. I contemplate that I had time to lose another train if it wasn't for the fact that it was late.
I finally get into the 9:03am train, which is pretty full and gets to the airport with some delay. During the trip I am thinking how it is possible that we spend billions of euros to build high speed railroads to save half an hour while the same amount of time can be lost because of technology repeatedly not working in the train stations. I arrive at the airport about 80 minutes earlier than my departure instead of the canonical two hours suggested for international flights. I hurry up and I manage still to get to the gate ten minutes before they start boarding. Although I get placed in seat 39F, the very last one. That means that you can't tilt the seat and that you are going to be the very last to get out of the plane, a critical feature if the plane lands late and you need to make a connection.
After a long flight, during which I ended up watching four movies, 10000 BC, Natural Treasure 2, Hercules and PS I Love You, I land in Philadelphia where I board a smaller flight to Boston. This time my seat is 6C, the second one after the first class seat. That's very good news since getting out first will give me better chances to catch the bus for Hanover, my final destination.
During the flight the captain is happy to inform us that, thanks to tail wind, we are going to land 25 minutes earlier. After that happens and the plane parks in front of the gate and everybody stands up, anxious to get out. But the door doesn't open. The captain first informs us that they are having difficulties with the connecting bridge, then that they are still having mechanical difficulties and that a mobile stair is on her way in case the problems could not be solved. We impatiently wait, seeing that freedom is just a few steps away. Sadly, jumping out of the plane is not an option. Finally, 25 minutes after parking, the captain informs us that the mobile stair arrived but it is going to connect at the back of the plane. It is 6:48pm and the bus starts going around the terminals at 6:55pm. Running would be an option if it wasn't that you have to wait for all of the people in front of you, that means all of them, again, to get out of the plane. The best ones are those that wait until is their turn to start organizing their luggages. Electrocution should be the only outcome for their behavior. After a short run, I manage to collect my luggage and step out of the airport at 6:56pm. The bus arrives just about 5 minutes later making me draw a sigh of relief. Only sad point, they are showing Natural Treasure 2 aboard, again.
Long story short, even here in the United States, the land of efficiency, they manage to have dozens of people lose their time for the most stupid reasons. Maybe my grandpa was right when he said that it was better during the Fascism when trains were never late. Too bad the world is not like Wikipedia, where if something is wrong you can actually fix it instead of cursing the people who are guilty of it. For everything else, I guess the only option is to have a little patience.
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