The first paper from my own lab is out in PLoS ONE, YAY!
Chen LL, Chung WC, Lin CP, Kuo CH (2012) Comparative analysis of gene content evolution in phytoplasmas and mycoplasmas. PLoS ONE 7: e34407. DOI: 10.1371/journal.pone.0034407
Showing posts with label science. Show all posts
Showing posts with label science. Show all posts
2009/12/06
What was I thinking?
I was going through my old files this afternoon to get rid of things that I don't need any more. A mid-term report from the Evolutionary Genetics course that I took during the first year of grad school caught my eye with the following paragraph:
"Godzilla godzillus is a large reptile species endemic to the Hollywood Desert in southern California (Emmerich 1990). Due to its popularity on pet market, human collection caused extinction of several natural populations during the past decade. Of the five remaining natural populations, three of them have very small population size (N<=60, Figure 1). To preserve the species, a captive breeding program was initiated at the Hollywood Fantasy Zoo (Emmerich 1998). However, the founding individuals used in this breeding program were all collected from one population (A1). This raises the concern that future restoration efforts will greatly change the genetic composition of the species. To access the level of genetic variation and pattern of genetic structure in remaining populations, this study collected samples from all five remaining populations in the Hollywood Desert."
I honestly don't remember doing such silly things. Good thing that they didn't kick me out of the grad program.
"Godzilla godzillus is a large reptile species endemic to the Hollywood Desert in southern California (Emmerich 1990). Due to its popularity on pet market, human collection caused extinction of several natural populations during the past decade. Of the five remaining natural populations, three of them have very small population size (N<=60, Figure 1). To preserve the species, a captive breeding program was initiated at the Hollywood Fantasy Zoo (Emmerich 1998). However, the founding individuals used in this breeding program were all collected from one population (A1). This raises the concern that future restoration efforts will greatly change the genetic composition of the species. To access the level of genetic variation and pattern of genetic structure in remaining populations, this study collected samples from all five remaining populations in the Hollywood Desert."
I honestly don't remember doing such silly things. Good thing that they didn't kick me out of the grad program.
2009/10/14
Sleep seminar
While falling asleep during a seminar may not be all that rare (I do that some of the time and see people do it all the time), listening to a seminar about the science of sleep is definitely a first for me. Having good sleep during the night is difficult for me most of the time for as far back as I can remember, so when I saw the seminar announcement entitled "Sense & Nonsense to Improve Sleep", my interest is piqued and I can't wait to know what Dr. Richard R. Bootzin have to say about the subject. Here are the things that I learned today:
1. Sleep problems in toddlers and teenagers are good predictors for other problems (depression, substance abuse, etc) 10+ years down the road. Presumably, the same logic applies to adults.
2. Having <6 or >9 hours of sleep per day is not good; 7-8 hours would be the optimal for most people.
3. The use of bright light (in conjunction with darkness) is one of the most effective ways to influence circadian rhythm.
4. The stories about those crazy cyclists who participate in the Race Across America are absolutely fascinating. The hallucinations about aliens and such when one is under tremendous physical/mental stress and sleep deprivation can make very funny stories.
1. Sleep problems in toddlers and teenagers are good predictors for other problems (depression, substance abuse, etc) 10+ years down the road. Presumably, the same logic applies to adults.
2. Having <6 or >9 hours of sleep per day is not good; 7-8 hours would be the optimal for most people.
3. The use of bright light (in conjunction with darkness) is one of the most effective ways to influence circadian rhythm.
4. The stories about those crazy cyclists who participate in the Race Across America are absolutely fascinating. The hallucinations about aliens and such when one is under tremendous physical/mental stress and sleep deprivation can make very funny stories.
2009/04/07
Conservation delimma
Dr. Donald Strong from UC Davis gave a very interesting talk on an invasive plant for our department seminar today. In addition to the ecology and evolution of this plant species, I found the implication on conservation very thought provoking.
So you have a new invasive species coming in and taking over everything, needless to say, many other species in the ecosystem are affected by these drastic changes. Now the problem is this: there are two endangered species of birds involved, one being harmed and the other being helped by these changes. You get rid of the invasive plant, one of the birds goes back to its old miserable way of life; you let the invasive plant goes unchecked, the other bird is going to suffer. It is like asking whether you are going to save your son or daughter. No really an easy question and probably have no good answer.
So you have a new invasive species coming in and taking over everything, needless to say, many other species in the ecosystem are affected by these drastic changes. Now the problem is this: there are two endangered species of birds involved, one being harmed and the other being helped by these changes. You get rid of the invasive plant, one of the birds goes back to its old miserable way of life; you let the invasive plant goes unchecked, the other bird is going to suffer. It is like asking whether you are going to save your son or daughter. No really an easy question and probably have no good answer.
2009/02/18
Evolution of human culture
As a part of the celebration for Darwin's Day, our department invited Daniel Dennett to give three talks at UA this week. I attended the first two, "The Evolution of Reasons" and "The Evolution of Words and Other Memes". Both are excellent talks and I really like the second one. The parallel between evolutionary biology and human culture/technology is really thought provoking. My favorite example is the analogy of languages as virtual machines that allow us to "digitize" and faithfully replicate memes.
All these reminded me of my first reading of The Selfish Gene by Richard Dawkins back in high school, which may be a key reason of why I ended up as who I am today.
All these reminded me of my first reading of The Selfish Gene by Richard Dawkins back in high school, which may be a key reason of why I ended up as who I am today.
2008/12/20
Bacteria genome and breast feeding
Unlike my earlier post, the two things in the title are actually quite tightly linked.
Read a paper about the genome sequence of Bifidobacterium longum infantis. Basically this is a bacterial species that dominates the gastrointestinal tract of breast-fed infants. By cracking the genome sequence, the scientists found that it has a whole battery of genes for utilizing human milk oligosaccharides that lack a nutritive value to human infants. In other words, this little critter is specialized in growing on breast milk (oh boy do the infants consume a lot of that, just ask my wife, a proud mother of 3 breast-fed babies) and thus out-compete other potentially harmful bacteria in infants' gut, all the while without taking up the nutrients that infants need.
Very cool science story about human-bacteria co-evolution indeed.
Read a paper about the genome sequence of Bifidobacterium longum infantis. Basically this is a bacterial species that dominates the gastrointestinal tract of breast-fed infants. By cracking the genome sequence, the scientists found that it has a whole battery of genes for utilizing human milk oligosaccharides that lack a nutritive value to human infants. In other words, this little critter is specialized in growing on breast milk (oh boy do the infants consume a lot of that, just ask my wife, a proud mother of 3 breast-fed babies) and thus out-compete other potentially harmful bacteria in infants' gut, all the while without taking up the nutrients that infants need.
Very cool science story about human-bacteria co-evolution indeed.
2008/12/18
Why I decided to work on bacteria
After working exclusively on bacteria genomes for a couple of months, recently I went back to the world of eukaryotic genomics to compile some data sets for comparison with my findings in bacteria. Now that I am totally spoiled by the availability and quality of bacteria genome sequences, working on eukaryotes is excruciatingly frustrating and I just have to vent here.
1. The taxon sampling is so sparse (both within and across phylogenetic groups). Often the lineages are either too closely or too distantly related, which makes it really hard to do comparative genomics.
2. When I get lucky and find a group that has just the right level of divergence, some of the genome sequencing projects seemed to be "in progress" forever. Seeing that the last update was from several years ago, I really doubt if they intend to finish what they started.
3. Okay now, what about the published genomes? Everyone knows that you are supposed to deposit the sequences in GenBank/EMBL/DDBJ when you publish the genome paper, so people can get the sequences to do more analysis later. Well, as it turned out, this is quite tricky as well. While most groups followed this guideline, many of the deposited genome sequences do not contain annotation of any kind. To get the annotation, you have to hunt down the files from various sources, and needless to say, everyone uses whatever file format and convention that caught their fancy.
4. Just when I think I am done with all the painful data collection/file format conversion and ready to roll, my whole data analysis pipeline simply blows up in my face. As it turned out, some annotations are just plain horrible; there are annotated proteins with less than 60 amino acids and more than 3 in-frame stop codons, or worse yet, "genes" with one single amino acid. I mean, come on guys, even a first-pass-fully-automatic annotation can do better than that. While my pipeline worked well for what it was designed to do, there is very little that it can do about the classic garbage-in-garbage-out problem.
All these frustrations reminded me why I decided to switch from eukaryotes to bacteria last year, and I really glad that I did.
1. The taxon sampling is so sparse (both within and across phylogenetic groups). Often the lineages are either too closely or too distantly related, which makes it really hard to do comparative genomics.
2. When I get lucky and find a group that has just the right level of divergence, some of the genome sequencing projects seemed to be "in progress" forever. Seeing that the last update was from several years ago, I really doubt if they intend to finish what they started.
3. Okay now, what about the published genomes? Everyone knows that you are supposed to deposit the sequences in GenBank/EMBL/DDBJ when you publish the genome paper, so people can get the sequences to do more analysis later. Well, as it turned out, this is quite tricky as well. While most groups followed this guideline, many of the deposited genome sequences do not contain annotation of any kind. To get the annotation, you have to hunt down the files from various sources, and needless to say, everyone uses whatever file format and convention that caught their fancy.
4. Just when I think I am done with all the painful data collection/file format conversion and ready to roll, my whole data analysis pipeline simply blows up in my face. As it turned out, some annotations are just plain horrible; there are annotated proteins with less than 60 amino acids and more than 3 in-frame stop codons, or worse yet, "genes" with one single amino acid. I mean, come on guys, even a first-pass-fully-automatic annotation can do better than that. While my pipeline worked well for what it was designed to do, there is very little that it can do about the classic garbage-in-garbage-out problem.
All these frustrations reminded me why I decided to switch from eukaryotes to bacteria last year, and I really glad that I did.
2008/11/13
Exponential regression in Excel
As it turned out, Excel calculates the R-squared values of exponential regression based on transformed data. For example, for a exponential curve y=ae^bx, Excel computes R^2 using ln(y) = ln(a) + bx.
I know I shouldn't rely on Excel to do my stats but occasionally I do use it to do some quick analyses before pulling out R. What happened today was I did the regression in Excel first to see the plot and then calculate the P-value in R. Luckily, I caught the discrepancy in the R-squared value and decided to find out what the problem was. It took me quite some time to figure it out, and needless to say, I am not happy about it.
Lack of capability is one thing; Pretending being able to do something and then screw it up is totally another.
[Edit to add on 03/16/2010]
I am a bit surprised to find that this appears to be one of the most read entries of my blog. Lots of people landed here through googling some combination of "excel", "regression", and other words.
Anyway, I have a slightly more detailed explanation of the problem with performing exponential regression in Excel, plus some simple tutorials of doing regression analysis in R on my wiki at:
http://wiki.chkuo.name/
Feel free to take a look there if you are interested, hope this helps.
I know I shouldn't rely on Excel to do my stats but occasionally I do use it to do some quick analyses before pulling out R. What happened today was I did the regression in Excel first to see the plot and then calculate the P-value in R. Luckily, I caught the discrepancy in the R-squared value and decided to find out what the problem was. It took me quite some time to figure it out, and needless to say, I am not happy about it.
Lack of capability is one thing; Pretending being able to do something and then screw it up is totally another.
[Edit to add on 03/16/2010]
I am a bit surprised to find that this appears to be one of the most read entries of my blog. Lots of people landed here through googling some combination of "excel", "regression", and other words.
Anyway, I have a slightly more detailed explanation of the problem with performing exponential regression in Excel, plus some simple tutorials of doing regression analysis in R on my wiki at:
http://wiki.chkuo.name/
Feel free to take a look there if you are interested, hope this helps.
2008/10/02
Bionumbers
Found out about this interesting database from EvoDir:
BioNumbers: http://bionumbers.hms.harvard.edu/
BTW, do you know that vulcanism releases 10^15 gram of carbon per year?
BioNumbers: http://bionumbers.hms.harvard.edu/
BTW, do you know that vulcanism releases 10^15 gram of carbon per year?
2008/07/19
Bioinformatics Career Survey
Just helping to spread the words here (via Bioinformatics Zen).
*Edited to removed the survey on 08/04/2008*
View the preliminary results here
*Edited to removed the survey on 08/04/2008*
View the preliminary results here
2008/04/18
Life is fragile
I read the obituary for Scott Williamson on EvoDir today and feel really sad about this news.
I met Dr. Williamson back in 2006 when he gave a talk in our department at UGA. I remember him as a brilliant (but shy) theoretician who works on some very interesting questions. I am quite surprised to find that he is so young. Life is fragile and I feel really sorry for him and his family.
I met Dr. Williamson back in 2006 when he gave a talk in our department at UGA. I remember him as a brilliant (but shy) theoretician who works on some very interesting questions. I am quite surprised to find that he is so young. Life is fragile and I feel really sorry for him and his family.
2008/04/13
An interesting quote
"A fishnet is made up of a lot more holes than strings, but you can't therefore argue that the net doesn't exist. Just ask the fish."
From Jeffrey Kluger on why it is a bad (and stupid) idea to refute evolutionary biology because there are many unanswered questions. Take that you ID supporters.
From Jeffrey Kluger on why it is a bad (and stupid) idea to refute evolutionary biology because there are many unanswered questions. Take that you ID supporters.
2008/04/12
Final submission of my disseration
The third chapter of my dissertation is published in BMC Evolutionary Biology today. This one describes the characteristics of lineage-specific genes in some apicomplexan parasites. With this citation info, I happily updated my dissertation and send it out for the final submission. Needless to say, that pretty much made my day (or my week for that matter). Really look forward to relax a bit over the coming weekend.
2008/03/19
Web 2.0 for science networking
I found a very interesting social networking site, SciLink.com. The idea was simple enough, they mine scientific publications to find links between co-authors. All you have to do is to sign up on their website, claim the papers that you have published, and you can see a collaboration network with you at the center.
They have some nice visualization tools on the site. But with my limited experience I have to say that this is not ready for prime time yet. The publication records in their data base are limited (mostly based on my searches of some big names in my fields). It's hard to imagine that people will go through the trouble of entering all publications by themselves. Also this probably won't work well before there is a critical mass. I will check back on this site sometimes later and hope that they are on their way to a healthy growth.
They have some nice visualization tools on the site. But with my limited experience I have to say that this is not ready for prime time yet. The publication records in their data base are limited (mostly based on my searches of some big names in my fields). It's hard to imagine that people will go through the trouble of entering all publications by themselves. Also this probably won't work well before there is a critical mass. I will check back on this site sometimes later and hope that they are on their way to a healthy growth.
2008/03/07
Doomed to be a scientist
I was too naive to think that getting my dissertation out of the door would help with this. Unfortunately thinking about my research projects (either tweaking the old ones or starting new ones) still got me all excited and stay wide awake for a couple hours in the middle of the night. It was fun but I am really tired now.
So I guess there's no escape; I let go of my other dreams when I graduated from the college and chose the path to a research scientist. There were some tough times and I can foresee more challenges are yet to come, but all in all I think I made a good choice. I should be grateful for how well things turned out.
This reminded me of a career development talk I went to awhile ago. The speaker (sorry I forgot his name, maybe I should try to find this in my emails) said that the main point is to have fun and not thinking about scientific achievement, fame, or money. He used the big biochemical pathway diagram as an example; every tiny arrow on the map was the collective work of many scientists' lifetime achievement and still subject to revision. Very few people can make the quantum leaps in our knowledge, the majority of scientists are more like worker ants in the colony. Compared to other professions with similar training requirements, the pay for scientists really isn't that great. So if it's not fun, you would be better off doing something else. I guess he got a good point and I am glad about where I am now.
So I guess there's no escape; I let go of my other dreams when I graduated from the college and chose the path to a research scientist. There were some tough times and I can foresee more challenges are yet to come, but all in all I think I made a good choice. I should be grateful for how well things turned out.
This reminded me of a career development talk I went to awhile ago. The speaker (sorry I forgot his name, maybe I should try to find this in my emails) said that the main point is to have fun and not thinking about scientific achievement, fame, or money. He used the big biochemical pathway diagram as an example; every tiny arrow on the map was the collective work of many scientists' lifetime achievement and still subject to revision. Very few people can make the quantum leaps in our knowledge, the majority of scientists are more like worker ants in the colony. Compared to other professions with similar training requirements, the pay for scientists really isn't that great. So if it's not fun, you would be better off doing something else. I guess he got a good point and I am glad about where I am now.
The secret key to mastery
Read an interesting article in the Time magazine (Mar 10, 2008 issue) about why experience or raw talent are poor indicators of performance. The article cited the research done by Anders Ericsson at Florida State and suggested that "dedicated, slogging, generally solitary exertion" are the keys to "first-rate performance". One of the most intriguing points is that "it should never get easier; if it does, you are coasting, not improving". That's sounds really comforting isn't it?
2008/02/22
The science of arranging chairs
I read on Improbable Research about an old paper by Donald Stone and Alice Stone (JSTOR link).
The title of this 1974 paper is "The administration of chairs" and it went into great details about the science of arranging chairs . The original paper itself was very interesting and I thought the term "Improbable Research" is a good description for it.
The title of this 1974 paper is "The administration of chairs" and it went into great details about the science of arranging chairs . The original paper itself was very interesting and I thought the term "Improbable Research" is a good description for it.
2008/02/20
How hard is hard enough
Not sure if it is my type A personality or the work ethic I got from my parents, I often worry about not working hard enough. Reading this article, On the Process of Becoming a Great Scientist, somehow gave me some reassurance that maybe I shouldn't worry too much about this (doesn't really help anyway). In the article, I find the part about enjoying the process of writing particularly helpful, especially given my circumstance of having to produce my dissertation soon. I think marathon is a good metaphor, there is no point of enduring the hardship if you are not going to enjoy it.
2008/02/14
SlideShare.net
Found this interesting and useful website for sharing presentations (http://www.slideshare.net/). Several BioPerl presentations made by Jason Stajich can be found here.
2007/10/04
Evolutionary bioinformatics is for lazy scientists
A while ago I attended a talk by Scott William Roy, in which he classified bioinformaticians as parasitic organisms. I think that's a pretty funny joke.
Today while listening to a talk by Eric Haag at our department seminar, it suddenly occurred to me that evolutionary bioinformatics is great for lazy scientists. Basically the experiments have been done by nature (the "evolutionary" part), and better yet, the data have been collected by other people (the "bioinfo" part). All we have to do is to play with the data on computers. Doesn't that sound easy enough?
Today while listening to a talk by Eric Haag at our department seminar, it suddenly occurred to me that evolutionary bioinformatics is great for lazy scientists. Basically the experiments have been done by nature (the "evolutionary" part), and better yet, the data have been collected by other people (the "bioinfo" part). All we have to do is to play with the data on computers. Doesn't that sound easy enough?
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