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I’ve been always interested in evolutional and phynogenic studies, I read some ABCs before I went to bed on that last night, and woke up this morning thinking, “why not try it out myself”?

Well, you know, a cladogram is something you see on a biology text book that shows how human evolves from ancient apes, and how we’re related to modern ones. Watching a well and carefully constructed cladogram is a great pleasure, because it reveals the evolutionary events happend millions of years ago. However, constructing it is another story, it appears to be very simple and actually the basic principle is simple. But there’re still many problem to be solved before we can make a reasonable tree, and conclude something base on it. The biggest headache may be choosing the gene. Luckily, many scientists have done lots of experiments to prove that using mitochonrion genes for phylogenetic purpose usually works because they change fast enough to see the difference between species from a genus, and conserved enough to see their common ancester. Plus it is mainly materinherited.

Forget about the aboves, I just wanna try out some softwares that I may be using in the future. So, I visited GenBank, and fetched some published mtDNA sequences. The gene I chose was the one encodes cytochrome b, it’s totally random, I don’t know which to use actually. I collected sequence information for 10 species, 9 of which are gobies(Gobiidae) and one Perciform Aspasma minima was chosen as outgroup. Again, I don’t have tons of theory to choose this one, I just want to see how things would turn out.

Next, I need a program to align the sequences and compute the tree. After trying out some of the many, I find phyloWIN easy to use and also powerful. The data file is attached in this blog, you can download it here. With just several clicks, a tree is drawn. The result turns out satisfying, which reflects the some main groups in Gobiidae.

Technorati Tags: genbank, Goby, phylogeny

Came across this blog about this Latin song, the Chinese lyric seemed not right, so I did it myself. Full of mistakes I guess:

The song can be downloaded here.

Technorati Tags: Chinese, Latin, lyric, translate

Today I received the invitation code from Google Analytics, and have it set up for Melopia. Before google analytics I had used the Weblog Expert to analyze the weblog of Melopia. It has been working very well, until I came back to campus, and dissapointedly found that the ftp could not be accessed from our network( blaming the network center), thus I stuck there for some time until I found Web2ftp, a web-based tool that let poor users like me to logon to their ftp from intranet.

Though the download speed is extremely slow using web2ftp, but it’s better than nothing, so I just let it be. And it’s always a joy to see visitors from all over the world, though there’re only less than 15 visitors per day on average. And Phonetica Latinae seems to attract most audiences. Unfortunately, our network seems to have more serious problems lately and I can’t even open web2ftp!

It’s often said that “A door is closed, a window is opened”. That is, google analytics save the day. with some simple steps, including placing a small piece of code before </body> tag, I had no problem during installation. Hopefully I can see some statistics tomorrow.

Another interesting analysing code I placed in Melopia is the visitor map service provided by clustrmaps.com, in the map we can see where are visitors from.

At last, I know, no matter what method or service I use to analyze the visitor data cannot change the interestingness(word created by flickr) of Melopia. Only more useful contents can increase my visitors.

Technorati Tags: google analytics, Web

Just back from the psycological experiment, the last one of this semester. Our task today is to open a rabbit’s skull(craniotomy) and stimulate different areas on the pallium. The rabbit was first anaesthesized, and we cut the head skin open. After that, we use a driller to drill two holes in the skull top, then the holes were extended.

I think such experiments are really cruel, because the animal must not be anaesthesized too deeply, or it may not respond to the stimulation. Our rabbit struggled several times, thus we added more dose of anaesthestic. But then, as expected, it didn’t have obvious responses. All we can record was the pallia controlling the lower jaw and the neck.

Lindera was very upset about the result, and she insisted trying over and over again. The rabbit was waking up from anaesthesia, so I decided it’s time to let it go. It’s not easy to kill an animal, but I knew that’s the only way to release it from pain. So I injected air to the ear’s vain, it died quickly.

We should honor these animals which sacrifice themselves for scientific studies. At least, as a biology student, we must respect the ethics of using experimental animals. And we must do our best to minimize the pain during experiment, and truely respect them from our hearts.

Technorati Tags: ethic, experiment, rabbit