Monday, June 1, 2009

Sodium Dodecyl Sulfate OR Bubble Bath


Conversations with the benchmate about a chemical called SDS (sodium dodecyl sulfate) we use for various purposes in the lab:


D: Hey, I just realized that SDS is actually a component of toothpaste, shampoo, shaving foams, dissolvable aspirins and especially bubble bath.

BM: Wow, really?

D: Yeah, I was making some 10% SDS for in situ buffers and the SDS powder looked so much like the bubble bath I have at home. Also, it's driving me crazy because it gets so foamy when I want to mix it in the water.

BM: Duuude, it is so ironic. We handle all that stuff with gloves in the lab and then we go home and eat the same sh*t.


(At least I have a fun benchmatey).





Info about SDS is from Wikipedia
SDS pictures from a Google search :)

Sunday, May 24, 2009

Evolution of House Cats

June 2009 Scientific American has this great article on the evolution of house cats. Two of my favorite subjects: evolution and cats, can it get better than that?



The article cites a research that examined DNA of 1,000 wild cats and domestic cats from different places in Asia, Europe, Africa and Middle East. The result shows that all domestic cats descended from one species, F. s. silvestris (pictures above), that lived in Middle East! Arright! Domestic cat is not from Egypt after all, which is quite surprising. This DNA analysis data is supported by a burial found in Cyprus. This 9,500 year-old burial has a human and cat skeleton next to each other. It is known that cats are not native to Cyprus, so people must have brought their kitty cats with them. Previously it was thought that Egyptians domesticated cats 3,500 years ago, which is much later.

When I was reading the article, I could not help but thinking what kind of grant proposal one should write in order to get funded for analyzing DNA from 1,000 cats from so many different places. I mean it is not like you do it at your local vet or PetCo. And then I realized, that grant proposal must have looked something like this:



And of course, research got funded...

Saturday, March 14, 2009

Witty protest of the Darwin cover censorship by Turkish

In Middle East Technical University (METU), one of the most prestigious universities in Turkey, there is a stadium, and on the concrete seats of this stadium there is a giant print that says: DEVRIM (means “revolution” in Turkish). According to the urban legend, this was written by a group of revolutionist students in 1968 with a formula they developed together with chemistry students, and this was such a formula that, no other paint could cover this white paint. All the attempts of deleting it, painting on it by the officials in the years that followed proved to be useless. Obviously, the chemistry students knew what they were doing. So the word “revolution” stayed on, reflecting the revolutionist spirit of this university for decades*.



Yesterday, protesting the recent censorship of Darwin cover by the Turkish national science council of Turkey (TUBITAK), students and faculty at METU got together on the letter “D”. They called this protest “Censoring the censorship”. Because, when you remove “D” from the word “DEVRIM” you are left with “EVRIM”, which means “EVOLUTION” in Turkish.


The head of the Association of Faculty at METU, Prof. Dr. Melih Ersoy, says, “TUBITAK is the institution that should be promoting and encouraging the scientific research and thinking. It is unacceptable and very worrying to see this institution replacing the Darwin cover of the magazine, especially in 2009, the Year of Darwin.”


Photographs by: İsmail Çiftçi

*Now one of the symbols of METU, the DEVRIM print was repainted in 2008, celebrating its 40th anniversary. Pictures of this event are here.

Thursday, February 12, 2009

Darwin Day


“If it be assumed that the characteristic differences between various domestic races are due to descent from several aboriginal species, we must conclude that man chose for domestication in ancient times, either intentionally or by chance, a most abnormal set of pigeons…”

He is... the father (well, one of the fathers) of evolutionary theory. He is the guy who shed such a light on the biological sciences, we started seeing what had been hiding in the dark and we asked ourselves "How did we actually do without the evolutionary theory before?". Because "nothing made sense, except in the light of evolution".

Today is Darwin's 200th birthday and the 150th anniversary of his masterpiece: "On the Origin of Species".


The last couple of months (besides from being unbelievably busy and feeling unbelievably bad about not writing posts for this brand new blog of mine) I have been thinking about writing an article on Darwin, or on something Darwin did, you know, something that had to do with Darwin at least, for Darwin Day (which is today, February 12th). With this in my mind, guess what where was I, when I got a simple idea (this article you are reading now)? The Library!

I was there for some other reason and suddenly I thought "Hey, why do I not go check out the shelves that have evolutionary biology books?" (of course I know where they are, come on!). I got there, and saw something I had never paid attention before: some books were in little cardboard cases that were made exactly for their size. Between the time my brain asked the question why the hell they were in these cases and my hand reached for the book, "They must be really really old books!", screamed my brain. Then immediately it sent signals all over my body telling it "Get excited yo! I likes old bookses!".

The book decided to cast it's "send mites and dust" spell on me as soon as I opened the box. I sneezed a couple times but was all right. And there it was, the second edition of Darwin's "Variation of Animals and Plants Under Domestication -Vol. 1", which was published in 1876.



Of course, I checked the book out. I've got to tell you this though, my friends, at the moment I saw that book's cover, I could see why some people are bibliokleptomaniac (by the way, this term does not exist in Wikipedia!). There was just something magical about this book being so old. It is just gonna be so painful to give this book back to the library.


Not that I am going to read the whole thing. I have to be realistic. It is quite thick, the paper is very thin, text size is unusually small (for our century anyway), there is tiny line spacing, I have a looooot of experiments to do and... the figures are great... I am definitely going to look at its pictures. Although this thought triggers other thoughts that make me feel ashamed as well, and eventually I end up remembering the fact that I am a lousy biologist, who has not yet read The Origin of Species. Yes, I admit, and I am not proud of it. So, I think, one of the greatest things that I could do for myself this year would be to read a book written by Darwin (I still have the right to choose which book). That said, I am pretty sure there are many many and many biologists like me - yeah I am talking about those of you who have not read The Origin of Species - (by the way, this knowledge makes me feel less worried about some government officials, or FBI whatever, coming to my door and putting a hold on my university diploma. Because there is just too many of us, they cannot handle that!). But let me tell you something! There is at least someone even worse than me: He is one of us who has not read THE BOOK. He even has a Ph.D. in evolutionary biology (I mean, at least I am more of a molecular-cell biologist of some sort, I am a "devo" person) (I know that you know my pathetic attempt to reflect my "bad" on someone else, and I am totally cool with that!). To celebrate The Darwin Year he started reading The Book and he is now blogging on it. His name is John Whitfield, and I definitely suggest his blog: Blogging the Origin.** (Great idea).

Anyway, let's get back to our book. When I got home, I first made some tea. (Turks gotta have their tea). Aaaand I started looking at the pictures in the book.


I "analyzed" its every corner. Front and back cover...



When I realized the book was borrowed only 6 times (including me) for the last 37 years, my brain got out of control with random thoughts again: "Who were these others who borrowed it? What kind of people were they? Did they actually read the book, or did they just look at the pictures like I'm doing now? Am I a nerd? Or a geek? What's the difference between these anyway? I should get more tea..." And so on, and so on... Yes, maybe I have not YET read The Book, but I am one of those 6 crazy people, who borrowed this book since 1972: Nıhohahahaha! (This translates into "crazy laughter" in Turkish Internet slang).



There was only one thing left for me to do: After looking at the pictures, I started taking pictures of the book, and decided to make it into some kind of photo blog entry, and write these very sentences that you are reading right now.

It is just not easy to write a happy birthday note for a 200 year-old Darwin.


Footnotes:
* If you'd like to read it, there is an e-copy of "The Variation of Animals and Plants Under Domestication" here.
** I should thank my friend Uygar for letting me know of this blog.
*** The first drawing is from Nature.com. The photographs are taken by me.

(On a second thought, I guess I am going to read this book!)

Wednesday, December 17, 2008

Hello Blogosphere!


PREFACE


A couple of weeks ago, when I found myself reading "PREFACE"s of several books I was about to borrow from the library, I felt like I was getting old and serious (not in a bad sense though). This was something I would have hardly done before. Now I understand why books have such intro pages, and who reads/needs them.

I had to read them, because there was a pile of 20 books on "religion and evolutionary theory" (which will be one of the popular topics I'll be writing on here), I did not want to borrow all of them because I am not an alien with 8 arms, so I needed a quick summary of what a book was about. I also wanted to know the vision of the writer. (As a part of growing up, another thing I knew was that not all books were worth reading, and I was smarter than a lot of people. Obviously, though, I was still too young to be modest, but lets talk about it later).

So, call me boring, and skip this very first entry of this blog if you like, but for those out there who do not have the time trying to figure out what the blog is about and what kind of a person I am, here is my very first PREFACE (sounds like the first grey hair growing out of my skull doesn't it?)

I am a graduate student (as we speak) working on limb development and regeneration. I live in New Orleans - USA, I am an expert of evacuation from hurricanes -which is a crucial qualification as a grad student if you live here-. I am originally from Turkey (where there are maybe 3 camels, no pyramids, and craziest creationists on the planet).

I love research and science, and I want this blog to revolve (and evolve) around science. I want it to be more conceptual than just discussing some hard core scientific data, or reporting what's new in the literature (although I'll probably do these as well). The idea of having this blog originates from the fact that, -I believe- most people in biological sciences tend to get lost in their specific research area, and they (including me) forget to look at the bigger picture. We almost lose our imagination. I live with the paranoia that the answers to my questions are so obvious and easy, but I cannot see them because I am obsessing myself with details. I am hoping that you smart people out there will come up with these answers and eventually write my Ph.D. thesis for me.

The tag cloud of this blog might look like this in a year:

regeneration, limb development, evolutionary biology, creationism, Gallus gallus, Xenopus leavis, alternative model organisms, science and religion, science education, open source science, creativity, "I love progressive", "I am confused"...

Finally, the name of the blog comes from, well obviously one of the greatest movies ever made. But also, besides from being a suitable definition of my thoughts, Frizzled is a receptor of Wnt signaling pathway. When I started graduate school, the first project I worked on was how the Wnt signaling pathway regulated kidney development. So now, I have a thing for this pathway :)

I hope you'll enjoy reading this blog and will share your frizzled thoughts so we can poke each others brains, bounce and get ideas from each other. Science has to become more "open source". And I'll be brainwashing you all here in this blog about that as well.

Ok good people of Earth, it's on!

Photograph by A. Murat Eren.