Looking back at 2015

Another year's passed. I am getting older and this makes me sad. Here's the summary of my 2015:

1. I have read 10 books. You can see some of them here. I will write more reviews for the ones I am missing and hopefully read at least 10 more books in 2016.

The Violinist's Thumb
The Devil's Doctor
Linus Pauling: And the Chemistry of Life
The Kaiser's Chemists
The Time Machine and the Invisible Man

Up from Generality: How Inorganic Chemistry Finally Became a Respectable Field

Energy from Heaven and Earth

Half-Life: The Divided Life of Bruno Pontecorvo, Physicist or Spy

Python Pocket Reference

2. I have posted 75 articles that I had read using #chempaperaday tag. As I said in my very first post, these are not the only articles I have read in 2015. These are the ones I post here. I am not posting any article related to my research, thesis or anything closely related with our lab. You can be sure I've read at least 150 papers in addition to the ones I posted here. I save and annotate them in my EndNote folders.

3. I took some MOOC's and obtained some CS and Python certificates. I wrote some useful code. I built the homepage of my own website.

4. I solved my first crystal structure (with the help of the crystallographer).

5. Poster presentation at ACS Boston.

2016 goals?

1. Publish 3 papers. 

2. Read at least 10 books.

3. Learn Flask. 

4. Get Data Science certificates. 

5. Build a web app.

6. Finish building the website.

Hopefully, everything will be much better in 2016! 

Happy new year!

Book: Regenesis: How Synthetic Biology Will Reinvent Nature and Ourselves

George Church is a great mind and scientist. I had the chance to listen to his talk in Museum of Science last year. So, when I saw the book by him, I didn't even hesitate one second. I knew it would be a great read. After reading it, I can say I was absolutely right. Whether you like biology or not, whether you know some biology or not, you should read the book. It is not only a book about synthetic biology and the future of it, it is also about humanity, the fate of humans and our society.

"Imagine a future in which human beings have become immune to all viruses, in which bacteria can custom-produce everyday items, like a drinking cup, or generate enough electricity to end oil dependency. Building a house would entail no more work than planting a seed in the ground. These scenarios may seem far-fetched, but pioneering geneticist George Church and science writer Ed Regis show that synthetic biology is bringing us ever closer to making such visions a reality. In Regenesis, Church and Regis explore the possibilities—and perils—of the emerging field of synthetic biology. Synthetic biology, in which living organisms are selectively altered by modifying substantial portions of their genomes, allows for the creation of entirely new species of organisms. Until now, nature has been the exclusive arbiter of life, death, and evolution; with synthetic biology, we now have the potential to write our own biological future. Indeed, as Church and Regis show, it even enables us to revisit crucial points in the evolution of life and, through synthetic biological techniques, choose different paths from those nature originally took. Such exploits will involve far more than just microbial tinkering. Full-blown genomic engineering will make possible incredible feats, from resurrecting woolly mammoths and other extinct organisms to creating mirror life forms with a molecular structure the opposite of our own. These technologies—far from the out-of-control nightmare depicted in science fiction—have the power to improve human and animal health, increase our intelligence, enhance our memory, and even extend our life span. A breathtaking look at the potential of this world-changing technology, Regenesis is nothing less than a guide to the future of life."

The above paragraph is straight from the Amazon webpage for the book. I had to quote it because I can't write anything better than that. It's an easy to read book so I am pretty sure anyone who has 3-4 hours on a weekend will easily finish reading it. You will not only learn how synthetic biology can change our future but also how important it has become in our lives without even realizing it. Moreover, if you want to be an entrepreneur in biotech there are tens of examples of them; how they were founded, how and why they succeeded (or didn't), the challenges and even future directions.

Before you look up for the definition of synthetic biology, let's see how George Church describes it:

"the science of selectively altering the genes of organisms to make them do things that they wouldn;t do in their original, natural, untouched state."

As usual, I have quotes :

"Creating a mirror world might give us a fresh lease on life, one free of disease and unwanted agricultural pest species."

"...species that are lowest in diversity are most vulnerable to extinction."

"Give me a selection, and I will change the world."

"Multicellularity tends to come with a hard consequence-you give up your immortality."

"...just as individuals respond differently to drugs and to pathogens, they also respond differently to information."

"What should we do? Doing nothing, or doing what is traditional or natural, is not even close to a recipe for survival. If we choose tomorrow to behave in a way that our primitive ancestors did, nearly all of our 7 billion humans will die."

Elitism

"Throughout my life, I have had a strong conscious and unconscious addiction to knowledge. Suppressing knowledge seems to me wrong and impractical. Obviously, knowledge can be used and misused. But, prevention of misuse, I firmly believe, must be kept separate from limitations on knowledge. Those believe that we are not yet ready for some knowledge consider themselves members of a world aristocracy that is ahead of everyone else in its value judgements. Some of the horrible events of the twentieth century may appear to justify their opinion. Nonetheless, I cannot help opposing aristocracy and elitism, whether they be an elite of nobility, race, money, morals, or even knowledge itself."

The quote above is from Edward Teller's Memoirs. 

Like him, I oppose any kind of "elitism." Today, I was thinking of people who consider themselves as smarter than other people based upon their education. Some people think a degree (especially an advanced degree) is a sign of intellectual capability. In fact, an advanced degree is just a degree that is earned mostly by hard work and sometimes even patience. A few exceptional people aside, most people just become highly professionalized in a certain field with an advanced degree. It does not show that are any smarter than a person without a degree. 

Update: #chempaperaday and other things...

It's been a very long time I haven't written any posts. Well, the Fall semester started and it's been incredibly busy. I teach two lab sections, grade papers, hold office hours, answer tons of emails from students (this was unexpected!), take my own courses and study for them AND do the assignments! I also try to keep my research alive and move on to further steps in my "projects." 

If anyone is wondering, #chempaperaday is still alive and I do read papers almost everyday. The problem is most of these papers are related with my research and I do not want to write about them. Obviously,  I am trying to make new compounds. So, just by following the papers I read, one might figure out what I am onto (more or less). That's why I will keep them to myself.

I have read other papers too. But, as I mentioned above I have been busy and trying to figure out my new life schedule. So, I couldn't really focus on the blog. Tens of different blog post topics and ideas have come to my mind while I was dealing with all those stuff. Now that I am more comfortable with my schedule and more organized, I will write posts more often. The next post is coming tonight!

Thanks if you are reading here.

Shopping for symmetry!

Symmetry is a part of life. In fact, it is really hard to find an object without any symmetry operations. I found some objects for you!

I miss my bike!

Due to the horrible weather around here and some technical problems, I still haven't started to ride my bike. I hope I can ride very soon.

"I  ride, I ride the winds that bring the rain
A creature of love and I can't be tamed"

 

Calm Before the Storm

It's an exciting night for me. Although I don't get excited often, this night is special. Tomorrow is officially the first day in grad school. So, my heart beats a little faster than it regularly does. I am not sure how many hours I will sleep (if I can sleep any).

I have always thought the best music was produced in 80's and 90's. OK, this one was released in 2000. But, it belongs to 90's for me!

The sky is so clear tonight;
It's so calm before the storm.
All the stars shine so bright
Like the world has been reborn.
I'm think I'm in a dream tonight.
It's still calm before the storm.
But I dream of rising light
A sign it's time to be reborn.

It's still calm before the storm.

Are you happy with your work?

I don't remember posting anything except chemistry here (I hope). But, this one deserves to be shared on this blog too. I have just seen this blog post on Brainpickings. I try not to read anything other than chemistry or science (and sci-fi and a little bit literature and a little bit of philosophy), but I couldn't help but reading this post and I saw several quotes that I can relate to my past and present life. I believe that you should quit your job if you are not happy with it. I can not see any excuses to keep working in the same job but not liking it. Maybe a few very extreme examples, but that's all. It's very simple. If you don't like what you are doing, just stop doing it. It's never too late.

You can easily translate some of these quotes into your research and science I think. So, I decided to write some of them here. By the way, I should mention that I have never read any of those "personal development" or "self-help" books. There is absolutely no chance that I will ever read one. I think you can only learn from experience (yours or somebody else's) in the life and quotes or autobiographies might be helpful too since they are usually directly related with experience. But, those books not! I will not discuss this with anyone. So, I am not planning to read the book in the article linked. But, I am glad I saw these quotes in the blogpost on Brainpickings:

“Life really begins when you have discovered that you can do anything you want.”

 "Much the same thing happens when you take a person and put him in a job which he does not like. He gets irritable in his groove. His duties soon become a monotonous routine that slowly dulls his senses."

"Whether you are flying the Atlantic or selling sausages or building a skyscraper or driving a truck, your greatest power comes from the fact that you want tremendously to do that very thing, and do it well."

 "The greatest satisfaction you can obtain from life is your pleasure in producing, in your own individual way, something of value to your fellowmen. That is creative living!"

"The next time you feel that you ‘haven’t the time’ to do what you really want to do, it may be worth-while for you to remember that you have as much time as anyone else — twenty-four hours a day. How you spend that twenty-four hours is really up to you."

How to Avoid Work: A 1949 Guide to Doing What You Love | 

Brain Pickings

 http://www.brainpickings.org/index.php/2012/12/14/how-to-avoid-work/

42nd Annual James R. Killian Jr. Faculty Achievement Award Lecture:Understanding and Improving Platinum Anticancer Drugs

If you have been following the blog for some time (or if you actually know me), you must know that I am also interested in metal based anticancer drugs. Today I attended Stephen Lippard's award lecture at MIT where he gave a talk about platinum anticancer drugs for 1.5 hours.

Here is the recognition for his work and award:

Stephen J. Lippard, who is widely acknowledged as one of the founders of the field of bioinorganic chemistry, is this year's recipient of MIT's James R. Killian Jr. Faculty Achievement Award.
Established in 1971 to honor MIT's 10th president, the Killian Award recognizes extraordinary professional achievements by an MIT faculty member.

In announcing this year's award at the May 15 faculty meeting, the award committee noted that Lippard's groundbreaking work has pushed back the frontiers of inorganic chemistry, while simultaneously paving the way for improvements in human health and the conquering of disease.

Lippard, the Arthur Amos Noyes Professor of Chemistry, has spent his career studying the role of inorganic molecules, especially metal ions and their complexes, in critical processes of biological systems. He has made pioneering contributions in understanding the mechanism of the cancer drug cisplatin and in designing new variants to combat drug resistance and side effects.

His research achievements include the preparation of synthetic models for metalloproteins; structural and mechanistic studies of iron-containing bacterial monooxygenases including soluble methane monooxygenase; and the invention of probes to elucidate the roles of mobile zinc and nitric oxide in biological signaling and disease. 

 Especially, he focused on one of his recent projects : Osmium complexes. I also think that he is equally interested in Pt(IV) complexes. It was great to see and listen to him again after ACS Dallas national meeting.

My ACS Dallas experience

Since this blog is also my diary, I thought it would be a good idea to write down the talks I have been to at ACS Dallas this year. 

First of all, it was the greatest experience I have had as an undergrad. I have seen so many great chemists and I had the chance to listen to some of them. Unfortunately, we left the meeting on Tuesday at noon, so, I missed many great talks. 

X-ray fluorescence imaging and metalloproteomics: Tying images of metals in cells to the proteins that bind them
Lydia Finney

Metal-halogen secondary bonding in iron(II), cobalt(II), and nickel(II) 2,6-dihalophenolate complexes: Insights into the substrate specificity of the hydroquinone dioxygenase PcpA
Timothy E Machonkin, Monica Boshart, Jeremy Schofield, Patrick L Holland, Dalia Rokhsana.

Phosphoryl transfer enzymes: Theoretical studies of native enzymes and ground-state and transition-state analogs
Charles Edwin Webster, Katherine N. Leigh, Roger G. Letterman, Nathan J. DeYonker.

Reversible pyranopterin cyclization in synthetic models of the molybdenum cofactor
Benjamin R. Williams, Sharon J. N. Burgmayer, Anna Kalinsky, Yichun Fu.

Nitric oxide reactivity of the site-differentiated cluster [Fe₄S₄(LS₃)L']²⁻
Eric Victor, Stephen J Lippard.

Bimetallic complexes of rhodium dibenzotetramethylaza[14]annulene ((tmtaa)Rh): Structure, reactivity, and thermodynamic studies
Bradford B Wayland, Gregory H Imler.

Synthetic analogs for reduced [2Fe-2S] cofactors and for Rieske centers Franc Meyer, Antonia Albers, Serhiy Demeshko, Sebastian Dechert, Eckhard Bill. Bioinorganic meets organometallic: A tetracarbene-oxoiron(IV) complex Franc Meyer, Steffen Meyer, Iris Klawitter, Serhiy Demeshko, Eckhard Bill, Oliver Krahe, Frank Neese Controlling catalytic processes through ligand design Robert H. Grubbs Catalytic additions of O-H, N-H and C-H bonds to alkenes John F Hartwig Reactivity of the coinage metals beyond electrophilic activation of n systems Didier Bourissou, Abderrahmane Amgoune, Maximilian Joost. Fixing nitrogen with iron complexes Jonas C Peters, John S Anderson, John Rittle, Sidney E Creutz. Redox non-innocent nacnac and pyridine-imine chelate complexes of first row metals Peter T Wolczanski, Valerie A Williams, Wesley D Morris, Brian M Lindley, Brian P Jacobs, Thomas R Cundari, Karsten Meyer. Design of new ancillary ligands with nitrogen and phosphorus donors Michael D. Fryzuk, Truman C. Wambach, Fraser Pick, Tatsuya Suzuki. Power curves of buried junction photoelectrochemical cells Daniel G Nocera Determining electronic configuration of diruthenium compounds: Coupling crystallography with magnetic studies Carlos A Murillo Small HOMO-LUMO energy gap favors the chemistry of low valent silicon and transition metals Herbert W. Roesky Phosphorus chemistry and Lewis acid catalysis Douglas W Stephan Werner complexes: A new class of chiral hydrogen bond donorcatalysts for enantioselective organic reactions John A Gladysz Nickel complexes of electron rich PCP pincer ligands: Bond activation and catalysis Warren Piers, Dmitry Gutsulyak, Javier Borau-Garcia, Etienne LaPierre, Masood Parvez. Tantalum and niobium methylidenes Daniel J Mindiola, Keith Searles. Anion complexation and sensing with organoantimony compounds Francois P. Gabbai Copper-oxygen intermediates relevant to metalloenzymes and other oxidation catalysts William Tolman Tuning of the first- and second-coordination spheres in nonheme iron complexes David P. Goldberg, Alison C. McQuilken, Sumit Sahu, Leland R. Widger. Shellfish are inorganic chemists: Characterization and synthetic mimics of marine biological adhesives Erik Alberts, Courtney Jenkins, Heather Meredith, Michael Johnston, Jessica Roman, Chelsey Del Grosso, Michael North, Natalie Hamada, Jonathan Wilker. DNA signaling among proteins with iron-sulfur clusters Jacqueline K Barton PS : I tried to fix the issues with the list, but I couldn't.

Update on Clayden's Organic Chemistry textbook "challenge"

As I mentioned in this post, I am trying to finish reading and understanding Clayden's organic chemistry textbook until the end of May 2014. Thanks to spring break, I was able to gain some more speed and today I have finished Chapter 26. Since there are 53 chapters, I thought it would be nice to write about my studies so far. 

Anyway, as you can understand from my blog's header and posts I am way more interested in inorganic chemistry than organic chemistry. But, organic chemistry knowledge is essential in inorganic chemistry too. Firstly, I want to design and synthesize ligands. In fact, I want to prepare a new AND useful ligand on my own. Without knowing the basics and details of organic chemistry, there is no way I can do this. Moreover, without organic chemistry, there is no way that I can even understand and appreciate the use/synthesis of some ligands that are already published. Having finished  Wade's textbook, I realized that I needed to learn more. Also, I know I am not so good at organic chemistry. So, I decided to be better at it with Clayden's.

First of all, my thoughts about the book mentioned in that post haven't changed. I am not an organic chemist, but as a student (the target reader of the book) I still find the book not organized for my educational purposes. It is very common to come across some reagent, reaction or even a functional group in the early chapters without learning anything about them first. Usually, there is a note saying that "...covered in Chapter X." When I compare it to my favorite organic chemistry textbook (Wade's), I still think this book doesn't follow the usual sequence (from simple to difficult). 

I did every single practice problem in the book. Most of the time, I really enjoyed the problems and I am planning to write some blogposts on some mechanisms. My favorite problems and examples are the ones that give or ask you the mechanisms of real drug syntheses. It's great to see that I can understand and design the same syntheses for some drugs. Organic chemistry is really cool! To my surprise, I was able to do ~70% of the problems without much effort. So, I am better than I had expected. Some problems that involve certain agents were really hard for me. Because, if you don't know which one to choose, you will have to go and seek help in tables or chapters. One thing I realized about myself is that I can make some educational guesses, but when it comes to mechanisms I sometimes choose wrong steps although I can draw the right product in the end. I think some problems have more than one routes, and sometimes I am just wrong but lucky. 

I have never done anything about protecting groups at the school, so Chapter 25 took me a while to understand. It's not hard but it was new to me.

Overall (26 chapters), this book is great and I am sure I will always use this book in my future career.

So, now I am ready to go to ACS Dallas and when I come back, I will go on studying. I also decided to read organic chemistry papers too. Maybe they will help me to pick up some tricks. Also I will be able to see more syntheses. Feel free to suggest me readings too.

By the way I did not give up #chempaperaday. In fact, I still read papers but the point of that challenge was that I had decided to read "extra" papers. Right now, I am only reading inorganic chemistry textbooks, books and publications. So, it won't be fair to post those papers.

Made Of Glass

This is how I feel now.

Life...

In case anyone is reading this blog, I just got caught up with life again. There are decisions to make and a road ahead. I need lots of thinking and planning.