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Archive for the ‘Random’ Category

roasted chestnuts = furfural

Posted by naturalproductman on December 15, 2014

C&E News had an interesting article on the scents of the season.

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Difference in media response

Posted by naturalproductman on December 10, 2014

I just thought I’d point some difference in responses between two recent retractions in Science vs. Nature.

There were two Nature papers recently retracted on stem cells from a group in RIKEN and it was all over the news in Japan.

On the other hand there was a Science paper recently retracted on a retro-“click” reaction reported by a group at the University of Texas, which was covered in C&E News.

Because I have been in both countries during the time these retractions occurred, I just thought I’d point out an interesting difference in response by the media (news coverage).

I remember being in Japan around January 2014 and turning on the news on the television and seeing a woman with a face full of tears at a press conference on almost every channel they showed the news. I wondered what it was about, and it was something about making mature cells into stem cells by treating them with acid. It was a big deal and a topic of discussion in probably every news show as well as of course your science news and blogs on the internet.

Meanwhile in the US, I don’t recall as much of the time when I heard about the Science retraction (looking back, it was around June 2014) but I remember seeing C&E News and other blogs (retractionwatch, pipeline corante) about the retraction in the US lab. The article was about reversing the click reaction (azide and alkyne coupling to make a triazole, and the paper was about doing the reverse reaction). I don’t think I have to be a science expert but it wasn’t as much of a big deal in the media – although still a serious debate about falsifying data and getting it published. I don’t remember seeing this story on the television.

I was just wondering, if the research was happening in the opposite countries (stem cell research in US and reverse click reaction in Japan), would a retro-click retraction of a Science paper be as big of a deal in Japan? And the other question: would a stem cell Nature paper retraction be as big of a deal in the US? Is it a difference between: (1) the importance of science in the media in the two countries, (2) the importance of the research areas (stem cell vs. basic science), (3) the genders of the lead authors (male vs. female), (4) a Science paper vs. 2 Nature papers, (5) a combination of all of the above, or (6) something else I did not mention?

Posted in Ethics, Random | 2 Comments »

Reminiscing about textbooks – top picks and why?

Posted by naturalproductman on November 26, 2014

Today I wanted to talk about the undergrad textbooks I had and highlight any interesting ones that stood out and why. Of course, these are all my subjective opinions and I am sure many people have their own favorites and reasons as well, so I invite any comments to talk about other opinions.

Inorganic Textbook:

Advanced Inorganic Chemistry by Huheey Keiter and Keiter was a great textbook. I remember going to the undergrad library and checking out the book on reserve and spending a few hours on Sunday just to read the book while I was taking my upper division inorganic chemistry class. What I liked about the book was that: it combined molecular orbital theory and practical applications (i.e. Tanabe Sugano diagram), it covered d-orbitals and had a good introduction to transition metal chemistry, which was a good introduction for any organometallic chemist. The problems in the end of each chapter were great.

There was some organometallic textbook by Hegedus as well, but I don’t recall too much theoretical explanations behind the different cross-couplings. But it is a good reference book to have if you want to be able to look up certain cross couplings.

Organic Textbook:

Organic Chemistry by G Marc Loudon was a good one for the straight chemist – the thing I liked about this book was that it flat out gave the explanations of concepts and in some parts of the book, it would have a little section for the practical application of the concept in biology. My memory of this book was that I would read it in the car during the summers just for fun.

Organic Chemistry by Vollhardt and Schore was another book that was pretty straightforward and easy to understand. I don’t recall the little sections that Loudon had though. I would also read this one in the car during summer for fun.

Organic Synthesis – The disconnection approach by Stuart Warren was a really nice book that was full of synthesis problems. I remember I went through that entire book of disconnections/retrosynthetic analyses over a two month period and after going through the entire book, I can safely say that I became a better synthetic chemist.

Physical Textbook:

Mcquarrie’s red Physical Chemistry textbook was pretty good – although I wasn’t too much of a math person in college because the multivariable calculus had given me nightmares. Sometimes it isn’t about the subject though, and it is more about the teacher. I think I just went to a fast paced undergrad competing with other top students. The classes were cutthroat and it was more of an environment where you would be left for scraps if you fell behind.

Biochemistry Textbook:

Lehninger’s book was good it had an online learning tool where you could go through some mini lessons on some topics.

To rank my top 3 books from my personal point of view, which reflects on my interests when I was younger: (1) Advanced inorganic, (2) Loudon’s organic, (3) Warren’s disconnection approach.

Posted in Random | 7 Comments »

Advice from Michael Doyle

Posted by naturalproductman on November 10, 2014

Michael Doyle gives advice about writing manuscripts in his ACIE profile article…basically he says to focus on the main points in the manuscript and all of the other details go to the supporting information. The intro persuades the reader to keep on reading. He started off his career as a professor at undergrad only institutions and moved to PhD ones and commented that at the undergrad only institutions, the resources are not as good but the students are top notch.

 

ACIE article

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Triphenylphosphine (oxide) removal solved!

Posted by naturalproductman on October 25, 2014

You might remember an older post on something about the difficulty in removing triphenylphosphine or triphenylphosphine oxide removal. But first, how about a brief background: why would someone use triphenylphosphine in the first place? Well I can think of several reasons:

(1) Baylis-Hilman reaction

(2) Any metal cross coupling reaction using palladium tetrakis triphenylphosphine catalyst

(3) Mitsunobu reaction

So my particular problem was using the palladium tetrakis reagent to remove an Alloc protecting group.

You can see the details of the solution in page S-104 in supporting information file. But basically in a nutshell, instead of using tetrakis, I used Pd(DBA)2 and trimethylphosphine (PMe3) as the ligand, which evaporates at 38 degrees celsius.

Posted in Methodology, Random | 2 Comments »

Chembiodraw 14.0 Downloading Problems on the Mac?

Posted by naturalproductman on August 9, 2014

Did anybody else have trouble downloading Chembiodraw 14.0 on their macs?

 

My Chembiodraw 13.0 site license expired so I tried to download the new version 14.0 on my mac, but ran into several problems. Every time I would contact the customer support by email or through their website, it would take a long time for a response. The best thing was to get them on the phone.

 

First you need to make sure you have version 10.9 operating system.

 

Even after getting version 10.9, I had trouble with installation of the program because there is some glitch when you download.  I was lucky enough to get a hold of someone when I called their Waltham Massachusetts phone number at 5:30 AM.

On Finder you have to go to the Users folder, then Shared folder, then Library folder, then Preferences folder.

 

Then under Get Info option after right clicking the preferences folder, you have to go to Sharing & Permission in the pop up window. Then you have to let everyone have Read & Write permission.

 

Seems like I am not the only one with this problem because it is under the FAQ section of cambridgesoft.

 

Hope this helps anyone with the time and headache I had.

 

 

 

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How long does it take to publish in ACIE?

Posted by naturalproductman on July 16, 2014

Ever wonder how long it takes to publish in ACIE?

 

Here’s an interesting article in Chimia that explains the process. Conclusion:  it takes about 13 days on average for a referee to review a submitted manuscript.

 

Chimia paper

Posted in Random | 1 Comment »

Problems with SENSATIONALIZING Science

Posted by naturalproductman on June 29, 2014

This is related to the previous post about the elevated impact factors that some journals have. I guess the effect of trying to publish in the big monster journals with impact factors over 30 is that you get people who want to publish there so their careers can sky rocket. As a result, these people may falsify data to convince people who are not familiar with proper control experiments to admit that the science was great.

Posted in Random | 4 Comments »

Random Discussion: Subjectivity of Journal Submissions

Posted by naturalproductman on June 28, 2014

Here’s an unusual thought here that I never really considered until recently but it is worth taking note:  why is Science, Nature, and Cell still such a high impact factor? Let me briefly explain the Science editorial process when they receive a paper. Step 1: Researcher submits a paper, editor office gets it. Step 2: Editor does a prescreen before even sending it to reviewers (real scientists) and determines if it is good enough to be in Science or not.

I read this rejection letter from one of the editors and it was stated in the last paragraph that:

“Papers are selected on the basis of discipline, novelty, and general significance, in addition to the usual criteria for publication in specialized journals. Therefore, our decision is not necessarily a reflection of the quality of your research but rather of our stringent space limitations.”

The paper didn’t make it through Step 2. I have a problem with Step 2. Reading the editor’s name this letter is affiliated to, one can do a pubmed search and find out if this person has a good enough background that is suitable to judge whether the paper is truly good enough for Science journal or not.

I can say that after looking at the background of the editor, they probably were not even qualified to understand that the paper was good enough. One can argue however that if it’s truly good science anybody could say that it is interesting. But from looking at today’s Science research articles that get published, I’m not really that impressed with the content. I mean yes, it is Science journal with an impact factor of over 30, but still, when the editor has a mere 11 publication (of them, none are in Science except for the editorial articles they have written), would you think that this person is qualified to judge if a paper is good enough for Science or not?

On the other hand, if you look at other journals, such as ACIE or JACS or Biochemistry or JBC. These journals actually have professors, who run their own labs and are still publishing as the editors. These are scientists who are doing research currently and are up to date with the exciting world of science.

Maybe this is just a bitter rant from someone who feels rejected, but still, I think I may have a point here. I do not mean to completely offend the qualifications of the editorial board of Science magazine but there is a big difference between these journals with impact factor over 30 and other top tier journals, which have editors, who run labs and are involved in actual experimentation and practicing actual science. I hope someone can enlighten me if I am incorrect.

 

 

 

 

 

 

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Academia vs. Industry

Posted by naturalproductman on May 17, 2014

Ever consider the pros and cons between academics and industry? Here’s a nice article from someone who had experience in both.

Plos article

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