1. Koichi Tanaka shared the Nobel Prize in Chemistry in 2002 for his contribution in the use of mass spectrometry to analyse biological macromolecules.
2. The unique thing about Tanaka is that he, unlike most Nobel laureates, did not have a Ph.D.. He also did not have formal training in chemistry, unlike most Nobelists. When he won the prize, his age was 43, considered very young given that most Chemistry laureates in the last two decades were considerably older and more experienced.
3. He graduated BS in Electrical Engineering, and worked for Shimadzu Corporation, a reknowned Japanese company that manufactures scientific instruments.
4. From his autobiography on www.nobel.se, one gets an impression that he was not a famous scientist prior to winning the Nobel. Nonetheless, the Nobel committee decided to acknowledge his contributions.
5. One also gets an impression that he never dreamed of winning the Nobel. To me, he seemed like a scientist in the purest sense: hardworking, creative, curious and dedicated to the intellectual knowledge.
6. Scientists are afterall humans, and sometimes seek recognition and fame in addition to the intellectual satisfaction. Koichi Tanaka appeared to be an exception.
7. Disclaimer: I have never met him, but I'd love it if I ever get the chance.
Monday, November 24, 2008
Thursday, November 6, 2008
Extraodinary Nobelists: Robert B Woodward.
1. R.B Woodward was, in my opinion, the smartest chemist of the 20th century. He won the 1965 Nobel Prize in Chemistry for bringing advancement to the field of organic synthesis.
2. He also co-authored with Geoffrey Wilkinson the seminal paper on the structure of ferrocene. Wilkinson went on to win the Nobel in 1973 (with Ernst Otto Fisher) for the work on ferrocene, but Woodward was left out. He complained, to no effect.
3. Woodward is also known for the Woodward-Hoffman rules, which were a unifying theory that governed a class of important reactions, the pericyclic reactions. Hoffman received a Nobel in 1980 (with Kenichi Fukui), but Woodward had passed away.
4. Woodward also worked on the cyclization of squalene oxide, the first step in the biosynthesis of cholesterol. His collaborator Konrad Bloch won the Nobel in Physiology in 1964.
2. He also co-authored with Geoffrey Wilkinson the seminal paper on the structure of ferrocene. Wilkinson went on to win the Nobel in 1973 (with Ernst Otto Fisher) for the work on ferrocene, but Woodward was left out. He complained, to no effect.
3. Woodward is also known for the Woodward-Hoffman rules, which were a unifying theory that governed a class of important reactions, the pericyclic reactions. Hoffman received a Nobel in 1980 (with Kenichi Fukui), but Woodward had passed away.
4. Woodward also worked on the cyclization of squalene oxide, the first step in the biosynthesis of cholesterol. His collaborator Konrad Bloch won the Nobel in Physiology in 1964.
Monday, October 6, 2008
Sexism in Science in the 80s: The case of Barbara McClintock
Barbara McClintock won the Nobel Prize in Medicine in 1983, but some historians compared her award to the Francois Jacob's and Jacques Monod's 1965 Nobel Prize in Medicine.
McClintock was awarded "for her discovery of mobile genetic elements", while Jacob and Monod (and Lwoff) were awarded "for their discoveries concerning genetic control of enzyme and virus synthesis"
Although McClintock's work were performed on maize and were published in the 1950s, while Jacob-Monod's work were performed on bacteria (which is academically more popular and important than maize) in the 1960s, the scientific community en masse began noticing the importance and relevance of McClintock's contribution only after Jacob-Monod's discovery. Some historians questioned why McClintock's work had to depend on Jacob-Monod's discovery to gain appreciation and acknowledgements, and suggested that McClintock was a victim of gender discrimination.
McClintock was inducted to the National Women Hall of Fame in 1986, and passed away in 1992 at the age of 90; she never married and never had any children. She was the biographic subject of several writings.
The info for this post were taken from Wikipedia (keyword Barbara McClintock) and the Nobel Foundation (www.nobel.se, keyword McClintock). McClintock's image is taken from the Nobel Foundation.
Ethics in Chemistry: Fradulent cases.
1. These are several actual cases that I can remember. The reader can google the keywords for additional info.
The case of Bengu Sezen vs Dalibor Sames.
The case of G.Buono, brought to light by Scott Denmark.
The case of Imanishi-Kari and David Baltimore.
Hwang Woo-Suk and the much publicized fraudulent cloning experiments.
2. There is a very good fictional story about a fraudulent scientist winning the Nobel Prize, entitled Cantor's Dilemma, written by Carl Djerassi. I recommend this to any interested readers.
3. I write this posting with the following point in mind: science is a noble profession, but scientists are after all humans. Some of them get seduced by the dark side, but most of them are good.
The case of Bengu Sezen vs Dalibor Sames.
The case of G.Buono, brought to light by Scott Denmark.
The case of Imanishi-Kari and David Baltimore.
Hwang Woo-Suk and the much publicized fraudulent cloning experiments.
2. There is a very good fictional story about a fraudulent scientist winning the Nobel Prize, entitled Cantor's Dilemma, written by Carl Djerassi. I recommend this to any interested readers.
3. I write this posting with the following point in mind: science is a noble profession, but scientists are after all humans. Some of them get seduced by the dark side, but most of them are good.
Sunday, October 5, 2008
Chemistry and Mathematics, reversibility, reproducibility, executability.
1. I am a chemist but along my academic journey, I learned some mathematics and simple programming. I love chemistry, but I don't hate mathematics.
2. Chemical operations are usually irreversible; mathematical operations, on the other hand are reversible.
3. Consider the operation of adding sugar to coffee as a representation of a chemical operation. If the chemist made an unintentional mistake and accidentally added salt instead of sugar, then that cup of coffee is pretty much irreversibly ruined, and there is pretty much little or no way to "fix" the mistake. Likewise in a chemical plant, if a mistake happens, then it might not be salvagable. Not all mistakes are unfixable, it all depends on the exact nature of the system.
4. In mathematics, most mistakes are reversible. If one accidentally entered the wrong number into an equation, he or she can simply click the "UNDO" button on his software, and correct his mistake. Even if there is no "UNDO" function, one can SAVE the mistake under a different filename, close the file, and RELOAD the original file.
5. In mathematics, operations are usually if not always reproducible. One can add two numbers 100 times and get the same result everytime. In chemistry, this is only true if a system has been fully optimized.
6. A mathematician wanting to test (execute) his idea usually needs only a computer, software, and access to the literature. An organic chemist wanting to execute (test) his idea needs the whole physical infrastructure-- ingredients, instruments and apparati.
7. The inherent features of chemistry that I described above-- irreversibility, reproducibility, and executability are also reasons that chemistry is unique. One such uniqueness is the possibility of unintentional discovery.
8. James Sumner made a careless irreversible mistake when he unintentionally left a flask of enzyme solution near the window during the winter of 1926, to unexpectedly find that the enzymes crystallized from solution. He went on to win the Chemistry Nobel Prize in 1946
8. Sir Alexander Fleming discovered penicillin, the world's first antibiotic, by accident. It saved the lifes of many Allied soldiers during World War II. The discovery of penicillin is a historical moment in medicine.
9. I write this post to highlight a point: there are two types of science. The first is very logical, reproducible, reversible, predictable and computable. Mathematics and computer programmming belong to this class. The scientists in this group are theoreticians, and deal mostly with ideas and theories.
10. The second type is what I call wet science: where the scientist deal with the physical tangible things. The scientists in this group are experimentalists. They are also logical, but they usually have an intuition about irreproducibility and unpredictability of what they do.
11. Interestingly enough, there is a branch of chemistry called computational chemistry aka theoretical chemistry where the chemist uses a computer to study and predict the behavior of chemicals.
2. Chemical operations are usually irreversible; mathematical operations, on the other hand are reversible.
3. Consider the operation of adding sugar to coffee as a representation of a chemical operation. If the chemist made an unintentional mistake and accidentally added salt instead of sugar, then that cup of coffee is pretty much irreversibly ruined, and there is pretty much little or no way to "fix" the mistake. Likewise in a chemical plant, if a mistake happens, then it might not be salvagable. Not all mistakes are unfixable, it all depends on the exact nature of the system.
4. In mathematics, most mistakes are reversible. If one accidentally entered the wrong number into an equation, he or she can simply click the "UNDO" button on his software, and correct his mistake. Even if there is no "UNDO" function, one can SAVE the mistake under a different filename, close the file, and RELOAD the original file.
5. In mathematics, operations are usually if not always reproducible. One can add two numbers 100 times and get the same result everytime. In chemistry, this is only true if a system has been fully optimized.
6. A mathematician wanting to test (execute) his idea usually needs only a computer, software, and access to the literature. An organic chemist wanting to execute (test) his idea needs the whole physical infrastructure-- ingredients, instruments and apparati.
7. The inherent features of chemistry that I described above-- irreversibility, reproducibility, and executability are also reasons that chemistry is unique. One such uniqueness is the possibility of unintentional discovery.
8. James Sumner made a careless irreversible mistake when he unintentionally left a flask of enzyme solution near the window during the winter of 1926, to unexpectedly find that the enzymes crystallized from solution. He went on to win the Chemistry Nobel Prize in 1946
8. Sir Alexander Fleming discovered penicillin, the world's first antibiotic, by accident. It saved the lifes of many Allied soldiers during World War II. The discovery of penicillin is a historical moment in medicine.
9. I write this post to highlight a point: there are two types of science. The first is very logical, reproducible, reversible, predictable and computable. Mathematics and computer programmming belong to this class. The scientists in this group are theoreticians, and deal mostly with ideas and theories.
10. The second type is what I call wet science: where the scientist deal with the physical tangible things. The scientists in this group are experimentalists. They are also logical, but they usually have an intuition about irreproducibility and unpredictability of what they do.
11. Interestingly enough, there is a branch of chemistry called computational chemistry aka theoretical chemistry where the chemist uses a computer to study and predict the behavior of chemicals.
Liquid Helium, NMR and Chemistry
1. Liquid Helium is a very useful material. It is the coldest substance on Earth (~5 Kelvin).
2. One of its uses is to cool superconducting cryomagnets.
3. Cryomagnets are used in Nuclear Magnetic Resonance (NMR) and Magnetic Resonance Imaging (MRI)
4. NMR is widely used in qualitative analysis. You can think of it as the chemist's "eye". Using NMR, we can "see" things, without it, we work in the dark.
5. For example, would you know the difference between regular sugar (sucrose), glucose, fructose and aspartame (an artificial sweetener)? If you were to use all five of your senses, would you know the difference?
6. This problem is quite easy if one knows NMR. Of course, chemists use NMR to tackle tougher problems, e.g. to solve the identity of a newly discovered, previously unknown formula of an experimental cancer drug.
7. Without NMR, life is very difficult for the chemist. Without liquid Helium, NMR is useless.
8. A friend once told me a story that the government of Pakistan was given an NMR machine for free in the 1980s. It was the country's first NMR instrument, and previously their chemists had to work in the "dark".
9. However, the NMR sat idly and was not used. The Pakistanis didn't have liquid Helium.
10. Most of us are familiar with Helium GAS, which is used in balloons. Helium GAS is a common industrial chemical, but LIQUID helium is quite troublesome. When shipped from the US to Asia, half of the liquid helium would have evaporated and escaped, according to the same friend.
11. Helium is very light. Once it escapes into the atmosphere, it would leave the planet into outerspace, as it is so light that the Earth's gravity couldn't hold it in the atmosphere. It is not a renewable resource.
12. Helium is obtained from mining. Natural gas sometimes contain a little bit of helium, besides methane and other petroleum gases. United States is the largest supplier of Helium in the world.
2. One of its uses is to cool superconducting cryomagnets.
3. Cryomagnets are used in Nuclear Magnetic Resonance (NMR) and Magnetic Resonance Imaging (MRI)
4. NMR is widely used in qualitative analysis. You can think of it as the chemist's "eye". Using NMR, we can "see" things, without it, we work in the dark.
5. For example, would you know the difference between regular sugar (sucrose), glucose, fructose and aspartame (an artificial sweetener)? If you were to use all five of your senses, would you know the difference?
6. This problem is quite easy if one knows NMR. Of course, chemists use NMR to tackle tougher problems, e.g. to solve the identity of a newly discovered, previously unknown formula of an experimental cancer drug.
7. Without NMR, life is very difficult for the chemist. Without liquid Helium, NMR is useless.
8. A friend once told me a story that the government of Pakistan was given an NMR machine for free in the 1980s. It was the country's first NMR instrument, and previously their chemists had to work in the "dark".
9. However, the NMR sat idly and was not used. The Pakistanis didn't have liquid Helium.
10. Most of us are familiar with Helium GAS, which is used in balloons. Helium GAS is a common industrial chemical, but LIQUID helium is quite troublesome. When shipped from the US to Asia, half of the liquid helium would have evaporated and escaped, according to the same friend.
11. Helium is very light. Once it escapes into the atmosphere, it would leave the planet into outerspace, as it is so light that the Earth's gravity couldn't hold it in the atmosphere. It is not a renewable resource.
12. Helium is obtained from mining. Natural gas sometimes contain a little bit of helium, besides methane and other petroleum gases. United States is the largest supplier of Helium in the world.
Breast cancer has a cure, but...[the story of taxol and taxus brevifolia]
1. I assume the reader knows what breast cancer is.
2. Taxol (also known as paclitaxel) is a chemical compound, a drug that is effective in treating breast cancer. It can be found and isolated from the bark of the pacific yew tree Taxus Brevifolia. Bristol Myers Squibb once held the patent rights of Taxol, but I believe their rights are now expired. The National Institute of Health has a page for Taxol.
3. Here's the problem: there are not enough yew trees to supply enough Taxol to treat all the cancer patients. Even if there are enough trees, the monetary cost of the drug could be prohibitively high. And even if the cost if affordable, how do we replenish all the trees once we use them up? Taxus Brevefolia takes a long time (20 yrs) to mature.
4. There was an attempt to solve this problem: to synthesize Taxol by chemical means rather than to isolate it from the tree. In order to be able to this, the scientists need to know the molecular formula (structure) of Taxol in order to design a synthetic pathway.
5. We know the molecular formula of Taxol. It was solved by Mansukh Wani and Monroe Wall from the Research Triangle Institute in North Carolina. It was painstaking work, and the formula is shown.
6. In the 90s, research groups around the world have tried and succeeded in making Taxol. However, after spending tens of millions of dollars, they could only make miligram quantities. The public needs hundreds of grams or kilograms of Taxol.
7. It is very difficult to scale-up a miligram production system to a kilogram system. As an analogy, if you can make a one-foot diameter pizza, would you be able to easily make a one-thousand-feet diameter pizza? Even if your oven is that big, there are other complications: the middle of the pizza will be undercooked, while the side will be overcooked.
8. I write this post to highlight the following point: it is one challenge to discover a cure, it is another challenge to manufacture kilograms of material once the cure has been discovered. Life is difficult (and therefore meaningful) for scientists.
9. The first challenge is tackled by a multidiscplinary group of chemists, biochemists, pharmacists, medical doctors, biologists, etc. The second challenge is tackled by chemists, chemical engineers, mechanical engineers, etc. Collaboration is important, and funding is also important. If the task is undertaken by a private company, then profitability is an important factor.
10. Back to breast cancer. So what are we going to do about it? I'm not an expert on cancer, I'm not an MD. If you suspect that you or somebody you know have breast cancer, please seek advice from a physician. If you would like to know more about breast cancer, a good place to start is the Susan Komen site.
11. Back to Taxol. There are small companies out there growing Taxus aggresively to produce more Taxol. The supply challenge continues to be tackled. Besides the technical challenges, these companies have to deal with profitablitiy issues as well. One such company is Natural Pharmaceuticals Inc., which I'm not affiliated to in any way.
12. Curing cancer is not an easy task. At least now you know some of the challenges faced by the scientist working in this area.
Five hundred years, all for one breakthrough.
Q1: How long did it take to invent an aeroplane?
SYC: The way I look at it, it took us 500 years.
All inventions begin with an idea. In the case of airplanes, the first person to conceive the idea, by my account, was Leonardo Da Vinci. He must have been quite familiar with physical motions, as you can see from the image above that his design did bear some resemblance to the modern-day helicopter.
We should realize that Leonardo (1452-1519) did his work before Isaac Newton (1642-1726) conceptualized gravity. Although Leonardo didn't succeed, he did sow the seeds. I don't think Isaac Newton tried seriously to invent any flying machine, but his contributions (calculus, Newton's laws, gravity) served as the fundamentals in physics.
One of the many reasons that these two legendary scientists couldn't and didn't successfully invent the airplane is because they were ahead of their time, and they didn't have access to an important ingredient: fuel. "The modern history of petroleum began in 1846 with the discovery of the process of refining kerosene from coal by Nova Scotian Abraham Pineo Gesner" according to Wikipedia (keyword petroleum).
Aviation had a breakthroughs and entered a new era when the Wright brothers of North Carolina, USA, invented the first airplane in 1903.
I write this post to highlight a point: it took more than 500 years and more than one type of expertise to invent the airplane. Da Vinci and Newton were good physicts, but they weren't petroleum engineers. No one expected them to do petroleum refinement, just like we don't expect our modern-day physicts to do petroleum refinement. Besides fuel and physics, advancement in other areas of science were needed. For example, material science was needed for the invention of new lightweight material used in the construction of the airplane.
We humans once had a profound goal: to invent an airplane. We stretched our research abilities to achieve this goal. The generations of scientists prior to the Wright brothers must have had to endure many dissapointments and failures, but at the same time, they had to convince their sponsors to continue to fund them despite their lack of breakthroughs. The funding agencies must have been equally frustrated because they kept sponsoring projects that never seemingly paid off.
In 2008, we are faced with ongoing or new scientific goals: to cure cancer, to further explore outerspace, to stop global warming, etc. While it is easy to define goals, it usually takes a long time to accomplish the goals. Scientists try hard, and I sometimes wonder if the present generation of scientists are ahead of their time (or whether we should be) in trying to solve the aforementioned challenges. If so, then like Leonardo, we will "seemingly" not accomplish any breakthroughs, but the future generations will look back and thank us for sowing the seeds. At the meantime, the present generation will keep having difficulties convincing funding agencies to fund us.
It took us 500 years to invent an airplane. If a group of scientists was to ask Congress for, say, one million, one billion, or one trillion dollars to fund an important project of which they can't promise a completion timeline, should congress support that goal? Would you if you're a member of the Congress?
What is cholesterol? What is it's physiological function? Should we care?
Question 1: What is cholesterol?
Question 2: How does it affect the human health?
Most laypersons would answer both questions together, and say "cholesterol is the thing that causes high blood pressure, heart disease, obesity, etc."
To me, the layperson has answered the 2nd question, but did not answer the 1st question. More specifically, the answer above answered the question "what is hypercholesterolemia".
For a chemist, the definition of cholesterol is something that can only be answered by drawing, and not by words. Therefore, according to any organic chemistry textbook, cholesterol is defined structurally as the image seen above.
Therefore,
Question 1: What is cholesterol?
SYC: See the picture above.
Question 2: How does it affect human health?
SYC: An excess of cholesterol causes hypercholesterolemia (heart disease, high blood pressure, etc.)
Consider a third question:
Question 3: What is the difference between bad-cholesterol and good-cholesterol?
The answer depends on whether one is asking a nutritionist or a chemist.
As a chemist, I would describe bad-cholesterol using drawing as [see the image above], and good-cholesterol as [see the image above], therefore, they are one and the same.
A nutritionist would answer differently. The following is answer is taken from Wikipedia.
LDL particles are often termed "bad cholesterol" because they have been linked to atheroma formation. On the other hand, high concentrations of functional HDL, which can remove cholesterol from cells and atheroma, offer protection and are sometimes referred to colloquially as "good cholesterol."
Finally,
Question 4: What can/should I do about my health/lifestyle to treat/prevent hypercholesterolemia?
SYC: I'm not a nutritionist. General knowledge suggests physical exercise and healthy diet. Contact your physician or nutritionist.
Sunday, September 28, 2008
Literature Update
http://pubs.acs.org/cgi-bin/abstract.cgi/joceah/asap/abs/jo8016296.html
Note: Cyclohexene to Benzene. Mild conditions.
Note: Cyclohexene to Benzene. Mild conditions.
Monday, September 22, 2008
Monday, September 8, 2008
Wednesday, August 27, 2008
Techniques
Molecular Structure from a Single NMR Experiment Kupče, E̅.; Freeman, R.J. Am. Chem. Soc.; (Article); 2008; 130(32); 10788-10792. DOI: 10.1021/ja8036492
HRMS Directly From TLC Slides. A Powerful Tool for Rapid Analysis of Organic Mixtures Smith, N. J.; Domin, M. A.; Scott, L. T.Org. Lett.; (Letter); 2008; 10(16); 3493-3496. DOI: 10.1021/ol8012759
HRMS Directly From TLC Slides. A Powerful Tool for Rapid Analysis of Organic Mixtures Smith, N. J.; Domin, M. A.; Scott, L. T.Org. Lett.; (Letter); 2008; 10(16); 3493-3496. DOI: 10.1021/ol8012759
Wednesday, August 20, 2008
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