Genetherapy

Archive for the ‘Chemistry’ Category

Ugg… what a pain.  The reaction I’m doing today produces a low molecular weight, light-sensitive ?,?-unsaturated ketone as a product.  It’s a derivative of methyl vinyl ketone.  Not only is it low-boiling, it also polymerizes upon standing in light.  Ugg…

Now, I’ve worked with light-sensitive reagents (like the iodomethane and methallyl iodide) before, so I’m comfortable turning off the light and covering the reaction with foil to keep out extraneous photons.  That’s not so bad, because when the reaction’s done, you can flip on the light to work up the reaction.

Not so when the product is light sensitive.  Gotta keep the light off.  Gotta extract in the dark.  Gotta dry the organic layer with foil around the flask.  Gotta rotovap in the dark with foil around the flask.  Worst of all, gotta run a column in the dark.  For that, I cut off some of the sides of a cardboard box and used them as a shield to block the light and holed myself up in the dark corner of my hood to run the column.  Then gotta rotovap the fractions corresponding to product in the dark in foil.  Take the mass in the dark…  Ugg.  Pain all around.  Oh yeah, I forgot I gotta keep the NMR samples in the dark while I acquire the spectra, too.

Plus, gotta keep the product away from light until I set up the next reaction (which is going on right now)… and that’s gotta be in the dark.  At least when this reaction’s done, I can turn the lights back on.

Fortunately, the first reaction worked quite well.  I ran two multi-gram reactions side by side in the dark and got quantitative yield on both.

So while I run off to find some vitamin D supplements, tell me what the most operationally painful experiment you’ve set up is.  I’m sure many of you have stories that make mine seem trivial.  What experiment’s the biggest pain to run?  I think any reaction involving FOOF (the most awesome, most onomatopoeic molecular formula evah) has to be up there.

I remember buying my first O-chem books back when I was attending DVC (Diablo Valley College), a not-so-little community college here in the Bay Area. At first I checked the bookstore and lost my lunch when I saw the price of the new books. The text was $215, the lab manual was another $70, and the solutions manual was $100. Unfortunately, a new edition had been released that year, so even though the professor said that we could use older editions, many of the problem sets wouldn’t match up, so we’d have to get the problems from our classmates. In the end, the cheapest and most convenient route was to go online and buy the international editions. Even after extending the method to all my other classes, I still paid almost $500 for books that semester. Now I attended DVC before California went belly-up, so my classes were still a great bargain at $18 a unit. Since I usually took ~19 units, my total tuition cost was around $350 a semester. The cost of the books were actually greater than my cost of tuition. The sad thing is, this wasn’t an unusual case. Luckily this wasn’t too much of a hardship for me; I had a job on campus and money saved up. However, I knew a lot of students for whom the beginning of the semester meant not eating lunch in order to save up gas money.

Now students have probably been complaining about textbooks since time immemorial. Aristotle probably complained that his scribe made spelling mistakes in his copy of The Republic. Most of the time our bellyaching is justified. Not only do textbooks cost a lot, but there is often a gross amount of errors in them. Everyone knows that the first time you find a caption or answer wrong, it makes the rest of the book suspect. Also, these errors give the publishers a reason to release a next edition…that never seems to fix even half of the errors. However, they do switch around problem numbers, add a few pages of new content, and possibly even rearrange chapters. So now the professors lesson and homework plan, that goes by chapter numbers, page numbers, and problem numbers, is moot. And the student is effectively forced to buy the new edition (price “adjusted for inflation”) or suffer some inconveniences. Most choose to simply buy the new edition since tracking down the old one can be difficult and you have to be quick. Also, sometimes bookstores won’t buy back the old edition so if you had it, and an edition switch occurred before you finished your course track, you are up the creek.

Some of these issues can be addressed with online textbooks. The idea of supplementing physical texts with online modules has been around and implemented by publishers for many years. However, I’ve yet to see a good entirely online chemistry textbook. The advantages of online texts are of many: accessible anywhere you get 3G or Wi-Fi and have your mobile device, interactive learning capabilities, easy distribution, instant update/revision, and low cost publishing (server fees). Of course this won’t necessarily result the publisher make more money, but at 4 billion (yea, you read that correctly, billion) dollars a year, the industry doesn’t really need much help.

The student, however, does. We need these online textbooks, not just to save our wallet, but also to help prevent being stuck with an expensive and lousy text for a year that does a poor job of explaining the material. That expensive O-Chem book I bought really was terrible and it forced my professor to do a lot of extra work in teaching us not to follow the book’s direction of simply memorizing 500 reactions, but to see the patterns and the underlying physical explanations. In the end, we learned from his powerpoints and I paid $215 for a glorified reference book.

Well, some people are pioneering an effort to create an “Open Access Textbook”. In a perfect example of “chem 2.0″, UC Davis Professor Delmar Larsen is the project director of the ChemWiki, a truly free online textbook written by everyone, for everyone. In an absolutely Herculean effort, the developers and Larsen (Mary Obrien, Ron Rusay, Brent Krueger, Michelle McCombs) are trying to create a free and complete, as in covering all branches, chemistry textbook using a community of students, faculty, and outside experts from around the world. Of course they aren’t there yet, and there is still a long way to go but hey, their text literally gets better everyday.

Now I know you probably have a lot of questions: what about correctness and plagiarism? Could such a thing ever be considered an Authority? What do the publishers say? Does anyone actually use the thing? Well, it just so happened that a couple of weeks ago, I was at Davis for the Borge fellowship visitation and I had a chance to talk with professor Larsen who agreed to answer some of these questions for me. In a couple of days, I’ll post the interview here. For now, I suggest you go and check out http://chemwiki.ucdavis.edu/ and browse not just through the core, but the wikitexts and community as well.

A student in a chicken suit gets tackled by organic chemistry lecturer Owen Priest at Northwestern University.

An excellent video on methane by the Periodic Table of Videos crew last month.
Safety Note: Samantha “Pants!” Tang is not wearing a lab coat, gloves, and her hair is not fully pulled back.

Also from the Periodic Table of Videos, Sam shows us the Traffic Lights reaction.
Safety Note: Sam does not wear gloves even while working with NaOH powder.
EH&S Note: Throws the solution down the sink.

Mitch

Photo: Techchee.com

This doesn’t exactly fit in with the direction I was planning on taking with the posts on space science, but a story on MSNBC.com on Wednesday got my attention.  The story discusses NASA’s long endeavor into the search for life outside of Earth.  It used to be called exobiology (which I find to be an awesome name), but is now referred to as astrobiology.

NASA has previously attempted to find life on Mars with the Viking program in the 1970s.  Probes were sent to Mars to look for life… Earth life, that is.  The tests the probes ran attempted to find life that would exist at physiological conditions on Earth, a supposition that perhaps seems silly in hindsight.

An option in line with NASA’s recent change in direction could have the potential to bring Martian samples back to Earth for another attempt to find life on Mars.  The program – still in theoretical infancy – would last some 3-4 years and could begin in 2018 with sending a joint US/European rover to Mars to collect samples.  In 2020, a return vessel would go to Mars, get the samples, and return.

The story talks about the potential hazards of bring unknown astrobiological samples to Earth and the need to handle them in the equivalent of a Biosafety Level 4 Lab.

Anyway, my point in bringing this up is to share with you a short story – a commentary, really – by one of my favorite science fiction writers ever: Isaac Asmiov.  Asimov (also a former biochemist at Boston University) developed the Three Laws of Robotics and is the author of the original robot series that inspired movies such as I, Robot and Bicentennial Man.  If you haven’t read any of his work, I highly recommend one of his collections of short stories, such as The Complete Robot.

The commentary you should read is titled “Not as We Know It: The Chemistry of Life” and outlines what NASA scientists should keep in mind: life outside of Earth probably won’t look like life on Earth.

(in talking about life on Jupiter): An objection that might, however, be raised against the whole concept of an ammonia background for life, rests on the fact that living organisms are made up of unstable compounds that react quickly, subtly and variously. The proteins that are so characteristic of life-as-we-know-it must consequently be on the edge of instability. A slight rise in temperature and they break down.

A drop in temperature, on the other hand, might make protein molecules too stable. At temperatures near the freezing point of water, many forms of non-warm-blooded life become sluggish indeed. In an ammonia environment with temperatures that are a hundred or so Centigrade degrees lower than the freezing point of water, would not chemical reactions become too slow to support life?

The answer is twofold. In the first place, why is “slow” to be considered “too slow?” Why might there not be forms of life that live at slow motion compared to ourselves? Plants do.

He continues on to describe, in his opinion, what life might look like under the natural conditions of the various planets.  What the background medium would have to be and what the life-sustaining molecules would have to look like.  A fascinating read and a must read, in my opinion.

I attended a Macintosh Users Group recently. (Yes, I am a Mac user.) This meeting was unusual. Natali Del Conte, a tech writer for CNet and CBS, was the featured speaker. She talked about being authentic, social networking, and how technology has changed how we get information. She argued that gone are the days that information is simply pushed to us and that Walter Cronkite is the most trusted name in news.

A detail I have come to think more about is what we know. I remember that stomach acid was thought to cause ulcers, but Marshall and Warren have received a Nobel prize for their discovery of the role of Heliobacter pylori and its role in peptic ulcers.

Mitch (Feb 08) and azmanam (Feb 02) have posted on congressional misunderstanding of science and false or poor science reporting, respectively, but I don’t think chemists are as cognizant of the accuracy or correctness of textbooks or peer reviewed papers. There have been a few cases in which errors have entered the chemistry world.

I wrote the the archivist at the Oregon State University Library inquiring about whether there was any correspondence regarding a paper Pauling published (there wasn’t). I wondered what the referees may have said.  Now, I have been thinking how this is like the comments to a blog post. One of the really interesting things about the new media, is errors can be pointed out. They can be argued and open to everyone.

I have been thinking about how our ideas of atomic theory have evolved. In doing so, I have been reading a fascinating series of transcripts from recordings deposited at the Center for History of Physics of the American Institute of Physics.

It was interesting that some people thought Niels Bohr had confused the literature with his papers. However, overall, what I liked was how these transcripts contained the personalities of the scientists, their interests, and in some cases their ideas (or biases) about topics being discussed. I felt these transcripts from leading scientists were like our modern internet (although generally without the details of the science).

Our modern internet has no rules. It can be difficult to sort out the wheat from the chaff. We need to learn who to follow and who to ignore. Peer reviewed journals only give the filtered result. The referees reports are confidential. Comments are not published except in blogs. Now that science is moving toward electronic publication, would a new model for scientific publication improve the scientific world?

Just to note that this is not unusual in chemistry. Organic Synthesis has long provided a kind of review for a select set of procedures. I don’t foresee H.C. Brown’s papers becoming ignored, but independent reports could prove useful. Similarly, critical steps to improving yields  would be helpful. You can find examples of this in the Organic Chemistry Forums.

Should online journals allow comments? Would it be useful? How could it be done? Would it be science?

Fathi Moussa

Lon Wilson

Last year I covered Khodakovskaya et al.’s paper regarding the benefits of growing tomatoes in carbon nanotubes (CNT).^[CB] At the time I was concerned with the potential health risks associated from eating carbon nanotubes, but today in ACS Nano my concerns are alleviated. A paper from Lon Wilson’s and Fathi Moussa’s research groups discusses the effects from administering oral doses of carbon nanotubes (concentration as high as 1g of CNT per kg body weight) to Swiss mice.^{[ACS Nano]} The authors summarize their work the best.

CNT materials did not induce any abnormalities in the pathological examination. Thus, under these conditions, the lowest lethal dose (LD_Lo) is greater than 1000 mg/kg b.w. in Swiss mice.

So feel free to eat all the CNTs you want in lab, assuming they are not functionalized, you do it only once, and you limit yourself to single walled carbon nanotubes. I think partly because the results of the oral administration of CNTs went without any interesting side effects to present, the authors also looked into what happens when you inject CNTs into the peritoneal cavity of mice.

The image on the left is the control while the image on the right is 14 days after injecting mice with CNTs at a concentration of 1g CNT per kg of mouse. Although it looks sickly, the mice injected with the high concentration of CNTs did not die. Well…, not from the CNTs anyways.

Link to paper: In Vivo Behavior of Large Doses of Ultrashort and Full-Length Single-Walled Carbon Nanotubes after Oral and Intraperitoneal Administration to Swiss Mice (ACS Nano)

Mitch

A graduate student at the University of Wisconsin-Madison suffered burns and the loss of their favorite chair due to a fire that was started in the lab. A small lab fire usually wouldn’t make for interesting news, but see if you can spot something strange in the redacted narrative from the Madison Fire Department.

E4 found dry chem extinguisher activated, smoke, dry chem created haze on fire floor. found burned cushion chair in stairwell that was pushed there from room where reportedly students were working with chemicals that were spilled on to a chair that then started on fire. students came up with the idea to use a dry chem extinguisher as well as push the burning chair down the hallway to the stair well. It was reported to us that (deleted) was one of the students who was already at the UW hosp being treated for burns to his hand. E4 saw no one on the fire floor upon arrival.

The student took a burning item out of the laboratory and put it in the stairwell. A follow up revealed the student was worried about other chemicals in the lab catching on fire, but to the best of my knowledge most laboratories are designed to contain a lab fire. If the fire had gotten further out of control and caught the hallway and stairwell on fire, Madison might be missing a building today.

For future reference young graduate students the correct method for dealing with a burning chair in lab is the following. Rush to the safety shower and turn the flow of water on, then with a non-flammable object push the chair under the shower. Do not transport flaming objects outside the lab!

The chemical that started the fire was ethanol. Apparently the student was cleaning a pipette with an open flame nearby. As the student was shaking the pipette dry, a few drops of ethanol landed onto the chair and caught on fire.

The fire department received the call at 11:17 pm.

More media coverage: UW student burned in lab fire (The Cap Times)

Mitch

A graduate student at the University of Washington suffered burns and the loss of his favorite chair due to a fire that was started in the lab. A small lab fire usually wouldn’t make for interesting news, but see if you can spot something weird in the redacted narrative from the Madison Fire Department.

E4 found dry chem extinguisher activated, smoke, dry chem created haze on fire floor. found burned cushion chair in stairwell that was pushed there from room where reportedly students were working with chemicals that were spilled on to a chair that then started on fire. students came up with the idea to use a dry chem extinguisher as well as push the burning chair down the hallway to the stair well. It was reported to us that (deleted) was one of the students who was already at the UW hosp being treated for burns to his hand. E4 saw no one on the fire floor upon arrival.

The student took a burning item out of the laboratory and put it in the stairwell. A follow up revealed the student was worried about other chemicals in the lab catching on fire, but to the best of my knowledge most laboratories are designed to contain a lab fire. If the fire had gotten further out of control and caught the hallway and stairwell on fire, Madison might be missing a building today.

For future reference young graduate students the correct method of dealing with a burning chair in lab is the following. Run to the safety shower and turn on the flow of water, then with a non-flammable object push the chair under the shower. Do not transport flaming objects outside the lab!

The chemical that started the fire was ethanol. Apparently they were cleaning a pipette with an open flame nearby. As the student was shaking the pipette dry, a few few drops of ethanol landed onto the chair and caught on fire.

The fire occurred at 11:17 pm.

More media coverage from The Cap Times: UW student burned in lab fire

Mitch

I was jealous when I saw Joel write about his boss using his iPhone’s light source for experiments (finally, a really useful science iphone app). I knew I had to one-up him for no other reason then I am a Google Android user. Below is a video of an app I made; the app will scroll through the visible spectrum. In the video the glass contains red wine.

During the video you can see the wine absorbing blue light when the camera pans over the glass for the first time. Next time it pans over the red wine the light is green and still not transparent, but as the light was turning yellow the solution became more transparent. By the end, the light was red and it transmitted through the wine just fine.

If I had an other Android phone on hand I probably could have made a decent visible spectrometer from this setup.

Mitch

Suspect in UAH shooting – credit Huntsville Times, Dave Dieter

News broke this afternoon that there was a shooting at the University of Alabama in Huntsville’s Shelby Hall. It took me a while to find that this is (among other things) the home of UAH’s chemistry department. While CNN hasn’t filled in the details, the Huntsville Times already has reported that biology Professor Amy Bishop was taken into custody and her husband has been detained for the deaths of 3 faculty members and the wounding of 3 others.

While stunning and tragic, this would not have rated a post except for the alleged reason for the shooting: denial of tenure. According to the New York Times:

WAFF, the NBC affiliate in Huntsville, quoted university officials as saying the professor began shooting after learning at the faculty meeting that she was being denied tenure…

Dr. Bishop had told acquaintances recently that she was worried about getting tenure, said a business associate who met her at a business technology open house at the end of January and asked not to be named because of the close-knit nature of the science community in Huntsville. “She began to talk about her problems getting tenure in a very forceful and animated way, saying it was unfair,” the associate said, referring to a conversation in which she blamed specific colleagues for her problems.

Wow. Denial of tenure must be crushing for an assistant professor, especially since the process must seem protracted, random and unfair (at times). The really surprising detail is that (allegedly) she brought a gun; that’s an indication of a willingness to use violence and a certain level of forethought as to the potential outcome of the meeting. (CORRECTED: see update below.) Academic science is high pressure indeed.

My (our) thoughts are with the families of the victims.

UPDATE: From the AP:

University spokesman Ray Garner said Saturday that the professor, Amy Bishop, had been informed months ago that she would not be granted tenure. He said the faculty meeting where she is accused of gunning down colleagues was not called to discuss tenure.

Cassandra Fraser

Recently, Cassandra Fraser’s group reported on a very cool property, reversible mechanochromic luminescence, observed in an easy to make material.^[JACS] The molecule of interest is the difluoroboron complex of avobenzone (BF₂AVB), that UV absorbing molecule in your sunscreen minus the boron and fluorines.

In broad general language, mechanochromic luminescence describes the ability of some materials to change colors after scratching under UV light. The image below shows BF₂AVB coated on weighing paper (A), a cotton swab is used to write “Light” (B), the surface is hit with a heat-gun (C), the surface is ready to be written on again with a cotton swab (D).

The image brings up all kinds of creative ways to write secret messages, especially as the letters will fade over time even without using a heat gun. But before the CIA intelligence wonks in the audience get ahead of themselves the material doesn’t seem to be completely reversible at room temperature without annealing. Cassandra Fraser has corrected me, apparently the wording of the paper was just awkward to my ear, the material is fully reversible at room temperature.

…even a small mechanical perturbation, such as a slight touch with the tip of a cotton swab, changed the green-blue BF2AVB film emission to yellow. The yellow emission gradually reverted back to green again at room temperature, with much faster recovery at elevated temperature. The written regions were no longer readable after annealing.

The field has, in short order, gotten tantalizingly close to the goal of a 100% reversible mechanochromic luminescent material at room temperature. Congrats!

Link to article: Polymorphism and Reversible Mechanochromic Luminescence for Solid-State Difluoroboron Avobenzone

Sam covered one of the first entrants to reversible mechanochromic luminescence a year ago: reversible mechanochromic luminescence is cool

Mitch

Cassandra Fraser

Recently, Cassandra Fraser’s group reported on a very cool property, reversible mechanochromic luminescence, observed in an easy to make material.^[JACS] The molecule of interest is the difluoroboron complex of avobenzone (BF₂AVB), that UV absorbing molecule in your sunscreen minus the boron and fluorines.

In broad general language, mechanochromic luminescence describes the ability of some materials to change colors after scratching under UV light. The image below shows BF₂AVB coated on weighing paper (A), a cotton swab is used to write “Light” (B), the surface is hit with a heat-gun (C), the surface is ready to be written on again with a cotton swab (D).

The image brings up all kinds of creative ways to write secret messages, especially as the letters will fade over time even without using a heat gun. But before the CIA intelligence wonks in the audience get ahead of themselves the material doesn’t seem to be completely reversible at room temperature without annealing.

The yellow emission gradually reverted back to green again at room temperature, with much faster recovery at elevated temperature. The written regions were no longer readable after annealing.

The field has, in short order, gotten tantalizingly close to a 100% reversible mechanochromic luminescent material at room temperature.

Link to article: Polymorphism and Reversible Mechanochromic Luminescence for Solid-State Difluoroboron Avobenzone

Sam covered one of the first entrants to reversible mechanochromic luminescence a year ago: reversible mechanochromic luminescence is cool

Mitch

(From Left to Right)
Dr. David Keith
Dr. Philip Rasch
Dr. Klaus Lackner
Dr. Robert Jackson

Geoengineering is a wonderful example of taboo science. Most people would fall within 2 camps. Camp 1 considers geoengineering with disdain as it mucks with the natural environment. Camp 2 probably wouldn’t want their government involved in planetary climate control. With those entrenched camps where do scientists fit in?

Scientists were called as witnesses before The House Subcommittee on Energy & Environment last week in regards to geoengineering. The witnesses invited were…

• Klaus Lackner (Geophysics,
  Earth and Environmental Engineering): Covering CO₂ sequestration
• Robert Jackson (Biology): Covering Biological and Land Strategies to lower CO₂
• Philip Rasch(Atmospheric Science but a chemist by training): Calling for a Manhattan project type approach to researching geoengineering
• David Keith (Chemical and Petroleum Engineering): Mainly advocating that some sort of global policy towards geoengineering needs to be developed. The most sane and coherent witness; scientists don’t usually fair well before politicians.

So why care about taboo science? The simple matter is that it would cost 1-2 billion a year to return the planet to pre-industrial levels of temperature, assuming they use cheap sulphates to do the job. This means any number of nations, frankly any wealthy cohort of industrialists, can take climate control into their own hands.

Since geoengineering is a delicate subject to broach to the public, transparency is crucial and wasn’t loss on the chairman Brian Baird (D-WA). Congressman Baird mentions how some citizens believe their government is placing psychotropic drugs in jet fuels, the so called chemtrails and remarked “…legitimate scientific research [in geoengineering] must not get tied up in these kind of things.”

However, all the scientists were taken aback by Randy Neugebauer (R-TX), my favorite exchange was the following.

Randy Neugebauer (R-TX)

Randy Neugebauer, “What percent of the atmosphere is CO₂?”
Scientist, “390 parts per million”.
Randy Neugebauer, “Less than one tenth of one percent…This tiny minuscule amount…[can't] be more important factor in our climate than solar activity”.

I’m not even sure where to begin to broach such a deep misunderstanding of climate change. I would have mentioned to Mr. Neugebauer that he would be dead if that minuscule amount of CO₂ was removed from the atmosphere, as all plants would die followed by animals in short order. The concept of small amounts having huge impacts in large dynamic systems is an important lesson to teach, even more so to do it dexterously. These types of exchanges went on for some time. I’m left wondering why Randy Neugebauer is even on the Subcommittee on Energy & Environment in the first place.

The ranking Republican, Bob Inglis (R-SC), had this to say in his last remarks, “I believe in a basic role of government is to do basic research, its an important function that we do.” It is nice to know that basic science research is appreciated by both sides, even though there is always a rogue member in every committee.

Press Release: Subcommittee Examines Geoengineering Strategies and Hazards

Mitch

I first heard this on National Public Radio and then I searched for it. In short, David Ehre, Etay Lavert, Meir Lahav, and Igor Lubomirsky report in Science, (Water Freezes Differently on Positively and Negatively Charged Surfaces of Pyroelectric Materials) water freezes at a lower temperature (-18°C) on the negatively charged side of a lithium tantalate plate with a strontium titanate film than on the positive side (-7°C, and -12°C uncharged).

Is this unique or is this a manifestation of something in our standard introductory organic chemistry textbooks? I thought it was the latter. Let me explain how.

For the purpose of thinking about this problem, let us assume the metal surface is simply a flat charged surface, without contour. If the surface has a negative charge, then the water should be attracted like a flagpole. One hydrogen should be anchored to the surface of the metal at right angles and the other hydrogen could spin about that axis with the flag hydrogen at 105°. It should not be surprising that this configuration should not be as good of a surface as one with greater rigidity.

If we compare with the positively charged surface, then both pairs of non-bonded electrons should be anchored to the surface and locking the hydrogens in a fixed position. This should limit the degrees of freedom and enable crystal growth.

(From Left to Right)
Dr. David Keith
Dr. Philip Rasch
Dr. Klaus Lackner
Dr. Robert Jackson

Geoengineering is a wonderful example of taboo science. Most people would fall within 2 camps. Camp 1 considers geoengineering with disdain as it mucks with the natural environment. Camp 2 probably wouldn’t want their government involved in planetary climate control. With those entrenched camps where do scientists fit in?

Scientists were called as witnesses before The House Subcommittee on Energy & Environment last week in regards to geoengineering. The witnesses invited were…

• Klaus Lackner (Geophysics,
  Earth and Environmental Engineering): Covering CO₂ sequestration
• Robert Jackson (Biology): Covering Biological and Land Strategies to lower CO₂
• Philip Rasch(Atmospheric Science but a chemist by training): Calling for a Manhattan project type approach to researching geoengineering
• David Keith (Department of Chemical and Petroleum Engineering): Mainly advocating that some sort of global policy towards geoengineering needs to be developed. The most sane and coherent witness; scientists don’t usually fair well before politicians.

So why care about taboo science? The simple matter is that it would cost 1-2 billion a year to return the planet to pre-industrial levels of temperature, assuming they use cheap sulphates to do the job. This means any number of nations, frankly any wealthy enough cohort of industrialists, can take climate control into their own hands.

Since geoengineering is a delicate subject to broach to the public, transparency is crucial and wasn’t loss on the chairman Brian Baird (D-WA). Congressman Baird mentions how some citizens believe their government is placing psychotropic drugs in jet fuels, the so called chemtrails and remarked “…legitimate scientific research [in geoengineering] must not get tied up in these kind of things.”

However, all the scientists were taken aback by Randy Neugebauer (R-TX), my favorite exchange was the following.

Randy Neugebauer (R-TX)

Randy Neugebauer, “What percent of the atmosphere is CO₂?”
Scientist, “390 parts per million”.
Randy Neugebauer, “This tiny minuscule amount…[can't] be more important factor in our climate than solar activity”.

I’m not even sure where to begin to broach such a deep misunderstanding of science and climate. I would have mentioned to Mr. Neugebauer that he would be dead if that minuscule amount of CO₂ was removed from the atmosphere, as all plants would die followed by animals in short order. The concept of small amounts having huge impacts in large dynamic systems is an important concept to convey, even more so to do it dexterously. These types of exchanges went on for some time. I’m left wondering why Randy Neugebauer is even on the Subcommittee on Energy & Environment in the first place.

The ranking Republican, Bob Inglis (R-SC), had this to say in his last remarks, “I believe in a basic role of government is to do basic research, its an important function that we do.” It is nice to know that basic science research is appreciated by both sides, even though there is always a rogue member in every committee.

Mitch

For those with an interest in journalism and time this summer ACS is offering a summer internship in the C&EN newsroom. Deadline is Feb 22nd.

Chemical & Engineering News, the weekly newsmagazine of the American Chemical Society, seeks an intern for our Science/Technology/Education department for the summer of 2010.

C&EN reports current events in the chemical enterprise, including recent advances in research, education, industry, funding, and regulatory policy. C&EN reaches all 154,000 members of the ACS each week, and its online edition receives more than 13 million page views per year.

The candidate should be a highly motivated student or recent graduate with demonstrated interest in science writing and at least a bachelor’s degree in chemistry or a related field. The intern will have a chance to write bylined news and feature stories for publication in C&EN. We offer a $1500 monthly stipend for three months. The intern ideally will be based in our Washington, DC, headquarters; however, exceptional candidates unable to relocate may be considered. Starting and ending dates are flexible.

Contact Amanda Yarnell for more information about this year’s internship.

Link: C&EN Internships

Update: There is also an associate editor position available.

Mitch

(See important update, below)

The Times of London yesterday ran a story that Jenny McCarthy needs to read (h/t HotAir.com).  The article details an investigation of the results of the 1998 paper in the Lancet medical journal which shows a link between thimerosal in MMR vaccines and autism.  The investigation concludes the author, Andrew Wakefield, manipulated data to show the link.

Confidential medical documents and interviews with witnesses have established that Andrew Wakefield manipulated patients’ data, which triggered fears that the MMR triple vaccine to protect against measles, mumps and rubella was linked to the condition.

The research … claimed that the families of eight out of 12 children attending a routine clinic at the hospital had blamed MMR for their autism, and said that problems came on within days of the jab. The team also claimed to have discovered a new inflammatory bowel disease underlying the children’s conditions.

However, our investigation … reveals that: In most of the 12 cases, the children’s ailments as described in The Lancet were different from their hospital and GP records. Although the research paper claimed that problems came on within days of the jab, in only one case did medical records suggest this was true, and in many of the cases medical concerns had been raised before the children were vaccinated. Hospital pathologists, looking for inflammatory bowel disease, reported in the majority of cases that the gut was normal. This was then reviewed and the Lancet paper showed them as abnormal.

How convincing was Dr. Wakefield’s article?  Vaccination rates in the UK dropped from 98% to below 80%.  Some 1350 cases of measles have been confirmed in the UK, a 2400% increase over the number of confirmed cases in 1998.

Besides the obvious implications of manipulated data, no one seemed too concerned that Dr. Wakefield’s sample in the 1998 paper included only 12 children.  Time after time after time, studies have tried to replicate Dr. Wakefield’s results.  Not surprisingly (anymore), no one was able to.  Yet, that doesn’t stop parents from receiving news time warning about vaccines, the CDC from needing to issue a statement on the safety of thimerosal, the HHS from issuing money from the vaccine injury fund (!), and major presidential candidates from telling town hall attendees that there is a “strong link” between thimerosal and autism.

I don’t even think this qualifies for an Ig Nobel award.  It’s just infuriating.

Update (2/2/10): Today, the Lancet Medical Journal officially retracted Dr. Wakefield’s original 1998 paper.  The retraction was the final domino to fall in officially discrediting the specious claim linking thimerosal and autism.  How long will it take to rid the vaccine-autism link from the minds of worried parents?  That’s a different question.  Hopefully, though, doctors can now use this to help persuade overly-worried parents that vaccines are indeed safe.

(From L to R)
Dr. Arun Majumdar
Dr. Chuck Vest
Dr. Anthony Atti
Mr. John Denniston
Dr. John Pierce

ARPA-E is one of the newest funding programs at the Department of Energy. It was authorized in 2007 with the passage of the America COMPETES Act, but was only funded when The American Recovery and Reinvestment Act of 2009 was passed with an initial $400 million. ARPA-E is unique in that its first Funding Opportunity Announcement (FOA) was kept broad and only asked for 8-page proposals for high-risk but high-reward “transformational” technologies. Yesterday (Wednesday) in the House Committee on Science and Technology ARPA-E was examined, the chairman for the hearing was Bart Gordon (D-TN).

Arun Majumdar, the current director for ARPA-E, gave several examples why federal funding is necessary for energy research and used a graph on worldwide shipments of solar photovoltaic cells to make his point that America is losing its edge in energy technologies.

Arun also gave some metrics on the ARPA-E awards. 3,700 concept papers were received. Only 340 were invited to write a full proposal. 37 projects were selected and $151 million was pegged for those projects. 45% went to small business, 35% went to educational institutions, and 20% to large industries. Also mentioned was the start of their Fellows Program for recent PhD students interested in energy/policy.

John Pierce, the vice president of DuPont Applied BioSciences, gave a statement that called for “external advisory panels” to guide the perspective of the ARPA-E agenda. Which sounds like something industry would want.

Link to more information on the hearing: Program to Foster Innovation in Energy Technologies Is Off to a Promising Start

Link to ARPA-E: Advanced Research Projects Agency – Energy

Mitch

(for other entries in the Chemistry in Space series, click here)

Who knew boiling a liquid was so complicated?  When you put a pot of water on the stove or heat your reaction-in-toluene solution in an oil bath several things happen.  The liquid closest to the heating element starts to get hot.  Convection circulates the hot liquid up and the cold liquid down due to the density differences of hot and cold liquids.  Eventually, the liquid near the heating element becomes hot enough to move into the vapor phase and bubbles start to form.  Buoyancy causes the bubbles to float to the surface and pop, while more convection continues to circulate the water.  Eventually, you get a rolling boil.

Everything changes in the microgravity environment of space.  Buoyancy and convection no longer play a role.  The heated fluids no longer circulate and the bubbles no longer naturally rise to the surface.  So what happens when you try to heat a liquid to boil in microgravity?  Astronauts tested this during the course of several space shuttle missions during the 1990s.  They arrived at some very interesting conclusions.

First, the liquid nearest the heating element starts to get hot, just as it does on Earth.  But it doesn’t rise and circulate due to convection.  It just gets hotter and stays next to the heating element.  It eventually gets hot enough to move into the vapor phase, just as it does on Earth, but the bubbles don’t rise to the surface and pop.  Instead, they stay next to the heating element and coalesce into one giant bubble.  Eventually, the size of the bubble becomes larger than the heating element and there is no longer any liquid in contact with the heating element.  This insulates the liquid from the heating element and leads to a “dry out” where there is no more boiling and the temperature of the heating element “begins to soar.”

(click on the image to go to the NASA page describing Zero G Boiling and to see an awesome movie of boiling in action)

All of this is predicted by theory, but it’s nice to have the chance to do some of those proof of principle experiments for the first time ever.  It reminds me of what some of the pioneers of science must have felt when working out some of the fundamental theories of chemistry and physics that we don’t even realize we take for granted today.

An interesting variation of this experiment was conducted impromptu by an astronaut on the International Space Station in 2003.  Don Pettit* was performing repair operations using a soldering iron.  He decided to put a few milliliters of water on the hot surface.  The water droplet formed a blob around the soldering iron and kinda wobbled there.  As expected, the water heated up and began to boil.  Surprisingly, though, this time the boiling looked much similar to boiling on Earth.

My working theory is the small amount of water and the inherent jostling of the system (the soldering iron looks like it was held by hand in front of the camera) caused enough motion in the water to move the bubbles around.  The bubbles could bump into each other and coalesce.  The size of the bubbles quickly reached the surface (unlike the bulk boiling experiment described above) and were allowed to pop.  Thus, it is by accident, in my opinion, that the boiling looks like it would on Earth.  It’d be interesting to repeat the experiment with the soldering iron held steady by vice grips or something.

(click on the image to go to the NASA page on the soldering iron boiling experiment and to see an awesome movie of this microgravity microboiling in action)

Here’s an overview page of boiling in space.
Here’s the NASA page on the 1990s boiling experiments.
Here’s the NASA page on the impromptu soldering iron boiling experiment.

*Also inventor of the super awesome zero-g coffee mug.

Carl “Dan” Fish, a worker at the Dupont plant in Belle West Virginia, died this past Sunday due to phosgene exposure. Only scant details about the incident have been released by DuPont thus far, but this is what we have been told.

On Saturday afternoon a site employee was exposed to Phosgene from a leaking transfer hose. The hose was not in service when the leak occurred but did contain a small amount residual Phosgene from an earlier use. The employee was transported to the hospital by the Kanawha County Ambulance Authority for treatment and observation as part of the standard protocol for exposure to this material.

Unlike previous chemistry related deaths this has gotten the attention of Washington. Senator Rockefeller (D-WV) released a statement Monday, Rockefeller Statement on Incidents at DuPont Chemical Plant, calling for a thorough investigation of the incident. Since Rockefeller is the chairman of the Senate Commerce Committee, the committee with oversight of the facility, and being a senator from West Virginia Dupont can look forward to being under intense scrutiny.

Update 1: The senior senator from West Virginia, Robert Byrd (D-WV), has released his own statement: Byrd statement on incident at DuPont chemical plant

Update 2: It took DuPont 20 minutes to identify the chemical exposure to Metro 911 services after the initial call for an ambulance: DuPont calls: ‘Can you give me some more information?’
Audio Files: 1st Call from Dupont Advising Medical Emergency, Cpt Wallace Contacting Dupont for more info (The Charleston Gazette)

Update 3: The U.S. Chemical Safety Board voted to investigate the incident that caused a braided steel hose connected to a one-ton capacity phosgene tank to suddenly rupture. The lead investigator will be Johnnie Banks and the CSB team will arrive Tuesday at DuPont: Board Votes to Initiate Investigation on Accidents at DuPont Chemical Facility in Belle, West Virginia (CSB)

Mitch (Our best thoughts from everyone at Chemistry Blog goes to his family and friends at this time)

SPIE an international society focused on all things light-based is having their big photonics conference in San Francisco this week. I had the opportunity to sit in the professional development speaker series and thought I would share some of the speakers’ insights.

Andrea Armani a 2nd year assistant professor at USC in chemical engineering spook on Leading a Well-Adjusted Research Group. She stated that she gives her students Fridays off from their main research endeavor and allows them to tackle any question they want; which is a very new generation Google-esque approach to student mentoring. She also explicitly establishes that a particular older graduate student will mentor a younger graduate student in the lab, so that the younger student will always have someone to answer their questions. The most interesting story told was how she deftly managed to diffuse the amorous advances of a student, a very awkward position indeed, and a situation not covered in the manual.

Thomas Tongue gave a talk on Peaks and Pitfalls of Professional Communication, but it mainly focused on how to deliver what he calls The Elevator Pitch. He says that in scenarios where you would like to collaborate with an other scientist, or a scenario where you feel you could contribute to a team in the company if only you were placed on it, that you essentially have 60-90 s with that collaborator or vice-president to make your best pitch. The pitch has to be clear, compelling, conceptual (not bogged down in technical jargon), concrete (a specific quantifiable metric should be given), consistent (story should flow well), customized for the the target audience, and always given in a conversational tone. His advice is similar in nature to what Peggy Klaus advocates in her book The Art of Tooting Your Own Horn without Blowing It but she terms them brag-a-logs. Peggy Klaus’s book is a good read for those interested in professional development and especially for those that have problems vocalizing their contributions.

I am glad SPIE offered these talks, as it can be difficult to extract this kind of information from PIs.

Mitch

Stephen J. Ebbens

Jonathan Howse

The current state of the art in nanopropulsion devices was recently reviewed by Ebbens and Howse in an article last Friday.^[SoftMatter] A short summary of the nano- systems is presented below with video action shots when I could find them.

The Whitesides

Catalyst: Pt
Fuel: H₂O₂
Propulsion: Bubble propulsion
Terrain: Aqueous meniscus
Max Speed: 2 cm/s
Mitch’s Name: The Karl Benz (since it was the first)
Article: Autonomous Movement and Self-Assembly

The Sen-Mallouk-Crespi

Catalyst: Pt
Fuel: H₂O₂
Propulsion: Self electrophoresis/Interfacial tension
Terrain: Settled near boundary in aqueous solution
Max Speed: 6.6 um/s
Mitch’s Names: The Ford Mustang of nanopropulsion. (It is a hot rod, get it?)
Article: Catalytic Nanomotors: Autonomous Movement of Striped Nanorods

The Jones-Golestanian

Catalyst: Pt
Fuel: H₂O₂
Propulsion: Pure self diffusiophoresis
Terrain: Free aqueous solution
Max Speed: 3um/s
Mitch’s Name: The Volkswagen Beetle
Article: Self-Motile Colloidal Particles: From Directed Propulsion to Random Walk

The Mano-Heller

Catalyst: Glucose oxidase and Biliruben oxidase
Fuel: Glucose
Propulsion: Self electrophoresis
Terrain: Aqueous meniscus
Max Speed: 1 cm/s
Mitch’s Name: The Komatsu Truck (because it is huge)
Article: Bioelectrochemical Propulsion

The Feringa

Catalyst: Synthetic catalse
Fuel: H₂O₂
Propulsion: Bubble/interfacial
Terrain: Acetonitrile solution
Max Speed: 35 um/s
Mitch’s Name: The F150 (has some exhaust issues)
Article: Catalytic molecular motors: fuelling autonomous movement by a surface bound synthetic manganese catalase

The Sen-Mallouk

Catalyst: Pt (CNT) (+cathodic reactions at Au)
Fuel: H2O2/N2H4
Propulsion: Self electrophoresis
Terrain: Settled near boundary in aqueous solution
Max Speed: 200 um/s
Mitch’s Names: The Ford Mustang GT (has more kick than the regular version)
Article: Bipolar Electrochemical Mechanism for the Propulsion of Catalytic Nanomotors in Hydrogen Peroxide Solutions

The Feringa v2

Catalyst: Glucose oxidase and catalse
Fuel: Glucose
Propulsion: Local oxygen bubble formation
Terrain: Free aqueous buffer solution
Max Speed: 0.2–0.8 um/s
Mitch’s Name: The Chevrolet Nova (more hot rod action)
Article: Autonomous propulsion of carbon nanotubes powered by a multienzyme ensemble

The Gibbs-Zhao

Catalyst: Pt
Fuel: H₂O₂
Propulsion: Bubble release mechanism
Terrain: Aqueous solution
Max Speed: 6 um/s
Mitch’s Name: The Rover
Article: Autonomously motile catalytic nanomotors by bubble propulsion

The Bibette

Engine: External magnetic field
Propulsion: Flagella
Terrain: Aqueous solution
Max Speed: unknown
Mitch’s name: The BMW Mini E (because there is no such thing as a magnetic car)
Article: Microscopic artificial swimmers

The Sagués

Engine: External magnetic field
Propulsion: Doublet rotation coupling with boundary interactions
Terrain: Settled near boundary in aqueous solution
Max Speed: 3.2 um/s
Mitch’s Name: The Smart ED
Article: Magnetically Actuated Colloidal Microswimmers

The Fischer

Engine: External magnetic field
Propulsion: Propeller drive
Terrain: Aqueous solution
Max Speed: 40 um/s
Mitch’s Name: The penis car
Article: Controlled Propulsion of Artificial Magnetic Nanostructured Propellers

The Najafi-Golestanian

Engine: Conformation changes in linking units
Propulsion: Time irreversible translations
Terrain: Free solution
Max Speed: ?
Mitch’s Name: The Eternal Concept Car
Article: Propulsion at low Reynolds number

Some devices that were not included by the authors of the review article, but should definitely be included in any list like this are below:

The Gracias

Engine: External magnetic field
Propulsion: Brute Force
Terrain: Aqueous solution
Max Speed: ?
Mitch’s Name: The Truck Cranes
Article: Tetherless thermobiochemically actuated microgrippers

Tetherless Microgrippers Grabs Tissue Sample – Watch today’s top amazing videos here

The Nelson

Engine: External electromagnetic fields
Propulsion: Flagella
Terrain: ?
Max Speed: 18 um/s
Mitch’s Name: The Tesla Roadster (simply awesome)
Article: Characterizing the Swimming Properties of Artificial Bacterial Flagella

Artificial Sperm – Watch more funny videos here

Link to Review Article: In pursuit of propulsion at the nanoscale

Mitch

As chemists we are members of the professional class, whatever that means, and are required to keep an updated curriculum vitae on hands for all occasions. As job hunting has brought this into focus for me recently I felt the need to share some of my insights.

Pronounciation and Origins
Curriculum is Latin for course. Vitae is Latin for life (technically the plural of life, unless you’re in second declension genitive). Put it together and it translates to course of life. As vitae is loaned from Latin it can be very confusing to pronounce. Dictionary.com has the correct pronunciation of vitae as vigh-tee. This is a little irking since scientists know how to pronounce Latin words and in Latin vitae would be pronounced vee-tigh (more-or-less).

Now to the point. It would be great if there was a place online for the chemical class to keep their CVs. As you develop more work experience it would be nicer to update one centralized CV than to update your word file and then redistribute your CV. Imagine having a link to your CV on your business card, it would be more employer friendly than having them hold onto your business card + several printed pages of CV. To that end, I made a website for that purpose.

I have been using it solely for my personal use, but if there was interest from other chemists I’ll be willing to open it up to a larger audience. Link below…

Mitch’s CV: chemicalvitae.com/mitch

The template is based on Paul Bracher’s CV template that he posted about oh-so many years ago. As I alluded to above, if you want one leave a comment and if there is enough demand I’ll open it up to public registrations. If demand is but a twinkle, I’ll setup the site with a lot less bells-and-whistles and keep registration limited only to the commenteers.

For those chemists that are worried about having too much information about themselves visible on the internet, I can block search-engines from visiting/indexing your profile. So only the people that you have given a link to your CV will be able to find it. Let me know what you guys think.

Mitch

Edit: Fixed some Latin grammar.

The below picture is of sodium chloride crystals.  I’ve made them dozens of times in left over aqueous layers that have been in my hood so long that all the water evaporated.

Crystalline sodium chloride is one of my favorite crystals to grow.  Very easy (although it takes a while), the crystals can get quite large and beautiful.  And they have the characteristic X running through them.  Especially awesome to me, because I did my undergrad at Xavier University.  It’s nice to know that even my chemistry loves XU

What makes this picture so cool, though, is the crystals were grown in space.  The picture is from NASA’s Image of the Day.  The crew aboard the International Space Station’s Destiny lab grew the crystals in a water bubble as part of the program to do chemistry in space.  From NASA:

Looking for all the world like a snowflake, this is actually a close up view of sodium chloride crystals. The crystals are in a water bubble within a 50-millimeter metal loop that was part of an experiment in the Destiny laboratory aboard the International Space Station and was photographed by the Expedition 6 crew.

Space has long fascinated me, and I’ve been trying to get the info and motivation to start a miniseries on chemistry in space.  So I guess today’s IotD is a good way to begin.  Stay tuned over the next several weeks to hear more about awesome chemistry in space!

I thought I knew the process involved in a postdoc interview, but it is a unique experience that people don’t share enough.

Lesson #1
The one thing that was never made clear to me is that you need to have an hour long talk ready to go. I was asked the night before my interview if I would be willing to give an institute wide 1-hour seminar while I was there. Unfortunately for my own professional development I politely chickened-out; I have some ACS talks of 20-25 min length but nothing prepared that would tell a cohesive story for a whole hour. Other postdocs that I have seen interview at Berkeley usually give talks to the group they want to join and not the big seminar talk.

Lesson #2
The interview is all day long. My day started at 9:00 am with a meeting with the professor I contacted, followed by a presentation to his research group of my thesis work. Afterwards it was 1-on-1 talks with his postdocs and a lunch with the group. Which is what I expected. After lunch came meetings with the other professors in the department, an aspect of the process that I was not expecting and was more under prepared then I would have liked to be. The final meeting of the day was with the professor I initially contacted followed by more specifics on what aspects of his work was most interesting to me. The whole process ended after 5:00 pm with an early dinner.

Lesson #3
You need to wear a suit. Fortunately my friends got that into my head before the interview.

Lesson #4
The last step in the process is getting the funds. I need to apply for a fellowship to get started, but as the institute manages the fellowship program I am applying to, I was told not to worry about getting it.

The whole day went well, and I look forward to that next step in academia. If anyone else has gone through this process please share your experience in the comments.

Mitch