Category: chemistry

Nobel Prize in Chemistry shared by three

October 8, 2014 • 4:02 am

Except for literature, it looks like from now on, given the collaborative and increasingly “big” nature of science, the science Nobels will usually be shared by the maximum of three people. Or at least so they have been so far this year. According to my CNN News bulletin:

Two Americans and a German won the Nobel prize in Chemistry this year for their work on optical microscopy that has opened up our understanding of molecules by allowing us to see their functions.

The winners are Eric Betzig, Stefan W. Hell and William E. Moerner, the Nobel committee announced Wednesday.

And the blurb from the Swedish Academy:

Surpassing the limitations of the light microscope

For a long time optical microscopy was held back by a presumed limitation: that it would never obtain a better resolution than half the wavelength of light. Helped by fluorescent molecules the Nobel Laureates in Chemistry 2014 ingeniously circumvented this limitation. Their ground-breaking work has brought optical microscopy into the nanodimension.

In what has become known as nanoscopy, scientists visualize the pathways of individual molecules inside living cells. They can see how molecules create synapses between nerve cells in the brain; they can track proteins involved in Parkinson’s, Alzheimer’s and Huntington’s diseases as they aggregate; they follow individual proteins in fertilized eggs as these divide into embryos.

It was all but obvious that scientists should ever be able to study living cells in the tiniest molecular detail. In 1873, the microscopist Ernst Abbe stipulated a physical limit for the maximum resolution of traditional optical microscopy: it could never become better than 0.2 micrometres. Eric Betzig, Stefan W. Helland William E. Moerner are awarded the Nobel Prize in Chemistry 2014 for having bypassed this limit. Due to their achievements the optical microscope can now peer into the nanoworld.

Two separate principles are rewarded. One enables the method stimulated emission depletion (STED) microscopy, developed by Stefan Hell in 2000. Two laser beams are utilized; one stimulates fluorescent molecules to glow, another cancels out all fluorescence except for that in a nanometre-sized volume. Scanning over the sample, nanometre for nanometre, yields an image with a resolution better than Abbe’s stipulated limit.

Eric Betzig and William Moerner, working separately, laid the foundation for the second method, single-molecule microscopy. The method relies upon the possibility to turn the fluorescence of individual molecules on and off. Scientists image the same area multiple times, letting just a few interspersed molecules glow each time. Superimposing these images yields a dense super-image resolved at the nanolevel. In 2006 Eric Betzig utilized this method for the first time.

Today, nanoscopy is used world-wide and new knowledge of greatest benefit to mankind is produced on a daily basis.

I don’t think anybody guessed this winner. Stay tuned for the literature and peace prizes tomorrow and Friday.

 

Google doodle celebrates Nobel Laureate

May 12, 2014 • 12:56 pm

When I saw today’s Google Doodle, which looks like this:

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I knew instantly that it had something to do with Dorothy Crowfoot Hodgkin (1910-1994), who won the Nobel Prize in 1964. In fact, she would have been 104 today had she lived. And you should know that this Doodle was about her, too, because I’ve posted about Hodgkin before, showing the model of penicillin that she made from X-ray crystallography, a field she helped found. Here’s that model, which I showed in my previous post, and which appears in the Doodle:

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It was for determining this structure, and that of vitamin B12, that Hodgkin got The Big Prize. You can read more about her at the link above. She remains the only British woman to ever get a Nobel Prize in science.

The attitude toward women scientists of her era, and her persistence in ignoring it, is expressed by a nice article in this January’s Guardian:

When, in 1964, she was awarded the Nobel Prize, did the press regard her in the same light as they would a man in the same position? Absolutely not. The Daily Telegraph announced “British woman wins Nobel Prize – £18,750 prize to mother of three”. The Daily Mail was even briefer in its headline “Oxford housewife wins Nobel”. The Observer in its write-up commented “affable-looking housewife Mrs Hodgkin” had won the prize “for a thoroughly unhousewifely skill: the structure of crystals of great chemical interest”.

. . . Hodgkin was a woman not prepared to let her gender get in the way of her work. When married, but still working under her maiden name of Crowfoot, she presented a key paper at a major meeting at the Royal Society in 1938 when eight months pregnant. Another long-term collaborator, Nobel Prize winner Max Perutz, referred to her appearance at this meeting in his speech at her memorial service: “Dorothy lectured in that state as if it were the most natural thing in the world, without any pretence of trying to be unconventional, which it certainly was at the time.”

The days have passed, I hope, when a woman who wins a Nobel Prize is described as a “housewife” or a “mother.”  But there are still too few women in science, and, as several recent studies have shown, still unconscious gender bias against them by scientists of both sexes. Yet I fear we’re still in the days when headlines might say “British woman wins Nobel Prize” when they wouldn’t say “British man wins Nobel Prize.”  The day will come, in our children’s lifetime, when all scientists will be judged not by the content of their chromosomes, but by the character of their science.

 

New chemical element found

May 7, 2014 • 1:12 pm

Well, element 117, which has the titular name of “ununseptium”, was actually discovered by a team of Russians and Americans four years ago, and has been submitted for recognition as an “official element,” but its creation was just replicated by a group in Darmstadt, Germany, and that should speed its acceptance. The new discovery and its implications are described in a piece by Clara Moscowitz in Scientific American. 

It’s amazing what physicists go through to make this stuff, but it had a fortuitious outcome:

To create 117, with the temporary periodic table placeholder name ununseptium, the researchers smashed calcium nuclei (with 20 protons apiece) into a target of berkelium (97 protons per atom). The experiment was so difficult in part because berkelium itself is tough to come by. “We had to team up with the only place on the planet where berkelium can be produced and isolated in significant quantities,” Düllmann says. That place is the Oak Ridge National Laboratory in Tennessee, which has a nuclear reactor that can create the rare element with a half-life of 330 days. It took the facility about two years to build up a large enough stock of berkelium for the experiment; when about 13 milligrams had accumulated, Oak Ridge scientists shipped it off to Germany for the next stage of the project. At GSI, researchers accelerated calcium ions to 10 percent light-speed and sent them colliding into the berkelium. If a calcium and berkelium nucleus collided head-on, occasionally the two nuclei would stick together, fusing to form a new element with a combined total of 117 protons. “We get about one atom per week,” Düllmann says.

One atom per week! It’s a triumph of our species that we can get one atom per week and then get enough of that stuff to identify it!

Now, as is usual for these trans-uranium elements, its half-life is very short: 0.05 seconds, but it’s identified by looking for the elements it forms upon decay: in this case (after several decays), lawrencium 266. That’s a new form of lawrencium (Lr, characterized by its 103 protons), for up to now the most common form of Lr was the 262 isotope, with 159 protons and half-life of 3.6 hours. Lawrencium-266, in contrast, has 163 protons and a half life of 11 hours. This has been seen as a confirmation of physicist’s predictions:

“Perhaps we are at the shore of the island of stability,” [Christoph] Düllmann says. [Düllmann led the German collaboration.]
 
No one knows for sure where this island lies, or even if it exists at all. Theory suggests that the next magic numbers beyond those known are around 108, 110 or 114 protons, and 184 neutrons. These configurations, according to calculations, could lead to special properties that allow atoms to survive much longer than similar species. “All existing data for elements 116, 117 and 118 do confirm that lifetimes increase as one goes closer to the neutron number 184, says theorist Witold Nazarewicz of Oak Ridge, who was not involved in the study. “This is encouraging.”

Well, I can’t say I understand the “island of stability” business at all (click the words in bold for more info), but perhaps one of our physics readers can explain that theory—if it’s not too arcane for general consumption.

Reporting from mid-book, Professor Ceiling Cat, Chicago.

h/t: Blue

The ninth pitch drop fell

April 22, 2014 • 9:31 am

What I’m about to describe is supposedly the world’s longest-running scientific experiment, and, although we already know the result, it gets demonstrated repeatedly: once every decade on average.

In 1927, Professor Thomas Parnell of the University of Queensland set up an experiment to demonstrate that some substances that appear to be solid, like pitch, are really liquids, and flow at an extremely slow rate. At room temperature, for example, pitch is solid, brittle, and can be shattered with a hammer. But Parnell wanted to show that it was really a liquid in the technical sense.

So, in 1927 Parnell heated up some pitch, poured it into a sealed funnel, allowed it to congeal for three years, and then snipped the neck of the funnel. Over the next 86 years (Parnell died 21 years into the experiment), generations watched the pitch slowly drip from the funnel (nobody’s actually seen a drop fall).

Here’s a photo of the setup:

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Longtime custodian of the famous experiment, the late Professor John Mainstone. (Photo from the University of Queensland.)

Up until last week, there had been eight drops, but a ninth just fell on April 10. Here’s a time-lapse video taken over the last two years:

Sadly, the fall isn’t so dramatic, as the latest drop simply glopped onto the one below it, still adhering to the funnel. They need to move that funnel higher up!

There’s another description of the experiment at the University of Queenland’s site, which gives a bit more information:

The experiment was set up as a demonstration and is not kept under special environmental conditions (it is actually kept in a display cabinet in the foyer of the Department), so the rate of flow of the pitch varies with seasonal changes in temperature. Nonetheless, it is possible to make an estimate of the viscosity of this sample of pitch (R.Edgeworth, B.J. Dalton and T. Parnell, Eur. J. Phys (1984) 198-200). It turns out to be about 100 billion times more viscous than water! The first picture in the slide show above is of the late Professor John Mainstone, longtime custodian of the experiment. In the 83 years that the pitch has been dripping, no-one has ever seen the drop fall.

The history (from Wikipedia):

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By the way, I’m told that very old windows are thicker at the bottom than at the top, supposedly the result of glass itself flowing downward. I have no idea whether this is true.

h/t: Robert

Fred Sanger died

November 20, 2013 • 10:01 am

According to the BBC News, Fred Sanger (I never heard anyone call him “Frederick”) died yesterday at age 95. He was the only English person to ever win two Nobel Prizes. These were both in chemistry. One, given in 1958 (and to Sanger alone), was for determining the amino acid sequence of insulin from cows, dispelling a common idea that proteins did not have a definite and repeatable sequence. The method, involving paper chromatography, was laborious.

The second prize was for a unique method of DNA sequencing (the so-called “Sanger sequencing”) that he published with in 1977 with Alan Coulson and S. Nicklen in the Proceeding of the National Academies of Science (click the link to see a paper that nabbed a Nobel).  Sanger, Wally Gilbert (who developed another method of sequencing DNA) and Paul Berg (who worked on the chemistry of nucleic acids) shared the chemistry Nobel in 1980.

Wikipedia gives a few interesting tidbits about the man:

He has lost his religious faith and calls himself an agnostic. In an interview published in the Times newspaper in 2000 Sanger is quoted as saying: “My father was a committed Quaker and I was brought up as a Quaker, and for them truth is very important. I drifted away from those beliefs – one is obviously looking for truth but one needs some evidence for it. Even if I wanted to believe in God I would find it very difficult. I would need to see proof.”

Ah, the old “lack of evidence” statement that turns so many scientists into nonbelievers.

Also, when reading his obituary I didn’t see any reference to “Sir Frederick Sanger,” and don’t ever remember him being called “Sir Fred.” That’s because of this:

He declined the offer of a knighthood as he did not wish to be addressed as “Sir” but later accepted the award of an Order of Merit.

Sanger was one of the good guys, known for his lack of cant and arrogance.

By the way, can you name the other three people who won the Nobel Prize twice? I’m sure you’ll know at least one, but think before you look up the answer (here).

sanger
Fred Sanger (1918-2013)

The world’s most politically correct salt

November 8, 2013 • 1:56 pm

From Amazon:

1. FDA approved
2. Non-GMO
3. Organic
4. Halall (sic)
5. Kosher, and, best of all
6. NO CHEMICALS!

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And really—approved by the NIH? Since when do they approve salt?

Picture 7

Some of the reviews are hilarious:

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Pure sodium chloride (a CHEMICAL) is white, and one reviewer suggests that the pink color comes from brine shrimp.

h/t: pyers

Paul Davies, chemistry, and the origin of life

January 14, 2013 • 6:50 am

How the unique properties of life originated from inert matter is still one of the great unsolved problems of biology. Creationists, of course, claim that our failure to solve it means that God did it: as Ingersoll noted in yesterday’s quote, “Our ignorance is God; what we know is science.”

And perhaps we’ll never know precisely how life began, for it happened in the distant past and involved chemical reactions that could not fossilize.  But I have confidence in three things: life originated naturally and not through God’s fiat; that we will show that this was possible within 50 years or so by demonstrating the evolution of life-like systems in the laboratory under primitive Earth conditions; and that while life may have originated more than once, all living species descended from only a single proto-organism (lots of evidence for that one). If we can demonstrate the origin of life in the lab through realistic experiments, then—although we may not know how it really happened several billion years ago—we can say that it could have happened naturally, and therefore we need not invoke God.

Paul Davies is an astrophysicist who spends a lot of time promoting the comity between science and faith, and who won the Templeton Prize in 1995. As Wikipedia notes:

An opinion piece published in the New York Times,[2] generated controversy over its exploration of the role of faith in scientific inquiry. Davies argued that the faith scientists have in the immutability of physical laws has origins in Christian theology, and that the claim that science is “free of faith” is “manifestly bogus.”[2] The Edge Foundation presented a criticism of Davies’ article written by Jerry Coyne, Nathan Myhrvold, Lawrence Krauss, Scott Atran, Sean Carroll, Jeremy Bernstein, PZ Myers, Lee Smolin, John Horgan, Alan Sokal and a response by Davies beginning I was dismayed at how many of my detractors completely misunderstood what I had written. Indeed, their responses bore the hallmarks of a superficial knee-jerk reaction to the sight of the words “science” and “faith” juxtaposed.[3] While atheists Richard Dawkins[4] and Victor J. Stenger[5] have criticised Davies’ public stance on science and religion, others including the John Templeton Foundation, have praised his work.

I’ve written about Davies’ accommodationism several times on this site; one example, in which he finds God in quantum mechanics, is here (see also his 2007 New York Times article asserting that science rests on faith.) But, to give him credit, Davies is also something of a polymath, and has an interest not just in physics, but in the early Ediacaran fauna and especially in the origin of life (“abiogenesis”). He’s apparently done technical work on the last issue, which I must confess I haven’t read (the literature on abiogenesis is huge). But in yesterday’s Guardian, Davies summarizes his work in a piece called “The secret of life won’t be cooked up in a chemistry lab.”

His basic claim is that science hasn’t solved the origin-of-life problem because it’s been left largely in the hands of chemists, and from-the-ground-up reductionist chemistry is not the way to solve it:

But a more fundamental obstacle stands in the way of attempts to cook up life in the chemistry lab. The language of chemistry simply does not mesh with that of biology. Chemistry is about substances and how they react, whereas biology appeals to concepts such as information and organisation. Informational narratives permeate biology. DNA is described as a genetic “database”, containing “instructions” on how to build an organism. The genetic “code” has to be “transcribed” and “translated” before it can act. And so on. If we cast the problem of life’s origin in computer jargon, attempts at chemical synthesis focus exclusively on the hardware – the chemical substrate of life – but ignore the software – the informational aspect. To explain how life began we need to understand how its unique management of information came about.

Well, he doesn’t mention that many biologists and biochemists have also worked on the problem, including Stanley Miller, Gerald Joyce, and Nobel Laureate Jack Szostak. But never mind. Davies goes on to say that the fundamental problem is not in the purview of chemistry, but in how biological information gets organized hierarchically:

Information theory has been extensively applied to biological systems at many levels from genomes to ecosystems, but rarely to the problem of how life actually began. Doing so opens up an entirely new perspective on the problem. Rather than the answer being buried in some baffling chemical transformation, the key to life’s origin lies instead with a transformation in the organisation of information flow.

Sara Walker, a Nasa astrobiologist working at Arizona State University, and I have proposed that the significant property of biological information is not its complexity, great though that may be, but the way it is organised hierarchically. In all physical systems there is a flow of information from the bottom upwards, in the sense that the components of a system serve to determine how the system as a whole behaves. Thus if a meteorologist wants to predict the weather, he may start with local information, such as temperature and air pressure, taken at various locations, and calculate how the weather system as a whole will move and change. In living organisms, this pattern of bottom-up information flow mingles with the inverse – top-down information flow – so that what happens at the local level can depend on the global environment, as well as vice versa.

. . . Walker and I propose that the key transition on the road to life occurred when top-down information flow first predominated. Based on simple mathematical models, we think it may have happened suddenly, analogously to a heated gas abruptly bursting into flame.

. . . The way life manages information involves a logical structure that differs fundamentally from mere complex chemistry. Therefore chemistry alone will not explain life’s origin, any more than a study of silicon, copper and plastic will explain how a computer can execute a program. Our work suggests that the answer will come from taking information seriously as a physical agency, with its own dynamics and causal relationships existing alongside those of the matter that embodies it – and that life’s origin can ultimately be explained by importing the language and concepts of biology into physics and chemistry, rather than the other way round.

Now I have to say that this is either way above my pay grade, is too abstruse for the general public, or is simply wrong. And I’ll take a chance here and say that the problem is not going to be solved using information theory or “top down” considerations. Yes, of course the environment played a role in the origin of life, but that doesn’t mean that we can’t take a reductionist approach. (As an example of “top down” control, Davies uses the fact that genes can be turned on by environmental factors, but of course that area of research progressed purely through reductionism, not through incorporating “environmental information theory.”)  To me, the problem of abiogenesis involves taking a set of original molecules that didn’t contain any information for a replicator, and then figure out what kind of processes enabled them to gain the ability to replicate. Along with that is the formidable problem of how the replicator became connected with a phenotype, in other words, how that replicator evolved to produce proteins and cells—and that is information.  All this can, I think, be attacked without any importation of “information theory” from the beginning. Information is a consequence of, rather than an a priori requirement for, understanding abiogenesis.

In fact I don’t know what Davies is suggesting here, and maybe his technical work has insights that are fruitful.  The Guardian article, though, is simply opaque, and there are hints from other work that Davies’ approach may not be fruitful.

One of these is a new book by chemist Addy Pross, What is Life? How Chemistry Becomes Biology. (The title, of course, is borrowed from Erwin Schrödinger’s famous book that had such a huge influence on the pioneers of molecular genetics.)

I have just received this book and have only glanced through it, but it’s a short volume describing the latest thought on the origin of life, and Pross’s own speculations on how it started. And it’s pure chemistry: no information theory needed. It does, in fact, what Davies says hasn’t been done: meshing the language of chemistry with that of biology.

I’m told by those who have read it that Pross has an intriguing and possibly correct idea about how a population of molecules can, through a process of biochemical natural selection, become replicators that get hitched to metabolism. The “information” of life then is a result of the process, not something that, as Davies asserts, needs be modeled in from the beginning. As Pross notes on p. 152:

A moment’s thought suggests therefore that the term “information” in its biological context is just “specific catalysis” when considered in a chemical context.

I’ll be reading this book in the next month or so, and will report back, but I wanted to say four things now:

1. If you’re interested in the origin of life, read Pross’s book. It’s written for the curious layperson, and is therefore perfectly suitable for the non-scientist readers of my site.
2. I suspect that Davis is wrong and that the reductionist approach, based on chemistry, is the way to solve the problem of life’s origin.
3. But I may be wrong, too, and somehow, in ways I don’t understand “top down information flow”—whatever that means—may be the key to the problem. But if the history of science is any guide, the problem will yield to chemists starting with a population of molecules existing under realistic early-Earth conditions.
4. The Guardian article is completely opaque to the nonscientific reader (indeed, to me as well), and seems more like p.r. for Davies’ work than a genuine attempt to explain to the layperson how life might have originated.

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h/t: Michael