Elliott Carter: 100th birthday

December 23, 2008

Turning 100 at Carnegie Hall, With New Notes. (New York Times, December 11, 2008.)

Another centenarian: Living to 100 (April 22, 2009).

My page for Biotechnology in the News (BITN) -- Other topics includes a section on Aging. It includes a list of related Musings posts.

There is more about music on my page Internet resources: Miscellaneous in the section Art & Music. It includes a listing of music-related Musings posts.

More, November 2012...

Elliott Carter, perhaps the oldest active composer ever, completed his final work three months ago, at age 103. Carter died on November 5, 2012, five weeks short of his 104th birthday. Elliott Carter, Master of Complexity. (New York Times, November 6, 2012.)

Some fun reading: Fuel cell gadget and growing diesel

December 13, 2008

A reader sent me the following two links, which are worth sharing. They are unrelated, except that both are broadly about energy issues.

Thought you'll enjoy. Especially the second story is very interesting and potentially of some importance.

* MTI Micro's Recharging Station Makes It Easier. (PC Magazine, December 10, 2008.)
* Tree fungus could provide green transport fuel. (A Jha, Guardian, November 3, 2008.)

As to the second... The basic claim is that they have a fungus which can grow on cellulose and make diesel fuel. That's nice. The problem is economics. There is a huge gap between finding such a bug and making it economical. The paper is good microbiology; it is from Gary Strobel at Montana State, who is well regarded. It is good to study it further, and try to develop it, as they suggest. Maybe something will come from it. Maybe some gene from it will prove useful. The caution is simply that one should not get too excited about such things, should not claim -- or believe claims -- that something has been solved.

There are two issues here. One is the use of cellulose as the feedstock, and the other is the kind of fuel being made. Both are interesting. But the barrier to using cellulose is the problem of breaking it down. Nature made cellulose to be strong; no one yet has a process for breaking it down that is economically practical in this context.

The Strobel article is The production of myco-diesel hydrocarbons and their derivatives by the endophytic fungus Gliocladium roseum (NRRL 50072). (G A Strobel et al, Microbiology, 154:3319, November 2008.) Browsing the intro can be good for overview. And maybe see the final section, Origins of fungal hydrocarbons and crude oil.

By the way, some of you may share a characteristic with this fungus. Apparently, it likes oatmeal.

There is something analogous going on here. Many of you know about Jay Keasling's project to make artemisinin. This is a type of anti-malaria drug of great interest. Unfortunately, the natural supply is limited and expensive. Keasling has led a group to re-engineer bacteria and yeast to make this drug -- with the goal of providing it at very low cost. (Much of the work was funded by the Gates Foundation. So the development costs need not be recovered from sales. The company set up to do the production is committed to providing the drug at low cost to developing countries.) In fact, they have made huge strides, and are actually succeeding in reaching the goals. Ok, good. Good science -- coupled with good '"social conscience."

Now, Keasling wants to modify the process to make "gasoline" (i.e., liquid transportation fuels). The logic is that the drug is not very different from gasoline -- in terms of chemical class. More specifically, he thinks it should be possible to modify the pathways to produce other compounds suitable for use as gasoline. Ok, that is plausible. The problem is cost. The market price of even an inexpensive drug is, say, 100 times the price of gasoline. It has been a tremendous achievement to improve the process to get the price of artemisinin down to "cheap". And now they want a further two orders of magnitude cost reduction? This is not a hidden problem. Keasling states it right up front. He knows it is a huge challenge to meet the economic target to make gasoline, but he thinks it is worth trying. Good. If he weren't optimistic, we would not find out whether it can be done. The caution is to not get excited and claim in advance that he has solved the problem.

Here are some things on Keasling and the artemisinin project:
* A campus news story on the funding of this project by the Gates Foundation: QB3 + Gates' millions = a cure? Helped by Microsoft's founder, Jay Keasling and his industry partners hope to create an inexpensive treatment for malaria. (1/12/05.)
* A status report -- a news story: Synthetic yeast to brew up vital malaria drug. (6/4/08.)

A Musings post on Keasling's "gasoline" project: Engineering E coli bacteria to convert cellulose to biofuel (December 13, 2011).

More on malaria is on my page Biotechnology in the News (BITN) -- Other topics under Malaria.

More about microbes making oil: Oil in the oceans: made there by bacteria (January 3, 2016).

There is more about energy on my page of Internet Resources for Organic and Biochemistry - Energy resources. It includes a list of some related Musings posts.

Also see: Nobel notes (October 13, 2015).

An unusual cyanobacterium

December 11, 2008

There is a recent report of an unusual cyanobacterium. One thing that makes it an interesting story is how they picked it up.

The key finding of interest is that it is a unicellular cyanobacterium that fixes nitrogen during the day.

So, why is that so remarkable?

Think about the inherent contradiction of being a nitrogen-fixing unicellular cyanobacterium.

A key characteristic of the cyanobacteria is that they are photosynthetic -- and make oxygen. They are the only bacteria to carry out this advanced form of photosynthesis; other bacteria make sulfur, for example, as their byproduct of photosynthesis. (The cyanobacteria were -- it seems rather certain -- responsible for the original oxygenation of the earth's atmosphere. And they are the basis of plant chloroplasts.)

But carrying out photosynthesis that makes oxygen is incompatible with nitrogen fixation. Why? Because the enzyme of nitrogen fixation is quite sensitive to oxygen. For a cell to make oxygen and fix nitrogen at the same time just won't work.

The cyanobacteria that fix nitrogen have worked out two solutions to this dilemma. Somehow they separate the two processes -- in space or time. Some cyanobacteria are multicellular; these then differentiate and make special non-photosynthetic cells for nitrogen fixation. But the unicellular cyanobacteria do it by the clock: they photosynthesize (and make oxygen) by day and fix nitrogen by night.

So, finding a unicellular cyanobacterium that fixes nitrogen during the day was striking. Not possible, it would seem. Analysis showed a simple enough solution: This bug lacks the system for oxygen-evolving photosynthesis.

A cute story, with an intriguing answer. And it might even be important. The bug is rather common in the ocean.

For an overview... A press release, from UC Santa Cruz: Mysterious microbe may play important role in ocean ecology. (11/13/08.)

The article is: Globally Distributed Uncultivated Oceanic N₂-Fixing Cyanobacteria Lack Oxygenic Photosystem II. (J P Zehr et al, Science 322:1110, 11/14/08.)

More about nitrogen fixation: Using light energy to power the reduction of atmospheric nitrogen to ammonia (May 20, 2016).

More about cyanobacteria:
* A primitive cyanobacterium (October 25, 2021).
* A whiff of oxygen three billion years ago? (April 6, 2015).

COOL AS HELL! Sea slug that runs on solar power (Really)

November 30, 2008

A reader sent this to me. It is part of a fascinating story.

A sea slug that gains the ability to turn sunlight into energy from the algae it eats is arguably the first functional plant-animal hybrid found in nature.

[Here we use the term "plant" in the broad sense of photosynthetic organisms with chloroplasts. More precisely, the algae and "land plants" are distinct groups, but the distinction is not an issue here.]

Read the story and watch a video here: Solar-powered sea slug harnesses stolen plant genes. (New Scientist, November 24, 2008.)

One of the basic (most fundamental?) differences between plants and animals is photosynthesis. They do, we don't.

But that is not entirely true. Corals are a well developed example of a photosynthetic animal -- due to symbiosis with algae. Corals really are animals -- but "primitive" ones, related to the jellyfish. (Coral bleaching -- an important environmental concern -- involves loss of algae.)

Beyond that, there have been reports of green molluscs. In early reports it was hard to be sure whether the animal was gaining energy from the "green". But now that seems quite clear, at least for some cases. The report here, with a green sea slug, adds to the information. Chloroplasts are not independent; they require genes in the host nucleus for full function. The work here shows that the animal has in its genome one of the genes known to be required. Thus it is clear that a gene has been transferred from the algal nucleus to the sea slug nucleus.

The work is interesting at multiple levels. One is simply understanding this "green animal" -- the fascinating idea reflected in the message title here. (In private musings, some of us have suggested developing photosynthetic farm animals, to improve the efficiency of food production. The existence of this green sea slug is something of a "proof of principle" -- though not offering any clue as to how to go about doing it. Or maybe we could just see green sea slugs.)

Beyond that, the work illustrates a couple of other important ideas.

One is horizontal gene transfer (HGT). The "normal" way to get genes is from your parents; "vertical" gene transfer. But getting genes from your friends or neighbors -- or your food -- is common among the bacteria. This HGT is much less documented in higher organisms; the transfer of a gene from algal nucleus to sea slug nucleus would seem to be such a case. The mechanism is unknown (though many hypotheses are plausible).

The second is the bigger issue of cell organelles and their symbiotic origin. The mitochondria in your cells originated from bacteria; long ago, some primitive cell ate some bacteria. Instead of digesting them, they incorporated them. Over time, most of the genes from the ingested bacteria were transferred to the nucleus; modern mitochondria contain only a few genes, but are largely dependent on host genes. Similarly, chloroplasts originated by such an event, involving the ingestion of photosynthetic cyanobacteria.

The acquisition of chloroplasts by sea slugs is another such event. Studying such events adds to our basic understanding of how we got here.

The article, which is freely available: Horizontal gene transfer of the algal nuclear gene psbO to the photosynthetic sea slug Elysia chlorotica. (M E Rumpho et al, PNAS 105:17867, November 18, 2008.) The introduction to the paper gives a nice discussion of the context. You can also get to a couple of short movies by clicking on "Supporting Information". (There is a link to the article in the news story; click on the doi number.)

For other "photosynthetic animals":
* Coral bleaching: how some symbionts prevent it (September 30, 2016).
* A photosynthetic salamander? (August 24, 2010). A vertebrate.
* Croatian Tethya beam light to their partners (December 16, 2008).

* * * * *

There is a significant challenge to the story that the sea slugs are truly photosynthetic. See the post: A challenge to the story of photosynthetic sea slugs (January 7, 2014).

More on the issue...
* Photosynthetic sea slugs; species vary (June 9, 2015).
* More on photosynthetic sea slugs (February 20, 2015).

Origin of chloroplasts

November 17, 2008

Scientists discover the chance meeting 1.9bn years ago that led to the eruption of life on Earth. (Mail Online, November 11, 2008.)

This is based on a meeting report, not a paper, at this point, and the news story itself is somewhat hyped. Nevertheless, this is probably interesting, and we can await details.

The basic idea, that chloroplasts arose from bacteria that managed to establish themselves as endosymbionts, is broadly accepted. The bacterial precursors of the chloroplasts must have come from the group we call cyanobacteria, the only group of bacteria with oxygen-evolving photosynthesis.

These cyanobacteria -- originally the free-living ones and later the chloroplast descendants -- are responsible for the oxygen in the atmosphere.

One of the comments at the end says "If the chances of an event are a billion to one, but there are a billion opportunities for it to occur then it should be expected." That makes an interesting point. However, remember that we really have no idea what those numbers are. Saying they are both "billion" conveniently matches the numbers. But "billion" might be off by many orders of magnitude.

What the record tell us, as data, is that all plant life we now see seems to be descended from a single lineage of chloroplasts. That means that the event happened only once -- or that it happened more than once, but only one line survived. The former is simpler, but it is impossible to exclude the latter.

The same kind of argument applies to the original emergence of life. So far as we can tell, all life on earth is related, and thus comes from a single origin of life event. That event occurred a billion or so years into the earth's history (assuming that life indeed started here directly rather than by an infection from elsewhere). Does that mean it is "rare"? There is no way to know. Some would suggest that the emergence of life is quite probable, at least under some conditions and over the geological time scale. They might even suggest that life started on earth many times, but only one line survived. Of course, these are the same people who suggest that life is common throughout the universe. Much fun, but that is something we do not know, and it is not likely we will find out. So it is good for fun discussion, but not likely to play much role in serious science.

Note that there is a story for mitochondria similar to that for chloroplasts. Mitochondria also arose from bacteria that were taken up by another cell and established a symbiosis. Lynn Margulis, now of U Mass, is the person generally given credit for the modern version of these ideas on the role of endosymbiosis in the development of modern eukaryotic cells. She gave a seminar here a year or so ago, which I think I mentioned. It is important to emphasize that the tools needed to recognize the connection between mito/chloroplasts and bacteria became available only in mid-late 20th century.

Also see... Origin of eukaryotic cells: a new hypothesis (February 24, 2015).

Sounds of atoms

November 12, 2008

This item has a fun aspect, but also reflects some good serious science.

It is based on a short note in Science. A good place to start is an MP3 file that is posted with the Supplementary materials for the article. Scroll down to the last item listed, an "audio file" -- 29 seconds worth. The file is described there -- but I suggest listening once before reading the details. Briefly, you are listening to the tip on a scanning tunneling microscope approach -- and reach -- the sample.

So what are these sounds? Well, they are not particularly natural, not the "sounds of atoms" (the tile of the item in Science, as well as my title here). But there is a serious purpose. What they have done is to take electronic signals from the instrument, and convert them into audio signals. Why? Because the ear is pretty good at recognizing patterns. (After all, that is sort of what "music" is all about.) By listening to the audio channel of their instrument, they can tell whether operation is "normal". Much easier -- and presumably, more fun.

There are also a couple of movie files listed on the page of supplementary materials, above the audio file. Same idea, but now the sound is coupled with the developing image. These are big files.

I wish they had posted an example where something was not working, and the sound helped them catch the problem. Still, an interesting (but not novel) idea -- and fun.

The full letter -- about a half page and with a cute little figure -- requires subscription access. It is at Life in science: Sounds of Atoms. (Science 322:190, 10/10/08.) There is also a link to it at the bottom of the page listed above (labeled "return to article"), the page of supplementary materials.

Article on scientific information

October 28, 2008

It is about the use of XML for coding information in online resources.

Open Access: Taking Full Advantage of the Content. (P E Bourne et al, Open Access: Taking Full Advantage of the Content. PLoS Comput Biol 4(3): e1000037, 3/28/08.)

More milk

October 16, 2008

This picture is from a current paper, from scientists in the Department of Earth System Science and Technology at Kyushu University in Japan. The work is relevant to many phenomena, "such as the overturn of the outer portion of the collapsed core of a massive star [2], the formation of high luminosity twin-exhaust jets in rotating gas clouds in an external gravitational potential [3], laser implosion of deuterium-tritium fusion targets [4] ... "

So the questions are...
* What is the figure about?
* Why are they studying this?

If you can work "Sierpinski carpet" into your answer, you get a bonus -- unless I conclude you just looked this up. But if you can actually explain to me what a Sierpinski carpet is, that would be nice.

The picture is actually of something very simple. It is quite possible that some of you have done this yourself. It would be suitable for a science lab at a wide range of levels -- though not with this fancy photography.

The article is freely available: The paper. (M Shimokawa & S Ohta, 2008.) The figure used above is Fig 1b of the paper, on p 16 of the pdf file. The quotation above is from page 2. For the title of the paper, and a clue as to what they did, put your cursor over the following "link": The title.

The link above is to a preprint. Here is the published article. (M Shimokawa & S Ohta, Fractals 20:97, March 2012.) (Figure 1b of the published article is different, but equivalent.

Previous milk post: Got milk? (October 13, 2008). (immediately below)

More coffee... Why you should freeze the coffee beans before grinding them (May 29, 2016). Links to more.

More fractals... Cauliflower math (July 26, 2021).

Self

October 8, 2008

If you see yourself in the mirror, you know it is you. The ability to recognize yourself in the mirror has been shown for various apes, dolphins, elephants -- and now magpies. Magpies are a member of the corvid group of birds, including crows and ravens -- and generally recognized as the birds with the most advanced brains.

The paper is very readable, with a good introduction describing the background, and info from other animals. The discussion gives a good balanced analysis of how one should interpret the significance of the test. The experimental set-up is also described clearly. All-in-all, a nice paper to browse. The "author summary" is a great place to start -- and maybe is enough if you don't want details.

One aspect of this work is simply the fun part. These are neat experimental systems. It is fun to see what they did. Another good example is a recent paper reporting that bees can count to 4. The first reaction is inevitably... oh yeah, how did you figure that out? So the paper becomes fun just to see how they did it. Of course, that includes the controls to try to sort out that the results were due to counting, not some other behavioral pattern.

The magpie-mirror paper is freely available: Mirror-Induced Behavior in the Magpie (Pica pica): Evidence of Self-Recognition. (H Prior et al, PLoS Biology 6(8):e202, August 2008.)

A short news story: Mirror test shows magpies aren't so bird-brained. (New Scientist, August 19, 2008.) It includes a video, and links to some of the mirror work with other animals.

Those of you who have had some chemistry may know about mirror-image molecules. It is common to make some comment about other mirror phenomena, for fun. Here is one of my favorites in this context. (It is fully identified on the image file, which includes figure legend.) Another mirror image phenomenon [link opens in new window].

More about the mirror test for self-awareness: Learning to use a mirror (June 22, 2015).

The post Teaching pigs to use a mirror (December 1, 2009) discusses work showing that a pig can use a mirror to help find hidden food.

More corvids... Ravens: planning for the future? (September 11, 2017).

The book Marzluff & Angell, Gifts of the Crow -- How perception, emotion, and thought allow smart birds to behave like humans (2012), is a delightful introduction to the corvids, the group of intelligent birds that includes the magpies. For more about the book, see my page Books: Suggestions for general science reading, for Marzluff & Angell, Gifts of the Crow.

More about the brain is on my page Biotechnology in the News (BITN) -- Other topics under Brain (autism, schizophrenia). It includes a list of relevant Musings posts.

This post is noted on my page Internet Resources for Organic and Biochemistry under Stereochemistry (Chirality).

Converting Oklahoma to natural gas

October 1, 2008

Below is a link to a recent paper on converting residual oil in the ground to natural gas.

The key background ideas here:
* Standard oil production processes leave over half of the oil in the ground.
* It is possible to convert "oil" to "natural gas" using microorganisms (bacteria and archaea).

The basic biochemistry and microbiology of how this would work is fairly well understood. The issues at hand are whether it can be turned into a practical and economic process.

This paper shows a small lab scale process, using samples of sandstone from a depleted oil field (in Oklahoma). The short message is that it works.

They do some crude calculations and estimate that such a process could produce several percent of the US natural gas supply. (I would presume that a real-field process would work more slowly than their lab process.) They make no estimate of cost.

They do note that such a process could work also on shale oil.

Remember, the main goal here is getting the oil out of the ground. Converting it to gas is a trick to get it out of the ground. Fortunately, oil and natural gas are about equivalent in terms of usefulness.

The paper is at: Bioenergy Production via Microbial Conversion of Residual Oil to Natural Gas. (L M Gieg et al, Applied and Environmental Microbiology 74:3022, 5/08.)

More about hard-to-recover fuels: Shale gas recovery using hydraulic fracturing (fracking) (October 7, 2013).

There is more about energy on my page of Internet Resources for Organic and Biochemistry - Energy resources. It includes a list of some related Musings posts.

What are these?

September 25, 2008

A one word answer, collectively describing the whole group, is desired.

Ready? Put your cursor over the word answer. (Do not click.)

To check yourself... Source (Science 321:206, 7/11/08.)

For those who do not have access to that, here is part of the figure legend: figure legend.

Other "What is it?" features include...
* What is it? (November 20, 2009).

More about these things... Tracking the pathogen of the Irish potato blight (June 25, 2013).

Weighing gold atoms

September 24, 2008

This is neat!

It is as if a violinist tunes his instrument. Then a gold atom is put on a string, and the violinist notices the change in frequency of the string -- due to the added mass. Of course, in that case, the change would be negligible, but the idea is just what they do here. The work is from Alex Zettl's lab at UC Berkeley.

Nanotube 'springboard' weighs clinging atoms. (New Scientist, July 21, 2008.)

A good page at Alex Zettl's web site: An atomic-resolution nanomechanical mass sensor (now archived).

The article is An atomic-resolution nanomechanical mass sensor. (K Jensen et al, Nature Nanotechnology 3:533, September 2008.) A copy is at Zettl's web site: pdf file. At least, browse the abstract.

The article noted here is also noted on my page of Introductory Chemistry Internet resources in the section on Units; dimensional analysis.

More about carbon nanotubes: Characterization of carbon nanotubes (December 3, 2013).

Among many posts about gold... Prospecting for gold -- with help from the little ones (March 1, 2013). Includes a list of gold-related posts. Added July 9, 2024.

Gasoline content regulation and air quality

September 19, 2008

This is from an announcement of a seminar -- with an abstract.

Agricultural and Resource Economics Seminar:
Clearing the air? The effects of gasoline content regulation on air quality.
Maximilian Auffhammer and Ryan Kellogg

Abstract:
This paper examines the effects of U.S. gasoline content regulations on ground level ozone concentrations. These policies are costly and have been shown to raise gasoline prices by 3-5 cents per gallon. We provide the first comprehensive empirical estimates of the regulations' air quality benefits. We exploit the fact that regulations vary by time and place of introduction, as well as by the specific gasoline content restrictions prescribed. We show that early regulations that targeted the evaporative emissions of volatile organic compounds (VOCs), one of the two main precursors to ozone, did not have a statistically detectable effect on air quality. For California, however, the targeted, more expensive removal of a class of VOCs particularly prone to forming ozone resulted in a large, measurable effect. Our findings suggest that allowing refineries the flexibility to remove the least-cost VOCs from gasoline is ineffective in improving air quality. Further, we show that the federal reformulated gasoline introduced in 1995 and 2000 reduced summertime ozone concentrations.

Arsenic and photosynthesis

September 9, 2008

Arsenic (As) is a quite fascinating element in biology. We most commonly think of it as toxic, with the current disaster of the water in Bangladesh serving to emphasize that. (I recently noted a paper on the source of that As, in the Himalayas.)

However, As is not all bad in biology. The development of Salvarsan, an anti-microbial agent based on As, was a major development (1910). Even now, As is still used medically. (All medical uses are limited by toxicity.)

Enzymes for As metabolism are common -- and probably ancient. Arsenic is thought to be essential for optimal growth in humans -- though the reason is not clear.

Of course, the bacteria show the greatest diversity of As biology. Bacteria are known that can use As as an oxidant, instead of oxygen. (They use arsenate ion, with As(V), for this.) And some bacteria have been found to use As as a reductant -- a source of electrons. (They use arsenite ion, with As(III), for this.)

Now a new report, in the Aug 15 issue of Science, of bacteria that use arsenite as the reductant to support the reduction of CO₂ in photosynthetic growth.

The most famous reductant (electron donor) for photosynthesis now, in modern plants, is water -- leading to the production of oxygen. The most common reductant for photosynthesis that does not produce oxygen is sulfide ion -- sometimes leading to production of granules of elemental sulfur. In fact, the bacteria here can also use sulfide, perhaps even preferring it to arsenite. However, they show here that two crude microbial sources oxidize arsenite in the light. And they show that a pure culture of one of the organisms can use arsenite as its sole electron donor for photosynthetic growth.

The bacteria here were isolated from Mono Lake, so for some of us this is a "local" story -- and another fitting piece in the saga of Mono Lake.

The bacteria studied closely so far do not seem to contain a "typical" arsenite oxidase. They do contain an arsenate reductase. Perhaps that enzyme is running in reverse here, or perhaps there is more to this story than apparent so far.

Finding As-dependent non-oxygenic photosynthesis suggests that a biogeochemical As cycle was established three billion years ago -- before the development of an oxidizing atmosphere.

Here are a couple of links to brief news stories on this:
* Arsenic-loving bacteria rewrite photosynthesis rules. (Chemistry World, August 15, 2008)
* In Lake, Photosynthesis Relies on Arsenic. (New York Times, August 18, 2008)

The article is: Arsenic(III) Fuels Anoxygenic Photosynthesis in Hot Spring Biofilms from Mono Lake, California. (T R Kulp et al, Science 321:967, August 15, 2008.) "A primitive form of photosynthesis in which arsenic is the electron donor occurs in purple bacteria in a California lake, perhaps a relic of early life forms."

* For more on arsenic in medicine, see: How arsenic works against a cancer (June 16, 2010).
* For a report of a bacterium growing with arsenic replacing phosphorus in general metabolism, see: NASA: Life with arsenic (December 7, 2010). That bug, too, is from Mono Lake, which has a high level of As. Note that the paper has little specific information about what replacements are actually occurring.

More from Mono Lake... A superhydrophobic fly -- that can survive in highly alkaline water (February 25, 2018).

More on biofilms... On sharing electrons -- II (June 9, 2013).

More about purple bacteria: A purple-green protist, with an unusual set of endosymbionts (September 25, 2021).

Image of a carbon atom that isn't there

August 17, 2008

A research group at UC Berkeley, headed by Alex Zettl, has observed individual atoms by "ordinary" electron microscopy. Not just any atoms, but light atoms -- carbon and even hydrogen. They can also observe missing atoms!

A really neat paper, featured on the cover of Nature. It is actually fairly straightforward transmission electron microscopy (TEM). The big trick was to use graphene -- a layer of graphite one atom thick -- as a support. At least some regions are sufficiently clean to allow single atoms of adsorbed light elements to be detected. And one thing that helps is that the graphene is a conductor, so electrons from the beam are easily dissipated, and the support withstands the rather long exposures needed to see these light atoms.

At left... Images of C atom (black arrow) and H atoms (red arrows) by electron microscopy. The C atoms have mass 12 daltons; the H atoms have mass 1 dalton. In further work they went on to make an image of a missing C atom -- a "hole". Surely, its mass is -12 daltons? For that picture, see Figure 3 of the paper listed below.

Is this all "honest"? In the paper, they discuss the interpretation of the spots at some length. They make detailed arguments to support the identifications. It becomes clear that their identifications are highly likely -- but not based solely on the EM. For example, they note that they could not distinguish H and He. But they identify the spot as H, because there is no He around, and anyway it wouldn't bind to the support. Similarly, the C could be off, but C is most likely.

[This reminds me of a story Bonnie Bassler tells of the identification of a novel regulatory molecule found in some quorum sensing systems in bacteria. Based on x-ray info -- quite good X-ray info -- she wrote a structure with a C connected to four oxygens. She thought it a bit odd, but that is what the data seemed to show. Only when a chem colleague strongly objected did they consider the possibility that they might have a boron atom instead -- with the X-ray pattern unable to distinguish B and C. She then tells of how she set out to learn everything that is known about B in biology -- a project that took something under a half hour. Indeed the compound turned out to be a borate ester -- one of the very first specific B-containing chemicals identified with a specific role in biology.]

In any case, back to the current work...

There is a good news story at Electron microscope sees single hydrogen atoms. (Physics World, 7/16/08.) The figure above is from this site; it is also part of Fig 2d from the paper.

There is a good summary of the work, with pictures, at Zettl's web site: Zettl: Atoms (now archived).

The paper itself is Imaging and dynamics of light atoms and molecules on graphene. (J C Meyer et al, Nature 454:319, 7/17/08.) A copy is at Zettl's web site: pdf file. As noted, the Figure shown above is part of Fig 2d of this paper; see Fig 3 for the image with a C atom missing.

Another way to get to the paper -- and more -- is to go to his list of publications: Zettl's list of publications. Scroll down to 2008. He posts pdf of most of his papers -- and his site has other neat stuff, including unusual fullerenes.

The paper is actually quite readable, at least for those with some chem and EM background. As always, if you find parts of the paper difficult, just skip those parts -- and enjoy the pretty pictures.

Also see: Seeing molecules under a microscope (September 19, 2009). This post involves developing atomic force microscopy to allow observation of the atomic structure of small molecules. It shares with the current post pushing back the limits of common techniques to allow novel atomic-level visualizations. And they both bring some neat pictures!

Also see:
* Visualizing atoms with electron ptychography -- approaching the theoretical resolution (June 5, 2021).
* A chemical bond to an atom that isn't there (October 31, 2018).
* How many atoms can one carbon atom bond to? (January 14, 2017).
* Graphene by the roll -- and soon in your living room (July 31, 2010). This post discusses advances in the production of graphene.

For more on AFM and EM, see a section of my page of Internet Resources for Introductory Chemistry: Atomic force microscopy and electron microscopy (AFM, EM). Some of the links are to galleries of AFM images. It also includes a list of other Musings posts on AFM and EM.

This post is listed on my page Introduction to Organic and Biochemistry -- Internet resources in the section on Aromatic compounds.

Global warming

August 3, 2008

There will be winners and there will be losers.

Global warming [link opens in new window]. (source unknown)

Also see:
* Is Arctic warming leading to colder winters in the eastern United States? (May 11, 2018).
* Economic analysis of the damages (and benefits) from climate change (August 26, 2017).
* Was there a significant slowdown in global warming in the previous decade? (May 30, 2017).
* Is the weather getting better or worse? (May 23, 2016).

Flu vaccine -- some good news

July 29, 2008

The following link gives some good news about flu vaccine development. The link is to a press release at Purdue. There is a good overview of the flu vaccine issues.

Note two developments, which really are quite distinct...

First, they do not use eggs for growing the vaccine virus. The (chicken) egg method works well most of the time (though it does produce a vaccine that cannot be taken by those allergic to eggs). However, it is relatively slow. Further, it is an interesting question whether it would work well for a bird flu virus that is good at killing chickens.

Second, the virus works against a range of flu strains, not just a single strain. A broad H5N1 vaccine has already been approved, but frankly it is not very good. This one is not claimed to be effective against all H5N1, but it works against at least one and possibly two subgroups. They suggest that this vaccine could be stockpiled in anticipation of an outbreak, even though a more specific vaccine might be developed when the outbreak occurs.

Testing has proceeded only as far as mice. It's not ready for prime time yet.

New vaccine may give long-term defense against deadly bird flu and its variant forms. (4/17/08. Now archived.) (At the bottom are abstracts of two of their recent papers on the work.)

Items on the flu, especially on the new 2009 flu, have been consolidated on the page Influenza (Swine flu)

Solar taxi

July 14, 2008

This post is based on a talk I attended.

The event. [The URL here is an archive site; the video of the event is no longer available.]

The story.

The simple story is that he has a solar-powered car -- and is traveling around the world without a drop of gasoline (for the land parts). The trip is -- openly -- something of a publicity stunt.

The car pulls a trailer with a panel of solar cells.

Now, it is not quite that simple. In fact, the solar trailer provides only part of the power. He has an additional solar installation "at home", which feeds into the grid. He takes credit for that, and charges the batteries from the grid wherever he is. Ok.

Fun! The talk was more a travelogue and pep talk than science or even technology, but it was worthwhile. He is a good speaker, and certainly an advocate.

He tells lots of stories about the countries he has visited. (He started in Switzerland, and went east.)

Among them...

Worst press -- quantitatively: Australia. Zero reporters showed up for his big press conference.

Worst press -- qualitatively: Saudi Arabia. The newspaper story quite misrepresented his trip. He suspects the oil kingdom did not want to publicize an alternative.

Worst highway incident: India -- though this sort of had a happy ending.

Worst bureaucracy: Hm, maybe China and Saudi Arabia. But he made clear his admiration for what the Chinese are doing, even while emphasizing the extreme bureaucracy.

Least useful place to visit: New Zealand. No one lives there (as he showed a picture of sheep). However, he did make a good university connection there (Otago), and they are going to build a second generation car for him.

Most difficult country to enter: US. Well, except for Japan -- which refused him entry, period. Why? Because Japan does not allow vehicles with Swiss license plates, due to lack of a treaty between those two countries. To an image of the Japanese flag, he made a joke about Japan not allowing his solar car in. (Folks, if you don't know what the Japanese flag looks like, you are missing the point.)

The complete video of the talk is at the CITRIS web site. Go to the first link given above, and click on "view lecture". Even if you watch just a few minutes, you will get the flavor. There are also a lot of photos at that site. The car was on display in front of the building; I think it was demonstrated after the lecture. Of course, there is much more at his site, the other link above.

Other posts about CITRIS events:
* Printed electronics: Using a printer to make a better can of soup (April 3, 2012).
* CITRIS: Zettl; new energy series (November 1, 2009).

More about traveling... Exoplanet Travel Bureau (February 21, 2015).

This could be you

July 8, 2008

This item was originally posted, with the title given here, a figure, and a comment: Imagine a kid having this as the first entry in his/her photo album.

Here are news stories that include the picture:
* Human Ovulation Moment Caught on Camera. (Cell News (blog), June 18, 2008)
* (No longer freely available) Human egg makes accidental debut on camera. (New Scientist, June 11, 2008)

The picture shows an egg emerging from the ovary -- the process of ovulation. The yellow thing is a human egg (or contains a human egg in it -- not entirely clear).

This guy had a camera inside this woman, and she ovulated as he watched.

What was he doing with a camera in there? An operation -- a laparoscopic hysterectomy. Catching the ovulation was just a happenstance.

A problem with interpreting such a picture, the way I sent it originally, was lack of context -- and any sense of scale. The ovary is the blur in the background. The red object is a single follicle of the ovary.

Arguably, the emergence of the individual egg could be considered the first step that could be specifically identified with a new life. It would thus be a suitable first picture in one's photo album of life. Of course, this particular egg probably had no such future -- tho it is not really discussed anywhere. This particular egg probably just dropped into the woman's peritoneal cavity.

The article: Laparoscopic observation of spontaneous human ovulation. (J-C Lousse & J Donnez, Fertility and Sterility 90:833, September 2008.)

Another egg: What are they? (September 14, 2011).

More... In the beginning... It's Izumo1 + Juno (May 23, 2014).

Also see...
* Involvement of the non-pregnant uterus in brain function? (February 11, 2019).
* Observing the birth of quadruplets (March 29, 2015).

Are you happy?

July 5, 2008

Big news story. Here it is from the source: the World Values Survey, University of Michigan Institute for Social Research. Happiness is rising around the world: U-M study. (6/30/08.) From there, you can link to the happiness chart -- and see how your country rates. You may find it interesting/instructive to compare with neighboring countries or such.

Note that the ratings are not for "now", but are based on integrating data over several years. So don't let a current situation weigh too heavily in your expectations.

Be cautious interpreting this. The survey itself is very simple, very elegant. But what is behind it is not always clear.

People sometimes note, for example, that the "poor" in the US are much better off than the poor in some country X, yet are unhappy. Why? Because they compare with what they know, what is around them, what they see on TV.

The study does some analysis, and notes that economics per se is only one factor, not always the most important. They emphasize the importance of freedom and human dignity. I suppose "hope" could be considered a key factor. But another side of that is knowing there is something better. People in closed societies may not know there is something to hope for. Witness the effort China goes to in order to keep news from its populace.

One key paragraph from the news release linked to above:

"Economic growth, democratization and rising social tolerance have all contributed to rising happiness, with democratization and rising tolerance having even more impact than economic growth. All of these changes have contributed to providing people with a wider range of choice in how to live their lives - which is a key factor in happiness."

I was surprised to see Colombia near the top, given what we hear about the social situation there. Perhaps what we hear is not representative. The dominance of former Soviet bloc countries near the bottom is striking; I was somewhat surprised, though, that the Baltic states were there too. (14 of the 19 countries with negative scores are in that area -- former Soviet republics, Soviet bloc, on down thru Yugoslavia. Ditto for 4 of the lowest 5 positive scores. Yet a number of counties in that area seem to be doing well, such as Poland, Czech Republic and the northern parts of Yugoslavia.)

Mainly for "fun". If something does intrigue you, read more, and see what is behind the numbers.

(Their idea of a "country" is not entirely clear. #2 on the list is Puerto Rico, which is not a country -- it is a territory of the US. There are some other non-countries on the list of countries.)

Also see... The Happy Planet Index (December 27, 2011).

Swirling tower

July 1, 2008

From a reader. Fun.

... something utterly fantastic! A moving skyscraper!

http://www.csmonitor.com/Innovation/Horizons/2008/0625/dubai-s-twirling-tower.

Be sure to get to the video where you can see the individual floors spinning independently.

Another post about an apartment complex: A bird nest (September 9, 2014).

Another house: A small house (July 1, 2018). Tenth anniversary Musings post.

More things spinning... A new record: spinning speed (October 12, 2018).