Musings: 2008 (archive)

Musings is an informal newsletter mainly highlighting recent science. It is intended as both fun and instructive. Items are posted a few times each week. See the Introduction, listed below, for more information.

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December 2008


December 23, 2008

'Tis amazing how often it comes up, both with native speakers and those learning English later.

The following bit of advice on the matter is apparently well known. I just came across it in a book I am reading.

"Form the possessive of nouns by adding 's, just an apostrophe, just an s, a semicolon, a w, an ampersand, a 9, or anything."

Something to ponder for the holidays, which all too often seem to be about possessions.

Other posts on English include:
* Punctuation (January 11, 2010)
* Spleling (June 11, 2009)

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.)

Croatian Tethya beam light to their partners

December 16, 2008

A question for you: Who invented fiber optic cabling?

You can't think of the name? That's ok. I'll settle for the species -- or even the phylum.

Try this: Nature's 'fibre optics' experts. (11/10/08.) "Sea sponges can beam light deep inside their bodies, and do so using the natural equivalent of fibre optic cables, scientists have found."

Some time ago, it was shown that the skeletal "hairs" on some sponges could transmit light -- with surprising efficiency. These hairs are basically glass (silica); they are called spicules. Now, there is evidence that the spicules actually function as light pipes in the sponge and are biologically important. The sponges harbor photosynthetic microbes -- and probably depend on them for food. But photosynthetic bugs need light, and it is rather dark down there. So the sponges pipe in light.

The paper is: Light inside sponges. (F Brümmer et al, Journal of Experimental Marine Biology and Ecology. 367:61, 12/08.)

Note that this might be considered another example of a photosynthetic animal.
* Also see: COOL AS HELL! Sea slug that runs on solar power (Really) (November 30, 2008).
* For a photosynthetic vertebrate, see: A photosynthetic salamander? (August 24, 2010).

The 2009 Nobel Prize in Physics related to fiber optics: Nobel prize in physics for the rediscovery of fiber optics (October 12, 2009).

More about fiber optics... Detecting earthquakes using the optical fiber cabling that is already installed underground (February 28, 2018).

This story is also noted on my page Introductory Chemistry -- Internet resources in the section on Solids.

More about sponges:
* Bending a rigid rod (May 17, 2013).
* Quiz: What is it? (October 31, 2012). See the answer.
* An unusual eye? (June 6, 2012).

More about silica: Long-term data storage in glass (August 14, 2013).

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).

A mammoth story

December 1, 2008

This item is particularly important for any who were planning to ask for -- or give -- a mammoth for Christmas.

A recent announcement of a genome sequence for a mammoth was greeted with much fanfare. Inevitably, news stories began talking of how one could use the genome sequence to recreate the animal. (The Jurassic Park scenario.)

A couple comments about the genome sequence work per se. First, it is a example of using the new sequencing technologies, with greatly increased throughput. Second, the published sequence is quite incomplete. They claim it is about 70% of the genome. It is an incredible achievement to get this much, but it is far from being "a genome".

A Neandertal sequence will come in due course.

News story: Woolly-Mammoth Genome Sequenced. (Science Daily, November 20, 2008.)

The following three items are from Nature. (The first may require subscription for access; the others seem freely available.)
* Two news stories accompanying the article:
1) Let's make a mammoth. (H Nicholls, Nature 456:310, November 20, 2008.) It is a good overview of the issues in going from genome sequence to making the animal. I think the article can be usefully read by people at all levels. If some parts get a bit heavy, just browse, and go on to the next point. (You'll probably learn more about elephants than you wanted to know.)
2) DNA sequencing: Mammoth genomics. (M Hofreiter, Nature 456:330, November 20, 2008.)
* The article: Sequencing the nuclear genome of the extinct woolly mammoth. (W Miller et al, Nature 456:387, November 20, 2008.)

For more on mammoths...
* Comparing woolly mammoth genomes over time (June 1, 2015).
* Uptake of small pieces of ancient mammoth DNA by bacteria: What are the implications? (May 13, 2014).
* Early American art: a 13,000 year old drawing of a mammoth (July 18, 2011).
* Mammoth hemoglobin (February 1, 2011).

There is more about genomes on my page Biotechnology in the News (BITN) - DNA and the genome.

November 2008

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).

Both ways

November 18, 2008

The infectious agents for some diseases can be passed from one animal to another.

It is common knowledge that we can get some infectious agents from other animals. But it works both ways. Our pets and other animals can get infectious agents from us, too.

There is a nice little (one page) news story about this in a recent issue of Microbe. It is J L Fox, Cats with MRSA, elephants with TB are parts of a "microbial storm". Microbe 3:451, October 2008.

That news story is no longer available online. An alternative: Cat Got Your MRSA? -- Pets Can Harbor Drug-Resistant Staph and Pass It to People. (M Hitti, WebMD, March 12, 2008. Now archived.)

There are various levels of transmission of diseases from one animal to another.

Every case of rabies or malaria in humans comes from another species. We just don't transmit these human to human. (I suppose we might transmit rabies, but the chances are low.) The example in the article of MRSA -- the drug resistant "staph" -- in cats and dogs falls here. Cats and dogs don't carry staph. People do. The pets get it from the people.

The Ebola virus is probably maintained in nature in bats. Somehow, it occasionally gets transmitted to humans -- but then is easily transmitted human to human. About all that saves us is that most people who get it die quickly -- breaking the transmission.

Some diseases of humans, now transmitted among humans, once were diseases of other animals -- and somehow crossed. Flu is a ongoing example... There is much attention given to a particular strain of bird flu that is deadly to humans. Fortunately, it is only poorly transmitted by humans, so almost all cases come from birds -- from rather intimate contact with birds. But given the nature of the flu virus, it is plausible, perhaps even likely, that the virus will adapt at some point to become a human flu virus. The 1918 flu pandemic was almost certainly due to such an event; it killed 50 million people.

Is this disease transmission relevant to food safety? Yep. Any animal we eat is a potential source of infectious agents. The good news is that this is rather well understood; good food handling should pretty much eliminate disease transmission from food animals. Almost all infectious agents are killed by proper cooking. (The one exception is the prion -- the agent of mad cow disease. But this is rare. There are also issues of toxins; these may not be eliminated by cooking, but this is a different issue.) There really is no reason to avoid any food animal because of fear of disease transmission.

Unfortunately, vegetables have become a source of disease agents -- as much due to our complex food system as anything. Vegetables may become contaminated with disease agents from animals. Importantly, we do not cook many of our vegetables, so if they are contaminated, we can fall victim. There have been incidents of this type in the news in recent months. (Certainly, if the lettuce is coughing, do not eat it.)

Also see my page BITN: Emerging diseases. That discusses disease transmission among types of animals.

Also see...
* Microbes on your fresh fruits and vegetables? (May 29, 2013).
* Rats, bananas, and tuberculosis (March 11, 2011).
* Q     or     Beware of goats bearing infections     or     It's one health. (February 20, 2010).
* Killer chickens (December 2, 2009). That post is primarily about transmission of disease from chickens bought as food.

For more about prions, see my page Biotechnology in the News (BITN) - Prions (BSE, CJD, etc). It includes a list of related Musings posts.

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).

Obama and science

November 13, 2008

For those who are impatient...

New Scientist posted an item on Obama and science. It is at: Obama promises new era of scientific innovation. (November 5, 2008.)

Time will tell.

Also see: Science in the White House (June 11, 2009).

More about Obama... Nobel Peace Prize (October 25, 2009).

2016: US Presidential candidates weigh in on science questions (October 18, 2016).

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.


November 10, 2008

A nice little article about bald eagles. Mainly for fun. Beauty Is Only Feather Deep. (C L Raven, American Scientist 94:392, September 2006.)

The bald eagle is an American symbol -- and sometimes people wonder why.

More about eagles: What is killing the eagles? (April 5, 2021).

For an item about another American icon in the skies: Turkey stories (April 19, 2010).

October 2008

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.)

Man's best friend

October 22, 2008

The article is "Genetics and the shape of dogs". Much of it is at a level suitable for general reading -- and it has lots of good pictures. Genetics and the shape of dogs. (E A Ostrander, American Scientist 95:406, 9/07.) Check Google Scholar for a freely available copy.

The dog occupies a special place in human culture -- an amazing story of domestication. We not only use dogs, but our social bonding with them is quite distinct. Is there any animal besides the dog with whom we are willing to share the bed, and even the dinner table? Their wolf ancestors are extremely social animals -- a base upon which to build. But the modern dog is largely a human creation; the characteristics of dogs are what humans have bred dogs to have. This domestication began millennia ago, but intensified rather recently. Most of what we know as the modern dog was developed only in the last couple hundred years or so.

The diversity of dogs, by both their behavioral characteristics and their obvious physical characteristics, is striking.

Analysis of dog breeds has taken some major steps forward. The dog genome has been (partly) sequenced. Beyond that, the genetics behind the various breeds has been largely elucidated. A quite small number of key developmental steps is the difference between dogs of distinctively difference appearance. (Of course, this fits well with our modern understanding of body plan development; the basics of animal body plan were laid out a few hundred million years ago, with only "minor" changes needed to produce animals from sponge to human. The underlying differences between dog breeds is tiny in this perspective.)

The article is a nice overview of the dog. There is some technical information in it, but it is also good for general reading. I think many will enjoy at least browsing it.

A related post on dog genetics, focusing on the coat: Bichon frise. (November 17, 2009.)

Also see: How many species of wolf are there, and why does it matter? (October 16, 2016).

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).

Got milk?

October 13, 2008

The question is: How long have people been asking that?

And the new answer is, a couple thousand years longer than we used to think.

As so often, the article is interesting not only because of the answer but because of the methodology. I think you may enjoy reading what they did, regardless of whether you care much about the answer.

News story: Stone Age Milk Use Began 2,000 Years Earlier. (National Geographic, August 6, 2008. Now archived.)

The article: Earliest date for milk use in the Near East and southeastern Europe linked to cattle herding. (R P Evershed et al, Nature 455:528, September 25, 2008.)

Next milk post: More milk (October 16, 2008). (immediately above)

More dairy history... The oldest known piece of cheese (April 25, 2014).

More herding... A biodegradable agent for herding oil slicks (September 18, 2015).


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).

Nobel prizes

October 8, 2008

As so often, it seems, the "molecular biologists" have captured two of the science Nobel prizes this year.

The chemistry prize was announced this morning, and went to three scientists associated with the story of GFP = green fluorescent protein. GFP was originally isolated from a jellyfish, so there is a neat story of its natural biology. But then it was developed into a major lab tool. It has crept into the popular press, because of the delightful pictures. Some of you may have seen pictures of green mice and self-lighting tobacco -- both based on GFP.

The Nobel trio here includes Roger Tsien of the University of California. San Diego, not Berkeley, but still, it is one big family. (Berkeley seems not to get many science Nobels anymore.) A midday seminar made use of his work (on other detection systems) -- and noted the announcement about him this morning. Tsien is one of those folks who could easily win more; he is just quite a scientist.

The Nobel announcement is at: Nobel prize announcement, chemistry, 2008.

But for those for whom this is new... try the GFP website, at GFP. At least, look at the pictures. (This site is really the reason for posting this item. I'm sure most of you know about the prizes.)

(And seriously, there is plenty of good chemistry in this work. At the heart of it was figuring out how this complex molecule is fluorescent -- and then how to modify that property.)

Among Musings posts about the use of GFP:
* Design criteria for mRNA: the start codon (May 2, 2022).
* Medical safety: What if pills were better labeled, so your phone could verify them? (April 23, 2022).
* How tau gets around (June 28, 2020).
* CRISPR connections: p53? cancer? (October 6, 2018).
* Regenerating a leg (September 1, 2009).

For more on GFP in the Tsien lab: Petri dish art (May 11, 2011).

This Nobel is also noted on my page Internet resources for Molecular Biology: Miscellaneous.

Earlier in the week, the "biology" Nobel (technically, Physiology or Medicine) was awarded to three scientists involved in the discovery of HPV (human papilloma virus) and HIV (human immunodeficiency virus).

HPV is a clear example of a virus causing cancer. That has long been a big question. It is important to understand that the answer is not yes/no. That is, there is no simple answer to the broad question of whether viruses cause cancer. Some viruses do. Broadly, cancer involves changes in control of cell growth. This is typically due to multiple mutations affecting various aspects of growth. Some viruses can, in effect, provide one or more of those mutations. That is what HPV does, and it is fairly well understood exactly what this virus does to cause cancer. Note that only some strains of HPV cause cancer. There is no broader implication that viruses in general cause cancer, or that cancer requires viruses. zur Hausen's work with HPV was an important part of developing this broader understanding.

The Nobel announcement gives some info on this: Nobel prize announcement, medicine, 2008.

This Nobel is also noted on my page Biotechnology in the News (BITN): HPV.

* * * * *

Next post that featured a Nobel in the title: Nobel prize in physics for the rediscovery of fiber optics (October 12, 2009).

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.

September 2008

Titanium biology

September 29, 2008

We had a seminar on titanium biology a few days ago. Ann Valentine, from Yale. Very interesting (and a good presentation), and I thought it would be good to share some of the highlights. The full story is on the supplementary page Titanium biology.

Posts about titanium include:
* Communication in diatoms (February 6, 2022).
* The major source of positrons (antimatter) in our galaxy? (August 13, 2017). Links to more.

What are these?

September 25, 2008

picture, to be identified

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).

Lasagna battery

September 25, 2008

From a reader... (I did not ask how this came up.)

"A "lasagna cell" or "lasagna battery" is accidentally produced when salty food such as lasagna is stored in a steel baking pan and is covered with aluminum foil. After a few hours the foil develops small holes where it touches the lasagna, and the food surface becomes covered with small spots composed of corroded aluminum. This metal corrosion occurs because whenever two metal sheets composed of differing metals are placed into contact with an electrolyte, the two metals act as electrodes, and an electrolytic cell or battery is formed. In this case, the two terminals of the battery are connected together. Because the aluminum foil touches the steel, this battery is shorted out, a significant electric current appears, and rapid chemical reactions take place on the surfaces of the metal in contact with the electrolyte. In a steel/salt/aluminum battery, the aluminum is higher on the electrochemical series, so the solid aluminum turns into dissolved ions and the metal experiences galvanic corrosion."
From: Lasagna cell.

So, would it be possible to get electrocuted by some leftover lasagna?

More about batteries... Fast charging batteries (March 13, 2009).

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).

Science cartoons

September 21, 2008

The site, and one of the cartoons, was noted in a recent journal.

Now archived: 2008 Science Idol Finalists.

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

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.

Why swatting flies doesn't work

September 15, 2008

It's nice to see that Caltech scientists are working on practical problems.

A news story -- with video: Fly's brain 'senses swat threat'. (8/28/08)

Several movies of the work are posted with the article. Go to Movies. Scroll down to the movies, under "supplemental data" after the main text.

The article itself is G Card & M H Dickinson, Visually Mediated Motor Planning in the Escape Response of Drosophila. Current Biology 18, 1300, September 9, 2008. Use the same link given above for the movies. The article is actually quite readable -- and much fun. Unless of course, you side with the flies.

Seriously, this is good neurobiology work. Working out how a simple brain reacts to a stimulus is good basic biology. Ours may be more complex, but we probably build on what the fly brain does.

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).

How do you imagine your house in 20 years?

September 2, 2008

From one of you...

Houses of the future are here!
Houses - 1.
Houses - 2.

Not sure it is a good idea to have a house that is soluble in solvents likely to be found around the garage.

On the other hand, it could make moving easy. Just dissolve the house, and then re-cast it at the new location.

Save your coffee cups!

August 2008

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.

Images of C and H atoms by electron microscopy.

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.

A robot that eats flies -- and more

August 4, 2008

A contribution... The world's six most useful robots. (June 22, 2008.)

(It would be nice if the article gave links for more information on the individual items. Still, it is a nice article.)

More about what robots eat: A robot that can feed itself (February 3, 2017). This is from the same lab as the title topic of the current post, which is item 1 of the linked story.

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).

July 2008

Working with Windows Vista -- Make it fly!

July 29, 2008

An article about working with Windows Vista, and improving its performance. The thread includes with some lively discussion. See Supplementary page: Windows Vista

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)

Making a wimpy virus

July 23, 2008

This story has gotten considerable attention.

As key background, one approach to making a vaccine is to use an attenuated form of the disease agent. The attenuated form is able to grow, and induce immunity, but not able to cause disease. The oral polio vaccine (Sabin) is of this type.

Traditionally, the attenuated form is made by a ritual, and the basis of attenuation is not clear. It is tested to see that it does not cause disease, but we typically do not understand why. The Sabin polio vaccine has actually caused some problems, as it mutates back to the virulent form.

So, a good goal would be to attenuate vaccine organisms by design -- intentionally building in changes that reduce virulence.

The work here is an example of rational design of an attenuated organism -- but using a strategy that does not really depend on understanding all the gene functions of the agent.

The genetic code uses 64 triplet codons to code for 20 amino acids. As that might suggest, there are multiple codons for some (most!) amino acids. For example, there are four codons for Thr (threonine): ACN, where the N indicates that any of the four bases are ok in the third position.

Now, it might seem that codons that code for the same amino acid, eg ACA and ACG, would be equivalent. (And that is often a good approximation.) Certainly they are "synonymous" -- coding for the same amino acid.

However, it turns out that not all synonymous codons are used equally well. Why? A simple reason is that the amount of tRNA available may differ. Thus, a codon with much tRNA available is translated "fast", and a synonymous codon with very little tRNA available is translated "slow". Of course, a basic observation is that organisms work -- even if not very well. In general, "fast" codons are used a lot, and "slow" codons are used less. It works out. And it is fairly well understood. People moving genes from one organism to another may consider whether they should change any codons in the gene so they work better in the new host.

What they do here is sort of the opposite. They design a variant of polio virus to use many "slow" codons. They made a few hundred mutations, each making translation more difficult. The result? A virus strain which grows poorly, induces an immune response, and does not cause disease (based on tests with mice so far).

And they have a nice acronym.

Press release from the lead university, summarizing the story: SBU Team Designs Customized Wimpy Polioviruses A Method That Could Be A New Path To Vaccines. (June 26, 2008; now archived.)

The paper is: Virus Attenuation by Genome-Scale Changes in Codon Pair Bias. (J R Coleman et al, Science 320:1784, 6/27/08.)

Also see: Polio: progress toward eradication (November 5, 2010).

My page for Biotechnology in the News (BITN) -- Other topics includes a section on Polio.

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).

Book: Life of Pi, by Yann Martel

July 13, 2008

A book recommendation from a reader. (It is not one of my usual science books.)

Yann Martel, Life of Pi.
Amazon link:

The book is really nice, I've enjoyed it as it is a mixture of a lot of different stuff, and most important in it is the position of the main character on freedom and religion. Don't be too critical, though..

My comments ...

I have just finished reading it, and I endorse the recommendation.

The book, published in 2001, received the Booker prize a few years ago -- a prestigious award to books from the British Commonwealth (so not all that well known in the US). I had not heard of it, nor of the author (who apparently is Canadian).

As noted, it can be read on various levels. I'm not sure I would make much of the religious part -- tho Pi's conversion to Christianity, Hinduism and Islam certainly is one interesting, and amusing, part of the book.

However one describes it -- I suppose I would lean toward "fantasy" -- it is well written and fun to read. If you foresee spending seven months on a lifeboat with only a tiger, it is a must read. Some have suggested it is a children's book. I think that underestimates the book, but certainly it is suitable for young teens.

Some of you may be interested to know that the book action starts in Pondicherry, in southern India.

One disappointment... The book has 319 pages, 5 more than I expected. I wonder if that is a production error.

This post is noted on my page Books: Suggestions for general science reading, for Martel, Life of Pi.

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).


July 8, 2008

A G story. Real science, about the G (guanine) in DNA.

The DNA double helix has become iconic, and many in the general public at least vaguely understand how DNA replicates via complementary base pairing. But these are simple points -- oversimplified.

The common DNA helix picture suggests that the DNA structure is uniform. But of course, to anyone with a bit of chemistry, that would be quite unreasonable. DNA is a heteropolymer -- contains different kinds of subunits -- and its structure varies with what subunits are present (the base sequence). That is biologically important.

Similarly, the idea that DNA replicates by base pairing is superficial. It is obvious to a chemist that the energy difference between right and wrong base pairs cannot possibly account for the observed high fidelity of replication. Much more -- loosely summarized as proofreading -- occurs to achieve the high fidelity replication.

The base G in DNA causes its own problems. Certain sequences that are rich in G tend to fold back on themselves, forming an intra-stand four-stranded structure known as a quadruplex. Not sure, but I suspect that the G-rich quadruplex first attracted attention in biology when it was found in telomere sequences. These are the sequences found at the very ends of chromosomes in higher organisms. The idea that the G-rich overhangs might form this quadruplex was appealing; maybe this is even good, a protective structure at the end.

But what about sequences inside the genome that might tend to form a quadruplex? Is this a concern?

In a recent paper, scientists used the worm model, C elegans. They found that mutant worms lacking the "dog" gene had high rates of deletion mutations -- in these G-rich regions. (It's not clear from this paper, but I bet that the gene name dog stands for deletion-of-guanine.) They thus suggest that the dog protein protects the genome from quadruplexes.

Relevance to us? The human genome sequence suggests that we have about 376,000 sites in our chromosome that might tend to form these G-rich quadruplexes. And we have a gene homologous to the worm "dog" gene. Not only do we have it, but the gene has long been known. It is called the FancJ gene; Fanc = Fanconi anemia. Mutations in the FancJ gene lead to genetic instabilities.

Thus we infer that known diseases in humans are due to problems with G-rich DNA sequences that might form quadruplexes; our normal FancJ gene protects us against these diseases. Note that the direct evidence here is solely from the worms.

The article is at: Mutagenic Capacity of Endogenous G4 DNA Underlies Genome Instability in FANCJ-Defective C. elegans. (E Kruisselbrink et al, Current Biology 18:900; June 24, 2008.)

And yes, the word guanine is related to guano.

More about telomeres:
* What to do if your telomeres get too long (March 19, 2017).
* A 115-year-old person: What do we learn from her blood? (November 18, 2014).

More about the quadruplex: Triplet-repeats: Do they act through the RNA? (September 24, 2017).

Another example of research on C elegans: Extending lifespan -- five-fold (January 12, 2014).

Another post about G -- a different G: Does anyone know how strong gravity is? (September 16, 2014).

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).

The vision thing

July 3, 2008

What happens if you cross green algae with blind mice?

The resulting mice can see.

Well, that is the idea. What they really did was to add a gene for a photoreceptor from a green alga to retinal cells of mice lacking photoreceptors, by genetic engineering.

And the treated mice indeed gained some vision. Not only did nerve measurements show responses, but the mice gained some useful vision, as judged by behavioral testing.

Obviously this has limitations; what they tried to do was limited. But it is also a remarkable success. Enough of a success that serious thought will be given to testing it in humans.

It is also a good reminder of the universality in biology. Moving genes from one organism to another is common nowadays, and gene function from such transfer is common. In this case, not only is there gene function, but also relevant physiological function -- with an algal gene in a mammal. The eye is one of the simpler parts of our body, and finding that algal and mammalian -- presumably including human -- photoreceptors can serve the same purpose is not a huge surprise.

A news story on this:
Blind mice see the light after algae protein treatment. (Thaindian News, April 28, 2008. Now archived.)

The article, via abstract at PubMed: Light-activated channels targeted to ON bipolar cells restore visual function in retinal degeneration. (P S Lagali et al, Nature Neuroscience 11:667, June 2008.) (Put the title into Google Scholar and you may find a freely available copy.)

More on animal vision: Butterflies and UV vision (June 29, 2010).

More on restoring sight: A camera-based device to restore vision (February 25, 2013).

(My title is a US political joke, which most of you are too young to understand. And it is not worth explaining.)

Swirling tower

July 1, 2008

From a reader. Fun.

... something utterly fantastic! A moving skyscraper!

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).

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