Musings: archive for 2009

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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2009 (This page):
December 29
December 21
December 16
December 9
December 2
November 23
November 18
November 11
November 4
October 28
October 21
October 14
October 7

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2008

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Archive items may be edited, to condense them a bit or to update links. Some links may require a subscription for full access, but I try to provide at least one useful open source for most items.

Please let me know of any broken links you find -- on any of my web pages. Personal reports are often the first way I find out about such a problem.


December 29, 2009


The 12 Psychology Studies of Christmas

December 28, 2009

The 12 Psychology Studies of Christmas. (December 22, 2009.)

Thanks for the contribution!

More Christmas posts: More resin for Christmas through better use of Boswellia (December 17, 2012).



The octopus and the coconut

December 28, 2009

Octopus in coconut shells. The figure shows, from top to bottom:
* A half coconut shell
* An octopus
* A half coconut shell.

This arrangement was made by the octopus.

Did you know that an octopus can build a shelter out of coconut shells?

Octopus snatches coconut and runs. (December 14, 2009.) The figure above is from this story.

The article is: Defensive tool use in a coconut-carrying octopus. (J K Finn et al, Current Biology 19:R1069, December 15, 2009.) It is a short article -- less than 2 pages. (The pictures are the same as those in the BBC story, above.) It includes an interesting discussion of what the criteria are for considering a behavior as "tool use". They suggest that this is the best example of tool use by an invertebrate -- one already known as being rather intelligent.

There are two movie files available at the journal web site. The first is quite spectacular! Have a look: Movies. Or, on the article web page, scroll down to "Supplemental Data".

After hearing the headline, I was a little disappointed with the story. I was hoping to see an octopus climb a palm tree.

Thanks to those who called my attention to this story. I finally chose the BBC news story -- as good as any I saw, and the best for pictures.

A subsequent post on tool use by animals: Complex tool use by birds (May 28, 2010).

Subsequent posts on octopi:
* How an octopus adapts to the cold -- by RNA editing (March 5, 2012).
* Octopus will only pay attention to television if it is "high definition" (August 20, 2010).



December 21, 2009


Neurobiology lesson (Bobby McFerrin)

December 21, 2009

From the session on "Notes and Neurons: In search of a common chorus", 2009 World Science Festival. If this isn't the time for a neurobiology lesson, just take it as another episode from San Francisco's inimitable performer Bobby McFerrin.

YouTube: Bobby McFerrin Demonstrates the Power of the Pentatonic Scale.

For more about the World Science Festival: World Science Festival. See "Archive" section for information on the 2009 festival.

There is more about music on my page Internet resources: Miscellaneous in the section Art & Music.

Thanks for the contribution!



Spiders

December 21, 2009

Farooq sends What a show off! The multi-coloured 'peacock' spider that reveals a spectrum of shades to attract a mate. (11/28/09.) The reason is shown at the right.

(This is reduced from the image at the news site. That is, the image size is reduced. The spider itself is actually quite tiny: it would easily fit on a finger tip.)

As the news story notes, the coloration is a distinctive feature of the male, and is part of its attractiveness to a potential mate. This would seem to be a classic case of sexual selection, as enunciated by Darwin: evolution selecting for traits that enhance mating success. This has been well studied in peacocks (the birds); there seems to be little information available on the peacock spiders.
Peacock spider

More about the peacock spider:
* Here is page with numerous pictures of the peacock spider: Peacock spider, Maratus volans. (11/29/08.) The pictures here, as well as the one at the top, are by photographer Jurgen Otto. Among the pictures are some with a direct view of the colorful flap in the raised position. There are also pictures of the spider with two legs raised straight up -- while maintaining a normal posture; I bet you can't do that. Apparently this guy is quite a dancer, too.
* And for information: Debunking an urban myth: The jumping spider Maratus cannot fly!. (by Julianne M. Waldock, Western Australian Museum, 2007.) The main point is that those flaps are not wings, but this brief article gives some other information about the history of this spider.


That colorful fellow reminds me of the happy-face spider. This is from a newspaper article (which is probably not of much interest at this point): Spiders invade the Bishop Museum this weekend. (9/17/96.)

And here is a whole page of happy-face spiders. This is from an article a few years back: Portraits of Evolution: Studies of Coloration in Hawaiian Spiders. (G S Oxford & R G Gillespie, BioScience 51:521, 7/01.)


The peacock spiders and the happy-face spiders strike us by their coloration. The stories behind the coloration seem to be different for these cases. As noted above, with the peacock spider, the male is highly ornamented in order to impress a mate. With the happy face spiders, the reason for the coloration is not clear. All the spiders shown on the page noted above are from one species; spiders of a single population are highly varied in their coloration. The genetics behind the varied coloration have been partially worked out, but no reason for it is yet apparent. The BioScience article above is a readable introduction to the story of the happy-face spiders (and another Hawaiian spider).

* * * * *

Another example of Darwinian sexual selection: Bird theater (October 19, 2010).

More about Hawaii: Hawaii's hot spot(s) (October 9, 2011).



HIV vaccine trial -- follow-up

December 19, 2009

The original post was HIV vaccine trial -- and quibbling about statistics (11/2/09). I have updated the post to include the final published paper. What is new is that I have also included the editorial that was published in the same issue of the journal. It is a two-page overview of the work, with a good plain-English discussion of what was learned from the trial. Recommended; a good place to start, and a good place to go back to if you found the coverage so far to be confusing.



December 16, 2009


Electricity in DNA: guarding your genes?

December 16, 2009

This is a fascinating item, tying together two seemingly distinct issues.

First... A couple decades ago there was considerable controversy about whether DNA could conduct electricity. The structure of DNA -- the stacked base system -- would seem to allow it; it was just a matter of showing it -- or not. In fact, people got various results. Over time, it became understood that the answer was probably yes, but that conduction was very sensitive to the DNA structure.

Second... We all understand the importance of maintaining the integrity of our genes. What we often do not appreciate is how difficult a task that is. DNA must replicate accurately, yet to do so seems to violate the laws of chemistry. Over time, we have come to understand how costly proofreading bridges that gap. Further, DNA is subject to damage. We understand that cells are full of enzymes that monitor DNA for damage, and repair it. But the notion of these proteins randomly monitoring your entire genome for defects almost makes this seem far-fetched.


So what is the connection? Jackie Barton (now chemistry chair at Caltech) was one of the pioneers in working out the conductivity of DNA. She now proposes that the electrical conductivity of DNA is central to monitoring it for errors. The basic idea is this... Two DNA repair proteins bind to DNA. One sends an electron down the conducting DNA. If the second protein receives that electron, it quickly falls off. Why is this an interesting process? Because the conductivity of DNA is extremely sensitive to the DNA structure; if there is a DNA defect, the electron is not transmitted. The protein does not fall off -- now "knowing" that there is a defect nearby. That is, the free conduction of electrons along DNA serves to signal "all clear", and the repair proteins can look elsewhere. This would lead to a huge improvement in the efficiency of the search for damage.

Evidence? Well, mainly circumstantial at this point, but the case is developing. (Barton is actually quite cautions in presenting the proposal, as seen in the paper below and in her recent talk here.) For example... The repair proteins contain a redox center (for our purposes, an "electron detector"). This redox center has no obvious role in the repair reaction of the enzyme, and had been quite a mystery.

It will be fun to watch how this story develops.

News story: Electricians shocked to find out how DNA repairs itself. (Naked Scientists, September 6, 2009.)

The paper is: Redox signaling between DNA repair proteins for efficient lesion detection. (A K Boal et al, PNAS 106:15237, 9/8/09.)



Where are the eyes?

December 16, 2009

Borislav asks you to look at the picture, and find the eyes. picture.

For more, see the supplementary page Fish eyes.

Other posts on the diversity of animal eyes include...
* Where are the eyes? (August 19, 2011). Same title. Different animal.
* How many eyes does it have? (March 12, 2010).



How molecules walk: a movie

December 15, 2009

Go to the website for Ron Vale's lab, and click on the main movie in the middle: Animated model of processive motion by conventional kinesin.

What's this about -- besides being cute? There are various molecules in your cells that "walk" around. One type is in muscle, where myosin walks along actin fibers. Another is kinesin, which carries cargo along microtubules within your cells. The movie here is an animation of how kinesin walks. It has two "feet", and they move along the microtubule track, one over the other, more or less as you walk. The orderly cycling is driven by the usual cellular energy source, ATP. In fact, this is a great example of how ATP (and related nucleotides, such as GTP) cause cycles of protein motion.

Much of this was worked out in Vale's lab, at UCSF (University of California, San Francisco). Vale gave a talk here recently, which prompted me to post this item. (One of his students -- now a Berkeley physics professor -- gave a talk on some of this a year ago; I never quite got around to posting it then.)

Look around his site. Among other things is a page of movie files. Explore!

For more on walking...
* Added May 28, 2014. "Moonwalkers" -- flies that walk backwards (May 28, 2014).
* What is it? (March 8, 2011).



A vaccine to make food safe

December 15, 2009

A recent post on food safety mentioned the problem of the E coli bacteria O157:H7. [Killer chickens - follow-up (12/9/09).] It is harmless to cows, but very bad for us. Thus the following news story caught my attention: After Delays, Vaccine to Counter Bad Beef Is Being Tested. (12/3/09.)

The simple story is the development of a vaccine -- for cows -- against this E coli. The story tells of some of the hurdles along the way, including the confusion over its regulation by the US government.

Remember, this is a vaccine for cows -- who are not harmed by this bug. The idea is to vaccinate the cows for our safety.

The news story gives numbers for both infections and deaths due to E coli O157:H7. Despite all the fear this bug engenders, the number of deaths it causes is less than 100 per year in the US. In contrast, ordinary flu causes 30-40,000 deaths.

For those who might like more about the confusing issues of food safety regulation, I recommend Marion Nestle's book Safe Food - Bacteria, Biotechnology, and Bioterrorism, listed on my page of Books: Suggestions for general reading.

Another post about E coli O157:H7... Don't eat the cookie dough? Or the flour? (February 20, 2012).



Appendix. Yours.

December 11, 2009

What is it for?

I was brought up with the idea that the appendix served no role, that it was something of a legacy (of what was not very clear), and that it would probably be lost eventually over evolutionary time as being of no value. Removing it was routine, and of no consequence (beyond the surgery itself).

However, a new idea has emerged: that the appendix is a reservoir of your normal gut bacteria. When your normal complement of bacteria has been upset (for example by an illness, especially with diarrhea), the appendix restores the gut biota and thus restores your health. I must admit that when I first heard this idea a few years ago, I shrugged it off as "silly". But it has been getting serious attention, and is enjoying some support. That does not mean it is right, but it is worth considering and exploring.

The idea that the appendix might be a bacterial incubator fits in with our increased understanding of the gut biota, including the importance of having the right bacteria.

This post was stimulated by a new paper, but I did not find a good news story for it. So, here is an older news story along with the current paper. For most people, the news story is sufficient for now.

The news story from a year ago... It provides a good introduction to the new proposal. Helpful Bacteria May Hide in Appendix. (6/17/08.)

The current paper: Comparative anatomy and phylogenetic distribution of the mammalian cecal appendix. (H F Smith et al, J Evol Biol 22:1984, 10/09.) The heart of the paper is comparative anatomy of the appendix, in diverse mammals.

Two parts of the 15-part Figure 1 are shown at the right. a = human; b = orangutan. The appendix is at the top.
Appendices: human, orangutan

Bottom line? Stay tuned. But don't be so sure that the appendix is useless.

Also see: Is Arthromitus a key bug in your gut? (1/16/10)



A small perk when living in Florida -- more

December 11, 2009

From: Maraca. I encourage you to read it aloud.

Since Musings is (primarily) about science... I think this comes under "biophysics". In any case, I learned about it from Science magazine (325:1208, 9/4/09).

This is a follow-up to A small perk when living in Florida (November 23, 2009). It is an unauthorized follow-up, and stands on its own.

More from Florida... Pythons in Florida (February 7, 2012).



December 9, 2009


Killer chickens - follow-up

December 9, 2009

This is a follow-up to Killer chickens (December 2, 2009). Various things...

One person wrote me that it is just taken for granted, in his country, that all chickens are contaminated with Salmonella. This reinforces the main point from the earlier message.

One of the "traditional" meat hazards many of us learned about is getting Trichinella worms from under-cooked pork. The rule was: always cook pork well-done. Interestingly, a new report on this just showed up -- and it shows that trichinellosis (or trichinosis) has almost disappeared -- at least from pork. This is presumably due to some combination of improvements in pig farming (including regulation and inspection) to reduce the incidence, plus the consumer-level protection of cooking pork well. Only 66 cases of trichinellosis were reported in the US over the recent 5 year period. (That is not per year, but total for 5 years.) Only 20% of those were associated with pork. (Bear is the most common source!) The report, which is short, very readable, and perhaps surprisingly interesting: Trichinellosis Surveillance --- United States, 2002--2007. (E D Kennedy et al, MMWR Surveillance Summaries 58(SS09), 12/4/09.)

The general picture that emerges... In the US meat supply, beef and pork are rather reliably safe; chicken is reliably contaminated. However, even "safe" meats are subject to sporadic problems. Therefore, good kitchen habits and thorough cooking are always useful precautions. As noted last time, preventing contamination of other kitchen items with contaminated meat prior to cooking is a serious issue. Fact is, the kitchen is probably the room in the house most likely to be a source of infectious disease.

Two sporadic problems with beef have become famous.
* One is due to Escherichia coli O157:H7. (Delightful name!) This gained the spotlight when it showed up at Jack in the Box; understanding what happened led to tightening the requirements for cooking beef. It is important to note that it is this particular type of E coli that is dangerous -- very dangerous, especially for children; other E coli are normal and presumably essential part of your gut biota. And this bad strain of E coli seems not to hurt the cows. E coli O157:H7 is still an issue; if you hear about a beef recall due to E coli O157:H7, take it seriously. (There are 18 beef recalls currently "active"; 9 of them involve E coli O157:H7.)
* The other famous beef problem was BSE ("mad cow disease") -- and the resulting human disease vCJD (variant Creutzfeldt-Jakob disease). The unusual infectious agent in this case, the prion, is not killed by cooking. It was propagated by human-designed farming practices that served to amplify the prion. Once the positive feedback loop was recognized, the practices were changed, and BSE has substantially faded away. Interestingly, an important clue to understanding the BSE cycle came from working out a similar disease in humans, kuru, which had been propagated through ritual cannibalism. (A perverse thought... How many more would have died from BSE had not the Fore of New Guinea developed their odd ritual -- and had not scientists worked it out before BSE struck?) Even with all the hype, only about 200 people actually got it, mainly in England; it is a serious disease, but poorly transmissible from cow to human. Prions are fascinating, but there is little need to worry about them from our food supply. (I have more on BSE on my page Biotechnology in the News (BITN) - Prions (BSE, CJD, etc).)

Most of our meat comes from "industrial" farming. Farming practices and regulation affect meat quality. We have not discussed those issues here very much. These change over time -- hopefully for the better. Those in other countries can check to see what you can learn about local meat supplies. (There is some discussion of why chickens are contaminated in the CR report; see the page on "Dirty Birds".)

The post A vaccine to make food safe (12/15/09) discusses a new vaccine against the E coli strain O157:H7. This is the E coli noted above as a serious food safety problem. The vaccine is to be given to cows, so they do not transmit it to us.

The following post is about the possible transmissibility of Alzheimer's Disease; it makes comparison with the prion diseases. Is Alzheimer's disease transmissible? (February 4, 2011).



Extrasolar planets

December 8, 2009

Think about... When you were born, how many planets were known? In our solar system? Beyond our solar system?

For most of you, the answers are nine and zero. Since then, our solar system seems to have lost one planet (or, rather, demoted it), but we now know of a few hundred extrasolar planets (also called exoplanets). The first extrasolar planet was announced, to great fanfare and perhaps some skepticism, in 1995. Now, they are announced in batches on a regular basis. New techniques are developed, each more sensitive than the last. This is one of the great scientific developments of our era -- a development entirely (or largely) within the lifetime of each of you.

The graph below is a summary of the extrasolar planets discovered so far. (This is from a recent paper, noted below; it shows about 370 extrasolar planets. A big new batch of planets was announced just after this paper came out.) The graph shows a point for each planet, based on its distance from its star (x-axis, labeled semi-major axis, referring to the size of its elliptical orbit) and mass (y-axis). Both axes are based on Earth as 1; note the point labeled E at (1, 1). All the planets of our solar system are shown, each identified by an initial. All the other symbols (including x) are for extrasolar planets. (Example: Find the symbol S, for Saturn. It is at approximately (10, 100). That is, it is about 10 times as far away from the sun as Earth is, and it is about 100 times more massive than the Earth.)

Extrasolar planets Extrasolar planets.

(Solar system planets are also shown, with their initials.)

More explanation above.


This is Figure 1 of the paper listed below.

So, what do we see?

The horizontal line near the top shows the size of the largest possible planet. Anything larger would more likely be a star.

The dashed line in the middle defines the limit of a key method for detecting planets. Finding planets below the line is difficult -- so far.

Most extrasolar planets found are between those two lines -- as expected.

Most planets of our solar system are below the dashed line. Only Jupiter and Saturn, our two largest planets, are above it. That is, the methods used so far are not likely to find Earth-like planets. (A common remark is that the search for extrasolar planet is mainly finding Jupiters.)

The failure to find "earths" so far is a methodological limitation. In fact, the authors emphasize that the distribution of known extrasolar planets, as seen above, is almost entirely due to the methodological limitations. The story of recent years has been a progression of better and better methods. And that continues. The Kepler spacecraft, launched earlier this year by NASA, is specifically designed to detect earth-like planets. We can only wonder what the graph above will look like a few years from now. Remember, only 15 years ago that graph would have been empty (except for our solar system planets). (UC Berkeley astronomy professor Geoff Marcy is one of the pioneers of exoplanet exploration, and is a co-investigator for the Kepler mission. Marcy was the first speaker in the current series of Astronomy lectures here; see Astronomy talks (6/22/09).)

The main point here is to show this graph, and discuss some of the information in it. For those who want more, here is the review article: Light and shadow from distant worlds. (D Deming & S Seager, Nature 462:301, 11/19/09.) The article discusses the various methods. The final sections of the paper discuss prospects.

Also see...
* Atmosphere suggests planet might harbor life (August 30, 2010).
* The first truly habitable exoplanet? (October 12, 2010).
* A post about the Kepler mission -- a large-scale search for extrasolar planets... The Kepler Orrery (June 3, 2011).



Lux aeterna: Mushrooms; Mozart

December 7, 2009

Mushrooms -- photographed in the dark. They glow!

This new mushroom species was discovered on twigs near Sao Paulo, Brazil -- while mushroom hunting at night. The discoverers named it Mycena luxaeterna. More about the name below.


The scale bar (upper right) is 5 mm.

This is Figure 2b from the paper. It is also in the news story listed below. Fig 2a, in the paper, shows the same scene with lighting, so you can see the fungus as it was found on the twigs. From Fig 2a you will recognize it as a mushroom.

News story: Seven New Luminescent Mushroom Species Discovered. (October 5, 2009.)

The paper: Luminescent Mycena: new and noteworthy species. (D E Desjardin et al, Mycologia 102:459, March 2010.) Desjardin is at San Francisco State University.

The music: Mozart's Requiem: final section. (Georg Solti and the Vienna Philharmonic. 6 minutes. A performance on the occasion of the bicentennial of Mozart's death. Details on the YouTube page.) Try to make out the opening words.

That final section of the Mozart Requiem is called "Lux aeterna" -- which you may have heard as the opening words. The species name for the fungus here, Mycena luxaeterna, "was inspired by and borrowed from Mozart's Requiem". (Just search the paper for Mozart.) "Lux aeterna" is Latin for "eternal light".

More... Lux aeterna: Mushrooms; Mozart -- follow-up (March 22, 2010)

Another post of work from the same lab: SquarePants in Borneo (September 24, 2011)

More from Brazil: Why would a plant have leaves underground? (January 21, 2012).



Dinosaurs in Tamil Nadu

December 7, 2009

Jai sends two news stories about the discovery -- and then the looting -- of a huge bed of dinosaur egg fossils in his home state, about 200 miles from where he lives. He notes (edited from two emails): "This news came in all national dailies and vernaculars. It is hyped as the largest such discovery in the subcontinent. ... But sadly, the egg fossils were looted by local villagers (may be expecting some reward???) either due to greed or ignorance."

* India's Jurassic nest dug up in Tamil Nadu. (Times of India, 10/1/09.)
* TN 'Jurassic' site treasure looted by villagers. (Times of India, 10/8/09.)

More about dinosaur eggs... The oldest dinosaur embryos, with evidence for rapid growth (May 7, 2013).



Bet hedging

December 5, 2009

It is often said that organisms are well adapted to their environment. It makes some sense, and we broadly understand how natural selection leads to such adaptation. But the real world is more complex than that. Well adapted to what environment? Environments vary. The basic environment of Earth has varied over the ages, and that has been important in the development of various waves of organisms. Further, the current environment for an organism is not constant. For example, man has learned to use clothes to deal with the variable environment. And many bacteria have "learned" (genetically) to use any of a range of foods, so they can take advantage of their varying environment.

The point is, then, that one way for organisms to be well adapted is to be adaptable. Some organisms are very well adapted to a particular set of conditions, but poorly able to deal with other conditions; we call these organisms "specialists". Other organisms excel at dealing with varying conditions -- they excel at how quickly they can adapt; we might call these organisms "generalists". Under constant conditions, the specialist may do better. However, under variable conditions, the generalist may do better over the long term.

An example of a specialist animal you may have heard about... The panda is specialized for eating bamboo. A bamboo shortage endangers the panda -- even though other food may be around. [For more about pandas: The panda genome (January 11, 2010).]

Of course, it is easiest to study adaptation in microbes, simply because they do things faster. A recent paper showed how bacteria exposed to a fluctuating environment adapt and produce a mixed population. Various members of the population are optimized for one or another condition. The population is not optimized for any specific condition, but for the collection of conditions. The population -- the species -- will survive well under any of the conditions, because it has hedged its bets, and pre-adapted to the variability. It is a cute example of something we have long assumed to be so.

The bacteria in this mixed population are (probably) identical genetically. However, they behave differently. In fact, analysis shows that a particular mutation is largely responsible for the mixed behavior. Thus we can summarize what happened here by saying that the major selective pressure was variability; mutations occurred that made the organism better able to respond to variability.

Bet-hedgers: bacterial colonies and cells. The figure shows bet-hedging bacteria, seen at two levels.

Part b shows bacterial colonies; the (white) scale bar is 2 mm. There are two major colony types, at left and right; the middle colony is "mixed".

Part c shows bacterial cells; the (black) scale bar is 10 µm. The small black "bars" are individual bacteria; some are surrounded by a halo (a capsule). (The cells with capsule give rise to colonies like the one on the right in part b -- a colony type referred to as opaque.)


The figure is part of Figure 1 of the paper.

Press release, from the Max Planck Institute (home base of one of the scientists involved): Bacteria expect the unexpected -- Scientists observe the emergence of a new adaptation strategy to rapidly changing environmental conditions. (11/5/09.)

The paper: Experimental evolution of bet hedging. (H J E Beaumont et al, Nature 462:90, 11/5/09.)



A flu shot for Santa Claus?

December 5, 2009

Hungary warns Santa Claus to get flu jab amid epidemic. (11/23/09.)

I guess this falls under the heading "Applied virology".

Aside from the fun aspect, it does raise an interesting public health issue, about people whose job puts them in contact with large numbers of vulnerable people.

Posts on flu have been consolidated on the page Musings: Influenza (Swine flu).



December 2, 2009


Killer chickens

December 2, 2009

A big news story from Monday, which is really important. Chickens -- the ones we buy in the store -- are major carriers of disease. Half or more of the chickens in the store are contaminated with bacteria that cause illness.

Some quick notes...
* Two kinds of bacteria are discussed: Salmonella and Campylobacter. The former may be more familiar to you, but the latter is probably more serious. For our purposes here, it doesn't matter much. Contamination with either is bad.
* Much of the story discusses differences in the contamination level from one brand to another, or with different processes. The best results show nearly half of the chickens being contaminated. So all these differences are really not important for us. One should just assume that chickens are contaminated.

Dealing with chicken safely is fairly easy. It involves two major points:
* Cooking the chicken sufficiently to kill the bacteria.
* Avoiding contaminating other things with the uncooked chicken, including its juices.

Remember, transmission of germs from one animal to another is common. It does seem that the chicken is currently the most serious threat to us as a source of disease. However, the precautions for handling chicken are reasonable precautions for handling any meat. Also remember that the animal you are most likely to get disease from is Homo sapiens -- an important reminder during this flu season.

* A short news story, for a quick overview: Consumer Reports: Two-Thirds of Chickens Tested Harbor Dangerous Bacteria. (PR Newswire, 11/30/09.)
* The report: How safe is that chicken? Most tested broilers were contaminated. (Consumer Reports, January 2010.)

Follow-up and related posts:
* Both ways (November 18, 2008). This is primarily about transmission of disease from humans to other animals.
* Killer chickens - follow-up (December 9, 2009).
* Killer chickens -- follow-up: some progress (June 7, 2010).
* Killer chickens -- A clue to the underlying problem? (August 27, 2010).
* Killer eggs: The American egg problem (September 8, 2010).
* Cooking pork (June 4, 2011).
* Don't eat the cookie dough? Or the flour? (February 20, 2012).
* Possible transmission of norovirus via reusable grocery bag (May 21, 2012).
* Are government safety inspections worthwhile? (June 12, 2012).
* Why mice don't get typhoid fever (November 26, 2012). A Salmonella story.
* Cockroach should be disinfected before eating it (February 12, 2013). Humans aren't the only ones to deal with food cleanliness.
* How do vegetables get contaminated? (August 31, 2013).
* Added April 28, 2014. Salmonella and food contamination; the biofilm problem (April 28, 2014).
* Added July 7, 2014. Tracking food poisoning through online reviews (July 7, 2014).
* Added September 6, 2014. Campylobacter -- how do the chickens feel? (September 6, 2014).

My page Internet resources: Biology - Miscellaneous contains a section on Nutrition; Food safety.



Teaching pigs to use a mirror

December 1, 2009

Could you find your dinner if it was hidden "around the corner"? Could you find it if you could see it in a mirror? (Hm, try it.)

We have discussed how animals respond to mirrors. The post Self (10/8/08) discusses work showing that a magpie can recognize itself in the mirror. The paper there discusses other mirror work.

Now we have a report of an animal making use of a mirror to find food. Pigs can learn how to interpret what the mirror image means, so that they go where the food is, not simply behind the mirror. As with so much animal behavior work, it is fun; it is particularly fun to read some of the odd incidents along the way. It is also hard to analyze the validity of the work. They obviously have considered and tested many possible interpretations, but it is hard to know if they have covered them all. I'm also somewhat concerned by how much emphasis they put on the relevance of their finding to animal welfare -- to how the animals should be treated. It almost comes across as a bias. That doesn't mean there is anything wrong with the work, but it does raise some suspicions. As always, the ultimate test lies in independent replication of the work.

A news story: Pigs Prove to Be Smart, if Not Vain. (11/9/09.)

(The cartoon at right is from this story.)
Cartoon: pig and mirror.

The paper is: Pigs learn what a mirror image represents and use it to obtain information. (D M Broom et al, Animal Behaviour 78:1037, 11/09.) From Cambridge University.

Why pigs? Why study aspects of behavior or intelligence in pigs -- or in magpies? Well, it is good to study such traits in a range of organisms. We study them in other primates (e.g., chimps) because they are our close relatives; learning what we do and do not have in common with them helps us understand our history. On the other hand, studying traits in less-related organisms helps us put things in a big perspective. Knowing that the ability to use a mirror arose in rather diverse animals tells us that this is not a trait unique to the human lineage. As to the specific choice of pigs... They are highly social animals, and are considered intelligent. And these are domestic pigs; working with them in the lab is relatively easy -- though not without some risk of the unexpected, as the paper notes.

Dr Dean Edell mentioned this item on his talk show. (For those who don't know... Edell is a doctor, now retired; he did an excellent medical-oriented radio talk show. He is good at emphasizing scientific logic.) He added that pigs have learned to use a joystick and play video games. A quick check of Google suggests there is something to that. Explore if you wish. If you find something worth posting, pass it on.

For more about pigs... Cooking pork (June 4, 2011).

Added June 23, 2014. For more about mirrors. Could we block seismic waves from earthquakes? (June 23, 2014).



NOTCH drugging

December 1, 2009

Jitesh sends: Researchers 'NOTCH' a victory in war on cancer. (Harvard, 11/12/09.)

A Harvard group has recently reported development of a novel type of drug. This opens up new possibilities for research, in addition to whatever therapeutic potential it turns out to have.

A simple version of the story is that the Notch protein is overactive in many human cancers; therefore one would like to inhibit it. They have developed a drug that indeed seems to inhibit Notch.

So why is this a big deal? Because people have come to think that proteins of the Notch type are "undruggable". To develop a drug that inhibits a protein, one needs a chemical that binds to the protein -- with specificity. That is, the drug should bind to the target (what you want it to bind to), but not to other things. A good approach is often to get it to bind to the target in a way that interferes with its normal interactions. The problem is that Notch normally binds to other proteins (large molecules), not to small molecules. It just doesn't seem to have good binding sites for small molecules. Finding small molecules that work with such proteins has proved difficult.

In some sense, the solution is obvious. If small molecules don't work, because this protein binds large molecules, then design a large drug. In fact, that is what they did: they created a small protein matched to Notch. But doing this is a quite a big deal. Designing novel large drugs is much more complex. And there is another problem: large drugs often do not get into the cell. Theirs does -- and the reason is not really clear.

Notch is a transcription factor: part of the apparatus that makes a mRNA (messenger RNA) copy of DNA genes. More specifically, it helps determine which genes get copied. That is, Notch is not involved in turning one chemical into another, but is a regulatory protein, controlling genes. There are many such regulatory proteins; they play major roles in cells functioning properly. Thus, not only is Notch important, but it represents an important class of proteins. So the report here of a drug that inhibits Notch, using a novel approach, opens up a new door to studying gene function.

Will their new drug be useful in treating cancer? Well, they do report some simple studies that are encouraging. But lots of candidates pass those tests, and ultimately prove not to be useful. We'll just have to wait and see whether it is a drug useful in the cancer clinic. But no matter, it should open up new research approaches, and perhaps will open up a new class of drugs.

* News story that accompanied the article: Chemical biology: A Notch above other inhibitors. (P S Arora & A Z Ansari, Nature 462:171, 11/12/09.)
* The article: Direct inhibition of the NOTCH transcription factor complex. (R E Moellering et al, Nature 462:182, 11/12/09.) (Put the title of the paper into Google Scholar, and you may find an available pdf of the paper.)

My page for Biotechnology in the News (BITN) -- Other topics includes a section on Cancer. It includes a list of some other Musings posts on cancer.



A smart rat

November 30, 2009

Have a look... Rat Made Supersmart -- Similar Boost Unsafe in Humans?. (11/12/09.)

Here is the paper. I do suggest that you read over the abstract. Genetic Enhancement of Memory and Long-Term Potentiation but Not CA1 Long-Term Depression in NR2B Transgenic Rats. (D Wang et al, PLoS ONE 4(10):e7486, 10/19/09.)

This is fascinating work, trying to understand how the brain works. It shows that increasing the amount of a particular protein, previously implicated in memory, has certain effects on enhancing memory. Similar results have been obtained with mice, and the biochemistry of this protein is similar in primates. Thus they suggest that the effect may be general.

Fig 2B from the paper. The Figure shows an example of the results. The experiment involves testing whether the rats retain a memory; 50% is the expected result with no memory. Wt (wild type) is the regular rat; the memory is largely lost by 1 day. Tg (transgenic) is the rat making more of the protein being studied; the memory is still significant at 3 days. Thus the greater level of the protein in the Tg rat has enhanced retention of the memory.

This is Figure 2B from the paper.

It is indeed fascinating to begin to understand memory at the molecular level. This is one of the great frontiers of modern biology. But talking about using the finding to make smarter humans is quite unwarranted. First, "smart" is more complex than this one trait. As the news story notes, it may well be that this trait could have both good and bad aspects. Second, we do not know the result holds for humans. It may be a good hypothesis, but it is not known. Testing of such things in humans must be done with great caution.

Making smarter humans by genetic engineering is a long long way off - if it ever comes. But what if... Someone finds a patient with serious memory problems, and the patient has abnormally low levels of this protein. Would that be a suitable situation for a test of this hypothesis in humans?

For more... Nature recently did a "news feature" on smart mice. Small, furry ... and smart. (Nature 461:862, 10/15/09.) This is an overview of several approaches to making smarter mice, and includes discussion of the downside of each.

Recall Personalized medicine: Getting your genes checked (10/27/09). Is there a connection? Careful!

For more on rats:
* A rodent that can't chew (November 5, 2012).
* Rats will free prisoners, and share their chocolate with them (January 18, 2012).

For a case of a possible (human) gene related to language: Is there a gene for "It's on the tip of my tongue"? (July 6, 2012).

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.



Results from the LHC

November 30, 2009

LHC results. (11/6/09.)

Did they really need a multi-billion dollar system to test this?

At least, you do not need to understand high energy physics to understand this. A little about gravity and some basic electricity are sufficient.



Evolution of the end of Origin

November 30, 2009

A cute little item appeared in Science recently. It shows four versions of a paragraph that Darwin wrote over a period of 22 years. Some of the variation may simply be word choice, but some may reelect subtleties of his thoughts. The whole item is a half page -- the bottom half of History of science: Evolution of the end of Origin. (R W D Nickalls, Science 326:801, 11/6/09.) The final version is in bold; in the others, bold indicates words that appear in the final version. One interesting point is that the final version is the shortest!

If you can't access that, there is a pdf of the item available from the author. It is labeled "preprint", but seems to be fully equivalent to the final version. It is at Author pdf of preprint.



November 23


A small perk when living in Florida

November 23, 2009

Jessica sends her own photos of the space shuttle launch last week (November 16). They were taken about 10 miles from launch site. She chose a sampling of three for posting here, and I downsized them for web posting.

#1         #2         #3

And a short video sequence, which Jakub shot from about 40 miles away, and posted at YouTube for you: Space shuttle video. "Mostly entertaining for the commentary, I think" -- notes Jessica. And it raises our consciousness about the need for cloud control.

For more about Florida: A small perk when living in Florida -- more (December 11, 2009).

More on the shuttle:
* Photography from the space shuttle (June 4, 2012).
* Space shuttle: some final photos (December 3, 2012).



Goethe, Huxley, and Nature

November 22, 2009

Nature: Aphorisms by Goethe. (T H Huxley, Nature 1:10, 11/4/1869.) An editorial, the very first article in Nature -- 140 years ago this month.

I was tempted to suggest that Goethe was the first to have his words published in Nature. But the page suggests that designation actually belongs to Wordsworth.

For those who may be curious, here is the Table of Contents (TOC) for that issue: Nature Vol 1 #1: Table of Contents. (The TOC should be freely available. However, the individual items will not be available, unless you have subscription access. If you see something you want, let me know.)

Another Musings post about the first issue of a journal: Bacteria induce simple "pre-animal" to become colonial (September 8, 2012).



Did Neandertal children hate broccoli?

November 22, 2009

There is a simple test, often done with school children... Have them touch their tongue to a special piece of paper. Most people -- about 3/4 -- say, yuck; the others have no response. The paper contains a chemical, called PTC, that is extremely bitter. Or at least, it is bitter if you have a functional taste receptor for PTC. About 1/4 of us have a defective taste receptor, and cannot taste PTC -- or the similar bitter substances in broccoli and cabbage, and their relatives. There is a good correlation between liking broccoli and not having the functional taste receptor. (It is not a perfect correlation; more is involved in liking foods.)

We have several taste receptors, for various tastes. For simplicity here, I will refer to just this one. For example, "taster" refers here to the ability to taste this particular substance. "Non-tasters" (for PTC) probably have quite normal response for other tastes.

In our modern era of molecular biology, we now know much more about this. Not only do we broadly understand taste receptors, but we know the difference between the receptor in tasters and non-tasters. It is largely due to one base difference in the DNA of the taste receptor gene.

So, what now? A group of scientists have analyzed the DNA from a Neandertal, and found that the person contained one copy of the taster allele (form of the gene) and one copy of the non-taster allele. Thus this person was heterozygous for the bitter taste allele; in modern humans, tasting is dominant, so we can guess that this Neandertal individual was a taster -- and that he may well have found broccoli distasteful.

With only one individual analyzed, we do not know how frequent tasting and non-tasting were. We only know that both alleles were present -- apparently the same alleles now found in modern humans. (To my knowledge, we know little about Neandertal eating habits for veggies; I use broccoli here simply as an example -- one you can relate to.)

Our closest living relatives, the chimpanzees, also have tasters and non-tasters. Interestingly, it was recently shown that the chimp non-taster allele is due to a different mutation than the one found in humans. A simple model is that the chimp-human ancestor was a taster, and that non-tasting has arisen in each lineage since then.

A good news story: Neandertals Led Bitter Lives. (Science Now, August 12, 2009.)

The article: Bitter taste perception in Neanderthals through the analysis of the TAS2R38 gene. (C Lalueza-Fox et al, Biology Letters 5:809, 12/23/09.) A very readable paper. As always, if you don't want the technical details, skip over those parts. But the introduction and discussion are good. (The news story above links to the article.)

A subsequent post on DNA sequencing from a Neandertal-era human: The Siberian finger: a new human species? (April 27, 2010).

Other posts about Neandertals include... Did Neandertals use cosmetics? (January 24, 2010).

Also see: Loss of ability to taste "sweet" in carnivores (April 6, 2012).

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



What is it?

November 20, 2009

What is it?

Want a hint? Put your cursor over the word hint. (Do not click.)

When you are ready... The source. (See the first item in the pdf file.)

Other "What is it?" features include...
* Next: What is it? (December 14, 2010).
* Previous: What are these? (September 25, 2008).



November 18


Bichon frise

November 17, 2009

Three genes largely determine the type of dog coat. Fig 3, 75% The pictures show examples of seven typical types of dog coats. The table at the left shows how these come from simple combinations of three genes. (More about this below.)

A previous post was an overview of recent work on dog genetics, by Elaine Ostrander, at NIH: Man's best friend (10/22/08). Since then there have been reports analyzing specific aspects of dog development. The dog story is intriguing for multiple reasons. The dog was originally domesticated by man thousands of years ago. The modern wolf is around for comparison; in fact, the wolf and dog are still a single species. In addition to that "ancient" history, there has been a more recent explosion of the development of dog breeds. Most of our modern dog breeds date from the last 200 years or so. And of course, couple all this with the special status that the dog plays in human society, both as a worker and friend.

Here is a study of the dog coat. Dog coats vary -- a lot, it would seem. But a careful study of many breeds shows that much of the variation can be accounted for by three genes. For each of these genes, there are two alleles (forms): the original allele -- still found in the wolf, and called "-", and a new variant allele, called "+", which confers a new phenotype (observed feature). With two alleles of each of three genes, there are 23 = 8 possible combinations. The table at the left of the figure above shows seven of those combinations. For example, row C shows the phenotype "wire and curly", which is due to the allele combination -++. Then, there is a picture of a dog of this type. (The missing combination is --+. They predict that this combination would not be distinguishable from ---.)

The article is: Coat Variation in the Domestic Dog Is Governed by Variants in Three Genes. (E Cadieu et al, Science 326:150, 10/2/09.) The Figure above is Figure 3 of this paper.

As to dog G, whose name is the title of this post... That's a dog? At least, the tongue is sticking out.

More dog genetics: Dog psychiatry: Implications for humans (October 3, 2010).



Enceladus and its plume

November 17, 2009

The Enceladus plume. A featured photo from NASA, shot by the Cassini spacecraft that is orbiting Saturn. The photo is striking, but do read the brief text below it. The Enceladus plume, discovered only a few years ago and highlighted here, is one of the mysteries of our solar system; it seems to be largely water. Does this mean that this tiny moon contains liquid water?

Thanks for the contribution!

More about Enceladus and its water: A water fountain for Saturn (October 23, 2011).

Also see: Clouds? Puddles? Does that mean it rained? (April 6, 2011). More from Cassini.



The promise of science?

November 16, 2009

The November issue of The Scientist ran an editorial and a feature article on the problem of scientific hype. I encourage everyone to read the former, which is short and to the point. Those who might want to partake in a serious discussion should tackle the article, too; it is something of a mess (in my opinion), but raises lots of good issues along the way.

The articles are:
* Authors of Our Own Misfortune. (R Gallagher, The Scientist, 11/09, p 13.)
* Promises, Promises -- Ill-judged predictions and projections can be embarrassing at best and, at worst, damaging to the authority of science and science policy. (S Blackman, The Scientist, 11/09, p 28.)

Most of us would probably agree that the problem, in some sense, is real. The question is what should be done about it. Scientists are supposed to be optimistic about their work -- as well as skeptical. And we have a general public that is not well educated about the nature of science.

I face this issue when posting things for Musings. The most exciting part of science is the new stuff -- just reported. By its nature, it is tentative, subject to further work. Some of it will not pan out. That's fine; that is the nature of science. I sometimes make a point of noting that something "has been reported" (rather than "proved"), or that something is tentative. But it is always understood; that is the nature of science.

* * * * *

A reply... To the promises of science: the thought of what could be, and therefore, how convincing the promise, often predicts -- at least -- the intensity of scientific pursuit. True, we may not have discovered the cure for the world's worst diseases, but think of the milestones and leaps we have made because someone, somewhere, published a story that we just might? Promises, if nothing else, lead to funding and research: the cornerstones of discovery. And, as many like to quote Edison for the phrase, if nothing else, we have discovered hundreds of ways NOT to do something...perhaps just as valuable, albeit, not as exciting? (I love the table of some prominent predictions.)

For more about Edison -- and sound recordings...
* Restoration of old sound recordings (July 23, 2011).
* Poetry (July 23, 2009).



The smallest violin

November 16, 2009
(with follow-up)

Violin, 1 cm. Musical instrument maker in Guangzhou builds tiny violin. (11/6/09.) The violin is about 1/30 of normal size.


For those who may be confused by the ruler... It is an ordinary ruler: the numbers are in centimeters; the little lines are millimeters apart.

The stated size of the instrument refers to the body, not including the neck.

If, for simplicity, we assume that the tones scale with the size of the instrument (shorter strings, higher frequency), then the open strings would sound five octaves above the normal violin. That would put them just above the highest notes of a (normal) piano. (The tone actually depends on more than the length of the string. But I have no information on the other factors.)

* * * * *

I have already received a response on this item. It made a point that occurred to me, too. The violin above is the result of traditional craftsmanship. What might be possible if we go beyond that? How about a computer-crafted microscopic violin? A nano violin? At some point, would we switch from simply miniaturizing the violin to retaining its functional essence but with a new design? Uh, what is the functional essence of a nano violin? If posts here stimulate such ideas, that is good!

More on violins: Spiders and violins (May 4, 2012).

There is more about music on my page Internet resources: Miscellaneous in the section Art & Music.



What to eat

November 13, 2009

Our nutritionists feed us the following item: Vegetarian Diets Can Help Prevent Chronic Diseases, American Dietetic Association Says. (7/3/09.) (It includes a nice picture!)

The paper referred to is a goldmine of information -- regardless of whether you want to follow a vegetarian diet. The simple story is that this is a "position paper" from the American Dietetic Association. The simple conclusion is that "appropriately planned vegetarian diets, including total vegetarian or vegan diets, are healthful, nutritionally adequate ... ." And this conclusion is based on a detailed analysis of such diets and human nutritional needs, as they are understood. The paper -- 17 pages -- is a summary of this analysis, nutrient by nutrient.

Two issues are addressed. One is whether the vegetarian diet satisfies nutritional needs; the second is whether it might actually have benefit. The report's main focus is the former. However, some evidence supports the latter, too.

Borislav and Dubravka emphasize:

Keep in mind that the paper deals with "carefully planned" diets, with diverse sources. The paper doesn't touch unhealthy approach to food consumption; i.e., you could eat only veg cookies and drink only veg juice. You would be a vegetarian for sure, but such practice is essentially destruction of your organism. Any diet can be well balanced, and this paper compares health effects of such diets.

For those who are new to subject; this paper is of enormous importance. This is practically the first time that so many experts on the field agreed that veg eating can be optimal / beneficial for humans of any age or condition.

The paper is intended for nutrition professionals. Don't expect to be able to design good vegetarian diets just by reading this paper. Nevertheless, you will find much information in it, and you should get an idea of some of the important issues.

The paper is available from a site maintained by the American Dietetic Association: Position of the American Dietetic Association: Vegetarian Diets. (J Am Diet Assoc. 109:1266, 7/09.) This page gives the abstract, and links to a freely available pdf of the complete paper.

A post that refers to another report from this group: Omega-3 fatty acids; fish oil (March 29, 2010), on dietary fat.

Also see... Red meat and heart disease: carnitine, your gut bacteria, and TMAO (May 21, 2013).



Crocodiles, humans, and stones

November 13, 2009

Did you know that a crocodile may have 10 kilograms of stones in its stomach?

Did you know that a crocodile stomach stone might be mistaken for a human-made tool?

Were crocodiles responsible for the stones we call tools?. (P Dempsey, Nature 461:341, 9/17/09.)

I don't know any more about it. It struck me as amusing (hey, there is a cute cartoon) -- but also possibly important. Let's see where it goes.

More on crocodilians:
* Crocodilians: Thick-skinned but very touch-sensitive (January 2, 2013).
* Space shuttle: some final photos (December 3, 2012). You'll have to look around a bit.



November 11


A new source of electricity

November 10, 2009

Joe sends Does Energy Grow on Trees?. (November 2009.) See the first item there.

The paper is: Ultra-Low Voltage Nanoelectronics Powered Directly, and Solely, from a Tree. (C Himes et al, IEEE Transactions on Nanotechnology 9:2, 1/10. From the University of Washington.) I encourage you to at least read the Introduction, for an overview.

What is the source of electricity from a tree? In a general sense, it is not particularly mysterious. There are various gradients of ions in living systems; they note some of them. It is not clear which they are tapping into. Tree, Figure 1
The figure at the right is
Figure 1 from the paper.

One of you is into large scale power systems. Could we get you to calculate how many maple trees it would take to power, say, a city of a million people?

Seriously, this is not a joke. In the paper, they build real devices that run on the tree power. They even suggest how this may be useful in real applications, such as environmental monitoring "in the wild", where trees are more plentiful than batteries. An important aspect of this is the development of tiny devices that have very low power requirements. That is, we have a convergence: the development of a low-power source and the development of devices that need low power. Apparently they are not alone in thinking this might be useful: see the "Note Added in Proof" at the very end of the paper.

That same convergence is behind using bacteria to generate electricity in microbial fuel cells (MFC). In MFC, the electrodes tap directly into the core metabolism -- into the electron flow that is part of the microbes burning their food. I introduce MFC on my page Internet Resources for Intro Chem: Redox reactions; fuel cells. The listing features a picture of a calculator powered by bacteria -- and includes links for more information.

The news story that starts this item is from a new source: the Career Cornerstone News, a publication of the Sloan Career Cornerstone Center. Joe encourages you to check it out, both as a source of info about science and, more centrally, about science careers. Other topics noted on the current page include "Degree Profile: Cardiovascular Technologist" and "Engineers Design Self-Righting Buildings" (for earthquake resistance).



Mission improbable

November 10, 2009

Last week I posted an item about the recent HIV vaccine trial. Among the things I noted there was quibbling about the statistics. [HIV vaccine trial -- and quibbling about statistics (11/2/09).] Well, there has been a lot written about this trial, including about the statistics. But I was quite surprised to get an e-mail from the Nutrigenomics list on this topic. Turns out they were distributing an interview with a statistician by the Science NOW news service (part of Science magazine). The interview is rather fun, and with a little luck you'll come away with a better feel for what "p = 0.05" means. It is not specifically about the merits of this trial.

The interview is at the Science Now and Nutrigenomics sites:
* Mission Improbable: A Concise and Precise Definition of P-Value. (Science Now, 10/30/09.)
* P-values and Science Meaning. (NUGO, 11/6/09.)

Some of you have not yet studied statistics. That's fine. I think you will still find the item fun and useful. It is good even if you just come away realizing that the p value is a way we express the uncertainty of a conclusion, and that its meaning confuses those who use it. (I wonder... maybe those who have not taken a stat course will understand this better than those who have taken the course.)

Added March 2, 2014. More about p: More on the story of p (March 2, 2014).

Added December 13, 2013. More about statistics and clinical trials: Chelation therapy -- a controversial clinical trial (December 13, 2013).

There is more about statistics on my page Internet resources: Miscellaneous in the section Mathematics; statistics. It includes a listing of related Musings posts.



Personalized medicine: cancer therapy

November 9, 2009

A recent post was about personalized medicine: Personalized medicine: Getting your genes checked (October 27, 2009). Specifically, it was about the possible value of having your genome tested to see what features it codes for. For example, testing might show your odds of getting heart disease, based on the specific gene variants (alleles) you have. The general feeling there was that the principle was sound, but that the information currently available made it of limited use, in general.

The current post is closely related: the same general idea of personalized genetic testing, but now focused on a specific application, cancer therapy. Individual people have different genes that affect their susceptibility to cancers and affect how specific anti-cancer agents may act. Further, cancers are different; that is the nature of cancer, which involves genetic changes. Thus testing of a person with cancer, specifically including testing the cancer itself, may well guide treatment. In fact, there has already been some success with this approach. Still, it is limited, in large part because the information is limited. Thus simply doing research by collecting information on individual cancers may be appropriate for a while.

Here is a news article from Science discussing this aspect of personalized medicine. Looking for a Target On Every Tumor. (Science 326:218, October 9, 2009.) The article discusses the successes and limitations of the approach, and offers a view of what should be done. Hopefully, this specific application helps to put the broader issue of genetic testing in perspective.

Also see: Genomic information: What not to do. (January 16, 2010).

My page for Biotechnology in the News (BITN) -- Other topics includes a section on Cancer. It includes a list of some other Musings posts on cancer.



Is the incidence of autism increasing?

November 6, 2009

A common statement is that autism is on the rise. Yet there is much confusion about this. It is clear that autism is diagnosed more now than in the past, for various reasons. Part of the reported increase is presumably due to better diagnosis. That still leaves open the question of whether there is a real increase.

Now, we have a report that provides a unified view of autism rates over several decades. It finds no evidence of any change in rate. The rates found here for adults of all ages are comparable to the widely reported rates for children. If this is indeed correct, it suggests that the rising numbers for autism are largely due to changes in diagnosis, not to a true increase in incidence. Thus there is little need to be looking for a cause that has changed in recent times.

Unfortunately, as I started reading more about the study, it became clear that it has serious limitations. The big one is that the number of people studied is quite small. The news story listed below does a good job of describing the limitations. So, I think what we have here is a first report: they did something no one had done before. Others should be able to build on this, with bigger studies and addressing some of the other concerns. Also, we do not seem to have a scientific paper for this, but rather a report from a government agency. That's not ideal, and emphasizes that this is step one; we need more.

* News story -- a good overview of the study, including its limitations: For the First Time, a Census of Autistic Adults. (Time, October 3, 2009.)
* The report, from the UK National Health Service (NHS), now hosted by the Health & Social Care Information Centre: Autism Spectrum Disorders in Adults Living in Households Throughout England - 2007, Report from the Adult Psychiatric Morbidity Survey. (September 22, 2009.)

This is a hot topic, and I'm sure this report will get much attention, including from those "with an agenda" of one kind or another. If you come across some good stuff, let me know, and I'll share it here.

Also see: Early detection of autism (June 14, 2011).

More on autism is on my page Biotechnology in the News (BITN) -- Other topics under Brain (autism, schizophrenia).



Novel Internet technology

November 6, 2009

Novel Internet technology (This is an archive of the original site.)

Is this the ghost of Feynman?

Thanks for the contribution.



November 4


Happy birthday

November 4, 2009

A few days late, but it was this past week. A commemoration of the first steps in building the facility that threatens to overwhelm us all. Celebrating 40 years... . (10/29/09.)

More birthday posts...
* Next: Happy Birthday (May 27, 2012).
* Previous: Happy Birthday (September 9, 2009).



HIV vaccine trial -- and quibbling about statistics

November 2, 2009

A different virus this week...

Over recent weeks there have been stories about a trial of a vaccine to prevent HIV infection -- to prevent AIDS. The stories vary, and there has been some confusion. Let's see if we can sort out some of this.

The most important point, I think, is that the trial showed a small effect: there was some reduction (about 30%) of HIV infection in the vaccine group (compared to an unvaccinated control group). The small effect is not "success", but it is worth following up.

The effect observed here is probably too small to be useful at this point. However, it is the best HIV vaccine result obtained so far. (In fact, it is about the only trial with any encouraging results.) Therefore, the researchers want to follow up: Why did this trial show a small effect, and how could it be improved?

So, what is the problem -- other than the effect being small? The first problem, which has been in some of the news stories, concerns the statistics. With such an experiment, one calculates a p value -- a probability that the results might be due to "chance". In this case, the p value comes out to around 0.05 (5%) -- a little more or a little less depending on exactly how it is calculated. No big deal. Except that there is a convention that p = 0.05 is commonly considered the cut-off between success and failure. Thus when the p appeared to be a bit above 0.05, some wanted to dismiss the result as not significant. But that is really an abuse of statistics.

Why? Well, if you phrase the question as "Did the trial prove that the vaccine is effective?", then, by convention, 0.05 is the proper cutoff. However, that is not the right question. No one is proposing to declare this as proof, and start vaccinating everyone. The practical question is whether the results here are worth following up. The trial gave the best result ever, and there is some hint of why. Clearly, this will be followed up.

As I understand it, there seems to be an emerging consensus that p = 0.04 is probably the best p value for the experiment. So, the p-skeptics will be silenced. No matter, the point is worth making.

The other confusion relates to the biology. The trial used two vaccines, one for the initial dose, and another for the booster dose. Both vaccines had been tested before, and neither gave any hint of providing any protection. In fact, many questioned the wisdom of doing the new trial, given that its two vaccine components had each failed so far. Is it possible that two vaccines together can do what neither can do alone? Indeed. The two vaccines work rather differently, and that might be relevant. Optimistically, the current trial shows the merit of that approach. I think that the main result of this trial will be work to test that idea -- and see if they can do better than the modest effect reported this time. But it is also possible that we have a false lead, a statistical fluke, and that it won't lead anywhere. The only way to know is to try.

A good news story: First HIV vaccine trial success. (10/20/09.) (If you find other articles about this issue, be sure to check the dates. Some discrepancies between articles will be due simply to when certain information was available.)

* The article is: Vaccination with ALVAC and AIDSVAX to Prevent HIV-1 Infection in Thailand. (S Rerks-Ngarm et al, N Engl J Med 361:2209, 12/3/09.)
* The article was accompanied by an editorial: HIV Vaccine Trial Results - An Opening for Further Research. (R Dolin, N Engl J Med 361:2279, 12/3/09.) The editorial is a two-page overview of the work, with a good plain-English discussion of what was learned from the trial. Recommended; a good place to start, and a good place to go back to if you found the coverage so far to be confusing.
* Both of those are freely available from the journal web site.

See Mission Improbable (11/10/09) for more about p values. That item was stimulated by this one, but is not specifically about this vaccine trial.

* See Why did the HIV vaccine work for some people? (September 27, 2011) for some follow-up on this vaccine trial.
* And then... Why did the HIV vaccine work for some people? Follow-up (May 1, 2012). This fills in the details of the item immediately above; it provides a published paper and the data.

Another approach to an HIV vaccine: A novel approach to providing immunity to HIV (March 12, 2012).

Some other posts on the complexity of HIV issues:
* Why are HIV-infected people more susceptible to Salmonella infection? (5/21/10).
* A bio-ethics controversy: HIV-TB interaction (7/13/10).

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



CITRIS: Zettl; new energy series

November 1, 2009

I have mentioned some of this to some of you before, but there may be new info here.

CITRIS is a multi-campus organization devoted to innovation. There is a particular emphasis on the IT in their name (information technology), but overall their work spans almost anything you can think of. Of particular interest, they have talks that are webcast live, and are then available from the archive for later viewing. (It seems to take them a couple weeks or so to post the video.)

One major attraction is their long-running series of Wednesday noon talks called "Research exchanges".

A recent event that might interest some of you was a talk by Alex Zettl, UC Berkeley physics professor. A couple of Zettl items have been posted here before:
* Weighing gold atoms (September 24, 2008);
* Image of a carbon atom that isn't there (August 17, 2008);
The talk consisted of three short vignettes of work from his lab: nano-motors; a solar-powered boat; and a radio made from a single nanotube. They all work. The talk was not very technical (for the most part); I'm sure that high school students would enjoy and follow a large portion of it. Zettl just exudes "fun" in his work. Considerable physics gets noted along the way, but if some is beyond you, it is not much of a barrier to following the main ideas. Much is novel, but it comes over as routine. We do just take it for granted that one operates the atomic force microscope (AFM) inside the electron microscope (EM)? The three segments were independent, so you can watch one part at a time. I strongly encourage you to give this talk a try.


2009 brought a new series of CITRIS talks, on a wide range of energy issues. These are called "i4Energy" seminars.

Updated September 9, 2013... Fall 2013: The i4Energy series has now been integrated into the regular Research Exchanges series.


For CITRIS events... go to CITRIS events. There you can choose a page for the Research Exchanges series, which now includes the i4Energy seminars.

A direct link for the Zettl talk: Zettl's CITRIS talk, 10/14/09.

More from Zettl: Loudspeakers: From gold-coated pig intestine to graphene (April 27, 2013).

Other posts about CITRIS events:
* Printed electronics: Using a printer to make a better can of soup (April 3, 2012).
* Solar taxi (July 14, 2008).

* * * * *

Another source of videos of good science talks at UC Berkeley is Science@Cal. See the post Astronomy talks (June 22, 2009). (This series started as a set of astronomy talks, but has now expanded to "science".)

* * * * *

Another series... Lecture videos: Berkeley City College (July 14, 2013).

* * * * *

Added May 27, 2014... UC Berkeley Physics Department seminars; video files available for most: Physics Department seminars, current and back to 2007. Click on the date for more information, including title. In general, these are high level talks for people in physics. Nevertheless, some may enjoy seeing some of these speakers.

An example: The Voyager Journey To Interstellar Space; talk by Ed Stone (50 minutes). (Physics Department, University of California Berkeley, March 3, 2014.) If you have trouble with that link, use the link above for the list of Physics Department talks; scroll down to Spring 2014, March 3. This video was noted in the post At the edge of the solar system (September 28, 2012).

Explore!



How do you make phospholipid membranes if you are short of phosphorus?

November 1, 2009

One of the first things you learn about biological membranes is that they contain fatty acids and phosphate. They are found together in a class of substances calleds phospholipids. The phosphate group plays an important role; it defines the polar end of the lipid molecule.

Phosphate is in short supply in some places in the ocean. And cells need it for other purposes -- such as making nucleotides and nucleic acids: e.g., ATP, DNA and RNA. What happens when the phosphate runs low? They just starve and die? Well, some of them switch to using sulfate in their lipids. This spares the phosphate for its more essential role, in ATP etc.

Why does that substitution work? Probably because much of what lipids do is defined by general physical properties, rather than very specific chemical interactions. At a simple level, the membrane is the bag that holds the cell together. I noted above that the phosphate group defines the polar end of the lipid molecule; sulfate can do that, too -- about equally well. Thus the substitution of something that looks fairly similar may work; the same substitution would not work for the nucleotides, where phosphate-specific chemistry is involved. In fact, there is a wide variety of lipids, variations on the theme illustrated by the phospholipid bilayer we usually hear about. There are even other ways to deal with a P-shortage than the S-substitution noted here.

Here is a delightful introduction to this story: No Phosphorus? No Problem! (There's More Than One Way to Skin a Phytoplankton). (3/23/09.) The page discusses much of the diversity of lipids (hinted at above), though it was stimulated by the report of the S-for-P substitution. The picture at the top shows you some basic lipid chemistry; it is not important that you pay much attention to that, if you are not familiar with the chemistry. However, I would note that it is the middle frame (5-6-7-8) that represents the common lipids we hear the most about. It is clear when you read the legend, but I would not have put things in this order, I think.

Yeah, that is a blog. So, is a blog a good source? It depends -- as with most any source. This blog is written by the eminent microbiologist Moselio Schaechter, and it is hosted by the American Society for Microbiology. Further, the specific point I am talking about here is directly supported by a current paper (listed in the blog and below).

The blog page also appeared, in a somewhat condensed form and without pictures, in Microbe magazine, in September; that is how I came across it, and I suspect some of you noticed it.

The paper is: Phytoplankton in the ocean use non-phosphorus lipids in response to phosphorus scarcity. (B A S Van Mooy et al, Nature 458:69, 3/5/09.)

* * * * *

* For a broader view of the P problem, see: A phosphorus shortage? (September 29, 2010).
* For a report of P being replaced by As, see: NASA: Life with arsenic (December 7, 2010). Note that there is actually no specific information about the lipids in this paper.
* Phosphorus long long ago... The origin of reactive phosphorus on Earth? (July 5, 2013).

For more about lipids, see the section of my page Organic/Biochemistry Internet resources on Lipids.



NASA finds a chemical of life on a comet -- follow-up

October 30, 2009

In a recent post, we noted the finding of the amino acid glycine on a comet: NASA finds a chemical of life on a comet (9/1/09). At the time of posting, the paper reporting the work was not available. It is now available, and I have added it there. Those with a little background with isotopes may find the paper good reading. But even without that, much of the paper is accessible and interesting; give it a browse! It is good to know they do not claim finding Nylon bags on the comet. Anyway, I bet most of you have never read a paper in a Meteoritics journal.



October 28


The new flu: your questions

October 28, 2009

The flu item posted last week generated some questions. I have posted a couple of the questions, with some responses.

See the supplementary page for Flu. The new content is at: The new flu: your questions (10/28/09). The post this follows up is immediately above it (dated 10/21/09).

Although the specifics are about flu, some of the issues are general, about the nature of infectious diseases.

Emphasize that posts such as this one provide some information, but cannot be complete. If they raise some questions to think about, that is good. There is no intent to provide medical advice.



Personalized medicine: Getting your genes checked

October 27, 2009

A few years ago scientists reported "the human genome": the sequence of bases in human DNA. Sort of. There is no such thing as "the" human genome; we all differ. However, that report serves as a baseline for further work. In fact, specific genomes have been published for a few individuals (including two of the scientists who were pioneers in the human genome project: Jim Watson and Craig Venter).

We all differ. Take two random people, and they probably differ in a few million ways in their genomes. And they probably differ in their odds of getting heart disease, or cancer, or whatever. In part they have different probabilities of getting, say, heart disease, because of their different genomes. Can we sort that out? Can we check a person's genome and advise them of their odds of getting heart disease -- and then suggest what they might do about it? That is, can we use a person's specific genome to customize medical information for them?

Such personalized medicine seems a good idea, at least in principle. In fact, we have been doing some of this for many years. Pregnant women have long had a test called amniocentesis, to see if the fetus is likely to have Down syndrome. People who know they are at risk for one or another genetic disease can have other tests done, sometimes as part of in vitro fertilization. Newborn babies are tested for a range of genetic diseases. (Not all the tests alluded to here are done by testing DNA directly; some tests are for specific characteristics derived from the DNA.)

The availability of the complete reference human genome -- and the technological advances it reflects -- allows for much more information to be developed. A major activity now for biomedical researchers is trying to find genes for human diseases.

But here's the problem... We all know about simple cases, where one gene plays a major role in determining a disease. There is one specific DNA difference between a person with sickle cell disease and a person without it. A person who carries the sickle cell version of the gene (the sickle cell allele) will have the disease; the person without that version will not have it. Very clean distinction. Same idea for, say, Huntington disease. However, for most diseases there are many many genes, each of which affects your chances of having the disease by a few percent. Since the effects are small, these genes are hard to find; preliminary reports of such effects often end up being discarded upon further testing. And if you do have a gene that really does increase your chances of getting heart disease by 20%, what are you supposed to do about it? What if you have two genes, one of which increases the chances by 15% and one decrease it by 20%? And what if we admit that we have not yet found other genes that could be just as important as those?

Why bring this up? Companies have been formed to provide people with their personal genome information. Give them some scrapings from your cheek -- and a thousand dollars or so -- and they will test your DNA and report back to you on what they find. Amazing! It would have been unthinkable a decade ago. But is it a good idea? The problem is that the quality of the information they provide is limited and of questionable usefulness, for reasons I introduced above. The principle is fine. Over time, the cost will come down and the quality of the information will improve. But for now, it is questionable.

What brought this up now is a nice article in a recent Nature with a serious discussion of the issue. The authors include genome pioneer Craig Venter. I encourage you to look over this article. An agenda for personalized medicine. (P C Ng et al, Nature 461:724, 10/8/09.) As a general perspective, they think the companies are doing high quality work, technically, but -- as I have suggested above -- the quality and usefulness of the information is questionable.

You can also get to the paper via the web site of the Venter Institute. Go to their page of press releases: Venter Institute press releases. Scroll down to the item for October 7, 2009. Click on its link; it takes you directly to the article at Nature.

My discussion here and the article both have a somewhat negative tone regarding the usefulness of these genetic testing services. Ok, but in some ways the picture is not negative. The human genome is an exciting development. Important knowledge about human biology, including disease, is coming from it. The companies providing these tests have a good idea; the problem is just that they are ahead of reality. What they are doing will likely become more and more useful over coming years. I should also add that there are individual cases where a person may want certain genetic tests done because of a personal situation; that is fine.

* * * * *

Follow-up. Even before formal posting, this item has generated some controversy. Good! What do you think? Has anyone had experience with using genetic information? Would you consider using it? Are you curious what your genes say? Would you adjust your lifestyle based on knowledge of your genetic characteristics? Would you use genetic information in choosing a spouse? In choosing an embryo? If you might do any of these, would you do so now, or would you wait until the method provides better information? Have you thought about these questions before?

Again, I want to emphasize that the somewhat negative tone of my post makes a couple of assumptions. It deals with the case where there is no specific reason to suspect a significant genetic issue, and it deals with the current state of genetic testing. Importantly, if a person knows that there is a family background of a genetic characteristic, testing focused on this is a quite different matter.

* * * * *

Here are some related posts. This is intended as a fairly complete list of all posts in the broad area of learning about the human genome and how we might use that information.
* Personalized medicine: cancer therapy (November 9, 2009).
* Genomic information: What not to do (January 16, 2010).
* Low-carb or low-fat diets: a rational choice? (March 14, 2010).
* Genome sequencing to diagnose child with mystery syndrome (April 5, 2010).
* The human genome - 10 years on (April 16, 2010). Perspective.
* Let parents decide (May 14, 2010).
* Personalized medicine -- and the entering students at UC Berkeley (May 25, 2010).
* The $1000 genome: Are we there yet? (March 14, 2011).
* Your genes: What do you want to know, and when do you want to know it? (March 22, 2011).
* Is whole genome sequencing a useful medical tool? (November 9, 2011).
* Cystic fibrosis: treating the underlying cause -- for some people (November 13, 2011).
* Why did the HIV vaccine work for some people? Follow-up (May 1, 2012).
* In humans, rare mutations are common (July 24, 2012).
* Genome sequencing of a human fetus (August 25, 2012).
* Accumulation of mutations in the sperm of older fathers (November 19, 2012).
* More genome sequencing for newborns? (September 17, 2013).
* Added October 22, 2013. Are there genetic issues that we don't want to know about? (October 22, 2013).

There is more on personalized medicine, including useful background and perspective, on my page Biotechnology in the News (BITN) - DNA and the genome. Especially see the sections "Examples of how genome information is useful" and "Recent items, briefly noted".

* Added October 22, 2013. My page for Biotechnology in the News (BITN) -- Other topics includes a section on Ethical and social issues.



Gravity tractor: protection from asteroid collisions

October 26, 2009

We have discussed the possibility of asteroids colliding with earth -- with possibly disastrous consequences. A recent post was: NASA mission to detect killer asteroids (9/9/09).

What do we do if we detect something headed in our direction? There is no clear answer to that. The following recent news story discusses one option being considered: British plan to tackle asteroids. (8/31/09.) As you read this, note there are numerous issues -- including the need to launch the device 15 years in advance of the expected collision. This emphasizes the need to detect objects on a collision course with earth well in advance.

Remember... This is a news story about an idea. It is not a report of a finished product. What is most important here is that we have a proposal -- an interesting one. We need lots of proposals, and then work on them to find out which things will really work.

More... NEOShield: defense against Earth being hit by an asteroid (February 6, 2012).

A record of previous events... Earth: craters (August 19, 2012).

A distinct problem is dealing with manmade debris in space. Here is a post on that topic: Cleaning up space debris (September 6, 2011).

Added September 16, 2014. More about gravity: Does anyone know how strong gravity is? (September 16, 2014).



Seeing atoms -- follow-up

October 25, 2009

I have added cross-references between two earlier posts, both of which involve the development of new techniques for visualizing atoms. They share the features of involving interesting methodological developments, and of having some neat pictures. They are:
Seeing molecules under a microscope (September 19, 2009);
Image of a carbon atom that isn't there (8/17/08).

Why did it take me a month to do this? The older post pre-dates the Musings files. I am (very) slowly adding some earlier items from my old e-mail files. In this case, the new post prompted me to try to find the old item. If you haven't, you might enjoy browsing some of the older items on the Archives page.



Nobel Peace Prize

October 25, 2009

It reminded me of this site. I thought I had distributed it previously, but don't see it in the files. Anyway, for fun... Nano Obama.

The paradigm of this prize also prompted me to suggest some others. I didn't look up all the details, so this is a bit sketchy.
* Nobel Medicine Prize to Richard Nixon, for declaring war on cancer.
* Nobel Medicine Prize to Margaret Heckler, for promising a vaccine against AIDS. (For those too young to understand... Well, if you are too young to understand, that is the point. This was a long time ago. About 1985. Heckler was Secretary of Health and Human Services for Reagan.)
* Nobel Physics Prize to (whom? Teller?), for telling us that fusion energy would be the ultimate energy source in twenty years. Actually, this was quite a good prediction. So good that we keep making it. (This prediction was noted in the post about a book that reviews predictions from Popular Mechanics magazine: Book Suggestions: Benford, The Wonderful Future That Never Was.)
* Nobel Economics Prize to the Nobel Peace Prize Committee. Not sure I understand why, but I never understand the Economics Prize.

Contributions?

More about Obama...
* Quiz: Barack Obama and polar bears (July 20, 2011).
* Obama and science (November 13, 2008).



October 21, 2009


The vegetarian spider

October 21, 2009

Figure 1A: spider eating plant So, what is the big deal?

Have you thought about what spiders eat? Perhaps the spiders most familiar to us are those that make a web, and catch food in it. Flies, for example. If anyone has reports of spiders catching flying plants in their webs, let me know.

But what about all the other kinds of spiders? Apparently, they are all carnivores (meat-eaters). At least, they are largely carnivorous, even if they consume some occasional nectar or pollen. Or so it was thought.

The new work reports the first known herbivorous (plant-eating) spider -- the first out of some 40,000 species of spiders. The spider itself has been known for over a century, but it was not known what it eats. One must wonder, then, how many other spiders have odd habits that we have not yet noticed.

There is more to this story. The spider doesn't just eat plants; it eats specialized leaf tips that are intended for the ants. So the story is not simply of the first known vegetarian spider, but of how it gets its food by intruding into a plant-animal relationship that itself is interesting.

For more...
* Here is a short news story that introduces the spider -- and the ants and the leaf tips. Vegetarian spider -- Small jumping species steals lunch from ants. (Science News, August 30, 2008.) Click on "Enlarge" -- if you are bold enough. This is based on a meeting a year ago; the work was recently published; see below. This story is no longer freely available.
* Unusual Spider Species Passes Up Live Prey for Plants -- A primarily vegetarian jumping spider gets ahead by taking advantage of ancient ant-acacia mutualism. (Scientific American, October 12, 2009.)
* Here is a news release about the current paper. Herbivory discovered in a spider -- Clever Central American species is the first spider known to science that feeds mainly on plant food. (EurekAlert, October 12, 2009.)
* Some movies of the spiders are posted with the article at the journal web site: Spider movies. (The movies should be freely accessible there, even if the article is not. I provide the article below. You can also get to the page for movies by going to the article page, and choosing "Supplemental data".)
* The news story that accompanied the scientific article: Nutritional Ecology: A First Vegetarian Spider. (D E Jackson, Current Biology 19:R894, October 13, 2009.) An excellent overview of the spider and its feeding habit.
* The article: Herbivory in a spider through exploitation of an ant-plant mutualism. (C J Meehan et al, Current Biology 19:R892, October 13, 2009.) The figure at the top of this item is Fig 1A from this paper.

For more about how spiders eat: Which end of the ant should you eat first? (June 4, 2010).

For more about spiders: How the spider avoids being attacked by the ants (January 10, 2012).

For more about the tree-ant relationship -- and the elephant connection: Why a tree cultivates ants (October 3, 2010).



The artificial zebra

October 21, 2009

Not sure whether this is biology or art...

I heard this on the BBC news a few days ago. Here is the story, with picture (actually a short video, if you are willing to endure the ad), from the BBC web site. Dye-job donkeys wow Gaza children. (10/9/09.) There are many levels to this, but let's just take it here for amusement.

Another zebra that isn't... Stripes protect zebra against horseflies -- another story of polarized light (February 26, 2012).



The new flu

October 21, 2009

See the supplementary page for Flu. The new content is at: The new flu: (10/21/09). There is also a follow-up to this post, immediately below it there (dated 10/28/09).



SETI

October 20, 2009

SETI = Search for Extra-Terrestrial Intelligence. It is a program to look for signals in space that bear the distinctive signature of being from intelligent beings.

Nature recently ran an interesting opinion piece about SETI -- noting that it was 50 years ago that they published a key paper putting forth the rationale for such a venture. I thought some might enjoy reading these two short papers. The 1959 paper has some technical stuff in it, but much is accessible. Skip what you must -- but be sure to read the final paragraph.

* An alien concept. (F Kaplan, Nature 461:345, 9/17/09.)
* Searching for interstellar communications. (G Cocconi & P Morrison, Nature 184:844, 9/19/1959.)
* A somewhat edited version of the Cocconi & Morrison article was later published in Cosmic Search, a magazine of the Big Ear Radio Observatory, North American AstroPhysical Observatory. This is freely available online: pdf of later version: Searching for interstellar communications.

I would have included a picture of the program's key findings -- had there been any.

For the record, I am not a fan of SETI. However, the program exists, and there is interesting logic behind it. It was fun to read the 1959 paper.

* * * * *

Many know SETI through the program SETI At-home, a distributed computing system. Another example of such a system is discussed in the post The Quake-Catcher Network: Using your computer to detect earthquakes (October 14, 2011).

Also see... The smartest chimpanzee? (September 29, 2012).



Using music to control a machine

October 17, 2009

Music to control a microfluidics device.
That music results in the controlled movement of four liquid droplets. Each tone controls one of the four droplets. For example... The first note is a G; it causes droplet A to move. Each time that G is sounded, droplet A moves.

For a good introduction: Music Is the Engine of New Lab-on-a-chip Device. (7/22/09.) This links to a couple of movies showing how the music controls the device. I suggest starting with the second one -- unless you are from the University of Michigan.

Although the first reaction here might be simply that this is cute, they are addressing a serious issue, and their proposal is potentially a meaningful solution. Microfluidics allows work to be done with tiny volumes -- so small that the problem is learning how to handle them. What they propose is acoustic control, with resonant cavities as the switches -- activated by "music". It seems to work. And it is cute.

The paper is: Acoustically driven programmable liquid motion using resonance cavities. (S M Langelier et al, PNAS 106:12617, 8/4/09.) The Figure above is from Figure 4 of this paper. You can see the movement of droplet A -- nine times -- by looking at the blue peaks in the bottom part of the Figure.



A good home -- for your mouse

October 15, 2009

It's from an article on Lab Toys -- on providing a proper environment for lab animals. It is also similar to the cover photo on the magazine. For those who may want more, the article is: Lab Toys. (A Katsnelson, The Scientist, 10/09, p 30. It may require subscription access; give it a try.)

Added July 11, 2014. Also see: Would wild mice use an exercise wheel? (July 11, 2014).



October 14, 2009


Lakes that explode

October 13, 2009

In a recent item, we talked about ice that burns. [Ice on fire (August 28, 2009).] Methane (natural gas, CH4), formed by some combination of geological and biological processes, is trapped deep underground (or in the deep ocean) in ice cages. It may be released -- gently and intentionally to yield a useful energy source, or violently to yield a disaster.

The current item has some similarities to that story of ice that burns. It involves a trapped gas, which may be released either usefully or destructively. In this case, the main relevant gas is carbon dioxide, CO2; it is produced by volcanic activity, and vented to a lake bottom. Under the high pressure at the lake bottom, the gas is quite soluble (think of a champagne bottle). Some of the CO2 may be converted to methane by bacteria. Now we have a gas that might be useful, if we can figure out how to harvest it. But the big concern is that something may disturb the gas at the lake bottom, resulting in a massive gas release -- an explosive release of the suffocating gas CO2, and perhaps also some methane. Think of opening that champagne bottle.

Such exploding lakes are known. Fortunately they are not common; to make one requires volcanic activity connected to a deep lake. In fact, only three such lakes are known, all in Africa. A few lake explosion events have been observed in modern times. On August 21, 1986, Lake Nyos in Cameroon "exploded" -- releasing a cloud of CO2; 1,700 people and 3,500 livestock were killed. A landslide or some volcanic activity may have triggered the explosion. Lake Nyos has now been (partially) vented, to allow it to safely off-gas.

Cow killed by Lake Nyos explosion, reduced
A dead cow, killed by an exploding lake.

Lake Kivu, in Rwanda, is also saturated with CO2. It is 2000 times larger than Lake Nyos.

A lakeful of trouble. (News feature. Nature 460:321, 7/16/09.) This is what brought the issue to my attention at this point -- along with the recent post about methane hydrates (ice on fire). It is mainly about Lake Kivu. Kivu is not only much larger than Nyos, but also contains much methane, produced from the CO2 by bacteria. Thus Kivu has the potential to be tapped as an energy source -- as well as the potential to cause a disaster.

For more about Lake Nyos: Wikipedia: Lake Nyos. The Figure above is reduced from one in this article.

Another Musings item on volcanoes: VPOW (July 14, 2010).

Added January 17, 2014. More on high pressures: Novel forms of sodium chloride, such as NaCl3 (January 17, 2014).

There is also a dead cow in the post Another disease has been eradicated. GREP (February 2, 2010).



Science in Eastern Europe

October 13, 2009

This item is mainly for those with a particular interest in Eastern Europe.

Nature ran a "news feature" on how science has progressed since the fall of the Berlin wall, 20 years ago. The two articles include some general discussion, and some data, with comparison to the EU and selected specific countries. The two articles are:
Scaling the wall. (Nature 461:586, 10/1/09.)
Beyond the bloc. (Nature 461:590, 10/1/09.)

An amusing tidbit... The University of Ljubljana in the tiny country of Slovenia has broken into the ranks of the "top 500 universities in the world" (Shanghai ranking). For a country of only two million people, that is a nice ratio of top universities to population.



The Lord has a new ring

October 12, 2009

Borislav sends: New ring detected around Saturn. (BBC, October 7, 2009.)

This was a big news story last week about a big "object" discovered in our solar system. Big but almost invisible.

Let's take a moment here to go through the story, guided by that beautiful figure from the news story. It is easy to get lost in all the big numbers, and the figure combines different scales.

Saturn and its ring system

The top frame shows Saturn and its classic ring system. The inner ring system was seen (but not understood) in the earliest telescopic observations, by Galileo in 1610, and was recognized as a ring-like structure by Huygens in 1655. The top frame also shows the "distant" and faint E ring, discovered in 1967. That whole top frame would just about fit within the orbit of our Moon.

Now, shrink that whole top frame down to the little white circle in the middle of the main frame. Circling around that entire internal Saturn system is the moon Iapetus -- in the orbit shown with a faint green line, which is about 10 times further away than the E ring, which seemed so far away in the top frame. And then there is the moon Phoebe -- out in the orbit shown with a faint yellow/brown line, four times further away than Iapetus, and in a different plane. Ok, we knew about Iapetus and Phoebe. What is new here is that large brownish "smear", extending from beyond Phoebe inward to about Iapetus. A ring. A ring that was previously unknown.

(Iapetus was discovered in 1671 -- by Giovanni Cassini, after whom the current Cassini spacecraft, exploring Saturn, is named. Phoebe was discovered in 1899. The count of known moons for Saturn is 61 -- or hundreds, depending on what one counts. Some of these were discovered by the Cassini craft. However, the new ring reported here was discovered using the Spitzer Space Telescope, not Cassini.)

Why was something so big unknown? Well, there is not much there. It covers a lot of space, but there is not much in it. The news story will give you some numbers about how low -- unimaginably low -- the density of the ring is. If we collected all the material in the ring, we could put it in a pile the size of a few city blocks. Yet this ring helps us fill in a story. The ring is probably made by things hitting Phoebe, releasing Phoebe material into the ring. These particles spread out over the ring, and some hit Iapetus -- thus explaining why one side of Iapetus looks like it has been bombarded with Phoebe-like material. It has.

* The paper is: Saturn's largest ring. (A J Verbiscer et al, Nature, 461:1098, 10/22/09.) Even just browsing the abstract may be useful. If you find the paper too technical, skip down to the very last sentence -- for a prediction.
* The published paper was accompanied by a Nature news story: Solar system: Saturn's colossal ring. (M S Tiscareno & M M Hedman, Nature, 461:1064, 10/22/09.)

As to the title of this item... You might check the Musings post of May 14 for another item whose content is partly Tolkien-inspired.

More from the rings of Saturn: Venus: an unusual view (March 18, 2013).

Added May 9, 2014. More about rings in the Solar System: Rings for Chariklo (May 9, 2014).



A solar prominence

October 12, 2009

The sun, with a prominence; reduced. What a photograph!


Even better... Bigger picture [link opens in new window].

The caption: "Figure 1. Extending over many thousands of kilometers and with a mass of more than 100 billion tonnes, a twisting solar prominence protrudes out of the Sun's corona in the bottom left of this image. Magnetic fields are heavily involved in the formation of these and other solar features, such as flares and coronal mass ejections. When these fields break apart and link up with each other, in a process called magnetic reconnection, such solar features can explosively release energy that can have consequences on Earth."

This is from Reconnecting magnetic fields. (J L Burch & J F Drake, American Scientist 97:392, 9/09.) The photo was taken by SOHO, the Solar and Heliospheric Observatory. (The photo itself is not new; I think it is probably from about 1997.)



Nobel prize in physics for the rediscovery of fiber optics

October 12, 2009

The use of fiber optics has been around long before Charles Kao came along. As we have noted here before, some sponges use glass light pipes to direct light into the photosynthetic symbionts that lie in otherwise dark parts of their body. See Croatian Tethya beam light to their partners (12/16/08).

The prize announcement is at: The Nobel Prize in Physics 2009. (October 2009.) The linked page "Scientific Background" (at right) gives some interesting historical background. It traces the idea back to Faraday and Tyndall, in the mid 19th century -- and then even further back to ancient Egypt. Kao did not invent fiber optics, but rather made key developments in the field.

This Nobel award was not only about fiber optics. Half the award went to two scientists for developing charge-coupled devices (CCD), which convert light to electrical signals. CCDs are the basis of modern astronomical observations, including those shown in this Musings set, and of modern digital photography.

More Faraday... Lyell on fossil rain-prints (May 6, 2012).

Added March 11, 2014. More about inventions... National Inventors Hall of Fame: 2014 inductees (March 11, 2014).



elgooG

October 12, 2009

elgooG logo !flesruoy ti yrT.

elgooG.

I recently posted an item about Haystack (next item, immediately below: Haystack (October 6, 2009)), which is designed to overcome government restrictions on Internet access. This reminded me of an earlier such effort. It has survived on its own, because it is fun. Because of the nature of the site, I have long listed elgooG on my page of Internet Resources for Organic Chemistry -- under Stereochemistry (the study of mirror image molecules).

The designers of Haystack and elgooG represent science at its best, harnessing technology for human good. There have been numerous such programs, with varying technical aspects. I got one reply about Haystack noting that it is easy to circumvent. Sure. They understand that. They keep changing the details, and distributing the information through the "underground".

Added April 11, 2014. More about Google: Google tracks the flu -- follow-up (April 11, 2014).

Added May 28, 2014. More that is backwards... "Moonwalkers" -- flies that walk backwards (May 28, 2014).



October 7, 2009


Haystack

October 6, 2009

Haystack is a computer program -- to attempt to restore communication to those whose governments restrict the Internet. I heard one of the Haystack people being interviewed, and decided to check the web site. Here is the FAQ: http://www.haystacknetwork.com/faq/. [Link no longer valid.] The page is now archived: archived page.

Part of the push and pull of the role of the Internet in modern society.

Also see related item, immediately above: elgooG (October 12, 2009).

* * * * *

More, November 3, 2010...

Such programs are difficult to implement, and typically require high maintenance -- to keep them ahead of the authorities. A reader expressed considerable skepticism about Haystack when I posted it initially; turns out he may have been right. Haystack has now been withdrawn, with allegations that it did not work very well in the first place.

The Wikipedia page provides very brief coverage, but is likely to be updated if there are further developments. As of now, I also recommend the BBC news story of September 14, 2010; this is currently reference 8. Wikipedia: Haystack (software).



Don't eat the bats.
    or
An ALS story: Guam and New Hampshire; food chains and biomagnification; cyanobacteria, cycad trees, and flying foxes; pond scum; and BMAA.

October 6, 2009
Updated January 2, 2014.

News story: Did a lake trigger a deadly disease? (Boston Globe, September 14, 2009) "Researchers hope to explain why Lou Gehrig's disease seems to occur more often in people who live near lakes and ponds where cyanobacteria bloom". [This story is no longer freely available. The text of the story seems to be at: text of news story. See the update below for more.]

Just seeing that opening line connected this news story to a fascinating story of a neurological disease in Guam. The news story above is actually very good. If you just start with it, you'll get all the connections. If you start with me here, I'll try to give you some background. With luck, I'll confuse you. That's good; it is a confusing story -- as so often with an incomplete story.

Let's start with a disease. ALS = amyotrophic lateral sclerosis. The Brits call it motor neuron disease, which may be more intelligible. It is a progressive neurodegenerative disease. The patient loses control of motor functions, and typically dies upon losing the ability to use the muscles for breathing. The disease is also referred to by the name of its first famous victim, Lou Gehrig, whose baseball career was cut short by ALS. Stephen Hawking is another famous ALS victim. In general, the cause of ALS is not known. A few cases are familial -- caused by mutations. But even with these, the reason the mutation causes the disease is not understood. Of course, with a disease that is mainly defined by its symptoms, there may be multiple causes; not all ALS may be the same.

BMAA structure. So to Guam. There is an ALS-like disease there. It is particularly common among those who eat flying foxes (which are really bats). Is there any connection? Yes, say researchers who have worked out the food chain. The real culprit is a chemical called BMAA (β-methylamino-L-alanine). (L-alanine is one of the common amino acids found in all organisms; BMAA is a variation, not commonly found in biology.) Some cyanobacteria ("blue-greens" -- bacteria that do modern plant-type photosynthesis) make small amounts of BMAA. Some of these BMAA-producing cyanobacteria grow in the roots of cycad trees -- and the BMAA ends up in the cycad seeds. People eat the cycad seeds; there is doubt that this results in enough exposure to BMAA to be a problem. However, the seeds are also eaten by flying foxes. And people eat the flying foxes -- and, it is said, get ALS from the BMAA that has been transmitted along the food chain. One aspect of this story is biomagnification: the increasing levels of the presumed toxin as it passes along the food chain. In fact, measurements have shown that higher levels of BMAA are present in the flying foxes than in the cycad seeds, which in turn have more than the bacteria. The story is circumstantial and not fully accepted, but has served to trigger a lot of work.

Now what? Clusters of ALS in New Hampshire -- with a possible connection to pond scum containing cyanobacteria. Sound familiar? No bats.


The paper behind this news story is not yet available. So, take this as a preliminary account. And remember that people have been arguing about the role of BMAA in causing neurodegenerative diseases in humans for many years, so we should not expect a simple answer soon.

Although an article is not available for now to go with the current news story, I do have two reviews with different views of the Guam situation. [See update below for the article on the current work.]
* A good recent review of the general BMAA story (via abstract at PubMed): Is there a role for naturally occurring cyanobacterial toxins in neurodegeneration? The beta-N-methylamino-L-alanine (BMAA) paradigm. (S Papapetropoulos, Neurochemistry International 50:998, 2007.)
* A review by skeptics, explaining why the "cycad hypothesis" (that is, BMAA) is not relevant to the Guam disease. The ALS/PDC syndrome of Guam and the cycad hypothesis. (J C Steele & P L McGeer, Neurology 70:1984, 2008.)

I had trouble coming up with a concise title for this item. The first part of the title is short. But it does not fit the New Hampshire situation, which got this item started. Further, the problem is not simply eating bats, but rather eating bats that have eaten cycads -- cycads that are infected with cyanobacteria -- with BMAA-producing cyanobacteria. Suggestions welcomed.

Added July 1, 2014. More on this story... How BMAA may cause motor neuron disease -- a clue? (July 1, 2014).

More about bats: How to find the blood (August 29, 2011).

* * * * *

Updated January 2, 2014. The original news story noted above is no longer freely available, and no article was available at the time of the original post. Now...

News story: Dangerous Waters -- Could there be a connection between blue-green algae and clusters of deadly neurological disease near our lakes? (UNH Magazine, Spring 2009.) (The work is from Dartmouth Medical Center and the University of New Hampshire.

The article: A cluster of amyotrophic lateral sclerosis in New Hampshire: a possible role for toxic cyanobacteria blooms. (T A Caller et al, Amyotrophic Lateral Sclerosis 10 Suppl 2:101, 2009.) There is a freely available pdf from the authors.



Athletes: Head injuries

October 5, 2009

Some of you may be interested in the possible long term effects of sports injuries, especially to the head. This is particularly an issue for children; the story here is about pro athletes.

News focus story: Neuropathology: A Late Hit for Pro Football Players. (G Miller, Science 325:670, 8/7/09.) "Emerging research suggests that hard knocks on the field may cause delayed brain damage in retired athletes."

As I was about to post this, the National Football League released its own survey of the incidence of memory problems in retired players. Dementia Risk Seen in Players in N.F.L. Study. (9/29/09) Note that this is not a formal medical study, and has not been published as a scientific article. Presumably, others will follow this up with more careful studies.


For more about sports...
* Baseball physics (July 31, 2011).
* Flow centrality: the key to a scientific analysis of the soccer game (July 11, 2010).



Failbot

October 5, 2009

Recent posts about robots resulted in a response -- a robot that actually does something. Or at least tries to. The Honda presentation.

Anyone here understand Japanese?

* * * * *

This item already has attracted a response! It follows ...

I think that it is not fair and almost impolite to write such an article about Asimo.

I am biased about this one, so...

Asimo irresistibly reminds me of Asimov's Giskard, as Giskard never got "humanoid" form, but always stayed "robot"-like and had profound impact on development of human civilization. Additionally, Giskard was the character who "invented" zeroth law of robotics.

For those who need some help with the allusions...
* R. Giskard Reventlov
* Three Laws of Robotics - Zeroth Law added.

Fun!

Now I will paraphrase Gates; "Be nice to robots. Chances are you'll end working for one." - So be nice to Asimo! :)

* * * * *

The previous robot item was about iCub: Prosthetic arms, prosthetic head ... (9/26/09).

The next robot item: Synthetic brains (1/25/10).



NASA weighs India, finds it deficient

October 2, 2009

The simple story here is that NASA says India is losing water. Actually, that was already known. What's neat is how they make the measurement.

The measurement is based on using a pair of satellites, and carefully measuring their positions relative to each other. This turns out to be rather sensitive to the local gravity -- to the difference in gravity sensed by the two satellites. The major contributor to the changes in gravity observed over time -- at least over short time scales -- is water. That is, NASA is taking repeated measurements of local gravity variations, and the best interpretation is that India is losing water.

The water problem is becoming an issue in many places, including here in California. As population increases, we are reaching the limits of our supply of fresh water. It is hoped that gravity measurements such as those reported here will be useful in understanding the water supply.

* GRACE home page. GRACE = "Gravity Recovery and Climate Experiment". Lots of good info there. Look around. Among the pages...
* Under Education: Tracking water movement on and beneath Earth's surface. An overview, with data tracking monthly gravity variations in the Mississippi River basin.
* Under News: Satellites Unlock Secret to Northern India's Vanishing Water. (8/12/09.) A NASA press release about the India work.
* The paper: Satellite-based estimates of groundwater depletion in India. (M Rodell et al, Nature 460:999, 8/20/09.)

And as I was putting this together, The European Space Agency announced the start of another project to examine earth's gravity variations. For a short intro: Satellite to begin gravity quest. (9/22/09.)

For some results from that mission -- more about gravity, see: The potato we call home: a study of the earth's gravity (May 3, 2011).

Added March 21, 2014. More about water in India... A practical system for removing arsenic from water (March 21, 2014).

More from GRACE: 2011: There was less water in the oceans (November 25, 2012).

Added June 20, 2014. More about groundwater: Groundwater depletion in the nearby valley may be why California's mountains are rising (June 20, 2014).



How bacteria swim and why -- a physics view

October 2, 2009

An article about a biological system -- but with something of a physics view. The focus is on how bacteria swim -- on bacterial flagella and their motor. This swimming system is an interesting machine. Further, it is connected to a sensory system, so that the bacteria (tend to) swim toward good things and away from bad.

This article is a bit old. However, the basics are still good and the article is delightful. People with various backgrounds should find parts of it interesting and useful.

Motile Behavior of Bacteria. (H Berg, Physics Today 53:24, 1/00.) Howard Berg was a pioneer in developing our modern understanding of bacterial motility and chemotaxis. There is also a copy of the paper freely available at DASH, the Harvard repository: copy: Motile Behavior of Bacteria. Click on "Download Full Text", near the top.

Caution. The size of the bacterial cell should be given in µm (micrometers). However, some web browsers are incorrectly showing mm (millimeters).
Bacterial flagella: motor, EM
The Figure shows a composite of electron microscope images of the "motor". It is part of Figure 2 of the article.

Berg's web site: Bacterial Motility and Behavior. Among the things there... movies of bacteria swimming.

More about swimming:
* Can giraffes swim? (August 6, 2010).
* Spinning gears -- driven by bacteria (February 1, 2010).
* Dancing algae (June 25, 2009).

Thanks to Jitesh for passing this on to us.



September 30, 2009


One way trip to Mars -- follow-up

September 30, 2009

Last week I included an unidentified picture with this item. I have now edited the item and identified the picture. One way trip to Mars (9/22/09).

I showed one person a draft of the original item before posting it last week. I asked if it was cruel for me to post it without identifying the picture. He said it was. So that is why I went ahead and did it.



Growing new teeth

September 29, 2009

Scientists have grown new, functional teeth -- for a mouse. They took stem cells, started tooth development under controlled conditions in the lab, and then implanted the tiny developing tooth in a tooth socket in the mouse. Tooth development continued, and resulted in a good tooth.

For an overview and picture: Mouse Tooth Grown From Stem Cells in Mouth. (8/3/09.)

The paper is Fully functional bioengineered tooth replacement as an organ replacement therapy. (E Ikeda et al, PNAS 106:13475, 8/11/09.)

Will this work for humans? Hard to know; I'm sure they will try. One important difference between mouse and humans here is that mouse (rodent) teeth grow continually throughout life, although I think they cannot make a new one if one is fully removed. Thus the environment in the mouse tooth socket may be more amenable to nurturing a replacement tooth than it would be for humans.

A reader sent me some information about this story; the above summarizes the highlights of our discussion. It is one part of the broader issue of learning about regeneration of body parts, including the possibility of making new body parts in the lab.

A recent Musings item on regeneration: Regenerating a leg (September 1, 2009).

More on stem cells: Do you need some new brain cells? (March 22, 2010).

More on rodent teeth: A rodent that can't chew (November 5, 2012).

There is more about regeneration and stem cells on my page Biotechnology in the News (BITN) for Cloning and stem cells. It includes an extensive list of related Musings posts.



Prosthetic arms, prosthetic head ...

September 26, 2009

iCub This is iCub.

iCub is 3 1/2 years old, and has nine younger brothers, with ten more due by the end of 2009.

He lives at IIT Genova (Genoa). Or should I say, he is at IIT Genova.


For a feature report on iCub, his family, and their education: The bot that plays ball. (Nature 460:1076, 8/27/09.) The paper is also at the iCub web site: The bot that plays ball. Of particular interest may be the plan to teach one of the kids language -- the same way you would teach any kid language, by speaking to him.

The picture above is from iCub's web page: iCub. The site also includes the Nature article, as noted above.

Other posts on robotics include:
* Added January 14, 2014. Cubli: a little cube that can stand on one corner and can walk (January 14, 2014).
* Failbot (October 5, 2009)
* Prosthetic arms (September 16, 2009)



The human mind: understanding death

September 26, 2009

Why did the "human mind" arise only once? In this short letter to Nature, a provocative idea is raised... A key feature of the human mind is self-awareness. Humans are (we presume) the only animal to know their own mortality. The idea suggests that knowing of death, and fearing it, served as a barrier to the development of the human mind. We are inclined to treat the human mind as a positive, but the proposal is that it might have been a negative.

Human uniqueness and the denial of death. (A Varki, Nature 460:684, 8/6/09.) See the right hand side of the page. It will be interesting to see whether any follow-up is published. Until then, just take this as an intriguing -- and disconcerting -- reflection on our nature.



Using DNA to make computer chips

September 25, 2009

Jitesh sends the following item on how DNA might be used to position computer chip components more closely than now possible: DNA 'organises itself' on silicon. (8/17/09.)

Briefly, the method uses common chip substrates and common etching techniques to create binding sites for special DNA molecules. Observation of the bound DNA molecules, using atomic force microscopy, shows that most are properly aligned as intended. The DNA molecules can now be used for the next level of positioning components. This offers the promise of positioning components with 6 nanometer resolution -- about 10-fold better than current practice.

Fig 2c. 175% In the figure, the whitish triangles are DNA molecules, which have been designed and synthesized in the lab to have this particular shape. A surface is prepared for them, with binding sites that are supposed to determine where the DNA binds, and its orientation. As you can see, they do very good at "where". And their results for orientation, while imperfect, are promising. The figure highlights one column where all the triangles are oriented as intended. (The DNA triangle with a dark circle is one that is oriented incorrectly; there are others.)

The white scale bar is 500 nm. The sides of the DNA triangles are about 127 nm.


The Figure is Part C of Figure 2 of the paper listed below.

Another good news story on this is: Self-assembled DNA Scaffolding Used To Build Tiny Circuit Boards. (8/20/09.)

The picture that is prominent in both news stories is cute, but it does not show one key feature. It does show the DNA molecules, but does not show them oriented. This picture is not from the paper. (It would seem to reflect an earlier stage of the work.)

This is a complex story. Many steps. One thing to note is that there is no biology going on here. Nature invented DNA as the molecule of heredity; a key part of how it works is that the two strands are complements of each other. The computer scientists use DNA and its feature of complementarity -- but they do not use any biology. They design the DNA they want, and make it using chemistry. Then they use the DNA to help them position computer components. Why is this good? Because the DNA has features that allow them to position things more closely than otherwise possible. Moore's law lives on -- if this works out.

The paper is: Placement and orientation of individual DNA shapes on lithographically patterned surfaces. (R J Kershner et al, Nature Nanotechnology 4:557, September 2009.)

This post shares an interesting technique with one from last week: Seeing molecules under a microscope (September 19, 2009). Both use atomic force microscopy (AFM). This post uses AFM as a routine observational tool. The previous post presents a development of the AFM technology itself. Note the size of the molecules (and the scale bars) in the two posts. This post focuses on observing DNA molecules about 130 nm across; the previous post focuses on observing a small molecule about 1.5 nm across. In fact, the problem there was not primarily size, but the nature of the molecule.

As these posts show, AFM lends itself to beautiful and fascinating pictures. For more, 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.



Pet Diary

September 25, 2009

From miscellaneous e-mail... (It's pretty good!)

What Pets Write In Their Diary:

* Excerpts from a Dog's Diary...

8:00 am - Dog food! My favorite thing!
9:30 am - A car ride! My favorite thing!
9:40 am - A walk in the park! My favorite thing!
10:30 am - Got rubbed and petted! My favorite thing!
12:00 pm - Lunch! My favorite thing!
1:00 pm - Played in the yard! My favorite thing!
3:00 pm - Wagged my tail and barked! My favorite thing!
5:00 pm - Milk Bones! My favorite thing!
7:00 pm - Got to play ball! My favorite thing!
8:00 pm - Wow! Watched TV with the people! My favorite thing!
11:00 pm - Sleeping on the bed! My favorite thing!

* Excerpts from a Cat's Daily Diary...

Day 983 of my captivity...

My captors continue to taunt me with bizarre little dangling objects... They dine lavishly on fresh meat, while the other inmates and I are fed hash or some sort of dry nuggets.

Although I make my contempt for the rations perfectly clear, I nevertheless must eat something in order to keep up my strength.

The only thing that keeps me going is my dream of escape. In an attempt to disgust them, I once again vomit on the carpet.

Today I decapitated a mouse and dropped its headless body at their feet. I had hoped this would strike fear into their hearts, since it clearly demonstrates what I am capable of. However, they merely made condescending comments about what a "good little hunter" I am. The bastards.

There was some sort of assembly of their accomplices tonight. I was placed in solitary confinement for the duration of the event. However, I could hear the noises and smell exotic food. I overheard that my confinement was due to the power of something called "allergies". I must learn what this means and how to use it to my advantage.

Today, I was almost successful in an attempt to assassinate one of my tormentors by weaving around his feet as he was walking. I must try this again tomorrow -- but at the top of the stairs.

I am convinced that all the other prisoners here are flunkies and snitches. The dog receives special privileges. He is regularly released -- yet, he seems to be more than willing to return. He is obviously retarded.

Other posts on dogs include:
* Do dogs respond to their owner's yawns? (May 29, 2012).
* Dog fMRI (June 8, 2012).
* It's a dog-eat-starch world (April 23, 2013).

Other posts on cats include:
* Quiz: The monkey-cat (October 26, 2011).
* See cat run (March 14, 2012).
* Big cat, little cat: Taqpep determines coat pattern (December 27, 2012).



September 23, 2009


What to do if you are about to drown

September 23, 2009

Grow. Upward. Fast.

At least, that is how rice does it -- those strains of rice that can survive deep water. They can grow almost a foot per day when submerged.

How it happens is fairly clear, and fairly simple. Ethylene, H2C=CH2, is a well-known hormone in plants; it is the ripening hormone for fruits, and is used to induce artificial ripening of fruit in warehouses. Ethylene is a gas. The growing rice makes ethylene. If the rice is submerged, the ethylene cannot easily escape; it builds up, and induces the growth spurt.

What's new is that scientists in Japan have found key hormone-related genes that are involved in the process. They have bred the genes into high-yielding rice strains, and they seem to work. Thus they seem to be on track to combining two beneficial traits into a single strain: high yield, and tolerance to deep water. Rice escaping deep water
The figure at right is a cartoon showing how the rice grows to escape rising water. The full figure, in the story in Nature listed below, also shows the hormone interactions that are involved. (It also shows an alternative approach some rice uses to survive flooding.)

* A short news story in the New York Times with the highlights: In Some Rice Varieties, Genes Fuel Fast Growth When the Water Pours In. (8/21/09)
* Good news story accompanying the article in Nature: Plant biology; Genetics of high-rise rice. (L A C J Voesenek & J Bailey-Serres, Nature 460:959, 8/20/09. And yeah, that first author really has four initials; he is Dutch.)

For more about rice... What color is your rice? Rice, diabetes, and arsenic. (December 12, 2010).

For more about avoiding drowning... How to survive flooding by making a waterproof raft (May 27, 2011).

A post about the opposite problem for rice: DEEPER ROOTING leads to deeper rooting -- and to drought tolerance (August 16, 2013).



Fat tax? -- Follow-up #2

September 22, 2009

The issue, briefly, is whether taxing "junk food" would be a good way to combat the epidemic of obesity. The original post is Fat tax? (9/9/09). The replies, including a new one, are posted on Fat tax page. More welcomed; I'll post things there anonymously. Facts, opinions, whatever.



One way trip to Mars

September 22, 2009

Glenn

It is expensive to send people into space. It is even more expensive to bring them back.

A One-Way Ticket to Mars. (A New York Times Op-Ed piece, L M Krauss, 8/31/09.)

Seems worthy of consideration. Thanks for the contribution.

For some context... As noted in the article, the US is in the process of re-evaluating its commitment to manned space travel. The report mentioned in the article has been delivered to the President. As expected, it emphasizes the cost.


The picture? Well, the Americans should recognize the man, and understand the relevance. Comments? (I'll add an explanation next week.)

Updated Sept 30, by identifying the picture... The picture shows John Glenn -- in 1998 at age 77, about to embark on a stint on the space shuttle as the world's oldest astronaut. The picture is available from many sources, such as the NASA page John Glenn Returns to Space. John Glenn was one of the original batch of American astronauts; in 1962 he became the first American to orbit the earth.

More about Mars... Water at the Martian surface? (August 27, 2011).

More on the shuttle: Photography from the space shuttle (June 4, 2012).



Prosthetic arms - follow-up

September 22, 2009

Original post: Prosthetic arms (9/16/09). An additional video was included.



Seeing molecules under a microscope

September 19, 2009

Pentacene: model and AFM image Farooq sends... "You may be interested in seeing the pentacene molecule under a 'microscope'! Very impressive images."

News story: Microscopes zoom in on molecules at last. (8/28/09.)


A sample is at left. The top frame (A) shows a model of the molecule called pentacene. The gray balls in the rings are carbon atoms; the white balls attached to the rings are hydrogen atoms. The bottom frame (C) shows an image obtained with the atomic force microscope. (This figure is from the paper, listed below. The bottom frame is also in the news story, above.)

For those of you who are just beginning to think about the size of molecules, he adds: "Just imagine the size of molecules, if we know that a drop of water contains billions of molecules. Have you ever dreamt of seeing molecules with your eyes? Do they actually look like the way we "imagine" them to be... For the first time in our recorded history, scientists have been able to have a high resolution picture of a relatively large molecule called pentacene."

Note the scale bar. 5 Angstroms = 0.5 nanometers. The molecule is about 15 A across -- about 1 A (0.1 nm) per atom.


There is some subtlety here. People have long been showing images of atoms using atomic force microscopes (AFM). So, what here is really new? Indeed, AFM has long seen atoms on solid surfaces. But here we see atoms -- all the atoms -- of a small molecule that is loosely bound to the surface. That turns out to be much harder. Why? Because the AFM probe is as likely to push the molecule around as it is to measure its structure. What they did here was to design a new AFM probe, with the tip being a single molecule (carbon monoxide, CO). This "gentler" probe, carefully controlled, scans the fragile surface without disrupting it.

The paper is The Chemical Structure of a Molecule Resolved by Atomic Force Microscopy. (L Gross et al, Science 325:1110, 8/28/09. The paper is from the Zurich lab of IBM -- where the atomic force microscope was invented.)

The 1986 Nobel Prize for physics was awarded for the invention of the AFM, and for developments in electron microscopy. Nobel site: 1986 physics prize.

* * * * *

An early bird noticing this item replied with a link to what the picture above reminded him of [link opens in new window]. Hm, there is a scale bar on the picture above.

* * * * *

There is another post on AFM just a few days later: Using DNA to make computer chips (September 25, 2009). I made some comments at the end of that post comparing how AFM is used in the two items, and offering more pictures.

* * * * *

Also see:
* Image of a carbon atom that isn't there (August 17, 2008). This post involves developing electron microscopy to allow observation of individual carbon and hydrogen atoms. 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!
* The 35 most famous xenon atoms (June 29, 2010). The Kavli Foundation honors a pioneer of "seeing atoms".
* Making big "molecules" from big "atoms" (December 7, 2012).

For more about AFM, 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.

Added March 28, 2014. More about carbon monoxide... Cooperation: a key to separating gases? (March 28, 2014).



Super Squirrel

September 19, 2009

They grow 'em big up there in the fresh air of the Canadian Rockies. The squirrel

Those of you who have studied some physics or some art are probably dying to tell me about perspective, and how close the critter was to the camera. But I'll just let the picture speak for itself.

Think about... Do you think the squirrel knew what he was doing? Look how well he has positioned himself.

For the "original" and a brief story, see The squirrel. (National Geographic, August 13, 2009.)

Thanks for the contribution!

More from squirrels -- some serious science: A 30,000 year-old plant, with an assist from a squirrel (March 10, 2012).

More wildlife photography... Bear photography (June 19, 2012).

Also see: Fossil discovered: A big stupid rabbit (April 22, 2011). Another big rodent.



September 16, 2009


Prosthetic arms

September 16, 2009

Prosthetic arm Thien contributes a presentation that he and his class partner made for a class last semester. The class was Technical Communication. The heart of the project was a presentation to the class -- a presentation of a technical topic at a level appropriate for the "businessmen" in the company. Their chosen topic, Prosthetic Arms, is closely related to the topic of robotics, which comes up here from time to time.

Here is their Powerpoint presentation; I think you will find it fun to look over. Prosthetic arm [Powerpoint file; link opens in new window]. (File size: 4.7 MB.)

The last slide offers a movie. The movie (about 2 minutes) is now at: Airic's_arm movie (company site; includes more information). The movie is also at Airic's_arm movie (YouTube).

It's a good movie. Thien notes: "It is not about any of the prosthetics we discussed, but this video demonstrates one company's arm that can move the arms and finger smoothly, pressure sensor (not breaking the screen), gripping power (dumbbell). It uses some technologies that we have researched, such as fluidic muscle." For more about this device, see the manufacturer's site, listed immediately above for the movie.


For those who want more...
Here is the written version, which served as notes for the talk. It contains more detail. Report [pdf file; link opens in new window].
And here is the list of references referred to in that written version: Work cited [pdf file; link opens in new window].

The picture at the start of this post shows Mesofluidic prosthetic fingers with FILMskin patch -- from a collaboration of Oak Ridge National Laboratory, NASA, and DARPA. It is Slide 8 of Thien's presentation (Figure 2 of the report), and is from an Oak Ridge article: New "Arms" for Disabled Soldiers -- Designing a better prosthetic arm for military amputees.

* * * * *

An additional video... Video: Cutting Edge Prosthetic Arms. (5+ minutes.) Some of it sounds like a promotional item from the military (which it is), but it contains some good footage. Recall that the original post also noted work supported by DARPA.

Other posts on robotics and related issues include:
* Prosthetic arms, prosthetic head ... (September 26, 2009).
* Reading the brain waves from speech (October 17, 2010)
* Berkeley Bionics: From HULC to eLEGS (October 22, 2010)
* eSkin: Developing better sense of touch for artificial skin (November 29, 2010)
* FDA to fast-track prosthetic arm (February 14, 2011)
* FDA to fast-track prosthetic arm -- Follow-up: videos (April 2, 2011).

Added January 29, 2014. More about prosthetic arms: 3D printing: simple inexpensive prosthetic arms (January 29, 2014).

More about regeneration and replacement body parts is on my page of Biotechnology in the News (BITN) for Cloning and stem cells. It includes an extensive list of related Musings posts.



Sustainable Energy - without the hot air

September 16, 2009

The topic title here is the title of a book, by David J C MacKay, Professor of Natural Philosophy in the Department of Physics at the University of Cambridge. The goal of the book, in the author's words: "I'm concerned about cutting UK emissions of twaddle...". Although the details in the book are UK-centric, surely we all share his concern.

As a starter... Energy: Can Civilization (at Least the U.K.) Run Sustainably?. (Book review by Marty Hoffert, Science 324:1517, 6/19/19.)

The book is freely available online: Sustainable Energy - Without the Hot Air. Try the 10-page synopsis. Between that and the review (above), you will have a good idea what it is about.

Greg has read the book (the author is one of his college profs). Greg writes...

"The book is well worth a read, even if you have little interest in the issues, simply because he gives such excellent examples of 'order of magnitude physics' at work. The physics isn't particularly complex (though there is more detail in the appendices), and it's surprising quite how much you can work out from some simple ideas."

So we have multiple reasons for giving this book a try. The subject matter, renewable energy, is important, and the book gives an insight into how scientists think. In addition, it is a good lively read -- and freely available online. So, give it a try. More about the book, mainly from Greg, on my page of Book suggestions.

One point that remains unclear is what a Professor of Natural Philosophy is in the 21st century.

Also see...
* Energy wastage: The set-top box (August 1, 2011).
* Alternative energy for a sustainable future (May 7, 2009).

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



Bilingual infants - sorting out "multiple speech structures"

September 14, 2009

Here is a new paper on the issue of children growing up bilingual. In a controlled test, they show that 12-month old infants do better at sorting out "multiple speech structures" than their monolingual counterparts.

See Bilingual infants - sorting out "multiple speech structures" (9/14/09). It is part of supplementary page on bilingual issues.



What are they?

September 12, 2009

What is shown in each picture?

Left Left

Both pictures are electron micrographs. Scale not shown, but you can assume they are similar. More specially, the black lines bordering each structure are about the same thickness. Ignore the labeling.

For identification, see supplementary page



Fat tax? -- Follow-up

September 11, 2009

The issue, briefly, is whether taxing "junk food" would be a good way to combat the epidemic of obesity. The original post is Fat tax? (9/9/09). I have posted a reply on Fat tax page. More welcomed; I'll post things there anonymously. Facts, opinions, whatever.



Origin of gas warfare

September 11, 2009

bee ball And you were thinking about Fritz Haber?

It's a fun story -- for those who like warfare. Japanese bees defend themselves from the hornet by surrounding it. The interior of the "bee ball" gets hot; it used to be thought that the heat killed the hornet. However, new work shows that the heat is not enough to kill a hornet. It also shows that the bee ball contains a high level of carbon dioxide; the CO2 is a key part of the lethal blow. That is, the bees gas their victim.

News story: Bees kill hornets with carbon dioxide emissions and local warming. (E Yong, Not Exactly Rocket Science (ScienceBlogs), July 5, 2009.) The picture above is from this news story.

The paper: Heat and carbon dioxide generated by honeybees jointly act to kill hornets. (M Sugahara & F Sakamoto, Naturwissenschaften, 96:1133, 9/09.) Very readable paper. Give it a try.

More on bees...
* Why are the bees dying? (January 26, 2010).
* Bees -- around you (June 11, 2009).

Added August 8, 2014. More chemical warfare by insects... The advantage of washing with formic acid (August 8, 2014).



September 9, 2009


Happy birthday

September 9, 2009

To the State of California, admitted to the Union on this date in 1850 -- the 31st state. Thanks in large part to chemical element #79.

Next birthday post... Happy Birthday (November 4, 2009).


NASA mission to detect killer asteroids

September 9, 2009

Collisions of heavenly bodies occur. We have noted various examples in recent posts, including the recent apparent collision of a comet with Jupiter (Collision! Jupiter injured (7/24/09)). Heavenly bodies hit earth, too. The ones most familiar are what we call meteorites. But there is a tremendous size range. It is thought that our moon was formed during a collision of earth with an object perhaps the size of Mars. And it is thought that a medium size object from space crashed off of Mexico 65 million years ago, setting in motion a train of events that led to the extinction of the dinosaurs. Whether we have all those details right, the collisions occur, and can be disastrous. And they will occur in the future, with potentially disastrous effect.

NASA is supposed to be cataloguing objects in space that pose a risk to earth. The news story below is an update: they are making progress, but less than we would like.

NASA cannot keep up with killer asteroids -- Congress assigned mission four years ago, but never gave NASA money. (MSNBC, August 12, 2009)

What do we do if we find an object is on a collision course with earth? No one has really answered that yet, thought many ideas are considered. If we have several years warning of an impending event, perhaps we can send up a mission and nudge the object a bit.

For more about what we might do, see: Gravity tractor: protection from asteroid collisions (October 26, 2009).

For more about that collision that created the Moon: The Moon: might it be a child with only one parent? (April 13, 2012).



Fat tax?

September 9, 2009

Should we tax "junk food"?

We do have a tradition of "sin taxes" -- taxing things we think are objectionable. Taxes on alcohol and tobacco are common examples. We also tax things as a matter of public policy -- related, but distinct. Gasoline taxes might be an example. Now, there is a move to tax fat. Are we asking the right question? Are we developing a good answer?

The link here is to a short post on the Nutrigenomics site; simply reading this gives you the idea. (If you want more, it links to the full report that is referred to.) Fat Taxes on Junk Foods. (8/23/09.)

I intend this post to stimulate thinking about the subject. I am not taking a position, either way. I do think that each such case has to be considered on its own merit. [In California (and perhaps elsewhere?) there is interest developing in the possibility of taxing marijuana.]

For follow-up, see Fat tax? -- Follow-up (9/11/09). Or, go directly to the supplementary page: Fat tax page.

Also see The junk food issue is global (April 7, 2012).



Dr. Smith?

September 5, 2009

I first heard about Dr. Smith? on the radio. He was being interviewed about his paper on zombies. Is this for real? Apparently. Check out his web page: Dr. Smith?'s web page, University of Ottawa. You can read about the zombies there, too. Scroll down to ""Of sewage, disease and zombies", where it starts "I started academic life in sewage."

The last character in his name is silent.

Next post about zombies: Death-grip scars from zombie ants, 48 million years ago (November 9, 2010).



Life that thrives on hot air

September 5, 2009

Life where life is impossible.

The Atacama desert of Chile is noted for its harsh conditions. Scientists study it partly to learn about the limits of life, and partly as a model for what life on Mars might be like.

Now, take Atacama, and ascend to 6000 meters (about 19,000 ft). Not much there -- except for occasional luscious green patches, near fumaroles, where gases from the earth interior make it to the surface. Some CO2. Some warmth. And thus some life. Of course, at the base of the life system are microbes.

For a news story as a brief introduction: Earth's highest known microbial systems fueled by volcanic gases. (PhysOrg, 3/3/09.)

The article, which is freely available: Fumarole-Supported Islands of Biodiversity within a Hyperarid, High-Elevation Landscape on Socompa Volcano, Puna de Atacama, Andes. (E K Costello et al, Applied and Environmental Microbiology 75:735, 2/09.) Scroll down to Figure 2 for some pictures of the area. (I also have its reference #22, the 1991 report that is the first modern description of life up there. If you want it, let me know.)

Added April 13, 2014. More from the Atacama desert: Whales in the Chilean desert -- the oldest known case of a toxic algal bloom? (April 13, 2014).



A new flute -- 35,000 years old (Follow-up)

September 5, 2009

See the original post, which includes the updates: A new flute -- 35,000 years old (7/1/09).



September 3, 2009


Warfare: the tymbal

September 3, 2009

"... [W]e pitted E. fuscus against B. trigona in a flight room equipped with high-speed infrared video cameras and an ultrasonic microphone"

Bats eat insects. In the dark; they use sonar to "see". Of course, some insects "defend" themselves. The new work tested possible reasons why certain moths (B. trigona) managed to avoid being eaten by the bats (E. fuscus); the results were best explained by proposing that the moths simply jammed the bat sonar. The moths make high speed ultrasonic clicks -- using their tymbal.

A news story, with good pictures and some video: Moths Outwit Bats By Jamming Sonar. (7/17/09)

The article (from which I quoted at the top): Tiger Moth Jams Bat Sonar. (A J Corcoran et al, Science 325:325, 7/17/09.)

More about moths: The story of the peppered moth (July 9, 2012).

More about bats: A plant that communicates with bats (September 7, 2011). This is about attracting echolocating bats.

Added June 18, 2014. More about ultrasonic (supersonic) insects: Introducing Supersonus -- it stridulates at 150,000 Hz (June 16, 2014).



Connecting a cell phone and a microscope

September 2, 2009

Think about it. What could you achieve with that?

News story: CellScope turns cell phone into microscope for disease analysis. (7/27/09, from the Daily Cal, the student paper at UC Berkeley.)

The paper referred to is freely available: Mobile Phone Based Clinical Microscopy for Global Health Applications. (D N Breslauer et al, PLoS ONE 4(7):e6320. July 22, 2009. doi:10.1371/journal.pone.0006320.)

Also see Device intended for medical diagnostics moves into the world of entertainment (October 20, 2010).

Added June 22, 2014. Another approach to simple microscopy: A ream of microscopes for $300? (June 22, 2014).

Another possible use of the cell phone as a tool in medicine was briefly noted in the post... What's around the corner? (January 7, 2011).

For possible biological effects of cell phone use, see... Effect of cell phone on your brain (April 11, 2011).

For more on cell phones...
* Added January 21, 2014. Windmills for your cell phone? (January 21, 2014).
* Traffic congestion patterns analyzed from cell phone records (July 7, 2013).

More about microscope developments... A microscope small enough that a mouse can wear it on its head (November 12, 2011).



Regenerating a leg

September 1, 2009

Maybe it has happened to you. You get in a fight or accident, and a leg gets cut off. No problem. Over coming weeks, a new one grows back, and you are fine.

The salamanders reading this are nodding with understanding.

The humans reading this are wondering.

But why not? It really does happen in the salamanders (and a very few other "higher" animals). Why is this ability quite uncommon among higher animals? Why can't we do it? Before we can answer that, it would help to know how it occurs.

What we observe in the regenerating salamander leg is a clump of cells, which then gives rise to the many cell types needed (e.g., skin, blood and muscle). The common view has been that the clump contains cells that are pluripotent -- cells we commonly call stem cells, with "many powers". These cells proliferate (multiply), and then differentiate (change) into the various cell types needed.

However, new work suggests otherwise. This work shows that the clump contains various kinds of cells, and each kind retains its identity. That is, the skin cells in the new leg come from skin cells in the clump, and so forth. The general way they showed this was to tag one or another cell type, and watch the fate of the tagged cells. The tag was GFP -- the famous green fluorescent protein.

Time will tell how valid this new view is. Other workers will try to verify the result and extend it. Do various regeneration systems work the same way? The goal? At a basic level, the goal is to understand regeneration. A bigger goal is to learn how to develop regeneration in mammals -- in humans, as a medical treatment. There is a sense in the field that we may have the capacity to regenerate, but that there is a brake on it. If only we could learn to control the brake.

* A short news story: Regenerative Medicine: Salamander reveals new insights. (7/10/09.)
* A more detailed but very readable overview of the work, which accompanied the article itself: Developmental biology: A cellular view of regeneration. (A S Alvarado, Nature 460:39, 7/2/09.)

Related Musings items include...
* Growing new teeth (September 29, 2009). Regeneration.
* Nobel prizes (October 8, 2008). GFP.
* Petri dish art (May 11, 2011).

For more about GFP, see my page Molecular Biology Internet resources: Miscellaneous; scroll down to two items on Green fluorescent protein. They include a web site devoted to this protein, and a link to the Nobel prize announcement last year.

More about regeneration is on my page of Biotechnology in the News (BITN) for Cloning and stem cells. It includes an extensive list of related Musings posts.



NASA finds a chemical of life on a comet

September 1, 2009

Jitesh Dundas sends Found: first amino acid on a comet. (8/17/09.)

Quite by coincidence, a few minutes after reading that item from Jitesh, I landed on the NASA site, where the following item was featured: NASA Researchers Make First Discovery of Life's Building Block in Comet. (8/17/09.)

This is a fascinating story, at multiple levels, but it is also important to not make too much out of the result.

The Stardust space probe, which visited a comet and sent back samples, is a tremendous achievement. Both stories above talk of the difficulties in the analysis of what was brought back.

So what does it mean? Well, it means that a comet has some glycine (an amino acid) -- a chemical that is a normal and important part of life on earth. We can plausibly suggest that small organic molecules, this one and others, are common on comets. Actually, that is not surprising, though this is the first real evidence on the matter, for comets. Did these comets deliver glycine to earth? Probably. It is commonly believed that much of the water on earth was delivered by comets; having some organic matter come along is not surprising. At this point, the amounts are not at all clear.

The real question we would all love to answer is whether this material from comets played a role -- maybe a critical role -- in the origin of life on earth. The new finding provides no direct evidence on that point. So let's not exaggerate and read much into this finding. It is exciting enough on its own.

A scientific paper for this item? I usually try to provide one. At least, I try to find the paper that is behind the news story, so I can judge whether the particular news post is reasonable. In this case, there is apparently a paper in press, but I do not have access to it. If I can get it later, I will let you know.

* * * * *

Here is the paper, at the NASA site: Cometary glycine detected in samples returned by Stardust. (J E Elsila et al, Meteoritics & Planetary Science 44(9):1323, 9/09.) A very readable paper, which presents evidence that the glycine found in the samples is likely of cometary origin. Key arguments are where it is found in the sampling device, and the carbon isotopes found in it. In contrast, they show that another amino acid found in their sample is likely of terrestrial origin -- more specifically, from the Nylon bags used for sample storage.



Tarsier; eukaryotic cells

August 31, 2009

tarsier The tarsier is one of the most "primitive" of the primates -- the line of organisms that led to monkeys, apes, and humans. By "primitive" here we simply mean that it is one of the oldest organisms that we would recognize as being on the primate line; it is near the base of the primate family tree.

Tarsiers are noted for having very large ... Well, I think it is obvious enough.

For a sense of scale, the adult tarsier may be 10-15 centimeters (4-6 inches) long -- not counting the tail -- weighing about 100 grams (1/4 pound).
 

The picture is the reason for this post. They had to stretch a bit to get that figure into the article, but the full article it is from is actually of some interest. It is about eukaryotic cells: cells that contain a "true nucleus". They also contain mitochondria; we recognize that the mitochondria in eukaryotic cells derive from bacteria (as do also the chloroplasts of plant cells). Somehow, long long ago, bacteria were taken up by some pre-eukaryotic cells, and -- instead of being eaten -- were "adopted". This process is called endosymbiosis. But its details remain elusive. This news feature discusses some of the available information, and some of the ideas for how eukaryotic cells got started.

On the Origin of Eukaryotes. (A "News focus" article, by C Zimmer, Science 325:666, 8/7/09.)

One of the pictures in the article shows a sampling of very diverse eukaryotic organisms -- including the tarsier shown above.

Tarsiers and lemurs are two modern primates that we consider near the base of the primate lineage. A couple of previous posts here were about Ida, the remarkable and contentious fossil find that is also considered near the base of the primate lineage. I did not use the terms in my Ida posts, but some of the discussion is about how Ida fits in with the lemurs and tarsiers. The posts on Ida are now consolidated on the page Ida.

Here is a post on another type of symbiosis of a bacterium with eukaryotic cells. It may or may not be a step along the pathway to the development of a new organelle. A new organelle "in progress"? (September 13, 2010).

More about eukaryotic cells: Are there really three domains of life? (January 12, 2013).

Added October 6, 2013. More about simple primates... Underground hibernation in primates? (October 6, 2013).

More about primates: Rukwapithecus and Nsungwepithecus (June 1, 2013).

Also see: Monogamy (January 30, 2013).



Dinosaur proteins -- update

August 31, 2009

Original item: Dinosaur proteins (7/6/09).

A recent post was about finding proteins in some dinosaur fossils. This was noted as a remarkable discovery -- and a controversial one. If the results hold up, they provide support for the idea that dinosaurs are most closely related to birds.

I have found another news story that is worth including. It is perhaps in the spirit of investigative journalism. It goes through the science and the controversy in considerable detail. It exposes the personalities of the players, but remember, the real issue is the science: what are the facts, as best we can determine them. There is some sense that the new work is better than the old -- thanks in part to the criticisms made. Whether the results will stand is something we can't tell. This is normal science. People report what they did, and then we see if their work stands the test of time. The more dramatic the result, the harder it may be to convince people. This is why we often say that a new paper "claims" or "reports" something, rather than "proves" it.

The new story is Origin of Species: How a T. Rex Femur Sparked a Scientific Smackdown. (E Ratliff, Wired Magazine, 6/22/09.) It's fairly long and detailed, but maybe worth it; good plot, well presented.



August 28, 2009


On collecting opinions

August 28, 2009

An item on animal behavior: On collecting opinions.



Ice on fire

August 28, 2009

Borislav recently sent me an item on an unusual and fascinating source of methane (natural gas). His e-mail title was "Ice On Fire - A Powerful New Energent? Or - Are We Sitting On a Time Bomb?" The source is called methane hydrate or methane clathrate -- or "ice that burns". We've had a lively discussion of this fascinating topic; the post here is something of a synthesis of our discussion, largely built on his original message. As you read through this, realize that there are many issues. The post here, including two news stories, barely scratches the surface. We have here a potential huge energy resource -- and a potentially huge disaster, which may come from our misuse, or just naturally. And then there are the questions of what this stuff is and where it comes from.

What happens if you torch an ice-cube? In most cases nothing, but one particular ice from Siberia burns rather vigorously! The first of the two news stories listed below starts with this Siberian ice.

* Ice on fire: The next fossil fuel. (New Scientist, June 24, 2009.) This article seems to no longer be freely available.
* Mining "Ice That Burns". (MIT Technology Review, June 8, 2009.)

These articles tell you a story about harvesting methane trapped in ice for use as a fuel. The methane gas is formed by high-pressure thermal decomposition of organic remains, and caught inside ice crystal structure.

A big unanswered question is the environmental price of using another C source as a fuel. Among the risks...

* Methane (CH4) is about 20 times more potent greenhouse gas than CO2. Thus, careless extraction of this new methane source could enhance global warming.

* In fact, methane may be released "naturally" from such deposits; such releases might occur with explosive force, causing geological disruptions, as well as atmospheric contamination. Global warming may enhance the risk of such events.

* Methane is flammable (that is why we use it); what if released methane ignited? Imagine a detonation of cubic kilometer of compressed methane.

If you, too, are fascinated and perhaps also confused... Good. Just be alert for more information on methane hydrate -- the ice than burns.

Also see...
* Lakes that explode (October 13, 2009).
* BP oil spill incident: the methane hydrate crystals (May 18, 2010).
* Fire from ice: is it practical? (May 13, 2013). A first effort to harvest methane from hydrate deposits.
* Added March 7, 2014. Svalbard is leaking (March 7, 2014).

There is more about alkanes on my page Organic/Biochemistry Internet resources in the section on Alkanes.



July 27, 2009


Royal Society suggests science books

July 27, 2009

The Royal Society offers a prize for outstanding science books. Here is information on the 2009 prize, including a list of candidates: http://royalsociety.org/The-2009-Royal-Society-Prize-for-Science-Books/. Click on "The books" at left for other years. [See below for updated links.]

One of the books (Shubin, Your Inner Fish) is already listed on my page of Book suggestions: Shubin. Also, I have listed another of Mlodinow's books, and it is quite good: Book suggestions: Mlodinow. I've got a couple others of them on my to-read list -- which gets longer and longer. Among the semi-finalist books, I have read Zimmer (Microcosm), which I also recommend: Book suggestions: Zimmer.

As an aside... Shubin gave a pair of lectures here this past year. They were superb. So, not only do I recommend his book (now backed by the Royal Society!), but I also commend him to you as a speaker.

Maybe some summer reading ideas here? Try them. And I'd be delighted to add your comments to my Book Suggestions page -- whether for these books, or other science-related books.

* * * * *

The winning book was Richard Holmes, The Age of Wonder -- How the romantic generation discovered the beauty and terror of science. I have now read that book and listed it: Book suggestions: Holmes.

* * * * *

More, June 7, 2011...

The Royal Society book prizes have been reorganized, and they have a new web site: Royal Society Winton Prize for Science Books.

For information on awards for previous years, scroll down that page. There is also information for previous years on the Wikipedia page: Wikipedia: Royal Society Prizes for Science Books.

* * * * *

More from the Royal Society: Royal Society opens its historic journal archives to free access (November 22, 2011).



A missing link

July 27, 2009

A missing link. [source unknown.]

A reader sent this to me, with the comment "This is not a Dilbert comic". At that point, I was trying to discourage too many cartoons -- and it seemed they were largely from Dilbert. I was concerned about too high a percentage of "joke" messages. This new Musings format is more flexible. If you think something is worth sharing, I will try to post it. Please include source information. Even better, send me the link to the item, in proper context at the source site.



Collision! Jupiter injured.

July 24, 2009

Many of you surely heard about this; it was quite a news story last week. It started when an amateur astronomer in Australia saw something unusual in his image of Jupiter. He reported it to the astronomers. Best guess as of now: something hit Jupiter, leaving a little scar. Little? The scar is about the size of the earth.

Here is a news story: Jupiter sports new 'bruise' from impact. (7/21/09.) Note the link to "1 more image"; that is the original view.

Recall recent post Collision of Earth and Mars (7/8/09). That item discussed the possibility of collisions between planets -- sometime in the future. The current story involves a much smaller object colliding, perhaps a few tens of miles across. But the current story is also about a real event, even though the details of what happened are not clear. The news story above includes some discussion of the only prior observation of a significant collision beyond earth -- a few years ago and also on Jupiter.

The next post on solar system collisions is about collisions with earth: (NASA mission to detect killer asteroids (9/9/09)).

The next collision with Jupiter... Jupiter injured again! (6/11/10).



How big are rain drops? And why?

July 23, 2009

John writes:
When I was a kid I used to wonder why some rain drops are bigger and some are very very small, and now years later researchers have come up with a video of a rain drop breaking up. Why raindrops come in many sizes. (7/20/09; the news story there includes the video.) I think it's very cool.

The article referred to is: Single-drop fragmentation determines size distribution of raindrops. (E Villermaux & B Bossa, Nature Physics 5:697, 9/09.) Figure 1 of the paper shows some data on the size distribution of real raindrops. The paper discusses the differences in drop behavior in the cloud and during free-fall.

Near the end, they say "An interesting extension would also be to consider the same fragmentation problem with, instead of liquid drops confined by surface tension, brittle solids with a weak tenacity (critical stress), such as snowflakes ..." Yeah, this is fun.

The journal has a high resolution version of the video posted at Journal supplementary materials. Choose the movie, which I might call "60 milliseconds in the life -- and death -- of a raindrop"

More rain... Lyell on fossil rain-prints (May 6, 2012) (and accompanying post).



The animal mind

July 23, 2009

Nature recently ran two short essays expressing different views on how to interpret similarities of behavior between humans and other animals. I think they are worth reading -- together.
* Can evolution explain how minds work?. (J J Bolhuis & C D L Wynne, Nature 458:832, 4/16/09.)
* Darwin's last laugh. (F B M de Waal, Nature 460:175, 7/9/09.)

The main point of contention is whether similarities should be considered as reflecting shared ancestry or convergent evolution. For an analogy, think about wings. We consider that wings in various kinds of birds are due to their shared ancestry -- all birds have wings, and all bird wings are related. On the other hand, we consider that bat wings and bird wings reflect convergent evolution: two distinct examples of organisms independently developing something similar. Both explanations for similarities are plausible. The challenge is figuring out which applies to each case. For wings, we have a pretty good idea which is which; for behavioral traits, we know much less. As you read these two essays, remember that in the long run the debate will be resolved by getting more data. What you are reading here are two views during an ongoing debate. Science in progress.

Both essays have good cartoons.

Understanding behavior and the mind -- more generally, the brain -- is one of the great frontiers of modern biology. A recent example of a Musings item on "human-like" animal behavior was Animals counting -- more (July 13, 2009). I have some books on the mind on my page of Book suggestions. Among them are books by Gazzaniga and by Searle. More from Gazzaniga... Split brains and yellow submarines (January 9, 2012).

For more on animal counting and related issues... On the Evolution of Calculation Abilities (June 20, 2011).



Thomas Alva Edison reads poetry

July 23, 2009

Edison: poetry [mp3 file; link opens in new window].

Edison's first recording on his new "phonograph" system was in 1877; he read a poem. The recording here is his "reconstruction", recorded in 1927 for posterity. It really is Edison -- at the age of 80.

It was long thought that Edison made the first sound recordings, thus that the 1877 original of this would have qualified as the first sound recording. We now understand that Edison was not first -- though he was first with something that was developed into a practical product. For more on the pre-Edison recording, see Physicists convert first known sound recording. (David Perlman, San Francisco Chronicle, March 2008.) There is a link to a sound file at the end of the article. The restoration discussed here was done, in part, at the Lawrence Berkeley Lab. There is more about this and other aspects of historic recordings in the Art & Music section of my page of Miscellaneous Internet Resources: Historic recordings.

* For more about Edison... Restoration of old sound recordings (July 23, 2011).
* The wisdom of Edison was also invoked in a reply to a post on the nature of science: The promise of science? (November 16, 2009).

More poetry... The Mudville story, on its 125th anniversary (June 3, 2013).



July 20, 2009


R. U. R.

July 20, 2009

A robot story. Perhaps the first robot story.

R. U. R. is a play -- a short play that is very famous. The title stands for Rossum's Universal Robots; it was written in 1920 by the Czech writer Karel Capek. The play -- the title of the play -- is considered the origin of the word robot. Beyond that, it is a delightful little play. Recommended.

An English translation of R. U. R. is freely available at: R. U. R. in English. The translation is by David Wyllie; the book is posted as part of a free book collection, eBooks@Adelaide, at the University of Adelaide.

The original Czech version of R. U. R. is available from Project Gutenberg: R. U. R. in Czech.

Wikipedia provides some basic background on R. U. R. : Wikipedia: R. U. R.. (This article includes both links to the play that I give above.)

I have added R. U. R. to my page of Book Suggestions. I'd welcome some brief comments on it from those who have read it recently.

Another Musings post that recommends a book from the Adelaide site: A book to enjoy (online) (February 16, 2010).



Eating frog legs -- and why the hind legs taste better

July 16, 2009

Some people like to eat frog legs. So do some dragonflies.

In recent years, deformed frogs have been getting a lot of attention. There are frogs with too many legs, and frogs with not enough legs. (The preferred number of legs, for a frog, is four.) Why the leg problem? Many thought it was an indicator of chemical pollution, or even of high levels of UV irradiation.

A few years ago, good evidence showed that extra legs were caused by infection with a parasite. The parasite interfered with normal development. Ok, perhaps, but that did not explain the missing legs -- other than to suggest that extra legs and missing legs were two distinct problems.

Now we have the cause -- or at least a cause -- of missing legs: dragonflies eat them. More specifically, the dragonflies eat the limb buds of the developing tadpoles. The resulting deformations of the adult frogs are due to the nature of the regeneration process.

Here is a good news story about this new work: Legless frogs mystery solved. (6/25/09) The title is not very good, but the story itself seems fine. It includes an explanation of why the dragonflies tend to eat the hind legs. Note the experimental work they did, where they surgically removed limb buds (but did not eat them?), and showed that the results were similar to what was observed with the predator.

The article: Explanation for Missing Limbs in Deformed Amphibians. (B Ballengee & S K Sessions, Journal of Experimental Zoology (Mol Dev Evol) 312B:770, 11/15/09.)

Comment: As the news story (but not its title) makes clear, there may be more than one cause for a problem. But one thing that concerns me is why frog leg number became an issue only a few years ago. If it is a natural biological phenomenon, it seems odd that it started only in 1990. Perhaps there is some reason why dragonflies did not chew on tadpoles before then. Or perhaps no one really paid any attention to the frog leg problem. Or perhaps there is more to this story. The Discussion in the article deals with some of the possibilities; good reading.

For more on frogs...
* What if you had eyes on your tail? (July 27, 2013).
* Quiz: What is it? (October 5, 2011).
* The political leapfrog (January 24, 2011).

Added January 28, 2014. More on dragonflies: Black silicon and dragonfly wings kill bacteria by punching holes in them (January 28, 2014).



Ant mega-colony takes over world

July 16, 2009

I was trying to think of a cute title, but I can't improve on theirs.

I knew that ants up and down the state of California were all part of one colony. But I had not realized that Europe had a colony several times larger. The new finding is that those two colonies -- and more -- are actually related: part of the same super-colony.

The main measurement discussed here is aggressive behavior: whether ants from two locations fight each other. If they don't, the interpretation is that they are "family". Some other information is given to support this. That includes chemistry: the ants seem to be distinguished by how they smell, due to hydrocarbons in the cuticle. They also make some interesting comments about human society.

* A news story: Ant mega-colony takes over world. (7/1/09.)
* The paper: Intercontinental union of Argentine ants: behavioral relationships among introduced populations in Europe, North America, and Asia. (E. Sunamura et al, Insectes Sociaux 56:143-147, 7/09.)

Could we extend this to humans? If we all smelled the same, would that lead to peace? Maybe we should all use the same hair spray. (I hate the smell of the stuff.)

The following post offers a video of a talk on this topic: Ant sociality: supercolonies -- a video of a talk (May 31, 2011).

Other posts about ants include:
* Why a tree cultivates ants (October 3, 2010).
* How to survive flooding by making a waterproof raft (May 27, 2011).
* Item immediately below.



The ant collector, with videos

July 16, 2009

More ants

A contributor several thousand miles away sends this site, which is from the California Academy of Sciences in San Francisco: Dr. Brian Fisher.

He notes ...

The ant collector: a man who risks his life to study ants.

The probability is that we know only a fraction of insects; this guy specializes in ants. He goes around the world into the most inhospitable areas and collects and studies ants.

You don't have to stride his page too much, just watch the short introductory videos at the homepage.

Now that we have you at the Academy site ... At the top right, is a link labeled "Previous: Dr. John McCosker". He is the shark guy -- and world famous. Pursue at your own risk.

Another link on Fisher's page is to AntWeb. I have a link to that site on my page Molecular Biology Internet resources: Sites that focus on specific organisms (or groups).

For other posts about ants, see the item immediately above; it includes links to more.

More from CalAcad... Our newest spiders: the cave robbers (September 5, 2012).



Element #112: Copernicium

July 15, 2009 (combined with earlier post, June 12)

In June: Element #112 is officially recognized. A New Chemical Element in the Periodic Table. (6/10/09.)

A month later, a name is officially proposed for chemical element #112: copernicium, Cp. Official approval is likely in late 2009 or so. Element 112 shall be named "copernicium". (7/14/09.)

The final approval, in November, established the symbol as Cn.

A person on the Chemed discussion list suggested a name based on the name of the Institute where it was discovered. Using good German language skill, he suggested that #112 be named helmholtzzentrumfurschwerionenforschungium. (Elements 108 and 110 have already been named after the location of the Institute.)

But, you say, #112 is already on your periodic table?? Indeed. It was discovered (first announced) in 1996. Many people go ahead and show a new element based on such a preliminary report. What's new is official recognition of #112, following good confirmation of the discovery.

Of the proposed name, Will writes:
"Unbeknownst to many, Copernicus (Kopernik) was a Pole. In fact, he and I attended the same university in Krakow. He graduated slightly before me, with the class of '95. 1495. Also, as an interesting linguistic side note to this elemental discussion, a "kopernik" in Polish is a man who works with copper. So it will be interesting to see if they name an element after a man who was named after another element."

There is more about all of the newer elements on my page Internet Resources for Introductory Chemistry. Elements there are 112-118, with only #117 missing so far, plus a controversial report of #122. There is also information about the names of all elements.

A Musings post on the discovery of: Chemical element #117 (4/13/10).

The next post about new names for chemical elements: Chemical elements 114 & 116: flerovium, livermorium (proposal) (December 5, 2011).



July 13, 2009


Animals counting -- more

July 13, 2009

We have previously noted work suggesting that bees can count.

This story in New Scientist discusses work on counting by various animals, including salamanders, chickens, and horses -- as well as the bees. Animals that count: How numeracy evolved. (New Scientist, 6/23/09.) The article surveys the big issues, including some of the problems with studying counting. It discusses the specifics of the work for several cases. It's fun to see how one studies counting by animals that cannot speak.

The article above seems no longer freely available. Here is another useful story on this topic, focusing on the specific article listed below. It is now archived at Chicks Are Smart, Scientists Confirm. (Discovery Channel, 4/1/09.)

A current paper that was the immediate impetus for the story: Arithmetic in newborn chicks. (R Rugani et al, Proc. Royal Society B 276:2451-2460, 7/7/09.)

Arithmetic in newborn chicks? Of course, that reminds me of a piece of music: 'The ballet of the unhatched chicks', from Pictures at an Exhibition, by Mussorgsky. Played here by Mina Ivanova, or Another version. This was posted earlier, in the context of Dancing birds. Scroll down to "Dancing birds -- follow-up", May 15, 2009.

Another post that includes a ballet... Quiz: What's the connection... (February 14, 2012).

For more on animal counting and related issues...
* Making smarter flies (July 18, 2012).
* On the Evolution of Calculation Abilities (June 20, 2011).



Hell

July 13, 2009

Hell.

For more... The source.



A new electric car

July 11, 2009

First Croatian car to be launched soon. (July 10, 2009.)

The previous item on electric cars is Electric cars (May 9, 2009).

For an analysis of the benefits of electric cars... Electric cars and pollution (April 5, 2011).



Is it language?

July 9, 2009

You come across a group of symbols -- on a piece of paper or an ancient cave wall or tablet. Language? How could you tell?

One way to get an idea is to look for patterns. In language, symbols are not entirely random, nor are they entirely ordered. Think about sequences of letters or sequences of words. So, go measure the randomness of the way the symbols appear -- even though you know nothing about any of them. That randomness is expressed as entropy -- much like the entropy you come across in your science classes.

A recent short paper in Science did just that -- on samples of writing from the Indus civilization of 4000 years ago (near the current India-Pakistan border). Many have thought the writings involved "real language", but evidence was controversial. In the new paper, they show that the Indus scripts have just about the same amount of randomness as other languages. And refining the analysis, they even discuss its relationship with other languages from that area.


News story: Indus Script Encodes Language, Reveals New Study Of Ancient Symbols. (ScienceDaily, April 30, 2009.)

The paper is at: Entropic Evidence for Linguistic Structure in the Indus Script. (R P N Rao et al, .Science 324:1165, 5/29/09. It is a collaboration between people at the University of Washington and several Institutes in India.) One page paper, and the main idea is quite clear from the graphs. Have a look!

Also see...
* Can French baboons learn to read English? (May 13, 2012).
* Are some languages spoken faster than others? (November 21, 2011).



Touching your partner

July 9, 2009

The bacterium Pelotomaculum thermopropionicum and the archaeon Methanothermobacter thermautotrophicus are good friends. Let's call them Pt and Mt. In fact, Pt and Mt grow better when they are together -- when they are touching.

The basic reason they grow better together is clear enough. Pt burns its food in a way that really doesn't work very well. The problem is that it makes a lot of hydrogen, which inhibits it. Mt to the rescue: Mt burns hydrogen. So, together they grow fine: what is a bad waste product of Pt is good food for Mt. Such co-metabolism is well known among microbes, and is termed syntrophy.

Not only do they grow well together, but Pt actually causes key growth genes of Mt to turn on. How? What kind of signal does Pt send to Mt to turn Mt's genes on? Some hormone? Recent work shows it is the physical interaction that turns on Mt genes. The flagella (hair-like structures usually associated with swimming) of the Pt bacteria interact with the Mt partner, turning its genes on when they are very close -- and touching.

A news story in Science discusses this, and another example of syntrophy, with some nice pictures. Microbiology: Getting in Touch with Your Friends. (Science 324:1150, 5/29/09.)

Relevance to higher animals? Certainly, syntrophy is relevant. The extreme case is represented by organisms (cows, termites) that grow on cellulose, but are quite unable to digest it without the help of their microbial partners. It's probably true for us, too, though it is harder to show clearly.



Collision of Earth and Mars

July 8, 2009

A few months ago, I teased one of you for suggesting that Earth and Mars were on course to collide. A recent news story made me wonder if I owed you an apology. But first, I checked the information behind the news story -- and found that it was rather exaggerated. Nevertheless, this is fun and interesting.

What's behind all this? Astronomers tried to calculate how the solar system would behave -- not just for the next few years or even few millions of years, but for five billion years. The longer calculations have much uncertainty in them, due to uncertainties in our knowledge of the planetary orbits. So, they do many calculations. As a result, they make statements about the probability of one outcome or another. Turns out... they think the solar system may do fine for five billion years -- about a 99% chance of that. (And somewhere around 5 billion years, the sun starts making real trouble.)

But it is those other 1% of the cases they looked at that cause excitement (or concern). The key culprit is the planet Mercury, which has a special attraction for Jupiter. (Hm, maybe we could say that Jupiter is the cause of the problem, with Mercury being its victim.) But Mercury might run into things along the way -- such as Venus. One of their calculations shows quite an interplanetary melee, with various collisions possible among the inner planets (Mercury to Mars).

Here are three things for you to read on this, at increasing levels of complexity. All are fun, assuming you enjoy the idea of planetary billiards.
* Report: Planets will collide in 5 billion years. (6/11/09.) This is the newspaper story I started with (from the San Francisco Chronicle). The title is wrong -- in saying that a collision will occur. As the story goes on, he clarifies, and you learn that this is something that might happen, with about a 1% probability.
* Planetary science: The Solar System's extended shelf life. (Nature 459:781, 6/11/09.) This is the news story in Nature, accompanying the actual article. It is by Gregory Laughlin, who is quoted in the newspaper story.
* Existence of collisional trajectories of Mercury, Mars and Venus with the Earth. The article. (J Laskar & M Gastineau, Nature 459:817, 6/11/09.)

So what about my possible apology? After reading the full story, I think not. At least not yet. Check back with me in a billion years or so, and let's see how the calculations look then.

A real -- or at least "suspected" -- collision in the solar system is discussed in the item Collision! Jupiter injured (7/24/09).

A possible consequence of complex gravitational interactions is that, in some cases, a planet might be ejected from its solar system, and be left to wander through space unbound to any star. Is it possible that life could exist on such an unbound planet? See... Steppenwolf: Life on a planet that does not have a sun? (July 2, 2011).

More on Venus: Sulfur dioxide in the atmosphere of Venus (February 16, 2013).



Funding scientific research

July 8, 2009

This item may be mainly for those involved in scientific research, or interested in how funding is determined. It addresses the question of evaluating ideas that are truly novel -- outside the mainstream.

Grant System Leads Cancer Researchers to Play It Safe. This links to a Nutrialerts item, but the heart of it is an article by Gina Kolata, a highly respected science writer for the New York Times.



July 6, 2009


Miniature helicopters -- and botany

July 6, 2009

If you were going to design a miniature helicopter -- the military would love them -- why might you consult an expert on trees?

Maple Seeds And Animals Exploit The Same Trick To Fly. (6/13/09.)

The basic finding is that maple seeds twirl as they fall, creating local vortices that slow their descent. (They are sometimes referred to as helicopter seeds.) Small flying animals (insect and bird) use a similar aeronautical trick to stay aloft. The same principle might be useful for a mini helicopter.

The full paper: Leading-Edge Vortices Elevate Lift of Autorotating Plant Seeds. (D Lentink et al, Science 324:1438, 6/12/09.)

More about seeds: Hard seeds or soft seeds? (April 26, 2013).



A plant that cheats

July 6, 2009

The plant that pretends to be ill. (BBC, 6/19/09.)

You've probably seen plants where some leaves have white patches -- normally. Why does that happen? After all, the white parts are not active for photosynthesis, so this "variegation" should be a disadvantage. Here they show, for one case, that the variegation makes the leaves look like they have been attacked by a particular moth; the moth then avoids them. How do they test their idea? By painting white streaks on green leaves, using typewriter correction fluid. The moths avoid the painted white patches.

For those who want more, here is the article: Leaf variegation in Caladium steudneriifolium (Araceae): a case of mimicry? (U Soltau et al, Evolutionary Ecology 23:503, July 2009.) The first few pages give some interesting background, and mention other cases of suspected mimicry in plants. They claim theirs is the first experimental test of the phenomenon.

More about moths: The story of the peppered moth (July 9, 2012).

More about plant defenses... Underground messaging between bean plants (July 29, 2013).

Added May 30, 2014. More mimicry... A plant that mimics the leaves of its host (May 30, 2014).



Dinosaur proteins

July 6, 2009

Two years ago paleontologist Mary Schweitzer stunned the scientific world by claiming to identify pieces of protein in a 68 million year old fossil of Tyrannosaurus rex. Why is that so stunning? Because protein -- and DNA -- don't survive well after death; they are rather unstable chemicals. People have been isolating old DNA for several years, but the initial work was fraught with controversy, and did contain mistakes. Over time, people learned how to get old DNA, and how to avoid contamination. Is that now happening for old protein?

Schweitzer has now reported new data with a different fossil to support her claim.

What does she learn from the work? The protein being studied is collagen, a major skeletal protein in animals. She claims that the dinosaur collagen is similar to bird collagen; this supports the close relationship between dinosaurs and birds.

Are we to believe this? I don't know. The initial claim was met with considerable skepticism, and a list of objections. Some of the objections have been addressed. Can other labs independently do this? Over time, we'll see. Let's just sit back and enjoy the show.

For more...
* Proteins, Soft Tissue from 80 Million-Year-Old Hadrosaur Add Weight to Theory that Molecules Preserve Over Time. (PhysOrg, 4/30/09.)
* Paleontology: 'Protein' in 80-Million-Year-Old Fossil Bolsters Controversial T. rex Claim. (Science 324:578, 5/1/09.) A one-page news story about the recent work.
* Biomolecular Characterization and Protein Sequences of the Campanian Hadrosaur B. canadensis. (M H Schweitzer et al, Science 324:626, 5/1/09.) The paper.

Follow-up posts...
* Dinosaur proteins -- update (August 31, 2009).
* Dinosaur proteins -- update #2 (June 27, 2011).

Also see...
* A dinosaur in color (April 5, 2010).
* Mammoth hemoglobin (February 1, 2011).
* Life at age 34,000? (October 8, 2011). Is it possible to find microbes that have been alive for tens of thousands of years?
* A 30,000 year-old plant, with an assist from a squirrel (March 10, 2012). Is it possible to resuscitate plants from 30,000 year old tissue?
* The Iceman's blood (May 14, 2012). 5,000 year old blood cells.
* A new approach for testing a Llullaillaco mummy for lung infection (August 17, 2012). More about analyzing old proteins.
* The oldest dinosaur embryos, with evidence for rapid growth (May 7, 2013). An independent claim of dinosaur protein.
* Added April 25, 2014. The oldest known piece of cheese (April 25, 2014).



Bilingual from Childhood

July 1, 2009

See Bilingual from Childhood -- reply (7/1/09). It is part of supplementary page on bilingual issues.

More replies or comments welcomed.



Light bulbs

July 1, 2009

How many of you light the house by heating a piece of wire until it glows white? Do you notice that it gets hot? In the winter, that might be nice, but in the summer it is quite an energy waste. Surely there is a better way. The fluorescent light is one better way -- with its own problems. And then there is the white LED; it would seem to be just perfect -- if only someone would invent one. Actually, there are white LED lamps, but they are not very good yet.

Here is a nice overview of these alternative forms of lighting. It is freely available: Time to Change the Bulb. (Nature 459:312, May 21, 2009.)

Also see:
* CFL and LED lights: energy-efficient, but toxic (March 3, 2013).
* A possible hazard of using compact fluorescent light bulbs (November 13, 2012).



A new flute -- 35,000 years old

July 1, 2009

Jessica sends: Flutes Offer Clues to Stone-Age Music. (6/24/09.)

And writes of it...

The oldest known instrument made by human hands.

"Scientists say they've found what they consider to be the earliest hand-crafted musical instruments in a cave in southwest Germany, less than a yard away from the oldest-known carving of a human. The flute fragments as well as the ivory figurine of a "prehistoric Venus" date back more than 35,000 years, the researchers report."

Although other flute fragments have been found in these caves before, to find one so well preserved and nearly in its entirety gives the researchers a chance to really see (and hear) the full depth of the musical capabilities of our early ancestors. I was often amazed in museums, seeing the quality of craftsmanship and creativity in works produced by ancient civilizations. Yet, these often only date back up to 10,000 years ago. Physical proof of music and artwork demonstrate the long history of our creative roots and this was such a striking article for me.

* * * * *

My notes...

The New York Times (NYT) article listed above refers to a paper in Nature; it is at: New flutes document the earliest musical tradition in southwestern Germany. (N J Conard et al, Nature, 460:737, 8/6/09.) A copy is at: pdf from author. I think many will find parts of this article quite accessible reading.

Here are two items that accompanied the paper in Nature. One is the Nature news story, which is very good. The other is a short conversation with the author about the work. These are:
* Archaeology: The earliest musical tradition. (D S Adler, Nature 460:695, 8/6/09.)
* Conversation with the author. See the left hand column, labeled Abstractions -- First author. (Nature 460:666, 8/6/09.)

The NYT article has a link to a short music clip. (See "Multimedia", at the left a few lines below the main figure near top.) This is played on a replica of one of the ancient flutes.

I have some items on ancient instruments on my web page: Ancient instruments.
* See the item there about the 9000 year old flutes from China. One of those flutes was in good enough condition to play. The music clip listed there is played with the actual 9000 year old flute.
* See the item about possible Neandertal flutes. The scientists in the work reported here do not accept the claim for Neandertal flutes. I followed up some on this point, and got the article that is reference #4 in the Nature paper. It summarizes the arguments used to support the claim that a bear bone with holes in it is a Neandertal flute. It then proceeds to refute these points. It is a long but readable paper, with lots of nice pictures of old bones. If this historical point intrigues you, I encourage you to try this paper. It is at: A Middle Palaeolithic origin of music? Using cave-bear bone accumulations to assess the Divje Babe I bone 'flute'. (F d'Errico et al, Antiquity 72:65, 1998.)
* I have added this new item to my page.



June 29, 2009


Bilingual from Childhood

June 29, 2009

See Bilingual from Childhood (6/29/09). It is part of supplementary page on bilingual issues.



Gaia's evil twin: Is life its own worst enemy?

June 26, 2009

See Gaia's evil twin: Is life its own worst enemy? (6/26/09). It is part of supplementary page on Gaia and James Lovelock.



Vanessa-Mae music; follow-up

June 25, 2009

The June 15 music post was of Vanessa-Mae playing the Bach Toccata and Fugue in d.

Brian offers some other tracks from the same album, some of which are original works. The music tracks are no longer available here, but people may enjoy the connections we made, and the links to information.

For more about the artist:
Wikipedia: Vanessa-Mae.
The Violin Player Vanessa-Mae.

For more about the Bach piece and the various postings of and about it, see the posting Visualizing music (June 18, 2009).

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.



Dancing algae

June 25, 2009

Earlier we had dancing birds. (See the item immediately below this one.) Now, how about dancing algae? Skeptical? Go look at the movies: Dancing algae. In particular, be sure to watch the one called "Dancing Volvox: minuet bound state".

The algae here are Volvox, a colonial green alga with flagella. The spinning of Volvox colonies was observed long ago -- by van Leeuwenhoek three centuries ago. Now, Cambridge University physicists provide more sophisticated observations, showing that the colonies interact -- dance around each other -- depending on the situation. And they explain the interaction by physical laws, suggesting that no biological signaling is needed.

Is this dancing of biological significance? They speculate that the clustering promotes fertilization during the sexual phase, and they say they will try to test this.

For those who want the details of the observations, and the discussion of the hydrodynamics, here is the paper: Dancing Volvox: Hydrodynamic Bound States of Swimming Algae. (K Drescher et al, Physical Review Letters 102:168101, 4/20/09.) Even if you don't want the technical stuff, the first page may be useful background.

Lest we confuse... There is no music here. The "dancing birds" coordinated their body movements with music. In contrast, the "dancing algae" are simply clustering and moving around each other in a simple physical environment; the pattern of their movements is suggestive of dance.

More about swimming: How bacteria swim and why -- a physics view (October 2, 2009).



Dancing birds -- more follow-up

June 24, 2009

The main new point is that when the articles appeared in print, there was a nice two-page commentary. If you enjoyed the original story, I encourage you to look at this. Biology of Music: Another One Bites the Dust. (W T Fitch, Current Biology 19:R403, 5/26/09.)

Second, the final published papers are now posted. (Earlier I had posted pre-publication versions.) These should be substantively as before except for having the proper citation information. Probably of no concern for most people.

Finally, I moved the earlier items to the archive page; I also consolidated multiple posts on one topic onto a separate page. So, you can find the earlier posts marked on the archive page at Dancing birds, May 6, 2009 and Dancing birds -- follow-up, May 15, 2009. Or you can go directly to the page that contains the content of both posts, and the new links noted above: Dancing birds. If you missed it, the second of those contains music of chicks dancing in their shells.



Hydrogen cars?

June 24, 2009

A current news feature from Science: Transportation Research -- Hydrogen Cars: Fad or the Future?. (Science 324:1257, June 5, 2009.)

The immediate impetus is the announcement that the Obama administration has decided not to continue with research on H-cars at this point. Regardless, the article is a good overview, outlining the pro and con of the idea. Three pages, and very readable.

There is a supplementary page for this item. The article posted here stimulated an e-mail exchange with Jakub, who has extensive experience with fuel cells. The supplementary page is based on our exchange. Hydrogen cars? - supplement.

A subsequent post on this topic, about a year later: Hydrogen fuel cell cars (June 8, 2010).



June 22, 2009


Astronomy talks

June 22, 2009

2009 is the International Year of Astronomy, commemorating the start of Galileo's telescopic work 400 years ago. UC Berkeley is hosting a series of lectures for the general public. I have been to a couple, and they have been quite good.

The following page lists the lectures, and provides videos: International Year of Astronomy 2009 Public Talks Hosted by the UC Berkeley Astronomy Department.

* * * * *

UPDATE: They have continued the series beyond 2009, and with a broader science spectrum of talks. A nice development! Web site for the new series: Science@Cal Lecture Series. Also, they now webcast the lectures live, and archive them online.

Some of these lectures are referred to in other posts:
* Berkeley Bionics: From HULC to eLEGS -- Follow-up (July 26, 2011). Talk by Homayoon Kazerooni.
* Ant sociality: supercolonies -- a video of a talk (May 31, 2011). Talk by Neil Tsutsui.
* Extrasolar planets (12/8/09). Talk by Geoff Marcy.

Other talks include...
* The Exploding Stars, Dark Energy, and the Runaway Universe. (Jeffrey Silverman, July 21, 2012.)
* The Quest for the Higgs Boson at Large Hadron Collider. (Beate Heinemann, January 21, 2012.)

Archives:
* Science@Cal, 2010-recent: Science@Cal archive, at YouTube.
* Original series of astronomy talks, 2009: Astronomy talks, 2009. (This is the page listed above.)

Of course, I encourage you to browse the listings to find those that interest you. Quality of the talks has been generally quite good.

* * * * *

Another source of videos of good science talks at UC Berkeley is CITRIS. See the post CITRIS: Zettl; new energy series (November 1, 2009).

Another series... Lecture videos: Berkeley City College (July 14, 2013).



Ida: follow-up

June 21, 2009

Ida is a 47 million year old fossil of an early primate. Posts about Ida have been consolidated on the page Ida.



Cloning: camel

June 19, 2009

A cloned camel was born recently. Scientist: First cloned camel born in Dubai. (4/14/09)

* * * * *

More, June 11, 2012...

More on this story... Cloning: camel -- update (June 11, 2012).

While checking out the new story, we found an article on the original cloning: Production of the First Cloned Camel by Somatic Cell Nuclear Transfer. (N A Wani et al, Biology of Reproduction 82:373, February 1, 2010.)



Visualizing music

June 18, 2009

The Bach, Toccata and Fugue in d minor, BWV 565. Again. This time, a YouTube video with an unusual visual aspect. Bach, Toccata and Fugue in d minor. Visualized by Stephen Malinowski.

From the contributor's comments...

To hear Bach organ piece live, on a large organ, is certainly one of the most profound aural bone-chilling experiences one can have.

Johann Sebastian Bach is considered one of the greatest western composers, and now you can see a fantastic visualization of his famous Toccata and Fugue in D minor:

There is more at Malinowski's YouTube channel: The artist at YouTube. Apparently he made a music animation machine. More at his site: Malinowski's web site. His page The Conductor Program - computer-mediated musical performance provides some background and technical information.

We have shared other versions of this piece, here and in my music posts:
* Played on tesla coils, See the Musings post below for May 31: Tesla coils -- music.
* An organ version, played by Marie-Claire Alain.
* A music post... For those who may prefer something that does not sound so "classical"... a version by Vanessa-Mae.

There is more about music on my page Internet resources: Miscellaneous in the section Art & Music.

More about Bach: Bach and the immune system (August 26, 2013).



Healthcare costs

June 18, 2009

Sorry about the dull title of this item.

Perhaps I should explicitly state the target audience: this is for anyone who is alive. The US is currently re-evaluating its health care system. Again. Or still. Those of you outside the US can read this to poke fun at us.

The article is from the New Yorker. It is journalism, but the author is a physician. Remember, it is easier to describe the problem than to fix it, easier to complain than to build. Further, the article is one person's view. So, take this in that spirit. It is a good read, with some good points. It is not the last word. The article is apparently considered important in the Obama administration.

The Cost Conundrum - What a Texas town can teach us about health care. (New Yorker, 6/1/09. Article by Atul Gawande.)

I've had discussions of health care systems with several of you. It is a complex topic. Each plan that is suggested has pro and con aspects. The challenge is to figure out a good balance; that means tuning the incentives that are built in to any system. In science we try ideas, then improve them as more information comes in; if would help if our political system learned that feedback system.

I try to be fairly neutral when posting things here, but I am happy if discussion follows.

More on health care:
* POCDx -- What's the barrier? (January 29, 2013).
* High-tech medicine: good or bad? (June 4, 2010).



What should a car sound like?

June 18, 2009

If you are inclined to answer the question in my header with something like "a car", good for you.

Car sound. (10/13/09.) (The item originally linked here is no longer available, so I replaced it with another story on the same topic. The new item is a bit more recent.)

Interesting issue. Fun, and some good science involved. I know there have been times when the lack of sound from a car caught my attention.



June 15, 2009


Curry and Alzheimer's disease

June 15, 2009

John sends: Curry a day could keep dementia away. (The Free Library, reprinted from ITN News, 6/3/09)

Now, is there something to this, or is John just trying to curry our favor? Well, there is some real background to it. In fact, he and I discussed earlier work on this some years ago, as he reminded me in his e-mail.

There certainly are data suggesting that countries with high consumption of curry have lower rates of Alzheimer's disease (AD). Of course, that proves nothing, but curry is interesting stuff; its key ingredient curcumin -- the yellow stuff -- certainly has biological effects. It is worth investigating.

So here we have some mouse data, which show an effect. Good. But there are uncertainties. One is that mice are not simply little humans; mouse data do not always aim us correctly. Second, there is still much mystery about the biology of AD. Those plaques... we really are not sure how important they are in the disease process. There are even reasons to worry that the effect seen could be bad for an Alzheimer's patient. (Note that the mouse data is only on plaques, not on memory.) Finally, we must emphasize that we have no idea what the side effects of large doses might be.

The story refers to a clinical trial in humans. I'm sure they will proceed with great caution.

A small clinical trial of curcumin on AD was reported in 2008. It was more or less equivalent to what we call a Phase 1 trial, mainly intended to scope the treatment, and check for major side effects. The trial showed no significant effects of any kind.

Bottom line... An interesting story, worth following. But don't jump to conclusions. There is really nothing so far to show that curry either prevents or usefully treats AD in humans. Time will tell.

More about curry: A curcumin-based drug and stroke treatment (March 16, 2011).

More about Alzheimer's Disease: Do cell phones prevent Alzheimer's Disease? (January 13, 2010).

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



Putting the MRI machine in the patient

June 15, 2009

Doug sent some information on a technical development that is both fascinating and potentially important. The short version of the story is the development of an MRI machine that can be inserted into a patient's artery. In Doug's first message on this, he started, "Cool! They've invented an intravascular MRI (IVMRI) catheter."

The rest of this item is from Doug, with only minor editing (mainly for format). He provides some background, and an introduction to this new development.

Coronary atherosclerosis, more commonly called "coronary artery disease" or simply "heart disease", is the leading cause of death in the US, ahead of even cancer. Coronary atherosclerosis occurs when fatty deposits, called atheromatous plaques, build up on the inside walls of coronary arteries, leading to reduced perfusion of the heart muscle [1]. This can lead to heart attacks when blood flow becomes so reduced that the heart muscle dies. The most accurate way of diagnosing atherosclerosis is a procedure called coronary catheter angiography, which is a specialized X-ray that involves injection of radio-opaque dye to visualize the coronary arteries in real-time [2]. But since this only tells that a narrowing is present, to help the cardiologist better determine the location and size of the plaque, another catheter, this one containing a tiny ultrasound transducer, can be inserted. This is called intravascular ultrasound, or IVUS [3]. Currently, coronary angiography with IVUS is the standard of care when atherosclerosis is suspected. However, IVUS has drawbacks: the images are notoriously difficult to interpret and it gives no information on the composition of the plaque, which is extremely important in determining whether the plaque is "vulnerable", or likely to break apart. It also requires a trained technologist to use. Rupture of a vulnerable plaque is the most common etiology (cause) of an acute myocardial infarction [4].

However, Israeli researches have developed a catheter that can create magnetic resonance images of arterial plaque [5]. By putting two tiny magnets on the tip of the catheter, a field of 0.2 Tesla can be generated, which causes the hydrogen atoms in the nearby tissue to align with the field. Then, a radiofrequency ("RF") coil is used to emit a pulse that causes the atoms to fall out of alignment. When they realign with the field, the atoms emit an RF pulse. This pulse is detected by the coil, and a computer than converts the data from the coil into an image [6]. Since atherosclerotic lesions have far greater hydrogen content then non-atherosclerotic lesions, they can easily be distinguished from each other. This will allow cardiologists to more accurately diagnose and treat patients with coronary artery disease.

In 2008 the first IVMRI system was installed, at ZOL Hospital in Genk, Belgium [7].

Reference and links. Some are on background material; #5 and #7 are the key links on the mini MRI machine.
1. Wikipedia: Atherosclerosis.
2. Wikipedia: Coronary catheterization.
3. Wikipedia: IVUS (Intravascular ultrasound).
4. Wikipedia: Vulnerable plaque.
5. Detecting Unstable Lesions in High-risk Patients: The Single-use, IntraVascular MRI (IVMRI) Catheter. (Cath Lab Digest, 3/04.)
6. Wikipedia: How_MRI_works. (Part of a larger page on Magnetic Resonance Imaging.)
7. TopSpin Medical announces first commercial installation of the Cathamaran(TM) Intravascular MRI System. (1/30/08)



Chemical element #112

June 12, 2009

This has been combined with a subsequent post: Element #112: Copernicium (7/15/09).



Science in the White House

June 11, 2009

This is an editorial in Science by John Holdren, the new Presidential Science Adviser. Some might enjoy reading it, for perspective. Science in the White House. (Science 324:567, 5/1/09.)

Also see: Obama and science (November 13, 2008).

I post this without any intent of partisanship etc. It is simply a one page statement of how he perceives his job. How it plays out remains to be seen. If people want to follow up on this with comparison or whatever, that is fine, but that is not my basic intent at this point.



Spleling

June 11, 2009

"AOCCDRNIG TO RSCHEEARCH AT CMABRIGDE UINERVTISY, IT DEOSN'T MTTAER IN WAHT OREDR THE LTTEERS IN A WROD ARE, THE OLNY IPRMOETNT TIHNG IS TAHT THE FRIST AND LSAT LTTEER BE AT THE RGHIT PCLAE."

Cmabrigde Uinervtisy site on spleling.

As often, there are good serious ideas behind the humor. I encourage you to read Matt Davis's page, linked above. He analyzes why the bad spelling "works", giving insight into the quite serious issues of the nature of written languages and how we read. He discusses why the letter scrambling may not work so well in some languages, and includes translations of the target text in several other languages.

Again emphasizing that this involves something important... Most of you regularly use a tool that deals with this issue. Think about it. Then move your cursor over this sentence for one possible answer. (Do not click.) Do you have others?

It occurs to me that several of you could contribute a new language to his page. I encourage you to consider doing so. The idea is to translate the statement (at least the first sentence, shown above, I suppose) into the new language; then, carry out the scrambling as described. If you send such to me, let me know if I can pass it on to him; I will specify that you be given the credit.

This has been around for a while. It recently resurfaced in a book review in Science (324:38, 4/3/09; the book is on the history of writing).

Other posts on English include:
* Punctuation (January 11, 2010)
* Possessives (December 23, 2008)

Also see...
* Are some languages spoken faster than others? (November 21, 2011). On human languages. I suspect this is related to the current post.



Bees -- around you

June 11, 2009

Two links here. The first is a news story in a UC Berkeley paper about bees in their natural environment. The second, which is referred to there, is a web site of the professor whose work is highlighted.

A must-see spot - if you're a Berkeley bee. "Gordon Frankie's Oxford Street garden is a popular stop for dozens of native bee species - and a laboratory for learning what plants they prefer." (5/1/09)
Urban bee gardens: A practical guide to introducing the world's most prolific pollinators into your garden. Frankie's web site, for the general public. Lots of interesting info, even if you are not inclined to invite the bees in. Sections include: Introduction - Why Make Yours A Bee Garden?; Bees: The World's Star Pollinators; Where Do Bees Nest In the City?; A Guide To Closer Bee Observations; Natives Vs. Exotics; Stinging: Facts Vs. Fears. And more.

More on bees...
* Origin of gas warfare (September 11, 2009).



June 8, 2009


The mouse genome

June 5, 2009

Good news for mouse fans: Mice have more genes than humans do.

So it seems after the recent announcement of the completed mouse genome. (You may have heard about it; it was a rather big news story last week.) Mouse 20,210; human 19,042. (This is the count for predicted protein-encoding genes.)

No gloating, mouse fans. These gene numbers wander around from one analysis to another. (I was surprised to see the human gene count down below 20,000.) It is still something of a guessing game to predict genes in complex organisms. Further, we now understand that multiple proteins are made from what appears to be a single gene. And we understand that variation in exactly when and where a protein is important.

About 3/4 of the genes of human and mouse are likely to code for the same functions. That leaves 1/4 to distinguish us.

This is mainly fun and games at this point. These numbers mean little. What really matters is that much genome information is being collected. Over time it will be analyzed at increasingly detailed levels. At some point we will move beyond the numbers and start pointing to specific genes as being responsible for specific differences.

A particular reason for being interested in the mouse genome is that the mouse is an important model organism for studies of human biology. We are both mammals, and thus share much basic biology. The mouse is small and fast-growing, so easier -- and cheaper -- to study. However, results from the mouse do not translate simply to man. A mouse is not just a tiny human. The more we know about the details of man and mouse, the better.

The largest genome (found so far)? About 46,000 genes. The poplar tree. But a poplar tree is not just a tall green human.

In another post, I claimed that the spruce genome was the largest -- for a quite different reason. The spruce genome has about 20 billion base pairs, and about 29 thousand genes. The poplar genome has a half billion base pairs -- and 46 thousand genes. Spruce has more base pairs than any other genome yet sequenced; poplar has more genes. Both are proper criteria, but they are quite different -- as you can see with these two examples. (Of course, numbers change over time. The numbers reported for these genomes will change some, and more genomes will be sequenced.) The spruce genome: it's big (July 1, 2013).

This item is related to the item on Biological complexity (May 20).

The paper is: D M Church et al, Lineage-Specific Biology Revealed by a Finished Genome Assembly of the Mouse. PLoS Biology, 7(5):e1000112, 5/26/09. It is freely available at: Mouse genome paper. The paper is quite technical, and probably more than you want. I note it for completeness, especially since it, like all articles in PLoS journals, is open access.

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



Fish story

June 4, 2009

Worm picture: Worm.

For more on this, see Fish story page.



Lituus

June 4, 2009

Bach makes the Musings page once again. Did you know that Bach wrote a work that called for two litui?

Greg sent the following:
1. 'Lost' music instrument recreated. (5/30/09)
2. YouTube item on the lituus. It's not really a video, but has an oral presentation of the story of resurrecting the instrument, some good pictures, and some bits of the music.

He added, "No, I didn't know what a lituus is either."


Ok, Greg has now established himself as our expert here on litui. Or so I presume. Any challengers?



June 1, 2009


Ida

May 31, 2009

Ida is a 47 million year old fossil of an early primate. Posts about Ida have been consolidated on the page Ida.



Tesla coils -- music

May 31, 2009

Borislav sent me links to three YouTube videos -- in three separate messages, over about 10 minutes. In the third, he said: "Sorry for the three emails, but I usually don't find stuff this cool! :)"

Here are the three. We suggest you play at least the first one before going on. (Each is very short: 1-3 minutes.)
1. Singing Tesla Coil - MIDI Controlled.
2. Awesome Tesla Coil Concert. Includes some explanation.
3. Faraday Fun - Imperial March.

He also said "I want to hear Bach on this!". And a couple days later, he sent:
4. Bach.
It is an excerpt from the Toccata and Fugue in d, BWV 565. How did he get this? He wrote to the group, saying he wanted to hear them play Bach; they replied with the link.

The group playing these works is ArcAttack, creators of the original Singing Tesla Coils. Their web site is ArcAttack. Choose "About" for some information on what they do, and choose "Video" for some more samples. You can also find more by searching YouTube.

For more on the work of #4, see the Musings post for June 18: Visualizing music.

Added October 15, 2013. Two of the works here are also part of the following Musings post: What to do with old floppy disk drives (October 15, 2013).

There is more about music on my page Internet resources: Miscellaneous in the section Art & Music.

More Faraday... Lyell on fossil rain-prints (May 6, 2012).

* * * * *

I realized that one person here might provide a professional commentary about this item. Larry's first career was as a professional musician. Larry responded -- with comments and memories:

Things that make me go hmmm?

Looks like these guys have found the next dangerous yet cool thing since Roy Horn of Siegfried and Roy was almost eaten by his pet tiger. I think the Tesla midi controlled art is very cool and innovative. From a former musicians point of view, I would hope someday the Sax player doesn't discover he's the path of least resistance.

The robotic drums... hey I thought of that first! I actually thought of trying something like that back in the 80's when I tried to make my Radio Shack Model 100 computer play John Coltrane solos, but I couldn't figure out how to make a mechanical device achieve a good saxophone tone without saliva.

In today's music when there are a few live musicians, to keep costs down most bands typically use a Mac and midi to provide strings, horn sections, background vocals and even stage lighting control. If you ever see 5 people on stage but hear an entire orchestra, look for a Mac Pro laptop computer (MS based machines historically have been too unstable for hardcore midi musicians).

Midi has gotten a lot more sophisticated since I used it years ago. Years ago if midi cables got too long or worn out, the signal would get dropped and the unit being controlled would lose sync with the master. That was a real catastrophic problem if the human drummer was playing to a click track and the click went away or changed tempo. (click track is designed to sync the human drummer to the computer driven instruments, typically you'll see drummers in big concerts with headphones on.)

Since I was a musician there's been a number of devices marketed that alleviated the noise issue on the midi lines. It seems with all the noise floating around generated by the Tesla drivers they would have to balance the fine line of to much signal filtering versus not enough which could be a huge challenge. What I mean by that is the robot controller could read noise instead of signal and lose sync with the computer in the middle of a song. At that point the drums could just stop or start playing a different pattern or start playing random beats and instruments. If they've got a good EE designer for the controllers he's probably using some very sophisticated noise suppression circuitry along with shielded cables. However if they're doing concerts, their show has got to be repeatable so I'm pretty certain they have it together. If they don't and the Robo drummer did its own thing... it's all jazz anyway!



Stem cells: an update

May 28, 2009

Stem cells are cells that can form different kinds of specialized (differentiated) cells. Some can form many different kinds of cells. That is, they have many possible fates or "abilities"; we call them pluripotent. The recent big stem cell news is finding that one can take various kinds of cells from an animal, treat them in the lab, and cause them to revert to a pluripotent state. These cells are called induced pluripotent stem cells, iPSC.

Nature has recently published a nice 4-page "news feature" summarizing recent developments.
Fast and Furious. (Nature 458:962, 4/23/09.) Their subtitle: "The field of induced pluripotent stem cells has gone from standing start to headlong rush in less than three years. Monya Baker charts the course so far, and the obstacles ahead".

It is somewhat technical in places, but I think many will find it of some value, at least to browse. Let me know if you have questions, or would like to see more on some parts of this. For those who may find the article somewhat difficult... I would emphasize... look it over, and try to learn something new from it. It is not a textbook, and you will not have a test on it. Look it over, and make some progress. Now you know more than you did.

An important point -- whether you read the Nature story or not... You hear a lot about stem cells being used to treat people. Maybe. Certainly that is the dream. But that is a long way off, for the most part. The more immediate use is for research, to learn about diseases. The article talks about this.

I have more on stem cells on my page Biotechnology in the News (BITN) - Cloning and stem cells



And the fuel cell said ...
and
Man-eating plants?

May 27, 2009

See the top item on the page: Graphic Science (Science 323:1543, 3/20/09.)

The item at lower right of the page may also be of interest. I wonder if you could breed these to something larger, and develop man-eating plants. Hm, what do the vegetarians here think of carnivorous plants?



Are you bilingual?

May 27, 2009

See Are you bilingual? (5/27/09). It is part of supplementary page on bilingual issues.



May 25, 2009


I think I created life.

May 21, 2009

One of you keeps extolling the virtues of the "Clean" function in chem drawing programs such as ISIS/Draw. I'm not sure what it really does. In fact, it usually seems to do nothing, unless I have actually somehow distorted a bond. However, I continued to be curious and to explore.

Using the new program Symyx Draw, I used the multi-chain tool to quickly draw a long chain of rather non-descript form on the screen. I think I had 100-150 carbons. Then, select it, and "clean". I was quite startled to see the following appear on the screen. Symyx Draw cleans.

Someone has identified this as a software bug.

I welcome attempts to reproduce this and improve on it. Happy to post more on this.



Brown fat

May 21, 2009

Brown fat is neat stuff. It could be the secret to weight loss: it lets us burn excess food, and simply release its energy as heat. The problem is, we don't have brown fat (at least if you are old enough to read this). Or do we?

The idea is simple enough, good biology. Normally, when we burn our food we capture some of the energy as ATP (bio-energy) and release some heat as a by-product. Ordinary fat (white fat) is a way to store excess food, for later use. But brown fat is sort of the opposite: in brown fat we burn our food, and make nothing useful at all -- we just release the heat. Its purpose to the animal may actually be heat production; it is sometimes called thermogenic fat.

Many smaller animals have brown fat, so much is known about it. Further, human infants have brown fat -- and it presumably helps them keep warm. But common wisdom was that we lose our brown fat at a very young age.

At the other extreme, pigs lack brown fat function, even in infancy. (They carry a mutation in the gene for wasting energy.) That is why baby pigs nest -- to keep warm.

There have been two recent developments of note. First, we may have brown fat, after all. It seems to be an interesting story why this was missed earlier. The brown fat is being detected -- rather accidentally -- during measurements of tumors. The measurements of brown fat are variable -- for reasons that are partially understood. A recent clue is that exposure to cold seems to activate our brown fat.

Second, work with mice has shown how brown fat cells are made. Scientists were able to develop brown fat cells in the lab, and then they carried the work over to real mice. An interesting part of this story is that brown fat is closely related to muscle. [The brown color is due to the high number of mitochondria (and their cytochromes), as also found in muscle.] Developmentally, brown fat and white fat are quite unrelated. But no matter the details and relationships, the point is that they learned how to induce brown fat formation.

Perhaps we will learn to induce the formation and function of brown fat in humans. Will this turn out to be a useful tool in combating obesity? Let's be cautious. That is a big jump. We may be able to induce brown fat, but it will take some time to test whether it is an effective and safe intervention. After all, brown fat must be quite carefully controlled, or else it could waste all your food. The brown fat story has been fun to watch over the last year or two, and I think more neat stuff is likely. Let's watch.

Two recent news stories on some of these developments with brown fat:
WebMD: Can Brown Fat Make You Thin? (4/8/09.)
Obesity: Be cool, lose weight (S R Farmer, Nature 458:839, 4/16/09.)

More about brown fat: Brown fat: different kinds respond differently to cold (September 20, 2013).

For more about lipids, see the section of my page Organic/Biochemistry Internet resources on Lipids.



Biological complexity

May 20, 2009

The article here explores an idea. It is an interesting discussion, with no particular conclusion. In fact, the "conclusion" of the paper includes the statement that "... there is little, if any, consensus on what the term 'complexity' means." So, enjoy the trip, but don't worry much about where it ends up.

A good view may be that there are many ways to look at biological complexity. Many interesting ways. A merit of the article is exploring various views of complexity.

Can Biological Complexity Be Rationalized?. (B J Finlay & G F Esteban, BioScience 59:333, 4/09.)

This article is probably more specialized that most I share here. At least with this format I don't need to bother everyone with an extra email for it. I just post, and you choose which to read, and at what level.

The item on the mouse genome (June 5) is related.



Money question

May 20, 2009

This is really for the Americans. Others can just enjoy (and snicker?).

a. How much is a dime worth? That is, how many cents? (No tricks. Has nothing to do with the price of metals etc.)

b. How do you know that? You did check? You looked at one to see what it says? I hope.

Why did this come up? Well, when you are satisfied with part b, put your cursor over the following word: explanation. (Do not click.)

The dime is a convenient reference point for thinking about weight. It weighs just about 2 grams. See, for example... A microscope small enough that a mouse can wear it on its head (November 12, 2011).



Space shuttle passes in front of the sun

May 19, 2009

Shuttle-sun.

"WOW!", says the contributor. Wistfully, I suspect.

For more by the same photographer... More.

More on the shuttle: Photography from the space shuttle (June 4, 2012).



May 18, 2009


On the road to life?

May 18, 2009

There was a big news story this past week -- a fascinating development in the story of how life may have begun. Unfortunately -- but probably not surprisingly -- the story has been accompanied by much hype. Some accounts have even proclaimed that they created life in the lab. Hardly. But what they did do was to show a plausible pathway for one key step.

As background... Modern biology is built around understanding three "informational macromolecules" -- large molecules that carry information. One of these is DNA, which carries your genes. Around 1960, we developed a simple view of the roles of these three types of molecules. Simplified, this is summarized as the Central Dogma of Molecular Biology: DNA --> RNA --> protein. That is, DNA "codes for" RNA, and RNA "codes for" protein.

So how did this get started? When a system involves inter-dependent parts, it can be hard to understand how it got that way. What did more primitive versions of the process look like? Which part came first?

In the case of DNA --> RNA --> protein, by the early 1980s it became rather clear that RNA was the best candidate for being first. The key was finding that RNA can do what DNA and protein do -- even if not as well. Thus we can easily envision an "RNA world", in which life used RNA, but not yet DNA or protein. That simplifies the system, and pushes the question back.

So where did RNA come from? Was RNA the original "gene", or was there something before it? Chemists have been working on "pre-biotic" chemistry for many decades, looking for plausible ways to get from "the primordial soup" -- whatever it was that was around before life began -- to life. A lot of fun stuff, and sometimes even interesting results. But one thing that eluded the chemists was finding how to make RNA. That is where the current work fits in. What they did was to fill in part of the story about how to get from the primordial soup to RNA. They showed a way to get to two parts of the RNA -- a better story than anyone had done so far.

Here is the announcement from the University of Manchester. It is not technical, but it does provide a good low-hype perspective. Organic chemists shed light on origins of life. (May 14, 2009)

The work was published in Nature.
* Here is the News story that accompanied it there: Origins of life: Systems chemistry on early Earth. (J W Szostak, Nature 459:171, May 14, 2009.)
* The article itself: Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions. (M W Powner et al, Nature 459:239, May 14, 2009.) (Caution, this article is rather heavy chemistry.)

A post on the history of the Central Dogma: Central Dogma of Molecular Biology (August 16, 2011).

Also see: A novel type of polymer -- and its possible relevance to the origin of life (March 15, 2013).



Climbing robot

May 15, 2009

Climbing robot.

This is from the University of Pennsylvania. Note that the page links to Boston Dynamics, where there is much more.

Thanks for the contribution!

More from Boston Dynamics: See cat run (March 14, 2012).



Dancing birds -- follow-up

May 15, 2009

Items on the Dancing Birds have been consolidated onto a single page. For this item, see Dancing birds -- follow-up.



The little people of Indonesia

May 14, 2009

A fascinating story about humans.

In 2004 scientists discovered fossil remains of tiny humans on the Indonesian island of Flores. By tiny, I mean they were about 3 feet (1 meter) tall, with a head about 1/3 the size of ours. Dating suggests they vary from about 100,000 to 17,000 years old. They have become known informally as hobbits. Formally? Homo floresiensis -- if you think they are a distinct species.

I will use the term "human" here in the loose sense of any animal that we would generally recognize as human-like.

What are they? How are they related to us? Well, some possibilities...

- Children? But they are not children; that is fairly easy to tell.

- Defective humans? That is, they might be pathological examples of "regular" humans. For example, there is a condition called microcephaly that leads to a small head. However, careful examination of the samples does not support this: the fossils are not consistent with any known pathological condition. The more general version of this suggestion is hard to rule out and remains possible. The main point for now is that there is no evidence for it. This point also illustrates a key problem: There is only one skull so far -- a serious limitation of the data set.

- Dwarfed humans? In some cases it has been found that large animals forced into small environments (such as islands) evolve into a smaller form. Maybe the hobbits are a dwarf line of something close to modern humans. A fascinating possibility! And for a while it was the favored hypothesis for many people. However, more detailed analysis of the remains makes this unlikely. Nevertheless, it may be that they are a dwarfed version of some older species of humans. That is, the idea of dwarfing may still hold, but their place on the human "family tree" may be rather far back.

So where does this stand? In some sense, about as it did: a fascinating observation, with no explanation yet, certainly nothing that is agreed on. Some ideas that have been presented seem unlikely. Current thinking is that it may be a branch of an ancient line. But details are elusive. As noted, the data set is limited. An important line of work is to look for more specimens. We shall see. Science in progress.

If the hobbits are ultimately recognized as a distinct species, it would seem to imply that three species of humans co-existed on the earth within the last 50,000 years or so. (The three: modern humans, neandertals, and the hobbits. Homo sapiens, Homo neanderthalensis, Homo floresiensis.)

Here are two good current stories on the hobbits:
A Tiny Hominid With No Place on the Family Tree. This article includes a picture directly comparing the skulls of Homo sapiens and Homo floresiensis. (4/27/09.)
Palaeoanthropology - Homo floresiensis from head to toe. (Nature 459:41, 5/7/09.) This article includes a photo of the Flores island fossil site, and a suggested human family tree -- with lots of dotted lines (for uncertainty).

Careful readers will note that the two articles do not entirely agree. So be it. In fact, the big message is that this is a developing story, and the conclusions are not at all clear.

A Musings post on another possible new human species: The Siberian finger: a new human species? (April 27, 2010).

More on the Hobbits..
* Hobbits: an update (May 1, 2010).
* Hobbit DNA? (May 28, 2010).
* The Hobbits: a dissent (August 15, 2011).

Much of Dean Falk's book The Fossil Chronicles -- How two controversial discoveries changed our view of human evolution is about the hobbits. I have listed the book on my page Book Suggestions: Falk, The Fossil Chronicles, 2011.

Fossil discovered: A big stupid rabbit (April 22, 2011). The post above introduces the hypothesis that the hobbits on Flores Island might be dwarfed due to the island environment. Another part of this "island rule" -- a broader hypothesis about how some animals adapt to such environments -- is that smaller animals may evolve to larger forms. The post here offers a possible example.



PHD: Piled Higher and Deeper

May 13, 2009

This is for those of you in graduate school. Or those who have been in graduate school. Or those who might go to grad school at some point. Or those who enjoy cartoons.

The theme might also be stated as what one can do with a Ph.D. from Stanford in robotics. In fact, the Science article listed below is part of their "Science careers" feature.

For the meat: PHD. By the way, this runs in the student newspaper at UC Berkeley.

Science ran a news story on this comic strip and its creator Jorge Cham. For those with access: Science: Piled Higher and Deeper: The Everyday Life of a Grad Student. (Science 323:1668, 3/27/09.)



Radio-tagged ants

May 13, 2009

Social insects are fun. Articles I post on bees always seem to attract comment. So here is a short item on ants. The methods are fun, as much as the results.

How House-Hunting Ants Choose The Best Home. (Science Daily, 4/26/09.) Includes a photo of an ant with a radio device.

Watching as Ants Go Marching.... (Science 323:1284, 3/6/09.)

Also see:
* Tracking termites (February 26, 2010) for another approach to tracking insects -- in the field.
* What's a dia? Bumblebees and reindeer don't agree. (December 6, 2010). Another example of radio-tagging insects.
* Ants: nurses, foragers, and cleaners (May 24, 2013).



May 11, 2009


Electric cars

May 9, 2009

Our automotive writer Brian Sy shares another of his reviews, this time a short review of a new electric car: the 2010 Aptera 2e. The review contains a couple of pictures of this thing. (That's a car?) I think you'll find the content of interest -- while also enjoying Brian's lively writing. Aptera 2e review [pdf file; link opens in new window].

As a bit of background, we had asked Brian for a comment on the Tesla sedan that has been announced: Tesla sedan. Brian replied with the Aptera review, which also mentions the Tesla. He also briefly noted of the Tesla: "Haven't dug too deeply into it, but hell, $50,000 for an electric mid-size luxury sedan that can do 0-60 in 5.6 and goes 300 miles? That pretty much makes it a BMW 550i except the gas is FREE."

The next item on electric cars is A new electric car (July 11, 2009). It is on the Dok-ing car.

Another review from Brian of a car of "environmental" interest: Cleaner cars: the Honda Civic Natural Gas car (December 9, 2011).

More from Tesla: Hyperloop: Ground transportation at near the speed of sound (August 19, 2013).

* * * * *

Update, December 2011... Brian notes that Aptera has recently gone out of business. This does not necessarily reflect on the merits of the car, but does reflect on the difficulties of the market. Aptera closes its doors. (CNet, December 2, 2011.)



Lovelock: The Gaia guy

May 8, 2009

See Lovelock: The Gaia guy (5/8/09). It is part of supplementary page on Gaia and James Lovelock.



Alternative energy for a sustainable future

May 7, 2009

A 2008 issue of Engineering and Science (E&S), the Caltech alumni magazine, was devoted to this topic. Good articles, written for the well-educated layman. Go to http://calteches.library.caltech.edu/710/, which is the table of contents for this issue, Volume LXXI, Number 2, 2008. Articles include:
"The Race for New Biofuels", by Frances H. Arnold;
"Solar Fuels I: Rods and Stones", by Douglas L. Smith;
"Solar Fuels II: The Quest for the Catalyst", by Harry B. Gray;
"From Solar Fuel Back to Electricity", by Marcus Woo.

I have listed this item on my page of Internet Resources for Organic and Biochemistry - Energy resources. Another good article from this magazine is listed there, under the title "Powering the planet". In general, I encourage you to browse E&S. It has good articles about a wide range of science (and some non-science).

Related Musings items:
* Cellulosics for energy: an update (October 30, 2010). Overview of the use of cellulosics -- and the slow progress being made.
* Joint Center for Artificial Photosynthesis (JCAP) (August 16, 2010).
* Sustainable Energy - without the hot air (September 16, 2009).
* Materials for solar cells (March 10, 2009).



Language development

May 7, 2009

This may be of particular interest to those of you who deal with Slavic languages.

Language development.



Dancing birds

May 6, 2009

Items on the Dancing Birds have been consolidated onto a single page. For this item, see Dancing birds.

More birds: Of birds and butts (February 2, 2013).



Swine flu

May 2, 2009

Posts on this topic have been consolidated on the page Musings: Influenza (Swine flu).



April 2009


Twins

April 30, 2009

Two by two. A nice story about twins. Much fun, with interesting questions, interesting information, and neat pictures. The pictures include a nine-banded armadillo with her genetically identical quadruplets genetically identical quadruplets genetically identical quadruplets genetically identical quadruplets. Apparently, that is normal for nine-banded armadillos. (Simply seeing one of these critters is always fun.) Do human populations vary in the frequency of twins? Apparently that is really not known for sure; it is one of the interesting questions discussed here. And how identical are identical twins? Another interesting question.

I think people with a wide range of backgrounds and interests will find it fun to at least browse this article.

The article, a News Feature, is: D Cyranoski, Reproduction: Two by two. Nature 458:826, April 16, 2009. "Could genes explain the remarkable rate of identical twins born in some remote villages around the world? David Cyranoski investigates a long-standing biological curiosity." For those with access, it is at Twins.

For more on armadillos, see: Leprosy: the armadillo connection (May 14, 2011).

Also see:
* Cannibalism in the uterus (May 31, 2013)
* In vitro fertilization: Will it suffice to transfer only one embryo? (May 19, 2013)



The Typewriter: the movie

April 30, 2009

Earlier, I posted a music item: Leroy Anderson's The Typewriter. A reader responded with the following delightful item: The Typewriter: the movie.



Google tracks the flu

April 30, 2009

You may have heard about this in the news. Google, in collaboration with the CDC, says they can track the flu by the frequency of searches on flu symptoms and such. The idea is not new, but their implementation of it is more advanced than prior efforts. The big advantage is the speed at which the info becomes available.

See http://www.google.org/flutrends/. That page shows what is happening. The page also links to more information, which includes the paper published in the Feb 19 issue of Nature.

Added April 11, 2014. Follow-up: Google tracks the flu -- follow-up (April 11, 2014).

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

Also see:
* Added July 7, 2014. Tracking food poisoning through online reviews (July 7, 2014).
* In what year was the word "slavery" most used in books? (February 23, 2011).



Cannibalism

April 27, 2009

There is reason to believe that Neandertals may have been cannibals, and the Neandertal specimen whose genome was sequenced was from what is now Croatia. Obviously then we must ask whether modern Croatians are also cannibals. Obviously. Actually, I might not have thought of it, except ...

Not long ago, Borislav and Dubravka sent me a recipe. Here are key excerpts, with Borislav's translation (after the // on each line):

Pašteta od boba // Bob pate

500 g boba, bez mahuna i ljuski // 500g of Bob, without shells and layers
1 češanj češnjaka - sitno nasjeckan // 1 garlic, finely cut
(etc)

...

Priprema: // Preparation

Kuhajte bob u kipućoj blago posoljenoj vodi 10 do 12 minuta dok ne omekša. // Cook Bob in boiling water ...

* * * * *

Now, Borislav tried to weasel out of this by suggesting that bob is a type of bean. Not sure I buy that. Occurs to me that I do not know anyone in Croatia named Bob. Further, I do not know anyone named Bob who went to Croatia and returned. Seems pretty good evidence that there are no Bobs there -- probably because they are, er, consumed. Also, look at it the other way. If I told Borislav I had a recipe that called for 500 g borislava, do you think he would believe me if I insisted that a borislav is a type of bean?

Beware. People's taste vary.

Borislav's next attempt to dehumanize me: BOB 2.0 (April 26, 2010).

Also see:
* Cannibalism in the uterus (May 31, 2013)



Living to 100

April 22, 2009

Who is the first Nobel prize winner to live to age 100?

Oldest Nobel laureate turns 100. (BBC, April 22, 2009.)

For those who have access, I would also encourage you to look at a longer "News Feature" in Nature: Neuroscience: One hundred years of Rita. (Nature 458:564, April 2, 2009.)

Another centenarian: Elliott Carter: 100th birthday (December 23, 2008).

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

* * * * *

More, January 8, 2013...

The object of this post died on December 30, 2012, at age 103. Here is a nice little item about her: news story on death of centenarian Nobelist. (The Scientist, January 1, 2013.)

Of course, this raises the question: Who is now the oldest living Nobel Prize winner? And we might make a variation of that question for those who don't think economics should be relevant... Who is the oldest living Nobelist in the real sciences? That question also has the merit of getting us to a Berkeley prof. You can check yourself at: Caskets On Parade -- List of Nobel Prize Winners. Check the second table there.



Science: virus-battery

April 15, 2009

Hot story!

A reader sent this to me: Viruses Used to Grow "Greener" Batteries. (April 3, 2009)

After you look over that short item, I think you will find the following, from MIT, helpful: New virus-built battery could power cars, electronic devices. (April 2, 2009)

Briefly, they use the virus as a template for growing electrode materials. The virus per se is not doing anything electrical. (So in that sense it is very different from the microbial fuel cells. In those, the bacteria are doing biology/chemistry. Generating electrons is a normal part of their day's work, and in the fuel cell we make use of the electrons from the bacterial metabolism. In the new case, the virus is more a scaffold. But one that can be manipulated to do things we think are useful.)

The work is from Angela Belcher, at MIT. She is something of a superstar in this area of bio-nano-whatever-you-want-to-call-it.

It is fun science. Clever ideas, relating things from diverse fields. It has the potential to be useful; certainly it is intended that way. So far, it is not -- it is just fun and exciting, and progress continues.

For those who want more, here is the paper: Fabricating Genetically Engineered High-Power Lithium-Ion Batteries Using Multiple Virus Genes. (Y J Lee et al, Science 324:1051, 5/22/09.)

More about batteries...
* Boiled batteries (July 19, 2010).
* Fast charging batteries (March 13, 2009).



Do robots dream of electric sheep?

April 10, 2009

Maybe Robots Dream of Electric Sheep, But Can They Do Science?. (4/2/09.)



Asteroid hits earth

April 3, 2009

Is that big news?

In this case it is big news because it was the first time that an asteroid hit earth according to predictions. It was detected a few hours before its impact, and it landed about where and when it was predicted to land. An airline pilot in the area dimmed his lights so he could watch the event. This may well have been the first time a human made plans to watch a collision of another heavenly body with earth. (However, it was not the first planned watching of an astronomical collision. That honor would surround the collision of the Shoemaker-Levy comet with Jupiter a few years ago. I think. Does anyone have anything better here? Watching Neil Armstrong walk out onto the moon does not count; only "natural" astronomical collisions.)

65 million years ago, a much larger asteroid landed in Mexico -- and wiped out a good portion of life on earth (direct and indirect effects, perhaps along with other events).

Now, we can make a good case that that event was good -- from our point of view. That impact wiped out most of the larger animals on earth, including the dinosaurs. Thus it opened up niches that were previously occupied. It seems to have led to the age of mammals -- which had previously been minor organisms on earth. And of course, the development of mammals led to the development of humans. Would there be humans (or, when would humans have developed) had not this impact event wiped out the dinosaur 65 million years ago? Something to think about.

However, if such an event were to occur now, it would wipe us out. Not so good.

So, we now watch the skies, looking for objects that seem on track to hit the earth. The idea is simple enough; getting the data is still difficult. The case described here is the first "success" -- in the sense of detecting an object still in the skies, and predicting, with reasonable accuracy, its landing.

Of course, with an object the size of the one that did in the dinosaurs, simply successfully predicting its landing would not be "success". What is essential in that case is to somehow alter its course. We don't have a good plan to do that yet -- and it would take more than a day's notice.

There are multiple stories in here. They include a fuller understanding of what happened 65 million years ago; what I wrote above is a simple version of the common consensus, but it is not all clear and people argue about the details. There are the issues of detecting near-earth objects, and then devising a plan for dealing with one that is headed our way. And then there is the political side... this is an interesting case of risk: an event that is very very improbable over any time period of immediate concern (yet ultimately inevitable). An event with huge possible consequences. How do we deal with that? How do we support work on studying it? How much resources do we devote to learning how to alter the course of an asteroid? And... What do we tell people -- and when -- about a possible collision? In thinking about this last question, remember that the first data that comes in is pretty rough. And remember that in between the tiny rock of last October and the one that did in the dinosaurs is a whole range of sizes, capable of a wide range of damage.

Here are two news stories, which should be freely available. They are from quite different times as the story developed. The impact was on October 7, 2008, in Sudan.
* First Images of Asteroid 2008 TC3 Impact Aftermath. (11/8/08.)
* Look! It's a near-Earth asteroid! (3/26/09.) This is a blog entry. It links to a news story -- which is not currently available.

The following very calm news story, from Nature, describes what happened -- from the original detection of the rock through picking up its pieces. The rock that fell to earth. (Nature 458:401, 3/26/09.)

Overall, this is a fun story of current events. But it is also a serious story. It is a scientific and political issue to worry about asteroids hitting earth.



Electric cows

April 1, 2009

From Nature (with updated link):

Research Highlights

Nature 458, 389 (26 March 2009) | doi:10.1038/458389a; Published online 25 March 2009

Biology: Electric cows

http://www.pnas.org/content/106/14/5708.abstract

Having previously shown statistically that cows and deer preferentially align their bodies north-south, Hynek Burda of the University of Duisburg-Essen in Germany and his colleagues now provide more evidence for these animals' magnetic sensing.

If this alignment is truly due to some sensing of the magnetic field, strong, nearby magnetic fields such as those from power lines should disrupt ruminant orientation.

Using satellite and aerial photographs, the researchers show that 1,699 cows grazing within 50 metres of overhead power lines at various European locations were randomly oriented. Field observations of 653 deer within 50 metres of power lines in the Czech Republic also revealed random orientation.

* * * * *

Hm, what more could I say?

The paper is: H Burdaa et al, Extremely low-frequency electromagnetic fields disrupt magnetic alignment of ruminants. PNAS 106:5708, 4/7/09. The link to it, above in the quote from Nature, should work.

For more on animals and the earth's magnetic field... Magnetic field perception (6/16/10).



March 2009


Progress toward a flu vaccine with broader specificity

March 30, 2009

As you may know, current flu vaccines are specific to single strains. As a result, the flu vaccine is re-formulated each year -- based on a "good guess" as to what strains are coming. Not only are the guesses sometimes wrong, but this is an expensive approach, and it does not deal with the possibility of some novel strain coming along -- such as one from the bird flu.

There is interest in developing vaccines of broader specificity. It has been a challenging problem, but perhaps there is some hope... Antibodies Could Radically Alter Approach to Flu. (2/23/09.)

The article referred to is listed near the end, along with an accompanying news story; links to the items are provided. The news story is particularly good.

Certainly this is good news -- a good idea. I do fear it is further from reality than the simple story might suggest. But that is why we test things. Let's see.


Posts on flu have been consolidated on the page Musings: Influenza (Swine flu).



Science: Love songs

March 26, 2009

What did you expect... Music: love songs ???

* For Mating Mosquitoes, 'Harmonic Convergence'. (New York Times, January 9, 2009.) Added December 3, 2013.
* Mosquitoes create harmonic love song before mating, a Cornell study finds. (Cornell Chronicle, January 8, 2009.)

The article title is: Harmonic Convergence in the Love Songs of the Dengue Vector Mosquito.

What an irresistible title!

And the idea is rather simple...

You know that mosquitoes buzz -- by beating their wings. The wing buzz is part of their recognition process for mating.

In the mosquito studied here (Aedes aegypti -- the vector for dengue and yellow fever), the females beat their wings at around 400 Hz, and the males at around 600 Hz. As part of courtship, they match their wing beats. Well, not exactly -- that is a rather large difference, and would be hard for them to match. What they do is to adjust their wings so that their harmonics match at about 1200 Hz, the 2nd harmonic for the males and the 3rd harmonic for the females. Much of the paper is about direct testing that they are matching these harmonics.

They were somewhat surprised at this, because they thought that 1200 was above the hearing limit for the mosquitoes. So they do further testing to show that the mosquitoes can actually hear up to around 2000 Hz.

A fun paper, of music and science. I've given the main idea here, but I encourage you to at least look over the paper. I think you will find much of it fairly accessible.

Now, should you sing to mosquitoes?

The article: Harmonic Convergence in the Love Songs of the Dengue Vector Mosquito. (L J Cator et al, Science 323:1077, February 20, 2009.)

Related Musings posts:
* Mosquitoes that can't fly (May 3, 2010).
* Dengue fever -- Two strikes and you're out (August 10, 2010).
* Added June 16, 2014. Introducing Supersonus -- it stridulates at 150,000 Hz (June 16, 2014).



A funny Dilbert

March 24, 2009

http://www.dilbert.com/strips/comic/2009-03-16/?Page=1



Mini dinosaurs

March 19, 2009

Big surprises come in small dinosaur packages (University of Alberta, March 20, 2009.)

The article is: A microraptorine (Dinosauria-Dromaeosauridae) from the Late Cretaceeous of North America (N R Longrich & P J Currie, PNAS 106:5002, March 31, 2009.)

More about small dinosaurs... Microraptor was piscivorous (May 25, 2013).



Fast charging batteries

March 13, 2009

Below is quite an interesting article. If it works as described it'd be quite a breakthrough.

Fast-Charging Lithium Ion Batteries Tested. (March 11, 2009.)

The paper is Battery materials for ultrafast charging and discharging. (B Kang & G Ceder, Nature 458:190, 3/12/09.)

More about batteries...
* Science: virus-battery (April 15, 2009).
* Lasagna battery (September 25, 2008).



Materials for solar cells

March 10, 2009

A new paper has gotten a lot of attention recently. It is from some big shots at Berkeley, on the potential of various materials for use in photovoltaic (PV) solar cells.

It has gotten considerable mis-interpretation, too. The main point is an economic analysis, showing that certain materials are worth studying further -- even though their current efficiency is very low. FeS is an example. It is readily available and cheap. It works, but not very well. They do not claim that FeS is ready to replace silicon, or that it ever will. Their claim is that it is worth working on, to see if they can get the cost down. And they note how, with cheap materials, it may work out that one can afford to operate at lower efficiency.

The lead author, Cyrus Wadia, gave a seminar on this last week. (He is finishing up his PhD thesis.) My sense is that his economic modeling makes good points, but that he has little to show in terms of actual progress experimentally. He would probably agree with that. He spent much time emphasizing how long it takes -- how many years, even decades -- to make an idea pay off in this area. Ok. This is basic research for now, and let's not expect any quick payoff.

Here is a readable news story from the university: Cheaper materials could be key to low-cost solar cells. (2/17/09.)

For those who want to wade through the whole thing -- or who just want to be impressed by fancy graphs whether they understand them or not, here is the paper: Materials Availability Expands the Opportunity for Large-Scale Photovoltaics Deployment. (C Wadia et al, Environ. Sci. Technol. 43(6):2072-2077, 2/13/09.) May require subscription for full access.

I know some of you are very interested in this topic, and understand it much better than I do. Comments welcomed. (However, comments that solely point out puns in this note will be ignored.)

By the way, the authorship illustrates another emerging trend. For three authors, there are six affiliations -- all on the Berkeley campus and adjacent LBL.

* * * * *

Follow-up, from a reader:

One thing that causes me to think on this is that, if you consider a Life Cycle Assessment approach to the question: "Is it economical to research a cheaper, albeit less efficient, material for possible future use," my first reaction is "how does the author quantify the expected gains/losses of man-hours, opportunity costs (time spent research this instead of researching a material with greater potential or a new material altogether), etc"? The cost function in the paper only considers resource extraction and transport costs, not the cost of R&D.

Another question then comes to mind: if a less efficient but less expensive material is used, does this directly imply the need for a greater area of solar coverage to accommodate the required capacity? I'm not very familiar with the correlation of solar panel size and capacity, so I can't say how much this would factor in. But you'd expect that unless there is greater expansion in residential, business roof top, urban applications, there may be some question as to how many more PV power generation sites (total area) would be needed to accommodate the capacity goals?

Not that I am discounting the work. At the personal level, I would love nothing more than a greater capacity shift to renewables and alternative energy. The article brings up an interesting and potentially a compelling argument for additional research. Not to mention, continues to expand the explosive PR for the solar industry. From what I've seen in needs documentation reports here, if you cannot demonstrate an improvement in levelized cost of electricity relative to the competition, it is far less likely that large investment ventures will go forward. For this reason I often see renewables given only a small percentage of consideration and projected allocation in the energy sector (particularly in the models we use to project future capacity in each industry, and much of the competitiveness is still a result of subsidies and similar support to help make the benefit/costs more competitive). Most of the talk regarding new investments focus on "clean coal", IGCC, and natural gas, and nuclear.

For the most part, I'll just let this stand on its own. It shows how complex such modeling can be, with judgment about what is important. In some fields, various modelers come up with quite different answers. But this is published, and others can publish their models, too. Over time ...

* * * * *

Related Musings items:
* Joint Center for Artificial Photosynthesis (JCAP) (August 16, 2010).
* Alternative energy for a sustainable future (May 7, 2009).

More about the roof-energy connection: What if your house could sweat when it got hot? (November 30, 2012).

There is more about energy on my page of Internet Resources for Organic and Biochemistry - Energy resources.



February 2009


Why is a raven like a writing desk?

February 17, 2009

A delightful little essay, about lots of things. It is both fun and insightful.

Have a look. It is open access, at: Why is a raven like a writing desk?. (H Wainer, American Scientist 96:446, 11/08.)



Happy 1234567890!!

February 13, 2009

From one of you.

You are probably not aware that today is 1234567890 s in UNIX time.

That number is number of seconds passed from January 1 1970 when computer time officially started.

Read more:
(Both links here are now to an archive version of the page.)
* Unix Time's 1234567890 Second Countdown
* 1234567890 Day

Happy 1234567890!! :)



The nature of science

February 4, 2009

A nice little article... Descriptive Science. A Casadevall & F C Fang, Infection and Immunity 76:3835-3836, 9/08. A "Guest Commentary". It was later reprinted in Microbe, December 2008, which is where I saw it.

The context here is microbiology, but the issues it raises are general.

We often discuss how we teach young students about the "scientific method". Sometimes it comes across as a rather rigid series of steps. Maybe that is inevitable when we have to write it down as a list. But in the real world it is more complex, a back and forth between observation and ideas.

An important skill in science is seeing the unexpected -- what happens that may be unrelated to the intent of the work. And sometimes we do things just to look.



January 2009


Anagram

January 29, 2009

Our immediate former president is known for, let us say, some idiosyncrasies of speech.

Consider the descriptive term for the way he speaks,
   Bush lilt

Rearrange those letters to form another word that some may feel describes his speech.

(This is "humor", not intended as political per se.)



Self-Sustained Replication of an RNA Enzyme

January 22, 2009

A fascinating paper -- which is getting much attention and too much hype.

What did they really do? Well, they made two pieces of RNA, each of which can catalyze making the other. That is, RNA molecule A catalyzes making B, and RNA molecule B catalyzes making A. It works -- indefinitely, as far as they tested, which led to a (calculated) 1025-fold increase in one case. Of course, "normal biology" occurred during the process; the products are quite evolved compared to the parents. (No proteins, or other bio-molecules, are present -- just the two enzymes and the "food".)

Fun stuff, with lots of potential for studying "the RNA world". It is from a lab with a long track record of working with ribozymes, that of Gerald Joyce at Scripps in San Diego. They consider it "an experimental model of a genetic system".

So what is the hype? Well, is this system alive? Did they "create life"? Such questions get news media attention, but they are not very helpful. Is it alive? Well, that presupposes we have a notion of what life is -- a notion so refined that we can deal with primitive cases. We don't; anyway, why would that be helpful? So I hope the focus is more on what the system does, and how it might be studied. What features of living systems does it show? Does it lack? Those questions can be useful for discussion.

Is this directly relevant to how life originally developed? Well, common wisdom is that life (or pre-life) went thru a stage when RNA (or something very similar) was the major bio-molecule (serving as both gene and enzyme). But it is a huge leap to suggest that this particular system is directly relevant. Again, let's just enjoy this system and see what it can do. It is simple enough that it is practical to study it in the lab -- with experiments on a time scale of hours.

Here is the press release on this from Scripps: Scripps scientists develop first examples of RNA that replicates itself indefinitely. (1/11/09.)

The article: Self-Sustained Replication of an RNA Enzyme. (T A Lincoln & G F Joyce, Science 323:1229-1232. 2/27/09.) Caution... The paper is fairly technical, but you can get the main ideas from browsing the first page or so.



Stem cell trials

January 20, 2009

One of you sent me the following two items, hot off the "press" from the BBC.

Both involve planned tests of stem cells in humans.

1) Stem cell stroke therapy assessed (1/18/09.)

2) Stem cell eye surgery to be tried (1/19/09.)

Be patient with stem cells. It is a broad and complex field. Many things are going on. Even these specific tests will take a while to analyze -- and maybe they will not work. But over time...

Science magazine just rated the new procedure for making human iPSC (induced pluripotent stem cells) the scientific breakthrough of the year for 2008. iPSC may be equivalent to embryonic stem cells in their potential, but easier to deal with.

You will even get a taste of the controversies surrounding stem cells, even of the disagreements between regulatory agencies. So it is, especially when something is new.

Hm, both of these items involve work from Scotland, and they were sent to me by the only person here (I think -- ??) with a degree from a Scottish university. Thanks!

There is more on stem cells on my page Biotechnology in the News (BITN) - Cloning and stem cells.



Can you run an airline?

January 11, 2009

Can you run an airline?

A reader sent this to me. I take no responsibility for it, but merely pass it along.

Caution, some is quite technical.

Any comments will be forwarded to the perpetrator.

More about airplanes... How to board an airplane (September 16, 2011).



Older items are on the page Musings: archive for 2008.


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