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Musings: 2009 (archive)

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

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   Introduction (separate page).
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2009
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2012:    January-April    May-August    September-December
2011:    January-April    May-August    September-December
2010:    January-June    July-December
2009: this page, see detail above.
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 octopus and the coconut

December 28, 2009

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. (BBC, 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: Movie 1. Or, on the article web page, check the menu bar at the left; scroll down to "Extra".

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).

Among other posts on octopuses...
* Sleep stages in octopuses -- do they dream? (July 13, 2021). Added November 18, 2024. Includes an extensive list of posts about octopuses and other cephalopods.
* 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).

A book, listed on my page of Books: Suggestions for general science reading. Sy Montgomery, The Soul of an Octopus -- A surprising exploration into the wonder of consciousness (2015).

More coconut... What's the connection: blue cheese, rotten coconuts, and the odorous house ant? (August 24, 2015).

December 21, 2009

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.

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! (J M Waldock, Western Australian Museum, 2007. Now archived.) 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 [link opens in new window]. 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 [link opens in new window]. 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.) Check Google Scholar for a freely available copy.

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).

Among many spider posts... The spider with the mostest ... (and such) (January 2, 2018).

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, September 8, 2009.)

More on electrical conductivity: What's the connection: rotten eggs and high-temperature superconductivity? (June 8, 2015).

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

How molecules walk: a movie

December 15, 2009

Go to the website for Ron Vale's lab -- movies, and click on the movie: 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. Explore!

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

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.

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

Also see:
* Does the appendix affect the development of Parkinson's disease? (December 11, 2018).
* Re-introducing captive animals into the wild: an orang-utan mix-up (June 27, 2016).
* Is Arthromitus a key bug in your gut? (January 16, 2010)

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 (December 15, 2009) 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.

More about eating pig: Why you should not eat larb: A story of trichinellosis -- locally (March 11, 2018).

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. (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...
* Habitable planets very close to a star (June 19, 2016).
* Exoplanet Travel Bureau (February 21, 2015).
* A post about the Kepler mission -- a large-scale search for extrasolar planets... The Kepler Orrery (June 3, 2011).
* The first truly habitable exoplanet? (October 12, 2010).
* Atmosphere suggests planet might harbor life (August 30, 2010).

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. (Science Daily, 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 on Borneo (September 24, 2011)

More basidiomycetes:
* An antidote to the mushroom toxin α-amanitin (June 12, 2023).
* Are yeasts important partners in lichens? (September 12, 2016). Mushrooms are the best known basidiomycetes.

More bioluminescence: Xystocheir bistipita is really a Motyxia: significance for understanding bioluminescence (May 9, 2015).

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

More Mozart:
* Treating epilepsy with Mozart (December 4, 2021).
* There is Mozart in the air -- encoded in orbital angular momentum (April 25, 2015).

There is a section of my page Internet resources: Chemistry - Miscellaneous on Chemiluminescence.

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

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.

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.)

More about adaptation: Robots that can quickly adapt to disabilities (June 23, 2015).

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 news story: Two-Thirds of Chicken Tested Harbor Dangerous Bacteria. (N Starkman, Civil Eats, November 30, 2009.) (This is a replacement news story; the one originally posted is no longer available. June 2019.)
* 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).
* Salmonella and food contamination; the biofilm problem (April 28, 2014).
* Tracking food poisoning through online reviews (July 7, 2014).
* Campylobacter -- how do the chickens feel? (September 6, 2014).
* The cost of food poisoning (October 14, 2014).
* Fugu poisoning incident in the United States (January 5, 2015).
* Food poisoning outbreak: Listeria infections from caramel apples and fresh apples (January 14, 2015).
* Is the lychee (litchi) a toxic food? (May 11, 2015).
* Using a plasma to kill norovirus (June 5, 2015).
* What do chimpanzees think about cooking food? (August 30, 2015).
* Chefs' preferences can lead to food poisoning (June 28, 2016).
* An organoid for the gut: at last, a culture system for norovirus (October 30, 2016).
* Disease outbreak from pasteurized milk (March 5, 2019).

My page Internet resources: Biology - Miscellaneous contains a section on Nutrition; Food safety. It links to related Musings posts. There is overlap between the lists of posts there and here, with no clear distinction between what the two lists cover.

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.)

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).

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? (National Geographic, 11/12/09. Now archived.)

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.

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 (October 27, 2009). 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. (November 6, 2009.)

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.

November 23, 2009

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. [Each link opens in new window.]

#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).

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).

More on the same gene, and other eating-related genes, in diverse humans: Genes that make us human: genes that affect what we eat (February 18, 2015).

Other posts about Neandertals include...
* Contributions of Neandertals and Denisovans to the genomes of modern humans (July 6, 2016).
* Did Neandertals use cosmetics? (January 24, 2010).

Also see:
* Measuring development of humor in children (October 4, 2022).
* 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.

November 18, 2009

Bichon frise

November 17, 2009

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 (October 22, 2008). 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).

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).

My page for Biotechnology in the News (BITN) -- Other topics includes a section on Ethical and social issues; the nature of science.

The smallest violin

November 16, 2009
(with follow-up)

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. It includes a list of related Musings posts.

What to eat

November 13, 2009

Our nutritionists feed us the following item: Vegetarian Diets Can Help Prevent Chronic Diseases, American Dietetic Association Says. (Science Daily, July 3, 2009.) (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 article: Position of the American Dietetic Association: Vegetarian Diets. (J Am Diet Assoc. 109:1266, July 2009.) I think it is freely available there.

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

Also see...
* Vegan diet increases risk of broken bones (January 9, 2021).
* Red meat and heart disease: carnitine, your gut bacteria, and TMAO (May 21, 2013).

November 11, 2009

A new source of electricity

November 10, 2009

Joe sends Does Energy Grow on Trees? (November 2009; now archived.) 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, January 2010.) You may be able to get a copy by putting the article title into Google Scholar. 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.
The figure at the right is Figure 1 from the paper.

One reader 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).

* * * * *

More about MFC: A robot that can feed itself (February 3, 2017).

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.

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.

November 4, 2009

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).

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.

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).

* * * * *

Video: The Voyager Journey To Interstellar Space; talk by Ed Stone. (50 minutes.) (Physics Department, University of California Berkeley, March 3, 2014.)

A search using Google Videos for the video name reveals other talks by Stone, including at least one, a little more recent, with the same name. I encourage you to check out a recent Ed Stone talk, even if it is not the one I listed above.

Explore!

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 (September 1, 2009). 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, 2009

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. Check Google Scholar for a freely available copy.) 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.

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 started 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. However, I have not maintained it as complete, due to the complexity and breadth of the topic. OLDEST FIRST...
* 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).
* Are there genetic issues that we don't want to know about? (October 22, 2013).
* The emerging role for genome sequencing of sick babies (October 27, 2014).
* The genetics of being a "morning person"? (April 15, 2016).
* What if zebrafish could get human cancer? (October 25, 2017).
* Distinguishing pathogenic and benign BRCA1 mutants: a high-throughput test (January 26, 2019).
* Project Baby Bear: Is it worthwhile to sequence the genomes of babies with mysterious ailments? (October 18, 2021).

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".

My page for Biotechnology in the News (BITN) -- Other topics includes a section on Ethical and social issues; the nature of science.

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.

October 21, 2009

The vegetarian spider

October 21, 2009

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).

Among many posts about spiders:
* The spider with the mostest ... (and such) (January 2, 2018).
* 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 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).

Using music to control a machine

October 17, 2009

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. (July 22, 2009.) 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, August 4, 2009.) 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.

More lab chips... Multi-organ lab "chips" (April 14, 2018).

More droplets: What determines the size of liquid droplets from a sprayer? (September 21, 2018).

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

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.

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.

Follow-up: Briefly noted... Lakes that explode -- II (October 13, 2021).

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

More on high pressures:
* What happens when the cork is removed from a bottle of champagne? (October 27, 2019).
* Novel forms of sodium chloride, such as NaCl₃ (January 17, 2014).

More from Cameroon: Using your phone to find Loa loa (August 14, 2015).

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

Among other posts on cows...
* Should we make antibodies to HIV in cows? (November 14, 2017).
* Polled cattle -- by gene editing (July 8, 2016).

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.

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).

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

A solar prominence

October 12, 2009

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.) Check Google Scholar for a freely available copy of the article, from the author.

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 (December 16, 2008).

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).

More about optical fibers: A novel type of optical fiber (November 8, 2014).

More about inventions...
* Zhemchuzhnikovite: a natural MOF (August 19, 2016).
* National Inventors Hall of Fame: 2014 inductees (March 11, 2014).

* Previous post that featured a Nobel in the title: Nobel prizes (October 8, 2008).
* Next: Nobel Peace Prize (October 25, 2009).

elgooG

October 12, 2009

!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".

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

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.

* * * * *

A major follow-up story: Early detection of brain damage in football players? A breakthrough, or not? (September 14, 2015).

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

There is now an extensive list of sports-related Musings posts on my page Internet resources: Miscellaneous under Sports. Added August 14, 2024.

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

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. (Now archived.)
* 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. (September 22, 2009.)

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).

* * * * *

More from GRACE about groundwater:
* Evaluating the world's water resources (August 11, 2015).
* Groundwater depletion in the Colorado River Basin (October 3, 2014).

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

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

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

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. (Now archived. Berg died in 2021.)

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.

Prosthetic arms, prosthetic head ...

September 26, 2009

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, August 27, 2009; it is freely available.) 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.

Other posts on robotics include:
* Creepazoids and the Uncanny Valley (May 15, 2016).
* 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)

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.

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. (Science Daily, 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.

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.
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. (August 21, 2009)
* 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, August 20, 2009. And yeah, that first author really has four initials; he is Dutch.)
* The article: The ethylene response factors SNORKEL1 and SNORKEL2 allow rice to adapt to deep water. (Y Hattori et al, Nature 460:1026, August 20, 2009.)

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

More about rice...
* How rice leads to global warming, and what we might do about it (September 2, 2015).
* How rice recognizes a Xoo infection (August 28, 2015).
* 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).

One way trip to Mars

September 22, 2009

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

More about astronauts and space travel: Which direction does blood flow in an astronaut? (January 7, 2020).

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

Seeing molecules under a microscope

September 19, 2009

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.

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.

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).

More about Banff wildlife... Trains, grains, and bears (May 24, 2017).

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

September 16, 2009

Prosthetic arms

September 16, 2009

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, which is from the company. The movie (about 2 minutes) is now at: Airic's_arm movie (YouTube). There is more information at: Airic's_arm -- Robot arm with Fluidic Muscles (Now archived from the company site; the movie is no longer there.)

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. (Now archived.)

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).
* Making better artificial muscles (March 13, 2018).

More about prosthetic arms:
* An artificial hand that can tell if a tomato is ripe (January 3, 2017).
* 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.

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?

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

Also see: A primitive cyanobacterium (October 25, 2021).

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? (September 9, 2009). 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

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...
* Zero? Do bees understand? (July 20, 2018).
* Bumblebees play ball (March 20, 2017).
* Why are the bees dying? (January 26, 2010).
* Bees -- around you (June 11, 2009).

More insect warfare...
* Bee wars (March 1, 2015).
* 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).

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.) Original link: http://www.nugo.org/nutrialerts/40368; Fat Taxes on Junk Foods (August 23, 2009).

Updated, October 4, 2015... The site given above is no longer available; I do not know what "the full report" refers to. As a substitute, I offer the Wikipedia page on the topic. It can't fill the role of the original item, but does offer an overview of the topic, and is maintained with current information. News story: Wikipedia: Fat tax.

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 two replies received in follow-up, see the supplementary page: Fat tax page.

Some results: The Berkeley soda tax: does a "fat tax" work? (August 30, 2016).

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

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.)

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

More extreme biology from the Andes: What if a hummingbird's body temperature dropped to below 10 °C on a cold night? (September 29, 2020).

More on biodiversity... On restoring ecosystems: priorities? (December 5, 2020).

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. (NPR, 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 from the same lab: Jamming of bat sonar, by bats (January 20, 2015).

More about moths and bats: Would moth wings make good sound absorbers? (July 19, 2022).

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

and... Which came first: butterflies or flowers? (March 9, 2018).

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

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

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. (July 10, 2009; now archived.)
* 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, July 2, 2009.)

Related Musings items include...
* Humans may be more like salamanders than we had thought (limb regeneration) (February 11, 2020).
* 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.

Tarsier; eukaryotic cells

August 31, 2009

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:
* Origin of eukaryotic cells: a new hypothesis (February 24, 2015).
* Are there really three domains of life? (January 12, 2013).

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

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

More about big eyes: The ogre-faced spider, with massive eyes but no ears, detects the sound of prey using its legs (February 9, 2021).

Also see: Monogamy (January 30, 2013).

August 28, 2009

On collecting opinions

August 28, 2009

An item on animal behavior: On collecting opinions [link opens in new window].

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 Science Books Prize.

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).

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. (New Scientist, July 21, 2009.) Note the link to "1 more image"; that is the original view.

Recall recent post Collision of Earth and Mars (July 8, 2009). 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 (September 9, 2009)).

The next collision with Jupiter... Jupiter injured again! (June 11, 2010).

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).

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

Also see: Do apes have a "theory of mind"? (February 19, 2017).

A book about animal behavior is listed on my page Books: Suggestions for general science reading. de Waal, Are we smart enough to know how smart animals are? (2016). The author is one of the essayists listed above.

Also on that page of Book suggestions are some books on the mind. Among them are books by Gazzaniga and by Searle. More from Gazzaniga... Split brains and yellow submarines (January 9, 2012).

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.

R. U. R. is freely available from Project Gutenberg, in the original Czech and in English translation:
* R. U. R. in English.
* R. U. R. in Czech.

Wikipedia provides some basic background on R. U. R.: Wikipedia: R. U. R..

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.

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.

Element #112: Copernicium

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

In June: Element #112 is officially recognized. New Chemical Element In The Periodic Table. (Science Daily (GSI), June 12, 2009.)

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". ChemEurope (GSI), July 15, 2009.)

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.

More about copernicium: Is copernicium noble? (January 3, 2020).

A Musings post on the discovery of: Chemical element #117 (April 13, 2010).

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

A novel sensor for infectious viruses, using nanopores lined with aptamers (November 6, 2021). More from GSI. What else can one do with Schwerionen?

July 13, 2009

A new electric car

July 11, 2009

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

The archived copy of that story may come up without the figure. Here is the figure: the car [link opens in new window].

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).

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.

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.

See update in next paragraph. http://www.nugo.org/nutrialerts/40276. 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.

Updated November 30, 2015. The Nutrialerts item listed above is no longer available. Here is the New York Times article referred to: Grant System Leads Cancer Researchers to Play It Safe. (G Kolata, New York Times, June 27, 2009)

July 6, 2009

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).

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

More about cheating: Are bankers fundamentally dishonest? (January 23, 2015).

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.

A new flute -- 35,000 years old

July 1, 2009

Jessica sends: Flutes Offer Clues to Stone-Age Music. (New York Times, 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.) Check Google Scholar for a copy. 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 page Internet resources: Miscellaneous under: Art & Music: 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.) Check Google Scholar for a copy.
* I have added this new item to that section.

June 29, 2009

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.

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).

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).

Another example of catalyst development... A simpler way to make styrene (July 10, 2015).

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.

June 22, 2009

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.

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).

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

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.
7. Topspin Medical Announces First Commercial Installation of the Cathamaran Intravascular MRI System. (January 29, 2008.) (This item replaces one that is no longer available.)

Also see: The role of mutation in heart disease? (April 25, 2017).

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:
* US Presidential candidates weigh in on science questions (October 18, 2016).
* The role of a government science adviser (April 22, 2014).
* 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.

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." (Berkeleyan, 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 city bees... The advantage of living in the city (July 27, 2018).

More on bees...
* What if there weren't enough bees to pollinate the crops? (March 27, 2017).
* Origin of gas warfare (September 11, 2009).

June 8, 2009

Fish story

June 4, 2009

Worm picture: Worm [link opens in new window].

For more on this, see Fish story page.

June 1, 2009

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.

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!

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?

May 25, 2009

I think I created life

May 21, 2009

One reader 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 [link opens in new window].

Someone has identified this as a software bug.

I welcome attempts to reproduce this and improve on it.

Also see: The origin of life's chemicals: making an almost-Krebs-cycle in the lab (June 10, 2019).

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.

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

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).

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. (New York Times, April 27, 2009.)
* Palaeoanthropology - Homo floresiensis from head to toe. (Nature 459:41, May 7, 2009.) 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...
* The modern pygmies of Flores Island (November 6, 2018). Discusses implication for the hobbits.
* Evidence for early Homo floresiensis (July 5, 2016).
* Homo floresiensis -- revised dating of the original "hobbit" site (June 25, 2016).
* The "hobbits": dentition suggests they were a distinct, dwarfed human species (November 30, 2015).
* Hobbits: Is the answer "Down syndrome"? (December 12, 2014).
* The Hobbits: a dissent (August 15, 2011).
* Hobbit DNA? (May 28, 2010).
* Hobbits: an update (May 1, 2010).

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.

More from Indonesia: Is Harry Potter responsible for the increased owl trade in Indonesia? (August 6, 2017).

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

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.

Language development

May 7, 2009

This may be of particular interest to those of you who deal with Slavic languages.

Language development [link opens in new window].

Swine flu

May 2, 2009

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

April 2009

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.

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)

Science: virus-battery

April 15, 2009

Hot story!

A reader sent this to me: Viruses Used to Grow "Greener" Batteries. (National Geographic, April 3, 2009. Now archived.)

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. (MIT, 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).

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. (November 8, 2008.)
* Look! It's a near-Earth asteroid! (Emily Lakdawalla, Planetary Society, March 26, 2009.) 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, March 26, 2009.)

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.

More about this asteroid: Another Solar System planet -- revealed by its diamonds? (May 22, 2018).

March 2009

Science: Love songs

March 26, 2009

What did you expect... Music: love songs ???

* For Mating Mosquitoes, 'Harmonic Convergence'. (New York Times, January 9, 2009.)
* 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... Could we repel mosquitoes by playing loud music they don't like? (May 18, 2019).

Also see:
* A mosquito-like robot (August 18, 2020).
* Introducing Supersonus -- it stridulates at 150,000 Hz (June 16, 2014).
* Dengue fever -- Two strikes and you're out (August 10, 2010).
* Mosquitoes that can't fly (May 3, 2010).

More on dengue is on my page Biotechnology in the News (BITN) -- Other topics under Dengue virus (and miscellaneous flaviviruses). It includes a list of related Musings posts.

Mini dinosaurs

March 19, 2009

News story: Big surprises come in small dinosaur packages. (University of Alberta, March 20, 2009.) Original link: http://folio.ualberta.ca/en/Archive/Volume%2046/Issue%2014/Big%20surprises%20come%20in%20small%20dinosaur%20packages.aspx. The item is no longer available, and I do not have a replacement news story.

The article, now freely available, 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).

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. 43:2072, 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).

Another life cycle analysis: Effect of food crops on the environment (November 20, 2015).

There is more about energy on my page of Internet Resources for Organic and Biochemistry - Energy resources.

February 2009

Happy 1234567890!!

February 13, 2009

From a reader...

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!! :)

January 2009

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: The Immortal Molecule: Scripps Research Scientists Develop First Examples of RNA that Replicates Itself Indefinitely Without Any Help from Biology. (January 8, 2009.)

The article: Self-Sustained Replication of an RNA Enzyme. (T A Lincoln & G F Joyce, Science 323:1229, 2/27/09.) Caution... The paper is fairly technical, but you can get the main ideas from browsing the first page or so.

Can you run an airline?

January 11, 2009

Can you run an airline? (Now archived.)

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).

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