Using your brain waves to log on to the computer

April 29, 2013

A news story about this work reminded me of a recent post, in which brain waves were sent from one animal to another [link at the end]. The news story is based on a talk given recently by Chuang's group. Even though the information available is limited, it seemed of interest to briefly note this new work.

Of course, it isn't the idea here that is novel, but the implementation. There are a couple of main themes in this work:

1) One is that they use an inexpensive commercially available device to collect brain waves. It is a single channel electroencephalogram (EEG) device, with a sensor worn on the forehead, as shown in the picture above. The signal -- the brain waves from the person trying to log on -- is compared to what the person has previously recorded; in a sense, it is just like a regular password system, but what is checked is what the person thinks, not what the person types.

This device is much simpler than the complex EEG sensors used when the goal is to assist people with disabilities. In the current work, the goal is relatively simple: they need only associate the brain waves with the individual. When brain waves are being used to perform tasks, a more refined signal is needed.

In fact, one of their conclusions is that they now get results with the simple EEG that are as good as previous results with the more complex "clinical" EEGs.

2) The other theme is what we might call consumer acceptance. Much of the talk is about what kinds of mental tasks people might find appropriate for this computer operation. They find that people vary in what they consider easy or boring. Their general conclusion is that it is probably best to allow users to select their own type of task.

Does it work? With their best system, they get an error rate of about 1% -- mostly due to false rejection of the proper user (rather than to acceptance of an improper user). As noted, an important point for them is that they achieve this with a simple device. They do not claim it is ready for real world use, but rather that it is worth studying further.

News stories:
* New Research: Computers That Can Identify You by Your Thoughts. (UC Berkeley School of Information, April 3, 2013.) Good overview.
* Thoughts could be future of security. (Daily Cal (UC Berkeley student newspaper), April 10, 2013. Now archived.) A more informal overview.

Chuang's group gave a talk about this work recently at a meeting; here is the paper they presented. It is freely available; the link here is to a copy from the authors: I Think, Therefore I Am: Usability and Security of Authentication Using Brainwaves. (J Chuang et al, 2013 Workshop on Usable Security, Seventeenth International Conference on Financial Cryptography and Data Security, April 2013.) Remember, this is a meeting talk, not a published paper. We note it here briefly as fun and interesting -- and potentially useful. And it is, for the most part, a quite readable paper. Formal publication of a peer-reviewed paper will presumably follow at some point.

Background post: Can one rat know what another rat is thinking? (April 8, 2013). A brain signal is sent from one rat to another; the receiving rat acts on the signal.

Examples of the use of brain-computer interface to assist the disabled.
* Brain-computer interface -- without invasive electrodes (December 28, 2016).
* Brain-computer interface: Paralyzed patients control robotic arm by their thoughts (June 16, 2012).

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

More about computer security:
* Computer security: web-based password managers (September 29, 2014).
* Can computers talk to each other? Could it be a new type of security threat? (June 18, 2014).

Hard seeds or soft seeds?

April 26, 2013

Interesting little story. Some plants make hard seeds, some make soft seeds; some make both kinds. Why?

The common view has been that seed hardness provides a physical basis for dormancy, promoting the lifetime of the seeds. A new article suggests another advantage of hard seeds: they may be less attractive to animals -- because they give off less of the odor molecules that attract the predators.

Their experimental approach is simple and fun. The scientists provide hamsters with an array of little dishes filled with various little things... soft seeds, hard seeds, and gravel. (In a given test, the hard and soft seeds are from the same type of plant.) They measure what the hamsters find.

In some experiments, the hamsters could see the seeds. In that case, hard vs soft made little difference. However, in some experiments, the seeds were under the gravel, and could be detected only by odor. In that case, the hamsters removed many more soft seeds than hard ones.

The simple conclusion, then, is that hard seeds are harder for the hamsters to detect by odor. That is, the hard seed is an anti-predator trait.

The authors speculate about the importance of various reasons for the seed types, but there is not much to go on. One particularly interesting speculation is about why a plant might make both hard and soft seeds. The soft seeds attract animals, and the hard ones may go straight through the digestive system. Thus the mixture serves to promote dispersal of the seeds.

A bit more explanation... A key feature of "hard" seeds is that they are impermeable to water. They do not easily germinate -- and start to metabolize -- when exposed to water. Thus the general feature of impermeability, which promotes dormancy, also reduces release of the volatiles that the hamsters detect, probably by preventing their production by metabolism. The key experiments, in which odor detection was important, used seeds that were not only buried but also wetted, to promote metabolism.

News story: Physical dormancy in seeds: a game of hide and seek? (New Phytologist Trust, March 8, 2013.) A useful brief overview.

The article: Physical dormancy in seeds: a game of hide and seek? (T R Paulsen et al, New Phytologist 198:496, April 2013.)

More about seeds: Miniature helicopters -- and botany (July 6, 2009).

More about detecting food by odor:
* Malaria-infected mosquitoes have greater attraction for people (May 28, 2013).
* What happens if you block the left nostril of a mole's nose? (April 19, 2013).

More, May 7, 2013... Comment. A reader questioned a word usage in this post. Is it proper to use the term predator to describe an animal that eats seeds? I had wondered, too, but gone along with the usage by the authors of the paper. Turns out that seed predation is a well-accepted usage; put the term in a search engine or Wikipedia, if you want.

Life in an Antarctic lake

April 22, 2013

Briefly noted...

Lake Vida is a lake in Antarctica. It is covered with ice, and has probably been isolated from external input for nearly 3,000 years. We would consider the conditions in Lake Vida to be rather extreme. The temperature is about -13 °C, and it is quite salty but devoid of oxygen. In a recent article, a team of scientists report that Lake Vida is teeming with life -- microbes.

Exploring the sub-surface lakes of Antarctica is a new and active field. It's also a difficult and controversial field. The idea is to isolate water from these underground lakes -- without contaminating them with anything from the outside world. It involves drilling a hole -- while maintaining absolute biological sterility. And doing it under some of the most inhospitable conditions on Earth.

In recent weeks there have been news stories about possible isolation of novel microbes from an Antarctic lake thought to be isolated for millions of years. The initial news report was followed by denials, and counter-denials. Unfortunately, at this point there are no real facts on that story.

The current article is a small step in the study of Antarctica's underground lakes: a published paper about a younger lake. It opens the subject of finding microbial life in such lakes. Published papers do not always turn out to be right, but at least a formal publication gives us something solid to look at.

The article is largely a description of what they found, both for chemicals and microbes. As examples... The lake water contains 20% salt. It is supersaturated with N₂O (nitrous oxide, laughing gas). There is a diverse collection of microbes (about 32 species across eight phyla, based on analyzing DNA), at around 10⁶/mL. It is presumed that the energy source for the microbes is inorganic chemicals, deriving from the rocks in contact with the lake.

News story: Hearty Organisms Discovered in Bitter-Cold Antarctic Brine. (Science Daily, November 26, 2012.) (One might guess that the first word of the title should be "hardy". The "error" apparently derives from a press release from one of the lead institutions involved in the work.) A useful overview.

The article, which is freely available: Microbial life at -13 °C in the brine of an ice-sealed Antarctic lake. (A E Murray et al, PNAS 109:20626, December 11, 2012.)

More from Antarctica:
* What do microbes eat when there is nothing to eat in Antarctica? (April 2, 2018).
* A quasi-quiz: The fate of bone and wood on the Antarctic seafloor -- and the discovery of new bone-eating worms (August 20, 2013).
* How were the Gamburtsevs formed? (December 7, 2011).
* How an octopus adapts to the cold -- by RNA editing (March 5, 2012).

Underground water on Mars? ... A lake on Mars? (August 24, 2018).

What happens if you block the left nostril of a mole's nose?

April 19, 2013

It veers to the right.

Humans have two ears, spaced some distance apart. Each ear sends a signal to the brain, which then integrates the two signals to obtain information about the direction and distance of the sound source. This is an example of stereo sensing.

Little is known about smelling in stereo. A new article shows that one animal seems to be able naturally to smell in stereo. It is the mole, shown above. This little burrower depends on smell as its primary sense for finding food.

The work began by noticing that the moles shifted their head back and forth while sniffing out a food source. This suggests that they are processing repeated sniffs to gain information about the source. This observation led a scientist to set up controlled conditions for studying how the moles respond to odor cues. The testing included tests not only for serial sniffing but for stereo sniffing: integration of the distinct information from the two nostrils.

A key piece of evidence came from experiments of the type noted in the title of this post. Here is an example of what they found in such a blocked-nostril test with one particular mole.

The overall observation is that blocking one nostril causes the mole to veer to the other side -- toward the side of its open nostril. This result suggests that the mole is using the information from the two nostrils separately to determine the location of the food reward.

News stories:
* Moles Smell in Stereo to Find Food, Dodge Predators. (National Geographic, February 5, 2013. Now archived.)
* Evidence Moles Can Smell in Stereo. (Science Daily, February 5, 2013.)

The article, which is freely available: Stereo and serial sniffing guide navigation to an odour source in a mammal. (K C Catania, Nature Communications, 4:1441, February 5, 2013.)

More about moles: The basis of intersexuality in moles (November 28, 2020).

Other posts about smelling include:
* Copper ions in your nose: a key to smelling sulfur compounds (October 10, 2016).
* What does blue light smell like? (July 18, 2010).
* How do you tell if bees are pessimistic? (August 5, 2011).
* Hard seeds or soft seeds? (April 26, 2013).

Infant cured of HIV?

April 15, 2013

It was a big news story in the popular media last month: an infant apparently cured of HIV. It is a potentially important story, so let's look at it. A big caution... It is also an incomplete story. At this point, what we have is a report at a meeting; no scientific paper has been published. If we take the basic facts presented at the meeting as correct, we must remember that this is one case. We think we know what happened, but cannot be sure. The only way to know whether the result holds more broadly is to test it more broadly. It is an exciting enough result that such testing will undoubtedly be done.

Here is the basic story... A child was born to an HIV-infected mother, who had received no treatment. The child was put on HIV-therapy 30 hours after birth -- even before test results were available; the testing showed that the child was indeed positive for the virus. Treatment continued for 18 months, but was stopped. The child has been off therapy for about a year, and appears to be free of HIV. Thus, if we accept the test results showing that the child was indeed infected and is no longer infected, this seems to be a "cure".

What's novel here? Normally, withdrawing treatment of an HIV-infected person leads to a rebound of the virus. The implication is that the virus is "hiding" in the body, in some latent form not susceptible to the ordinary treatment. Treatment works fine, but relax the treatment and the virus rebounds. In the new case, the treatment was relaxed, and no rebound occurred. One possible interpretation is that the treatment began so early after infection that the virus never established its latent or hidden infection. That would be an exciting point, if it really holds.

As we noted at the outset, neither the facts nor the implications are entirely clear. This is a case report, not a controlled experiment. Was the child truly infected? Is it indeed disease-free, or at least virus-free?

If the story is correct as presented, we do not know for sure why it worked here. Perhaps this child was, for some reason, a special case. Nevertheless, we learn from single reports; we at least ask good questions. In this case, the implication is that we should treat immediately after exposure. This might apply to babies born to mothers who were infected but untreated. However, the number of such cases is small in the developed world, and acting on this in the developing world will be challenging.

News stories:
* Toddler 'functionally cured' of HIV infection, NIH-supported investigators report. (NIH, March 4, 2013.) From a funding source.
* Doctors Cure Baby Born With HIV For First Time. (Medical News Today, March 4, 2013.)
* In Medical First, a Baby With H.I.V. Is Deemed Cured. (New York Times, March 3, 2013.) If you read this, try to read it through to the end. Some things are a bit mixed up along the way.

Here is the abstract of the presentation given at the meeting: Functional HIV Cure after Very Early ART of an Infected Infant. (D Persaud et al, 20th Conference on Retroviruses and Opportunistic Infections, March 4, 2013. Now archived.)

More July 21, 2014 (1)...

Here is the article that was later published about that initial report: Absence of Detectable HIV-1 Viremia after Treatment Cessation in an Infant. (D Persaud et al, New England Journal of Medicine 369:1828, November 7, 2013.) Check Google Scholar for an available copy, including an author manuscript at PubMed Central.

More July 21, 2014 (2)...

The follow-up news is not good. Now, a year later, the child is clearly infected.

We had limited information at the time of the initial post, and we have even less at this point on the update. Nevertheless, we should note the setback.

News story: HIV Returns in "Cured" Child -- A Mississippi girl who was thought to have been "functionally cured" of HIV as an infant once again harbors detectable levels of the virus. (The Scientist, July 11, 2014.)

* Previous post on HIV... A simpler assay for detecting low levels of HIV, using gold nanoparticles (January 3, 2013).
* Next... How HIV destroys the immune system (March 3, 2014).

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

Caffeine boosts memory -- in bees

April 12, 2013

Who would try feeding caffeine to bees? Coffee plants. (And some citrus plants.) The nectar of coffee flowers contains caffeine -- just a little, not enough to taste too bitter. Perhaps enough to make the bees come back.

A new article looks at how bees respond to caffeine. The basic experimental design is familiar. Bees are offered choices. A scent leads to a reward -- of sugar. The question is whether the bees learn to associate the scent with the reward. In this case, one variable was the level of caffeine.

The following graph shows how the bees responded.

We see, then, that caffeine can enhance the ability of bees to remember what they learned, and that the level of caffeine required is about what is found in the nectar of some flowers. Thus the scientists suggest that what they studied here, under lab conditions, is likely to be relevant "in the field". They suggest that the plant benefits from providing some caffeine in its nectar, by getting more pollination. It's already known that caffeine at high levels is an insect repellent; finding a beneficial effect of low caffeine would be an interesting development. The results here are consistent with that, but certainly not sufficient. For example... Would it be possible to do field studies and show that increased caffeine leads to more pollination?

News stories:
* Bees Get a Buzz from Flower Nectar Containing Caffeine. (Science Daily, March 7, 2013.)
* Coffee and Citrus Plants Boost Bee Memory With Caffeine. (C Wilcox, Science Sushi (Discover blog), March 7, 2013.)

* News story accompanying the article: Neuroscience: Caffeine Boosts Bees' Memories -- Caffeine in floral nectar enhances the memory of bees for the flowers' scent by altering response properties of neurons in the bee brain. (L Chittka & F Peng, Science 339:1157, March 8, 2013.)
* The article: Caffeine in Floral Nectar Enhances a Pollinator's Memory of Reward. (G A Wright et al, Science 339:1202, March 8, 2013.)

For more about caffeine...
* Chocolate: 1200 years old (February 18, 2013).
* Your desire for caffeine: It may be in your genes (May 31, 2011).

More on bees:
* What should a plant do if it hears bees coming? (December 10, 2019).
* Bees and flowers: A 30-volt story (June 21, 2013).
* Novelty-seeking behavior (May 26, 2012).
* The traveling bumblebee problem (January 11, 2011).

More about pollination:
* What if there weren't enough bees to pollinate the crops? (March 27, 2017).
* A "flower" that bites -- and eats -- its pollinator (December 27, 2013).

More about memory: Near-death experiences: are the memories real? (August 11, 2013).

Also see: Why some citrus fruits are so sour (April 22, 2019).

Can one rat know what another rat is thinking?

April 8, 2013

Sure. Send the brain signal from one rat to the other.

A new article reports doing just that. We note it briefly...

A recent post showed that a rat could respond to an infrared (IR) sensor that was connected to its brain [link at end]. As a result, the rat gained the ability to respond to IR light, effectively adding a new sense to its sensory repertoire. The new work is from the same group of scientists; in some ways, the new work is similar to that reported in the earlier post. Each is a small step in a big field involving learning about brain signals.

The authors refer to the new work as establishing a brain-to-brain interface (BTBI). The general plan of an experiment is as follows... One rat is given a behavioral test, and makes a decision. Electrodes implanted in the brain of this rat transmit brain signals from this "encoder" rat. Those signals are then transmitted, in real time, to a "decoder" rat, whose actions are then observed. Both rats face the same situation; it turns out that the decoder rat does what the encoder rat had chosen -- with a significant probability.

In one test, just to emphasize the point, the scientists connected two rats on different continents. The encoder rat, making the original decision, was in Brazil; its brain signal was connected to a decoder rat in the United States, who acted on the decision made by the rat in Brazil. How did the signal get from one to the other? Via the Internet, of course. The decoder (receiver) rat did just fine at making use of the information.

This work has something of a "stunt" aspect, and some of the discussion of it includes hype about what might be done in the future. Ok, but the point is that this is all part of the big story of learning about brain signaling. In the IR post, rats learned to use the signal from an external electronic device. In the current post, brain signals are obtained from one rat and transmitted to another. In other work, we have already noted examples of humans benefiting from such applications, even though they are quite primitive at this time. As to developing computers based on such interconnected animals... Well, that illustrates a line of work the authors want to pursue. It's good that they are enthusiastic about their work. Let's see what they learn from it.

News stories:
* Intercontinental mind-meld unites two rats -- But critics are skeptical about predicted organic computer. (Nature News, February 28, 2013.)
* First direct brain-to-brain interface between two animals. (Kurzweil, March 1, 2013.)

The article, which is freely available: A Brain-to-Brain Interface for Real-Time Sharing of Sensorimotor Information. (M Pais-Vieira et al, Scientific Reports 3:1319, February 28, 2013.)

Movies. There are two movie files for this work. One shows a couple of test sequences. The second is an interview with the lab head about the work. You can find them at the lab web page: First brain-to-brain interface allows transmission of tactile and motor information between rats. (Nicolelis lab, Duke University.) (The first is also available with the article, at the journal web site.)

Background post: Can rats touch infrared light? (February 25, 2013). As noted, this work and the current work are from the same lab. This post includes links to other relevant Musings posts.

More...
* The brain-machine interface -- at the World Cup (July 2, 2014).
* Using your brain waves to log on to the computer (April 29, 2013).

And more... Computer scientist thinks; psychologist moves finger (September 24, 2013).

More about enhancing rat brain function... Can blind rats learn to use a geomagnetic compass? (June 29, 2015).

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

Thanks to Borislav for alerting me to this work.

Why the facial tumor of the Tasmanian devil is transmissible: a new clue

April 5, 2013

Briefly noted...

We previously noted the case of the facial tumor of the Tasmanian devil [link at the end]. An unusual feature of Devil facial tumor disease (DFTD) is that it is transmissible. The animals bite each other -- and transmit the cancer; the population of Tasmanian devils has become endangered.

Transmissible cancers are extremely rare, and not understood. Usually, the immune system serves as a barrier to cancer transmission to a new host, even of the same species. Obviously that barrier is not effective with DFTD. A new article offers some explanation of what is going on with this transmissible tumor.

Briefly, the scientists find that the tumor is failing to display tumor antigens, thus making the tumor invisible to a new host. That's different from what was expected, that the devil tumor might not have any distinctive tumor antigens. Further, they think that the failure to display the tumor antigens is not due to a mutation in the display system, but to some operational problem. It's there, but is turned off. In fact, in the lab they can get the tumor to display antigens that could be used to target it.

What are the implications? It's too early to know, but at least it represents a better understanding of a novel disease. Knowing a more specific cause of the problem allows work to proceed focusing on that specific cause. There are tumor antigens and maybe they can be expressed. Further, knowing that poor antigen display is a key issue raises some hope that a vaccine might be useful.

News story: Hope for Threatened Tasmanian Devils. (Science Daily, March 11, 2013.)

The article, which is freely available: Reversible epigenetic down-regulation of MHC molecules by devil facial tumour disease illustrates immune escape by a contagious cancer. (H V Siddle et al, PNAS 110:5103, March 26, 2013.)

Background post: The devil has cancer -- and it is contagious (June 6, 2011). Includes pictures.

An important follow-up: Immunization of devils: a treatment for a transmissible cancer? (April 24, 2017).

Another transmissible cancer? ... Is clam cancer contagious? (April 21, 2015).

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

More about epigenetic marks: A DNA test that can distinguish identical twins (July 17, 2015).

The benefit of providing alcohol to the eggs

March 30, 2013

Given a choice, fruit flies may choose to lay their eggs where there is a high concentration of alcohol (ethanol). Why? To protect their offspring from parasitic wasps, which would lay their eggs in the larval flies. The wasps cannot tolerate the alcohol. On the other hand, the flies, whose natural environment is fermented fruit, can tolerate alcohol.

Thus it is clear that the flies respond to the presence of the female wasps in a way that benefits the fly offspring. (The flies do not respond to male wasps -- just to the females, the ones that lay eggs in their offspring.) The authors consider this something of an immune response. More specifically, they call it a behavioral immune response, an interesting idea. They also refer to it as medication; the article title uses this terminology.

How do the flies know there is a female wasp around? The scientists do additional experiments in which they manipulate the sensory responses of the flies. Flies with their olfactory (smell) system disrupted respond normally in these tests. However, flies with their visual system disrupted fail to respond to the wasps. Thus the scientists conclude that the flies detect the wasps -- and distinguish male and female -- visually.

News stories:
* Fruit flies defend eggs using alcohol. (Naked Scientists, February 21, 2013.)
* Fruit flies medicate their larvae with alcohol. (Phys.org, February 22, 2013.)

The article: Fruit Flies Medicate Offspring After Seeing Parasites. (B Z Kacsoh et al, Science 339:947, February 22, 2013.)

More about parasitic wasps: Cockroach should be disinfected before eating it (February 12, 2013).

More on fruit flies:
* "Moonwalkers" -- flies that walk backwards (May 28, 2014).
* Making smarter flies (July 18, 2012).

How many moons hath Pluto? Follow-up

March 26, 2013

Original post: How many moons hath Pluto? (July 20, 2012). That post, less than a year ago, presented the newly discovered fifth moon of Pluto. Aside from the fun of discovery, knowing the moons of Pluto is important because we have a spacecraft on its way to Pluto; the success of the New Horizons mission depends on it not hitting the moons. We ended that post by wondering, at least implicitly, how many more, undiscovered, moons Pluto might have.

Here we have a new study with something of an answer to that question. Now, we need to be clear: they did not find anything; they did not even look. Rather, they ran computer simulations of how they think moon formation occurs around Pluto. The following figure summarizes one of their computer results.

That figure shows three more moons. But they don't know how many there might be. One estimate is that there might be ten more -- all too small to detect by current methodologies, but large enough to damage the New Horizons spacecraft. The message? New Horizons will have to fend for itself as it approaches Pluto, looking for unknown moons and adjusting its course as needed.

By the way, that disk around Pluto has never been seen either. It's for New Horizons to find and measure -- data that will feed back to the models of how the moons formed. That is, the computer simulations here and the upcoming observations by New Horizons will not only serve to protect the spacecraft, but also to enhance our understanding of moon formation.

The number of moons of Pluto is both fun and important. Stay tuned.

News story: The Many Moons of Pluto. (Astrobites, March 8, 2013.)

The article: The Formation of Pluto's Low Mass Satellites. (S J Kenyon & B C Bromley, Astronomical Journal 147:8, January 2014.) A copy of the manuscript, as accepted for publication, is freely available at the arXiv.

More about a dwarf planet: Ceres is leaking (February 18, 2014).

Bacteria on human teeth -- through the ages

March 24, 2013

What makes this interesting is that scientists were able to extract DNA from the decayed teeth. The calcified dental plaque seems to protect the bacterial DNA from being lost over time. They then identified the types of bacteria that were present. They did this for 34 early European skeletons, spanning several thousand years and various lifestyles. From their results, they concluded that the nature of the human oral microbiota -- the bacteria in our mouth -- changed at two key times in human history. One was the transition from hunter-gatherer to farmer, and the other was the industrial revolution. They further suggest that these changes were important for our understanding of modern oral disease.

It's interesting that they were able to do this. It is another testament to the revolution in sequencing DNA -- and in carefully handling ancient DNA. I think it's fair that the conclusions here should be taken as preliminary. In the big scheme of things, they have a small data set at this point, only 34 individuals. What is important is they have established the approach; more data -- a wider variety of samples -- is bound to come. We are just beginning a story of how the human oral microbiota has adapted to changing human lifestyles.

News stories:
* Calcified Bacteria Sheds Light on the Health Consequences of the Evolving Diet. (SciTech Daily, February 18, 2013.)
* Prehistoric Plaque and the Gentrification of Europe's Mouth. (E Yong, Not Exactly Rocket Science (National Geographic blog), February 17, 2013.) Now archived.

The article: Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions. (C J Adler et al, Nature Genetics 45:450, April 2013.)

A recent post on the gut microbiota: Malnutrition: is more (or better) food the answer? (March 8, 2013).

A recent post on the skin microbiota: A virus that could treat acne? (October 21, 2012)

For a broader perspective on our microbiota: Sharing microbes within the family: kids and dogs (May 14, 2013).

Added November 13, 2024. More from dental plaque: Division by 14: a new mode of bacterial growth (November 13, 2024).

More from the analysis of old DNA: Tracking the pathogen of the Irish potato blight (June 25, 2013).

More from the study of old teeth:
* How to eat if your jaw looks like a circular saw -- a follow-up (March 8, 2015).
* The case of the missing incisors: what does it mean? (September 13, 2013).

More about tooth decay:
* How the teeth are sensitive to cold (June 14, 2021).
* Is fluoride neurotoxic to the human fetus? (December 13, 2017).

Also see: It's a dog-eat-starch world (April 23, 2013).

There is more about genomes on my page Biotechnology in the News (BITN) - DNA and the genome. It includes an extensive list of Musings posts in the broad areas of genomes and sequencing.

The Obama lizard

March 20, 2013

About 65 million years ago the dinosaurs became extinct. The common view is that they were the victim of a major calamity, including the collision of an asteroid with Earth. It wasn't just the dinosaurs; a good fraction of species became extinct.

A new article examines the effect of this mass extinction event on snakes and lizards. These groups of reptiles had been thought to survive the extinction rather well. However, the new analysis suggests otherwise.

During the course of the work, the scientists discovered three (extinct) lizard species that had not been previously identified. They named one of them after the US President; it is shown above.

News story: Asteroid That Killed the Dinosaurs Also Wiped out the 'Obamadon'. (Science Daily, December 10, 2012.)

The article: Mass extinction of lizards and snakes at the Cretaceous-Paleogene boundary. (N R Longrich et al, PNAS 109: 21396, December 26, 2012.)

More about extinctions: The 6th mass extinction? (April 4, 2011). The 5th of those mass extinctions is the one discussed in the current post.

More about Obama: Quiz: Barack Obama and polar bears (July 20, 2011).

and then... The Trump moth (January 31, 2017).

More about dinosaurs:
* How the birds survived the extinction of the dinosaurs (June 6, 2014).
* The oldest dinosaur embryos, with evidence for rapid growth (May 7, 2013).
* Do animal bones have something like annual growth rings? (August 7, 2012).

More about lizards: An advanced placenta -- in Trachylepis ivensi (October 18, 2011).

The proton -- and a 40 attometer mystery

March 17, 2013

How big is a proton? It has actually been measured. Various methods have been used over the years, and an official value for the size of the proton is recognized. Now we have a new measurement -- actually a refinement and confirmation of one reported a few years back. The new measurement has created a new problem.

The new measurement was done by measuring the spectrum of muonic hydrogen. A muonic hydrogen atom is like a hydrogen atom -- but with a muon (instead of an electron) orbiting the single proton. The muon has the same charge as the electron, but is about 200 times heavier; the basic ideas of the structure and properties of an atom should hold for muonic hydrogen, but the numbers are different. Thus, measurement of the exotic muonic hydrogen offers a new approach to measuring the properties of the proton.

We might write an ordinary hydrogen atom as e^-p⁺, where e^- is an electron with charge -1 and p⁺ is a proton with charge +1. Then, a muonic hydrogen atom is µ^-p⁺; µ^- is a muon with charge -1.

The scientists measure the spectrum of muonic hydrogen: what wavelengths of light does it absorb? That measures the difference between certain energy levels in the atom, values that are sensitive to the positive charge nearby. Because the muon is much heavier than the electron, it is much closer to the nucleus, and more sensitive to the precise size of the proton. It's all very logical -- just incredibly demanding technically. Muonic hydrogen atoms don't last very long; the scientists have only a few microseconds to take their measurements for each muonic hydrogen atom they produce.

The following figure summarizes the measurements -- old and new -- of the size of the proton. (By "size of proton" here we mean a specific property, called the root mean square charge radius. It is, in simple terms, the size as measured by looking at the charge distribution in the proton.)

Thus we have a discrepancy. At this point, no one understands why. Is there some problem with one set of measurements -- a problem not taken into account in the error analyses so far? Is there some reason why a proton might actually have a different size when combined with a muon? All we can do now is to note the discrepancy and ask some questions. The paper itself ends with an extensive discussion of some of the possibilities. For now, we do not know the size of the proton (to within about 40 attometer). That means that our understanding of this particle, key to atoms and chemistry, is incomplete.

News story: Physicists confirm surprisingly small proton radius. (Phys.org, January 24, 2013.)

* News story accompanying the article: Physics: How Big Is the Proton? (H S Margolis, Science 339:405, January 25, 2013.)
* The article: Proton Structure from the Measurement of 2S-2P Transition Frequencies of Muonic Hydrogen. (A Antognini et al, Science 339:417, January 25, 2013.)

Those who have some chemistry might make a quick estimate of the size of the proton... Atoms are about 0.1 nanometers (1 Angstrom) across, and the nucleus is about 1/100,000 of the size of the atom. Do the arithmetic, and you will get an estimate for the size of a nucleus: about 1 femtometer. Of course, the smallest nucleus is simply a proton. That estimated value is indeed close to the values measured, as discussed above.

More from the atomic nucleus...
* Data on 31 isotopes of cadmium support a new model for the structure of atomic nuclei (December 1, 2018).
* Discovery of the neutron: 80th anniversary (February 27, 2012).
* Quark soup (August 15, 2011).

My page of Introductory Chemistry Internet resources includes a section on Nuclei; Isotopes; Atomic weights. It includes a list of related Musings posts.

Also see... What is the charge on atoms of anti-hydrogen? (July 15, 2014).

More muons... Using your smartphone to detect cosmic rays (April 7, 2015).

Thanks to Greg for helpful discussions of this post.

A novel type of polymer -- and its possible relevance to the origin of life

March 15, 2013

The three polymers that carry sequence information in our modern biological world are DNA, RNA, and protein. Among these, it seems likely that RNA is the oldest. Thus we can imagine some primitive stage in which RNA alone -- of those three -- was present, carrying out the roles of all three modern polymers. That stage is sometimes termed the RNA World.

So where did RNA come from? RNA is meaningful only in the polymer form, and it is not obvious how polymeric RNA might have formed originally. A new article offers a hint of how this might have happened. The scientists make small chemical subunits that have some features of RNA bases; importantly, they spontaneously "pair" and assemble into a polymer in aqueous solution.

That stacking is the key point. They show that it is possible for something like an RNA base pair to spontaneously stack into a polymeric form. And they understand why the stacking occurs: it is due to the hydrophobic interaction between the single units -- just as with modern nucleic acids.

How close is this to being RNA? We have already noted that they formed a 3-part structure, not a 2-part structure as in the modern base pair. But the individual parts are somewhat like the RNA bases, in that they include nitrogen-containing aromatic rings with hydrogen-bonding groups on the edges. In fact, one of the subunits has a pyrimidine ring, which is the core of two of the modern nucleic acid bases. Further, the polymers they get are quite long, as much as 18,000 units long -- long enough to reasonably call them gene-sized.

Thus they suggest that that they have revealed a possible pathway for how RNA-type polymers might have originally formed. Is this what really happened? We have no way to know, but it is interesting chemistry to demonstrate possibilities.

News stories:
* Molecules Assemble in Water, Hint at Origins of Life. (Science Daily, February 20, 2013.)
* Self-Assembling Molecules Offer New Clues on Life's Possible Origin. (Science Now, February 11, 2013.)

The article: Efficient Self-Assembly in Water of Long Noncovalent Polymers by Nucleobase Analogues. (B J Cafferty et al, Journal of the American Chemical Society (JACS) 135:2447, February 20, 2013.)

Other posts that may relate to the origin of RNA or, more broadly, to the origin of life include...
* An RNA replicator network (March 26, 2022).
* Another possibility for the origin of ribo- and deoxyribo- nucleosides (July 5, 2020).
* The magnesium dilemma: a step toward understanding how RNA might have been made in "protocells" (February 22, 2014).
* The origin of reactive phosphorus on Earth? (July 5, 2013).
* Did life start in a geothermal pond? (February 28, 2012).
* On the road to life? (May 18, 2009).

A good book on the origin of life is noted on my page Books: Suggestions for general science reading: Deamer, First Life (2011).

A post on the history of the Central Dogma, which ties together the roles of DNA, RNA and protein: Central Dogma of Molecular Biology (August 16, 2011).

There is a connection of this story to an unfortunate story of child poisoning a few years back. That story involved milk that had been contaminated with melamine. Investigation showed that the toxicity was due to a complex formed between melamine and cyanuric acid. The latter is the CA of the current work; melamine is very similar to the blue part of TAPAS. For more on that melamine story, see my page of Internet resources for Introduction to Organic and Biochemistry, in the section on Amines, amides.

Melamine toxicity: possible role of gut microbiota (April 21, 2013). More about that story of melamine toxicity.

More about self-assembly: Nanolympiadane: chemical synthesis of the Olympic rings (October 11, 2020).

What caused the C-14 increase in the year 775 AD?

March 11, 2013

In an earlier post, we noted a recent report of an unusually high content of carbon-14 (¹⁴C or C-14) in tree rings for the year 775 AD [link at the end]. Since C-14 production is stimulated by gamma (γ) rays, the tree ring anomaly pointed to an anomalous source of gamma rays for that time. Some possible sources were considered; none fit with what was known.

A new article suggests another possible source: a short gamma ray burst (GRB). Such a GRB, lasting less than two seconds, might have been due to a collision of two "small" objects, such as neutron stars or white dwarfs. It is plausible that such an event, at a suitable distance, might not have been observed.

It's an interesting story. But remember, the scientists have no evidence whatsoever for such an event. What they do is to add another type of event to the list of candidates, and explain why it is perhaps more reasonable than the others suggested so far. In fact, the paper is probably a more thorough discussion of the candidates than we have seen so far. They do suggest that it might be possible for astronomers to find the object that gave rise to the gamma ray burst.

This remains a story in progress. It started with careful observations of tree rings, with one-year resolution. Those observations of tree rings are leading to questions about the nature of our galactic environment.

News story: Did an 8th Century Gamma Ray Burst Irradiate Earth? (Science Daily, January 21, 2013.) For the most part, this is a good overview. (However the part about beryllium-10 is partly incorrect; ignore it.)

The article, which is freely available: A Galactic short gamma-ray burst as cause for the ¹⁴C peak in AD 774/5. (V V Hambaryan & R. Neuhäuser, Monthly Notices of the Royal Astronomical Society 430:32, March 21, 2013.) In some ways, this is a quite readable paper, as it summarizes the main arguments. However, be forewarned that you will be overwhelmed with numbers; with a little judgment, you can read past most of them and get the main ideas just fine.

Background post: Tree rings, carbon-14, cosmic rays, and a red crucifix (July 16, 2012). The observed C-14 blip was between the years 774 and 775; for simplicity, I have referred to this as 775.

Malnutrition: is more (or better) food the answer?

March 8, 2013

Perhaps not, according to a new article, which suggests that the underlying problem in some malnourished children may be the microbes in the gut. It is a clever piece of work, and it opens up new approaches to considering malnutrition.

Here is the idea. The scientists study the specific type of malnutrition known as kwashiorkor. It's a disease where a distinctive feature is the swollen belly; you've probably seen pictures. They focus on discordant twins -- twins where one has the disease and one does not. It is assumed, reasonably enough, that the twins had more or less the same diet. The key finding was that those with and those without the disease had different gut bacteria. That is interesting, but alone tells us little. In particular, it says nothing about any causal relationship. Does the disease cause a change in the gut microbiota, or is it possible that the gut microbiota changes for some reason, and that contributes to the disease process?

As a second test, they fed children with the disease a "therapeutic diet" -- an inexpensive nourishing food product used to treat malnutrition. A simple summary of what they found is that there was some improvement in the gut microbiota, but it was incomplete.

A third type of experiment is perhaps the most intriguing. They tested the effect of the various collections of microbes on nutrition. Of course, they did this in mice, not humans. The basic finding was that mice with gut microbes from the healthy kids fared better than the mice with gut microbes from the kwashiorkor kids. This would appear to be a direct demonstration that the gut microbes of the kwashiorkor kids are themselves part of the problem. This is a well-controlled experiment, in mice. We do not know its relevance to humans; that has not even been tested.

Let's, for the sake of discussion, assume that the mice result holds with humans. It raises numerous questions -- some of which are probably easy to address. Is the disease onset due to some event that affects the gut microbiota, and makes the kids unable to metabolize their food properly? Could we diagnose children likely to get kwashiorkor before they get it, by testing their gut microbes? If so, could we do something about it? Does knowing about the role of microbes lead to a treatment? Would replacement of gut microbes help? Or would a different choice of foods help, by helping to stimulate the preferred microbes? Lots of question, as so often the case when we get a novel intriguing result. It's a clue, a piece of the puzzle.

News stories:
* Gut microbes at root of severe malnutrition in kids. (Washington University, St. Louis, January 30, 2013.) News release from the lead institution.
* Gut Microbes Contribute to Mysterious Malnutrition. (E Yong, Not Exactly Rocket Science (National Geographic blog), January 30, 2013.)

* News story accompanying the article: Microbiology: Undernutrition - Looking Within for Answers. (D A Relman, Science 339:530, February 1, 2013.)
* The article: Gut Microbiomes of Malawian Twin Pairs Discordant for Kwashiorkor. (M I Smith et al, Science 339:548, February 1, 2013.)

Among posts about the microbiota...
* Treating malnutrition by improving the gut microbiome (May 29, 2021). More, from the same lab. (But it is not a direct follow-up of the same situation.)
* Our microbiome: a caution (August 26, 2014). The hype of microbiome research.
* Melamine toxicity: possible role of gut microbiota (April 21, 2013). Was the toxicity of melamine in the poisoning incidents a few years ago mediated by gut bacteria?
* Bacteria on human teeth -- through the ages (March 24, 2013). The oral microbiota.
* A bacterial cocktail to fight Clostridium difficile (January 19, 2013). An example of treating a disease by directly changing the gut microbiota -- again in mice.
* Antibiotics and obesity: Is there a causal connection? (October 15, 2012). Does the gut microbiota affect obesity -- as well as malnutrition?

More about twins: A DNA test that can distinguish identical twins (July 17, 2015).

Better violins through better fungi?

March 4, 2013

This is one of those stories that come up from time to time... a fascinating idea, with little information available. So we just briefly note it.

A Swiss group claims that treatment of wood with certain wood-rot fungi leads to violins that sound better. The fungi reduce the density of the wood. The idea is that reduction of the wood density leads to improved acoustical properties. If the fungal treatment is carefully controlled, this is done without undermining the structural integrity of the wood. Presumably much of the work involves figuring out the details. The news story refers to a test in which a violin made from fungi-treated wood was rated by listeners as better than a Stradivarius violin. See the video below.

The current news story is based on a talk by the lead scientist. We don't have much more to go on at this point. It's an interesting story, with interesting science behind it.

News story: Treatment With Fungi Makes a Modern Violin Sound Like a Stradivarius. (Science Daily, September 8, 2012.)

Video: Stradivari's Heirs - How Scientists Uncover the Secrets of the Stradivari. (YouTube, 4 minutes.) This is apparently a "trailer" for a film made in 2011 about the story.

The lab: Bio-engineered wood. From EMPA, in St Gallen, Switzerland. Scroll down to "Tonewood" and "Mycowood" for this project. Or choose the higher level heading "Applied wood materials" from the menu at the left for a broader view of the institute. It is an interesting site to explore.

More on violins:
* Briefly noted... The salt content of great 18th century violins from Cremona (March 16, 2022).
* Spiders and violins (May 4, 2012).

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

More on fungi: SquarePants on Borneo (September 24, 2011).

More about wood density: Making wood stronger (March 19, 2018).

Also see... Using old clothes as building materials? (February 5, 2019).

More about rot: How fish rot -- and the implications for studying fossils (April 6, 2010).

Prospecting for gold -- with help from the little ones

March 1, 2013

In large parts of Australia, gold is found in commercially useful amounts a few meters below the soil surface. But finding it takes work. It requires drilling samples, and testing them, to see where the Au is.

It turns out that the termites that are so abundant there have already done the drilling step -- and deposited samples of the deep soil in their mounds. Why not, then, just measure the gold in the termite mounds?

This is an example of bio-prospecting: using some kind of biological sample as an indicator of minerals nearby. What's new here is the specific example. Although the work here is with termites that build substantial mounds, they suspect that many types of termites or ants would work. (If you haven't seen a termite mound, check out the Phys.org news story; the mounds are quite amazing.)

News stories. Some of the news stories on this work also refer to an earlier paper, in PLoS ONE in 2011, by the same group. That's fine, but I am focusing here on the new paper on gold.
* Termites and ants stockpile gold in their mounds, researchers find. (Phys.org, December 10, 2012.) Includes a picture of a termite mound (as well as the termite picture shown above).
* Termites Strike Gold: Ant and Termite Colonies Unearth Gold in Australia. (Science Daily, December 9, 2012.) The termites shown in this news story are a different kind of Australian termite.

The article: Source of anomalous gold concentrations in termite nests, Moolart Well, Western Australia: implications for exploration. (A D Stewart et al, Geochemistry: Exploration, Environment, Analysis, 12:327, November 2012.)

More about termites (and ants)...
* What if two of the world's most destructive pests spent the evening together in Fort Lauderdale? (April 4, 2015).
* Ants: nurses, foragers, and cleaners (May 24, 2013).
* Tracking termites (February 26, 2010).

More about gold...
* Goldene: 2-dimensional gold (July 9, 2024). Added September 24, 2024.
* Water disinfection in nanoseconds (April 3, 2023). Added July 9, 2024.
* A gold-based spray to treat heart damage (May 17, 2022). Added July 9, 2024.
* Air pollution: progress towards a process for ammonia oxidation (April 5, 2019). Added July 9, 2024.
* A simpler assay for detecting low levels of HIV, using gold nanoparticles (January 3, 2013).
* The golden ear: A nano-ear based on optical tweezers (July 13, 2012).
* Weighing gold atoms (September 24, 2008). Added July 9, 2024.

A camera-based device to restore vision

February 25, 2013

Briefly noted... The US Food and Drug Administration (FDA) has approved a device that will restore partial vision to people with certain types of blindness. The device is based on using a camera, with the electronic signal from the camera being sent directly to the retina.

News story: Limited Sight Restored by Retinal Implant. (MedPage Today, February 14, 2013.)

The purpose of noting this here is to juxtapose it with the accompanying post, immediately above. The basic logic is the same in both cases.

Other posts about restoring vision include:
* Connecting the senses (April 26, 2011).
* Restoring sight by use of stem cells to regenerate a new cornea (July 13, 2010).
* The vision thing (July 3, 2008).

More about vision: What if there was a gorilla in the X-rays of your lungs? (July 26, 2013).

A living organism powered entirely by electricity?

February 22, 2013

A striking feature is the unusual way these bacteria divide. As you can see from the one at the bottom left, they divide lengthwise, rather than across.

The more important point for now is how these bacteria are getting their energy. You can't really tell, but in the above figure the bacteria are attached to a graphite electrode. In the work reported in a recent article, the bacteria are being fed with an electric current -- which seems to be their sole energy source.

These bacteria normally grow by "burning" iron. More specifically, they oxidize Fe²⁺ ions to Fe³⁺ ions. This works, though it is a difficult existence. For one thing, the product Fe³⁺ precipitates out, covering the growing cells with rust. This makes it difficult to study these bacteria in the lab.

The scientists also knew that these bacteria would grow attached to a piece of iron; this suggested that their biochemical machinery for oxidizing the iron was, in part, on the outside of the cell. If so, perhaps they could get the bacteria to attach to a piece of graphite and then just feed them the electrons they would get by oxidizing the iron. They tried it, and it seems to work. The bacteria grow, apparently rather normally, but do not get coated with rust.

The iron or the electricity are the energy source for the bacteria. They still need other kinds of food, as "material". For carbon, they use carbon dioxide, "fixing" it just as plants do.

News story: Scientists trick iron-eating bacteria into breathing electrons instead. (Phys.org, January 29, 2013.)

The article, which is freely available: Cultivation of an Obligate Fe(II)-Oxidizing Lithoautotrophic Bacterium Using Electrodes. (Z M Summers et al, mBio 4:e00420-12, January 29, 2013.)

Another example of unusual electron metabolism in bacteria: On sharing electrons (May 3, 2011).

More about iron chemistry... 2 + 2 = 4: Chemists finally figure it out (October 9, 2015).

Of disasters, asteroids and meteors

February 19, 2013

Last week I juxtaposed two short items [links at end]. One was a news feature that discussed rare but inevitable major disasters, such as super-volcanoes. The other noted the fly-by of an asteroid later in the week -- a close encounter, but one of no real consequence, since the orbit of the asteroid was well established. The juxtaposition was intentional. However, there was no intent to imply that any significant event would actually occur. No intent. And no premonition.

Friday morning (the day of the asteroid fly-by) a headline news story was about a meteor strike in Russia, with some damage and several hundred people injured. (The number of injuries has since risen to about a thousand, mostly minor. The damage is estimated as several million dollars.) Two BBC announcers ("presenters", in BBC lingo) were arguing about whether it was related to the asteroid fly-by. They contacted an astronomer, who assured them it was not. Just a coincidence. The next morning, I learned we had had a meteor strike in northern California. Another one. We had two significant meteor strikes last year; one has already been the subject of an article in Science, because of the unusual composition. (None of the California meteor strikes noted here caused any injury or significant damage, so far as I know.)

What's going on? It's just the Universe doing its thing. In a sense it is what that news feature on disasters was about. Events happen. Small ones happen more frequently, bigger ones less frequently. Occasionally, there are super-disasters.

The asteroid that passed by -- the one event that was predicted -- was big enough that it could have devastated a city, perhaps injuring or killing millions. We only discovered it last year; had it been on path to hit Earth, we would not, at this point, have had any way to change its course. (We could have evacuated the target area.) The meteor that targeted Russia exploded before it hit ground; the damage was due to the shock waves, and the injuries largely due to people being hit with debris. In the big scheme, it was a minor event. To the people of the affected area, it certainly was significant, though not devastating. The three meteors that hit northern California in the past year were of similar size.

Here are some news stories about the meteor events; most are from the popular media. Remember that immediate reports of current events may not be entirely accurate.

Last Friday...
* Fireball Lights Up Northern California Skies: Reports. (Space.com, February 16, 2013.)
* Meteor Streaks Across Russian Urals, Leaves Nearly 1000 Injured. (Huffington Post, February 15, 2013; now archived.)

Last year, in northern California...
* Massive Fireball Over California Coast - October 17th, 2012. (American Meteor Society (associated with Pennsylvania State University), October 2012.) The page links to reports of recent meteor events -- many of them.
* Minivan-sized Asteroid Exploded Over California. (Discovery News (later, Seeker), April 23, 2012. Now archived.)

Background posts:
* Reasons to hide tonight? (February 11, 2013).
* An asteroid alert (February 11, 2013).

More about one of those northern California events noted above: Formation of the Moon: the California connection (October 10, 2014).

More about meteors...
* Libyan desert glass, King Tut, and the hazards of meteorite strikes (May 31, 2019).
* The origin of reactive phosphorus on Earth? (July 5, 2013).

More about asteroids: What has six tails -- and is beyond Mars? (November 20, 2013).

More to worry about... A visit from a star? (March 8, 2017).

There is no intent to post more on this topic next week.

Sulfur dioxide in the atmosphere of Venus

February 16, 2013

There is a clear pattern: red points are near the top. As noted, red points are the oldest points. Thus we see that the SO₂ level on Venus has been decreasing since those earliest time points -- over a time scale of just a few years. You can see that simply from the color pattern of the points. (You can also see a trend toward higher SO₂ levels nearer the equator.)

The results shown above, taken along with other data for SO₂ in earlier years, suggests that the SO₂ level on Venus fluctuates rather dramatically. Why? Well, they don't know, but one possibility is volcanic eruptions. Results such as those reported here may be the first evidence for active volcanism on Venus. Regardless of that interpretation, the work is impressive simply in the measurements it reports and the trends it finds.

News story: Have Venusian Volcanoes Been Caught in the Act? (Science Daily, December 3, 2012.)

Both of the following are freely available:
* News story accompanying the article: Planetary science: Rising sulphur on Venus. (L W Esposito, Nature Geoscience 6:20, January 2013.)
* The article: Variations of sulphur dioxide at the cloud top of Venus's dynamic atmosphere. (E Marcq et al, Nature Geoscience 6:25, January 2013.)

A post about atmospheric SO₂ and volcanoes -- on Earth: Why isn't the temperature rising? (September 12, 2011). SO₂ is a million time more abundant in the atmosphere on Venus than in ours.

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

More about Venus: Venus: an unusual view (March 18, 2013).

More about atmospheric SO₂ and volcanoes -- on Earth: SO₂ reduces global warming; where does it come from? (April 9, 2013).

Planet Venus was also mentioned in these posts:
* GJ 1132b: "the most important planet ever found..." (December 18, 2015).
* A new trick for the Kepler planet-hunters (June 25, 2012).
* Collision of Earth and Mars (July 8, 2009).

Cockroach should be disinfected before eating it

February 12, 2013

You probably spend time cleaning your food. But did you know... Parasitic wasps that eat cockroach clean their food, too. A new article reports that larval wasps, living inside the cockroach, secrete a potent antibacterial mix.

How can we see what is going on inside the cockroach? Because the scientists had opened it up, and inserted a clear window (a coverslip) into the roach body.

Based on their evidence, the scientists believe that the wasp secretes the antibiotics to clean its food. Their story is incomplete: they do not directly show that the secretions are necessary for the larval survival. It would be interesting if they can figure out a way to test that.

News story: Researchers discover wasp larva disinfect their food before eating. (Phys.org, January 8, 2013.) A good overview of the work, with a description of the larval life cycle. (It includes a picture of the adult wasp. It's a quite pretty little critter, perhaps as suggested by its common name, the emerald cockroach wasp.)

The article: Larvae of the parasitoid wasp Ampulex compressa sanitize their host, the American cockroach, with a blend of antimicrobials. (G Herzner et al, PNAS 110:1369, January 22, 2013.)

Movie. There is a movie posted with the article. It shows a wasp larva inside the cockroach, and shows the larval secretions. It's not dinner-time viewing, but it is interesting. Go slowly at the start, so you figure out what is what; it is well-labeled, but may move faster than you want. The movie runs about 30 seconds. From the article web site, above, choose Supporting information. The movie is also available at movie: Ampulex compressa sanitize their host. (YouTube)

More on parasitic wasps...
* The benefit of providing alcohol to the eggs (March 30, 2013).
* Wasp hides under ladybug (January 3, 2012).

More on cockroaches:
* Why and how some cockroaches avoid glucose (October 11, 2013).
* Acrobatic cockroaches inspire robot design (September 16, 2012).

The post started with a comment about keeping your food clean. If you need a reminder why... Killer chickens (December 2, 2009) (and several posts linked there).

More on antibiotics and disinfectants is on my page Biotechnology in the News (BITN) -- Other topics under Antibiotics.

An asteroid alert

February 11, 2013

There will be an asteroid in the neighborhood this week. An asteroid half the size of a football field will be passing closer than any previous asteroid that has been tracked. It will fly under some of our communications satellites. It will miss the Earth by 28,000 kilometers -- assuming NASA did the calculations right.

News story: Asteroid to Give Earth Record-Setting Close Shave on Feb. 15. (Space.com, February 1, 2013.)

See the accompanying post, above.

There is also a post that is something of a follow-up to both of these: Of disasters, asteroids and meteors (February 19, 2013).

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

The role of the immune system in making stem cells

February 8, 2013

An intriguing and confusing story -- one that may turn out to be important.

Some background. One major type of stem cell being studied is the induced pluripotent stem cell (iPSC). iPSCs are made from various types of body (somatic) cells by reprogramming them to an embryonic-like stage, where they are pluripotent: capable of making any cell type. The basics for making iPSC were developed in 2006 by Shinya Yamanaka, who shared the Nobel prize last year for this work.

To induce the reprogramming of adult cells to become embryo-like requires adding some "factors". The original way to do this was to add a virus that coded for the needed factors. This works, but using the virus raises some concerns. Therefore, people developed other ways to deliver the factors, without a virus. Such virus-free procedures work, but not very well. Why a virus-free procedure works poorly has been mysterious. And that leads us to the new work.

The key experiment in the new work is to use a non-viral method of inducing reprogramming -- but also add a virus, a "blank" virus, with no relevant genes. Turns out, adding the virus improves the efficiency of reprogramming. That is, even though all known needed factors were provided independently of the virus, there was something about adding a virus that improved the procedure.

The authors go on to show that the virus seems to be acting by stimulating the immune system. More specifically, it is acting through one of the toll-like receptors (TLR) of the innate immune system. Thus, the original Yamanaka success seems to have involved not just the identified factors, but also the virus itself, via the innate immune system. This is a small step toward better understanding the reprogramming process. I'm sure we will be hearing more about this and other developments. It's a reminder that the iPSC process is still new, and only partly understood.

News story: Viruses Affect Cell Reprogramming -- Viral vectors used to carry transcription factors that de-differentiate cells into a stem-cell-like state are themselves a key factor in efficient reprogramming. (The Scientist, October 25, 2012.)

* News story accompanying the article: ''Transflammation'': When Innate Immunity Meets Induced Pluripotency. (L A J O'Neill, Cell 151:471, October 26, 2012.)
* The article: Activation of Innate Immunity Is Required for Efficient Nuclear Reprogramming. (J Lee et al, Cell 151:547, October 26, 2012.)

For more on stem cells:
* Bacteria can make mouse stem cells (April 6, 2013).
* Geron sells its stem cell business (January 23, 2013). The business side -- of products based on embryonic stem cells.
* Using patient-specific stem cells to study Alzheimer's disease (February 24, 2012). An example of how iPSC are used to study disease.

There is more on stem cells on my page Biotechnology in the News (BITN) - Cloning and stem cells.

More on the innate immune system and TLRs: Why mice don't get typhoid fever (November 26, 2012).

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

A new SARS-related virus seems to be emerging -- and an "ethics" story

February 4, 2013

We have noted various new viruses [links at end]. One point of such stories is to allow us to watch the course of a new virus. We even hope that our societies (and public health institutions) learn from each new virus story so that we are better able to deal with one that may be serious; we must emphasize that in the early stages we have little way to know which will be serious. We now have another new virus to watch -- and it is killing humans.

Some of you may remember the SARS virus, which emerged in 2002. Fortunately, the SARS virus was not easily transmitted from one person to another, and good containment procedures brought the SARS epidemic to an end. SARS was on the scene for less than a year, but killed over 700 people -- 10% of those known to be infected -- during its brief stint.

We now have a new virus, which first drew attention in September 2012. It has killed five people so far -- five confirmed deaths, out of nine known to be infected. The virus has been isolated, and is undergoing study; it is a corona virus, the same general type as the SARS virus. This post is prompted by one recent paper on the new virus. The point is not so much the specific findings, but to bring the story of the new virus to your attention. We will watch it over the coming months. Will this new SARS-type virus do more or less damage than the original SARS? If it does do only limited damage, is that because we did something good to stop it, or because it just wasn't a very good virus?

What is in the new paper? One thing they tested was whether the new virus uses the same receptor as the SARS virus. (The receptor is the surface structure on cells where the virus attaches.) Simple studies show that it does not; for example, cells without the SARS receptor can be infected by the new virus. That's disappointing; if it used the same receptor, we would have a head start in knowing how it infects. Secondly, they tested the host range of the new virus: what kinds of cells can it grow in? Many. It grows in cells from a wide range of animals.

News stories:
* New SARS-Like Virus Infects Both Human and Animal Cells. (Science Now, December 11, 2012.)
* New coronavirus can infect cells from multiple species. (CIDRAP, December 11, 2012.) See links on the page to "MERS-CoV" or "SARS" for more, including recent news. MERS stands for the newly established name for the virus, Middle East Respiratory Syndrome.

The article, which is freely available: Human Coronavirus EMC Does Not Require the SARS-Coronavirus Receptor and Maintains Broad Replicative Capability in Mammalian Cell Lines. (M A Müller et al, mBio 3:e00515-12, December 11, 2012.)

The "ethics" story? Viruses can be the subject of international disputes. We have noted a previous example [link at end]. The new virus is raising its own international issues. It was isolated in one country, and then sent to a leading lab in another for further characterization (including the work discussed above). This has lead to concerns and questions. Among them is the tension between the scientist who isolated the virus and the authorities in the country where that happened.

As you read the following news story... The purpose here is not to blame anyone. The issues raised need to be addressed. The previous dispute was resolved by an international agreement, mediated by the World Health Organization (WHO). We hope further agreements will be worked out to deal with situations such as this new one. The goals should be clear: efficient development of understanding of new diseases -- which do not respect international boundaries. The concerns of developing countries are often understandable, and need to be respected -- without endangering public health anywhere.

News story: Tensions linger over discovery of coronavirus. (Nature News, January 14, 2013.)

Background posts about new viruses:
* The Heartland virus (October 2, 2012)
* Schmallenberg virus (January 20, 2012). Links to follow-up.

Follow-up for the new MERS virus: Where is the MERS virus coming from? (September 22, 2013).

More MERS... MERS in the United States (May 18, 2014).

The previous international microbiology dispute, and its resolution: International relations: sharing flu viruses (May 28, 2011).

Influenza is a continuing story of new viruses. Many posts on various flu issues are listed on the supplementary page: Musings: Influenza.

Two sections of my page Biotechnology in the News (BITN) -- Other topics are relevant to the virus story here. One is specifically on SARS, MERS (coronaviruses), and one is on the more general topic of Emerging diseases (general).

There is a section of my page Biotechnology in the News (BITN) -- Other topics on Ethical and social issues.

A better understanding of the basis of color vision

February 1, 2013

We'll come back to the figure in a moment, but first let's look at some background. The basis of our visual system is the absorption of light by a photoreceptor pigment in the eye. The pigment has two parts. One is retinal, a derivative of vitamin A; the other is a type of protein called opsin. Retinal binds to the opsin; this bound complex is the photoreceptor.

It is the retinal part of the photoreceptor complex that absorbs the light. But when you look at the various kinds of photoreceptors, such as the three color receptors in humans, they all have the same retinal; it is the opsin protein that varies. Somehow the chemical environment in the various opsin proteins changes the absorption spectrum of the bound retinal. Exactly how this happens has not been clear.

That gets us to the new work. The scientists set out to explore that effect of chemical environment on the color. It turns out that opsins are fairly difficult proteins to work with in the lab, so they used something else: another retinal-binding protein. They made a range of changes in the protein, by introducing mutations into the gene. They then measured the absorption spectrum of the complex of each of them with retinal. The paper contains full spectrum information, but the photos above give the idea -- very well.

In the figure above, M1 through M11 are the various opsin proteins they made. In each case what you are seeing is the color of a solution containing the indicated protein with bound retinal. There is quite a range of colors. The first tube contains retinal, with no protein at all. It appears colorless to our eye; actually it does absorb light, but only in the ultraviolet part of the spectrum. The full figure in the article contains the full spectra, and a table showing the absorption maximum for each species, as well as for natural visual pigments.

For example... Protein M1 absorbs blue light, with its maximum absorbance at 425 nm. This is very close to the blue photoreceptor for humans. By absorbing blue light, the solution of the protein appears yellow.

The red receptor M11 has an absorbance maximum at 644 nm. That's far beyond our red receptor, and beyond any retinal-based photoreceptor seen in biology. In fact, it is more red-shifted than many thought would be possible.

By making all these proteins and seeing how each one influences the absorption spectrum of the retinal, they learn more about how receptors for color vision work.

News story: Detailing Color Vision -- Scientists engineer a spectrum of artificial pigments to understand how animals see in color. (The Scientist, December 6, 2012.)

* News story accompanying the article: Biochemistry: Redder Than Red. (T P Sakmar, Science 338:1299, December 7, 2012.)
* The article: Tuning the Electronic Absorption of Protein-Embedded All-trans-Retinal. (W Wang et al, Science 338:1340, December 7, 2012.)

The role of opsin proteins and retinal (vitamin A) in vision was noted in the post An unusual eye? (June 6, 2012).

And more...
* The eyes of Cnidaria (jellyfish): the big picture (August 19, 2018).
* Color vision: an overview (December 1, 2014).
* How can the mantis shrimp see so many colors of UV? They use filters (August 30, 2014).

A source of dietary vitamin A was discussed in the post Golden rice as a source of vitamin A: a clinical trial and a controversy (November 2, 2012).

Vitamin A (and hence retinal) is made from carotenoids. Carotenoids were featured in the post Red and green aphids (June 2, 2010). That post includes some information on the structures of various carotenoids and how they are made. Cut a molecule of beta-carotene in half, and you get, with just a bit of adjustment, two molecules of vitamin A.

More about vision: What if there was a gorilla in the X-rays of your lungs? (July 26, 2013).

Also see a section of my page Internet resources: Biology - Miscellaneous on Medicine: color vision and color blindness.

POCDx -- What's the barrier?

January 29, 2013

The first barrier for some might be, what does POCDx mean? It means point-of-care diagnostics; the simpler form POC is also used. POC is about providing medical testing that can be done on-the-spot, with fast and inexpensive results. Sort of.

Much work is being done to develop POCDx; there is a POCDx group at Berkeley. But getting POCDx to work requires more than making clever inexpensive tests; they must be integrated into the medical system. A talk at a Berkeley symposium in early January emphasized that POC was not just about technology but about the broader problem of health care systems. The talk was by Madhukar Pai, an India-trained doctor now at McGill University, and it was one of the high points of the day-long meeting. Pai noted that he had recently written an article on the topic -- and that is the point here.

The article, which is freely available: Point-of-Care Testing for Infectious Diseases: Diversity, Complexity, and Barriers in Low- And Middle-Income Countries. (N P Pai et al, PLoS Medicine 9(9):e1001306, September 4, 2012.) (Since I mentioned that our speaker was M Pai... The lead author, whose name is listed here, is his wife, who is also a physician at McGill.) Worth at least a browse for anyone interested in health care systems. And it is relevant to all, not just developing countries. The cost of health care in the US is a serious problem; POCDx offers one line of hope for improvement in our inefficient system. (Some have joked that India will lead in the improvement of US heath care, for this reason. We don't need to take that too literally, but it expresses a useful idea.)

More on health care:
* High-tech medicine: good or bad? (June 4, 2010).
* Maternal mortality (May 7, 2010).
* Healthcare costs (June 18, 2009).

Examples of POC developments:
* Ultra-fast PCR (March 14, 2023).
* The paperfuge: a centrifuge that costs 20 cents (April 17, 2017).

Fish with bigger brains may be smarter, but ...

January 25, 2013

As background, humans are noted for having a large brain, but that brain is expensive. The human brain is about 2% of the body, but uses about 20% of the energy. Interestingly, the total energy consumption by humans is about what one would expect for the body size. Something must be compensating for the increased energy consumption by the brain. This issue has long been recognized, but is not entirely understood. One suggestion is that humans have less digestive system, compensating for the greater brain. Some have even suggested that the key to developing a bigger brain was learning to cook food, making it easier to digest. Some of this is little more than speculation at this point.

Now the fish. A team of scientists has decided to look at the big-brain issue with guppies. It's an interesting story; however, it is not at all clear what we should conclude from it at this point.

Here is an overview of what they did... They selected for fish with larger brains. (In parallel, they also selected for small-brained fish.) The resulting fish not only had larger brains, but were smarter -- as judged by how they did on a math test. That is, the brain was not only larger but better. The downside? The large-brained fish had smaller guts and produced fewer offspring.

Let's look at some of the specifics...

The work started by selecting for large-brained fish. This is logically straightforward, and turned out to be easy. They took the fish with the largest brains, and bred them. In parallel, they did the same for small-brained fish. Interestingly, over just two generations, they developed two populations of fish with 5-10% difference in relative brain size. That they did this so easily means they were largely exploiting natural genetic variation within the population.

Here is what they found in one test comparing the two populations...

And now some data showing the cost of having the larger brain...

What do we learn from this? The first point is simply that they can do all this -- that they can select for larger (and smaller) brains, and study the effects. That is, they seem to have developed an interesting experimental system. Do the results here tell us anything about humans? Do they even tell us much about fish?

What they did here seems logical, but there are many questions about the work. I've noted some along the way, but I can think of more... They do this one "math" test to show that the fish with larger brains are smarter. Are their results here really significant, or was this some kind of fluke result? What other abilities would these fish show -- or not show? They test their small- vs large- brained fish; what about the original "normal" fish? (Maybe the large-brained fish test the same as normal, and the small-brained fish are odd.) Even if the fish chosen for large and small brains by this procedure have certain features (intellectual and otherwise), is that general? What would happen under different conditions? What would happen if these fish were bred for extended periods with limiting food, where a smaller gut might be a problem?

I don't have answers to these questions. That's the point. What they did here was interesting; the results are intriguing. But let's be cautious about interpreting this. It is hard to know what the significance is -- without much more work. The good news is that the fish system is simple enough and fast enough that they should be able to do more work. Let's see what bigger story -- and bigger brain -- develops.

News story: Big Brains Are Pricey, Guppy Study Shows. (Science Daily, January 3, 2013.) The story is a good description of the work, but I think it is overly generous in stating the significance. The logic is fine. However, I really see this as more of an initial effort along a new and interesting line than anything conclusive at this point.

The article: Artificial Selection on Relative Brain Size in the Guppy Reveals Costs and Benefits of Evolving a Larger Brain. (A Kotrschal et al, Current Biology 23:168, January 21, 2013.)

More about the brain size-gut size problem... Sliced meat: implications for size of human mouth and brain? (March 23, 2016).

Posts on brains include:
* A possible genetic cause for the large human brain (March 25, 2017).
* Mice with human brain cells (April 13, 2013).
* Is it possible that mental retardation could be prevented by a simple prenatal treatment? (January 14, 2013).

Posts on fish include:
* Helicoprion -- a fish with 117 teeth, arranged in a spiral (March 9, 2013).
* Did you see what the sawfish sawed? (April 27, 2012).

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

Stretchable electric wires

January 22, 2013

Have you ever cut through the insulation of an electrical wire? Did you notice that the metal part -- the inner part that conducts electricity -- drips out onto the floor? No? Well, it would if that inner metallic part were liquid -- as proposed by a group of scientists from the University of North Carolina in a recent article.

Why would you want to do that? Their goal is to make wires that can be stretched. That's not a new idea, but attempts to date have had limited success; ordinary metals just aren't very stretchable. Their approach here is novel. Wire has an outer part, the insulating sheath, and an inner part, the conducting metal. The approach here is to separate the functions of the outer and inner parts more completely. Stretching is the job of the outer sheath; the inner part just conducts electricity. Thus they focus on making a plastic for the sheath that can be stretched. However, the core is a liquid metal. When the sheath stretches (or relaxes), the conducting liquid metal just conforms to the sheath.

Liquid metals? You may know that there is one metal that is liquid (at room temperature), but mercury presumably would not be a good candidate because of toxicity. Perhaps you recall that there is another metal with a melting point just a bit above room temperature; it will melt in your hand. That is gallium. What they do is to dissolve something in the gallium, to lower its melting point. The alloy of gallium and indium that they use has a melting point of 16 °C.

Does their liquid-core wire work? Yes. They provide some lab measurements, and some real use. They use the wire as part of the cable for an earphone or an iPod charger, and show that it works fine, even while the experimenter repeatedly stretches the wire to several times its original length and relaxes it. The movie files listed below capture these exercises.

The following graph illustrates one key feature of their novel wires: the mechanical properties are now due entirely to the outer insulating sheath.

Are there any problems with this liquid-core wire? Yes. If you cut through the insulation, the inner metallic part drips out onto the floor.

News story: Liquid Metal Used to Create Wires That Stretch Eight Times Their Original Length. (Science Daily, December 18, 2012.)

Movies. There are two short videos posted with the article. There is also a video at YouTube, which is equivalent to #2. In the video, someone is stretching and relaxing the earphone cable, but the sound continues normally. Ultra-Stretchable Wires. (YouTube, 37 seconds)

The article: Ultrastretchable Fibers with Metallic Conductivity Using a Liquid Metal Alloy Core. (S Zhu et al, Advanced Functional Materials 23:2308, May 13, 2013.)

A stress-strain curve for a fiber was presented, with more explanation, in the post Spider silk: Can you teach an old silkworm new tricks? -- Update (February 11, 2012).

More about stretchable electronics: Supercapacitors in the form of stretchable fibers -- suitable for clothing (May 2, 2014).

More about unusual wires: On sharing electrons (May 3, 2011).

More about electrical insulation: Using an electrical conductor as an insulator (September 12, 2021).

More gallium... Capturing carbon dioxide using gallium (April 4, 2022).

An easier way to get infected with malaria

January 18, 2013

The normal way one gets infected with malaria is to be bitten by a mosquito that is carrying the parasite, Plasmodium falciparum (Pf). Now, a team of scientists has developed a way to directly inject people with the parasite, avoiding the need for a mosquito.

Why would you want to do that? It's for lab work. One difficulty in studying malaria is starting the infection. The ability to infect a study population directly with a defined dose of parasites will facilitate lab work, including drug testing.

The key part of the work was to develop a well-defined product. The scientists, from a company called Sanaria (get it?), describe it as "aseptic, purified, vialed, cryopreserved Pf sporozoites" (from the abstract; sporozoites are the form of the parasite that mosquitoes inject when they bite you). They now report the results of a small Phase 1 trial of their product.

They seem to have achieved their primary goal: the development of a preparation of malaria parasites that can be easily handled, and delivered to people in a controlled manner. This small trial needs follow-up, but it is encouraging. If this holds, the ability to provide controlled infections will facilitate malaria research.

It is also possible that this line of work could lead to a malaria vaccine. There is evidence that inactivated sporozoites could be effective as a vaccine. However, there has been no reliable delivery method. The current work seems to provide that reliable delivery method; this should allow work on a sporozoite-based vaccine to proceed with the ability to do controlled tests. In fact, they have already reported some work on this.

News story: Injectable Formulation of Malaria Parasites Achieve Controlled Infection. (Science Daily, November 13, 2012.)

The article, which is freely available: Controlled Human Malaria Infections by Intradermal Injection of Cryopreserved Plasmodium falciparum Sporozoites. (M Roestenberg et al, American Journal of Tropical Medicine & Hygiene, 88:5, January 2013.)

More on malaria...
* A vaccine against malaria -- with 100% efficacy? (October 20, 2013).
* Malaria-infected mosquitoes have greater attraction for people (May 28, 2013).
* Genes that protect against malaria (January 19, 2010).

And see my page Biotechnology in the News (BITN) -- Other topics under Malaria.

If you would rather read about mosquitoes... Mosquitoes are delectable things to eat (August 21, 2010).

Is it possible that mental retardation could be prevented by a simple prenatal treatment?

January 14, 2013

Let's look at some results. We will fill in the background later.

Something interesting is happening here. What is this about? What are DS mice, and what is this peptide?

DS mice are mice considered a model for Down syndrome (DS), the most common cause of mental retardation in humans. The human DS disease is due to having an extra copy of one chromosome (#21); the DS mice also have an extra copy of a chromosome, one that is partly equivalent to the human 21. We need to emphasize that the precise nature of human DS is not clear, and it is not clear how good the DS mice are as a model of human DS. Nevertheless, DS mice show a learning deficit, as shown here (the DS-placebo results). And the peptide treatment helps.

The "peptide" is actually a pair of small proteins, used together. They are neurotrophic growth factors, known to be involved in brain development. Previous work had suggested they have some benefit for DS mice. What is novel here is the treatment of the mice in utero, leading to an improvement in learning in the adult mice. That is, it would seem that a genetic error affecting brain development can be reversed by a prenatal treatment. That's an interesting finding. Understanding this, and finding whether it is relevant to this -- or any -- human disease requires further work.

News story: Prenatal Intervention Reduces Learning Deficit in Mice. (Science Daily, November 29, 2012.)

The article, which is freely available: Prenatal Treatment Prevents Learning Deficit in Down Syndrome Model. (M Incerti et al, PLoS ONE 7(11):e50724, November 29, 2012.)

More about Down syndrome: Down syndrome: Could we turn off the extra chromosome? (November 15, 2013).

Posts on brains include:
* Fish with bigger brains may be smarter, but ... (January 25, 2013).
* A drug treatment for an autism-like condition in mice (November 9, 2012).

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

More about growth factors: Targeting growth factors to where they are needed (April 21, 2014).

Carl Woese and the archaea

January 12, 2013

A historic paper -- from just 35 years ago. It is Carl Woese's paper declaring what has come to be known as the three-domain model for classifying organisms. It's not only a paper of historic significance, but it has long been recognized as such.

There are a couple of reasons to take note of this classic paper here.
* An accompanying post, immediately above, offers a challenge to Woese's three-domain model.
* Carl Woese died recently, on December 30, 2012, at age 84.

What Woese did in 1977 was to compare the gene sequence for a particular gene (for the small ribosomal RNA) for a range of organisms. This was an early example of using gene sequence to determine relatedness of organisms. The key result was that the genes from one group of organisms, which had been considered bacteria, were as different from the other bacteria as from the eukaryotes. This group of organisms was the methanogens. Woese suggested, then, that there are three "equal" groups -- or domains -- of organisms: the bacteria, the archaea, and the eukaryotes (using modern terminology).

So we have a new article challenging the Woese model coming out more or less as he dies. Does the new work diminish the importance of Woese's work? Hardly. We can break down Woese's contribution into three parts.
* He established an experimental approach for measuring relatedness, using genome sequence.
* He established the distinction between the archaea and the bacteria. That is, he recognized the archaea as a distinct group. (Back in 1977, he called them "archaebacteria".)
* He proposed the three-domain model.

The first two stand. Woese introduced using genome sequence for phylogenies, and he brought us the archaea. The third dominated discussion for many years, but seems open to question. Woese had few archaea in those days. The new work makes use of much more information on the archaea, and primarily deals with the relationship between the archaea and the eukaryotes. We do not yet know if the new work will stand; some think it makes the best case yet for the alternative, eocyte, model. If the eocyte model wins, it can be thought of as building on what Woese did. Woese introduced us to the archaea; they are more complex than he knew at the time.

News story: Carl R. Woese, who discovered a new domain of life, dies at 84. (University of Illinois, December 31, 2012.)

The 1977 article is recognized by the journal that published it as a PNAS classic. The first two articles listed here are PNAS items, from 2012, about the original article. The "Profile" is a brief overview; the "Perspective" is a more detailed scientific analysis. Both contain modern versions of the three-domain model. The third here is the original article. All are freely available.
* Profile: Woese and Fox: Life, rearranged. (P Nair, PNAS 109:1019, January 24, 2012.)
* Perspective: Phylogeny and beyond: Scientific, historical, and conceptual significance of the first tree of life. (N R Pace et al, PNAS 109:1011, January 24, 2012.)
* The article: Phylogenetic structure of the prokaryotic domain: The primary kingdoms. (C R Woese & G E Fox, PNAS 74:5088, November 1977.) It's a short article that remains quite readable to this day. Those with some background in microbiology, or at least biology, may enjoy looking over the original article.

Related accompanying post (immediately above): DNA: Are there really three domains of life? (January 12, 2013).

And more...
* The Asgard superphylum: More progress toward understanding the origin of the eukaryotic cell (February 6, 2017).
* Our Loki ancestor? A possible missing link between prokaryotic and eukaryotic cells? (July 6, 2015).

More about the domains of life... The largest known virus (August 5, 2013).

More about methanogenic archaea: What caused the mass extinction 252 million years ago? Methane-producing microbes? (October 12, 2014).

More about ribosomal RNA: Ribosomes with subunits that are tethered together (October 5, 2015).

* Previous history post... DNA: Watching the hopping supercoils (November 24, 2012). (This is not primarily a history post, but includes some history in the note at the end.)
* Next... The Mudville story, on its 125th anniversary (June 3, 2013).

My page Internet resources: Miscellaneous contains a section on Science: history. It includes a list of related Musings posts.

Book on the Archaea... See my page Books: Suggestions for general science reading: Forterre, Microbes from Hell (2016).

Making an artificial ion channel from DNA

January 8, 2013

There are various reasons why a story catches my attention and gets considered for a Musings post. Striking pictures are one way to get my attention.

Ion channels are common -- and important -- in biology. Ion channels in the cell membrane allow common ions, such as Na⁺, to get in or out of the cell. Such ions are the basis of voltage differences across cell membranes, and ion channels are central to the operation of the nervous system. What makes this one special is that they make it almost entirely from DNA. The idea is to design strands of DNA that will self-assemble into the desired structure, the ion channel in this case. (Just to be absolutely clear... We are not talking here about DNA coding for the channel; the DNA is actually the construction material for making the channel.)

They do an interesting "trick" to help get the channel device to stick to the membrane. Look at the diagram (the upper picture). The small orange (carrot-like) things? They are modified DNA structures with cholesterol attached. The cholesterol helps to hold the device to the membrane. Cholesterol is not part of natural DNA; here, it is attached to some of the DNA bases. The heart of the construction process involves making use of DNA base pairings, but it is fine to have other structures attached. (The red part at the bottom of the diagram? That is the part that goes through the membrane. The set of red cylinders forms a pore in the middle.)

Importantly, they test the blobs-with-DNA-based-channels; they work! The scientists observe a voltage across the membrane when the channel device is inserted.

A striking picture got my attention. But there is more here than just a pretty picture. The work involves constructions with DNA -- not just to make a structure, but to make a functional device. This is probably one of the most complex DNA constructions done to date.

News story: Artificial ion channels created using DNA origami. (Phys.org, November 16, 2012.)

* News story accompanying the article: Chemistry: Functional DNA Origami Devices. (M S Strano, Science 338:890, November 16, 2012.)
* The article: Synthetic Lipid Membrane Channels Formed by Designed DNA Nanostructures. (M Langecker et al, Science 338:932, November 16, 2012.)

A recent post on "DNA technologies": Making big "molecules" from big "atoms" (December 7, 2012).

Nanopores -- another revolution in DNA sequencing? (June 22, 2012). The use of the channels in this new work is somewhat similar to how channels are used in the new method of sequencing DNA using nanopores. (In fact, the protein used in that method by some groups was one of the models they used here to guide their work.)

Here are some posts that note the function of natural ion channels. One discusses a disease related to an ion channel.
* A drug treatment for an autism-like condition in mice (November 9, 2012).
* How an octopus adapts to the cold -- by RNA editing (March 5, 2012).
* How to find the blood (August 29, 2011).

How porcupine quills work

January 5, 2013

The picture above is the tip of a quill from a North American porcupine, as observed by scanning electron microscopy (SEM). The amount of tip shown in the picture is about a half millimeter. Note that the tip is not smooth, but rather has flap-like features -- called barbs.

The picture of the quill is trimmed and reduced from one in Ed Yong's story listed below. Similar SEM figures in the paper show the barbs. The picture linked above is also from that story. (You did see a face in there? If not, go back and look again.)

So what brought this up? A team of scientists, largely from Harvard and MIT, has studied the forces required to insert and retract quills, as well as quills that have had their barbs removed. They then designed artificial porcupine quills, using what they learned from studying the real thing. They suggest that what they learned may be useful in designing improved medical devices such as needles or sutures.

Perhaps their key discovery is that barbed quills penetrate the skin more easily than de-barbed ones -- even though the barbed quills are larger (in diameter). This is probably because the uneven surface of the barbed quills penetrates mainly at the outermost part. Thus the force of penetration is focused onto a small region of the quill. Of course, as is well known, removal of barbed quills is difficult.

News stories:
* Inspiration from a Porcupine's Quills. (Science Daily, December 10, 2012.)
* Why porcupine quills slide in with ease but come out with difficulty. (E Yong, Not Exactly Rocket Science (Discover blog), December 11, 2012.)

The article: Microstructured barbs on the North American porcupine quill enable easy tissue penetration and difficult removal. (W K Cho et al, PNAS 109:21289, December 26, 2012.)

A previous post about better needles for inoculations... A better way to deliver a vaccine? (July 25, 2010).

And sutures and such...
* Fixing the heart with some glue and light (July 27, 2014).
* Smart sutures (November 3, 2012).

This work is, in part, an example of bio-inspired (or bio-mimetic) development. For more about this emerging field, see my Biotechnology in the News (BITN) topic Bio-inspiration (biomimetics). It includes a listing of some other Musings posts in the area.

One example... Bending a rigid rod (May 17, 2013).

Crocodilians: Thick-skinned but very touch-sensitive

January 2, 2013

People have known about the ISOs for a while, and known that they are sensory organs. However, their biological function has been unclear. A new article reports more in-depth work on the ISOs of crocodilians (alligators and crocodiles). Among the findings... crocodilian ISOs are more sensitive to the touch of a hair than are human fingertips.

The paper includes anatomical work, examining the structure of the ISOs and their connection to the nervous system. It also includes functional tests, such as the one noted above.

What are the ISOs for? Think about the situation... an armor-plated animal -- with ultra-sensitive mechanosensory sites. They can detect small water ripples, such as those caused by possible prey. And they can detect contact with prey and whatever else is around. It seems likely that the high density of the ISOs around (and in!) the mouth aid is distinguishing food from debris -- and from the kids. Female alligators gently carry their young in their jaws.

News story: Despite Their Thick Skins, Alligators and Crocodiles Are Surprisingly Touchy. (Science Daily, November 8, 2012.)

* News story accompanying the article: Croc jaws more sensitive than human fingertips. (K Knight, Journal of Experimental Biology 215(23):i, December 1, 2012.)
* The article: Structure, innervation and response properties of integumentary sensory organs in crocodilians. (D B Leitch & K C Catania, Experimental Biology 215:4217, December 1, 2012.) There is a 3-minute movie file associated with the article. It is freely available from the article web site; choose "Supplementary Material". That takes you to a description of the various scenes, and a link to the movie file. Some scenes include a human hand, which will give you a size comparison.

If you find yourself paying more attention to parts of the structure other than the little bumps, you should know that the work here used juveniles, only a few centimeters long. As noted above, the movie file with the article lets you compare the size of the animals with a human hand.

More on the crocodilians:
* Crocodiles, humans, and stones (November 13, 2009).
* Space shuttle: some final photos (December 3, 2012). You'll have to look around a bit.

More about the sense of touch... eSkin: Developing better sense of touch for artificial skin (November 29, 2010).