The Antikythera device: a 2000-year-old computer

August 31, 2011

It's among the oldest known geared devices -- of a complexity unknown for many centuries.

The object shown above was pulled from the sea in 1900. It's from a shipwreck that occurred 2000 years earlier -- a shipwreck encountered by accident by divers looking for sponge. The stories of what this device does and how that was learned are fascinating.

It's known as the Antikythera device, from the Greek island near its discovery. It has been examined by various techniques over the years, including increasingly sophisticated forms of X-ray analysis as they were developed. Over time, a picture has emerged. It consists of a system of gears that carries out various astronomical calculations and displays the results on dials. It is, therefore, a calculator -- perhaps even a computer. (What's the difference? It's not very clear -- and not very important here. It's just a teaser: This 2000-year-old device might reasonably be considered a computer. Those who read the book will get one man's opinion, but it does not help much.)

It's not news that such astronomy was known, and considered important to the ancients. What is historic here is that this is a very old geared device. When discovered, it was the oldest known geared device -- a thousand years older than the previous record holder. It is still one of the oldest known such devices. It is plausible -- though uncertain due to the sparse record available so far -- that this is a forerunner of modern geared devices, including clocks. A forerunner, perhaps -- but it is also more complex than any such devices known so far up to at least the 14th century. Further, the nature of the device is an insight into ancient Greek technology: quite small and intricate, requiring high precision manufacturing.

The fossil record of machines has much analogy to that of organisms. Fragments. A sparse record. Understanding each individual device/fossil is a challenge. And the story of how various fossils are related is tentative, subject to more information becoming available. This device revolutionizes our views of the history of geared machines. A plausible history begins to emerge, but it is very incomplete. We need more fossil clocks and computers!

The story of the Antikythera device has peaked in recent years, though study continues. The story has been told in various scientific papers. Usefully, it has been told in a general-interest science book by Jo Marchant. I have noted this book on my page of Book suggestions: Marchant, Decoding the Heavens. The journal Nature has published various articles, both technical and news, on the device. I encourage you to check out their video, listed below, as a good introduction.

Videos. Here is a two-part video produced by Nature, in conjunction with a paper on the device in 2008. Each part is about 10 minutes. Together, they are a good introduction and overview.
* Part 1    * Part 2
A search on Antikythera videos will turn up more, including one on a model made with Lego blocks. (Watch dates. The story of the Antikythera device is a developing story. You may find older videos -- or readings -- with information that is no longer current.)

An article. This one discusses the interpretation of the inscriptions. Reflections on the antikythera mechanism inscriptions. (M K Papathanassiou, Advances in Space Research 46:545, August 10, 2010.)

Among other resources...
* Wikipedia: Antikythera mechanism. The picture above is from this page. It shows the largest piece.
* Interactive Relighting of the Antikythera Mechanism. Among the technologies used to analyze the device was one developed by HP (Hewlett Packard). It involves reflectance imaging -- detailed analysis of the surface under various lighting conditions. This page is an entry point to their work, with some examples. Click on "PTMs" for more about the method -- and a picture of an artefact a thousand years older then the Antikythera device! (Now archived.)

Added July 11, 2024. More about the device: Which calendar did the Antikythera device use? (July 11, 2024)

More on computing history:
* Alan Turing, computable numbers, and the Turing machine (June 23, 2012).
* Book suggestions: Swade, The Cogwheel Brain - Charles Babbage and the Quest to Build the First Computer (2000).

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

More on gears... Quiz: What are they? (September 27, 2013).

More about shipwrecks... An ancient navigation device? (April 16, 2013).

Posts on sponges include... Bending a rigid rod (May 17, 2013).

More from the Greek seas: Underwater "lost city" explained (July 25, 2016).

More old things... Claim of oldest fossilized cells refuted (May 3, 2015).

How to find the blood

August 29, 2011

To him, blood is dinner. Vampire bats live on blood. They sneak up on an animal in the dark, and go directly for a vein. How do they know? Scientists have long known that the bats are able to detect heat -- as infrared (IR) radiation. They do this using a special organ, known as a pit, near the nose. But how do they detect IR radiation of this type? That is not a common trait!
The picture is reduced from the one featured in the Nature news story, listed below.    closer view.    Hm, maybe I should have chosen a picture that better shows the teeth -- barely noticeable here. I chose this one as being cute.

New work explores this further, and finds the heat sensor. In fact, they find the specific molecule that is sensing heat. It is an interesting story.

As background... We all have heat sensors. Just approach the hot stove, and you will know. Over recent years we have come to know that we detect the heat through a specific protein, a heat sensor. It is an ion channel in the cell membrane. When the channel protein gets hot, it changes shape, and allows specific chemicals (ions) to flow; the ions are what initiate the nervous system response.

The new work shows that the vampire bats have re-tuned this regular heat-sensing protein, which normally helps to protect us from noxious heat, so that it detects normal body temperature. They make two versions of this heat sensor; the one tuned to detect body heat of their victims is made only in the facial pit structure.

Overall, then, they provide good evidence that a novel form of this ion channel protein has been re-tuned so that it is sensitive to body heat. Its localization to the facial pits is consistent with that use. Thus we seem to have the molecular basis for one step in how vampire bats find their target.

Some snakes also have IR sensors to detect body heat. Some, such as the pit vipers, have an anatomical structure somewhat like that of the vampire bats. However, the molecular basis of the pit viper heat sensor is different. It seems, then, that this heat sensing trait arose independently in the two groups of animals.

News story: What Steers Vampires to Blood. (UCSF, August 3, 2011.)

* News story accompanying the article: Neuroscience: Heat-thirsty bats. (M B Fenton, Nature 476:40, August 4, 2011.) This provides a useful introduction to vampire bats, as well as to the heat sensing.
* The article: Ganglion-specific splicing of TRPV1 underlies infrared sensation in vampire bats. (E O Gracheva et al, Nature 476:88, August 4, 2011.)

More about vampire bats:
* The biological basis of sanguivory (March 2, 2018).
* What can we learn by looking at the DNA in vampire bat feces? (May 27, 2015).

Other posts on bats include...
* Don't eat the bats.     or     An ALS story: Guam and New Hampshire; food chains and biomagnification; cyanobacteria, cycad trees, and flying foxes; pond scum; and BMAA. (October 6, 2009).
* Water: a bat's view (December 3, 2010).
* Baseball physics (July 31, 2011).
* A plant that communicates with bats (September 7, 2011).

A post about developing an artificial sense for infrared light: Can rats touch infrared light? (February 25, 2013).

Also see:
* How the teeth are sensitive to cold (June 14, 2021).
* Heart health and python blood (December 28, 2011).
* Making an artificial ion channel from DNA (January 8, 2013).

For more about lipids, see the section of my page Organic/Biochemistry Internet resources on Lipids. It includes a list of related posts.

Mayhem at the center of the Milky Way

August 23, 2011

This post is about some colorful writing. The first news story listed below starts, "The Milky Way's center houses a supermassive black hole so sleepy that it probably hasn't swallowed a decent meal for years." Now, that gets attention. I've included another news story, and the article they refer to.

The topic is some speculation about what's going on at the center of our galaxy. More specifically, it's about a burst of star formation a few million years ago. They suggest this could relate to a collision of black holes as part of a galactic collision. It's important to note that, while there are interesting ideas here, this is largely speculation. In fact, the paper listed below is a draft -- apparently posted to solicit comment. An important part of this will be for the astronomers to suggest alternatives, and then to suggest what observations might help distinguish among the proposed explanations. So, enjoy the story -- especially the first item listed below. Don't take it too seriously, at least for now.

News stories...
* Black Hole Collision May Have Set Off Fireworks in the Milky Way. (Science Now, July 27, 2011.) Check it out, for some fun science writing -- and a good presentation of the story.
* Massive Black Hole Smashed Into Milky Way 10 Million Years Ago -- Evidence is emerging that a small galaxy, with a huge central black hole, must have recently collided with the Milky Way, say astronomers. (The Physics arXiv Blog, MIT Technology Review, July 19, 2011.)

The article, which is freely available at the arXiv: Can A Satellite Galaxy Merger Explain The Active Past Of The Galactic Center? (M Lang et al, July 18, 2011.) Caution: The version posted is a draft of an article. It has not yet been submitted to a journal, and has not been peer-reviewed. The authors have posted the draft in order to solicit comments. It is possible that other versions will be posted later. (The date on the article and the date on the arXiv page are incompatible. No big deal.)

More on black holes...
* Gravitational waves (February 16, 2016).
* How would you die if you visit a black hole? (May 6, 2013).
* Black hole: simulation (March 15, 2010).

More on galactic mergers...
* LEDA 074886 (April 2, 2012).
* What is it? (February 7, 2011).

More about the Milky Way:
* We are all Laniakeans (October 21, 2014).
* Dung beetles follow the Milky Way (February 24, 2013).

Medical ethics: pregnancy reduction

August 20, 2011

Good presentations of ethical dilemmas should make everyone squirm a bit. After all, if there weren't good points on each side, it wouldn't be a dilemma, would it? The following item from the New York Times should fill the bill. For now. we'll just let the article stand on its own. I really encourage everyone to read it through -- and squirm a bit.

The Two-Minus-One Pregnancy. (New York Times, August 10, 2011.)

What is your "first" or "main" reaction?

Another post on IVF ethical issues: Let parents decide (May 14, 2010).

A post about embryo screening... In vitro fertilization: Will it suffice to transfer only one embryo? (May 19, 2013) A key goal is to reduce the number of embryos implanted.

Also see... A gene that reduces the chance of successful pregnancy: is it advantageous? (May 18, 2015).

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

Speech: Taking turns

August 17, 2011

A recent Musings post was on the ability of chimpanzees to listen [link at the end]. The big theme was that human language requires more than just the ability to speak. Exploring these other aspects in other animals may offer insights into the development of human language. In that post, we looked at the ability to listen -- a necessary component of language. In this post, we look at the ability to "take turns" in a "conversation". In the new work, scientists examine the ability of a very talkative type of monkey to respect the taking-turns rule.

In summary, then, the young do not seem to know the rule for taking turns in a conversation, but adults do. This is similar to what is found for humans. That is, "taking turns" is a rule that develops -- and it does so in this monkey and in humans.

As always, it is important to note the limitations, and to be cautious about over-interpreting the results. We do not know if the rule develops from learning, or from innate development. We do not know if it develops the same way in both monkey and human. And even with these two examples, we must not assume it occurs for all related animals. In fact, they suggest that chimps do not respect the taking-turns rule. At the end of the paper, they offer a good discussion of how one might interpret the new work, including its limitations.

The article is short and much of it is quite readable. I encourage you to have a look. It is freely available: Youngsters do not pay attention to conversational rules: is this so for nonhuman primates? (A Lemasson et al, Scientific Reports 1:22, June 23, 2011.)

Background post: Speech: Are chimps good listeners? (July 25, 2011)

Other posts on language include:
* How children acquire language skill: the role of conversation (December 3, 2018).
* Can chimpanzees learn a foreign language? (March 10, 2015).
* Mountains and human language? (June 28, 2013).

For more on monkeys...
* The first chimeric monkeys (February 5, 2012).
* Prejudice against outsiders -- in monkeys (May 10, 2011).

Quark soup

August 15, 2011

Ice crystals consist of water molecules that are held together to form a recognizable higher order structure. If you put enough energy into an ice crystal, the interaction between the water molecules is overwhelmed; the crystal loses its structure, leaving a collection of individual water molecules loosely interacting in the liquid state. We call this behavior "melting"; for water-ice, it occurs at a temperature of 273 K (0 °C).

Somewhat analogously, neutrons and protons -- the familiar particles of the atomic nucleus, and collectively called nucleons -- each consist of three quarks. Perhaps, if one put enough energy into the nucleons, the interaction between the quarks would be overwhelmed, leaving a collection of quarks, loosely interacting in a liquid-like state.

A new paper reports that this happens. What's particularly important is that theory and experiment are in good agreement on how much energy is needed. Agreement between theory and experiment suggests that physicists understand what is happening. How much energy does it take? In the language of the plasma physicists, it takes about 175 million electron-volts (MeV) to melt nucleons. They convert this energy value to the common temperature scale using the Boltzmann constant (1 eV = 11605 K); it's about 2x10¹² K -- two trillion Kelvins.

Do we care? Well, aside from it representing an advance in our basic understanding of matter, the universe presumably went through the reverse of this transition shortly after the Big Bang. Thus this paper helps with our understanding of the early universe.

We started this post with ice crystals. Adding energy (raising the temperature) broke the crystals down to their components, the water molecules. Adding more energy would break down the water molecules to their components, the atoms of hydrogen and oxygen. And so forth. The new work is about a later stage, where the individual nuclear particles (nucleons) are broken down to their components, the quarks. The Big Bang created a very hot universe; as the early universe cooled, the same kinds of processes occurred -- in reverse. It's thought that the state of the universe was something like what was achieved here for about a microsecond -- starting about 10^-12 second after the Big Bang. When the universe had aged to about 10^-6 second, it had cooled enough that the quarks combined to form particles such as protons and neutrons. This brief time when quarks dominated the universe is known as the quark epoch. [Wikipedia: Quark epoch.]

After reading a draft of this post, a physicist offered some other energy numbers -- in the same units -- for comparison. He notes... Separating the proton and electron of a hydrogen atom takes ~10 eV. Separating the proton and neutron of a deuterium nucleus takes about 2 MeV -- about 200,000 times more. We now see that "melting" nucleons, to make something like a liquid phase of quarks -- takes 175 MeV -- another 100 times that.

News story: When Matter Melts: Scientists Map Phase Changes in Quark-Gluon Plasma. (Science Daily, June 24, 2011.) Good overview.

* News story accompanying the article: Physics: The Limits of Ordinary Matter. (B Müller, Science 332:1513, June 24, 2011.) The figure above is from this article. This is actually a rather readable overview of some complex physics. Give it a try!
* The article: Scale for the Phase Diagram of Quantum Chromodynamics. (S Gupta et al, Science 332:1525, June 24, 2011.) The article is an interesting international collaboration between scientists in India, China, and the USA (Lawrence Berkeley). The lead author is a theoretical physicist from the Tata Institute of Fundamental Research in Mumbai. The experimental results, which were previously published, are from Brookhaven National Lab in New York state. In fact, the current paper involves interpreting the earlier experimental results in terms of the energy requirement for the nucleon → quark transition.

Also see:
* 3D printing: Make yourself a model of the universe (December 19, 2016).
* On the testability of scientific models (March 14, 2015).
* IceCube finds 28 neutrinos -- from beyond the solar system (June 8, 2014).
* The proton -- and a 40 attometer mystery (March 17, 2013).
* A galaxy far, far away: the story of MACS 1149-JD (October 12, 2012).
* Discovery of the neutron: 80th anniversary (February 27, 2012).

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

Can genes be patented? The Myriad case -- Reversal

August 10, 2011

Among the posts in this story...
* Can genes be patented? The Myriad case (April 2, 2010). Original post.
* Can genes be patented? The Myriad case: The Last Word (June 26, 2013).

Briefly, in that original post, we noted that a court had ruled invalid a set of patents on isolated genes. The current news is that an appeals court has overturned that decision. That is, the gene patents are now legal.

Please read the original post before trying to make much of this. Remember, the issues here are legal -- and there are disagreements. In fact, the new ruling was by a split vote. There are also more parts to the story than noted in my brief summary above.

News stories...
* Court of Appeals Rules that Myriad's Patents on BRCA Genes Are Valid. (GEN, July 29, 2011.) Not particularly well written, but it does give an overview of the various issues.
* Myriad Genetics Ruling That DNA Is Patent-Eligible. (Corporate Law Report, August 3, 2011. Now archived.) Links to multiple legal commentaries.

What else are feet good for?

August 8, 2011

Electron micrograph (SEM) of part of a tarantula foot -- making silk. This is Figure 5E of the paper. Scale bar for this part is 20 µm. From the figure legend: "Fig. 5. Silk-secreting spigots on tarantula spinnerets (SEM images). ... (E) Indian ornamental spigot shank with scale-like ornamentation and a silk droplet at its tip." Spiders commonly make silk for webs or other structures; the silk is extruded from spinnerets on the abdomen. The new paper shows that tarantulas also extrude silk from their feet; the silk is used to help them hold on to vertical surfaces -- sort of like a climbing rope.

News story: Tarantulas Shoot Silk From Feet, Spider-Man Style -- To keep balance, spiders spin silk using foot "spigots". (National Geographic, May 16, 2011. Now archived.) Features a picture of the lead author's pet tarantula. Good overview of the work.

* News story accompanying the article: Tarantulas shoot silk from feet. (K Knight, Journal of Experimental Biology 214(1):i, June 1, 2011.)
* The article: Tarantulas cling to smooth vertical surfaces by secreting silk from their feet. (F C Rind et al, Journal of Experimental Biology 214:1874, June 1, 2011.) The paper starts with a discussion of the controversy about an earlier report that tarantulas might make silk on their feet. It ends by discussing the possibility that silk production in the feet was the primitive form in spiders, with abdominal production coming later.

More about silk: Spider silk: Can you teach an old silkworm new tricks? (October 13, 2010).

More about spiders and such:
* Why do many tarantulas have blue hair? (March 7, 2016).
* Tarantulas in the trees (November 11, 2012).
* How the spider avoids being attacked by the ants (January 10, 2012).
* How to seat a spider in front of the computer (September 28, 2010).

More about feet: A shoe (August 9, 2010).

Aerospace engineers develop explosive device for supersonic delivery of vaccines

August 2, 2011

Vaccines without painful -- and expensive and hazardous -- needles. Many are working on some substitute for the traditional injection. We have noted one example before: A better way to deliver a vaccine? (July 25, 2010).

Now we have a new approach -- and it certainly is an exciting approach. The lead authors of the paper are from the Department of Aerospace Engineering at the Indian Institute of Science, Bangalore. Their basic approach is to put an explosive device on the skin (at the site of the intended injection), ignite it -- and, voila, you are injected.

How big an explosion? In terms of TNT (trinitrotoluene)... The explosions here are equivalent to 0.168 milligrams of TNT. (That's about 2x10^-10 tonnes of TNT.) The explosion is big enough to generate supersonic shock waves -- at a very tiny area: the injection site. That's really the point. It is the energy of the shock wave that delivers the injection sample into the skin.

In the paper they present data to show that vaccinating mice with this device is effective -- as effective as ordinary vaccination. (In fact, they have some evidence that the vaccination is more efficient, thus allowing use of lower doses. The greater efficiency may be a general property of vaccination in the skin per se.)

What should we make of this? They have developed a novel system for administering vaccines (or drugs, such as insulin) into the skin. Animal testing shows that the device works. They hope to start testing with humans. The news story discusses some of the economics of the device -- indicating that the authors have at least considered that important issue. Ultimately, the value of the device will depend on whether it is safe and effective -- and economical and practical -- with humans. It is a candidate for that further testing. Time will tell.

News story: IISc designs India's first needleless drug device. (Live Mint, February 22, 2011. I am unfamiliar with Mint -- or Live Mint. Mint is apparently a business-oriented newspaper in India.)

The article: Needleless Vaccine Delivery Using Micro-Shock Waves. (G Jagadeesh et al, Clinical and Vaccine Immunology 18:539, April 2011.) The Introduction notes other medical applications of shock waves.

More on shock waves...
* What happens when the cork is removed from a bottle of champagne? (October 27, 2019).
* Blast detector (December 29, 2010).

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

More on needleless delivery of vaccines: The nasal spray flu vaccine: it works in the UK (April 12, 2017).

More on vaccines is on my page Biotechnology in the News (BITN) -- Other topics under Vaccines (general).

Baseball physics

July 31, 2011

Bat meets ball -- the crack of the bat. A distinctive sound. The essence of the American "national pastime".

It's a simple physics problem. A collision. If the ball simply hit a solid wall, it would bounce back. But it hits a swinging bat, and the energy of the bat is transferred to the ball. Analyzing collisions is a mainstay of physics. However, there is a catch: collisions vary in how the energy is transferred. In an idealized elastic collision, the transfer of energy as kinetic energy (energy of motion) is complete. However, when one drops a mudball on a floor, the ball does not bounce back at all; this is an inelastic collision. Real collisions may have elasticity anywhere between these extremes.

So, how well is kinetic energy transferred between bat and baseball? That is, how elastic is the bat-ball collision? It depends -- on the nature of the bat and the ball. A new paper explores how the elasticity of the collision varies with certain conditions, such as the temperature and humidity of ball storage, and whether the bat is "corked".

In this work, they measure the coefficient of restitution (COR), using bats and balls with various treatments. The COR is a measure of the elasticity of the bat-ball collision. A COR of 1 would be a completely elastic collision. A COR of 0 would be a completely inelastic collision. A bat-ball collision with higher COR means that the ball will go further; a higher COR would lead to more home runs.

Here are two examples of their findings, shown together in Figure 4 of the paper. Both of these deal with how baseballs are stored prior to use. In one experiment, they looked at the effect of humidity. Balls were stored at various humidities for six weeks, all at the same temperature (72 °F, which is about 22 °C). Measurements of ball weight showed that it took 1-3 weeks for the balls to equilibrate to the new humidity. Balls stored at the various humidities were then tested for their COR. These results are shown with open symbols and the dashed line; the scale for relative humidity is at the bottom. In the other experiment, they looked at the effect of temperature (T). Balls were stored at various temperatures for 24 hours. Balls stored at the various temperatures were then tested for their COR. These results are shown with solid symbols and the dotted line; the scale for T is at the top.

You can see that storing the balls at higher humidity leads to a decline in COR, as you might expect. You can also see that storing the balls at higher T leads to an increase in COR. The reason for this is not entirely clear; it may be in part due to moisture changes. The big conclusion is that ball storage conditions matter.

News story: The Physics of Cheating in Baseball. (Smithsonian, June 24, 2011.)

The article: Corked bats, juiced balls, and humidors: The physics of cheating in baseball. (A M Nathan et al, American Journal of Physics 79:575, June 2011.)

One aspect of the paper bothers me. The title of the paper refers to cheating -- an aspect picked up on by many of the news stories. However, only one of the variables they study in the paper (corked bats) involves a possible cheating -- where what they study is subject to rules. In fact, the word cheating does not appear in the paper except in the title. The paper is about the physics of baseball. It is unnecessary to bring up cheating in order to discuss the paper.

The particular experiments shown above were motivated in part because one major league baseball team in fact stores baseballs at higher humidity in order to reduce home runs. The work shows that this may work as they hoped. So far as I know, there is no cheating here; there are no rules on ball storage. Perhaps there should be -- guided by work such as reported here.

Baseball fans will enjoy reading what they did with corked bats -- and will perhaps be surprised at their results.

More baseball...
* Effect of climate change on baseball games (June 10, 2023). Links to more.
* The origins of baseball -- two million years ago? (August 18, 2013).
* The Mudville story, on its 125th anniversary (June 3, 2013).
* Baseball and violins (May 15, 2012).

Other posts about sports...
* The turtle that plays basketball (November 12, 2010).
* Flow centrality: the key to a scientific analysis of the soccer game (July 11, 2010).
* Athletes: Head injuries (October 5, 2009).

There is now an extensive list of sports-related Musings posts on my page Internet resources: Miscellaneous under Sports. Added September 8, 2024.

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

More about collisions: Sandstorms and midair collisions (September 16, 2013).

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

Quiz: Barack Obama and polar bears -- answer

July 27, 2011

Original post: Quiz: Barack Obama and polar bears (July 20, 2011). As a reminder, the quiz simply asked... "What do Barack Obama and polar bears have in common -- in terms of their ancestry?"

The answer is now included at the end of the original post.

Speech: Are chimps good listeners?

July 25, 2011

Speech and language are distinctive parts of being human. One part of speech is listening. Speech would not be very useful unless we could listen. Listening includes anatomical issues (ears), and neurological issues (interpreting the sounds). How did all these various aspects of speech and listening develop? We know something about the anatomical features, but much less about the neurological aspects. Is the ability to listen -- the ability to distinguish and interpret the sounds of speech -- already present in pre-speaking ancestors? Did the abilities to speak and to listen develop side by side?

A new paper was motivated by questions such as those. Briefly, they investigated the ability of a chimpanzee -- one who was well trained to understand human speech -- to understand distorted speech.

The figure below shows the key results. This is Figure 3 of the paper. In each test, the chimp was presented with a word, either with natural speech or a distorted synthetic speech. The animal tried to identify the word by choosing from among four candidate words. (Thus 25% would represent random success; this level is noted by the dashed horizontal line.) Humans were also tested; although the general intent of the tests was the same, the procedure used for humans was different. Since this is a preliminary test, and the protocols used for chimp and human were not the same, we will look for the main effects, and not worry about small differences.

Let's start with the left block of results, for the chimp. We see that with natural speech, the chimp scored about 80% (white bar). The chimp was presented words in a type of synthetic speech called noise-vocoded (NV). The chimp scored about 55% with these distorted words (the two darker bars -- which don't really differ). Now, look at the left-most of the two data sets for humans. This compares human results for natural and NV speech. Humans do better on both parts than the chimps; the decline from normal to NV speech is similar for chimp and human. The remaining tests compare natural speech with another type of synthetic speech, called sine wave (SW). There are two sets of results for chimps and one for humans. Again, the big picture is that the results for chimp and human are similar.

The overall "big picture", then, is that the chimp -- one experienced with human speech -- tested about as well as humans on understanding two types of distorted speech. Remember that the test is measuring not just the ability to recognize the sound, but to interpret a distorted sound in terms of known words. The significance of this result is unclear; the discussion in the paper on this is quite good. I think for now, we simply note that they did this -- an interesting experiment. Hopefully, it opens the door to further work exploring how the chimp "listens".

News stories:
* Chimp recognises synthetic speech. (BBC, July 7, 2011. Now archived.) Includes a couple of pictures of the chimp, one of them "at work".
* Chimp has an ear for talk -- Language-trained ape recognizes distorted speech surprisingly well. (Science News, July 8, 2011.) Includes audio clips to show the various types of speech tested. (I suggest you try the "natural speech" one last.) [September 10, 2012... This article is no longer freely available.]
* Chimps Are Good Listeners, Too. (Science Now, July 1, 2011.)

The article: A Chimpanzee Recognizes Synthetic Speech with Significantly Reduced Acoustic Cues to Phonetic Content. (L A Heimbauer et al, Current Biology 21:1210, July 26, 2011.)

The Supplemental Information linked to the article includes two short audio files that illustrate the types of speech used here; I think you can access these regardless of whether you have access to the article itself. Each file has one word, in the three speech types tested: natural, noise-vocoded, and sine-wave. (Unfortunately, the first one is "normal", so you hear the distorted speech styles already knowing what the word is.) (One program questions the file type of these audio files, but plays them fine.)

Also see...
* Do apes say "hello"? (September 14, 2021).
* If you are talking with someone, how can you tell if they are paying attention? (May 8, 2017).
* The smartest chimpanzee? (September 29, 2012).
* Can French baboons learn to read English? (May 13, 2012).
* Are some languages spoken faster than others? (November 21, 2011).
* Speech: Taking turns (August 17, 2011). On speech -- in monkeys.
* What makes us human? A new approach (April 25, 2011). On chimpanzees.

Recovery from natural disaster: can the poor benefit?

July 22, 2011

A disaster occurs. Over time, the survivors rebuild. What is the long-term result? Is it possible that the long-term result is "good" -- good for the poor or disadvantaged? If so, what conditions might promote getting a good result?

A paper on this topic appeared recently in a prestigious scientific journal. The paper is a case study of one incident. They argue that the poor did benefit, and they suggest why it worked out this way. The secret, they suggest, is to allow bottom-up control of the recovery. It's an intriguing paper.

Here is their data. This is Figure 1 of the paper. They divide the population into thirds, by the amount of land they owned (a measure of economic status). The lowest third, the most land-poor, is denoted by blue bars, at the left of each set; see the key at the top of the figure for more. The first set of data, labeled 1999, is from shortly after a hurricane. The bars show the change in land holdings compared to a 1998 baseline, before the hurricane. All three groups lost land; the poor lost the most -- on a percentage basis. The other two data sets are for two times a few years after the hurricane. Both years show the same general effect: the poor have gained the most land -- again, on a percentage basis. (Just look at the overall bar height for now. The dark bars within the big bars of these two data sets show the amount of land gained "by claiming primary forest".)

That graph is the heart of their story. It leaves much unanswered, including what has happened in the near-decade since their last data. (They do note that the area survived flooding in 2008 with little effect.) In the paper, they discuss how the recovery occurred, and why they think this worked out rather well. Although one can point to many holes in the story, and question assumptions, it is an intriguing story -- worth a look with an open mind. Remember, this is a "natural experiment". They just happened to be studying this particular society when a hurricane occurred. They observed, and now they report what they saw, and provide their comments.

News story: Climate-Related Disasters May Provide Opportunities for Some Rural Poor, Study Suggests. (Science Daily, March 14, 2011.)

The article: Climate-related disaster opens a window of opportunity for rural poor in northeastern Honduras. (K McSweeney & O T Coomes, PNAS 108:5203, March 29, 2011.)

More about floods: Flooding in The Netherlands: natural or manmade? (September 19, 2015).

More about hurricanes: The effect of hurricanes on lizards (August 14, 2018).

Early American art: a 13,000 year old drawing of a mammoth

July 18, 2011

That's it. A drawing of some elephant-like animal -- probably a mammoth or mastodon. The drawing is about 3 inches long and 2 inches high (7.5 cm x 4.5 cm). The drawing was found engraved on a fossil bone, in Florida. The bone -- and drawing -- were discovered by an amateur fossil hunter, who recognized the possible importance, and took it to university researchers. Here is a picture showing the drawing in the context of the full bone. The bone is about 16 inches (40 cm) long. The bone [link opens in new window].

Finding a drawing of a mammoth made by a human means that the human knew what a mammoth looked like. Since the mammoths went extinct about 13,000 years ago, this is evidence that humans were there 13,000 years ago -- humans with the artistic talent and instinct to draw the fauna.

Some of you with roots outside the Americas may be laughing at me for posting this. 13,000 years? You call that old? Yes, I do. America was the last continent to be inhabited by humans. The time of the first arrival of humans in America is not entirely clear. It is almost certainly within the last 20,000 years; until very recently, even the 13,000 year age of this item might have seemed suspicious.

News stories. The text of the following two items is substantially the same. The former may be easier to read.
* Earliest Art in the Americas: Ice Age Image of Mammoth or Mastodon Found in Florida. (Science Daily, June 21, 2011.) The picture above is from this page.
* Bone fragment is only Ice Age artwork from America to show a "proboscidean". (Smithsonian, June 22, 2011.) The larger picture, linked above, is from this page.

The article: Earliest Art in the Americas: Incised Image of a Proboscidean on a Mineralized Extinct Animal Bone from Vero Beach, Florida. (B A Purdy et al, Journal of Archaeological Science 38:2908, November 2011.) Much of the paper is about establishing that the bone is authentic.

For more on mammoths and such...
* Did the First Americans eat gomphothere? (July 29, 2014).
* Uptake of small pieces of ancient mammoth DNA by bacteria: What are the implications? (May 13, 2014).
* If the elephant can't find its dinner, should you help by pointing to it? (October 18, 2013).
* To kill a mastodon (November 15, 2011).
* Mammoth hemoglobin (February 1, 2011).
* A mammoth story (December 1, 2008).

More about prehistoric art:
* Images from 30,000-year-old motion pictures (July 22, 2012).
* Leopard horses (December 2, 2011).

For a book on the earliest Americans, see my Book Suggestions page: Meltzer, First Peoples in a New World -- Colonizing Ice Age America (2009).

A human protein that can sense magnetic fields

July 15, 2011

The Musings post Magnetic field perception (June 16, 2010) noted a nice discussion of magnetic field detection by animals. Now we have a report of a human protein that seems to be able to detect magnetic fields -- when transplanted into the fruit fly Drosophila. Let's look at what they did, and then discuss the meaning of the result.

The figure below (Figure 1a from the paper) shows the key results. It's a complex figure, so let's go through it slowly. There are four experiments, each of which has two parts. The basic design is that a batch of flies is tested in a T-maze, in which one arm has a magnetic field. They measure the number of flies in the arm with the magnetic field and the number of flies in the arm without the magnetic field; the result is expressed as a "preference index" for the magnetic field. The two parts of each experiment involve flies that are "naive" (untrained) and "trained". In the training the flies learn to associate a magnetic field with a reward of food.

We'll start with the two controls, one positive and one negative. Then we'll look at the key experiment with the human protein.

Restoring the responses by adding back the fly gene shows that they are studying the right gene. That the human gene also works shows that -- well, that the human gene can substitute for the fly gene. This is a standard type of test, and it is common that a defect in one organism's genome can be remedied by a related protein from another species.

However, we must also recognize the limitations. It may be that the human protein can function in the fly, but this does not mean it does function that way in humans. For example, it is possible that the protein is capable of a magnetic response, but that it is not connected up to the nervous system in humans for that response. They properly conclude that their results suggest that the possibility of a magnetic response in humans, with the involvement of this protein, should be studied further.

News story: Can Humans Sense Earth's Magnetism? Human Retina Protein Can Function as Light-Sensitive Magnetic Sensor. (Science Daily, June 21, 2011.)

The article, which is freely available: Human cryptochrome exhibits light-dependent magnetosensitivity. (L E Foley et al, Nature Communications 2:356, June 21, 2011.)

More on magnetic reception in animals... The nature of a bio-compass? (June 10, 2016).

Another example of studying the senses in fruit flies: What does blue light smell like? (July 18, 2010).

For more on using Drosophila as a model system... Making smarter flies (July 18, 2012).

More on cryptochromes... An unusual eye? (June 6, 2012).

More about magnetic fields: What if your compass pointed south? (October 24, 2014).

Does XMRV cause CFS? We have a verdict. Maybe.

July 11, 2011

In October 2009, a report appeared claiming an association between xenotropic murine leukemia virus-related virus (XMRV) and the mysterious human illness chronic fatigue syndrome (CFS). A few months later, a second paper appeared on the issue, claiming there was no association. Ah, a scientific dispute -- and a Musings post: A virus that is or is not associated with chronic fatigue syndrome (February 12, 2010). Scientific disputes get resolved by collecting further evidence. By mid-2010 we had two new papers -- one on each side. And we got another Musings post, a follow-up that is linked to the original. We should also note that the same virus was reported to be associated with prostate cancer, and similar confusion surrounded that claim.

This is an important issue, because CFS is poorly understood, and typically untreatable. The claim of a virus being involved is intriguing -- a possible lead, or even breakthrough. We need to emphasize that even those claiming an association between the virus and the disease have no evidence that the virus is involved in the disease process. But if this virus -- a retrovirus -- is involved in CFS, then drugs against retroviruses (such as those used against HIV) might be useful. In fact, some have administered these drugs to patients; to my knowledge, no meaningful results from controlled experiments have been reported.

Work has continued -- as has the dispute. Are both sides right -- and CFS is heterogeneous? Or is one side finding a virus that is not there? Or is the other side failing to find a virus that is there? All of these are plausible; it takes focused work to sort out the possibilities. At least to some extent, people on the two sides have cooperated to try to do definitive experiments.

Various weaknesses of the XMRV story have cropped up over the last couple of years. However, two new papers would appear to deal a death blow to the claim that XMRV is associated with CFS. Article #1 finds no evidence for the virus in a sampling of CFS patients -- using the "best possible" testing; their sampling includes several patients for whom positive results had been obtained by other labs. Further, they show that viral nucleic acid (DNA) contaminates some common lab materials; this can explain why some may find a virus that is not there. They also find that human serum inactivates the virus, making establishment of infection unlikely. Article #2 uncovers the likely origin of the virus, as a laboratory recombinant. Further, they are able to examine the original sample of a prostate cancer that had been reported to have the virus; the original sample does not have it, but after passage through mice, it does. This strongly suggests that the original finding of the virus in the tumor was an artifact of lab work.

Overall, the key points are:
* Testing does not reproducibly show the virus. This include testing of the same patients.
* One reason for that variability of testing has been found: common lab materials, including commercial reagents, may be contaminated with the virus.
* The particular virus XMRV now appears to have been made during lab work a few years ago. This point does not preclude that it might cause disease, but it could not have done so a few years ago -- since it did not exist then. Implicating this new virus in CFS (or prostate cancer) makes little sense, since the diseases existed long before this virus did.
* Various characteristics suggest that the virus is unlikely to establish infection in humans.

Both papers involve complex experiments, with complex technical issues. I have noted only some highlights. I do not intend that my brief descriptions here are sufficient to convince you of the conclusion; instead, I intend simply to give an idea of what was found. However, it is fair to state that most -- but not all -- workers in the field, looking at these new papers and the sum total of the evidence, do not think that XMRV is associated with CFS (or with prostate cancer).

News stories:
* Retraction Sought, Refused on XMRV-CFS Study. (MedPage Today, May 31, 2011.) Discusses the scientific content of both new papers, as well as a personal dispute.
* Mouse Virus Erroneously Linked to Chronic Fatigue Syndrome, Study Finds. (Science Daily, May 31, 2011.) This item is mainly about paper #1.

The articles:
1) No Evidence of Murine-Like Gammaretroviruses in CFS Patients Previously Identified as XMRV-Infected. (K Knox et al, Science 333:94, July 1, 2011.)
2) Recombinant Origin of the Retrovirus XMRV. (T Paprotka et al, Science 333:97, July 1, 2011.)

Here is a Q&A page from the National Cancer Institute summarizing the new consensus view. It includes an extensive list of references. XMRV and Human Disease Association: Questions and Answers. The page was actively maintained during the debate. The link here is to an archived version, dated May 31, 2011. It includes the new articles discussed here, and seems to be the end of the active phase for the page.

Another mouse virus... What is in the rubella virus family? (November 15, 2020).

The problem of human birth

July 8, 2011

Human birth is difficult. The birth canal just isn't big enough. It's a well-known problem, with serious consequences. The underlying reason for the problem is understood... It stems from two developments in the human lineage: a larger head, and a smaller pelvis. The latter change correlates with the change to standing upright.

One might wonder whether, over time, humans would evolve to somehow make birth "easier" -- or safer. A new paper sheds some light on this. By genetic analysis they show that genes associated with gestation time have been changing (evolving) faster than average. (Gestation time is the time of development in the womb. Longer gestation time means a larger baby.) This would suggest that human evolution has in fact been dealing with the birth problem. Little is known about the control of birth timing; their genetic analysis offers some hints.

Some background (from Figure 1 D of the paper)... The graph shows body weight at birth vs gestation time (age at birth, we might say) for various animals. Humans are shown by the circled red point. Other primates are shown in blue, and other mammals in black. The first observation is that the (blue) curve for primates is shifted to the right: for a given birth body weight, primates have longer gestational periods compared to other mammals. Then, look at the point for humans. It is to the left of the curve for the primates. That is, humans have a shorter gestational period than expected, compared to other primates. The log-log scale, labeled with the values of the natural logs, may make it hard to get a sense of the numbers. To guide you... On the x-axis, the ln values of 5 and 6 correspond to gestational periods of 148 and 403 days, respectively. On the y-axis, the ln values of 6 and 8 correspond to birth weights of 403 and 2981 grams, respectively. (The latter value is about 6 1/2 pounds.)

They also explore whether these genes with accelerated evolution affect the likelihood of premature birth. They show that variation in one of them, the gene for follicle-stimulating hormone receptor (FSHR), accounts for some of the variation in birth timing. Thus there is an immediate practical aspect to recognizing and understanding these genes. Will knowledge of why birth timing varies help us control it?

This is a complex story. The work here is rather preliminary. Emphasize the general ideas: the questions they ask, and the leads they find. The conclusions they reach are rather soft at this point -- but intriguing.

Aside from whatever the limitations of the data are at this point, it is not at all clear what the "best" solution would be. Earlier birth may make the birth process easier, but also leads to birth at an earlier stage of development -- including brain development. (If it is too early, we have premature birth -- with its own problems, as noted above.) Is evolution dealing with the size of the birth canal? The compactness of the head? (or its shape?) Would human intelligence be enhanced if we would go back to walking on "all fours" -- at least for women?

News story: Evolution Points To Genes Involved In Birth Timing. (Medical News Today, April 14, 2011.)

The article, which is freely available: An Evolutionary Genomic Approach to Identify Genes Involved in Human Birth Timing. (J Plunkett et al, PLoS Genetics 7(4):e1001365, April 14, 2011.)

Also see:
* Kangaroo mother care for premature babies: start immediately (June 27, 2021).
* Using caffeine to treat premature babies: risk of neurological effects? (April 27, 2019).
* The rising rate of caesarean section births: an intriguing correlation (April 15, 2019).
* Human birth: When to cut the cord? (December 11, 2011).

A post on maternal mortality: Maternal mortality (May 7, 2010).

More about the timing of birth: When should the eggs hatch? (June 11, 2013).

Making electricity in your windows: sharing the solar spectrum

July 5, 2011

This is clever! At first glance, it might seem that capturing solar energy to make electricity and letting solar energy through -- the normal function of a window -- would be at odds. If you've seen solar panels, they are black, to absorb as much of the solar energy as possible; that's not the best color for windows.

However, the solar spectrum is complex. The only wavelengths we can see are, well, the visible wavelengths. What if we designed a window that used the non-visible solar energy to make electricity? That is exactly what is reported in a new paper. It's not a completely new idea. What they did that was new was to begin to approach a practical way of doing it. The trick is to use a different type of solar cell, based on organic "pigments" -- ones chosen to absorb only infrared light. These have advantages for sharing the solar spectrum, and for ease of fabrication into combined window-solar cell devices.

The paper reports production of combined window-solar cell devices. As windows, they are about as transparent as some ordinary windows. As solar cells, they are useful, but have somewhat low efficiency.

Is this going to become a commercial product? It's too early to tell. This is an early step from a university lab. It's a long road to make a device that is practical and economical. As typical of a pioneering research paper, these issues are not really dealt with at this point. The news story listed below is a good discussion of many of the practical issues involved. The point for now is that we have a significant step toward getting onto that road.

News story: Turning windows into powerplants -- New technology from MIT could enable a building's windows to generate power, without blocking the view. (MIT. April 15, 2011.) Good overview of the advance, and of some of the technical and economic issues involved in making progress implementing it. Recommended!

The article: Transparent, near-infrared organic photovoltaic solar cells for window and energy-scavenging applications. (R R Lunt & V Bulovic, Applied Physics Letters 98:113305, March 17, 2011.) You might check the abstract for a good summary. The first page starts with a useful introduction to the topic. After that, this paper gets to be fairly dense physics.

Other posts on solar energy include:
* Could vibration (or loud music) improve the performance of a solar cell? (December 11, 2013).
* A Christmas present: Using concentrated sunlight to split water and CO₂ (February 18, 2011).
* Engineering cyanobacteria to make high-value chemicals (September 21, 2010).

More about high-tech windows... Windows: independent control of light and heat transmission (February 3, 2014).

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

Should τ replace π?

July 1, 2011

News story: 'Tau day' marked by opponents of maths constant pi. (BBC, June 28, 2011 -- τ day.)

Look over the news story, and browse some of the comments at the end for a range of views. It's fun, but also has some things to think about.

Traditionalists might want to listen to π. Make sure your sound is "on". (This site is listed on my page of Miscellaneous Internet Resources, under both Mathematics; statistics and Art & Music -- Science.)

Also see: Pi (November 10, 2014).

Posts about a different tau include: How tau gets around (June 28, 2020).

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

Should the music industry use MRI scans to predict the success of new songs?

June 28, 2011

The music industry would love to be able to predict the success of a song. What if you could take an objective measurement? Stuff a teenager in an MRI machine and play the song. Measure the kid's brain activity -- and predict how the song will sell. A new paper suggests this approach might be worth considering.

Here are the key data. This is Figure 2b of the paper. The y-axis shows a measure of a song's success: the number of albums sold. The x-axis shows a measure of brain activity that they found, by MRI, when teenagers listened to short clips from the song. There seems to be a correlation between these two measurements. The correlation coefficient shown is 0.32. Remember that it is R2 that is a measure of the "importance" of the correlation. In this case, R2 is about 0.1. Importantly, the MRI measurement was a better predictor of success than the opinions expressed by the listeners.

What are we to make of this? Two things strike me, at this point. One, the idea is not at all unreasonable. Two, the data here are very limited. With that perspective, it is easy enough to "judge" this work. Let's take it as a preliminary observation. It raises a question. Now they need to do good focused work to test the idea more thoroughly. Upon careful testing, the idea may fall apart completely -- or it may get better. Novel scientific papers are often that way. It's the nature of novelty: the first report may be rather rough. The real judgment comes after further work. But surely there is enough here to warrant that further testing -- and to provide summer jobs for some teenagers.

If you do read over how they did these measurements, I think a number of possible improvements will be clear.

News stories. Here are two. The first one is the one I first came across. I found it intriguing, but not very clear; it is from a general news source, not specializing in science. I looked for more information, and found the second story, from a source that generally has high quality science reporting. Particularly note that the second story is much more upfront about the limitations of the work.
* Study: Pop Songs Literally Get Stuck in Teens' Heads. (Time, June 14, 2011.)
* Teen Brain Data May Predict Pop Song Success, Study Finds. (Science Daily, June 13, 2011.)

The article: A Neural Predictor of Cultural Popularity. (G S Berns & S E Moore, Journal of Consumer Psychology 22:154, January 2012.) A draft copy is available at the Social Science Research Network: pdf copy.

The lead author is described as a neuroeconomist, and is at the Center for Neuropolicy, Emory University. The two italicized words are not in my spell checker. Or dictionary.

Other posts on MRI include:
* DNA testing -- for rejection of a transplanted heart (May 24, 2011). MRI is among other methods discussed, besides what the title suggests.
* Dog fMRI (June 8, 2012). This is from the same group as the work in this post.

Another post on cultural aspects of songs: Tracking new songs as they cross the Pacific (June 21, 2011).

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

More about testing consumer preferences: Is it ok to eat while standing up? (January 14, 2020).

Ten Great Public Health Achievements, 2001-2010

June 26, 2011

Public health is much in the news -- successes and failures. It is easy to get lost in specific news, and lose sight of the big picture. The US Centers for Disease Control and Prevention (CDC) has recently published two articles highlighting recent achievements -- while also noting much that needs to be done. One article focuses on the US; the other takes a global view. They are written by the same person, and have a consistent format.

The writing is rather dry, and there are lots of numbers. Nevertheless, even a browse of the section headings may be interesting. Then, maybe you will stop and read an occasional section in more detail. I encourage you to have a look.

Did you know that child mortality (deaths of children less than five years old) decreased by 20%, worldwide, over the decade? That half of child mortality is in Africa (with 13% of the population)? That the measles vaccine saved 13 million deaths over that decade?

The reports were published in Morbidity and Mortality Weekly Report (MMWR), a publication of the CDC. MMWR is freely available online.
* Ten Great Public Health Achievements --- United States, 2001--2010. (R Koppaka on behalf of the Domestic Public Health Achievements Team, CDC; MMWR 60:619, May 20, 2011.)
* Ten Great Public Health Achievements --- Worldwide, 2001--2010. (R Koppaka on behalf of the Global Public Health Achievements Team, CDC; MMWR 60:814, June 24, 2011.)

Among Musings posts on big issues of public health...
* International relations: sharing flu viruses (May 28, 2011);
* Poliovirus eradication: an update, with some good news and some bad news (May 22, 2011);
* One health (November 15, 2010).

A post on one major issue of child mortality: Sudden infant death: a genetic factor affecting breathing? (April 30, 2018).

Vaccine development: Silk: Stabilizing vaccines and drugs (July 29, 2012).

Quiz time... answer

June 22, 2011

Original post: Quiz time... (June 15, 2011). As a reminder, the quiz asked... What is the connection between the figure at the right (look at the eyes) and the music at: music?

I have updated the original post to include the "answer". Go to the original post: Quiz time... (June 15, 2011).

On the Evolution of Calculation Abilities

June 20, 2011

The apparent ability to count or to do simple arithmetic is found scattered among various animals. We have noted some examples in Musings, in large part because they intrigue us. Of course, it is part of a serious effort to understand how brains work -- including the human brain. The story of counting and arithmetic in various human societies is fascinating, too. There are both innate biological aspects, as well as cultural and learned aspects.

I recently came across a nice review of this whole field; my title for this post is the article title. It's well written, and should be largely readable by the general reader. Along the way you will learn why it is sometimes best to say that 5 plus 5 is "about 10", and why the Sikuani Indians of Colombia say "aniha-kae-behe kae-taxu-behe kaetaxuwusito" to mean the number 16.

The article, which is freely available: On the Evolution of Calculation Abilities. (A Ardila, Frontiers in Evolutionary Neuroscience 2:7, June 2010.) It's fun. At least, browse.

Among posts on animals doing math -- rather complex math in this case: The traveling bumblebee problem (January 11, 2011).

For more on animal math...
* Monkey math (June 1, 2014).
* Making smarter flies (July 18, 2012).

Also see: The animal mind (July 23, 2009).

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

The sperm count problem

June 18, 2011

A strange story. It's strange not because of the scientific content, which is both interesting and important. It's strange because of how the science was done -- and reported. We have discussed various scientific controversies, but this one is quite unusual.

You may have heard... sperm counts have been declining -- for humans. It's considered a concern for two reasons. First, it could limit reproductive potential. (Hm, with over-population, isn't that good?) Second, it may reflect environmental contamination -- by chemicals known as endocrine disrupters. That is, some argue that the decline in sperm counts is due to industrial chemicals in our environment. The real question is whether it is true. The Danish report that is the basis of the common claim has been much criticized, and other studies are inconclusive.

Now there are some new results, also from Denmark. The work is generally considered high quality. The new results show no evidence of any decline over the 15 year period studied (and the values do not seem at all low). Ok, new data -- good work, and an apparent result which should be of interest. The results have been posted at the web site of the Danish National Board of Health (the funding agency), and written about in the journal Epidemiology.

So what is so strange about that? What makes this story strange is that the scientists who did the study object to the results being made public. They are not involved with the papers about their work! Why is not entirely clear. So what we have is some posted data, and some discussion of it. The work is potentially important. If there is some reason why the apparent conclusion is not appropriate, we should know. Hopefully, events will cause the authors to properly publish their work, so we know the full story. For now, we know "the answer" but not the full story.

The graph. This is from the Bonde et al "Commentary" article, listed below. That article gives its original source, and discusses the unusual background of the figure, which is why it is controversial. As you can see, there is no particular trend in sperm counts evident from this data set. (2006 was apparently a bad year for sperm.)

All the items below are short and readable, and deal both with the scientific issue and the publication issue. I encourage people to read at least some of these items.

News story: In Update on Sperm, Data Show No Decline. (New York Times, June 6, 2011.)

Articles in Epidemiology. Remember that the scientists who did the work are not authors of either of these items. Both articles include links to web sites that may have some useful discussion, including the views of the scientists -- but these web materials are in Danish.
* Editorial, via PubMed: On Sperm Counts and Data Responsibility. (A J Wilcox, Epidemiology 22:615, September 2011.)
* The "Commentary" article, presenting the data, via PubMed: Trends in Sperm Counts - The Saga Continues. (J P Bonde et al, Epidemiology 22:617, September 2011.)

Also see: The bisphenol A (BPA) controversy (September 19, 2010). The post introduces the controversy surrounding this chemical, but does not go into the specifics. In fact, BPA may be an endocrine disrupter -- one of those chemicals that some consider part of the problem for the current issue, sperm count decline.

I really encourage you to be very cautious about reaching conclusions, both regarding sperm counts and BPA. The important point here is to understand the scientific uncertainties; these are unresolved issues. In the light of uncertainty, it is fine to choose to be conservative in the choices you make. But that is different from claiming that the answers are known.

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

Early detection of autism

June 14, 2011

In medicine, early detection is generally considered good. However, early detection of autism has been a challenge. Autism is defined by behavior; there is -- so far -- no biochemical test. Stretching our understanding of autism to allow diagnosis at younger ages is a challenge; a successful test would provide useful information for those studying the condition, and might be useful in allowing earlier treatment.

A group of scientists centered at the University of California San Diego now claim that routine screening of year-old babies for autism -- and for other developmental disorders or delays -- is both practical and fruitful. The test itself is not new; what is new here is setting up a system for administering it systematically and learning how to deal with the results. The test carries an intimidating name: Communication and Symbolic Behavior Scales Developmental Profile Infant-Toddler Checklist (CSBS-DP-IT-Checklist). It is a questionnaire that can be filled out by the parents in about five minutes -- and evaluated in about two minutes. They achieved widespread use of the test, with suspect children being referred to therapy earlier than would have been common. It seems to be a useful step.

News story: Five-Minute Screen Identifies Subtle Signs of Autism in One-Year-Olds. (Science Daily, April 28, 2011.) Good overview of what they did, the progress they reported, and the goals for further work.

The article, via PubMed: Detecting, Studying, and Treating Autism Early: The One-Year Well-Baby Check-Up Approach. (K Pierce et al, Journal of Pediatrics 159:458, September 2011.)

* Previous post on autism: Is the incidence of autism increasing? (November 6, 2009).
* Next: A mouse carrying a serotonin-transport gene that contributes to human autism (May 18, 2012).

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

With 24 eyes, can they see the trees?

June 11, 2011

A year ago we noted the fascinating visual system of the box jellyfish: How many eyes does it have? (March 12, 2010).

What do all these eyes do? An important point to realize at the start is that these are very simple organisms. They lack a "brain" -- a centralized structure coordinating the nervous system. They do have a simple nervous system, but it is delocalized. It may follow, then, that the eyes have special local functions, too; that is, an eye may be connected to "local" nerves, for a specific purpose. We noted this possibility in the earlier post.

The eyes with lenses are particularly intriguing; they are more complex than the eyes of most jellyfish, and are of about the same general design as our eyes. They are image-forming eyes, not just light detectors. The new work is on the upper lens eyes ("ule"; see figure in previous post). These eyes always point upwards, regardless of how the animal is oriented; this is because of a weight at the end of the stalk carrying the eyes. The scientists noted the tendency of the animals in a particular population to stay very near the edge of the canopy formed by the trees. (This was a good location for food.) So, they hypothesized that the animals can see the canopy -- can see the trees (or, at least, the forest). Here they test this hypothesis.

Here are some key results. Consider the top frame of the figure, labeled "4 meters". They place a bunch of jellyfish inside a transparent cage about 4 meters (horizontal distance) from the canopy of trees over their lagoon. The left side of the figure shows the paths taken by individual jellyfish. That's rather messy, but you can see that there is more action on the side nearest the canopy. The right side is a "summary"; there is one point for where each jellyfish ended up. You can see that most of them ended up on the canopy side. The bottom frame is the same idea, but now with the jellyfish about 12 meters from the canopy. The results show that they move more or less randomly; they are apparently too far away from the canopy to see it. These two frames are parts of Fig 3 of the paper. The full figure shows more distances tested.

The summary of their observations is that the jellyfish seem to be able to see the canopy if it is within about 8 meters. Interestingly, they do some measurements on the eyes, and then estimate that the eyes should give reasonable images out to about 8 meters. Thus observation and theory seem in agreement. Further, seeing the canopy leads to a behavioral response (swimming in correct direction). The case is developing that these animals -- thought to be among the most primitive types of animals -- have image-forming eyes that are used to direct behavior. They do that despite the absence of a "brain".

News story: Box jellyfish stable-eyes vision to hunt prey. (ScienceBlogs: Neurophilosophy, posted by "MO", who identifies as a molecular and developmental neurobiologist, April 28, 2011.) Good background, as well as a discussion of the current work.

The article, via abstract at PubMed: Box Jellyfish Use Terrestrial Visual Cues for Navigation. (A Garm et al, Current Biology 21:798, May 10, 2011.)

More on jellyfish vision: Associative learning coupled to the visual system of box jellyfish. (June 27, 2024). Added June 27, 2024.

More about the nervous system of jellyfish: When do jellyfish sleep? (September 29, 2017).

More about jellyfish... Caltech engineer turns rat into jellyfish (September 22, 2012).

More on simple visual systems... An unusual eye? (June 6, 2012).

More on simple brains... Can memories survive if head is lost? (November 23, 2013).

More on vision:
* The limits of the human visual system: can humans detect single photons? (October 7, 2016).
* Color vision: The advantage of having twelve kinds of photoreceptors? (February 21, 2014).

Chemical elements 114 and 116 officially recognized

June 8, 2011

Two new chemical elements have been officially recognized: #114 and #116. The discovery (or, rather, synthesis) of these elements was reported some time ago. Over time, enough data has accumulated that the International Union of Pure and Applied Chemistry (IUPAC) is satisfied; they now declare the elements accepted.

Over coming months, official names will be proposed -- by the discoverers. The news story below hints at some names, but I would treat this as just "rumor". The proposed names will then be put out for comment, and in due course IUPAC will approve official names.

News story: New chemical elements synthesized by Russian team recognized. (RIA Novosti, June 3, 2011. Now archived.) The story also notes that they plan to work soon on trying to make element #119.

Also see:
* Four new chemical elements officially recognized (January 12, 2016).
* Chemical element #117 (April 13, 2010). A post on the original announcement of a chemical element.
* Element #112: Copernicium (July 15, 2009). A post on the official naming of an element.

My page Introductory Chemistry -- Internet resources has sections on "Names of elements" and on various of the newer elements. The section on #114 notes its original discovery, in 1999, and its confirmation, in 2009.

The naming proposal is in the post: Chemical elements 114 & 116: flerovium, livermorium (proposal) (December 5, 2011).

The devil has cancer -- and it is contagious

June 6, 2011

Borislav noted the following news story, which is a nice overview of a fascinating topic: Drumming up support for Tasmania's unsexy beast. (Los Angeles Times, March 27, 2011.)

There are several issues here, at various levels of biology.

First, we have an animal that is not well known. In most of the world, marsupials are unfamiliar, known to us largely through zoos and occasional cultural icons. Only the opossum is common outside of Australia. The kangaroo, of course, is our familiar marsupial, but it is no more typical of marsupials than "rat" is typical of eutherian (placental) mammals. The Tasmanian devil is a carnivorous marsupial now restricted to the Australian island-state of Tasmania.

The Tasmanian devil is now an endangered species. Why? Because it has cancer. It? Yes, the species has cancer -- a cancer that is rapidly spreading through the population, and which is inevitably fatal. Why is it spreading? Because the cancer is itself transmissible; the cancer is infectious. Genetic analysis of the tumors from various individuals has shown that the tumors are closely related to each other -- and not to their host animal.

Caution: The figure linked here is not for dinnertime viewing. Here is a picture of a devil with the cancer [link opens in new window]. The figure is from a web page, now archived, of the Australian Wildlife Health Network. Scroll down to "Save the Tasmanian Devil (STTD) Program".

Transmissible cancers are uncommon. In fact, there are only a couple of well-characterized transmissible cancers. But why? A cancer is a growth that has become rather independent of the host. We know it can spread within the host, a process known as metastasis. In the lab, it is common to transplant human tumors to mice. But there is an important catch: this works well only with special mice lacking an immune response (so-called nude mice, which also lack hair). In fact, tumors are normally recognized as foreign upon transfer to a new host, and are rejected as any foreign tissue would be. Similarly, tissues transplanted from one human to another are typically recognized as foreign, and rejected. Somehow, the tumor is not rejected, and spreads easily around the population. This lack of rejection upon transfer is really the unusual feature. The reason for the lack of rejection is not entirely clear, but must somehow reflect the immunological nature of the cancer and the immune system of the devils. One part of this is apparently that the devils are very closely related, and share key immunological features.

Does that story leave you a little uneasy about whether some cancers might be transmissible among humans? It should. It's not well understood what is going on. The immunology of cancer is a messy story, and transmissible cancers are rather new on the scene. The story of the Devil facial tumor disease (DFTD), which threatens an interesting creature, is getting attention from a small but growing band of researchers. Time will tell how this plays out -- for the Tasmanian Devil, and for our understanding of cancer.

More on the DFTD:
* Immunization of devils: a treatment for a transmissible cancer? (April 24, 2017).
* Tasmanian devils: Are they developing resistance to the contagious cancer? (September 6, 2016).
* Why the facial tumor of the Tasmanian devil is transmissible: a new clue (April 5, 2013).

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

Previous post on marsupials: The kangaroo family tree: the American ancestry of kangaroos (August 13, 2010).

Previous post on cancer: Does radiation treatment of cancer cause new cancers? (April 8, 2011).

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

The Kepler Orrery

June 3, 2011

It's perfectly ok to skip down and check out the video listed below. It's fun. You can come back and read the explanation later.

An orrery is a model of the solar system -- a working model, showing how the planets orbit around the sun. The solar system? Maybe that should say our solar system (and our sun). Of course, our solar system was the only solar system known until recently. The first planets outside our solar system were discovered in 1995; we now know there are other solar systems out there.

Musings has noted these extrasolar planets (or "exoplanets"; links below). However, we are now in a new era of extrasolar planets. The spacecraft Kepler, launched in 2009, has the primary goal of searching a region of the sky for planets -- and solar systems. Kepler's basic approach is simple: it looks for the reduction in light from a star as a planet crosses in front. Its strength is the sensitivity of its detection system, partly because it is in space, free of the earth's atmosphere. In February 2011 NASA announced the first big batch of Kepler discoveries. This data set, based on observations over the first four months of operation, offered us more candidate extrasolar planets than obtained by all previous searches combined.

The Kepler orrery shows all the solar systems in this new batch that have at least two planets characterized so far. It's cute, but it is also a profound symbol of the new era of extrasolar planets.

The video -- just over one minute -- is at YouTube: Kepler Orrery. (Do a web search on Kepler Orrery, and you will also find some later versions.)

A good news story about the February data release: Kepler Planet Hunter Finds 1,200 Possibilities. (New York Times, February 2, 2011.) It's worth it for the first sentence!

For general information about the Kepler mission:
* Kepler Overview -- Kepler: NASA's first mission capable of finding Earth-size and smaller planets around other stars. (NASA) See their menu at the left for more.
* Kepler (spacecraft). (Wikipedia)

More from Kepler:
* How many exoplanets are known? Three (four?) fewer than we thought (May 31, 2022). A re-evaluation.
* A new trick for the Kepler planet-hunters (June 25, 2012).

Musings posts from the pre-Kepler era of extrasolar planets:
* The first truly habitable exoplanet? (October 12, 2010).
* Extrasolar planets (December 8, 2009).

Planet discovery -- in olden times: The first report of a new planet (March 13, 2011).

More on planetary discovery:
* Habitable planets very close to a star (June 19, 2016).
* The youngest (known) planet? (October 30, 2011).

A post about Kepler himself... Book review: Kepler (February 3, 2010). Kepler's Astronomia Nova (New Astronomy), from 1609.

More from NASA: MESSENGER orbits Mercury, shoots Debussy (June 10, 2011).

And more... Exoplanet Travel Bureau (February 21, 2015).

Ant sociality: supercolonies -- a video of a talk

May 31, 2011

The post Ant mega-colony takes over world (July 16, 2009) discussed the relatedness of Argentine ant populations around the world. UC Berkeley professor Neil Tsutsui, who works in this field, recently gave a talk here on the broader topic of ant sociality. The lecture was part of the Science@Cal series; it was an excellent talk, and is now available as an online video.

Here is a link to a video of the talk: Extreme Sociality: Supercolonies of the Invasive Argentine Ant. (Neil Tsutsui, Science@Cal, May 2011.)

Tsutsui lab web page. (Tsutsui was not part of the work referred to in the earlier post. However, he was acknowledged in the paper for contributing California ants to the study.)

For general information about the Science@Cal series, which started as a series of astronomy talks for the International Year of Astronomy: Astronomy talks (June 22, 2009).

Other Musings posts on ants include: How to survive flooding by making a waterproof raft (May 27, 2011).

International relations: sharing flu viruses

May 28, 2011

Health is global. Viruses know nothing of national boundaries, and they now travel by airplane. Public health is an international matter.

A specific issue is that new strains of a pathogen need to be shared with the major labs studying the disease. A few years ago, a "developing country" refused to do so. Their reason was that they felt they were being exploited. They were concerned that the developed countries would use their virus to make profitable drugs or vaccines, and that the developing country would not share the profit or the benefit.

The WHO (World Health Organization) has just negotiated an agreement that tries to strike a reasonable balance between the various concerns. The news stories listed below outline the dispute and the agreement. As you read these, most important is to recognize the valid concerns of both sides. The details of the agreement are perhaps less important; time will tell how well it works.

News stories:
* WHO Resolves Impasse Over Sharing Of Flu Viruses, Access To Vaccines. (NPR, April 18, 2011.)
* Infectious diseases: 'Breakthrough' Deal on Flu Strains Has Modest Provisions. (M Enserink, Science 332:525, April 29, 2011.)

Another such dispute... A new SARS-related virus seems to be emerging -- and an "ethics" story (February 4, 2013).

Many posts on various flu issues are listed on the supplementary page: Musings: Influenza.

The "one health" idea emphasizes the flow of diseases among various organisms. The current post is about the flow of diseases among countries. Of course, those are related issues. One health (November 15, 2010).

For a broad overview of public health... Ten Great Public Health Achievements, 2001-2010 (June 26, 2011).

More about WHO: The role of WHO: the view of its director (December 1, 2015).

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

What is it?

May 25, 2011

If it's rather obvious what it is, then... How big is it? and What is it made of? Of course, the figure at the left is a diagram. Perhaps you would like to see an actual photo of one.

I'll post an answer, with proper source information, next week [see immediately below].

Answer (posted June 1, 2011):

The figure at left is similar to the one in the original post (immediately above), but now with dimensions shown. Clearly, it is something of a "nanoflask". The "actual photo" of it, linked above, is also a clue; some of you probably recognized that as an electron micrograph. What is it made of? DNA. It is an example of how the base pairing properties of DNA can be used to make complex structures. How big is it? Well, we could estimate that at various levels. Simplest is to ask what size "box" it would fit in. That is, just look at the overall size and shape. For this purpose, it is a cylinder with diameter 40 nanometers (nm) and height 70 nm. Thus, we can calculate the size of a cylindrical box for this flask: the volume is about 90,000 cubic nanometers. That is 9x10-20 liters, or 90 zeptoliters (zL). Of course, the flask itself is somewhat smaller, and the inside volume is smaller yet. (If the prefix zepto is unfamiliar, see my page Metric Prefixes - from yotta to yocto. The page includes examples to give a sense of scale for most of the prefixes. For example, at the other end of the volume scale, the volume of the earth is about 1 yottaliter.)

News story: DNA Nanoforms: Miniature Architectural Forms -- Some No Larger Than Viruses -- Constructed Through DNA Origami. (Science Daily, April 14, 2011.)

The article: DNA Origami with Complex Curvatures in Three-Dimensional Space. (D Han et al, Science 332:342, April 15, 2011.) The figures in this post are parts of Figure 3 of this paper.

Other posts on "DNA technologies":
* The nano-alphabet (June 29, 2012).
* Nanorobots: Getting DNA to walk and to carry cargo (August 7, 2010).

Other "What is it?" features, and other quizzes, include...
* What are they? (September 14, 2011).
* Quiz time... (June 15, 2011).
* What is it? (March 8, 2011).

Other posts dealing with small containers include... Making a small container that has an opening in it (September 10, 2019).

A simpler bicycle

May 23, 2011

Bicycles are complicated. It is not well understood how they work. In an effort to better understand how a bicycle works, Dutch engineers have designed and tested a simpler bicycle. The new bicycle is shown at the right. (This is Figure 2A of the paper.)

You might find it useful to compare this with a standard bicycle. The linked figure (Figure 1) shows a diagram of a standard bicycle along with a diagram of a theoretical model of the new, simpler bicycle. (The model shown in this figure uses skates rather than wheels. The bike they made -- shown above -- uses wheels.)

You're wondering??? You might want to jump ahead and see this simple bicycle in action. There is a nice video with the Popular Science news story listed below; that same video is #1 with the paper. You should also remind yourself that the word bicycle refers to the device having two wheels. The name does not specify that it must have a seat, or other parts you may be wondering about.

Why did they do this? As noted above, it is not clear how a bicycle works. One useful feature of a bicycle is that it tends to stay upright. Riders learn how to assist, but a riderless bike will tend to do it "all by itself". Why? There are some ideas, but no general agreement. So, the purpose of the test bicycle is to test how a bike stays upright. The test bike is simpler, and two key aspects that many thought were critical to the self-righting ability of a bicycle have been changed. These are the gyroscopic action and the position of the wheels. The positioning of the front wheels make them much like the front casters on a shopping cart at the grocery store, and could well lead to self-righting.

The results? Look at the video, if you haven't already. The simplified bike, lacking two suspected self-righting features, rights itself just fine.

Their conclusions are cautious. They do not claim that they have disproven that the proposed features lead to self-righting. Instead, they claim that those features are not essential for self-righting. That is, they claim that there may be various ways to promote self-righting. They also suggest that the optimum bicycle may not yet have been designed.

Think about that next time you fall off a bicycle. (By the way, putting a large mass on the frame (e.g., on the seat) is likely to make the bicycle less stable.)

News stories:
* A Bicycle Built for None: Riderless Bike Helps Researchers Learn How Balance Rolls Along. (Science Daily, April 15, 2011.)
* Video: Scientists Build a Riderless Bike That Stays Up On Its Own. (Popular Science, April 19, 2011. Now archived.) Includes a video; this is movie #1 with the paper.

The article: A Bicycle Can Be Self-Stable Without Gyroscopic or Caster Effects. (J D G Kooijman et al, Science 332:339, April 15, 2011.) Click on "Supporting Online Material" (SOM) for some movies. They are listed on the SOM page, with descriptions, and then linked there. Of these, #1 is perhaps most useful; it simply shows the new bicycle in operation. The description of this movie is quite amusing. Note that #1 is also included with PopSci news story, above. The others show some details; they are narrated in Dutch.

Here is the legend for movie 1, from the SOM... Movie s1. The Experiment. The video Video1BasicExperiment.mp4 shows a typical experimental run. In order to effectively capture the experiment on film many different camera positions were tried. The main objective was to show that the bicycle once released follows a straight line. When it is perturbed, it stabilizes and then continues on a straight line in a new direction. The difficulty was finding a viewing position from where clearly can be seen that the bicycle actually goes through these three stages. Multiple fixed positions were tried, with both zoom and panning motions, however the most effective camera position turned out to be mobile, on a skateboard that closely followed the bicycle. One person carried out the experiment with the bicycle, the cameraman stood on the skateboard and only concentrated on filming the bicycle while a the third person pushed the cameraman forward and ensured that the distance between the bicycle and camera stayed roughly constant.

Previous post on bicycles: MIT invents a better bicycle wheel (April 24, 2010).

More gyroscopes:
* Gyroscopic seeds (June 15, 2018).
* Dolphins, bulls, and gyroscopes (September 10, 2010).

More about pedaling: Renewable energy for the school bus: let the kids pedal (April 24, 2012).

Development of a new species of lizard in the lab

May 20, 2011

Scientists at the University of Kansas have created a new type of lizard. They used methods that would seem to be entirely natural, and the resulting lizard should probably be considered a new species.

As background... lizards have some unusual biology. They are vertebrates, and generally reproduce sexually as we might expect. However, they have an unusual ability to form hybrids. Many of the hybrids are sterile, so are dead-ends. However, there are numerous lizard species with the unusual ability to reproduce parthogenetically: that is, the female is the sole parent. (She lays eggs, which hatch and develop normally; the key point is that fertilization is not needed.) There has been suspicion that parthenogenetic lizards may have arisen via hybridization.

In the new work, the scientists allowed two lizards, from different species, to mate. (The particular species were chosen as follow-up to some earlier work, which had been suggestive but incomplete.) Offspring were obtained. Among them were four females that were not only viable, but capable of reproducing -- all by themselves (i.e., parthogenetically). They have now followed these offspring through four generations, and the new species seems stable.

It's important to emphasize that the new species was formed entirely naturally. No genetic engineering, or other "unnatural" manipulation, was involved. In fact, their intent was to mimic what they thought was going on in nature.

Is it proper to consider this the formation of a new species? Using common guidelines, it would seem so. The resulting lizards are now reproductively isolated from the parent species. Since they reproduce parthogenetically, i.e., by cloning, that is easy to show.

Unfortunately, there is no general agreement on how species are defined, especially for organisms without sexual reproduction. So it is hard to give a definitive answer; there may well be some discussion of this point among biologists. However, if the new lizard had been found in nature, it is likely that it would have been called a new species. If you'd rather leave the species question open for now, think about this work producing a new "type" of lizard, probably by a pathway already used in nature. We should note that this is not a common way to make new species in nature.

Above we noted that the four females discussed here were "among" the offspring. What else did they get? Two more animals, which they think are males. About those they only say, "The reproductive status of the presumed males is still under investigation and will be reported in due course."

News stories:
* All-Female Lizard Species Created in Lab. (Wired, May 3, 2011.)
* New species of lizard created in lab that reproduces by cloning itself. (PhysOrg, May 6, 2011.)

The article: Laboratory synthesis of an independently reproducing vertebrate species. (A A Lutes et al, PNAS 108:9910, June 14, 2011.)

For more on lizards...
* Twenty percent of the females are genetic males (October 6, 2015).
* An advanced placenta -- in Trachylepis ivensi (October 18, 2011).

Another new species: Making a new species in the lab (July 26, 2015).

More on hybrids... Hybrid formation between organisms that diverged 60 million years ago (May 8, 2015).

Studying cancer development by analyzing the genomes of individual cancer cells

May 16, 2011

Cancer is complex. There is a broad view that cancer develops as multiple mutations affect the growth properties of the cancerous tissue, allowing it to grow without the host's usual growth constraints. People talk of a cancer evolving -- changing over time by random mutations, with natural selection determining what thrives. (Some people even suggest that a cancer might be considered as a distinct species. If nothing else, this is an interesting and provocative view.) With the modern tools of genome sequencing, people are now trying to analyze what these genetic changes are, by sequencing the genomes from numerous cancers. Such studies suffer from the basic fact that any such analysis yields a vast zoo of mutations, most of which probably have nothing at all to do with the cancer. As an example of cancer genome analysis... The post Finding cancer genes (September 19, 2010) discussed an analysis of the genomes of some ovarian cancers; mutations in a particular gene were found in a substantial fraction of the cases, and seem likely to be relevant to the cancer.

New work has added an interesting aspect to the study of cancer mutations. Instead of just analyzing the genome from the cancer, they analyzed the genome of individual cells from the cancer.

An example, from Figure 2b of the paper. They analyzed the genome of 100 cells from a particular tumor. From that genome information, they assembled a chart showing the relatedness -- the family tree -- of those 100 cells. It is very much like a common genealogy chart, except that this one is based on observed genome differences, not on knowing who derived from whom. That is, we infer who derived from whom by looking at the genomes.

The chart offers an unprecedented view of what is happening in the tumor.

The chart is analogous to a "tree of life" chart showing how different organisms are related. In fact, comparing genomes is now a key tool in making such tree-of-life charts.

The paper is quite complex, and some of the discussion seems excessive. After all, they have now done this for a total of two tumors; making broad generalizations seems unwarranted. The reason for posting this item is simply to note the technological development -- that they can now do this at all.

News story: With New Method, Researchers Can Infer How Tumors Evolve and Spread. (Science Daily, March 14, 2011).)

The article: Tumour evolution inferred by single-cell sequencing. (N Navin et al, Nature 472:90, April 7, 2011.)

One of the requirements for making this work practical is low cost sequencing, a development discussed in the post: The $1000 genome: Are we there yet? (March 14, 2011).

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

How to fold a bag

May 13, 2011

Consider an ordinary paper grocery bag. You've emptied it. Wouldn't it be nice to fold it flat, for storage. Try it. I bet you can't do it -- at least while following the rules.

You may realize you knew that. Think about cardboard boxes. When cardboard boxes are folded flat, one opens the bottom (as well as the top). If your grocery bag were made of cardboard -- or of steel -- you really wouldn't be able to fold it flat. You get by with a bit of cheating with the paper bag, but that would not work with a rigid bag.

So what are the rules? What is this cheating we accuse you of? Again, if you haven't done it yet, go try it with an ordinary paper bag: try to fold the bag flat.

The basic rule is that you are supposed to fold it along the creases. That's all you are allowed to do. With a rigid material, such as the cardboard box, that's all you can do. With paper, we cheat a bit, and flex the paper itself.

What now? Engineers at Oxford University have figured out how to make a bag that will fold flat. A rigid bag: a steel bag. It's not an easy problem; much of the work is computer simulation -- and trial and error.

A bag that can be folded flat -- a computer simulation. (One more step is needed beyond what is shown, but that is easy enough.) The basic shape of the bag (frame a) is "normal". What's novel is the pattern of creases, where folds occur. This is Figure 4 of the paper. After doing the simulation, and finding out what should work, they made such a bag. Figure 5 of the paper shows that a real bag, made as the simulation suggests, does fold flat. You can see Figure 5 in the paper, and parts of it are in some of the news stories.

This is fun. Is it useful? Folding boxes is a big deal; it's often done by robots. The news reports say that the authors are in contact with manufacturers of cartons regarding their proposed better box.

News stories:
* Paper, Plastic, or Steel? (Science Now, March 30, 2011.)
* Origami solution found for folding steel shopping bags. (PhysOrg, March 31, 2011.)

The article: A solution for folding rigid tall shopping bags. (W Wu & Z You, Proc. R. Soc. A 467:2561, September 2011.) Some may enjoy a look at Appendix A, to see how one makes a mathematical model of a grocery bag.

Previous folding story: Folding towels (April 10, 2010).

And more...
* A robot that can fold itself up (December 9, 2014).
* A box that will fold up upon command -- heat- or light-actuated switches (September 3, 2011).

More bags:
* Should bags be made from torrefied paper? (May 14, 2023).
* Doggy bags and the food waste problem (January 4, 2017).

Prejudice against outsiders -- in monkeys

May 10, 2011

It's us vs them. Much of what goes on in human society seems to have this undertone. Whether we call it prejudice or discrimination or racism or nationalism or tribalism, conflicts between groups are common. There is hardly a feature of humans that is not the basis for such behavior. Broadly, we can refer to such behavior as "in-group vs out-group", or, in shorthand, "us-vs-them".

We can even understand why such behavior may be beneficial. Imagine a sparsely populated earth, with family groups scattered around. It is, perhaps, reasonable to be suspicious of an "outsider". However, in our modern, densely packed world (think "globalization"), we now have some ideal against such discrimination by group membership. Is the us-vs-them bias biologically encoded in us? Is our modern cultural egalitarianism up against our innate biology? In asking these questions, I am not presuming an answer. The point is to ask the questions, and see what we can learn about our innate biological nature. A recent Musings post explored whether the hormone oxytocin might be involved in such responses: Is the hormone of love also the hormone of discrimination? (January 29, 2011).

Is us-vs-them bias unique to humans? I'm sure we could imagine why it might be one way or the other, but can we actually tell? Now, a group at Yale University has modified a standard psychological test that is used to study such biases in humans to do similar tests with rhesus monkeys. It is interesting how they do the test. And the answer? The monkeys, too, show bias against outsiders.

Here is one of their experiments... It takes a bit to describe it, but the basic idea is fairly simple, and used in a variety of psychological tests. (In fact, the same basic test was one of those used in the paper noted above.) The underlying idea is that the monkeys will look at something "strange" longer than they look at something "ordinary". So, they offer the test monkeys some pictures, and measure how long they look. In this experiment, each test is with a pair of pictures. One part of the pair is a monkey -- either an insider or an outsider. The other part of the pair is another object they know the monkeys consider good (a fruit) or bad (a spider).

The results are summarized in the following figure. Look first at the left side, for males. The two curves are different. What is behind these two curves? They are labeled "consistent" (dark symbols) and "inconsistent" (light symbols). "Consistent" means that a picture of an insider was paired with a good object (such as fruit), or that an outsider was paired with a bad object (such as a spider). That is, "consistent" means that both objects were good or both were bad. In contrast, "inconsistent" means there was one good object plus one bad object, such as an insider and a spider.

The pattern is clear. The males quickly adapted to the "consistent" pictures, and spent little time looking at them. However, they kept looking at the "inconsistent" pictures for several seconds, with no trend toward accepting them over repeated tests. Interestingly, the females adapted similarly to consistent and inconsistent pairs. See the right side of the figure.

Be cautious about interpreting this work, especially its possible relevance to human behavior. The key point here is that they have introduced a new method to allow study of the monkeys. They have some interesting -- but preliminary -- results. These need to be validated and extended. Even then, it is a big jump to understand the significance of the results for humans. (What is the significance of the sex difference shown above in the monkeys?) Understanding the behavior in monkeys may give us useful clues to explore. Further, it may be good to see how other animals, especially other primates, respond to such tests.

News story: Human Prejudice Has Ancient Evolutionary Roots. (ScienceDaily, March 18, 2011.) Beware of hype in the title. The article itself is generally good. Remember that titles and headlines are often written by someone other than the author, and are intended to attract attention. [This was originally at http://www.sciencedaily.com/releases/2011/03/110317102552.htm. It was removed when the article was retracted, If you really want to see it, check the Internet Archive.]

The article, via abstract at PubMed: The Evolution of Intergroup Bias: Perceptions and Attitudes in Rhesus Macaques. (N Mahajan et al, Journal of Personality and Social Psychology 100:387, March 2011.) Check Google Scholar and you may find a freely available copy.

For more on monkeys...
* Pink corn or blue? How do the monkeys decide? (June 9, 2013).
* The first chimeric monkeys (February 5, 2012).
* Speech: Taking turns (August 17, 2011).

A gene for obesity

May 7, 2011

The article title may get a yawn. Another paper dealing with the details of energy balance -- in mice. However, towards the end of the article they make a connection to humans. They show that a mutation leading to increased activity of this protein correlates with increased obesity in Mexican Americans. That's consistent with the effect seen with mice. The effect is small, but statistically significant -- and confirmed by an independent analysis of a second population.

Interestingly, the mutation was not associated with greater obesity in non-Hispanic whites. There are a couple of possibilities for this finding. One is that the whole effect is a mistake -- an artifact of the particular analysis. The other possibility is that indeed the mutation is giving different effects in different populations, due to some combination of differences in genetic background or lifestyle (such as diet). It will take a while to sort this out.

For now, the work is a tantalizing hint. Regulation of energy balance is complex; the basic subject of the paper deals with the complexity. What is the relevance? Well, maybe it is relevant -- along with other things. Humans are complex, and we vary.

News story: Feast, Famine and the Genetics of Obesity: You Can't Have It Both Ways. (Science Daily, December 16, 2010.)

The article: CRTC3 links catecholamine signalling to energy balance. (Y Song et al, Nature 468:933, December 16, 2010.)

Among other posts that probe aspects of obesity...
* An obesity gene: control of brown fat (October 2, 2015).
* The junk food issue is global (April 7, 2012).
* Fructose; soft drinks vs fruit juices (November 7, 2010).
* A virus associated with obesity? (October 4, 2010).

For more about obesity, see the section of my page Organic/Biochemistry Internet resources on Lipids. The list of Musings posts there includes more on obesity and related issues.

Electric cars and pollution -- Follow-up

May 4, 2011

Original post: Electric cars and pollution (April 5, 2011).

A reader expressed concern that the post could be misinterpreted. The article is not a complete analysis of electric cars vs traditional gasoline-powered cars. It focuses on one issue: the effects of fuel usage, electricity vs gasoline, on emissions. In fact, it compares the fuels for the same vehicle: the plug-in electric hybrid (PHEV). Other analyses might, for example, also consider manufacturing and maintenance issues of electric vs gasoline engines, but these are beyond the scope of this article.

The confusion comes, in part, from the term "electric cars" in their title -- and then in mine. It would have been better to refer to use of electricity as fuel than to electric cars per se. The paper is quite clear, but the title suggests something else..

I have added this point to the original post.

On sharing electrons

May 3, 2011

The way we get energy is to burn our food. For example, we eat -- and burn -- sugar. This process involves removing electrons from the carbon atoms -- four electrons per C atom. Where do the electrons go? Well, for us they go to oxygen. We -- and most higher animals -- use oxygen, O₂, as the electron sink; the oxygen gets the electrons and forms water, H₂O. Sugar + oxygen → carbon dioxide + water; this biological process is commonly called "respiration", but overall it is chemically just like ordinary burning.

But what about organisms that grow without using O₂? Where do their electrons go? There are various answers to that. Examples of other electron sinks that some organisms may use include nitrate ion, NO₃^-, and the iron(III) ion, Fe³⁺.

Sometimes things are more complicated. Some time ago, it was found that bacteria may work together to get rid of their electrons. One species might transfer its electrons to H⁺, making molecular hydrogen (H₂), which is liberated. And then another species would use the H₂, transferring the electrons to something else. This inter-species electron transfer via hydrogen helps both species grow.

More recently, it was found that some bacteria make electrical wires, and attach themselves to minerals. They get rid of their electrons through the wires; the minerals -- outside the cells -- are the electron sink.

And now? A report that these types of cells can connect up -- electrically -- with other cells. One species produces excess electrons, transfers them to the other via the electrical wires, and the second sends the electrons off to their ultimate sink. It's another demonstration of the diversity of bacteria, and of the interactions between organisms.

What they did was to inoculate two bacterial strains together. When growth was good, a portion was transferred to fresh medium. The graph shows the growth of these bacterial mixtures, over time. The y-axis shows how long it took to achieve good growth at each step; that is, a high value here means slow growth. Each line is for one replicate culture. (This is Figure 1 of the paper.) The graph shows that it initially took 30 days to achieve good growth, but over time this reduced to about 5 days. Clearly, the pair of bacterial strains had -- somehow -- adapted so they could grow better.

The enhanced growth was accompanied by the formation of aggregates, visible to the naked eye. The figure at left shows a cross section of one such aggregate, stained with a red stain for one strain and a green stain for the other. The picture shows that both strains of bacteria are within the aggregate. The scale bar is 100 µm, or 0.1 mm. This is at about the limit of what one can see with the naked eye. Individual bacteria are on the order of 1 µm -- much too small to see. But the aggregate here is a half millimeter across, a quite visible dot. This is Figure 2C of the paper.

Analysis of the bacteria showed that one of them had acquired a mutation enhancing the production of a cytochrome, a protein involved in electron transfer. The particular cytochrome is known to be involved in extracellular electron transport. Intentional addition of such a mutation re-created the effect; this kind of experiment shows that what they found is indeed relevant. In contrast, adding a mutation that interferes with hydrogen transfer had no effect. Together, these results suggest that the electron sharing in this case is due to the wires, containing a cytochrome, and not due to hydrogen transfer.

People have speculated about the possibility of direct electron transfer from one organism to another via electrically conductive wires, but this is the first time it has been shown. At this point, the process has been shown only in the lab under some special conditions. However, they suspect that it occurs in nature.

News story: Interspecies Electron Transfer: Anaerobic Bacteria Found to Cooperate. (Science Daily, December 4, 2010.)

The article: Direct Exchange of Electrons Within Aggregates of an Evolved Syntrophic Coculture of Anaerobic Bacteria. (Z M Summers et al, Science 330:1413, December 3, 2010.)

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

And...
* Better bacterial conductivity (November 3, 2020).
* A battery for bacteria: How bacteria store electrons (May 2, 2015).

More on unusual ways to energize bacteria: A living organism powered entirely by electricity? (February 22, 2013).

More cytochromes: Carbon-silicon bonds: the first from biology (January 27, 2017).

More on stretching things: Stretchable electric wires (January 22, 2013).