Musings: May-August 2011 (archive)

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Musings: May-August 2011 (archive)

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

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

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August 31, 2011

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.)

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).

The hydrogen economy -- in the mid-Atlantic

August 30, 2011

The ultimate energy source for most life around us is the sun. However, in the 1970s scientists began to work out the story of life at deep sea thermal vents; these are basically undersea volcanoes. There, life is based on chemical energy coming from the earth's interior. Specifically, oxidation of methane (CH₄) and sulfides (such as hydrogen sulfide, H₂S) drive the system. Microbes carry out these reactions, and thrive; they are the base of the ecosystem, as the primary energy collectors.

New work shows that hydrogen gas is also one of the energy sources for thermal vent life systems. In some ways this is not a surprise. It has long been known that H₂ is present. Further, hydrogen metabolism is simple and yields much energy. However, use of hydrogen at thermal vents had not been established. In the new work, they show that the gill tissues from mussels near thermal vents have the key gene for metabolizing hydrogen. Under lab conditions, the tissues do in fact metabolize H₂. Hydrogen metabolism can be attributed to the bacteria living in the gill tissue by genome analysis.

Here is another of their intriguing experiments...

What they did was to sample the environment near a vent, and measure the local hydrogen concentration and temperature (T). The graph shows the hydrogen concentration (y-axis) vs T (x-axis). They separate the data points into two groups: those in mussel beds (red), and those not (blue). The basic observation from the graph is that samples from the mussel bed have lower hydrogen level than expected for that T. Thus they infer that the mussels are consuming the hydrogen. (It is the bacteria within the mussels that actually carry out hydrogen metabolism.)

(This is Figure 3 of the paper. You can also see that the mussels like cold water.)

I can think of questions to ask about this, but it is a remarkable experiment. Measuring the H₂ concentration is quite a technical feat. Not many people have operated a mass spectrometer at the ocean floor.

Overall, their results make it likely that this deep sea thermal vent biosystem operates, in part, on hydrogen.

News story: Researchers discover hydrogen-powered symbiotic bacteria in deep-sea hydrothermal vent mussels. (PhysOrg, August 11, 2011.) A good overview of the work, plus pictures of the mussel beds and the vent area.

* News story accompanying the article: Microbiology: Hydrogen for dinner. (V J Orphan & T M Hoehler, Nature 476:154, August 10, 2011.) For those not familiar with deep sea vent life, this is a good introduction.
* The article: Hydrogen is an energy source for hydrothermal vent symbioses. (J M Petersen et al, Nature 476:176, August 11, 2011.)

Thanks to Jitesh for alerting me to this story.

Also see:
* Was hydrogen the energy source for the origin of life? (February 1, 2022).
* Life on 10 zeptowatts (September 13, 2020).
* Is there food on Enceladus? (May 21, 2017).
* Is clam cancer contagious? (April 21, 2015).
* How does worm "fur" divide? (January 4, 2015).
* Steppenwolf: Life on a planet that does not have a sun? (July 2, 2011).
* Hydrogen fuel cell cars (June 8, 2010).

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.

Here is an example of their evidence on the heat sensors. This is Figure 3b of the paper.

The basic idea of the experiment here is simple, though it is technically quite complex. They measure the current through the ion channel as a function of temperature (T). The graph shows current on the y-axis (log scale); the x-axis is related to T.

Even with that brief description... The two graphs each show a "kink". In one, labeled (at the top) as having the S version of the channel protein TRPV1, the kink is at about 30 °C. In the other, labeled as having the L version of the channel protein, the kink is at about 40 °C. The former, the S version, is the novel form that is specifically found in the facial pits; it is this form that is suitable for detecting the heat of a vein.

Let's look at that T scale, on the x-axis, more closely. The scale says 1000/T; that is, the graph uses the reciprocal of T, rather than T. That means that T "runs backwards" -- high T to the left. You can now see that as we raise the T (go left!), the current increases, as the channel opens. (Chemists will recognize the type of graph here as an Arrhenius plot.)

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.

Water at the Martian surface?

August 27, 2011

It captured the attention of the news media -- and of the public. Water on Mars. Near the surface -- perhaps on the surface. Now -- photographed by a NASA spacecraft. Liquid water is a key requirement for life "as we know it", and finding liquid water at the Martian surface certainly feeds the imagination. So, what's the story?

The figure at left is an example of the key evidence. It's based on a photo taken by the HiRISE camera on the Mars Reconnaissance Orbiter. Look at those dark streaks. The authors call them recurring slope lineae (RSL). They do look like water, don't they? Importantly, the streaks appear in summer, and disappear in winter. And they appear in places where it gets warm -- warm enough to melt water-ice (or, at least, brine: concentrated salt solutions). Animated sets of photos showing the seasonal recurrence of the RSL at various sites are available below.

And that about takes care of the facts. The rest is a discussion of what the RSL might be, with water (or brine) being one of the choices. An instrument that should be able to identify water showed no water signal with the RSL. There are various possible explanations for that discrepancy. For example, the water may be just under the surface, affecting its appearance. The paper is modest in its claims, but clearly the intent is to raise the possibility that surface water is part of the modern Mars story. The possibility.

This is Figure 1C of the paper, and has been used widely in news stories. The general credit for the figures is: NASA/JPL/University of Arizona.

If only we could send something (or someone) to where those streaks are to make a direct observation! But that is not going to happen for several years. Until then, we have some tantalizing pictures and some speculation. That's fine. Time will tell. For now, we just have "the possibility"; it is certainly premature to claim that water has been found at the surface of Mars.

News stories...
* Briny Water May be at Work in Seasonal Flows on Mars. (University of Arizona Office of University Communications, August 4, 2011.) Press release from the lead institution. Good presentation of the work, including the uncertainty of interpretation. Under "Et Cetera" (at the right), it links to the lab web page, which includes numerous animations showing the seasonal changes. (Each animation is a series of photos of the same site over time.)
* New Evidence for Flowing Water on Mars. (Universe Today, August 4, 2011.) Includes one of the animations.

The article: Seasonal Flows on Warm Martian Slopes. (A S McEwen et al, Science 333:740, August 5, 2011.) The "Supporting Online Material", linked to the article page, includes a table (Table S5) that shows what evidence is consistent or inconsistent with various interpretations of the streaks. The interpretations involving brine flow generally fare best -- other than the specific identification of water. If the flow is underground, near the surface, with the streaks reflecting changes in properties of the surrounding soil, that avoids the issue of failure to directly observe water. Bottom line... They have fascinating images of seasonal changes; what they mean is uncertain.

Thanks to those who suggested this item. It was on my list to do, but the extra votes helped to ensure it got finished.

More about Mars...
* A lake on Mars? (August 24, 2018).
* Is Mars wetter than Earth -- underground? (February 9, 2018).
* What causes gullies on Mars? (September 8, 2014). This post is from the same team of scientists.
* One way trip to Mars (September 22, 2009).
* Spirit (February 20, 2010).
* Genome from Mars (September 22, 2010).
* Mars: craters (August 11, 2012).

* * * * *

Update, June 13, 2018... More recent work, from the same scientists, makes it more likely that the RSL are due to flowing sand. Key evidence is that the flows are found only at substantial slopes. In any case, RSL are still of interest. News story, which links to the article: Recurring martian streaks: flowing sand, not water? (Phys.org, November 20, 2017.)

August 24, 2011

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).

Predicting vaccine responses

August 22, 2011

People vary in their responses to a vaccine.

The figure at right illustrates this. Two flu vaccines were administered. One, labeled TIV (trivalent inactivated vaccine; blue bars), is the common injected vaccine. The other, labeled LAIV (live attenuated influenza vaccine; black bars), is administered intranasally. Each bar shows the response of one person, measured 28 days later. You can see that the responses of individuals -- the amount of antibody they make -- vary widely. This is true for both vaccines.

Why is there such variation? And could we tell before waiting for the response to develop? That is, could we predict who will and who will not develop a good antibody response to a vaccine? A new paper explores these questions, and comes up with some interesting -- and preliminary -- results. Their approach is rather brute force: they simply measure gene expression by the individuals 7 days after the vaccine, and look for differences between responders and non-responders. That is, they compare day 7 gene expression patterns with the day 28 antibody response. (They look at gene expression on both day 3 and day 7. The two days apparently give similar results. It is not clear in the paper which day's data are used.)

For the TIV, they found about a thousand genes whose early expression seemed correlated to the later antibody response; that is out of about 20,000 human genes. A few of these genes are shown in the figure at the left.

Now, you may well find this figure overwhelming -- or at least, amusing. But what it shows is a gene network: a group of genes that are functionally related. Further, the coloring shows how these genes responded compared to the antibody levels achieved (for the TIV). Red indicates genes whose expression was positively correlated with a good response; blue indicates genes whose expression was negatively correlated with a good response. That is, the analysis has shown a functionally related set of genes that seems to predict the ultimate response.

This is Figure 4b from the paper; it is also in the Science Daily news story.

We learn two things from this analysis... First, we learn that the function of certain genes does predict the antibody response. Second, we find some clusters of related genes that seem related to the antibody response; this gives us some clues about important functions involved in the antibody response. Thus, we have gained some information about the questions posed above.

Is this useful? Well, it's very preliminary -- but intriguing. The good news is that they find differences in gene expression between responders and non- responders to the vaccine. They've done this with two flu vaccines here, and in earlier work with another vaccine (yellow fever). The genes involved are mostly different in each case, but with a few genes that seem to be involved in multiple responses. That could be very interesting to follow up. For now, this is largely a research project, to help us better understand vaccine responses. It is possible that predicting which people will respond -- either shortly after vaccination or perhaps even before -- could be useful information, but that is for the future.

News story: Quick Test Can Predict Immune Responses to Flu Shots. (Science Daily, July 10, 2011.)

* News story accompanying the article: Solving vaccine mysteries: a systems biology perspective. (L Trautmann & R-P Sekaly, Nature Immunology 12:729, August 2011.)
* The article: Systems biology of vaccination for seasonal influenza in humans. (H I Nakaya et al, Nature Immunology 12:786, August 2011.)

Also see: Who gets sick from the flu? (September 20, 2011). This later post deals with the variability of infection responses between individuals. The post above deals with variability of vaccine responses between individuals. The approach is similar for the two papers. Is there any actual connection between what is being studied? Interesting question. I don't think we can tell at this point.

And more... Why vaccine effectiveness may vary: role of gut microbiome? (February 27, 2015). This is from the same lab.

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

Posts on flu and flu vaccines are listed on the page Musings: Influenza (Swine flu).

Why did the HIV vaccine work for some people? (September 27, 2011). This post raises some similar issues for an HIV vaccine.

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.

Where are the eyes?

August 19, 2011

The picture shows a purple sea urchin (Strongylocentrotus purpuratus). It was photographed off the Southern California coast; these purple sea urchins are common around there. The organism is responsive to light. The question for you is: Where are the eyes? Think about that before reading on.

Source: Figure is reduced from main figure at Strongylocentrotus purpuratus (Stimpson, 1857). The photo -- and the page, with more information and more beautiful photos -- is by Dave Cowles, Walla Walla University.

According to