Justice should be blind -- and well fed

April 29, 2011

The legal system is supposed to act on the relevant facts of a case, free of bias (e.g., about race) or any extraneous factors. That is the ideal we strive for; it is sometimes summarized in the phrase "justice is blind". Of course, we all know that human systems do not live up to the ideals. Sometimes, bias is evident. Sometimes, we are just mystified. Someone even quipped, "Justice is what the judge had for breakfast."

A new paper, in the prestigious scientific journal PNAS (Proceedings of the National Academy of Sciences, US), examines how the decisions of judges on similar cases vary during the working day. Their results, while not literally supporting the "breakfast" quip, certainly remind us of it, and require further attention.

One activity of a judge is to examine petitions from defendants, for matters such as parole. These are short acts; the judge spends about 6 minutes on average on each case, and handles many such cases in a single session. Thus one can analyze the nature of the decision vs time (or position) within a single court session.

The graph shows the key results. This is Figure 1 of the paper. The ordinate (y-axis) is the fraction of decisions that are favorable to the defendant. The abscissa (x-axis) is, loosely, time during the day. More precisely, it is the position of the case in the sequence of cases -- what they call the ordinal position. The dotted lines indicate breaks -- meal breaks. The circled points are for the first case of each session during the day. The major trend is clear: The first case in each session (the three circled points) has about a 65% chance of being decided favorably for the defendant. As each session continues, that probability trends lower -- eventually reaching zero.

Much of the paper is about explaining details of the court system, looking for possible variables that might be affecting the results. They do not find anything. They are left with the conclusion that the position of the case in the session affects the outcome -- that meal breaks affect the outcome. They do not know why. For example, it might be the meal itself that affects the decisions. However, it might also be the break from the stress of decision-making. There is nothing in the analysis at this point to clearly distinguish those possible explanations. The key point here is to show that there is an effect -- a big effect.

The paper analyzes courts in Israel. From the description of the courts and the cases, I would say the system is similar to US courts (though with different scheduling). Since the paper focuses on human issues, such as food and mental freshness, the general results are likely to hold anywhere.

News story: A Judge's Willingness to Grant Parole Can Be Influenced by Breaks. (Science Daily, April 14, 2011.)

The article: Extraneous factors in judicial decisions. (S Danziger et al, PNAS 108:6889, April 26, 2011.)

More about justice: Police training (July 19, 2020).

Connecting the senses

April 26, 2011

Imagine the following test... Step 1. You are presented with an oddly shaped object. Step 2. You are then presented with two objects, and asked to identify which is the one from step 1.
The figure at right shows some examples of pairs of objects used for the tests. This is Figure 1a from the paper.

Seems simple enough, and it does not matter whether step 1 is done by feel or sight, and whether step 2 is done by feel or sight -- or even whether the two steps are done with the same sense. After all, your brain integrates the information into "the object" -- regardless of which sense you use; you have no problem combining information obtained with the different senses.

Now imagine a 12 year old boy, blind from birth. He has surgery to restore sight, and is given this test shortly after the surgery. He can't do it. He can do it if both steps are done with the sane sense. That he can do it if both steps are by sight shows that his vision is ok. However, he cannot do step 1 by feel and then step 2 by sight. (They did not test the opposite combination.)

What I described there has been done, in a study by Project Prakash, which provides sight-restoring surgery to children in India, and is also able to carry out some testing. The paper reports results for five children, ages 8 to 17. What I wrote above summarizes the first key finding; medical and test details are in the paper.

First key finding? What is the second? For three of the children, they were able to repeat the testing. Each child showed major improvement in the touch-sight part of the test -- in one case being re-tested only five days after the initial test.

These results show that the role of the brain in processing sensory information is complex. The integration is not "automatic", but it occurs rapidly enough that it cannot be due to growth of new brain cells. The full story remains to be told.

News stories...
* MIT Study Of Blind Children In India Reveals Insights Into Brain Development. (Asian Scientist, April 14, 2011.)
* Shedding light on a longstanding puzzle -- Study of blind children in India helps answer a 300-year-old philosophical question. (MIT, April 11, 2011.) From one of the institutions involved. (At least one of the authors is an MIT professor who is also involved with Project Prakash.)

The article: The newly sighted fail to match seen with felt. (R Held et al, Nature Neuroscience 14:551, May 2011.) It's a short and readable article; give it a try.

More on the interrelationships of the senses:
* Can you see your hand in total darkness? (April 14, 2014).
* What does blue light smell like? (July 18, 2010).

More on restoring sight:
* A camera-based device to restore vision (February 25, 2013).
* Restoring sight by use of stem cells to regenerate a new cornea (July 13, 2010).

Music-making technology -- for the physically disabled

April 23, 2011

This item is along the lines of some others we have noted: robotic devices, controlled by the mind. But the specific application here is particularly interesting: the purpose of the device is to allow those with extreme physical disability to make music. There is considerable literature attesting to the therapeutic value of music. For some people, "music" includes making their own, not just listening.

With that perspective, what they do is "straightforward"; it is also rather preliminary at this point. The idea is to allow a person to control a musical device using their mind. The test subject is a person with "locked-in syndrome", capable of little physical movement except for the eyes. The subject learns to make music, using eye motions to control the computer. (Actually, the control is done by measuring the brain waves associated with the eye movements.) It's very limited music at this point, but a start to an interesting project. The test subject has expressed pleasure at what she has done so far.

News stories:
* Music is all in the mind. (Nature News, March 18, 2011.)
* Thoughts Make Music For Patient With Locked-in Syndrome. (Medical News Today, March 22, 2011.)

The article: Brain-Computer Music Interfacing (BCMI): From Basic Research to the Real World of Special Needs. (E R Miranda et al, Music and Medicine 3:134, July 2011.) The article is largely a general overview, and is not very technical.

Among posts on mind-controlled devices:
* Brain-computer interface: Paralyzed patients control robotic arm by their thoughts (June 16, 2012). A major development.
* FDA to fast-track prosthetic arm -- Follow-up: videos (April 2, 2011).
* Reading the brain waves from speech (October 17, 2010)

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

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

Using stem cells to study a heart condition

April 19, 2011

When we hear about stem cells, it is often in the context of using them to treat a disease or defect. Indeed, that is one of the long term dreams. However, stem cells can be useful as research tools in the lab. New work offers a good example.

The stem cells here are induced pluripotent stem cells (iPSC); these are stem cells based on taking cells from an individual, and causing them to "regress" back to a stem cell-like state. This ability to generate stem cells from an individual means that we can develop stem cells that carry certain specific disease genes. In the current work, they generate stem cells from patients with a certain type of genetic defect in heart rhythm, called long QT syndrome (LQTS). They then cause the stem cells to form various kinds of heart cells, and these can even be assembled into simple tissues. As a result, they are able to do lab studies of heart tissue carrying specific defects -- something not easily done by other means.

Here is an example of the results. They assemble such "artificial" heart tissue in the lab, using cells from a normal person and cells from a patient with LQTS. The figure shows an electrical measurement made on the two groups of cells. The difference is evident. FPD = field-potential duration; it is related to the QT interval. This is Figure 2e from article #1 listed below.

One useful aspect of this work is that they can study drugs. This includes drugs that might affect the condition, but it also means that they can test for side effects of other drugs. A common issue is finding that a drug affects heart rhythm; a lab system such as the kind developed here could be useful for screening for such side effects.

This is early work. Pretty much everything with stem cells is early stage work. The key idea here is using stem cells in the lab to study human physiology in ways that have not been practical before. This is a useful development -- much more modest than using stem cells therapeutically, but much closer to reality.

Two papers on this were published together; they represent similar work from independent labs. The term "Timothy syndrome" refers to a specific type of LQTS.

News stories:
* Stem cell help for Long QT. (The Naked Scientists, January 16, 2011.) A useful brief overview of paper #1. It includes a diagram of the heartbeat, showing what QT refers to.
* Skin Cells Used to Develop Possible Heart Defect Treatment in First-of-Its-Kind Study. (Science Daily, February 10, 2011.) A good presentation of paper #2. This is the most thorough of the news stories, but reading the shorter ones above may be good for starters.

The articles:
* 1. Modelling the long QT syndrome with induced pluripotent stem cells. (I Itzhaki et al, Nature 471:225, March 10, 2011.)
* 2. Using induced pluripotent stem cells to investigate cardiac phenotypes in Timothy syndrome. (M Yazawa et al, Nature 471:230, March 10, 2011.)

For more on stem cells:
* Using patient-specific stem cells to study Alzheimer's disease (February 24, 2012). This, too, involves the use of patient-specific iPSC.
* Cardiac stem cells as a treatment for heart damage: preliminary results are "very encouraging" (November 29, 2011).
* Children with two fathers (January 3, 2011).

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

For more on heart beats: Lighting the heart (August 31, 2010).

For more on heart disease: DNA testing -- for rejection of a transplanted heart (May 24, 2011).

Measuring radiation: The banana standard

April 17, 2011

There is a lot of radiation in the news, and you may be getting confused with all the different ways to measure it. It may be refreshing to find a unit of radiation that you can relate to: the banana. It may be whimsical, but it is also interesting and instructive.

It's well known that bananas are a good source of the mineral potassium. That is the basis of the point. Naturally occurring potassium is radioactive, as it contains about 0.01% of the radioactive isotope potassium-40 (K-40 or ⁴⁰K). The K-40 isotope gives off quite strong emissions; it also has a very long half life (over a billion years), so will always be around. Since all biological materials contain potassium, they (we!) are all radioactive. In fact, exposure to other organisms -- including our friends -- is a significant source of background radiation.

With the common banana being a known K source, the idea of using the banana as a reference for measuring radiation has some appeal. We can all relate to being exposed to one banana per day.

For an introduction to the banana standard: Wikipedia: Banana equivalent dose. (The radioactive sample shown above is edited from a figure at Wikipedia: Banana.)

I don't want to attempt any comprehensive presentation of the units that are really used for radioactivity. However, a brief survey might be in order. A useful start is to realize that the various units for radioactivity may actually be measuring different things. For each type of measurement, there may be different units, including official SI units.

One thing to measure is the number of radioactive decay events -- simply count them. This is most simply and directly presented as disintegrations per minute, or dpm. Common units that count decay events are the becquerel (SI) and curie.

There are different kinds of radiation, so simply counting events is not a good measure of the risk from an exposure. Thus one way to measure radiation is to measure the energy adsorbed from the radiation. Units for this energy include the gray (SI) and rad.

The types of units discussed above measure different things, but they are objective. Unfortunately, the effects of radiation on organisms is complex. Biologists have attempted to account for this complexity with something called the effective dose. The effective dose is a measure of the biological importance of the radiation. Units for this include the sievert (SI) and rem.

On average, a person receives about 2 mSv (millisieverts) of radiation per year, from natural "background" sources. An X-ray may contribute a few mSv -- a significant but still small increase in risk. It is likely that no one outside the Three Mile Island facility received more than a mSv from the 1979 accident. (These numbers are from the page: Wikipedia: Sievert.)

Eating one "standard" banana per day is equivalent to about 36 microsieverts over a year. This should not be taken too literally; the Wikipedia article notes that there are some complexities about what the banana standard really means. In any case, it is fun, and a reminder of our common exposure to low doses of radioactivity.

Other posts on radiation include:
* How radioactive is your avocado (and some other common exposures)? (November 16, 2016).
* Effect of low dose radiation on humans: some real data, at long last (July 24, 2015). And accompanying post.
* Berkeley RadWatch: Radiation in the environment (February 24, 2014).
* An improved CT scanner, with a reduced radiation dose (February 5, 2013).
* Does radiation treatment of cancer cause new cancers? (April 8, 2011).

My page of Introductory Chemistry Internet resources includes a section on Nucleosynthesis; astrochemistry; nuclear energy; radioactivity. That section contains some resources on the effects of radiation.

Other posts on bananas include:
* Food security: the potential of enhanced cultivation of enset (February 22, 2022).
* The genome of Musa acuminata (August 8, 2012).
* Rats, bananas, and tuberculosis (March 11, 2011).
* What does blue light smell like? (July 18, 2010).

Bouba and kiki: A puzzler

April 12, 2011

Look at the two objects at the right. One is a bouba and one is a kiki. Which is which? Saying that you do not know is not helpful. Most people actually do know -- even if they have never heard the terms before. And they know regardless of their language. So, fairly quickly, make your choice. Perhaps you have a conscious reason, or perhaps it just seems obvious. Make your choice, and then read on.

For basic background: Bouba/kiki effect. (Wikipedia.) The figure above is from this page. The page includes reference to the original 1929 work that got the topic started, as well as to more recent scientific papers. Note that the spelling of the terms varies from one use of them to another.

Why did this come up? Because the American Museum of Natural History (New York City) has a major exhibition Brain: The Inside Story, and one of their activities involves Bouba and Kiki -- now in human form. Kiki and Booba. (AMNH, November 30, 2010. Now archived.)

Also see: Bright lights and pupil contraction (March 2, 2012). It's not really related, but...

Capsaspora owczarzaki and you
    or
Where did animals come from?

April 10, 2011

The modern era of DNA sequencing and genome analysis -- the last decade or so -- has brought huge amounts of new evidence on the relationships between organisms. Sometimes people look at the genome similarities and differences between closely related organisms, such as various primates. Sometimes they look at broad issues, such as the overall "tree of life". For example, how did the line of organisms we call animals develop? What were the key steps in making the transition from a unicellular organism to a simple animal? It turns out that the genomes of all animals, from the simplest sponge to vertebrates such as us, are remarkably similar. Many key molecules of human development are there in the simplest animals. And now the story goes back further, as information comes in for even simpler organisms, perhaps representative of those that gave rise to animals. The current news is about Capsaspora owczarzaki, an amoeba. It, too, has some of these same key molecules, as do other pre-animals that have been examined.

The emerging story is that the development of the various types of animals was largely due to subtle changes in how key regulatory molecules acted. The basic "toolkit" for being an animal -- sponge or human -- was developed long ago. This leaves much to be figured out, but it establishes a framework that is quite satisfying.

News story: From Single Cells, a Vast Kingdom Arose. (New York Times, March 14, 2011.) Highly recommended, as a general overview, whether you go on to the more technical article below or not.

The article: Unexpected repertoire of metazoan transcription factors in the unicellular holozoan Capsaspora owczarzaki. (A Sebé-Pedrós et al, Molecular Biology and Evolution 28:1241, March 2011.)

As I was finishing this item, I finally got around to the January issue of The Scientist. It includes a nice feature article closely related to this post. The broad theme is the development of multicellular organisms. For most of the era of life on earth, most life was unicellular. Then, multicellularity developed, as now seen in all the macroscopic organisms we routinely encounter. Multicellularity was clearly one of nature's great innovations. How did it occur? The story above addresses part of this; the article in The Scientist is a broader overview, and very readable. Highly recommended. From Simple to Complex. (J Akst, The Scientist, January 2011, p 38.) Lead-in: "The switch from single-celled organisms to ones made up of many cells has evolved independently more than two dozen times. What can this transition teach us about the origin of complex organisms such as animals and plants?"

A previous post on the use of genome sequences to determine relatedness of organisms: The Siberian finger: a new human species? -- A follow-up in the story of Denisovan man (January 14, 2011).

A post on the early history of skeletons: The earliest biomineralization? (January 24, 2012).

More about amoebae...
* Trogocytosis -- How an amoeba chews its food (May 16, 2014).
* The largest known virus (August 5, 2013).

Weather report from Titan: Clouds? Puddles? Does that mean it rained?

April 6, 2011

Musings doesn't do many weather reports. However, if this one holds up, it is remarkable. Rain. A billion (10⁹) kilometers from here. The first report of rain somewhere else than on Earth. Of course, we have an "eye-in-the-sky" watching: the Cassini spacecraft. Even then, it did not directly see the rain, but merely circumstantial evidence that makes it likely that the rain happened. The rain report is for Titan, the big moon of Saturn. The rain of course is methane, CH₄.

Titan is cold. Any water that might be there is permanently solid (with only a trace in the vapor phase). However, the temperature does allow methane to cycle between gas and liquid phases -- much as water does here on Earth. Lakes of methane are now rather well characterized on Titan. The lakes change with time, and there are seasonal patterns. In fact, much of the paper involves interpreting the observed rain in terms of seasonal variation, just as we have Spring rains here.

Th heart of their observations is that they see clouds, and then see dark regions on the surface, which they interpret as being "puddles" of liquid methane. These puddles disappear, presumably by evaporation. Figures in the paper show what they see, but of course it is the interpretation that matters -- and that is hard for an untrained observer.

News story: Seasonal Methane Rain Discovered on Titan. (Wired, March 17, 2011.)

* News story accompanying the article: Planetary science: Precipitation Climatology on Titan. (T Tokano, Science 331:1393, March 18, 2011.)
* The article: Rapid and Extensive Surface Changes Near Titan's Equator: Evidence of April Showers. (E P Turtle et al, Science 331:1414, March 18, 2011.) See "Supporting Online Material" for more, including diagrams where they show their interpretation of the figures.

More about Titan...
* Weather forecast: Clouds will form near North Pole within two years (April 9, 2012).
* Quiz: NASA's boat (June 29, 2011).

More from Cassini... Enceladus and its plume (November 17, 2009).

More about rain...
* What would raindrops be like on other planets? (April 13, 2021).
* The aroma of rain (June 13, 2015).
* Lyell on fossil rain-prints (May 6, 2012) (and accompanying post).

* Previous post about turtles: Where is turtle #92587? (February 22, 2011).
* Previous post about an article written by a Turtle: none.

The 6th mass extinction?

April 4, 2011

The paper discussed here has received a lot of attention. My initial reaction to hearing about the work was that the paper was likely to be too complicated to understand. I was pleasantly surprised to find that much of the paper was very readable and very interesting. I encourage people to have a look, at the news story and at some of the paper. I should also caution that the paper has a political element; it is important to be cautious. The paper raises a question, and discusses what is known; importantly, it discusses how we know -- and what the problems are. The discussion is very interesting. Emphasizing an answer is missing the point, from a scientific viewpoint.

There are two basic background points that the paper builds on:
* Our best estimate is that there have been five "mass extinctions" of life on earth in the last 540 million years (the period where there is an abundance of complex organisms). A mass extinction is defined by the loss of 75% of the species in a short time (geologically speaking). The most recent of these is perhaps the most famous. It was about 65 million years ago, and included the extinction of the dinosaurs; this event was associated with an asteroid colliding with Earth. The extinction of the dinosaurs opened up niches, and allowed the proliferation of mammals -- including humans. We thus recognize that extinctions are part of nature -- and are not entirely bad.
* We are now going through a time of loss of biodiversity. It may be caused, in part, by human activities.

So, they ask: Is this the 6th mass extinction? In order to address this, they need to make clear what the "rules of the game" are. How do we count species -- now, and for the distant past? What are the types of evidence we use, and what are the limitations of the analyses? These are the aspects of the paper that I found most interesting; they constitute a serious overview of how we know about mass extinctions.

News story: Has Earth's Sixth Mass Extinction Already Arrived? (Science Daily, March 5, 2011.)

The article: Has the Earth's sixth mass extinction already arrived? (A D Barnosky et al, Nature 471:51, March 3, 2011.)

More about extinctions:
* Did selenium deficiency play a role in mass extinctions? (February 5, 2016).
* What caused the dinosaur extinction? Did volcanoes in India play a role? (April 13, 2015).
* What caused the mass extinction 252 million years ago? Methane-producing microbes? (October 12, 2014).
* The Obama lizard (March 20, 2013).

More about the effect of humans on biodiversity: The ultimate census: the distribution of life on Earth (June 22, 2018).

Soft drinks (sugar) and blood pressure

April 1, 2011

Soft drinks again. Recall Fructose; soft drinks vs fruit juices (November 7, 2010). That post focused on the special effects of fructose, a natural sugar that some people consume in high quantities via soft drinks that have been sweetened with high fructose corn syrup.

Now we have a new report, which suggests a link between sugar consumption and blood pressure. The sugar consumption is for all sugars, not just fructose; the focus is on sugar-sweetened beverages (SSB), whether soft drinks or juices, as a major source of sugar. By looking at the accumulated databases of health information, they find a correlation between the consumption of SSB, and blood pressure (BP).

A key limitation of this type of study, as we have noted before, is that it does not look at causality. That is, they find that people who drink lots of SSB tend to have higher BP -- a correlation. However, we do not know that the SSB is causing the BP changes. Interestingly, they refer to one paper in which there is a direct test of BP changes upon drinking SSB; that paper also shows an effect of the SSB on BP. Thus the current paper should be taken seriously, though it certainly needs more careful follow-up.

The magnitude of the effect suggested here is about 1.5 torr (mm Hg) per can of SSB. This may seem small, but for those who regularly consume multiple cans of soft drink -- or equivalent amounts of juices -- each day, this can add up. Note that this would represent a substantial calorie intake, as well as possible contribution to BP.

News stories:
* Sugary soft drinks linked to high blood pressure. (BBC, March 1, 2011.)
* Sugar-Sweetened Drinks Associated With Higher Blood Pressure. (Science Daily, March 1, 2011.)

* Editorial accompanying the article: Sugar and Salt in the Pathogenesis of Elevated Blood Pressure. (K Stolarz-Skrzypek, Hypertension 57:676, April 1, 2011.)
* The article: Sugar-Sweetened Beverage, Sugar Intake of Individuals, and Their Blood Pressure: International Study of Macro/Micronutrients and Blood Pressure. (I J Brown et al, Hypertension 57:695, April 1, 2011.) The paper discusses other studies of sugar effects, both short and long term, on BP. (Those interested in the prospective study mentioned above should check out reference 30 of this paper.)

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

Human origins, and the species question

March 28, 2011

We have noted recent developments in understanding human origins, including genome work. It is a remarkable development that we now have information about the genome of two ancient populations of hominids, the Neandertals and the Denisovans. In both cases, there is evidence for some inter-breeding between the ancient population and what we call modern humans, Homo sapiens. We noted this, with its implications, in the post The Siberian finger: a new human species? -- A follow-up in the story of Denisovan man (January 14, 2011).

Inevitably, we ask: are these ancient populations part of our species, or not? The traditional view has been to consider Neandertals as a distinct species of human, but the inter-breeding results lead us to question that. The two papers on Denisovans make different statements on the species issue.

A recent news feature in Science addressed this species question. The main focus of the story was discussing various views of ancient human migrations. However, of immediate relevance is a "side-bar" (p 394) on "The Species Problem". It briefly summarizes a range of views on what "species" means in modern biology. The bottom line is that this is something of a mess. No big surprise; as we learn more, it is common enough in science for an idea we thought we understood to become murky. Reading this short sidebar is a useful introduction to the species problem. As a specific, you will see why the group studying the Denisovan man decided to step back and not take a position on whether or not that is a new species of human.

The article: A New View Of the Birth of Homo sapiens -- New genomic data are settling an old argument about how our species evolved. (A Gibbons, Science 331:392, January 28, 2011.) As noted, the side-bar on the species question is the main reason for this post.

More about ancient humans: An interesting skull, and a re-think of ancient human variation (November 12, 2013).

A modified chicken that cannot transmit bird flu

March 26, 2011

The 2009 influenza (flu) virus seems to have passed without causing much problem. But the specter of a serious flu pandemic remains -- and remains substantially a mystery. What is likely is that a serious flu will involve birds -- including domestic poultry. A serious strain of bird flu is active in Asia, causing substantial economic losses -- and causing fear about what might happen if the virus adapts to humans. Thus the idea of reducing flu infection in birds is of interest -- both to protect the birds per se, and to protect us.

New work offers a novel approach to reducing bird flu. It's already possible to vaccinate birds against the flu, But that has the same disadvantages as vaccinating humans against the flu. What if we could engineer the birds to be intrinsically resistant to the flu? That is the idea of the new work. They genetically modify the birds to make a small piece of RNA that mimics a key part of the viral genome -- a part needed for the virus to replicate. As a result, the viral polymerase (replication system) sees this "decoy" RNA -- rather than the virus. With the polymerase tied up with the decoy, there is little virus replication.

Here is an example of some of their preliminary work, showing that the decoy can inhibit the viral polymerase enzyme. No chickens or viruses here, just cells with various genes being added to test the proposed interaction. This is Figure 1C from the paper, and summarizes two types of experiments.

The first three bars are for one experiment. The left-most bar, labeled pLentilox, is the control; enzyme activity is 100%. (The control here is simply the vector used in the rest of the experiment for carrying decoys, but without anything added; that is, it is an empty vector.) Decoy 5 is the decoy they designed; you can see that it greatly reduces the enzyme. Decoy 7 was designed so that it does not affect the enzyme, and indeed it does not; a control such as this helps to make the point that the first decoy is working for the intended reason. The two right-most bars are for another type of experiment. Non-TG is the control, at 100%. TG-D5 uses the same decoy 5 we saw above, and again it inhibits the enzyme.

The experiments above establish that the idea has merit: a decoy can inhibit the viral enzyme, It's now time to test whether this works in real chickens with real viruses. They modify chickens to produce the decoy, and they present some results on how these modified chickens respond when challenged with flu virus. They find that the modified birds infected with flu may get sick and die, but virus transmission is greatly reduced. Blocking transmission is the key to blocking the spread of an infectious disease, so the results are encouraging.

This is an intriguing piece of work. It is logical, and the data show a good effect. However, there are reasons to be cautious -- as both the Science articles make clear. The work here should be taken as preliminary: an interesting finding that deserves to be followed up. Only with careful follow-up will we know how effective it is over the long term, and what side effects there might be. On the plus side, if it works, it probably can be extended to other flu virus hosts, particularly the pig, and perhaps to other viruses. Each case will need to be worked out, but if one case works well, others will follow.

News story: Chickens Modified to Not Spread Bird Flu. (Discovery News, January 14, 2011.)

* News story accompanying the article: Avian influenza: Transgenic Chickens Could Thwart Bird Flu, Curb Pandemic Risk. (M Enserink, Science 331:132, January 14, 2011.)
* The article: Suppression of Avian Influenza Transmission in Genetically Modified Chickens. (J Lyall et al, Science 331:223, January 14, 2011.)

Many posts on the flu are listed on a supplementary page Influenza (Swine flu).

More decoys: Making decoys that trap the SARS-2 virus (August 10, 2022).

More on disease transmission... Should you ask your doctor to go BBE? (May 12, 2014).

Your genes: What do you want to know, and when do you want to know it?

March 22, 2011

This post is prompted by a news feature in a recent issue of Science. The topic is familiar enough: getting information about your genes, part of the broad issue of personalized medicine. The article starts with a little story that is, frankly, rather scary. So, I think it is worth sharing.

The article: What Would You Do? (J Couzin-Frankel, Science 331:662, February 11, 2011.) Lead-in: "As technology makes it easier to sequence people's DNA for research, scientists are facing tough decisions over what information to give back."

This is not a new topic. Numerous Musings posts have dealt with the emerging story of personalized medicine; some have dealt with the ethical issues. An early post, with links to many others, is: Personalized medicine: Getting your genes checked (October 27, 2009). Most recently we presented the declining cost of genome sequencing -- a point that makes the current story all the more relevant. That post is: The $1000 genome: Are we there yet? (March 14, 2011). (The articles for that post and this one are together in that issue of Science.)

Sometimes it is tempting to blame the advancing knowledge for creating ethical issues. However, in a sense it is only the details that are new. Some years ago, in the early days of recombinant DNA work, there was concern that such work would create ethical problems. I gave talks about various aspects of the new work from time to time at local high schools. One point I made was to discuss an ethical problem resulting from parents refusing a standard medical treatment for their child, and the attempt of the state to take the child from the parents so they could treat the child. This case was from the current news -- and had nothing to do with any advanced technologies. Ethical issues usually, by their nature, involve different values we hold coming into conflict with each other. It is the nature of values that they will conflict. Let's promote the discussion of the values and how they might apply to one problem or another, so that individuals can make decisions they are comfortable with -- for themselves.

Consistent with the previous point, I post this item without intending to favor any particular outcome. Read the article, learn about what is known, think about the values involved and how they may conflict -- so you can make decisions for yourself. You can't avoid the question.

Bird lays egg

March 19, 2011

At age 60, that is news.

Borislav sends the following news story... Oldest recorded wild bird raising a chick. (USA Today, March 8, 2011. Now archived.) We don't have any more information, but the article discusses why this is interesting -- as well as fun. We'll just let it stand.

The date on the story listed above is March 8. Three days later, Mother Nature added a footnote: Japan tsunami: Thousands of seabirds killed near Hawaii. (BBC, March 16, 2011.)

* * * * *

Update, 2021... Wisdom the albatross has hatched yet another chick at the age of 70 -- She's the oldest known wild bird in history - and she's pretty awesome! (Fermin Koop, ZME Science, March 8, 2021.)

* * * * *

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

More about seabirds: Why don't penguins fly? (August 24, 2013).

More birds: Of birds and butts (February 2, 2013).

More about bird eggs... What is the proper shape for an egg? (September 18, 2017).

A curcumin-based drug and stroke treatment

March 16, 2011

Curcumin is the yellow stuff in the spice turmeric. It is a common ingredient of curries. Various possible health effects have been suggested for curcumin. These suggestions come from simple correlations, that people who eat lots of curcumin have less of some disease, followed by some lab work in model systems. At its best, the work shows some effect in an animal model, and offers some explanation for why it works. Nevertheless the question of its usefulness in humans usually remains an open question.

We noted an interest in using curcumin to treat Alzheimer disease [Curry and Alzheimer's disease (June 15, 2009)]. So far, limited testing has been reported in humans, with no clear benefit.

John now sends a news story about the possible use of a new drug derived from curcumin to treat stroke. Animal results have shown promise. The good news is that they want to do testing in humans. It is an important part of this story that they have used curcumin as the starting point, but the drug being tested is a derivative -- a derivative designed to better cross the blood-brain barrier. By modifying the curcumin, we can no longer simply call it curcumin. For example, one reason for the interest in using curcumin is that it is already widely consumed, and regarded as rather safe. However, once we modify the molecule, we can no longer assume that it has the same safety profile. After all, the purpose of the modification was to get more of it into the brain. It remains to be seen whether this increases side effects as well as effectiveness.

Modifying a potential drug to change specific properties is a standard tool in drug development. Having new options for treating stroke would be welcomed. Thus the new work is welcome. However, caution is important. Do not assume that anything in particular will work out, and do not weigh very heavily anything you know about curcumin as being relevant to a possible new drug that is related to curcumin. This is what drug testing is about, and the annals are littered with well-intentioned but failed drugs.

News story: Spice drug fights stroke damage. (BBC, February 10, 2011.)

Articles:
* Via abstract at PubMed... Delayed treatment with a novel neurotrophic compound reduces behavioral deficits in rabbit ischemic stroke. (P A Lapchak et al, Journal of Neurochemistry 116:122, January 2011.) Use of the new drug in a rabbit model.
* Neuroprotective and neurotrophic curcuminoids to treat stroke: a translational perspective. (P A Lapchak, Expert Opin. Investig. Drugs 20:13, January 2011.) Overview. This could be a good place to start. Browse and check the section headings. The article includes chemical structures for curcumin, and for natural and synthetic derivatives.

A background post is listed above.

Also see: Can we pinpoint a specific molecular explanation for tissue damage following a heart attack? (March 24, 2015).

The $1000 genome: Are we there yet?

March 14, 2011

The main purpose here is to discuss a single graph. In fact, the main purpose is to discuss a single curve on that graph.

Look at the red curve on the graph at the right. It shows, in round numbers, the cost of DNA sequencing over the last decade, The scale for this line is on the right -- a log scale. (The curve is so well-labeled that one hardly needs to check that scale.) The curve starts in 2000, about the time the human genome project was announcing a "complete", though rough, human genome. That project cost a few billion dollars, but much of that was development costs. As of that time, they estimate the cost of sequencing as $10,000 -- per million base pairs (Mbp). The human genome is about 3 billion base pairs, so that would be about $30 million to sequence a human genome. The cost of DNA sequencing has dropped dramatically over the decade. On average, the cost has dropped by half every year or so -- a faster pace than the famous Moore's Law for computers. The graph now shows $1 -- per Mbp. That would be about $3,000 for a human genome.

As the original human genome project wrapped up, a new goal was formulated: the $1000 genome. That's a nice round number, and the graph here is rough. Nevertheless, we are about there. The cost of sequencing the human genome has come down by a factor of 10,000 over the decade. If you need your genome sequenced, it is now practical. If you just want your genome sequenced, for fun or curiosity, why not?

Caution... Although it is now practical for an individual to get his or her genome sequenced, our ability to understand the genome information is still limited. Nothing here is intended to encourage anyone to actually get their genome sequenced. The point is that cost per se is no longer the critical limitation.

The graph is part of a news story, generally discussing the pressure that genomics is putting on computer systems. The lower curve in the graph shows the cumulative amount of genome sequence known; it is overwhelming the computer systems needed to analyze it. Those interested in the computer issues may find the article of interest. It is: Will Computers Crash Genomics? (E Pennisi, Science 331:666, February 11, 2011.)

Among many Musings posts on sequencing, the following seem especially relevant here...
* The $1000 genome: we are there (maybe) (January 27, 2014). An announcement, from a supplier of sequencing equipment.
* More genome sequencing for newborns? (September 17, 2013).
* DNA sequencing: an overview of the new technologies (June 22, 2012). An accompanying post discusses nanopore sequencing.
* How many human genomes have been sequenced? (November 30, 2010).
* Genome sequencing to diagnose child with mystery syndrome (April 5, 2010).

* A subsequent post also is about how we deal with genome information: Your genes: What do you want to know, and when do you want to know it? (March 22, 2011). (The articles for that post and this one are together in that issue of Science.)

* A post on cancer genome sequencing... Studying cancer development by analyzing the genomes of individual cancer cells (May 16, 2011).

* Using DNA sequencing to monitor a patient: DNA testing -- for rejection of a transplanted heart (May 24, 2011).

* Is whole genome sequencing a useful medical tool? (November 9, 2011). What is the role of genome sequencing in medicine?

* Also see: Using DNA for data storage (March 5, 2013). That's storage of computer data. DNA sequencing is how you read it.

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

Rats, bananas, and tuberculosis

March 11, 2011

Before going on, what do you think is the story line connecting the elements of the title?

When ready, go have a look at one of the following news stories:
* Detecting Tuberculosis: No Microscopes, Just Rats. (New York Times, January 3, 2011.)
* Rats vital in curbing spread of TB. (APOPO, January 20, 2011. Now archived.) A page from the organization doing the work. Links to much information. (APOPO? It is a Dutch acronym: Anti-Persoonsmijnen Ontmijnende ProductOntwikkeling; in English: Anti-Personnel Landmines Detection Product Development. The name of the organization refers to another use for the rats.)
* Also note that an update to this post has been added at the end.

Stories about using an animal, such as a dog, to detect some disease are common enough. The logic behind them is straightforward: the animal is trained to distinguish some feature, usually the odor, of a diseased sample compared to a normal sample. Rarely do we hear of the details behind the detection, such as what specific molecules are being detected. Perhaps more importantly, rarely do we hear of such a test actually getting serious consideration for practical use. It's not entirely clear how close this is to practical use, but maybe. The point is that rats are quite good at detecting tuberculosis (TB), and the use of rats is probably less expensive that currently used tests (at least the more sensitive ones). (The bananas? They are used as reward for the rats during the training phase.)

Quite good? The rats detect most cases that were already noted by the routine field test (examining a stained sputum sample under the microscope). (Why the rats missed a few cases is not addressed.) Interestingly, the rats detected a huge number of samples that the routine test did not. Are these false positives? Well, more careful examination has already suggested that a third to a half of them are real positives, but had been missed in the initial screening. So what about the rest? Are they false positives? They don't know. It may be that the rats are simply more sensitive, and are detecting samples with a low level of TB bacteria. An important part of the follow-up will be to sort this out.

The article: Short Report: Using Giant African Pouched Rats to Detect Tuberculosis in Human Sputum Samples: 2009 Findings. (A Poling et al, American Journal of Tropical Medicine and Hygiene 83:1308, December 2010.) It's very short (main text is less than two pages), and includes some good discussion of the sensitivity issues.
Figure is reduced from main figure at Wikipedia: Gambian pouched rat.

Other posts on TB include...
* A new vaccine against tuberculosis? (November 9, 2018).
* How did tuberculosis get to the Americas? (January 24, 2015).
* A bio-ethics controversy: HIV-TB interaction (July 13, 2010).
* Both ways (November 18, 2008).

For more on rats: A rodent that can't chew (November 5, 2012).

Another example of using animals to help with medical diagnosis: Can pigeons diagnose cancer by reading patient X-rays? (December 29, 2015).

Also see:
* Bomb-sniffing grasshoppers? (November 8, 2020).
* Copper ions in your nose: a key to smelling sulfur compounds (October 10, 2016).
* When life imitates art... Bacteria blink for arsenic (April 15, 2012). Biosensors.
* Leprosy: the armadillo connection (May 14, 2011). The bacteria that cause tuberculosis and leprosy are related: both are from the genus Mycobacterium.

More, January 30, 2012...

Here are some recent stories. The new paper provides more evidence of the same type as shown earlier; the questions raised above are not really addressed.

News story: Tanzania: Trained Giant Rats Sniff Out Land Mines And TB. (I Eveleens, African Spotlight, January 3, 2012. Now archived.) This story also notes the use of the same type of rat in detecting land mines.

Article, which is freely available: Using giant African pouched rats to detect tuberculosis in human sputum samples: 2010 findings. (A M Mahoney et al, Pan African Medical Journal 9:28, July 18, 2011.)

Who is #1: the most DNA?

March 7, 2011

The twentieth century brought a basic understanding of heredity at the molecular level. Briefly, the chemical known as DNA carries genetic information, and the basic unit of information is the "gene" that codes for one protein chain. The discovery of the structure of DNA by Watson & Crick is symbolic of this understanding. [The original Watson-Crick paper on the structure of DNA (October 25, 2010).]

If genes or DNA are the underlying basis of heredity, surely it is good to have more of them? Surely, more complex organisms have more? But no. Biology is not so straightforward, First, there is no particular relationship between the number of genes and the amount of DNA. That is, the gene density in the DNA varies widely from one organism to another. Second, neither measurement correlates well with any measure of complexity. Clearly, the basis for genome size -- whether measured by amount of DNA or by number of genes -- is a complex story.

No matter the importance, it is human nature that we like to keep score. In recent months, two newcomers have taken over the #1 spot on genome size lists. One is discussed in this post, and one is discussed in the accompanying post, below: Who is #1: the most genes (for an animal)? (March 7, 2011).

The first paper is based on work measuring the DNA content of various plants found at the Royal Botanic Gardens at Kew (England). They show that a particular plant, Paris japonica, has a larger genome than any eukaryote previously reported. In this case, genome size refers to the amount of DNA in the haploid (1C) chromosome set.
The figure at right is reduced from the main figure in the ScienceDaily news story listed below.

Here is an example of how they measure the genome size, from Figure 1C of the paper. They prepare nuclei from a mixture of their sample ("2") and a reference material whose genome size they know ("1"). They then add a fluorescent dye that binds to DNA; the amount of dye bound is a measure of the amount of DNA. They then measure the fluorescence from each nucleus. The graph shows the number of nuclei (y-axis) with a particular amount of fluorescence (x-axis). You can see that the data is largely in two peaks -- one for each kind of nucleus. It appears that nuclei of peak 2 (the sample, at about 300) are about 3 times bigger than the nuclei of peak 1 (the reference, or standard, at about 100). The little table in the figure shows the detailed analysis, and shows that the nuclei of peak 2 are 2.807 times bigger. Since the genome size of the reference is known, they multiply that by 2.807 to get the genome size of their sample. It is 152 picograms (pg) -- for "1C", the haploid DNA content.

A 152 pg genome for this little plant. That is about 15% larger than that of the lungfish, the previous champ. For comparison, humans have about 3 pg of DNA in the 1C (haploid) set.

Some things to note about this work...

First, it is about amount of DNA, not number of genes. As noted above, these vary quite independently. We do not yet know the number of genes; however, it is likely that the gene number in this plant is not much different than in other plants.

In order to claim that this genome is the largest eukaryotic genome, they have to ignore one measurement that has been reported. There is an old report of the genome of an amoeba, Amoeba dubia, that is about five times larger than the genome reported here. There has long been skepticism about that result, and they choose to set it aside.

They note that their plant, like many plants, has undergone genome duplication -- twice! That is the plant may behave as a diploid, but actually is octuploid. Thus the large genome size is not fundamental to this group of plants, but reflects duplication events. This is an interesting but incomplete story in how organisms evolve. One reason biologists look at genome sizes is to try to see the evolutionary story.

News stories:
* Jaume and the Giant Genome. (The Scientist, February 2011.)
* Rare Japanese Plant Has Largest Genome Known to Science. (Science Daily, October 7, 2010.)

The article: The largest eukaryotic genome of them all? (J Pellicer et al, Botanical Journal of the Linnean Society 164:10, September 2010.)

A good general resource on genome sizes is the Animal Genome Size Database, maintained by Ryan Gregory at the University of Guelph. Choose the Statistics page (menu bar at the left) for a nice overview -- of all genome sizes, plant and microbial as well as animal. The figure near the bottom of the Statistics page is good perspective. [This database is also listed on my pages Internet Resources for Molecular Biology: Genomes and Unusual microbes: Microbes with too much DNA.]

Thanks for Borislav for calling this new plant genome work to my attention.

* * * * *

The accompanying post, below, is related to this one: Who is #1: the most genes (for an animal)? (March 7, 2011). At the end of it are some general comments.

More about genome duplications: On genome duplications (September 10, 2015).

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

Another post from a journal of the Linnean Society... Was Linnaeus's original elephant African or Asian? (December 7, 2013).

Child development: nature vs nurture? Year 2 as a window of opportunity.

March 5, 2011

It is generally accepted that children of higher socioeconomic status (SES) do better in school than children of lower SES. Why, and what might we do about it?

A new study shows that the differences are clear by age 2 -- but minimal at only ten months. Further, they show that genetics plays a role in the progress made by the children of higher SES. It is as if the poorer environment of the children of lower SES prevents them from realizing their full potential, from realizing what genes would allow -- and that there is a key step in this process during the second year of life.

A key tool used here, and widely in biology, is study of twins. So-called identical twins come from the same fertilized egg; the more technical term, monozygotic twins, derives from this fact. They are genetically identical, at least to a first approximation. Fraternal twins come from different eggs, and therefore are no more genetically similar than any siblings. Thus the general idea is that differences between identical twins and fraternal twins reflect differences in the role of genetics.

As so often, it is important to distinguish their facts and their interpretations. They did certain tests, and found certain results. The nature of the tests is actually not very clear in the paper itself, which simply refers to them. The news stories give you a better idea what was done. Then we raise the question of SES vs development. What aspect of SES, precisely, is relevant to the developmental steps tested here? What genetic features are relevant? Would we get different results if we studied other aspects of development? As the news stories make clear, the authors want to look at such questions. That is, the work here helps aim them to further work; it does not reach a simple conclusion on its own. Nevertheless, it does lead to some optimism: if we could learn what the critical aspects of child development are, at any particular age, we would have the prospect of making improvements. That's worth pursuing. At the same time, we must be careful to avoid reaching premature conclusions. Let the research work proceed.

News stories:
* Children's Genetic Potentials Are Subdued by Poverty. (Association for Psychological Science, January 31, 2011.)
* Being Poor Can Suppress Children's Genetic Potentials, Study Finds. (Science Daily, January 11, 2011.)

The article: Emergence of a Gene x Socioeconomic Status Interaction on Infant Mental Ability Between 10 Months and 2 Years. (E M Tucker-Drob et al, Psychological Science 22:125, January 2011.)

More on child development: Measuring development of humor in children (October 4, 2022).

More from the same journal (as the current post):
* What if there was a gorilla in the X-rays of your lungs? (July 26, 2013).
* How to talk to yourself (June 11, 2010).

Alzheimer's disease may be delayed in people who are actively bilingual

March 1, 2011

Both Alzheimer's disease (AD) and bilingualism have been discussed in Musings before. (Some links to a sampling of such posts are at the end of this post.) But it was a surprise when Borislav told me about a study combining these two topics.

The basis of the study is simple. They take a collection of AD patients, and collect background information about them. In particular, they classified the patients as monolingual or bilingual, and compared those two sets of patients.

The table at the right shows some of their results. The data here are a subset of more complete data shown in their data table (second page of the article).	Language group	Age at AD onset	Years of education
	Monolingual	72.6	12.6
	Bilingual	77.7	10.6

The key observation is that AD appeared at a later age in their bilingual patients, by about five years. This is a quite large delay.

Studies such as this must be interpreted with caution. The study basically shows a correlation, not causation. What is the real cause? As one example of ruling out a possible confounding variable, the table (above) shows that the effect is not simply due to educational background; in fact, the monolingual patients had more education. In their full table (in the paper), they also show that the effect is not simply due to having a higher status job. Again, the monolingual patients rated higher on that scale. (I do not know anything about that scale; they simply refer to a standard scale they used.) A confounding variable they cannot eliminate is immigration. Not surprisingly, there is a much higher frequency of immigrants in the bilingual group. Does this matter? There is no basis for answering that now, but they note the concern.

If the correlation shown here turns out to be significant, it fits with a pattern that activities that enhance brain use can delay AD. A goal is to define this better: what kind of use, or what parts of the brain?

News story: Being bilingual may delay Alzheimer's and boost brain power. (Guardian, February 18, 2011.)

The article: Delaying the onset of Alzheimer disease -- Bilingualism as a form of cognitive reserve. (F I M Craik et al, Neurology 75:1726, November 9, 2010.) Check Google Scholar, and you may find a freely available pdf. (Reference 7 of this paper addresses a similar question, including the immigration aspect; in fact, that work was stimulated by earlier work from the people who wrote the current paper. It, too, does not lead to a clear conclusion at this point, but those interested in following this story closely should check it.)

Other posts on AD include:
* Reversing Alzheimer's disease (March 4, 2011). Immediately above.
* Is Alzheimer's disease transmissible? (February 4, 2011).

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

Several posts on bilingualism have been consolidated onto the page: Musings: Bilingual.

Robots should learn to crawl first, then walk

February 27, 2011

That's the way we do it, so why shouldn't robots do it that way, too? There is a whole class of robots that learn from their experiences, but typically their body remains fixed. Would they learn better if they started with simpler bodies?

That's the essence of the question asked by "roboticist" Josh Bongard at the University of Vermont. Computer simulations showed that robots with an evolving body did indeed do better. Preliminary experimental work supports that.

An interesting aspect of the work is the interplay between biological thinking and engineering thinking. In this case, thinking about biology offered some guidance about robot design -- not answers, but rather questions to ask. An interesting question is whether we learn some biology from the work here with robots -- simulated or live.

News stories:
* For Robust Robots, Let Them Be Babies First. (University of Vermont, January 20, 2011.) This is from the author's university, and may be basically a press release. It is a quite good presentation of the ideas, and may be a good place to start.
* Metamorphosis key to creating stable walking robots. (New Scientist, January 10, 2011.) A short but useful overview of the work; includes the overview video.

Video. There is an "overview" video, which is included with some news stories, and is available separately at YouTube. This contains a narration that helps some with making sense of what is being shown. Overview video, at YouTube. More videos with the paper, below.

The article: Morphological change in machines accelerates the evolution of robust behavior. (J Bongard, PNAS 108:1234, January 25, 2011.) The paper itself is very dense, with complex and unclear figures; it is probably difficult reading for all but the robot connoisseurs. There are some videos to accompany the paper. Unfortunately, they, too, are rather confusing -- partly because the time compression is inconsistent and unclear. But they are cute. If you want to try these, it may be best to start with the "Supporting information" pdf, posted along with the article at the journal site; it describes and links to the videos.

For more about designing things inspired in part by looking at biology, see my section for Biotechnology in the News (BITN) on Bio-inspiration (biomimetics).

Another Musings post on bio-inspiration: Why don't woodpeckers get headaches? Designing better shock absorbers (April 18, 2011).

A recent post on robots: Robot uses coffee as a picker-upper (December 17, 2010).

For more on walking... What is it? (March 8, 2011).

Cellulose: improved processing

February 25, 2011

A recent post noted that the development of cellulose for making biofuels is progressing slowly. [Cellulosics for energy: an update (October 30, 2010).] Of course, work is proceeding. This post briefly notes two recent papers that report progress. Each of them is scientifically interesting, and does represent some progress toward understanding and improving cellulose production. It will take many such steps to develop a process that is economically practical.

Paper #1 is probably simpler to understand. If we think of cellulose as a long polymer of glucose residues, we might write it as (Glc)_n; Glc is a standard abbreviation for glucose, and n is simply a large number. Complete breakdown of cellulose might be thought of as (Glc)_n → n Glc; that is, a chain of n glucose residues is converted to n glucose molecules. However, common methods of breaking down cellulose give small chains of glucose, such as (Glc)₂ or (Glc)₃. What they did in the new work was to genetically modify the yeast so that they could use these short glucose chains. Once the yeast have been modified, one no longer needs to add extra enzymes to do those steps; further the short chains tend to inhibit cellulose breakdown, so getting the yeast to remove them improves the rate of cellulose digestion.

Here is an example of their results, from Figure 2C of paper #1. The graph shows the concentration of ethanol vs time for two fermentations. Growth was on cellulose, with cellulase enzyme added to break it down. The two fermentations differ in that one used a yeast strain that had been engineered to take up and use the short glucose chains. The upper curve (solid dots), is for the engineered strain. You can see that it makes ethanol faster, and makes more of it. The results show that the engineered strain is improved "as advertised". What they do not show here is that the improvement is of economic benefit compared to other ways of solving the problem.

The short glucose chain (Glc)₂, connected as in cellulose, is known as cellobiose. Similarly, (Glc)₃ is cellotriose -- and so forth. Collectively, such short chains are called cellodextrins.

Paper #2 is more mysterious -- but interesting. Bottom line, they have a new enzyme that stimulates cellulose digestion. Well, even that is not quite right. In this work, they are not studying cellulose at all, but rather chitin. Chitin -- the structural material of lobster shells -- is chemically and structurally similar to cellulose, so there may be a connection. And they say that other groups have evidence for a similar helper enzyme with cellulose. What does this new enzyme do? They suggest that it has two features: it binds very tightly, and it produces unusual ends when it breaks down the chitin. Both features may help to open up the material for further digestion. It's not very clear -- but they do show that this new enzyme, however it works, does help.

News stories:
* #1 Researchers Expand Yeast's Sugary Diet to Include Plant Fiber. (Science Daily, September 10, 2010.)
* #2 Researchers Identify Enzyme That Breaks Down Chitin; May Lead to Cheaper Biofuels. (Green Car Congress, October 14, 2010.)

The articles:
* #1: Cellodextrin Transport in Yeast for Improved Biofuel Production. (J M Galazka et al, Science 330:84, October 1, 2010.)
* #2: An Oxidative Enzyme Boosting the Enzymatic Conversion of Recalcitrant Polysaccharides. (G Vaaje-Kolstad et al, Science 330:219, October 8, 2010.)

Engineering E coli bacteria to convert cellulose to biofuel (December 13, 2011). A milestone. Not an economic process, but an interesting technical achievement.

A recent post on another approach to development of alternative energy: A Christmas present: Using concentrated sunlight to split water and CO₂ (February 18, 2011).

More about chitin, and its derivative, chitosan: Some shrimp in your wine? (August 27, 2016).

Where is turtle #92587?

February 22, 2011

92587. (Sea Turtle; updated as new data becomes available.) The main figure is an animated gif file; give it time to load, so that you see the data.

For a bit of background: Turtles Are Not Just Drifters. (E Pennisi, Science 331:281, January 21, 2011.)

More about turtles...
* Magnetic turtles (July 5, 2015).
* Why might it be good to put lights on fish nets? (September 9, 2013).
* The turtle that plays basketball (November 12, 2010).

An article by a Turtle... Weather report from Titan: Clouds? Puddles? Does that mean it rained? (April 6, 2011).

Dust

February 19, 2011

Dust is important. We may find it a nuisance, at the personal level. However, dust in the atmosphere affects the weather, as it adsorbs or reflects energy. Further, dust contains minerals, and the global movement of dust provides a transfer of nutrients from one place to another. For example, large amounts of the critical nutrient iron are transported by dust clouds.

One source of dust is "desert". Such dust varies. Why? One possibility is that dust varies depending on rainfall: wet soil prevents surface soil from being transported by wind. But beyond that? Do human activities affect dust?

The new work looks at long term dust records from the Sahel region of the Sahara Desert -- one of the largest dust sources on earth. Their analysis shows that dust levels correlate with rainfall up to about the 18th century. After that? Much more dust. Why? Well, it correlates with the introduction of agriculture in the area. Does that mean that the human activity of agriculture increases dust? That's their suggestion. It will be interesting to see how the suggestion is received.

The graph shows the key findings, from Figure 3 of the paper. Both axes are rather complicated, but we can simplify them. The y-axis is about the amount of dust for the year. The x-axis is about rainfall: note the labels "wet" and "dry". Now, look at the points on the graph. Most of them fall into a broad region near the bottom -- which they bracket and label "600 BC to 1700 AD". During this time there is a general trend: more dust in dry years. Then there are three points above those, each with a date. Each century is showing more and more dust. The 1700s may be almost "normal", but certainly the 1800s and 1900s show much more dust than expected from the main part of the graph. This graph is the heart of their argument; it is data. Dust has increased dramatically since about 1800. The idea that it reflects agriculture is one interpretation of the result; let's wait and see what others think of it.

News story: Modern agriculture a major control of increased rates of dust flux from continent to ocean. (Wired, July 14, 2010.)

The article: Increase in African dust flux at the onset of commercial agriculture in the Sahel region. (S Mulitza et al, Nature 466:226, July 8, 2010.)

Musings posts about dust...
* What happened to the Neandertals? (October 8, 2010). Volcanoes are another source of dust. Although such dust affects both solar radiation to the earth and re-radiation from the earth, the net effect is cooling. This post suggests that an extreme burst of volcanic activity might have caused such major climate change as to be a factor in the extinction of the Neandertals.
* Geoengineering: a sunscreen for the earth? (February 20, 2010). If atmospheric dust can cool the earth, it was inevitable that someone would suggest that we intentionally add dust to the atmosphere in order to combat global warming. It's controversial, but the idea remains on the table as one geoengineering approach.

This post has nothing to do with the post on smart dust: Smart dust: A central nervous system for the earth (July 20, 2010). This is about ordinary dust; perhaps we could say dumb dust.

More from the Sahel: Wind-borne mosquitoes repopulate the Sahel semi-desert after the dry season (October 14, 2019).

I started to write this item some months ago, actually alongside the "Smart dust" post. Somehow, it got set aside. Recently, the topic of dust came up in a private discussion. We went back to this post and decided it was worth finishing up. This is an example of how readers affect the selection of topics.

Farming by amoebae

February 15, 2011

We know about farming carried out by mankind -- and we know of farming by ants and some other insects. Now, biologists at Rice University (where I used to be on the faculty) claim to have uncovered the simplest known agricultural system -- and the smallest farmers.

Dictyostelium discoideum (or "Dicty" among friends) is a tiny organism, now commonly called a social amoeba; it is also called a cellular slime mold. In good times, Dicty lives as single-celled amoebae, eating bacteria. When food becomes scarce, the cells come together to form a multicellular "slug", which differentiates into multiple cell types. This leads to the production of spores -- and to dispersal of the organism. Thus the cellular slime molds have characteristics both of unicellular and multicellular organisms.

So, how does farming enter the picture? The new finding is that some strains of Dicty don't eat all the bacteria in the environment. Instead, when the food begins to be scarce, they start hoarding it -- and they put the bacteria in the spores. This gives an advantage to the spores if they arrive in an area where the food is poor -- but may be a disadvantage (just a cost) if the spores arrive in a food-rich area.

Is this really "farming"? Well, the purpose of using the term is to draw comparisons. So the response should be to analyze the situation, looking for similarities and differences -- thus increasing our understanding. The term itself is beside the point.

It's a delightful story, well presented in all the readings listed below.

News story: Like Humans, Amoebae Pack a Lunch Before They Travel. (Science Daily, January 20, 2011.)

* News story accompanying the article: Evolutionary biology: Farming writ small. (J J Boomsma, Nature 469:308, January 20, 2011.)
* The article: Primitive agriculture in a social amoeba. (D A Brock et al, Nature 469:393, January 20, 2011.)

For a delightful book about the social amoebae, see John Tyler Bonner, The Social Amoebae -- The biology of cellular slime molds on my page Books: Suggestions for general science reading. Bonner was one of the pioneers of work on these organisms. The book is something of a memoir, as well as a wonderful overview of the organisms -- from an old-school biologist who loves the organisms themselves, not just genes.

More about amoebae... The largest known virus (August 5, 2013).

More about farming: The case of the missing incisors: what does it mean? (September 13, 2013).

More about lunch: Astronomers identify source of peryton signals received by radio telescopes: it is the microwave oven in the observatory kitchen (April 24, 2015).

A post about a quite different kind of "slime mold": How slime molds learn (June 11, 2019).

A new approach to making large molecules, using a Vernier process

February 12, 2011

Sometimes the idea for a Musings post starts with a figure; the question is then whether we can build a good story around a figure that catches attention. Here the figure shows some chemistry -- and it is a striking figure. Further, there is a good story, partly because the authors do a good job of explaining their chemistry in a non-technical way.

This story is best told with some fairly large pictures; even the figure above gets better at full size. So the rest of this post is on a supplementary page: A new approach to making large molecules, using a Vernier process.

A post about a related chemical, from the same lab: Hückel at 40 -- that's n = 40: the largest known aromatic ring (February 1, 2020).

Caterpillars that whistle

February 8, 2011

It's actually been known for a long time that some caterpillars make sounds. How and why has not been clear. New work sheds some light on how and why one type of caterpillar sounds off.

The "how" is rather unusual. When the caterpillar is startled, its head jerks back. This compresses the air behind it, which then leaks out through holes in the body. That's the source of the sound: air being squeezed out of the body. One test of this was to cover the holes; that prevented the sound.

The "why" seems fairly straightforward. The sound can startle and scare off predators. This is shown in the second movie; see below.

There are two movies available. Movie 1 shows the response of the caterpillar to being "attacked" with forceps. Listen! (The caterpillar? That's it; the thing being attacked. Well camouflaged, isn't it?) Movie 2 shows what happens with birds. In this case, the caterpillar is not shown, but you can hear it.

News story: Blow It Out Your Sides: Caterpillars Can Whistle. (Live Science, December 10, 2010.) Movie 1 is included here (but not Movie 2).

* News story accompanying the article: Whistling Caterpillars Startle Birds. (K Knight, Journal of Experimental Biology 214:ii, January 2011.)
* The article: Whistling in caterpillars (Amorpha juglandis, Bombycoidea): sound-producing mechanism and function. (V L Bura et al, Journal of Experimental Biology 214:30, January 2011.) Both movies are available under "Supplementary material".

More about caterpillars: Studying predation around the world: What can you do with 2,879 fake caterpillars? (July 28, 2017).

What do you think will be the most important technology of the next 30 years?

February 7, 2011

Here's a chance for you to think about our future -- and maybe even win a prize.

Borislav sends a page announcing a contest: Which technology do you think will have the biggest impact on human life in the next 30 years? (New Scientist, in collaboration with Statoil and the Royal Academy of Engineering.) This is now an archived page.

The main purpose of noting this in Musings is to promote thinking about an interesting topic.

If you are interested in submitting an entry...

* Be sure to read the rules, both about the content and the administrative rules such as privacy.
* The contest topic is engineering, and the time span is three decades.
* Contest deadline is March 1, 2011.
* The web site says that the contest is for EU residents. It is not clear how this is enforced. It may be that anyone can submit ideas, but only EU people can officially win.
* This is about promotion as well as being a legitimate contest. By default, they will use the e-mail address you use with your submission to send you advertising. Check the boxes on the entry form to restrict this, as you wish. Read the privacy rules.

Entries are posted at the site; click on "Entries".

I won't post any discussions here unless you give me explicit permission. But just as a starter (and I do not plan to submit anything)... Think about the problems we have. How many of them would be ameliorated if the human population were, say, half of what it is now? Would it be good if a major goal were to achieve some such population reduction? How could this be done -- fairly? What about the side effects, in terms of altered age distribution of the population during the transition?

Is Alzheimer's disease transmissible?

February 4, 2011

Don't panic. The practical answer, for the real world, is "probably not". But the full story is more complex, and quite interesting.

Consider a couple of diseases. One is Alzheimer's disease (AD). It is a neurodegenerative disease, progressing slowly and inexorably. The other is the type of disease we call prion diseases; bovine spongiform encephalopathy (BSE) or its human form, variant Creutzfeldt-Jakob disease (vCJD) are perhaps the best known prion diseases. Prion diseases are neurodegenerative diseases, progressing slowly and inexorably.

In introducing these two diseases I described them with similar terms. Is it possible that they have further similarities? Not long ago, the common view would have been "no"; they certainly seemed quite distinct -- based on knowing very little about either one. One reason for considering them as distinct is that prion diseases are transmissible. The classic prion disease of sheep, scrapie, spreads though flocks. BSE spreads through herds of cattle by using material from infected cows as food for the next generation. And eating BSE-infected beef is how humans get vCJD. In contrast, there has been no evidence that AD is transmissible.

In recent years, we have come to understand that each disease acts through a toxic protein. That is the amyloid-β peptide, derived from the amyloid precursor protein, for AD, and the prion protein for the prion diseases. In either case, the protein, whose normal function is not clear, goes awry and causes neurodegeneration. Much is murky about the details, but the protein starts to aggregate, and it is likely that some such aggregated form is the disease-active form.

We have also learned that not all prion diseases are acquired by infection. Prion diseases occur spontaneously, and their frequency can be enhanced by mutations -- just as for AD.

Thus over time, scientists have begun to recognize similarities between AD and the prion diseases. And they began to wonder once again if AD might be transmissible. After all, part of the prion story is that the disease-protein enhances its own production, and that seems to hold for AD, too. Before looking at the new work on the transmissibility of AD, we need to make one more point about prion diseases. We normally think of them being transmitted orally, as in the examples above. However, oral transmission is extremely inefficient. (There were hundreds of thousands of cows with BSE, but only a couple hundred cases of vCJD derived from it.) For lab work, prion transmission is done by intra-cerebral inoculation -- injecting the protein directly into the brain.

Readers can probably guess where this is going, so let's get to the -- first -- point: scientists injected AD protein into the brains of mice, and showed that it enhanced AD. That is, at least under these special conditions, AD can be shown to be transmissible. In fact, this was done a few years ago. The new work extends this, and shows that intraperitoneal injection (into the abdominal cavity) of the toxic AD protein can lead to enhanced disease.

So what does this all mean? That's not entirely clear. No one is suggesting that AD and prion diseases are the same disease, or even closely related. But they may share more features than we had realized. People working on these diseases now share their ideas and models. Further, the story is about more than just AD and prion diseases. There are also Parkinson's disease and Huntington's disease. Each of these is a neurodegenerative disease, progressing slowly and inexorably. Each seems to involve a particular protein that has gone awry, and tends to aggregate. A broad conclusion that may be emerging is that the protein that is toxic when produced endogenously can also be toxic if it is taken in -- if it gets to the right place in the body. How this might work can be understood vaguely, since the protein enhances its own aggregation, but beyond that it is quite unclear. In some ways, the result makes sense, given the emerging understanding of the disease process.

Given the title -- and the finding, some may wonder whether this means that AD might be transmissible (contagious) in humans. This seems unlikely, though we should be careful to not exclude the possibility. We should also note that a low level of transmission could be hard to detect -- but also of low consequence. One key argument against transmission of AD is simply that there is no evidence that it occurs. Second, the prion experience suggests that transmission is inefficient. The only known examples of substantial prion transmission to humans involved special situations where a positive feedback loop had been introduced. In both cases, further transmission was stopped simply by eliminating that feedback loop. The overall picture would seem to be that transmission of AD is unlikely, except possibly under special conditions; if such conditions occurred and were recognized, transmission would be stopped by changing the relevant conditions.

News story: Peripheral Induction of Alzheimer's-Like Brain Pathology in Mice. (Science Daily, October 21, 2010.) (October 30, 2011: The story that was originally listed is no longer available.)

* News story accompanying the article: Medicine: Prion-Like Behavior of Amyloid-β. (J Kim & D M Holtzman, Science 330:918, November 12, 2010.)
* The article: Peripherally Applied Aβ-Containing Inoculates Induce Cerebral β-Amyloidosis. (Y S Eisele et al, Science 330:980, November 12, 2010.)

More on this...
* Transmissibility of Alzheimer's disease? (June 1, 2016). Overview.
* Transmission of Alzheimer's disease in humans? (September 27, 2015).

More about Alzheimer's disease:
* Alzheimer's disease may be delayed in people who are actively bilingual (March 1, 2011).
* The Alzheimer's disease peptide: Why does it accumulate? (January 22, 2011).
* My page for Biotechnology in the News (BITN) -- Other topics includes a section on Alzheimer's disease. It includes a list of related Musings posts.

More about prions:
* Prion diseases -- a new concern? (March 19, 2012). New concerns about the transmissibility of prions from one species to another.
* The prion disease BSE/vCJD was briefly noted in the post: Killer chickens - follow-up (December 9, 2009).
* For more about prions, see my page Biotechnology in the News (BITN) - Prions (BSE, CJD, etc).

Also see:
* Possible role of gut bacteria in Parkinson's disease? (March 17, 2017).
* Huntington's disease: Is it an amino acid deficiency? (October 4, 2014).

Robot uses coffee as a picker-upper -- Follow-up

January 31, 2011

Original post: Robot uses coffee as a picker-upper (December 17, 2010).

I came across another good news story on this, so will add it. The stories posted originally are also good, and the whole topic is fun, as well as potentially useful -- a simple flexible robotics gripping device.

Here is the additional story (which I have also added to the page for the original post): Get a grainy grip -- Robot hands may work better if they look more like beanbags than fingers. (American Scientist 99:29, January 2011. Now archived.)

Is the hormone of love also the hormone of discrimination?

January 29, 2011

Oxytocin is a fascinating hormone. In rats, it stimulates mothers to nurse their pups. In prairie voles, it promotes monogamy. In humans, it promotes trust and love.

Is oxytocin the magic road to world peace and brotherhood? Not so fast! As work on oxytocin progresses, we find that the story is more complex -- as so often in biology. It now seems that oxytocin works within our own group, but does not promote good feelings to "outsiders". It is a common feature of humans populations that we have some natural preference "for our own kind"; it is easy to imagine how that could promote survival.

A new paper reports several psychological tests showing that oxytocin promotes "ethnocentrism" -- that preference for our own kind. Further, they try to analyze the effect, and see whether it is due to a positive effect, an attraction for the "in-group", or due to a negative effect, a negative response to an "out-group". The results support the role of a positive effect, and are quite mixed for the negative effect.

Here is an example of what they did. The test here is a standard psychological test, the Moral Choice Dilemma Task. "A famous example is that of a trolley running toward five people, who will be killed if nothing is done. Hitting a switch will divert the trolley to another track, where it will kill only one person." [p 3 of the pdf, under "Experiments 4 and 5".] That is, the choice is whether or not to throw the switch -- and kill one person, but save five. In this use of the test, the one person who would be sacrificed is a member of the in-group or an out-group. The subjects being tested were under the influence of either oxytocin or a placebo.

The graph shows the results from one such test. (This is Figure 3A of the paper.) Look at the right side, labeled "placebo". The two bars are about the same height, indicating little or no preference for sacrificing a member of the in-group or out-group. Now look at the left side, labeled "oxytocin". The in-group bar is now lower than the out-group bar. That is, the participants with oxytocin were less likely to sacrifice an in-group member than an out-group member. Now compare the two in-group bars: the one for oxytocin is lower. That is, with oxytocin the participants were less likely to sacrifice a member of their own group. In contrast, the two out-group bars are about the same height, suggesting that there was little or no effect of oxytocin on how the participants reacted to the out-group members.

There are big cautions associated with this work. It is important that the work be extended, with various kinds of tests and various populations. At some point, we need to know something about dose-related effects, and what the endogenous hormone level is for the people being tested. A particular concern relates to the testing here for a negative effect. Some experiments show a small negative effect: that oxytocin seems to cause a negative response to the out-groups. Some of the news reports have hyped this, suggesting that oxytocin may promote, e.g., racial discrimination. The authors emphasize that the negative effect they see is small and mixed, and needs to be tested further. In any case, we should presume that oxytocin is only one part of the story -- regardless of what the details of the story turn out to be. That is, oxytocin is one factor that affects our feelings.

News story: Research finds the hormone of trust has limits. (Medical Xpress (was Phys.Org), January 12, 2011.)

The article: Oxytocin promotes human ethnocentrism. (C K W De Dreu et al, PNAS 108:1262, January 25, 2011.)

More about oxytocin: Role of oxytocin in monogamy in prairie voles (May 22, 2023).

Another primate with big eyes... Monogamy (January 30, 2013).

Also see: Prejudice against outsiders -- in monkeys (May 10, 2011).

Paleobioboron

January 26, 2011

The chemical element boron has a rather enigmatic role in biology. It is required for optimal growth of plants, but very few specific B-containing biochemicals are known -- and for the most part they were discovered only in the last decade or so. The discovery of a boron-containing signaling molecule in bacteria came as quite a surprise.

Now we have a story of bio-boron from long long ago -- from the Jurassic era. The picture above shows a 150-million year old fossil of a red alga; the new work claims that the redness of this fossil is due to a class of boron-containing chemicals (which they call borolithochromes). This is a novel class of biochemical! Nothing like it is known from modern organisms.

There are two types of concern about this work. The first is whether the proposed structure is correct. This is straightforward: further work will clarify the structure. But the other concern is more interesting and more difficult. Did this chemical exist in the original alga, or was it somehow made during all the intervening time (e.g., during fossilization)? For example, it is conceivable that aromatic compounds and other borates, both from the original organism, reacted to form these compounds during fossilization. The authors offer some circumstantial evidence that the compounds are indeed biological, but they recognize that the case is incomplete. Fossils are not the real organism, and it is difficult to sort out how the fossil developed.

Perhaps the most important follow-up of this work should be to look for these boron compounds in modern organisms similar to the fossil organisms. No such compounds are currently known from modern organisms, but the red algae are not the best-studied organisms. If such compounds are found in modern organisms, it will support the idea that the compounds found in the fossil may indeed be biological. Further, and perhaps even more important, the compounds will become bio-markers that may be useful in classifying organisms. If no such compounds are found in modern organisms, there is no clear conclusion. Regardless, the fossils are pretty, and these novel boron compounds are the reason why.

News story: Shade of Red Preserved in Jurassic Fossils. (Wired, October 26, 2010.)

The article: Boron-containing organic pigments from a Jurassic red alga. (K Wolkenstein et al, PNAS 107:19374, November 9, 2010.) The figures above are Figures 1A and 3 from this paper.

More about boron: An unusual hydrogen bond, involving boron (March 26, 2016).

Other posts featuring pictures of fossils include:
* Death-grip scars from zombie ants, 48 million years ago (November 9, 2010).
* The oldest known plants (November 2, 2010).

The political leapfrog

January 24, 2011

Yeah, this is about politics. It is about an issue that gets attention in American politics. It is also an issue in state politics here in California. The article caught my attention partly because of a recent discussion with a reader, also a Californian, about some of the implications of last fall's election, both at the state and national levels. With luck, the discussion here is not particularly partisan; the basic points are symmetrical across the political spectrum. (I'd be curious to hear whether those in other places find any of this fits with their experiences.)

As some basic background... Elections for state and national legislators are held in two phases. Procedures vary some by state, but this is typical... In the first round ("primary" election), each party chooses its candidates; that is, the voters in a party choose among the possible candidates of that party. In the second round ("general" election), all the voters choose among candidates from all the parties, and the winner is elected. The US political system is dominated by two political parties... The Republican party ("R") is to the "right" of the political spectrum, as conservative; the Democratic party ("D") is to the left, as liberal. (There are other parties, and they may influence the political debate. However, it is rare for them to elect any candidates.)

The observation that underlies the paper is that it seems that politics is becoming increasingly polarized. For example, the legislative bodies (US Congress and California state legislature) tend to have members with relatively extreme positions -- on one side or the other. Why? Is this because these extreme positions are dominant in the population? Or is there something about the electoral system that tends to lead to the election of candidates with extreme views?

The current paper explores this by polling the electorate and comparing their views with how their members of Congress actually voted. They do this over a period when the Congress switched from being controlled by the Republicans to being controlled by the Democrats. Their results suggest that the Republican Congress was more conservative than the electorate -- even more conservative than the Republicans in the electorate. Further, the Democratic Congress was more liberal than the electorate -- even more conservative than the Democrats in the electorate. That is, the overall position of the Congress leapfrogged the position of the electorate.

Why does this happen? The argument is that it may follow from the nature of our two-stage election procedure outlined above. It is commonly considered that the people with the more extreme positions are more active politically, both in giving time and money. Thus the primary elections, within each party, may be biased toward the more extreme candidates.

Is there anything we can do? In fact, California took an interesting step last year. The voters passed a ballot proposition that revamped the two stage election system with the intent to reduce the influence of the political extremes. In the new system, the primary election will include all candidates from all parties; the top two will go on to the second round -- regardless of party. The idea is that candidates will have to appeal more to the middle of the political spectrum in order to win the first round. (Not surprisingly, the major political parties strongly opposed this proposition, which was openly intended to reduce their power.) The 2012 elections will be the first with this new system. It will be interesting to see what effect it has.

News story, now archived at: Political Leapfrog Hops Over Most Americans. (Miller-McCune (now Pacific Standard), October 30, 2010.)

The article: Leapfrog Representation and Extremism: A Study of American Voters and Their Members in Congress. (J Bafumi & M C Herron, American Political Science Review 104:519, August 2010.)

Those who want a picture can go look on their own. You might want an elephant, the symbol of the Republican party; a donkey, the symbol of the Democratic party; or an elephant-donkey hybrid as a symbol of the emerging spirit of bipartisanship. Or perhaps you would want a picture of Arnold Schwarzenegger.

A previous post on politics: Do your genes affect your politics? (December 5, 2010).

More: Scientific curiosity -- and politics (May 22, 2017).

A previous post on frogs: Eating frog legs -- and why the hind legs taste better (July 16, 2009).

The good and bad of the immune system -- a sheep story

January 21, 2011

The immune system protects us from disease. Hm, obviously, it doesn't always work. Maybe we should have more -- a "stronger" immune system. But there is a downside to having too strong an immune system: in humans, we commonly see that downside as autoimmune diseases. We don't fully understand how this all works; the immune system -- or, better, the immune systems -- are quote complex, and only partially understood.

Now we have a report on the immune system of a wild animal population. The work seems to, once again, show that the immune system has both good and bad effects.

They studied a population of sheep on a remote island off the coast of Scotland. They measured a marker of how strong the immune system was; that leads to the first key observation... the animals varied. Some animals had a stronger immune system than others, just as one would expect for any natural population.

What were the consequences? Well, females with stronger immune systems survived harsh winters better. (They suspect that the harsh winters were accompanied by increased threat of infection.) However, animals with stronger immune systems had fewer offspring. (They don't know why.) Thus overall, it seems that under mild conditions animals with weaker immune systems fared best (had more offspring), whereas under harsh conditions animals with strong immune systems did best. Thus a mixed population is maintained over the long run. This is likely a common situation.

Recall Why African-Americans have a high rate of kidney disease: another gene that is both good and bad (August 17, 2010).

Here is an example of their results. This is from Figure 2B of the paper. The bars show the survival (of females) over the winter, under various conditions. ANA- and ANA+ distinguish animals with low and high levels, respectively, of an immune system marker; the cutoff is somewhat arbitrary, but the idea is fine. Red bars show the results for several mild winters; survival is high, and the ANA- sheep do a bit better. Blue bars show the results for several harsh winters; survival is much lower, but the ANA+ sheep, with stronger immune system, do better.

The paper is both interesting and frustrating. It is interesting because it deals with the "real world" -- a natural population of animals in the wild. A key point -- that the population is heterogeneous -- is something that is often not seen in lab experiments; in fact, one often goes to great lengths to avoid heterogeneous populations. The heterogeneity of natural populations is important. We sometimes casually say that organisms are optimized for their environment. However the environment is variable, so the whole idea of being optimized for the environment is a simplification. Having variability within the population is one way that the population is optimized; different animals within the population have an advantage under different conditions. This is true for humans, too. An example we often hear about is the ability to use food efficiently. It's a great trait when food is scarce -- yet leads to obesity when food is plentiful. What's frustrating about the work with natural populations? The ability to do experiments. What is reported here is rather limited.

News story: Wild Scottish Sheep Could Help Explain Differences in Immunity. (Science Daily, October 29, 2010.)

* News story accompanying the article: Immunology: Infection Protection and Natural Selection. (L B Martin & C A C Coon, Science 330:602, October 29, 2010.)
* The article: Fitness Correlates of HeritableVariation in Antibody Responsiveness in a Wild Mammal. (A L Graham et al, Science 330:662, October 29, 2010.)

Among other posts on the complexity of the immune system... Dengue fever -- Two strikes and you're out (August 10, 2010).

More about sheep: What can we learn from reading (the DNA from) old parchments? (January 30, 2015).

A person without fear -- due to a brain lesion

January 18, 2011

Evidence has been accumulating that the region of the brain known as the amygdala is key in the emotion we call fear. Now, study of an accident of nature provides some important support for this view -- and it is an interesting story.

The work involves a patient, coded as SM, who has lesions in both sides of her amygdala. Part of the study involves testing SM for her reactions to standardized stimuli, generally accepted as promoting fear. SM shows little or no fear with these stimuli, though she reacts normally to stimuli for other emotions. Further, an extensive analysis of SM's life shows a consistent pattern of absence of fear, despite incidents that most of us would consider harrowing.

They discuss some cautions in interpreting this work. Importantly, SM's lesions are not precisely confined to the amygdala. The new work is not proof of the role of the amygdala in sensing fear, but it is one more piece of evidence. An important merit of the work is that it is a real human.

Fear is a natural emotion, and very primitive. It is a good survival instinct: if in doubt, run.

News story: When the Brain Knows No Fear: Fear Discovery Could Lead to New Interventions for PTSD. (Science Daily, December 16, 2010.)

The article, via abstract at PubMed: The Human Amygdala and the Induction and Experience of Fear. (J S Feinstein et al, Current Biology 21:34, January 11, 2011.)

Thanks to Thien for alerting me to this story.

A 2008 paper provided evidence that veterans with certain types of damage to the amygdala were less susceptible to post-traumatic stress disorder (PTSD). This is reference 35 of the new paper. It is an example of how the understanding of fear and amygdala might be useful. PTSD may, in some ways, be thought of as a condition of excessive fear. Is it possible that it could be treated by somehow inhibiting the amygdala?
* News story: Study suggests some brain injuries reduce the likelihood of post-traumatic stress disorder. (EurekAlert, December 23, 2007.)
* The article, via abstract at PubMed: Focal brain damage protects against post-traumatic stress disorder in combat veterans. (M Koenigs et al, Nature Neuroscience 11:232, February 2008.) The paper is freely available from an author's web site: Author copy of pdf file.

For another aspect of fear and related emotions, see the post Racial stereotyping reduced with Williams syndrome (May 10, 2010).

For more about PTSD: Post-traumatic stress disorder (PTSD): a clue to its biochemistry (April 15, 2011).

The Siberian finger: a new human species? -- A follow-up in the story of Denisovan man

January 14, 2011

Original post: The Siberian finger: a new human species? (April 27, 2010). Briefly, scientists found an ancient finger bone in a cave, called Denisova, in Siberia. They were able to extract DNA, and sequence it. In this first report, they reported the sequence of the mitochondrial genome, which was recognizably human, but distinct from either modern or Neandertal humans. The evidence suggested that the finger represented a new type of human, possibly a new species. Regardless of the details, the story was fascinating simply because it opened up a new chapter in the story of the human race starting from a single finger.

Now, less than a year later, the same group reports the nuclear genome from the finger of this "Denisova man" (actually a woman). Instead of just having 16 thousand bases of information -- about the rather special, maternally inherited mitochondrial genome -- we have about 3 billion bases of information from its main genome. The big story is that the novelty of Denisova man is confirmed; the nuclear genome, too, is distinct from both modern and Neandertal humans. Beyond that, there are some differences in detail, and some fascinating new points.

The key difference is how they see the Denisova sequence relating to the others. From the mitochondrial sequence, they proposed that the Denisova sequence was older, as if Denisovans were ancestral to both modern and Neandertal humans. This is reflected in the figure in the earlier Musings post. Now, based on the nuclear genome, they propose that Denisovans were a sister group to the Neandertals. They do not know the reason for the discrepancy, though they do discuss some possibilities. In general, nuclear genome information is more likely to reflect the true history of the organism. However, two points to emphasize... First. both mitochondrial and nuclear genomes point to the Denisovans being a novel ancient group of humans. Second, the evidence is still limited. The authors are quite clear when interpreting their data that they are offering hypotheses based on the data so far, and indicating how these data suggest lines of further work. Unfortunately, the news coverage is not always so clear.

A new point that comes up is that some segments of Denisovan genome sequence are found in modern humans -- but only in Melanesians (Papua New Guinea, and nearby south Pacific islands). This implies some interbreeding between the Denisovans and the Melanesians -- and raises an obvious question given that the only known Denisovans so far are from Siberia. This leads to a hypothesis about the distribution of Denisovans; hopefully this will be tested with more data.

The figure summarizes their current views; this is Figure 3 from the paper. The first main point in the figure is to see how the human lineage has split. Start at the bottom, with a single ancestral population. At some point, moving upward, the population splits into two. (This is labeled tv on the y-axis.) The right-hand branch further splits in two, giving the Denisovans and Neandertals -- both now extinct. The left-hand branch splits -- eventually into four groups shown here, all modern humans from various geographical regions. ("French" and "Han" are taken as representative of European and Chinese, respectively.) The second main point is to see two instances of gene flow (transfer) from one of the now-extinct groups to modern humans; see the two arrows, labeled f1 and f2, between these two groups. These gene flows point to inter-breeding between the populations. One of these is the transfer of genes from Neandertals to modern humans -- all but the Africans, who had already split off; this was introduced in their earlier work on the Neandertal genome. The second gene transfer is from the Denisovans to the Melanesians; this is introduced in the new paper. Remember that this is presented as the best fit to the data so far. And there is limited data, especially on the right-hand side (the extinct groups). More data leads to better understanding; available data allows the development of hypotheses that can be tested. The story of Denisovan man is very much a new and preliminary story. The development and testing of hypotheses is the most important part of the story.

With the earlier work there was talk of whether the Denisovans should be considered a distinct human species. With the current work, and the repositioning of the Denisovans, they prefer to just avoid that term. It is hard to know where to draw to line between one species and another. Maybe it is a species, maybe just a population (tribe?). What's important now is to follow the leads and learn more about the nature and distribution of the Denisovans.

Finally, they discuss one more Denisovan fossil: a tooth. The tooth, like the genome, is neither modern nor Neandertal. This is the first evidence about the morphology of the Denisovans. Again, more would be welcomed!

News story: Siberian Fossils Were Neanderthals' Eastern Cousins, DNA Reveals. (New York Times, December 22, 2010.)

* News story #1 accompanying the article: Palaeoanthropology: Fossil genome reveals ancestral link -- A distant cousin raises questions about human origins. (E Callaway, Nature 468:1012, December 23, 2010.)
* News story #2 accompanying the article: Human Origins: Shadows of early migrations. (C D Bustamante & B M Henn, Nature 468:1044, December 23, 2010.)
* The article: Genetic history of an archaic hominin group from Denisova Cave in Siberia. (D Reich et al, Nature 468:1053, December 23, 2010.)

For more about human ancestors:
* An interesting skull, and a re-think of ancient human variation (November 12, 2013).
* Did Lucy butcher a cow? (February 11, 2011).

A general discussion of the species question, motivated in part by the findings for Denisovan man: Human origins, and the species question (March 28, 2011).

For more on the use of genome sequences to determine relatedness of organisms: Capsaspora owczarzaki and you     or     Where did animals come from? (April 10, 2011).

Also see: Archaic human genomes: update (September 2, 2011).

Also see: Life at age 34,000? (October 8, 2011). Is it possible to find microbes that have been alive for tens of thousands of years?

For more about Denisovan DNA in modern humans: What is Denisovan man telling us about Asian-Pacific man? (October 25, 2011).

Also see: The Iceman's blood (May 14, 2012).

Another example of using nuclear genome vs mitochondrial genome for understanding ancestry... A polar bear update (June 3, 2012).

More on ancient DNA... How long does DNA survive? (October 23, 2012).

Also see: Using DNA for data storage (March 5, 2013). That's storage of computer data.

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

Antibiotics in ancient times

January 10, 2011

A fascinating story. It's long been known that some ancient human bones "glow" (actually, fluoresce) -- just as if they had the antibiotic tetracycline in them. Many suspected this was likely due to contamination of the bones with tetracycline-producing bacteria over the ages.

New work shows that the tetracycline is actually an intrinsic part of the bones. This suggests that the antibiotics were incorporated during life, rather than being later contamination. Further, the tetracycline is widespread in the bones, even with a child. This suggests that there was frequent exposure, not just an occasional event.

Ok, that is the "easy" part. Actually, it wasn't easy at all, but required some quite sophisticated chemistry to figure out. But it is easy in that it is the factual part. What does it mean? Of course, here we have little to go on, with plenty of room for speculation. And as happens from time to time, the authors are cautious in the paper, but more provocative in the news.

The particular samples here are from Sudan, around the 5th century. The society was known to do fermentation: they made beer. It is thus plausible that they also fermented other bugs -- whether they understood the details of the process or not. The big question of interest is whether they knew the golden stuff was good for their health. That is, did they actually grow up this stuff in order to use it for medical treatment? The authors emphasize that the exposure was frequent, which suggests to them it was intentional. Maybe, but it doesn't quite follow. And even if it was intentional, it doesn't follow that they did it for medical reasons. So, let's be cautious about concluding what they did and why. But let's also be open. The new work shows regular exposure to tetracycline, and that raises interesting questions. Perhaps people will bring new findings to bear on those questions.

News story: Ancient Brew Masters Tapped Antibiotic Secrets. (Science Daily, September 2, 2010.)

The article: Brief Communication: Mass Spectroscopic Characterization of Tetracycline in the Skeletal Remains of an Ancient Population From Sudanese Nubia 350-550 CE. (M L Nelson et al, American Journal of Physical Anthropology 143:151-154, September 2010.)

I wonder... If they used antibiotics regularly, did they have a problem with antibiotic resistance? Here is a Musings post on antibiotic resistance: Restricting excessive use of antibiotics on the farm (September 25, 2010).

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

Also see: The history of brewing yeasts (October 28, 2016).

What's around the corner?

January 7, 2011

The problem at hand is illustrated by the Figure at the right. Clearly, there is no direct line of sight from the camera to the person in the room. Can we, despite that, get the camera to take a picture of the person? Now, you might suggest that we put a mirror on the door. Ok, good idea -- for the specific problem as posed here. But that is not a good general solution to the problem of seeing around corners -- as will be clear when you look at the range of proposed applications.

So, what are we to do? How about doing something like radar or echolocation, but using waves reflected off the door? Measure how long it takes for a photon to travel from the camera to the door to the person and back to the door and then to the camera. We know how fast light travels, so if we measure how long it takes for the light to return, we can calculate how far away the person is. But how do we tell where the person is? That takes more measurements, at various angles. At least in principle, take enough measurements, and the computer should be able to sort it all out.

The speed of light is 30 centimeters per nanosecond -- or about a centimeter every 30 picoseconds. (A nanosecond is a billionth of a second; a picosecond is a trillionth of a second.) To be able to judge distances to within a centimeter, they use a camera with a trillion frames per second -- and a light pulse that is much shorter than that.

Some of this is not new. They make quite a point that they are building on known technologies -- combining and stretching them to try to go a bit further. The hard part is the signal analysis. For some perspective, have a look at the following figure: "Higher Dimensional Light Transport: Popular imaging methods plotted in the Space-Angle-Time axes". It's complex, but the main point is to see the new method along with some other methods. This figure and the one above are from the project web page listed below. Versions of these pictures appear in various articles and news stories.

Let's see if we can explain the idea of how this works. The following figure is from the lower frame of Figure 8 part b of the 2009 presentation. It is a diagram to illustrate how we can see "around the corner".

The camera apparatus consists of a light L and an array of sensors, denoted here by S1 and S2. The goal is to see a pattern of two objects plus a space between them, at P1, P2, and P3; the objects are conveniently considered as mirrors. The problem is that the objects are behind an "occluding wall". Consider a light beam from L. Two such beams are shown, in red. One is a solid line, one is dashed. Let's just follow the solid line. Remember, a key point of their camera is that L is giving off short pulses of light -- each carefully aimed at a particular angle. The two beams here are separate events! The "solid" beam hits the diffuser, at D2. The diffuser is optically complex (think surface of door as an example), and various things happen to the beam. For example, parts of the beam bounce back to the sensors; see the solid blue line from D2 to S1. The sensor records the arrival of this "single-bounce" signal -- records the time of its arrival. Other parts of the (solid red) beam are reflected from D2 toward the objects at P1 and P3 (and toward the non-object at P2); see more solid blue beams. The beams that hit the objects are reflected back to the diffuser (green), and on to the sensors (yellow). These are triple-bounce signals, and the time of their arrival is a measure of the total distance traveled -- thus a measure of where the objects are.

If you can follow the solid beam around, good. Try to see that the sensors see single-bounce signals and triple bounce signals -- the latter involving the objects. The time it takes for each signal to arrive at a sensor depends on the total distance. A computer sorts out all the info received at the sensors, and computes where the objects are -- even though they cannot be directly seen. That's the idea.

What have they actually done? Well, they have developed the proposal, which recognizes that the devices they need, such as high-speed pulsing lasers, are available. They have begun to develop some mathematical theory and some software to implement it. And they have actually done some simple tests -- proof of principle -- in the lab. They understand that many challenges remain; they discuss some of them both on the project web page and in the paper. It's an interesting problem!

News story: Laser camera takes photos around corners. (BBC, November 18, 2010.)

Project web site: Looking Around Corners using Femto-Photography. (Camera Culture Group, MIT Media Lab.)

That project web site page links to two meeting presentations:
* A Kirmani et al, Looking Around the corner using Transient Imaging. IEEE 12th International Conference on Computer Vision (ICCV), 2009. In the published volume, it is p 159. This is listed on their page under References; choose Local copy to get a freely available pdf of the published version.
* Further down their page is an item labeled Presentation. This is a talk given in October 2010 by project leader Ramesh Raskar. The video -- of the actual talk -- is about 12 minutes; the first part of it is about this project, and the second part is about using a cell phone to measure your vision (the Netra project). The talk presents the main ideas, but without any actual demonstration of the system. It is fun, but not very deep. (The first slide says "Every photon has a story.") (For more on the cell phone as a tool in medicine... Connecting a cell phone and a microscope (September 2, 2009).)

Thanks to John for contributing this topic.

More about light: Is the speed of light really constant? (May 20, 2013).

Echolocation:
* On a similarity of bats and dolphins (September 15, 2013).
* A plant that communicates with bats (September 7, 2011).

Where did our oceans come from?

January 4, 2011

Three-fourths of the Earth's surface is covered by water. Where did all this water come from? The actual amount of water is not so high -- only about 0.02% of the rocky mass of the planet.

The simple answer is that we do not know its source. The common view is that the water was largely delivered to the planet by comets and such. However, a new paper from MIT geologist Linda Elkins-Tanton suggests that it could have arisen from the water in the original minerals that came together to form the Earth.

The paper has gotten considerable attention. I guess people are intrigued by the idea that our oceans are home-grown rather than imported. But we should emphasize that this is just a model. She does calculations to show how an ocean might develop from initial minerals, under certain conditions. The results make it plausible that the model could have applied to early Earth.

Where does this leave us? With two models for the source of earthly water. Both are plausible; what is unclear is in the details -- and the numbers. I'm sure that people will try to refine the details, and will debate the merits of the competing models. Perhaps one will end up seeming more likely, perhaps not. Perhaps both processes contributed to our earthly water supply. Let's just be open to these possibilities, at least for now.

Does it matter? Well, mankind always wants to know more. So it is part of our general understanding of nature. The model applies generally to "rocky planets", so has implications beyond the Earth. The paper notes that home-grown water would allow more time for life to emerge. Ok, but that solves a non-problem, and seems to be mainly to get attention.

News story: Growing Earth's Oceans. (Science Daily, December 8, 2010.) Good overview of the background and the model.

The article, which is freely available: Formation of early water oceans on rocky planets. (L T Elkins-Tanton, Astrophysics and Space Science 332:359, April 2011.)

More on the origin of Earth's water: Were comets the source of Earth's water? (February 3, 2012).