Does it matter what time of day you milk the cow?

December 28, 2015

By reputation, milk induces sleep. Does that mean that milk is a drug, not just a food? If so, should we wonder whether the details of milk preparation affect its pharmacological activity?

That's the idea behind a new article, which compares the effect of cow milk on mice depending on what time of day the cow was milked.

In this work, the scientists compared the effects of "Night milk" (milk collected from the cow at night) and "Day milk" on several behaviors in mice. Each behavior is related to sleep or to sedation. Here is an example...

I chose to discuss falling frequency here because it showed the biggest effect. Look at the graph above, and it's easy to see that there is an effect. The effects on other behaviors were small. Among the behaviors studied were the time required to fall asleep and the duration of sleep. Both showed small but statistically significant effects.

The scientists analyzed the milks. The Night milk contained about ten times more melatonin than the Day milk. The Night milk also contained about 25% more tryptophan. (These results were expected, based on earlier work.)

Are the observed effects consistent with what one might expect from the levels of melatonin and tryptophan found in the Night milk? Qualitatively, yes. Quantitatively? The authors do not address this, but it should be done. If there is agreement, it would strengthen the case that Night milk is more effective at promoting sleep. If there is not agreement, it would show that the story is incomplete.

Perhaps the most important point here is raising the question. If we are going to use milk as a drug, maybe we should examine it as carefully as we would an "ordinary" drug. It should not be a surprise that the composition of cow milk varies during the circadian cycle; whether it matters is open for testing. The current paper is a step.

News story: Night milk: milk taken from cows at night might be the sleep aid you need -- Sedative effects of night milk have not been tested on people but the high amounts of tryptophan and melatonin suggest it may be healthier than Ambien. (M Gajananm, Guardian, December 15, 2015.) Note the excessive interpretation in the sub-headline there; concentrations are facts, but "healthier" is open for discussion.

The article: Milk Collected at Night Induces Sedative and Anxiolytic-Like Effects and Augments Pentobarbital-Induced Sleeping Behavior in Mice. (I J I dela Peña et al, Journal of Medicinal Food 18:1255, October 26, 2015.)

A recent post about melatonin and sleep: How caffeine interferes with sleep (December 11, 2015).

More... Evening light: how it affects our sleep (July 30, 2019).

A recent post about milk: Breastfeeding and obesity: the HMO and microbiome connections? (November 14, 2015).

and then... Cockroach milk (August 21, 2016).

Also see...
* The nutritional value of yogurt? (September 28, 2018).
* Polled cattle -- by gene editing (July 8, 2016).
* Does it matter what time of day you get a vaccine? (October 26, 2012).

GJ 1132b: "the most important planet ever found..."

December 18, 2015

That gets attention, doesn't it? Even with the qualification that follows: " ... outside the Solar System." It's from the news story in the journal. There are so many new planets being discovered these days that it can be hard to get attention.

Yes, GJ 1132b is interesting. Perhaps not up to the standard suggested by the title here, but interesting. In fact, the authors seem to have said "most intriguing". That's more reasonable.

So what's the deal? First, GJ 1132b is about Earth-size. Moreover, it is Earth-like. It's rocky, based on measuring its density. That means it is also Venus-like.

Second, it's rather close, at least by astronomical standards. About 39 light-years away.

Third, it has an interesting Sun. GJ 1132 is a red dwarf star, small and cool. Cool star, but the planet is only a million miles away (it orbits the star every two days!).

What's the point? The temperature on GJ 1132b may be about 230 °C. That is too hot for life (or for liquid water), but it makes GJ 1132b the coolest rocky planet yet found. It's cool enough that it may well have an atmosphere -- and that's why it is interesting. An atmosphere, and close enough to us that we should be able to study it. That its star is small and dim is a bonus; the starlight interference will be smaller. It would be the first case where we are able to get information about the atmosphere of an Earth-like planet beyond our Solar System. That's interesting, even intriguing.

Planet GJ 1132b is referred to both as Earth-like and Venus-like. Of course, in terms of size, it is both. Earth-like is a major focus for planet hunters. The new planet is too hot for life. Venus is hot with an atmosphere; that's why some refer to it as Venus-like.

The news stories listed below are good at describing why the new planet is interesting. The article itself documents the technical information.

News stories:
* Astronomers eager to get a whiff of newfound Venus-like planet. (Science Daily, November 11, 2015.)
* A Relatively Nearby Earth-Sized Planet. (P Gilster, Centauri Dreams, November 11, 2015.)

* News story accompanying the article: Astronomy -- A small star with an Earth-like planet. (D Deming, Nature 527:169, November 12, 2015.)
* The article: A rocky planet transiting a nearby low-mass star. (Z K Berta-Thompson et al, Nature 527:204, November 12, 2015.) Check Google Scholar for a freely available copy at ArXiv.

More from a dwarf star... Habitable planets very close to a star (June 19, 2016).

A post about Venus: Sulfur dioxide in the atmosphere of Venus (February 16, 2013). Links to more.

A recent post about exo-planets: Most Earth-like (habitable) planets haven't formed yet (October 27, 2015).

Also see... Atmosphere suggests planet might harbor life (August 30, 2010). Discusses how one studies the atmosphere.

The WHO report on the possible carcinogenicity of meat

December 12, 2015

It was a big news story a few weeks ago: the World Health Organization (WHO) reported that processed meat is carcinogenic, and red meat may be carcinogenic.

It's an interesting story, even important. But it is also confusing. Here are some comments about the report. They are based on my reading of some of the materials, plus listening to an hour discussion of it; one of the panelists was on the WHO team that prepared the report.

It's important to keep fact and opinion separate with such a story, so let's start with some facts...

Preparing such reports is a normal activity of WHO. More specifically, it is an activity of the International Agency for Research on Cancer (IARC), within WHO. The IARC team that prepared the report is a team of scientists.

WHO did not test anything. They did not do any experiments. The report is based on an analysis of what has been published. WHO has standards for evaluating the quality of trials, and they have rules that guide their decision-making process.

WHO defines their terms. It is important to understand what it is they claim. Their definition of "processed meat" may be especially important.

The report has not yet been published. There are summaries available. The full report will be published, in a WHO monograph; I do not know when.

Ok, those are facts. Let's look at some of the issues. This part may include my analysis and opinions.

The main findings are stated as broad generalities: processed meat is shown to be a human carcinogen; red meat is a possible carcinogen. These characterizations are based on standards established by WHO.

They have compared processed meat with cigarettes -- and caused considerable confusion by doing so. The comparison is intended to reflect the confidence in the conclusion, not the magnitude. That is, they are just as confident that their analysis shows processed meat is carcinogenic as they are for cigarettes. However, the magnitudes are very different.

Here is an example of a magnitude, using round numbers. If one eats 50 grams of processed meat per day over a lifetime, there is (says the report) a 20% increase in the risk of cancer. Since the baseline risk is about 5%, it becomes 6% with the consumption of processed meat. (The 50 grams, or about 2 ounces, is about two strips of bacon.) These magnitude numbers are sometimes reported in a way that is not clear. It is not two strips of bacon, but two strips of bacon per day over a lifetime. It is important to understand the dose that is involved.

A concern about that statement is what "processed meat" refers to. The report is very clear in saying what they mean, but it is not what most people would mean by the term. For the report, it refers to a wide variety of meats, processed in various ways. (Processing is traditionally done for preservation, but it may also be done for taste.) But that's confusing. Meats are processed in various ways. There is no reason why the various treatments should have similar effects. One would presume that some forms of meat processing are more carcinogenic than others. Lumping them is confusing. Why did they do this? Apparently because they were unable to reach conclusions for individual types of processed meats. That may well reflect limitations of the tests that they analyzed; remember, they did not do any tests, but merely analyzed what was already reported.

This leads to another point of interest... Why are processed meats carcinogenic? Or, better, why is a particular type of processed meat carcinogenic? In fact, there has long been evidence that certain types of "curing", using nitrates, could lead to the formation of nitrosamines, a type of chemical that is known to be carcinogenic. In one sense, it might not matter why something is carcinogenic. If it is, let's avoid it. But in this case, they claim that a heterogeneous class of things is carcinogenic. It really would be nice to sort that out.

What about meat, which they conclude is a possible carcinogen? What meat? Red meat, which means mammalian muscle. The stuff we typically eat, from cows and pigs and such (but not birds).

It's odd that meat is carcinogenic. If meat means mammalian muscle, that's us. That would mean we are carcinogenic. Now, maybe it's only carcinogenic to the digestive system. Maybe.

This gets us back to the issue, why is it carcinogenic? In fact, it's well known why meat is carcinogenic -- at least one reason. It's the way we cook it. High temperature treatment of meat leads to "char", which is quite likely carcinogenic. If this is the main reason they are getting a signal from meat, wouldn't it be good to make a distinction between "meat is carcinogenic" and "how we cook meat makes it carcinogenic". (That also gets us out the hole of ourselves being carcinogenic.)

Some of the points I raised above were among my first thoughts when I heard about the report. Interestingly, they came up during the discussion; the panel member who was involved in the report understood the points, and had proper responses. The comments are not criticisms of the report as much as a reflection on the state of our knowledge. (However, I do wonder why they say some things the way they do. They have a penchant for saying things that are predictably confusing.)

Eating meat is a normal activity for many animals (and even an occasional plant). Cooking it and preserving it are not. (Cooking makes meat more digestible, and we like the taste. Treatment of meat to preserve it was an important development for mankind, before refrigeration.) How much of what WHO found is fundamental to meat, and how much is due to the things we do to it -- all with the best of intentions?

What to do? We can divide that into parts, what an individual should so and what the scientific community should so.

The effects described here are small. If you want to reduce your consumption of meat and especially processed meat, fine; it's not likely it will make much difference in your risk of cancer, but it is a proper step. Further, it would be good to compare the effect with other risks you take. Those who might consume unusually large amounts of meat or processed meats would have a stronger case; it would also be good to learn about other problems from eating large amounts of meat, which are beyond our scope here.

The more important implications are for the scientific community. The work raises lots of questions.

News stories:
* WHO Confirms Eating Meat Causes Cancer, But How Did This Once Healthy Food Become So Deadly? (D Dovey, Medical Daily, October 26, 2015.)
* Processed meat can cause cancer. (Science Daily, October 27, 2015.)

A Q&A posted by WHO at their web site: Q&A on the carcinogenicity of the consumption of red meat and processed meat. (IARC, WHO, 2015.) This is good, though at times you may have the feeling you are dealing with a government report.

News story published by the WHO panel in a scientific journal: Carcinogenicity of consumption of red and processed meat. (V Bouvard et al, Lancet Oncology 16:1599, December 2015.) Check Google Scholar for a freely available copy. Two pages; a good overview by the authors of the study. As noted, their full report will be published separately, and is not yet available.

More about meat...
* Growing meat without an animal? (April 11, 2018).
* Red meat and heart disease: carnitine, your gut bacteria, and TMAO (May 21, 2013).
* Carnivorous algae -- that hunt large animals (October 7, 2012).

More about the WHO, a political organization that deals with science: The role of WHO: the view of its director (December 1, 2015).

And then... Is glyphosate (Roundup) a carcinogen? (March 6, 2016).

Next cancer post... How vitamin C kills cancer (December 15, 2015). This is the post immediately above.

My page for Biotechnology in the News (BITN) -- Other topics includes a section on Cancer. It includes a list of related posts.

My page Internet resources: Biology - Miscellaneous contains a section on Nutrition; Food safety. It includes a list of relevant Musings posts.

Biomimetics -- an overview

December 9, 2015

Biomimetics can be thought of as learning from nature -- engineers learning from nature. A famous recent example is learning how the gecko attaches to walls, and then designing artificial materials that work on the same principles.

A recent feature article in The Scientist discusses several examples. Some of them have been the subject of Musings posts. The article is a good read; skip around as you wish.

News feature, which is freely available: Inspired by Nature -- Researchers are borrowing designs from the natural world to advance biomedicine. (D Cossins, The Scientist, August 2015, p 34.)

A recent post about biomimetics: Shark skin inspires design of a new material to reduce bacterial growth (March 13, 2015). This is one of the topics included in the current article.

See my Biotechnology in the News (BITN) topic Bio-inspiration (biomimetics). It includes a listing of Musings posts in the area, and has additional information.

When the laundry piles up... An econophysics critique of smart meters

December 6, 2015

This post is about an article in a physics journal; the topic is when you should do the laundry. The authors didn't actually do any laundry; this is a theoretical analysis of laundry, using the tools of econophysics, whatever that is. In all seriousness, it is an interesting and provocative analysis of a current issue in energy resources.

What's the real issue? Smart meters. These are meters that measure your electricity usage and report it continuously back to your electricity company. This lets the company bill you using different prices per unit of electricity depending on when you use it. The idea is that electricity is more valuable during certain times, referred to as peak usage; therefore, peak-usage electricity should cost more. If you do your laundry at night, during off-peak times, they will charge you less than if you do it during the day, when demand is high.

In fact, your smart meter can do more than that. It can turn your washing machine on all by itself, presumably late at night when electricity is cheap. (This assumes that your washing machine is intelligent enough to understand the smart meter; modern washing machines are, or soon will be.)

We understand that power plants have a finite capacity, and that usage patterns vary. For things where you can choose, it is good to use electricity when demand is lower. And it is reasonable that the electricity company charges less for off-peak usage, to encourage you to make that choice. Sounds good. Or is it?

A new article, from the Institut für Theoretische Physik, Universität Bremen, challenges the alleged benefit. The authors argue that attempts to control electricity usage using feedback from the usage level could backfire: it could lead to catastrophic swings in usage, which would defeat the purpose. Imagine the following, extreme scenario... usage declines, so the price is reduced. Everyone turns on their washing machine -- manually or automatically, it doesn't matter; the point is that the lower price triggers demand. The result? A higher overall demand than happens during the usual peak period.

The authors show the effect by computer modeling. It makes sense.

Comment... Isn't this just a problem with the nature of the feedback? This is all about computer software, at the electric company. It monitors usage and sends out commands (or information) that adjust usage. That makes some sense. (We'll ignore privacy concerns here. In particular, we'll assume that accepting usage commands is voluntary.) If the company computer sends out commands to use more electricity than is available, that's not so good. Surely, good software can figure that out.

Smart meters have been the subject of considerable debate, with good arguments for them, and some concerns. The current article raises an interesting issue, but it should be solvable. It's one thing to suggest that feedback from usage to price may be good, but that doesn't mean that any feedback procedure that is suggested is good; details matter.

News stories:
* A seemingly obvious way to make the electricity market better may actually make it worse. (L Zyga, Phys.org, July 23, 2015.)
* Smart Meter Time Varying Pricing Can Lead to "Catastrophic Consequences" for the Grid. (K T Weaver, Smart Grid Awareness, July 27, 2015.) This is from an anti-smart meter site. Despite the obvious bias, it's a useful presentation. Just be aware that it presents only part of the story.

The article: Econophysics of adaptive power markets: When a market does not dampen fluctuations but amplifies them. (S M Krause et al, Physical Review E 92:012815, July 22, 2015.) Check Google Scholar for a copy.

Previous post about laundry: Folding towels (April 10, 2010).

Also see a section of my page Internet Resources for Organic and Biochemistry on Energy resources. It includes a list of some related Musings posts.

The role of WHO: the view of its director

December 1, 2015

The World Health Organization (WHO) is an agency of the United Nations (UN). It has been much criticized for how it handled the Ebola outbreak -- and that wasn't the first time. Fact is, WHO is a political organization -- and it behaves as such.

Science magazine recently did an interview with the head of WHO. It's interesting. In offering it here, I am not endorsing anything or anyone, but merely allowing one relevant party to speak. We need to think about how the world community handles medical issues; WHO is part of the effort.

Interview, freely available: In wake of Ebola epidemic, Margaret Chan wants countries to put their money where their mouth is. (K Kupferschmidt, Science Insider, October 14, 2015.) This is an interview with Margaret Chan, WHO director-general, by a member of the news staff at Science. A short version of the interview appeared in the magazine, 350:495, October 30, 2015. The interview also briefly discusses the problem of increasing antibiotic resistance.

Recent Ebola post, which is relevant here: After Ebola, what next? and how will we react? (September 5, 2015).

There is a section on my page Biotechnology in the News (BITN) -- Other topics for Ebola and Marburg (and Lassa). That section links to related Musings posts, and to good sources of information and news.

Something good WHO did... International relations: sharing flu viruses (May 28, 2011)

More WHO...
* WHO: We need to prepare for Disease X (May 13, 2018).
* The WHO report on the possible carcinogenicity of meat (December 12, 2015).

Claiming knowledge one does not have: it's particularly common with those who think they are experts

November 29, 2015

What do you think of the "1975 Public Affairs Act"?

When a representative group of Americans was asked that, in the late 1970s when it might have been current, a third of the respondents expressed an opinion, one way or the other. That is, a third of those questioned claimed some knowledge of the Act.

That's an interesting finding -- because there is no such Act.

That is an example of people claiming knowledge they don't have. It's a nice example, because it is easy to tell whether they really have the knowledge they claim: there is no such Act. This phenomenon is called over-claiming.

A recent article extends the study of over-claiming to explore the effect of expertise. Are those who think they know a field well less likely to make excessive claims of their knowledge in the field -- or more likely? More likely, say the results. That is, "experts" are more likely to over-claim knowledge than non-experts.

It's an odd article, in that most of the results, which are quantitative, are presented as narrative, with almost no tables or figures.

Here's a brief summary of one experiment... Test subjects were randomly assigned to two groups. Each group was given a little geography quiz. After taking the quiz, they were asked to rate their knowledge of geography. One quiz was quite easy, the other was quite difficult. Those who took the easy quiz rated themselves as more knowledgeable about geography than did those who took the difficult quiz. That is, it seems that the easy quiz induced a feeling of expertise in the subject matter. Both groups were then asked to rate their familiarly with some geographical locations, some real and some not. The group that took the easy quiz was more likely to claim knowledge of non-existent locations. The authors interpret this as showing that the feeling of expertise induced by the easy quiz led to an increase in over-claiming.

The work describes a phenomenon. It does not explain it. Even the finding that it relates to one's perception of expertise is more description than explanation. It does not tell us whether people over-claim knowledge because it is human nature to do so, or because our culture (education?) teaches us to do so, or who knows what. In particular, there is no claim that it is because people deliberately lie.

Perhaps you are aware of the phenomenon. You may see it in politicians and in advocates for positions you disagree with. Yes, that's all probably true. But be careful. You may well show it, too -- along with those on your side. Whatever the reason, it is likely common. We don't carefully and critically examine everything we know. At the very least, when it matters, you should do so. When someone's "knowledge" is questioned, it would make sense to go check, go look it up.

Science, at least collectively, understands this. It is fundamental in science that knowledge is tentative, subject to questioning and further work. Of course, individual scientists may well express high confidence in their knowledge, for better or worse. And our education system tends to transmit "facts", often with little understanding of their source or certainty.

It's an intriguing article. Sorting out the causes of over-claiming is for future work. For now, we simply recognize the phenomenon of claiming knowledge one does not have. And we recognize that being knowledgeable does not prevent over-claiming; it may even make it worse.

"Continuing to explore when and why individuals overclaim may prove important in battling that great menace -- not ignorance, but the illusion of knowledge." That's the final sentence of the article.

* * * * *

You might wonder, regarding the story at the top of this post... Maybe there was something of a similar name that was in the news. That is, maybe this was confusion, not over-claiming. That is a proper kind of question to ask. I don't know in this case (but one can check it out, in the reference quoted in the current article). We must emphasize that the phenomenon of over-claiming is not based on one such story, but on much accumulated evidence.

Is over-claiming related to one's genuine knowledge of the subject, or to one's self-evaluation of expertise? Those are somewhat distinct issues, and the article discusses both. The particular experiment above focuses on the latter.

News stories:
* Self-proclaimed experts more vulnerable to the illusion of knowledge. (Science Daily, July 20, 2015.)
* 'Learned' people easily may claim facts impossible to know. (B Friedlander, Cornell Chronicle, June 11, 2015.) From one of the institutions involved in the work.

The article: When Knowledge Knows No Bounds: Self-Perceived Expertise Predicts Claims of Impossible Knowledge. (S Atir et al, Psychological Science 26:1295, August 2015.) The example I posed at the start of this post is taken from the introduction in this article. They give a reference to the study, which I did not check.

I think there is some connection between this and the recent post Using a smartphone as your extended brain (November 17, 2015).

Two fine books, listed on my page of Books: Suggestions for general science reading are relevant to the topic...
* Gleiser, The Island of Knowledge -- The limits of science and the search for meaning (2014).
* Kahneman, Thinking, Fast and Slow (2011).

Organ transplantation: from pig to human -- a status report

November 23, 2015

One source of organs for transplantation could be non-human animals. Pigs may be the best candidate as organ donor for humans: they are of similar size, and similar physiology, in that they are omnivorous. And we know how to grow them on a large scale.

Musings has noted such work before [link at the end]. We now have a nice update, as a Nature news feature. It discusses the range of difficulties that must be dealt with. Despite some technical progress, the big answer so far is that it doesn't work very well.

There has been some success with use of pig corneas, and with pancreatic islet cells that are encapsulated. These are useful steps, but not true organ transplants.

A recent advance is the improved ability to do gene editing. Tools such as CRISPR allow us to make changes to the pig genome as we wish. Of course, that doesn't tell us what the right changes are, but it does facilitate the work.

Challenges remain; tools develop. Research continues. It will help us understand biology better, and perhaps someday may lead to a good source of organs. The news feature here is a useful overview and update.

News feature, which is freely available: New life for pig organs -- Gene-editing technologies have breathed life into the languishing field of xenotransplantation. (S Reardon, Nature 527:152, November 12, 2015.)

Background post: Pigs as organ donors for humans (February 16, 2010). Also see follow-up post, linked there.

New developments...
* Pig hearts can sustain life in baboons for six months (January 7, 2019).
* Long term survival of a pig heart in a baboon (April 30, 2016).
* How to do 62 things at once -- and take a step towards making a pig that is better suited as an organ donor for humans (January 17, 2016).

Also see: Using human stem cells to make chimeras in pig embryos (February 25, 2017).

More about CRISPR: CRISPR: an overview (February 15, 2015). Includes a complete list of posts on CRISPR.

There is more about replacement body parts on my page Biotechnology in the News (BITN) for Cloning and stem cells. It includes an extensive list of related Musings posts.

More about gene editing is included on my Biotechnology in the News (BITN) page Agricultural biotechnology (GM foods) and Gene therapy. It includes a list of related Musings posts.

Using a smartphone as your extended brain

November 17, 2015

Modern phones give us instant access to all the world's information, it would seem. So we look up things. Things perhaps we should know, perhaps do know. Of course, the phone is a stand-in here for use of the Internet, a specific example of how we access the Internet. The broad question is, how do we use the Internet? Along the way, we might ask... Do people differ in how they use the Internet? If so, why?

A recent article offers some evidence on the matter. The general theme of the article was to explore how people use the Internet, via their smartphone. More specifically, the scientists asked whether they could correlate such usage with other characteristics of the people.

Here is an example of the results from the new article. The table is not easy reading. We'll walk through some parts of it slowly. I'll give an overview of the experiment and the results, but then focus on specific examples from the table. If you find the broad view confusing, the examples may help.

What do we see? A useful place to start is with the asterisks that denote significance. For both tests, the results for overall SP usage and for SP search engine usage are significant. However, the results for SP usage for social media and entertainment are not. That is, whatever it is we are testing here, it relates to search engine use, not the other uses. "Search engine use" might be interpreted as using the SP for "knowledge"; perhaps it is the only one of the uses that we would interpret that way.

So, let's focus on the search engine usage. For both tests, scores decrease as SP search engine usage goes up. What are these two tests?

The cognitive ability test, on the right, is easier to explain. It is a test of one's ability to do certain things, such as some math. It is in the general vein of an IQ test. The trend of cognitive ability score vs SP search engine usage shows a correlation: people who use search engines more have lower test scores. (You just looked something up using your phone? That means you're dumb? No, not at all. We all look things up, but some people are more likely to than others. And so forth. Be cautious about interpreting all this!)

The cognitive style test, on the left, may raise some new issues. Recent decades have developed the idea that we have two broad types of thinking. One is generally described as fast and intuitive; the other as slower and analytical. Both of these are normal, and both have advantages. Of course, people vary in their propensity to use one or the other.

The cognitive style test is a measure of how analytical the person is. A higher score means that the person is more toward the side of the spectrum showing slower, more analytical thinking; a lower score means that they are more toward the side showing faster, more intuitive thinking. It would be good to avoid any connotation that one side is better than the other; they are two parts of normal human thinking.

The results for the cognitive style test suggest that those who tend to act fast-and-intuitive are more likely to use their SP search engine.

Taken together, the tests reported here suggest that people vary in how they use the Internet. We look things up, using the Internet as an extended memory. Some people do that more than others; the current work correlates that with certain features. Interesting tests.

The work opens up many questions. For example...
* Are the results reported here reproducible? It is possible that the results of such experiments vary, for various reasons including the nature of the people tested. A single experiment is a step, but not necessarily the final answer.
* What is the cause-effect relationship for the effect? Some would suggest that the presence of easy information, on the Internet, is making us less likely to think. There is nothing here that supports such a claim; the authors note that explicitly. It is just as plausible that some people are more inclined to look things up. And maybe, there is more than one reason for what is observed.
* And then there are some "big" questions... Is this good or bad? How should we be using the phone, or the Internet? These may be fun to discuss, but I really would suggest that it is premature to conclude much. It is sad to find that people think having more information available to more people is bad.

News stories:
* iPhone, Therefore I Am. (S Greenfield, Psychology Today, April 2, 2015.)
* Is your smartphone making you stupid? (Kurzweil, March 6, 2015.)

The article: The brain in your pocket: Evidence that Smartphones are used to supplant thinking. (N Barr et al, Computers in Human Behavior 48:473, July 2015.) Check Google Scholar for a copy.

Comment...

The general topic addressed here came up in discussion recently, so a note about the article caught my attention. I'm not sure what to make of all this. But if this post serves to promote some thinking or discussion about the topic, that's good. Just be cautious about jumping to conclusions.

One person responsible for raising these questions in the popular mind is the journalist Nicholas Carr. In 2008, he wrote an article for the Atlantic: Is Google Making Us Stupid? (N Carr, Atlantic, July 2008.) It's available, go have a look. The title is catchy, and gets attention. And the article raises questions. But it is important to distinguish raising questions and pretending that we have answers.

Carr later expanded the article into a book. The article usefully serves to raise the questions. The book is a long-winded elaboration; I spent much of the time with the book wondering what the point was. Some of the history is fun to read, but not important. Carr is not good at evaluating evidence, and his elaboration is unconvincing to those who think critically about evidence.

Some are using Carr's book to claim that the Internet is making us stupid. That's not justified. I wouldn't conclude much of anything from what Carr wrote, other than that there are questions. We have new tools. More people have more access to information than ever before. Why do some want to paint this as bad?

There is also a Wikipedia article on the topic, with the title of the article as its title. It tries to provide some balance of views, but is rather messy. If you browse it, you will get a sense of the debate. Don't try to make much more out of it.

* * * * *

A book, listed on my page of Books: Suggestions for general science reading... Kahneman, Thinking, Fast and Slow (2011). Kahneman is a key figure in developing the ideas of cognitive style, of fast and slow thinking, that are used in the analysis above. He is a psychologist -- who won the Nobel prize in economics, because his ideas have proved insightful. The book is long, but quite readable. It is an enjoyable book about how people think. If you find the topic of this post interesting, you should at least learn what Kahneman did.

Above I have criticized one book and recommended another. Why the distinction? Kahneman is a scientist, whose contributions are behind much current work in psychology. The book is a presentation to the public of what he has accomplished. In contrast, Carr is not a scientist. He is an observer of the field; he has questions and concerns, but he lacks understanding. His goal is not to present what is known, but to raise concerns. Both are valid books, but they are different. You shouldn't uncritically accept any book you read. In particular, you should distinguish whether what is being presented is broadly accepted or not.

Also see:
* Political bias in Internet access? (January 23, 2017).
* Claiming knowledge one does not have: it's particularly common with those who think they are experts (November 29, 2015).

Other posts about using smartphones include... Can you detect the SARS-2 virus with your phone? (March 2, 2021).

Breastfeeding and obesity: the HMO and microbiome connections?

November 14, 2015

Some have suggested that there is a relationship between breastfeeding and the subsequent development of obesity in the child. However, tests of the idea have led to confusing results.

A new article tries to relate the development of obesity not simply to breastfeeding but to specific features of the breast milk. The results are intriguing, though very preliminary.

The focus is on a class of chemicals called human milk oligosaccharides (HMO). These are complex sugars (or sugar derivatives). An important feature of them is that people cannot digest them. Why does a mother put things in the breast milk that her child cannot use? The hypothesis is that they are there to feed the intestinal bacteria, the microbiome. The breast milk influences what develops in the microbiome, and that affects the subsequent development of the child.

In the new work, the scientists followed a small group of infants through age six months. They measured the growth of the children, including the amount of body fat. And they analyzed the mothers' milk for HMO.

Here is an example of the results...

That's interesting. Let's go on. The next figure provides a more specific clue -- and a big caution.

I will resist trying to interpret that graph. After all, the main point is perhaps that it's not very clear what it means. The set of data is certainly not normally distributed (in the statistical sense of "normal").

The authors are quite aware of the limitations of their work here. They emphasize that the findings should be taken as preliminary, subject to further testing. That is, this small test leads them to formulate new hypotheses, such as the possible importance of this HMO, LNFPI. Don't go out to buy this stuff for your kid; the results here do not justify that. What they do justify is further work. Further work that may lead to better understanding of the connections between breast milk, the gut microbiome, and obesity.

The key advance here is to focus on specific components of the breast milk, rather than simply whether or not the infant is fed breast milk. Not all breast milk is the same.

For two of the specific HMO, there seemed to be a trend in the other direction: more of that sugar in the milk correlated with more fat. What does that mean? Is it possible that these HMO have some other benefit? Or are they "mistakes". In any case, they help emphasize the complexity of the story.

The hypotheses is that the microbiome is one factor in obesity, not the sole -- or even primary -- factor.

News stories:
* Obesity May Be Associated with Carbohydrates Found in Breast Milk. (D Semedo, Obesity News Today, November 2, 2015.)
* Factors in breast milk may play a role in transmission of obesity. (Science Daily, October 29, 2015.)

The article: Associations between human milk oligosaccharides and infant body composition in the first 6 mo of life. (T L Alderete et al, American Journal of Clinical Nutrition 102:1381, December 2015.)

A possible connection between obesity and the microbiome was made in the post: Obesity, gut bacteria, and the immune system (May 24, 2010).

More about breastfeeding: Barium, breast milk, and a Neandertal (June 17, 2013).

More about milk: Does it matter what time of day you milk the cow? (December 28, 2015).

Another example of natural sugars that may be more important for their effect on the microbiome than on their direct nutritional content: Influence of the food additive trehalose on Clostridium difficile? (February 23, 2018).

More on the microbiome...
* How a "low-gluten" diet may benefit those who are not gluten-sensitive (January 27, 2019).
* How intestinal worms benefit the host immune system (February 27, 2016).

Among many posts on obesity: Olfaction and obesity? (July 18, 2017).

My page Organic/Biochemistry Internet resources has sections on Carbohydrates and Lipids. They include a list of related Musings posts; the list in the Lipids section includes many on obesity.

Making use of CO₂

November 10, 2015

One approach to dealing with the high level of carbon dioxide in the atmosphere is to remove it. But then what? What do we do with it? One possibility is simply to bury it; that leads to a combined process known as carbon capture and sequestration (CCS).

It is also possible that we might put it to use. CO₂ is a chemical used in industry; we might take the CO₂ we remove from the atmosphere, and use it. In one sense, the best use would be to convert it to fuel, something like gasoline. An advantage of making a fuel is that there is a huge market potential.

All this is logical. The problem is working out a practical economical process. In particular, it takes a lot of energy to use CO₂; if we spend a lot of fossil fuel energy to use CO₂, that may defeat the purpose. Many are working on the problem. There are technical successes; practical implementation is still largely for the future.

A recent news feature in Nature gave a nice overview of the field. It discusses possible uses of CO₂, and the work being done towards making the use of atmospheric CO₂ practical. It's worth a browse. It's a status report, not a claim of success.

The news feature, which is freely available: How to make the most of carbon dioxide -- Researchers hope to show that using the gas as a raw material could make an impact on climate change. (X Lim, Nature 526:628, October 29, 2015.)

Photosynthesis is one "natural" use for CO₂, and we might stimulate that... Fertilizing the ocean may lead to reducing atmospheric CO₂ (August 24, 2012).

Progress towards a valuable product... Making carbon nanotubes from captured carbon dioxide (June 3, 2018).

Another approach: Capturing CO₂ -- and converting it to stone (July 11, 2016).

Also see a section of my page Internet Resources for Organic and Biochemistry on Energy resources. It includes a list of some related Musings posts.

Analysis of uranium samples from World War II Germany

November 7, 2015

A new article reports analyses of samples of uranium (U) left from World War II German labs. These are labs where German scientists were, we might presume, trying to figure out how to control the fission reaction; such control could lead to making a reactor for nuclear power, or to a bomb.

Here is an example of the results...

The scientists also measured the levels of two rare isotopes, one each of U and of plutonium (Pu), which are made upon bombardment with neutrons. The levels of both were at about the levels found in natural samples. In fact, for the Pu, the level was lower in the U samples than in the original ore. This reflects that the U had been purified from the ore, leaving Pu behind. Fission is triggered by neutrons. Had the samples been exposed to much neutron bombardment, the levels of these isotopes should have been high. The results suggest that the samples had not received a sustained high dose of neutrons.

World War II ended 70 years ago. We're still trying to figure out what happened -- and what might have happened. This article makes a small contribution to figuring out World War II.

In other tests, the scientists were able to authenticate the date of the materials, and to determine the likely source of the ore from which the U was extracted.

News story: Forensic investigation of uranium from German nuclear projects from the 1940s. (M Wallenius, Phys.org, September 16, 2015.) If this is labeled right, the news story was provided by the head of the research team, who is also an author on the article.

The article: Uranium from German Nuclear Power Projects of the 1940s -- A Nuclear Forensic Investigation. (K Mayer et al, Angewandte Chemie International Edition 54:13452, November 2, 2015.)

More uranium:
* Role of biological processing in the formation of a uranium ore (June 30, 2017).
* File dates and human settlement in Polynesia (November 16, 2012).

More about measuring fission products: Berkeley RadWatch: Radiation in the environment -- Follow-up (May 6, 2014).

More about atomic bombs: Atomic bombs and growing new brain cells (November 1, 2013).

More from World War II: Alan Turing, computable numbers, and the Turing machine (June 23, 2012).

Also see: A better way to oxidize americium? A step toward improved processing of nuclear reactor waste? (December 7, 2015).

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

My page of Introductory Chemistry Internet resources includes a section on Nucleosynthesis; astrochemistry; nuclear energy; radioactivity. It includes a list of related Musings posts.

Added February 12, 2024. This post is also listed there in the section Lanthanoids and actinoids.

How the MERS virus spread in Korea: role of super-spreaders

November 3, 2015

The outbreak of Middle East respiratory syndrome coronavirus (MERS-CoV, or MERS for short) on the Arabian peninsula continues. There have been about 1600 cases worldwide, with 3/4 of them in Saudi Arabia. The death rate is about 35%.

In May, the virus took a plane trip to the Republic of Korea (South Korea), starting a MERS outbreak there. Over two months there were 186 cases. That's the second largest country total, and the only substantial number outside the Arabian peninsula area. The Korean outbreak had 37 deaths.

A new article details the Korean MERS outbreak. It contains more than any casual reader would want to know, but the first point is simply to note how well the disease was tracked, to produce this data set. MERS is a new virus, poorly understood. The kind of information recorded here is useful in understanding disease spread.

The following figure shows one of the simplest analyses: when and where the cases appeared.

It's the most basic description of the outbreak: a record of when and where the cases arose. You can already see that most of the transmission occurred within the health-care system. "The majority (98%) of patients were infected with MERS-CoV in healthcare facilities." (p 272 of the article.)

If you'd like a bit more... Transmission pattern (Figure 4) [link opens in new window]. This figure shows the chain of transmission. It is based on the above figure, plus additional information about the cases. You may not want to spend much time with this; simply recognizing that it exists is good.

But I do note... From the figure above, one might guess that the index patient went to hospital C. It turns out that things were more complex, as seen on the linked figure here. He went to hospitals A & B, then to C. Hospitals A & B were the source of only two infections; C was a hotspot.

The red circles show patients who spread the disease. The number in the circle is the patient number. You can see that Hospital C not only was a hotspot, but a source of five patients who spread the disease further.

Of particular note is the role of a small number of people who transmitted a large fraction of the cases. These people are termed super-spreaders. One patient transmitted 85 cases, nearly half of the total. The five leading transmitters were responsible for 153 of the cases (83%).

One of the super-spreaders was the index patient, #1, the man who brought the virus to Korea. He transmitted 28 cases. But he was also special: it was nine days after he first showed symptoms that he was properly diagnosed. During that interval, he was in contact with several hundred people, many of them hospital staff. That is, this person was exposing people, including health-care workers, even before anyone was aware that MERS existed in the country.

The initial phase of an outbreak is a special challenge. Not only are undiagnosed people around, possibly spreading the disease, but the presence of the disease at all is not yet recognized. What level of infection control should a hospital take to deal with unknown diseases?

The authors look for characteristics that might define a super-spreader. It's not clear. In fact, it is hard to know for sure whether being a super-spreader is a characteristic of a patient per se or of the environment they happen to be in.

One cannot help but think of the Ebola outbreak while reading this article. Among the similarities... the importance of transmission in health-care settings, and the importance of tracing contacts as part of disease control. Of course, contact tracing was much easier for this modest size outbreak in a society with excellent health-care.

Perhaps the main point of this post is a little insight into how a disease, a new disease, is tracked. And it reminds us of the challenge.

News stories:
* 83% of Korean MERS cases stemmed from 5 patients. (Korea Herald, October 25, 2015.)
* Korea highlights MERS super-spreaders, reports death. (J Wappes, CIDRAP, October 26, 2015.)

The article, which is freely available: Middle East Respiratory Syndrome Coronavirus Outbreak in the Republic of Korea, 2015. (Korea Centers for Disease Control and Prevention, Osong Public Health and Research Perspectives 6:269, August 2015.) The journal is from the Korean agency, and the article is published with the agency name as author. (There is a list of "authors and KCDC EIS officers who contributed to this article" in the Acknowledgments. EIS? Epidemic Intelligence Service.)

* Previous post about MERS: Camels and the transmission of MERS: blame the kids? (March 30, 2015).
* Next: A MERS vaccine, for camels (January 22, 2016).

There is more about MERS on my page Biotechnology in the News (BITN) -- Other topics in the section SARS, MERS (coronaviruses). It includes links to good sources of information and news, as well as to related Musings posts.

The importance of identifying contacts or even possible contacts... An Ebola vaccine: 100% effective? (August 7, 2015).

How much would it cost to make a brain?

November 1, 2015

Twenty five cents. (0.25 USD.) So says the senior author of a new article.

These are mini-brains, little blobs of tissue a millimeter or so in diameter. They show many normal brain activities; for example, they form synapses, and transmit electrical signals. The news stories emphasize that these brains do not show cognitive function. (But I must wonder... it is not obvious that any such test was done.)

What are they good for? Drug testing would be one use. These mini-brains are cheap and easy to make, and they last for a month or so. They would be well suited for testing the effect of drug candidates on brain activity.

How does one make such a mini-brain? Take a rat brain, dissociate the cells, and let them reform in a dish into small aggregates, or "neural spheroids".

For those who really want the economics... The cost number, 25 cents per brain, is not in the article itself. It does come from the author, and is noted in the news stories. It includes the cost of making the new brains, but not the general fixed costs of the lab.

It's an interesting approach. What may be particularly important is to notice the diversity of types of mini-brains that are appearing. There may be many ways to make a brain, with different ones suited for different uses. Learning how to make and use mini-brains is part of developing our understanding of the brain.

News stories, both with good overviews of the work:
* How to Make a Mini Brain. (Neuroscience News, October 1, 2015.)
* How to grow a functional 3-D mini-brain for 25 cents. (Kurzweil, October 2, 2015.)

The article: Three-Dimensional Neural Spheroid Culture: An In Vitro Model for Cortical Studies. (Y-T L Dingle et al, Tissue Engineering Part C: Methods 21:1274, December 2015.)

A recent post on mini-brains, but a very different type: Autism in a dish? (September 4, 2015). The mini-brains discussed here are made from stem cells: in this case, special stem cells from individual patients of a specific disease.

More on nervous systems: An artificial neuron? (November 6, 2015).

More organoids (and such):
* Multi-organ lab "chips" (April 14, 2018).
* An organoid for the gut: at last, a culture system for norovirus (October 30, 2016).

More inexpensive things: Making better artificial muscles (March 13, 2018).

My page for Biotechnology in the News (BITN) -- Other topics includes a section on Brain (autism, schizophrenia). It includes an extensive list of brain-related Musings posts.

Most Earth-like (habitable) planets haven't formed yet

October 27, 2015

We are in an era of discovering exo-planets -- the first known planets beyond our Solar System. A particular interest is finding planets that might host life, so-called habitable or Earth-like planets.

A new article says that this may be a bad time to look for such planets. Most haven't formed yet.

The article builds on our improved understanding of the universe, much of it based on the observations by the Hubble Space Telescope, plus the Kepler mission for finding exoplanets. Importantly, there is now good evidence for vast dust clouds in the universe. Inevitably, these will condense -- forming new stars and their planetary systems, including habitable planets. The authors model all this, and suggest that 92% of the ultimate set of habitable planets have not yet formed.

That conclusion is different from one in an earlier Musings post [link at the end]. That post focused on the point that the rate of star formation had slowed down; astronomers agree on that point. But the authors of the previous work did not consider the magnitude of the remaining dust. They concluded that most stars (and therefore most planets) that would ever form had done so. The new article suggests that there is enough dust left to support continuing star formation for a very long time -- perhaps a trillion years. The rate of star formation will be very slow, but the time scale is huge; as a result, the authors of the new work suggest that most stars and their planetary systems belong to the future.

It's fun. It's another step in our understanding of the universe. We'll see how others react to the new model. Of course, it is testable, though the time scale will make it a challenge.

News story: Theoretical Study Suggests Most Earth-Like Worlds Have Yet to Be Born. (SciTech Daily, October 20, 2015.)

The article, which is freely available: On the history and future of cosmic planet formation. (P Behroozi & M S Peeples, Monthly Notices of the Royal Astronomical Society 454:1811, December 2015.)

The American journalist Lincoln Steffens said something along the line... The greatest painting has not yet been painted; the greatest poem is still unsung. To that we now add... The most habitable planet has not yet formed.

The statement from Steffens comes in various forms. One is at Bartleby's: Steffens quote. It's intended as a statement of optimism about the future. I remember it well; it was at the heart of a speech I gave in 8th grade.

* * * * *

Background post about star formation: Star formation has slowed down (December 4, 2012).

Exoplanets... Habitable Exoplanets Catalog (July 27, 2012). The catalog fails to list those not yet found -- and those not yet formed.

And... GJ 1132b: "the most important planet ever found..." (December 18, 2015).

More from the Hubble: Europa is leaking (February 10, 2014).

Chernobyl exclusion zone: mammal populations

October 24, 2015

More from Chernobyl. A new article provides new data on the habitability of the region around the Chernobyl nuclear accident. It's interesting. And it's easily misinterpreted.

The scientists tracked the populations of various mammals (elk, boar, wolves, hares and others) in the "exclusion zone" around the accident site and compared them to nearby uncontaminated regions. The basic finding is that the populations of mammals are not significantly different in the exclusion zone. (In one case, the population is much higher in the exclusion zone, perhaps due to the absence of humans.) Some of their data suggests that animals returned to the exclusion zone within a year after the accident.

Comment...

That's fine. The question is what it means. The elk don't read the signs. People would probably move into the area if they needed some space and didn't see the signs. It's worse than that... We don't know how much time these animals are spending in the exclusion zone; dose of radiation depends on exposure time as level as well as the level. Further, we don't know whether the animals are suffering any consequences from their time in the exclusion zone.

A previous post was about birds in the Chernobyl area. The authors of that work studied the physiology of the birds, and showed that they had signs of oxidative stress. The birds were in the area, and they had adapted to the radiation -- at a cost. We don't know how well this will work in the long run, but at least it offers some understanding of what the animals are doing. [Link at the end.]

The new article presents useful data. It is good that the authors have collected all this, and published it. But the article spends most of its space trying to establish that all is well. It makes only the briefest mention that there might be limitations to the significance.

My comments are not intended as a judgment about whether it is safe to be in the Chernobyl area. That's not a simple matter. That animals seem at home in the area does not vouch for its safety. My comments also are not intended as any claim of error in the article. It's that the way the work is presented is subject to misinterpretation -- as evidenced by the news coverage listed below.

News stories:
* Researchers Discover Abundant Populations of Wildlife in Chernobyl Exclusion Zone. (Sci.News, October 6, 2015.)
* Chernobyl has become an unlikely wildlife haven. (S DeWeerdt, Conservation, October 6, 2015. Now archived.)

The article, which is freely available: Long-term census data reveal abundant wildlife populations at Chernobyl. (T G Deryabina et al, Current Biology 25:R824, October 5, 2015.) It's a 2-page paper. Go look if you'd like to see some data.

Background post about animals at Chernobyl: Are birds adapting to the radiation at Chernobyl? (August 3, 2014).

More about Chernobyl: Effect of Chernobyl exposure on the rate of new mutations in the next generation (June 1, 2021).

More about wildlife... Human-wildlife conflict -- what is the proper way to get rid of a pest? (July 12, 2017).

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. It also includes a list of related Musings posts.

Cancer metastasis: An early detection system?

October 20, 2015

Metastasis -- the transfer of a cancer to new sites -- is probably responsible for the most cancer deaths. It is now relatively easy to remove a primary tumor, but if a few cancer cells are left, they can establish multiple secondary tumors at other sites. Much attention nowadays is devoted to studying metastasis.

In recent years, scientists have come to realize that cancer cells can be found in the blood stream. These circulating tumor cells (CTC) reflect an early step of the metastatic process. These cells are present at very low levels; scientists are just learning how to find them. Work on CTC is an emerging area of active work, but it is not clear where it will lead.

A new article reports an intriguing development. The scientists implant a small sponge-like scaffold in mice with cancer. The scaffold attracts and collects CTC.

Here are some results...

How does this thing work? Apparently, the immune system notices it, and treats it as a foreign body. With an immune horde around it, it becomes an attractor for cancer cells. The authors think that invasion of the scaffold is actually analogous to the establishment of a metastatic lesion.

It's intriguing. It's also early -- as usual for novel discoveries. This is a single type of test, with mice. Would it work in humans? For what cancers and under what conditions? We'll see.

Why might this be useful, if it pans out? First, it is an early detection system. If a person has been treated for cancer, and is likely at risk for metastasis, the device could be implanted and checked at intervals for early signs that the metastatic process is underway. Second, it might actually reduce metastases -- by the simple act of removing metastatic cells. The importance of this point is more speculative for now.

News story: New Device Prevents Breast Cancer Metastasis In Mice. (A Venosa, Medical Daily, September 9 2015.) Caution... hyped title.

The article: In vivo capture and label-free detection of early metastatic cells. (S M Azarin et al, Nature Communications 6:8094, September 8, 2015.)

Previous post on cancer -- and indeed on metastasis: Anti-oxidants and cancer? (October 18, 2015).

Next: Could a tapeworm with cancer transmit the cancer to its human host? (November 16, 2015).

More on metastasis: Metastasis: How clusters of tumor cells get through narrow capillaries (June 3, 2016).

Another sponge... A sponge that will soak up phosphate pollution from water (August 14, 2021).

My page for Biotechnology in the News (BITN) -- Other topics includes a section on Cancer. It includes a list of related posts.

Anti-oxidants and cancer?

October 18, 2015

Oxygen is a very reactive chemical, which we use to burn our food. Some of the possible intermediates formed during oxygen use are even more reactive. These species, such as the superoxide ion, O₂^-, are collectively called reactive oxygen species (ROS), and are considered quite dangerous.

Enter anti-oxidants. Organisms that survive around oxygen have many defenses against it. One is an enzyme that degrades that superoxide ion mentioned above. (That enzyme is called superoxide dismutase.) Further, there are chemicals around that can rapidly react with ROS, sacrificing themselves for the good of the cell. These chemicals are collectively known as anti-oxidants; they include glutathione and common vitamins such as C and E.

So, anti-oxidants are good for us? Maybe we should take more of them? Maybe they would treat cancer?

Those are perfectly good questions to ask, but be careful about what you expect -- or assume. Like so many things in biology, the full story is complex.

A new article examines the effect of some anti-oxidants on mice with melanoma. The following figure shows some key results...

The experiment shows that the anti-oxidant NAC increases the number of metastases. It's metastases that lead to most cancer deaths nowadays. Thus the effect of the anti-oxidant is of concern.

The big question is the significance of the result. That's not clear. Previous work had shown a variety of effects of anti-oxidants on cancer, with no clear picture. The current article goes on to show how the anti-oxidant works in this case to promote metastasis. It seems to promote migration and invasion of the cancer cells. Along the way, it increases the level of glutathione, thus affecting the natural oxidation balance in the cells. The scientists also show some evidence for another anti-oxidant (a vitamin E derivative); the overall effect may be similar. Other work has suggested different mechanisms of action. There may be no one general answer.

The detrimental effects seen here should make clear that we should not assume that an anti-oxidant would be useful in treating cancer. The work does not preclude that there might be favorable cases, but they need to be shown.

My usual disclaimer on medical matters... I don't give medical advice. This post is about an article, and I have comments about what is in the article.

News story: Antioxidants Facilitate Melanoma Metastasis -- Two compounds boost the ability of melanoma cells to invade other tissues in mice, providing additional evidence that antioxidants can be beneficial to malignant cells as well as healthy ones. (A Azvolinsky, The Scientist, October 7, 2015.)

The article: Antioxidants can increase melanoma metastasis in mice. (K Le Gal et al, Science Translational Medicine 7:308re8, October 7, 2015.)

ROS damage and the anti-oxidant glutathione were discussed in the post Are birds adapting to the radiation at Chernobyl? (August 3, 2014).

Possible role of ROS and oxidative stress in heat attack damage: Can we pinpoint a specific molecular explanation for tissue damage following a heart attack? (March 24, 2015).

A post that mentions the issue of anti-oxidants and cancer: Is folic acid good for you or bad for you? (April 10, 2010).

More...
* How oocytes limit oxygen-induced aging (August 20, 2022).
* Science myths (February 23, 2016).
* How vitamin C kills cancer (December 15, 2015).

More about melanoma:
* A connection between eating fish and skin cancer? (June 20, 2022).
* Can fecal transplantation be useful in treating cancer? (April 27, 2021).
* Fair skin and cancer: What is the connection? (March 12, 2013).

More about metastatic cancer:
* Metastasis: How clusters of tumor cells get through narrow capillaries (June 3, 2016).
* Cancer metastasis: An early detection system? (October 20, 2015).
* Diagnosis of prostate cancer in a 2100 year old man (November 8, 2011).

My page for Biotechnology in the News (BITN) -- Other topics includes a section on Cancer. It includes a list of related posts.

Nobel notes

October 13, 2015

The Nobel prizes were announced last week. All three science prizes have a connection to Musings posts, so I thought I would note them here. In no case, did we discuss the specific work that was the subject of the award; that was typically "long ago".

For each, there is a link to the Nobel announcement quoting the first sentence or so, an outside news story, and 1-2 Musings posts.

Physiology or medicine

Nobel announcement: The 2015 Nobel Prize in Physiology or Medicine. The award is "... to William C. Campbell and Satoshi Omura for their discoveries concerning a novel therapy against infections caused by roundworm parasites, and ... to Youyou Tu for her discoveries concerning a novel therapy against Malaria." (October 5, 2015.)

News story: Antiparasite Drug Developers Win Nobel. (K Zusi & T Vence, The Scientist, October 5, 2015.)

Related Musings posts, one about each of those two drugs:
* A post about the anti-roundworm drug ivermectin: Using your phone to find Loa loa (August 14, 2015).
* A post that notes work on the development of a microbial process to make the anti-malaria drug artemisinin: Some fun reading: Fuel cell gadget and growing diesel (December 13, 2008).

Physics

Nobel announcement: The 2015 Nobel Prize in Physics " ... recognises Takaaki Kajita in Japan and Arthur B. McDonald in Canada, for their key contributions to the experiments which demonstrated that neutrinos change identities. This metamorphosis requires that neutrinos have mass." (October 6, 2015.)

News story: Neutrino 'flip' wins physics Nobel Prize. (J Webb, BBC, October 6, 2015.)

Related Musings post: IceCube finds 28 neutrinos -- from beyond the solar system (June 8, 2014).

Chemistry

Nobel announcement: The 2015 Nobel Prize in Chemistry " ... is awarded to Tomas Lindahl, Paul Modrich and Aziz Sancar for having mapped, at a molecular level, how cells repair damaged DNA and safeguard the genetic information." (October 7, 2015.)

News story: DNA Repair Pioneers Win Nobel. (T Vence, The Scientist, October 7, 2015.)

Related Musings posts:
* A gene for breast cancer: what does it do? (May 4, 2010).
* Electricity in DNA: guarding your genes? (December 16, 2009).

Nobel prizes get mentioned in Musings posts from time to time. The last post that featured a Nobel in the title was In vitro fertilization: an improvement and a Nobel prize (October 15, 2010). If you want to see more about posts that note a Nobel, put the following into Google: Nobel site:bbruner.org/musing

A novel drug candidate that is active against all stages of the malaria parasite

October 10, 2015

Malaria is a complicated disease. It is caused by a parasite, but that parasite has multiple growth phases -- in mosquitoes and in humans. For example, in humans there are distinct growth phases in the liver and blood.

The complexity of the malaria parasite's growth presents a major challenge to drug development; a drug effective against one stage is typically not effective against another.

You might wonder... Aren't there things the parasite does in all stages? Sure, but they may not be good drug targets. Remember, the basic biology of a malaria parasite is the same as basic human biology. Both are eukaryotes; developing drugs that are active against one eukaryote and not another has long been a difficult problem. Of course, there might be good targets we haven't found yet.

A recent article reports finding such a target -- and a drug that inhibits all stages of the parasite in a mouse model system, with low toxicity.

The drug inhibits protein synthesis in the parasite. But it is more or less an accident that the scientists could find a drug that inhibits the step in all parasite stages but not in the host.

The authors show that their new drug is effective against current drug-resistant strains. They estimate that the drug should be quite inexpensive. The low cost coupled with its broad effectiveness suggests it could be useful as a prophylactic drug, reducing the chances of getting an infection.

Of course, the immediate challenge is to see whether it works in humans. It's a long journey from drug discovery to establishment, and many drugs fail along the way. The current drug is interesting, but the work here it is only a first step.

News stories:
* New single-dose malaria treatment could eventually help millions. (S Petrova, The Conversation (and reprinted here by Medical Xpress), June 18, 2015.)
* New antimalarial compound discovered -- Promising lead kills parasites in both humans and mosquitoes. (Wellcome Trust Sanger Institute, July 2, 2015.) From one of the institutions involved in the work.

The article: A novel multiple-stage antimalarial agent that inhibits protein synthesis. (B Baragaña et al, Nature 522:315, June 18, 2015.)

A recent post on malaria: Pop goes the hemozoin: the bubble test for malaria (January 24, 2014).

More... How an American weed might interfere with control of malaria in Africa (November 13, 2015).

More on malaria is on my page Biotechnology in the News (BITN) -- Other topics under Malaria. It includes a listing of related Musings posts.

Twenty percent of the females are genetic males

October 6, 2015

Sex determination in reptiles can get confusing. Some reptiles use a system involving genes and chromosomes that is somewhat like ours. One sex has two sex chromosomes of the same kind; the other sex has two different sex chromosomes. In humans, the females have two X chromosomes (XX), whereas males have one X and one Y chromosome (XY). In the lizards discussed here, the males are ZZ, and the females are ZW.

There is nothing important about the details, or the difference from what mammals do. The point is that one can tell the genetic sex by identifying the chromosomes.

In some reptiles, sex is determined by temperature (T): the T during egg development.

The lizard known as the bearded dragon has both systems.

The T part of the system has been demonstrated in the lab; it leads to lizards that are genetically male becoming female.

A new article reports examining dragons from the wild. Twenty percent of the females the scientists found should be male, according to their chromosomes. That is, they found ZZ females in the wild. Lots of them. They had a male set of chromosomes, but female anatomy -- and they reproduced as females. In fact, ZZ females reproduced better than the traditional ZW females; they had more offspring.

That's a bit weird, isn't it? But it may be more than that. First, it is a chance to watch a change in sex determination occurring in nature. We know some lizards use one system and some use another; here we may be watching a lizard change from one to the other.

A change from one [system of sex determination] to the other? Think about what happens... Cross a ZZ female with a (normal) ZZ male. All the offspring are ZZ. The W chromosome gets lost. Getting a mix of males and females is now entirely dependent on the environment, the T.

Second, the change may be important -- a challenge to the survival of the bearded dragons. Both of the systems for sex determination work. However, the T-based system has a vulnerability. The sex ratio of the animal depends on the environmental temperature. That's ok. Somehow, the animal has adapted so that it produces a reasonable sex ratio under the conditions it encounters. But what if the environmental T changes rapidly -- so rapidly that the organism cannot adapt? There is a risk of this happening as we experience rapid climate change. There are reptiles for which significant changes in sex ratio have occurred over recent years, and there is concern about the future of some of these species.

The bearded dragons may be undergoing an interesting change, from one mode of sex determination to another. They may also be sealing their own fate if they do this at a time of rapid climate change. That may be quite uncertain at this point, but the story alerts us to the issue. That is the big story here.

News stories.
Update: Two new stories listed May 2022 to replace stories no longer available.
* Reptile sex goes wild in the outback, UC research finds. (Claudia Doman, University of Canberra, July 2, 2015.)
* Australian "dragon." If it's hot, eggs hatch with female genitalia but male genetics. (David J Tenenbaum, Why Files, July 2, 2015. Now archived.)

News story: Lizard Swaps Mode of Deciding Its Sex -- Sex assignment in bearded dragons can flip from one based on chromosomes to one driven by temperature, researchers report. (K Grens, The Scientist, July 1, 2015.) Discusses the current work and the "big story" significance.

* News story accompanying the article: Evolution: Reptile sex determination goes wild. (J J Bull, Nature 523:43, July 2, 2015.)
* The article: Sex reversal triggers the rapid transition from genetic to temperature-dependent sex. (C E Holleley et al, Nature 523:79, July 2, 2015.)

More about lizard reproduction...
* Facultative endothermy: a lizard that is warm-blooded in October (February 1, 2016).
* When should the eggs hatch? (June 11, 2013).
* An advanced placenta -- in Trachylepis ivensi (October 18, 2011).
* Development of a new species of lizard in the lab (May 20, 2011).

More about sex chromosomes or sex determination...
* Quiz: The monkey-cat (October 26, 2011).
* On his right side, he is female (April 24, 2010).

More about climate change: Is the weather getting better or worse? (May 23, 2016).

What's the connection: Narcolepsy and the flu vaccine (or getting the flu)?

October 3, 2015

Not obvious, is it?

Do you remember the new flu strain that emerged in 2009? It provoked extensive vaccination programs. In Europe, there was an increased incidence of narcolepsy. Investigation showed that it correlated with getting one particular type of flu vaccine. Further, one study has found a correlation between the seasonal incidence of flu and narcolepsy.

What's going on? Is it just coincidence, or is there some real connection? A recent article offers a clue.

Before we look at the new information... What is narcolepsy, and what do we know about how it occurs? Narcolepsy is a condition in which a person has a strong tendency to fall asleep during daytime. In recent years, it has been worked out that narcolepsy is typically caused by failure of a hormone called hypocretin. Many people with narcolepsy can now take hypocretin as a drug, resulting in good control of their narcolepsy.

What kind of connection might there be between flu and narcolepsy? The evidence above, showing some correlation between flu and narcolepsy, might suggest that they share some biology. Perhaps, for example, the flu virus, in a vaccine or in a natural infection, stimulates an immunological response that just happens to interfere with the narcolepsy pathway. There is no reason that "should" happen, but sometimes two proteins are closely enough related that there is some immunological cross reaction between them.

The new analysis finds that a part of the flu virus is very similar to the receptor for the narcolepsy hormone. This viral protein induces antibodies to itself, as expected. Those antibodies also recognize the receptor for the narcolepsy hormone, thus preventing that hormone from acting -- and thus causing narcolepsy.

The logic of that is good; I suggest you go through that paragraph slowly enough that you follow what people think may be going on.

One piece of evidence is that the vaccine that seemed to promote narcolepsy contained more of the offending protein than did the vaccine not correlated with narcolepsy. Further, people who had been vaccinated with it had more of the offending antibodies.

It is not clear where this is going. The story is intriguing and plausible, but incomplete. If the story holds up, a hidden problem has been uncovered -- and can be dealt with. There have been some suggestions of a flu-narcolepsy connection before, but some of the work was not reproducible. The new work needs to be integrated with that.

News story: On the Flu Vax-Narcolepsy Link -- Researchers identify a peptide present in the swine-flu vaccine linked to narcolepsy that may be responsible for the sleep disorder. (A Azvolinsky, The Scientist, July 1, 2015.) Good overview.

The article: Antibodies to influenza nucleoprotein cross-react with human hypocretin receptor 2. (S S Ahmed et al, Science Translational Medicine 7:294ra105, July 1, 2015.)

Even with the offending vaccine, narcolepsy was a rare side effect. The incidence of narcolepsy was on the order of one in ten thousand.

The authors explicitly note that, based on what we know at this point, the benefits of the flu vaccine outweigh this possible side effect. Part of that evaluation is that a natural flu infection may have the effect, too. There is considerable uncertainty here at this point, and it is good to learn how to minimize an adverse effect. However, there is no intent here to suggest that the flu vaccine should be avoided.

* * * * *

Narcolepsy was briefly noted in the post Dog psychiatry: Implications for humans (October 3, 2010).

Another example of confusion in the immune system: Why are HIV-infected people more susceptible to Salmonella infection? (May 21, 2010). Links to more.

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

* Previous "What's the connection" post: What's the connection: blue cheese, rotten coconuts, and the odorous house ant? (August 24, 2015).
* Next: What's the connection: ships and lightning? (October 14, 2017).

Fish make their own sunscreen

September 29, 2015

Briefly noted...

Many organisms have a chemical that acts as a sunscreen; after all, they are in the sun, and need protection from ultraviolet irradiation. Some make their sunscreen; some get it from their diet. (And some buy it at the supermarket.)

A recent article shows that a fish makes a sunscreen, called gadusol. This came as something of a surprise... Vertebrates were not known to have the genes for making it, and it was suspected -- even assumed -- that fish got it from their diet.

The discovery was made first in the zebrafish, a small fish commonly used for lab work. The scientists identified specific zebrafish enzymes for making gadusol. Analysis of genome databases showed that the gadusol genes were found in many fishes, and also in amphibians, reptiles and birds, but not mammals.

To show that the fish genes for making the sunscreen were intact, the scientists transferred them to yeast -- which then made the compound. This might be the basis of a commercial system for making gadusol. Beyond that, the article raises interesting questions about how the gadusol genes got to vertebrates and why they are not in mammals.

News story: Fish and other animals produce their own sunscreen: Copied for potential use in humans. (Science Daily, May 12, 2015.)

* News story accompanying the article; it is freely available: Shedding light on sunscreen biosynthesis in zebrafish -- Zebrafish can synthesize a sunscreen compound called gadusol, which was previously thought to be acquired only through the diet. (C A Brotherton & E P Balskus, eLife 4:e07961, May 12, 2015.)
* The article, which is freely available: De novo synthesis of a sunscreen compound in vertebrates. (A R Osborn et al, eLife 4:e05919, May 12, 2015.)

Previous fish post: The opah: a big comical fish with a warm heart (July 13, 2015).

More zebrafish:
* Scoliosis: an animal model (July 22, 2016).
* The answer is cereblon (March 16, 2010).

Other posts about sunscreens include...
* How some tardigrades are resistant to ultraviolet light (October 27, 2020).
* How do you know if you have been in the sun too long? (August 5, 2016).
* How can the mantis shrimp see so many colors of UV? They use filters (August 30, 2014). One of the filters discussed there is the same compound, gadusol. (The post does not name the specific compound, but refers to its roles.)
* A possible hazard of using compact fluorescent light bulbs (November 13, 2012).
* Geoengineering: a sunscreen for the earth? (February 20, 2010).

Transmission of Alzheimer's disease in humans?

September 27, 2015

This is a story that may seem scary. But set that aside; it is a fascinating biology story, about our increasing understanding of an important disease. The practical implications are not clear, but probably less than we might fear.

Alzheimer's disease (AD) is a progressive neurodegenerative disease, with increasing prevalence with age. There is nothing in the traditional knowledge of the disease to suggest it can be transmitted from one person to another.

We have learned a lot in recent years about AD at the molecular level, although the story is still incomplete. Interestingly, that increased understanding has led scientists to wonder whether AD might in fact be transmissible, at least under special circumstances. It "should" be transmissible.

Central to the AD story is a small protein called AB or AB-42; that stands for amyloid beta 42, the number giving the size (number of amino acids) of the protein. This protein aggregates into what are called amyloid plaques, a characteristic feature of the disease. Much attention has been devoted to figuring out how these plaques form and what they do. One point is that small aggregates serve as "seeds" to promote further aggregation.

This feature of a protein forming aggregates, and serving to seed aggregate development, reminds us of another type of disease: the prion diseases, such as bovine spongiform encephalopathy (BSE) and Creutzfeldt-Jakob disease (CJD). That comparison makes us think about another characteristic of prion diseases: they are transmissible, at least sometimes. Transfer of the aggregated protein from one animal to another can lead to the disease in the recipient. In the lab, this transfer is often done by direct inoculation into the brain. Some prion diseases can be transmitted orally. (One form of CJD is acquired by eating beef that has the BSE prion.)

If AD is, in some ways, like prion diseases, is it possible that AD can be transmitted? The question forces itself on us. In fact, experimental transmission of AD in lab animals has been shown. This was first done by direct inoculation of the protein aggregate into the brain, and it led to disease symptoms in the recipient. In follow-up work, the AD aggregate was injected into the abdominal cavity, with the same result. This was discussed in an earlier post [link at the end]; I encourage you to go back and review that post somewhere along the way here.

We now have an article suggesting that transmission may occur for humans. Of course, no one intentionally inoculates AD proteins into humans. However, it has happened accidentally, and we now have some information on the consequences.

What kind of accident led to people being given AD protein? Human growth hormone (hGH) is a useful drug. hGH used to be prepared from tissue from human cadavers. Such preparations of hGH benefited many, but we now understand that they may have also transmitted disease. In fact, a couple hundred cases of a prion disease, CJD, are attributed to transfer of prions by such cadaver-derived hGH.

Perhaps you can guess where this is going. In new work, scientists have examined the brains of people who died of CJD long after receiving such cadaver-derived hGH. They found that some of those brains had evidence of AD pathology. They had levels of AB plaque higher than expected for their age.

Did they have AD? There is no evidence for that. These people had reported no signs of the cognitive decline that is characteristic of AD in a living person. However, they died rather young. It is plausible, though not certain, that these people were on the way to AD.

That's about it. Some people who received fairly crude preparations of human brain protein show some evidence for AD pathology. It is suggestive, but incomplete. The limitations include that there are only a small number of samples, that the people did not have "real" AD, and that there may be alternative explanations for the results. Nevertheless, it is suggestive, and needs follow-up.

What are the implications? One is that we might expect a burst of AD from others who received this treatment, as they age. That's bad, but it is limited, as the treatment is no longer done. (All hGH is now made using recombinant DNA technology, and is highly purified.) Another implication is that we need to take care that surgical instruments do not transmit AD.

Most importantly, if the suggested interpretation holds up, the evidence for AD transmission helps us to understand the disease. Both this work and the broader AD story are incomplete, so any conclusions are tentative at this point.

The following figure shows an example of their results. This figure is not directly related to any of the points made above, but is interesting.

News stories. Both of the following stories give good overviews of the work, including its limitations.
* Autopsies reveal signs of Alzheimer's in growth-hormone patients. (A Abbott, Nature News, September 9, 2015.)
* Can Amyloid Spread Between Brains? A study of deceased patients who received injections of cadaver-derived growth hormone hints at the possible transmissibility of Alzheimer's disease. (J Akst, The Scientist, September 9, 2015.)

* News story accompanying the article: Neurodegeneration: Amyloid-β pathology induced in humans. (M Jucker & L C Walker, Nature 525:193, September 10, 2015.)
* The article: Evidence for human transmission of amyloid-β pathology and cerebral amyloid angiopathy. (Z Jaunmuktane et al, Nature 525:247, September 10, 2015.)

Background post about the transmission of AD-like disease in mice: Is Alzheimer's disease transmissible? (February 4, 2011).

More AD:
* Added April 12, 2024. The gut microbiome and Alzheimer's disease (April 12, 2024).
* Added April 9, 2024. Evidence for transmission of Alzheimer's disease by medical procedures (April 9, 2024).
* Transmissibility of Alzheimer's disease? (June 1, 2016). Overview.
* BRCA1 (the breast cancer gene) and Alzheimer's disease? (February 8, 2016).

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.

For more about prions, see my page Biotechnology in the News (BITN) - Prions (BSE, CJD, etc). It includes a list of related Musings posts.

How PBRs survive major earthquakes; why being near two faults may be safer than being near just one

September 22, 2015

What is a PBR? Here's one...

It is a precariously balanced rock -- or PBR. It's just a few miles from the San Andreas fault, a major earthquake fault in southern California. The rock probably has been there for several thousand years, and has been exposed to many major earthquakes.

How is it possible that such a PBR can survive major earthquakes? It has been something of a mystery, one that intrigues seismologists. We now have a new article that suggests an answer.

The simplest argument one might think of is that it's just a matter of luck. However, the numbers make that very unlikely. There are many such rocks, and many large quakes.

Importantly, PBRs near faults are not randomly distributed. They are in certain areas. Is it possible that these PBRs are in areas that, for some reason, experience less ground motion than we expect in a nearby major quake?

What's striking is that the PBRs are in regions very near two faults. That may be the key. The faults are actually connected, and energy is transferred rather directly from one to the other. The authors suggest that the direct transfer of energy between connected faults protects surface features, such as the PBRs. That is, surface motion is reduced because there is more below-surface connection.

If their suggestion holds up, there may be another consequence -- in addition to protecting some rocks. If the faults are more connected than we thought, then a major quake on one of them might cause more damage than we expect, precisely because the quake could more easily jump to the other fault.

One active field in seismology is trying to predict seismic hazards. That means understanding the strain on faults. It also involves predicting how far a quake is likely to propagate. The current work suggests that we may be underestimating that latter point, because faults are more connected than we thought. On the other hand, being right near the connection of major faults may be the safest place around.

News story: Precariously balanced rocks provide clues for unearthing underground fault connections -- San Jacinto, San Andreas interaction weakens earthquake shaking near them. (University of California, Irvine, August 4, 2015.) From the lead institution. Includes a picture of an even more spectacular PBR, though one not related to the current study.

The article: Reconciling Precariously Balanced Rocks (PBRs) with Large Earthquakes on the San Andreas Fault System. (L G Ludwig et al, Seismological Research Letters 86:1345, September 2015.) Note that the term PBR is from the authors.

A recent post about earthquakes: Fracking: the earthquake connection (June 19, 2015).

A post about earthquake predictions: Earthquake: Are the geologists responsible for the damage? (November 17, 2014).

More about earthquakes...
* Another million earthquakes for California (June 30, 2019).
* Earthquakes induced by human activity: oil drilling in Los Angeles (February 12, 2019).
* Detecting earthquakes using the optical fiber cabling that is already installed underground (February 28, 2018).
* Does the moon affect earthquakes? (October 21, 2016).

More intriguing rocks... How rocks travel (November 14, 2014).

Flooding in The Netherlands: natural or manmade?

September 19, 2015

There have been 32 major floods in southwestern Netherlands in the last half-millennium. About a third of them were intentional floods created by humans in the context of war. That's a key finding of a recent article analyzing the nature and impact of flooding in that low-lying country.

The author delved into the historical record, actually for a thousand years, then focused on the last 500 years. He found floods that were natural, but also floods that were induced by man, for both offensive and defensive purposes. The use of floods, as with other weapons, sometimes turned out well, sometimes not. The most recent induced floods discussed are from World War II.

It's an unusual scientific article. You may find it fun to browse.

News story: Floods as war weapons. (Science Daily, June 9, 2015.)

The article, which is freely available: Flooding in river mouths: human caused or natural events? Five centuries of flooding events in the SW Netherlands, 1500-2000. (A M J de Kraker, Hydrology and Earth System Sciences 19:2673, June 9, 2015.)

More about flooding...
* Recovery from natural disaster: can the poor benefit? (July 22, 2011).
* How to survive flooding by making a waterproof raft (May 27, 2011).

More about war...
* Bee wars (March 1, 2015).
* Does the Christ child lead to war? (September 30, 2011). A possible war-climate connection.

Wind... Atmospheric rivers and wind (May 9, 2017).

Chagas: the guinea pig connection

September 15, 2015

Briefly noted...

Chagas disease is prevalent in some areas of tropical South America. Incidences as high as 40% are found in some communities.

Chagas is caused by a protozoan, Trypanosoma cruzi; it is transmitted by a beetle-like insect known as the kissing bug.

Epidemiological evidence has suggested a connection between the disease and guinea pigs. However, the role of the guinea pigs has been a mystery. A new article offers a possible explanation, at least for one village. It's about the price of alfalfa.

Here's the idea... When the price of alfalfa rises, it becomes too expensive to keep feeding the guinea pigs. So the villagers have a feast -- and eat the guinea pigs. The guinea pigs are an alternative host for the parasite. The feasting time reduces the guinea pig population. In some cases, this leads to small populations with high incidence of infection. That in turn enhances the infection of the insect vector, which transmits the parasite to humans. It's a complex web of interactions, with feedback loops that lead to enhanced transmission -- triggered by a rise in the price of alfalfa.

The evidence is mainly indirect. The proposed model is a hypothesis with limited evidence, but perhaps it is a useful start that can guide further work. It's interesting to read how the authors explored the question. And they do suggest a solution: a price ceiling for alfalfa could reduce the incidence of Chagas disease. It's testable.

News stories:
* Possible explanation for high incidence of Chagas in some Peruvian communities. (B Yirka, Phys.org, June 18, 2015.)
* Guinea pig feasts may explain high rates of deadly parasite in Peru. (L Wade, Science magazine, June 16, 2015.)

The article: Bottlenecks in domestic animal populations can facilitate the emergence of Trypanosoma cruzi, the aetiological agent of Chagas disease. (M Z Levy et al, Proceedings of the Royal Society B 282:20142807, July 2015.)

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

More about guinea pigs:
* Why don't black African mosquitoes bite humans? (December 19, 2014).
* and maybe Golden rice as a source of vitamin A: a clinical trial and a controversy (November 2, 2012).

Hydrogen sulfide and superconductivity -- update

September 12, 2015

Original post: What's the connection: rotten eggs and high-temperature superconductivity? (June 8, 2015). On July 15, we added a brief note at the end, with some new information.

Briefly, the story is that hydrogen sulfide has been shown to act as an electrical superconductor at higher temperatures than found previously for any substance. It seems likely that the actual superconducting material is not H₂S itself, but a reaction product under the high pressures used, likely H₃S.

The work has generated much excitement, but so far all we have had are preprints posted at ArXiv. We now have a formally published article. The more recent article posted at ArXiv, noted in the July 15 addendum, has now been published in Nature. There is no new content, but the news stories are new. The one from Nature News notes the very limited independent replication of the work so far, based on informal inquiry of those likely to be able to do so. I should add that the information on this point here is somewhat different from what the same author said in his previous news story. A caution to keep in mind.

I am listing the new items here, but will also add them to the original post as another addendum. Remember, if you cannot access the Nature article, the versions posted at ArXiv are freely available. The news stories in Nature are freely available; they link to the ArXiv items.

News stories:
* New temperature record: Hydrogen sulfide becomes superconductive under high pressure at minus 70 degrees Celsius. (Phys.org, August 18, 2015.)
* Superconductivity record sparks wave of follow-up physics. (E Cartlidge, Nature News, August 17, 2015.) Includes a useful list of references to the related articles.

* News story accompanying the article: Superconductivity: Extraordinarily conventional. (I I Mazin, Nature 525:40, September 3, 2015.)
* The article: Conventional superconductivity at 203 kelvin at high pressures in the sulfur hydride system. (A P Drozdov et al, Nature 525:73, September 3, 2015.)

On genome duplications

September 10, 2015

When the genome of the common yeast, Saccharomyces cerevisiae, was sequenced, it was found that some parts of the genome appeared double. Somewhere along the line, the genome apparently had undergone a complete duplication. In fact, such "whole genome duplications" are found in diverse organisms, including vertebrates. It's a "quick" way to get more genes; the extra copies are free to take on new functions, or to get lost.

How does genome duplication occur? In general we don't know, but two scenarios are plausible...
1) The genome, literally, doubled, because of some unusual cell division event. (Remember, genome duplication occurs during every cell cycle. But genome duplication is quickly followed by cell division, restoring the original genome in each cell.)
2) Two organisms with similar genomes hybridized, and for some reason ended up forming a new organism with a combined, doubled genome.

In neither case do we understand why the event might have happened; both scenarios involve some unusual event.

So, which was it? As you might imagine, we have no direct evidence on the matter. For reasons that aren't very important, scenario 1 has become widely accepted.

A new article now provides evidence for scenario 2. It's based on an interesting prediction about the consequences of the scenarios.

Consider the initial cell of the new organism with the expanded genome. There is an interesting difference in its genetics under those two scenarios. In scenario 1, the duplication leads to a cell with two identical copies of everything. In scenario 2, the fusion leads to a cell with two similar copies of things, but no specific prediction beyond that. That is, in scenario 2, the two genomes are merely "similar", but how similar depends on the details.

Why do they have to be "similar"? Because the two genomes seem to be compatible enough to form a viable hybrid. You don't buy that? That's fine. Maybe they don't have to be so similar. That doesn't change the basic idea; in fact, it expands the range of possibilities.

What's the new evidence? Detailed analysis of duplicated genes in yeast suggests that the genes are older than the organism. That is, the genes had already diverged when the duplication occurred. That's consistent with scenario 2, but not scenario 1.

How strong is the data? Well, people will quibble about that. Estimates of age from genetic data often have huge uncertainties. Perhaps what this article does is to make us re-examine scenario 2.

Scenario 2 has an interesting "advantage". Since the initial organism with the duplicated genomes has gene sets that have already diverged, there really are (or, at least, may be) new genes when the hybrid forms. If they are beneficial to the organism, they could show their benefit right away. In scenario 1, the gene sets are identical at the time of genome expansion; any benefit would come later. It's important to note that this argument proves nothing. It certainly does not prove what happened. It simply notes a difference in how the two scenarios could play out.

Does the argument apply to other genome duplications? That must remain an open question, pending some data. There is nothing that precludes both scenarios from operating.

News stories:
* In a Rethink of Yeast's Double Genome, Ancient Mating Is an Idea on the Rise. (GEN, August 10, 2015. Now archived.)
* Studying yeast provides new insight to genome evolution. (Centre for Genomic Regulation (CRG), Barcelona, August 7, 2015.) From the lead institution. The page links to a press release that is available in English, Spanish, and Catalan.

* News story accompanying the article. It is freely available: Origin of the Yeast Whole-Genome Duplication. (K H Wolfe, PLoS Biology 13(8):e1002221, August 7, 2015.) Good overview of the work and its implications. If you want more than the news stories, give this a try, even if you skip some of the more technical parts.
* The article, which is freely available: Beyond the Whole-Genome Duplication: Phylogenetic Evidence for an Ancient Interspecies Hybridization in the Baker's Yeast Lineage. (M Marcet-Houben & T Gabaldón, PLoS Biology 13(8):e1002220, August 7, 2015.)

A post that notes the issue of genome duplications: Who is #1: the most DNA? (March 7, 2011).

* Previous post about yeast:
Do human genes function in yeast? Yeast-human hybrids. (August 21, 2015).
* Next: How to confuse a yeast -- a sensory illusion (January 15, 2016).

More ascomycetes... Penidiella and dysprosium (September 11, 2015). This is the post immediately above.

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.

After Ebola, what next? and how will we react?

September 5, 2015

The West Africa Ebola outbreak seems to be winding down. It's not over, and we're not sure where virus is hiding, but the current case count is tiny. Liberia has just been declared Ebola-free -- for the second time. Mop-up will continue, but it is a time for optimism.

It has been the worst Ebola outbreak in recorded history. It was enhanced by being in an area with no previous experience with the disease, and with a higher population density than in previous outbreaks. Response was slow, both locally and from the international community.

What have we learned? What will we do in the next disease outbreak?

Next outbreak of what? That is the first interesting question, and one that we cannot answer. The Ebola outbreak took us by surprise; the next disease outbreak probably will, too. If the same outbreak occurred again, we would deal with it much better, because of the experience, and the additional tools such as the new vaccine. But we don't know what or where the next disease outbreak will be. We can only make a list of candidates, at least candidates that we know about. We can prepare for some of them. We can also make generic plans for how to deal with outbreaks that catch us by surprise -- as they surely will. How do deal with them quickly.

A recent issue of the journal Nature had a section "Ebola: Did we learn?"; it was featured on the cover. Nature is not alone in addressing these questions, while the waning Ebola is still on our mind. (How quickly will we forget?) I encourage you to look over the section.

Here is one of the stories in that feature section, perhaps the central one on the theme of learning and preparing. You can browse the table of contents of the issue for more. All are freely available, I think.
* The next time: The world is ill-prepared for the next epidemic or pandemic. But the horror of the Ebola outbreak in West Africa may drive change. (D Butler, Nature 524:22, August 6, 2015.)

A recent post on Ebola: An Ebola vaccine: 100% effective? (August 7, 2015).

More: Ebola survivors: are they a risk to others? (June 5, 2016).

A recent post on one of those other diseases that might worry us: In the shadow of Ebola: The story of Lassa virus (August 26, 2015).

One major player...
* WHO: We need to prepare for Disease X (May 13, 2018).
* The role of WHO: the view of its director (December 1, 2015).

There is a section on my page Biotechnology in the News (BITN) -- Other topics for Ebola and Marburg (and Lassa). That section links to related Musings posts, and to good sources of information and news. There is also a section there on Emerging diseases (general).

Effect of artificial lighting on the environment

September 3, 2015

Sometimes we express concern that human activity affects "nature". For example, there is concern that use of underwater sonar may affect marine animals, such as whales.

Have you ever thought about how artificial lighting affects other animals? Does the lighting in a harbor affect the animals in the water? A new article reports that it does.

The scientists developed a controlled test, though it was done in a natural environment (Menai Strait, UK). They put standard surfaces under the water at a particular position. They provided controlled lighting, at levels similar to what is found in well-lit harbor areas. After a period of time, they examined the surfaces. Depending on the organism, the scientists either counted the number of organisms attached or the surface area that was covered by attached organisms. They examined a variety of invertebrates.

Here is a sample of what they found...

Conclusion: artificial lighting may affect how marine invertebrates attach to underwater surfaces. The effect may be in either direction, depending on the animal.

That general conclusion should not be a surprise. It is well known that many of these organisms are affected by light. Now it is documented, in the context of artificial lighting. Further, the test system can be the basis for further work, perhaps testing the effect of suggested changes in lighting procedures.

An interesting comment in the article is that LED lighting may be a particular concern. It has a wider spectrum that lights commonly used before. Further, the lower energy consumption may encourage additional lighting.

So... Do we light the bridge because it improves traffic safety? because it looks pretty?

News stories. They include some discussion of the possible consequences.
* Harbour light 'attracts ship-damaging creatures'. (R Morelle, BBC, April 29, 2015.)
* Coastal light pollution disturbs marine animals, new study shows. (Science Daily, April 29, 2015.)

The article: Night-time lighting alters the composition of marine epifaunal communities. (T W Davies et al, Biology Letters 11:20150080, April 2015.)

A post about the effect of sonar on whales: Effect of simulated sonar on whale behavior (March 16, 2014).

A post about a possible use of underwater lighting: Why might it be good to put lights on fish nets? (September 9, 2013).

A post that raises the issue of the effect of lighting on us: Does it matter when you eat? Or whether you leave a light on at night? (December 1, 2010). Use of artificial lighting may affect humans, too. It disturbs our natural circadian rhythm. The implications are not clear, but are of concern to some. (Artificial lighting is a serious problem for astronomers, because they depend on a dark sky for some of their observations.)

Posts about lights include:
* Effect of LED street lights on insects (September 4, 2021).
* How to light a cave (August 30, 2021).
* CFL and LED lights: energy-efficient, but toxic (March 3, 2013). The current work used LED lights. They chose that in part because they considered it the most likely lighting type for the future.

Light pollution... A world atlas of darkness (July 29, 2016).

More on pollution: Deaths from air pollution: a global view (October 23, 2015).

My page of Introductory Chemistry Internet resources includes a section on Lighting: halogen lamps, etc.