Briefly noted...

December 11, 2019

1. Visitors from beyond the solar system. Two years ago, 1I/'Oumuamua. A mysterious object, it looked to some like a flying cigar; some wondered if it carried surveillance equipment. Astronomers got just a glimpse of it as it left the solar system. Now, 2I/Borisov. At least, it looks like a comet, and -- having been noticed early -- it will be the subject of much scrutiny. A short news feature reflects on these I-things -- the first major visitors to the solar system from beyond, at least in the age of modern astronomy. (The new I catalog... The I in the designation means interstellar.)
* News feature: How two intruders from interstellar space are upending astronomy. (A Witze, Nature News, November 20, 2019. In print Nature 575:434, November 21, 2019)
* Added May 15, 2023. Also see: Briefly noted... A hydrogen-powered comet? (May 15, 2023).

2. A new 1980s-quality computer. It doesn't use silicon transistors. It is based entirely on CNT (carbon nanotube) transistors. The current article represents major progress in making a functional computer based on CNTs. The future? We'll just have to wait, but some think CNTs could be the way to go.
* News story: A Carbon Nanotube Microprocessor Mature Enough to Say Hello -- Three new breakthroughs make commercial nanotube processors possible. (S K Moore, IEEE Spectrum, August 28, 2019.) Links to the article. (The three brekthroughs are RINSE, DREAM, and MIXED.)
* This item is noted on my page Introduction to Organic and Biochemistry -- Internet resources in the section on Aromatic compounds. The section includes graphene and CNT.
* Added June 20, 2023. Also see: Wooden transistors (June 20, 2023).

3. Vaccine against African swine fever (ASF). ASF is a viral disease that has recently become of serious economic importance. We now have a preprint reporting a vaccine that is highly effective against the major strain in current Eurasian outbreaks. I suggest reading the abstract and introduction for an overview.
* Here is the preprint, which is freely available: Development of a highly effective African swine fever virus vaccine by deletion of the I177L gene results in sterile immunity against the current epidemic Eurasia strain. (M V Borca et al, BioRxiv, December 2, 2019.)
* I have noted this item on my page Biotechnology in the News (BITN) -- Other topics under Vaccines (general).
* A news story: Sterile immunity possible against ASFv, US scientists say. (V ter Beek, Pig Progress, December 9, 2019.)
* Here is the published article: Development of a Highly Effective African Swine Fever Virus Vaccine by Deletion of the I177L Gene Results in Sterile Immunity against the Current Epidemic Eurasia Strain. (M V Borca et al, Journal of Virology 94:e02017-19, April 2020.)

Turning E. coli into an autotroph (using CO₂ as sole carbon source)

December 9, 2019

The following graph, from a new article, shows something impossible...

Growth on CO₂ as the sole carbon source -- a phenomenon called autotrophy -- is typical of plants. There are some autotrophic bacteria, but E coli is not one of them. At least, it wasn't one of them until now. The new article reports modifying E coli to make it autotrophic; the green growth curve shown above shows the result.

Growth on organic materials, as typical of animals and ordinary E coli, is called heterotrophy.

Autotrophic growth requires an energy source. (Ordinary E coli use sugar both for making cell mass and for energy. But CO₂ is not an energy source.) For plants, the energy source is light. Autotrophic bacteria use various energy sources; some use light (photoautotrophs), others oxidize some chemical, such as hydrogen gas or Fe²⁺ ions, as an energy source (chemoautotrophs).

What is the energy source for the autotrophic E coli? Formic acid (HCOOH). But doesn't that count as a C-source? No, because the bacteria have been designed so that the formic acid is used only for energy, and none of its C enters into making cell mass.

The following figure shows the idea of how this bacterial strain is designed...

Now go back to the top graph... The dashed line there shows the utilization of formate (right-hand y-axis).

What does it take to make E coli autotrophic? The idea is to install a complete system for CO₂ fixation, including Rubisco and a functioning Calvin-Benson cycle in the bacteria, just as in plants. The scientists knew which enzymes are in the normal E coli and which were needed. It's a logically straightforward (but technically complex) project to add the genes for the missing enzymes. Lab evolution then helped get it right; that is a major emphasis of the article.

What is the point of all this? For now, it is just a demonstration. They did it to see if they could. The strain grows rather slowly on CO₂, and actually releases more CO₂ (from the formate) than it consumes, so it is not suitable for using up CO₂. If you read things that suggest a use for such a strain, it is speculation at this point (as the authors are well aware). But it is an autotrophic Escherichia coli -- the first success at turning a heterotroph into an autotroph.

News stories:
* Lab-Evolved E. coli Consume Carbon Dioxide -- Bacteria that take in inorganic carbon could have applications in sustainable biofuels. (E Makowski, The Scientist, November 27, 2019.) Now archived.
* Laboratory-evolved bacteria switch to consuming carbon dioxide for growth. (Science Daily (Cell Press), November 27, 2019.)

The article, which is freely available: Conversion of Escherichia coli to Generate All Biomass Carbon from CO₂. (S Gleizer et al, Cell 179:1255, November 27, 2019.) Much of the article is very readable, discussing the issues, strategies, and limitations.

A few days ago, a preprint appeared reporting similar work in a yeast. Energy was based on oxidation of methanol (which proceeds via formate). The preprint is freely available: A synthetic Calvin cycle enables autotrophic growth in yeast. (T Gassler et al, BioRxiv, December 3, 2019.)
* The article has been published: The industrial yeast Pichia pastoris is converted from a heterotroph into an autotroph capable of growth on CO₂. (T Gassler et al, Nature Biotechnology 38:210, February 2020.)

* * * * *

More about chemoautotrophic bacteria:
* Growing on manganese ions as an energy source (September 15, 2020).
* Is photosynthesis the ultimate source of primary production in the food chain? (April 2, 2017).

More about the Calvin-Benson cycle for CO₂ fixation: Discovering how CO₂ is captured during photosynthesis: The Andy Benson story (June 15, 2013).

Also see... A novel enzymatic pathway for carbon dioxide fixation (March 12, 2017).

Briefly noted...

December 4, 2019

1. Quality of animal research. A short news-feature-type story about developments in the use of animals in medical research.
* Freely available... Fixing the Flaws in Animal Research -- Many preclinical studies carried out in vivo are poorly designed and generate irreproducible data, but efforts to address the problem are on the rise. (D Kwon, The Scientist, September 1, 2019. In print, with a slightly different title: p 63 of the September issue.) Now archived.
* One of the scientists discussed in this story is Thomas Hartung. He was the lead scientist behind the work described in the post Predicting the toxicity of chemicals (September 11, 2018). That work is noted in the current article.

2. Lesson from a comet: a new way to make oxygen gas? Throw something at a wall hard enough, and it may break. For example, throw a molecule of CO₂ at a wall, and it may break into pieces, such as CO + O. Occasionally, a CO₂ molecule may be bent enough that it forms a cyclic version of CO₂, which then breaks into C + O₂. The story starts with the unexpected finding of O₂ on a comet, as the Rosetta spacecraft studied Comet 67P/Churyumov-Gerasimenko. Why would there be O₂ on a comet? It was suggested that the O₂ may be produced by collision of CO₂ molecules with the comet surface. That led to lab work to show such a reaction, along with theoretical studies of what is happening. It works. Not very well, but it is a first step.
* News story: Comet-inspired reactor could create oxygen for astronauts. (J Strickler, ZME Science, May 29, 2019.) Links to the article, which is freely available.
* A post about the approach of Rosetta to Comet 67P... Twins? A ducky? Spacecraft may soon be able to tell (August 4, 2014).

Health care: Can the computer give racially biased advice?

November 30, 2019

It sure can. For example, what if you trained the computer on a set of data that was racially biased?

A recent article explores the issue, not with hypotheticals, but with an example of a major program used to guide medical care in the United States.

The following graph shows the basic finding...

That is, for a given risk score, blacks are sicker than whites. But they are treated by their score, not by how sick they are. The computer has discriminated by race.

The article contains analyses comparing blacks and whites for several specific conditions; the general pattern holds. For example, for any specific risk score, blacks have higher blood pressure than do whites.

Why does this happen? Why does the computer discriminate by race?

The authors look into the origin of the algorithm, and find that it is based on health care costs paid in the past, not on medical status. For various reasons, blacks have historically spent less on health care, for any specific condition. The computer bases the patient's risk score on their previous medical costs (from insurance records), not medical condition. But previous costs do not properly measure medical condition, when applied across races; therefore, the computer program is racially biased, providing a lower standard of care to blacks for the same medical condition. (The computer does not record race per se.)

Study of the algorithm began when the scientists noticed that black patients seemed to have worse outcomes than white patients with the same risk score.

The article shows that treatment costs for the coming year are about equal for blacks and whites, for any given risk score (Figure 3A). This reinforces that the computer is predicting costs, not medical outcomes.

After the basic study was completed, the authors initiated contact with the company that wrote the algorithm. The company is collaborating with the authors to address the issues raised here. See the Discussion section of the article and also the Competing interests section of the Acknowledgments for more about the relationship.

News stories:
* How computer algorithms help spread racial bias in US healthcare, and how they can help fix it. (Tech Xplore (A Khan, Los Angeles Times), October 25, 2019.)
* Widely used health care prediction algorithm biased against black people. (K Manke, University of California Berkeley, October 24, 2019.) From one of the institutions carrying out the study.

* News story accompanying the article: Social science: Assessing risk, automating racism -- A health care algorithm reflects underlying racial bias in society. (R Benjamin, Science 366:421, October 25, 2019.)
* The article: Dissecting racial bias in an algorithm used to manage the health of populations. (Z Obermeyer et al, Science 366:447, October 25, 2019.)

Among earlier posts on health care: Healthcare costs (June 18, 2009). Links to more.

Also see: Identifying individuals from their genomes: a controversy (December 5, 2017).

Fracking by mice

November 18, 2019

Musings has discussed fracking in several posts. It can be a controversial topic.

A new article reports that fracking is a normal part of life for mice. By extension, that probably holds for all mammals.

The term fracking is short for hydraulic fracturing. It involves the use of fluid pressure to break a structure. That structure might be a rock formation that is trapping oil or gas. Or it might be a cluster of cells in an early embryo.

Caution... The article discussed here is rather difficult. We have a bit of wordplay to strike up interest, and the biological problem addressed is interesting and important for understanding development. But the actual work, by a team of biologists and physicists, is complicated. If we can open up the idea of what this is about, that is fine for now.

The following figures show the role of fracking in the development of a mouse. The first is a diagram, with an overview. The second is an example of the experimental results from the article.

The diagram...

Some results...

That's an idea of what happens. Microlumens arise between cells in the early embryo. The microlumens effectively coalesce into one large lumen, the blastocoel, as fluids follow paths of low resistance. With the physicists and biologists collaborating, the team hypothesizes that the process of development of lumens, including coalescence, involves fluid pressure, arising from osmotic forces. That story of lumen life cycles is new to most biologists, but a well-understood process to physicists.

There is much more to be done to understand all the details, but the current article has given us a new perspective... A key step in the development of the mouse body (and presumably the body of any mammal) is a physical fracture -- mediated by fluid pressure.

News stories:
* Controlled hydraulic fracturing sculpts mammalian embryos into shape. (A Williamson, Phys.org, August 15, 2019.)
* Inflate your embryo. (M Le Verge-Serandour, The Node, September 17, 2019.) A short version of the story from one of the authors of the article.

* News story accompanying the article: Development: Embryonic self-fracking -- Mammalian embryos use controlled hydraulic fracturing to sculpt their shape. (M Arroyo & X Trepat, Science 365:442, August 2, 2019.) Excellent.
* The article: Hydraulic fracturing and active coarsening position the lumen of the mouse blastocyst. (J G Dumortier et al, Science 365:465, August 2, 2019.)

Previous post about fracking: Fracking and earthquakes: It's injection near the basement that matters (April 22, 2018).

Previous post about mice: Cats, fats, and Toxoplasma. And mice. (October 21, 2019).

Briefly noted...

November 13, 2019

1. The effect of space travel on humans: a study of identical twins. We need to learn more about the effects of space travel on humans. Of course, we collect much data, but how can we compare data from people in space with unrelated people who didn't go into space? The ideal answer is obvious, and NASA had a chance to do it, with the identical twin astronauts Scott and Mark Kelly. It's an interesting story, though going through the details of what was found is probably more than most people want. At least, look over the news story, which is by an expert biologist.
* News story: NASA twins study highlights key risks for long-term space travel: Cosmic rays and microgravity. (R Lewis, Genetic Literacy Project, April 16, 2019.) Links to the article.
* Related:
- Fidelity of DNA replication in micro-gravity (January 11, 2022).
- Which direction does blood flow in an astronaut? (January 7, 2020).

2. Beware the magnetic stir bar. They are called stir bars, not catalysis bars. But what if they are not clean? A recent article explores the problem, and shows that stir bars can easily accumulate enough firmly-bound contaminants to affect reactions. Routine cleaning is not sufficient to decontaminate them. Those who use stir bars should read the article behind this post. For others, it is a fun story.
* News story: Stir bar contamination may inadvertently catalyze reactions -- Traces of metal nanoparticles embedded in used magnetic stirrers can interfere with chemical reactions. (M Peplow, C&EN (Chemical & Engineering News), March 28, 2019.) Links to the article.
* The article: Phantom Reactivity in Organic and Catalytic Reactions as a Consequence of Microscale Destruction and Contamination-Trapping Effects of Magnetic Stir Bars. (Evgeniy O Pentsak et al, ACS Catalysis 9:3070, April 5, 2019.)

3. E-cigarettes and the issue of vitamin E acetate. This has been a big news story in recent days, so I will note the article here. It is very short and readable. Briefly, the scientists found vitamin E acetate in the lungs of people with damage from e-cigarettes, but they have no direct evidence at this point of a causal link. That chemical is one of several that have been under suspicion. As so often, this is science in progress.
* The article, which is freely available: Evaluation of Bronchoalveolar Lavage Fluid from Patients in an Outbreak of E-cigarette, or Vaping, Product Use - Associated Lung Injury -- 10 States, August-October 2019. (B C Blount et al, Morbidity and Mortality Weekly Report (MMWR) 68:1041, November 15, 2019.)

A half-millennium record of climate change, from the grapes of Burgundy

November 9, 2019

The grape harvest was early in Beaune, in the Burgundy region of France, in 1393. In fact, 1393, 1413, and 1420 stand out in the historical record for having early grape harvests in the century from 1350-1450. That was, we might suspect, due to unusually warm weather those years.

Those comments are based on a new article about climate change. It offers some insight into French climate history. It's a particularly interesting story because of the data source.

Look...

Where did this record of grape harvest days (GHD) come from? From the records in Beaune, where GHD is an officially-established event. But as we cautioned above, it is not simple. The GHD records are well known, but have been incorrectly presented over the ages. The current work involved critical analysis of a variety of sources, including many original (contemporaneous) sources, and getting the best information possible for the GHD. Much of the article is about building the data set, and includes discussion of the uncertainties that remain. It is a work of historical scholarship.

We suggested that the grape harvest might be related to temperature. Data? Here it is....

So this graph establishes that there is a good correlation between the local temperature and when the grapes are harvested. There is no T record back to 1350, but there is a record of when the grapes were harvested (to be picky, back to 1354). That grape harvest record, along with the correlation, allows us to estimate what the T was in the summer of 1393 in Burgundy.

Back to the top graph for a moment. As we noted, the top 5% of the points are labeled -- the earliest grape harvests. Visual inspection shows that the frequency of early harvests has varied over the centuries. For example, they were uncommon during the 1800s, a time associated with low T. More recently, there is a different pattern.

News stories; both contain good pictures.
* French wine grape records show accelerated warming over the past 30 year. (R Arthur, Beverage Daily, September 2, 2019.)
* Burgundy wine grapes tell climate story, show warming accelerated in past 30 years. (European Geosciences Union, August 29, 2019.) From the journal publisher. Note some pictures at the very bottom of the page, showing original archival data; one is from 1385.

The article, which is freely available: The longest homogeneous series of grape harvest dates, Beaune 1354-2018, and its significance for the understanding of past and present climate. (T Labbé et al, Climate of the Past, 15:1485, August 29, 2019.) From the University of Burgundy, among other places. One affiliation there is to the Institut Universitaire de la Vigne et du Vin; put that into Google with the word translate, if you need to. It's a generally readable article, with much interesting historical discussion.

Among wine-related posts...
* Improved ostracon analysis reveals 2600-year-old request for wine (July 23, 2017).
* Some shrimp in your wine? (August 27, 2016).

More grapevines:
* What do we learn from the sulfur isotopes in the California vineyards? (June 28, 2022).
* Acne, grapevines, and Frank Zappa (August 1, 2014).

Also see: What happens when the cork is removed from a bottle of champagne? (October 27, 2019). Another post where I noted the author affiliations, also from the French wine country.

Brain development: comparing human and chimpanzee lab-grown brain organoids

November 5, 2019

Organoids. Pieces of organ-like tissue grown in the lab. Typically, from iPSC (induced pluripotent stem cells), differentiated in the lab to develop into something like primitive lab-grown organs. Organoids let us study how organs develop, under controlled lab conditions.

Cerebral organoids. A fancy term for brain organoids. Pieces of brain tissue differentiated and grown in the lab. Interesting stuff.

And now... A team of scientists reports growing monkey, chimp, and human brain organoids in the lab -- and comparing them.

The answer? They are different.

This article may be of interest simply because they did it. That's true with a lot of work on organoids, especially brain organoids. It's early days in the field. We're going to learn a lot from organoids. We may even find them useful as biological materials (e.g., for transplantation). But for now, we're just stepping in -- and that in itself is interesting.

The article is crammed with data. But don't expect a big answer; it's too early for that.

Here are a couple of graphs, comparing brain organoids from three primates...

That's about it, for now. We are beginning to compare the development of brain tissue for humans and other primates under controlled lab conditions. The work makes use of the recent technologies of iPSC, organoid development, and nucleic acid sequencing. The authors use terms such as "gene-expression atlas" to denote that they have provided a chunk of data that underlies further work. Inevitably, such work will lead to better understanding of what make us human.

News stories:
* How human brain development diverged from that of great apes -- Cell atlas of great ape forebrain development illuminates dynamic gene-regulatory features that are unique to humans. (ScienceDaily (Max Planck Institute for Evolutionary Anthropology), October 16, 2019.)
* Human 'mini-brains' slow at developing among primates. (P Ghosh, BBC, October 16, 2019.)

The article: Organoid single-cell genomic atlas uncovers human-specific features of brain development. (S Kanton et al, Nature 574:418, October 17, 2019.)

An early post on brain organoids: Artificial brain-like structures grown from human stem cells in the lab (October 1, 2013). Links to more.

More... Briefly noted... Brain organoids grow eye precursor structures (March 2, 2022).

More about brains is on my page Biotechnology in the News (BITN) -- Other topics under Brain. There is a list of related Musings posts.

More organoids: Snake venom gland organoids (March 17, 2020).

My page Biotechnology in the News (BITN) for Cloning and stem cells includes an extensive list of related Musings posts.

The microbiome of babies born by C-section

November 2, 2019

Over recent years, we have developed some general ideas about the human gut microbiome...
- It is important for good health.
- It is first acquired during birth.
- Babies born by cesarean section ("C-section"), bypassing normal birth, have normal health.

Those three points do not fit together well. One can imagine what the missing pieces might be, but data are limited.

A new article provides perhaps the most comprehensive comparison yet of the microbiomes of babies born by normal vaginal birth and by cesarean section. It focuses on the first three weeks after birth, the "neonatal" period. It is an early report from the Baby Biome Project.

The following figure provides a useful visual summary of some of the major findings...

So, C-section babies have different gut microbiomes, though the difference declines substantially over the first few weeks and months. C-section babies get more of their early gut microbiome from "the environment", which, of course, is variable.

The testing also included the mother. For vaginal births, a baby's gut microbiome most closely corresponds to that of the mother's microbiome of the gut -- not the vagina.

For C-section births, many sources may contribute -- including the hospital environment.

Many questions remain. Perhaps most important... Does it matter? The authors do not have any health outcomes to report here. However, they can comment on the general reputation of some of the bacterial groups found. The red-coded bacteria, such as Bifidobacterium, are considered important for good health. And some of the blue-coded bacteria are potential pathogens. The patterns suggest that the C-section babies are relatively low in the good bugs and high in the bad bugs. Although the microbiome differences are reduced over time, it is possible that they have an early impact, including their effect on instructing the immune system.

The scientists will continue to follow these kids, even into adulthood.

News stories:
* Microbiome Affected by Babies' Delivery Method, but Long-Term Effects Remain Unknown. (GEN, September 19, 2019.)
* Babies born by C-section have different gut bacteria. (Neuroscience News (University College London), September 21, 2019.)

The article: Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth. (Y Shao et al, Nature 574:117, October 3, 2019.)

The analysis also indicates significant effects of antibiotics given to the mother prior to the birth and of early breastfeeding in affecting the early gut microbiome. Those points are noted, but are smaller effects, and are not the focus of the current article.

* * * * *

The final half-paragraph of the article (with reference links omitted): The disrupted transmission of the maternal gastrointestinal bacteria (particularly pioneering Bacteroides species) through delivery by caesarean section and maternal intrapartum antibiotic prophylaxis predisposed newborn babies to colonization by clinically important opportunistic pathogens that circulate in the hospital environment. However, the clinical consequences of the perturbations of early-life microbiota and the carriage of immunogenic pathogens during this critical window of immune development remain to be determined. This highlights the need for large-scale, long-term cohort studies that also sample home births to better understand the consequence of the perinatal factors in hospital birth and establish whether perturbation of the neonatal microbiota negatively affects health outcomes in childhood and later life.

* * * * *

A previous post on the topic: Your gut bacteria: where do you get them? (July 30, 2010). The article of that earlier post is reference 1 of the current post.

More on C-sections: The rising rate of caesarean section births: an intriguing correlation (April 15, 2019).

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.

A lithium-ion battery that might be good for a million miles?

October 29, 2019

A recent article makes a bold claim: a lithium-ion battery that could last for a million miles (1.6 million kilometers) of car use.

The specifics there are a little arbitrary, but the scientists have data. The following figure is a bottom-line comparison of their new battery with a common reference battery...

Battery performance depends both on the chemistry and on the physical structure. The work here is done with batteries called NMC532/AG. That stands for LiNi_0.5Mn_0.3Co_0.2O₂/artificial graphite, with large single crystal NMC. These are batteries that have been extensively studied in the authors' lab. (Note that the letters and numbers in the name represent the composition.)

They discuss some of the failure modes for such batteries, and point to specific improvements they have made. However, they also acknowledge that they have no information about some failure modes, more characteristic of larger scale batteries.

There is much discussion of electrolytes, with their pro and con features -- and trade-offs. This is a complicated issue, which we won't go into here.

The million-mile claim? Charging cycles (under specified conditions) is a clear measure of battery lifetime. But then the authors add some assumptions, for perspective. They make assumptions about the usage level of the battery, in charging cycles per day and miles driven per day. That allows them to put forward estimates of battery lifetime in other terms, ones that people can relate to. The million-mile claim is of that type. The data shown in the figure above is real data. (The million-mile claim would represent about a doubling of battery life over what is now available.)

Another major application for such batteries is grid energy storage. The authors estimate a 20-year lifetime for their batteries in such use.

The article is provocative -- openly so. But it contains much data showing the improvements in the new battery, and explanations of how they did it. As always, one article does not a truth make. We'll see over time whether the work reported here leads to practical improvements -- ones that can be implemented at a large scale and economically. (We'll leave it to the news stories to speculate exactly where Tesla is on this development curve.) The authors challenge the community to implement what they have done, and to exceed their performance results. They suggest that their battery should be the reference standard for now.

News stories:
* Million-mile battery unveiled by ground-breaking research. (Tech Xplore (S Davies, Institute of Physics), September 27, 2019.)
* Tesla May Soon Have a Battery That Can Last a Million Miles -- Elon Musk promised Tesla would soon have a million-mile battery, more than double what drivers can expect today. A new paper suggests he wasn't exaggerating. (D Oberhaus, Wired, September 23, 2019.) Includes discussion of the relationship between the university lab (Dalhousie) behind this work and Tesla.

The article, which is freely available: A Wide Range of Testing Results on an Excellent Lithium-Ion Cell Chemistry to be used as Benchmarks for New Battery Technologies. (J E Harlow et al, Journal of The Electrochemical Society 166:A3031, September 6, 2019.) The article acknowledges the financial support of Tesla.

A post about improving lithium-ion batteries: Making lithium-ion batteries more elastic (October 10, 2017).

More... Briefly noted... Electronic structure of lithium atoms (March 8, 2022).

Among many posts about batteries... Using the walls of a building as a rechargeable battery? (May 24, 2021).

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

Spontaneous formation of hydrogen peroxide from water

October 26, 2019

Is hydrogen peroxide (H₂O₂) made spontaneously in a bottle of water (H₂O)?

If so, would we expect the reaction to be dependent on the oxygen (O₂) in the air?

What if the water was aerosolized (turned into tiny droplets)?

And why am I asking these questions? That one is easy. A new article forces them on us.

Let's look at some results from the article...

Formation of the chemical that fluoresces green in the droplets indicates that the aerosolized water made H₂O₂. That peroxide oxidized the added chemical to produce the fluorescent product, which was observed.

The next figure shows the effect of droplet size...

Droplets matter. The smaller the better.

What about the need for molecular oxygen? Look...

On the basis of evidence such as presented above, the authors suggest that water can spontaneously make some hydrogen peroxide. The process requires tiny droplets, and does not require molecular oxygen.

It is an intriguing result, and quite unexpected. (How did they find it? It came up accidentally during other work on chemistry in microdroplets.)

The authors speculate how the peroxide is made. They note that the intense electric field at the surface of a tiny -- and highly curved -- droplet is strong enough to cause a hydroxide ion, OH^-, to lose an electron. That leads to making the hydroxyl radical (OH). Two hydroxyl radicals can then join to make HOOH -- hydrogen peroxide. They have no direct evidence for this proposed mechanism, but it seems most likely for now.

If this holds up, it could be useful. H₂O₂ is useful in industrial processes. However, its synthesis is not fully satisfactory. The process described here is simple, inexpensive, and environmentally friendly. It produces only a low concentration of H₂O₂, but for many uses that is fine.

News stories:
* Water surprise: microdroplets have potential to produce hydrogen peroxide. (R Trager, Chemistry World, September 11, 2019.)
* In a Totally Unexpected Finding, Water Has Spontaneously Produced Hydrogen Peroxide. (P Dockrill, Science Alert, September 1, 2019.)

* News story accompanying the article: Production of hydrogen peroxide enabled by microdroplets. (C Zhu & J S Francisco, PNAS 116:19222, September 24, 2019.)
* The article: Spontaneous generation of hydrogen peroxide from aqueous microdroplets. (J K Lee et al, PNAS 116:19294, September 24, 2019.)

More about droplets affecting chemical reactions:
* The role of tiny droplets in driving unfavorable reactions -- such as those needed to get life started (January 17, 2023).
* Speeding up a chemical reaction by dividing up the container (February 28, 2014).

Other posts involving the exotic hydroxyl radical include...
* Interaction of pollution sources: Can the whole be less than the sum of the parts? (March 9, 2019).
* Nuclear-powered bacteria: suitable for Europa? (March 27, 2018).

Also see: Speech droplets: Can you transmit an infection to someone by yelling "Stay healthy" at them? (June 14, 2020).

Harvesting water from "dry" air -- an update

October 22, 2019

Two years ago, Musings reported on the development of a chemical that could be useful for harvesting drinkable water from "dry" air (that is, at low humidity) [link at the end]. It was a significant development, but the productivity was still too low for practical use. A new article reports a ten-fold improvement in productivity.

The new article reports an actual installation in a real-world desert (in California), with three days of continuous operation. Importantly, they collected the water from the chemical several times per day, rather than once a day, as done earlier.

The general idea is that the chemical collector binds water from the air. From time to time, the collector is heated, which drives the water off. The water is harvested, and the collector is ready for another round. This basic idea was presented in the background post, which I suggest you read again along with this one.

To allow water to be harvested from the collector chemical at any time of day, the new device includes a solar panel and a battery, to provide energy. The energy can also be used to run fans, which facilitate air movement through the collection device.

The following figure shows some data -- and some pictures.

The type of chemical used here as a collector is, as before, a MOF, or metal-organic framework. The current device uses a new MOF, which operates better than the previous one and is cheaper. In developing MOFs, attention has shifted some from the capacity to the speed of the exchange reactions. That is important for doing multiple cycles per day, as in the current work.

This real-world trial produced water at about ten times higher productivity than the previous device. Economics is complex. The article does not discuss the economics, but the authors are moving toward commercialization, as discussed in the news stories.

News stories:
* Water harvester makes it easy to drink water from thin air. (R Sanders, University of California Berkeley, August 29, 2019.) From the lead institution.
* Crystalline nets harvest water from desert air, turn carbon dioxide into liquid fuel. (R F Service, Science, September 3, 2019.) This story focuses on the current article, but includes some other things. (The two parts of the title are about two unrelated projects.) The general theme is the use of MOFs.

The article, which is freely available: Rapid Cycling and Exceptional Yield in a Metal-Organic Framework Water Harvester. (N Hanikel et al, ACS Central Science 5:1625, October 23, 2019.)

Background post: Harvesting water from "dry" air (July 1, 2017).

Next MOF post... Capturing NO₂ from polluted exhausts (December 7, 2019).

Using ultrasound to recharge an implanted medical device

October 19, 2019

Consider a medical implant, such as a pacemaker. How do we get power to it? A recent article explores a new possibility: it uses ultrasound to transfer energy across the intact skin into the body, and a triboelectric generator implanted under the skin to change the form of the energy from sound to electricity.

What's a triboelectric generator? It's a device that converts movement into electricity. It's a well-known type of energy transformation. What's new here is trying to do it within the body.

The work here starts with the development of a generator that can work within the body. It is based on a membrane that vibrates in response to the ultrasound; the vibrations are coupled to electrode materials that generate electricity from the varying contact with the membrane (i.e., from movement).

TEG = triboelectric generator. The authors call their device a VI-TEG, for vibrating and implantable triboelectric generator.

Here are some results to show that the general idea works...

That test shows that one can generate electricity from ultrasound. It is a simple test, without the complications of having living tissue around.

The following figure shows how this might be set up in a person. The actual test here is with a piece of pig tissue (which is similar to human tissue).

It's hard to tell how useful this will be. The numbers are fairly soft at this point, and there is no information about long term performance. For now, it's an interesting approach, worthy of further development. The prospect of being able to charge up a medical implant without breaking the skin provides a strong incentive.

News stories:
* An implantable device that produces energy using ultrasound. (B Yirka, Tech Xplore, August 2, 2019.)
* Ultrasound System to Charge Medical Implants. (Medgadget, August 5, 2019. Now archived.)
* Prof. Sangwoo KIM develops transcutaneous ultrasound energy harvesting using capacitive triboelectric technology. (SKKU News, August 5, 2019.) (SKKU? Sungkyunkwan University.) Includes Figures 1-3, in full, from the article (but without legends).

The article: Transcutaneous ultrasound energy harvesting using capacitive triboelectric technology. (R Hinchet et al, Science 365:491, August 2, 2019.)

A post that includes use of ultrasound as a visualization tool: Unusual twins: neither monozygotic nor dizygotic, but... (March 11, 2019).

More ultrasound: An ultrasound device you can wear (September 17, 2022).

In this post, the abbreviation TE is used for triboelectric. In a recent post, TE was used for thermoelectric. Beware. Both are interesting and somewhat unusual ways to generate electricity, but they are different. The thermoelectric post: An air-conditioner you can wear? (August 19, 2019).

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

An armadillo's distress call

October 15, 2019

Listen... call. (25 seconds; at YouTube.) The video is also posted with the article as supplementary material.

Armadillos are usually silent. However, this species of armadillo is well known to make noise, though the new article is apparently the fist scientific analysis of what that sound is. The animal here is Chaetophractus vellerosus, with the common name screaming hairy armadillo.

And they are solitary. To whom is this animal talking? In the current work, the scientists analyze the acoustic features of the armadillo call. They suggest that the call is typical of distress calls in diverse vertebrates. A distress call may startle a predator. For small predators, that may work. The distress call may also attract attention from others around, who may attack the perpetrator or aid the victim. That is, the distress call has a wide audience; it's not subtle.

An excerpt from the authors' Discussion section (first paragraph)...

The weeping call is a harsh, loud, broadband, and long sound composed of five note types: crying notes, inhaled notes, inhaled sobbing notes, exhaled sobbing notes, and grunt notes. The general arrangement and number of the note types were highly variable between individuals of both sexes; however, some predictable syntactic patterns between successive note types were evident. Crying notes were the most common, distinctive, and loudest sounds in the call, and there were no differences in acoustic parameters among sexes. The acoustic structure, probable lack of sexual dimorphism, and the behavioral contexts in which individuals of the screaming hairy armadillo produced the weeping call (hand-held disturbance and dog trapping) indicate that this is a distress call.

News story: Why the screaming hairy armadillo weeps. (Nature, August 6, 2019.) Very brief, but useful. Features a nice picture of the animal.

The article: The weeping vocalization of the screaming hairy armadillo (Chaetophractus vellerosus), a distress call. (J P Amaya et al, Journal of Mammalogy 100:1427, October 22, 2019.)

Previous post about armadillos: An armadillo the size of a beetle (April 8, 2016). Links to more.

Asian Zika in Africa

October 12, 2019

Zika rose to fame a few years ago when it became associated with microcephaly. That association became clear during a major Zika outbreak in Brazil. The microcephaly association changed the status of Zika. Instead of just being another moderate -- and fairly obscure -- virus infection, it was now a significant cause of disability.

That association was something of a surprise. Though experience with Zika, mainly in Africa, was not extensive, there was no hint of an association with microcephaly.

Further study has revealed that there are two distinct types of Zika strains: Asian strains, which cause microcephaly, and African strains, which do not. Musings has discussed the origin of Asian Zika [link at the end].

Recently, microcephaly that is apparently related to Zika infection has appeared in Africa -- in particular, in Angola and Cape Verde. Why? A new article investigates the matter.

Here is one clue...

It's clear that the Zika recently found in Angola is most closely related to Brazilian Zika. Using best estimates of how fast such viruses change, the scientists calculate that the new Angolan Zika probably split off from Brazilian Zika in 2016.

Here is another clue...

That combination of features makes it plausible that a Zika virus caught a flight from Brazil to Angola, serving to establish a new line of Zika in Africa -- a line that causes microcephaly.

The article actually has very limited data; there is much discussion of what is not known. The conclusions are based on reasonable inference from what has been found so far; confirmation is needed. If the conclusions hold up, the article represents a good example of detecting a new disease (in a particular place) fairly early. Will knowing about it so early help people control the new Zika that has returned to Africa?

News stories:
* Study implicates Asian Zika strain in African microcephaly cases. (L Schnirring, CIDRAP, September 26, 2019.)
* Zika's Asian Genotype Impacting Women in Africa. (D W Hackett, Zika News, September 27, 2019. Now archived.) Also mentions some other recent Zika news.

The article, which is freely available: Emergence of the Asian lineage of Zika virus in Angola: an outbreak investigation. (S C Hill et al, Lancet Infectious Diseases 19:1138, October 2019.)

A background post about the origin of Asian Zika, the kind that causes microcephaly... A recent genetic change that enhanced the neurotoxicity of the Zika virus (December 1, 2017).

Also see: Are non-African Aedes aegypti mosquitoes better at carrying Zika? (January 5, 2021).

Next Zika post: A Zika vaccine test: protection of the developing fetus? (January 24, 2020).

There is a section on my page Biotechnology in the News (BITN) -- Other topics on Zika. It includes a list of Musings post on Zika.

Traumatic brain injury: long term effects?

October 8, 2019

Football. Traumatic brain injury (TBI). The tau protein. Alzheimer's disease. They all seem related, but we have limited understanding of how. One difficulty is that it is a long-term story. Further, the individual points are hard to measure.

New advances in brain imaging are allowing observations of what was previously invisible. A new article uses a new type of brain imaging to explore the long-term consequences of even a single TBI. The findings are striking, though we should note that their significance is not clear at this point.

Here is a summary of the data...

What is being measured here? The immediate measurement is positrons; that is what a PET scan does. The "trick" is to couple the positron emitter to something of interest. In this case, it is a molecule, called Flortaucipir, that specifically binds to tau. The results are presented on a statistical basis... The brain scan yields a signal region-by-region. Computer analysis shows the score for each small region, or "voxel" (volumetric pixel).

Here is a figure that shows the brain scans for the 21 people with TBI. What's shown is not raw scan results, but the calculated results for tau, shown on a color scale. There is a color scale bar at the bottom. Briefly... bright colors (reds, yellows) are for high scores for tau. Darker colors, especially blues, are for lower scores. Remember, the participants are in order by overall score. So you can see that the scans are mostly bright (abnormal) at the top, ranging to mostly blue (normal) at the bottom. Figure 1 from the article [link opens in new window].

What do we learn from all this? New tools allow better observations. We can now see that people who received a head trauma even decades earlier show evidence of it that can be detected by a modern brain scan, reflecting unusual protein levels in the brain.

The tau-PET scans correlated with tau level in the cerebrospinal fluid. High levels of tau also correlated with apparent damage to white matter. However, the current work was not able to show a connection with cognitive decline; it is a small study group, with incomplete data.

The authors consider this a small pilot study, showing progress in monitoring tau in living people. More specifically, the results suggest that single TBI events can have effects on tau that can be detected decades later.

News stories:
* Tau Pathology Present Decades After a Single Brain Injury -- Patients who suffer a traumatic brain injury may exhibit abnormally abundant tau protein many years later, a new in vivo imaging technique reveals. (R Williams, The Scientist, September 9, 2019.) Now archived.
* PET Identifies Tangles Decades after a Single Traumatic Brain Injury. (ALZFORUM, September 7, 2019.)
* Expert reaction to study on single traumatic brain injury and protein tangles in the brain. (Science Media Centre, September 4, 2019.) A range of views, with much emphasis on the limitations of the study.

The article: In vivo detection of cerebral tau pathology in long-term survivors of traumatic brain injury. (N Gorgoraptis et al, Science Translational Medicine 11:eaaw1993, September 4, 2019.)

A post on using PET to measure brain injury... Early detection of brain damage in football players? A breakthrough, or not? (September 14, 2015). Includes useful general information about PET scans.

More PET: Brain imaging to detect and distinguish tauopathies, including Alzheimer's disease (January 18, 2021).

Posts about tau include:
* How tau gets around (June 28, 2020).
* Alzheimer's disease: a role for inflammation? (January 18, 2020).
* Alzheimer's disease: What is the role of ApoE? (November 6, 2017).

More about brain injury:
* Briefly noted... Concussions in women athletes (August 18, 2021).
* A sniff test to see if a person is conscious (August 4, 2020).

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

Does vaccination against yellow fever affect incidence of severe dengue?

October 4, 2019

Dengue virus presents a strange phenomenon: infection with one strain of dengue can enhance the severity of subsequent infection with another strain. The phenomenon, commonly called antibody-dependent enhancement (ADE), is not well understood, but it obviously has practical implications.

If one strain of dengue can enhance the infection with another strain of dengue, what about related viruses? Dengue is a flavivrrus, a group with several important pathogens, including Zika and yellow fever (YF). These viruses are commonly transmitted by the same types of mosquitoes. The question of whether one of them enhances another member of the flavivrrus family is of concern.

Musings has noted articles exploring the possible interaction between dengue and Zika [link at the end]. A recent article explores the possible interaction between yellow fever and dengue. Specifically, the scientists ask whether vaccination against YF affects the likelihood of having the severe type of dengue.

The following figure summarizes the findings...

It seems simple and reassuring: yellow fever vaccination does not impact on the severity of dengue disease.

Comment...

The article seems straightforward. But, perhaps to be a bit provocative, it is also somewhat disconcerting.

Underlying this work is a mystery: why strains of dengue virus, in some circumstances, enhance each other's infection. That in itself is an odd phenomenon, which is poorly understood. We now worry about possible interactions with other members of the dengue family (the flavivrruses). Results for Zika-dengue interactions have suggested there are some interactions, but the work is not at all clear.

So we now have a study of YF-dengue interactions. It is encouraging -- as far as it goes. How far is that? Are there other pieces of this story that have not yet been uncovered? With no real understanding of how ADE works, it is hard to know.

News stories:
* News Scan for May 08, 2019. (CIDRAP, May 8, 2019.) Scroll down to the second item... "Study: Yellow fever vaccine does not increase dengue severity".
* Yellow Fever Vaccination Does Not Increase Severe Dengue Risks. (D W Hackett, Vax Before Travel, May 8, 2019. Now archived.)

The article: Yellow fever (YF) vaccination does not increase dengue severity: A retrospective study based on 11,448 dengue notifications in a YF and dengue endemic region. (M J Luppe et al, Travel Medicine and Infectious Disease 30:25, July 2019.)

A recent post about the interaction of Zika and dengue viruses: The effect of prior dengue infection on Zika infection (April 20, 2019).

More about the viruses is on my page Biotechnology in the News (BITN) -- Other topics under Dengue virus (and miscellaneous flaviviruses). There is a list of related Musings posts. (There have been no previous posts about yellow fever, except for incidental mention of it.)

Why can't lithium metal batteries be recharged?

October 1, 2019

First... Distinguish two kinds of batteries that have similar names: lithium metal batteries and lithium ion batteries. The latter are the common rechargeable batteries found in many devices; they do not involve free elemental lithium. Lithium metal batteries have a lithium metal electrode. Current commercial lithium metal batteries are "primary" only (disposable); we will come back to this point in a moment. The history of the two types is intertwined -- as is their chemistry. It is reasonable to think of both of them as subclasses of lithium batteries. (Wikipedia has useful pages on both of them, if you want more.)

This post is about lithium metal batteries -- those with a lithium metal electrode. More specifically, it is about trying to recharge them.

Lithium metal batteries allow high energy storage -- due to the low mass of the lithium atom. However, attempts to make them rechargeable have failed. It is not clear why.

Two possible causes have gotten the most attention. One is that some of the metallic lithium (Li⁰) is inactive, probably because of some structural problem. The other is that some of the lithium ions are sequestered and are unavailable.

A new article reports work to distinguish the two proposals. The following figure shows some results; we'll describe what the scientists did below.

The graphs make clear that the variable efficiency of these batteries relates to unavailable lithium metal, not sequestered lithium ions.

How did the scientists do this? They used a reaction known to most who have taken a chemistry class: lithium metal reacts with water to release hydrogen gas.
2 Li(s) + 2 H₂O(l) --> 2 LiOH(aq) + H₂(g)
The basic idea of what they did was to react the electrode sample with water and measure the hydrogen gas produced; that gave them the amount of Li metal in the material. The idea is simple, but implementing it in their context is not; development of this assay is one major issue in the article.

The hydrogen measurement directly gave them the data shown in part e, above. The results in part f were determined by difference, not by an independent measurement.

Having identified the main cause of the problem, the scientists go on and report observations on the nano-level structures. It seems likely that the problem is small pieces of Li breaking off the anode during the charging cycle. The extent of this breakage varies with the details of the battery, including the electrolyte, but no current design reduces it sufficiently. The scientists suggest what might be done about it. It will take further work to see whether these ideas are fruitful. The big point of the current work is to identify the problem.

News stories:
* What really weakens lithium battery efficiency? (I Paredes, Physics World, September 6, 2019.)
* Main culprit behind lithium metal battery failure. (Science Daily (University of California - San Diego), August 21, 2019.)

The article: Quantifying inactive lithium in lithium metal batteries. (C Fang et al, Nature 572:511, August 22, 2019.)

Previous post on batteries: A low-temperature battery (July 29, 2018). It is a type of lithium-ion battery.

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

Briefly noted...

September 25, 2019

Do humans perceive magnetic fields? There is no convincing evidence for it, but it is still a fascinating idea. In a recent article, a team of scientists looked for effects on brain waves. They used magnetic fields similar to those of Earth -- fields within normal human experience. The results are complicated. There were consistent effects on the brain waves -- for some people under certain conditions. There was no conscious response or recognition. It's intriguing. Let's see what happens next. Can others independently validate the basic findings? If they are real, do they have any practical effect in modern humans, or are they simply a vestigial response? Is it possible that some people, or even some cultures, do learn to make use of magnetic information?
* News story: First Neuroscientific Evidence that Humans Have Geomagnetic Sense. (E de Lazaro, Sci.News, March 19, 2019.) Links to the article, which is freely available. There was considerable news coverage. If you want more, put the article title into a search engine.
* A post on biological effects of magnetic fields: Looking for genes for animal magnetism (June 11, 2017).

Consumption of microplastics by humans: a report and review from WHO

September 23, 2019

In the previous post, immediately below, we discussed a recent article that estimated the consumption of "microplastics" by humans. Two months after that article appeared, the World Health Organization (WHO) issued a report on the topic, focusing on drinking water. They also were involved in a review article that appeared a few months ago, with considerable detail.

The article discussed last time showed that bottled water was a major source of microplastics. Beyond that, the article is perhaps noteworthy for all the uncertainties it raises, including whether it matters.

The WHO report reinforces that last point.

The main thrust of the report is that there is no evidence suggesting any harm due to microplastics taken in via the GI system. (Inhaled plastics is another issue, not discussed in this report.)

Here are some of the possible types of harm the report discusses...
- Physical effects of the pieces.
- Effects of chemicals intrinsic to the plastics, such as monomers, additives, and degradation products.
- Effects of chemicals that absorb to the plastic.
- Role of plastic surfaces in encouraging growth of pathogenic microbes (e.g., biofilms).

That's quite a list of possible harms. The report makes clear how limited the information is at this point for many of them. It has extensive lists of recommendations -- questions that need further study.

Both parts of the message are important. To date, there is no evidence for harm from human oral consumption of plastics. But many aspects of the problem need more study. (The report does suggest that dealing with known problems, such as disease transmission via food and water, should be higher priority.)

The report is about 120 pages; it is written for the general audience. It is well-organized, with "boxes" highlighting key points along the way. Those wanting to explore a little should find it easy to browse. Those who want more of the technical background should check the review article.

Consumption of plastics is a fairly new issue. We have limited information at this time; that's a call for more work.

News stories:
* Microplastics in Drinking Water Don't Threaten Human Health: WHO -- A new report finds no evidence of a current danger from microplastics, but the World Health Organization urges further research. (A P Taylor, The Scientist, August 22, 2019.) Now archived.
* Microplastics in water: no proof yet they are harmful, says WHO -- Report calls for more research and warns against complacency over the issue. (J Watts, Guardian, August 21, 2019.)
* The Dangers of Microplastics in Drinking Water. (Multipure, September 19, 2019.) From a company that provides water purification systems for home use.

The report, Microplastics in drinking-water, is freely available. Go to the WHO news story WHO calls for more research into microplastics and a crackdown on plastic pollution. (WHO, August 22, 2019.) Links to the report and to related WHO pages.

The review article, which is freely available: Microplastics in freshwaters and drinking water: Critical review and assessment of data quality. (A A Koelmans et al, Water Research 155:410, May 15, 2019.)

Recent post on a specific article on human consumption of microplastics: Consumption of microplastics by humans: the bottled water problem (September 20, 2019). This is the preceding post, immediately below. It includes links to some related posts.

Added June 18, 2023. Also see: Plasticosis (June 18, 2023).

Added June 18, 2023. A general post on plastics, with links to much more: History of plastic -- by the numbers (October 23, 2017).

Briefly noted...

September 18, 2019

Hurricane deaths? A major hurricane devastated Puerto Rico in 2017. However, there has been considerable disagreement about how many people were killed by hurricane Maria. Much of the public disagreement was political, but underlying that was a serious question: How do we determine the deaths from a disaster? It may be easy enough to count how many people were killed directly, but the effects are complicated and long-lasting. A Nature news feature earlier this year gives a nice overview of the topic. As usual for Musings, the goal here is to emphasize the underlying issues, not the politics.
* News feature, freely available: Death, statistics and a disaster zone: the struggle to count the dead after Hurricane Maria -- Intense controversies surround studies of how many people perish in conflicts and disasters, but researchers are developing new ways to measure mortality rates. (C Arnold, Nature News, February 5, 2019. In print, with a different title: Nature 566:22, February 7, 2019.)

What can we learn from 17,000-year-old cat feces?

September 16, 2019

In this case, as reported in a new article, we learn that the cat had worms.

Those are the basic observations. A macroscopic sample that is probably from a medium-sized carnivore. And an egg, seen under the microscope, that is tentatively identified as belonging to a common group of intestinal parasites.

DNA analysis extends the observations. The carnivore is a cat. A hefty cat -- a puma (perhaps 80 kg). The parasite is specifically identified as Toxascaris leonina.

Radiocarbon dating of the coprolite sample indicates it is about 17,000 years old. That is about 6,000 years younger than the surrounding material. The reason for the difference is not known, but the authors note the value of direct dating of the sample itself.

The worm here thus becomes the oldest example of an intestinal parasite confirmed by DNA analysis. And the coprolite sample is the oldest such sample to be directly dated using C-14.

In the Discussion, the authors note that these parasites came to the area (in Southern Argentina) before humans. That contradicts some ideas for how the worms were introduced.

News stories:
* Oldest Known Parasites Found in Ancient Puma Feces -- Researchers isolate roundworm DNA from animal excrement that is about 17,000 years old. (C-Y Hou, The Scientist, August 28, 2019.) Now archived.
* 16,000-year-old puma poop yields a sample of Ice Age parasites -- The Ice Age roundworm DNA is the oldest genetic sequence ever recovered from feces. (K N Smith, Ars Technica, August 28, 2019.)

The article: Ancient parasitic DNA reveals Toxascaris leonina presence in Final Pleistocene of South America. (R S Petrigh et al, Parasitology 146:1284, September 2019.)

More feces:
* What can we learn by looking at the DNA in vampire bat feces? (May 27, 2015).
* The effect of defecation by whales on global warming (August 2, 2010).

More old things, with DNA analysis... The oldest known identical twins (December 7, 2020).

Previous post about nematodes: Worm count (August 27, 2019).

Briefly noted...

September 11, 2019

N = 1 trials. An N = 1 trial is a clinical trial with one person. A treatment is given, with variation, to one patient over an extended period. For example, each week might, randomly, be with or without the drug. People vary in their responses to drugs or other treatments. An N = 1 trial focuses on what happens with one person. In contrast, an ordinary clinical trial gets the average result for a study population. A recent news feature gives an interesting overview of N = 1 trials. It includes some history, and discusses various modern views on such trials.
* News feature: N-of-1 Trials Take on Challenges in Health Care -- From personalizing clinical practice to aiding biomedical research, individualized clinical trials have been heralded as a solution to several problems plaguing modern medicine. But they've yet to be widely adopted. (C Offord, The Scientist, July 15, 2019.) Now archived.

Modeling the role of hydrogen cyanide in the pre-biotic formation of life's chemicals

September 8, 2019

The following figure is featured in the abstract of a new article...

Now, the scientists did not actually carry out the second step. But they discuss it at considerable length. The chemicals in the center seem to be good precursors on the way to making protein and RNA, and that's a good step toward life.

They did not actually carry out the first step either. But what they did do was to carry out some rather complex computational chemistry simulating what might happen to a solution of HCN in water -- a solution that was likely present on the early, pre-biotic Earth. Their conclusion from the computational explorations: HCN + water could have yielded key chemicals needed to make life. It is even plausible that life could have arisen from HCN + water alone.

Conditions? The near-boiling water of the early oceans would have provided enough energy for these reactions, according to the simulations. (Some work, including the pioneering work of Miller and Urey, has involved the use of extreme energy sources, such as lightning.)

So? Well, it's fun. Origin-of-life stories are often fun. It proves nothing; we will probably never know what actually happened to start Earth life. However, it opens up new possibilities for experimental work. Can scientists test some of the predictions of this article? That's a good role for computer simulations.

There is a related figure in the article. We don't need any detail from it, but some may find it interesting, so here it is: Figure 1 [link opens in new window]. Part B (right side) is an expanded version of the middle part of the figure above; that is, it shows the chemicals made from HCN + water -- in their simulations. Part A (left side) is an interesting summary of actual lab work on pre-biotic synthesis, dating back to Miller and Urey.

News stories:
* New insights into the origin of life. (Science Daily (American Chemical Society), August 7, 2019.)
* Scientists uncover new insights into the origin of life. (T Puiu, ZME Science, August 7, 2019.)

The article, which is freely available: Insights Into the Origin of Life: Did It Begin from HCN and H₂O? (T Das et al, ACS Central Science 5:1532, September 25, 2019.)

Posts about pre-biotic chemistry include:
* A special role for cyanide in the chemistry of early life? (April 25, 2022).
* Miller-Urey revisited: the role of the glass container (January 22, 2022).
* The origin of life's chemicals: making an almost-Krebs-cycle in the lab (June 10, 2019).

Previous post about cyanide, in its more familiar role as a poison: Domestication of the almond (August 26, 2019).