Musings: 2024 (current posts)

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Musings: 2024 (current posts)

Musings is an informal newsletter mainly highlighting recent science. It is intended as both fun and instructive. See the Introduction, listed below and in the navigation bar at the top, for more information.

In mid-2023, Musings transitioned to a new format, for a semi-retirement phase. With some adjustments, it is now similar to the earlier "briefly noted" format. The format is flexible, and contributions can be in various formats by agreement.

Posts on this page, for 2024, have largely been adjusted to conform to this new format.

If you got here from a search engine... Do a simple text search of this page to find your topic. Searches for a single word (or root) are most likely to work.

   Introduction (separate page).
This page:
Current posts -- 2024
   New items
   December    November    October    September    August    July    June    May    April    March    February    January

Older items are on the archive pages, listed below.

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New items

The next posts will be on a new page, starting perhaps about January 8, 2025.

December 2024

How a dolphin signals it wants to play

December 11, 2024

Did you smile when you saw that picture? If so, you may have yourself a play partner.

This is reduced and trimmed from the figure in the news story listed below.

More animal behavior, more about dolphin communication. The work is based on extensive and careful observation of the animals. A key conclusion is that the dolphins signal their desire to play by the big open-mouth smile shown above. As always, remember, the interpretations of such work tend to be very human.

To be fair, there is nothing in the work reported here to suggest that the dolphins communicate with humans this way.

* News story: Dolphins 'smile' at each other when they are feeling playful. (Sanjana Gajbhiye, Earth.com, October 3, 2024.)
* The article, which is open access: Smiling underwater: Exploring playful signals and rapid mimicry in bottlenose dolphins. (Veronica Maglieri et al, iScience 27:110966, October 18, 2024.)

More about dolphin communication: Do dolphins talk to each other? (November 19, 2016)

More about smiles: Can a sea anemone make you smile? (June 21, 2021).

Understanding the lanthanum deficit in the universe: lab-scale measurement of the rate of nucleosynthesis

December 4, 2024

Heavy chemical elements are made in the stars, where there is enough energy to drive the nuclear reactions that lead to heavier nuclei. Those processes, broadly called nucleosynthesis, were long divided into two types: s (slow) and r (rapid). Not surprisingly, as more data became available, it became clear that the real world is more complex. As an example, recent observations have found less lanthanum that the older models predict. It is now clear that some types of stellar nucleosynthesis are i (intermediate).

The experimental work reported in a new article is about measuring the rate of decay of cesium-140 to barium-140. That process involves conversion of a neutron into a proton (a beta decay, increasing the atomic number by one without affecting the mass number). It can be followed by measuring the gamma rays emitted. This reaction can be related to the nucleosynthesis of lanthanum. The measurements have implications for the rate of neutron capture by Ba-139, which is related to the process for making lanthanum nuclei. It's all complex, with a variety of related reactions; lanthanum production itself is not directly accessible. The overall point is a better sense of what determines the rate of lanthanum production, which is less than had long been expected from older models.

* News story: Lanthanum Less Abundant Than Previously Thought -- Measurements related to the production of lanthanum in stars where elements are thought to form via the "i process" indicate that less of the element is produced than models predict. (Katherine Wright, Physics 17:78, May 17, 2024.) Good overview.
* The article: First Study of the ¹³⁹Ba(n,γ)¹⁴⁰Ba Reaction to Constrain the Conditions for the Astrophysical i Process. (A Spyrou et al, Physical Review Letters 132:202701, May 17, 2024.)

This post is listed on my page Introductory Chemistry Internet resources in two sections: Lanthanoids and actinoids and Nucleosynthesis; astrochemistry; nuclear energy; radioactivity.

November 2024

If a fish doesn't cooperate, is it ok to hit it?

November 20, 2024

A recent article makes extensive observations of hunting behavior of octopuses and fish -- working together. It's quite a feat of field work -- and what the animals do is quite complex. Among the observations is that an octopus may hit a fish that is not doing "its job".

The usual caution about animal behavior work... It can be very interesting to observe animals, especially in nature, but be careful in the interpretations. It is natural for us to see patterns in what we observe, but it is all too easy to anthropomorphise. As you look over the work reported in the article, you might admire the work, but take the interpretations as hypotheses.

* News story: Octopuses hunt with fish and punch them when they don't contribute -- Octopuses are getting more and more interesting with each new study. (Mihai Andrei, ZME Science, September 30, 2024.) Good overview. Includes some discussion of alternative interpretations.
* News story accompanying the article: Behavioural ecology: Shared leadership beneath the waves -- A field study of multispecies groups of marine animals that engage in collective foraging finds that leadership can be shared between individuals of different species. (Susanne Hoffmann, Nature Ecology & Evolution 8:2010, November 2024.)
* The article, which is open access: Multidimensional social influence drives leadership and composition-dependent success in octopus-fish hunting groups. (Eduardo Sampaio et al, Nature Ecology & Evolution 8:2072, November 2024.)

More about octopuses: Sleep stages in octopuses -- do they dream? (July 13, 2021). Includes an extensive list of posts about octopuses and other cephalopods.

Sharing resources: How to get a bird to help you find honey (September 4, 2016). A post about another example of cooperation between animal species: honeyguide birds and humans.

Division by 14: a new mode of bacterial growth

November 13, 2024

The best known bacterial division process is binary fission: the cell grows, then divides into two. There are other modes of division, including filament formation, which may be followed by septation and division, typically forming one new cell at a time. A new article shows an interesting variation. The cell forms a filament, then rather synchronously forms numerous septa along the filament and divides into multiple cells. The number of daughter cells per division varies -- but examples were seen with as many as 14 daughter cells from a single division step.

Significance? First, it is about diversity in Nature. The authors also suggest that it might help determine the nature of dental plaque. The bacterium studied here is Corynebacterium matruchotii, a major component of plaque biofilm.

* News story: Open Wide: Human Mouth Bacteria Reproduce through Rare Form of Cell Division. (Emily Greenhalgh, Marine Biological Laboratory, September 3, 2024.)
* Direct link to the video included in that news story. (20 seconds, time lapse.) The first few seconds show a single cell elongating, septating, and dividing into several daughter cells. After that, the video gets confusing.
* The article, which may be open access: Tip extension and simultaneous multiple fission in a filamentous bacterium. (Scott Chimileski et al, PNAS 121:e2408654121, September 3, 2024.)

More from dental plaque: Bacteria on human teeth -- through the ages (March 24, 2013).

This post is listed on my page Unusual microbes.

Asteroids as a food source for astronauts

November 6, 2024

Could we eat asteroids? Do we "cook" them first? A recent article explores such questions. There is considerable organic carbon on some asteroids. A process known as pyrolysis could convert it to things suitable for supporting microbial growth.

No asteroids were harmed in this work. The current work is mathematical modeling using what is known about the composition of asteroids and about the relevant processes. There is a lot of uncertainly in the numbers, but the authors suggest that as little as 5000 metric tons of asteroid could support one astronaut for one year. The point of the work is to open up the topic for further consideration.

* News story: Future long-term astronauts may end up eating asteroids (thanks to bacteria) -- How could we feed astronauts on lengthy space missions? These researchers have a quirky idea. (Mihai Andrei, ZME Science, October 7, 2024.)
* The article, which is open access: How we can mine asteroids for space food. (Eric Pilles et al, International Journal of Astrobiology 23:e16, October 3, 2024.)

* More about the composition of asteroids: Briefly noted... Uracil found on asteroid (March 29, 2023).
* More about food for space: Briefly noted... Yeast as a primary food in space? (January 24, 2023).
* More about pyrolysis: Flash photo-pyrolysis: converting banana peels to useful chemicals (March 5, 2022).

I have listed this post on my page Internet resources: Biology - Miscellaneous under Nutrition; food and drug safety.

October 2024

The dynamics of gamma ray production in thunderstorms

October 30, 2024

Gamma rays were found coming from thunderstorms in the 1990s, when they were accidentally observed by a NASA satellite. Musings has discussed some of the work to characterize what is happening (see background post noted below), but the story is still quite incomplete. Recently, an international team made extensive systematic observations of thunderstorm γ rays, using a plane originally intended for spying. It is clear that thunderstorm γ rays are quite variable, with some storms not showing them at all. The work did connect the two types of gamma activity previously described. Extended γ glows sometimes seemed to lead to short intense bursts of high energy γ rays. Both kinds of activity could occur without lightning. The scientists even suggest that γ ray development may be related to the processes that lead to lightning. Thus the work may be a significant step toward understanding thunderstorms, a fascinating and complex -- and important -- atmospheric activity. The spy planes will allow collection of much more data.

Are thunderstorms a radiation hazard to people? The levels of gamma rays measured so far should not be of concern on the surface of Earth, or even to passing aircraft.

The project is also a bonanza for acronymologists, with a double example of nested acronyms. The project is known as ALOFT -- Airborne Lightning Observatory for FEGS and TGFs. FEGS = Fly's Eye Geostationary Lightning Mapper Simulator. TGF = terrestrial γ-ray flash. Of course, the work is, in part, from NASA.

* News story: Surprising Discovery: NASA's Retrofitted U2 Spy Plane Reveals Tropical Lightning Storms Are Radioactive. (SciTechDaily (Duke University), October 6, 2024.)
* News story accompanying the article: Atmospheric physics: Glowing γ-rays solve thunderstorm conundrum -- Aircraft observations of high-energy rays emitted by thunderstorms reveal that they are both intense and dynamic. Long-lasting glows that switch to rapidly flickering flashes could offer clues to how lightning forms. (Joseph R Dwyer, Nature 634:36, October 3, 2024.)
* Two articles:
1) Flickering gamma-ray flashes, the missing link between gamma glows and TGFs. (N Østgaard et al, Nature 634:53, October 3, 2024.)
2) Highly dynamic gamma-ray emissions are common in tropical thunderclouds. (M Marisaldi et al, Nature 634:57, October 3, 2024.)

Background post: Lightning and nuclear reactions? (January 28, 2018). The article of the earlier post is reference 28 of the current article 2.

A one-electron bond between two carbon atoms

October 23, 2024

Start with the labeled C-C bond in molecule 1, at the left. It looks fairly ordinary. But it is actually somewhat stretched, due to the effects of the surrounding ring systems.

Oxidation of molecule 1 results in loss of one electron from that C-C bond, leading to the cation labeled 1^•+. The C-C bond is now a whopping 2.921 Ångstroms long, more than 1 Å longer than in molecule 1. It is now about twice as long as a typical C-C bond.

The dot in the label for the ion and on the bond itself is for the single electron in the bond.

This is part of Figure 2e from the article.

The ion shown there is stable. The scientists isolated it as a salt with the triiodide ion, and did a variety of analyses, including X-ray crystallography. It is quite clear from both the experimental results and theory that the C-C bond has one electron. Such one-electron bonds were proposed nearly a century ago (by Linus Pauling), and occasionally implicated in various processes. This is the first direct evidence for such a bond between two C atoms. What made the current work succeed was that it involved a direct attempt to stabilize such a bond, based on the surrounding framework.

* News story: One-electron covalent bond between two carbons pushes limits of bonding. (Victoria Corless, Chemistry World, October 4, 2024.)
* The article: Direct evidence for a carbon-carbon one-electron σ-bond. (Takuya Shimajiri et al, Nature 634:347, October 10, 2024.)

More carbon: A new form of carbon -- hard enough to scratch diamond (March 1, 2022). Includes a list of some posts about novel forms or behavior of carbon.

A nuclear clock

October 16, 2024

Timekeeping requires reference points. For example, we might note that the seasons come at regular intervals, so we define the time of one cycle of the seasons as a year. Good idea, but not very precise. In the modern world, atomic clocks are the most precise references for timekeeping. They are based on one specific electronic transition. In principle, we might do even better with nuclear clocks, but they have been experimentally inaccessible. A new article reports progress. An unusually low energy transition in the nucleus of a rare thorium isotope can be probed with an unusually high energy UV source. The article connects time as measured with an atomic clock to time as measured with this new "nuclear clock". Can they turn this into a practical timekeeping device? As so often with a preliminary finding, the answer is, we'll see.

* News story: Scientists Inch Closer to World's First Nuclear Clock - A New Tool to Probe the Mysteries of the Universe. (Tibi Puiu, ZME Science, September 5, 2024.)
* News story accompanying the article: Metrology: Countdown to a nuclear clock. (Adriana Pálffy & José R Crespo López-Urrutia, Nature 633:43, September 5, 2024.)
* The article: Frequency ratio of the ^229mTh nuclear isomeric transition and the ⁸⁷Sr atomic clock. (Chuankun Zhang et al, Nature 633:63, September 5, 2024.)

Also see... Atomic clock measurements of the difference in gravity over one millimeter (May 4, 2022).

A nuclear-powered battery for your phone?

October 9, 2024

The possibility of tiny sources of nuclear power has long intrigued scientists. A new article reports a new approach, which may have the potential to be practical. The basic plan is to use a tiny amount of americium (commonly used in smoke detectors), embedded in a matrix where the radioactive emissions (alpha particles) lead to light production. The light is then transformed to electricity -- known technology (photovoltaic cell) -- which is used to charge a battery. The overall result is about 8,000 times more efficient than previous attempts at such micronuclear devices.

* News story: Researchers create tiny nuclear-powered battery thousands of times more efficient than predecessors. (Bob Yirka, Tech Xplore, September 19, 2024.)
* The article: Micronuclear battery based on a coalescent energy transducer. (Kai Li et al, Nature 633:811 September 26, 2024.)

* More americium: A better way to oxidize americium? A step toward improved processing of nuclear reactor waste? (December 7, 2015).
* This post is listed on my page Introduction to Organic and Biochemistry Internet resources under Energy resources.
* ... and on my page Introductory Chemistry Internet resources under Lanthanoids and actinoids.

The physics of paper cuts

October 4, 2024

A piece of paper can cut you, You probably know that. Some kinds of paper are more likely to cut than others. A new article explores how that works, using both an experimental model (an artificial finger) and computer simulation. If the paper is too thick, it is like a dull knife, indenting the surface rather than breaking it. If the paper is too thin, it is likely to just buckle rather than break the surface. The conclusions all seem reasonable; now there is some data behind them. Paper of 65 µm thickness is about optimum -- for cutting you. (Table 1 suggests that a page from the journal Science is more likely to cut you than a page from Nature.)
* The opening of the article... "Paper cuts are ... endemic among literate persons (globally 86% aged 15+ years [2]) and may lead to severe microbial infections [3,4]."

* News story: Scientists uncover the physics behind paper cuts. Here are the types of paper most likely to cut you. (Tibi Puiu, ZME Science, August 1, 2024.)
* The article: Competition between slicing and buckling underlies the erratic nature of paper cuts. (Sif Fink Arnbjerg-Nielsen et al, Physical Review E 110:025003, August 23, 2024.)

Relevant background posts: Nothing obvious.

September 2024

Yesterday: Earth got a new moon in orbit

September 30, 2024

We have noted before that Earth occasionally captures asteroids into orbit, where they may remain for weeks or perhaps a few years. 2024 PT₅ was captured yesterday (September 29, 2024) -- or at least that is what was predicted, according to a new article. It will remain in Earth orbit until November 25, when the gravity of the Sun displaces it, according to the predictions.
* The new moon is about 10 meters in diameter. Professional-level equipment will be needed to see it. If you're not ready to observe 2024 PT₅ on this visit, you might plan ahead for the next visit, in 2055.

* News story: Earth will soon have a new mini-moon in September - but only briefly. (Tibi Puiu, ZME Science, September 19, 2024.)
* The article, which is open access: A Two-month Mini-moon: 2024 PT₅ Captured by Earth from September to November. (Carlos de la Fuente Marcos & Raúl de la Fuente Marcos, Research Notes of the American Astronomical Society 8:224, September 2024.) For a pdf file of a draft of the article, scroll down to "Article and author information" and choose "AAS-provided PDF".

The idea that Earth has small temporary moons from time to time was introduced in: Briefly noted... 1. How many moons hath Earth? (September 5, 2018).

An injectable pacemaker for the heart?

September 25, 2024

Installing a heart pacemaker requires a significant surgery. What if we could just inject a pacemaker into the heart, at least in an emergency? A new article reports progress toward that goal. What the scientists have done is to develop a "parts kit" that can self-assemble into a functional pacemaker. At this point, they have tested it in the lab with isolated chicken embryo hearts and with zebrafish. They are ready to test it in mammals, injecting the parts kit directly into the heart (more precisely, into the region around the heart). The current version will last about five days -- before self-degrading into harmless pieces that are excreted. The injectable pacemaker is intended for emergency use, such as in the wild or in a war zone, stabilizing heart function for a few days until proper surgery can be done.
* What powers this temporary pacemaker? An ordinary mobile phone should work just fine.

* News story: Injectable heart stimulator for emergency situations. (Åsa Hansdotter, Lund University, August 27, 2024.)
* The article, which is open access: In situ assembly of an injectable cardiac stimulator. (Umut Aydemir et al, Nature Communications 15:6774, August 8, 2024.)

Another approach for developing a pacemaker: Lighting the heart (August 31, 2010).

Building the bio into a biodegradable plastic

September 18, 2024

A recent article reports a process for incorporating bacterial spores into a plastic during manufacture. When "the time comes", the spores can be activated, the bacteria grow and make an enzyme that will degrade the plastic (a polyurethane). The starting bacterial strain (Bacillus subtilis) was chosen for its ability to degrade the plastic. It was modified to survive during production of the plastic -- at 135 °C. Testing showed that the plastic would degrade under ordinary compost conditions (without special additions to the compost for this purpose). Interestingly, incorporation of the bacterial spores into the plastic improved some of its mechanical properties.

* News story: Biodegradable 'Living Plastic' Houses Bacterial Spores That Help It Break Down. (University of California San Diego, April 30, 2024.)
* The article, which is open access: Biocomposite thermoplastic polyurethanes containing evolved bacterial spores as living fillers to facilitate polymer disintegration. (Han Sol Kim et al, Nature Communications 15:3338, April 30, 2024.)

Also see...
* Good enzymatic degradation of polyesters, by manufacturing the plastic with the enzymes in it (May 4, 2021). The current work is in the same vein as this earlier work, now using organisms rather than just enzymes. The use of bacterial spores may make the new process more robust.
* A general post on plastics, with links to much more: History of plastic -- by the numbers (October 23, 2017).

A better way to get a blood sample, using a leech-like device

September 11, 2024

If a leech gets a blood sample from your arm, you may not even notice. If only doctors could be so gentle. Maybe they can, thanks to a device reported recently. It was, quite frankly, designed to mimic what a leech does. It attaches to the arm by light suction, and uses an array of microneedles to penetrate the skin. The scientists think that their new device is practical and inexpensive; it is ready for testing with humans.

* News story: Blood sampling device inspired by leeches could make needles obsolete -- Innovative blood sampling device mimics leech mechanics for painless, efficient diagnostics. (Tibi Puiu, ZME Science, May 2, 2024.)
* The article, which is open access: A Bioinspired and Cost-Effective Device for Minimally Invasive Blood Sampling. (Nicole Zoratto et al, Advanced Science 11:2308809, May 15, 2024.)

* Previous posts mentioning leeches: none.
* More microneedles: Treating a heart attack using a microneedle patch (January 11, 2019).

Rotifers make antimicrobials -- using bacterial genes

September 4, 2024

We have previously noted that one type of tiny animal, the bdelloid rotifers, have a very high level of horizontal gene transfer (HGT). A new article reports a useful function for one set of genes the rotifers acquired from bacteria: they make novel antimicrobial agents. In this case, the bacterial genes protect the rotifers from fungal infections that would otherwise be fatal.

These rotifer antimicrobials may be worth attention. The antifungal agents reported here are novel, presumably because the genes have been evolving there for millions of years. Further, they have passed at least one test for safety in animals. But how safety in rotifers extrapolates to safety in humans needs to be checked.

* News story: New study shows tiny animals steal antibiotic recipes from bacteria. (University of Oxford, July 19, 2024.)
* The article, which is open access: Bdelloid rotifers deploy horizontally acquired biosynthetic genes against a fungal pathogen. (Reuben W Nowell et al, Nature Communications 15:5787, July 18, 2024.)

Background post on rotifers, their fungal infections, and horizontal gene transfer: Lesbian necrophiliacs (March 8, 2010).

August 2024

A step toward roses without thorns

August 28, 2024

Prickles, as the plant biologists call them. They occur in numerous and diverse plants. A new article explores the genetics behind the trait of having or not having prickles. Turns out it is rather simple, with one key gene often making the difference. This allows the scientists to mutate out prickles in some plants. Here is an example...

Desert raisins, Solanum cleistogamum.
Left: Wild type, with prickles on the berries.
Right: Berries after genetically blocking prickle formation.

This is part of Figure 5 from the article.

Roses without thorns? The team has evidence that the same gene is involved. However, rose genetics is a bit messy. We'll see.

(It is common that thorns are manually removed from cultivated rose plants, so there is an incentive to pursue this. We also note that there are some thornless roses. The issue here is modifying current commercial crops to make them thornless.)

* News story: Plant biologists discover an ancient gene family is responsible for plant prickles across species. (Phys.org (Cold Spring Harbor Laboratory), August 1, 2024.)
* News story accompanying the article: Evolutionary biology: A sharp discovery -- Plant prickles are controlled by genes involved in the final step of cytokinin biosynthesis. (Elizabeth A Kellogg, Science 385:495, August 2, 2024.)
* The article: Convergent evolution of plant prickles by repeated gene co-option over deep time. (James W Satterlee et al, Science 385:ado1663, August 2, 2024. Not in print edition.)

* More about thorns... Why a tree cultivates ants (October 3, 2010).
* and roses... Briefly noted... Two new genomes (August 8, 2018). See item 1 there.

Treating prion disease with CHARM, to reduce production of the prion protein

August 21, 2024

The progression of prion diseases depends on the continued production of the normal prion protein. This is true even when the disease was initiated by "infection" with an exogenous prion agent, such as that for BSE. Animals lacking the gene for the prion protein have been made by genetic engineering; they cannot get prion diseases. That might lead to the development of cattle strains that cannot get BSE, but does not provide a direct route to treatment. Is it possible we could turn off the prion gene in an animal that has begun to develop a prion disease?

A recent article reports some success in treating prion disease by turning the prion gene off -- or at least, turning it down. In addition to the basic result, the method they used is interesting -- and complicated. The heart of the method is that the viral vector leads to the production of a small protein that binds to the prion gene promoter -- and targets a DNA methylase to that promoter. The resulting methylation of the prion gene promoter silences gene expression. Thus, this is a form of epigenome editing; it affects expression of the target gene, but not the DNA sequence of the gene. Tests in a mouse model are promising, but of course there is much more to do.

The scientists call their method Coupled Histone tail for Autoinhibition Release of Methyltransferase (CHARM).

* News stories:
- Epigenetic Editor Silences Toxic Proteins in the Mouse Brain, Offering Promising Path to Treat Deadly Prion Diseases. (Monica M Bertagnolli, NIH, July 25, 2024.) Good presentation of the approach.
- CHARMed collaboration creates a potent therapy candidate for fatal prion diseases -- A new gene-silencing tool shows promise as a future therapy against prion diseases and paves the way for new approaches to treating disease. (Greta Friar (Whitehead Institute, MIT), June 27, 2024.)
* News story accompanying the article: Medicine: An epigenetic editor to silence genes -- A new class of editor has improved delivery, durability, tunability, and safety. (Madelynn N Whittaker & Kiran Musunuru, Science 384:1407, June 28 2024.)
* The article: Brainwide silencing of prion protein by AAV-mediated delivery of an engineered compact epigenetic editor. (Edwin N Neumann et al, Science 384:eado7082, June 28 2024. Not in print edition.)

* A previous post about developing a treatment for prion disease: Briefly noted... First in-human trial of an antibody against a prion disease (April 26, 2022).
* For more about prions, see my page Biotechnology in the News (BITN) - Prions (BSE, CJD, etc). It includes a list of related Musings posts.
* Also see: CRISPR: an overview (February 15, 2015). This originally included a complete list of posts about CRISPR. It was expanded to include posts more generally about genome editing. Now, epigenome editing.

Effect of climate change on timekeeping

August 14, 2024

The length of the day, in astronomical terms, depends on the speed of rotation of the Earth. Occasional adjustments are made to our human-based timekeeping system to compensate for real-world irregularities in that rotation. Most common has been adding a leap second, to reflect slowing of the Earth's rotation. The new twist is that climate change is affecting the Earth's rotation. The melting of polar ice is affecting the distribution of mass on Earth, thus changing its rotation. The effect is to slow the rotation. The full context is complicated; in some sense, the new finding may be good news. The recent changes in Earth rotation have been in the opposite direction, with the rotation speeding up, which would lead to the need for a negative leap second. (This was noted in the Musing post linked below.) Melting of polar ice would counteract this change, at least delaying the need for a negative leap second.
* There is ongoing discussion of how to maintain official time. The new finding here may be welcomed simply for relieving the immediate pressure to consider a negative leap second, while the broader timekeeping context is being reconsidered.

* News story: Melting polar ice is changing Earth's rotation and slowing down time. Here's how this will affect the leap second -- Climate change is now altering how we keep time. (Tibi Puiu, ZME Science, March 28, 2024.)
* News story accompanying the article: Forum: Metrology... Melting ice delays leap-second problem -- Humans' effect on the polar ice sheets is slowing Earth's rotation, posing challenges for its alignment with the official time standard. Two researchers discuss the science behind the slowdown and the impact it has on timekeeping. (Sections by Patrizia Tavella & Jerry X Mitrovica, Nature 628:273, April 11, 2024.) Good discussion, with context.
* The article: A global timekeeping problem postponed by global warming. (Duncan Carr Agnew, Nature 628:333, April 11, 2024.) Put the title into Google Scholar, and you may get a freely available copy. (Caution... I had trouble downloading one of the listed files, but another was fine.)

For more about the Earth's rotation, including the issue of a possible negative leap second... Briefly noted... A record short day (August 23, 2022).

Role of DNA damage and inflammation in storing memories?

August 7, 2024

Caution, this may be a confusing story. But it also sounds like it is potentially quite important. We store memories in the details of neuron structure. How? and how do they get there? Those points are less clear. A recent article explores some phenomena that seem to be associated with the formation of long-term memories. The work suggests that DNA damage and the resulting inflammation are part of the story of storing memories. One piece of evidence is that mutant mice lacking a key step in the DNA-directed inflammatory response are deficient in forming long-term memories. It may be that the brain has co-opted a piece of the innate immune system for its own purpose.

* News story: Making long-term memories requires DNA damage, researchers discover. (Medical Xpress (Albert Einstein College of Medicine), March 27, 2024.)
* News story accompanying the article: Neuronal inflammation makes memories persist. (Benjamin A Kelvington & Ted Abel, Nature 628:40, April 4, 2024.)
* The article, which is open access: Formation of memory assemblies through the DNA-sensing TLR9 pathway. (Vladimir Jovasevic et al, Nature 628:145, April 4, 2024.)

* TLR9, the DNA-sensing receptor of the inmate immune system, was introduced in the post: Does it matter what time of day you get a vaccine? (October 26, 2012).
* More about brains is on my page Biotechnology in the News (BITN) -- Other topics under Brain.

July 2024

Hypermutation and defense in bacteria

July 31, 2024

Hypermutation and defense in bacteria. The adaptive immune system of vertebrates generates a vast library of antibodies by a complex set of processes broadly referred to as hypermutation. Immune cells proliferate, with a high rate of mutation in the antibody genes, due to various "unusual" processes. Scientists have recently explored a type of hypermutation, using error-prone reverse transcription, in bacteria. The hypermutation is focused on a few genes, which may be sensors of viral antigens. Thus they suspect that the process is associated with resistance to viruses -- a type of immune response. The bacteria are colonial, almost multi-cellular -- making them highly susceptible to viral spread. (They are a species of Thiohalocapsa, commonly known as pink berries, due to their macroscopic appearance.) The article includes considerable speculation, but the basic findings are intriguing.
* News story: How to win an arms race: lessons from "pink berries". (Roo Weed, MicroBites, June 14, 2024.)
* The article, which is open access: Targeted hypermutation of putative antigen sensors in multicellular bacteria. (Hugo Doré et al, PNAS 121:e2316469121, February 14, 2024.)

More hypermutation... A novel approach to providing immunity to HIV (March 12, 2012).

Naked mRNA vaccines (without the lipid coat)?

July 24, 2024

A problem with the current formulation of mRNA vaccines is that the lipid coat is reactogenic, causing side effects. The significance of the side effects varies -- a lot; they can be serious, though more often they are just annoying. On the other hand, using naked (free) mRNA could reduce the effectiveness, because of the instability of mRNA. A recent article reports progress toward developing effective naked mRNA vaccines. Key developments include injecting into skin (which has more immune cells, compared to the usual muscle site), and using a jet injector (to enhance uptake, compared to the usual syringe and needle). Results are encouraging -- but limited at this point. The scientists are planning a clinical trial for 2026.
* News story: Must mRNA be cloaked in a lipid coat to serve as a vaccine? (Phys.org (Innovation Center of NanoMedicine), April 3, 2024.)
* The article, which is open access: Carrier-free mRNA vaccine induces robust immunity against SARS-CoV-2 in mice and non-human primates without systemic reactogenicity. (Saed Abbasi et al, Molecular Therapy 32:1266, May 2024.)

Background... Briefly noted... mRNA vaccine history (November 3, 2021).

COVID posts are listed on my page for BITN -- Other topics in the section SARS, MERS (coronaviruses).

A fractal molecule in nature

July 17, 2024

Scientists recently found that the enzyme citrate synthase from the cyanobacterium Synechococcus elongatus self-assembles into Sierpinski triangles. Why? Probably just an evolutionary accident; mutational analysis has not revealed any role for the unusual structural pattern. But the structural repetition did confuse the software used to analyze the electron microscope images.

* News story: Discovery of the first fractal molecule in nature -- Scientists at the Max Planck Institute in Marburg found for the first time a natural protein that follows a fascinating mathematical pattern of self-similarity. (Max Planck Institute for Terrestrial Microbiology (Marburg), April 10, 2024.)
* The article, which is open access: Emergence of fractal geometries in the evolution of a metabolic enzyme. (Franziska L Sendker et al, Nature 628:894, April 25, 2024.)

Previous post about fractals: Cauliflower math (July 26, 2021).

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

Which calendar did the Antikythera device use?

July 11, 2024

The Antikythera device was introduced in the background post listed below. It is likely that the device tracked the year using a line of holes around one ring, known as the calendar ring. The question is, what kind of year -- for this ancient device? That is, how many holes were there? The condition of the device makes it difficult to get a good count. A new article reports a sophisticated statistical analysis of the best images available. The conclusion? Most likely 353-356 holes, a much narrower range than earlier estimates. It is consistent with the 354-day year used by the Greeks in the era of the device. A 360-day year is just barely within the 99% limits of their estimate; a 365-day year is quite implausible.

* News story: Astronomers decypher 2,000-year-old ancient Greek computer with the help of gravitational waves science -- The oldest computer in the world is revealing its secrets. (Tibi Puiu, ZME Science, July 4, 2024.)
* The article, which is freely available (only) as a pdf at this special link: An Improved Calendar Ring Hole-Count for the Antikythera Mechanism -- A Fresh Analysis. (Graham Woan & Joseph Bayley, Horological Journal, July 2024, p 282.) The journal is the official journal of the British Horological Institute. Horology? It's the study of timekeeping, the measurement of time.
* The mention of gravitational waves is about statistical methodology. Indeed. both of the current authors are involved in the gravitational wave project (LIGO).

Background psot about the Antikythera device: The Antikythera device: a 2000-year-old computer (August 31, 2011).

Goldene: 2-dimensional gold

July 9, 2024

Scientists have reported making gold monolayers. By analogy with the more famous 2D form of carbon, they call it goldene. But making graphene is relatively simple; the basic structure is found in the common substance graphite. In contrast, metals do not tend to make 2D structures. Thus the work required developing a novel synthesis; the work started quite by accident while studying titanium silicon carbide. As with graphene, goldene has novel properties. For example, a gold monolayer is not a good electrical conductor. The main point for now is that the article presents a novel material.
* News story: Scientists make the first single-atom-thick sheet of gold. It's called 'goldene' -- The new material could revolutionize catalysis and more. (Tibi Puiu, ZME Science, April 16, 2024.)
* The article, which is open access: Synthesis of goldene comprising single-atom layer gold. (Shun Kashiwaya et al, Nature Synthesis 3:744, June 2024.)

* Among posts about gold... Prospecting for gold -- with help from the little ones (March 1, 2013). Includes a list of gold-related posts.
* Posts about graphene and such are listed on my page Introduction to Organic and Biochemistry -- Internet resources in the section on Aromatic compounds. Added September 24, 2024.

Is there similarity between the fingerprints from different fingers of the same person?

July 2, 2024

The traditional view is that all fingerprints are completely different. For forensic use, one must match the print to the specific finger. A recent article uses an AI system to analyze a library of fingerprint sets. The finding is that the various prints from one individual are related. That's interesting in terms of understanding fingerprint development. It may also have forensic use, though this will need further development.

* News story: Your fingerprints are not unique, new AI finds -- An AI program reveals a shocking secret about human fingerprints that even forensic scientists found shocking. (Rupendra Brahambhatt, ZME Science, January 12, 2024.)
* Interview with the lead author, an undergraduate at Columbia University: AI fingerprint breakthrough could aid future forensics. (Naked Scientists, January 12, 2024.)
* The article, which is open access: Unveiling intra-person fingerprint similarity via deep contrastive learning. (Gabe Guo et al, Science Advances 10:eadi0329, January 12, 2024.)

More about fingerprints: Briefly noted... How fingerprints develop (June 2, 2023).

June 2024

Associative learning coupled to the visual system of box jellyfish

June 27, 2024

Jellyfish are primitive animals. However, some have eyes -- many eyes. In a previous post, Musings discussed work on the behavioral implications of jellyfish eyes. The work has now been extended, showing that these jellyfish can learn to associate cues (visual and mechanical) with behavioral responses. The work shows that the ability to learn is a property of even one of the simplest nervous systems known.

* News story: Box jellyfish show surprising ability to learn without a brain -- Learning from experience was believed to be restricted to more advanced creatures, but in a first, Caribbean jellyfish were shown to learn from past mistakes. (Sukanya Charuchandra, Advanced Science News, October 4, 2023.)
* The article: Associative learning in the box jellyfish Tripedalia cystophora. (Jan Bielecki et al, Current Biology 33:4150, October 9, 2023.)

For background about vision in the box jellyfish... With 24 eyes, can they see the trees? (June 11, 2011). The article discussed in this background post is reference 15 of the current article; both articles are from the same group.

Ed Stone dies

June 25, 2024

See "update" at the end of At the edge of the solar system (September 28, 2012).

Converting type B blood to type O

June 19, 2024

Scientists have reported finding bacteria that can remove carbohydrate antigens from blood cells, converting them to be effectively type O. The bacteria come from the gut, where they apparently feed on the mucus on the gut lining. The cells of the gut lining are coated with a variety of sugars, and these bacteria have a collection of enzymes that remove those sugars. The enzymes also do a good job on blood cells. The scientists suggest that their current process is already good enough to convert type B blood to useful type O. Results with type A blood are encouraging but not yet good enough to be useful. The common blood types are actually more complex than we usually make them sound; that makes the conversion more complex than one might expect, but the work here actually provides information about the additional complexities.

* News story: Scientists find a way to convert blood types and make them mutually compatible for transfusion -- New enzyme technology could transform some blood types into universal donor blood, addressing global blood shortages. (Tibi Puiu, ZME Science, April 30, 2024.)
* News story accompanying the article: Microbiome: Gut microorganism enzymes unlock universal blood. (Timothy J Satchwell et al, Nature Microbiology 9:1161, May 2024.)
* The article: Akkermansia muciniphila exoglycosidases target extended blood group antigens to generate ABO-universal blood. (Mathias Jensen et al, Nature Microbiology 9:1176, May 2024.)

More about blood types: Progress toward a universal source for red blood cells, avoiding the need to match blood type (February 23, 2021).

"Tidal" effects of Mars on Earth climate?

June 12, 2024

A recent article reports finding 2.4 million year cycles in the nature of deep-sea sediments. That corresponds to a known cycle in the gravitational interaction of Mars and Earth -- an astronomical "grand cycle". The observed effects reflect changes in ocean circulation, and could well have effects on climate. (Mars is about 10 times the mass of the Moon, but is about 100 times farther away -- at closest approach.)

* News story: Every 2.4 Million Years, Mars Does Something Unexpected to Our Ocean's Depths. (Michelle Starr, Science Alert, March 12, 2024.)
* The article, which is open access: Deep-sea hiatus record reveals orbital pacing by 2.4Myr eccentricity grand cycles. (Adriana Dutkiewicz et al, Nature Communications 15:1998, March 12, 2024.)

Also see: Does the moon affect earthquakes? (October 21, 2016).

Making diamonds in 15 minutes at ambient pressure

June 5, 2024

Making diamonds in 15 minutes at ambient pressure. A new article reports a different approach for making diamonds under conditions milder than usual. They make diamonds at atmospheric pressure. They do use a high temperature, though somewhat lower than common. They report making significant amounts of diamond films -- in a few minutes (rather than a few days, as common for making synthetic diamonds). And they don't even need a seed diamond. The key is the liquid metal alloy used as the solvent. It will be interesting to see how this work develops. A potential advantage is easier scale-up, since extreme pressure is not needed.

* News story: Making Diamonds at Ambient Pressure -- Scientists develop novel liquid metal alloy system to synthesize diamond under moderate conditions. (Institute for Basic Science (Korea), November 28, 2023.)
* The article: Growth of diamond in liquid metal at 1 atm pressure. (Yan Gong et al, Nature 629:348, May 9, 2024.)

More about making diamonds... Making lonsdaleite -- with diamonds in it -- at room temperature (December 8, 2020).

May 2024

Testing CWD prions in human organoids

May 29, 2024

Organoids are clumps of organized tissues, made from stem cells. A recent article looks at whether CWD prions can propagate in or damage human brain organoids. It is a very human model system. The general answer is no, thus suggesting a strong species barrier between the CWD prions from cervids (deer and such) and humans. The authors note limitations of the work... The exact nature of organoids is not fully understood. They did not test everything possible. And importantly, there is no certainty that new prions that might arise in cervids would have the same properties as those they tested.

* News story: NIH study shows chronic wasting disease unlikely to move from animals to people -- Study of cerebral organoids reinforces evidence for substantial species barrier. (NIH, May 17, 2024.) The current article is the first one listed there (dated 2024).
* The article, which is open access: Lack of Transmission of Chronic Wasting Disease Prions to Human Cerebral Organoids. (Bradley R Groveman et al, Emerging Infectious Diseases 30:1193, June 2024.)

Added June 12, 2024.
The article above has gotten a lot of attention. Unfortunately, some people emphasize the immediate negative results and fail to note the limitations of the work. CIDRAP, a respected independent source on infectious diseases, discusses the concerns in a follow-up news story: NIH researchers never said there is no risk of CWD spillover to humans. (Mary Van Beusekom, CIDRAP, June 6, 2024.) Includes a link to an earlier "Statement" from CIDRAP about the article.

I have listed this item on my page Biotechnology in the News (BITN) -- Prions (BSE, CJD, etc) in the section Posts in my Musings newsletter.

Related Musings posts include...
* Human cortical organoids can survive -- and function -- in rat brains (October 22, 2022).
* Unusual nature of CWD; implications for transmission to humans (September 24, 2022).
* Also see previous item, immediately below.

Testing prion strains in fruit flies

May 22, 2024

The common prion diseases are based on a particular protein, found in mammals. What if we transferred the gene for that protein to flies (Drosophila)? They become susceptible to prion infection. Further, a recent article reports that such flies can be used to test the nature of prion strain variants. Strain testing with flies is much cheaper and much faster than with other systems available so far.

* I have not found a good news story for this item. The abstract of the article, below, will serve.
* The article, which is open access: Genetic modulation of CWD prion propagation in cervid PrP Drosophila. (Alana M Thackray et al, Biochemical Journal 480:1485, October 2023.)
* The following page is an overview of the project, not just the current article. (It is from a site describing publicly funded research.) Rapid bioassay of cervid prions in PrP transgenic Drosophila: addressing the threat to animal and human health from Chronic Wasting Disease. (UKRI, updated April 18, 2024.)

* I have listed this item on my page Biotechnology in the News (BITN) -- Prions (BSE, CJD, etc) in the section Posts in my Musings newsletter.
* Also see next item, immediately above.

Harvesting methane from the air?

May 15, 2024

Various ideas for removing carbon dioxide from the air are being considered. But what about methane? In the short term, it is an important contributor to climate change. There are bacteria, called methanotrophs, that can grow on methane. However, they do not do well on the low methane levels in the atmosphere. A recent article reports a methanotroph that can grow at relatively low methane levels. It offers the possibility of removing CH₄ from the air, especially in areas of high methane concentration -- near sources of atmospheric methane.

* News story: Bacteria that 'eat' methane could slow global heating, study finds -- Technology has the potential to make deep cuts to emissions of the potent greenhouse gas but requires major investment. (Oksana Pyzik, Guardian, August 22, 2023.)
* The article, which is open access: A methanotrophic bacterium to enable methane removal for climate mitigation. (Lian He et al, PNAS 120:e2310046120, August 21, 2023.)

Also see...
* Among posts about capturing CO₂... Precipitating CO₂ from air (July 30, 2022).
* Climate change: Should we focus on methane? (March 24, 2012).

What if the sidewalk would remove the snow for you?

May 8, 2024

It's a simple idea. If concrete could generate heat when it gets cold, it could melt the snow. To do that, the concrete includes a liquid that will freeze at an appropriate temperature (near 0° C). Freezing releases heat. A new article reports some success in getting this to work. The key is developing a material that is liquid in the concrete, freezes when it gets cold (releasing heat), and is compatible with the concrete. A pilot test on the university campus shows that the self-heating concrete works. Practical in the real world? We'll see.

* News story: Drexel's Self-Heating Concrete Is One Step Closer to Clearing Sidewalks Without Shoveling or Salting -- Field Testing Shows Concrete Can Warm Itself When Temperatures Fall. (Drexel University, March 18, 2024.) Includes a photo from the pilot test (though it is not labeled).
* The article: Development of Self-Heating Concrete Using Low-Temperature Phase Change Materials: Multiscale and In Situ Real-Time Evaluation of Snow-Melting and Freeze-Thaw Performance. (Robin Deb et al, Journal of Materials in Civil Engineering 36:04024102, March 18, 2024.)

See an earlier post on engineering the properties of concrete: Using the walls of a building as a rechargeable battery? (May 24, 2021).

Retraction: High-T superconductivity?

May 1, 2024

See retraction note at the top of: Superconductivity near room temperature: let's try again, now using lutetium (March 21, 2023).

April 2024

Possible transmission of CWD to humans?

April 24, 2024

We have noted that there is no evidence for transmission of CWD to humans. A recent meeting presentation suggests a possible pair of cases. The key point is that two people who hunted deer in the same area, with a known significant level of CWD, both developed a prion disease. The argument that they acquired the disease from deer is not strong, but it may open up an area for further observation. (The disease was characterized as CJD, but there is no simple way to show it wasn't due to CWD.)

* News stories:
- Study Suggests Possible Link Between CWD and Fatal Human Disease - But with Many Open Questions. Should you be alarmed? Probably not if you read the fine print. The study merely concludes that a link can't be ruled out and that more study is needed. (Will Brantley, Field & Stream, April 18, 2024.) A brief item about the new work, with some flavor of the response. The subtitle is a reasonable summary.
- Does 'zombie deer disease' pose risks for humans? (Jennifer Chesak, BBC, April 19, 2024.) A broad discussion of the CWD risk, written earlier this year. It was updated to include a brief mention of the current report.
* The article -- actually an abstract of a meeting presentation; it is open access: Two Hunters from the Same Lodge Afflicted with Sporadic CJD: Is Chronic Wasting Disease to Blame? (P7-13.002). (Jonathan Trout et al, Neurology 102 (17_supplement_1), April 9, 2024.) From the 2024 Annual Meeting, American Academy of Neurology.

Some background: Unusual nature of CWD; implications for transmission to humans (September 24, 2022). CWD = chronic wasting disease.

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

Improving ventilation reduces COVID

April 17, 2024

The topic was introduced in the background post listed below. A new article provides some data. The incidence of COVID was reduced with better ventilation. The quality of ventilation was judged by air flow measurements, CO₂ levels, and the quality of air filters. The simple measurement of CO₂ proved to correlate with COVID incidence. The careful (but small) study was made possible by a special situation. A small school for children with severe disabilities was kept open during the pandemic, with special attention.

* News story: Study links air quality improvements to fewer school COVID cases. (Lisa Schnirring, CIDRAP, April 4, 2024.)
* If you would like to see the news story from the university... The one linked on the page above is garbled. Here is a link to the original: Air Quality in Schools: Shielding Kids with Intellectual and Developmental Disabilities from COVID. (Susanne Pallo, University of Rochester Medical Center, March 28. 2024.)
* The article, which is open access: Ventilation during COVID-19 in a school for students with intellectual and developmental disabilities (IDD). (Martin S Zand et al, PLoS ONE 19:e0291840, April 3, 2024.)
* The (US) CDC has recently posted a page about improving ventilation, to reduce COVID and, more generally, respiratory infections. News story: CDC releases ventilation guidance for curbing indoor respiratory virus spread. (Lisa Schnirring, CIDRAP, March 25, 2024. First item on the page.) Links to the CDC page. Direct link to the CDC page: Ventilation Can Reduce Exposure to Respiratory Viruses in Indoor Spaces. (March 22, 2024)

Background post: Briefly noted... Improved ventilation to reduce COVID transmission (September 23, 2020).

COVID posts are listed on my page for BITN -- Other topics in the section SARS, MERS (coronaviruses).

The gut microbiome and Alzheimer's disease

April 12, 2024

A recent article reports an interesting experiment, with provocative results. The simple story is that transplanting gut microbes from (human) Alzheimer's disease (AD) patients to healthy young rats led to cognitive decline in the rats. The treated rats showed less development of new neurons in the hippocampus. Does this mean that AD leads to changes in the gut microbiome, and that such changes feed back to affect the brain? These are questions that need to be addressed.

* News story: Is Alzheimer's disease transmissible? Experiments with gut microbiota yield surprising results. (Vladimir Hedrih, PsyPost, February 19, 2024)
* Commentary accompanying the article: Microbial manipulation of memories and minds. (Carolina Gubert & Anthony J Hannan, Brain 146:4791, December 2023. Excellent, as an overview of the current work, broader context, and the questions raised by the findings.
* The article, which is open access: Microbiota from Alzheimer's patients induce deficits in cognition and hippocampal neurogenesis. (Stefanie Grabrucker et al, Brain 146:4916, December 2023.)

Background post: Transmission of Alzheimer's disease in humans? (September 27, 2015).

Also see the preceding post, immediately below, for a related article. Both posts involve, in some broad sense, transmission of cognitive deficiency.

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.

Evidence for transmission of Alzheimer's disease by medical procedures

April 9, 2024

The article discussed above provided evidence that amyloid plaque related to Alzheimer's disease (AD) was transmitted by hGH used in medical procedures; there was no direct evidence for consequences, such as cognitive deficiency. A new article provides evidence that people who got that treatment did indeed get AD. It is not possible to prove they got the AD from the medical treatment, but it is likely. Thus there is now good evidence that AD can be transmitted by the amyloid plaque. Establishing that as a principle is interesting. It should be stressed that the specific procedure used here is no longer used, and that other routes for AD transmission seem unlikely.

* News story: Scientists document first cases of acquired Alzheimer's due to decades-old childhood treatment -- New findings indicate old childhood growth hormone treatments may be linked to early onset Alzheimer's disease. (Tibi Puiu, ZME Science, January 30, 2024.)
* News story accompanying the article: Neurodegenerative diseases: Evidence for iatrogenic transmission of Alzheimer's disease. (Mathias Jucker & Lary C Walker, Nature Medicine 30:344, February 2024.)
* The article, which is open access: Iatrogenic Alzheimer's disease in recipients of cadaveric pituitary-derived growth hormone. (Gargi Banerjee et al, Nature Medicine 30:394, February 2024.)

More about transmission of AD: Transmission of Alzheimer's disease in humans? (September 27, 2015).

Also see the next post, immediately above, for a related article.

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.

Bitcoin and the origin of life

April 3, 2024

Well, sorta. The team of scientists used the vast computer network called blockchain to explore what would happen if a collection of likely primordial chemicals was given a long time to react and develop. It is the largest simulation of suspected origin-of-life chemistry. Interestingly, some metabolic sequences similar to those of modern life emerged, leading to the sustained production of certain chemicals. It is hard to know what to make of such work. Perhaps most important for now is that they have introduced a new tool for studying pre-biotic chemistry. We'll see where this leads in further work.

* News story: Chemists Use Blockchain To Simulate Over 4 Billion Chemical Reactions Essential To The Origins Of Life. (Astrobiology (Cell Press), January 25, 2024.)
* The article: Emergence of metabolic-like cycles in blockchain-orchestrated reaction networks. (Rafał Roszak et al, Chem 10:952, March 14, 2024.)

More pre-biotic chemistry... A special role for cyanide in the chemistry of early life? (April 25, 2022).

March 2024

Tardigrade resistance to stress -- how do they do it?

March 27, 2024

Tardigrades (water bears) are noted for their resistance to environmental stresses; see the background post listed below. A new article reveals part of the molecular mechanism involved in sensing stress and triggering formation of the "tun" state of dormancy. Briefly, reactive oxygen species (ROS), such as oxygen radicals, oxidize the amino acid cysteine; the oxidized cysteine is central to signaling. Addition of ant-oxidants blocks the transition that allows the animals to survive the stress. When the stress is removed, the cysteine oxidation is reversed -- and normal life activity resumes. One more part of the story.

* News story: Tun Formation in Tardigrades is Mediated by Reactive Oxygen Species, Study Shows. (Sci.news, January 18, 2024.)
* The article, which is open access: Chemobiosis reveals tardigrade tun formation is dependent on reversible cysteine oxidation. (Amanda L Smythers et al, PLoS ONE 19:e0295062, January 17, 2024.)

Background post: How the tardigrades resist desiccation (April 10, 2017). The article of this earlier post is reference 16 of the current article.

Oldest mosquito fossils: bloodsucking males

March 20, 2024

A recent article uncovers some old mosquitoes, preserved in amber. They are of interest for two reasons. First, they are the oldest mosquitoes we have seen. Second, they are males with mouth parts that suggest they drank blood. In modern mosquitoes, only the females suck blood.

* News story: Oldest mosquito fossil shows males were once bloodsuckers too -- Oldest fossil mosquito found in Lebanese amber suggests ancient males also fed on blood, revising our knowledge of mosquito evolution. (Tibi Puiu, ZME Science, December 4, 2023.)
* The article: The earliest fossil mosquito. (Dany Azar et al, Current Biology 33:5240, December 4, 2023.)

A recent post about mosquitoes: Briefly noted... The mosquito microbiome - inside and out (February 28, 2023).

This item is listed on my BITN-Other topics page under Malaria. This section also includes some general items about mosquitoes.

Can plants serve as carrier in the transmission of prion diseases?

March 13, 2024

A recent article shows that plants can take up prions via their roots, with resulting prion accumulation in the parts of the plant above ground. Mice fed such plants can acquire prion disease. As so often with prion work, the real-world implications are not clear, but this is another example of how hardy prions might spread through the environment. (The work here was done with two lab-adapted prion strains, from transmissible mink encephalopathy and scrapie.)

* News story: Plants can take up CWD-causing prions from soil in the lab. What happens if they are eaten? (Mary Van Beusekom, CIDRAP, February 22, 2024.)
* The article, which is open access: Plants as vectors for environmental prion transmission. (Christina M Carlson et al, iScience 26:108428, December 15, 2023.)

More about prion transmission: Can ticks transmit CWD prions? (May 28, 2023).

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

Lab-grown coffee

March 6, 2024

Musings has discussed developing meat grown in lab culture; see background post listed below. Now, coffee. The idea is simple... Grow coffee cells in the lab, roast them -- and brew. A recent article describes considerable work on the process -- and the product. How is the product? Mixed reviews for now. Promising, but further work is needed. In principle, growing coffee in a controlled fermentation process offers better control over the nature of the product.

* News story: Production process for cell-based coffee published. (European Biotechnology, December 12, 2023.) This is fairly light on the current article, but it has some interesting broader points. It notes a suggestion that the coffee process may be economically much more favorable than cell-based meat. And it notes similar work to develop a cell-based cocoa process.
* Also see... An interview with the group leader back in 2022: Lab-Grown Coffee. (Vera Koester & Heiko Rischer, Chemistry Views, January 4, 2022.) It focuses on the coffee work, but is also more broadly about "cellular agriculture". Author HR of this item is the senior author of the article listed below.
* The article, which is open access: Proof of Concept for Cell Culture-Based Coffee. (Heikki Aisala et al, Journal of Agricultural and Food Chemistry 71:18478, November 29, 2023.)

Background post: Tuning the protein and fat content of cultured meat (February 2, 2021).

Also see a recent post about coffee: A thermotolerant coffee plant, with high quality beans (June 8, 2021).

February 2024

An edible food wrapper, based on bacterial cellulose

February 28, 2024

A good portion of plastic use -- and waste -- is from food wrappings and bags. A recent article reports development of a new type of biodegradable wrapping. It is based on bacterial cellulose, which can be made by a fermentation process. The wrapping product is complex, with various ingredients to achieve various goals. The results suggest the product is practical by several criteria, including that it is biodegradable, even edible. (There is no economic analysis in the article.)

Cellulose is made by various bacteria. The chemical nature and biosynthesis is the same as for plant cellulose. However, bacterial cellulose is usually free of other components (such as lignin), and is highly crystalline. One of the more prolific cellulose-producing bacteria is Komagataeibacter xylinus (previously known as Acetobacter xylinum). The organism used in the current work is from a traditional fermentation; it is likely this species.

* News story: Material scientists set out to beat plastic packaging on three fronts. They succeeded. (Emma Bryce, Anthropocene, July 7, 2023.)
* The article: Edible, strong, and low-hygroscopic bacterial cellulose derived from biosynthesis and physical modification for food packaging. (Ka Man Cheung et al, Journal of the Science of Food and Agriculture 103:6625, October 2023.)

This post is listed at: History of plastic -- by the numbers (October 23, 2017).

... and on my page Organic/Biochemistry Internet resources under Carbohydrates.

A personal note... I was involved with an early effort to develop a practical process for the large scale production of bacterial cellulose. For an example of the work, see US Patent 5079162 -- and note the "inventor" listing. (The work was a collaboration between Cetus Corporation, where I was, and Weyerhaeuser. The project was later sold to Kelco; they indeed developed it into commercial products. The current work is about a far more complex product.)

Is it worthwhile to sleep for four seconds?

February 20, 2024

Well, if you do it ten thousand times in a day, you will accumulate over ten hours of sleep. That seems to be the approach of one group of Antarctic penguins, as reported recently. Interestingly, the work was done on penguins in the wild, rather than under controlled lab conditions. The animals had electrodes implanted in their brains prior to the work, but were then observed back in the wild, with extensive monitoring of the environment. As so often, novel findings raise more questions than they answer. In this case, questions about the nature of sleep and questions about the operation of penguin colonies.

* News story: Penguins obtain large quantities of sleep via seconds-long microsleeps -- New study shows the most fragmented sleep ever recorded in an animal. (Max Planck Institute for Biological Intelligence, November 30, 2023.)
* News story accompanying the article: Ecology: Penguins snatch seconds-long microsleeps -- Chinstrap penguins fall asleep thousands of times per day in the wild. (Christian D Harding & Vladyslav V Vyazovskiy, Science 382:994, December 1, 2023.)
* The article: Nesting chinstrap penguins accrue large quantities of sleep through seconds-long microsleeps. (P-A Libourel et al, Science 382:1026, December 1, 2023.)

Also see...
* Sleep genes and Alzheimer's disease? (May 28, 2022).
* Does penguin language conform to the laws of human language? (February 18, 2020).

This post is listed on my page for Biotechnology in the News (BITN) -- Other topics in the section on Brain.

Evidence for fission of superheavy elements in stars

February 13, 2024

Observations of elemental abundances in 42 stars show that the abundances of some elements seem correlated. The correlations suggest that the elements arose together, by fission of heavy elements. As a (simplified) example, the abundances of silver (Ag; atomic number Z = 47) and europium (Eu, Z = 63) are correlated; they may have arisen by fission of nuclei of darmstadtium (Ds, Z = 110). The full data is more complex, but consistent with their models of fission processes. The work provides the first good evidence for such heavy element fission in stars. It also suggests the existence of superheavy elements there. (We explicitly note that there is no claim of directly detecting superheavy elements in stars, and no claim implicating elements heavier than those already made on Earth. So far.)

* News story: First hints of nuclear fission in cosmos revealed by models, observations -- Fission models find clear fingerprints of nuclear process never before directly observed in stars. (Los Alamos National Laboratory, December 7, 2023.)
* The article: Element abundance patterns in stars indicate fission of nuclei heavier than uranium. (Ian U Roederer et al, Science 382:1177, December 8, 2023.)

I have listed this item on my page Introductory Chemistry Internet resources in the section Nucleosynthesis; astrochemistry; nuclear energy; radioactivity. There is a list of related Musings posts.

Enhancing hypnotizability

February 7, 2024

A new article reports transient enhancement of the ability of people to be hypnotized, by magnetic stimulation of the brain. The treatment is guided by neuroimaging of the individual, and is non-invasive. The induced hypnotizability was reported in a sample of people with the chronic pain disorder fibromyalgia. The hope is that stimulating hypnotizability may allow the use of hypnosis, an effective treatment, on more people.

* News story: Stanford scientists boost hypnotizability with transcranial magnetic brain stimulation. (Eric W Dolan, PsyPost, January 4, 2024.)
* The article, which is open access: Stanford Hypnosis Integrated with Functional Connectivity-targeted Transcranial Stimulation (SHIFT): a preregistered randomized controlled trial. (Afik Faerman et al, Nature Mental Health 2:96, January 2024.)

* There are no previous Musings posts on hypnosis or fibromyalgia.
* I have listed this item on my page Biotechnology in the News (BITN) -- Other topics under Brain.

January 2024

How much greenhouse gases do people emit?

January 31, 2024

Of course, we emit CO₂ from burning our food. That is presumably carbon-neutral, since the food is derived from atmospheric CO₂. A new article examined how much methane (CH₄) and nitrous oxide (N₂O) people emit. Both are more potent greenhouse gases than CO₂. The big answer is that the amounts are measurable, but are minor contributors to the global greenhouse gas budget. Attempts to sort out why people vary in emission of these gases were not very fruitful; the study was too small to yield much on that question. It is likely that both gases arise largely from our microbiota.

* News story: We calculated the UK's greenhouse gas emissions from people breathing out -- here's what we found. (Nicholas Cowan & Mathew Heal, The Conversation, December 13, 2023.) From two of the authors of the article.
* The article, which is open access: Measurements of methane and nitrous oxide in human breath and the development of UK scale emissions. (Ben Dawson et al, PLoS ONE 18:e0295157, December 13, 2023.)

Also see: Space-based observation of atmospheric methane -- and the Four Corners methane hotspot (December 29, 2014).

Hydrogen gas as an anti-aging agent?

January 24, 2024

A new article reports that treatment of aged mice with hydrogen gas improved repair of damaged bone. The treatment was done by injecting a scaffold material with a high absorbed content of H₂ near the damage site. Development of the scaffold material was a central part of the work. It is thought that the H₂ acts as an anti-inflammatory agent, but its effects are broad and complex; there may be various mechanisms. An intriguing article.

* News story: Hope for seniors: Hydrogen-releasing scaffold aids bone regeneration in Chinese study. (Liang Shuang, China Daily, December 14, 2023.) (This story incorrectly says the work was done in rats.)
* The article, which is open access: Local H₂ release remodels senescence microenvironment for improved repair of injured bone. (Shengqiang Chen et al, Nature Communications 14:7783, November 27, 2023.)

More aging: How about having your immune system remove senescent cells? (September 27, 2020).

This item is listed on the page for BITN -- Other topics in the section on Aging.

Nitrogen-9 and 5-proton decay

January 16, 2024

Nitrogen atoms have seven protons in the nucleus. The common isotope of N also has seven neutrons, giving us N-14. That isotope accounts for over 99% of the N around us. In fact, that is the lightest stable isotope of N. A new article provides evidence for the existence of N-9 -- with only two neutrons. Lifetime? Immeasurably small, apparently about 10^-21 seconds (1 zeptosecond). In fact, it is not really a bound nucleus, but rather an observable resonance structure, at the limits of nuclear existence. It gives off five protons (more than half of the original nucleons) in three steps, leaving a helium nucleus (alpha particle). It is the first nuclear decay process found to give off five protons.

* News story, from the publisher's news magazine: Five Protons Spew Out of Extreme Nucleus -- A highly unstable nucleus that decays by emitting five protons has been observed, offering an extreme case for testing nuclear models. (Michael Schirber, Physics 16:186, October 27, 2023.)
* The article: Strong Evidence for ⁹N and the Limits of Existence of Atomic Nuclei. (R J Charity et al, Physical Review Letters 131:172501, October 27, 2023.)

Another "lightest" isotope: Briefly noted... The lightest uranium (November 30, 2021).

This item is listed on my page Internet resources: Introductory Chemistry under Nuclei; Isotopes; Atomic weights.

How reindeer see in the dark of the arctic winter

January 9, 2024

During the winter, reindeer feed on white lichen (often called reindeer moss). It is invisible to the human eye against the snowy background. Reindeer eyes undergo seasonal structural changes; these changes extend the reindeer vision into the ultraviolet (UV). New work shows that the lichen is visible in the UV during twilight. The white lichen absorbs UV, whereas the white snow reflects it. The work explains how an unusual feature of reindeer vision is advantageous, allowing them to find food in the extended twilight of the long arctic night. The article also suggests that the vitamin-rich lichen may provide protection against UV damage. (Interestingly, the work was done on the habitat of a reindeer herd in Scotland.)

* News story: Reindeer have a secret superpower that helps them find food the dark Arctic winter. (Fermin Koop, ZME Science, December 19, 2023.) (Yes, there seems to be a word missing in their title. Maybe they will fix it at some point.)
* The article, which is open access: Reindeer and the quest for Scottish enlichenment. (Nathaniel J Dominy et al, i-Perception, in Volume 14, December 15, 2023.) A short readable article, with interesting discussion of reindeer and UV. The article acknowledges the unusual nose of one famous reindeer, but also suggests that it is his "blue-eyes that allow him to find dinner". (p 5 of the pdf)

More about reindeer: What's a dia? Bumblebees and reindeer don't agree. (December 6, 2010).

Among many posts on animal vision... Chromatic aberration: is it how cephalopods see color with only one kind of photoreceptor? (October 14, 2016).

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