Musings: May 2019 to ?? (current posts)

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

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   May 15 (Current e-mail)
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New items

Posted since most recent e-mail; they will be announced in next e-mail, but feel free...

Could we repel mosquitoes by playing loud music they don't like?

May 18, 2019

Well, here are some results, from a recent article...

This test measured how long it took for mosquitoes to make their first bite, under controlled lab conditions.

The variable was whether or not music was playing: Audio player status, OFF or ON.

The victims were hamsters. (The mosquitoes were Aedes aegypti. Females were used for the test; only females bite for blood meals.)

It is clear that the mosquitoes were much slower to bite when the music was playing.

   This is Figure 3 from the article.

Here is the music... Music video: Skrillex - Scary Monsters And Nice Sprites. (YouTube, 4 minutes.)

The article contains other data from such tests. The music reduced the number of bites over a set time period, and also reduced the frequency of matings. That is, there is a general pattern that the activity of the mosquitoes is disrupted by the music.

Is there some reason to do such tests? Yes -- and it is something that has been noted in Musings [link at the end]. Mosquitoes communicate with each other during mating rituals with sound -- from their wings. Further, the scientific literature contains many studies of the effects of extraneous sounds on insect behaviors.

What else can we say about this? Not much. There are no other variables in the work. Just OFF/ON. The article includes a vibragram of the song, which shows that it contains "strong sound pressure/vibration with constantly rising pitches" (Section 2.2). The authors conclude that the song is "noisy".

There are reasons to find this article amusing -- starting with its title. However, the broad issue of how sound affects insect behavior is interesting. Can we learn to use sound as a weapon against insects? Perhaps we should be open to the possibility.

News stories:
* Blasting This Skrillex Track Will Reduce Mosquitoes' Desire to Bite, Study Finds. (J Bowler, Science Alert, April 1, 2019.)
* Here's how Skrillex's music could help fight Zika and dengue fever. (M Sanicas, ZME Science, April 4, 2019.)

The article: The electronic song "Scary Monsters and Nice Sprites" reduces host attack and mating success in the dengue vector Aedes aegypti. (H Dieng et al, Acta Tropica 194:93, June 2019.)

Background post on how mosquitoes sing: Science: Love songs (March 26, 2009). The article discussed in this post is among many references in the current article on insects and sound.

Among other posts on repelling mosquitoes: Can chickens prevent malaria? (August 12, 2016). The synergy between the current post and this older one needs to be tested.

There is a section of my page Biotechnology in the News (BITN) -- Other topics on Dengue virus (and miscellaneous flaviviruses). It includes a list of related Musings posts.

There is more about music on my page Internet resources: Miscellaneous in the section Art & Music. It includes a list of related Musings posts.

Progress toward making a homogenous product from diverse lignins

May 17, 2019

Wood contains lignin and cellulose. The lignin presents a special problem for those wanting to make useful products from wood. Lignin contains multiple types of subunits, and the chemical linkages between subunits are not easily attacked. Musings has noted the problem before [link at the end].

A recent article develops another approach to using lignin. Briefly, the products from a general treatment of three kinds of lignin are fed to a specially-developed bacterial strain, which converts all of them to the same final -- and useful -- product.

The following figure shows the plan. For now, just follow the general flow; don't worry about the details of structure (which are hard to read at this scale).

The top row shows the structures of the three types of lignin, and gives each one a letter, which is from one of the key chemicals involved.

The second row (thin box) shows some general processing, which leads to the three specific chemicals at the top of the main (bottom) box.

That big bottom box shows how a particular strain of bacteria metabolizes those three chemicals. In particular, note two red "X", showing steps that the scientists "knocked out" in the new strain they developed. As a result of those two knock-out changes, the metabolism of all three starting materials is diverted to a single final product: PDC (near the lower right, just above the red X there).

This is Figure 1 from the article.

If you want details of the chemical structures, check the web site for the article, which includes a high-res version of the figure.

Briefly, the three types of lignin units differ by the number of -OCH3 (methoxy) groups on the ring: 2, 1, 0 from left to right. Those groups are difficult to modify, but are important for the properties of the ultimate product.

With the original strain, before the red-X knockouts, all three starting chemicals end up being converted to pyruvate + oxaloacetate, as shown at the lower right. Those chemicals are part of general metabolism.

The following figure gives an idea of how it works, though this experiment only tests two of the three types of lignin.

The left and right sides of this figure are for two of the three types of lignin. In each case, the modified bacterial strain is grown on glucose, and given the lignin product: vanillic acid (left) or p-hydroxybenzoic acid (right). Growth of the bacteria is measured (top graphs), as are the concentrations of some metabolites (bottom graphs),

The top row shows the growth of the bacteria over time. The general result is that the bacteria grew in both cases (even if one of the growth curves looks odd).

In the bottom graphs, the red curve rises in both cases. That is for PDC, the desired product.

Some curves decline. They are the curves for glucose (yellow) and for the lignin material that was added at the start in each case (green or blue). That is, the things that were fed were used up, and the desired product accumulated. Checking the numbers on the y-axis, it appears that about 2/3 of the lignin material was converted to PDC in each case. (Actual conversion, average from multiple tests: 81% and 73%.)

(One curve is very low all the time; that is for one of the intermediates, but it need not concern us here.)

The bacteria used in this experiment, on two lignin types, had only one of the red-X blocks (the one at the lower right). The second block is needed only for the third lignin type.

   This is Figure 3 from the article.

In another test, the scientists used a mixture of lignin types with the final doubly-blocked bacteria. PDC was made at about 60% efficiency.

That the conversion to PDC is, reproducibly, less than 100% suggests that some of the lignin material is being consumed for growth. Thus there may be other pathways involved. Further work to reveal and block those pathways could be worthwhile.

Why make PDC (2-pyrone-4,6-dicarboxylic acid)? It is a dicarboxylic acid, and may be useful in making polyester plastics. Again, an important issue here is moving toward making one single (major) product.

It's a new type of development. As usual with articles of this type, there is no economic analysis -- and no claim that they have achieved a useful process.

News stories:
* Engineered microbe may be key to producing plastic from plants. (Science Daily (C Barncard, University of Wisconsin-Madison), March 6, 2019.)
* Biological funneling of aromatics from chemically depolymerized lignin produces a desirable chemical product. (Great Lakes Bioenergy Research Center, March 8, 2019.)

The article, which is freely available: Funneling aromatic products of chemically depolymerized lignin into 2-pyrone-4-6-dicarboxylic acid with Novosphingobium aromaticivorans. (J M Perez et al, Green Chemistry 21:1340, March 21, 2019.)

A background post about processing lignin: Turning lignin into a useful product (April 11, 2015).

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. Why is this post about energy resources? Indirectly... Utilization of lignin is coupled to that of cellulose; the latter is often used for biofuel.
* Also see the section on that page for Aromatic compounds.

May 15, 2019 (Current e-mail)

Briefly noted...

May 15, 2019

Ebola vaccine. The Ebola news from the current outbreak in the Democratic Republic of the Congo (DRC) is mostly depressing. However, results from vaccination, announced recently, are encouraging. The vaccination work was done by the ring strategy discussed in earlier posts, administering vaccine to contacts of known cases. Analysis suggests that the vaccine is 97% effective. Further, the death rate of those who do get the disease after vaccination is very low. The announcement, from the DRC and WHO, is preliminary; a proper scientific article is promised.
* News story: Ebola cases climb by 44 as vaccine trial affirms high efficacy. (L Schnirring, CIDRAP, April 15, 2019.) Links to the report, which is freely available; see the item near the end "Apr 13 INRB WHO preliminary VSV-EBOV results".
* For more about Ebola... Ebola and Marburg (and Lassa) (a section of a BITN page). This news is noted there. The section also has a list of Musings post about Ebola, including the vaccine and the ring-vaccination approach.

Failure to regenerate heart tissue: role of thyroid hormone

May 14, 2019

Regeneration of heart muscle, to repair a damaged heart, is an important topic. At least, humans think so, especially as more reach extended ages. It's not so clear that Nature thinks the topic is high priority.

Why don't humans do heart regeneration? One level of answer has become clear over recent years. Most of the muscle cells in human hearts are not ordinary diploid cells. They are mostly polyploid (with multiple chromosome sets). The advantage of that is not particularly clear, but the disadvantage is clear: being polyploid makes ordinary cell division difficult.

If you look at a wide range of vertebrates, there is a general correlation: the higher the percentage of diploid cells in heart muscle, the more likely that heart regeneration will succeed. But that just pushes the question back... Why do we have so few diploid heart muscle cells?

The following figure, from a new article, offers some clues...

Three graphs. For all of them, the y-axis is the percentage of cardiomyocytes (CM; heart muscle cells) that are diploid, for various animals. (Caution... the scales are not the same.)

That percentage of diploid CM is plotted against the standard metabolic rate (SMR; part A), body temperature (part B), and level of T4, a thyroid hormone (part C). (The standard metabolic rate is normalized to body weight. That may sound complicated, but it is a known factor: small animals have faster metabolism than big ones for the same amount of mass. They simply correct for that known factor.)

In each case, there is a good trend. The % diploid CM declines as the other plotted parameters increase. We don't need any more detail than that from this figure.

   This is Figure 2 from the article.

Those graphs show correlations. Is it possible that any of these things might be related by cause? In fact, it is known that thyroid hormone is involved in the control of body temperature and metabolic rate.

Is it possible that thyroid hormone controls the nature of cardiomyocytes -- and therefore heart regeneration? That question is subject to experimental testing; the article goes on to do some tests.

A simple test would be to elevate thyroid hormone levels in an annual that normally shows good heart regeneration. Zebrafish, for example; it is a common subject for studying heart regeneration in the lab. Doing that led to a marked reduction in heart regeneration in a standard test.

A more interesting test would be to see if we could stimulate heart regeneration in an animal where it usually fails -- by blocking the action of thyroid hormone. This is a technically complicated test, but the basic logic is straightforward. Mice were genetically engineered so that thyroid activity in the heart was blocked. Such mice were given an artificial heart attack, and their recovery was followed.

Here are some results...

The graph shows ejection fraction (EF) percentage vs time. The EF% is a measure of heart function.

Before you get lost in a blur of data points (and asterisks), look at the final data set, to the right, for day 28 following the heart attack. It's clear that the red-square mice are doing much better than the black-circle mice.

The red squares are for the engineered mice, where the thyroid hormone doesn't act on the heart. The black circles are for ordinary (control) mice.

It's quite clear: the mice recovered from their heart attack much better if the action of thyroid hormone in the heart was blocked.

Let's fill out what the data shows. The first data set is labeled baseline; this is before the heart attack. The two types of mice gave similar results, with EF above 80%. (The vertical line by that data set says NS, for not significantly different.)

At the first measurement following the injury (7 d), the EF is lower. Visual inspection suggests a small difference between the two types of mice, but statistically it is NS.

What happens after that is interesting. For the engineered mice, the heart function gradually improved. By the end of the experiment, it was about what it was at baseline. The control mice showed steadily declining heart function.

   This is the right-hand part of Figure 4G from the article. The full Figure 4 shows a variety of data consistent with the small part shown here.

Consider this mouse experiment along with the zebrafish one mentioned briefly before that... The evidence supports a role for thyroid hormone in controlling the ability to regenerate heart tissue.

It's interesting for two reasons. First, there is a story of how warm-blooded animals developed. We know that thyroid hormone is a key player in that story; we now associate that with loss of ability to regenerate heart tissue.

Second, we must wonder about the implications for human health. including possible therapeutic intervention. Some comments...
- We have no direct evidence about what is going on in humans. We might, of course, suspect that humans follow the general picture developed here, but we have no details. For example, we do not know whether the mouse experiment discussed above would work in humans -- even if we could do it.
- That mouse experiment is not possible with humans. Further, we don't know what kind of intervention would be needed. We might imagine having a drug that inhibits thyroid action in the heart. However, it seems unlikely that giving such a drug at the time of heart injury would be helpful. When would it have to be given? We don't know.

It's a fascinating article. It should stimulate a range of work. But it's important to realize that any application to human health is speculative at this point.

News stories:
* Warm-Blooded Animals Lost Ability to Heal the Heart. (C Intagliata, Scientific American, March 7, 2019.) Podcast, with transcript.
* Hormone Made Our Ancestors Warm-Blooded but Left Us Susceptible to Heart Damage. (J Alvarez, University of California San Francisco, March 7, 2019.) From the lead institution.

* News story accompanying the article: Evolution: Lost in the fire -- Thyroid hormones tip the balance between regeneration and temperature regulation. (S Marchiano & C E Murry, Science 364:123, April 12, 2019.)
* The article: Evidence for hormonal control of heart regenerative capacity during endothermy acquisition. (K Hirose et al, Science 364:184, April 12, 2019.)

A post about the importance of diploid cells for regeneration: Heart regeneration? Role of MNDCMs (November 10, 2017).

A post about heart regeneration in zebrafish: Zebrafish reveal another clue about how to regenerate heart muscle (December 11, 2016).

Among posts about thyroid function...
* Bigger spleens for a bigger oxygen supply in Sea Nomad people with unusual ability to hold their breath (July 2, 2018).
* How the giant panda survives on a poor diet (August 2, 2015).

Among posts about the complexity of warm-bloodedness... Facultative endothermy: a lizard that is warm-blooded in October (February 1, 2016). Links to more.

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

Caffeine: is it good for solar cells?

May 13, 2019

A recent post was about how caffeine improves the health of premature babies [link at the end].

We now have an article about how caffeine improves the health of solar cells.

Let's start with some bottom-line data, so you can see that there is a significant effect...

The graph shows the power conversion efficiency (PCE) of the solar cells over time. PCE is shown normalized to the initial value, set as 1.0 (for each device). That is, this is a test of the stability of the solar cells. (The actual value for the initial PCE was about 20%.)

The red curve is for the regular solar cells (controls). The black curve is for the solar cells with caffeine.

The control solar cells lose efficiency from the start. They are down by about 1/3 over the first 100 hours (4 days). The caffeinated solar cells are still operating at about 85% of initial efficiency at the end of the test (1300 hours = 54 days).

   This is Figure 4A from the article.

That is, caffeine improves the health of the solar cells. By a lot.

What's going on?

First, this work is about a specific type of solar cell, called perovskite. That term refers to a type of crystal structure. Perovskite solar cells are a recent development. There has been considerable progress, with the efficiency of perovskite cells now approaching that of traditional silicon-based solar cells. (As noted earlier, the cells in the current work were operating with about 20% efficiency, which is quite good. The caffeine led to a slightly higher efficiency.)

Perovskite cells have the potential to become a major type of solar cell; they are cheaper and easier to make than traditional cells. However, they have one major limitation: they are unstable. The current work addresses that limitation -- with some success, as the figure above indicates.

Is this all a joke? Well, it may have started as one, according to the news coverage. But then someone did the experiment -- and looked at the details of the chemical structures. Not only does a little caffeine (1% by weight) improve the performance of these solar cells, but the scientists have a good idea why. The caffeine fits into the molecular structure and stabilizes it.

Is this a practical improvement? Probably. Caffeine is an inexpensive chemical, available in large quantities. To be fair, conventional silicon-based solar cells are even more stable than what is shown above for the caffeine-perovskite cells. There is more to be done, but the article is an encouraging development.

News stories:
* Researchers figure out how coffee can boost (some) solar cells. (A Micu, ZME Science, April 26, 2019.)
* Science: Caffeine improved the performance of perovskite solar cells. (Solar Builder, April 29, 2019.)
* Caffeine boosts perovskite solar cells. (B Dumé, Physics World, April 30, 2019.) Excellent overview.

The article: Caffeine Improves the Performance and Thermal Stability of Perovskite Solar Cells. (R Wang et al, Joule, in press. Scheduled for June 19, 2019. issue.)

Background post on caffeine... Using caffeine to treat premature babies: risk of neurological effects? (April 27, 2019).

Among recent posts on solar energy... Is solar energy a good idea, given the energy cost of making solar cells? (March 24, 2017).

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.

Why are some icebergs green?

May 11, 2019

Ice is complicated. Not just the various Roman-numbered forms you hear about from exotic lab work, but natural ice -- the stuff you find in Antarctica.


An Antarctic iceberg.

At the far left, it is a "bubbly blue-white". But some of it is quite green.

   This is Figure 3 from the article.

Why is part of the iceberg green?

The bluish ice at the left is glacier ice, made by snow consolidating into large rigid blocks of ice. Glacier ice is pretty much pure water, just as the snow is. The color is the normal color of large amounts of water.

The green ice is marine ice, formed as sea water freezes out. This happens at the bottom surface of ice, where sea meets ice. Marine ice contains things from the sea.

Marine ice can be various colors, presumably due to different "contaminants" from the sea. So, why is some of the marine ice green? The short answer is that we don't know. A recent article explores the question, but it may be more interesting for the exploration -- and the pictures -- than in actually finding an answer.

The figure also shows snow, which is presumably white -- though you couldn't tell that from this picture. Snow, too, is a form of ice, so we have three kinds of ice there.

Another figure in the article shows five kinds of ice in a natural Antarctic scene. Included is an ice cloud.

There are two general ideas for what causes the green icebergs. One is dissolved organic matter. We're not talking about algae growing on the surface. The green color is within the ice, and distributed rather uniformly. Maybe it is cellular debris, which might be within the sea. Green? It's not that the organic matter is green, but that it shifts the spectrum so that the ice appears green rather than blue. The other suggested cause of green ice is iron. The color of iron (more specifically, its oxides) is a complicated topic, but it is certainly plausible that it could make for green icebergs.

Here are some results...

The figure shows spectra for several kinds of ice -- all from one Antarctic iceberg.

Spectra. Albedo spectra. Albedo refers to the fraction of light reflected. An object with high albedo reflects a lot of light. (Albedo = 1 means total reflection. Albedo = 0 means no reflection; the object is dark.) The scientists are measuring the spectra for light reflected from various kinds of iceberg ice.

You can see that the two ices labeled as blue (top two on the left, where they are labeled) reflect mainly light with short wavelength: bluish light. For the two ices labeled as green, much of that blue light has also been removed. The green ices reflect less light, and it is more spread over the entire spectrum, with a slight peak in the middle.

   This is Figure 7 from the article.

That figure takes us from a qualitative observation of how we describe the ice color to a quantitative analysis of the nature of the reflected light.

Beyond that... There is much more analysis. The authors measure the amounts of dissolved organic matter and iron in iceberg samples. They end up arguing that iron, in the form of iron oxides, is the more likely cause of the green color. But the arguments are complex and incomplete. The spectral properties of ice with iron oxides are not well understood. The article has considerable discussion of the limitations of the work, and concludes with a plea for more data.

News stories. Both of the following stories provide excellent overviews, with more spectacular pictures.
* Why Are Some Icebergs Green? (C Prend, Oceanbites, February 1, 2019.)
* Mystery of green icebergs may soon be solved. (American Geophysical Union (AGU), March 4, 2019.)

The article, which is freely available: Green Icebergs Revisited. (S G Warren et al, Journal of Geophysical Research: Oceans 124:925, February 2019.)

Among posts about the Antarctic... IceCube finds 28 neutrinos -- from beyond the solar system (June 8, 2014). Links to more. But this one includes a picture.

Among posts about ice... Why is ice slippery? (September 9, 2018).

A post about iron in the oceans... Fertilizing the ocean may lead to reducing atmospheric CO2 (August 24, 2012). In the current work, the authors suggest that the iron in the icebergs is effectively being transported from the Antarctic continent to the iron-deficient oceans. If so, the high-iron icebergs could be playing an important role in determining the biological productivity of the Southern oceans. That issue is addressed in the post linked here.

May 8, 2019

Briefly noted...

May 8, 2019

Where should a self-driving car park during the day after it takes you to work? Parking is now so expensive in dense urban areas that it may be in the car's self-interest to not park at all. Instead, it should just cruise around the streets all day, probably at about 2 miles per hour -- thus increasing congestion on the streets. That's the conclusion of a recent analysis. It's a plea for reconsideration of policies.
* News story: Mean streets: Self-driving cars will "cruise" to avoid paying to park -- Autonomous vehicles "have every incentive to create havoc," transportation planner says. (J McNulty, University of California Santa Cruz, January 31, 2019.) Has an invalid link to the article, so...
* The article: The autonomous vehicle parking problem. (A Millard-Ball et al, Transport Policy 75:99, March 2019.)
* A post about self-driving (autonomous) cars: The moral car: when is it ok for your car to kill you? (July 23, 2016).

Denisovan man: beyond Denisova Cave

May 7, 2019

The story of Denisovan man is one of the great science stories of the decade. It is about a newly-discovered type of human, with the first publication on the topic in 2010. It started with a finger bone and a few teeth found in Denisova Cave, in Siberia. Those early samples of Denisovan man yielded enough DNA that we have a Denisovan genome, and can now track Denisovan genes in humankind throughout the modern world. But it is important to realize that those few samples have constituted the only direct physical evidence about Denisovan man. It is a story with much mystery, a scientific story very much in progress. Musings has noted several parts of the story [links at the end].

Now there is something new. Look...

A jaw bone (mandible).

To clarify...
- The left side (brownish) is real. The right side (gray) is a digitally constructed mirror image of the left side to make a picture of an entire symmetrical jaw.
- The image has been processed to remove extraneous mineral material on the outside.

That is, the picture here is based on a real bone, but with some processing.

   This is Figure 1b from the article.

This is the Xiahe mandible. A new article reports the characterization of the Xiahe mandible as being from a Denisovan. (Xiahe, where the bone was found, is a county in Gansu province, China.)

Why is this bone so exciting?
- First, it is now the largest sample of Denisovan man we have.
- Second, it is not from Denisova Cave. It is from China, from the Tibetan plateau.

The big question is, what is the evidence this is a sample of Denisovan man? The main results to support that claim are summarized in the following figure...

That's a genealogy chart of several hominids. You can see that the Xiahe specimen (thick line) clusters close to the Denisova Cave sample.

What's the basis of that grouping? The Xiahe sample has not yielded any usable DNA. However, it has yielded some protein (collagen). Sequencing of ancient proteins is another recent development -- and that is the basis of the grouping shown here.

   This is Figure 2 from the article.

How good is the story that the Xiahe specimen is Denisovan (or closely related)? Perhaps the biggest uncertainty is simply the limited amount of data at this point. "Denisovan" and "Xiahe" are each defined by one sample. The progress with Denisovans over the current decade has been remarkable. This is one more step. We'll see how it holds up.

Further comments...

The Xiahe specimen is dated to about 160,000 years ago. It is older than the Denisova Cave specimens. It is also the oldest known human sample from the Tibetan Plateau.

The specimen was found in 1980. What's new here is the analysis.

Although the only physical specimens of Denisovans were from Siberia, the genetic evidence has pointed to a widespread distribution, especially through east Asia. It has been hoped for some time that analyses of specimens from China would turn up Denisovans there. Xiahe would appear to be step 1 in that direction. Surely, there are more Denisovans to be found in China. We also note that knowing this one jaw may bring attention to other samples that look similar in existing collections.

Previous genetic work had indicated that modern Tibetans got genes for survival at high altitude from Denisovans. Finding that the Denisovans were the first people in the Tibetan highlands complements that nicely.

News stories:
* Denisovan Fossil Identified in Tibetan Cave -- A mandible dating to 160,000 years ago is the first evidence of Denisovan hominins outside the Russian cave where they were first discovered in 2010. (S Williams, The Scientist, May 1, 2019.)
* Scientists found that the Tibetan Plateau was first occupied by Middle Pleistocene Denisovans. (Institute of Tibetan Plateau Research, Chinese Academy of Sciences, May 2, 2019.) From one of the lead institutions involved.
* How We Found an Elusive Hominin in China -- An ancient jawbone collected by a monk has been identified as the first Denisovan discovered outside of Siberia. (J-J Hublin, SAPIENS, May 1, 2019.) By one of the authors of the article. Excellent overview of the work, with good context.

The article: A late Middle Pleistocene Denisovan mandible from the Tibetan Plateau. (F Chen et al, Nature, in press.)

Among posts on Denisovans...
* Contributions of Neandertals and Denisovans to the genomes of modern humans (July 6, 2016).
* The Siberian finger: a new human species? (April 27, 2010). The original post, about the first article.

I usually don't refer back to "Briefly noted" items, but there are two that deserve mention here...
* Briefly noted... Denisova Cave (April 10, 2019).
* Briefly noted... A Neanderthal-Denisovan hybrid (August 29, 2018).

Among posts about ancient proteins:
* Reconstructing an ancient enzyme (February 26, 2019).
* Did the Neandertals make jewelry? Evidence from ancient proteins (February 26, 2017).

Y-Y: the first

May 5, 2019

What's Y-Y? Two atoms of yttrium joined by a single covalent bond.

The rare earth metal yttrium is a useful catalyst, but its chemistry is not well understood.

A new article reports the first observation of Y-Y bonds. They are a bit unruly; it helps to keep them caged.

The first figure is a drawing showing the structure of a cage with an yttrium dimer inside...

Y2@C82. The @ sign means "inside of". That is, this is Y2 inside a C82 cage. It is a well-defined molecule; the Y2 can't get out.

The Y-Y is shown in blue.

   This is part of Figure S10a from the article supplement.

The "cage" is a fullerene. This one is somewhat larger than the classical C60; many sizes of fullerenes are known. It wasn't long after fullerenes were first characterized that people started finding things inside them. The term endohedral was coined for such things, and the @ sign introduced to denote the unusual relationship.

The following figure shows some detail of that compound -- and more...

Part a (top) shows the same chemical as above. This drawing shows a cut-away to make it easier to see the bonding inside the cage.

You can see that there are two Y atoms, with a bond of about 3.6 Å (Ångstroms) between them. That's just about the bond length predicted.

The structure shown here is based on X-ray crystallographic measurements.

That is the evidence for covalent Y-Y single bonds. Such bonds are found in this chemical, and a closely related one in the study.

The study also showed something different in some cases. This is illustrated in part d (the bottom structure of this set). It's another cage, similar but a little bigger: C88. And it has 2 Y atoms. But in this case, there is also a C2 unit inside the cage, with a Y on each side of it. That is, this is Y2C2@C88.

The distance between Y atoms here is nearly 4.3 Å, considerably more than the directly-bonded Y-Y distance of the previous case.

The dihedral angle shown on the figure is the angle between the planes of the two triangles formed by the C2 and one of the Y. (At least, I think that is what it refers to. It doesn't seem to say.)

   This is part of Figure S8 from the article supplement.

So the study reveals two kinds of structures: cages with Y-Y and cages with a non-linear Y-C2-Y. The scientists found Y-Y in C82 cages, and the more complex structure in larger cages.

One should remember how these compounds are made. One does not set out to make a specific fullerene chemical. Instead, carbon material is burned at high temperature. The resulting soot is studied for its content of fullerenes, the cage chemicals. In the current work, the burning was done in the presence of yttrium oxide, so some of the resulting cages contained Y.

The work involved purifying and characterizing individual components from the soot. That experimental work was accompanied by theoretical work, predicting the properties of such Y-containing cages.

Overall, the work here enhances our understanding of an unfamiliar element.

News story: Fullerene cage stabilises first yttrium-yttrium single bond. (T Easton, Chemistry World, April 16, 2019.)

The article, which is freely available: Crystallographic characterization of Y2C2n (2n = 82, 88-94): direct Y-Y bonding and cage-dependent cluster evolution. (C Pan et al, Chemical Science 10:4707, May 7, 2019.)

Other posts that mention yttrium:
* Penidiella and dysprosium (September 11, 2015). Notes the terminology of rare earth elements and lanthanoids.
* Lead-rich stars (August 30, 2013).

Among posts about novel chemical bonds... A chemical bond to an atom that isn't there (October 31, 2018).

Don't confuse the Y-Y of the current post with the YY of a previous post... YY in the mouth? (April 4, 2014).

A thermal management system, based on carbon nanotubes, for your jacket

May 3, 2019

Do you have separate jackets for "cool" and "cold" weather? What if you could just use a single jacket, and throw a switch on it to change it from being a cool-weather jacket to a cold-weather jacket? Better yet, what if the jacket knew how cold you were, and just made the switch by itself?

A recent article offers a step toward the development of such an intelligent jacket.

To start, we need to understand how a jacket works to keep you warm. It's actually simple... Your body gives off heat -- as infrared (IR) radiation. The jacket traps the IR. As a result, you benefit from that heat you gave off.

If you get too warm, you take off the jacket. It would be easier if you could just tell the jacket to let some of the IR through. And easier still, if the jacket took action on its own. How could the jacket tell if you got too warm? You start to sweat. The humidity goes up. So, if the jacket responded to higher humidity by allowing IR to go through, it would serve the purpose.

Here's some data...

The graphs show the IR transiittance of two materials as the humidity changes.

It would have been simple if the authors had plotted IR vs humidity, but they did it differently. The graphs show both IR and humidity over time. IR is shown with the dark curve (and left-hand y-axis scale); humidity is shown with the light curve (right-hand y-axis scale).

The big picture... In one case the two curves are similar; as humidity increases, so does IR transiittance. In the other case, they are not; the IR transiittance remains fairly constant -- and low -- as the humidity changes.

   This is part of Figure 4 from the article.

The upper graph is for the new material that the scientists have designed. They call it a metatextile. The lower graph is for the control material. Accompanying thermal analyses (by IR imaging!) show that the new material becomes cooler as the humidity rises.

What is this new material? It's based on a common textile yarn, but modified so that it responds to humidity by changing structure and IR transmission. A key part of the modification involves carbon nanotubes.

The following figure shows the idea...

The squiggly lines show the IR (as labeled in one case, lower left). The IR at the bottom is what the person gives off; the IR at the top is what passes through the fabric. On the left side, the squiggly lines at top and bottom match. The material lets IR pass through. On the right side, the squiggly lines at the top are small, showing that IR loss from the material is low.

Look at the arrows showing the transition. "Cold/dry" shifts the material to the right, where it blocks IR loss and keeps you warm. "Hot/wet" shifts the material to the left, where it irradiates and keeps you cool.

The terms open and closed may be confusing. The authors' use the terms to refer to transmission of IR. But we also note... What's shown here are the individual yarns. The tighter an individual yarn, the more open the overall fabric.

   This is part of Figure 1 from the article.

Overall... When the humidity changes, the fabric structure changes. That happens because the fabric has a mixture of hydrophobic and hydrophilic regions. Therefore, it is distorted when the humidity changes. That changes the bulk porosity of the fabric. It also changes the organization of the carbon nanotubes -- and that changes the IR transmission. Together, the two effects (on bulk porosity and IR transmission) help the material retain heat when cool, but lose heat when warm.

So that's the idea... If you get too hot, you sweat. Your jacket responds by letting heat out. At least in principle, the current article shows how it works.

What if it rained? The authors acknowledge (in one of the news stories) that could be a problem.

News stories:
* 'Cool' Textile Automatically Regulates Amount of Heat that Passes through It. (, February 11, 2019.)
* Smart textile uses sweat as switch to keep wearer cool or warm. (J Urquhart, Chemistry World, February 8, 2019.) (They mix up the water binding properties of the fabric components. Whoops. And this is a chemistry site!)

The article: Dynamic gating of infrared radiation in a textile. (X A Zhang et al, Science 363:619, February 8, 2019.)

A post about controlling IR transmission by windows... Windows: independent control of light and heat transmission (February 3, 2014).

Among posts about sweat: What if your house could sweat when it got hot? (November 30, 2012).

Posts about carbon nanotubes (and related structures) are listed on my page Introduction to Organic and Biochemistry -- Internet resources in the section on Aromatic compounds.

Older items are on the archive pages, starting with 2019 (January-April).

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Last update: May 18, 2019