Musings: September 2020 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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Posted since most recent e-mail; they will be announced in next e-mail, but feel free...

Because of distractions, Musings may be irregular for a while.

September 16, 2020 (Current e-mail)

Briefly noted...

September 16, 2020

Nitrogen-fixing maize (corn). Scientists have found and begun to characterize a strain of corn that fixes molecular nitrogen, N2, from the air. The strain has aerial roots that secrete a mucus that supports the nitrogen-fixing bacteria. The novel corn is cultivated in a region of Mexico with poor soil. If the trait could be transferred to other corns, it could be of considerable value.
* News story: The Corn of the Future Is Hundreds of Years Old and Makes Its Own Mucus -- This rare variety of corn has evolved a way to make its own nitrogen, which could revolutionize farming. (J Daley, Smithsonian, August 10, 2018.) Links to the article, which is freely available.
* This is a story from 2018, which I stumbled across last week. Very interesting, but too old for a regular Musings post. So we just note it here.
* A background post that seems relevant: Why growing maize (corn) is bad for us (June 25, 2019).

Growing on manganese ions as an energy source

September 15, 2020

Have you ever examined manganese dioxide, MnO2, up close? Here are some pictures, from a recent article...

Scanning electron micrographs of MnO2 nodules.

The scale bars at lower right of each part are, from left to right: 20, 10, 20 µm.

That is, the pieces shown here are on the order of 0.1 mm across -- tiny, but visible to the naked eye.

   This is part of Extended Data Figure 4 from the article. (Not in print edition, but Figure 1f gives one example.)

What makes these MnO2 nodules of interest is that they were made by bacteria. The bacteria were growing on manganese ions, Mn2+, as their energy source, oxidizing the Mn2+ to Mn4+. The Mn4+ appears in the form of MnO2, which is insoluble. That is, the MnO2 nodules are the waste products from burning fuel.

Manganese is an abundant element on Earth, with much of it in the form of Mn2+. Oxidizing that to Mn4+ is good chemistry. In fact, the reaction is known to occur biologically. However, no organism was known that could exploit the reaction as its primary energy source.

(For comparison... Fe plays a major role in redox reactions for most organisms. Bacteria that get their energy by oxidizing one form of iron ion to another, Fe2+ to Fe3+, have long been known.)

One argument against the Mn2+ reaction becoming popular may be evident from the pictures above. We may find those pictures beautiful, but to the bacteria, it may be something like making a prison for oneself. But that is not an argument against it happening.

A few years ago, a team of scientists at Caltech (accidentally) found a bacterial culture that appeared to be carrying out the Mn2+ oxidation on a large scale. It was a mixed culture, of considerable complexity, so it was not clear what any particular bacteria were doing. They have now followed up, with substantial purification of the mixed culture. The current article is the first report of any (reasonably well characterized) life form growing using the energy from the oxidation of Mn2+ ions.

Interestingly, it is still a mixed culture, with two kinds of bacteria. Attempts to isolate a Mn2+-utilizing monoculture have failed; apparently, the second member of the culture has an essential role, though the scientists do not know what it is. The major member (80-90%) is thought to be the Mn-oxidizer.

It is common for microbes to grow together in Nature. Sometimes it is obligatory that they do so. Isolating pure cultures of individual organisms has long been a tradition in microbiology, but it is increasingly understood that it may not be appropriate for all organisms. It is still true that the overwhelming majority of bacterial species that we can recognize cannot be grown in the lab, singly or otherwise.

The microbe pair grow together, oxidizing Mn2+, and using the energy from that oxidation for growth. They use CO2 as their primary carbon source, just as photosynthetic organisms do, but here the energy for CO2-fixation comes from the chemical oxidation.

The scientists have sequenced the genomes and begun to analyze the transcriptomes (mRNA content) for both members. And they have offered names for both: Manganitrophus noduliformans and Ramlibacter lithotrophicus.

Use of Mn2+ as a primary energy source for a living system can now be considered an established fact.

News stories:
* Bacteria with a metal diet discovered in dirty glassware. ( (California Institute of Technology), July 15, 2020.)
* Serendipitous history in the microbial making. (K Freel, Molecular Ecologist, July 24, 2020.)

The article: Bacterial chemolithoautotrophy via manganese oxidation. (H Yu & J R Leadbetter, Nature 583:453, July 16, 2020.)

A post about some interesting speculations on the biology of manganese: Photosynthesis that gave off manganese dioxide? (July 21, 2013).

More manganese... Manganese(I) -- and better batteries? (March 21, 2018).

A post about an unusual chemoautotroph -- one that was made in the lab: Turning E. coli into an autotroph (using CO2 as sole carbon source) (December 9, 2019).

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.

Life on 10 zeptowatts

September 13, 2020

It's census time in the United States, and also in the sediments below the ocean floor.

A recent article presents results from the latter, and some of them are intriguing. The following figure gets us started, with some results for three kinds of microbes (bacteria and archaea)...

Look at two of the pie charts in part A. The one at the upper right shows the counts for these three types of microbe. The one at the lower right shows their rate of energy usage -- which is called power. The numbers are global totals; the types of microbe are identified only by their color codings for now.

Divide those two numbers and you get power per cell. For the "orange" microbes, that is 2.4 gigawatts divided by 6.27x1028 cells. That is 3.8x10-20 watts/cell. About 40 zeptowatts/cell.

Part B shows the results differently, with the number of cells found (y-axis) vs power (x-axis). The peak is about 10-20 watts/cell. 10 zeptowatts/cell.

Note that the first number (40 zW/cell) is the mean, whereas the second (10 zW/cell) is the mode. The distribution has a significant tail on the high end, which is why the mean is higher than the mode.

The figure also shows results for two other kinds of microbe, green and lilac. We'll focus on the orange microbes, the ones with the lowest energy usage.

   This is Figure 1 from the article.

Let's use the second number, 10 zeptowatts/cell. It's simple and in the ballpark.

That's not much energy. In fact, it's close to estimates of the theoretical minimum needed to maintain cells in suspended animation, without death. And it is about a hundred-fold less than previous measurements of the power needed to maintain cells.

Thus it would appear that these microbes are maintaining themselves in nature near the lower limit for life, in terms of energy usage.

It has long been suspected that there are microbes at the low energy limit. Well, logically there must be. But what is it? The current work extends our analysis of where microbes are on Earth to a case where they are surviving but not dividing, on an energy supply 1/100 of the previously measured limit.

There is an interesting implication, if all these numbers are actually correct. The sediments measured here are over a million years old. If these cells are simply maintaining themselves, without having enough energy to divide, that suggests that the current cells, the ones being measured, are the same cells originally deposited. That is, these cells are a million years old.

Don't take that as a claim. It is an implication, if the basic numbers and arguments are correct. There are many reasons they may not be. But it certainly is a challenge, and further work will undoubtedly try to shed more light on the question of long term maintenance of microbes in nature.

What is the basis of the measurements? Geologists drill deep into the ocean sediments, and extract "cores" -- long samples of material over a range of depths. (Some of these cores were originally made for exploring for minerals.) The cores can then be analyzed in the lab, by various methods. These analyses yield estimates of the numbers of cells and the amount of organic carbon metabolized. The latter can be interpreted in terms of energy consumed. The measurements are then fed to a computer model. (The details of what was measured are not clear from the article alone, and I can think of questions I might have about the analysis and assumptions. That uncertainty does not detract from the general description of what was accomplished.)

What are these three colors of microbes? The type of particular interest, shown in orange, is methanogens. Green is for aerobes (using oxygen). Lilac is for sulfate-reducing microbes. The three types reflect varying redox potential of the sediments. The orange microbes, the methanogens, are from the greatest depths, with lowest redox potential.

For fun, here is a map. It shows where the methanogens are found...

The map is color-coded by the cell power. The red and yellow areas of the map are for the methanogens with the highest power/cell.

Note that the power range shown here agrees with that in part B of the top figure.

   This is Figure 2C from the article. Other parts of the full figure show the maps for the two other classes of microbes noted in Figure 1, above. They are all quite different.

News stories:
* New study reveals lower energy limit for life on Earth -- An international team of researchers led by Queen Mary University of London have discovered that microorganisms buried in sediment beneath the seafloor can survive on less energy than was previously known to support life. The findings have implications for understanding the limit of life on Earth and the potential for life elsewhere. (Queen Mary University of London, August 5, 2020.) Excellent overview of the work, despite a little hype near the end.
* Life at its limits -- Microbes in the seabed survive on far less energy than has been shown ever before. (EurekAlert! (GFZ GeoForschungsZentrum Potsdam, Helmholtz Centre), August 5, 2020.) (This page incorrectly refers to sulfate being oxidized; it is reduced. The main content of the page is fine.)

The article, which is freely available: Widespread energy limitation to life in global subseafloor sediments. (J A Bradley et al, Science Advances 6:eaba0697, August 5, 2020.)

For reference... Humans operate at about 100 watts. Divide that by the number of cells, about 30 trillion, and you get 3x10-12 W = 30 picowatts = 3x109 zeptowatts.

* * * * *

More about methanogens: What caused the mass extinction 252 million years ago? Methane-producing microbes? (October 12, 2014).

A post about life at the bottom of the ocean: The hydrogen economy -- in the mid-Atlantic (August 30, 2011).

September 9, 2020

Briefly noted...

September 9, 2020

Does a grammar checker improve the readability of a text? Not according to a test reported in a recent article. It improves the grammar, but readability is a different issue. Perhaps that is not a surprising conclusion, but it is contrary to the claims of the company making the grammar checker.
* News story: Grammar tools do not improve readability. (O-J Øye, Science Norway, August 20, 2020.) Links to the article, which is actually a book chapter, based on a meeting presentation. Is it peer-reviewed? Don't know. (Careful... The publisher's page includes separate links for the book and for the chapter.)

Treating croplands so they take up more CO2 from the air

September 8, 2020

CO2 reacts with silicate rocks to form carbonates. It is a natural process, a type of weathering. It could be the basis for removing CO2 from the air. Musings has previously noted one proposal to make use of this chemistry for reducing atmospheric CO2 [link at the end].

A recent article explores using this approach on ordinary farms. If farmers spread silicate rock dust on their fields, there would be vast areas of CO2 uptake. How well would it work? How much would it cost? What might be the side effects, pro and con? The article does some modeling, and suggests that the approach is worth considering.

The following figure gives an idea of the potential...

Each graph is for one country. The upper left graph (part a) is for China, the single largest contributor.

The black line shows CO2 removed from the air (y-axis) vs fraction of the country's cropland used for the removal (x-axis). Remember, this is modeling; the results here are calculations of what could be removed with one or another set of assumptions. (The shaded region around that line shows 90% confidence limits; the uncertainty is largely due to varying rock quality.)

As an example, consider 25% coverage of the country's farms. Look at 0.25 fractional coverage on the x-axis, and read the y-value: it is about 0.25 -- that is Gt/yr (gigatons of CO2 per year).

The values are similar for the other two countries shown here. The total for the three countries is probably about 0.7 Gt/yr (at 25% coverage).

CDR = carbon dioxide removal. "Net CDR" (on the y-axis label) means that they have taken into account the energy costs of the process (such as grinding the rock).

The black and green curves, each with 90% confidence limits, are for two different scenarios. The black is for BAU = business-as-usual. The green assumes policies have been set to limit the global temperature increase to 2 degrees. The results are similar for the two cases.

This is part of Figure 1 from the article. The full figure shows similar graphs for nine more countries. The set of 12 countries shown in the full figure includes the seven non-European countries with the largest potential contributions, plus the five with the largest contributions from Europe. (The largest European contributor would be about #6 worldwide.)

The scientists do the prediction worldwide. The three countries shown above are those that would make the largest contributions. The total for the world is about 1 Gt/yr. Again, that is at 25% coverage; by using more cropland, the number could double.

Table 1 of the article provides a different way of getting that perspective. The second section of that table is for a goal (total) of 1.0 Gt CO2/yr. You can see that the three big contributors each contribute about 0.25 Gt, at a coverage of about 25%. (The data used here is a little more complicated than just the black curve shown above, but the end result is similar.)

How significant is that amount? Commonly stated goals call for removing 10 Gt/yr of CO2. If the new proposal led to removing 1 Gt/yr, that would be a significant contribution.

What would it cost? They estimate (US) $80-180 per tonne of CO2. That cost is in the ballpark of other proposed methods for removing CO2 from the air. (Table 1 of the article, mentioned above, also shows cost numbers by country.)

Where does the rock dust come from? The authors note that it is common stuff, often just remaining in piles from other processes. New mining to produce the rock could be considered, but only as a last resort.

Side-effects? The rock dust is likely to be good for the soil, leading to improvements in agricultural yields. This is the kind of effect that could help promote acceptance. It is also possible that some rock sources could be toxic.

Bottom line... It is an interesting proposal, deserving further analysis and testing. The current article is entirely modeling. Though the basis of the method is well-known chemistry, there is no experimental work here.

News stories:
* Spreading rock dust on farmland could capture surprisingly large amounts of CO2, fast -- The technology and infrastructure already exist - and the strategy could provide a substantial income source for farmers. (E Bryce, Anthropocene, July 17, 2020.)
* Applying rock dust to croplands could absorb up to 2 billion tonnes of CO2 from the atmosphere. ( (University of Sheffield), July 9, 2020.)

* News story accompanying the article: Environmental science: Atmospheric CO2 removed by rock weathering -- Large-scale removal of carbon dioxide from the atmosphere might be achieved through enhanced rock weathering. It now seems that this approach is as promising as other strategies, in terms of cost and CO2-removal potential. (J Lehmann & A Possinger, Nature 583:204, July 9, 2020.)
* The article: Potential for large-scale CO2 removal via enhanced rock weathering with croplands. (D J Beerling et al, Nature 583:242, July 9, 2020.)

Background post... Capturing CO2 -- and converting it to stone (July 11, 2016). In that case, the CO2 was delivered into natural basalt formations. In the new work, the same chemistry is exploited, in a dispersed system. Links to more about geoengineering.

COVID-19: How well does the virus replicate in children?

September 6, 2020

The nature of COVID-19 in children is confusing. The big observation is that children seem less affected than adults. But not all the pieces fit.

Two new articles report that children tend to have higher levels of the virus than do adults, especially in the early stages of infection.

Let's look at some of the basic results from the two articles on viral load in children vs adults. The general approach is the same... The standard test... take a sample (often the famous nasal swab), and measure the amount of viral RNA by quantitative PCR. (The level of virus is assumed to closely correlate with the level of viral RNA.)

Here are the key results from article 1...

The graph shows the viral RNA vs patient age.

Viral RNA is shown here as CT. That is cycle threshold, the number of cycles of PCR required to reach the threshold for detection. The lower the CT, the more virus there was in the sample.

The horizontal line within each data set shows the median. Focus on that (while realizing that the data distributions are very broad). You can see that the viral load is highest for the young children and lowest for the adults.

The authors estimate that the difference in CT medians here corresponds to 10-100 fold difference in viral RNA level.

   This is the Figure from article 1. (It is the only data presentation in this short article.)

Here are the key results from article 2...

This graph also presents viral RNA vs patient age, but the details are different.

First, the y-axis scale is indeed the amount of viral RNA, in copies per mL -- on a log scale. (The lowest points shown are at 1, for 101 = 10 copies/mL. But these points actually mean <40 copies/mL. Why? The authors state that the limit of detection was 40 copies/mL; all values appearing to be zero were plotted as 10 copies/mL.)

The patients are divided into two major groups: pediatric (red), and adult (black). The dividing line is age 22.

Within each age group, there are three sub-groups, based on the time of onset of symptoms; see x-axis labeling. The first group is for measurements made 0-2 days after onset of symptoms.

Observations (again, focusing on the medians)...
- For each age group, the level of viral RNA declines during the infection. In fact, the highest viral RNA levels are seen at the very beginning of the symptomatic phase.
- Comparing the two age groups at a particular stage of infection... The pediatric patients have higher viral RNA level for two of the three stages. (I assume that the median for the right-hand group is in the big cluster of points at the bottom.)

   This is Figure 2B from article 2.

The big picture from both studies is that children have high viral loads, perhaps even higher than adults.

The age categories are different for the two articles, and it's not obvious that the two sets agree. The distributions are broad, which is to be expected; comparison of medians and other measures of the middle data, helps to reduce the influence of outliners. Further, some of the data sets are quite small.

Despite the cautions, both articles point to children having high virus levels. Whether they have higher levels than adults is perhaps a weaker claim at this point, but not too important.

If children have high viral loads, they are potentially a source of virus transmission, though that has not been measured directly. Why they don't get as sick is a different issue; it is not due to having less virus.

As so often, the information about COVID is not simple.

The results shown in the second figure are also a reminder that virus levels are high early in the infection. It is not addressed here, but that is consistent with there being high virus levels prior to symptoms -- allowing for good viral transmission by people who are asymptomatic.

News stories:. The first two are specifically for article 1, which was published online in late July. The last two are specifically for article 2, which was published online in late August.
* News Scan for July 31, 2020 -- Kids 5 and younger could spread COVID-19 as much as adults, study finds. (CIDRAP, July 31, 2020.) First item on the page.
* Children Often Carry More Coronavirus than Adults Do: Study -- It's not clear if their high viral load makes kids more likely to infect others. (A Heidt, The Scientist, July 31, 2020.)
* Researchers show children are silent spreaders of virus that causes COVID-19 -- Comprehensive pediatric study examines viral load, immune response and hyperinflammation in pediatric COVID-19. (EurekAlert! (Massachusetts General Hospital), August 20, 2020.)
* Kids with COVID have more viral RNA in their airways than adults do. (M Van Beusekom, CIDRAP, August 20, 2020.)

Two articles, which are probably temporarily freely available:
1) Age-Related Differences in Nasopharyngeal Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Levels in Patients With Mild to Moderate Coronavirus Disease 2019 (COVID-19). (T Heald-Sargent et al, JAMA Pediatrics, in press.)
2) Pediatric SARS-CoV-2: Clinical Presentation, Infectivity, and Immune Responses. (L M Yonker et al, Journal of Pediatrics, in press.)

The page for BITN -- Other topics includes a section on SARS, MERS (coronaviruses). That section now includes COVID-19. It lists Musings posts on coronaviruses.

How to get common fluorescent dyes to work in the solid state

September 4, 2020

There are some very good fluorescent dyes that don't work -- don't fluoresce -- very well as solids. A new article solves the problem. The method should be widely applicable.

The following figure shows the problem -- and that it has been solved.

Start with the bottom row... five disks, each with a thin film of one dye. UV light is shined on the disks. Not much happens.

The top row shows the same dyes, now incorporated using the new method, called SMILES. Each dye tested now fluoresces more brightly.

(The oxazine fluorescence can be hard to see; adjust your viewing angle. It indeed is the least successful of the dyes tested here, but is far brighter in the SMILES form than alone. Quantitative data in the article confirm these points.)

   This is Figure 5A from the article.

Why the dyes don't work in the solid phase is well understood. The fluorescent molecules are so close together that they quench each other. (That is, the electrons excited by the UV dissipate, through another molecule, without emitting any light.) Of course, that explanation makes evident how to solve the problem. It's just a matter of doing it, in a practical way.

The following figure shows the problem and the solution, with some chemical detail for one specific dye.

Part D (left) starts with the structure of the dye molecule. This dye is rhodamine 3B (R3B in the top figure, at the left). It is a cationic dye; there is a positive charge on the N at the lower right of the structure.

Since the dye is cationic, it must be incorporated into the solid with an anion; in this work the anion is perchlorate, ClO4-.

The bottom of part D shows the structure of the solid from these two ions. Note the color coding, used consistently in the figure: blue for the dye, with different shades of blue for convenience, and red for the perchlorate.

Two distances are marked, both 8-9 Å. That is the distance between two dye molecules. For now, just note them.

Part E shows the magic ingredient, a chemical they call cyanostar (after the five cyano groups on the outside).

The top of Part F shows how cyanostar does its magic: two cyanostars form a complex with one perchlorate in the center. This complex is the active anion in the final structure.

That leads to the next structure, just below in part F: the dye cation plus the cyanostar-perchlorate anion. They form a nice ordered structure, with the dye molecules held apart, due to the cyanostars. The cationic dyes align with the perchlorate anions, but the spacing of those anions is determined by the cyanostars.

Two distances are shown on this structure, one horizontal and one vertical. Both are about double the distances shown for the cyanostar-free structure (bottom of part D). It is this structure, with the dye molecules held apart, that led to the bright response in the top figure.

   This is part of Figure 2 from the article.

The top figure shows that the cyanostar solution worked for five dyes tested, representing different chemical classes of dyes. The generality holds because what the cyanostar does is to space the perchlorate anions. Thus it works for a variety of cationic dyes. There is nothing in the method that is dye-specific (though of course it must fit, and be chemically compatible). The cyanostar itself is colorless; the optical properties of the product come from the dye.

The scientists go on to show that the benefits of the cyanostar are retained upon incorporation into common polymers. Figure 10 of the article shows examples. This is a step toward using the new method in real-world applications.

SMILES? Stands for small-molecule ionic isolation lattices. (They need acronym help.)

News stories:
* Chemists create the brightest-ever fluorescent materials. (Nanowerk News (Indiana University), August 7, 2020.)
* New Fluorescent Material Could Boost Optics Technology. (R Lea, AZoOptics, August 13 2020.)

The article: Plug-and-Play Optical Materials from Fluorescent Dyes and Macrocycles. (C R Benson et al, Chem 6:1978, August 6, 2020.)

A recent post about fluorescence: Electronic monitoring of plant health; it might even allow an injured plant to call a doctor (June 21, 2020). In this case, quenching was exploited in making the measurement.

Older items are on the archive pages, starting with 2020 (May-August).

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