text:
What is sigma factor PvdS?
I am using MEME suite tool for de novo motif discovery and when I use TomTom to compare my motifs with known motif database, I find that my genes could potentially be upregulated or downregulated by sigma factor PvdS. I would like to understand what sigma factor PvdS exactly means.
I am not really able to interpret the UniProt page. It indicates the protein: sigma factor PvdS and gene: PvdS. Then it is difficult for me to put together the GO-Molecular Function and the GO-Biological Function in order to understand what sigma factor PvdS means.
From the paper by Miyazaki et al., I find:

In response to iron limitation Pseudomonas aeruginosa PAO induces production of pyoverdin, a low-molecular-weight siderophore able to capture ferric ion with a very high affinity. The pvd genes involved in the pyoverdin biosynthesis are organized in a chromosomal region termed the pvd region, and expression of some pvd genes is regulated at the transcriptional level. Two sets of promoter regions for the pvd genes were defined that were transcriptionally derepressed under iron-limiting conditions. Analysis of transcription from such promoters in Escherichia coli led to isolation and identification of a positive regulatory gene, pvdS, for expression of the pvd genes, and pvdS was localized in the pvd region.

From this extract, I can understand that PvdS is a positive regulatory gene that is, from Wikipedia:

A regulator gene, regulator, or regulatory gene is a gene involved in controlling the expression of one or more other genes. Regulatory sequences, which encode regulatory genes, are often at the five prime end (5') to the start site of transcription of the gene they regulate.

And so PvdS regulates the expression of the pvd gene involved in the pyoverdin biosynthesis.
Then in the paper by Tracey et al I find that:

PvdS is an alternative sigma factor regulated by the global iron regulator Fur

So putting all the pieces together, can I say that my genes could be upregulated or downregulated by this PvdS sigma factor, that is a sigma factor that means a protein needed for initiation of transcription in bacteria and this protein, in this particular case, is encoded by the regulatory gene PvdS that regulates the expression of the pvd gene involved in the pyoverdin biosynthesis?  And thus the PvdS sigma factor is a protein for initiation of transcription of the pvd genes?
Thank you in advance.

This is a site for specific problems about biology that can be regarded as of general interest. It is not a site for discussing the research data of particular individuals. As for the function of the actual pad gene, you have found out more than anyone here is likely to know. I assume that you know what sigma factors are, or can read about them.

Clarification of the Question
It appears to me that the question posed in the title of this question, “What is sigma factor PvdS?” is answered by the poster — it is a sigma factor that is specific for, and allows transcription of, genes involved in pyoverdin synthesis in Pseudomonas aeruginosa. I assume that the poster knows that a sigma factor is a subunit of bacterial RNA polymerase that must associate with it before it is capable of initiating transcription. (The information is readily available on Wikipedia or in Berg et al.)
The bulk of the actual question is devoted to describing the results of computer analysis of the genome of an unspecified archaeon. Towards the end the poster poses a question:

…can I say that my genes could be upregulated or downregulated by this PvdS sigma factor…

[The sentence continues for several lines. The emphasis is mine.]
I therefore interpret the question as asking

What conclusions can be drawn from computer analysis of the type
performed, with particular reference to the biological system
described?

Answer
It is necessary to emphasize at the outset that the conclusions that can be derived from studies performed in silico are severely constrained.
Sequence similarity allows you to suggest that an experimentally uncharacterised gene might encode a protein with a similar function to a related gene. No more. Only experimental analysis of the protein allows you to state what its function actually is.
The usual type of annotation of such proteins (and by extension their genes) is one of:

hypothetical xxxxxx protein
putative xxxxxx protein
possible xxxxxx protein
xxxxxx-like protein
xxxxxx-domain protein

Likewise, the occurrence of a motif that allows pyoverdin genes to be recognized by a transcription factor in P. aeruginosa can only suggest that a functionally uncharacterized gene from a different organism might be similarly recognized and its transcription regulated in a similar manner.
In the example in question the most it is possible to say is that a system of gene regulation similar to that in P. aeruginosa may exist in the archaeon. To go any further one would need to identify (the gene for) for the putative sigma factor, show that it allowed the RNA polymerase to bind to the genes, and either show this affected transcription directly or perform genetic experiments that would allow the same conclusion.
Furthermore, I would be wary of describing the putative sigma factor as ‘PvdS’ unless the proteins predicted to be encoded by genes on which this motif is found bear a similarity to the genes for synthesis of pyoverdin, from which its gene name, pvdS, is derived. (A BLAST search should, of course, be done on the genes to determine this — probably blastx.)

I think the OP is not a native English speaker and so some of the question phrasing is cumbersome as a result. I interpreted "could" as similar in meaning to your "suggest".

Since the objection about the fact that I was discussing my research data and the different votes to close the question for the same reason (I think), I removed the last part (I already imagined that it could be source of troubles). So just knowing what sigma factor PvdS means would be great ! @David

Anyway, I was asking if my genes could be regulated by the same factor indicated by the software (sigma factor PvdS) . I did not ask if they might encode a certain protein...

@Manuela The principle for genes is the same, but I have now spelled it out. It is of little use asking what "could" be on a site which is concerned with objective answers to precise questions in biology. Many things are possible, but how probable is an objective judgement. The key point of my answer is that you can only go far in silico — to draw any real conclusions (certainly publishable ones) you need to do experiments or convince an experimental scientist that they are worth doing.

@Armand I am aware that the poster is not a native speaker as I have helped her previously. My impression is that she wants to go further than "suggest" — modal verbs in English and romance or germanic languages do tend to differ in usage, but they are one of the things that are emphasized and one learns early on in a language. Even if this were so she is asking a question that is impossible to answer without seeing all of her data, and is even then off-topic as it does not constitute a general biological problem.

Thank you @David for the answer ! As regards the first part of my question, I still have a doubt: is PvdS the gene that encodes the sigma factor that allows transcription of genes involved in pyoverdin synthesis in Pseudomonas aeruginosa ?

For the second part (interpretation of the motif), thank you! I wanted only to know if this motif could have any relevant meaning (=if this suggests a meaning for the motif, as @Armand said). I think that when you do de novo motif discovery using MEME or other softwares, the results are always suggestions.

So, finally, the very last suggestion: did you mean that I should compare the proteins encoded by my genes and the proteins encoded by the genes for synthesis of pyoverdin to say if they are recognized for transcription by the same factor (PvdS) ? Is this a little replacement of the experiment? Or did I completely misunderstand your last suggestion?

@Manuela —My guess is that you are at some advanced level of education with a training in the numeric sciences but no real knowledge of molecular biology trying to use bioinformatics tools on a problem. It would helpt to know if it is one of your own devising, one given you in a Bioinformatics course or in a lab where you are doing a project is relevant in terms of advice. To answer your question, you should do a BLAST search on each of the genes (or probably better protein translations) that have the motif associated with PvdS to see what they are related to. Surely you know BLAST?

@David no there is no bioinformatics course or lab. It is just for an exam project and I took data from ncbi after reading a paper. I have a physics background and I wanted to go towards biophysics, so yes no real knowledge of molecular biology, unfortunately, thus interpreting some results is difficult for me ... Anyway, yes I know BLAST, so thank you for the suggestion ! The fact was simply that I was surprised to find this common motif in two genes which encode proteins with similar biological function but of two different organisms which belong to two different domains.

As your archaea genome must have been published and, I imagine, the genes annotated, BLAST may not be necessary, at least in the first instance. Just assemble the annotations and see if they indicate genes that encode proteins similar to those in the pyoverdin synthetic pathway or perhaps some other pathway. If there is no useful annotation, then you would need BLAST.  If the putative proteins do not hang together (obviously there may be exceptions), your argument probably doesn't either.


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From an evolutionary standpoint, why don’t couples attempt to have as many kids as possible?
Many couples have 4 or 5 kids, but it is unusual for a couple to have 10 or 15. Shouldn’t humans have evolved to want as many kids as possible to maximize the chances that their genes are passed down?

Remember that until 100 years ago even in developed countries, conditions were very different than now -- women often died in or near childbirth, children often died of disease during childhood, hormonal birth control was not available, etc.

Because many humans are intelligent creatures. and place their personal well-being ahead of abstracts like evolution?  I mean, why on Earth would I give a damn about whether or not my genes are passed on?

There's strong cultural component to it. It is not uncommon in strongly religious communities to make as many children as possible. Also, baby-boom took place not so long ago, while average number of children in a modern European family is 1-2 (depending on the country).

Typical family sizes (especially in developed countries) are much smaller than they used to be, because cultural factors influence behaviour (do you want to have 10-15 kids if you can't afford to give them a good education?) From Kopf and Livni 2017:

More fundamentally, maximizing the number of offspring does not necessarily maximize reproductive fitness, because the amount of resources/care you give to each individual offspring matters; if you have too many offspring, maybe none of them will grow up to be high-quality/reproductively successful. This trade-off affects non-human organisms as well; there is an entire literature in evolutionary biology on optimal reproductive tactics that includes this issue (Pianka 2008).

Kopf, Ephrat, and Dan Livni. “The Decline of the Large US Family, in Charts.” Quartz, 2017. https://qz.com/1099800/average-size-of-a-us-family-from-1850-to-the-present/.
Pianka, E. R. “Optimal Reproductive Tactics.” In Encyclopedia of Ecology, edited by Sven Erik Jørgensen and Brian D. Fath, 2567–72. Oxford: Academic Press, 2008. https://doi.org/10.1016/B978-008045405-4.00841-7.

Wow. Great answer, thanks!

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text:
Vitrification of Humans for Later Revival
In the video from Tom Scott "I promise this story about microwaves is interesting.
" high success rate in multiple reanimations of a hamster was stated by scientist interviewee J. E. Lovelock who worked on these experiments. In the near end of the video the scientist says that it is not possible on larger organisms partially because you cannot get antifreeze agents to diffuse into the cells quickly enough. Searching on this topic I found out that antifreeze is required because if ice forms it expands and damages the cell walls and more. Although in how Lovelock was describing the experiments, it seemed as if they quickly cooled the hamster to between 0 and 1 degrees celcius, see "Reanimation of rats from body temperatures between 0 and 1° C by microwave diathermy" and "Resuscitation of Hamsters after Supercooling or Partial Crystallization at Body Temperatures Below 0° C.". From the original Nature article

Hamsters, chosen because of their known adaptability to body temperatures between 2.5° and 38° C.,
were cooled by the method recently described by
Andjus and Smith for rats. After transfer to icy
water, the deep body temperature was recorded from a
colonic thermocouple connected to a potentiometer
or a microvoltmeter recording with an accuracy of
±0.3 deg. C. In our experience the hamster ceases
to respire at body temperatures between + 2.5° and + 6° C., and heart beats are no longer visible at +1.8 - 3.5° C.

it is then said that

After cessation of
respiration, the animal was transferred to a 50 per
cent propylene glycol bath maintained at - 4 ° to - 7° C., which reduced body temperature to zero in
7-10 min. Under these conditions, some animals
became supercooled so that body temperature might
reach - 5·5° C. or even below in a further 50-70 min.

Propylene glycol being an ingredient in antifreeze also being non-toxic which is seen in its use as a food additive. Although nowhere in this method is it said that it somehow is administered into the hamster so that it can diffuse into the cells themselves. It is also said that an estimated 15% of total body water crystallized (froze/became ice). These hamsters were then successfully revived. Why does Lovelock then say that it does not work on humans because of antifreeze not diffusing fast enough? From searching around one reason is that it does not work because it is not possible to cool a human body quick enough, although if it became possible to vitrify a body quick enough and heat it up quick enough. Would it then become possible to revive humans and or bigger animals?
My main question is how and why does it matter how big the animal that is being frozen matter? What exactly makes it possible on hamsters and not on for example a dog or a human being? I understand that it takes significantly longer to cool a human being compared to a hamster. But I do not understand how for example the heart cells do not die in the process of cooling a hamster compared to a human. The cooling pattern is the same for both, and the heart in both cases will be deprived of blood therefore oxygen. The amount of expansion caused by potential ice formation will be the same on hamsters and humans because the size of the cells are roughly the same.

Are you familiar with Kleiber's law? Would it be a sufficient answer for you?

I think you may be "assuming facts not in evidence" :)  You are focusing on the size of the animal. However, your quote notes, "Hamsters, chosen because of their known adaptability to body temperatures between 2.5° and 38° C., ", that is hamsters were chosen not for their size, but because they were known to be able to adapt to temperatures as cold as 2.5C.
Determining the mechanisms of how hamsters can adapt to such cold temperatures would certainly be interesting.

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text:
Evolutionary reason green bottle flies are shiny
Just noticed some green bottle flies in my backyard. They are shiny. A shine like that attracts attention (of potential predators) and probably takes some work to maintain. This made me wonder why they might have evolved this. The Wikipedia article on them suggests this is used by males to identify mates.
It is further supported by this paper linked by @DkNguyen.
But common houseflies don't shine like that. They rely on pheromones instead. Why these very different strategies?
What surprises me is that the two fly species (green bottle flies and house flies) are probably closely related because they share so many other traits. And yet, their mating strategies are so radically different. I'm looking for where this branching off happened on the tree of evolution and what could have caused it.

My attempt at an explanation:
For the most part, I see the shiny green bottle flies outdoors. Either when there is poop, or a carcass or something with a strong smell. This seems to be supported by the following article: https://www.aardvarkpest.co.uk/blue-green-bottle-fly/
On the other hand, the common houseflies I mostly run into indoors where there aren't many strong smells from the things they might eat (which is not to say they necessarily evolved in this environment, just that it plays to their strengths). This suggests that the shiny green bottle flies are attracted to food that smells strong and that they are relying primarily on their sense of smell to seek out food. This probably means that if they use their sense of smell for finding mates too, it's going to overload that sense, causing them to not be as effective at finding mates and procreating.
This seems like a good reason for evolution to select for switching the mechanism of finding mates to one based on vision rather than smell in cases where the smell is relied on for other important tasks.
Are there any papers or other material to support or refute any of the reasoning in this chain?

The guys dig it. Also, apparently they have good colour vision. https://www.sciencedaily.com/releases/2017/02/170214162804.htm

@DKNguyen Want to turn your comment into an answer?

Not really, not since I don't think there is enough there and I don't really want to look further. There's probably something more definitive out there.

Does this answer your question? Why do some bad traits evolve, and good ones don't?

Not quite. I get the general answer, but my question is more specific. The two fly species (green bottle flies and house flies) are probably closely related because they share so many other traits. And yet, their mating strategies are so radially different. I'm looking for where this branching off happened on the tree of evolution and what could have caused it.

"Probably closely related" — is there some reason you haven't looked this up? Since one of the expectations on this site is that posters demonstrate prior research, doing that might improve this questions reception. However, the page linked by MaximilianPress is in all likelihood the best answer you will get — evolution has a large random component so trying to say why these two flies do things differently could require reconstructing the entire evolutionary and ecological history of these two flies and their ancestors ...

Look up references that support that the two are closely related? I felt that was quite obvious, but I can do that. Also, while it might be true that MaximillianPress's answer is the best I'll get, I don't think answering this one is as hard as you're making it out to be. One plausible theory is that the common ancestor relied only on pheromones and that they were exposed to an environments where the smell signal was compromised (perhaps because of what they were eating), forcing them to slowly abandon the smell mechanism and switch to a more visual mechanism.

Also, I think the fact that evolution is random is besides the point. It wouldn't work any other way. That's not an excuse to throw up hands and say "well, its random" :)

They are in different families — I don't off the top of my head known how many millions of years of separation that represents, but flies have been around for 100s of millions of years and families represent some of the deepest levels of separation. 2) This means that there have been a (large) multiple of 10^8 generations (with random mutations) since the last common ancestor. Does that help you understand why the assumptions behind your question are naive?

I didn't know these two things, so thanks for pointing out. But still, I feel these alone don't say much; turtles and crocodiles have been fairly unchanged for 100s of millions of years and a mind boggling number of generations as well. I feel most traits of green bottle flies and house flies like the way they fly, speed at which they process information, lifespans, etc. have hit local optima and the way they look for mates is one of the few traits that separate them. Maybe I'm still naive, but I find the answer I posted satisfactory.


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how do we feel electricity on skin even though merkel cells are pressure sensitive only?

Note: Here I am not talking about electric shock (one feels when a lot of electricity passes through), I am talking about smaller sensations one feel directly on the skin.

Note: I am not able to find any correlation graph between feature of electricity that determines the intensity of feeling i.e., voltage, current or frequency. So is there any research paper or anything else around that can shed light on this? This will be very helpful.

I have studied that humans sense touch because of the "Merkel cells" in the skin, and Merkel cells are essentially pressure sensors. I don't think electricity leads to pressure changes, So then how do we feel the sensation of electricity on skin. Is it because electricity directly interface with neurons some how?
If I am not able to explain the question here is a more practical way of thinking about it:
If I touch two electrode close on the skin (or maybe possibly one even though I am not sure one can do the trick) and pass electricity how will skill feel it.

Do you mean static electricity?  (I've never felt anything else that wasn't a shock.)  I'd suspect that the static electric charge on body hair is causing them to move, activating pressure receptors.

Why do you assume electricity isn't passing through your skin just because it doesn't feel like a shock? Electricity doesn't always feel like a shock. For example, when electrodes cause your muscles to twitch.

@jamesqf I am not just talking about static electricity. One practical example that you might have felt could be if you take a 9v battery and touch it on your tongue you will feel sensation that can't be described as shock. Similar things are possible to do on skin at higher voltages.

@DKNguyen ya electricity is definitely passing through skin (and I am not assuming it isn't. But for my particular application I am interested in sensation directly felt on skin.

In the skin, there are 4 types of tactile receptors, dependent on whether it is glabrous or hairy skin;

Meissner's corpuscles
Merkel cells
Ruffini endings
Pacinian corpuscles

Ruffini endings are thought not to be sensitive to electrical stimulation, the other 3, however are. These other 3 can readily be electrically activated and each type can be separately targeted by changing stimulus and placement parameters. Activation is normally due to pressure differences. However, the nerve endings are basically axons, and these can be activated electrically as well Kajimoto et al. (2002).
Some parts of the body have high densities of these tactile receptors, such as the fingertips and the tongue. That's why electrical stimulation has been applied as a means to convey information via the skin. Take for instance the BrainPort device (Fig. 1); this device consists of a camera hooked to a tongue-display unit (TDU). The TDU translates camera pixels into tactile images on the tongue, brought about by 144 electrodes. It is designed to substitute vision for blind people. (Stronks et al., 2016).

Fig. 1. BrainPort device. Source: Nau et al. (2014)
References
- Kajimoto et al., Electronics and Communications in Japan, 85(6) 120-8
- Nau et al., Front Hum Neurosci (2014): fnhum.2014.00291
- Stronks et al., Exp Rev Med Dev (2016); 13(10): 919–31

Thanks for answer I also read your answer to this question https://biology.stackexchange.com/questions/37207/why-can-humans-feel-electricity and it was also helpful. But is there research on correlation between electrical features and sensations on body.


text:
Why are more children being hospitalized with Covid-19?
I see that more children are being hospitalized with Covid-19. If I recall correctly, throughout the pandemic, researchers have thought that children were more resistant to the virus because they are often exposed to other viral pathogens, and therefore often have a Type I IFN response activated (which I've taken it is very effective at preventing infection).
I'm curious to know why more children are being hospitalized now. Some possible reasons that come to mind are that the coronavirus has evolved to better subvert the Type I IFN response, or that it has evolved to be able to better infect cells that are mounting a Type I IFN response, or that children are being exposed to fewer pathogens now (than they were even recently), or that the number of children hospitalized is independent of the number of children infected.

Since Delta is so much more transmissible than earlier variants, it's likely that many more children are being infected than previously. More infected -> more hospitalized.

Children have the lowest vaccination grade. They're also a lot less likely to keep their distance from each other.

Right now, at least, it's not clear whether anything significant has changed biologically for children with respect to the Delta variant.
What is known for certain, however, is that Delta is very infectious, and that the vast majority of kids are still unvaccinated, either because they are under 12 and not eligible or because they are teenagers whose parents didn't feel a sense of urgency to vaccinate.
In the US, where COVID is surging and more than 70% of adults are vaccinated, just comparing vaccination rates for different age groups means that we should expect to see a far larger fraction of the infected being children than in the previous waves. There's a lot of infections going on right now, and thus as a baseline, even if the danger for any given child is the same as with the prior variants, we should expect a lot more sick kids than before.

Add to this the anti-mask crowd and the start of in person schooling and we will see many more sick before this thing is behind us.

Washington Post reported on August 3rd that 57% of US adults had at least one vaccine dose. Has the number changed that much in less than a month, or is there an inaccuracy in one of these figures?

@electronpusher You are getting the figures in the article confused.  Currently 59.9% of all people in the US (including children) have at least one dose. When you remove children under 18, it's currently 72.3% of adults.  Children in the 12-17 age bracket are currently at 44% with at least one dose. All of these numbers were just a few percent lower two weeks ago.

Is Delta more infectious than other variants though? Yes, it's very prevalent, but you probably wouldn't call this year's strain of influenza more infectious than last years, and the year before that and so on. So while your statement that it's very infectious is true (every SARS-CoV-2 variant is), it may mislead some people who may think that Delta is somehow worse than other variants, while it just has better fitness in the current population.

@JohnEye Although the exact r-value isn't certain, the data so far shows the Delta variant to be far more infectious than other strains. See, for example: https://context-cdn.washingtonpost.com/notes/prod/default/documents/8a726408-07bd-46bd-a945-3af0ae2f3c37/note/57c98604-3b54-44f0-8b44-b148d8f75165.#page=1

The document was criticized recently on This Week In Virology podcast for various reasons, the exaggerated and weakly-supported claims about infectivity among them, see for example here (link with timestamp): https://youtu.be/EmdBoM8g9m4?t=3700 The whole episode is quite interesting and the hosts go into considerable details about R0 estimates, how much of a slippery number this is since it changes with vaccinations, naivety of population, human behavior, seasons, policy, cultural factors etc, and they discuss how difficult it is to untangle these factors and produce anything useful.

@JohnEye Yes, evaluation of the situation is still in flux and there are caveats on any number. Current evidence still generally points toward "significantly more infectious", however, and arguing the point is splitting hairs with respect to the question at hand.


text:
What is this bug? (Northern Italy)
I found two of these going around my room, looks like they entered from the window. Size is about 8-10 mm. Colour a very light translucent brown.
Any ideas of what it could be and if it's dangerous? The image is blurry as it was startled by the light and started running around :)
I live in Northern Italy and weather is humid heat (32° C, 62% RH) if that helps.

That looks like a sow bug, but white. The ones in my area are brown.

Welcome to Biology.SE. Identifications questions should include: 1) one or more clear closeup photos of the organism (photos from multiple angles if possible); 2) the species-identification tag; and 3) habitat information. Please [edit] your post to include as much of this essential information as possible. ——— Please also take the [tour] and then go through the [help] pages starting with [Ask] questions effectively on this site.


text:
How to understand the biophysics and math behind a 0.2 second delay between the pulse in my arm and my ankle?
I recently had a test with six blood pressure cuffs; 2 each on arms, ankles and big toes. During the test I could feel the pulses in my arms and legs, and noticed a distinct ~0.2 second delay between the pulse in my arms and ankles.
I used my pulse rate at the time and the fraction of the pulse period between arm and leg to get the 0.2 seconds, and I unscientifically give myself a +/- 20% error bar on that number.
I was at first quite surprised, because the speed of sound in water is roughly 1500 meters per second, and since water and presumably blood is mostly incompressible I couldn't figure out what could cause such a long delay.
Then I realized that arteries must be somewhat elastic, and that the propagation of the pulse must involve the mass/inertia of the blood and the restoring force of the artery, and so this was a biophysics problem of some kind.
It turns out that the results of the test include a report of the propagation velocity which was of the order of 1100 centimeters/second. I'm not sure how that connects with my estimate of 0.2 seconds as it implies a distance of 2.2 meters and there's no way that my elbow is 2.2 meters farther from my heart than my ankle (I'm ~1.7 meters tall).
Questions: How to understand the biophysics and math behind a 0.2 second delay between the pulse in my arm and my ankle?

Is there an equation that relates the delay between arm and ankle pulse to the elasticity of the arteries?
How is the velocity calculated from the measure delay in this case?

Since @bob1 outpaced me with his answer, I will give just a short comment. He has correctly warned you that the $\text{PWV}$ is not equal to the sound propagation velocity. In the Moens-Korteweg equation, you can see that the $\text{PWV}$ depends strongly on the dimensions of the artery, its elastic properties, and also on the blood pressure (indirectly, by changing the elasticity $E$). From the physiological perspective, this means that the  $\text{PWV}$ is not constant throughout the circulatory system. Furthermore, measuring $\text{PWV}$ has generally a large measurement error.

Finally, the measurements of $\text{PWV}$ are generally on the order of $\text{m/s}$ (with outliers up to approx. $25 ;\text{m/s}$). Your result ($11; \text{m/s}$) seems to lie on the upper part of the distribution. Some graphs for the age and pressure dependence can be found here and here.

It's like the difference between voltage propagation down a wire and movement of the electrons themselves, if that helps

@Domen - I'm a virologist not a cardiology person at all, so I would love if you could provide a better/more complete answer. I just did some quick googling, so am sure to have missed some salient points.

So it turns out that your estimate is not bad, by simple velocity calculation, I get it to be a little over 50% out (see below), but as you say, there is some error in your measurement. However, it turns out the pulse wave velocity is much more complicated than that, and subject to some debate in the literature.
The speed at which the impulse propagates is not the speed of sound, but rather the speed of the impulse from your heart, and varies according to aterial stiffness (thinner arteries are faster, larger slower as they are more floppy). The equations for calculation are similar to those used to calculate the velocity of sound in a medium. There are two of these, where $P$ is pressure and $V$ is volume and $\rho$ is density of the blood:
The Frank/Bramwell-Hill equation
$$
PWV = \sqrt{\frac{V.dP}{\rho.dV}}
$$
And the Moens-Korteweg equation ($E_{inc}$ = vessel wall elasticity, $h$ = wall thickness, and $r$ = radius
$$
PWV = \sqrt{\frac{E_{inc}.h}{2.r.\rho}}
$$
Now these are super complicated for the average person to measure and it seems a bit difficult to work with, so it can be simplified to a the classic $velocity = distance/time$.
If you look at the structure of the arteries in the body, all the major blood ones to distal portions of the body feed off (unsurprisingly) the same source, the aorta.
Now to estimate the difference in time you need to work out the time it would take to propagate to each point.
I'm not too far off you in size (~10 cm taller), and did some very rough estimates of how far my elbow is from my heart and about how far my heart is from my ankle, and I got ~40 cm for elbow and ~135 cm for ankle.
You gave a propagation speed of 1100 cm/s, so substituting that into the simple equation:
$$
\text{time} = \text{distance}/\text{velocity}
$$
So 40 cm distance:
$$
\text{time} = 40/1100
$$
$$
\text{time} = 0.0364  \text{ seconds}
$$
and 135 cm distance
$$
\text{time} = 135/1100
$$
$$
\text{time} = 0.1227 \text{ seconds}
$$
$$
\text{Difference in time} = 0.1227-0.0364
$$
$$
\text{Difference} = 0.0863 \text{ seconds}
$$


text:
Is this a bed bug? Looks like a skeleton
Is this a bed bug? Germany, the size of specimen is 0.6 mm.

Does this answer your question? Insect identification - Is this a bedbug?

Please provide your location and approximate size of the specimen if you want an ID.

Looks similar to the picture in your answer, but I don't know. I have a new picture uploaded.

The body shape, cerci, size, and in-home concern have me thinking this is a cockroach nymph.
It doesn't resemble the nymph of any of the really common global pest species (e.g., German, Oriental, brown banded; see here), and narrowing down otherwise is difficult. I don't know the exact species (as my internet keeps crapping out when I search for European-based websites). So I will -- for now -- show you imagery of a nymph of a common pest cockroach for comparison:

 Pest Off Solutions


text:
Safety of Covid-19 vaccine for pregnant women
Is there any possibility that the protein produced by COVID-19 mRNA vaccine taken into body could cause negative effect for unborn babies?
In particular, isn't it possible the protein could be used as part of the baby of the pregnant woman?
In addition, mRNA can be broken by thermal fluctuation, so I worry that this broken mRNA might produce unexpectedly harmful protein for the body. Is this risk possibly realized?

Why do you think the protein would 'be used to become part of the pregnant woman' or 'produce unexpectedly harmful protein for the body'?

In a very recent case, an unvaccinated mother gave birth to her baby, held her once, and she died 10 days later of Covid-19. How, when the vaccine is so new, can we determine all of its effects on intrauterine offspring? However, the lack of a mother has definite known negative side effects.

The CDC has evaluated COVID-19 vaccines for pregnant people, and has determined that they are safe.
The main worry that they were addressing, however, was not either of your concerns (which do not make sense biologically). Instead, they were looking at whether the reaction of the body to the vaccine would be a potential cause of miscarriage.  The answer is: no, it's not.
Instead, we should be encouraging pregnant people to get vaccinated so that they will be less likely to die or become seriously ill, which will definitely have a bad effect on their unborn baby.

Thank you for your prompt answer. ok, I am totally new to biology and my concern might be off the point, but I am sincerely trying to understand why scientifically this mRNA vaccine is believed to be safe. Could you kindly answer SPECIFICALLY what does not make sense biologically?

How can you prove that the protein made by the mRNA does not affect unborn baby?
How can you rule out the possibility that the proteins made by broken mRNA is not toxic to human?

I would suggest studying some of the basics on how cells, proteins, and pregnancies work. mRNA is being degraded continually unless it's stabilized, so when mRNA gets broken, it gets rapidly recycled and you get no product, not a toxic product. As for impact on unborn babies, big proteins won't pass the placental barrier at all, so they simply cannot get to the baby in the first place.

As for "how do we prove ... ?", "how do we rule out ...?"  The only way to prove that the vaccines are safe for pregnant women, or more precisely to evaluate their risk (since nothing is 100% safe), is to run a randomized clinical trial. This is (1) slow, (2) expensive, (3) unethical because we don't have any reason to believe that they're unsafe (so it wouldn't be fair to the pregnant women we left in the control group who got COVID). "Prove it" is a bit like "prove I won't be eaten by a crocodile on my front porch" (even if I live in New Jersey).

@jakebeal, you could add the second and third sentence of your comment to your answer ...

Some immunoglobulins (IgG) are known to cross the placenta. They usually help the infant, not harm them, making a potential case for the safety of the vaccine. (Also, sorry that I repeated one of your points to the OP. I had not read your answer at that point.)

@anongoodnurse True, though the transfer of IgG is mediated by a specific targeted mechanism, so the basic point about proteins not passing through remains, and I hope the (inevitable) exception doesn't confuse the OP.

Thank you all for kindly answering question from layman. My knowledge on biology is from what I've read the textbook of essential cell biology, so not enough to understand papers on mRNA vaccines, but thanks for explaining in easy words.
@BenBolker I get your point, maybe my words were too strong, the proof of safety is like devil's proof.

@jakebeal OK, so there is enough reason to believe harmful proteins will not enter placenta generally. I will believe it.

@jakebeal What about the first question? it will take a while (~hours to days?) for mRNA to be broken by brownian motion, so if the broken mRNA is still able to produce corresponding protein, aren't there any possibilities that one of those proteins might be harmful to human?

@HQMA Cells regulate mRNA quite aggressively for many reasons, including preventing production of harmful proteins by RNA-based viruses. Those same mechanisms will generally prevent what you are worrying about. See, for example, this survey: https://www.nature.com/articles/nrm2104

@jakebeal Thank you for your comment, it's good to know there are such arguments to suggest the safety


text:
Understanding expected mean number of breeding seasons
I've recently come across an equation for the expected mean number of breeding seasons after the first breeding season, as a function of the annual survival rate (S) and the probability of breeding,
$$
\mathbb{E}(\#\text{ of breeding seasons}) = \dfrac{1}{-\ln(S)} \times \text{breeding probability}
$$
I'm having a hard time understanding what the term $1 / -\ln(S)$ represents. Any ideas?

It's just a continuous version of the discrete calculation. The discrete version is the (infinite series) sum
$$
\sum_{i = 0}^\infty S^i \cdot bp
$$
adding up every (chance of survival to season $i$) x (breeding probability given that survival).
Making this continuous converts the equation to
$$
\begin{split}
 & \int_0^\infty bp \cdot S^i \, di \\
  = \enspace & bp \int e^{i \ln S} \, di
\end{split}
$$
integrating gives
$$
\left.bp \cdot \frac{e^{i \, \ln(S)} }{\ln(S)} \right\vert_{0}^{\infty}
$$
Evaluating gives
$$
= \frac{bp \cdot e^{-\infty} }{\ln(S)} - \frac{bp \cdot e^{0} }{\ln(S)}
$$
(remembering that $0 <= S < 1$, so $\ln(S) < 0$)
$$
= bp \cdot 0 - bp \cdot \frac{1}{\ln(S)}
= bp \cdot \left(0 - \frac{1}{\ln(S)}\right)
= bp \cdot \frac{-1}{\ln(S)}
$$

This makes sense, thanks!

@BenBolker Thank you so much for the example that LaTeX works here! I will work on completing the formatting.

I think your explanation is correct. The expected value of the exponential distribution is:
$$t \sim \text{e}^{-\lambda t} \implies \langle t \rangle = \int_0^\infty t \ \text{e}^{-\lambda t} \; \text{d}t = 1/\lambda.$$
For the exponential survival function, we have to identify the parameter $S$. Since $S$ is the number of survived individuals after one year, we derive:
$$S = \text{e}^{-\lambda} \implies \lambda = - \ln S.$$
Therefore, the life expectancy is simply:
$$\langle t \rangle = -\frac{1}{\ln S}.$$
Because the probability of a breeding to happen each year is independent, we can multiply the life expectancy by the probability that the breeding happens in a one year period. This gives us the final result:
$$\langle \# \text{ breedings} \rangle = \langle t \rangle \cdot P(\text{breeding}) = -\frac{1}{\ln S}\ P(\text{breeding}). $$

This is also a good explanation! Thanks for the help.


text:
Why does Diphenylamine only react with the deoxyribose of purines?
The deoxyribose in DNA in the presence of acid forms β-hydroxylevulinaldehyde which reacts with diphenylamine to give a blue color with a sharp absorption maximum at 595nm.
In DNA, only the deoxyribose of the purine nucleotides react with Diphenylamine, so that the value obtained represents half of the total deoxyribose present.
Why is this the case?

Why not start with researching what happens when DNA (not just the deoxyribose part) is placed in acidic solution?

As you have correctly stated, the DNA cannot directly react with diphenylamine. First, it has to be cleaved so that the deoxyribose is exposed. In acidic solution and at high temperature, a depurination occurs several orders of magnitude faster than depyrimidination, because N-7 of the purine can be protonated and assist the cleavage.
See this mechanism of the acid-catalyzed depurination:


text:
Bug identification
Germany, cca 0.6mm, dead Bug, i haven't see before

This is an immature cockroach, possibly Planuncus vinzi.
Here is a map of the observed distribution of the Planuncus genus:

And here is an extract of a gallery of nymph-stage Planuncus cockroaches:

To view the full gallery: https://www.inaturalist.org/taxa/732965-Planuncus/browse_photos?term_id=1&term_value_id=5
You can change the "Life stage" attribute from 'nymph' to 'adult' to see what the fully-grown versions look like and see whether they look more familiar to you in that form.


text:
Could p-loop bind fully protonated ATP?
The phosphate tail of ATP binds the p-loop motif, evolutionary conserved, going back to since forever. In the dominant model, the deprotonated hydroxyl groups are complexed with Mg2+, at least two of them.
I was wondering about a hypothetical model (could consider it "fantasy" or just thought experiment, without disclosing if there is any actual credible reason to think about it. )
If the three deprotonated hydroxyl groups were actually protonated, is there still a fit in the p-loop? This would remove the Mg2+, since it is substituted by H+, charge-wise.
That ATP does not actually get protonated like that in the dominant models, is neglected in the question. I am just wondering about fit in the p-loop. To have a way to think of that, imagine the ATP might be slightly modified, or some other input altered, but the p-loop itself is the same, and the phosphate tail except here it is fully protonated.

A really simple answer is that hydrogen bonds are stronger when the hydroxyl groups on the phosphates are deprotonated, because hydrogen bonds are like a competition for a proton, but, hydrogen bonds form between hydroxyl groups even when one is not deprotonated.

This gets a bit more interesting if a few facts are considered. The deprotonated group has, relatively speaking, less negative charge. Otherwise, it would be able to hold onto the proton just as well. And since the hydrogen bond acceptor is the group with most negative charge, the deprotonated one would only be favoured because it lacks the proton, not because is has less negative charge in itself. This is a fact but it does not in itself say much. But consider the following.
In a "lock and key" setting with a specific type of fit, the deprotonated group might actually be the hydrogen bond donor. This is very counter-intuitive, but, it relies on the groups being forced close to each other to start with. Then, the combined negative charge of the groups, will actually protonate the deprotonated group, and it will be the donor to the more negatively charged other group. It is a fact that, with added negative charge, the ability to attract a proton increases. And hydrogen bonds rely on physical closeness.
So, the p-loop/ATP complex is acting like a base, using a lock-in-key fit for... protons.


text:
Identification of moth in Pandemis heparana trap
While monitoring Pandemis heparana in an apple orchard in South Tyrol (middle of August), I frequently observed huge moths accumulating within the trap. The trap itself is working with pheromones for Pandemis heparana.
The moth is 4 cm long and at least 1.5 cm in diameter. It is quite solid and has upper wings which are brownish and lower wings which are bright orange with a distinct black part at the end of the wing.

Can you help me to identify this moth?
Edit: The moth was dead when i touched it.

There's a group of moths known as the "Underwing moths" for their brilliant coloured hindwings. I think these are used to startle predators when they get too close. They have the brilliant red/orange with a black border. If you could open the wings fully, it would help with ID significantly.
The genus is Catocala, which translates to "beautiful lowerone"
For some moths of Austria, you can browse images here, which is how I found the genus name.


text:
Cell Theory- does the first cell not contradict cell theory
In cell theory, we have cells arise from other existing cell.
But the first cell did not arise from existing cell, and that means there are some other condition which allows cell to be formed.
I understand the chance of forming the cell without other cells has a low probability, but given it is still possible, does that not contradict the statement itself that you must have other cells to form new cells even ignoring the first cell as a special case?

Can you please clarify what it is about the standard models of abiogenesis that you do not understand?

@jakebeal Thanks - I understand we can create cells from non-living material, but I do not see why we can leave that out in cell theory, and say cells are only created from other existing cells. We can say this is the only way cells are created by living material (ignoring cases which cells arise from non-living material), is from other cells, but then all living materials have cells (from the definition of cell), and so that makes that statement trivial?

I think this is mostly a confusion of the meaning of "laws" that govern fields like physics and the "laws" that govern biology. Biology tends to stubbornly break any sort of "law" you try to constrain it with (besides those of physics), but that doesn't necessarily make biological "laws" less useful, it's just that we tend to take for granted how things need not be as they are in biology.

Sometimes the probabilities of events are so low, that we can neglect them for all practical purposes. A classical example in thermodynamics: if we have a gas in a container, there is a non-zero probability that all the molecules assemble in one half of this container, while in the other part we have vacuum. It never happens in practice - the probability of such an event is $\propto 2^{-N_A}$, and if one observes a container, one would have to wait for longer than the age of the universe (which is much longer than our lifespan, the existence of the humankind, and the existence of life). Thus, we can confidently treat it as a law, and claim that the sea had never opened in front of Moses.
Same about the acquisition of the cellular membrane: the event might have happened only once in a few billion years, and in very special conditions, which are not at all common nowadays. It is negligible for all practical reasons, to the precision that makes it possible to consider it a law.

It's also worth noting that existing life will inhibit the emergence of new life, as existing life will tend to quickly eat anything with the potential to become new life.


text:
The Portion of the Earth's Biomass Attributable to Ants
An exterminator came to the house today (bad ant problem).
He claimed that 20% of the earth's biomass is comprised of ants.
I was surprised by this statement.
I figured that I would post the question here (hope that's OK) and ask if someone can, generally speaking, either confirm this assertion or refute it.
If the exterminator's statement is false, what would be a more accurate estimate? If you can provide a reason or two, I would appreciate it.
Thank you.

I've suggested this question as a duplicate of the one linked above because, even though it doesn't specifically refer to ants, the graph in the answer shows that arthropods (which includes ants) are a measly 1 gigatons, compared to the 450 gigatons of plants. If you dig into the supplemental information, you find that terrestrial arthropods are less than 0.2 gigatons, and a lot of that isn't ants (e.g., 0.07 Gt termites), so ants are way under 20% even just of animals.

This is an incorrect statement. According to an answer to a question in a different SE, https://skeptics.stackexchange.com/questions/7602/is-the-total-biomass-of-ants-roughly-equal-to-the-total-biomass-of-humans, ants comprise roughly 15-20% of the (terrestrial animals), which is only a small percentage of the total biomass that includes sea life and plant life, among other forms of biomass, on earth.

If you read the sources for that Skeptics post carefully, they claim “On average, ants monopolize 15–20% of the terrestrial animal biomass…”. So, that excludes all aquatic life and non-animal terrestrial life, including plants. So I’d say the 20% figure given by OP is likely off by orders of magnitude.

@Alex K Thank you for providing the link to the Sekptics posting. It is helpful.

@acvill I said "total dry biomass" to mean terrestrial animals, thanks for the suggestion.

@AlexK in a biological context, "dry biomass" typically refers to dehydrated mass (that is to say, organic material minus water weight). Also, there is nothing about the phrase "dry biomass" that suggests it refers to animal biomass exclusively. Your answer could be a good one if you correct the language to accurately reflect your linked source, and rewrite your conclusion ("This is a possibly true statement") to reflect the fact that terrestrial animal biomass is a small fraction of earth's total biomass.


text:
Why is syphilis not resistant to penicilin?
How is it that we are dealing with so many antiobiotic resistant infections in iatrogenic settings, and yet this very old bacterial pathogen has still not acquired resistance to penicilin (the oldest antibiotic to which it has had the longest relative exppsure to)??

While rare, it does happen--reports of penicillin-resistance go back to at least 1949

First off, Treponema Pallidum-the bacteria which causes Syphilis-is EXTREMELY SENSITIVE to Pencillin; even a small does can wipe them out! Secondly, since Syphilis has been around for centuries without mutating into a form immune to Pencillin this suggests TP doesn’t have ANY protective measures against antibiotics-making it highly susceptible. Lastly, resistance rates remain low globally, meaning strains which develop immunity don’t survive long against antibiotic treatment


text:
Biology Experiment Algae pH & temperature help?
I am planning a Biology investigation for my IB IA on the impact of temperature and pH on algae growth. Does anyone have tips on how to measure the growth rate of algae? What algae is the most suited for such an experiment? Also, how do I change the pH of the water containing algae? I'm a beginner, any ideas would be a great help!

Welcome to the site - can you tell us what sort of equipment you have access to? In particular do you have access to pH meter, microscope, hemocytometer, low mass scales, drying oven,

Perhaps spirogyra? Make sure any tap water is left overnight to gas off the chlorine compounds.

i have access to a wide range of equipment, all those you listed I can use

In general is a good idea to check the scientific literature in the subject. In the section "materials and methods" you could find how people do stuff like measuring growth or controlling pH.
Of course, many of the methods described there could be out of reach, but you can get ideas and ask here more specific questions.
For this specific question a quick search lead me to this paper "Standard Methods for Measuring Growth of Algae and Their Composition"


text:
Does hormone participate in metabolic activites?
strong text
My take on question-

All hormone are not water soluble, some are fat soluble also so this option is definiely wrong.

Thyroxine Hormone is do stored in the body in Follicle of thyroid gland, All is not mentioned so we can say this option is not wrong.

Hormones are destroyed after use, and that's a fact, so this option is also correct.

Now here comes the tough part

Hormone do not participate in the metabolic activities, well signaling is not participating as far as I think, Hormones do not act as A Substrate or as A enzyme, so this option seems correct to me, but I am not sure, Does Signalling means Participating??

The molecules of most of the hormones are small. I don't know what to make of it, well if compare simple one molecule Hormones like Epinephrine and Melatonin to Peptide hormone, Peptide hormone seems large,this options is so Ambiguous I need help in this

Ah, good old bad exam questions. Invoking subjective, arbitrary and ambiguous adjectives and verbs. My very rough and blunt appraisal would be that many hormones are indeed widely and relatively small -ish. They are often 're-usable' after binding since their binding to receptors is often reversible. Some endocrine cells store hormones, while other hormones are entirely in flux. Some hormones are soluble, others aren't, yet others are not but are emulsified by things like micelles (e.g. casein). Some hormones certainly participate in metabolism; think insulin's role in glucose metabolism.
First, let's just acknowledge the lax definition of hormone before we go into each one-by-one.

Most hormones are small molecules

Generally correct. I think most biologists would be okay with saying this is generally true. They are necessarily small in many cases because they function in long-range endocrine or paracrine signaling and must satisfy preconditions for such functions. Consequently, it's easier to make a long list with small molecular weight hormones than it is to make a list of large molecular weight hormones.

Hormones are destroyed after use

Generally incorrect. That depends what destroyed and use mean. If by use one means binding to a receptor to transduce a cascade, then a single hormone molecule typically can be re-bound to the same receptor on one cell, and/or can be received by different cells. Some hormones are 'destroyed' by endocytosis and subsequent lysis within the endomembrane system, others have to be inactivated by proteases or filtered from bodily fluids by, say, kidneys.

Hormones are stored in the body

Some are, others are not. Steroid hormones, being lipophilic, cannot be stored in vesicles, and so are synthesized in mitochondria and smooth endoplasmic reticulum as precursors. I would be cautious to claim that precursors are hormones, so let's say with confidence that these cannot be stored. However, many other hormones that are usually not lipophilic, such as amino-acid based hormones, are typically stored in secretory granules. See here or here.

All hormones are soluble in water

False. Counterexample: steroid hormones are insoluble in water, which is why they are carried by transport proteins in the aqueous medium of the blood.

Hormones do not participate in metabolic activities

False. Counterexample: insulin.

Hormones do not participate in metabolic activities
False. Counterexample: insulin     , Isnt the participation means, being the substrate or enzyme, Insulin does signal transduction by kinases , which ultimately leads to GLUT 4 to insert in cell membrane, this is isn't metabolism , anbolic or catabolic, as the signal transduction only lead to influx of glucose, not in metabolism of glucose, in short i am not able to digest that signal transduction is also a paraticpitation in metabolism, it is facilitating metabolism

You are right that insulin does not directly participate in chemical pathways. It is a central player in the metabolism of glucose. It directly influences the availability of glucose for glycolysis! ATP is catabolically consumed to begin glycolysis. How about the case of adrenaline? Does adrenaline not increase the availability of oxygen? This is semantic confusion that the question leaves open to interpretation, hence the preface. But certainly one can reason that metabolism, defined as the total set of life-sustaining chemical reactions in organisms, excludes insulin as a participant!


text:
Is lignification within plants a reversible process? If so which factors can reverse lignification?
Lignification is an important process in plants such as trees to allow for structural rigidity. Is this process reversible by the plant and if so which factors influence this reversibility?

A quick search found Ursache, 2021 that says in the abstract lignification is "thought to be irreversible", but I haven't chased it down.

Do you mean specifically delignification that occurs in vivo by means of metabolic processes in the same plant that performed lignification? Delignification is a well-known process of microbial decomposers e.g. white rot (https://bnrc.springeropen.com/articles/10.1186/s42269-019-0094-x), and which could presumably occur in living tissues infected by some pathogen, but I don't think that's what you mean.

I edited your post to make it more concise — please re-edit if you think I've altered your meaning, but try keep your posts as clean and clear as possible. To thank someone for a helpful/useful comment just upvote it (as I did). It would also be helpful if you added in more background — i.e. tell us where you've looked for answers, more about what you do know about the topic, and where exactly you still have questions. Also, can we assume that by "factors" you mean enzymes or are you more interested in things like environmental conditions?

I'm interested in any factors that's why I let it unspecified. A quick google scholar search did not return any results if plants are capable of reversing lignification. As I'm pretty limited time-wise I offered a bounty..


text:
Is unihibited exhalation beneficial for someone with a contagious respiratory disease?
If someone has a contagious respiratory disease (I'll refer to as CRD - eg. COVID, FLU, etc.) I'm wondering if the process of exhaling could be beneficial for them.
My first thought is that exhaling would be beneficial because expelling the virus from the lungs (which is the same process that makes it contagious) could lower the viral load in the lungs.  Instead of those virii replicating in their own lungs it would be expelled.  It would seem that wearing a mask in a case where a person has a CRD would be detrimental because the virus would be caught by the mask when they breathe out (which is why masks protect other people) but then could be re-inhaled when they breathe in.)
On the other hand, it could be that for someone to be contagious they would have such a viral excess that the amount they would re-inhale would not be significant.
It is clear that if someone might have a virus and be might be contagious should wear a mask around other people.  The question is, would such a person benefit from not wearing a mask when they are not around other people (in a closed room or car or outside away from people) or would it not make a difference?  For example, I've often seen people driving around in a car by themselves while wearing a mask.  It's not clear to me if this is a harmless practice or is detrimental to them.

Short answer
No, there isn't going to be any benefit to an infected person by allowing them to breathe out virus particles freely. The number of viral particles breathed out is tiny relative to the number captured in a diagnostic swab, which itself is tiny relative to the virus contained in the entire rest of the respiratory tract. Simple exhalation is just not an effective manner of removing virus.
Longer answer
Fabian et al 2008 measured exhaled virus from subjects with influenza.

Concentrations in exhaled breath samples ranged from <48 to 300 influenza virus RNA copies per filter on the positive samples, corresponding to exhaled breath generation rates ranging from <3.2 to 20 influenza virus RNA copies per minute.

Granados et al 2017 estimated viral loads of influenza on the order of 10^5 to 10^8 copies per milliliter, median around 10^6.6 (from 200 microliter extracts of clinical samples).
There are 1440 minutes in a day, if we go from the top end that's 20*1440 = 28800 exhaled particles over an entire day, easily an order of magnitude less than would be picked up by a diagnostic swab and likely a fraction of a percent. That doesn't even account for the fact that a diagnostic swab is itself not taking any sizable fraction of the infected particles in that individual, nor that new particles are being generated throughout the day.
Wanting to confirm a bit, I went to another source. Milton et al 2013 collected particles of two sizes from breath exhalations, as well as swabs from the same subjects. Median swab concentrations were around 10^5 to 10^6 on different days, similar to those from Granados. Virus particles from the coarse and fine exhaled particles were much lower; the peak was in fine particles on the first day with a median over 30 minutes of 610 particles (plus another 23 in the coarse particles), the same as the high end of Fabian.
It is not feasible that these tiny numbers would have any influence on the severity of the infected individual's illness. If it were, you'd be much better off just getting a bunch of respiratory swabs (no, this won't actually work)! It is feasible, however, that these particles go on to infect others, and that's what mask-wearing is trying to avoid.
As far as people alone in cars, likely the main benefit to them is that by keeping their masks on rather than removing them repeatedly, they're avoiding contact between their hands and anything that's ended up on the mask, and avoiding bringing the mask that they'll breathe through into contact with whatever has ended up on their hands.

Fabian, P., McDevitt, J. J., DeHaan, W. H., Fung, R. O., Cowling, B. J., Chan, K. H., ... & Milton, D. K. (2008). Influenza virus in human exhaled breath: an observational study. PloS one, 3(7), e2691.
Granados, A., Peci, A., McGeer, A., & Gubbay, J. B. (2017). Influenza and rhinovirus viral load and disease severity in upper respiratory tract infections. Journal of Clinical Virology, 86, 14-19.
Milton, D. K., Fabian, M. P., Cowling, B. J., Grantham, M. L., & McDevitt, J. J. (2013). Influenza virus aerosols in human exhaled breath: particle size, culturability, and effect of surgical masks. PLoS pathogens, 9(3), e1003205.

Thanks for the great answer.

Based on what you're saying, it seems a comparable analogy would be that when a fire spews out burning ashes, it can start other fires.  But keeping the sparks contained in the original fire is not going to make it burn any stronger.

While I don't doubt your short answer, I'm not sure I follow the long one, either.

@anongoodnurse The short form of the long answer is that the number of viral particles breathed out is tiny relative to the number captured in a simple swab, which itself is tiny relative to the virus contained in the entire rest of the respiratory tract. Simple exhalation is just not an effective manner of removing virus.

Ah, thank you! Senior moment... no, several minutes, there. :-/


text:
Why do babies urinate when they hear "SHHH.." sound?
I have noticed it many times in the region where I live. I don't know if its common World wide. But I think someone else would have noticed it. So why does this happen ?

I have no sense of the tags to be used here . So please someone add it if possible .

This sounds like hearsay; we appreciate questions that are founded on scientific grounds. I would suggest this to be carried over to Reddit or a similar nonscientific forum

I think it's necessary to show evidence (not merely anecdote) for a phenomenon before asking "why" it occurs.

In general, babies do not naturally urinate when hearing that sound.
However, there is a technique of instilling a Pavlovian response in your baby to urinate when hearing that sound.  You start by holding the baby diaper-free, and making the sound when they urinate, so that they make that association between the sound and the sensation of urination.  After lots of reinforcement, you can get the baby to urinate when it hears the sound, so babies are potty-trained earlier than they otherwise would be.
It's part of a process called "elimination communication"
https://en.wikipedia.org/wiki/Elimination_communication
It's less common in Western countries, probably because most people prefer to, and have the means to either buy lots of disposable diapers, or have the means to easily wash their cloth ones over and over again.

I always thought that it is the onomatopoeia for the sound of peeing, invoking the same response as the sound of running water.


text:
At what calcium concentration does the Sodium-Calcium Exchanger (NCX) "turn on"?
I am interested in the comparison between the Plasma Membrane Calcium ATPase (PMCA) and the Sodium-Calcium Exchanger (NCX) which are two pumps on the plasma membrane of cells that serve to move calcium out of the cell and maintain relatively low resting calcium concentrations. Typically, I see the statement that the PMCA has high affinity for calcium but a low pumping capacity, whereas the NCX has a low affinity for calcium but a high pumping capacity.
In the literature, I can find relatively simple models of the PMCA as well as data of estimated dissociation constants for it. However, I am having a much harder time finding the concentration of calcium where the NCX becomes relevant. It might be because the NCX also depends on sodium concentrations, membrane potential, etc., which gives rise to much more complicated models. However, there must be some research that backs up the "NCX has a low affinity" claim.
So, what is the typical calcium concentration range where the NCX becomes relevant, such as a calcium dissociation constant where the pump is at 50% of its maximum capacity?

Check https://en.wikipedia.org/wiki/Sodium-calcium_exchanger

@PCM I don't the the answer to my question there.

I'm not sure but I think you will find that these are "always on" pumps, so at any concentration they can be pumping. By relevant you mean physiologically?

@bob1 Good point. More quantitatively, I'm asking about something like a dissociation constant where we would expect the pump to operate at 50%. I know that's a huge simplification for the NCX, but I feel like there should still be some sort of estimate.

I could not find the $K_d$ of NCX proteins in KEGG BRITE, BRENDA, SuperTarget, DrugBank, Uniprot, or PDSP Ki databases...
(Also, I cannot understand the use of the word 'relevant' in the question you asked.)
Still, the requested thermodynamic constants can be found in publications.
Taken from Z.Li et al.(1994)

NCX2 ($Na^+$) : the $K_d$ values for $Na^+$ $(28 \pm 2 mM, n=2)$ are very similar before and after $\alpha$-chymotrypsin treatment and are somewhat higher than those measured for NCX1(e.g. Hilgeman, 1990; Matsuoka et al., 1993)

NCX2 ($Ca^{+2}$) : The fitted $K_d$ values are 1.6 and 1.4 $\mu$M with Hill coefficients of 2.4 and 1.1 respectively. The reason for the shift in the Hill coefficient is unclear.

Also, B.Linck et al.(1998) studied NCX1,NCX2,NCX3 comprehensively. They reported the $K_d$ of these proteins in various situations and environments. These two results seem conflicting... Maybe because they worked on different types of tissues in their studies...
Taken from B.Linck et. al.(1998)

Exchange currents recorded from NCX2-expressing
cells (Fig. 8B) were not as well regulated as those
previously reported from oocytes (22) [=> Z.Li et. al. paper] and were smaller
than those obtained from NCX1-expressing cells.

Looks like B.Linck's paper is much more reliable, though. But I may not share all the graphs of the paper here.(copyright stuff)
I skimmed through the papers, honestly... So feel free to dive into these papers yourself. Cheers!


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Why can mRNA come out of the nucleus but not enter it?
I am a mechatronics engineer who stopped learning biology after high school - but this is bothering me.
mRNA is, if I recall correctly, created in the nucleus of the cells and migrates out of the nucleus inside the cytoplasm where it will be translated by ribosomes.
mRNA vaccines inject mRNA molecules inside the body, which are apparently transported by their nanolipidic particle coating across the cell membrane, correct?
I understand that the DNA→mRNA transcription is probably not reversible, but I do not understand how the mRNA is only able to cross the nucleus-cytoplasm membrane in one direction.
Care to explain? Bonus kudos for clarifications on the rest of my doubts.

mRNA vaccines are not "transported" by their lipid coating (no active transport involved). It's just that lipids are attracted to the nonpolar plasma membrane and expelled from polar water.

Nuclear pores control what gets in and out of the nucleus.  In general, mRNAs are only allowed out, they don't go back in.  Reverse transcriptases, of course, will put mRNA back into DNA, but only some viruses, like HIV, have those enzymes.
https://portlandpress.com/biochemj/article-abstract/477/1/23/221793/Into-the-basket-and-beyond-the-journey-of-mRNA?redirectedFrom=fulltext

Interesting, thanks! Do you mean that, unless a person is infected by rare specific viruses, no reverse transcriptase is present in the body and therefore the mRNA cannot reenter the nucleus?

It is very hard to categorically say something is impossible in biology; there are always exceptions.  But your cells are full of your mRNA all the time.  When you get infected with most viruses, like COVID, there is foreign mRNA in your cells.  In general, this does not cause permanent change to your DNA, let alone clinically pathogenic change.

Just note that reverse transcriptase works in the cytoplasm to create a DNA copy of an RNA, so it does not allow mRNA transport to the nucleus, it just creates DNA which could then be transported to the nucleus.

I think this is the beginning of a good answer, but it doesn't directly address OP's question: "but I do not understand how the mRNA is only able to cross the nucleus-cytoplasm membrane in one direction". Yes, nuclear pores control the flow of mRNA out of the nucleus, but they also allow things into the nucleus (like proteins). What is the mechanism by which mRNAs are exported but not imported?

@acvill: this would indeed be particularly interesting to know!

@swbarnes2 has it been shown that RNA viruses do not change DNA?

How many colds have you gotten in your lifetime?  Do you think they've all changed your DNA?

Transcription Regulatory proteins are able to enter into nucleus because they posses a specific strings of amino acid sequence called Nuclear Localization Sequence. Nuclear Pore Complex don’t let anything without that sequence pass. Nucleus membranes are temporarily dissolved during cell division and reconstituted once the process is complete so technically it’s a possibility that some enzymes could happen to be there. However during cell division, DNA is all wrapped up (DNA-nucleosome-chromatin-chromosome) so not much regulation (much less damaging alterations) can be done during this time.
And let’s just say things do go wrong and this particular cell starts to act wonky, your immune cells will recognize the “defective” cell and either engulf it to destroy it or trigger its self destruction through Apoptosis. Pretty neat huh? Inspite of all the failsafe mechanisms, some viruses do manage to disrupt DNA by inserting transposons which in some incidences could trigger/suppress oncogenes, protooncogenes, tumour suppressor genes etc with dire consequences.
Sorry David! Pardon my zeal for proteins. My comment was more for the previous posters and not the OP.
Post transcription, mRNA is modified (introns removed, spliced), 5’capped, Poly A tailed added on. 7-MethylGuanosine m7G cap plays an important role in mRNA transport and metabolism. m7G Cap attracts and binds proteins such as eukaryotic translation initiation factors and Cap Binding Proteins. They not only guide mRNA where to go (ribosomes on ER) but also protect them from being degraded by exonucleases (very efficient enzymes that break down RNA and DNA)
mRNA has a lifespan of mere 1-3minutes.
So to answer your question, cytoplasmic mRNA (foreign or m7G capped cellular RNA) tend not to make it back because

The proteins it’s bound to lack the Nuclear Localization Sequence to get past the Nuclear Pore Complex or 2. Gets degraded very quickly by exonucleases.

Reverse Transcriptase (RNA dependent DNA Polymerase) is not just found in viruses. Telomerase (that lengthen telomer caps on chromosomes) also is a reverse transcriptase. Look up human TERT. Like all polymerases it needs specific binding sites and requirements. RT just doesn’t transcribe any ol RNA into cDNA hybrid FYI. The viruses that insert viral genome into cellular DNA have evolved to bypass all the cellular fail safes.

Welcome to SE Biology. Please finish the [Tour]. Please also read the question and note that it is about the transport of mRNA. Your answer is about proteins and makes no mention whatsoever of mRNA.

Sorry I can’t spend any more time specifically to look up citation to back up my post.  randomly came across it and sensed an underlying concern regarding mRNA vaccine becoming  incorporated into your DNA.  For reasons outlined above the chances are extremely slim to zilch. Don’t get me started on the amount of noncoding and  considered junk DNA already on our chromosomes. As for citations, you can easily look it up based on the names I provided or  I’m sure other cell biologists  can back me up.  Should be working  or spending time with my kids anyway. Adios and hope I helped OP

@NunyaBeezenez Welcome to Stack Exchange! This site works different than most others. Answer posts are absolutely expected to support their assertions by citing references and including links.


text:
What are the roles of ATP and ADP in muscle contraction?
I've always known that the hydrolysis of ATP generates ADP, P, and energy, so I'd assume that if energy is necessary in a given process, ATP hydrolysis should occur (or another exothermic process).
What I don't understand is how this works in muscle contraction. I assume that part of my misunderstanding might be due to the lack of knowledge of how the contraction works at a molecular level, as well as how this phenomenon relates to the contraction at the macroscopic level (my arm contracting), hence I'm writing this question.
From a number of sources, including the image below (which is taken from an book in Italian, so I don't include the text; with reference to the figure, stadio means stage, by the way) and the one in this related question, I understand that the mechanical energy is released (i.e. the muscle exerts power on the external world) both when P is released when ADP is released, but definitely not when ATP is hydolised.
Now I do understand that the cycle in the image has to repeat a tremendous number of times while I simply raise my hand to say hello, for instance, but my knowledge of physics tells me that, whatever the amount of energy required to raise my hand is, the two power srokes summed up on all the elmentary cycles have to provide that energy (plus some more to overcome losses, like joint friction or whatever).

But where is the energy that the two power strokes are exerting coming from? It looks like the energy is coming from the release of ADP and P, which makes me think that this is itself an esothermic process, otherwise how could it result in power strokes?
And also, why is ATP needed, then?
From the image I see that the ATP hydrolysis happens between stage 5 and stage 1; does this mean that stage 1 is a high energy state?

In the meanwhile that I write, I start to think that probably the core of the matter is that I mistakenly thought that ATP is what provides the energy for the mechanical action, whereas probably it provides the energy (between stage 5 and 1) that is stored in the myosin (stage 1), such that when the mechanical energy is required (between stage 1 and 2), the myson is able to release it (from stage 2 to stage 4). Does this make any sense?

As a first approximation, I think your explanation makes sense. You can imagine the system having a spring, and the hydrolysis of ATP providing the energy to load the spring  (store the energy in the myosin). Afterwards, this energy is released as mechanical work in the power stroke(s).
However, this analogy will not lead you far because things get complicated, especially if you want to study this process from a physical perspective. In biological textbooks (such as the one you provided), you will find the whole cycle being portrayed as going in one direction only (clockwise red arrows in your image). But because this is happening in the molecular world, most of the reactions/processes are actually reversible. In fact in molecular motors (such as your example with myosin), thermal motion frequently leads to backward steps, especially when the muscle is under high load. This can nowadays be directly measured with various single-molecule techniques:

The simplified biophysical models for molecular motor are ratchets, using thermal motion. They are in a way analagous to Maxwell's demon. But the same way as Maxwell's demon is not feasible because it violates the second law of thermodynamics, a molecular (Feynman–Smoluchowski) ratchet cannot generate macroscopic work by solely extracting the thermal motion. And that is where the energy of ATP comes into play: the energy is used to keep the system out of equlibrium and break the symmetry of motion in space and time (steps forward become more frequent than steps backward).
My answer is really far from being self-sufficient or self-explanatory, but I hope it provides at least some starting keywords for your further research of the topic.


text:
Why are basophils and eosinophils considered granulocytes?
I have read that granulocytes are a type of leukocytes that have granules (hence the name) visible by microscopy. But then there is something called a granulocyte/monocyte progenitor cell, which I thought would give rise to these structures. From this progenitor cell neutrophils and monocytes are created, but not eosinophils nor basophils. Furthermore, monocytes are agranulocytes. I believe my questions are all related:

Based on what I’ve read (stated above), I can only assume there is a difference between granulocytes and granulocyte progenitor cells. So is there a difference? And if is what is the purpose of differentiating between a granulocyte and a granulocyte progenitor cell?

Why are monocytes not considered a granulocyte, when they arise from the granulocyte progenitor cell?

Why are basophils and eosinophils considered granulocytes?

granulocytes are a type of leukocytes that have granules (hence the name) visible by microscopy

Yep, that's it; like you said, that's where they get the name: their appearance. Not their function or progenitor, just their appearance, and they were named long before the other factors were understood. That history goes back to at least the mid 1800s:

Paul Ehrlich's techniques, published between 1879 and 1880, for staining blood films using coal tar dyes, and his method of differential blood cell counting, ended years of speculation regarding the classification of white cells.
...
In 1846, Thomas Wharton Jones (1808-1891) described "granule blood-cells" in several species including humans. The term "granule cell" had also been used by Julius Vogel (1814-1880), who had previously observed similar cells in inflammatory exudates. Vogel, in turn, was aware of the work of Gottlieb Gluge (1812-1898), who had observed "compound inflammatory globules" in pus and serum that resembled eosinophils. Almost 20 years before Ehrlich developed his staining methods, Max Johann Schultze (1825-1874) performed functional experiments on fine and coarse granular cells using a warm stage microscopic technique and showed they had amoeboid movement and phagocytic abilities. Despite these earlier observations, it was Ehrlich's use of stains that heralded the modern era of studies of leukocyte biology and pathology.

Progenitor cells are cells that haven't yet matured into functional fully differentiated cells; usually the name "progenitor cell" is reserved for cell populations that are nearly differentiated and won't result in more than a couple/few final cell types. So, no, a "XYZ progenitor cell" is not the same as an "XYZ cell".
It seems like there is not a settled terminology for various classifications of immune cell progenitor cells, with different publications using different terms. For example, a figure on Wikipedia uses "myeloblasts" to describe cells that undergo either granulopoiesis to become some granulocyte, or they become monocytes:

(from https://en.wikipedia.org/wiki/Granulopoiesis#/media/File:Hematopoiesis_(human)_diagram_en.svg)
They don't really name any general granulocyte progenitor, instead showing them all splitting off together. Others refer to "myeloid progenitors", "granulocyte/monocyte progenitor"/"GMPs", "granulocyte/macrophage progenitor" (as monocytes become either dendritic cells or macrophages), and others.
I don't see any source where a "granulocyte progenitor cell" becomes a monocyte, only that a "granulocyte/monocyte progenitor cell" does; the "granulocyte/monocyte" label seems most clearly interpreted as "granulocyte and monocyte" progenitors, so I see nothing conflicting with these cells giving rise to both granulocytes and monocytes. I also do not see evidence that there is a stage of differentiation in which a particular cell will possibly become a monocyte or neutrophil, yet will not become eosinophil nor basophil; every textbook-style reference I find shares the pattern from the Wikipedia image above or discusses a stage of differentiation in which a cell is either fated to become a monocyte or any of the granulocytes. Given the complexity of differentiation, it's certainly possible some paper has made that claim, but I see no evidence for it.

Thank you for your in detailed response. I was reading the kaplan book and they had a figure but it wasn’t really discussed. However, this does explain the trouble I ran into with other related content.


text:
Anybody know what kind of bug/cricket this thing is? I can't narrow it down enough
Spotted just walking about down the road.

Welcome to the site, please take a [tour] and visit the [help] to learn what makes a good question to be asked here. Specifically for identification purposes we need good quality photos, preferably from several angles, a location (general, district/county level would be good), and an approximate size.

Grasshopper, immature, I do not know the specific species.

Location is the U.S. I have a video but the site would not let me post it.

Please [edit] your post to include all the requested information (hover over or click on the species-identification tag for details) — comments are ephemeral and often overlooked so they should not be used to convey important information. In addition, as mentioned by @bob1 we need a location much more specific than "U.S." — as a random example, the fauna of central Texas and costal Maine are very different! I believe there are services that will convert (portions of) a video into a GIF that can be included — you may also include a link to the full video.

@ErgoNot try using a site like ezgif.com to convert your video to a gif (which can be uploaded into your post. Just make sure you optimize it to be <2mb for the system to allow it to be included in your post.

It could be a immature lubber grasshopper ( adults look rather different).


text:
Aren't tortoise bones fused with the shell? How did this tortoise (in the post) survive without it?
I've just read this story about a tortoise that lost a good portion of its shell in a forest fire here in Brazil and got a 3D-printed prostheses.
Here's the picture of it:

The way it looks like, it seems there were no bones fused with the shell, and that the shell was just a thin layer hovering over its body below, like the bones were entirely contained inside the body and you could just remove the shell.
What really happened here?
Were all the bones burned until they all fell off?
Wasn't the spine supposed to be there to?
How could this be even survivable?
Or maybe in this species the shell is not fused with the bones?
Thanks!

The shell has several layers. I believe this specimen has lost the kreatin scutes (very painful!) and the inner layer that has become visible is the bone layer.


text:
Predicting protein folding with Alphafold
I’m trying to figure out how to use Alphafold, which is a biological analysis software for predicting the folding of amino acid sequences. I’ve been trying to follow the directions on the creators’ website for downloading it and using it but there’s one part I don’t understand (see the sections mentioned in the link below), and because a mistake here could be costly, I would like to understand it before I make a mistake. To me, the website seems to be saying that I have to download the software, and then also download the two terabytes worth of data that the model was trained on, and that having both the sotware and the training data will allow me to predict the folding of new amino acid sequences (kind of like if I’d have to train the model myself). This seems odd to me because although I don’t know much about modelling software, it was my understanding that the software creators use data to train a model, find what model would best predict new inputs, and then give you that pre-set model.
My question - do I have to download both the Alphafold model and all that data in order use the software to predict the folding of new amino acid sequences? In particular, if I really only just want a visualization of the folding and accompanying statistics, is this the simplest way for someone with little background in programming (although my university does have the storage capacity for the data if need be)?
(See the Model Parameters and Running Alphafold sections of this github link: https://github.com/deepmind/alphafold)

I’m voting to close this question because it is asking for details concerning the installation and use of software. Re: "do I have to download both the Alphafold model and all that data in order use the software to predict the folding of new amino acid sequences?"

@acvill thanks for your comment. I disagree, I think it’s about the best way to analyze the folding of specific protein sequences

Because the focus of my question, and my untimate focus, is on analyzing the folding of protein sequences, I do strongly believe that falls within the scope of allowed questions on this site. In addition, because Alphafold is a groundbreaking method and its source code was only released recently, this question will be relevant to current and future researchers who will analyze protein folding using the software

Your question consists of two parts: (1) do I have to download 2+ TB of model and data to use the software? Their github page makes it clear that, yes, you do, if you want to run it AF locally. Domen gives a alternative, but this question is outside the scope of the site. (2) is AF the simplest way to predict the folding of new amino acid sequences? Similar general questions about coding recommendations for protein modeling have been asked and closed in the past.

That said, general questions about computational protein structure prediction are on-topic and well-received. I suggest taking a look at the ongoing discussions on biostar concerning the use and accessibility of AlphaFold.

Questions regarding analytical methods, such as those related to bioinformatics or biological simulation, that do not ask explicitly about the underlying biology are considered off-topic. One place where this is covered in the [help] is the page "What topics can I ask about here?".

In addition to the other comments, these sorts of software are usually run on high performance computing clusters, which have large numbers of CPUs/GPUs as well as the storage needed. Most computers would struggle to run this locally without a specialist build.

If you have little experience with programming, I strongly suggest using the official Google Colab notebook for AphaFold. It really involves only some button clicks and pasting the amino acid sequence.
This notebook folds without templates, but there is another unofficial notebook that uses the template generation.


text:
How would a "synthetic defective interfering SARS-CoV-2" work in practice? Wouldn't it require a large fraction of all cells to be infected?
The abstract of A synthetic defective interfering SARS-CoV-2 is as follows.

Abstract
Viruses thrive by exploiting the cells they infect, but in order to replicate and infect other cells they must produce viral proteins. As a result, viruses are also susceptible to exploitation by defective versions of themselves that do not produce such proteins. A defective viral genome with deletions in protein-coding genes could still replicate in cells coinfected with full-length viruses. Such a defective genome could even replicate faster due to its shorter size, interfering with the replication of the virus. We have created a synthetic defective interfering version of SARS-CoV-2, the virus causing the Covid-19 pandemic, assembling parts of the viral genome that do not code for any functional protein but enable the genome to be replicated and packaged. This synthetic defective genome replicates three times faster than SARS-CoV-2 in coinfected cells, and interferes with it, reducing the viral load of infected cells by half in 24 hours. The synthetic genome is transmitted as efficiently as the full-length genome, suggesting the location of the putative packaging signal of SARS-CoV-2. A version of such a synthetic construct could be used as a self-promoting antiviral therapy: by enabling replication of the synthetic genome, the virus would promote its own demise.

I've highlighted "in coinfected cells"" because it seems to be key to how this would work as a "self-promoting antiviral therapy". To my understanding, the competition happens only within cells that have been infected with both viruses.
Just for example to describe my question, let's say that in an infected individual undergoing antiviral treatment with a synthetic defective interfering virus only $1 \times 10^{-3}$ pulmonary epithelial cells are infected by either virus. A naive application of statistics suggests only $1 \times 10^{-3}$ of cells infected with the disease-causing virus would also be infected by the synthetic defective interfering virus, while 99.9% of them would not be.
At that point I don't see how this is helping; it would require a large fraction or perhaps most, rather than only a small fraction of all of the patients pulmonary epithelial cells to have been infected before enough competitive events would take place for the synthetic defective interfering virus to actually cause the disease-causing virus to be threatened with "extinction" due to competition.
Is that how this would actually have to work in practice?
Question: How would a "synthetic defective interfering SARS-CoV-2" work in practice? Wouldn't it require a large fraction of all cells to be infected?

Could not find tags similar to competition and antiviral-therapy, help with tagging is appreciated.

I'd like to add on Armand's answer about the delivery method of DI RNA. The author has stated that in additional work that’s nonetheless unpublished, the workforce has now used nanoparticles as a [supply vector][1] and noticed that the virus declines by greater than 95% in 12 hours. If the delivery efficiency of DI RNA is guaranteed, the fraction of coinfected cells should be a concern anymore.
Resources
[1]: https://www.sciencedaily.com/releases/2021/07/210706153039.htm

Interesting! What does "delivery efficiency of DI RNA is guaranteed" mean? Essentially 100^% of cells that the SARS-CoV-2 can potentially infect are already pre-infected by the defective interfering virus first? They would just go into each sell and not cause harm to it, but instead just "sit tight" and quietly wait for the disease causing virus to co-infect the cell? Or does it simply need to be a substantial fraction, and the "self-promoting antiviral therapy" makes so many DI viruses as soon as the disease-causing virus starts to co-infect that they can keep up locally with the infection?

Well, that’s the problem here: you can’t pre-infect the cells with DI virus first. In the absence of WT genome, the DI RNA, even though delivered into the cells, will quickly degrade inside the cells because they are unable to replicate and package their genome. Presumably, even a small amount of RNA can interfere with the WT virus and result in the demise of each the virus and the DI genome. But the current coinfection only results in a 50% reduction in virus load over 24 hours, and this shouldn't be sufficient for therapeutic function.

Okay thanks for the insight; I'm getting the idea now.

The authors note in their article that this is only a proof of principle. In particular, they write "An efficient delivery method should be devised to increase the initial amount of DI RNA and to deliver it in vivo. "
Your question is well-founded, as nobody seems to know how such a therapy would actually work in practice.

Personally I don't think this strategy is useful, but I could be wrong.

Thanks for your answer; I was afraid that I was missing something. I'm sure the competition is scientifically interesting by itself, and even if not a realistically viable therapy as-is it may offer insight into new antiviral schemes.