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How to select a microscope for deep microscopy? Specifically for Deep Learning/ML model development
I am new to biology and microscopy. I am a data scientist. I am faced with a question on selecting a good microscope that enables automation of scanning the slides. And cellular object detection using deep learning.
Considering, my lack of background I am only looking at the resolution of scanned output and the ability of the microscope to provide images that can integrate with a workflow that I am about to develop. As one of the first applications, I am looking to detect sperm cells stained with Christmas Tree stain (head = red/pink, tail = yellow/green) using brightfield microscopy.
What are the other criteria I should worry about? What questions should a data scientist ask?
Any general advice will also be valuable.

Optics Optics Optics - there are a few questions you need to ask yourself and then supply in your question here, the first of which is "what are you looking for?" (cells? what sort?, stained (yes/no, what stain?) The second of which is "how am I looking for it?" This one might involve words like brightfield, fluorescence, confocal . Thirdly - how magnified? Stick to a quality brand (Nikon, Zeiss, Olympus) and you can't go really wrong, but be prepared to spend $100 K. Talk to your local sales reps!

The first application is the detection/localization of sperm cells using a Christmas tree stain. Brightfield, that is what the team I am working with mentioned. 40x.

There's already an automated platform out there for the use-case.  I've edited your question to include the information from your comment.

I would advise someone new to biology and microscopy to outsource this particular decision to someone who is not new to biology and microscopy: you need a collaborator. I realize this is probably what you intend to do by asking here, but I think you'll need more hands-on advice and guidance in this endeavor than you can get through StackExchange.

@BryanKrause I had just come to the same conclusion. I was going to start answering the question, but then realized that I would need to explain pretty much every part of the microscope and its purpose, which would take me far too long to write up, and be far too unwieldy to work in this format.

I do collaborate with Biology scientists. But I am the only one from a data science background. My question is more limited to the intersection between microscopy and data science. What questions should a data scientist ask when buying a microscope?

@kosmos: for list of information with possible questions to be induced see here. The questions you should be asking boil down to "what are the best things for my scenario?". This will include lenses, camera (CCD, colour/false colour), mounts, stage automation, illumination, image enhancements (DIC/Normarsky, Phase contrast, others), and even then it will come down to some opinion based things. You really really need to talk to an expert. I suspect that you will need mostly information about the camera data output and maybe drivers etc.

@kosmos I think the two sides of that question are best served by a conversation between A) You. You're the data scientist. You know what your processing pipeline is going to look like, so you have an idea what data you are going to need to input, and B) Someone who is an expert in microscopy. In particular, automated microscopy, which itself seems like a niche area to me. It's something where you're better off sitting down and having a back-and-forth conversation with someone who has the complementary experience to yours. Probably also a useful third party would be a sales rep.

@Bryan Krause thanks for your advice. There are biologists in my group but not experts in microscopy; not in an in-depth way.  We are actually talking to sales reps, but difficult to verify their claims. Considering a $100k budget, which is not small for the lab, I have a responsibility to ensure that the new microscope will enable data science applications such as sperm cell detection and potentially more.

@bob1 I have raised some questions with the sales rep and have requested a meeting with their technical team. My first question is the ability of the microscope/scanner to integrate with the pipeline. Particularly issues with proprietary formats. Regarding image quality, my assumption is that if the human eye can identify it, the machine could be trained to do that with sufficient data.  I find that object detection in microscope images has a challenge that cells are too small amidst a lot of background objects. Considering this and in general, what would you comment on this assumption?

I think you really need to provide more information on just what you're attempting to do.  Just what do you mean by automating the scanning of slides?  Do you have humans preparing the slides and putting them on the microscope?  Or do you want an automated pipeline to do some or all of that?  For the former,  you could probably (though I'm no expert, by any means) use a much less expensive microscope with a high resolution USB camera.  Especially if you're still in a development phase, where your main concern is getting the software to work.

Not sure this is answerable here. I suggest trying to get a demo or better yet tell the sales rep that you need to "test drive" their product for x days — where x is significantly more time than your worst case estimate for how long a test run would take. Maybe invoke/invent a manager/supervisor/bean counter who is skeptical and thinks a competitors cheaper scope would be more than sufficient for your needs?  Probably works even better if you actually have specifics about alternatives ...

For detecting objects like cells, you need a good enough spatial resolution that comes from the choice of objective (the higher the NA, the better the resolution).  No need to worry too much about that, though, if your object is larger than ~1 um. You also need a high dynamic range from the detector, preferably 16-bit or higher, and to make sure that the experimenter will use it. Proprietary software is a problem, mostly if you want to do real-time detection. You can always build your microscope to custom specifications but that requires expertise.

@vkehayas Thanks for your comment. It is not real-time detection.

@tyersome These microscopes are quite expensive and getting one for trial is a bit of a problem, especially if they need to come from another country.

@kosmos In my experience, the more expensive something is the easier it is to get one for a trial. The sales folk know you are making a big investment and are willing to do anything to make it happen. You say you have biologists but not microscopy experts in your group. Biologists aren't good enough - get a microscopy expert, too. For things like proprietary format...that probably comes from the camera rather than microscope. Every camera I've used could output in some sort of bitmap format. Video was more problematic.

@kosmos if you are doing single image, most software(!) can output in tif format, but this might not be enough for you, depending on your pipeline. I've had good use with Spot cameras, they have excellent resolution, great optics and good software. They also have a development kit for integration with custom software, which might be useful for you.

@kosmos regarding your questions in comment - yes, and no. I'm no expert in machine learning or anything, but the trained human eye is very very good at picking up patterns. If the cells are too small cf. other objects, increase the magnification. Optical magnification is better than digital, for reasons that should be clear to you.

@bob1 thanks for your comments.

@kosmos - ignore my comments re spot cameras, they were good about 10 years ago, looks like they haven't increased the pixel resolution (5-12 MP) since then. This may not be a problem for you though, and most microscope cameras are in that range anyway. Another option is to get adapters for a D-SLR camera.

Are automatic sliders available as extensions to microscopes? By automatic slider, I am looking at a process where a few hundred slides are prepared and placed on the slider and it automatically pushes it to the microscope. The microscope does the scanning. The scanner/camera captures the image and stores it on to the cloud or on-premise storage. These images are then either seen by an expert or processed by automated software. I see there are cameras that could be added to microscopes. But looking for automatic sliders as well which work with the cameras.


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Atom or Cell? Which is the basic unit of life?
As it is said that everything in this universe is made up of atom and molecules and atoms is called the building block of matter. But then why the cell is called the basic unit of life, why not atoms?

What do you think distinguishes "life" from "not life"?

I think you have a misunderstanding of the term unit as used in unit of life. Unit here refers to the smallest building block that is somewhat complete and operational in the relevant context (here: life).
Cells are called the units of life because all life we know is composed of cells. (There are some borderline cases like viruses, but even those rather resemble a cell than an atom.) On the other hand, if you cut a cell in half, it is certainly not operational or alive anymore.
You wouldn’t call atoms units of currency, even though all coins and bank notes are made up of atoms (ignoring digital currency for the sake of the analogue).

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Why there aren't any pandemic diseases by prions?
Learning biology in school, I became interested in the fact that there aren't any diseases by prions which are globally infectious (as far as I know), unlike diseases by viruses (ex. COVID-19, SARS etc.) or by bacteria (ex. plague, ...). Why is it?
cf. Here are some my hypothesis

Prions are not efficient pathogens because they don't have DNAs.
Such prions are not yet discovered or does not exist.
There exists lots of people who are immune to such diseases.

Are there any answers to the questions? Or is there any answers?

Add #4: Prions are bound up in cells, and not readily transmitted through the environments.  You might contrast respiratory viral diseases like COVID or influenza, that are transmitted through the air, with ones like AIDS that require exchange of body fluids.

Kuru, a neurodegenerative spongiform encephalopathy, is considered by many to have reached epidemic proportions in Papua New Guinea in the 1950s, caused by cannibalism of dead relatives, mainly by women & children. Carleton Gajdusek received a Nobel prize for his work on Kuru. (For a disturbing BBC documentary on Carleton Gajdusek, see Storyville The Genius And The Boys)

I think it requires cannibalism.

I thought CJD could be spread by surgical instruments (and that 'conventional' sterilization methods is not enough to 'kill' the prion)? (See Iatrogenic Creutzfeldt-Jakob disease via surgical instruments, for example)

@Jamesqf hepatitis and AIDS are pandemics affecting millions of people, so why would that vector not a threat? quote: Worldwide, 500 million people are estimated to be infected with hepatitis B or C. ... isn't that a pandemic, because it's not transmitted readily through the environment?

@aliential: The difference is in rate of spread, and limits on who it can spread to.  E.g. AIDS took ~25 years from the first known case (1959) until it was recognized as a virus, COVID took a few months from the first case to worldwide pandemic.

I think that you could argue that some prion diseases do form epidemics or outbreaks. In some cases it does appear that people have referred to BSE/vCJD as pandemics. There is even some journalism on the topic, and see also here.
Infection by prion from the environment does occur at some rate, and it is true that it is these prions are the more transmissible. See Table 1 in that linked paper for more information; it appears that the discovery of prion excretion through e.g. feces is relatively recent.
For less transmissible variants it is true that you usually have to directly ingest a fair amount of prion from (i.e. eat) an infected individual to be affected, which is a harder means of transmission because it implies cannibalism (which is not that uncommon biologically, but still).

Might be noted that the pandemic-like outbreak of BSE supposedly was the result of (unintentional) cannibalism, as cow feed producers included waste from meat processing in their products.

@jamesqf a good point. So which transmission mechanism is most efficient can be expected to vary a lot across environments; obviously a feedlot / meatpacking supply chain has a significantly different ecology from a "natural" population.

In order to get large outbreaks via cannibalism/consumption one typically needs not just cannibalism but group cannibalism, i.e. one individual gets eaten by several others https://royalsocietypublishing.org/doi/full/10.1098/rspb.2006.0449?casa_token=geTGhZcyauUAAAAA%3AHpSSymG2SBv6cfyuFXu5fztS6XifIweORmi36i7YA-LfXdyP72bO3kM6FBbNisnRmTXJhccS-7WR

Viruses mutate relatively fast, i.e. Aids mutates 100,000 times faster than Eurkariotic DNA. Actually, viruses mutate on average once every time they reproduce into a new copy / per genome replication.
The DNA segment that encodes healthy PRPC protein which can be hyjacked and converted by a prion has 3kb base pairs, and there are only 30 mutant version of PRPC known as prions detailed since 1970, compared to thousands of different versions of Covid-19 since 2019. The mutant prions dont use RNA, they actually latch on to the healthy versions inside the human body and changes them to mutants.
We can say that prions evolve 10,000 to 100,000 times slower than other bodily fluid viruses like hepatitis and AIDS. Those mutations serve to keep the viruses fit, resistant to new environments, new species, new biochemistries.

Prions don't have a nucleotide component, it is entirely protein, so prions and viruses (or any nucleotide containing organisms) aren't comparable directly in terms of evolution.  It's also that they are incredibly slow - takes years (decades?) to see the effects in any individual.

Precisely, the question was comparing prions to quote: like diseases by viruses (ex. COVID-19, SARS etc.) or by bacteria (ex. plague, ...). So I detailed the difference in replication process and mutation rate...

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What are those berry-like plants in this photo?
I found this photo on a Flickr gallery and I have no idea what this plant is. Is it supposedly a type of berry or something?

I really think you should be giving full attribution to the owner of the flickr photo or gallery. Or at least a link to the source.

A google image search finds:
https://www.flickr.com/photos/15110103@N08/2044059567
which was taken in The Hague, Netherlands. And also identifies the tree.

Without knowing the geography of where the photo was taken, we could guess this is a European Mountain Ash (Sorbus aucuparia) which is fairly widespread in North America and Europe (but doesn't really grow in South America, Asia, Africa, Australia)..
You can look up this plant for information on the berries. They contain vitamin C, but don't have much other desirable properties.

There was no exact location on the Flickr page, so I couldn’t put the date.

@Kylethedownvotedisliker definitely an Sorbus tree, sometimes known as Rowan or Whitebeam. Pinnate leaves with serrations, red pome-like fruit in corymbs, very distinctive.


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Different flowers have same colour
I notice that certain (wild) flowers have the same colour, although they are not closely related. For example, the yellows of the dandelion (Taraxacum) and the buttercup (Ranunculus) are, at least to my eyes, identical (my observations are in the Netherlands).

I know that the colour is intended to attract insects; is this parallel evolution or are there certain biochemicals which provide colour and are easy for the plant to synthesize? Or something else?
Edit: I used the buttercup and dandelion because that was the first pair I found physically close enough for a photo; the cowslip, celandine and charlock mustard are all (to my eyes) the same yellow. I have also seen similar blues, reds and violets, and shall try to collect examples next time I go cycling on the dyke.
When I look at colour tables like https://en.wikipedia.org/wiki/Web_colors#Extended_colors I see numerous colours which I do not recall ever seeing in wild flowers.
Edit2: I retract my remarks about blues, reds and violets; it's hard to judge colours when cycling past and when I pluck the flowers and compare directly there's a definite difference, for example:

However I still find the yellows very similar; here the charlock (left) is lighter but the buttercup, celandine and dandelion look identical to my eyes.

Comments seem to suggest a biochemical cause; can anyone confirm (or disprove) it?

I don't have an answer, but note that many insects see a different spectrum that we do — for example bees can see into the ultraviolet, but IIRC don't see reds. Consequently, what we see isn't necessarily a good representation of what an insect pollinator sees — in fact the UV pattern on a dandelion may be very different from that on a buttercup. Search for "UV" images of buttercups and dandelions to see example images.

Antheraxanthin, is the pigment that is causing the yellow colour in dandelions. It is built from a basic carotene molecule. Carotene is a another basic pigment that is found in many plants specifically to produce colour. Antheraxanthin in dandelions, is associated with photoprotection from the sun. Possible topics you should explore to understand your questions are: carotenoids, flavonoids, and anthocyanins, all of these molecules groups are associated with flower pigmentations.

link Here is a article about buttercups, apparently the the pigment molecule in buttercup is also a derivative of  carotenoids, just like dandelions. Though the purpose for the presence of the pigment is totally different. As mentioned by @tyersome, the pigment in buttercup produces different UV colour, which some animals see and this feature brings about different physical properties such as reflectivity that is seen in buttercups and not dandelions.

Wow! You guys are fast! tyersome's link seems to exclude parallel evolution, and Sentma's data suggests a biochemical explanation. Is anyone confident enough to make an answer?

@NL_Derek, could you make your question a bit more clear, at its current state it is a bit vague.

You might consider that there are many fewer colors (at least to human perception) than there are species of plants with showy flowers.

@Sentma is this an improvement?

WRT those color tables, note that there are many more colors there than can be distinguished by the average human.  Honestly,  can you tell the difference between LawnGreen, Chartreuse, and GreenYellow,  or between Firebrick and IndianRed?

@jamesqf valid observation, but my point is that I don't recall ever seeing a flower with, for example, LightSlateGray or RosyBrown.

@NL_Derek: Perhaps you haven't looked hard enough?  Here's a local wildflower that approaches RosyBrown: https://en.wikipedia.org/wiki/Paeonia_brownii  You could probably find grays in for instance Aril & Arilbred irises.  Like this one: https://garden.org/plants/view/527214/Arilbred-Iris-Iris-Eyes-on-You/  (I really can only approximate the particular shades myself.)

@jamesqf your remarks led me to check further and I have now restricted the question to yellow. Also I suspect Dutch dykeside wild flowers are less varied than in your locality, alongside yellow and white I see mostly shades of blue, pink and purple/violet.

@NL_Derek: Perhaps - I've never been to the Netherlands.  (And the Aril Irises are definitely not wildflowers hereabouts, being native to the Middle East.)  But even within some species, there are considerable color variations.  For instance, the common wild California poppy (Eschscholzia californica) is usually a bright orange, but it's not that uncommon to see plants with bright yellow flowers, or intermediate shades: https://en.wikipedia.org/wiki/Eschscholzia_californica

I think parallel evolution is likely due to the cost to produce the pigments in plants.
Xanthophylls and carotenes are made from only carbon, oxygen and hydrogen. This provides most of the yellow colours without using up nutrients.
Anthocyanins and betalains also need nitrogen, which can be a limiting nutrient for plants.
Wikipedia has a section on plant pigments at:
http://en.wikipedia.org/wiki/Biological_pigment

+1 for the Wikipedia link


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Why is there not an immune response to injected immunoglobulins?
When you inject immunoglobulins as a treatment for certain diseases, the immunoglobulins are a foreign substance.
I can appreciate that maybe the constant region would be similar to the hosts as it is from another human and these don't change a lot.
However, in the variable regions, wouldn't there be the possibility that the antigen receptor region could be the complement to the patient's own antibodies? Wouldn't this trigger an immune response and destroy the injected Ig's? Yet we seem to do this procedure, so why doesn't this process occur?

Does this answer your question? Why does not the host produce any immune response to antiserum antibodies?

No, it mainly discusses animals not human antibodies. Also, it doesn't explain why human to human transplant of immunoglobulins doesn't create a reaction

If a head-to-head "match" between antibodies from two different people was to occur, a similar match would most likely have occurred already in the donor. People have the same tissues after all.
But in the donor; the B lymphocytes producing the antibodies had to go through the processes of "central tolerance" and "peripheral tolerance".
This would weed out the cells producing autoantibodies.
Theoretically, nasty autoantibodies in the recipient could react with innocent antibodies in the donor though.

Intravenous immunoglobulins (IVIG) are human blood products purified from the plasma from many healthy donors.
These are natural proteins that your body normally makes to help you to fight infections and to serve other functions for the immune system. In addition, all immunoglobulins are screened to eliminate the possibility of carrying pathogens or other diseases 1. Since the body's immune response is activated by the recognition of T cells to the antigen, these naturally produced, screened IVIG will not trigger an immune response against them.
However, IVIG are not 100% safe. Injection of immunoglobulins can cause some adverse effects, such as fever, headache, chills, etc. These adverse effects are usually transient and mild, but there are few cases of severe side effects. You can find more details in this paper.
Resources

https://www.rheumaderm-society.org/ivig/

Guo Y, Tian X, Wang X, Xiao Z. Adverse Effects of Immunoglobulin Therapy. Front Immunol. 2018;9:1299. Published 2018 Jun 8. doi:10.3389/fimmu.2018.01299

Re: "these naturally produced, screened IVIG will not trigger an immune response against them." In rare cases, they may indeed do so. Screening has no effect on this, rather it would be sequence differences in the Ab genes between the donor and recipient. In practice, such sequence differences are minimal enough between humans that no effect is normally observed.  For animal Abs injected into humans, a reaction is more likely, so such Abs are often first engineered (before or after antigen selection) to replace much of the molecule with human sequences (see "chimeric" or "humanized" Abs)

Screening of IVIG is very good, but not perfect, in identifying pathogens, and so there is a quite small risk of infection for the recipient.


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Why doesn't muscle strength depend on its length?
In case of tug of war the more people participate the more strength they represent. And in case of muscles - the longer it is, the greater the number of myosin heads bind to actin when muscles contract. So why doesn't length matter?
UPDATE:
Since I've found multiple answers that compare muscles to ropes, let me comment on why those explanations don't work for me. Ropes don't have "muscle" strength, they have tensile strength. So this analogy can only compare tensile muscle strength to tensile rope strength.
In the end I'm pretty sure I'll find out that tensile strength constraints the muscle strength. And that's probably going to be the reason why muscle strength doesn't grow with length - something does not allow it, otherwise it would get damaged.
But I'd like find out what exactly prevents further contraction. Is it mechanical receptors on the muscle cell which block deploarization? Mechanical receptors in tendons which send nervous signals (but then - do tendons get thicker in proportion with the muscle)? Something else?

Does this answer your question? Why is muscle force more dependent on cross-sectional area than on fiber length?

@kmm, I haven't seen that question, though I tried hard to look for it. Thanks for pointing out. But no, unfortunately there are no satisfying answers there :(

@kmm, I've updated the question to explain why the rope analogy doesn't answer the question.

To those who vote for closing: this site doesn't have an answer to my question. If you close it - someone else in the future will have to ask this question again. Otherwise no one will ever answer it.

The close votes are for this question being a duplicate (which I think it is). Whether or not you find the answers here or on the other question satisfying does not change that this and the other question are basically asking about the same concept.

@kmm, yep, I'm not arguing with that. It's just unfortunately this usually means the question won't be answered at all (unless moderators will bump it up, which they probably won't). So we'll wait for yet another duplicate..

I think you probably just need to take the leap to understanding a muscle pulls more like a rope does than like a spring, and tensile strength is the best way to think about it. That's what the answer on both this question and the target duplicate are saying, and that's why people are considering it a dupe. Dupes are dupes because the question is effectively the same; if there is an old question you want a new answer on you could offer a bounty.

@BryanKrause, this analogy game will bring us only so far :) A motor protein is a motor protein. It doesn't matter if goes in parallel or in a sequence - it will exert a force and therefore the muscle will become stronger. Unless there's an additional complexity hidden somewhere (which is probably the case). Bounty or not it seems like there are simply no people here who work in this field and can give a good answer. Hence we get more and more of "rope" answers.. So maybe you're right - this dupe won't help.

If you put me between two Hafþór Júlíus Björnsson and we all linked hands and pulled on each other, we would not have a pull strength of two Hafþór plus me. Each Hafþór would pull at one Hafþór, but they'd pull me apart. Think of them as two thick muscles and me as one thin muscle. You can make the chain as long as you want, we can never pull with more than my strength, you'd just stretch me until I broke. Even the chain of Hafþórs would only pull at one Hafþór, because if a Hafþór is pulled at 2X their strength they would also lengthen.

@BryanKrause, if we assume that 3 Hafþórs don't break the weakest Hafþór then they do add up to more strength. In fact together they pull 3x as strong as 1 Hafþór. Sure, as we add more and more Hafþórs one of them will break eventually. At that point we reach the max strength. Getting back to muscles: if we add more myosin in a row - they will too pull stronger. But something doesn't let them even though now they can. So it's not that the muscle isn't getting stronger, it's that something limits it. I'd like to find out what that is and how it scales with the muscle length and width.

Myosin pulling is like a rope. It can't pull twice as hard or it breaks. If I can lift a Hafþór I can lift a Hafþór. It doesn't help me if that Hafþór can also lift another Hafþór; to pull them both I'd need to be twice as strong. If I want to double the strength I need them side by side me, not in a chain.

I think you're missing that there is nothing in the middle to pull against. The chains are all pulling each other down the line so the total strength isn't summed. If Hafþór on one end pulls, the next Hafþór has to pull the same just to stay in the same place.

Alternatively maybe it helps to consider Newtons 3rd law?

@BryanKrause, that's because our analogies are imperfect. If we return back to the tug of war.. Hafþór is actually pulling on the rope. Not on another Hafþór. So the more Hafþórs (myosin) we have the harder they pull on the rope (actin). And in your muscles you don't have 1 myosin head per muscle cell - you have many of them in a sequence. And you have many sarcomeres in a sequence. If you remove half of them - you'll have half of Hafþórs (myosin heads) pulling on actin.

Ok then that's what you are missing: you're imaging some central rope of near infinite strength that everything acts on, like people in a tug of war. That's wrong. None of my analogies involved tug of war. Myosin pulls different actins together, like maybe the myosin is the arms and the actins are the bodies in the chain. The only ground points are the tendons at each end of the muscle, in between it's all muscle fibers pulling against each other. Bob drew the scenario reasonably below, besides the tendon/ligament confusion.

No one in the linked duplicate referred to tug of war, either, except someone in the comments with the same confusion as you, and someone else responded to them and explained how this doesn't work.

@BryanKrause, I now realize what was my problem, I've put it in a separate answer. Thanks!

It's simply that the fibers are arranged end-to-end. If you simplify this down and imagine a single muscle fiber you have actin and myosin like this:
ligament-|actin-myosin-actin-myosin-actin-myosin

If you think of this as a strand of cotton pulling on a weight (ligament). Each group only pulls along the length, so the strength is not multiplied, but rather related to the strength of the individual fibre.
In reality muscles are stacked into bundles, which are much stronger as all the fibers can contract pulling with the strength of the multiple ends. Like this:
         |actin-myosin
         |actin-myosin
ligament-|actin-myosin
         |actin-myosin
         |actin-myosin

This is like the multiple strands of cotton making up a rope, the strength comes from having lots of them distributing the load.
This is something called physiological cross-sectional area, which describes the strength of a muscle by estimating the cross-section of the muscle across its thickest part.

The confusion I had is that I thought that myosin pulls on actin with a force which some how isn't the maximum possible. And if we were to add another sarcomere in a series - each myosin would have to work harder and together with the new sarcomere they would exert a greater force.
But this of course isn't how it works. Myosin doesn't have a notion of a varying strength, it's binary: it either attaches to actin or not. If we were to try to pull apart actin or myosin harder by their "tails" (by a neighbouring sarcomere) - actin would've started to "slip" from myosin. Therefore putting more sarcomeres in series would not make the muscle stronger - we'd simply add more "slipping".
The other possibility in a theoretical world would be to make actin and myosin strands longer and add more myosin heads (we'd have to reinforce lots of structures though). This way we could've made the muscle stronger by making it longer. But that's not how it works: a longer muscle cell merely means more sarcomeres in series.
Thanks @Bryan Krause for nudging me into the right direction in the comments.


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Differentiating molecules based on peptide sequence? How to annotate?
I want to differentiate between classical class I and non classical class I MHC molecules in a model organism using well conserved structural features within classical MHC I molecules (eg intradomain disulfide bridges within class I a1 domain). To do this I need to align the peptide sequences of transcripts of that model organism with transcripts of classical MHC I human genes and see which genes from those transcripts have those structural features. So I am looking for a tool to align and annotate those structural features in a replicable manner
Additionally if you have any other bioinformatic ideas /computational analyses on how to find classical MHC Class I molecules on an organism which is poorly annotated that would highly appreciated!

Check out http://www.bioinf.jku.at/software/msa/ You can do the alignment in R and annotate there in a very replicable manner once you learn the package. You can also align it in Clustal Omega (use the protein option to align), or unitprot.org/align


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Novel bacterial strains of bacteria first isolated on the International Space Station, did the space environment lead to these genetic changes?
Question
Methylobacterium ajmalii sp. nov., Isolated From the International Space Station (Bijlani et al. Frontiers in Microbiology, 12, p. 534, 2021) is a thorough analysis of "novel strains" of bacteria isolated from the International Space Station (Characterization of the total and viable bacterial and fungal communities associated with the International Space Station surfaces)
Question: Bijlani et al. 2021 is written at a very dense and technical level that is challenging for me to understand. I'd like to know:

Does the article suggests these may be newly discovered species or only that they are novel strains of known species of Earth bacteria?
Does the article suggest that the environment on the ISS selected for these species or strains, and they resulted from some genetic changes due to the ISS environment, or if we looked hard enough we'd expect to find the same ones on Earth and they just happened to be identified first on the ISS because of the rigorous studies of those samples?

Background
I was lead to the paper after seeing the ink the BBC's Could humans have contaminated Mars with life? which is primarily about a different topic.
The paper is one of 10 papers the 2021 topic Extremophiles: Microbial Genomics and Taxogenomics.
The ISS is a unique closed environment with plenty of surfaces with sometimes problematic mold growth, and a population of usually 3-6 humans with regular rotations every 5 to 6 months who maintain an array of biological experiments including a sustained effort to try to grow vegetables and flower hydroponically and in soil.
The atmosphere is maintained similar to Earth's surface (oxygen/nitrogen ~1 bar) with 60% relative humidity and often has a CO2 concentration slightly higher than the astronauts would prefer.

The authors propose that this is a distinct species based on a number of physiological and genetic tests. To quote the summary of your linked paper

In summary, the phylogenetic and genetic distinctiveness and differential phenotypic properties were sufficient to categorize these three ISS strains as members of a species distinct from other recognized Methylobacterium species. Therefore, on the basis of the data presented, strains IF7SW-B2T, IIF1SW-B5, and IIF4SW-B5 represent a novel species of the genus Methylobacterium, for which the name Methylobacterium ajmalii sp. nov. is proposed.

This indicates (emphasis mine) that they think that these isolates are distinct enough from species that we have found on Earth to make the isolates a species. This is a species that we haven't found on Earth, but unsurprisingly it is closely related to species from the same genus that have been found on Earth and on the ISS

The authors make no statements about how the species came to be there that I could see, only that it is a novel species from the ISS, which has not been found on Earth. No mechanisms for arisal are postulated, and the authors wisely did not speculate on this at all (speculation on results is frowned upon in science). One of the reasons they did not speculate on this will be that testing mechanisms whereby speciation has occurred is very difficult, especially as they would need to mimic in the lab the conditions in the ISS and show which conditions were important for the speciation. These experiments would be technically challenging and very time consuming.

It is worth noting that we don't really know the rate of species differentiation on Earth, let alone in space, partly because Earth is so covered in bacteria that proving that one evolved in the environment is difficult as it is hard to prove that you didn't just miss it last time you looked. To quote the paper I linked above:

For example, a single gram of soil can harbour up to 1010 bacterial cells and an estimated species diversity of between 4·103 to 5·104 species .

However, the ISS is one environment where it might be easier to see these sorts of events because it is relatively micro-organism free, and we have prior samples to go back and compare to. For some comparison of the numbers, I turn to the second paper you linked, which found:

Of the total bacterial and fungal isolates that grew, 133 bacterial isolates and 81 fungal isolates were identified by Sanger sequencing...   ...When the ASVs were summarized to the genus level, 121 taxa were detected, 77 of which could be assigned to known genera

and

Overall, the number of bacteria (combination of R2A and BA growth) isolated from the ISS from all 24 samples ranged from 6.7 × 103 to 7.8 × 1010 CFU/m2

So quite high numbers of cultivatable bacteria (CFU = colony forming units, a measure of how many bacteria will grow per sampling), indeed as high as those found in a gram of soil, but very low species diversity compared to the soil.
It is still difficult to prove that this is a new species evolved strictly on the ISS, but it does seem logically likely that evolution will happen on the ISS, as it does anywhere that life is present (as far as we know).

+n! Thanks you for writing such a thorough post at a level that I can readily understand and appreciate, and outlining several important concepts that apply here. I will think about follow-up questions like "Can a new bacterial species arise in as short as 10 or 20 years given unusual human habitat conditions?" and "Simple way to understand how scientists decide when two strains of bacteria are actually sufficiently different that they are two different species?" But first will reread this a few more times, then re-read this paper, then look through previous Q&A here before posting.

@uhoh - no problem. The answer to your first one is yes. Model bacterial replication takes ~20 min under ideal conditions, so about 3x an hour. Multiply that by a year and you get something like 26,000 rounds of replication. This is plenty to speciate on - think where our ancestors were 26,000 generations (~780,000 years) ago.


text:
Why do T cells have MHC II receptors?
I have seen the answer to this question which says that T cells do not express MHC II proteins which would make sense.
However, my textbook "The immune system" by Peter Parham disagrees. It says that T cells do gain MHC II receptors after activation.

*Activated T cells express MHC class II molecules, whereas resting T cells do not.

I cannot see why this is needed. MHC II molecules are for CD4 cells (helper T cells).
If the T cell presenting the antigen was a CD4 cell, then that seems useless, because this cell was already the one that could recognise this particular antigen - so why show it to others? The chance that another T cell that could recognise it too would be incredibly small no?
I guess I can see the merit of a CD8 T killer cell to show the antigen, as it could alert other CD4 T cells to come assist (although cytokines seem like a better method...)
So what is the purpose of T cells, in particular CD4, of showing MHC II proteins?

That's the description in my book which has the same image.
The book is: Janeway's Immunology (9th Edition)
Article discussing MHC Class II expression in humans:
https://doi.org/10.4049/jimmunol.168.2.763
Excerpt from the book:

The processing and presentation of pathogen-derived antigens has two
distinct purposes: inducing the development of armed effector T cells,
and triggering the effector functions of these armed cells at sites of
infection. MHC class I molecules bind peptides that are recognized by
CD8 T cells, and MHC class II molecules bind peptides that are
recognized by CD4 T cells, a pattern of recognition determined by
specific binding of the CD8 or CD4 molecules to the respective MHC
molecules (see Section 4-18). The importance of this specificity of
recognition lies in the different distributions of MHC class I and
class II molecules on cells throughout the body. Nearly all somatic
cells (except red blood cells) express MHC class I molecules.
Consequently, the CD8 T cell is primarily responsible for pathogen
surveillance and cytolysis of somatic cells. Also called cytotoxic T
cells, their function is to kill the cells they recognize. CD8 T cells
are therefore an important mechanism in eliminating sources of new
viral particles and bacteria that live only in the cytosol, and thus
freeing the host from infection.
By contrast, MHC class II molecules
are expressed primarily only on cells of the immune system, and
particularly by dendritic cells, macrophages, and B cells. Thymic
cortical epithelial cells and activated, but not naive, T cells can
express MHC class II molecules, which can also be induced on many
cells in response to the cytokine IFN-γ. Thus, CD4 T cells can
recognize their cognate antigens during their development in the
thymus, on a limited set of ‘professional’ antigen-presenting cells,
and on other somatic cells under specific inflammatory conditions.
Effector CD4 T cells comprise several subsets with different
activities that help eliminate the pathogens. Importantly, naive CD8
and CD4 T cells can become armed effector cells only after
encountering their cognate antigen once it has been processed and
presented by activated dendritic cells.

Unfortunately the most recent review specialized on this topic (I found) dates back to 2004, and it's pretty confusingly written, IMHO. The general gist of it appears to be that T cells can act as APC cells under some conditions (aka T-APC) and it was generally thought that this serves a down-regulatory function for T cells, e.g.

There is considerable evidence, dating as far back as
1978, in support of the notion that human activated
T cells can function as APC (so-called T-APC) and
thereby affect the activities of other T cells. [...]
Most reports show that MHC class II–mediated antigen
presentation by T-APCs provides downregulatory signals
by inducing either apoptosis or clonal anergy in activated
T cells or cytotoxicity in resting T cells.
This T-T presentation-induced anergy does not appear to
result from TCR ligation in the absence of costimulatory
molecules, because activated T cells themselves express
CD80 or CD86.

More recent work has found that trogocytosis is possible between T cells, i.e. they can pass each other peptide-bound MHC. In particular trogocytosis explains some mysteries in this area, such as how mouse CD8 T cells, which cannot express the MHC-II gene, themselves actually acquire such receptors on their surface.
One such recent paper proposes that such T-T interactions differentiate CD4 T cells into regulatory ones vs Th17 pro-inflammatory ones:

We investigate the functional outcome of T-T cell antigen presentation by CD4 T cells and find that the antigen-presenting T cells (Tpres) predominantly differentiate into regulatory T cells (Treg), whereas T cells that have been stimulated by Tpres cells predominantly differentiate into Th17 pro-inflammatory cells.

The introductory section of this 2021 paper contains a useful minireview of the directions of research  (some of them being apparently somewhat contradictory to each other, if more specific conditions of the experiments aren't taken into account)

Another important mechanism of intercellular communication within the immune system is trogocytosis (Joly and Hudrisier, 2003), where T cells and natural killer (NK) cells acquire micrometer-sized fragments of the APC membrane (Carlin et al., 2001; Vanherberghen et al., 2004). These fragments can contain immune-modulating membrane receptors such as killer inhibitory receptors and major histocompatibility complex (MHC) class I and II complexes. Previously it was shown that MHC-II vesicles are released by APCs and acquired by responding T cells (Arnold and Mannie, 1999; Patel et al., 1999). T cells also acquire peptide MHC (pMHC) complexes at the IS [immunological synapse] via a process that requires T cell receptor (TCR) internalization and TCR signaling (Huang et al., 1999; Hudrisier et al., 2001). In addition, they acquire CD80 and CD86, ligands of the co-stimulatory receptor CD28 (Hwang et al., 2000; Sabzevari et al., 2001). This could convert T cells into APCs. Both CD8 T cell-dendritic cell (DC) interactions and secondary T cell-T cell interactions are required to generate protective CD8 T cells (Gérard et al., 2013), and CD8 recall responses depend on CD8 T cells taking up MHC-II from DCs to present it to CD4 T cells and obtain their help (Romagnoli et al., 2013). In contrast, other results have suggested that pMHC acquisition by T cells may play an inhibitory role (Dhainaut and Moser, 2014). For instance, T cell antigen presentation to other T cells has been associated with the induction of anergy, apoptosis, and even tolerance (Chai et al., 1998; Mannie et al., 1996), and may represent a mechanism to limit clonal expansion (Tsang et al., 2003).

I believe in the article you provided it is stated that the function of MHC class II molecules on activated CD4+ T cells is still unclear. It is believed that these MHC class II molecules-presenting T cells have potential ability to act as antigen presenting cells and induce immune response by activating other T cells. They are also capable of inducing down-regulatory signals for immune response by inducing anergy in activated T cells and cytotoxic resting T cells. In addition, they have also been reported to transduce intracellular signals into T lymphocytes.


text:
How does a diploid sporophyte form in non-recurrent apomixis?
I came across this definition of non-recurrent apomixis which occurs in angiosperms-

In non-recurrent apomixis, both the egg-cell and embryo are haploid and embryo is developed directly from an egg-cell without fertilization.

If this is the case, how does a diploid sporophyte develop from the haploid embryo? Are there any examples of the same?
I think most likely it would be by free nuclear divisions, that seems like the best bet, but I'm not sure if that's how it occurs.


text:
What can be used for DNA preservation?
I am neither a student nor really advanced in biology, I am just writing a tabletop role-playing game scenario that I want as realistic as possible. In the story, the players find an old laboratory where genetic mutations were studied, but as the electricity is off since 40 years, most of the embryos are "rotten". I still need to have some embryos still "fresh" so someone could get DNA from it and continue the experiment.
Problem is, I thought about formol (the experiment is supposed to have taken place in the 1980's, so the health problem is not one right now), but I've read that formol alters and destroys the DNA. I've seen older ways with alcohol, but the process doesn't seem as efficient.
What liquid (or technic) could have been used in the 80's to preserve embryos and their DNA so we could still exploit it 40 years later, and with not electricity?

70% alcohol preserves DNA well.

Hi Lyzvaleska, and welcome to Biology.SE! You mention you've read that formol destroys DNA, and that alcohol preservation seems less efficient.  Can you link to sources for these claims?

dry/lyophilized DNAs are also rather stable. https://www.idtdna.com/pages/support/faqs/are-lyophilized-oligos-stable-when-stored-frozen-

@acvill For the formol destroying DNA, I've seen it in a french source (but can't seem to put my hand on it right now anymore) that it could alter the DNA. For the alcohol, I saw claims about being less efficient, but apparently it was more of a visual problem and the evaporation. But it looks like that alcohol fits my needs perfectly :)

There are a few plausible ways:
As someone mentioned in the comments; Alcohol works well for this. We have samples from a hundred years ago (e.g. Thylacine), which have been stored at room temperature in a museum for that period of time and have had DNA easily extracted from them.
Unfortunately for many species, alcohol preservation fell out of favour due to it shrinking (by dehydration) specimens, so that they no longer look "realistic" in terms of morphology (something that is very important for classical identification methods). In addition, ethanol and other alcohols tend to evaporate fairly fast if not sealed properly. For these reasons aldehyde based solutions came into favour about 100 years ago. The downside to this is that formaldehyde and other aldehydes cross-link the genetic material, making it more or less impossible to extract and use.
Another possible method is dehydration - mummification. Small samples like embryos or tissues can be dehydrated quite fast. In the absence of water, these samples should last more or less forever - we can extract DNA from mummies in many places around the world, but these ones might interest you in particular.
There are also specialist chemical solutions such as RNAlater that are routinely used in labs for preservation of precious genetic material.
Given that we knew these sorts of things in the 1980's and that the lab was staffed with competent scientists, and that they knew that the lab was going to shut down but would re-start at some time in the future, then it is entirely plausible that they would have used alcohol or something like RNAlater.
In the absence of this knowledge, but still competent scientists, it is much more likely that they would have used some sort of cold (frozen) storage method;  whether this was cryopreservation (liquid nitrogen), such as is used for storage of cells or a specialist -80 $^\circ$C freezer or a -20 $^\circ$C freezer like you might find at your house. Some samples may have been still stored in chemical preservation in the interests of space-saving in freezers though.


text:
How much light can pass through the human eyelid?
My sister tells me that at night when the lights in the room are off that she can see the ambient outdoor light from neighboring buildigns and streetlights through her eyelids (i.e., when her eyes are closed). I, on the other hand, can't see anything. I can easily fall asleep even when the lights in the room are on; my sister can too, but when I tell her to sleep with the lights on because I have work to do, she just stares at the light and says that she can't sleep.
So, quantitatively, how much light would be able to pass through a normal human being's eyelids. And would ambient outside light be enough to pass through?

Define what you mean by "a normal human being".  You seem to assume that you are, and your sister is not.  But try an experiment: sit in a normally lighted room, close your eyes, and notice what you see.  Now place your cupped hands over your eyes.  Notice a difference?  Then you're probably normal :-)  (Though this might vary depending on the melanin content of your skin...)

Adding to @jamesqf 's personal experiment idea, note that visual sensitivity in humans spans many orders of magnitude an the dark-adapted eyes will notice smaller changes in light. Turn off the lights at night and sit by the switch for 5-10 minutes, then, keeping your eyes closed, flick the switch back on. I'd be surprised if you don't notice a difference, though what level of light is bothersome is surely going to vary from person to person.

Yep, this is a how-long-is-a-piece-of-string question. You could make some assumptions based on data on thickness of eyelids in the population and melanin content in general for specific populations- though that's a huge variable in itself.

@jamesqf by normal person, I mean just any average joe. Like most experiment would have an average reading right?

@Brien Lim: Yes, but without doing experiments (or being much better at using search engines than I am) on a bunch of average Joes (or Jills, since your sister seems to have markedly different sensitivity), how can this be answered?  And if we find that in fact there's a lot of difference between individuals, who's to say what's "normal"?

Short answer
About 0.79% of the light gets through on average, but there is variability across wavelengths and individuals. (variability between individuals seems to be correlated with density of macromolecules in the eyelid).
Long answer:
This is called "eyelid spectral transmittance".
Lucky for you, Bierman et al (2011) sought to determine the answer to this question.
Using a custom LED wand that actually emitted light under the eyelid for a sensor on the outside to read, they found quite a bit of variability both across wavelengths as well as across 27 test subjects.
They report their findings in terms of optical density, which is explained as follows:

A measure of the transmittance through an optical medium. Optical density equals the log to the base 10 of the reciprocal of the transmittance.... In spectroscopy, optical density is the measure of absorbance, and is defined as the ratio of the intensity of light falling upon a material and the intensity transmitted. Abbreviation OD.

We can use the equation  A = -log10(1/T) to convert their findings of OD to transmittance and then multiply by 100 to get a percentage of light that can pass through.

Their result of an OD of 2.1 ± 0.3 SD = a transmittance of 0.79%

They do note that  eyelid thickness, and/or the density of macromolecules in the eyelid account for most of the variation in transmittance between subjects.

 Bierman, A., Figueiro, M.G. and Rea, M.S., 2011. Measuring and predicting eyelid spectral transmittance. Journal of biomedical optics, 16(6), p.067011.


text:
What role does the eardrum and ossicles play in hearing, versus cilia?
Modern electronic sound recording equipment employs a physical membrane that triggers the piezoelectric effect in a metallic element, to transform sound waves into electric signals.
I had always thought that the eardrum (or tympanic membrane) was the main instrument of hearing in vertebrates, that it physically transduces sound waves into nerve signals. However, in looking into it, I find that the eardrum transmits sounds to inner ear anatomy, where more structures are encountered before the sound waves become nerve signals.
I also find that small hairs, cilia, are sensitive to sound, and appear to be what actually turns sound waves into nerve signals, perhaps analogously to rod and cone cells in the eye. These cells line the ear canal, and when I read about them, they seem to be the real mechanism of hearing, and not the ear drum or inner ear bones.
At this point I'm confused as to actually how sound waves are transduced into nerve signals in vertebrates. Can someone explain the the roles of the various parts of anatomy in vertebrate hearing, in the overall, big picture? What roles do the large parts play, versus the microscopic cilia?

Sounds are pressure waves in air, but the inner ear is a liquid-filled space. This presents an impedance matching problem where sound is reflected rather than transmitted.
The eardrum and inner ear bones perform this mechanical impedance matching/transduction of air-to-liquid sound. From Purves' Neuroscience:

Sounds impinging on the external ear are airborne; however, the environment within the inner ear, where the sound-induced vibrations are converted to neural impulses, is aqueous. The major function of the middle ear is to match relatively low-impedance airborne sounds to the higher-impedance fluid of the inner ear. The term “impedance” in this context describes a medium's resistance to movement. Normally, when sound travels from a low-impedance medium like air to a much higher-impedance medium like water, almost all (more than 99.9%) of the acoustical energy is reflected. The middle ear (see Figure 13.3) overcomes this problem and ensures transmission of the sound energy across the air-fluid boundary by boosting the pressure measured at the tympanic membrane almost 200-fold by the time it reaches the inner ear.

Some sources will refer to this as "amplification" which is correct in some ways (without it, sound would be too "weak" in the inner ear) but doesn't quite explain the whole problem.
Inner hair cells do the actual sensory transduction, converting vibrations into electrical signals when the "hairs" are stretched apart mechanically, causing a fragile "tip link" to pull on a physical channel, opening it and allowing ions to flow through. The cochlea is a frequency-analyzer, vibrating at different frequencies along its length and allowing different hair cells to respond maximally to different frequencies of sound.

As a side note, although you asked about vertebrates, aquatic vertebrates like fish don't have these middle ear bones, their hearing is quite different from the mammalian ears I am most familiar with. I'm not sure at all about hearing mechanisms in aquatic mammals that evolved from terrestrial ancestors, like whales and dolphins, but that might be a good subject of a later question.

The auditory system (Fig. 1) is basically comprised of 3 main parts - the outer, middle and inner ear (the cochlea).
Generally spoken, the outer ear captures sounds, the middle ear transmits them, the inner ear acts as a transduction system to translate the acoustic pressure waves into electrical signals.

The pinna of the outer ear funnels acoustic waves into the ear canal (meautus) and amplifies it. The pinna changes the transfer function that aids in sound localization in the vertical plane (Fig. 1A).
The middle ear conveys the pressure waves from the ear drum (tympanic membrane) to the ossicle chain, amplifying the sound further (Fig. 1A).
The inner ear is where the action is, see Fig. 1B for a sectional view. The cochlea is a fluid-filled tube. The ossicles transfer the acoustic energy into the fluid of the scala vestibuli. From there it travels through the cochlea as a traveling wave that rides on the basilar membrane (Fig. 1C). The traveling wave in turn sets the hair cells in motion. These hair cells have hairs (cilia) that allow current to pass when deflected. This in turn leads to release of neurotransmitter that in turns activates the auditory nerve to generate action potentials that are transmitted to the brain (Fig. 1D).

Fig. 1. The auditory system. source: Morgan et al. (2020)
Reference
- Morgan et al., Medizinische Genetik (2020); 32: 2


text:
Does Remdesivir cause bone marrow suppression?
According to Wikipedia, Remdesivir is a prodrug of GS-441524 which is a nucleoside analog.
I know that nucleotides are the building blocks of both DNA and RNA, meaning nucleotide analogues that prevent the creation of viral RNA can also prevent the creation of normal cell DNA, meaning they can cause problems in dividing cells. This is also reflected in the nucleotide analogue article of Wikipedia:

They are not specific to viral DNA and also affect mitochondrial DNA. Because of this, they have side effects such as bone marrow suppression.

So does Remdesivir cause bone marrow suppression?
If not please explain why.

From Off-Target In Vitro Profiling Demonstrates that Remdesivir Is a Highly Selective Antiviral Agent:

Overall, the cellular and biochemical assays demonstrated a low potential for RDV to elicit off-target toxicity, including mitochondria-specific toxicity, consistent with the reported clinical safety profile.

This isn't a very complete answer, but the wikipedia article doesn't go into detail or link references explaining the mechanism by which nucleoside analogues suppress bone marrow function. So I can't say if the assay results in my link rule out a suppression effect by remdesivir


text:
What is the minimum number of chemical elements required for life on earth? Does it vary between kingdoms?
As a non-biologist, I assume that there are certain elements that occur in all life forms as we know them. Examples might be carbon, hydrogen, oxygen and so forth. There are also elements that are rarely, if  ever, required for life on earth. My question is not about what elements might be required for life (although such information might be interesting for me and other readers). Rather it is about what the minimum possible number of elements that any life form on earth has, if we know the answer to that question. Also, if it is known, (how) does this differ between the plant, animal and other kingdoms?

You are far more likely than me to know what tags might be appropriate here. Please feel free to edit.

What are you defining as life? Viruses? Prions? bacteria and above certainly, but where's your cut-off?

@bob1 Whichever entities/notional kingdoms that an answerer might consider to be forms of life are fine, so long as it is explained in the answer. (Although, I wasn't thinking of prions and barely know what they are).

Prions are self-replicating proteins that can turn other proteins into more prions, they cause diseases like Creutzfeldt-Jakob disease (vCJD is also known as "mad-cow disease"), they replicate, evolve etc... don't worry, they aren't really alive, but then neither are viruses technically, which can't replicate themselves independently of another organism and always need some part of that organisms replication machinery to function. However, if you accepted prions as life, the minimum would be C, H, O, N, S I think.

I think I would add P to the list provided by @bob1 (ATP/NAD)

Hmmm. Four downvotes, but no constructive comments to explain how to ask a better question. Sigh ...

@user338907 Is that an answer perhaps?

@Araucaria - The reason for the down-votes is likely that it is impossible to define because there is such a variety of life that there will be no 1 magic number of elements. The most we can do is list a minimum of elements that are found in all life-forms, which would presumably make life possible, but that is specifically not what you asked for.

@bob1 +1 But presumably if there are elements that are found in all life forms, there are life forms that don't need any or many more than those elements. The vastness of different life forms that exist doesn't really have too much effect on this. For example, if we know of a life form that only needs those elements that are necessary for all life forms plus two others, then every other life form requiring more than that is out of consideration. No?

minimum to have any life or life as earth currently has?

@John I suppose that it's probably best to restrict it to life as earth currently has.

then you will need basically every element aside from the very unstable ones and the noble gasses, very few are not used in some life somewhere. even fluorine occurs in some life. it would be easier to list the elements NOT used in life.

@John I meant the minimum for a life form that currently exists on earth! (Narrow scope meaning of (any). I misunderstood the 'any' in your comment.

If we change the question to "what is the minimum number of elements common to every form of life?", my lists would be as follows. (I am not considering either viruses or prions to be 'alive').
The following elements are surely common to all forms of life (List 1):

H (1), C (6), N (7), 0 (8), Mg (12), P (15), S (16) [#7].

In addition, the following elements are very likely to be common to all forms of life (List 2):

Na (11), Cl (17), K (19), Ca (20), Fe (26), Cu (29), Zn (30) [#7].

If we broaden things to include elements occurring in any form of life I would add (List 3):

B (5), F (9), Si (14) [!Seemingly], V (23), Cr (24), Mn (25), Co (27), Ni (28), Se (34), Mo (42), Cd (48), Sn (50) [!Maybe], I (53) , W  (74) [#14].

No element in either list has an atomic number greater than 74 (Tungsten). (In the list given by Frieden (1972), the highest is I (53)).

For List One (and as pointed out by @bob1), H (1), C (6), N (7), 0 (8), S (16) are all present in proteins. P (15) is present in ATP and NAD. We must surely also include Mg (12), as the true substrate of almost all ATP-requiring enzymes is a complex of Mg++ and ATP. I can't see that any element can be removed from this list, but it could be argued that we need to add some from List 2.

For List 2, Fe (26) is present as haem in haemoglobin and the cytochromes, and (not necessarily complexed to heme) in other components of the electron transport chain. It might be possible that anaerobic life is possible without iron, in which case Fe (26) needs to be demoted to List 3 (but I doubt it). Zn (30) occurs in many enzymes (including yeast and liver alcohol dehydrogenase). It might be possible for a life form to exist without requiring Zn, but I don't know of any examples.

If we restrict consideration to plants, then Mn (25) needs to be promoted to List 1 (Mn is an essential component of Photosystem II, the enzymic system responsible for the 'splitting' of water in photosynthesis). As life as we know it would be impossible without PS, Mn (25) should possibly be in List 1 without qualification.

List 3 will probably always be contentious, but here are my thoughts:

B (5) is present in boromycin the only naturally-occurring compound containing Boron (as far as I am aware). It has long been considered essential for some plants, but this is contentious. See The importance of boron in biological systems and Boron: the essential element for vascular plants that never was
Edit B (5). @john has pointed out that B is required by some cyanobacteria, and has provided the following reference: Boron Requirement in Cyanobacteria. Its Possible Role in the Early Evolution of Photosynthetic Organisms.
The authors (Bonilla et al.) point out that B is a trace element that "although required in higher plants, has no role in animals or fungi". They suggest that B (possibly as boric acid?) can stabilize membranes by forming cis-diols with glycolipid -OH groups, a role previously suggested to account for B requirement in plants. (References to the original plant research may be found in Bonilla et al.).

This, I think, justifies B being included in List 3: required for some forms of life (but not a minimum requirement for life).

F (9) occurs in fluroacetate (See also The natural production of chlorinated compounds by G W Gribble)

Si (14). A paper in Science in 1972 suggests that Silicon is an essential element for the chick (news to me!). Frieden (quoted below) has this to say: "Possible structural unit of diatoms; recently shown to be essential in chicks. "

V (23). Occurs in haloperoxidases (See Coordination environment changes of the vanadium in vanadium-dependent haloperoxidase enzymes.  The vanadate ion is very similar to phosphate. See The role of vanadium in biology)

Cr (24) Whether Chromium is an essential trace element is controversial. It may play a role in insulin action (see Wikipedia) but this is not universally accepted (the Wikipedia article gives a good summary of the current position). Some bacterial can reduce chromium but this seems to be a detoxification mechanism (See also Chromium: is it essential, pharmacologically relevant, or toxic?). Frieden states "Essential in higher animals; related to action of insulin." but this, it appears, is still controversial. Possibly Cr (24) needs to be deleted from List 3.

Co (27) is a component of Vitamin B12

Nickel (28). Urease, the first enzyme crystallized (by Sumner in 1926), an accomplishment that played an essential role in establishing that enzymes are proteins, was shown in 1984 to contain Nickel (see Urease (Wikipedia))

Se (34) Selenium (as selenocysteine) is directly incorporated on the ribosome into some enzymes (SelenoCys is considered "the twenty-first amino acid")

Mo (42) is a component of quite a number of enzymes, including xanthine oxidase and is often associated with a pteridine cofactor.  See Molybdenum and Molybdenum-Containing Enzymes

Cd (48) A carbonic anhydrase from the marine diatom Thalassiosira weissflogii contains cadmium. It is thought that in oceans depleted of Zn, diatoms can use Cd as a zinc substitute. (See Biochemistry: a cadmium enzyme from a marine diatom and
Structure and metal exchange in the cadmium carbonic anhydrase of marine diatoms)

Sn (50) There have been some reports that Tin is an essential trace element for rats and humans (see Case study: bioavailability of tin and tin compounds and Frieden (quoted below)), but the evidence appears to be very scanty. Tin probably should be deleted from List 3.

I (53). Iodine is known to be a component of the thyroid hormones

W (74) Tungsten The first enzyme to require tungsten, a NADP-linked formate dehydrogenase from Clostridium thermoaceticum was purified and characterized in 1983. Since then a number  of tungstoenzymes (at least ten) have been identified, including acetylene hydratase. In many cases (and in a similar fashion to molybdoenzymes), W is often bound to a pterin cofactor. (See Tungsten in biological systems)

I think The chemical elements of life by E.Frieden, published in Scientific American in 1972, is still relevant, and I have relied heavily on the table on p55 of this publication in compiling the above lists
I haven't considered Sr (38), Nb (41), Ba (56) or Ta (73) but from Tungsten in biological systems  it appears that there is a case for these elements to be included in List 3

Should I take it, then, that there may be life forms that have only around 14 elements (list 1 + list 2)?

Note boron is important in cyanobacteria. http://www.plantphysiol.org/content/plantphysiol/94/4/1554.full.pdf and there a few notable organoboron compounds. https://www2.chem.wisc.edu/areas/reich/OrgMet/boron.htm

I think you can safely move Fe into list 1, even if heme (or haem) had never existed, Iron-Sulfur cluster proteins are ubiquitous among all cellular life, including obligate anaerobes. I can only think of one synthetic biology experiment in which E. coli was engineered to grow (very slowly) without making new Fe-S clusters, but they didn't even attempt to show growth in iron-limiting conditions. You're also probably right about being able to move Mn and Zn up to list 1 without further qualification.

@MikeyC Thanks. I agree with all you say, especially about non-heme iron. (Will update again over the weekend)


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Why aren't native predators in Australia able to handle the mice problem?
Australia is currently dealing with a mouse infestation problem, but Australia is awash with different types of predators that presumably eat lots of mice like animals.  Snakes in particular are well suited to kill mice, especially in close quarters. Snakes can fit in places most other predators can't due to their size. Additionally large invertebrates (like huntsman spiders) should also be able to take on some of the mouse load.
And it would be one thing if this was the first time the population ever boomed like this, but mice population booms have apparently have happened since Australia has existed. So why aren't we seeing large spikes in those predators when mice populations boom like this?

it takes time for the predatory population to respond - mice can breed in as little as 6 weeks (42 days), snakes take 45-70 days from laying to hatching, don't know how long from hatching to breeding...

Well for one thing we hunted many of the native predators to extinction. For another why haven't predators wiped out mice on other continents, because predators rarely wipe out their prey.

@bob1 yes but this has happened before, and I've seen no mention of increasing predator populations.

No doubt people have killed most mouse eating snakes in populated areas where mice find food easily. I see the same thing here in east TX; Copperheads ( mice eaters ) were common when I moved here 25 years ago. More people moved in and killed every snake they could . Now these same people are the ones who whine the most about the increase in mice and rats.  I have encountered many copperheads , they were about the most docile type snake I know .

a) you've got most of Australia's predators in your list: spiders and snakes.  Snakes aren't that populous and spiders don't have a huge appetite: 1 mouse per week would be overfeeding.  Dingoes don't eat 'em coz that's a cat's job.  We have no native cats, no rodent eating mammals like stoats, ferrets etc.  Basically it's up to eagles & goannas.  and b), Australia has existed for over 65,000 years.  Rodent plagues have been around for 200.

The mice aren't invading Australia, they are invading the wheat producing zones, where the tractors are leveling the land and putting on pesticides. The local frog, amphibian and snake populations downstream of the farmer's fields is strongly affected by the farmland, and so are the birds of prey, if they weather the pesticide use, they have to hide in dense trees, hollow logs, caves, and old barns, which are very lacking in Australian farmland.
If the government enforced laws for field edge habitats for local ecology, then there would be less mice.
Have a look at the map of wheat producing areas.
Rodent Outbreaks: Ecology and Impacts pages 225-238
PDF Google book
The map of mice infestations:

From pestsmart.org.au, though no longer available.

and a map of Australian climate:

wikimedia

Very nice answer and awesome images! Makes me wonder how a cold desert can be so directly adjacent to a hot desert, but perhaps it's just a matter of definition.

@Sixtyfive: See https://en.wikipedia.org/wiki/Desert_climate. A few different definitions are in use, but in all cases there's a temperature cutoff directly from "cold desert" to "hot desert". There are no in-between types. (And the names shouldn't be taken too literally. The Gobi Desert is a "cold desert" climate, but at the height of summer, temperatures there regularly rise above 100 °F or 40 °C.)

@sixtyfive The barrier of the warm vs cold desert is defined where the annual temperature average is higher and lower than 18'C, Koppen was a botanist, he devised regions based on vegetation types, the mix of temperature and rain where the same plant-types can grow. The temperature map is very different: https://www.researchgate.net/profile/Ferne-Edwards/publication/232319271/figure/fig1/AS:203062393217069@1425425255862/Average-annual-temperatures-in-Australia-showing-states-territories-and-their-capital.png Vs rainfall maps http://www.bom.gov.au/climate/how/newproducts/images/annrain2.jpg

Central Australia at Uluru and the cold desert regions can both sometimes be freezing on the thermometer for three/four months of the year, averaging 5'C at night. I think it's the summer that is hotter by about 10'C, i.e .30 vs 40'C.


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Is the covid-19 vaccine-induced copy of the protein spike also damaging cells?
In recent scientific articles, it has been discovered how the spike protein not only is a respiratory disease but also damages blood vessels cells directly, and is connected with higher risk of trombosis.
So, does the Spike Protein produced by the covid-19 vaccine also bring the same risks and damage?
How many spike proteins the immune systems produces after being instructed by the vaccine, and how do they behave afterwards ?
Thank you
EDIT: adding some references
-1) https://www.salk.edu/news-release/the-novel-coronavirus-spike-protein-plays-additional-key-role-in-illness/
-2) https://scitechdaily.com/covid-19-is-a-vascular-disease-coronavirus-spike-protein-attacks-vascular-system-on-a-cellular-level/
-3) here it says how the "creation" of the spike protein happens-> Can spike protein induced cell fusion be triggered by the mRNA vaccine?
EDIT2: Someone in the comments pointed out how articles 1 and 2 reference the same paper, and one paper doesn't constitute discovery.
But how the spike protein which are "created" after the vaccine, behave? Are they the same as the one from Covid-19?
Are they harmful? if not, why ?

Both of those news releases reference the same paper. One paper does not a discovery make. Do you have any references to any other published papers showing the same thing?

I'm sorry, I don't :(

@Cris scientists are natural skeptics. I'm not saying the results of the paper are incorrect, but there needs to be corroborating work done independently - it's how the scientific method works.

Yes, I totally understand. But my question remains. Regardless of damages on blood vessels, are the other damages created by the spike protein in the virus itself, still acting when this same protein is produced by immune system after receiving instructions from the mRNA? (sorry if I said something imprecise)

Where did you read that spike proteins are "created" by the vaccine? Vaccines induce the production of antibodies that bind to viral structures, not the structures perse

here: https://biology.stackexchange.com/questions/98449/can-spike-protein-induced-cell-fusion-be-triggered-by-the-mrna-vaccine?rq=1 "they only lead to the production of the spike protein in the cell."

@MikeKatz45 your comment is true of most vaccines but several of the new covid vaccines cause the body to produce antigens, to which the immune system then creates antibodies.

Ah very well I see now, so we are not sure if the spike has the trombogenic effect even if its modified to not fuse as the linked question says

@MattDMo: Funny how only the Chinese financially sponsored this research (despite the fact that the paper has some American co-authors). Anyway, it's the dose that makes the poison; "damages some cells" is true of bare mRNA released into the bloodstream as well. Downregulation of some ACE2 receptors, which is what the paper claims, isn't that big of a deal unless it happens at a massive scale.

The spike proteins expressed by cells that take up mRNA or ChAdOx vaccines are modified so they cannot induce membrane fusion. However, the research article you refer to indicates that circulating spike protein damages endothelial cells simply by binding ACE2, which suggests vaccine derived spike protein could still cause this kind of damage if it enters the bloodstream somehow:

we show that S protein alone can damage vascular endothelial cells (ECs) by downregulating ACE2 and consequently inhibiting mitochondrial function.

Spike protein is necessarily attached to a membrane, so for it to damage cells by binding ACE2, bits of membrane containing the spike would need to be exported from the cells. The SARS-CoV-2 genes that allow it to do this in a real infection are not present in the vaccines, of course. The only other route I know of by which S protein could theoretically enter the blood is in exosomes. This article analyzed circulating exosomes from COVID patients and did not detect any viral proteins:

We did not identify viral proteins via the purification of exosomes; thus, we can conclude that viral particles were not purified together with exosomes

Research creating hybrid S-protein that can make spike-coated exosomes indicates the natural spike protein does not get into exosomes:

the S protein could not be detected in the sample from pSwt-transfected cells. In contrast, the SGTM protein could be detected in the pelleted supernatant of pSGTM-transfected cells.

I was not able to find any studies looking for spike protein in exosomes of vaccinated people, but it should be less likely than for the actual virus.

Thank you, so the vaccine derived spike protein also does damage after inoculating the vaccine? "how many" spike proteins are going to be present in the bloodstream after injection compared to a real infection? What do you mean "if it enters the bloodstream somehow" (since the vaccine is actually injected into the bloodstream) ? could you explain in more detail this part ?

@Cris, "it" in "if it enters the bloodstream somehow" refers to the subject in the clause, which is "vaccine derived spike protein" and not "vaccine".

as mgkrebbs says, when the vaccine is injected into the bloodstream it is mRNA, which cannot bind to ACE2. The vaccine enters a cell and causes the cell to produce spike protein. The spike protein can bind ACE2, in theory, but it is stuck to the cell and cannot reach. There does not appear to be any way for the spike protein from a vaccine to reach ACE2, so it should not be able to cause damage in the way described by your article.

Thank you. Thus if I understood correctly, the mRNA containing the message instructs the cells to produce S proteins, but they are stuck into the cells and therefore cannot bind to other cells' ACE2? How many of these S proteins are produced after mRna injection, and how many of them are necessary for immune system to recognize them and develop immune response? How does this recognition happens, after targeted cells finish production of the mutant S protein?

I don't really know. You should probably ask another question for that. Here is a question related to yours, reading it will give you some background information: https://biology.stackexchange.com/questions/96886/do-mrna-vaccines-cause-transfected-cells-to-be-killed-by-cytotoxic-t-cells?rq=1

Spike protein is necessarily attached to a membrane, so for it to damage cells by binding ACE2, bits of membrane containing the spike would need to be exported from the cells. Won't bits of membrane of the cells that get killed by the immune system end up in the extracellular matrix?

That's a good question. My impression is the immune system would kill the cells displaying spike through phagocytosis, so the membranes would be recycled and the proteins digested. But I don't know enough about immunology to say for sure.

The Chadox1 Astrazeneca vaccine doesn't have the PP mutation, it is still able to drive cell-cell fusion. Most of the damage likely comes from the reaction of the immune system against cells expressing S on their surface, particularly at the 2nd dose.

Are you sure that spike protein cannot enter the bloodstream? From my sources, the median concentration of spike in plasma of vaccinated individuals is 47 pg/ml on day1/2. The spike concentration in an infected individual is most of the time below 70 pg/ml, and I am still looking for more accurate data. Reference can be provided upon request.

Yes, I'd like to see the reference, and No, I'm not completely sure.

Funny how only the Chinese financially sponsored this research you're talking about, despite the fact that the paper has some American co-authors. Anyway, it's the dose that makes the poison. This research may been published in good faith, but its findings have been used by anti-vaxxers out of context.
Downregulation of some ACE2 receptors, which is what the paper claims (in its title), isn't that big of a deal unless it happens at large scale. The study itself says that

vaccination-generated antibody and/or exogenous antibody against S protein not only protects the host from SARS-CoV-2 infectivity but also inhibits S protein-imposed endothelial injury.

In other words, they concede the condition is probably self-limiting in the immunocompetent.
Following [Moderna] mRNA vaccination (which has the highest dose of mRNA among the approved mRNA vaccines), levels of spike protein in the blood have generally too low to detect except by "ultrasensitive single-molecule array (Simoa) assays" and more importantly (with rare exceptions) anti-bodies cleared the spikes from blood in a few days, following the 1st dose, and from everyone in the test group a couple of days after the 2nd dose.

S1 antigen was detected as early as day 1 postvaccination, and peak levels were detected on average 5 days after the first injection.

The mean spike peak level was 62 pg/mL ± 13 pg/mL. After the second vaccine dose, no S1 or spike was detectable, and both antigens remained undetectable through day 56. For one individual (participant 8), spike was detected at day 29, 1 day after the second injection and was undetectable 2 days later.

Alas the latter paper lacks a comparison basis with what's detected following actual infections with SARS-CoV-2. Anyway, in correspondence to the press the lead author of this latter study concluded that

“We found that within a few days of the antigen appearing, the individuals developed antibodies that removed the antigen from the bloodstream,” he added. “Our conclusion was that the vaccine is working as intended.”

In other words, it's not a real clinical concern in most people. I'm not like totally dissing these findings, as they might be related to the myocarditis side effect of mRNA vaccines, but the fact that the latter most often happened after the 2nd dose suggests it's not the spike directly that's involved in that one.
By the way, "damages some [heart] cells" is true of bare mRNA (vaccine) released into the bloodstream as well, in animal models and in sufficient dose, at least in terms of detected inflammatory response. (For what's that worth, a co-author of this latter study is "the inventor [of] an intranasal influenza vectored SARS-CoV-2", i.e. no injection needed.)


text:
why secondary/booster vaccine shots may sometimes induce worse side effects?
Background:
I had my first shot about 1.5 months ago, I just had my shot yesterday. Unmistakable fever like symptom started within 4 hours. within 10 hours the whole body started aching, accompanied with chill, tiredness and headache.
2 details in this chain of event I can't explain:
(I believe those 2 details are related, I just couldn't connect the dots)
1
base on the 2 conclusions I just accepted without truely understanding them:

fever is an innate immune system function
adaptive immune system kicks in after days

it is hard to explain the lack of fever after the first dose (maybe the body is just treating the first dose as a local wound with some oppotunist bacteria getting in). It is even harder to explain the extreme quick onset of fever after the second dose (maybe I have left over CD4 CD8 plasmaB cells in response to first shot still wondering around or not commit suicide yet in the body?)
2
muscle and joint pain should be due to white blood cells releasing cytokine. The vaccine's lipid particles are injected into my arm muscle, not major blood vessels. Those lipid particles couldn't travel far into my whole body, lipids alone do not last long. They should only merge with or "infect" mostly local cells around the injection site. local pain, local ache makes sense, why did the whole body's immune cells ALL decide to release cytokine? shouldn't the aching be a gradient though out the body? starting from the site of injection, it should hurt the most, gradually the pain will be lowered the further away from the site of injection.
P.S.
the whole question is based on the knowledge that adaptive immune response takes days to take effect.  I just assumed the 2nd shot's side effect which takes merely hours to manifest couldn't be the adaptive immune response. However, I am thinking now, maybe the side effect is the continuation of the adaptive immune response from the first shot?
PS2 NEW INFORMATION
apparently nanolipids don't just stay locally
body ache is immensely way more complicated

This is a personal medical question, so it may get rightfully closed. But I think the underlying biological question, and how you pose it, is excellent. I also think that the understanding we have on the mechanisms of immunogenicity of the COVID-19 vaccines is still limited; it takes time to study them to a level that would satisfy your answer. I hope you understand that. I think a question about why secondary/booster vaccine shots may sometimes induce worse side effects is a good one, perhaps you can try to do your own research on that, and ask here once more, if this question gets closed.

To summarize the question, you are asking why:

the first and second vaccine shot did not induce the same immune response in terms of fever.
you experienced muscle and joint pain throughout your body even though the vaccine was injected into your arm muscle.

Regarding #1, your guess is mostly correct. According to Dr Melanie Swift, co-chair of the COVID-19 Vaccine Allocation and Distribution Work Group at Mayo Clinic:

When you take two doses of a COVID-19 vaccine, the first dose is the first time for your body to see the spike protein that the COVID-19 vaccines produce, and your body begins to develop an immune response. But that happens slowly. Then when you come back with a second dose, your body is ready to attack it. Your body is primed by that first dose of vaccine. The second vaccine dose goes into your body, starts to make that spike protein, and your antibodies jump on it and rev up your immune system response. [Source]

As for #2, I believe that the pain and soreness near the injection site is a separate symptom from the muscle and joint aches throughout the body.
The paper COVID-19 vaccine-related myositis has an explanation for the localized symptoms near the injection site:

With intramuscular vaccination, muscle is exposed to modified contaminant agents through direct inoculation, which elicit an immune response to the injected antigen. [...] Although similar to the COVID-19 infection itself the exact mechanism causing damage to the injected muscle is not known, it is worth reporting our observation of myositis suggesting a causal relationship to the novel, modified mRNA COVID-19 vaccine-adverse event, myalgia.

So, the arm symptoms seem to mostly be a localized reaction to modified contaminant agents which are injected.
As for the muscle and joint aches throughout the body, these are part of the general immune response which the body exhibits against the spike proteins which are eventually created. You are right that these symptoms are caused by cytokines, which are created by macrophages and neutrophils.
While it is true that the spike proteins will be manufactured by cells near the injection site, and will be detected there, this will trigger an immune response all throughout the body. This is similar to how a respiratory infection triggers an immune system throughout the body, and not just near the respiratory system.
As explained in an article on Breakthroughs.com, cytokines are chemical messengers which tell the body to produce more immune cells to help combat the infection. Their effects are intended to impact the whole body, which is why they cause symptoms on the level of the whole body, such as fever and muscle aches.

To summarize, "adaptive immune response takes days to take effect" is true, but that's the time it takes to adapt, not to react. Once the adaptation is done, it can respond immediately to the known antigen. The purpose of the vaccines is to eliminate that delay.


text:
Evolution equations of a 2-gender age-structure model?
This sounds a bit complicated but I want to grab more feelings on age-structured problems. Less than 2 days to the exam so I appreciate any help.
So suppose we get 4 age classes in a population census and we don't count the people in the eldest age class again. We model females and males separately. Let $u_{i,n}$ and $v_{i,n}$ be the number of females and males in age class $i$ at census $n$, respectively. $s_i$ and $t_i$ are the fraction of females and males, respectively, surviving from age class $i − 1$ to $i$. $m_i$ is the (expected) number of children from a female in age class $i$.
If a fraction $\alpha$ of births are females and $1 − \alpha$ are males, what are the evolution equations for (1) $u_{1, n}$ to $u_{4, n}$ and (2) $v_{1, n}$ to $v_{4, n}$ respectively?

I tried putting forward the Leslie matrix for female: $$\begin{bmatrix} \alpha s_1 m_1 & \alpha s_1 m_2 & \alpha s_1 m_3 & \alpha s_1 m_4 \\ s_2 & 0 & 0 & 0 \\ 0 & s_3 & 0 & 0 \\ 0 & 0 & s_4 & 0 \end{bmatrix}$$ Is this correct?

If I try to repeat the thought process in part 1, we must use $u_{i, n}$ to write out the equations for males in the 1st age group, i.e. $v_{1, n+1}$ (unless both gender can give birth): $$v_{1, n+1} = (1-\alpha)t_1\left(\sum_{j=1}^4 u_{j, n} m_j\right).$$ Is this a way to determine "the evolution equation for $v_{i, n+1}$ in terms of the population structure at census
$n$"?

In case I have to find the gender ratio (e.g. for a certain age class or overall) in census $n+1$ or in long run, should I find the largest eigenvalue of both Leslie matrices for both gender, and proceed to find the respective eigenvectors for both gender, and then add the terms together to compare?

Thanks in advance.

Good luck on your exams! I sure am glad I’m not the one taking them. (I had a dream last night about needing to solve a math problem much simpler than this one. Unfortunately the numbers kept changing!)


text:
What is this insect wing, based on its vein pattern?
I've heard that it's possible to identify insect species uniquely based only on the vein patterns of their wings.  Is this true?  If so, what is this?

The image is taken from an unsolved Internet puzzle game from a few years ago.  (The creators of the puzzle are no longer to be found, so I can't ask them).  I believe the wing is probably from some species of cicada, but I couldn't be sure, and if possible I'd like to know what particular species of cicada.
Also, is there any kind of formal classification/notation for insects' wing venation?  Might shed some light on what the puzzle makers actually meant by the dratted thing!  (You can remove this bit, or I can, if it's considered to be asking two questions at once.)

In case the answers here are not enough to solve the puzzle, you could post it at our sister site puzzling.SE.

There is a way to classify insect wings: the Comstock-Needham system.
From Wikipedia:

The Comstock–Needham system is a naming system for insect wing veins, devised by John Comstock and George Needham in 1898. It was an important step in showing the homology of all insect wings. This system was based on Needham's pretracheation theory that was later discredited by Frederic Charles Fraser in 1938.

The system assigns names to the enlarged longitudinal veins of the wings and provides subnumbering for different branches of those veins. The system also names cross-veins and cells (transparent areas between veins) relative to the major longitudinal veins.
Again, according to Wikipedia:

the major longitudinal veins are named:
> - costa C, meaning rib
> - subcosta Sc, meaning below the rib
> - radius R, in analogy with a bone in the forearm, the radius
> - media M, meaning middle
> - cubitus Cu, meaning elbow
> - anal veins A, in reference to its posterior location

The cells are named after the vein on the anterior side

Since the questions asks about identifying the wing based on the given image - do you have any idea what it is?

As I said in the question, I think it's a cicada.  The whole puzzle has a recurring cicada theme, and also from looking at some photos elsewhere in an online article about different types of insect wings that seems to be the best match ( http://www.metafysica.nl/wings/wings_14.html , scroll down to type 6, "Megadipterygia", although I think the author made that classification up).