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Which kind of inflorescence(s) does Sonchus oleraceus have?
Many capitulum inflorescences, several corymb inflorescences with capitulum inflorescences as the end nodes of each corymb inflorescence, or one compound corymb inflorescence with capitulum inflorescences as the end nodes?

A picture would be of great help here.

@Darlingtonia picture uploaded. Thanks.

Thank you. I'm a little concerned this is a homework question. What have you found about capitula (capitulums?) and corymbs that might help with the question?

@Darlingtonia I read some materials that say Sonchus oleraceus's capitulums are arranged as corymbs or raceme at the end of stem. I'm confused what on earth the inflorescence of Sonchus oleraceus is. Isn't the inflorescence of a plant fixed?

A flowering plant's inflorescence is the grouping of flower clusters on the plant. Inflorescences are categorized based on the architecture of the arrangement of flowers within them.
As members of the sunflower or daisy family, Asteraceae, Sonchus has it's flowers compressed into tight heads called capitula. A sunflower might casually appear to be a single flower, but close examination will reveal that it is made of many (dozens in the case of Sonchus) smaller flowers. In the photo above, each yellow petal, including those in the interior of the disc, originates from a separate flower. As such, the inflorescence of Sonchus is a capitulum.
However, Asteraceae is an extremely diverse family, and the arrangement of capitula can be an important character in classifying and identifying these plants. Because of this, the same inflorescence terms applied to a group of flowers can also be applied to a group of capitula. In Sonchus one can (often) call the arrangement of capitula a corymb*. One definition of corymb is "a flat-topped or round-topped inflorescence, racemose, but with the lower pedicels longer than the upper".
So, strictly, the inflorescence of Sonchus olearaceus is a capitulum, and the capitula are arranged in (approximate) corymbs.

*The first resource I found listed Sochus as "corymbiform to subumbelliform" which means, roughly, ranging from a corymb (but maybe not exactly) to not-quite-an-umbel.

Thank you for your analysis. I think there exists a difference between an inflorescence and a sub-inflorescence in an inflorescence. For example, a sub-inflorescence of a compound corymb is also a corymb. As to Sonchus olearaceus, the capitulum seems a sub-inflorescence, not an independent inflorescence, but I did not find the name of this type of compound inflorescence. All the named compound inflorescences I find have sub-inflorescence the same inflorescence type as the  compound inflorescence itself such as compound umbel, compound corymb, and  compound racemose.


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Is colocalisation of a protein with a presynaptic marker sufficient evidence to say that the protein is a component of axon terminals?
I am reading journal papers about the subcellular localisation of the insulin receptor (IR) in neurons.
I have read a paper stating that IR is highly enriched at synapses, localising to both the presynaptic axon terminal and the postsynaptic density compartments.
The above statement saying that IR localises to presynaptic axon terminals comes from immunofluorescence images of cultured neurons where IR colocalises with synaptophysin puncta.

^ https://pubmed.ncbi.nlm.nih.gov/16978790/
In contrast, another paper showed via subcellular fractionation of the rat brain that IR is enriched in the post-synaptic density (PSD) fraction (through analysing the IR levels in the PSD fraction via Western blotting).
I think this is stronger evidence compared to immunocytochemistry.
To say that a protein is a component of the presynaptic terminal is colocalisation with a presynaptic marker (e.g. synaptophysin) sufficient evidence? Or should there be other forms of evidence to back this statement up?

Colocalization of a protein with another structure is necessary but not sufficient to say that the protein is a component of that structure.
Mixed into the concept of a structure's existence is the concept of an observational timescale. A presynaptic terminal is a structure that exists over specific timescales; all of its constitutive (and identity-conferring) components must colocalize with it, over all of its lifetime. Otherwise it would be more apt to specify something which colocalizes over more limited timescales to be cofunctional structures with the presynaptic terminal.
Experimental techniques tend to probe specific timescales. For example,  immunostaining is based on the assumption that the dissociation rate constant for a specifically bound state is small compared to nonspecific bound states (allowing for the 'washing' steps to have sufficient efficacy). So, in general, spatial correlation of two molecular structures, based on a single observational approach, is insufficient evidence to qualify the structures as parts of a whole.

Empirical science is not based on proof, but on evidence.
No one study is the final word on anything. "Sufficient evidence" is entirely up to the person operating on the evidence and what they plan to do with it. Sufficient for further study? Certainly. Sufficient for using insulin injections to cure every mental/cognitive issue? Of course not.
I think I'd focus less here on the different measurement techniques and more on the model systems used, in addition to Ryan's points about timescales.

source: Stack Exchange

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/

sort: votes


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Relationship between Km and IC50 in cellular uptake assay
I'm going to describe the scenario in general terms at first so as to try and get to the theoretical content of the problem, but I'll post a link to the paper which got me thinking about it at the bottom of the post.
The setup for the assay is as follows. There is a membrane transport protein $P$ which can transport multiple substrates, of which we'll focus only on two, call them $S_1$ and $S_2$. To measure transport via $P$, we have a radiolabeled version of $S_1$ which I'll label as $S^{rad}_1$. The assay protocol is to first incubate cells overexpressing $P$ with a mixture of $S_1$ and $S^{rad}_1$ as well as other molecules of interest, wash off any remaining radioactive substrate which has not been taken up, dissolve the cells, and measure the resulting radioactivity in each condition. We can directly observe the $K_m$ for $S_1$ by measuring the initial rates at which $P$ transports $S_1$ at varying concentrations of $S_1$. We'll further assume that the ratio of $S_1$ and $S^{rad}_1$ is constant. Because $S_1$ and $S_2$ can both be transported by $P$ (assume via identical mechanisms), $S_2$ will act as a competitive inhibitor to the transport of $S_1$ if we add it into the incubation solution during the assay. If we keep $S_1$ and $S^{rad}_1$ constant and then vary the concentration of $S_2$, we'll observe less uptake of $S^{rad}_1$ as $[S_2]$ increases due to $S_2$ out-competing the former. We can then get an $IC_{50}$ value for $S_2$ with regards to the transport of $S_1$. My question, then, is: how does the $IC_{50}$ of $S_2$ when it is inhibiting the transport of $S_1$ relate to the $K_m$ of $S_2$ when it is being transported by $P$? Does there even exist such a relationship or would we have to use a radiolabeled version of $S_2$ to observe any data about its $K_m$?
I believe this is an accurate generalized description of the scenario at hand, but please point out/correct any mistakes I have made! As I mentioned, this scenario was inspired by a published journal paper which you can find here:
https://jpet.aspetjournals.org/content/295/1/392.long
In this paper, succinate acts as $S_1$ and N-Acetylaspartate, aspartate, and glutamate independently take on the role of $S_2$. In Fig. 2, the authors provide inhibition curves for succinate transport as the concentration of NAA, aspartate, and glutamate vary. They are able to fit this data to get $IC_{50}$ values for the three molecules, but they then, in the abstract, extrapolate these $IC_{50}$ values to be identical to the Michaelis-Menten constants for the substrates. This is the primary source of my confusion, as intuitively I don't feel that it is a valid assumption that $K_m = IC_{50}$ when the competitive 'inhibitor' can also act as a substrate for the transport protein. However, I haven't been able to find any information about this topic online and it's certainly not my strength as a new researcher hence my asking here instead.
Thank you for reading and for any help you are able to provide!

Another clue that something is going awry here is that I don't believe the paper (or my generalized scenario) assume anything about how the 'inhibitors' interact with the protein. That is to say, even though the authors show that NAA does get transported, their fitting of the $IC_{50}$ and then extrapolating this to the Michaelis-Menten constant does not make any assumptions about the fate of the 'inhibitor'. Obviously, a competitive inhibitor which lodges itself in the active site and prevents transport has no $K_m$ yet you could apparently claim its $IC_{50}$ as such.

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


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Are there any "good" gases which "accidentally" diffuse into the lungs and get exhaled?
The purpose of breathing is to bring oxygen into the body and to rid the body of waste gases such as carbon dioxide and excess water vapor. This is done by diffusion with the blood. I am wondering whether the respiratory system also "accidentally" removes good gases from the body via diffusion and exhalation. (These good gases do not include oxygen, since it doesn't diffuse from the blood into the lungs.) This might be useful if a person has low amounts of a good gas and breathing too much, such as doing too much exercise, is the culprit.
Such good gases could come from food. Just like alcohol vapor is exhaled, maybe these gases might be exhaled too. Good gases could also come from a specific metabolic process.

Related:  https://biology.stackexchange.com/questions/111813/besides-carbon-dioxide-and-water-vapor-what-waste-gases-are-removed-through-the

Your question might get more attention (i.e. additional suggestions) if the title were changed on the lines I suggested, e.g. "Are there any important gaseous metabolites or signalling molecules in humans that may be lost through exhalation?".

Biological scientists do not usually ascribe moral attributes to metabolites, despite the use of the term ‘good’ in reference to lipids by those who communicate with the public. So I think it better to rephrase the question more precisely, as something like:

“Are there any important gaseous metabolites or signalling molecules in humans?”

One gas that comes to mind is nitric oxide, which is a natural signalling molecule that causes vasodilation of smooth muscle. The production of this is stimulated by the erectile-disfunction drug, sildenafil (marketed under the trade name, viagra).
Thus, nitric oxide fits the bill (and, in so far as a penile erection is considered a ”good thing” — most men will be of that opinion, nitric oxide can even be considered a ”good gas”).
Nitric oxide has certainly been detected in the exhaled breath of normal individuals, but the majority is excreted in the urine as nitrite or nitrate.
So I would look for causes other than heavy breathing to explain the decline in its tissue concentration, and any unwelcome effects that this might have for the individual.

Is nitric oxide actually exhaled?

@mathlander — NO is exhaled, as can be found from the paper you linked to. I have modified my answer providing information on the metabolism of NO from this and another paper.


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Can I have LAMP on the bench / in the field?
I am interested in LAMP for detecting small amounts of DNA (loop-mediated isothermal amplification and yes, I know the initials don't match).
I am trying to figure out exactly how clean/(sterile?) everything needs to be.
On one hand:
-papers repeatedly stress that the assay is very sensitive and to avoid contamination
-these very nice guidelines (https://www.rtlamp.org/get-started/rt-lamp-open-access/) include the requirement for a PCR hood. I think this website is otherwise reasonable and thorough as it mentioned that HNB dye should be in its trisodium form (which most papers do not mention)
On the other hand:
-I'll be working with DNA, not RNA; less fragile
-the point of LAMP is supposed to be that it requires more basic equipment than PCR. If it still requires a clean bench, that sort of flies out of the window.
-a quick search for 'field LAMP amplification' found a publication (https://pubs.rsc.org/en/content/articlelanding/2022/ew/d2ew00433j - 'In-field LAMP assay for rapid detection of human faecal contamination in environmental water'). But I don't have enough experience in the field to tell whether this is a reasonable approach.

I don't do chemistry or bench work, so I can't speak to conditions required for LAMP in the lab. However, I know people who have developed a portable LAMP set-up that works in the field. It's still something of a prototype, with testing going on, but this paper provides you some idea. The process doesn't require very stringent cleaning. So to answer your question, yes, you can use LAMP in the field. I'd assume in the lab too, since the field set-up is portable and I've seen them use the unit in the lab.
https://www.sciencedirect.com/science/article/pii/S0956566320305820

Hello. Thank you. The paper that you linked is not really about LAMP - maybe you meant one of the references in it, or something else altogether? If you can adjust that, I will accept the answer.

I changed the reference. The Introduction includes multiple references to LAMP in the field.


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Can simultaneous double pathogen infections happen, or are they prevented?
Is there something in immunology that prevents a simultaneous infection with a 2nd pathogen? For example, I've never heard of someone getting both dengue and malaria together. Or, say, Ebola and Marburg fever.  Of course, sheer probability makes it unlikely but is there something more fundamental that prevents it?
Maybe a more tractable version of the question is within the class of viruses or one type e.g. respiratory viruses. Is there something that prevents getting infected by multiple pathogens at once?

You can absolutely have two infections occurring together.
One term which is used is 'co-infection'. Also 'secondary infection', in case where either the first infection or the treatment made it more likely for the second infection to occur. For example, secondary infections causing pneumonia were a big issue with Covid19.
I have done a quick google search on 'dengue malaria co-infection', and cases do exist. In this paper (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3614227/ - Concurrent malaria and dengue infection: a brief summary and comment), the authors comment on the fact that for this particular combination of diseases, the co-occurence is indeed quite low. They have various hypotheses:

The vectors for either disease are specific to geographically distinct areas, e.g. mosquitoes that prefer city vs rural areas.
(I've seen it contradicted in another paper but no time to search).
Pure statistics: the likelihood of getting both diseases is much less likely than getting one, especially if getting one disease results in behaviour modification (e.g. staying at home sick).
Underdiagnosis: if you go to the doctor with one obvious disease, you probably will not get tested for other co-infections you might have.

It is possible that, for other pairs of diseases, immunity may play a role (your body is already on high alert from one infection) but that can also provide a risk (your body is so exhausted from fighting infection #1 that you can't fight infection #2). I am not aware, though, of any general statement that would apply to all diseases.

Another particularly good example would be the hepatitis D virus, which requires the hepatitis B virus to be present for it to replicate (though not all cases are coinfection, HBV carriers can also get HDV for example).

Something from not too long ago - man diagnosed with Covid, Monkeypox, and HIV: https://www.webmd.com/covid/news/20220826/italian-man-covid-monkeypox-hiv-same-time

Another related term is "superinfection". Especially common in immunocompromised populations and/or when antimicrobial therapy was inappropriate.

I've got COVID and a bacterial chest infection as we speak... Feels a very relevant example

Another factor factually making a secondary, subsequent infection less likely is that the immune system is all revved up already. The second pathogen encounters a really hostile environment. During an acute infection the body is in an exceptional state which it is not able to maintain in ordinary times (I guess because of detrimental side effects -- think fever --, auto-immune issues and resource issues).

@ScottishTapWater Wishing you a speedy recovery! May your body kick the butts (and other body parts) of all relevant bacteria and viruses.

@ScottishTapWater Yup:  Back in college I had strep throat and mononucleosis at the same time.  Doctors are looking for one diagnosis, it confused them at first.

There are viruses that require coinfection.  The Hepatitis D virus is incomplete and can only reproduce in a host who is also infected with Hepatitis B.

Very interesting point, although quite a special case.


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Why does hyperventilation make you feel like you need to breathe more?
Calm Clinic claims:

"The problem is that hyperventilation makes your body feel like you're not getting enough oxygen. Essentially, it makes you feel like you need to take deeper breaths and take in as much air as possible. This makes all of the symptoms of hyperventilation worse."

As far as I know, the brain controls breathing rate by measuring the amount of carbon dioxide in the blood. So is this true? If so, why?

Hyperventilation alone does not cause you to feel that you're not getting enough oxygen. Rather, it's what causes hyperventilation that does that (thus resulting in hyperventilation.)
The Calm Clinic explains this quite well (while only mildly contradicting your quote):

During periods of intense anxiety, the body is sent into a state of fight or flight, when the brain signals to the body that danger is afoot. When this happens, you automatically start breathing quickly, as this oxygenates your blood and prepares your body to respond to a threat by fighting or fleeing. If the threat that has triggered your fight or flight response (whether real or imagined) persists, you’re likely to continue hyperventilating until you start to experience other unpleasant physical symptoms.

The focus of your question is

"...This makes all of the symptoms of hyperventilation worse." [emphasis mine]

You can hyperventilate by breathing too quickly or too deeply; either way, in people without underlying medical disorders, hyperventilation is usually caused by stress/anxiety. Anxiety makes your heart rate increase, and causes a perception of the need for more air (not the actual hyperventilation). It is often accompanied by some degree of chest tightness, which many people reasonable attribute to a problem with their heart. These things tend to cause more stress, so it's a cycle. The symptoms of hyperventilation are dizziness/lightheadedness, tingling in your hands/feet and around your mouth, and more but less common symptoms.
Under normal circumstances, hyperventilation leads to a period of decreased respiratory rate to allow for arterial blood to build up that critical buffer, HCO3.
Dealing with Anxiety Symptoms: Hyperventilation
(written for laypersons)

I meant to emphasize this sentence: "Essentially, it makes you feel like you need to take deeper breaths and take in as much air as possible."

That's fine. I hope you understand I was emphasizing that hyperventilation does not create more air hunger; the stress causing the hyperventilation does. A common symptom of anxiety is the feeling that one can't take a deep enough/satisfying breath. If this happens, a yawn will often break that cycle for a while. Yawns are wonderful things for stress. Most people can cause themselves to yawn at will.


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Bottleneck in population that is already experiencing inbreeding depression
What would be the result when a population experiences a bottleneck, while already manifesting inbreeding depression?
I only found this article and it suggests that the inbreeding depression would decrease by a few points. I couldn't find anything else relevant, only about how a bottleneck increases inbreeding (obviously).
What are the relevant Mathematics?


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Telomerase and End Replication in Eukaryote
Here is a picture of using telomerase in solving end replication problem (Courtesy: Molecular Biology of the Cell, Alberts, Garland Science Pub.)

Now lets consider the $3'$ end here, we are extending this end, and then using DNA Pol we extend the $5'$ end, even though the $5'$ end would still be truncated w.r.t $3'$ end but the original strand would be maintained. Now we know that this Telomerase enzyme is active in stem cells but NOT in somatic cells. So far so good.
Now if I consider the above layout in more detail: Lets consider what happens after the above replication cycle:

This is because in the 1st replication cycle, we have added more nucleotides to $3'$ end, as well as possible few more nucleotides to $5'$ end as well. Now this would create overhangs on each $3'$ end of my DNA. And I am confused on these overhangs. Either the replication machinery deletes these overhangs ( which I am not sure whether it happens), OR the second replication would start on these overhang DNAs. A possible issue with the second approach (i.e replication with overhangs intact) is that the length of each strand would keep on increasing with each replication cycle as we are keep adding new nucleotides to $3'$ end in every replication cycle!!
Can someone shed some light on how the second cycle would happen, and whether the overhangs would get deleted or it would remain (in this case strand length would keep on increasing)?

The overhangs are needed for telomere function and maintaining chromosome stability, so they aren't deleted. This is an active area of research, so the amount of detail you need to know depends on your level of study. They undergo processing instead of being deleted, involving nucleases. Note that DNA polymerase is filling in most of the gap. It will continue doing this in subsequent replications, so the slight single-stranded region left over won't grow. I'm assuming you mean "single-strand length" by "strand length." If you mean overall telomere size, then it depends on if the cell is somatic or not, which you pointed out.
(The 3′ overhangs can also form structures called T-loops, where the single-stranded overhang "invades" the double-stranded telomeric DNA. This helps protect the chromosome ends from being recognized as damaged DNA, maintaining genome stability.)


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Help me identify this wasp-like insect
I've never seen wasps with long legs like that.
It's not big, about 1-2cm in length (not counting legs).
Could you identify this?
UPD: location is central Ukraine

The details of the insect are listed below:
Common Name: Craneflies
Zoological Name: Ctenophora flaveolata
Location(mostly found at): Eastern Europe
Here is the Biological Identification,
Kingdom: Animilia
Phylum: Arthropoda
Class: Insecta
Order: Diptera
Family: Tipulidae
Genus: Ctenophora Meigen
Features: The species are large (about 20 mm long, with 25-mm wingspans), shiny black craneflies with large yellow, orange, or red markings to mimic wasps. Males have comb-like antennae. The larvae are saproxylic. The species are confined to old deciduous forests, orchards, and other habitats with continuity of the presence of dying and fallen trees. Ctenophora species are important bioindicators.
Source: Ctenophora (fly)

This is mostly a copy from Wikipedia. You have to mention your sources when you copy stuff. On the SE network, however, it is discouraged to copy-paste anything ad verbatim as it can be plagiarism, especially when sources are not mentioned.

Sorry, I forgot to mention the source. Thanks for the comment.


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How do we know that the DNA we share with other species (especially primates) isn't fully the result of transposable elements?
I recently read a couple studies that concluded the 25% of genetic similarity between cows and reptiles is actually primarily due to TEs (transposable elements) rather than common ancestry.
Here's the link to the study for more information: https://www.theatlantic.com/science/archive/2017/10/how-a-quarter-of-the-cow-genome-came-from-reptiles/542868/
Now, I'm a strong believer in evolution, but I'm wondering if there's even the slightest possibility that the 97-99% number floating around when it comes to human and chimp/bonobo genetic similarities isn't exactly accurate, especially with the existence of TEs. I supposed my question is, simply put, could TEs serve as an alternative explanation to common ancestry for humans and modern apes? Also would this undermine the ERV/retrovirus remains argument as well?

Never say never in biology. But it is not plausible that TEs explain the similarity in great apes (including humans).
Much (most?) of the argument for similarity is and has always been due to essentially identical coding sequences, which are mostly not affected by TEs.
More convincingly, the high degree of synteny between great ape genomes (including humans) is extremely unlikely if generated by independent random processes. For example, there is only one major difference in the gross ordering of elements on the chromosomes between humans and chimps.
The bovine/reptile similarity from TEs is mostly noticeable because it's on a background of quite low similarity at the coding level, and essentially no similarity at the synteny level. The BovB element is <20% of the cow genome. I don't know of high-level similarity numbers for the overall genomes of those organisms because I don't think the genomes are even alignable enough to compute those statistics, but I imagine they are quite low.

Thank you for your answer! Is it likely that TEs could at least be used to explain away the same ERV remains in human/primate genomes or is even that unlikely?

@MihirDhawan since you seem to be new to the Stack Exchange network, please read What should I do when someone answers my question? in the [help].

@MihirDhawan Certainly, humans and great apes are quite closely related so they have quite similar TE profiles, both active and defunct. Perhaps I am not understanding the question? In other words, they share TEs rather trivially through common descent, rather than through horizontal transmission (which is what makes that bovine case interesting). If what you are asking is "does horizontal TE transfer occur between apes and humans?", then that should probably be a separate question, as it's a bit different in scope.

@MaximilianPress Yes, I think that's what I'm trying to ask--does horizontal TE transfer happen between apes and humans. Thanks again, I'll post it as a new question!


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Identify blue/translucent jelly-like animal on beach
A few weeks back a beach in California had lots of this animal (if it is an animal?). Can anyone identify what it is?
They had a distinct blue bottom and a see-through top.

Hey, funny seeing this question here. My wife and I just visited a beach in San Diego yesterday and also noticed these creatures. At the time I just Googled "flat animal on beach with fin" and found out it was by-the-wind sailors as someone already answered. They are very alien looking. Wonder what caused them to come to shore in such large numbers.

With billions of years to work with, evolution comes up with some truly amazing and beautiful creatures.

 By-the-wind sailors
This appears to be Velella (a monospecific genus), commonly referred to as by-the-wind sailor.

More specifically, this is Velella velella, and is also less commonly referred to as sea raft, purple sail, or little sail in addition to usually being called by-the-wind sailor or even sometimes simply Velella.

 Source: Wikipedia
As can be seen from the above image, this 40-80 mm long [source] organism has a translucent sail with a lower bluish body that includes (not visible in your image or mine) small tentacles -- see below (as well as here):

 Source: Wikipedia
For more detailed description, see Scripps Institution of Oceanography:

A clear, chitinous semicircular to triangular sail sticks up above the water with a blue float beneath made of concentric circles of gas-filled chambers. Small tentacles extend below the circular chambers. The sail is angled left or right.

Like the better-known man o' war (see below), this carnivorous hydrazoan (think hydra or other related cnidarians like jellyfish), floats on the water's surface, using wind to direct its small, rigid sail while dangling tentacles below armed with nematocysts catch and stun prey. From Wikipedia (my emphasis):

Having no means of locomotion other than its sail, V. velella is at the mercy of prevailing winds for moving around the seas, and are thereby also subject to mass-strandings on beaches throughout the world. For example, most years in the spring, there is a mass stranding that occurs along the West Coast of North America

You can also see a report about these guys washing up on California beaches in mid-April from the Orange County Register.

Educational video of these sailors available here: YouTube

 Man o' war' is incorrect
Note: my initial gut reaction was that it was a small, beat-up Portuguese man o' war (Physalia physalis), often referred to as the Pacific man o' war (or even a "blue bottle") in the Pacific Ocean. A colonial marine siphonophore  (within class Hydrazoa) made of many smaller "zooids". Like Velella, it also floats on the water surface with its "pneumatophore" (a gas-filled bladder that forms a dorsal "sail" that can be pushed around by wind above the ocean) while tentacles armed with nematocysts dangle below to capture/stun prey.

Like your specimen, the man o' war's sail (or "pneumatophore") appears to be somewhat translucent with the lower portion often taking on a blue coloration (or sometimes purple, pink, or mauve) [source] like your organism. It's also not irregular to have many of these wash ashore all at once, as seen here.

However, the size and morphology (especially small size of the "sail", lack of obviously large bladder, and the clear concentric-circle morphology) of your specimen all pointed to another organism (and clearly toward Velella as stated above).

For what it's worth, NPR had a brief story on By-The-Wind-Sailors this week.


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What is the nature of seedless fruits?
Can seedless fruit be produced in nature without humans interfering with the fruit? And would that be considered a spontaneous mutation?

Is a mule "seedless fruit"? What might the difference be? Whether there's a spontaneous mutation or a hybrid that cannot reproduce doesn't matter, since the vast majority of these will not even be recognized by anyone (they can't propagate.) Furthermore, fruit can be seedless without genetic abnormalities, but based on growth conditions (granted this is very hit or miss.) Have you never found a seedless apple? (I have. I peel and cut up apples. Apples without seeds are not extremely rare.)

Questions here are expected to demonstrate prior research, like things you've read that motivate your question or show where you've gotten in trying to find an answer. It's also expected to look at existing questions here, for example searching https://biology.stackexchange.com/search?q=seedless

Some examples: https://biology.stackexchange.com/questions/19093/confusion-regarding-seedless-grape-and-the-normal-process-of-germination https://biology.stackexchange.com/questions/16754/how-are-oranges-in-the-us-or-anywhere-made-seedless https://biology.stackexchange.com/questions/80153/how-can-seedless-fruits-not-be-gmo - do any of these answer your question? If not, why not?

Seedless fruits are the result of a biological process called parthenocarpy – the development of a fruit without prior fertilization. Seedless plants are not common, but they do exist naturally or can be manipulated by plant breeders without using genetic engineering techniques.
Spontaneous mutations are naturally occurring alterations in the DNA due to slippage in natural processes. Also, as said before, The seedless plants are rare but can occur naturally ,i.e., without any human interference. So, yes it can be considered as spontaneous mutation.
If you cross a horse and a donkey, you get a mule. Mules can't reproduce — they are, in essence, "seedless".
Source: Seedless fruit is not something new


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Are there any affordable devices for measuring ghrelin levels at home, similar to blood sugar monitors?
I'm interested in finding an affordable medical device that can measure ghrelin levels, similar to how blood sugar level monitors work. I understand that ghrelin level measurements typically require laboratory analysis of blood samples, making it more complex and costly than glucose testing. However, I'm curious if there have been any recent developments in this area or if there are any devices available for public sale.
I've searched online for such devices but haven't found any clear answers. Most of the information I've encountered indicates that ghrelin measurement is primarily done in laboratory settings. I'm hoping someone here might have more up-to-date information or know of any devices that have been introduced to the market.

There are some home kits, but they are professional kits. You can buy one of them if you know how to use it:
https://www.assaygenie.com/human-ghrelin-pharmagenie-elisa-kit-sbes0025/
It costs around $780.
I know it costs a lot, but there are no cheaper alternatives.
Also, I tried to find out if there are any simpler monitoring machines, but unfortunately there is no such thing for Ghrelin (at least till now).

I wouldn't exactly call a colorimetric ELISA a home kit, unless your home happens to be equipped with a 450nm microplate reader, full set of pipettes, etc. I also fixed your link to point to the human kit.

Yes, you are right. But I discussed with you what I could find out.

"What you could find out" was probably the first result of a search engine query. Everybody and their brother makes human ghrelin ELISA/EIA kits, some significantly cheaper than the one you found. Answers should have some level of personal expertise behind them, not just the ability to use a search engine.


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Has anyone quantified how many transcription factor-inducer pairs are available for use in genetic circuits?
I know of at least 12 orthogonal small molecule sensors which come from the "marionette" strain paper (https://www.nature.com/articles/s41589-018-0168-3#Sec9). There are others scattered throughout the literature. Has anyone tried to count the number of these that exist. Let's, for now, exclude the fact that some may only work in specific organisms. I am curious about the total count of these systems and how quickly (slowly?) we are expanding the synbio toolkit.


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Volumes of the four heart chambers
We know that the left ventricle which feeds blood into the aorta is typically the largest chamber of the heart.
I'm looking for the typical absolute and relative sizes of the four heart chambers.

Welcome to Biology StackExchange! It is expected that you do some researching on your own prior to posting the question. For example, have you tried the simple method of Googling your question? It gives you the answer right away.

which species are you after?

It's tagged human anatomy.

@Domen, That doesn't tell me because ml/m2 is not a measure of volume.

@David, the values are corrected for the person's height, so that the volumes are divided by $\rm height^2$. See for example Fuchs, A. Normal values of left ventricular mass ... (2016).

@Domen, That requires further explanation, because why per height² and not per height or height³ which would be volume, which I might assume the heart volume scales with.

@David, we cannot discuss this in the comments. Please read the guidelines on How to Ask a Question on StackExchange. Then edit your question accordingly, and someone will be able to write a good answer.

The volume is not the same in all the organisms having four chambered heart. But if you are talking about humans, here are the measurements:
The mean volume of the right atrium (RAMV), right ventricle (RVMV), and left atrium (LAMV) was 22.3 +/- 6.5, 40.3 +/- 6.5 and 28.7 +/- 8.2 ml/m2, respectively.
Source: Measurement of four chambers' volumes and ventricular masses by cardiac CT examination

ml/m² is not a volume. What on earth is meant here?

It is Left Atrial End-Diastolic Volume Index. The unit ml/m² is used to define the size of the atrium with respect to the flow of blood.

ml/m2 is an indexed volume.

From an echocardiographic perspective I direct you to the consensus statements in our field (1). Keep in mind echocardiographic measurements are generally considered less anatomically accurate compared to cardiac MRI or cardiac CT. Since you have asked for absolute and relative sizes I have mainly just included measurement indexed to BSA from which you can determine the absolute depending on the persons height and weight:
Page 7. Normal LV EDV (2-SD range):
62-150mL (Male), 46-106mL (Female)
P.39.e8 Normal ranges and severity partition cutoffs

Page 10. Normal LA volume range (indexed to BSA):
16-34mL/m2 (Male), 16-34mL/m2 (Female)
Page 20. Normal RV EDV range (indexed to BSA):
35-87mL/m2 (Male), 32-74mL/m2 (Female)
Page 30. RA volume (indexed to BSA):
25±7mL/m2 (Male), 21±6mL/m2 (Female)
References:

Lang et al. 2015 "Recommendations for Cardiac Chamber Quantification in Adults: An Update from the American Society of Echocardiography and the European Association of Cardiovascular imaging" Journal of the American Society of Echocardiography.


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What keeps a muscle fiber in tension?
Someone in massage therapy told me that muscles require some chemical reaction to relax, and that magnesium helps with that.
Looking into it, every source online I've found states that muscles relax on their own.  On one hand, this makes sense because flexing requires energy and our arms would fall to our sides without it.  On the other hand, it doesn't make sense because sometimes muscles hold "tension" (knots) even when they aren't flexed.
I've also read that muscles use ATP only to move, but then have a chemical bond to hold in place (kind of like a ratchet system).  At the same time, running out of ATP will lead to relaxation.  This would indicate ATP is required to keep a muscle contracted.
Conversely, I've read that magnesium helps with blocking calcium, a part of muscle contraction.  This would indicate that calcium is part of some sort of chemical bond.  Chemical bonds tend not to not consume energy to remain bonded.
Other sources state that "muscle tension" is less about the fibers and more about other things (fascia).  That may be the answer to what a "knot" is.
Overall, I'm very confused about what keeps a muscle contracted, and what relaxes it.
If a muscle fiber was contracted in a vacuum, would it stay like that?  Is it chemically bonded in that state?  Or is it somehow held in place by the expenditure of ATP?  Why would the absence of ATP lead to fiber relaxation?

EDIT: thanks to @BryanKrause, the "physiology" section on Rigor Mortis contains details which seem to imply the existence of permanent chemical bonds that require a reaction to release (https://en.wikipedia.org/wiki/Rigor_mortis)

I think there's a good question in here, but I also think it's built on an assumption that a "muscle knot" is a thing that exists and is caused by a muscle that is somehow semi-permanently contracted. Can you cite any reliable source that this is the case? Otherwise, the rest of the question doesn't make much sense, despite all the background reading you've done.

Contrast with: https://en.wikipedia.org/wiki/Hypertonia https://en.wikipedia.org/wiki/Cramp https://en.wikipedia.org/wiki/Tetany https://en.wikipedia.org/wiki/Spasm

Some more relevant information: rigor mortis

@BryanKrause, the only part of this post that is actually a question is in bold; the rest exists to show a bit of the reasoning and information I working from.  Is there anything wrong with the bolded part of the question?

@Darlingtonia.  Amazing!  This does indicate that there is a semi-permanent bond when muscles are contracted that requires "replacing ADP with ATP" or  "breakdown of muscle tissue by enzymes [in death]" to relax.

Possible duplicate: https://biology.stackexchange.com/q/110761/16866


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PCR primer design for specific region
I want to amplify a specific region of my genome. I want the segment to be as precise as possible but the primers that would align to the start and end of the target fragment are not optimal in terms of qualities checked for primer design (GC content, melting temperature, etc).
Is there a way to amplify a specific segment of the genome as precisely as I want in this instance? Are there some tricks that one can use when primer pairs are not optimal?
Thank you!

Can you share the first 50 bases of the start and last 50 bases of the end? I find it hard to believe there is no primer length available you can use.

have you looked into primer design tools like primer3?


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Resazurin not turning pink
I want to add resazurin to my media as an anaerobic indicator.
To my understanding, the resazurin is blue when first added to the media, then turns pink after autoclaving, and finally it turns colorless when adding a reducing solution (sulfide in my case). However, I’m having trouble to make the media change from blue to pink. I’ve autoclaved and it’s still blue. My media contains KCl, NH4Cl, KH2PO4, Na2SO4, NaHCO3. I'll add sulfide and other metals after autoclaving.
Should I flush my media before autoclaving? what controls that first reduction step? Heat alone seems not enough to reduce the resazurin. Should I add another reductant in addition to sulfide?
I’d appreciate your comments and insights on this.
Thank you!


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Induced mutation for fruit
If we induce a plant to be polyploidy would that affect other parts of the plant, for example when the plant produces a pollen grain would it still be (n) or would it be different?

When and how are you inducing polyploidy? Keep in mind that some plants already are polyploid.


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Have elephants (or any species other than humans) been known to cover their dead?
I was just reading this blog on HarperCollins website about 5 animals that grieve. Of elephants, the following claim is made:

They bury their dead and pay tribute to the bodies and to the bones. [my emphasis]

Now, I don't doubt that elephants "pay tribute to the bodies", which I take as mourning, as THIS VIDEO (WARNING: if you are an animal-lover, these two videos may be disturbing to you and THIS VIDEO appear to show some sort of concern over the dead. I am aware of the complex emotional lives of many animals, such as cows experiencing PTSD-like symptoms from wolf attacks, or any number of animals that experience PTSD-esque symptoms. Or, how a mother orca carried around her dead calf for 17 days, and I could go on for awhile here.
My point is that I am not doubting that elephants experience a complex inner-world. What I am questioning is elephants' (or ANY creature's) propensity to cover their dead. I find the suggestion that they "bury" their dead, as doubtful almost to the point of disregarding it entirely (for an elephant to dig a grave large enough for another elephant, or to dig up enough material to cover another elephant to effectively "bury" it would be a tremendous amount of work and truly astounding, indeed). However, it would not be too terribly surprising to find them covering their dead. The question would be, to what extent? For example, is it a single branch or a single scooping of dirt with the trunk by a single member of the herd, or is it a concerted effort by the group to cover the deceased with a good amount of material?
The only place I can find with an apparent expert mentioning this behavior is in a Daily Mail article from 2013. It is a passing mention of the behavior:

According to Charlie Mayhew, of the Tusk Trust, elephants will ‘bury’ their dead, covering carcasses with branches and even taking the tusks to be placed at a different spot.

I can find no other mentions of this behavior, outside similar briefly passing mentions in places such as Quora or Facebook.
So, the PRIMARY question is do any animals bury their dead? The reason I have focused primarily on elephants here is because they are the only species mentioned by my Google searches that exhibit this behavior. SECONDARILY, I would like to know what form these "burials" take; i.e., like I mentioned earlier, how much covering of the deceased is performed, and by how many individuals. ULTIMATELY, someone will find a YouTube video or (even more preferentially, multiple) videos showing the act. Thanks for any help you can give.

Elephants are very intelligent and they do so.

Yes.
I was able to find a book1 (see p. 237-239) and a paper2 (I couldn't access this one) suggesting elephants bury their dead and other animals in African elephants (Loxodonta africana). I also found references to a paper/article in the American Psycologist3 that apparently catalogued some reports of these event in the 1980's (see reference 22 in Pinel et al. referenced below, this ref may be the same as ref 2.).
I believe the elephant burying behaviours are simply covering the animal with dirt or other items (leaves etc). How extensively they get covered, I don't know.
However, there are apparently two mammalian species (besides humans) that physically bury their dead. These are the rat4 (Rattus norvegicus) and the mole rat (see pay-walled NY Times link in 5, if you can access either of them) (Heterocephalus glauber). It seems that both species bury their dead in response to release of chemicals related to decomposition.
In the case of the common rat, dead rats of the same species are buried only between 5 and 40 hours post-mortem. In naked mole rats, it seems that the dead are dragged to the latrine/toilet area, which is then subsequently filled in and a new one dug.
Refs:

Douglas-Hamilton, I., Douglas-Hamilton, O. (1977). Among the Elephants. United Kingdom: Collins. (read for free at Archive.org)

Siegel, R. K. (1977). Religious behavior in animals and man: Drug-induced effects. Journal of Drug Issues, 7(3), 219–236. https://doi.org/10.1177/002204267700700302

Siegel RK. The psychology of life after death. Am Psychol. 1980 Oct;35(10):911-31. doi: 10.1037//0003-066x.35.10.911. PMID: 7436117.

Pinel JP, Gorzalka BB, Ladak F. Cadaverine and putrescine initiate the burial of dead conspecifics by rats. Physiol Behav. 1981 Nov;27(5):819-24. doi: 10.1016/0031-9384(81)90048-2. PMID: 7323189.
Format:

Piel, A., & Stewart, F. (2015). Non-Human Animal Responses towards the Dead and Death: A Comparative Approach to Understanding the Evolution of Human Mortuary Practices. In C. Renfrew, M. Boyd, & I. Morley (Eds.), Death Rituals, Social Order and the Archaeology of Immortality in the Ancient World: 'Death Shall Have No Dominion' (pp. 15-26). Cambridge: Cambridge University Press. doi:10.1017/CBO9781316014509.003 (you can see this chapter through google books - do a title search)

note the mole rats likely evolved the behavior for the same reason ants bury their dead.

Those pages are missing from the first source on Archive. Are you somehow able to see them, or did you read that from a book you actually have?

Also, where did you read that about the naked mole rats dragging their dead to their latrine? I could not find that on the page you listed, or under the "Behavior" tab on that website. It would be interesting considering it says that they get their sent from their latrines, so maybe they stop using a latrine once they dump one in?

@JimmyG. Here;s the quote from ref 5 on naked mole rats: Mole rats (Heterocephalus glaber) show a comparable behaviour, quickly detecting a corpse in their den, before dragging, kicking, or carrying it to the communal latrine. ‘When the latrine is filled they seal it off with an earthen plug, presumably for hygienic reasons, and dig a new one.’1 What the 1 is, I have been unable to determine, can't see any footnotes, doesn't fit ref style in article; may refer to table 2.1 in article but also doesn't fit other table refs.

@JimmyG. I see page 237 in the book linked; I read it on Archive. The linked book does have some problems with the colour plates and the scroll bar, but gets past that once you are past the plates. Exact page link: here

@JimmyG. sorry for the mixed comments - Presumably the mole rats make a new one, as it seems they seal off the old one. My local library has allowed me access to the NY Times article, so quote: For some animals, the death of a conspecific is a little tinkle of the dinner bell. A lion will approach another lion's corpse, give it a sniff and a lick, and if the corpse is fresh enough, will start to eat it....

@JimmyG. ...For others, a corpse is considered dangerous and must be properly disposed of. Among naked mole rats, for example, which are elaborately social mammals that spend their entire lives in a system of underground tunnels, a corpse is detected quickly and then dragged, kicked or carried to the communal latrine. And when the latrine is filled, said Paul Sherman of Cornell University, "they seal it off with an earthen plug, presumably for hygienic reasons, and dig a new one."

The quoted (Professor) Paul Sherman is at Cornell and does work on behaviours of animals, including naked mole rats; so entirely plausible that he would know. You can look at his Cornell page here and look through some of his books/articles.


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Sequence homology of cytokeratins
I am reading https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7962860/ and do not understand what it means by high sequence homology of cytokeratins in the following text:
"Sequence homology of cytokeratins is very high, but when the proteins are digested into peptides by trypsin they generate many unique peptides. In the amyloid deposits the cytokeratin peptides identified were mostly unique to one protein"
What does high sequence homology of cytokeratins imply about the amyloids?
What is the relationship between the sequence homology of cytokeratins and whether the generated peptides were identified to be mostly unique to one protein or multiple proteins?
Is it harder to remove amyloids that have high sequence homology of cytokeratins?

Going through the quote:

Sequence homology of cytokeratins is very high,

There are many human cytokeratin genes and corresponding proteins, and they have very similar sequences of amino acids.

but when the proteins are digested into peptides by trypsin they generate many unique peptides.

The serine protease trypsin breaks the varieties of cytokeratins into many different polypeptide pieces.  The fact that there are many resulting peptides could be due to the fact that the variety of original cytokeratins in fact have distinguishable differences near the cutting points that trypsin  operates on, despite all the cytokeratins being from a protein family with high residue sequence homology.  (Some of the unique peptides could also be due to there being multiple places in the consensus amino acid sequence of the cytokeratin family at which trypsin cuts the proteins, but the paper does not delve into that detail.)

In the amyloid deposits the cytokeratin peptides identified were mostly unique to one protein.

Given that there are many possible unique peptides resulting from trypsin digestion, it seems somewhat surprising that most of the peptides that show up in the amyloid deposits happened to come from an identifiable single type of cytokeratin.  They are hinting that this particular cytokeratin likely has an important relationship to the process involved in causing the disease (and hence perhaps should be studied more closely than galectin-7, which has previously been thought to be involved).


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ID Large brown/grey spider with light stripe along back

Giant spider on my door. Walked up to the door this morning and saw this beautiful lady waiting for me. I moved her to a tree so she can rest.

Can you please add the location?

Looks like a wolf spider.

(though I can't see the eyes to definitively rule out a fishing spider; though, fishing spiders don't as often have a bright streak long their backs -- a characteristic your specimen shares more with wolf spiders).

Wolf spiders tend to be relatively large/robust, with strong bodies and legs. They are often brown or grey and can display striping on their legs.
Your image is not great and you lack sufficient detail (size, location,etc.) for a more certain ID. However, two examples of wolf spiders in the genus Tigrosa have similar characteristics to your image:
Tigrosa grandis:

 Source: bugguide.net; Credit: Andrew Williams (2009)
Tigrosa helluo:

 Source: bugguide.net; Credit: Ashley Bradford (2007)
If you provide more detail, I could try to update my post accordingly.


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Was there a flu season in paleolithic times?
In temperate climates, flu viruses rise and recede with winter. This is for a number of reasons, including lack of vitamin D production in darkness (which weakens the immune system), dry air (humidity causes viral particles to become trapped in water droplets and fall), and people huddling together inside when it's cold (increasing the likelihood of spread).
So, was there a flu season in prehistoric times, specifically the paleolithic (i.e. before 10,000 BCE)? The first two causes would still apply for prehistory, but the last one might not, since people didn't have houses to live inside back then.
Also, in modern times, flu strains are reintroduced to the northern hemisphere at the start of flu season by travel from the southern hemisphere, but that did not occur in prehistory, which might have stunted the spread of the flu. Another factor is the low population density of prehistory, which may have prevented the formation of viral reservoirs in human populations. There may also have been significant variance by region, considering this is still a factor today. For example, the flu follows a more complex and less predictable seasonal pattern in tropical climates versus temperate.

Edited, focused version of an old closed question that went unanswered.

Looks pretty much the same to me. What did you change? How do you know that migration from the Southern hemisphere didn't occur? Humans have been building shelters (wood houses even) for hundreds of thousands of years. So many suppositions stated as "facts".

I removed mentions of cold viruses (which are several hundred viruses, many distantly related) to focus on the flu, and limited the timeframe to the Paleolithic (which is more narrowly defined than prehistory). There was obviously no transcontinental air travel in prehistory, preventing flu viruses from spreading between hemispheres the way they do today. Houses were much less common before the Neolithic, when humans began farming.

The first transcontinental flight (non-stop) was in 1923, 5 years after the terrible Spanish flu of 1918, which went around the globe twice, almost 30 years before transcontinental flight actually started with three airlines flying (only the North Atlantic, btw.) Houses were far from uncommon; the ancient Pueblo people on North America had multistory-dwelling villages before 10,000 BCE. I think you might be making a lot of unfounded assumptions. People huddled in tents a million years ago. A cough in a tent is pretty significant.

This question is about flu season, not the Spanish flu. Even if there was not transcontinental flight in 1918, there was rapid long-distance travel by ship and rail which obviously was not occurring in prehistory. This would certainly have an effect on the circulation of flu strains. The Pueblo people absolutely were not making multistory-dwelling villages before 10,000 BCE; they did not even exist as a culture back then.

The flu (HnNn Type A variants) is the flu; it spread before air travel; that was my point. The Spanish flu was only a particularly virulent-for-the-young variant. You're mistaken about the ancestral pueblos, and the city of Jericho was a city before 9000 BCE (some scholar date it to pre-agriculture.) Why don't you add some evidence of research to support your claims? You're more likely to get an answer that way.

I'll wait until others add cited evidence of research to support their claims. I added reference links in the previous discussion, but no one else (including you) bothered to, which made it seem pointless. Where is your source that the Pueblo people had multistory-dwelling villages before 10,000 BCE? That is a remarkable incorrect claim.

Overall, to me, this question doesn't appear on-topic for this site. This question seems like it might fit on [history.se], as the question is primarily about history, as opposed to a theoretical discussion of transmission and virulence under specified, or assumed, conditions. However, I'm not familiar with the History site, so I strongly recommend reading that site's on-topic page to verify that this would be on-topic. I'm also not a significant participant on this site, so my judgement that this is off-topic here may be wrong.

Flu, as we understand it, is zoonotic, which means it's from animals. In this case, pigs and chickens. I think it's well understood that the flu we know and understand today didn't exist until sometime after humans started farming pigs and chickens. That doesn't mean there weren't illnesses like the flu, just probably not the flu we have today.

@frеdsbend - Human influenza most likely was passed to us by birds, including migratory water fowl. Here's an article for laypersons.

@anongoodnurse I still wonder about the importance of 1) domesticated animals (chickens, pigs, etc.) in transferring the virus from infected wild birds to humans vs 2) humans hunting and touching infected wild birds vs 3) those darn infected wild birds not wearing their masks and coughing on us in closed spaces and giving it to us directly.

@anon Pandemic flu, maybe, which is the topic of that essay, but they rightly say that's not at all a given. It certainly isn't true for H1N1, literally called swine flu because it came from pigs. Seasonal flu circulates among humans, and feeds back into animals sometimes creating pandemics in them. For example, 1918 flu created a pandemic in pigs at the same time, though which species had it first is not known. As uhoh's comment above hints, it's foolish to dismiss the likely impact pig and chicken farming has had on shaping modern seasonal influenza.

@frеdsbend H1N1 was around before the name "swine flu", which AFAIK was coined for the 2009 H1N1 outbreak in USA/Mexico (before this it was known as as swine-origin). The 1918 + 1977 influenza pandemics were H1N1. Some variants of it are endemic in humans and some in birds too. Swine are not the only sources of this influenza strain. Phylogenetics tells us avians are the source of all influenzas (though C/D??); and you can easily isolate virions from water where birds concentrate, so not to dismiss agriculture, but catching it from the wild is certainly possible.

@frеdsbend - I read a fair number of scientific papers on the origin(s?) of human influenza virus(es). The phylogenetics bob1 mentions is the study of the genetic material of the viruses in order to determine the lineage of viruses, i.e. the where and when of a virus. Human influenza virus is an extremely old virus genetically, is most closely related to the influenza viruses affecting the Class Aves, predating pig and chicken farming, predating agriculture, predating any written history. The confidence you have in your (erroneous) opinion is unearned.

@uhoh - your comment is funny and thoughtfully put. The evolution (happening now) of influenza viruses is very heavily studied because of the worldwide morbidity and mortality of the virus, and because of the terrible consequences of a novel avian-to-human mutation that has a high degree of infectivity (the nightmare scenario: a deadly pandemic like that of 1918). While I have no doubt our close contact with birds has resulted in the deaths of some, it has not (to my knowledge) contributed to any serious epidemics. Bat influenza is also a threat, just fyi.


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What kind of insect is this? It looks like a huge spider with one long antenna and six legs

It looks like a huge spider but with six legs and has one very long antenna. It also looks like it has claws. Please I would like to know what sort of insect it is. So I would know measures to take if it is dangerous.
Details:
This picture was taken in Nigeria at night. It's raining season here too.

Similar critter: https://biology.stackexchange.com/questions/93794/what-insect-is-this-looks-like-a-spider-but-with-six-legs-and-long-antennae

While not completely sure, it definitely looks like an Arachnid. Upon further research, I have narrowed it down to either Amblypygi (i.e., whips spiders, tailless whip scorpions), or Solifugae (i.e., camel spiders, wind scorpions, sun spiders). Using whatever perceptional abilities I have, I have made the educated guess that the appearance of the arthropod you posted most closely resembles that of Amblypygi.
The "antenna" is part of the anterior legs (first pair), and not an actual antenna. The other leg of the pair is missing. The appendages in the front that are long and folded are not legs, but pedipalps.

this is a whip scorpion, family Phrynichidae

@JimN So, are we in agreement on what this is? The family of Phrynichidae are in the order of Amblypygi. But, Phrynichidae are not "whip scorpions", unless you meant "tailless whip scorpions" (whip spiders). Whip scorpions are in the order of Uropygi.

I'm sorry, I did mean 'whip spider' ! Let's put the common names aside. I agree with order Amblypygi, Family Phrynichidae. This paper mentions two species of the Damon genus in Nigeria: D. johnstonii and D. medius, and many other species in neighbouring countries, but other genera exist as well

Hm, my previous comment didn't include the paper URL? : https://www.sciencedirect.com/science/article/pii/S1439609205000425


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Is it possible for two fraternal twins to be completely different at the genetic level?
Given that the 46 chromosomes split evenly during meiosis, if the even pairs of the male gametes match with an even pair of the female gametes, the offsprings in theory should be carrying chromosomes the other does not posses, and thus in theory share no genetic material, despite coming from the same parents. This follows the assumption that each chromosome is unique and share no genetic materials with the other chromosomes.

Chromosomal abnormalities aside, every human offspring has 23 chromosomes from mom and 23 from dad.
If chromosomes were inherited as whole units (they are not), the odds of one sibling, fraternal twin or not, having exactly the opposite set of chromosomes would be 0.5^46 = 1.4x10^-14, or about 1 in 70 trillion. That is, the odds of selecting the other chromosome 1 from dad is 0.5, same for chromosome 2, etc, and the same for each chromosome from mom.
Because of crossing over, the odds are even lower.
"Possible" is not very meaningful at these probabilities.

The other answer correctly notes the probability is vanishingly small, equivalent to successfully calling a coin flip many times in a row. I'll also note that due to pedigree collapse, even two "unrelated" members of a population share some ancestor if you go back far enough - both your mother and father carry some small amount of identical DNA inherited from the same individual. For this bit of DNA, it doesn't matter if the offspring inherits from the father or the mother, they're inheriting the exact same DNA which can be traced back to the same ancestor. Fraternal twins can't differ at these otherwise normally variable loci, as the mother and the father don't have distinct DNA to give.


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Can drugs be administered through penis?
I was reading this paper on routes of drug administration and noticed that it mentioned intravaginal drug administration. It looks like this is a good way to take drugs because there are a lot of blood vessels which means you absorb a lot of the drug and you bypass the first-pass metabolism effect which catabolizes a lot of the drug before it gets to your liver.
I noticed there’s no mention of penile drug administration. Would there be any advantage of taking drugs this way, either by insufflation into the urethra or by injection into the penis? I googled it and it sounds like there are no drugs that are administered this way except for penile injections - similar to Botox, but for your penis, and not used for absorption purposes.

The urethral mucosa is very sensitive (in both males and females) and it would undoubtedly cause significant discomfort - or more - to place and leave medications in it. I can't think of any advantage the urethra would offer when the rectum, which is much less sensitive, is a possibility and a known site (often used for seizures in infants). The paper you linked to is a good one; there are many routes of drug administration available without causing undue pain. Fyi, the first pass effect is metabolism by the liver before the drug reaches arterial circulation.

Just use suppositories.

there's documented case of weirdos administering recreational drugs in every way possible including the penis, so there are surely documented cases of lsd, opiods, and other drugs going that way.


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Please help strang micro warm like thing found in dogs kennel in Conyers Georgia
I found this strange tiny warm under my five months old puppy's cage can someone please help find out what it is their was about thirty of them her cage is cleaned regularly and is dry and cozy I've checked her poop nothing in it but she is constantly scratching and losing hair rapidly no flea's on her

Welcome to the site - we would need to know where in the world you are, and preferably get some better pictures and a sense of how big these "worms" are. Could the scratching be caused by shedding (spring/summer coming in the Northern hemisphere...)? Do you groom the puppy and get these off her, or were they only found on her bedding?

If you're concerned about the health of your puppy, please take them to a veterinarian.


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What actually causes temporal isolation
Temporal isolation is caused when members of the same species are available to reproduce at the same time. How is such a phenomenon even possible, is it caused by mutations which lead to a certain percent of the population to reproduce at Time A and the other at Time B?

As the question is written, it could be answered on several levels, and may benefit from clarification. Are you looking for how general reproductive isolation can arise? You ask how the phenomenon is possible, so are you looking for examples of temporal isolation? You mention mutations, so is your question specifically about the genetics of temporal isolation? Remember that temporal isolation is likely found in an extremely diverse set of organisms, so it will not be caused by just one gene or one mechanism.


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How random is genetic recombination?
Two parents can have a very large number of different potential offsprings, and it's common knowledge that the daughter chromosomes in meiosis are produced randomly, i.e. in crossover, the exact spots where the parent chromosomes are "cut" and genes are exchanged are random, with a larger probability at recombination hotspots.
I can't understand how the crossover process can just be completely random, what is exactly different in each trial that leads to different outcomes? Is there something at the molecular level that actually determines the outcome (e.g. the exact positioning and the orientation of the chromosomes or other cells/molecules involved in the process)?

Overall, the crossover locations within a chromosome can be seen as random. More specifically, hot-spots depend on population (Fig 1) and sex (Fig S2) (in human) and can be predicted [1].


text:
is there periost beneath the articular cartilage?
I have read that : "The articular capsule surrounds the joint and is continuous with the periosteum of articulating bones." Does that mean that the periost forms the articular capsule in joints and there is no periost beneath the articular cartilage? Or is there additional periost beneath the articular cartilage?
Thanks a lot!


text:
What are the data behind the claims of high predictive power of biomarker tests for sleep deprivation?
Today's (6th May) Guardian is reporting that blood tests for tiredness have achieved high predictive power:

Prof Clare Anderson, at Monash University, in Melbourne, Australia, who is leading efforts to develop a blood-based test, said: “When you look at the major killers on the road, alcohol is one of them, speeding is another, and fatigue is one of them. But even though the solution to fatigue is quite simple, which is to get more sleep, our capacity to manage it is impaired because we don’t have tools to be able to monitor it like we do with alcohol.”
Anderson’s team has identified five biomarkers in blood that can detect whether somebody has been awake for 24 hours or more with greater than 99% accuracy.
Follow-up studies conducted in conditions closer to real-world situations have also indicated that these biomarkers can detect whether or not someone has slept. “We still get close to 90% accuracy at being able to detect sleep loss, which is pretty high considering all the things that are going on in people’s lives beyond just sleep,” Anderson said.

What is the data behind these statements?
Previous Reading:
Pubmed search "Clare Anderson[Author] biomarker" gives two papers, one assessing a classifier to detect lack of sleep but using blue light and skin temperature and nowhere near the reported predictive power.
The second appears to be a preliminary study for this work: Circadian and wake-dependent changes in human plasma polar metabolites during prolonged wakefulness: A preliminary analysis but does not seem to support such predictive power, from the abstract:

We observed metabolites that were significant at the group-level but not significant in a single individual, and metabolites that were significant in approximately half of individuals but not group-significant.
Owing to large inter-individual variation in rhythm timing and the magnitude and direction of linear change, acrophase and slope estimates also differed between group- and individual-level analyses.

Google Scholar gives 34 papers that cite this.  Of these one appears relevant, but has very different numbers:
Developing preliminary blood metabolomics-based biomarkers of insufficient sleep in humans
This uses 65 biomarkers to identify those with insufficient sleep, but reported far lower predictive power that is well below what would be required for law enforcement and is very far from "close to real-world situations":

The top-performing biomarker model was developed by linear SVM modeling, consisted of 65 compounds, and discriminated insufficient versus adequate sleep with 74% overall accuracy and a Matthew’s Correlation Coefficient of 0.39. The compounds in the top-performing biomarker model were associated with ATP Binding Cassette Transporters in Lipid Homeostasis, Phospholipid Metabolic Process, Plasma Lipoprotein Remodeling, and sphingolipid metabolism.

Other papers that seemed relevant, with particular emphasis on work authored by Prof Clare Anderson, do not obviously have the data.  I include a summary of the ones I looked at, for completeness but if anything they seem to support the difficulty for getting the sort of predictive power that would be necessary to reach the legal threshold of beyond reasonable doubt:
Using a Single Daytime Performance Test to Identify Most Individuals at High-Risk for Performance Impairment during Extended Wake
Identifying individuals particularly susceptible to sleep deprivation.  The existence of such people would seem to be a challenge for any such biomarker based test.

Laboratory-based studies have demonstrated significant inter-individual variability in the response to sleep loss due to extended wake, such that some individuals are able to maintain high levels of neurobehavioral performance on tasks of sustained attention, even when they subjectively report sleepiness whereas other individuals appear to be particularly vulnerable to sleep loss.

Circadian lipid and hepatic protein rhythms shift with a phase response curve different than melatonin
This does show five biomarkers used to measure sleep, but does not describe their use for prediction.  It does show a graph of how they vary over time, and the variation does not look conducive to such accurate predictions, though I know modern classifiers can spot things the human eye cannot.
Individual metabolomic signatures of circadian misalignment during simulated night shifts in humans
Looks at biomarkers during sleep disruption, but does not seem to support the quote predictive power:

On the individual level, the response to the night shift protocol was highly diverse, with phase shifts of rhythmic metabolite profiles ranging from a 0.2-h advance in one subject to a 12-h delay in another subject, revealing an individual metabolomic signature of circadian misalignment.

Endogenous circadian regulation and phase resetting of clinical metabolic biomarkers
Looks at biomarkers during sleep disruption, does not look at predictive power.
Diferential Impact of Sleep Deprivation and Circadian Timing on Refexive Versus Inhibitory Control of Attention
Analysis of ocular motor tasks throughout 40 hours of sleep deprivation.

Maybe contact the Guardian and ask them to change their terrible citation policy.


text:
Relationship between an Integrin-binding peptide and the Collagen type that it models
Recently, I have been investigating whether collagen can interact with integrin α2 (the product of human gene ITGA2). There is a structure in the protein data bank (PDB ID: 4BJ3) in which an integrin domain is bound to what appears to be a peptide fragment of human collagen type XXVI (gene COL26A1). However, the sequence of this peptide differs from that in UniProt (Q96A83) for this collagen, which raises the questions:

Why are the sequences in the PDB file different from the sequences in UniProt?
Even though there are differences between the sequences, can I still assume that chain C/D/E in 4BJ3 represents the protein translated from COL26A1 and that COL26A1 can interact with integrin α2?

The PDB structure contains 4-hydroxyproline, a post-translational modification of proline commonly found in collagen. This is not a standard amino acid and doesn’t have a one letter code, which is why it is designated as “X” in your alignment. In the PDB file it’s called HYP. In the paper reporting the structure, it’s designated “O”. Note that it aligns with proline in the UniProt entry.

I have edited the title to make it a little shorter and more focussed on the biology. I have revised my answer after having done some work on the problem. The timeline shows how the synthetic peptide evolved from work with larger collagen fragments. In fact the methodology of studying binding was affinity purification, but I cannot locate the paper that mentioned this — too many already.

Summary
The entry for 4BJ3 on the web pages of RCS Protein Data Bank contains information regarding a “collagen-like, GFOGER peptide” (authors’ words) that is at the best misleading and at the worst incorrect. This peptide is totally artificial, designed to have the integrin binding motif, GFOGER, flanked by model collagen GPP repeats so that it adopts a triple helical structure. The web page editors (I presume) have presented it as a mutated form of the α1 chain of collagen type XXVI, presumably because it scored highest in a sequence alignment. However the alignment is clearly on the basis of the GPP repeats, and this collagen has two mismatches in the key integrin GFOGER motif, specifically in the functionally important F and E residues. It is clear from the literature that the peptide was designed to study the interaction occurring in the integrin-binding collagens type I, II and IV — indeed collagen type XXVI was unknown at the time of design.
Collagen type XXVI completely lacks the GFOGER motif or any similar motif that has been shown to bind integrins. Although the possibility cannot be excluded without experimental evidence, the assumption would be that collagen type XXVI does not bind integrin α2.
The GFOGER peptide is not derived from collagen type XXVI
The PDB structure 4BJ3 is described in a file that can be downloaded from the RCS Protein Data Bank, and in the associated publication. According to these sources it consists of domain I of integrin α2 (residues 171–368) in a complex with a triple-helical “collagen-like, GFOGER peptide” of  sequence [GPO]2GFOGER[GPO]3, where O represents hydroxyproline.
The web page for this structure at the RCS Protein Data Bank allows one to view the protein, and contains additional information, prepared by the site curators and web editors. This includes a “Protein Feature View” in which the GFOGER peptide is aligned to Uniprot entry Q96A83, the conceptual translation of the α1 chain of collagen type XXVI:
This is the section that the poster appears to have found, and from which he has produced an alignment that includes X, which is actually the hydroproline in the synthetic peptide. Here this is replaced by P.

I have annotated the alignment to emphasize the GFOGER region and the differences (broken circles). Of the three mismatches, two are in the crucial GFOGER region which is the basis of the interaction between collagen and integrin, and both (‘F’ and ‘E’) are at critical positions.
It is clear that the choice of alignment with collagen type XXVI is not based on anything originating from the authors and makes no biological sense. How did it arise?
I have conducted Blast searches with the sequence of the synthetic peptide and found no exact hit. The highest scoring hit is with type XXVI, even though an intelligent scoring system would have demanded perfect alignment with the GFOGER motif. I assume that a person with an informatics background, but unfamiliar with the biology, accepted this.
It is misleading and wrong!
What is the GFOGER peptide derived from?
To answer this question I tracked back through the literature, following the references in the Introduction or Methods sections, starting from the 2013 paper and ending in 1986. To summarize:

1986: Collagens Type I, II and IV bind to a platelet membrane adhesion protein (Cell 46, 913-920) — Subsequently this was designated VLA-2 and later integrin α2β1.
1994: Artificial collagen-like peptide crystalized, confirming the triple-helix that had been proposed in the 1950s (Science 266, 75–81).
1994: Domain I of integrin α2β1 shown to contain binding site(s) for collagen.
1997: Domain I of integrin α2β1 crystalized (J.Biol.Chem.  272, 28512–28517). Molecular modelling suggested that a glutamic acid side chain (E) from collagen could coordinate to the integrin through a metal ion'
2000: Crystal structure of a complex between domain I of integrin α2β1 and the “GFOGER peptide” (Cell, 101, 47–56). The rationale for the synthesis of this peptide is clearly stated: “…We therefore designed the shortest peptide that would fold into a stable triple helix and that had the glutamate at its center. We synthesized a 21-residue peptide with the sequence [Ac-(GPO)2GFOGER(GPO)3-NH2]
and showed that it folds into a triple helix…”

There are further papers that could be cited, but this makes the provenance of the peptide clear, as also its relationship to collagens I, II and IV. The date of 2000 for the description of this peptide is also significant given the fact that collagen XXVI was not reported until 2002 (J.Biol.Chem. 277, 37678–37684).
Nevertheless could collagen XXVI still bind integrins?
I know of no direct experiments on this topic. What I have done is to perform Blast searches with those hexapeptides that have been shown to interact with integrin, with or without activation of the later. The results were:

Peptide
Integrin

GFOGER
Type I     (α1

GFOGER
Type II (α1)

GFOGER
Type IV (α3,α4,α5)

GFOGER
Type VII (α1)

GFOGER
Type XI  (α1, α2)

GLOGER
Type I (α1,α2)

GLOGER
Type II (α1)

GLOGER
Type VII (α1)

GASGER
Type I     (α1)

GASGER
Type XXIII (α1)

GMOGER
Type I (α1)

GMOGER
Type II (α1)

GMOGER
Type III (α1)

GMOGER
Type IV (α6)

GMOGER
Type V (α2)

GMOGER
Type IX (α3)

GLOGEN
Type III (α1)

GLOGEN
Type XXII (α1)

GLOGEA
Type II (α1)

It is evident that collagen type XXVI does not contain any of these motifs. Thus, in answer to the poster’s question:

Although one cannot exclude that it possesses a hitherto unidentified integrin-binding motif, there is currently no justification for assuming that collagen type XXVI will bind integrin.

Advice to anyone using the RCS Protein Data Bank
Read the documentation on the actual structure file, and the paper in which the structure is reported.

Thank you for sharing your informative answer and your advice.
Using genes to refer to proteins is a practice that I learned from some literature 123.This seems likely to impose an extra burden on people unfamiliar with the genetic symbols.
I have revised the question accordingly.

@WanNIE — Using gene names to refer to proteins is convenient (a) where the name of the gene product is not known (b) when tabulating data with space limitations (c) where their is ambiguity in protein nomenclature (although this may also be true of gene names.   Point (b) is probably the major factor in the paper you cite. Otherwise only collagen researchers would know what COL26A1 and COL11A2 are (I would have no idea), and it is bad practice to use these without the names of their products. The authors of the paper make no reference to any gene in their paper.

@WanNIE — Before I amend my answer could you clarify whether you wish to know whether the collagen human collagen type XXVI interacts with integrin, or whether the peptide GPOGPR does?

Sure, I want to know whether the collagen human collagen type XXVI (COL26A1) interacts with integrin and especially with the alpha2 subunit.

By the way, this paper states that the Wnt/Beta-catenin pathway can regulate the expression of genes in extracellular matrix (ECM)-receptor interaction, including COL11A1 (Collagen alpha-1(XI)), COL26A1 (Collagen alpha-1(XXVI)), LAMC3 (Laminin, gamma 3), and ITGA2 (Integrin, alpha 2). Does this implicitly suggest that there is a high possibility of an interaction between COL26A1 and ITGA2?

@WanNIE — No, co-expression says nothing about interaction. I think you are approaching this from the wrong end. You need to go back into the last century and see what studies had been done that relate directly to the interaction of these two proteins: antibody co-precipitation, electron microscopy or whatever. It would only have been on the basis of this sort of evidence that anyone would prepare a library of peptides to find what part of the collagen interact. But it may be that only certain collagens interact, so you need to read about the characteristics of individual types.

I checked ENSEMBL and the reason is not due to known alternative splicing but still allows for the possibility that they investigate a different sequence/allele due to mutations.
Importantly, in the (open source) paper, you can read that ..

GFOGER constitutes a high-affinity motif for all the collagen-binding
integrins reported to date [12]–[14].

Therefore, I would highly doubt that you can assume that COL26A1, if it does not posses that sequence, would be bound equivalently. Also, this quite frankly indicates that you are wrong with your premise, that the PDB shows COL26A1.

I agree, and have given you credit for this. And human collagen type XXVI alpha 1 does not contain this sequence as a sequence comparison or a Blast search with the peptide GFPGER will demonstrate.


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Is there any research on whether a choanozoan might have invaded a similar enough holozoan to make the first metazoan?
My mind was piqued by the idea of endosymbiosis of a bacterium penetrating the cell of an archaean being a precursor to the advent of eukaryotes. And I thought that perhaps something analogous to this sort of thing was also precursor in the advent of metazoa.
For instance, could the first metazoan have been the penetration of an "entrepreneurial" sperm-like choanozoan into the single-celled body of another, genetically similar enough, holozoan? a holozoan, perhaps similar to pluriformea or ichthyosporea? And that choanozoan and other holozoan... those two species found their greatest evolutionary advantage, their quickest ticket to diversification of their descendants, was to work together. To rework their genomes against each other's. And metazoa are actually two holozoan species that intertwined their evolutionary fates with each other's. And their specific genetic distinctivness was sacrificed for the advantages of shuffling their genetic material together. And the success of metazoa is actually the continued reproductive success of those two species. And that subsequent descendant-phyla offload certain functions to one species or the other, resulting in the many diverse levels on the spectrum of sexual dimorphism, that we see throughout non-social species, and also in gender roles as expressed in social animal species. And that conception of a metazoan zygote is the reenactment, eon after eon, of the first joining of those two cells of those two species. The hunting choanozoan swims through an ocean, searching through chemoreception for a cell that has evolved to attract it, enticing it to slam its genetic material into itself. Hunting the waters for something calling to its chemoreceptors. Smelling for a smell familiar enough, a smell that indicates that it is genetically compatible enough, to constitute an invitation. And "maleness" could also actually be thought of as "choanozoa-ness" and "femaleness" could be thought of as the likeness of whatever other holozoan species the first "egg" might have been.
Has anyone heard of any more formal research or speculation into an idea like this?


text:
Why does SNS engage epinephrine/norepinephrine (at the effector organ) while the PNS uses acetylcholine?
Why does SNS engage epinephrine/norepinephrine (at the effector organ) while the PNS uses acetylcholine?
Is there some advantage of E/NE in terms of being faster or more long-lasting vs. AcH that resulted in this utilization?
Thank you!!


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DIfferent Definitions of relative Fitness
I have got a question concerning the definition(s) of relative fitness.
There seem to be two major definitions in the literature:
$$
\text{relative fitness 1} = \frac{\text{absolute fitness of a type}}{\text{average absolute fitness of all types in the given population}}
$$
$$
\text{relative fitness 2} = \frac{\text{absolute fitness of a type}}{\text{maximum absolute fitness in the given population}}
$$
Now, my question is: What difference does the different normalization make with respect to the calculation of long-term evolutionary dynamics in the most simple models?
In particular: While relative fitness 2 can be held constant over generations because it does not depend on the (changing) relative frequencies of the given types, relative fitness 1 depends on the (changing) relative frequencies of the given types and therefore cannot be held constant over generations - is this correct?
I hope one of you can help:)

It would help your question to provide sources/references for the different definitions you've found.


text:
What is the thinking behind the naming of arachidonic acid?
Arachidonic acid, the double bonded fatty acid, is occasionally misrepresented as having to do with spiders (arachnids). The Wikipedia entry explains that it's instead elated to "arachis" = peanut in New Latin. Alas, peanut oil does not contain any of it. Bizarre! What went through the mind of the person who named this lipid and caused all the confusion and mispronunciation by learners? Is there any good reason for the name?

I’m voting to close this question because it is not about a problem in biology, but about the trivial name given to a compound over 100 years ago. It is little more than a rant, disguised as a question, the answer which can not possibly be known "what went through the mind…".

There are finitely many letters and possible combinations of them making words, and many many things to be named. Inevitably, some of the words will be similar or even homonyms. To me, having some really limited and basic knowledge of Latin and (Ancient) Greek, there is no real confusion here. All terms related to spiders have a different stem containing an n, namely arachnophobia arachnologist, Arachnida ...
Regarding the naming, it was suggested in 19131 based on its similarity to arachidic acid, which is indeed a (minor) constituent of peanut oil.

1 Martin, S. A. et al. The discovery and early structural studies of arachidonic acid. J Lipid Res. 2016

Thanks Domen. That's just the paper I was looking for. I'm citing here to document the answer for readers here: "The name, arachidonic, was suggested in 1913 based on its relationship to the well-known arachidic acid (C20:0). It took until 1940 before the positions of the four double bonds were defined at 5,8,11,14 of the 20-carbon chain." Arachidic acid seems to a minor constituent of peanut oil at around 1%.


text:
Does Mitochondrial Eve existence suggest genetic fitness, and what evolutionary developments map to her time period?
I am not sure of the size of the population at the time of Mitochondrial Eve, but I assume it must have been reasonably large.  It seems to me that without bias, each female at that time should have an equal number of descendants. It seems very unlikely that every other bloodline would die out unless Mitochondrial Eve's descendants had an evolutionary advantage.
Is it commonly accepted that Mitochondrial Eve's descendants have an evolutionary advantage?  If so, what advantages is ascribed to her descendants?

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There's an illustration here of the kind of way things might pan out in the absence of selection. One certainly oughtn't to expect every girl born to a given generation to have even a roughly equal no. descendants through the female line thousands of years later.

Please see the following related answers:

What is a Mitochondrial Eve and Y-chromosomal Adam
Does mitochondrial eve have to exist?
Is it tautological that all living humans descended from a single male and single female human ancestor?

Because mitochondrial lineages that provide a selection advantage are more likely to spread in a population, Mitochondrial Eve (ME) is more likely to have belonged to such a lineage. However, there is no real reason to suspect that ME in particular, or her descendants, had any special evolutionary advantage over other humans existing at the same time.
The identification of Mitochondrial Eve—the most recent mitochondrial ancestor of all living humans—changes over time as mitochondrial lineages in a population go extinct. When this happens, the assignment of ME jumps ahead in time to the most recent ancestor of the remaining lineages.
Extinction of a mitochondrial lineage can be entirely random (though selection helps), and is a consequence of reproduction in a finite population. The likelihood of lineage extinction is negatively correlated with it's proportion in the population. In a population without selection, each member wouldn't have an equal number of descendants, they would an equal likelihood of having some number of descendants (e.g., their number of offspring would be drawn from the same distribution). Under this scenario, and with a finite population, eventually all lineages except one will go extinct.*
All we know about any particular ME is that she was female, and had at least two daughters who themselves each had at least one daughter.
This simply follows from the definition of ME.
We have good evidence that the current ME lived about 150,000 years ago, meaning we can also be confident that she was an anatomically modern human.
Other than those facts, the current ME is anonymous, and we know little about the total population of human mitochondria at the time she was alive.
While significant beneficial mitochondrial mutations occurred sometime before ME, and some may have appeared for a subset of existing mitochondria, it's unlikely that ME herself was the origin of any functionally important mutations.
So, beyond the general statements that mutation and selection occur in mitochondria, and that ME was a member of the successful lineage who had some daughters, there's nothing particularly special or unusual about her.

*The lineage that remains is said to be "fixed" in the population; the chance of this is equal to that lineage's starting proportion of the population. Note that other mutations can occur in that lineage during the process of it becoming fixed, so that all offspring are part of that lineage, but don't have identical DNA.


text:
Two-compartment model for depot intramuscular injections
I am trying to learn pharmacokinetics.
Let us consider an intramuscular depot injection of $5 \,\pu{mg}$ ($5\cdot10^9 \,\pu{pg}$) of a drug, whose half-time is 4 days. Let us say that the initial plasma concentration is $C(0) = 50 \,\pu{pg/ml}$. After 3 days a blood test was taken and showed the plasma concentration $C(3) = 170 \,\pu{pg/ml}$.
We consider a two-compartment model in which:

first-order absorption to the central compartment with rate $k_a$

first-order distribution from the central compartment to the peripheral compartment with rate $k_d$

first-order elimination from the central compartment with rate $k_e$

We plot the amount in the serum, by solving the system of differential equations:
$$
\left\{
\begin{array}{l}
\frac{dx_1}{dt} = - k_a x_1 \\
\frac{dx_2}{dt} = k_a x_1 - k_d x_2 - k_e x_2 \\
\frac{dx_3}{dt} = k_e x_2
\end{array}
\right.
$$
Where $x_1$ is the amount in the depot, $x_2$ is the amount in the central compartment, and $x_3$ is the amount in the peripheral compartment.
We find that the amount of the drug in serum reaches, say $0.15 \,\pu{mg}$ ($1.5\cdot10^8 \,\pu{pg}$) on day 3. If we divide that by the amount of serum (e.g. $2.8 \,\pu{l} = 2800 \, \pu{ml}$), we obtain $$C(3) = \frac{1.5\cdot10^8 \,\pu{pg}}{2800 \, \pu{ml}} = 53571 \,\pu{pg/ml}$$ However the real concentration is just $170 \,\pu{pg/ml}$. Where does this all drug amount go? Why is there such a large mismatch?
I feel that I am missing something very basic.

Note: Here is an example of a two-compartment model.

You said you fit the model, right? What are you fitting it to? Can you plot x1, x2, x3 as a function of time?

@BryanKrause Yes, I fit the model using the method of residuals. Since I cannot measure x1 and x3 directly, I used x2 only based on my measurements (blood tests). The curve does fit relatively well. It's just the number on a different scale. This is where I have this problem.

Well, you have all the numbers you need to calculate x1 and x3. Can you plot them all (the predictions, that is)?

I suspect there's either a problem with units, or something weird is happening with your model because you don't have enough information to distinguish between kd and ke.

@BryanKrause Yes, I can plot them. They fit the curve fairly well. Most importantly, the model gives x1 + x2 + x3 = 5mg for t = 0 ... +Infinity. It is possible to distinguish kd and ke due to phasing. I.e. distribution completes before elimination and it's easy to estimate elimination. With absorption faster than distribution and elimination, the model (and reality) gives a hump (peak) after 1-2 days. Like I said, it fits well. Just the scale is very different, which is the question here.

@Julia, it is difficult to comment the outcomes without your data and fitting protocol. I suggest you add data together with fits to the question.

Can you add the plot to your question? It makes absolutely no sense that you say it both fits well and that the concentration on day 3 is different from what you measure. And, based on the differential equations you posted, there is absolutely no separability of those parameters if you only have x2 measurements, so either you're using different differential equations or making other assumptions not mentioned in this post.

@Domen Here's the fitting protocol. https://www.pharmacy180.com/article/two-compartment-open-model--extravascular-administration---first-order-absorption-2527/ I need to figure out how to add an image here.

@Julia, no need for images, post your data, for example upload it to pastebin.

@BryanKrause I'd love to have these experimental data (x1 and x3) and I agree, it makes perfect sense to have them to accurately validate the model, but really, there is no way to accurately measure the amount of a drug in a depot or tissues. If you saw any studies on how to that on a human body, please let me know.

@Domen What specifically are you looking for? 1) The experimental measurements of x2 2) ka, kd, ke 3) calculated curves for x1, x2, x3? I just want to make sure I do the right thing.

I know, I'm not suggesting you collect those data from x1 and x3, just pointing out that the model you present has no way to distinguish them. Kd + Ke is constrained, but not Kd and Ke separately. But yes, those three things: data, fitted K values, and plotted curves will help us figure out where the problem lies.

I think I found my problems. The experimental data I have are starting at the point in time when drug distribution is supposed to be complete (i.e. the beginning of the steady state). That is, at that time all the drug amount is supposed to be distributed to tissues (peripheral compartment). This is the 1st problem. The second problem is using the amounts in the system of equations, not the concentrations. The system of equations should use concentrations.