text:
Aging from inception until forming of reproductive elements
Aging from inception until forming of reproductive construct.
For example, it takes two months for Spermatogonia to develop.
Why is DNA damage over generations not accumulated?
I have this study.
https://www.biorxiv.org/content/10.1101/2021.03.11.435028v1.full
Is that consensus on the subject?

Somewhat relevant are the answers to these questions: Is each generation getting older?, and How are new people created from the DNA of an aged person, and DNA damage theory of aging and sex.  Also related: Why doesn't mitochondrial DNA accumulate damage over successive generations?.

Excellent ansert/comment. Thanks.

Does this answer your question? How are new people created from the DNA of an aged person. i.e. Why are we young?


text:
Is there a function for urea in sweat?
In ureotelic organisms, ammonia is converted to urea for excretion primarily in the liver and, to a lesser extent, in the kidneys. However, sweat also contains trace amounts of urea. Is this small amount just a residue from the blood or is it produced in sudoriparous glands and is, therefore, an adaptation (a backup route in case of liver/kidney failure, or maybe it has a function in chemical communication, as a pheromone)? Or does it have another, maybe vestigial, function?
Is there a function for urea in sweat? If so, what is it?

Tl;DR: Urea is a metabolic waste excreted from human body. As such it does not have any function in human body. It is a major product in the waste excreted from kidneys although trace amounts can be found in sweat. The concentration of urea increases when kidneys fails to function normally. Hence, they are excreted through sweat glands, observed as "frosts" on the skin among uremic patients.
Long answer:
Urea is a normal metabolic waste which are excreted by the kidneys but are also excreted from human body via sweat. In fact, sweat contains trace amount of urea, about 22.2 mmol/L (Huang.et.al. 2002; More on the concentration of urea in thermal sweat has been discussed by Bulmer, 1957). Urea is excreted by eccrine glands. As such, it is also thought to be an excretory organ (urea transferred across eccrine glands is discussed by Komives. et.al, 1966). However, the concentration of urea and uric acid doesn't affect much in the homeostasis function (as they are in negligible amount compared to metabolic waste in kidneys. Sweat seems to play the role of thermoregulation):

urea readily crosses the eccrine glandular wall and cell membrane and therefore concentrations of urea in sweat are expected to be about the same as that of the plasma. Some studies report very high urea concentrations in sweat , up to 50x that of serum, and suggest that this is evidence for a selective transport mechanism across the sweat gland, especially in patients with kidney damage, to clear the blood of high urea concentrations (Al-Tamer et.al., 1997).
[...]
Other studies have shown that uric acid and creatinine excretion via sweat is insignificant compared with elimination rates through the kidneys. Taken together, there is limited evidence that the sweat glands excretory function makes a substantial contribution to homeostasis.

As noted by Keller et.al. 2016, the concentration of urea and uric acid in sweat increases when kidneys fails to function normally:

In humans, urea is excreted in sweat, largely through the eccrine sweat gland. The urea concentration in human sweat is elevated when compared to blood urea nitrogen. The sweat urea nitrogen (UN) of patients with end‐stage kidney disease (ESRD) is increased when compared with healthy humans. The ability to produce sweat is maintained in the overwhelming majority of ESRD patients.

Also, urea concentration in sweat seems to be different among genders:

The sex difference in sweat UN was a surprising finding. In humans, the menstrual cycle is known to change the characteristics of thermoregulation and electrolyte balance. Estrogen lowers core body temperature at rest and during heat stress. Additionally, estrogen replacement therapy increases total body sodium.

source: Stack Exchange

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

sort: votes


text:
Mushroom Identification: Brown gilled mushroom in Ohio lawn near rotting stump roots
Even though I ID a lot on this site, I'm rather unqualified to ID mushrooms (even with the help of sites like urbanmushrooms.com).
Can anyone help me ID this mushroom species?

Attributes:

Morphology: convex cap; gills possibly free, adnexed, or sinuate (I really can't tell!); stem is equal or slightly club-shaped
Color: Brown cap; white gills; white/brown stalk
Size: 1.5-2.5 inches tall; cap 0.25-1 inch diameter
Other sensory: cap texture is smooth/waxy similar to white button mushroom one buys in a grocery store; smell is minimal but perhaps slightly musty?
Location: Eastern Ohio (Ohio Valley, about 10 miles West of the Ohio River)
Habitat: growing in recently moist (though almost dry) grass near (but not on) a rotting stump.  Violets, clovers, and other herby weeds also growing in lawn nearby.
Timing: Mid July; found on a sunny day after a week of on-and-off rain

More photos (click to enlarge):

You will need a spore print ; put a cap on newsprint in an undisturbed location for a day or so. The newsprint gives both a white and black background reference.

@blacksmith37 already in that process... waiting [not so] patiently

those mushrooms grow a lot near me.

I was advised by Walt Sturgeon, author of Appalachian Mushroom: a Field Guide as well as members of Poisons Help; Emergency Identification For Mushrooms & Plants Facebook group that this is likely Marasmiellus luxurians.

 Credit: Walt Sturgeon 2018 | Source: Mushroomobserver.org
Mushroomexpert.org provides the following supportive pieces of info:

Ecology matches: "growing gregariously or in tight clusters in woodchips, or on lawns (probably fruiting from dead, buried roots), and, rarely, fruiting directly from logs and stumps; summer and fall."

Location matches: "widely distributed and relatively common east of the Great Plains".

Walt Sturgeon suggested the following when I asked him about comparing this to similar-looking Entoloma:

Marasmiellus has a white to buff spore print.  Entoloma spores are ruddy pink.  A spore print is made by removing the stem and place the mushroom gill side down on white paper. cover with a bowl. wait several hours and there should be a spore deposit on the paper.

My spore prints did appear to be white.

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


text:
Which member of the Hemiptera family could this bug belong to?
Today I found this little bugger on the outside stucco near Vienna (AUT). Though I'm a big fan of bugs in general, certain members of the Pentatomidae, or their super-family the Pentatomoidea, especially the Palomena prasina (European shield bug) is not one of my favourites since their stink glands on the abdomen can secrete a foul-smelling and long-lasting secretion.
To my surprise, this quite beautifully ornamented bug with a length of about 7-8 mm didn't seem to tend to secretion even when stressing him a bit with a cotton swab (Disclaimer: no bugs were harmed during this test).

Can anyone help me identify this bug which seems to belong to the Hemiptera family (just my assumption, please correct me if I'm wrong).

Nezara viridula, Green Vegetable Bug (and other names).
Probably fifth instar, as the body is mostly green.
http://en.wikipedia.org/wiki/Nezara_viridula
Found by searching images using the terms:
green stink bug with four rows of yellow dots

Photo by Charles Schurch Lewallen, under Creative Commons license. Found at https://bugguide.net/node/view/8819

Thx for your id and the link, looks like the one I photographed is the Fifth instar. I didn't know they moult five times before reaching maturity and have different color morphs - quite impressive!

You are right, I change my answer.


text:
Can you identify this caterpillar?
Hi on my walk home in may i found this larvae crawling on a small road between grass and fields. All the yellowish larvae i know are looking totally differend than this. The origin of this picture is in the middle of Germany. The larva is is around 5 cm long and 1 cm tall.

Thank you


text:
Thermodynamically, how did the first cell arise?
Living cells are biochemical systems that constantly perform chemical reactions. One of the important consequences of these chemical reactions is the capacity of a living cell to replicate itself. The daughter cells will also constantly perform chemical reactions.
From an evolutionary perspective, new cells always arise from old ones via cell division. The first cell on premordial Earth must be readily performing chemical reactions in order to replicate. A raft of biochemicals must have for some reason aggregated to form the first cell and begin chemical reactions.
An important effect of highly orchestrated chemical reactions inside a living cell is that biological order is maintained, at the expense of increased entropy in its surroundings. However, this observation is an effect of cellular organization and activities, not the cause.
I feel thermodynamics is important in explaining how a raft of biochemicals came together in the first place to organize the earliest cell, and how these biochemicals started to engage in highly orchestrated chemical reactions. Then, what is the exact theory?

I'm a little bit unclear on what you're trying to ask. There is a whole literature on this subject, which is normally termed abiogenesis. What is it about the standard textbook explanations of abiogenesis that you need help to understand?

Simple question. Simple answer. Nobody knows.

For a provocative paper and a great introduction to this topic, see Towards an evolutionary theory of the origin of life based on kinetics and thermodynamics, where the importance of irreversibility and autocatalysis/self-replication is emphasized.

The first amino acids
For how life arose from no life, the Miller-Urey Experiment demonstrates how in primordial Earth conditions, a spark in the atmosphere (analogous to lightning) could have initiated synthesis of the many of the same amino acids (and amines) life uses today.
My understanding was that the spark broke some bonds between the gases (and water vapor) in the air, allowing atoms to re-bind in new combinations to make amino acids.
Here’s a 25-Page Biographical Memoir from the NAS on Stanley Miller, page 3 is where they start discussing this experiment. Miller published this experiment in the early 1950’s, in which he identified 5 amino acids. However, NASA and others revisited the same experiment and discovered Miller under-reported amino acids present, a result from the limited equipment available at the time. They have found 14 amino acids and 5 amines. Miller’s vials from an unpublished experiment of similar nature produced 22 amino acids.
In addition, amino acids have been found on meteorites, suggesting that they are capable of spontaneous synthesis.
The first replicating life
There is a lot less known about this, as we’re still researching it now. Not only this, but there are currently several different going theories.
Keep in mind, the Central Dogma of molecular biology describes genetic flow as DNA—> RNA—> PROTEIN.
The reason why there are different theories (and so many models within them) around the chemistry-to-biology (CTB) transition does not lie in which monomer is more likely to synthesize spontaneously, rather it is almost literally a chicken-and-the-egg situation. Everything is a precursor for everything.

Proteins are made by amino acids, which are polymerized by metabolic processes. Proteins are made by other proteins, and directed/coded for by RNA.
RNA is made by the monomer building blocks of ribose (sugar), phosphate, and a base (A, U, G, C). The bases are biosynthesized from metabolic pathways. RNA is elongated, and read by proteins.
Metabolism is driven by proteins and largely by ATP, which contains the nucleobase adenosine found in RNA (& DNA).

Protein first
Since amino acids are the monomers of proteins, it is a likely (and simple) possibility that a spontaneous reaction bound amino acids in the right order and configuration to create the first protein that enabled life. This protein’s function could likely be to polymerize/elongate amino acid chains into proteins.
This theory is supported and demonstrated by this study, which suggests that the first “protein” catalyzed the elongation and proper folding of other amino acid chains, including creating more copies of itself.  0.3% of the possible permutations of monomer sequences give a “protein” the elongation capability described, which though small, is an exciting possibility considering the age of the Earth and timeline of life. What’s more, polypeptide formation does not require as much precision as RNA synthesis, as speculated characteristics of proteins and amino acids comport with the computer modeling shown by the study.
Though this theory seems to contradict the central dogma, we must keep in mind that thermodynamically the reactions occurring at the origins of life were spontaneous, so the “pattern” of genetic flow present in most life might not be a direct indicator of “what came first.” This is supported by the existence of prions (pathogenic proteins), and the fact that simple organisms don’t always use mRNA to synthesize proteins (alternatively, they use “nonribosomal peptide synthetases”).
The limitation of protein-first models is that proteins don’t really “work backward” into RNA. Though nucleic acids acids contain components of amino acids from their biosynthesis, the are pretty different molecules.
Some models suggest this protein-first theory, AS WELL as an RNA first theory (see below). The idea is that self-replication of biological molecules started with proteins, but nucleic acid-based “life” also evolved, seperately. RNA self-replication probably took longer to reach, but outcompeted protein “life,” explaining today’s life as well as providing an explanation for the above limitation.
Organisms can “uptake” other organisms and incorporate them into their own cells. 2 commonly-cited widespread examples include organelles mitochondria and chloroplasts, both thought to originally be independent prokaryotes themselves.
RNA first (aka The RNA World Hypothesis)
Some theories suggest RNA came before functional proteins. In fact, this has been the de facto theory, because we had no mechanism to explain how proteins could self-replicate - something that has recently been demonstrated. In addition, this follows the central dogma, and would explain not only the development protein synthesis but also genetic information storage (the latter of which cannot be directly explained by the protein-first theory alone).
An idea behind this is that some RNA was able to auto-synthesize the first RNA-replicating enzymes. This sounds like a catch-22, but this study had found some RNA strands when joined can self-create an enzyme that replicates itself - the literal chemical makeup of this enzyme are RNA-oligonucleotides.
However, these RNA fragments in the lab have been take from existing ribozymes, so they may not be an accurate indicator for the first, spontaneously-created enzymes.
Limitations from and only RNA-first model stem from the fact that currently RNA synthesis/replication processes are detailed, intricate, and fragile. The chances of spontaneous reactions alone creating this process seem minuscule (though as mentioned earlier life took a LONG time to develop).
Until recently, another cited limitation concerned the fact that no known organisms replicate RNA. However, some viruses manage to code for RNA-replicated proteins, and (as mentioned earlier) RNA’s capability of self-replication has been recently discovered, be it in a lab setting.
Other theories
The last main debated theory concerns metabolism. This idea suggests metabolic processes occurred before the first life form, since many metabolic processes known today synthesize amino acids and nucleic acids from chemicals in our diet (how our body make the building blocks).
However, such a huge part of what makes metabolism today possible is driven by enzymes, which are proteins. Because of this, all of these processes would have to be dramatically slowed down in rate to mimic spontaneous reactions in primordial conditions, and on top of that there would have to be an explanation for how energetically unfavorable reactions in metabolism would occur. Most of these energetically unfavorable reactions in current metabolism harvest the potential energy in ATP, which longhand is adenosine triphosphate. The molecule adenosine is also used as one of the bases in nucleic acids, which at some level inherently contributes towards to the RNA World Hypothesis.
Primordial amino acids (that have not been retained in today’s life) serving as the hidden first building blocks of life is not an uncommon theory. However, this concept rarely stands alone - it typically contributes to either the protein-first or RNA-first theories.
Proto-RNA theories propose an unknown “stepping stone” molecule like RNA. Evidence of this inherently will be limited.
Some ideas cite a meteor or space rock on which life was present collided with Earth, transferring life to Earth.

Once self-replication AND translation (RNA-protein) have been established, Darwinian evolution can explain the rest.

Additional resources
How Structure Arose in the Primordial Soup (Quantamagazine)
Life’s First Molecule Was Protein, Not RNA, New Model Suggests (Quantamagazine)

What simple organisms use "nonribosomal peptide synthetases” to syntheisize proteins ?

All organisms replicate RNA, do you mean self-replicate RNA? the big advantage of the RNA world hypothesis is the entire RNA to protein translation process is made of RNA components. both ribosomal subunits, tRNA, Its all RNA. proteins are made by RNA not proteins, they are modified by other proteins. you also may be interested in more recent work on self-replicating self-catalyzing RNA. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3943892/


text:
Why does ATP act as an allosteric inhibitor of glycogen synthase?
Why is ATP an allosteric inhibitor of glycogen synthase? Wouldn't high levels of ATP in the cell mean that the cell has sufficient energy, and in this case wouldn't excess glucose be stored as glycogen? However ATP acts as an inhibitor of glycogen synthase.
What is the physiological basis/biological reason for this?
Reference:
Vasudevan D.M, Sreekumari S, Kannan Vaidyanathan 2021. Textbook of Biochemistry (For medical students) 9th ed. Pg.147
Nuttall FQ, Gannon MC. Allosteric regulation of glycogen synthase in liver. A physiological dilemma. J Biol Chem. 1993 Jun 25;268(18):13286-90. PMID: 8514767.

This question was asked (with similar phraseology) and answered on SE Chemistry in 2017. https://chemistry.stackexchange.com/questions/72741/why-does-atp-inhibit-glycogen-synthase  What’s going on here?

The answer there only explains the inhibition of glycogen phosporylase in detail while the question is about glycogen synthase. Moreover it explains the chemical aspect but not the physiological aspect of this inhibition. It was even suggested that the question be moved here, but no one seems to have done it. So, I posted another question.

I doubt whether you will find a more comprehensive answer than that on SE Chemistry, where the answerer offers to respond to comments. As for physiology there is nothing about it in the original or your version of the question, or I do not understand what you mean. My own objection to the question is that it provides no documentation for or details of its premise that “ATP is an inhibitor of Glycogen Synthase”. Until I am provided with this I suspect that it is a distortion or misreading. Please edit the question to include.

By physiological basis, I mean the biological reason for the inhibitory effect. I have edited to include the references.

Thanks for that. The question really boils down to the status of the 1993 paper. I was surprised to find PubMed only lists about seven citations, the latest in 1997. This suggests to me that the conclusions of the paper are not generally accepted, for whatever reason, despite being in the Indian text book you cite.  Whether or not this is justified is another matter. I will revise the question accordingly when I have a moment, and do some research on it later.

Thanks! I couldn't find this mentioned in either harper or lippincott, so I am also a bit doubtful about the validity of this claim. I'll try doing some research on my own too!


text:
Are there complexity requirements on potential hosts to be susceptible to parasites?
Are there lower bounds to complexity for hosts and how are these described or modeled? In other words, one would expect an organism to have a certain amount of "surplus tissue" in order for parasites to be able to feed on it, at least without killing the host too soon for the parasites to thrive.  For example, humans have surplus blood (we can draw a lot of blood and survive), making it possible to live with a few leeches, ticks, etc. Is this supposition really true? That is, do we know that "very simple" organisms cannot have parasites? If so, how do we characterize what is "too simple to be a host" and does it have anything to do with having "surplus tissue"? (I assume "surplus" is not the term used in parasitology because I haven't seen it in the books...)

yes it most at least have cells otherwise it does not qualify as a host.

"Complexity" is a difficult term to operate with in biology; most people that use it don't have an idea of how they'd like to operationally define it, and without an operational definition it isn't meaningful.
Phages are effectively parasites of bacteria - one could bicker that a virus can't be a parasite because it's not "alive", but I think this is just a semantic argument about what it means to be alive, and many of the definitions that exclude viruses are problematic because they those same terms exclude animal parasites.
Not all parasites are of the "feed on the host just a little bit" variety, either. Parasitoid wasps, for example, typically consume the entire target host, sometimes paralyzing it at the same time an egg is laid. Cordyceps is another fun group of (mostly) parasites, whose targets include other fungi and insects.
The only limit seems to be that the host must somehow be of use to the parasite. It must also be complex enough to be considered a living organism in its own right: you can't have a parasite of something that's already dead, for example, since that has a different meaning. I think these meanings are rather tautological, rather than interesting, though, so I'd answer your title question to say "no, not in any meaningful, non-tautological way".

Thank you this is very interesting! I guess I asked the  question a bit wrong: I meant specifically hosts that are multicell organisms and specifically parasites that feed on a host for an extended period (as opposed to consuming it or killing it entirely). In these restricted senses, one would expect (although I am asking because I'm not sure) that the host must have "surplus tissue" to be able to yield to the parasite without dying. I guess I am interested in this from an evolutionary perspective: do we see the entry of parasites as correlated to the development of "surplus tissue"?

@Antoshka I don't think you'll be able to do anything mathematical here in order to develop any "rule", just to look at examples, and biology is pretty good at coming up with exceptions to any rule you think you found. It's certainly not true that parasites of the type you describe only feed on "surplus" tissue: tick infestations can be fatal to deer, weakening them to the point they cannot recover.


text:
What is 'protein' in food?
I know that proteins perform a lot of functions and as a result there are a lot of different types of proteins in our bodies. When I eat food that has x grams of 'protein', what is this? A homogenous mix of proteins? A heterogenous one? Is it specific set of them that are general enough to be used by my body despite coming from a different organism? How can it be sure that my body can use the kind of protein in the food?

When we say "protein" with respect to food, what is generally meant is material that contains amino acids.  Every protein is, at its heart, a long string of amino acids, which then gets processed through some combination of folding, cutting, and bonding together with other molecules.
Much of our food is made out of cells, whether animal (e.g., meat), plant (e.g., vegetables, fruits, grains), fungal (e.g., mushrooms), or bacterial (e.g., yogurt).  Every cell has a widely heterogeneous mix of proteins, comprised in turn of a widely heterogeneous mix of amino acids.  Milk-based foods aren't cellular, but also have a wide range of amino acid content, because mammals produce milk as a complete food source for their babies.
Inside your body, digestion breaks the proteins, whatever they might have been originally, down into amino acids, and that's what you really need to pay attention to in terms of nutrition.
The human body can synthesize the majority of amino acids out of other molecules, but there are nine essential animo acids that we have to get from our food.  Any diet that provides a sufficiency of those amino acids, no matter what sort of proteins they may be originally bound up in, will provide what you body needs in terms of protein.

I suspect that the actual bacterial biomass in a standard yogurt is pretty darn low.

@Arthur well, if we take a standard yogurt — e.g. specified by a Russian standard, GOST 31981-2013, we get the requirement of ≥10⁷ CFU of particular bacteria (see §3.1). Dunno whether it's high or low, but the numbers are available.

@Ruslan 10^7 CFU per gram if Google reads the Russian correctly·  But even assuming we could say 1 live cell=1CFU (as I do below to get a crude guesstimate), we don't know how many dead bacterial cells are in there.  Presumably not 0.  Taking sizes for lactobacillus cells from Britannica and assuming they're mainly water from the point of view of density we get something like 1 part in 10^5 by mass live cells, or "pretty darn low".  I'm no biologist so couldn't even begin to work out the live:dead cell ratio - but can't trivially find it

It's a mix of all the proteins in whatever organism the food is coming from. Some (especially vegetable/grain) sources might have fairly specific proteins present because you are eating a specific part of that organism which is enriched in that particular protein, but ultimately the specific proteins don't matter much unless you have some sort of allergy. The reason it doesn't matter much is that your body won't use the whole proteins at all.
All proteins you eat are digested into their constituent parts: amino acids. Essential amino acids are those that a human cannot synthesize themselves, so it's important that the diet contain all of these. Vegetarians/vegans in particular should be familiar with the concept of "complete protein", or combinations of food sources that serve as "complete", to ensure they have access to all the essential amino acids.

As one might suspect, if a label says just "protein" without being more specific, it means any protein, without being more specific.
The reason we are not that interested in the details is that the body denatures most proteins in the acidic stomach and the intestines and breaks them up into their building blocks, the amino acids, without really taking a close look at them. (It's a bit like breaking up your brother's Lego stuff when you simply need grey bricks: It doesn't really matter whether it's his Millenium Falcon or his Saturn V.) The amino acids are then absorbed through the intestinal wall. They are used to synthesize the proteins our body needs (build your own star ship).
Our body can synthesize many of the 21 amino acids from scratch, some of them always in sufficient amounts; but nine of them must be ingested with food. They are called "essential" amino acids. They are like the special corner pieces you so badly need to finish your design and that are not so common.
If they are missing, which can happen with a non-varied diet, the body cannot use the other amino acids to create its needed body proteins and instead synthesizes carbs and fat from them. Therefore, a diverse diet is needed to fully utilize protein in food as building blocks for the proteins the body needs. That's the — important — exception to the rule that all food proteins are nutritionally equal.

Which is why eating collagen-rich food if you think you're body needs to build more collagen (like for joints) doesn't make any sense.  Even this site: https://www.webmd.com/diet/foods-high-in-collagens#1 gets it wrong: if your body is going to break the collagen down into amino acids, what difference does it make whether those amino acids come from collagen or from some other protein?

@MikeMaxwell if nothing else, one would think that eating collagen would ensure that you get all the amino acids required to build collagen in the human body.

The two most common amino acids in collagen are glycine and proline. ( https://en.wikipedia.org/wiki/Collagen ) The glycine-proline-hydroxyproline is the most important sequence motif for collagen structure. Neither glycine nor proline are essential amino acids (and hydroxyproline is made by post-translation modification of proline), so I think @MikeMaxwell has a point.

The other answers are correct: foods you eat include a mix of proteins, which are mostly cut into their constituent amino acids in your digestive system. However, while a burger (meat or veggie), might contain thousands or millions of distinct proteins, there are some proteins that much more common than others. For example, in blood plasma, there are more serum albumin molecules than all the other protein molecules combined.
Meat
In meat, the predominant proteins are actin, myosin, and tropomyosin. As might be expected, the function of these proteins is to allow muscles to move and apply force. Myosin heads "walk" on actin tubules. Connective tissue proteins collagen and elastin are also a major components. The function of these proteins is to provide structure and elasticity. Blood proteins such as serum albumin, myoglobin and hemoglobin are also included. The major role of serum albumin is to regulate the osmotic pressure of blood (keeping cells from accumulating too much water and bursting or losing too much water and dessicating). The function of myoglobin and hemoglobin is to carry oxygen.

Myofibrillar proteins are the main components of meat, and there are around 20 or so different types in this particular group. In perspective, out of the overall 50%–55% of myofibrillar protein, myosin and actin alone account for around 65%–70% of this figure.

From: Meat: Food and Science of the Animal Kingdom.

Actin, by Thomas Splettstoesser, CC BY-SA 3.0
Beans, peas, lentils
Pulses (peas, beans, lentils) contain mostly legumins and vicilins, which are oligomeric storage proteins. Hence, they serve no function other than to store amino acids that the new plant can use to grow from the seed. Legumins form from 6 subunits and have a total mass of 300–400 kDa. Vicilins are heteromeric or homomeric trimers with overall masses of 145–190 kDa.

Phaseolin, a vicilin storage protein in beans.
Milk
The major protein in dairy milk is casein. These proteins have an unusually high amount of proline, which inhibits secondary and tertiary structure formation. Their function is to supply amino acids to infant mammals and carry essential nutrients such as phosphorus and calcium. Together α-, β- and κ-caseins make up about 70% of cows' milk, with the rest consisting of lactoalbumin and lactoglobulin.  They comprise 20–45% of the proteins in human milk, depending on stage of lactation.


text:
Are there mammalian species in which the male makes no contribution after coitus?
It seems that live bearing is very high cost relative to egg laying. Therefore, I would expect that in a live bearing species the male would always have a post coital role.
Is this the case?

Are you claiming that, say, polar bear and tiger fathers help to raise their young?

I am not claiming I'm asking what advantage live bearing has over egg laying?

Can you clarify your question? The question you're explicitly asking here ("are there mammalian species in which the male makes no contribution after coitus") has clear answers, but in the comments you say that you want to know what advantage live bearing has over egg laying - which is a different question.  Can you be more explicit about the steps in your logic and say more precisely what your question is?

and, FWIW "sociality" (as in your title) is yet another topic - usually refers to associations of unrelated or distantly related individuals (not parent-offspring or parent-parent interactions)

there are two very different questions here, I suggest asking them separately .  And a better way to frame your first questions is what allowed eusociality to evolve in mole rats  the only vertebrate that is eusocial. its not insects and mammals it is insects and one mammal. Also I suggest you first ask what the benefits of live birth are because there are some pretty solid benefits.

I've adapted the question closer to what it originally said plainly and fitting the answer given. Eusociality is really a different thing altogether; I'd recommend asking that as a separate question as others have suggested, perhaps framing it on what you can learn from Ben's answer. Probably worth reading generally about eusociality before asking, too, in order to frame a clear question. "what advantage live bearing has over egg laying" is a third separate question, also only barely related to the others.

Narrowly speaking, the answer to your question is "yes, most of them".  West and Capellini (2016) analyze a data set comprising 529 mammalian species, of which only 65 have any form of male care of offspring. This figure from their paper shows that it is common in some primates and some carnivores (I haven't zoomed in to see exactly which clades these are), and otherwise rare.

West, Hannah E. R., and Isabella Capellini. “Male Care and Life History Traits in Mammals.” Nature Communications 7, no. 1 (June 14, 2016): 1–10. https://doi.org/10.1038/ncomms11854.

I'd think it would depend on how you define "care".  Is it just male-female pairings, or herd/pack animals, where the male(s) protects the entire group, including young?


text:
Can Shark bodies be preserved?
Under normal conditions, Shark bodies, which are made of cartilage are not preserved and only the teeth can only be preserved. I searched whether Shark bodies can be preserved in ice and I got this CNN article link about a megamouth shark. I'm guessing this was washed up or something, its preserved in ice at the Smithsonian.
I think sharks could encounter ice or some other preservative material and get trapped, like frozen saltwater, iceberg, or amber. So is there a definitive answer if shark bodies can get preserved in such material?
UPDATE
I realized frozen salt water would not be a preservative because sharks don't live near the polar seas and ocean, but that does not rule out the possibility of shark catching a current, because warm currents spread out to the poles, and cold water spread out to the equator.

https://www.google.com/search?q=can+amber+be+found+on+the+ocean+floor&rlz=1CASFJY_enUS951&oq=can+amber+&aqs=chrome.0.69i59j69i57j0l8.3723j0j7&sourceid=chrome&ie=UTF-8&safe=active&ssui=on

Do you mean preserved by some natural means, or by humans?  For the latter, you might read the rather amusing book "The $12 Million Stuffed Shark": https://us.macmillan.com/books/9780230620599

Natural Preservation.

Ahem, greenland shark locations...

Now I really want a shark preserved in amber… d***!

define preserved, there are plenty of whole body shark fossils.

Yes, it's possible if they are in very cold, low oxygen waters. Fossils of manta rays are fairly common, and there are examples of complete shark fossils preserved by silt and limestone.
Sharks can also be curated using epoxy, formaldehyde, alcohol and other preserving substances. There are famous preserved sharks, one is called Rosie, a great white from Australia, and the other is by Damian Hurst, a tiger shark.


text:
Spider identification North-West Italy
I would like to know what kind of spider is the one I killed and if it is somehow dangerous.

Location: city in North-West Italy.
Dimensions: ~1.5 cm, with legs opened.
Time of day: around midday, but the external jalousie of my window was closed, so it was dark when I found it.

It seemed to have some sort of marking on its abdomen, but colors were very dark, so it was difficult to view it properly.
Edit: The marking was some sort of symmetrical shape covering quite all the abdomen. Colors were very dark and it was difficult to distinguish it properly from the rest of the abdomen.

Unfortunately I didn't photograph it when was alive, and intact, because I found it out of my window and I didn't want to lose its tracks while getting my phone.
For what I know, the most dangerous spider that can be found here is the Loxosceles rufescens (Mediterranean recluse spider); it seems different, but obviously I'm not an expert.
Thank you very much!

Welcome to Biology.SE. You've done a good job on supplying the information needed for ids, but I'm not sure what you mean by a "form on its abdomen". Do you mean a marking and if so is it a different color, texture, or something else? Any additional information you can [edit] into your post will increase the chances of getting an accurate id.

Here is a gallery of species observed and submitted to the iNaturalist website... filtered the species by limiting the search to 'typical spiders' (excludes tarantulas or other weird things) and limiting the search to NW Italy. Sorted by most-commonly observed first. You can click on the "N Observations" to see the submitted photos that are currently IDed to that species (not necessarily a correct ID) https://inaturalist.ca/observations?nelat=46&nelng=13&place_id=any&subview=map&swlat=42&swlng=4.5&taxon_id=120474&view=species


text:
Disposing biohazardous material
I had conducted some disc diffusion tests with E.coli and S.epidermidis.
Now, I wanna dispose these petri dishes and was wondering the correct way to do it. Many websites mention adding bleach to the agar and disposing them in biohazardous waste bags right away.
I've decided to do the same. But, the lid for all the petri dishes I have are very loose. If I simply dispose the petri dishes in waste bags, I think that the lids are gonna come off and the bacteria may infect the waste bags.
Should I seal the petri dish with some tape like a parafilm so the lids won't come off or is it not a problem that the bacteria may come out onto the waste bags?
(No websites mention the issue of loose lids while disposing, so I wonder if this is a problem at all)

You don't have an autoclave available?

No, I'm not a professional researcher, a high school student. I just did this exp. at home...so I don't have one

Autoclave is standard, but bleach can be used. In your case, you'll want all the culture media and dish surfaces to have contact with the diluted bleach solution. I would prepare diluted liquid bleach as described in the link below and pour some in a plastic wash tub to a depth where you can put all your petri dishes etc in and have them fully submerged. Let them sit for at least 30 minutes in the solution, then recover the solids and put them in trash, and dispose of the bleach solution with MUCH dilution down the toilet. Pay attention to the safety suggestions and warnings in the link!
This U of Toronto web page has good info on disinfecting using bleach.


text:
Recombinations between Distant coronaviruses
With recombination I mean long ones, say > 1000 nucleotides, so that the two parents must be coronaviruses and the two pieces of genomes must have compatible genomic coordinates for the recombinant to be viable.
Though co-infection by distant CoVs (for example SARS-related with HKU2-related) are often found in nature, most recombinations occur between closely related coronaviruses.
One thing preventing distant recombination is the TRS (a small motif causing most sub-genomic mRNA junctions) which must be compatible when the 5' part of an ORF is included in the transferred piece of genome. Another one is the complicated interactions between the host and viral proteins and RNA.
However, some rare distant recombinations might occur.

An example is Deltacoronavirus which is a distant genus except in the spike where it falls into Alphacoronavirus (though a bit distant to others).

There are also two Alphacoronaviruses: HKU2 (a normal one) and Wencheng shrew CoV (a distant one) that form a separate "genus" in the spike.

Swine enteric coronavirus (SeCoV) is a near perfect recombinant between two distant alphacoronaviruses, PEDV and TGEV (both responsible of enteric swine diseases).

Are there other examples of recombination between distant Coronaviruses? Note that I mentioned one proven and three putatives recombinations, ie. we often don't have the triplet [major parent, minor parent, recombinant] as it is the case with SeCoV.
Discussing related lab experiments might be interesting as well (of note replacing VSV's G protein by various attachment&fusion proteins often produce viable chimera).

In every case recombinations are rare as not many were found in the 2 million SARS-CoV-2 sequences, but they end being common when looking at the long-term evolutionary history of a given lineage.

Recombination between distant viruses is less likely to produce a viable virus, which is why is rarely observed (recombination rate in a cell may be nearly as high as for similar viruses).


text:
Why does wheat consume more water than rice that is, unlike wheat, flooded?
Why does wheat consume more water than rice that is, unlike wheat, flooded? I thought rice was the villain of the piece when it comes to water consumption.

Welcome to Biology.SE. This community has agreed that questions that show little or no prior research effort are off-topic on this site as are "homework" questions unless you have shown your attempt at an answer. Please [edit] your question and tell us where you've looked for answers, what you do know about the topic, and where exactly you still have questions. Under researched questions may be subject to down-voting and closure. In addition, you should not expect other users to follow links or search for information in multipage ...

... documents. Instead, quote or summarize the relevant information (with references).  ——— Also be aware that this is not a forum or tutorial service; it is a Q&A site where specific questions relating to biology get specific answers. Please take the [tour] and carefully read through the [help] to learn more about the site, including what is on-topic and what is not, and how to [ask] a good question.


text:
Is there a term that distinguishes extracellular "transport" proteins from membrane-bound "transport" proteins?
I've been researching genetics and biochemistry in my free time and I've noticed that proteins such as albumin and apolipoproteins that facilitate extracellular transport and proteins such as GLUT1 which transports glucose across the cell membrane or MFSD12 which transports cysteine into the melanosomes of melanocytes are all referred to as "transport proteins" or "carrier proteins". Maybe its just my opinion as a layman but as far as I can tell these are two distinctly different processes, I don't see the logic in referring to these by the same name. One is a protein bound to a membrane that facilitates diffusion across that membrane and the other is a protein that spends the majority of it's lifetime shuttling molecules around outside the domain of any cell.
I'm wondering if maybe there is a set of terminology that distinguishes between the two?

The short answer to this question is NO.
To understand the reason one needs to appreciate certain things about proteins and about research into them. A primary objective in research into proteins is to understand how their structures determine how they work, not to classify them by function. Of course, assigning similar proteins to groups and using phrases to describe them is helpful, but as science progresses broad categories may be found to be invalid or unhelpfully wide, and even when valid it may be more helpful to consider narrower categories, with the practitioners being aware of the overall picture.
I have given introductory lectures on proteins to undergraduate students, and would list some of the diverse roles they can play. I might have said something like “some catalyse reactions, some play a structural role, some transport substances across membranes, others carry molecules from one location to another…”. For stylistic reasons I have used two different verbs “transport” and “carry” — and if I wanted to make headings for a list I might use “carrier proteins” and “membrane transporters”, but these are not official categories and others might use other descriptions.
As @bryankrause commented, “carrier transport proteins” such as apolipoprotein, albumin, zinc carriers, haemoglobin etc represent very diverse types and are generally not considered together after first introduction. The term “carrier protein” has problems as it may be mentally associated with “acyl-carrier protein”.
As for the “membrane transporters” it is instructive to look at the index to the respected text, Berg et al. Biochemistry — Chapter 13 which considers such proteins under the title “Membrane Channels and Pumps”. This has a subheading “Many molecules require protein transporters to cross membranes” but  then proceeds to use specific terms for different classes like “ion channel proteins”, “secondary transporters”, “ion pumps”.
In conclusion protein researchers tend to focus mainly on descriptive phrases and precise specialist sub-categories when talking about functional groups. The nearest thing to biological taxonomy is perhaps structural classifications such as SCOPe.


text:
Is there a formal name for the dissolved caterpillar substance produced during metamorphosis?
Is there a formal name for the dissolved caterpillar substance produced during metamorphosis? I've seen this described as a protein-rich soup, a horrid meltdown, larval tissue breakdown, metamorphic goo, etc. Wondering if it has a more specific scientific name?


text:
Vitamin B12 deficiency Megaloblastic anemic
I have two doubts regarding Megaloblastic anemia which shakes my mind
(1) first is- I know that vitamin B12 is required for thymidine synthesis which is further required for DNA synthesis and so if there is vitamin B12 deficiency than the DNA synthesis will get impaired which will affect the progression of cell cycle in the proliferating cells. This is what I know ,, now my question is that if the deficiency interferes with cell cycle progression then how bone marrow hyperplasia can be seen in vit. B12 deficiency??
(2) my second question is that how B12 deficiency interferes with nuclear maturation or rather what actually nuclear maturation is?
What  nuclear maturation signifies ?


text:
Do some flowers excrete urea or uric acid?
Sometimes when I sniff a flower up close, I can't but help smelling a faint urine like odor. From my layperson's understanding, uric acid and urea both are responsible for giving urine its characteristic smell. Do flowers excrete either of these chemicals?

are you just smelling ammonia?

It's very faint. It's the same smell you get in some cigars too, except they call it floral.

May I know, is it for all flowers or only a few? Can you identify those flowers ?

The Biology.SE community has agreed that questions that show little or no prior research effort are off-topic on this site as are "homework" questions unless you have shown your attempt at an answer. Please [edit] your question and tell us where you've looked for answers, what you do know about the topic, and where exactly you still have questions. Under researched questions may be subject to down-voting and closure.

For example, did you try searching for "flower smell urine"? This gives multiple results including an article in Scientific American.


text:
What species is this larva?
I'm trying to identify the species of what I think may be some kind of Lappet Moth larva? (wild guess based on some internet sleuthing)  But the markings don't really match nicely with any photos I can find.
It's light grey/blue-ish, with sparse tufts.  Horn-like hairs at the head and not much going on at the tail.  It's about 75 mm long (not quite 3 inches).
It was found in a bag of grass clippings after mowing the lawn.  Geographic location is the Bruce Peninsula in Ontario, Canada.  Did not find any others like it on the property.  It's unfamiliar to me (first time I've seen one like it).
Can anyone more positively identify?

Might be American Lappet Moth (Phyllodesma americana), check the trees above for more. If convenient, stretch it out a little, or make it angry to see possible orange bands.


text:
Flower Identification
I found a flower along the banks in north India ( near Ganges ) and I am not able to identify it. According to its leaves I thought it as Prosopis cineraria but I am not sure about it..
Leaf - pinnately compound
Flower- yellow coloured and
clustered
Other features include thorns on raches axile

Its Vachellia farnesiana Wikipedia link
Common name - Sweet Acacia, दुर्गंध खैर durgandh khair (In India)

Is it also called "Babool" as a common name?

Yes, "gandh babul". Common names may vary region to region also.

Can I please know, why my answer was downvoted ?

Well, I don't know...


text:
Can you identify these tiny black insects please?
I'm afraid I don't know anything about them except that there are suddenly thousands of them invading my house since about a week ago, and I'd like to repel them. Found in Cambridge, UK.
They are really tiny, about 3 mm long and smaller than a dry grain of rice. I've never seen them fly, just crawl around slowly. They get into everything, including the screen of my monitor!

I tried searching Google for tiny insects but none of the pictures or descriptions that I found seem to match these (I'm pretty sure they are not ants, lice, bed bugs, termites or silverfish).
If you have any idea how to repel or kill them humanely and without dangerous chemicals, I'd really appreciate that too.

Can you provide a clearer picture ?

I would ask did anything happen just before they appeared like a warehouse delivery or 2nd hand book purchase etc. Book lice or dust lice is a possibility. The photo is not clear enough to tell

They have wings so it looks like a flying insect, so not book lice or any of the others suggested so far. Can you describe how they invade (or at least how you find them) and what the conditions are in Cambridge at the moment (heat, humidity) and anything unusual you have noticed around (smells, fungi, plants blooming or fruiting etc.).

As a gardener, whenever I hear the words “tiny black insects”, my first thought is thrips, whether it’s thrips or not, and in spite of the fact that there are many tiny black insects to choose from!

In lieu of any better thoughts: Thrips (Thysanoptera). A large diverse group of tiny insects generally approximately 1 mm long. Well known for being invasive pests of many plant species, and being capable of transmitting a number of plant viruses. Which of the many species this would be, I don't know, but likely a common one like the Onion Thrips (Thrips tabaci).
According to Wikipedia:

In addition to damaging plants, thrips may invade houses and infest household objects such as furniture, bedding and computer monitors - in the latter case by forcing their way in between the LCD and its glass covering.

They all have a fairly well defined body shape, with an elongated abdomen and wings that are often shorter than the abdomen. They are known to rapidly reproduce, outstripping predator control, so you can get clouds of them around if the conditions are right.
If you have crops or gardens near you, thrips might be the insect you are seeing.

Thank you, someone here told me they were thrips too, so I'll go with that!


text:
Why doesn't RNA polymerase just rotate?
I read A little help understanding DNA supercoiling , Understanding DNA supercoiling , and Why does underwinding create topological strain of DNA? , but there's still something I don't get. Transcription creates positive supercoils ahead of the RNA polymerase and negative supercoils behind it, and according to my TA's, this causes enough mechanical strain to sometimes even stop transcription from occurring. Why doesn't the polymerase just rotate around the DNA to relieve the strain?
The video below is helpful to communicate what the question is asking. The model I was taught is that the polymerase proceeds on a linear path, not a helical path, and thus the transcription bubble forces positive supercoils ahead and negative behind. The video shows this with a pen in place of the polymerase and a shoelace in place of the DNA; displacement of the pen tightens coils downstream and loosens them upstream. The way this seems to depart from reality is the desk or backdrop in the video, which keeps the pen from spinning, and the air, which offers no friction or thermal energy. In real life, the polymerase isn't a pen and the DNA isn't sitting on a desk and the surrounding medium is aqueous and of course the whole thing is at a smaller physical scale such that heat is experienced differently. But why doesn't the pen (polymerase) just spin?
https://www.youtube.com/watch?v=J4YlcD59-yw
P.S. I also looked at Does RNA polymerase move around DNA or does DNA rotate beneath the polymerase?, but I'm not sure what to take from that thread. Some answers disagree and others only mention unwinding, which afaik is a much lesser source of strain compared to the lack of rotation.

Comments are not for extended discussion; this conversation has been moved to chat.

Consider that:

RNA polymerase (RNAP) is a large complex (~400 kDa in bacteria); inertia and drag would hinder its rotation.
RNAP is attached to its RNA transcript, which becomes increasingly large as transcription proceeds thus increasing inertia and drag. Additionally, if RNAP were to begin to rotate around DNA, the transcript could begin to wrap around the DNA.
The RNA transcript is often bound by proteins/ribonucleoproteins, including ribosomes in prokaryotes (which undergo cotranscriptional translation), further increasing the complex’s size and making it more difficult to rotate.

These ideas are discussed in the original paper which proposes the “twin transcriptional loop” or “twin supercoiled domain” model to explain the observation of transcriptionally coupled DNA supercoiling:
Liu LF, Wang JC. 1987. Supercoiling of the DNA template during transcription. Proc Natl Acad Sci USA 84(20):7024–7027.
For this model to work, the torque required to supercoil DNA, which would cause rotation of the RNAP complex, must be overcome by the frictional torque opposing rotation of said complex. A mathematical treatment in this paper estimates that RNAP itself with a modestly sized transcript and a single ribosome bound would not be sufficient to introduce significant supercoiling in dilute aqueous solution.
However, they estimate that a larger transcript with 20 ribosomes attached would have sufficient frictional torque opposing RNAP rotation to cause some supercoiling of DNA. Furthermore, the authors recognize that this model in dilute aqueous solution is not representative of actual conditions within a cell, where the presence of other macromolecules could impede RNAP rotation much more significantly than water alone.
Additionally, RNAP itself, the RNA transcript or the proteins which bind it may be physically anchored to some cellular structure during transcription. For example:

RNAP can be bound to DNA outside of the transcription bubble through some intermediary regulatory protein
Ribosomes translating extracellular or membrane-bound proteins are attached to the cell membrane in prokaryotes.

Such physical anchoring of the transcription complex would certainly prevent its rotation around the DNA helix.

It is perhaps also important to point out that cells have topoisomerases which relieve the superhelical strain generated by transcription (among other processes). If the torque on RNAP caused by supercoiling is negated by these topoisomerases, there isn’t really another force which would cause RNAP to rotate. Nevertheless, supercoiling as a result of transcription does occur in vivo and has important implications on genomic structure and gene regulation. See the following paper for a review:
Ma J, Wang MD. 2016. DNA supercoiling during transcription. Biophys Rev 8(Suppl 1):75–87.


text:
What is the name of this black and white dove/pigeon?
July 19, 2021. My sister found this bird outside near our bird feeders. We’ve never seen one of this coloring or size before, and I’m not sure it’s native to where we live (Northern New Jersey). It has a white plastic tag with numbers on the leg, so I’m thinking it’s either tagged for scientific research or it’s domesticated.
It was resting on the ground instead of sitting in the trees like the other wild birds that frequent our yard. My sister was able to get within 10 feet of it to toss it some bird seed and set out a bowl of water. Any other wild bird around here would’ve flown off if she was within 15 or 20 feet, which makes me think it’s either domesticated, has had contact with humans, or is injured. The bird opened its wings at one point, but didn't fly or flap them at all throughout our interaction with it.
I apologize for the image quality, I couldn't get too close to the bird or it would shy away. In the picture it's sitting down with its legs folded under it. From what I saw, it has a rounded or wedge-shaped tail that fades from white to black at the tip. The body is pure white. The wings are white but with about 3 black stripes across the outer tip. It's shaped like a dove or a pigeon and stands approximately 10 inches at its head.

What's the size?  Is it any different in size from the common pigeon (or rock dove) frequently seen in cities?

I believe it was a little bigger than rock doves. I have mourning doves that frequent my bird feeders and this black/white dove was about a third larger than the mourning doves. I'm estimating it was about 8-10 inches tall at its head when standing up and maybe 10 inches from chest to tail tip? I may be off with the measurements, I couldn't get too close to it.

Welcome to Biology.SE. Domesticated (and feral) Rock pigeons are highly variable in both size and coloration. They are around 33 cm (~12-14 inches) from beak to tail (which is the standard length measurement for birds), which seems compatible with your estimates. Do an internet image search for "Rock pigeon" to get an idea of how variable these birds can appear. It seems likely this is a "racing pigeon" that's gotten injured or lost. Try using binoculars (or a telephoto camera) to see the band and you might help it get home.

Possibly some breed of show/fancy pigeon.
For example, see Damascene Pigeons:

 Source: YouTube
You can see some discussion/images of black/white pigeons in the pigeon genetics newsletter, and you can see the below image of some additional black/white varieties:

https://i.ytimg.com/vi/Vz3YY7qzN1k/maxresdefault.jpg


text:
Help indentify this species of snake/worm
I stumbled upon this snake during my routine walking in the nature park near me. The location is southern India.

Time if observation is 6 30 PM.
The length was approximately 1 feet. I could see the tongue coming out just like normal snakes.
The tail was pointed. Guessing it to be red boa.

I would say not red boa - head shape is wrong as is colouration. I would hazard a guess at Kerela shieldtail based on the pics here: http://indiansnakes.org/

Body shape, coloration (especially lateral yellow stripe) and location all lead me to think this is some species of Uropeltis snake, all of which are endemic to India.

Wikipedia  lists 25 species in this genus, and at least some species are only differentiated by closely examining the number of scales or size of shields.

One common species is Uropeltis eliottii, but I'll admit the coloration looks a tad too dark for your specimen.

 Source: The Reptile Database
According to Wikipedia and The Reptile Database, this species is endemic to southern India.
In 2018, a new species, Uropeltis bhupathy was described by Jins et al (2018) from the Anaikatty Hills of the Western Ghats of Tamil Nadu (is this near you?), and I think the scale coloration looks closer to your specimen.

 Source: Jins et al (2018)

 Jins, V.J., Sampaio, F.L. and Gower, D.J., 2018. A new species of Uropeltis Cuvier, 1829 (Serpentes: Uropeltidae) from the Anaikatty Hills of the Western Ghats of India. Zootaxa, 4415(3), pp.401-422.

The color difference could be caused by the camera and the lighting (e.g. the scales reflecting light). I would guess your answer is right. Some cameras misrepresent colors, too; I have one that makes everything look more blue and less red than it appears. But yeah, we'd probably have to interrogate the questioner considerably to find out (about whether a flash was used, if a light was shining on the snake, if the snake was very reflective, if red things look less red with that camera, etc.)


text:
How easy is it for quantum dots to enter the intracellular portions of cells?
As quantum dots have better quantum yield than organic dyes, many are being developed as a substitute for them. Nonetheless, could these substitutes be small enough to enter inside cells as current dyes do, or would they be operate outside a cell?

How big are quantum dots and what is their chemical nature? Likewise for the dyes you mention. If you want someone here to do the biology, you need to research and supply the chemistry.

@David quantum dots is a rather generic term, which describes many types of (mostly semiconductor) structures, with sizes of a few tens to hundred nanometers. The caveat is that these are usually an integral part of a much bigger semiconductor crystal. What is meant here are probably the QDs embedded in small colloidal particles - perhaps of micrometer size. Still, their chemical nature may vary wildly.

As far as I can tell, they do not (readily) cross the plasma membrane. This paper, "Cell-Penetrating Peptide-Functionized Quantum Dots for Intracellular Delivery", discusses strategies to deliver quantum dots into cells. These include:

Passive delivery done by coating the quantum dots in something that allows them to be endocytosed more readily (the authors do not seem to be optimistic about this strategy)
Mechanically faciliated delivery (e.g. microinjection)
Peptide-facilitated delivery by complexing the quantum dots with a cell-penetrating peptide

Since people are going through all this effort to get them in, it does not seem like they are cell-permeable without substantial modification.


text:
Why is heparin contraindicated in patients with severe uncontrolled hypertension?
Heparin is a parenteral anti coagulant- prevents clot formation by inhibiting factors 2 a and 10 a mainly. Now, patients with severe uncontrolled hypertension- have persistent bp of more than 140/90. Here we are considering the force exerted by the blood on the wall of the arteries. Increased pressure of blood means, blood is trying to flow through a smaller diameter of the vessel, hence you can say that blood flow is decreased in such patients. Shouldn't heparin be useful in patients of hypertension because it will prevent clots from blocking the blood flow ? Why is it contraindicated ?

I would suggest that your question is more appropriate for SE Medical Sciences, where you are more likely to receive an authoritative answer.

Thank you for the suggestion.


text:
Which species is this in below picture? Can you please give me some details or reference link?

Can you name this species ? What are some characteristic ?
Size: 2.5 inches to 3 inches
Diameter: 1mm to 2 mm
Can crawl like millipede but little slow.
Always in red colour
Get fold like in one of image tile when touch.
After sometime it able to crawl again.
Has too many thin and small legs both the sides.
Mostly seen in June to August
Don't know if venomous.
Place : North India about 150km south from Himalya Mountain.

Could you please edit your question add more details, for example: how big was this animal? Where did you find it and at which season? Could you observe any details that might be hard to see on the images? etc. pp

For hints on the information we need for species-id questions you can click on the tag under your post.

It's a millipede, but which one is very difficult without locality.


text:
Sabouraud dextrose agar breaking?
I recently started growing some Geotrichum Candidum (GC) on Sabouraud dextrose agar (SDA) beds. The SDA was poured into sterilized petri dishes. After setting the plates in a cooler (20 C) for a day, I then inoculated the plates with a tiny smidge of GC. The GC is growing happily in that environment.
However, today on day 3, I noticed a crack across the SDA like shown in the picture below.
What does this mean? Did I prepare the plate wrong? Or is my GC just a bit naughty and somehow burrowing into the SDA?
Please note I am not a trained biologist, I've learned the skills I require for my activity from online resources and advice.

It could just be the agar drying out.

My initial thought. The cooler is at 80 % relative humidity though. Isn't that enough?

I suppose evaporation can occur at any relative humidity less than 100%. Is the agar shrinking in terms of thickness and/or peeling away from the side of the plate? These are also signs of desiccation.

I see no signs of desiccation on the surface nor on the edges of the agar.

After closer inspection it seems to be desiccation. I've added a 1/4 teaspoon demineralized water in the lid (inverted dish).

@neydroydrec If that turns out to solve your problem, can you please add it as an answer to your own question? Then  it will help the next person with a mysterious crack in their agar.

Sure. Waiting for results.

I cannot be entirely sure about the cause as I have not been able to reproduce this situation subsequently, but based on the comparison of what I did before and do now, it seems the cause was the wrong dosage of agar per water, i.e. an excess of agar.
Hoping this may help others.


text:
Do breakthrough infections spread attenuated virus?
No vaccines are 100% effective, so it's possible that patient A catches Covid-19 even after receiving two doses of vaccine. I understand that the risk is low, and the symptoms will generally be mild.
Now, patient A infects patient B who is not vaccinated.
Will patient B experience mild symptoms, or will their chances of hospitalization, ICU and death be the same as they were at the beginning of the pandemic?

Why should B show mild symptoms?

@Chris, I read that a virus is often attenuated by introducing it into a species in which it does not replicate well (https://www.sciencedirect.com/topics/neuroscience/attenuated-vaccine). I thought that the virus does not replicate well in a vaccinated person either; then I felt that I was jumping to conclusions and I thought I'd better ask here.

Attenuating viruses is a long process and nothing you can achieve with one infected person. This virus replicates pretty well in humans, so this is not a factor.

I would bet that, if it's replicating well enough to become transmissible, it's probably not going to attenuate. But that's just my handwaving explanation without having a closer look at the literature.

There's no way to know what effect passage through one vaccinated individual would have on an unvaccinated individual. The relationship between a virus's fitness in a particular host and the severity of disease it causes in that host is not straightforward, but generally we would expect a virus variant that can infect a vaccinated host well enough to pass on to another to be MORE aggressive and therefore cause more severe illness. With SARS-2 specifically, there's a chance a vaccine-selected variant could be milder, if the way it evades immune response is by more selectively limiting infection to those cells in the lungs that are involved in forming respiratory droplets and aerosols. (here is a reference if you want to read about mucosal vs. systemic immunity in COVID) My gut feeling is that such a mutation is much more complicated and therefore less likely than mutations that increase immune evasion and replication speed; which would lead to more severe disease.
Passage through animals leads to attenuation because the cellular machinery and immune response are different. A virus optimized for cows is no longer optimized for humans. A vaccinated human is still a human though, the mutations that work in one will work in the other.
Here is a paper discussing how HIV adapts to the immune system of individual infected humans, and how those strains are 'pre-adapted' to closely related hosts. You may find it relevant.


text:
Make plant experience 2 growing seasons per year by moving it across equator semiyearly
If I take a typical plant (such as e.g. a rosemary plant or an avocado sapling) across the equator from Florida to Brazil and back every year, so that the plant experiences Spring in both places, will the plant experience two growing seasons? Or is there some genetic wiring in the plant to prevent this?

Is this a theoretical question? Because if you live in Florida, you would probably know that you can have already two growing seasons there.

Oh, can you elaborate on that? I don't live in Florida, so the question is theoretical in that regard--but the question is a practical one.

Maybe a real practical question would be better to post then. For theoretical questions you can better go to e.g., stack exchange biology

@benn I'm not sure what you mean. Are you suggesting the question would be more practical if I put in the actual state I lived in? That seems unrelated to what I'm interested in.

I mean, please ask what you really want to do, instead of describing a hypothetical situation (in places where you don't live). Just ask, I have this plant, I live here and there, how can I do this or that with it? You'll probably get a better answer than for this question, don't you think?

Thank you for the pointers @benn. The question I've asked is the one I'd like to have answered though

You know it's illegal to shuffle live plants around as described, right? Generally, afaik, plants can't tell time and perennials take the cue from the environment, so yes, you would get two growing seasons ala hothouse tomatoes. Some plants might need more time than others, so how well the plant would actually do depends on many specifics. For example, the stems might be to thin to support the fruit or flowers triggered by the seasonal sun because they didn't have enough time to vegetate and bulk up in the spring wind.

I’m voting to close this question because this is an hypothetical question, while this community wants actual problems (see tour). Or it would be better placed on stack exchange biology, since it is theoretical and has nothing to do with real gardening.

Hi @benn, just to repeat, this is not a theoretical question. This is a practical question that I'm concerned with. I've replaced the state that I'm in just to stay as anonymous as possible on the internet.

@dandavis Thank you for the message! I was not aware of legality issues surrounding this.

@dandavis: Plants take cues from the environment, so they might need a certain amount of cold, or other cues, before breaking dormancy.  This is something that you might expect to evolve in order to avoid the effects of an early cold snap in the fall.  In fact, many plants do require a certain number of "chill hours".  See e.g. https://ucanr.edu/blogs/blogcore/postdetail.cfm?postnum=16468

I think you'll find there's no "typical" plant.

@Armand interesting, could you elaborate?


text:
When does a virus become a different species?
Related:
When does one decide to refer to a virus as a new variant?
I've been thinking about all the news related to "variants" of the SARS-CoV-2 virus, including the infamous "Delta Variant". One thing that strikes me as odd is that there seems to be no discussion on the possibility of a variant of this virus evolving so much that it becomes a distinct virus species - something other than SARS-CoV-2 but clearly descended from it.
I know that biologists typically define a species as a set of organisms whose members can produce fertile offspring (that is, if two populations either cannot produce offspring or can only produce sterile offspring, they are considered two different species), but this definition would not seem to work here as viruses do not reproduce sexually.
So, is there a general definition or consensus on when a virus lineage has experienced sufficient genetic drift from its sister lineages that it is a brand new virus rather than a variant? Is it based on percentages of base pairs changed? Is it based on changes in the clinical effects of infection (e.g. if a human Influenza virus underwent a mutation that made it unable to infect humans but highly infectious to the spleens of small marsupials, then it would be a new virus, even if the mutation consisted of only a single base pair change)?
Somehow, I'm imagining that a future 31st century biology textbook is going to say something like this:

While SARS-CoV-2 is no longer with us, its descendants live on as a family of viruses that cause Exploding Camel Brain Syndrome as well as a distinct cluster of closely related species that cause muscle inflammation in dogs.

Take two coronaviruses and the closest relatives of both, if they have the same host species, same geographical distribution and are genetically close enough then they will experiment a lot of recombination and the phylogentic tree will become messy enough to make clear that they are not distinct species. Conversely if they don't have the same hosts or geographical distribution then they tend to be quite divergent genetically.

The general issue of what exactly a "species" is has been addressed numerous times here, in different forms. Some good answers can be found at:
Defining "species" (Are species an emergent property or an ensemble of quantitative differences?)
How could humans have interbred with Neanderthals if we're a different species?
When has an organism evolved enough to be called a new species?
and a so far unanswered question:
References for historical momentum in asexual species definitions
I think Remi.b's answer that says:

The concepts of lineage and clade / monophyletic group are much more helpful. IMO, the only usefulness of this poorly defined concept that is the "species" is to have a common vocabulary for naming lineages.

is the place to start. A virus "species" is just a label to a lineage at one point in time. When we discover separate lineages of a virus, historically they have gotten a new label. It's then possible follow the lineages from there into strains/substrains, etc.
SARS-CoV-2 was first identified as the cause of a novel illness with a placeholder name 2019-nCoV. Its relation to the earlier SARS-CoV lineage was quickly identified and it's now been grouped alongside SARS-CoV-1 as a strain of the SARS-CoV species. So, given that SARS-CoV-1 and SARS-CoV-2 are considered strains of the same species, it seems highly unlikely that any variants of SARS-CoV-2 will be known as their own species any time soon.
One could consider other virus lineages as well. Influenza A is a species whose subtypes are described by two antigens, H and N, giving the perhaps somewhat familiar naming convention like "H1N1" or "H3N2". Each of these has contained different lineages often named by those causing illness in humans or animals, but at no time have these been considered separate species, they are all still considered the same species Influenza A.
The naming conventions for influenza A are pretty solid from long-term study and following precedent. The International Committee on Taxonomy of Viruses sets some conventions for naming, but their principles are:

Stability
To avoid or reject the use of names which might cause error or confusion
To avoid the unnecessary creation of names

None of these attempt to put any standardized distance between what are considered "different" versus the "same" species across different lineages. The ICTV code says this in vague terms, bold mine:

The criteria by which different species within a genus are distinguished shall be established by the appropriate Study Group. These criteria may include, but are not limited to, natural and experimental host range, cell and tissue tropism, pathogenicity, vector specificity, antigenicity, and the degree of relatedness of their genomes or genes. The criteria used should be published in the relevant section of the ICTV Report and reviewed periodically by the appropriate Study Group.

So, different study groups choose which criteria to use, and these need not be the same criteria each time. Introducing any would likely result in this situation. Instead, we have a fairly ad-hoc system given there is no particular biological meaning to "species" except as a lineage label, and this system is governed as much by scientific history as by any set level of genetic similarity. In the interest of maintaining stability, it seems unlikely that new virus species will be recognized under existing known virus species without novel discovery.

ICTV says monophyly is the major characteristic: A species is a monophyletic group of viruses whose properties can be distinguished from those of other species by multiple criteria. from 3.20 ICTV code. Criteria include but not limited to Natural and experimental host range, cell and tissue tropism, pathogenicity, vector specificity, antigenicity, and the degree of relatedness of their genomes or genes

@bob1 Yes, but monophyly doesn't tell you where to draw the species line (as compared to some other level of classification). The other characteristics are vague and not consistently applied in different lineages.

I totally agree, you can randomly pull a branch out of the IAV H1 tree and call it monophyletic. Classifications in virus below about the family level are pretty wishy-washy in general. There are some where we can easily call it a species, but for many families it is very difficult.


text:
Is Thylakoid membrane continuous with the Inner membrane of Choloroplast?
This article mentions that thylakoid membrane is  continuous with the inner membrane of cholorplast

Thylakoid membrane encloses the innermost compartment or thylakoid
lumen. The inner membrane of chloroplast is sometimes continuous with
the thylakoid membrane. Thylakoid membrane is composed of
phospholipids and galactolipids. It is similar to the inner membrane
of chloroplast and also shares some characteristics with the
prokaryotic membranes such as cyanobacteria

but a answer on stack exchange on mentions that they are closed at the end

. Each , of these lamellae is composed of double membranes joined at
the ends & each membrane is 100-200 angstrom thick....

Accordind to me thylakoid membrane should be continuous with inner membrane because it has originated from the same membrane, but i am not sure about it??

key word, "sometimes" also what makes you think they originated from the same membrane, chloroplasts were likely one free living bacteria.

There is a third membrane (thylakoid membrane) enclosed inside the chloroplast, not any more membranes. This is independent of the double chloroplast membrane. It folds to form the thylakoids, enclosing the (continuous) thylacoid lumen.

Chloroplasts are surrounded by a double membrane similar to the double membrane found within a mitochondrion. Within the chloroplast is a third membrane that forms stacked, disc-shaped structures called thylakoids. Embedded in the thylakoid membrane are molecules of chlorophyll, a pigment [...] The thylakoid membrane encloses an internal space called the thylakoid lumen or space. Other types of pigments are also involved in photosynthesis, but chlorophyll is by far the most important.

Image (CC) and information source: OpenStax, Concepts of Biology


text:
In lichen, do the fungi consume the oxygen produced by algae?
Is the oxygen produced by algae in photosynthesis consumed by the fungi, specifically in marine lichens where oxygen is less abundant? I am wondering this because of a speculative evolution project.

Exchange of gases between lichen symbionts has been demonstrated for Flavoparmelia caperata. Note that this is a foliose lichen species, though the findings may be generalizable to marine lichen.

We discovered the first evidence that photosynthetic O2 and respiratory CO2 mutually power the lichen symbiosis, together with the previously recognized exchange of Calvin-cycle sugars and water.

Ten Veldhuis MC, Ananyev G, Dismukes GC. Symbiosis extended: exchange of photosynthetic O2 and fungal-respired CO2 mutually power metabolism of lichen symbionts. Photosynth Res. 2020 Mar;143(3):287-299.

Thank you! This was very helpful

@katzenklavier if mine was indeed a helpful answer, I would appreciate if it was accepted. Seeing no other answers in the weeks since this was posted, I think this is reasonable.

done, sorry, I'm not to knowledgeable about this site


text:
Can anyone identify this seed, pit, or nut?
I found this on the recessed top of the intake manifold of my car engine.  It may have been there for weeks.  It was likely brought there by a rat or squirrel who was unable to chew through the outer shell/husk.  The white part seems to be where an animal gnawed on the outer portion.  Note the orange color where it was apparently not chewed on.  It likely was deposited in my engine compartment by a critter somewhere in inland/coastal southern or central California.  The air temperature when I found it (while changing a headlamp) was 106 degrees F (41 degrees C) and the temperature of the engine routinely gets well above that.  It has been well-toasted.
The size-reference coin is a US one cent piece that is about 19 mm in diameter.
I think it had the very faintest citrus aroma when I first found it and I thought it was a small orange (orange outer skin, white pith) that had been dehydrated and then chewed on by a small animal.  Then I shook it and it rattled - clearly not an orange.  When I cracked it open with a large pair of pliers I found the 'nut' that you see in the images.  It smells faintly nutlike and has a slightly waxy/oily finish - something like the appearance of a skinned hazelnut.  Note that the 'nut-meat' has shrunk away from a dark, shiny skin.
I haven't cut or tasted the nut-meat myself on the off chance it is toxic.
Are there any forensic botanists out there?

I'm going to go with California Beaked Hazelnut (Corylus cornuta).
While it is hard to tell from the chewed outer, it has the reddish-brown colour of hazelnut shell, and inside the shell is a dark brown papery layer. The nut (without the papery layer) is smooth and rounded

Certainly looks very similar to hazel nuts I grew in IL

This one is somewhat larger than any hazelnut I have ever seen.  And I don't think I've ever traveled in that particular car as far north as any of the areas noted as its natural growing area.  But that doesn't mean that it wasn't transported to somewhere I had travelled and was picked up by a naïve squirrel who couldn't figure out how to open it.

@OCPatch - people grow them in their gardens too; they are certainly available from nurseries. The nuts get up to about 4 cm/1.5 in long, so that's pretty big for a hazel, but not outside the realms of size for your one. The main argument against is the bumpy shell to my mind - hazels are all smooth AFAIK. Could be a pit from a (large) fruit?

@bob1 - Good point about people maybe having them as a novelty plant.  If it weren't for the orange and white husk I would have guessed it could have been a small avocado pit.  It could have been a small whole avocado but for the red/brown/orange outer skin and the hard, dried husk on the outside.


text:
What is the weight percentage of all people as compared to all Natural life?
If we compare the total mass  with the mass of all Naturally living beings with all creatures on Earth, be they bacteria, viruses, fish, insects, plants, etc., then what is the weight percentage of all people?
I ask this because I saw it mentioned that once people and all life they cultivated made up 0.1% of all animals and now 98%. With an exclamation mark. I am not sure if these were percentages of the total number of animals or their weight. I guess it is the number.

Why is the question downvoted? Please give a reason. I dont care about downvotes but I dont like irrational ones. Is it about the word Natural? What is Natural?

This has been studied in this paper, and they came up with:
Total biomass = 550 gigatons of carbon
Human biomass = 0.06 gigatons of carbon
So this would make humans about 0.01% of all biomass.  If this sounds like a little, a couple of points are worth mentioning:

They highlight that the mass of humans is an order of magnitude higher than that of all wild mammals combined.
Global human-made mass exceeds all living biomass.  This is mostly concrete and aggregates.

Graphical representation of the global biomass distribution by taxa. (A) Absolute biomasses of different taxa are represented using a Voronoi diagram, with the area of each cell being proportional to that taxa global biomass.  (B) Absolute biomass of different animal taxa.

Biomass and anthropogenic mass estimates since the beginning of the twentieth century on a dry-mass basis.

Wow! Great answer. Luckily we form a small part. For every person 100 000 kilo!

10,000 Kg actually.

I'm surprised that livestock and humans are so close in mass. I'd thought that livestock would be higher, given the inefficiency of meat.

@jakebeal I'm sure human omnivory helps, but also that the life of livestock is so brief. Chickens are slaughtered around 6 weeks age, pigs at 6 months, beef just over a year. A dairy cow produces about 10X its weight in milk per year (though of course a lot of that is water), a hen >3X its weight in eggs.


text:
Can enzymes be externally administered?
I was reading about Tay Sachs disease - it is essentially the deficiency of the enzyme hexosaminidase. Why can't the disease be treated by administering the enzyme (prepared artificially/extracted from other living things)to the patient?

A good start for your research is to look at where the enzyme normally acts, and how a replacement enzyme might get there.

The idea of using enzyme replacement therapy for Tay-Sachs has been around for a long time (here, for example). I don't know what the present status is, but a quick look at New Approaches to Tay-Sachs Disease Therapy seems to suggest that things haven't changed that much.  One problem is that an enzyme administered in the periphery will not cross the blood-brain barrier.

In general, yes, administration of enzymes in some form or another can be used to treat a deficiency. A common example of this is the use of lactase to treat lactose intolerance. Since lactose intolerance results from the body not producing enough (or any) lactase, you can take oral lactase to alleviate the symptoms:

Lactase products are tablets or drops that contain lactase, the enzyme that breaks down lactose. You can take lactase tablets before you eat or drink milk products. You can also add lactase drops to milk before you drink it. The lactase breaks down the lactose in foods and drinks, lowering your chances of having lactose intolerance symptoms. - NIDDK

For some deficiencies, a general strategy used is gene therapy, which provides a functional copy of a gene to an affected person's cells. The advantage of gene therapy is that, rather than repeatedly dosing with enzyme, you give the cells the ability to make the enzyme/protein that is lacking, which results in a longer-lasting therapy. This can also facilitate delivery to hard-to-reach places (e.g. you might not want to repeatedly inject enzyme into the liver, or brain, but if there's a vector that can target that tissue you can just inject it intravenously).
I'm not overly familiar with Tay-Sachs, but there is some good information in the comments that one of the commenters will hopefully expand into an answer.


text:
What's happening in the "C" and "T" stripes of a covid test kit?
I have a COVID home test kit which produces C and T (control and test) stripes when the solution is applied to the strip. Something similar happens in pregnancy test kits.
I understand the purpose of a control and test response, but what is the difference in mechanism?
In a negative test, why will C show up even though T does not?
In a failed test, why will C not show up even though T does?
Also, these stripes are somewhat distant from the spot at which the solution is applied. Why the separation?

@tyersome Laboratory techniques in biology are on-topic here, and though I think there is an argument that it would fit more securely at Medical Sciences it's reasonable to have it here as well.

@BryanKrause — OK, I'll withdraw my close vote.

This is a lateral flow assay.

[image source]
A sample is applied at one end of the strip and flows across to the other side by capillary action. It first encounters antibodies against the target antigen and which are conjugated to some reporter (in the image above, the reporter is colloidal gold). When the sample contacts these antibodies, they too will begin to move across the test strip. If the target antigen is present in the sample, in your case COVID, these antibodies will bind to it.
The sample then crosses the test line. The test line contains antibodies, immobilized to the strip, against the target antigen. If the sample contains the target antigen, it will bind to these antibodies and stop moving. Since the antigen is also bound to the reporter antibodies encountered earlier, these antibody/reporter conjugates will become concentrated at the test line and produce a visual change on the strip.
Finally the sample encounters the control line. The control line contains antibodies against the reporter antibodies. Regardless of whether the target antigen is found in the sample, the reporter antibodies will bind here and produce a visual line. The purpose of the control line is to give a visual indication that the sample has in fact travelled across the whole strip.
In a negative test, the lack of antigen means the reporter antibodies will not stop moving at the test line and will only be bound at the control line.
There are several possible reasons for a failed test (when no lines are visible or the test line is visible and the control line is not). Among these, it’s possible the sample has simply stopped migrating across the strip before reaching the test and/or control lines. Or it could be that the antibodies have degraded due to improper or prolonged storage such that they no longer bind properly.

Note that this answer is just a general description of a sandwich lateral flow assay. There can be variations of this procedure in specific tests.

There's another possible explanation for test failure - antibodies failed to bind. This could be a result of improper storage, with too hot most likely, followed by degradation of the antibodies (time).

@bob1 That’s a great point, thanks. I’ve updated the answer accordingly. Feel free to edit further.


text:
Why is it good practice to prepare western blot samples in pairs when you have two experimental groups?
I have done some Western blots where I have analysed the expression levels of a certain protein in brain homogenates from wild-type and knockout mice. When preparing brain homogenates, I was advised to prepare them in pairs, so that on the same day two brain homogenates, one from a wild-type mouse and the other from a knockout mouse were prepared.
I know that paired analysis is useful for comparing differences visually on the blot between samples from two experimental groups. However, I was wondering whether there are any other benefits (e.g. for statistical analysis) to preparing samples in pairs for a Western blot analysis besides just ease of visual comparison? Any insights are appreciated.

This point is not unique to Western Blot, but to any case-control study: if there is variability inherent in the preparation procedure, this variability will be reduced when the two samples are prepared simultaneously. This is perhaps easier understood using an analogy: if a toaster fits two toasts, but there is variation in the toasting time - the toasts that were in the toaster together are likely to be cooked/burned to the same level.
Statistically, one takes the full advantage of such improvements when using the statistical techniques specifically designed for paired data, such as paired difference test (see also paired samples t-test). But even unpaired statistical methods are likely to show better performance (in terms of identifying significant results).


text:
which carbohydrates are produced in the Calvin Cycle?
I understand the structure of simple carbohydrates (di- and monosaccharides, etc.,) but I'm encountering inconsistent/confusing nomenclature while trying to understand the Calvin Cycle.  One source shows that "the carbohydrate products of the Calvin cycle are three-carbon sugar phosphate molecules, or 'triose phosphates', namely, glyceraldehyde-3-phosphate (G3P)."  Are F6P and E4P also carbohydrates?  Are ALL n-carbon sugar phosphate molecules classified as carbohydrates?

yes they do.  you can delete your comment.

Sorry typo. I meant F6P and I meant product. But think about where I’m coming from. The Calvin cycle may have many intermediates, but it is means to convert three molecules of carbon dioxide to a triose phosphate product. The subsequent conversion of triose to hexose may be part of the dark reactions but is not part of the Calvin Cycle. It just feeds into a linear pathway akin to gluconeogenesis.

doesn't address my question at all

If your question is not in the title but about the definition of carbohydrate, you can easily find the answer on the web rather than posting here. Hint: try the Berg chapter on Carbohydrates and the following section 11.1. The phosphate does not contribute to the definition but does not cause an exclusion.


text:
When do Blue Jays form their crests?
I've noticed that not all Blue Jays appear to have a crest. I know that at certain times the crest may be down and less visible, but I notice in most images of juvenile Blue Jays they don't appear to have a crest. I'm curious if the crest forms later on or if Blue Jays are born with a crest?

Short answer
It seems like blue jays form their crests as adolescents, after their first post-juvenal molt before their first winter.

Longer answer
The top of the head of a bird is called the pileum, with the very top called the crown. As far as I can tell there is no particular distinction between "crown feathers" and "crest feathers", rather the presence of a "crest" is because the crown feathers are longer and stand out from the rest of the head.
Juvenal plumage
Blue jays born with their natal down will molt within the first two weeks to get their juvenal plumage. Dwight (1900) is quite descriptive of the juvenal plumage, but does not mention any crest, only that the pileum is a "flax-flower blue separated from the blue-tinged white forehead and white superciliary line by a narrow black line".
Crown feathers are longer after the first prebasic molt, forming a crest
The first prebasic molt refers to the (partial) loss of the juvenal feathers. Bancroft & Woolfenden (1982), examining young birds captured in Florida, found 8% in the first prebasic molt of the crown/head area in the first half of August, 89% in the second half of August, 78% in the first half of September, and 54% in the second half of September. So it seems most birds are getting through this molt by mid-September.
Dwight (1900) writes that "young birds become practically indistinguishable from adults" around this time and that compared to the juvenal plumage, bold mine:

the blue of head, back and wing coverts now distinctly barred with black and much brighter, and the crest feathers longer

I haven't found mention of crest feathers rather than crown feathers in descriptions of the juvenal plumage, with one exception I'll get to below, so I'll tentatively say that a blue jay forms its crest as part of this first prebasic molt in which the first winter plumage is evident.
Blue jay crest in behavior
The crest position of blue jays differs across behavioral contexts, ranging from erect to pressed against the head. Conant (1972) mentions the crest specifically as part of several different postures/behavioral contexts (parentheses are my paraphrasing):

In neutral posture, the crest and plumage are relaxed

While a Blue Jay is asleep, the crest is relaxed and the body plumage is usually fluffed

(while "investigating"): the crest is fluffed

(during "mild aggression"): the crest is fluffed

(during "intense aggression"): crest is fully erect or ruffled

(during avoidance/submissive posturing): the crest is relaxed or sleeked

(during "courtship feeding solicitation"): the crest is relaxed or sleeked

And finally, the one section that makes me a little uncertain, Conant (1972) describes the "nestling alarm freeze" behavior of nestlings when their nest is disturbed or they hear an alarm call:

The crest and body plumage are sleeked, wings closely appressed to the body, and tail closed.

My guess is that she's using "crest" here to mean the crown feathers, and just referring to them as the "crest" since that's the word used when describing the other behaviors that primarily involve birds with adult plumage. However, it raises a bit of doubt and perhaps the other descriptions missed that there is also a crest in the juvenal plumage, hidden in the alarm/sleeked position under the watchful presence of predators scientists. Dr. Sheila Conant is now Professor Emerita at the University of Hawai'i at Manoa; one could ask her, but I think it has been awhile since she studied blue jays closely.

Bancroft, G. T., & Woolfenden, G. E. (1982). The molt of scrub jays and blue jays in Florida. Ornithological Monographs, (29), iii-51.
Conant, S. (1972). Visual and acoustic communication in the blue jay, Cyanocitta cristata (Aves, Corvidae). The University of Oklahoma.
Dwight, J. (1900). The sequence of plumages and moults of the passerine birds of New York. New York Academy of Sciences.