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What causes people to feel sleepy due to recycled air?
I notice this the most in cars, when I set the air con to recycling air (instead of pulling in fresh air). After a while, I start to feel sleepy, and the sleepiness passes almost as soon as I open a window or change the air con setting to bring in fresh air.
I notice it also in shopping centers, or long bus rides, where there is inadequate fresh air. I know a lot of people who get sleepy from this, but also some people who just notice the air smelling 'stuffy' - but there's no particular smell, just 'stuffy'.
What causes recycled 'stuffy' air to smell stuffy? Is the sleepiness to do with increased Co2 / decreased O2 due to people breathing? Then is the 'stuffy' smell just the smell of CO2?
Any ideas how big of a change in concentrations we're talking about? Wikipedia says concentration of O2 in air is 20.95%. So are we talking about a drop by less than 1%, or a drop by a few %, etc.?
Is this 'stuffy air' bad for you? e.g. hypothetically if I have trouble sleeping, could I seal my bedroom (as sealed as an ordinary passenger car is), install an air con, and have it start recycling air when it's bedtime. Would this be bad for me long term?

do you have any reference besides your own experience to confirm that other people are also feeling sleepy with recycled air?

Yeah, just google "recycled air drowsiness". It doesn't seem to be unusual, and there are some articles / forum threads where people talk about CO2 levels. Although nothing about O2 levels (Does higher levels of CO2 necessarily mean lower levels of O2?). I'm more interested about whether it's bad for you, i.e. the sealing my bedroom and using an aircon hypothetical.

Happens with me too!! :D But wouldn't recycled air also have lesser oxygen?

@Polisetty yup that's kind of what I'm wondering about...

It's more of a psychosomatic phenomenon.  Your car isn't air tight, even if you have the internal air switch on.  Hence you can sleep in your car with the windows up and not die.  If it was O2/CO2 content you'd never know the difference and not be able to identify it as stuffy. Neither of those gases have a smell.  Likely it is reminiscence of smells in that air or the warming of the air that is making you sleepy.  If you actually sealed your bedroom, depending on it's size and your height from the floor, you could die from the CO2, so i would say take some Ambien.

Lot of questions in your post. You should try to emphasize one of them

Good question. CO2 doesn't smell though, it's one of the many odourless gases. That stuffy feeling is a very mild CO2 toxicity. But there would most likely need to be a change of more than 1% for a significant change in comfortability as we exhale 15.74% of that of that 20.95% unchanged. The sleepiness is caused both by the mild CO2 toxicity and the lack of O2 to your brain and muscles. Installing an air con largely depends on the size of your room (bigger is better), your age (younger is better), and your overall health, specifically how much physical activity your sustain on a day to day basis. Assuming you sleep for 8 hours you would only need 0.2 kg of O2 (0.6kg/24hr is needed for the avg. person at rest). If your room was the size of a twin bed (hypothetically) there would be around 0.15kg of O2. Taking the exact measurements of your room, you can calculate the amount of oxygen available using the molecular masses available on a periodic table. Personally, I feel you should be fine even without an air con but consider the factors listed above.
This is a very useful equation: kg = number of moles over molarity. But, you can always use a site like this: http://www.unit-conversion.info/molar-mass.html.
This is a copyrighted material so I can only give a reference: Organic and Biochemistry for Today, 7th Ed. ISBN 0538734310 Seager, S.L.; Slabaugh, M.R. Thomson/Brooks/Cole

Isn't it 75.13% of the 20.95%?

No 15.74% (approximately, most text books will give a range orbiting around 15.7%)

Which part of your answer is the reference relevant to?

It's semantics.  You've stated it "15.74% of that 20.95%", which sounds like 20.95% times 0.1574 giving you a return of 3.30% from the 20.95%.  75.13% of that 20.95% is 15.74%.

Carbon dioxide is not the only waste product which is exhaled. NASA scientist Wolverton goes into detail in his book, "How to Grow Fresh Air".  We exhale 70% of the body's waste products in gaseous forms.  Breathing these in repeatedly and at ever-higher concentrations causes a whole host of health problems, starting with, you guessed it, an inability to stay alert and sustain full brain function.


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bird identification by its singing
What bird is singing on background in this video?
https://www.youtube.com/watch?v=ckFIDeanJgg

First bird sounds at about 0:18

The bird singing at the beginning sec. 0:18 is a Nightingale (Luscinia megarhynchos). A recording with the same beginning is here http://www.xeno-canto.org/379628

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Can a mathematical function be assigned to ECG diagram?
This is a 12 lead electeocardiogram of a 26 year old male:
This is the graph of function $5sin(7x)sin(.5x)cos(3.25x)$
 This graph look quite similar to the ECG diagram.After sketching this graph, I thought whether ECG diagram could be assigned roughly to a mathematical function.
Question: Has anyone ever tried to even roughly assign the diagram to a mathematical function? Is it even possible?

The links are broken or I can't open them from my android

Fourier series was my first guess, too. Is there any particular reason you would like to do that? I'm asking because if fitting is your concern, wavelet decomposition may be easier to work with. By the way, the links work for me.

I’m voting to close this question because it's not about biology.

Yes a function could be assigned to an ECG diagram. I don't know if that would be helpful in any kind of research. Anyway I believe that from a mathematical point of view that if you manage to include all the equations shown in the picture into a single one you should get what you are looking for.

I have not made the diagram it was taken from this paper https://www.researchgate.net/publication/286584223_Design_of_a_synthetic_ECG_signal_based_on_the_Fourier_series by Radana Kahankova.

I was a high school back then when I asked this question. Obviously I had no emphasis on the graphical analysis being useful. haha

Try this:
$f(x)=-20(e^{\left(\operatorname{mod}\left(x-10,\ 20\right)-10\right)}*(e^{5\left(\operatorname{mod}\left(x-10,\ 20\right)-10\right)}-57*e^{4\left(\operatorname{mod}\left(x-10,\ 20\right)-10\right)}+302*e^{3\left(\operatorname{mod}\left(x-10,\ 20\right)-10\right)}-302*e^{2\left(\operatorname{mod}\left(x-10,\ 20\right)-10\right)}+57*e^{\left(\operatorname{mod}\left(x-10,\ 20\right)-10\right)}-1))/(e^{\left(\operatorname{mod}\left(x-10,\ 20\right)-10\right)}+1)^7$

Er, how does anyone know whether this is right or not?

Just copy the tex and paste it here: https://www.desmos.com/calculator

To be clear, there is really no biological reason to do this. ECGs are not collections of these sorts of functions. Fitting something like this is just a curiosity and gives you no understanding that you can't find in the original signal.

@Amad I see what you did here. You ploted a graph that slightly resenbles an ECG (Only QRST). Appreciate your intend to answer but I am afraid this is not what the author of the question's looking for.

@BryanKrause Haha I was a teenager back then when I asked this question and had no interest in the biological importance of the graphical analysis

@Mockingbird Yeah, that's kind of what I figured, I'm just going to close it. It's effectively a variant of https://math.stackexchange.com/questions/54506/is-this-batman-equation-for-real which is also closed over at Math.SE.

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Why fingers in human fists get folded in absence of neural stimuli?
Background:
I noticed that the fingers in our fist tend to get folded in absence of neural stimuli. The same thing happens in case of our hands and legs.
Question:

What is the mechanism behind this phenomenon?
Is there any positive or negative outcome of this phenomenon?

https://www.reddit.com/r/explainlikeimfive/comments/2yupq3/eli5_why_do_our_fingers_naturally_curl_when_our/

I would assume that as a result of the lengths of the tendons and the arrangements of the various flexor + extensor muscles, the slightly folded positions (curved) fingers, hands, legs, etc. are the "default" positions, in which both antagonistic muscles are in their relaxed state (thus without neural stimulation)
The evolutionary benefit of the slightly curved fingers, hands, legs, etc. may have been more relevant in our primate ancestors than it is today


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A good software for agent based modelling?
Hello i'm gonna start my master degree in systems biology and i'm thinking of working with agent based modelling, but i really don´t know which platform can be the best to simulate interactions between cells, like chemotaxis communication or between molecules. Some of my advisors have recommended me Netlogo because his simplicity and good interface, but i don´t know if it is enough powerful to run simulations of many interactions between a lot of agents. I hear that MASON is also good but you need a little background in java programming. So, which one do you think it could be the most appropriate or which other platform can you recommend me that also can be good?

Can you please elaborate a little more on what you are trying to achieve / to simulate? Don't be afraid of needing "little background in Java" as you will learn quickly.

My boss is a big fan of Repast HPC, but since Repast is a C++ framework it might not be the right choice for you. It takes a loooong time to write a good C++ program (even for someone who already knows the language fairly well), although it will run very quickly once it's written. A one or even two year long Master's program will end up going by surprisingly quickly, so if I was in your shoes I'd choose to start with the simplest thing possible (ie Netlogo). Once you have a finished product, even if it's somewhat more simplistic than you'd like, it'll be much easier to work your way up from there.
Really though, consider the choice of modeling framework to be part of your research project! Only you can come up with the right choice for your project, though as a practical matter you should heavily favor any framework that at least one person in your department already has some experience using. Things will go wrong, you will have questions, and Stack Overflow won't be able to answer all of them.
Here's a list of the more interesting agent-based modeling frameworks that I found from a few minutes of googling:

Repast HPC

pros:

C++ based
The only performance focused one of the bunch

cons:

C++ based
For simple models, would be like building a supercomputer to use as a pocket calculator

Netlogo

pros:

Focused on being accessible to non-programmers
Scripting language seems pretty straightforward

cons:

In my experience frameworks that try to implement their own scripting language in an attempt to be accessible to non-programmers ultimately end up being much more complicated to use than frameworks based around an established language. But I'm not the target audience.

Mesa

This one is Python based, so it's the one I would personally try first since I find Python to be the best language for quickly writing scientific programs of reasonable complexity. That's my own personal bias, so your mileage may vary

MASON

The fact that Repast HPC does not imply that a user will need to modify the model by him/herself. It should not be a "con". Also, it does not take so much time to code in C++ in comparison to other languages as long as the project is important enough. Disclaimer: I know nothing about the softwares.


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The Fish-Tetrapod Transition, evolution of the "elbow" in Stem Tetrapods
The Acanthostega and Tulerpeton limbs seem to form "elbows" in an axis perpendicular to the flexor and extensor plane of the fin. They seem to "flex" their "elbow" forwards, pre-axially. And, I assume, keep it permanently "flexed", a bit as if their humerus, ulna, and radius has been one single "V-shaped" bone. This adaptation positions the primordial hand forwards. Is this pretty much correct? Why I wonder, I always understood elbows as bending in the flexor/extensor plane, but in the first terrestrial life it seems to be in the pre-axial/post-axial plane. That probably has implications for how limbs continued to evolve, and for the embryogenesis of limbs in mammals like humans. I found that interesting.

keep in mind the orientation of limbs has changes between early terrestrial life and yourself. A salamanders forelimb bends very differently than yours. Consider you are looking at a 2D representation of a 3D structure. Also what makes you think those early limbs could not flex in the flexor/extensor plane?

Link to get you started. https://www.geol.umd.edu/~jmerck/geol431/lectures/d05limbs.html

Try reddit/ask paleontology or something. That question confused me. Simply put "it looks like these species had limbs at a fixed angle, is that correct?" Not really! You'd have to find cartilage wear marks and round joint zones on the bone to figure that out, and the litterature barely gives much info on the biomechanics of the forelimbs.

The current research doesn't venture many details on the elbows/radius/ulna and locomotion biomechanics.
For the moment they just say the elbow was "slightly flexible" and that the bones were transitioning towards a round shape.
You can research deep into the resources and will perhaps find more.
Here are a resource which give context, found via "locomotor performance in stem tetrapods"
https://www.researchgate.net/publication/236460049_Historical_Perspectives_on_the_Evolution_of_Tetrapodomorph_Movement
There's also a 3D study of the legs here: https://www.researchgate.net/publication/227857349_Three-dimensional_limb_joint_mobility_in_the_early_tetrapod_Ichthyostega
https://sandykawano.weebly.com/locomotor-biomechanics-for-moving-onto-land.html

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Generating Cartesian coordinates of each atom in protein chain from the internal coordinates using python or some software
I am trying to compute Cartesian coordinates of backbone atoms and side-chain atoms (C beta alone) for a given set of internal coordinates (bond lengths, bond angles and dihedral angles) I have written a code for the backbone alone (i.e) to construct cartesian coordinates of each atom in backbone from the respective internal coordinates(without side chains). However I got to know that this can be done in a software (maybe in PyMol or VMD). I am completely a beginner in this field of biochemistry/bioinformatics/biophysics. Does it really possible to do this in software like PYMOL/VMD? I'll be very happy if I can do this in python itself. I want to generate cartesian coordinate of a given tetrapeptide for all possible Ramachandran angles (within the allowed region)

Do you have the structure of the tetrapeptide provided or you want to run a simulation and get all the possible dihedral angles (they are not called Ramachandran angles)?.

No, I have just bond angles, bond lengths (standard values). Now for a given set of dihedral angles (Ramachandran angles) for tetrapeptide I need to generate the cartesian coordinates. I need to simulate the structure. I don't want the minimum energy structure. I just want to get the structure of tetrapeptide for a given set of internal coordinates ). @RoniSaiba

VMD by itself can't generate MD trajectories. You will need some other software like NAMD or the like to do so. However, once you have a trajectory, you can write a script (in Tcl) for VMD which will give you the cartesian coordinates of the atoms in a txt file which you can then process in python, R etc. Here is a Tutorial on how to use NAMD and VMD to get the job done. You will have to first make a .PDB of your tetrapeptide. You can use Avogadro to do that.

Is it a biology or bioinformatics STACK forum question ??? It could be also a chemistry one if talking about molecular dinamics ?? A penny for your thoughts

Have a look at Biopython
There are specific questions about the specific internal coordinates on Bioinformatics forum i.e. :
https://bioinformatics.stackexchange.com/questions/18849/help-using-biopythons-ic-chain-functionality-for-getting-protein-3d-coordinates
or
https://bioinformatics.stackexchange.com/questions/19570/read-pdb-file-extract-dihedral-angles-modify-dihedral-angles-reconstruct-cart/19597#comment28645_19597


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Why are Ramachandran angles of first and the last amino acid not necessary to define the full 3D structure of a protein chain?
I have come across an online ppt slide of the bioinformatic algorithm where it is said that first and the last amino acid Ramachandran angle is not necessary to tell all its internal coordinates. Is it really not necessary for any simulations while predicting the 3D structure of proteins? For instance, if we have a protein chain of N amino acid sequence, there will be 2N dihedral angles. Of which we need to specify only the 2N-2 (apart from the first and the last amino acid dihedral angles) dihedral angles. Why the two angles are ignored? Let's assume all the bond angles and bond lengths are provided for the entire chain.
I have seen this statement in the following ppt, slide number -9, titled representation of internal coordinates, under bullet point 3.
https://www.cs.umb.edu/~nurith/cs612/Manipulation.pdf

Welcome to Biology.SE! Please take the [tour] and then go through the [help] pages starting with [Ask] questions effectively on this site and [edit] your question accordingly. In particular, we expect you to do research on your own and then, informed by what you have learned, ask any questions you still have (ideally with references to reliable sources). What's different about the bonding of the terminal residues? See also this sites criteria for "homework", which can apply to questions even if they are not assigned as homework. Thanks!

Think about the case of a chain of N=3 points in space. There are only angles associated with the middle point, the two endpoints don't have angles associated with them because they only have one incident segment rather than two.


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Allowed Deviations in fixed bond length and bond angles in peptides from the typical values
I am using frag builder python module to generate peptide structures to compute the interaction energy for ensemble of peptides of a given sequence for a fixed bond lengths and bong angles. However, the fixed bond angles are slightly deviating from the typcial values seen in the literature. For instance, the bond angle of $C_{\alpha}--N--C$ is less than the typical value of 121 degrees and the bond angle of $C_{\alpha}--N--C$  as produced by frag builder is 111.7 degrees. Hence peptide plane is still planar. Yet the distance between the two successive $C_{\alpha}--C_{\alpha}$ is 3.721 A. Is it quite wrong to deviate by 10 degrees?

I don't know "frag builder" protocol; can you please provide a citation? Building a conformer is relatively simple compared to subsequently energy minimizing it. Can you also hint at the size of the peptide, and what it's interacting with? The planarity of the peptide plane depends on how its moieties are H-bonding to other groups.

@Ryan Fragbuilder article: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3961104/ . Size of the peptide I am working on various sizes of peptides such as 6, 10, 18, and 34. The planarity of the peptide bond is unaffected. as it is still planar.

@Ryan Also, it is just interacting with itself in a vacuum. I am minimizing only van der Waal interactions and electrostatic interactions.  I will extend this minimization with the solvation effect later.

Single-conformation descriptions of the native-state ensemble, under ambient conditions, are expected to have close to ideal geometries. This is a result from Statistical Mechanics; the probability of non-ideal geometries (say a given conformer $i$ with internal energy $E_i$ compared to a native/ground-state energy $E_0$) scales with their Boltzmann factors, $e^{-\beta (E_i - E_0)}$. But many backbone dihedral angles are isoenergetic, especially outside of tertiary structural constraints.
FragBuilder has fairly extensive treatment allowing for rotamer sampling and conformer regularizing. I expect you used its built-in energy minimization with the MMFF94 force fields, as in (code quoted from 1):
pep = Peptide(sequence)
pep.regularize()
print pep.get_energy()

So the question can be rephrased, can the dihedral angles $\phi$ and $\psi$ be more than ten degrees from their ideal values? And the simple answer is yes. That's well within the variation of conformations within a given rotameric energetic minimum.
Here's one study looking at these dihedral angle fluctuations in solution. It cites the Dunbrack library. In that paper, they study the dependence of side chain dihedral angles on main chain ones, and they sample angles $\phi$ and $\psi$ in 10 degree bins showing that a large variation in these angles is possible, especially outside the context of regular secondary structures.
I wanted to cite a current paper from a good theoretician, so I found this from DJ Wales. Here they use a state of the art sampling approach to generate a tripeptide library, whose statistics are compared to experimental structures. You can read their procedure, but I'll quote the relevant part here:

For each tripeptide, the low-energy conformations contain many $\phi$,
$\psi$ combinations, and the observed rotamers of the central amino
acid are averaged over these backbone configurations, resulting in a
backbone-independent library...Using tripeptide structures allows
local spatial effects on rotamers to be probed without interference
from stabilization in protein folds.


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Are parasympathetic nerves different from motor and sensory nerves?
So the nerves leaving the spinal cord are either motor or sensory (only?). But what about the cranial nerves? For example, the cranial nerve vagus is a parasympathetic nerve. Are parasympathetic nerves divided into categories of motor or sensory? Or is it just a parasympathetic nerve?
If it is indeed composed of motor and sensory nerves, then what about these nerves coming from the spinal cord? Should they not be of a broader name? Just like nerve vagus is of the parasympathetic nervous system.
So, it goes like this: parasympathetic -> n. vagus -> motor or sensory, right?
What about: ? -> n. median -> motor or sensory

There are many ways to divide and sort peripheral and spinal cord nerves and axons.
One division is into "autonomic" (further divided into sympathetic and parasympathetic) and "somatic" nervous system; the somatic nervous system is the part controlling the skeletal muscles and also involving the somatosensory system: touch/pressure/etc, as well as proprioception and proprioceptive reflexes.
Another division is directional: afferent versus efferent. Afferent nerves/fibers transmit information towards the central nervous system; efferent nerves/fibers transmit information away from the central nervous system, such as to control muscles.
Usually, when I hear "sensory" and "motor" I would assume someone is talking about afferent and efferent parts of the somatic nervous system. They're not necessarily considering the autonomic system at all (there's a bit of a tradition in some subfields in biology/physiology to forget that others exist). But there are also some sources that seem to prefer avoiding introducing the terms afferent and efferent for students and still use sensory and motor. I can't know what is being done in the specific text you're reading.
That doesn't mean that the autonomic part of the nervous system doesn't involve sensory or motor functions, just that "sensory" is often shorthand for "somatosensory" and "motor" shorthand for "skeletal motor".
If you want to talk about nerves within the parasympathetic system (or autonomic more generally) are carrying information into the CNS or out of the CNS, I'd recommend using the words "afferent" or "efferent", though nothing is wrong about calling them sensory and motor, you just want to be clear you are not talking about somatic nervous system functions. Using those terms, cranial nerve X/vagus nerve is primarily made up of both afferent and efferent fibers of the autonomic nervous system.
However, nothing is quite so simple in biology, and the vagus also carries some skeletal muscle efferent fibers and sensory afferents.
For the cranial nerves more generally, I think it's important to recognize that the cranial nerves are not all homologous even though they're numbered in sequence - someone just naively counted all the "pipes" coming out of the brain and ordered them. I would not attempt to generalize among them besides that feature (and even the simple idea that "cranial nerves leave the brain" is a bit suspect!).
Some of the cranial nerves are really no different from the somatic nerves coming out of the spinal cord, they just happen to come out really close to the brain. Others, like the olfactory nerve and optic nerve, are quite special: they don't come out of the brainstem but rather the cerebrum, and arguably the optic nerve doesn't even really leave the brain if you consider that the retina is embryonically brain tissue.
For a quick summary from Sonne J, Lopez-Ojeda W. Neuroanatomy, Cranial Nerve.:

Cranial nerves I (olfactory), II (optic), and VIII (vestibulocochlear) are considered purely afferent. Cranial nerves III (oculomotor), IV (trochlear), VI (abducens), XI (spinal accessory), and XII (hypoglossal) are purely efferent. The remaining cranial nerves, V (trigeminal), VII (facial), IX (glossopharyngeal), and X (vagus), are functionally mixed (sensory and motor).


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sympathetic nervous system and vasoconstriction
At the moment I am very confused and I would highly appreciate any explanation.
When the sympathetic nervous system is activated because we are for example exercising, our blood vessels constrict. The reason for this is apparently so that we increase the blood pressure and we get more venous return. However, now comes my confusion, by causing vasoconstriction, yes, we increase pressure, but we decrease blood flow, so how does it increase venous return and also the stroke volume??
Is it that the sympathetic NS constricts arteries or veins or both? And why do we need to increase the blood pressure during exercise anyways? We just need to get more blood flowing to the muscles and brain and wouldn't this be done by vasodilation instead as it increase blood flow?
Thanks very much in advance.

Can you please provide a quote of where you read this (with a link)? We can't identify where your confusion comes from if we don't have the exact, written words and source of your information. Some of it is clearly wrong. (If it was your professor, you might ask them.) Thanks.

@Nur Ahmed, Great questions. You have astutely picked up on some of the complex mechanics of the circulatory system during exercise. Depending on exactly what you're talking about (pre-capillary sphincters or conducting arteries) both vasodilation and vasoconstriction occurs during exercise (respectively). One error in your reasoning: vasoconstriction actually does not increase blood flow, this is because cardiac output increases to compensate. Arterial vasoconstriction makes increased venous return make sense, the tube is tighter so more gets through to the other end.

@Nur Ahmed Increased venous return increases filling of the heart and so stroke volume increases. My understanding is the sympathetic nervous system primarily constricts arteries, although you should do some research there if you want to know if it constricts veins, or by how much comparatively. We need BP to increase during exercise to maintain perfusion pressure which would otherwise drop due to dilation of capillary beds. More blood does need to go to the brain and muscles but systemic vasodilation would stop that from happening by sending it to the gastrointestinal tract, etc too.

I will be answering my own question now since I finally seem to grasp the physiology and just in case of someone also being confused :) I can still be corrected though
So the sympathetic nervous system constricts SPECIFIC arteries and constricts ALL veins of the systemic circulation. Let's assume that this person is in fear.
So, I used to wonder, since constricting a tube, there will be less blood flow through it per unit time, so how does constricting the veins give rise to more venous return? So this is the thing, the veins actually store blood during rest! Also, remember that veins are not completely circular like arteries! They are like flattened circular tubes. So now when we constrict these veins, we make the tubule more circular and we propel more of that blood that was hanging in the veins because the movement of blood in the veins is slow and moves against gravitational force. Also, the resistance of the veins increases BUT so does the pressure. So you might think that the increase in resistance does not allow the desired venous return, BUT, the increase in pressure overweighs the increase in resistance. The increase in pressure produces this pressure gradient between the veins and the right atrium; the blood moves down the pressure gradient and it moves down this gradient faster as the gradient rises.
The sympathetic nervous system releases catecholamines, that being norepinephrine and epinephrine. There are these receptors with which these hormones interact with. In one case, when this hormone interacts with one type of receptor, it cause vasoconstriction, and when it interacts with another type of receptor, it cause vasodilation.
There are CERTAIN adrenergic receptors in CERTAIN places. In the veins, there are the receptors that cause vasoconstriction, specifically, these receptors are alpha 1 adrenergic receptors. Then we also have beta 1 adrenergic receptors in the heart, where when these interact with the hormone, they cause vasodilation. So we need vasodilation in the coronary arteries so that more blood can flow through them and allow the heart to work harder as the blood brings to the cells its metabolic needs, such as oxygen, glucose etc.
We also have beta 2 adrenergic receptors found in skeletal muscles, which after an interaction with the hormone, causes vasodilation and increases perfusion. As a result, allowing the muscles to work harder as they get more blood carrying its metabolic needs.
All in all, alpha adrenergic receptors cause vasoconstriction and beta adrenergic receptors cause vasodilation. Epinephrine excites more of the beta adrenergic receptors of the vessels; epinephrine has a slight vasodilator effect because epinephrine excites more of the beta adrenergic receptors of the vessels. Norepinephrine excites more of the alpha adrenergic receptors of the vessels. But high levels of epinephrine causes vasoconstriction of for example the skin arteries because there are more alpha adrenergic receptors in the skin arteries. Also, high levels of epinephrine causes vasodilation of the coronary arteries as there are more beta adrenergic receptors. Low levels of epinephrine causes vasodilation of for example the skin arteries as the beta adrenergic receptors have more affinity for epinephrine as the epinephrine cannot be easily stolen by the alpha adrenergic receptors to cause an overall vasoconstriction.
During fear, the sympathetic nervous system is trying to pump more blood to the brain and skeletal muscles so that we are more conscious and more ready to fight or run away. Therefore, for example, the skin does not need much blood in this situation, and hence the blood moves away from the skin towards the heart to be pumped to the brain. The arteries of the skin contain mainly alpha 1 adrenergic receptors, hence vasoconstriction occurs during high levels of epinephrine, and less blood is available for the skin. This is one reason why you get pale during fear.
Also, one very important difference to bear in mind, is that constriction of arteries DECREASES blood flow because it decreases perfusion, and the constriction of veins INCREASES blood flow because it increases venous return.
In conclusion, "sympathetic activation can cause arteries to dilate or constrict depending on the receptors it acts on. Sympathetic activation causes constriction of arteries in the skin, but it also causes constriction of veins in the systemic circulation, which improves venous blood flow and thus venous return to the right atrium of the heart. Sympathetic activation almost always improves the pumping action of the heart, whether its effect is on the arteries (e.g. dilation of the heart arteries and the resulting increased blood flow to the myocardium and increased pumping activity of the heart chambers) or on the veins (constriction of the veins and the resulting improvement in venous return, an increase in end-diastolic volume and an increase in the stroke volume of the heart chambers)" (My Professor).
And the very very narrowed down conclusion, is that THE SYMPATHETIC NERVOUS SYSTEM IS TRYING TO CENTRALISE THE BLOOD TO THE BODY WHERE IT IS NEEDED THE MOST, AND IT DOES THIS BY CONSTRICTING THE ARTERIES OF AN AREA OF THE BODY WHERE BLOOD IS NOT NEEDED MUCH, BY CONSTRICTING THE VEINS OF THE SYSTEMIC CIRCULATION TO IMPROVE VENOUS RETURN, AND BY DILATING THE ARTERIES OF AN AREA OF THE BODY WHERE BLOOD IS NEEDED THE MOST TO IMPROVE PERFUSION.
That was long but pretty amazing.
Sources: Wikipedia (Adrenergic receptor), Guyton and Hall medical Physiology Textbook, My Professor, Alila Medical Media (Mechanisms of Venous Return, Animation)


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Why is a genome of an organism only given in the 5' -> 3' direction?
If u look up a genome of a certain organism or virus, it's always given in the 5' to 3' direction. I understand that one can derive the other direction very easily by just constructing the complementary strand.
Since genes can lie on both strands, why is only one strand given?

Think a little about how complementary strands bind to each-other with respect to 5' and 3' ends....

Welcome to SE Biology. We use standard English here, rather than text abbreviations so please edit your question, replacing "u" by "you". This may seem pedantic, but it is all part and parcel of our aim to provide good clear questions that will attract answers of lasting use. All nucleic acid sequences are written in the 5' to 3' direction, to indicate the asymmetry of the phosphodiester bond, so are you asking for both strands to be presented, or the reverse complement of the genome sequence? And in what context? Cite a Genbank page and explain to us how you would like it different.


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Is there a resource/paper containing information about which co-activators are often associated with a given transcription factor?
Given a list of human transcription factors, I would be interested in which co-activators they are often associated with.
I imagine that one could combine co-expression, pull-down, and other kinds of data to get an idea here.

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related chapter:  Coactivators  •Encyclopedia of Cancer, 2008• Vol.1, p.714-714

useful information:  https://www.mdpi.com/2072-6694/12/8/2296/htm

This website can be used to search for protein interactomes:
http://www.interactome-atlas.org/
might help you.

Your answer could be improved with additional supporting information. Please [edit] to add further details, such as citations or documentation, so that others can confirm that your answer is correct. You can find more information on how to write good answers in the help center.

Most eukaryotic TFs (transcription factors) are thought to act by recruiting cofactors (Reiter et al., 2017).

“Coactivators” and “corepressors,” are cofactors and these are mediators of TF effector activity.

Do you mean you need the information of cofactors?


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Can the coding strand for an RNA act as the template for another?
Can the same strand of DNA act as a sense strand and an antisense strand at two different occasions of transcription and result in two different proteins?

Welcome to SE Biology. Please finish the [Tour] to learn more about how this site works. Could you clarify please. Are you only interested in total or partial usage of both strands for synthesizing proteins (partial being just overlap between the ends of ORFs with the opposite directionality, which is quite common in bacteria). And do you require that the two proteins to use the same reading frame (which I suspect would lead to frequent stop codons) or different ones? (And thanks for using sense and anti-sense, my own preferred terms.)

Yes, the DNA strand that is usually the sense strand, coding for the mRNA and protein sequence can also become the antisense strand if transcription happens in the reverse direction. This phenomenon called antisense transcription is a relatively recent discovery has been discovered to be quite pervasive in all types of organisms by sequencing all the transcripts in the cell, a method called transcriptomics.
Although the antisense transcript is usually a short non-coding RNA which plays regulatory roles influencing the stability of the sense transcript by it's complementary binding, in rare cases it can form a protein if it has the required site to initiate translation (ribosome bidding site) and the codons to make a protein.
Source - Pelechano, Vicent, and Lars M. Steinmetz. "Gene regulation by antisense transcription." Nature Reviews Genetics 14.12 (2013): 880-893.
Wikipedia - Antisense RNA
These old papers from 1994 talk about antisense proteins -
Do "antisense proteins" exist? J protein chem, 1994
Antisense overlapping open reading frames in genes from bacteria to humans Nucleic acids research, 1994


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Human biology - liver regeneration after laprascopic segmentectomy
I am trying to understand to what extent human patients can regenerate liver mass after laprascopic segmentectomy: what part of liver will be regenerated and how fully.
My work with sources is not very good, but here is what I have found so far:
Michalopoulos, G. K., & DeFrances, M. (2005). Liver regeneration. Advances in biochemical engineering/biotechnology, 93, 101–134.:
"Following surgical resection of the two anterior hepatic lobes of rodents accounting for ~68% of liver tissue, the remaining lobes undergo compensatory hyperplasia restoring the liver to its original presurgical mass"

However, the article notes that:
"..PHx model doesn't apply to most common clinical scenarios.. patients who must regenerate liver mass after hepatic surgery often have cirrhosis, hepatic viral infection, steatosis.."
From this question (If the liver can regenerate why can alcohol abuse permanently damage it?) I gathered that only healthy hepatic tissue in liver can regenerate: the epithelial tissue.
Cytotoxic drugs like alcohol lead to steatosis and cirrhosis. Cirrhosis is the substitution of epithelial tissue by connective tissue. This connective tissue not only can't regenerate: it doesn't perform hepatic functions.
Assuming that the patient has otherwise healthy liver tissue, if a laprascopic resection of liver segment Sg3 has been performed, what part of the liver will be regenerated?

Thank you in advance, and I would be happy to edit/update my question with more info.

The healthy human liver has remarkable ability to regenerate in only a few months after resection.
In a study of 98 healthy donors who underwent left lobectomy donation, Chen and colleagues found that donors started with a mean liver volume of 1154 cm³, had an average of 276 cm³ removed, and then had an average liver volume of 1065 cm³ 6 months later (2006. PMID 17100722). Thus, on average, 68% of the donated liver volume had regenerated in those 6 months.
In my research, I was unable to find a systematic study of the location or direction of regeneration. Although hyperplasia appears to be the mechanism of regeneration (Marongiu et al 2017. PMCID 5352916), intuitively, we should suspect that the remaining liver will increase in volume rather than the removed lobe suddenly re-spouting somehow like a salamander's tail.
This set of 3 CT scans from a study by Esschert and colleagues provides anecdotal evidence for this intuition (2009. PMCID 2710489):

Figure 1 from Esschert et al 2009 showing post-operative liver regeneration after 3 months, available here.
In addition to the return of liver volume, donors also have no evidence of decreased liver function at least as long as 5 years post-operatively (Murad et al 2016. 27144969).
The above studies do not appear to delineate whether surgeries were performed open or laparoscopically, but I suspect that any effect of the less invasive laparoscopic procedure would only improve regeneration.
As an interesting aside, even after performing as many as 4 separate resections for patients with recurring hepatocellular carcinoma, Yamaguchi and colleagues found continued high rates of liver regeneration (over 90%) (Yamaguchi et al 2018. PMID 29947985).

Thank you for your excellent answer, Ian! Great first post!


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Odds of finding superbug in soil?
There are tons of soil, rock, etc. being dug up, dug into, and moved all around the world each day. Paleontologists likewise regularly excavate fossils and both buried and frozen specimens, and biologists take samples of permafrost, soil and underground bodies of water.
Given all of the upheaval of these ancient and underground substrates and specimens, I'm wondering what the odds are that we unearth a superbug?

by superbug, I mean an otherwise unknown microorganism that modern medicine does not have a way to kill.

I understand that this is likely too broad of a question to be answered here (but feel free to try!), so I will break this down into a more relevant set of questions to inform my research.

How many microbes (# of species and/or density) typically exist in a cubic meter of soil? (or some other volume)

This article seems to be a good start.

Do these microbe abundances and diversity change with depth?
What is the deepest place in the crust that has been found to harbor life?

This article from 2010 suggests almost 1400 meters. Have we found deeper?

What is the deepest place in the crust that has been found to harbor life?

The deepest living animal:

That award goes to the "Devil Worm" (Halicephalobus mephisto), a nematode that has been found living at 3.6 km below the surface!!

Halicephalobus mephisto is tiny (only 0.5mm long), and represents the deepest multicellular organism ever found.

The original paper can be found here: Borgonie et al. (2011)

I should note, that the paper found definitive Halicephalobus mephisto at 1.3km depth, but found rRNA gene sequence belonging to a specimen of Monhysteridae at the deep 3.6km depth.

Do these microbe abundances and diversity change with depth?
According to  Inagaki et al (2015), microbe density is very low at low depths:

By counting the cells of these microbes, they also conclude that it is a small community, with just one cell in a cubic centimetre of sediment in some sections of the sediment

It's an interesting question and I hope this answer doesn't seem flippant, because that is not my intention. The odds of finding a microorganism that has never encountered humans (or any mammal) but has evolved the ability to infect them seem rather low, in my opinion. For an organism to be pathogenic it must have the means evade the host immune system. This is an adaptive trait requiring co-evolution with the host. You can find a textbook discussion of pathogens in Molecular Biology of the Cell. Importantly, there's a section titled Pathogens Have Evolved Specific Mechanisms for Interacting with Their Hosts which answers your question rather well:

In contrast [to the normal microbial flora], dedicated pathogens do not require that the host be immunocompromised or injured [to cause an infection]. They have developed highly specialized mechanisms for crossing cellular and biochemical barriers and for eliciting specific responses from the host organism that contribute to the survival and multiplication of the pathogen.
In order to survive and multiply in a host, a successful pathogen must be able to: (1) colonize the host; (2) find a nutritionally compatible niche in the host body; (3) avoid, subvert, or circumvent the host innate and adaptive immune responses; (4) replicate, using host resources; and (5) exit and spread to a new host. Under severe selective pressure to induce only the correct host cell responses to accomplish this complex set of tasks, pathogens have evolved mechanisms that maximally exploit the biology of their host organisms.

Also keep in mind that the appearance of superbugs is due to intense selective pressure by the use of antibiotics. Such a scenario is not applicable to organisms we've never encountered before.


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If a person has a specific mutation in a gene, is it more likely he has other mutations in that gene?
If a person has a specific mutation in a gene (2281 del/ins in a single copy of the Bloom BLM gene), is he more likely than the general population to have other types of mutations in the same gene?

A priori, no! Why would it? Do you have any specific hypothesis in mind you would like to discuss?
Below are some expectations from a simple model and possible reasons for why this expectation may break down under more complicated models.
Simple model
Under a simple model (panmictic population and a few other simple assumptions), the number of mutations a given individual has in any sequence considered follows a poisson distribution. Assuming that all mutations occuring have a constance selection coefficient $s$, a constant dominance coefficient $h$ and that the mutation rate for the sequence of interest is $U$, then the number of mutations an individual carry comes from a Poisson distribution with mean $\frac{U}{2hs}$ (Crow 1970).
This model is simple but is probably a pretty good approximation to reality. Below are three assumptions that are not necessarily true and that would yield to a higher variance in the number of mutations (that is a higher probability for an individual that already carry a mutation to get a second mutation).
Population structure
In reality, populations are often not panmictic. As the genetic load depends upon the population size. More specifically, the smaller the population, the higher the genetic load (or the higher the number of mutants alleles present in the population) (Kimura et al. 1963).
Past evolutionary and demographic history
Populations are not stable through time. Some population have recently gone through a bottleneck, others a quickly expanding, some are shrinking, some have recently suffered from a plague, etc... Such processes can all cause populations to differ in the number of mutations they carry and therefore would increase the variance in the distribution of number of mutations individuals carry.
Within a specific short enough sequence, physical linkage associated with specific past evolutionary process will create a relatively long lasting linkage disequilibrium.
Condition-dependent mutation rate
It has been shown in Drosophila melanogaster that individuals with poor genotype tend to have a higher mutation rate causing their lineage to accumulate even more mutations (Sharp and Agrawal 2012).

I would add that there are mutations in certain genes that increase the likelyhood of mutations in general or genomic instability. But i agree that mutation in one gene is not likely to increase mutations in that gene. https://www.ncbi.nlm.nih.gov/pubmed/16020738

I agree theoretically it's unlikely, I wonder though if there is empirical data to support this from the 1000 genomes project.

thanks! so, correct me if I'm wrong, but all 3 arguments are supporting higher variance in the total number of mutations for an individual, NOT for a higher variance in the number of mutations of the SAME gene, correct?

Yes, you are right. However, higher variance in the total number of mutations also increases the variance in the number of mutations for any sequence of interest, including a specific gene.

I think you're missing the most important factor: variation in coalescence time across the genome. The fact that the individual has one polymorphism in the gene means that the coalescence time of their two copies is not very short, and so they are more likely than average to have additional polymorphisms in the gene.

@DanielWeissman This is exactly the same as "Past evolutionary and demographic history", isn't it? Demographic (population bottleneck) and evolutionary (high background selection) is what is affecting coalescent time.

@Remi.b I think the last sentence of that section is going in the right direction. Let's be clear though: the effect I'm talking about is present in completely stable, completely neutral populations. (In fact, bottlenecks can decrease the strength of the effect.)

The answer of course depends some on the details (e.g., whether or not the mutation is neutral), but in general, yes, polymorphisms should cluster along the genome. Roughly speaking, the presence of one polymorphism indicates that the most recent common ancestor of this individual's two copies of the gene probably lived pretty far in the past, so there's been a lot of time for them to accumulate additional mutations.
I'm being a little sloppy here about polymorphisms within an individual vs differences from the reference genome, but the logic is the same.

Bear in mind that the average mutation rate of DNA polymerase is about 1 error for every 1 x 10^6 bases.  So the probability of mutation is independent at each base pair, but low - there's nothing that would prevent another mutation, but there also is nothing that says it is demanded.
There is, however, a phenomenon known as compensating mutations - a second mutation that compensates for a detrimental effect of an earlier mutation.  For example, if I have a mutation in a gene that codes for a protein, and that mutation changes an amino acid that is a contact point for protein folding (or a similar structural component), the protein may not fold correctly until there is a compensating mutation in the region of sequence coding for the residue that interacts with that first amino acid.  Compensating mutations would tend to be positively selected if the protein function is significantly affected....

Any sources you could add?


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Does protein consist of repeating units of amino acids?
I am currently studying the chapter called macromolecule. I get that a nucleic acid consists of repeating units of nucleotides, and I personally think "the repeating units" does not mean the nucleotdes are all the same, as nitrogen bases have four types either in DNA or RNA. How about the protein molecule. A protein molecule is made up of amino acids. However, I am sure about whether a protein molecule are made up of same and repeating units of amino acids. Theoretically, the R group in each protein is differed from one another. Therefore, does that mean we cannot state that a protein molecule is made up of repeating units of amino acids?

They are repeating units in the sense that all of the units are amino acids. The R group is different in different amino acids (it is not just different theoretically). The different R groups contribute to the different shape, structure, function of proteins, and if all were the same, then we would have a very limited range of proteins.You will still say it is composed of repeating units, since all units are amino acids, and there are no foreign groups between them.
Similarly, all repeating units of DNA/RNA are nucleotides, even if they aren't the same nucleotides.

Proteins are composed of repeated units of aminoacids with different R groups.
CO-CH(R1)-NH - CO-CH(R2)-NH - CO-CH(R3)-NH -
See how the aminoacid backbone is repeated again and again even if the R groups attached to that backbone is different.

Proteins are heteropolymers of amino acids. Many Amino acids are joined together by peptide bond. During peptide bond formation C terminal of former amino acid & N terminal of successive amino acid join  , that's why proteins always start with the N terminal and end with C terminal.
4 Amino acids are shown in the section. This order repeats itself many times.
The image shown above is only a primary structure. Functional  and structural proteins can never exist in this form.In reality a protein coils around itself or attains a fixed shape due to intermolecular and intermolecular  interactions ; like the Beta pleated sheath in fibroin(silk protein) is due to hydrogen bonding.


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Does a gene code for protein molecules or a DNA codes for protein molecules?
To my understanding, a gene consists of a unique sequence of nucleotides that codes for a polypeptide or an RNA molecule. In my textbook, it is stated that DNA codes for protein molecules.
So I thought, a gene only code for 1 protein molecule or 1 RNA molecule
However, DNA can code for a number of protein molecules or RNA molecules, as a gene is a stretch of DNA.
Is my understanding correct?

Your understanding is correct in that DNA encodes RNA, and this is a one-to-one relationship generally (although there are exceptions, see link below).  However, a given RNA can encode myriad proteins via translation.  This is because of different translation start sites and splicing of RNA.  You can read about this relationship between DNA/RNA/protein (the 'central dogma' of molecular biology), here:
https://en.wikipedia.org/wiki/Central_dogma_of_molecular_biology
But in the title of the quesiton you also ask about whether a gene or DNA encodes protein.  A gene is comprised of DNA; if someone talks about a gene, this just means a transcribed sequence, i.e. a region of DNA that is made into RNA.  Whether or not this is then translated does not impact its definition as a gene.  If it is transcribed, you could call it a 'protein-coding gene', otherwise you can call it a 'non-coding gene'.


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How would evolution explain parastitic wasps?
I read this article about wasps that can do "brain surgery" on cockroaches.
https://www.wired.com/2014/02/absurd-creature-of-the-week-jewel-wasp/
How does evolution create such a thing?

The brain surgery along with many of the other steps in the reproduction process seems to be very precise.  Any error here or there could lead to a bad result
Even if by happenstance the first wasp figured out a good way to do brain surgery, how would its offspring know to do the same thing?

Thanks.

Welcome to Biology.SE! Please take the [tour] and then go through the help pages starting with [Ask] questions effectively on this site. In general we encourage you to do some research on your own and then, informed by what you have learned, ask any questions you still have (ideally with references to reliable sources). In particular, we expect you to look for similar questions on this site before posting — there are many including the one I've flagged. Thanks!

I encourage you to check out some of the online resources available for learning more about evolution. For example, this a useful introduction to evolutionary theory from UC Berkeley.
You might also find a book like "The Blind Watchmaker" helpful for understanding how complex behaviors and structures arise through evolutionary processes.


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Can someone identify these fungi?
Found them in Gujarat, India.
Found growing among potted plants

This may be Clitocyte odora commonly known as aniseed toadstool.

They can be found growing in small groups along the side of tree roots.

it is widespread in the temperate zones, occurring in Asia, Europe, and North America

Young specimens have a light blue texture on the cap which fades to grey in age. The gills and stem are white with no ring.

Reference

If there is a white skirt it is probably a verdigris argaric:
https://en.wikipedia.org/wiki/Stropharia_aeruginosa


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Can DNA be used directly to determine the age of a mutation?
I've studied that proteins found in a sample as biochemical evidences for evolution. Its variation in structure and configuration can be used to date the age when that mutation occured, effectively dating the sample. But can't DNA be directly used for the process? Proteins also require transcription and translation, increasing error. I think proteins make phylogenetic detection easier, but doesn't transcription and translation give more room for error?

A similar question has been asked previously and I supplied an answer here. Your remarks about transcription and translation errors are irrelevant. One is using the sequences of the proteins that are correctly transcribed and translated. Those that are not will probably be degraded. They will certainly not predominate.

I think that this question for which there are already two answers encompasses yours Comparative evolutionary study: is amino acid or nucleotide comparison more useful?

Dayhoff matrices are a way of looking at the acceleration of evolution in the protein sequences. But why wouldn't you use the genetic code for pseudo time?

Hi and welcome to Bio.SE! I think with a little tweaking this could be a great question, and I am not sure yet if it is a duplicate as David suggests. I have voted to close this question because it is unclear what the question is. I think without an example of the problem, it cannot be answered. What studies that use protein for time have you come across? Are they carbon dating, building a phylogenetic tree, or something else?

Yes, you are right.  Proteins are specified by DNA sequences, so DNA sequencing is a more direct way to obtain essentially the same information.  Note that mutation dating via DNA or proteins is approximate.  It involves a lot of assumptions about continuous rates of mutation, but in fact mutation is a stochastic process and does not have a knowable continuous rate.  The sequence of mutations can be determined with high confidence, but the rate can only be determined approximately.

No. DNA sequencing is an inferior method for evolutionary studies in general because the DNA diverges much more rapidly than protein. There is already a question on this topic. I’ll see if I can find it.

More rapid divergence does not equate to inferiority for evolutionary studies!  It would (ideally) amount to a higher "clock rate", which would (ideally) amount to higher accuracy.

See my answer to the related question which I give a link to in my comment to the poster.

This approximate time is often called pseudo-time.


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What proof do we have that visual attraction to other humans is a natural biological trait?
There's another question answered that relates to this, but the sources don't show enough evidence of how it is a natural biological trait that we're born with.
Even though there's evidence that culture influences some of our behaviors on visual attraction towards other people, is there any evidence this stems from something that is a natural biological trait?

I think your question might fit on a sister stack, but you need to better define "natural biological trait". You mean if it is 'pre-programmed' in our brains? If it is genetic? What are you looking for? Secondly, and not less importantly, what do you mean by visual attraction? What kind of outcome measure would you use for that?


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Can I find out what resistance bacteria has based on strain? where do I look for that info?
I have a list of strains across various organisms for example:
Escherichia coli - ATCC 25922, CGSC 6152, W3110RL.
Pseudomonas aeruginosa - ATCC 27853, PAO1, APAE1111.
I'm failing to find any resistance information on these strains, as in what strain is resistant or susceptible to what antibiotic. Is there a way to find out?
Thanks.

There are many official websites that holds information and collection of microbial strains, here you can find a selection of them: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4241729/

@Dirigible Answers should be in answers rather than comments.

@Dom, are you looking for a database of resistance genes carried by these strains, or do you want information on minimum inhibitory concentrations?

Start with the ATCC product sheets (Just google the ATCC Number). They have lots of information about common uses, history of the strain, references, and sometimes some antibiotic susceptibility info. Keep in mind, if it has been kicking around a lab for a while, you might want to double check some of the MIC values, as they're known to change with serial passaging in broth cultures. But that's mostly if you need rather exact values.

If database and literature searches fail, you can plug the GenBank accession numbers for your genomes into the CARD Resistance Gene Identifier. It takes either protein or nucleotide sequences, though nucleotide seqs. undergo ORF calling first. For example, plugging in NZ_CP009072.1 for E. coli ATCC 25922 gives 7 perfect hits to known antibiotic resistance genes. Granted, carrying the genetic determinants of resistance is different from phenotypic resistance, but it's a place to start.


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How is minimum infectious dose defined?
I'm a bit confused by the concept of a minimum infectious dose (MID). It seems from what my research so far has turned up, that while any dose greater than 0 could potentially cause an infection, for most pathogens the likelihood of this occurring is low enough to be dismissed.
What I'm now trying to figure out is, what metric is used to define the MID? Is it the amount of the pathogen which is expected to cause an infection in 50% of those exposed (similar to an LD50?) Is there some other value used instead?
Secondly, is there a specified relationship between the received dose, as a multiple of the MID, and the likelihood of infection (for example if the MID caused an infection in 50% of people, then perhaps 2 MIDs would cause infection in 75% and 3 MIDs would cause infection in 87.5%).
Note, I am not asking about how the MID is empirically measured, but rather about the conceptual underpinnings of the concept itself. Also, any links you can provide to additional resources would be most appreciated. Google is useless these days now that the search results are flooded with nothing but SARS-CoV-2 specific articles.

Minimum infective dose is the minimum number of infectious particles that causes infection/illness in 50% of those given that dose.
Practically this is only really measurable in a controlled laboratory setting, but one can estimate it for real world circumstances as well.
It isn't easy to know how exactly the probability will vary around the MID - there are too many factors related both to the individual and the pathogen to make simplistic assumptions (like assuming each individual infectious particle has an independent probability of leading to infection). It is typical that higher initial exposure (particularly for foodborne illness, but seems to be an issue with SARS-CoV-2 and other respiratory viruses as well) leads to more severe illness, however.


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What would happen if somebody was administered caffeine while sleeping?
I know that drinking caffeine before sleep can disrupt your sleep and REM cycle, but I was wondering what would happen if hypothetically someone slept for 8 or so hours before being administered a dose of (just to give a number) 50mg of caffeine through an IV.  Would they be woken up?  If they stayed asleep, what would happen?  Thanks everybody!

Could you tell us what the purpose of the question is? In what context is this likely to happen and for what reason? If you're writing a work of fiction, then our [writing.se] site may be of interest to you, and our [worldbuilding.se] site can help you with hypotheticals - but be sure take their tour, read their help center and to include a worldbuilding context.

There is no reason why caffeine would wake anyone up who is already asleep. Caffeine works because it's shape is very similar to adenosine molecules, they can therefore fit into the same receptors and prevent adenosine from binding. Adenosine is part of the reason we feel sleepy late in the evening and so preventing its binding like caffeine does will reduce that feeling of drowsiness. This hypothetical scenario could in theory lead to the person feeling less rested the day after because it would cause more adenosine to stick around afterwards. This reason is also why caffeine very early in the morning can make people feel drowsy later and is a bad idea overall.
Source for the basics:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3153505/


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What is this unusual Plantago?
I found this plant in Rouen (Normandy, France) in a plant bed on the side of a street (May 15th, 2024).
It looks like a Plantago lanceolata but some of its inflorescences are not the usual single spike at the end of the stalk but rather look like several spikes bunched together. This is clearly visible in the second photo.
All the other Plantago lanceolata that I could find nearby were the regular form.
Do you know if this is a known variety or just the result of a random mutation?
And also what would be the correct botanical term to describe this kind of inflorescence?

It's not a species; flowers just do this sometimes, e.g. an echinacea stem with two heads. Weird to see, but not terribly rare.

This might be an example of fasciation, which has many causes including pathogens and physical damage. It could alternatively be an infection by a phytoplasma.

After some more research I was able to find an article about mutations in Plantago lanceolata.
The author observed that mutations in the flowers of these species were more frequent when the plant had been damaged, after hay cutting for instance. But these mutated plants only rarely produced descendants with mutations.
He was however able to cultivate a variety that produced 80% of descendants with abnormal inflorescences.
So the plant I observed is almost certainly Plantago lanceolata and, as others noted in the comments, it's not that unusual for these species to have mutated flowers.
Here is an illustration taken from the article showing various abnormal inflorescences.

L. Blaringhem (1923) Etudes sur le polymorphisme floral. IV. Sexualité et métamorphose des épis de Plantago lanceolata L., Bulletin de la Société Botanique de France, 70:4, 717-725, DOI: 10.1080/00378941.1923.10836897

Excellent, nice to see someone come back and provide an answer to their own question.


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How do organelles divide?
I'm sure by the nature of this question you will come to know my amateurish knowledge in biology. During mitosis, they simply state that the organelles just replicate...while we are provided somewhat detailed information regarding the division of the cell. How do the nucleus and the other organelles divide? Mitochondria used to be prokaryotes apparently so do they divide by binary fission? while we're on that what exactly are the organelles composed of? There is a spike in protein production during interphase...so how do the organelles even go about dividing?

Well, the nucleus does not divide per se. Remember, the nuclear membrane dissolves during mitosis. It starts reforming after metaphase. Here is a review detailing the process and the mechanisms which are known. By extension, the Endoplasmic reticulum gets portioned as it is derived from the nuclear membrane.
Organelles also rely on the cytoskeleton and associated motor proteins for distribution between the daughters. A debated aspect in this regard is whether the organelles are distributed at random or is there an active process that ensures similar distribution between the daughters.
Finally, on to mitochondria. Till this point we have assumed symmetric cell division i.e. both daughters get almost equal amounts of maternal material. But in stem cell divisions, the non-stem daughter is smaller in size. Interestingly, this paper shows that the stem like daughter gets younger mitochondria (less damaged mitochondrial DNA).
As you can see, it is impossible to cover all the organelles in a single answer. And we are not even considering physiological differences between different cell types. Cheers!


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Do human populations differ in core body temperature?
Human body temperature is a very complex and tightly regulated system. Hypothermia or fever of only 1-2K (i.e. changes of about 5%) already cause major symptoms and changes of 3-4K (i.e. about 10%) are life threatening. Many humans live under relatively cold outside temperature conditions and maintaining an inside 36-37 degree C in these conditions is very energy consuming (most probably a reason why the body temperature in the periphery is several degrees lower), indicating very strong evolutionary constraints on not changing the core temperature too much (I remember a professor in biology classes in university saying that most fungi have a growth minimum around 37 degree C). However, other mammals have higher or lower body temperatures than humans which suggests that the 36-37 degree C of humans are not a universal gold standard (in mammals).
Probably, for a long time in hominin evolution maintaining the core body temperature was not extremely energy consuming due to tropical conditions. This could have changed during the out-of-Africa migration some 100-60 thousand years ago. Of course this is somewhat difficult assess because early modern humans started to wear protective clothing. In fact, wearing clothes is a most probably adaptive trait to save energy while maintaining core body temperature. Still, it is unclear to me whether physiological adaptations took place as well. Furthermore, there is considerable variation between individuals and also within individuals, the latter in response to environmental conditions and/or behaviour (e.g. exercise), which in principle allows natural selection to change the trait and also shows that slight shifts in body temperature are not harmful individuals.
My question is: Are there significant differences in core body temperature between human populations? Please note that my questions is not why the (average?) human core body temperature has this particular value or why it is different from other mammals or birds.
There is a somewhat related question (also on Skeptics.SE) about lower core body temperature in Japanese people. As far as I know, this difference is rather a measurement thing than a real biological difference, so my question remains unanswered.

Yes there are different physiological temperatures in different ethnicities. To know which temperature range differences are inherited and which are learnt by living in different climates requires surveys of people who are from the same region.
This study states a 0.35 degrees difference between a japanese and a malaysian, 36.95 and 37.3, it's alot.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3929238/
The following study states states a 0.15 degree difference measured with similar precision,
https://www.ncbi.nlm.nih.gov/pubmed/20824480
This graph shows that the human body temperature is 36.2 at rest, at night/morning and 37.5 in the middle of the day. :
http://millar.bio.ed.ac.uk/andrewM/WE%20book99/Part2-examples.html#tth_sEc8.3.4.2
That may account for the 1 degrees difference in Japanese studies, they measure first thing in the morning/ at rest/at night, and japanese body temperature of 0.15-0.35 lower that some other ethnic groups.
There are geographic differences if you test the homeostasis response of different populations, the inner body temperature responses, the temperature of the extremities, sweating responses, the physiological responses and the blood cell characteristics.
Mitochondria has also been shown to be selected by climate type. Populations living in colder environments have lower mitochondrial diversity and that the genetic differentiation between pairs of populations correlates with difference in temperature, and they have found certain genes mutations in the ND3 and ATP6 that seem to be independantly implicated in similar climate adaptations.
The temperature is measured in lots of zones of the body and of the extremeties and the capillary flow. That doesn't account for habituation and acclimatization to tropical or northern climates.
The tropical population was found to have different thirst and sweating efficiency, and to change temperature at different rates to compensate for the same ambient conditions and exercise.
Some schools in China enforce that children run around in shorts in the snow in the winter and at playtime so that they regualte their body in the cold. Some northern people are apparently able to override the unconcsious response of the physiology that can raise body tempereture very effectively, and be able to hold in cold tanks for surprisingly long times.
Cold and hot weather are a strong force on natural selection, as illustrated by mitochondrial adaptations, because an advantageous in temperature regulation brings about a global performance advantage. The physiology of temperature regulation has been subject to many theories and studies, and they have found physiological conditionings can be honed by genetic adaptations in different populations.
Even chimpanzees have similar temperatures:
The cycles of increasing and decreasing body temperature of chimps
are exponential and symmetrical, with an amplitude of 2.6-2.9?F
(2-3 AM - 2-3 PM) and a 24-hour mean of 99.0?F, or 98.7?F. The S.D. of the 17 daily means was 0.53?F; and
of the values at any single hour, 0.63'F....Thus, in the bulk of the species the temperature ranges daily from
37.5- to 39+?C whereas the ordinary range in man is 36.5 to 37.5?C. Low
values are similarly reported for several primitive primates.
some references: http://rspb.royalsocietypublishing.org/content/276/1672/3447 https://www.jstor.org/stable/1377087
Actually this study states a 0.35 degrees difference between a japanese and a malaysian, 36.95 and 37.3, and study referenced afterwards states states a 0.15 degree difference,
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3929238/
https://www.ncbi.nlm.nih.gov/pubmed/20824480

That is very interesting! Can you provide references for your claims, though?

Hi, it's an interesting quesiton and it gives me a subject upon which to educate myself. I read through 4 papers and 10-20 graphs to get the figures, and saw also a dozen other related research papers. for example http://rspb.royalsocietypublishing.org/content/276/1672/3447  https://www.jstor.org/stable/1377087  https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3929238/  especially the ncbi page study which answers your quesiton with a high degree of certainty. ill add them to the text. thanks.

Hi, I hadn't seen the above study, which measures a difference of 0.35 between malay and japanese, it's considerable, i had seen the following study from the same researchers states a 0.15 degree difference is similar conditions: https://www.ncbi.nlm.nih.gov/pubmed/20824480


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Selective breeding of organisms to survive on Mars
It seems that there may have been life on Mars, and it's also tempting to terraform and colonize the planet. This question is about testing the hypothesis "Can primitive life survive on Mars?". This is closely linked to the lithopanspermia hypothesis, that life can be seeded from bacteria on meteorites.
The hypothetical experimental setup is as follows:

Take microorganisms that live in the upper atmosphere and can survive high radiation
Recreate their natural environment in a lab, and let them live there
Slowly change the environment to be more similar to Mars: pressure, temperature swings, radiation, relative gas concentration
See if they are able to adjust

My question is: Is this possible? Has anyone done it, or is doing it currently? I know tardigrades are being sent to the moon, but they're hardly thriving there.
My apologies if the non-expert question is off topic. If you can suggest a more appropriate place to ask, I'll keenly do so.

Some consider the invasion of extraterrestrial environments on a moral ground, but that's not what I'm asking here.

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Why does plasmid recombination require precise "copying and pasting" but microinjection doesn't?
Just learning about biotechnological techniques of gene transfer at the moment. With bacterial plasmid recombination, from a high-school level, we are taught that:

The desired gene is cut using a particular restriction enzyme
The plasmid from the host is also cut using the same restriction enzyme
The desired gene is inserted into the space that was cut out from the plasmid.
The plasmid is put back into the bacteria and the gene can now be expresesd.

This makes logical sense.
With microinjection, however, we are taught that the gene is just directly injected into the cell using a needle and that it somehow manages to use it? How does that actually work? How does the extra gene just somehow get put into the existing DNA without cutting out a section like you have to do in plasmid recombination? Furthermore, if you can just insert the DNA into the cell with microinjection without all of the hassle of precise "copying and pasting" done in plasmid recombination, then what is the point of using plasmid recombination?

You can't microinject a bacterium for one thing - far too small, so you need all the components in one place to get the gene expressed and make the plasmid replicable.  This will include things like promoters, start sites, Kozak sequences, terminators, resistance genes, ori, etc.
Genes to be microinjected need, at a minimium, sites to make them insert into the host genome by recombination, or need similar components to a plasmid; promoters etc. It's not like this isn't also a precise science in how to get it to work, it's merely that microinjection is one of the techniques used to insert genes into the nucleus of eukaryotic cells.

You can't really determine the exact location of where the insertion will be, and I believe the microinjection you're talking about is using transposons (e.g. P elements).


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Does succinic acid provide any caloric value in humans?
Would the ingestion of pure succinic acid provide any caloric value in humans? I couldn’t find any nutritional information about it via Googling, but I read on Wikipedia that it’s converted into fumaric acid, which after Googling I found does have a caloric value of around 2.74 Kcal/g.
I don’t fully understand exactly how succinic acid is metabolised though, be it where it’s metabolised or the amount of it that can be metabolised, so I’m simply lost with the numbers.


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Do complementary DNA sequences/codons produce the same amino acids?
I haven’t been able to confirm this anywhere. If this were not the case, when transcription occurred, if the transcription were based upon the incorrect side of the DNA molecule, a completely incorrect output would result. Complementary sides should be aliases of each other, but I have not been able to find anywhere whether this is the case.

Isn't this trivial to answer using a chart of the genetic code? How do you think transcription would start on the "wrong" side?

Welcome to the site. Please take a [tour] and visit the [help] to find information on what we do here. In particular pay attention to the homework policy, which would cover your question. You could self-answer your question by thinking about strandedness and direction of transcription!

@BryanKrause In the very least, in this image, the sequence UUU does not produce the same results as AAA: https://ars.els-cdn.com/content/image/3-s2.0-B9780128008836000112-f11-05-9780128008836.jpg

“Complementary sides should be aliases of each other” — are you assuming that complementary strands should produce the same proteins when transcribed and translated? Why do you believe this to be true?

If DNA intends to code for one set of amino acids, would it not be wrong for a ribosome to build a polypeptide from different amino acids than one side of the DNA molecule intended for? Essentially, if one side of the DNA molecule depends on the other side of the DNA molecule, why would it ever be the case that complementary sequences don’t produce the same amino acid outputs? Since DNA is symmetric, I don’t see how the ribosome would be able to determine which side is intended to hold the information, in the case that complementary bases within codons don’t code for the same bases.

@acvill Does the whole “DNA transcription to RNA to translation within the Ribosome” process have some way of determining which side of the DNA molecule was supposed to be read? Since DNA is supposed to be complementary throughout, if I wanted to store some sequence on one side, I wouldn’t be able to just continue on storing more information on the other side of the molecule- the other side would be reserved for a chemical mirror image of my stored information. If one side holds the desired code and the other simply holds the backup copy, I only intend for the desired side to be read- but how?

Transcription is a highly regulated process, cells aren't just producing random RNAs from random stretches of DNA.
The transcription machinery needs to bind to DNA to get started, which requires a promotor sequence. It's not necessary for DNA to "read" the same way forwards and back, because it'll only be transcribed in the correct direction.

My question is not about the direction of transcription and translation, but rather, which side of the molecule the process begins copying from (i.e. not along the molecule, but across to the mirror side). If one side’s sequence deterministically depends on the other’s, is it the case that either side (i.e. codons containing exactly complementary bases) would produce the same output? If not, then why? Is there some way of ensuring that only one side of the mirrored DNA structure is read?

Yes, only that side "fits". DNA is directional (the ends are referred to as 5' and 3' ends). If you read the whole Wikipedia page on transcription or an equivalent chapter in a biology textbook I think it'll become clear. If you wanted to transcribe the other side, you'd have to start at the "end" and work backwards.

Thank you. I think this directionality shows me where the cracks of my question lies.


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Does vaccinating people with cowpox give people immunity to smallpox?
I've just recently learned about the body's defense mechanism about how lymphocytes from memory cells that are specific to a pathogen after being infected by a pathogen for the first time, but then I saw that vaccinating people with cowpox can give people immunity to smallpox, which is similar to cowpox. Why can this happen? Shouldn't the memory cells formed in this case be specific to only cowpox?

cowpox and smallpox are nearly the same disease, much like how the bat strain of covid and the human strain of covid are very related diseases. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0007666

As suggested by John, I think it is worth interrogating what you mean when you say that cowpox is "similar" to smallpox. What is similar between them? What is different between them? What would make the memory cells be "specific" to one or the other? Possibly, look into the history of smallpox vaccination: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9709930/

I think the key point here is to note that pathogens are assembled from multiple subassemblies, which are themselves composed of various proteins. It's these subassemblies of proteins which B cells develop antibodies for, in which case we call that subassembly an "antigen." The antibodies then attach to those antigens, which tags the pathogen for removal by other cells, destruction by proteins (in the case of membrane attack complexes), or otherwise prevents that part of the pathogen from doing whatever it would normally. There are also T cells, which have their own kind of antigen receptor (T-cell receptors). Have fun looking into those! You might check out "The Red Queen: Sex and the Evolution of Human Nature," by Matt Ridley, which is all about the Red Queen hypothesis, and dives into the major histocompatibility complex.
So, in the case of smallpox and cowpox, they share common antigens. That's what's being referred to in papers like "A comparison of the antigens present on the surface of virus released artificially from chick cells infected with vaccinia virus, and cowpox virus and its white pock mutant." Smallpox and cowpox are both orthopoxviruses, which you can learn more about from ViralZone's description.


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UV light-induced mutagenesis during gel extraction
this is a very short question I did not find the answer for online, neither on this nor other fora. At the beginning of my cloning protocol, I extracted the band with the sequence of interest directly from the gel upon electrophoresis, and failed to minimise the exposure time of my sample to UV (did not switch off the lamp between cutting of different bands). Now, the gel was sitting in the cast tray the whole while (altogether maybe 30 to 50 seconds), and I wanted to know whether this eliminates the risk of mutagenesis, or at least minimises it, due to the absorption of UV light by the cast tray. Thank you.

I've imaged gels for a few minutes on UV, then went to cut out bands. I managed to get successful plasmids from them after miniprep. Always check your minipreps for proper gel digestion and confirm by sequencing.

Thanks for your answer. Do you remember the size of your inserts? Mine are about 2.5 kb. I will have them sequenced next week, but was just curious as to whether the cast tray is made of plastic that absorbs UV light.

The gel tray does not absorb UV, otherwise you wouldn't be able to see the bands in the gel.

@MattDMo They often absorb a little, when I slide the gel off the tray and put it directly on the transluminator, the bands get brighter. I wouldn't bet on the tray making the difference between damaged and undamaged DNA though.


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What makes a protein structure discernible?
In Lehninger's Principles of Biochemistry, Pg. 116 states that "parts of proteins lack discernable structure." What exactly makes this protein not readable? Is it the complexity of the shape that makes it difficult for scientists to understand the structure?

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There are two main methods for discerning a protein's structure; x-ray crystallography, and more recently cryo-electron microscopy. Both methods work by firing a high-energy beam through the sample and observing how the path of the beam has been changed by passing through the sample. The data obtained by measuring the beam includes "signal" information on the structure of the sample, but also a lot of random data, or "noise". If the signal from large numbers of copies of identical proteins can be averaged together coherently, it can be separated from the noise and the positions of the atoms that make up the protein can be determined. In crystallography, this is achieved by getting the proteins to arrange into a crystal, and in cryo-EM by a computational process after data has been collected. Either way, if the many copies of the protein are not quite identical, the signal averaging will not work, and the positions of the atoms cannot be determined as accurately, or at all. In some cases, the protein has two or a few distinct structures that it switches between, and these can be separated and determined accurately. In other cases, the protein only takes a specific shape when it is bound to another molecule, and just flops around randomly when nothing is bound. Here is the abstract of a review on this second type of protein:

Many gene sequences in eukaryotic genomes encode entire proteins or large segments of proteins that lack a well-structured three-dimensional fold. Disordered regions can be highly conserved between species in both composition and sequence and, contrary to the traditional view that protein function equates with a stable three-dimensional structure, disordered regions are often functional, in ways that we are only beginning to discover. Many disordered segments fold on binding to their biological targets (coupled folding and binding), whereas others constitute flexible linkers that have a role in the assembly of macromolecular arrays.

Finally, some proteins will not crystallize unless a portion of their sequence is removed. These portions may have a consistent structure, but it can't be determined by crystallography.


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How do the High-Energy Electrons During Chemiosmosis Come from Water?
On Pg. 199 of Campbell, this is stated.

Both* work by way of chemiosmosis, but in chloro- plasts, the high-energy electrons dropped down the transport chain come from water, while in mitochondria, they are extracted from organic molecules (which are thus oxidized).

*Both refers to the to chemiosmosis in mitochondria and in chloroplasts (during photosynthesis).
My question is, how do the high-energy electrons in the transport chain for chemiosmosis come from water? Aren’t these high-energy electrons derived from light harvesting done by the light-harvesting complexes?

The light harvesting complexes use light energy to "lift" electrons to a higher energy state from which they can be used to reduce organic molecules (by way of an electron transport chain and NADPH), leaving a "hole" or cation behind in the LHC and thereby oxidizing it. If these complexes were not re-reduced by something, they would become non-functional after absorption of a single photon. So, they are re-reduced by removing electrons from water to generate molecular oxygen, which happens in photosystem II. So the photosystems I and II act as a series of "pumps" that make otherwise thermodynamically "uphill" (unfavorable) electron transfer from water to NADPH spontaneous, but they do not act as a net source of electrons--water does.


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Single cell organism's brain
Multi cellular organisms have brain.But what about single celled organisms do they have brain to control the cell's work?If they have something what that part called?You can say that the nucleolus do that work
then all cells have nucleolus.Then why multi cellular organisms have brain?

Single cells do not have brains. Plenty of multicellular organisms do not have brains either. Multicellular organisms such as fungi, plants, sponges do not even have nervous systems, and many organisms with nervous systems (like some jellyfish, molluscs, arthropods...) do not have something you could call a brain (I mean, I guess arthropods have a brain in that it's how you call the ganglion they have in the head, but it's not always that much bigger than other ganglia).
Organisms do not actually need a centralized control to function. You can do a lot in a multicellular organism simply with cellular signalling (each cells reacts to its environment in certain ways, sometimes emitting molecules that cause other cells to react in certain ways and so on), and single cells work similarly inside themselves, different parts of the cell "work together" by producing or consuming chemicals that others react to (or other physical processes).
Brains (i.e. a centralization of the nervous system) allow more complex behavior, to coordinate perceptions and actions in more precise and flexible ways.
This Wikipedia article on Chemotaxis for example describes how cells can move along a gradient of a useful or dangerous chemical, and gives some of the molecular mechanisms for this to happen:
https://en.wikipedia.org/wiki/Chemotaxis
Here is an article that seems to describe cell signalling in some detail:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1679905/

I think you have misconceived what a brain actually means. A brain is an organ, which is very different from the organelles of microorganisms.
Organ: a collection of cells that carry out a specific function.
Organelle: a structure enclosed in a membranne that exists in the cytoplasm of a cell.
The brain is a collection of neurons, of sometimes just cells that respond to  stimuli. Therefore, a unicellular organism does not have a brain. All they have are organelles.
How do unicellular organisms respond to stimuli then?
On the surface of the cell membrane are proteins (receptors). When a receptor is activated i.e. a molecule binds to it, it will set of a signalling cascade (think of a waterfall, or domino). This cascade which consists of other enzymes will ultimately end with the desired enzyme being activated and it catalyzes a desired reaction.
That is how cells react to stimuli. Strickly speaking, they do not have brains, but they can make decisions, they are forced to make a decision (they cannot make a choice, if a signalling molecule is present it will activate a pathway, it must unless another molecule regulates it).

We welcome new contributors to SE Biology, but suggest they read about the sort of questions that are on topic here, and in particular that one should "only answer well-asked questions". In my opinion this is not of a standard suitable for this site.  And I don't think your answer is particularly logical. How is a decision different from a choice?

Hmm, this sounds very philosophical. Logic gates "make" decisions, but it is not an active choice.

Not at all philosophical. I am using English as it has developed being applied by and to  sentient beings. If a technical field such as computing science happens to use an English word in a non-standard way, this is irrelevant to its meaning among ordinary people and even biologists.  (A decision is different from a choice, in actual fact, but both are non-deterministic. It is enough for you to argue that the responses of cells to their environment is deterministic.)


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Where can I find information on the anatomy or biology of seeds?
Where can I find information on the anatomy or biology of seeds?
For example if I want to know the anatomy (some sort of drawing) of a green bean where can I go to find such information?
Searching Google does little to nothing to describe this process, let alone provide a good picture or drawing. The images of Google do return some results, but they are posts that were made by people on Twitter or Pinterest. Even Google Scholar does not have a lot of research papers on such info.
Seems like the only option is to purchase Text books which cost upwards of $200 each.
Please help....

I have found that when learning about a new area starting with a relatively accessible and reliable source like Khan Academy is very helpful. Wikipedia is also generally a good starting point and you can then check their references. Online platforms called MOOCs offer free (or very low cost) courses on a wide variety of subjects — two I am familiar with are Coursera and edX. Finally, textbooks with a good level of detail are also freely available online e.g. from NCBI.

Well, I was able to find this on google, which seems to collect a very large amount of information on different aspects of seed biology. I don't know if it has every species/feature that you care about, but there is a lot of general information there (including images).
Note that it has an "unsafe" web address (I clicked through and my computer wasn't taken over yet).
See also this, found by google.
See also this, from a german academic source.
There are also an enormous number of technical reports like this and this from the USDA.

Hi, I guess this is my point. That there are only images but no official "safe" sites for such information.

@wwjdm If you are asking for whether there is a perfect catalog of comparative anatomy for the features that interest you in all the plants that interest you, I guess that is probably a no. However, I don't think it is too hard to look at e.g. the german source that I link to for general info, or to google scholar search "seed comparative anatomy beans" or whatever. What is an "official" site? the "unsafe" one is run by Ohio State University. The German one is also academic, the USDA is the USDA. No fancy web design in any of these places, but they are pretty official.

Thanks the USDA one you sent is good.

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