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Do cuttlefish know how to mimic animals since the moment they are born or do they learn by observing?
I can't seem to find information anywhere else so I hope somebody can help me out.
So, as the question states, I saw a cuttlefish mimicking a hermit crab the other day and I was wondering if cuttlefish carry information of what they can mimic as spiders carry information of how to make a web (innate behaviour) or if they learn how to mimic by observing other animals.

I am surprised a question with bounty has drawn no comments at all.

I haven't been able to find any definitive research/answers, but, based on the usage of their mimicry (camouflage and sexual), and some of its features (alteration of the surface texture of their skin, electric camouflage, development+change through lifetime), I'd hypothesise that it's most likely a mixture of the two. They likely have a large innate capacity to use the form of mimicry young cephalopods do, which is further developed socially/as a learned behaviour, which subsequently causes the change in the nature of their mimicry.
Cuttlefish texture change (Primary research article)
Transient sexual mimicry (Summary article (Nature))
Research has shown that cuttlefish mimicry develops and changes as they grow; it has also been shown to differ based on the location of the creature. There is also evidence of cephalopods learning socially, so it does indicate that their behaviour is at least partially learned. (Source + additional references- reed.edu ->Visual Mimicry in Cephalopods -> Ontogeny)


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How to watch a Zebrafish embryo in detail?
How much microscope zoom would I need to watch the development of a Zebrafish embryo in certain detail? Thanks guys!

It might help if you clarify what you mean by "certain detail".

Observing the development of cord and eyes would be a good start.

From personal experience, it should be sufficient to observe zebrafish at 10-20x magnification for broad structural changes during development.  If your microscope has a 10x eyepiece, then that would be 1-2x zoom. If you are observing sub-cellular changes, you would benefit from higher magnification.

source: Stack Exchange

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How is the probability of Rh type inheritance calculated?
I found somewhere on the Internet that, if parents are both Rh-positive, their children have 93.75% chance of being RH-positive and 6.25% chance of being RH-negative.
My question is: How is this calculated?

There are four possible parental genotype combinations (R = Rh+ allele, r = Rh- allele):
m  f
RR RR
Rr RR
RR Rr
Rr Rr

Only the last can produce Rh- offspring. The probabilty that the Rr Rr combination leads to a rr genotype in the F1 generation is $1 \over 4$. Since there are four combinations, the probability that the Rh+ parents are Rh Rh is also $1\over4$. Thus the probability of the offspring to be Rh- is $${1\over 4} \cdot {1 \over 4} = {1 \over 16} = 0.0625$$ Thus, the probability of Rh+ in the F1 generation is $$1 - {1 \over 16} = {15 \over 16} = 0.9375$$
Note: This is the rationale behind the values you state in your question. I am pretty sure that these four combinations are not equally distributed in a population. You would have to need to know the allele frequencies.

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What structures (i.e. organs) are suspended by tensile forces?
In several areas of biomechanical literature I have read, the concept of "tensegrity" has arisen. Definitions are as follows:

“The integrity of a stable structure balanced by continuous structural
  members (cables) in tension and discontinuous structural members
  (struts) in compression.” (Zhang, 1)

and then

“A tensegrity structure is recognized by its distinct set of
  compression elements (struts) that appear to float within a network of
  tensioned cables.” (Scarr)

I am highly skeptical about its applicability. Some authors (e.g. Evan Osar) suggest that tensegrity can be applied to the spine. However, the spine fundamentally does not fit the definitions provided above because its non-tensile components are connected / touching. Tensegrity involves floating
My Question:
Are there any areas of the body that would potentially qualify under this definition of tensegrity?
One example I can think of is the suspension of organs in the body, but I am unsure about this.

Sources:
Osar, Evan. Corrective Exercise Solutions to Common Shoulder and Hip Dysfunction. BookBaby, 2012.
Scarr, Graham. Biotensegrity: The Structural Basis of Life. Handspring Publishing, United Kingdom, 2014.
Zhang, Jing Yao, and Makoto Ohsaki. Tensegrity structures: form, stability, and symmetry. Vol. 6. Springer, 2015.

Do you really mean suspended in air? Because there aren't structures suspended into the air-filled spaces in the body.


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Worm compost cannot have cooked food
I live in the Netherlands and it is getting fashionable to compost with worms. After investigating a few websites I noticed that most websites suggested that I cannot feed the worms leftovers from citrus fruits. This seems logical. I then started noticing that people advise against feeding the worms cooked food.
I'm no biologist but I cannot imagine a reason why cooked food is bad for the worms. Could anybody explain why this might be in layman’s terms?

If you can, please add some references to this claim (as I am a biologist and can't imagine a reason either).

The only thing I can think of is that cooked foods often have added fat which might attract animals or that cooked foods tend to compress and don't allow for aeration but neither of these seem particularly concerning if there's a good mix of other things in the compost as well

I've been putting cooked food in my small domestic worm farm for years.  It works ok and the worms seem happy enough but downsides are that it can get a bit smelly in warmer weather and attracts flies.  My suspicion is that fly larvae and other small organisms on the top layer end up breaking down anything the worms can't handle.  The meat content in the cooked food would tend to be very low, primarily veg and carbs.  Also very little processed food goes in.  Final compost is excellent feeding for rhubarb, fruit and veg.

I think that "compost with worms" sounds like a mix of composting and worm farms. The two environments are a bit different: Worm farms are a fine culture using agriculture/garden waste of leaves and natural garden detritus, and compost can be more messy and contain food, cardboard, paper, waxy hay, twigs and detritus. Cooked food can form mouldy gooey masses which houses different funghi and bacteria groups than those present in garden detritus.

There are a few reasons for not feeding cooked foods to worms (Eisenia spp.) in a smaller household size worm farm. It's not because the food is cooked but what it often contains.
The earthworm used in vermiculture is usually Eisenia fetida (red wigglers) though other Eisenia species are sometimes used. All Eisenia are epigeic species meaning they live in the junction of decomposing organic matter (such as leaf litter, aging manure, rotted fallen trees) and their natural food is decaying plant matter and bacteria that are also digesting the organic matter. They don't make use of small dead animals (meat and fat).
In large scale commercial vermiculture operations, leftover and past-due-date foods from restaurants, institutions, nursing homes and schools are used along with plant matter and carboard and paper. I'm not sure how they balance cooked foods but possibly much less is used than plant matter.
The fact food is cooked isn't the problem but what's in it and/or what happens to it when added to the bin. If you have leftover vegetables and fruit that's been cooked with no added salt, it's perfectly acceptable. A certain amount of sweetened cooked fruit is also fine as the worms will eat that too. But ready-made foods usually have preservatives, salt, fats and spices added. Either worms won't eat it, leading to odour caused by mouldy rotten food, or it can make them unthrifty and even killing off your worms if it's fed them repeatedly.
Fats and meat along with cheeses and dairy products will also not be eaten so shouldn't be used. Sites about vermiculture say onions and garlic can 'burn' the worms skin which is the problem with citrus fruit. They can be used but in very small amounts and should be mixed well with their other food.
Vermicomposting for Business, Farms, Institutions & Municipalities
Wormy FACTS and Interesting Tidbits about Eisenia fedita


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Somatic cell cloning always produces female offspring?
I was looking at the somatic cell cloning of goats.
One of the advantages of the process said was

All offspring produced are female.

Now I'm confused.
How is this the case?
I know that the embryo after electrofusion is injected into a surrogate mother, but I don't understand how the advantage is that they are "all ... female."

What is the sex of the somatic cell donor?

@AlanBoyd I don't know! That's what I was confused by.

Probably you should provide a link to your source.

For most species of livestock only the females are of economic value. And if you clone a female, you will only get female offspring.
I can also imagine that you would want to use an oocyte and somatic nucleus from the same animal. This way, you also preserve the mitochondrial DNA from your golden goat. And males just don't make eggcells.
It could also potentially avoid any incompatibilities between host and donor, somewhat comparable to donor organs. But I don't know if this is actually an issue.


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What is the actual speed of nerve impulses in humans?
For an undergrad assignment I read a biology paper that mentioned the speed of nerve imuplses to be 440 km/h in myelinated fibers. However, our biology teacher told us that this reported conduction speed is not true. So my question is:
What is the actual speed of myelinated fibers?

It would be good if you can tell us what you did to arrive to your answer. And it would be good if you can include any relevant background information. Not everyone who answers questions on this site is a specialist in every field; but a lot of us do have good research skills, and we may be able to review your work to see if it makes sense. But the only way we can do this, is if you provide us with enough information to do so.

I saw in a few books that the speed of the myelinated fibre was 120m/s in human beings but then after sometime I saw the speed of the myelinated fibres was 440km/h in bbc documentary which is similar to 120m/s but one speed is in (m/s) and the other is in (km/h), when I convert the 120m/s into km/h so I got 432km/h therefore I needed to be sure that the error of 8km/h in 440km/h and 432km/h does not matter so I can proof it to my Teacher, I hope that you understand my question.

Short answer
A conduction velocity of 440 km/h is possible in thick, myelinated fibers. However, this number is probably more representative of the upper range of conduction velocities, rather than a conservative average.
Background
First off, there are a heap of variables that affect neural conduction velocities (in myelinated fibers) in complex ways (Waxman, 1980), including but not limited to:

axon diameter;
myelin thickness;
internode distance;
temperature;
axonal milieu;
age of the subject.

Having said that, in humans myelinated, thin A-delta fibers the average conduction speed was established at 19 m/s (Gyberls et al, 1983), or 68 km/h. A range of pain-conducting fibers exist, with different diameters. As a result, they range in their conduction velocities from 0.5 m/s (2 km/h for thin C-type fibers) to 120 m/s (432 km/h for thick A-alpha type fibers).
Hence, the 440 km/h is certainly possible in thick myelinated fibers. Note I just highlighted pain-conducting fibers here as an example, and other classes of neurons may feature even faster conduction in their axons.
References
- Gybels et al., J Neurophysiol (1983); 49(1): 111-22
- Waxman, Muscle & Nerve (1980); 3(2): 141–50


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Maximum parsimony tree - Am I right, or is the correction model right?
Alright. Monday we have a test, and now I was making a practise test.
We have to make a maximum parsimony tree. We must do that monday again, so I want to know if I am thinking wrong, or if the answer model is incorrect.
The sequences are:
Seq     1    2    3    4    5    6    7
1       A    T    A    A    G    C    C
2       T    C    A    C    C    T    G
3       A    T    C    C    G    A    C
4       T    G    C    A    C    T    G

This results in:
          1    2    3    4
----------------------------
   1  |
   2  |   6
   3  |   3    6
   4  |   6    3    6

And eventually, this results in:
          1,3     2,4
-----------------------------
1,3  |
2,4  |    6

This is the tree in the correction model:

My tree has two 1,5's instead of the two 3's at the root of the tree. Because 6 is the last distance. 6/2 = 3, so both branches should get a distance of 3. But, according to some examples I saw on the internet, it's a distance of 3 to the end of tree then, and not 3 to the next node. And there is already a distance of 1,5 in further benches at both sides, so only 1,5 remains (because 3 - 1.5 = 1.5).
So, am I wrong, or is the correction model wrong? Then I know how I must do it at the real test.
Sorry if my English is bad, and it's a little hard to explain because English is not my native language, but if I am right, you should know what I mean.

From your description, this is a distance-based clustering tree (UPGMA), not a parsimony tree. And in this case I believe you are correct, since if you sum up all branches from 1 to 2 or 3 to 4 (1.5 x 4) you will have the original pairwise distances. (The same for 1-3, and 2-4, which are easier.)


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Are there differences in cell membrane cholesterol levels between cell types?
With different cell types, and cell functions, are there distinct levels of cholesterol in each cell type's cell membrane, or do all cell types have a similar amount of cholesterol?
I am assuming certain cell types require different levels of cell membrane stability, and as such, different levels of cholesterol in that cell membrane.

Yes, there are differences in cell membrane's cholesterol levels among different human cell types.
This table from Alberts (2002) shows the difference in cholesterol composition in a liver cell, a red blood cell and a Schwann cell/oligodendrocyte (myelin):

Table: Approximate Lipid Compositions of Different Cell Membranes
Besides that, the table shows that there is difference in the cholesterol composition among different membranes in the same cell (compare plasma membrane, mitochondrion and ER). Actually, that's a more famous difference, depicted in this figure from Lehninger (2000):

Figure: Lipid composition of the plasma membrane and organelle membranes of a rat hepatocyte. The functional specialization of each membrane type is reflected in its unique lipid composition. Cholesterol is prominent in plasma membranes but barely detectable in mitochondrial membranes.
Sources:

Alberts, B. (2002). Molecular biology of the cell. New York: Garland Science.
Lehninger, A., Nelson, D., Cox, M. (2000). Principles of biochemistry. New York: Worth.

You're right, different cells have different quantities of cholesterol within the membrane. For example a red blood cell will have more cholesterol in it's membrane compared to an epithelial cell in the small intestine. This would be because the blood cell is free floating within the body rather than being physically adhered to something, so a greater level of stability is needed. It is solely dependent on the cells function.

Thank you for the answer! can you provide any links to literature that provide evidence of this?


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Phagocytosis and bacteria
Invading Bacteria are phagocytosed by phagocytes. Phagocytes are specialised white cells. But, if a non-phagocyte cells are infected with bacteria how those cells handle this situation? Do they succumb to the bacteria?

For cells to become infected with bacteria, some bacteria will still be present in the blood. These are still engulfed by phagocytes in the same fashion. However once engulfed the antigens on the surface of the Bacteria are placed on the surface of the phagocyte, this is known as an antigen presenting cell (APC). Specialized lymphocytes known as Th Cells bind to these antigens and then divide. These then stimulate Cytotoxic T cells which secrete a chemical known as perforin. The perforin makes holes on the membrane of 'non-phagocyte' infected cells allowing water to enter. This essentially causes the cell and the bacteria to explode, known as cell lysis.
So basically the infected cell is simply destroyed unless hydrolytic enzymes break down the Bacteria.


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Identifying this spider
I think this is a spider. 8 legs, 2 body sections, and 2 really long Palos? Anyways, can anyone identify this bug, or point me to a resource where I could classify it?

Welcome to Biology.SE! Please include your location and an approximate size of the species. And also add multiple close-up images from different sides. See here for more information

That's not a spider, that's a solifuge (also an Arachnida): https://en.wikipedia.org/wiki/Solifugae .@Anon answer is correct, despite lacking any reference or image for comparison.

It's camel spider, they have large pedipalps, big chelicerae, and their body is covered by little "hairs". As far as I know, there are only 2 families of that order in North America

Welcome to Biology.SE! Please add some more details and references to your answer, along with some images for comparison.

Some spider species are easy to identify as they're relatively common and well-known or though less common, have unusual or distinctive enough markings/coloration, they won't generally be mis-identified.
Since you live in the US, the species will be better identified by another American rather than someone from other another continent. Bug Guide (hosted by the Department of Entomology at Iowa State University) has an ID Request page where images can be posted and amateur and professional experts will look at and identify. You need to register but it's free. The clearer and more detailed your photo(s), the faster it'll be viewed and answered.
It's worth joining. There's a lot to learn and you may find learning about 'bugs' addictive with no bad effects?

I hardly think my answer warranted a downvote. Not living in the US, I didn't recognise it. The OP did ask for identification OR to be pointed to a resource that could help. BugGuide is an excellent resource for identifying arthropods.

I agree with @Jude: downvote might be justified if there was something misleading identification in the answer, but here there is no identification attempt. One could argue that this could have more typically been a comment rather than an answer, but given the fact that the original poster requested for identification resources, this may qualify as an answer.


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How does the adaptive immune system store information?
I am quite curious about this:

Where and how is knowledge that the adaptive immune system accumulates stored?
What is the "memory size limit" of this storage method if there is any?
Why cant this knowledge be transferred between individuals like we transfer computer antivirus definitions?

Are you thinking of the adaptive immune system? There is also "knowledge" in the innate immune system, in the form of generically coded receptors, but that part is fixed for each individual.

Yes, this question is about knowledge acquired during the life of a person, not present since birth

Welcome to Biology.SE! Although the question is nice, biologists generally don't recommend using such an analogy since both these pictures (of immune system and computer storage) don't superimpose clearly. I'd recommend you first study more about immune system, especially adaptive immune system and HLA.

@another'Homosapien'  I agree the computer analogy is not great, but it could still be interesting to consider information content of adaptive immunity (like the number of possible hypervariable region sequences etc).

@roland that would be interesting, but it would also be problematic to scale this up (which would eventually become necessary). Also, I wanted to first make this sure that the OP knows what stuff we'd talking about while using this analogy.

There is probably no precise answer to this question since, as others pointed out, the adaptive immune system is not really comparable to a computer. That said, here are a some items you might want to look into.
Question 1: the main site of information storage for the adaptive immune system is a special region of DNA in T and B lymphocytes that encodes immunoglobulins, the proteins that these cells use to recognize foreign organisms. The sequence stored in this special DNA region can be rearranged by hypermutation and recombination mechanisms. This occurs early in the life of T and B lymphocytes, so that each cell gets a unique DNA sequence. Those cells that later on happen to recognize invaders will multiply as part of the immune response, and they will later survive as memory cells, so that their specific DNA sequences are retained. If the same infection happen again later in life, these memory cells will help the immune system respond more quickly.
Question 2: the region of DNA used is on the order of 1 million bases long, and it has been estimated that the human immune system can generate around $10^{11}$ different immunoglobulins. How to interpret these numbers in terms of "memory size" is not clear to me though. On one hand, 1 million bases is equivalent to 250 kbytes (each nucleotide base storing 2 bits); but on the other hand, $10^{11}$ as an integer can be stored in 37 bits. I guess it depends on what level of information you consider.
Question 3: there is no mechanism for directly transfering information between lymphocytes. Lymphocytes cannot read and write their DNA at will, and they are not able to simply copy sequences from each other. Rather, their diversity comes from first randomly re-shuffling their immunoglobulin-coding DNA, followed by selection of the successful cells --- this is a brute-force, random-search method, like evolution itself. Also, lymphocytes from unrelated individuals will generally interpret each other as invaders, causing an immune response. However, it is possible to experimentally "edit" the "memory" of lymphocytes extracted from blood using genetic techniques. This has for example recently been explored to "train" cancer patients own lymphocytes to attack cancer cells, in some cases with remarkably good results.

Thanks, this is the information I was looking for! Sorry if I didn't formulate my question properly, as I come from computer science background.


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Why do I feel my schoolbag to be heavier after meals?
I am not sure this is related to psychology or not.
My friend casually commented to me that he feels his bag to be heavier after his meal. So I started observing my perception of weight of school bag after every meal. I did this for 3 weeks ( 1 log per day i.e. lunch, 5 days a week, 15 observations).
For 15 observations, 13 times I felt my bag to be heavier. These 13 times I had regular class after lunch. The other 2 times, I had an exam an hour later my lunch.
Is it psychological and / or body function related ?

Could certainly be physiological. After eating more blood is diverted towards the smooth muscles around organs for digestion. This will mean your skeletel muscles have decreased blood flow so less nutrients such as Glucose available to make contractions. As you have less energy available to contract the skeletal mucles you're more than likely to feel slightly weaker.
On the contrary it may he purely psychological! :) Good question though!


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Why do turtles ride on alligators?
I often see pictures of turtles riding alligators, I even saw that in a zoo once, but why do they do that?
Is it some sort of camouflage technique for the turtles? And why doesn't the alligator get it off?

turtles will crawl onto anything to get out of the water and bask, fallen logs are common and they likely cannot tell the difference between a still alligator and a log.  It might also be possible that the turtles do know what the gator is and are hoping to tag along and pick up scraps after it strikes.
I image that for the gators thrashing around to dislodge the turtle has to high a risk of scaring off prey so they just put up with it.


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What is the mass of a human retina?
I'm struggling to find a reference for the mass or density of a human (monkey or rabbit would also work) retina.
I'd appreciate any help!

I did some research and I found this site : https://www.covance.com/content/dam/covance/assetLibrary/posters/StrubleEVER14.pdf
It has the weight for ocular tissues for different kinds of animals ( rabbit , human  etc. ).
I also found that the area of a retina is 1094 mm² and the thickness is 0,12 mm , so if you can find the density you can find the mass.
(found on this site https://faculty.washington.edu/chudler/facts.html#sensory )

Are you sure that the referenced value of 2500 mm^2 is not the surface area? Because there is no way that the retina is 5 cm x 5 cm.

I'm sorry . I did some more research and you are right. The actual area of the retina that i found is  1,094 mm^2 (Link that i used https://www.ncbi.nlm.nih.gov/books/NBK11556/ )


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Ion-exchange vs Gel Permeation Chromatography for proteins
For extracting Lysozyme from egg white which method would you recommend and please help me understand why.
Lysozyme has a higher isoelectric
point (pH 10.5) and a lower molecular mass (14 307 Da) than most proteins so both these methods make quite a bit sense. Use Sephahdax G100 for gel permeation chromatography and CM-Sephadex G25 ion exchanger for ion exchange.
From what I can understand, Gel Permeation will separate the egg white based on Mr of the various proteins and compounds. There is quite a bit of variation in the Mr of egg white proteins but lysozyme, in fact, doesn't have the lowest Mr as Cystatin and Ovomucoid have lower Mr. Furthermore, GPC requires around at least a 10% difference in molecular weight for a reasonable resolution of peaks to occur. The range of Mr is also quite broad in this method. Will this be disadvantageous perhaps? So GPC does have the plus side of it having a well-defined separation time due to the fact that there is a final elution volume for all unretained analytes.
Now Ion exchange chromatography is very specific in the nature of how the exchanger interacts with the mixture being separated. Lysozyme has a PI of 10.7 which is much higher than the rest of the proteins in the egg white. As with GPC we use 0.05M Tris-EDTA, pH 8.2, containing 0.05M NaCl as the standard. Can this setup result in Gibbs Donan effect or chromato- focusing ?
I'm currently leaning towards GPC as the option to yield the purist product especially seeing as it can be desalted afterwards with G25.
Please help guide me in the right direction. I'm quite new to this but am ready and very willing and keen to learn and expand my abilites.

Note that GPC does not just separate proteins by Mr but by a combination of shape and Mr (though shape will be less important for you since most small proteins are quite globular)

Thank you very much for this interesting piece of information. I will keep this in mind for a sample containing perhaps a mixture of globular and membrane proteins.

I know this is an old question, but I would question why you don't just purify the lysozyme by crystallization from crude extract followed by polishing with IEC and SEC...

Here is source on how to crystallize directly from egg white. http://www.jbc.org/content/164/1/1.full.pdf&ved=2ahUKEwjehu-86aHjAhWrM-wKHc-5ChIQFjACegQIBBAB&usg=AOvVaw3ZNa3B5FmbhPGFiTZMpTdj

Since lysozyme is so well studied, your best bet is to search the literature and see what methods other people use. See this paper, for example. They report that lysozyme can be affinity purified on Sephadex, but they also reference other methods in the introduction that you could take a look at.
Both of the methods you described sound reasonable. The only way to know which is best is to try them and see. In fact, the best approach, depending on your application, would likely be to use both methods for optimal purity. Even when I affinity purity a protein, I will still often perform ion-exchange as a polishing step.

Here is what I have come up with. Thank you for all your help.
Ion Exchange Chromatography(IEC) will yield the purist product from a single application. The main reason is due to the fact that Gel Permeation Chromatography is compromised by the close proximity of Lysozyme (14.3 KDa) and Cystatin (12.0 KDA) in their molecular mass. Sephadax G100 separates a large range of molecular mass but the downside of large range is low sensitivity at such close proximity. It won’t be able to discriminate between these two proteins during the elution. Due to Cystatin only compromising 0.05% of the sample it will be even more difficult to pick up this contamination even though it is not large. Furthermore, Sephadax G100 will retain Lysozyme for very long as it is one of the smallest in the sample. Hence, a large amount will be retained and a diluted sample will be produced. It should also be taken into account that GPC has a low resolution, low capacity and does not permit high flow rates. GPC is the fastest and most simple method to produce a cruder sample in comparison to IEC. IEC in this case uses CM-Sephadex G25 which means no Lysozyme will be lost due to particle size properties and Mr allowing it to get caught in the matrix as opposed to GPC. This results in a more concentrated sample. If we compare the pI of all the proteins, Lysozyme (10.7) and Avidin (10.0) both are the only cations at initial pH 8.2 . This means lysozyme can easily be removed as pH is continuously decreased through the use of the cationic exchanger without denaturing it or any sample being lost. GPC is only useful as an additional step to IEC using G25 to further purify the sample through desalting and dialysis.

Your answer is much better than mine.


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Why doesn't submersion in water kill fungi?
I have read that fungi cannot live without air. Does a couple of minutes in a swimming pool full of chlorinated water kill them as it would a mammal? I've never heard this suggested. Will they survive by enjoying trapped air? Or by "holding their breath" for a long time?

Is oxygen soluble in water?

So would they die if submerged in halon or carbon monoxide?

Mammals have a brain, heart and other vital organs that consume a lot of energy (and therefore oxygen). Fungi don't need that kinda stuff and therefore don't need a lot of oxygen (they can hold their 'breath' for a very long time).

Is your question why chlorinated water doesn't kill fungi, or why they don't drown when submerged like mammals and many other animals would. In the case of either, are you sure that the premise is true?

@HarrisWeinstein   Good question. Let me revise my question...

There is a lot of anecdotal evidence that frequent visits to the pool help with fungal infections. Surely, someone from the scientific community must have noticed too, right? So why don't we frequently hear people suggesting to go swimming to treat these infections?
Because scientific results suggest the opposite!
Incidence of occult athlete's foot in swimmers

In our results, 22 swimmers had positive cultures (15%), 8 of these cases had no lesions (36%). They included 7 infections with Trichophyton mentagrophytes (87.5%) and one with T. rubrum (12.5%). We observed one case with a dual infection. Only one sample from the inanimate environment was positive. This study showed a significant incidence of occult athlete's foot in swimmers. To control this endemic problem, adequate preventive measures must be taken.

Foot Infections in Swimming Baths

A 10% random sample of all bathers at a public swimming bath were examined for tinea pedis and verruca.
The overall incidence of tinea pedis was 8·5% and of verruca 4·8%. The incidence of tinea pedis in 205 male adults was 21·5%, in 288 boys 6·3%, in 60 adult females 3·3%, and in 220 girls 0·9%. The incidence of verruca in juveniles ranged from 4·2% in boys to 10·5% in girls.
It was clear that both infections spread within the baths, and since a relatively small proportion of users admitted to taking precautions to avoid contracting or developing infections it seems advisable that more publicity about recommendations on foot care should be provided.

Onychomycosis in Icelandic Swimmers

The prevalence of
culture-positive onychomycosis was 15% in women and 26% in
men. Our results suggest that onychomycosis of the toenails is
at least 3 times more prevalent in swimmers than in the rest of
the population.

Does this mean that not only is going to the swimming pool not a cure of fungal infections, but it is actually the cause? Well, maybe not. While the articles show that there is a larger incidence of fungal infections among swimmers, they only show correlation, not causality. People who partake in sports activities have a bigger chance of having these infections than the general public. These are also the people who are more likely to go swimming.
To settle the matter for good, we need an article named "Prevalence of fungal infections among occasionally swimming couch potatoes" :-)

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What is the name of this flowering plant?
My mother is in hospice, and this beautiful flower is outside her window. She would like to know the name of "her" flower.
The flower is growing in Eastern Kansas and we are approaching the first day of summer here

Where's it growing? What's the season there? Can you add more pictures of the plant (close-ups)? See this for more information.

It looks like a variety of canna lily. There are several flowers that have opened on the tip of your plant, as in the photo below.

The flower is growing in Eastern Kansas and we are approaching the first day of summer here.   I will try and post better pictures of the flower and its leaves.  Thank you all very much for the help so far.


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Success of computer simulations in biology, new discoveries
In an interview with Tim Hunt, Hunt makes the following comment:

There are some people nowadays who think you can sort of model everything on a computer. But I'm not one of those. I don't think anyone has actually discovered anything modeling something on the computer because there are so many different way of doing things...how Nature herself actually chose to do it.

The claim starts at 4'25'' in the link interview.
Have biological simulations ever led to biological discoveries? What purpose have they served?

I think this question is too broad and open-ended, and probably somewhat opinion-based in terms of what "discovery" means - though I'm open to a difference of opinion. As a neuroscientist, I'd say I definitely disagree with the idea that no one has actually discovered anything by modeling, but I also agree that there is a good deal of misinformation about what modeling can actually do, which leads to silly arguments for example from animal rights groups that imply scientists study animals just to torture them because they should be able to do everything on a computer...

I don't think the question is so specific to Biology but rather to the use of numerical modelling in science in general. IMO, the question is off-topic here and should rather be asked on Philosoiphy.SE.

Beware of people speaking outside their expertise, modeling is difficult in cellular mechanics becasue we only know a small fraction of what is going on and our current computers cannot even handle all of that at once. Of course protein structure prediction is fairly important modeling, which he studied, so he should still know better.

I think this is an appropriate question for biology and also I think that asking this question of biology is different from asking it of other scientific disciplines because there are many more data points in biology than there often are in, say, physics. Physics simulations could involve mere handfuls of atoms.  Biological simulations would be more complex.

Personally, I have not used computer simulations to "discover" but I've used them to identify which of the ideas I've developed a priori are possible.

I am happy to re-word the question, if possible.

I like the question, but it's a bad fit for this site. I agree with the closure. "Computational" is a vague term & arguably includes all biology. Hunt's own work is a series of models for biological systems. I am sure his students have gained insights from computational work along the way. In this case, I don't think Hunt understands what he is commenting on or, less cynically, is being too imprecise. For other scientists stepping out into another field and instantly falling over, see that Michio Kaku does not understand evolution.

seems that the answer is "yes": "Simulation reveals how bacterial organelle converts sunlight to chemical energy" https://www.sciencedaily.com/releases/2019/11/191114115845.htm

In my opinion, this question is a question of philosophy of science, not Biology but here are my thoughts anyway.
Science by definition is a methodology that requires the creation of a hypothesis under a specific model and testing the prediction of this particular hypothesis.
Such modelling can be done either analytically (math) or numerically (with a computer). Typically, numerical modelling is being used when there the mathematical tools fail to offer a solution for the system analyzed. To me rejecting, numerical modelling is like rejecting modelling and is therefore like rejecting the scientific method altogether.
Computational modelling has brought a lot in pretty much any field of biology (and pretty much any field of science), so much so that it is hard to know where to start to fully address this claim. There are many models that were only verbal as mathematical tools were not sufficient to bring more quantitative predictions. For many of these models, computer modelling could offer quantitative predictions that could then be further tested.

Hi Remi - congratz on reaching the #1 rep! Well done, mate :)

@AliceD Ha ha Thank you! I might not stay in this position for long as Chris and you are pretty close. The three highest reputed users are very close.

You're really gaining a lot of rep and you should be, as you're writing up a lot of good stuff. I'm hardly gaining any rep these days now I'm (pro-tem) mod on two sites :-)


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Tree identification - Oregon
A bit west of Portland. It doesn't look native to me, and we didn't plant it. This is the first year it flowered, so I decided to see if I can get it identified. If it matters, the flowers are aromatic.

This is a Privet (Genus Ligustrum). It appears to be Ligustrum vulgare which is known as Common Privet, or sometimes European Privet.
It is a common woodland understorey shrub in Europe, often planted as garden hedging in urban areas as it is semi-deciduous and responds well to repeated pruning. You could never really call it a tree, it is a shrub species.
The white flowers as you say are quite fragrant and pleasant. They develop into shiny black/dark purple berries.

I would normally add some photos of my own, but yours are so good they show all the characteristic features very well.


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What is the difference between an active and inactive T helper cell?
1- Are all inactive T helper cells "T memory cells" ?
2- Is there anything such as active T memory cells ?
3- I have noticed that there is also a third type of T helper cells but i dont know what it is called. They are used in the beginning of the humoral response process (they bind to initial APC cells and then divide producing active t helper cells and inactive t memory cells). How are these different from the active and inactive T helper cells ?


text:
Animals with substantial five-fold symmetry besides starfish? Any land animals?
Animals with four, six and eight legs are widespread while the concept of seven legs (fictitious Heptapods) are the makings of amazing scifi short stories and blockbuster movies.
Are starfish the only types of animals currently (or ever) with five mostly equal sized appendages and substantial five-fold symmetry? Are there theories why five is unusual on land but common in the sea?
update: There is an interesting subtlety here. This answer points out that a sea star's legs are the little things under the five appendages, so I've adjusted the question to address instead five-fold symmetry and five appendages.

below: "Ophiopetra lithographica from the Lower Hienheim Beds (Lower Tithonian,Upper Jurassic) near Regensburg, Germany" from here.

below: "A green brittle star - Ophiarachna incrassata" from here.

below: "Une ophiure superbe (Ophiolepis superba) à la Réunion." from here.

I suggest that you will find it very interesting if you knew that actually there is a land animal with five limbs. If you are interested check here . I didn't want to post it as an answer because I thought it does not fully answers your question ;) . I forgot to mention that the land-animal I mentioned doesn't show symmetry to the fifth "limb".

@The_Mad_Fish I was a little hesitant to click your link until I saw it was the NewScientist. I clicked and then a big Aha! yep, well done :)

hahaha I hope that I covered you lol ;)

Many (if not most) of the Echinoderms (to which starfish belong as well) have five-fold symmetry, such as many sea liliy (Crinoidea) and sea urchin (Echinodea) species.
Five-fold symmetrical sea lilly:

Sand dollar (type of sea urchin):

Maybe you could add that they are, however, *Bilaterians (as opposed to Radiata), as their larvae, representing the ancestral state in the group, have bilateral symmetry.

I should have recalled sand dollars, thanks. OK so there are diverse members of an entire phylum, that's great! Echinoderms are also the largest phylum that has no freshwater or terrestrial (land-based) representatives so that settles it.

@AlexDeLarge that's an interesting feat.


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Identifying a beetle from northern California
Just found this organism crawling across my wall on the second story at around 12:30 AM. We're in Sonoma County in California. Our best guess so far is a soldier beetle, but the coloration doesn't seem to match any images we can find online. It's body was about 1.5 inches long and was a uniform brownish-tan color with black eyes. It may be worth noting we're in the middle of the worst heat wave we've seen in 15 years of living here.

This is a long-horned beetle, family Cerambycidae; the site http://www.sbcollections.org/cbp/DB_Query.aspx?Field=family&Value=Cerambycidae has a list of California species, with links to pages on each species (there are 387; not all species pages feature illustrations -- those that do figure museum specimens).  From that list the first that resembled your photograph is that covering Centrodera spurca (LeConte 1856), which has been found in Sonoma County; given that I haven't gone through the entire list there are likely other possibilities.
Centrodera spurca

I agree it's a long-horned beetle (so +1) but a picture to compare it to would be helpful. I edited to add. Not sure if it's the same beetle, though. They look like they can easily be mistaken within the group.


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What is the actual chance of sibling incest child suffering from a genetic disorder?
This is not a question about the (a)morality of incest or current laws. However, there seems to be a widespread misconception about the impact of sibling incest on the genetic health of the eventual offspring.
What is the average chance that an offspring of a random sibling couple will suffer from a genetic disorder compared to an offspring of any random unrelated couple?

There is an average answer - I am specifically asking about random human couples.

Fair enough. I don't know that there is an answer, though. Different populations have different genomes and risks, and it depends on how closely related (e.g. small gene pool population) the parents are. You'd have to look at multiple studies, probably many of which have not been done. So, still, probably no reliable answer.

Usually when we talk about genetic disorder risks for closely related pairings, the concern is the high probability of homozygous recessive alleles.
Lazarin et al. 2013 screened ~23,000 individuals for 108 genetic diseases and found 24% were carriers of a known allele for some disease. Including carriers of multiple alleles, the total frequency comes to about 38% (this is a lower bound because only known alleles can be screened; there may be many other variants that are not known to science that cause the same symptoms).
That means about a 62% chance that one of an individual's parents carries one of these alleles (1-.62*.62 - note that this 62% has nothing to do with 1-.38, just a mathematical coinicidence with rounding).
If a parent is a carrier, each sibling would have a 50% chance of also becoming a carrier; the probability that both siblings are carriers would be 25%. The probability that an offspring from those siblings would be homozygous recessive would be another 25%. .62*.25*.25=3.9% (note that these are all lower bounds, the chances would be much higher if there were multiple recessive alleles present or if both parents were carriers for the same gene).
However, this is limited to Mendelian mutations just for this subset of known alleles. There are many many more conditions and disorders that have more complicated genetics that we may or may not understand, so that the original question becomes nearly unanswerable. In fact the paper I cited only paid attention to what were considered "major" disorders and even left out the Mendelian alleles known to cause more minor issues (including clotting disorders that can easily lead to death in the right circumstances). There are also many mutations that don't cause a clearly defined disorder but cause some other more limited issues that could predispose the offspring to other illnesses.
Lazarin et al. 2013 refers to estimates that each individual carries about 4-5 lethal recessive mutations. Given that siblings are very likely to be carriers of the same particular recessive mutations, this would significantly impact any offspring well beyond the estimates for the known disease alleles.
References
Lazarin, G. A., Haque, I. S., Nazareth, S., Iori, K., Patterson, A. S., Jacobson, J. L., ... & Srinivasan, B. S. (2012). An empirical estimate of carrier frequencies for 400+ causal Mendelian variants: results from an ethnically diverse clinical sample of 23,453 individuals. Genetics in Medicine, 15(3), 178-186.

Thanks for the answer. I was wondering if we could extrapolate from the many real world examples of offsprings of first cousins - there must be millions of children, right? And the probability of homozygous recessive alleles in first degree relatives should be exactly 4 times higher, right? Actually I found an article saying exactly that https://www.larasig.com/node/2020.

Nicely done. There were all Americans, I presume? Mendelian vs. non-Mendelian aside, there are subsets of populations in which I would expect much higher rates of lethal (recessive) genetic mutations, the most obvious being Ashkenazi Jews. All in all, I think this question is not answerable, because the studies just haven't been done.

@anongoodnurse Yes, Americans, including a slice of all ethnicities although some are under/overrepresented. Africans/African-Americans were underrepresented. Ashkenazi Jews are quite overrepresented, probably because the study is from people undergoing preventative screenings and that community is aware of the risks. I agree the question as asked isn't totally answerable, but I think it's reasonable to estimate. What I tried to address in my answer is that the issue isn't just the known alleles but all the de novo or unknown alleles.


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Do the recent findings of an ape-like creature in Europe with human-like teeth change the Out of Africa narrative?
http://www.telegraph.co.uk/science/2017/05/22/europe-birthplace-mankind-not-africa-scientists-find/
Two fossils of an ape with human-like teeth were discovered in Greece, and Bulgaria, and they are about 7.2 million years old.
Does this change the narrative of the 'Out of Africa' theory?
Have scientists in the relevant fields commented on this yet?

Of course every researcher wants to find something exciting and new. As the linked Telegraph article identifies their fossiles as the oldest hominins ever found, arguing that the lineages between pre-humans and chimpanzees therefore split in Europe, with pre-humans then migrating back to Africa to be consistent with other evidence.

Does this change the narrative of the Out of Africa theory?

Not at all since the Out-Of-Africa hypothesis is about the African origin of all modern humans (Homo sapiens), i.e. that the species originated in Africa and then spread over the rest of the world. It is not about where possible, early ancestors may have originated. The ape from the article, Graecopithecus freybergi is claimed to be one of the oldest Homininesa, but that does not change the claim of the Out-Of-Africa hypothesis.
Reference
a Fuss, Jochen, et al. "Potential hominin affinities of Graecopithecus from the Late Miocene of Europe." PloS one 12.5 (2017): e0177127. https://dx.doi.org/10.1371/journal.pone.0177127


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Is the blastopore imaginary?
I've been told in my zoology class that the blastopore is an imaginary pore found in gastrula, from which mouth develops first in protostomes and anus develops first in deuterostomes. But we've also been told about the famous blastopore grafting in newts experiment by Spemann-Mangold. So how can you graft something which is imaginary? Is the blastopore really an imaginary pore?

Ithink they were referring to the fact it is not actually a pore in the normal sense of the word but instead an invagination. It has been imaged many times https://www.researchgate.net/profile/Jr-Kai_Yu/publication/6564822/figure/fig2/AS:281320203800598@1444083371979/Figure-2-Expression-of-Nodal-the-Nodal-antagonist-Lefty-and-organizer-related.png

From Merriam-Webster:

Definition of pore
1 :  a minute opening especially in an animal or plant; especially :  one by which matter passes through a membrane

The blastopore is a real thing, it is not imaginary. It is the point where the mouth or anus eventually develops. I'm guessing the reason your zoology class referred to it as imaginary, however, is probably because it isn't really a pore (and especially it is not a pore into the blastocoel). It sort of looks like a pore, but it's just a little indentation (and may even be considered a blastopore before the indent forms); it doesn't really become an opening until later, and the process of gastrulation doesn't actually involve anything going inside the blastopore, it's just a folding in of the cells on themselves.
In summary, I think your understanding is sound, good job, and I just wouldn't get too hung up on the "imaginary" part.


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What species of snake found in central Alabama, US?
The snake in the image below was found in the attic of a home in a relatively well-forested suburb of central Alabama, south of Birmingham about 20 minutes. It was safely released outside in the wooded backyard area. What species is the snake in the image below?
Some additional details that may be helpful follow. It emitted musk while being coaxed into the box. I don't recall seeing much striping, except near its head, as can be seen in the image below. I did not get a good look at the belly color, but I believe from the glimpses I got that it was similar to the lighter color on its back and sides. It appeared to be close to 3 feet (~90 cm) long.
I attempted to use Google to identify the snake, and the closest matches were various rat snakes. None had quite the same patterning.

Definitely looks like some species of rat snake (genus Pantherophis). Based on the size, location and coloration, I'd say it's a dark variant of a Gray rat snake (Pantherophis spiloides).

It might also be a cross between a black and grey rat snake (i.e., Pantherophis spiloides x obsoletus).

 Source: Todd Pierson

 Sources: Alan Brumbeloe | Bill Funderburk
Description: Adults usually 99-183 cm long; dark to light gray with darker gray or brown blotches

Unlike other Pantherophis, whose conspicuous juvenile pattern fades into adulthood, gray ratsnakes do not undergo drastic ontogenetic changes in color or markings. These snakes retain the juvenile pattern of dark elongate dorsal blotches separated by four, or more, pale gray body scales, a light gray crown with dark striping that forms an anteriorly facing spearpoint, and a solid band which covers the eyes and extends rearward to the posterior upper labial scales. The venter is usually off-white or pale gray with darker irregular blotches, and a double row of black spots behind the divided anal plate of the vent. The dorsal scale rows around midbody are usually weakly keeled. Because the gray ratsnake shares its range with other members of its genus, hybrids of midlands x eastern ratsnakes are not uncommon. [Source].

Note, According to here one could have a difficult time IDing juveniles between species of rat snakes:

The juveniles of all subspecies [of rat snakes] resemble the gray rat.

However, your specimen's size indicates it's likely an adult, and therefore its strong patterns preclude the black rat snake.

Distribution:  commonly found in the forests of eastern and central United States, including throughout Alabama:

 Source: Trey Dunn
Behavior: Gray ratsnakes are agile climbers and can be found in tree tops as well as barns/sheds/buildings close to forests

The gray ratsnake will defend itself by raising its head and bluffing a strike. If handled, these snakes will musk a victim by releasing the foul-smelling contents of their cloaca, and will bite if necessary. [Source].

It looks like a gulf hammock rat snake. Beloved to be a subspecies that started as a cross between yellow rat snake and grey rat snake. I know they occur in northeast Florida perhaps they are in Alabama as well.

We expect answers on species ID questions to be more than just an unsupported guess; it's best to use references from reliable sources to support an ID, and explain how that ID was reached to the exclusion of other possibilities.


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Do lobsters possess a nervous system to feel pain?
I was reading an article, which it mentions that lobsters do not have a nervous system:

Lobsters have very poor eyesight and no nervous system. They walk slowly
  on the sea floor but are capable of swimming backwards by the curling
  and uncurling movement of their abdomen.

But in Wikipedia, I read that only 3 types of multi cellular animals do not posses a nervous system:

The only multicellular animals that have no nervous system at all are
  sponges, placozoans, and mesozoans, which have very simple body plans.

Which none of them seemed like a lobster to me. In this answer, it is claimed that every living organism feels pain somehow.
Now I would like to know the answers of these questions:

Is the article about the lobsters true? They have no nervous system which means they feel no pain even if killed?
Is the claim in the answer true? Literally one of the claims must be wrong, since they conflict with each other somehow.

As for the answer you linked to, it states: I believe every living organism (even single cell ones) experience pain somehow, which is hardly a scientific claim. Also: The scientific answer depends on how you define pain, which is an important caveat. If you were to define pain as the ability to sense damaging stimuli (which to me seems inappropriate), then every organisms indeed can feel pain.

@canadianer Well yes, when a living organism can heal itself, it means it can feel the damage. I was actually wondering about the same pain that most of the animals (including humans) feel; the unbearable feeling.

"I was reading an article, which it mentions that lobsters do not have a nervous system:" - Neuroscientist chiming in here... this is a really good cue you should stop reading the article if you are looking for science.

@JackJohansson "...when a living organism can heal itself, it means it can feel the damage"- How so? Unless you're extending "feel" past a conventional meaning, then there countless organisms that this is isn't remotely true for.

@HarrisWeinstein - would love to know how you determine whether or not another organism can feel.

@canadianer Me too believe that on the basis of similarity. But yet it could not be tested ( problems of qualia ) yet.

Lobsters have "No nervous system"? it goes against my very basic understanding of animal anatomy and histology.

@AlwaysConfused I didn't write the article.

@JackJohansson I Didn't meant it is your claim. I just meant the website's claim sounded very odd to me.

@AlwaysConfused That's why i asked it here. But the comments seem like its a crime to ask.

@JackJohansson Would anyone here told not-to ask questions here? looks like none of the currently visible commentators said not to ask questions. Yes, moderation is tough here, but to me it seems the question is not being criticized... rather the web article is being criticized.

@youcantryreachingme Possessing a nervous system is a good start.

I do not have a link to this but I read that lobsters will fight over territory or mates or whatever and the loser of such a fight will avoid the winner for some time afterward. So whatever the lobster uses for a nervous system allows it to both remember and recognize other lobsters. (Yellow jacket wasps will fight for "pecking order" and remember whom they have fought before and feed peacefully next to each other once hierarchy position is established.)

Before answer, What intuitively seems:

Lobsters structurally contains sense-organs like eye and antennae, and output organs like muscles through which they move. So plausibly these organs should be plausibly connected to its controllers, i.e. neurons. The basic histology found in very primitive multicellular animals like Hydra, Planaria to advanced animals like human.
Lobsters are able to respond the stimuli.  They move, they prey their food, they met for sexual reproduction. So it is very unlikely they do it without a very complex nervous mechanism.
Lobsters are not surprisingly different in structure than any other crustacean arthropods. So it is very unlikely that lobsters would have so much drastic anatomical difference from other allied members.

What references says:
Arthropods:

The arthropod body plan can be seen as an elaboration of the segmented body of an elaboration of the segmented body of annelids, although arthropods show a higher degree of cephalization than do  the annelids. The outer surface of the arthropod is a rigid, many-layered cuticle,  and the segments of the body bear jointed appendages.
The nervous system of arthropods consist of a 'brain' in the form of dorsal- ganglion ,  connected by a nerve collar  around the gut to the first ganglion  of the ventral- nerve cord. The nerve cord is double, with segmental ganglia. Probably because of  the heavy external skeleton, the arthropods have a great variety of sensory organs connecting their central nervous system  with the external environment.

-Advanced BIOLOGY, Principles and Applications/ CJ Clegg and D G Mackean/ Reprint 1999/ John Murray publication.
Crustaceans:

According to australian museums website (home)

they have a small brain behind their eyes and a series of ‘mini brains’ or ‘ganglia’ (the plural of ganglion) in the nerve cord that runs along the body on the ventral (underneath) side.

A simple google  There are many papers and books about crustacean nervous system such as
The Nervous System of the Crustacea, with Special Reference to the Organisation of The Sensory System/M. S. Laverack/Springer,
The central nervous system of simple Crustacea/ w.a. Hilton/Wiley online library,
A book The Crustacean Nervous System/ Editor: Konrad Wiese/ Google Books (Multiple places discus Lobsters, most not free-accessible),   etc.

Here are some screenshots from the above mentioned Google book article.

Diagrams and photos of nerve-features of Procambarus, a crayfish(not to be confused with fish).

Nervous system diagram contains nervous system diagrams of Homarus, a
 lobster.
The same google book preview also shown the development of ladder like double-nerve-cord .

Developmental stages of  ventral ladderlike nerve cord in Homarus.
On the same Google book preview I found a more functional diagram (neuron response curves) of the crayfish,  Procambarus

....................
Lobsters:

According to The Lobsters Conservancy' s webpage on lobster's nervous system; it mentions very clearly that lobsters have nervous system.

Lobsters have compound eyes, as do most arthropods, but these are stalked to provide a broader field of view and increased binocular spread. In clawed lobsters, each eye has 13,500 ommatidia which are light capturing, image forming organs. Lobster eyes are adapted for use in low-light environments, but appear to be only monochromatic (no true color discrimination ability). How good is their eyesight? How much do they rely on it, relative to other sensory systems like smell, taste, or touch? Lobsters, with their eyes perched on top of their heads, certainly detect shadows of potential predators looming above them - - whether that detection is perceived simply as quick changes in light intensity or whether an image is formed is not known. Lobsters also use some obvious visual displays in agonistic encounters. Still, chemical and tactile senses appear to be the keys to successful social encounters and prey detection. However, vision in lobsters has not been well studied.
Even though lobsters live in a watery world, they have highly developed systems of both smell and taste. The first antennae, properly known as antennules (little antennae), act as the "nose" of the lobster. Hundreds of fine hairs cover the antennules and are the actual organs of smell. These hairs are incredibly sensitive to amino acids, the building blocks of all proteins, of which animal tissue is made. However, the hairs are densely packed on the antennules and this proves to be a problem in a watery environment. Water is much more viscous (sticker) than air, as oils are more viscous than water. When fine structures are densely packed together and placed in a water environment, the water between these structures is not easily moved - - in other words, a boundary of nonmoving water is formed around the structure. In order for a lobster to be able to smell something, or to be able to walk towards a smell, it has to constantly sample the chemicals in the water to determine their changing concentration. Lobsters do this in the same way that humans do - - they sniff. Sniffing is accomplished by flicking the antennule downward quickly - - this removes the old water and replaces it with new water and a new odor sample. Flicking can be easily observed by watching a lobster in a tank (at an aquarium,restaurant, supermarket, or lobster pound) for just a few moments. Because lobsters have two antennules, they can determine the direction of the smell by comparing the difference in concentrations between the two antennules. Humans use a similar mechanism for distinguishing between different concentrations (noise levels) of the same signal to determine the direction of sounds.
Lobsters also possess proprioreceptors - - sensory hairs that are internal and provide information about limb movement, posture, and equilibrium. These are generally located at joints and within muscles and are stimulated when the joint is bent or straightened and when the muscles are stretched. Proprioreception is critical to maintaining proper posture and coordination during movements.
Lobsters are also capable of producing and detecting low-frequency sounds. Clawed lobsters produce a growl or rasplike sound by contracting a small sonic muscle in the base of the large antennae. These sounds are not made during social interactions, but have been recorded for lobsters resting in their shelters and can be felt (not heard) when a human pulls a lobster from its tank or natural habitat. Their purpose is completely unknown, but may have something to do with defense. In contrast, spiny lobsters possess a stridulatory organ at the base of the second antennae that makes a variety of sounds: rasps (during aggressive encounters or when predators are nearby), slow rattles/flutters (when secluded), pops (when the lobster is out of its shelter), and mating calls. They do not, however, possess the functional equivalent of ears and thus do not hear these sounds in the same fashion as we do. But sounds are simply vibrations that travel through the medium they are produced in (air or water) and thus, they can be detected by mechanoreceptors that are sensitive to water vibrations.

Though, however; this webpage did not display the references for their so detailed informations.

The dispute :
The above mentioned website, Wikipedia, and some other website mentioned about this dispute. Several of the website (including OP's mentioned) supported the view that lobsters/ crustaceans don't feel pain; some put a more-or-less neutral opinion (like wikipedia, Lobsters conservancy). Some website such as PETA strongly offended this view and clearly expressed it as a popular believe.

Some people believe that shrimps, crabs, and lobsters—all of whom are more closely related to insects than to vertebrate animals—cannot feel pain at all. But recent scientific studies have shown that crustaceans have central nervous systems very much capable of generating the sensation of pain. Crustaceans release stress hormones (analogous to our adrenal hormones) in response to painful events. If you’ve ever seen a lobster or crab lowered into a pot of boiling water, you’ve seen these animals fight just as hard for their lives as any other animal would in the same situation. A lobster can’t scream, but that doesn’t mean he doesn’t feel agony in the time it takes for him to boil to death. And crustaceans suffer in other ways—they are often transported alive to restaurants and grocery stores and crowded into tanks where they are so stressed that their claws must be banded shut to prevent them from attacking each other.

My opinion about this problem; is nothing but people might overthinking a certain  belief, and the logical barrier to both prove or disprove it, is the problems of qualia.. And also, "lobsters don't have nervous system" is a drastic misinformation, a really bad news for science; But basically lobsters are no different from other animals.

this answers whether they have a nervous system but does not answer whether or not they feel pain. (a copy pasted peta article is not a reputable source) Plenty of animals  with a nervous system have only a reflex response to pain with no awareness of it, (sea slugs are the classic example). You went through a great deal of effort to show the former and could have easily tracked down the referenced paper for the former.

Yes they feel pain, at least in certain areas of their body without a doubt. Research has been done to test whether they feel pain consciously (a signal to the brain that is perceived allows for learned response) or if it is just a reflex response (Nociception), and there is good evidence they actually perceive it especially in the antenna.
source
Source 2

Now that's something i liked to know, despite the other comments that aren't any constructive. Thanks!

@JackJohansson Actually comments are not for answering, (this help article discusses usage of commenting here) and it may take time to get answer. Because there are rules for  answering, and it may take time to reach the potential answerer. Though short hint as comment sometimes tolerated here, basically if an user post an answer in form of comment, it receives high criticism. Mainly because answering as comment makes them less-trackable, and comments are very prone to deletion.

Can you please provide a source?

There already is one but I'll add another.

To answer if lobsters have a nervous system:
YES

References:
Mapping of serotonin-like immunoreactivity in the lobster nervous system
BS Beltz, EA Kravitz
Journal of Neuroscience 1 March 1983, 3 (3) 585-602
http://umaine.edu/lobsterinstitute/education/life-of-the-american-lobster/anatomy-biology/

Bonus picture:


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Size of deoxyribonucleotide
What is the diameter of each type of deoxyribonucleotide (if the types are significantly different in diameter, if they are fairly similar one value would suffice)? I.e., if a hole was to be created through which only a single deoxyribonucleotide could pass at a time, how small would it have to be?

DNA is about 20 angstroms wide, so each of the two strand is about 10 angstroms wide. That width is the average between a larger purine unit and smaller pyrimidine unit, so let's round up to 12 or 13 angstroms for the larger unit.

While this answer gives a reasonable approximation for nucleotides constrained in a double helix, it should be noted that nucleotides have conformational isomers and they could potentially be smaller when free in solution. Purines especially can form a syn conformation which is much more compact than the anti conformation found in B-DNA.


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What does it take to start producing(cultivating) probiotics?
Is there a DIY way?
Is it possible to make a bacteria strain from scratch based on an existing one ? (for example lactobacillus reuteri).

have you looked elsewhere for potential ways?

Is "probiotic" a scientifically meaningful term?

you are right @jamesqf but I don't know the correct english word to refer to this commercial name...

@VanceLAlbaugh yes I looked online but I didn't found nothing useful..

Probiotic prebiotic and synbiotic, are used to indicating health promoting bacteria, compounds that stimulate growth of probiotic bacteria relative to other bacteria and a mixture of both respectively.

@Alessandro Carrese: Don't feel bad.  I'm a native English speaker (and I think a fairly well educated one), yet I really have no idea what "probiotic" means beyond being a marketing term in the health food industry.

I did a master's thesis involving enzymes from a probiotic bacteria. Many of the known probiotics were cultivated from faeces but others have also been isolated from breastmilk. Many of the probiotic bacteria are strict anaerobes and can only be succesfully cultivated in modified atmosphere. You may need to use selective plating with various prebiotic compounds such as Galactooligosaccharides or similar compounds in order to control bacterial growth. I recommend incubating at 37°C or slightly below depending on how well controlled your incubator is.

Thanks for correcting my spelling mistakes. I have a question about references... Is it allowed to self reference a peer reviewed article?


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Why does regular bread yeast fail to thrive in pond water?
I thought I'd try adding regular yeast to water taken from my 75 gallon pond, with the idea that the yeast would be a good "bottom of the food chain" kick start to feed the little beasties, along with warmth and light, to allow the creatures to multiply faster than they would in the pond, to be added back the pond as feed. But to my surprise, the yeast won't grow in the pond water, at least, not like when you make bread with it. I've tried adding sugar, molasses, and "proofing" the yeast, but each time, the yeast does not thrive. Is something eating it as soon as it starts to grow, or is something using a nutrient it needs, or what?
The pond is established, with lots of plants, only a few fish, and ammonia levels are 0 ppm. It is an (apparently) thriving ecosystem. My question is, why won't yeast grow and froth up in that water?

How much sugar are you adding to the 'growth medium'?

I'm adding about a teaspoon of table sugar to a half gallon of water, same amount for molasses. With tap water, the water/sugar/yeast mixture foams and froths within minutes. Using pond water, it does not.  I even got a mixture of tap water, one cup water, one teaspoon sugar and a tablespoon of yeast. After ten minutes, this mixture was foaming and frothing, when added to the pond water, yeast activity stops, as near as I can tell.

For any microbiologists reading this, the supplementation is approximately 0.1% sugar.

What exactly is 'yeast' in your experiment?

I'm using regular bread yeast.

Is it fresh yeast or dried yeast?

I'm using regular bread yeast.

The yeast is packaged dry yeast. It is definitely good yeast, since after the first try I made sure the yeast was good by "proofing" it.

I am not a specialist of fish, but yeast infection is a thing. For the sake of your thriving ecosystem, I would advise you to ask on pets.SE or somewhere similar if having yeast in a pond is a good idea at all.

A few random thoughts.
I think that one problem here is that by using dried yeast you aren't really measuring growth or survival. Over a short time period much of the fermentation that you see probably has very little to do with viable cells. Dead cells in dried yeast act as permeable packages of enzymes and can promote fermentation.
Following on from that, it may be that components of the pond water can poison the fermentation carried out by the dead cells.
Thirdly, if you are using frothing as a measure of CO₂ production it is possible that there are components of the pond water that collapse that foam by removing stabilisers (probably protein).
Next, Saccharomyces isn't an obvious choice for use as an aquatic micro-organism since it is adapted/selected for growth in high sugar concentrations.
If I was trying to do this I think I would try to culture from the dried yeast under conditions where you do see activity, add lots more sugar (as if you were brewing), and look for actual production of yeast cells. Yeast settles out of suspension very easily so you might be able to pour off most of the liquid and add the cells to your pond. But I have no idea how well such cells will do in a pond.

Thank you for your thoughts. I think my question is actually related to your second paragraph,  "it may be that components of the pond water can poison the fermentation carried out by the dead cells". I'm trying to understand what that would be.

It was never my intention that the yeast survive in the pond. I was using yeast to feed the "little beasties", to promote their growth, which could then be added to the pond. I just find it interesting that with the substitution of pond water for tap water the yeast does not become active. I WAS using frothing as an indication of carbon dioxide production. I put the lid on the bottle and no (or very little) carbon dioxide production. I got the idea because yeast is used to feed brine shimp and daphnia.

Now I think the simplest explanation would be that something is eating up the sugar before the yeast has time to rehydrate and become active.


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What is this plant growing on Asian spider-flower?
I found a densely-clustered plant (circled in red in photo) growing on top of an Asian spider-flower. I know what Asian spider-flower looks like. I'm in Chennai, India. What type of plant is this?

(Click the Image to enlarge it)

can you post a closer picture?

Are you telling about something yellowish thread like climber plant? it may be some sort of parasitic climber, probably Cuscuta reflexa or Cassytha filiformis.

@AlwaysConfused I added new image.

@user33380 typically plants are very difficult if not impossible to identify without close-up pictures of leaves, stems, flowers, and/or fruits. If you can take any up-close pictures, you'll likely have much better luck getting this plant identified. See here for more hints regarding asking good [tag:species-identification] questions. Thanks.


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Pee Shiver: Any reliable research about this phenomenon?
I came across 2 webpages about the science of pee shiver.
Link 1
Link 2
I wonder if there any reliable scientific research about this phenomenon. The 2 webpages I have hyperlinked attribute this to ANS(Automatic Nervous System) or sudden decrease of temperature in exposed body part while peeing.
But these 2 are just hypotheses, not proved reseach. Is there any?

Sadly, nobody really knows why this happens. Interestingly, those 2 links are the only 2 major theories about this :P

@another 'Homo sapien' I think the hypothesis of relating pee shiver to autonomous nervous system is more realistic.
What do you think?

Yeah, that temperature one does not seem much satisfactory. However, I did not study either of them in detail, so I can't approve any right now...maybe somebody would also like to share opinion ;)

Really is there such a phenomenon? I never perceived it yet.

@Always Confused Yes, there is. I frequently perceive it.

@Mockingbird Maybe because I live in a very hot climate. Yet I never perceived it when I was in tour to any Himalayan region. BTW I could not found any wikipedia article on it. May be that has been not created yet, or maybe that exist in some other technical names.

It's been found that many people don't notice this phenomenon with themselves.

@Always Confused Perhaps you should try drinking too much water, then holding your bladder for too long, then pee. you might perceive it. And speaking of hot climate, I live in a tropical climate. Yet, I perceive it


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Water absorption plant physiology
Can the movement of water in plant outside xylem be multidirectional ,like in case of sucrose transport?

Do mean bulk flow? If not then yes. As in osmosis during transport of organic substances in phloem at source and sink.


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What sea animal is this?
I am in a remote village and a young boy (second pic holding tail) says this thing is his friend. This creature is safe, we held it for pictures and released it after. None of us know what this is and we do not know who to contact. The young boy plays with it every day so it is safe but it still is strange.
These are salt water shores, not fresh water.
Someone mentioned a dugong but it is far too skinny I think. I didn't get pictures of the head as we didn't know if it had sharp teeth.
Image is taken in a remote village in Kavieng, Papua New Guinea.

The creature's head looked like this.
Link:
 polartrec.com/files/members/cara-pekarcik/images/dsc_0160.jpg
I'm no expert, but I don't believe seals are in Papua New Guinea, it's almost a hybrid of few things.

Clearly a merman :p.

It is sure something that looks like a mammal... check any dolphin species or something like a sirenid... manate amybe? or something like seal.

The vertebral column is so pronounced! Doesn't appear like a dorsal fin.

Do you have a picture of its face?

I wish we did but all of us were too scared in case it might've had sharp teeth, it wasn't aggressive at all but since we have no medical nearby it was too risky

If you have any additional photos, please provide them.

Also, please orient us. We are looking at the dorsal (i.e. back) side of the animal, aren't we?? (Or is the animal upside down?)

Did you notice whether it had a blow hole?

Hi sorry it's 1am so my replies are slack, but yes you're looking at the dorsal side, and it did not have a blow hole. If I were to describe the head it looked awfully similar to a leopard seal but that's just a comparison. There weren't any other fins visible either. Such a strange thing we saw! Funnily enough, mermaids are huge in this culture and it was suggested by locals haha

@Jude Thanks for the responses. If possible, please take additional photos of this animal. Since you said it comes to play with the kid every day, I assume you'll have more opportunities to photograph?

What on earth is happening here??? This animal isn't any kind of seal (because of the dorsal fins) and it isn't any kind of dolphin because it doesn't have blow-hole and a find on his spine.... I strongly recommend that it is a sirenid... like sea-cows, but it is small. Because as you mentioned it plays with kids it maybe be a juvenile sea-cow... that's my opinion and I am not 100% sure :). Very interesting case by the way.

Will definitely be taking more pictures this afternoon, it's raining today but I don't think that will make a difference. Im a little worried as villagers believe this is genuinely a siren/mermaid/sea spirit in their culture and want to kill it as it brings death - very hard to persuade them and it sucks because it's a gentle little guy. Keep in mind this is a very isolated village and they were brought up on these beliefs unfortunately. The spine also was naturally pronounced - in the first pic we didn't hold up the tail

I also don't know how to link pictures but the creature head looked like this https://www.polartrec.com/files/members/cara-pekarcik/images/dsc_0160.jpg   And I'm no expert but I don't believe seals are in Papua New Guinea... its almost a hybrid of a few things. I'd also like to apologise to the person who edited my post, thank you! English is my third language so you helped me out

It would be interesting to know how long this animal has been around, and if it has been observed feeding, whether it looks healthy or not. I believe the provided answer is right (dugong). I read on wikipedia: "The dugong is a national animal of Papua New Guinea, which bans all except traditional hunting." -> Killing "mermaids" is not permitted, and I hope the animal will be treated with due respect.

This is off topic, but could you contact the Wildlife authorities and bring this creature to their notice. I think this is the best thing to do when one finds an unidentified animal and there's risk of death. @Jude

The animal should get proper protection

Could it just be a dead Pacific sleeper shark? On its back, given the colouration size, and the fin is set as a fish not a mammal they are twisting is!

It's probably a dugong, based on the location, lack of a dorsal fin, split tail, lack of a blowhole, and narrowing of the snout.
The prominent vertebral column looks unusual, but that might come from the strange posture it is being held in or from malnutrition.
This publication from the Australian government shows necropsy of several dugongs (note, this PDF contains graphic necropsy photographs), including one that was malnourished (see page 53). This individual shows some of the characteristics of the OP, including pronounced vertebral column and a clearly visible neck. The text notes the presence of these features as well.

Adult dugongs showing signs of malnutrition: a) with neck becoming visible
  and prominent backbone

Sadly, the other dugong pictures I found that look most like this specimen are also ones from news sources that are often dead or injured or needing some other human assistance. Some other examples:

Queensland couple come to rescue of beached dugong
Dugong dies from propeller wounds
Trang fishermen asked to help slow-moving male dugong
Rare Dugong saved in Maliangin Community Marine Sanctuary

Some pictures do show a prominent vertebral column near the tail in animals that seem otherwise healthy, but those images don't show the rest of the animal well (thanks to @theforestecologist):
http://www.oceanwideimages.com/images/11147/large/dugong-58M1444-20D.jpg
http://www.oceanwideimages.com/images/11144/large/dugong-58M1444-17D.jpg
As an extra piece of trivia, dugongs and their manatee cousins have been closely associated with mermaid legends.
Of course, a better picture of the animal's head, especially in profile, would make identification much more clear.

I knew it was a dugong... but a juvenile, since it doesn't have so much fat tissue that adults dugongs have... I believe that the unusual spine is because of the lack of food. Maybe because it is young its mother didn't learn to it the main seaweed nutrition that dugongs have.

Most pictures I can find from dugongs have more moon like shaped tails whereas the OP's picture clearly shows a strong split. Based on which pictures did you think that these tails were similair?

I agree about the tail, but perhaps this is really just an illusion from the way the animal is being held in the OP's pictures? I did find two pictures (here and here) that show a strongly pronounced spinal ridge leading from dugong taild like in the OP's photos.

I'm going to withhold an upvote for the time being due to the strangeness of the OP's specimen. Though I think you're likely ultimately correct that this is a dugong, I'd like to see you present a stronger case (e.g., address the following: skin color, ridge along back [feel free to use my photos], Rick Beeloo's comment about the tail, the narrow neck, the pointed nose, etc.).. I also don't think your photos are at all convincing :p

@theforestecologist Thanks for the extra pictures, I'll add them, and some as well as some more argument. I may wait a bit, though, for OP to post some more pictures, I think they will be quite helpful and the only way to make this definitive. Partly this is just a matter of process of elimination. There is no way this thing can be a seal, there is no seal with a tail like that (and no seals that live where OP is, though that's less convincing). There is no way it can be a dolphin/porpoise/etc because there is no blowhole. Etc..

@RickBeeloo In the linked Wikipedia article and many other (somewhat more reputable sources), one of the best differentiating features of dugongs versus manatees is the shape of their tail; dugongs have a fluked tail, manatees do not. I think the "fluke" is exaggerated in the pictures because of how the tail is held, like theforestecologist mentions.

Great find with that necropsy paper. You've convinced me. +1 for the effort! :D. Perhaps request to reproduce the malnourished dugong photo here?

@theforestecologist Thanks for the cleanup edits, much appreciated. This answer sort of ballooned into quite a mess. I think I won't bother requesting to reproduce the photo, unfortunately; it's an official Australian government publication, not a scientific one, that reserves all rights and requests written requests in the post for reproduction.

After looking over the links you included, I'm certain your answer is the right one. The prominent spinal ridge on this specimen seems to indicate starvation.

I know you said there was no blowhole on this animal but is it possible that the blowhole was closed and just a slit so not noticed?
The tail looks very much like a dolphin species but the low crest along the spine and no dorsal fin in sight is very puzzling. Your description of the head and your region of the world made me think of the Australian snubfin dolphin (Orcaella heinsohni) that's a recent discovered dolphin species near Papua New Guinea.
From New Guinea's Newly Discovered Species (from 2011)

In the waters south of New Guinea, an unexpected discovery was made in 2005. The snub-fin dolphin, Orcaella heinsohni, was once thought to be a member of the Irrawaddy species of dolphin. However, researchers found that snub-fins have different coloration, skull, fin and flipper measurements. That makes them the first new dolphin species recorded for at least 30 years. A skull of the new dolphin species was collected from Daru, Papua New Guinea. Scientists believe these dolphins occur mainly in protected, shallow, coastal waters, specially adjacent to river and creek mouths. The expected range of O. heinsohni is the coastal zones of Australia and Papua New Guinea.

Here's an image of the head shape.

Courtesy Daniele Cagnazzi
(from Support Our Snubfin Dolphin)

Could it possibly be a steller's sea cow
Well by the looks of it

spinal cord
the mouth
the fork tail
grass which it feeds on if u see the water in the photos
Well i could just be wrong but who knows

I think is blackchin guitarfish. Like that. But this picture not enought.

I completely disagree. It isn't a Blackchin guitarfish.

Please add support/citations for your answer. As of now, this appears to be an unsupported guess and will likely be downvoted. Please improve/expand upon your answer . Thanks.


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What species of moth is this?
Please help identify this species found at home.  I think it's a moth. Size is about 1 cm.
Is it harmful if found at home?
Location: urban home in Hong Kong

 Click photo for full-size picture

Please update the question with your location.

Its size is about 1 cm.

Thanks for the size. Please add your location. What country/state/province do you live in? What kind of area is your home in (urban vs wooded vs farm etc.).

Hong Kong, of sub-tropical climate ;  urban home, a flat on the 10th flor of a multi- storey building


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What determines whether a regulatory T cell suppresses a naive T cell binding the same antigen-presenting cell?
Here's what I learned about how regulatory T cells work:
There is a self-recognising naive T cell around.
A regulatory T cell that recognises the same self-antigen binds the same antigen-presenting cell as one of these T cells.
It suppresses activation of the naive T cell.
However, let's say the antigen-presenting cell is presenting foreign antigen on some of its MHC molecules. The naive T cell binds the  antigen and there happens to be a regulatory T cell nearby binding a self-antigen on the same antigen-presenting cell.
Does the regulatory T cell suppress the naive T cell? Is it just do with proximity, or do both cells have to bind the exact same antigen?

There a strong implication for a feedback loop mechanism for IL-2.
If a Treg is bound to an APC, it downregulates IL-2. It will then require exogenous IL-2 to be maintained. This IL-2 comes from a nearby naive T cell which is also binding a self-antigen. When that happens it upregulated IL-2. When it upregulates IL-2 and dumps it to all nearby cells which are then taken up by the nearby Treg. That causes Treg to continue its normal function by suppressing all nearby cells. It's an IL-2 negative feedback loop. It's all about proximity. What you are suggesting is not feasible since T cells recognise APC cells by MHC class II which are loaded by phagocytosis, meaning that the self-antigen has to be taken from outside of the cell. That means the APC would have to engulf two different self-antigens and displayed them on separate MHC class II which I guess is probably possible...
Check out this paper and figure 2:
http://www.cell.com/cell/pdf/S0092-8674(08)00624-7.pdf

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


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Are tendons and ligaments classified under the muscular or bone system?
Are tendons and ligaments classified under the muscular system or the bone system?
Basically they are not bones or muscles and that's why I have doubt.

You can join the muscular and skeletal system in the musculoskeletal system, which would contain tendons and ligaments.

tendons and ligaments are classified under muscular system as they are made up of white and yellow tissue

tendons are extension of muscle connective tissue.

Tendons are intrinsically part of muscles. Ligaments are not. So for your question, we need to create a classification system which is a bit artificial, based on the tissue structure of the various components of the musculoskeletal system.

The musculoskeletal system is made up of hard and soft tissues. The hard tissue includes bones and cartilages (articular cartilages), while the soft tissues are the muscles, tendons, synovial membranes, joints capsule and ligaments. (emphasis mine)

Here is an illustration of the biceps brachii muscle (arm) from Kenhub:

It looks a little different in real life, but this clearly illustrates how tendons (the white things at the ends of the muscle) are part of the muscle. So, to answer your question, tendons are part of the muscular system (a term that I have never used as a physician. I would just say "muscles".)
Ligaments are supporting structures of fibrous tissue of nearly the same composition as tendons, but do not arise from muscle per se. (For a reason I cannot comprehend, little research is devoted to the embryonic development of ligaments.)
These are the ligaments of the elbow (and more fibrous connective tissue):

Clearly they are not bone, and they are not muscle.
If you need to artificially divide muscle vs. skeletal systems, then:
Muscle: muscle and tendons
Skeletal: bone and cartilage
"Other": ligaments, bursae, synovial fluid and membranes, etc.
The easiest thing to define is what is bone and what is not bone. Then bone may well stand alone, even without cartilage. But no one would say cartilage is part of the "muscular system".
So I hope you see that this way of separately classifying tissues which are meant to work together is artificial and perhaps misleading.

If ligaments are not part of muscle then why do we consider sacrotuberous ligament a remnant of biceps femoris ?

@JM97 We don't. The sacrotuberous ligament spans the sacrum to the ischial tuberosity and about half the time is confluent with the long head of the biceps femoris. It's not considered a remnant thereof.

https://en.m.wikipedia.org/wiki/Sacrotuberous_ligament

Some ontologies such as the FMA and Uberon draw a distinction between the skeleton and the skeletal system, with the former consisting only of bones/cartilage, and the latter including ligaments and joints. A broader concept musculoskeletal system includes muscles/tendons with skeletal system elements.
This link shows the uberon concept of 'skeletal ligament' and its placement within the skeletal system:
http://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_0008846