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Etymology of PAX proteins
What is the reasoning behind naming proteins first found in Drosophila as paired box? All I could find on internet is that it was first found in Drosophila as a protein with paired domain, but I couldn't find anything about the term box along with it. Could anyone please signify the terms paired and box in the name of that protein?

According to InterPro, a paired domain is a DNA-binding element consisting of paired N-terminal and C-terminal subdomains, separated by a linker. PAX proteins follow this motif, and as such typically represent a class of helix-turn-helix transcription factors.
Box is the more interesting term here. In genetics, a box can be used to describe any regulatory element of a gene, including its promoter, UTRs and any enhancer or silencer elements. More loosely they also use box to describe coding segments of a gene, but in older publications.
Going back to Drosophila, however, studies in embryogenesis initially identified a protein called paired, a.k.a. prd. Homology studies into mammalian transcription factors found the presence of a prd-like domain in human HUP transcription factors, and these were renamed to PAX (ref). Thus, the naming of PAX family proteins classicaly denotes the presence not of a PRD regulatory element, but of a coding region for a prd-like domain in the gene product.

Can I say that they form the shape of box when they attach to a transcription factor?

@JM97 I think that would be difficult to prove!

In addition to the other answer, the following is some historical context on the naming of these genes.

1980 October: Discovery of pair-rule genes in Drosophila.
Nusslein-Volhard C, Wieschaus E. 1980. Mutations affecting segment number and polarity in Drosophila. Nature 287:795-801.

We have undertaken a systematic search for mutations that affect the segmental pattern depending on the zygotic genome... In [pair-rule mutants,] homologous parts of the pattern are deleted in every other segment

1986 May: Isolation of the paired gene in Drosophila.
Kilchherr F, Baumgartner S, Bopp D, Frei E, Noll M. 1986. Isolation of the paired gene of Drosophila and its spatial expression during early embryogenesis.

Here we report the isolation of the pair-rule gene paired (prd)... Transcripts of prd exhibit a pattern of seven evenly spaced bands during late syncytial blastoderm, reflecting a double-segment periodicity...

1986 December: Characterization of the paired box domain in paired.
Bopp D, Burri M, Baumgartner S, Frigerio G, Noll M. 1986. Conservation of a Large Protein Domain in the Segmentation Gene paired and in Functionally Related Genes of Drosophila. Cell 47:1033-1040.

...we show here that the prd gene contains a third domain about twice the size of the homeo domain, the paired box...

1988 May: First use of the abbreviation Pax to describe paired box containing murine homologs to paired.
Deutsch U, Dressler GR, Griss P. 1988. Pax 1, A Member of a Paired Box Homologous Murine Gene Family, Is Expressed in Segmented Structures during Development. Cell 53:617-625.

With the objective of isolating murine paired box homologs, a mouse paired box sequence (Pax 1) was identified that shows extensive nucleotide and amino acid sequence homology to all three known Drosophila paired box genes.

In response to a comment on the other answer:
Paired box refers to a DNA sequence/motif. The actual paired domain is a DNA binding motif present in some transcription factors. The crystal structure of the paired domain from prd has been solved. PDB: 1PDN. Expectedly, it doesn't really look like as box.
Xu W, Rould MA, Jun S, Desplan C, Pabo CO. 1995. Crystal structure of a paired domain-DNA complex at 2.5 Å resolution reveals structural basis for Pax developmental mutations. Cell 80:639-650.


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What is this fungus that is growing on my plant, and is it dangerous?
This fungus is growing on a plant in my front yard and I do not know if it is dangerous for my health or for the plants health. Can you please identify it? I live in Dominican Republic, a tropical island in the Caribbean Sea.
Here are some photos from my yard:

It is probably not good for the plant by the looks of it. But I think this question should be moved to gardening.se

Looks more like an insect invasion...

Also, please add your location.

My answer won't apply if your plant isn't a cycad (a species from the genus Cycas) as only cycads are affected. Cycad aren't native to the Dominican Republic but have been planted as ornamentals in many parts of the world. If your plant's a cycad, I'm convinced that what your plant has is NOT a fungal but insect infection - something far more serious for your plant but not harmful for you or other people.
Please compare photos provided to make sure of identification. Even enlarging your top photo,  it's not quite focused or clear enough to be sure. It appears that your white 'fungus' is actually Aulacaspis yasumatsui or the Asian cycad scale insect. Athough native to southeast Asia, it's been spreading to many places where cycad are found. Whether it's reached the Dominican Republic yet, I don't know but its been in Florida since the mid-1990s and is found in a number of Caribbean countries. It's now a very serious pest of cycad worldwide, resulting in the death of many.
Here are some photos for you to compare. I did my best to find photos that show greater detail for you to check. If the photos fit what you have, you need to treat your plant to prevent it dying and for the infestation spreading to other cycad on the island. I've no experience with this but the information on how to deal with this pest comes from Central Florida Palm & Cycad Society so they should know the best way to treat this.
Treatment of Asian Scale

 Image from Forestry Images courtesy of Jeffrey W. Lotz

 Image from Central Florida Palm & Cycad Society

Jude as your answer indicate the photos have not been taken you you, in that case the source of the pictures needs to be mentioned. Thank you.

Will do. It's weird but when I answer using my phone, either from Chrome or the SE app, most images from a URL won't load. So I end up downloading the images and posting them that way. Using my tablet, images load fine but I don't always have the tablet charged.

source: Stack Exchange

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sort: votes


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What is the difference between taxonomical aids Flora, Manual and Catalogue?
The three type of books mentioned above are taxonomical aids that offer information about species found in an area. However, the exact difference between them is not clear to me. Please explain.

They seem to be non-standard terms. Manual/catalogue can refer to anything.

Flora just tells about the plant species living there but manual tells about all the species living there And catalog is best defined as an array of the species in an understandable manner

A Flora describes plants and where they live. Floras typically include a dichotomous key for identification purposes and often times will include range maps as well. Floras are almost always designed to be simultaneously regionally constrained and regionally exhaustive/complete (i.e., includes all plants that grow in that region or at least all taxonomic divisions of specified taxa). See Example.
A manual applies much more broadly to plants, and typically instructs you on a subject (e.g., identification/differentiation of species).  A manual does not need to be exhaustive and its scope is typically user defined (though often based on the scale/range of it's underlying subject). However, some have used the term manual to be more or less synonymous with Flora or otherwise similar document (e.g., see here).
A catalog is simply a listing of all species organized in some way. These are usually alphabetical (vs. taxonomically organized like a typical Flora). You will also never find a key in a catalog and will often find less phytographic detail.
See Chapter 6 in Describing Species: Practical Taxonomic Procedure for Biologists by Judith Winston for further assistance.

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Lizard species identification

I managed to photograph a lizard in Haruvit Forest, Israel. I would like to know - what lizard species is this? Size appr. 20-25cm

Could you estimate the size of the lizard?

Try to assign a size relative to something. for example, would the lizard fit in your hand, or it closer to the size of your foot?

About 20-25 cm.

This lizard is likely a Roughtail Rock Agama (Stellagama stellio or Laudakia stellio). They are colloquially referred to as hardon (or hardun) lizards.
According to Wikipedia:

Like many agamids, stellions can change color to express their moods. They bask on stone walls, rocks, and trees. They are usually found in rocky habitats, and are quite shy, being very ready to dive into cracks to hide from potential predators.

More from natureisreal:

The most commonly seen local lizard where I live in central Israel is probably the roughtail rock agama (laudakia stellio stellio), known locally as a hardon or hardun. They are rather sinister looking with rough dark armoured skin, but perfectly harmless. If frightened they run away and hide in the crevice of a rock or tree, inflating their skin and opening their mouth wide to wedge themsevles into the space, making it impossible to dislodge them. Sometimes I see a large dark male surveying his territory from the top of the nearby water tower.More usually they are to be seen during the warmest times of day sunning themselves on rocks, to the extent that it seems that each rocks has its own resident hardon, and believe me, this country is full of rocks, and that makes for a lot of these lizards...


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What is this (seed/berry)-like object and where is it coming from?
I've been finding these little green (seed/berry) like objects in my garden for three years now.

This picture shows either a large variant or simply  a later lifecycle stage of development.
At their smallest, they look artificial - kind of like nerds candy - almost too green to be natural.  In the picture above, it is obvious that the item is a berry, but at the smallest sizes, my first thought was that it was fertilizer.  And indeed, I would've continued to think that if not for two things:

We re-mulched our garden two years ago, and didn't fertilize (nor have we ever, but this house is only 3 years old).
When you squeeze even the smallest sized objects, they squirt juice or water.

When the larger berries are crushed, many little seeds come out along with liquid; and it looks almost like a miniature pickled tomato.
There is nothing in my garden that produces any kind of visible berries; and I've never seen one of these attached to a plant.  That is part of what makes them so odd (and part of what made me think they were fertilizer); I always find them mixed (sometimes deeply) in soil or mulch.
If no one knows after a couple days, I'll go take a picture of one of the baby ones to help.  Any thoughts?
Location: Brighton, MI (USA).
Update:. Here are some other shots.  These are both flash shots because it is overcast today.  These are also of the younger variant because I couldn't find any  of the mature berries today.  Hope this helps.

Other photos that would help: close-up of where the 'stem' joins the 'fruit' (assuming that's what it is); sectioned (sliced in half with a razor) rather than squished, and maybe an 'in situ' shot of one where you found it in the surroundings of your garden?

Barring further details or photos, your fruits remind me of the drupe  from a hackberry (Celtis spp.)  tree.

Hackberry drupes are relatively small, often being only about 6-10mm in diameter.
Examples:
1,
2.
Do you have any warty looking trees nearby?
(like this).
Do you ever see the fruits in a different color? (purple, black, red, orange)?

I think you are right.  In response to your questions:  Different color: maybe purple - though I wouldn't necessarily realized they were the same with other colors.  We have a nearby golf course with warty trees, though it's quite a long stones throw away.  But my sense is that you are likely spot on

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Is there a difference in how Gas is produced which determines if it becomes a burp or flatulence?
I know that some gases are heavier than air and in the case of a gas leak it's best to escape to higher ground, while some gases are lighter than air such as Helium. However unlike Helium I haven't seen a burp burst into flames while I have had the unfortunate pleasure of being present at a party where flatulence was lit on fire.
So I am wondering if there is a difference in how the gas is produced which determines if it's becomes a burp or flatulence.

The gas expelled as a burp originates from the stomach. It is either gas swallowed together with food or gas that was dissolved in the drink. One prominent example for the latter is sparkling water where $\ce{CO2}$ is dissolved in the water at high concentration as carbonic acid ($\ce{H2CO3}$). Because of the acidic environment in the stomach the equilibrium between carbonic acid and $\ce{CO2}$ gas is shifted. Consequently $\ce{CO2}$ accumulates and needs to be expelled as a burp.
The gas expelled as a fart is mainly produced by microorganisms in the intestine and usually contains a lot of methane which makes it flammable.


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Why do crows sit on treetops even when it is cold?
It is cold outside: -1 degrees Celsius, wind 14 km/h and snow from time to time. I was wondering why crows (maybe birds in general in Northern Europe) are calmly sitting in relatively windy places even though there are plenty of potentially warmer places to go to. (see picture at the bottom).
My first guess was that it isn't cold enough for them However, I couldn't find support for this online, so it's not possible to know for certain.
NB1: This is my first post - let me know if something is inappropriate.
NB2: I am not a biologist, so please be patient.
I'd appreciate links/references where I could get information that gets closer to finding an answer to the given question.

I'd assume that they're staking out their territory most likely, or trying to attract a mate. Furthermore they might do this in order to experience the "bird-perspective", which could origin from either the fear of other predators, or the enhanced overview of the surroundings –– which could be vital for foraging

Birds (crows inclusive) have better heat conservation adaptations as compared to humans. Some of these are (but not limited to):
-Hollow tubes in feathers which provide insulation reducing heat loss.
-Reduction of appendage length especially in species that dwell in cold regions.
So conditions we perceive as cold are relatively warm for birds.

My first guess was that it isn't cold enough.

From this question on biology.se I can say it could be warm for them as it addresses birds surviving at -40C. Plus some of the answers and comments on the same question cover a couple of adaptations that birds exhibit to strive in such conditions.
edit: links that provide additional information on the same
-http://toughlittlebirds.com/2012/12/26/how-do-birds-keep-warm/
-https://beyondpenguins.ehe.osu.edu/issue/arctic-and-anarctic-birds/how-do-birds-stay-warm
-http://birding.about.com/od/birdingbasics/a/howbirdskeepwarm.htm
-http://gardenwalkgardentalk.com/2013/02/19/how-do-birds-keep-warm-in-winter/

Also WRT to wind, birds have (obviously?) evolved aerodynamic streamlining, so would not experience as much heat loss from wind.


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Can the dendrites of sensory neurons be a meter long?
The typical textbook structure of neurons is a cell with a short dendritic tree and a long axon. The dendrites receive information and send it to the axon via the cell body (soma). The axon is a long structure designed to send the information to distant parts.

A neuron. source: ASU School of Life Sciences
In sensory neurons of skin receptors, however, the dendrites are considered to receive information about the outside world, i.e., the dendrites are the receptive parts of sensory neurons. They generate action potentials that are sent to the soma. But I've been told that the soma of sensory neurons are located in the dorsal root ganglion of the spinal chord?
Does this mean that the dendrites of sensory neurons are exceptionally long? Suppose I feel a prick in my finger, do the pain receptors really have dendrites a meter long all the way to the dorsal root?

I made some extensive edits to your excellent question. I think it still contains your initial question and my answer still addresses your problem. However, I've added a dimension to it to make it interesting for this community at large. I hope you can agree. +1

Absolutely... Thanks for taking the time to do it.. #christiaan

Short answer
Axons can be over a meter long, but dendrites are never that long. Distance in the body is covered by axons. The dendritic part of skin receptors is generally considered to be the receptor part and the receptor part only. The elongated structure leading to the soma, as well as the axonal part to the spinal cord are generally considered to be one and the same axon, the soma being attached to the axon in this case.
Background
The sensory receptors in the skin have their cell bodies located in the dorsal root ganglia situated adjacent of the spinal cord (Bourinet et al., 2014). In the case of pain receptors it is shown in Fig. 1. The same basic structure holds for the touch receptors in the skin.

Fig. 1. Signaling of pain receptors in the skin. source: Bourinet et al. (2014)
The cell bodies are located in the dorsal root ganglia of the spinal cord. Action potentials are sent from the dendritic region in the skin to the cell body in the ganglion. From there on it is transmitted to spinal interneurons in the spinal cord and up to the brain.
The nomenclature of these sensory neurons is generally as follows: in the cell body the axon splits in two. The afferent part that transmits the pulses from the skin to the cell body and the part that transmits the signal from the soma away from the cell body to the spinal cord are both considered as a part of the axon. The dendritic region is generally considered to be the nerve ending (Fig. 2C). So the axons of peripheral sensory neurons, as well as motor neurons for that matter, can indeed be over a meter long (Lodish et al., 2000).

Fig. 2. Types of neurons. Arrows indicate the direction of conduction of action potentials in axons. (A) Multipolar interneurons. The dendrites receive signals at synapses with several hundred other neurons, and there is a single long branching axon. (B) A motor neuron innervating a muscle cell. Typically, motor neurons have a single long axon extending from the cell body to the effector cell. (C) A sensory neuron in which the axon branches just after it leaves the cell body. The peripheral branch carries the nerve impulse from the receptor cell to the cell body, which is located in the dorsal root ganglion near the spinal cord; the central branch carries the impulse from the cell body to the spinal cord or brain. Both branches are structurally and functionally axons, except at their terminal portions, even though the peripheral branch conducts impulses toward, rather than away from, the cell body. source: Lodish et al. (2000)
References
- Bourinet et al., Physiol Rev (2014); 94(1): 81-140
- Lodish et al., Molecular Cell Biology, 4th ed. New York: Freeman (2000)

there are axon's in giraffe that are 15ft (4.5m)long.

Great answer -- the visuals are key. worth briefly mentioning "unipolar", though? You describe it, but never use that "vocab" word.


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Hemiptera sp preimago?
Which species of Hemiptera is this preimago, seen in 2015 in Rome?

Can you please download the image from flickr and upload it here? You can credit flickr and the photographer.

What is the question?

I am the photographer. Can you help me identifying this species? Thank you again! Elena

@Elena You should add the picture here. And you should edit the question to add details such as geographical location, environment type, climate, habitat or whatever you can tell about the organism. Have a look at other [tag:species-identification] questions.

I think this is an Aphid because it has long, thin legs and two-jointed, two-clawed tarsi and resemble the Russian wheat aphid very much. They are very common in temperate zone and is a major plant pest.
Here's how the Russian wheat aphid looks:

Source:Website of tasmanian government


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Species Identification: Beetle having trunk!
Today morning I found this beetle in Cynodon dactylon grass. It had this beautiful head bearing a trunk like structure. I'm wondering what beetle it is
Images:

Approximate size: 1.75 cm
Temperature: 29°C
Location: Uttar Pradesh, India

Did a bit of research. Its one of the Snout beetles from the family Curculionidae. Couldn't get any further.

Looks like a weevil (Curculionoidea). What was it's approximate size?

@theforestecologist I guess around 1.75cm

This is a weevil called Cleonis japonica. Here is a link to a specimen which was collected in 1904. (http://weevil.info/sites/weevil.info/files/Cleonis_japonica.jpg)
Here is a link to same site and one other which show where it was found.
(http://weevil.info/content/cleonis) and (https://www.iso.org/obp/ui/#search)
NP means nepal. Here is a link to something which I hope is a little more descriptive.
https://www.zin.ru/Animalia/Coleoptera/pdf/arzanov_grebennikov_2017_cleonini.pdf
I wish you had taken better pictures.


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By what physiological mechanism do we not feel microbes (bacteria, etc.) living on our skin?
 Background
I know our bodies have a handful of ways to threshold our awareness of sensory stimuli:

Neural density

Sensory acuity
I assume really tiny stimuli could fit between receptors

e.g., Oaklander (2001) found nociceptor densities of 2-4000/mm2

Impacts summative abilities to surpass postsynaptic impulse thresholds

Varying thresholds of individual receptors.

Dubin & Patapoutian (2010), for example, show variations in classes of neurons based on their temperature (°C) and mechanical force (milli-newtons) thresholds (see thresholds listed in Tables 1 and 2).

Reticular formation involvement in regulating what we are consciously aware of

My question:
Which of the above physiological mechanism(s) are primarily responsible for our lack of sensation (or lack of conscious awareness) regarding microbes on our skin?

Update: My question is explicitly about physiology. Regardless of the impacts, benefits, evolution ,etc. of not feeling them, they're there. But even though we're covered in microbes, we don't sense them -- how not? I want to know by what physiological mechanism(s) we don't feel microbes on our skin.

I don't think any metazoan has evolved mechanisms to 'sense' microbes in the way you are describing. Microbes are everywhere, in fact, more microbe cells than human cells in adults. So, it is not that 'we don't feel them', quite but the opposite: we don't know how it feels to be 'sterile' of microbes. From the time we are born until we die, we are constantly hosting microbes, just as we don't 'feel' the atmosphere pressure, or gravity: these all are environmental constants to us. For such environmental constants, why would we be conscious of its presence/absence if it has no adaptive value?

I'd argue that we do have awareness of such organisms, only via smell: https://www.medicalnewstoday.com/articles/173478#what-is-body-odor, https://www.healthline.com/health/sudden-change-in-body-odor, https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0588-z

@TumbiSapichu  sure. I allude to some of your comment  in my post -- perhaps some part of our brain (e.g., the RF) prevents us from "feeling" them. Even if we don't know what it feels like to be sterile, you're suggesting that we feel something but we don't know how to interpret it (or that we haven't had reason to evolve a way to be conscious of it). That would be suggestive of CNS level of regulation (vs the PNS options I also propose in my question). I understand that no metazoans (including us) feel microbes, but my question is why (in a physiological sense) that is the case.

Nociceptors probably aren't the most relevant sensory receptors for the question; they aren't really responsible for any feeling of "touch"; you'd expect them to be activated only if a microbe released something chemical like damaged tissue does.

@Bryan I know they're not. It was just an example paper (the 1st I found) demonstrating density of a type of sensory receptor. I mention it solely for an example of receptor density. I assumed that the density of other sensory receptors are in the same ballpark (though, perhaps this was an incorrect assumption for me to make?). Regardless, I guess it's not really relevant to understanding the main question: which of these reasons would be most responsible for us not feeling microbes?

Ask yourself, what benefit would it have?
Keep in mind you will always bee covered in them, this is the state you evolved in. Thus sensing them would serve no purpose, and sensory organs are expensive in terms of resources so why would we evolve a useless sense?

But I'm not asking about the benefit. I realize there is nothing to gain feeling them. But that doesn't make them not there. And so even though we are covered in bacteria, we don't sense it. My question is about physiology. I want to know by what physiological mechanisms we don't feel microbes on our skin.

@theforestecologist because we lack a mechanism to detect them, I don't understand what more you could want, it is like asking why humans can feel beta particle emission.

but is that true? Are we lacking detection or awareness? You say this very definitively (and it may be true), but I haven't been able to find literature discussing the mechanism. Is this entirely an issue of PNS not sensing or of CNS not making us aware? If the PNS, is it because thresholds aren't met (for mechanoreceptors for example), or some other reason? I get that you want to simplify the answer because the question doesn't seem important to you. However, I have a biology student who asked me quite earnestly for an answer, and I'd like to provide one if such knowledge is known.

your not going to find a paper about a lack of a mechanism, scientists don't usually write papers about non-existent hypothetical structures. There is literally an infinite number of things we can't sense. For explaining it to a biology student the answer is to think of what senses we do have and what purpose they serve, they need to flip their thought process and think of what we can sense and how each mechanism works. we can't sense it because there is no mechanism to sense it because we can only sense things we have mechanisms to generate sensory signals for.


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Do any non-human species have juveniles that cannot communicate with adults?
Human babies take 1+ years to begin learning how to speak (though sign language can be learned a bit earlier1).
I know that cries, yells, and other non-linguistic sound are a simple form of communication, but they don't actually get across a specific point (e.g., what is causing a cry).
I understand that no other species use language, per se, and that linguistic development is complex and therefore requires time.
However, I'm wondering if other species have similar periods in which the adults "don't understand" the babies/juveniles.

In other words, do any other animals have a period of communication development early on in life before which the juvenile's cannot communicate with adults?

Boughman & Moss (2003) mentions the development of call types in some birds based on exposure to parents or certain social groups, but it doesn't quite address how these individuals communicate prior to the development of these calls (if at all). The paper also discusses individualization of sounds and recognizing variations to identify individuals, but again, this doesn't quite capture my question about a period of ontogenetic communication incompatibility.

1. Fitzpatrick, E.M., Thibert, J., Grandpierre, V. and Johnston, J.C., 2014. How HANDy are baby signs? A systematic review of the impact of gestural communication on typically developing, hearing infants under the age of 36 months. First Language 34(6):486-509. pdf
2. Boughman, J.W. and Moss, C.F., 2003. Social sounds: vocal learning and development of mammal and bird calls. In Acoustic communication (pp. 138-224). Springer, New York, NY. pdf

Plenty of species don't meet their parents. I don't suppose those meet your criteria?

@JohnDvorak they do not. I'm interested in the ontogeny and ethology of communication, not its absolute absence

Problem is, human baby crying still counts as communication. It's a far cry from Shakespeare, but I doubt that even chickens or baby eagles fare any better than just one utterance (no idea how to support that claim with studies though...). And it's not purely a matter of age either - get plopped into a random country in Africa or Asia, and you'll soon learn just how much you can say just by pointing at the right thing and saying "this".

@John Dvorak:  And similarly, there are multitudes of people with whom I share a common language, but seemingly can't communicate beyond what could (with some effort) be done by pointing & grunting.

Following up on the comment by @JohnDvorak — there is pretty good evidence that human babies communicate in ways that are much more sophisticated than just screaming until they get what they want. See for example: this review and this article. Based on this (and personal observations that some individuals seem to do a very good job of understanding what babies want) I think the premise that humans have non-communicative juveniles isn't well supported!

@theforestecologist We are starting a Bioacoustics Stack Exchange for people interested in the studies of non-human animal sounds and the impacts of sounds on animals. Please join us! https://area51.stackexchange.com/proposals/126698/bioacoustics?referrer=YjZmYjUxYzJkNDI1YmY5NDk3NzdhMzViMmZlNzI4ZDdiYTAyMWQxNTM5ZWFiNzRhODNkMmFiMzIxZjI3MmY1N_gFvrICTvBsmYNJ2ptRM6lIZEAV-VGkXtIwNyVDja680

@ASimonis thanks for the heads up-- yes I'm aware (and excited!), and I'm pseudo-interacting with it (limited by time constraints). As per this comment (and the other dozen you've made site-wide the last few days advertising Bioacousitcs SE): Such serial advertising (or really any post advertising other SE sites) has been deemed inappropriate and spammy (meta post). Please desist from writing such comments. They will be flagged as spam and deleted. Chat is where to be active

Thanks for the heads up @theforestecology. I'm sorry if the comments were inappropriate - just trying to figure out how to help our community grow and thrive. I was not aware of the Chat space, but now I am and will check it out.  Much appreciated! :-)

@ASimonis no worries. Just trying to prevent you from getting spam flagged. Carry on! (well, without posting ads for Bioacoustics :p). See you in chat sometime :)


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Range map atlas for insects?
I often use BONAP's North American Plant Atlas, for researching plant taxa ranges.

BONAP maintains relatively complete phytogeographic and related botanical databases for all free-living vascular plants found in North America (north of Mexico). For over four decades, we have worked collaboratively with many federal and state government agencies, private groups and individuals across the continent to produce and edit our databases

It generates incredibly useful range maps, and I can search by higher taxa (i.e., genus) to investigate many species based on their ranges at once. For example, Fagus:

However, I have so far been unable to find a similar online atlas (or any range-map query tool) for insects.
Does anyone know of any similar range-map resources for insects?

I'm most interested in maps for the US, but global maps would be incredibly awesome :)

I've found some interesting resources while searching including invasives distribution maps, and a way to view taxa lists for all known species in user-inputed locations. Cool stuff :)

Some additional range map sites: (1) InfoFlora -- plants of the Swiss Alps;  (2) inaturalist -- an "open-source" catalog of organism sightings with maps

I've just recently discovered a range map site for ants: antmaps.org.

 Image: Interactive range map for L. niger from antmaps.org
From the site's about section:

antmaps.org is not a database per se, but rather a client-end tool for visualizing and interacting with the GABI database. The Global Ant Biodiversity Informatics (GABI) project (Guénard et al. 2017 Myrmecological News) is an attempt to consolidate and curate a comprehensive global database of ant species distributional records, including literature records, museum databases, and online specimen databases.
As of July 2018, the database includes records from over 9300 publications, most major digitized museum collections, and specimen databases such as AntWeb. In total, the database now has over 1.9 million records including around 15000 described ant species and subspecies. The GABI data are currently housed in a PostgreSQL database that synchronizes once per week with antmaps.org.

The site also suggests other useful ant websites:

Antmaps.org is intended to complement other invaluable web tools for myrmecology such as AntWeb and AntWiki.

Citations:
 Guénard, B., Weiser, M., Gomez, K., Narula, N., Economo, E.P. (2017) The Global Ant Biodiversity Informatics (GABI) database: a synthesis of ant species geographic distributions. Myrmecological News 24: 83-89.
 antmaps.org paper to cite if you view data using this tool: Janicki, J., Narula, N., Ziegler, M., Guénard, B. Economo, E.P. (2016) Visualizing and interacting with large-volume biodiversity data using client-server web-mapping applications: The design and implementation of antmaps.org. Ecological Informatics 32: 185-193

I think the Global Biodiversity Information Facility (GBIF) may be what you are looking for https://www.gbif.org. It is not limited to plants and insects.

GBIF seems to be very good given it's amazing breadth of taxa. Thanks!

Now I've found a range map site for lepidopterans of North America:
https://www.butterfliesandmoths.org/taxonomy

The Butterflies and Moths of North America (BAMONA) project is indebted to thousands of individual citizen scientists who participate in data collection and review. Nearly all of the sighting data and photographs available on the BAMONA website are submitted by volunteers who take the time to share and document their sightings. Volunteer regional coordinators are responsible for data quality control and general scientific oversight, and many coordinators put in hundreds of hours of volunteer time each year.

Once you select a given species, the site generates a range map of known and historical records.
For example, for Lophocampa maculata:

A comment on another SE post has made me aware of yet another source for arthropod maps:
European Centre for Disease Prevention and Control's Tick Maps:

The tick maps are published regularly to provide the ECDC stakeholders, the scientific community and the general public with updated information on tick distribution at ‘regional’ administrative unit level (NUTS3 or equivalent and NUTS2 in Austria, Belgium, Denmark, Germany, The Netherlands, England (UK), Scotland (UK) and Wales (UK)).

Screenshots of the main page and an example map can be seen below:

The ECDPC site also provides maps for mosquitoes  and sandflies in the included European countries.

Nice! Maybe we should start a Wiki for this kind of info.


text:
Medical terminology for asymmetrically-shaped paired body parts?
Some people have different sized feet [source], a limb that is slightly longer than the contralateral (on other side of the body) limb [source], or other instances of paired body parts being different sizes.
These size differences in paired body parts on the same individual is referred to as hemihypertrophy (or hemihyperplasia).
However, what is the terminology used to describe variation of shape/form of paired contralateral body structures?

In other words, what is the general term for contralateral asymmetry?

For example, some women's breasts are asymmetrically shaped ("breast asymmetry"), and some people's fingers are different shapes (for example, unilateral brachydactyly type D).

 Source: Wikipedia
I assume a term other than "asymmetry" is used, but I have not come across any such generalized terminology.


text:
Identify round, green, flying insect with spikes in South Carolina (USA)
The tables have turned -- I need some help IDing an insect:
I've been unable to identify an insect that I came across about 6 years ago in South Carolina (USA).
We were doing a vegetation survey in a northern South Carolina forest when I felt a pinch (or bite) feeling on my hand. When I looked down a seemingly nearly round insect was at the site of the pain but flew away shortly after.
I have no photo of the insect, unfortunately, but I can best describe it as being light green, round (0.5-0.75 cm diameter) and shaped like a deep (i.e., slightly recessed) dinner plate with a ring of soft spikes around the perimeter of the slightly raised edges of its round body. I unfortunately have no recollection of the head or wings.
Here is a rough sketch of what I remember:

The spikes were very reminiscent of the backside of some adult scale insects (such as here) [seen below].

Given it's similarity to some scale insects, I've always assumed it was some species in the Coccoideae superfamily, but I have never been able to find a matching species.
Anyone have any ideas?

The only green spikey insect I've found to date is Spissistilus


text:
For which wing characteristic are Plecoptera (stoneflies) named for?
I'm coming across variable etymological meanings for the order Plecoptera (stoneflies).
Some sources indicate the meaning is "wicker/braided-winged", while others suggest "folded/pleated wing" -- both referencing different characteristics of the wings!

From Wikipedia: "The name "Plecoptera" literally means "braided-wings", from the Ancient Greek plekein (πλέκειν, "to braid") and pteryx (πτέρυξ, "wing"). This refers to the complex venation of their two pairs of wings, which are membranous and fold flat over their backs."

From Dr. John Meyer online Entomology class notes (NCSU): "The name Plecoptera, derived from the Greek "pleco" meaning folded and "ptera" meaning wing, refers to the pleated hind wings which fold under the front wings when the insect is at rest."

I understand that my latter source is much more reliable than Wikipedia, but the prior etymology shows up more frequently from searching.

To confuse things more, Merriam-Webster blends these two etymologies together: "New Latin, from pleco- (from Greek plekein to plait, weave) + -ptera"

I'm trying to create a key of insect orders using their names, but this mismatch in characteristic has stumped me as both seem plausible.

 Source: lesinsectesduquebec.com
Anyone know which of these stands true? (reputable source would be appreciated!)
(I don't really care about the etymology per se; I would like a source indicating the proper origin of the order's name so I know which is accurate)

Unfortunately an incomplete answer, hopefully others can add to this or fill out the details missing.
After a bit of searching, I found the original reference:
Plecoptera was named by Burmeister in 1939. I believe that this was a split of a previous clade, probably the Megaloptera.  The book is available on Google books in the following link: Burmeister 1939 Handbuch der Entomologie: Ordnung Gymnognatha.. The relevant clade can be found on page 863. Unfortunately it is in German and using gothic script, so I can't read it. I will attempt to download the PDF and text recover, then pass through a translator, but as a lot of the terms will be specialist I don't hold out much hope.
Edit: it seems the wing position/folding is discussed on the lower part of page 865 and page 866, but the translation is garbled, so a competent German reader would be needed for proper translation. The following is from the top of page 866:

The consequence of this arrangement is that the rear field of the orthoptere
wing can also be folded lengthways, the o
Sembloden, however, is not capable of such a folding. In br
For the Fåden, however, it will be in a state of rest under the Vorde
field bent, and lies with this and the upper wings horizontally or similar
the body, as in the walking orthopedic; while in i
following guild, with the same dislocation of the wing formation and F
tion, the position at rest is po, as with the jumping
Orthopterics, in which the wings form the body like a dady bebeck
Incidentally, there are also individual cases of orthoptera v
where the back panel cannot be folded, e.g. B. in heterosexuals
mia (p. 488.). With regard to the distribution of the veins in the w
As far as the wings are concerned, it should be noted that both wings fit into it
exactly match, which is again not the 3rd with orthopedic patients
is.

However, most of the references that I could find that talked about the name use the "folded" "plecos" form, if that bears any weight. The ptera bit is certainly "wing" as in Archaeopteryx, which translates to (archaeo) old-wing (pteryx).

Thanks for the effort here. It's not everyday you get a description about an insect that includes dady bebecks and heterosexuals :p. Quite amusing. I'll have to ask a German colleague what they think about all this!

@theforestecologist thanks. I thought it was quite amusing myself. I just downloaded the book and captured the text in base Evince on a Linux system. Then copied and pasted into Google translate. As you can see there is a lot missing or problematic, I suspect malformed characters from the printing and distortion/missing from the scanning. It seems that "dady bebeck" is actually "dach bede(ch?) in the original, so it might mean "where the wings cover you like a roof"

What I most appreciate is that I'd come across Burmeister's name in my own research, but the copy of his 1939 manuscript I found only had ~400 pages instead of the complete version you found. The index itself only went up a few hundred pages! I couldn't figure out why there was no mention of Plecoptera, but clearly your longer version makes all clear. (well, at least clearer! :p). My German colleague actually died last night, so improving the translation just became a bit more difficult on my end. Again, thanks for the upfront research! Let's see if someone can help clean up this translation

@theforestecologist. I'm sorry for your loss.  If it is any help, the volume I linked was edition 2, I think noted as "Bd.2 abt.1", so a revision of the one you (and I) found initially. I think that that first edition was a 1835 one, whereas we needed the 1839. The lack of Plecoptera was what gave away that it was the wrong one.

Ah. Good deal. Thanks, bob1


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Brain centers vs areas (and how they relate to nuclei)
I'm looking for a reputable source that can provide succinct definitions differentiating the following terms in the central nervous system (CNS; particularly in the brain):

Area

Center

Nucleus

Examples include Wernicke's area, piriform area, deglutition center,  olivary nuclei, vestibular nuclei, etc.
Really, I'm trying to corroborate my experiences having seen many examples of each but never having seen official definitions of either centers or areas. I know well that a nucleus is a cluster of cell bodies in the CNS [ex: source]. I also feel as though areas are regions with functionally-related roles, and that they tend to be associated with the cerebral cortex. Centers seem to be deeper functional regions.
What I'm not clear on is what the official differences between an area and a center are, whether (or to what degree) either term is inclusive vs exclusive of nuclei, and to what degree the relationship of all three words overlap either structurally or functionally.

I do know that Tortora & Derrickson (15th ed, 2017) indicate explicitly that certain centers are nuclei, but I'm not sure whether this more broadly describes all centers or is simply indicates a narrow example of a center.

Examples of nuclei in the medulla ...include the cardiovascular center and medullary rhythmicity center.

Motivation: trying to find a reputable source to provide a simple definition for my students. I usually just run with broad explanations based on repeated exposure of each, but I think my students would appreciate a cited, specific definition of each term.

I think the answer is that ultimately there are no specific definitions of these terms, and likely some exception to any rule one can craft. That's a hard thing to cite, though. I'll hunt around and see what I find.

@Bryan I'm glad you said that. Because after teaching A&P for the last 10 years, I've never seen such formal definitions. Still, there must at least be some sort of first usage or something for guidance. Perhaps I'll explore this from a historical word usage perspective to see if I find anything more definitive

Anatomists are the enemies of formality. Thinking it over more, some things like "area" seem primarily used in neocortex, at least the examples I can think of, which probably denotes that those areas aren't discrete "nuclei" or anything but more of a vague region (given that aside from some subtle cytoarchitecture they're not histologically separate from other adjacent areas). "Center" may be the least well-defined of the group.

I am not aware of an official organization that handles neuroscientific terminology so I doubt you will get official answers. However, brain areas are defined based on some criterion, e.g. anatomical landmarks, cell density changes etc. Nuclei are usually clusters of neighbouring brain areas that often participate in a common brain function (e.g. auditory or visual thalamic nuclei). In my subfield of neuroscience, center is never used. I've heard it in cognitive neuroscience studies and is associated to me with an implication of functionality (e.g. the "fear" center).

If you want to provide your students with some explanation of what one of the terms means, perhaps you may consider the idea of discussing how and why they were proposed. The situation is relatively clear if you choose for example the Broadmann areas and you can find plenty of material. I have not seen any information on how/when/why the "nucleus" term was first used.

"Anatomists are the enemies of formality" One example about this are the basal ganglia, which are located in the CNS, so they should be called basal nuclei. The mistake is already settled down in the CNS nomenclature, although some people tried to name them basal nuclei (e.g. Haines, fundamental neuroscience)


text:
Do patella bones form in people born with the inability to walk?
The patella is a sesamoid bone that typically doesn't completely from and ossify until ~3-6 years of age (e.g., Source). My long-standing understanding (supported by a claim in Saladin's college A&P textbook1 sitting on my shelf) was that sesamoid bones form "in response to stress."
Well, I had a student in my anatomy class this morning ask me the titular question about people born with leg paralyses or other congenital issues preventing them from walking. To their point, if such congenitally paralyzed people never walk and therefore never place stress on the knee via the quad tendon, would they ever form a sesamoid bone (i.e., the patella) in the knee?
I've done some digging and found evidence of "nail patella syndrome" (e.g., here) which results in people not forming a complete patella. However, I was unable to quickly narrow down any sources discussing lack of patellar growth due to congenital leg paralysis.

1.  Saladin, K. S. 2015. Anatomy & Physiology: The Unity of form and function. 7th edition. McGrawHill, Education, New York, NY

In mice, patella would form, but not separate from femur.
On the development of the patella:

Previous studies have suggested a central role for mechanical load in
the initiation of sesamoid development.
Our finding that the patella initially forms as part of the femur and
is later separated by joint formation led us to revisit the issue of
mechanical contribution to patella development. To achieve this, we
studied patella development in mutant embryos devoid of contracting
muscles, as a result of the naturally occurring autosomal recessive
mutation muscular dysgenesis (mdg; Cacna1s). These mice lack
excitation-contraction coupling and, consequently, their skeletal
muscles lack contractility.
Histological analysis of sagittal sections of hindlimbs identified at
E13.5, in both mutant and control littermates, the existence of
patella progenitors, which were part of the femur. However, at E14.5,
whereas in the control we observed joint formation between the patella
and the femur, in mdg mutants this process was not detected.
Consequently, at E16.5 the mutant patella was still part of the femur.
These results suggest that, although muscle contraction does not
affect patella initiation, it plays a crucial role later during the
separation phase.

I know, you asked for human, but it is the only relevant information I found. However, while sources mention a role of physical stress in the calcification of sesamoid bones, the preceding formation of cartilage seems unaffected. Now, given the information that ossification occurs in mice without physical stress, I personally would conclude that the human patella would also calcify in paralyzed persons. Strictly, the question whether the patella forms, should be answered, if a non-detached patella counts.

Very good find! Thank you for this! +1. I will hold off accepting your answer, though, to see if anyone ever stumbles across any info regarding patella detachment, especially in humans. (I would have never thought such a topic was so difficult to research!)


text:
What is the actual molecular mechanism for muscle relaxation?
A number of my students asked what happens to the sliding filaments when muscles relax. For example, in an individual sarcomere, do all myosin heads release all at once or one/few at a time?
More generally, what is the process/mechanism by which muscle relaxation occurs? What is actually happening to cross bridges themselves at a molecular level step-by-step from the point of full contraction to full relaxation?
Background to prove prior research: I know that AcH will be removed from the synaptic cleft of the NMJ, ceasing action potential generation due to stopping the influx of Na+. And I know that this causes calcium to stop being released by the sarcoplasmic reticulum (and that calcium pumps are even activated to transport Ca2+ back in). Finally, I know that without Ca2+, troponin moves tropomyosin back over the myosin binding sites of actin.
My question is really focused on what happens next. Some myosin heads must still be bound to actin during and following this process. How are they released? One at a time? All at once?.... What triggers this? (I know ATP will bind to each head causing it to release, but does the body intentionally flood/saturate the sarcoplasm with ATP to cause this to happen quickly, or is there some controlled regulatory mechanism?).
Does an individual sarcomere have a controlled slide back, or does it "snap back" into relaxed state all at once?

You have it pictured correctly. Myosin unbinds spontaneously from actin when it binds ATP which is maintained at near-constant levels regardless of the contractile state. It's the sudden drop of Ca2+ (from pumping into the sarcoplasmic reticulum) that causes troponin to change conformation and (with tropomyosin) occlude the myosin head from rebinding. This is the "steric blocking hypothesis" for how troponin-tropomyosin inhibits contraction. A good reference for this is Ebashi from circa 1960 (mentioned in the Lehman review below).
You have a related and more subtle question about the coordination of this process at the scale of a sarcomere. Because the Ca2+ concentration is globally coordinated between sarcomeres, and because tropomyosin is an elongated protein that connects multiple regulatory regions, the thin filament (actin plus troponin-tropomyosin) switches its regulatory states rather cooperatively, so that the whole muscle fiber switches on and off rather uniformly. This is more subtle and recently characterized structural biology.The most direct evidence for cooperative switching comes from a series of papers from McKillup&Geeves (also mentioned in the review below).
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5479050/


text:
Vaccination and Immunisation
Why are oral polio vaccines advantageous over the killed ones?  I was told that the orally given polio vaccine prevents infection by causing intestinal immunity. How does it do that? Also, how does this make it superior over the intravenously injected polio vaccine?

What research have you done on your own to answer these questions yourself? For example, Google searches or even simply reading the Wikipedia pages for polio vaccine and intestinal immunity would give you a lot of information. The Biology.SE community has agreed that questions that show little or no prior research effort are off-topic on this site unless you have shown your attempt at an answer. Please [edit] your question and tell us where you've looked for answers, what you do know about the topic, and where exactly you still have questions.

There is a killed oral polio vaccine?

Just look up the 'cutter incident'. Use of OPV is more of a historical and silly reason than the IPV. For example, India after recent eradication of polio has started to switch from OPV to IPV. There are serious plausible risks of using OPV but was still used due to one cutter incident that tainted IPV

@polisetty thanks. For your reference. It did help. PS: irrelevant though I wanna say this :/ (don't blame me) I guess I know you! Vashishta polisetty?

@user129402 yup :) Hope I'd known you too.. only if you could give yourself a name :P

@user129402 because it's the virus's natural route to infection, hope you now understand.

Oral polio vaccines are delivered in the site of the potential infection. You may think about them as about a realistic simulation of the infection. As it is not scientifically sound explanation, please see the answer about whether intramuscular vaccination leads to intestinal IgA secretion which protects against intestinal route of infection.
Oral polio vaccine (Sabina) contains attenuated (alive but weakened) polio virus, which can proliferate and compete in the environment with the really dangerous wild polio virus. That way also people which has not been  directly vaccinated may be protected - both by development of immunity after less severe infection, and by reduction of exposure to the wild virus.
The route of delivery is much more acceptable by children.


text:
How to read from flow chart
So I got the following picture and question:
a) Assume that F1 = 10 mmol h$^{-1}$ and the flow is not negative (ie f$_i$ ≥ 0,
i = 1, ..., 8). What is the most you can produce of the polymer DCDE (i.e.  determine F$_{obj}$).?
b) What can be said about the upper and lower limits of the flow values F2, ..., F8 when F$_{obj}$ is maximized?
I thought that you would want everything to flow through F4 and there onto F$_{obj}$ (where mmol h$^{-1}$ would double). However if this was true I don't understand question b, since in that case there would only be one possible flow value for F2,...,F8.


text:
Biology Intuition and Origin of the "facts"
I am a graduate physics student but also taking biology classes. I am new to the field of bio. Most of what we do in class seem like memorizations and stating-facts. I am wondering:

How can I develop intuition for biology? (Aside from memorizing and practicing.) I am not even sure what intuition would be like in the case of biology?
Where are all the known facts in biology (and chemistry) come from? Have to be from EXPERIMENTS though, I hope to understand the origins of the I-was-being-told-this-way facts such as the composition of DNA and the types of bonding. By understanding, I don't necessarily mean the exact experimental procedure, but the general idea of how everything came about. (I am mainly interested in molecular and cell bio).
Much appreciation for any input!

It feels different to learn biology than learning learning physics, just like it feels different to learn statistics than learning computer science. Every field is just a bit different! There's not much you can about it! That being said, of course, knowledge comes from experimentation. If your professor does not offer you explaination of how we discovered the things he present to you, then I am sorry but in the general term we cannot do much for you. Just learn for yourself. For example, on the structure of DNA, you might want to read about the experiments by Watson and Cricks.

Maybe you are asking "why are things the way they are". Again, I am sorry if your professor does not offer you such knowledge but I am afraid we cannot answer that question in such general terms here. Maybe the study of evolutionary biology will give you a bit more of a feeling of answering the "why" question. There is a famous phrasing saying nothing makes sense in biology except in the light of evolution. You might want to have a look at an intro course to evolutionary biology.

I'm voting to close this question as off-topic for the reasons explained above.

As someone who was trained in physics but is working in bioinformatics. I can only echo @Remi.b 's comments. Physicists tend to want big abstractions and simple rules, but biology is a maze of exceptions and edge cases, not to mention emergent phenomena. "In Surely You're Joking Mr. Feynman", Richard Feynman describes a summer he spent working in a biology lab. He was amazed at how easy it was to ask questions that no one knew the answer to, and how hard it was to frame and conduct the experiments that tackled the question.

Most biology textbooks I saw in my days as a student used at least partially an experimental approach to describing the facts presented, since the purpose of learning about biology in a general sense is often to understand "how biology is done" (which seems to be your desire as well) rather than just the facts. If your courses/books aren't doing that, I'd suggest simply picking up a different textbook.

Another possibility is that you are in a higher-level class that's trying to setup a backbone for teaching something new. It would be far too time-consuming to go into the background behind all of those facts, they're just reviewing them so that you can proceed in the course. A lower level course could go into more depth.

Thanks very much for the input. I do lack the experience in the field.

It's just that for instance in physics, I can boil, say Einstein's Equation in general relativity, down to the basic F=ma. But right now I just don't see how I can do the similar with biology. For instance, explaining DNA down to the atoms (?) or boiling down a certain disease into the make up of polymers (?) Again, I seem to not have much intuition in the field of biology at all. Sorry if I came across as too ignorant.

Experiments: Incubators, test-tubes, fridges, spectrometers, centrifuges, forceps, test tubes, petri dishes, microscopes, scales and balances, chemistry tests, electron microscopes, calipers, stains, statistics, population sample collections. You can't boil a disease. you can observe it by microscope and measure it. The most important equation that you need to know is that Biology = Chaos and measurements. ex. you can boil your body = 99 percent CHON organic chemistry by mass.

Googling "landmark experiments in biology" came up with a lot of hits, what was wrong with the experiments cited in any of those works?  Mendel's pea experiments should be easy enough to understand.
Honestly I don't see how it will benefit you to know the organic chemistry work that went into determining the chemical structure of adenine.

don't close it  yet, i'll explain to him that biology has 80,million species, 800 million proteins that are invisible and unkown, and organisms with 100ds of different tissues that vie in between all the physical forces of speed, heat, etc, and that he should at first study BioPhysics if that's what he's comfortable with.

Not to be snarky, but I'm not sure what you are asking for. All of biophysics on an index card?
There are over 200 billion atoms in a single copy of the human genome and there are highly non-linear interactions between many of those atoms. Now extend that to the interactions between the 10 trillion copies of the genome in a typical human. Note that many of those copies are chemically interacting after some fashion. In your physics education have you every solved, even numerically, a system of 10^24 particles all with highly non-linear interactions? Simple rules like F=MA are not going to help at all because the emergent properties end up dominating everything.
The crazy thing in biology is that the emergent behavior of complex systems sometimes does offer incredible simplifications. I spend my days pretending that the human genome consists of strings of symbols that obey simple statistical properties. The incredible thing is that such an absurdly simplifying model sometimes does provide useful results and insights.
Biology is generally the study of these emergent properties, which are not generally derivable from simple rules of basic physics. That is why there is so much memorization. Intuition is not magic. Intuition is simply the inarticulate expression of our training and experience. That means there is no way to develop intuition without memorization or practice. You may have some intuition for some areas of physics, but that has presumably came after years of studying physics in secondary school, undergraduate, and graduate school. Intuition in some field of biology will have the same price tag.
I can offer some help with the experimental background for molecular biology. Read The Eighth Day of Creation. It's a well written, semi-popular history of molecular genetics and includes details on many of the key experiments.

Famous experiments roughly chronological:
1400's they gave elephants wine in the tower of london and belived in 4 elements and blood letting.
Human and animal dissections
Observation of oxygen generated by plants in light
Observation of red blood cells and micro-organisms
First notions of the Cells, cell theory
First microscopes at the same time as first telescopes
Major experimental biology for inheritance of flower colors by Mendel
Advanced medecine and use of electricity on corpses
Theory of evolution using many specimens and case studies
Methodical ecology treaties and reports for many animals by Fabre
Methodical reports of ocean fossils and sea life, fossil biology
First scientific reports of antisceptics
Measures of plant O2 production as a function of light color and temperature
Discovery of vaccines
Discovery of penicillin and antibiotics
Synthesis and measure of soil chemistry
First precise measurements of pH
Discovery of cell nucleus
Discovery of virii
Discovery of DNA
First electron microscopes
Beginning of centrifuge, spectroscopy,
Consider the diversity of animal species and cosmic bodies.
In cosmology you have 10-15 Clades of cosmic bodies, 50 of fundamental particles, 4 forces. There are only 100 common elements.
In biology, 80,000,000 species, 1,000,000 Clades of animals/plants/funghi, 100,000,000 different Enzymes and Proteins which are all invisible, and that beat supercomputers since 2003, 1000,000,000 different organic chemicals.
Microbiology flourished in tandem with Astronomy with the development of dutch lenses used for navigation. Cell theory is a biological equivalent to cosmology.
Biology has 3.9 billion years of cumulative encoding and additive development, as in that every being is like an SHA64 algorythm, that cumulative complexity is arranged into a tree.
Physics doesn't have friends and foes, cumulative memory, encryption, computation ability, 1 billion chemicals, cell walls and cells, number of legs, appendages, reproduduction, division, child rearing, it's a completely different recipe.
Physics is simpler. It's the same as being stuck inside one single protein, where the edge of the protein is the cosmological boundary, and being able to gather masses of data about the contents of that boundary and the nature of the physical universe. The maths formula to represent every protein is probably as big as the universe, there's no size and time boundary in either, except that we are seeing inwards that complexity.
biology is reined by chaos, so the maths of it has many billion degrees, you are talking about an equation with a,b,c,d,e,f,g,h,i,j,k, etc with billions of variables, and the maths formulas are billions of lines long. how are biologists supposed to deal with that?
Physicists are stunned by schrodinger's cat, probability issue.
What is the probablity of predicting where an animal will be on the same time on 2 different days? If you can write equations for that, then physics and biology will be the same. Biologists are not even going to try to write an equation for that kind of thing! they just have to use statistics all the time.
The maths of Biology are the biggest chaos system that man has ever peered into.
They are so incredibly confusing and unfathomable.
Try to write some equations in biology to predict movements of elements. you can't equate a bird like a photon, they are more chaotic and complex.
Biology has trees. Where do trees exist in physics? The biology tree has 80 million known branches.


text:
What is the difference between RFLP and DNA fingerprinting?
Is RFLP (restriction fragment length polymorphism) analysis the same as DNA fingerprinting? I looked for information online and I don't understand the difference.

What do you understand about each concept, and where exactly are you stuck? In particular, have you read through the Wikipedia article on DNA profiling, the very first result when googling DNA fingerprinting?


text:
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.


text:
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


text:
Can cancer cells transmit from one organism to another?
I know cancer cells are very resilient, so would it be possible for them to survive outside of the original organism for long enough to be absorbed by another? Furthermore, would that type of "infection" be possible?

Yes. Devil facial tumour disease is an example:
https://en.wikipedia.org/wiki/Devil_facial_tumour_disease
Look here for other examples of transmissible cancers.
I have not heard of any human transmissible cancer.


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Fruit identification - What is this green long fruit?
I found this fruit in the South of France, but I have no Idea what it is. It's a green, hard fruit. I tried to cut it to see the inside (on the following pictures).
It fell from a big tree, but I don't remember much information about it.

Thanks in advance!

Do you have a photo of the plant?

Reminds me of Theobroma cacao, which almost certainly wouldn't grow that large (or at all?) in France (I wouldn't think). I'm not sure if any other Malvaceae plants grow similar fruits. I'll admit that the seemingly-circular stipule scar on the stem is reminiscent of a magnolia, but I don't know of any with a fruit like that. Overall, I ca't say I know European flora all that well...Can you provide more information (location, tree photos) and perhaps more pictures (seeds, tree leaves, etc.)?

Could it be a Ceiba speciosa pod? We have a lot of Silk Floss trees near where I live and they grow these types of pods. When they are fully developed, they burst open and are filled with cotton-like floss and dark seeds. I have never seen an unripe one opened up, but it definitely looks like the ones on the trees. The trees themselves are easily identifiable as well. They are large with greenish trunks that have thorns growing along the surface. Also, if you had previously seen the tree with large pink-purple flowers, that would be a good indication.
https://en.wikipedia.org/wiki/Ceiba_speciosa

Please provide some reasoning with support.

I agree that the OP's specimen looks like a member of the Malvacaea and could very well be Ceiba speciosa. The OP's lack of more useful pictures and your (now improved) post still do not have me convinced, however. I find it strange that the OP mentioned but I don't remember much information about [the tree], when the trunk of C. speciosa would be quite memorable I believe.  I'd recommend finding an image of C. speciosa fruit to include in your answer and adding some indication about how such a tropical fruit could be found in France. Both would strengthen your answer. Thanks!

Thanks, it totally looks like Ceiba Speciosa ! I really don't remember the trunk tought, I think it was partially hidden behind a wall. But I've seen another specie of Ceiba ("Ceiba Insignis") in the same town, so it makes sense.


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What is the literal meaning of the scientific name for the cactus wren?
What does the scientific name Campylorhynchus brunneicapillum mean? I simply want to find a way to decipher the meaning of scientific names. In the past I had to translate the names syllable by syllable using an abbreviated Latin dictionary to get a rough idea of the meaning. I can not find an on-line Latin translator that works - and not all scientific names are Latin.


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What is the name of this South India plant?
Location: South India.
Month: June.
Branches of the tree:

Lower part of the Plant:

Plant's leaf:

Whole plant:

Hi Welcome to Bio.SE! Please upload all of your images using the url option of the image uploader. Simply adding links is dangerous because they might become nonworking and your question becomes unusable /unamswerable. Thanks!


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About the formation of protein
There is a question in my textbook which asks: "What does the glucose produced from photosynthesis form?" However one of the answers said that glucose forms protein.  But I'm quite sure that amino acids form protein, don't they?  I would be grateful if anyone out there could help me out.

What research have you done before asking it here? Hint: glucose is an energy source.

I only know that excess protein can be converted into glucose in our body for energy, but i dont know how glucose can be converted into protein :(

Who asked converting glucose into protein? Also, it is possible to convert gluocse to amino acids.

Can you be more specific about "one of the answer" ? Was this a multiple-choice thing ? What was the exact sentence involved ?

Photosynthesis results into formation of a carbon skeleton (a 3C or 6C skeleton). These newly formed carbon skeleton can be used to form a large number of bio-molecules which are required by a cell. For example the glucose can enter into aerobic respiration and the intermediates thus formed are used for synthesis of several molecules.

As you can specifically see from the above figure, alpha ketoglutarate is converted into glutamate which is then used for synthesis of proteins.
Alpha ketoglutarate is a keto acid can easily be aminated to give rise to amino acid.

Good answer. The often taught idea that photosynthesis produces glucose is an oversimplification. It would be better to think of it as a process of carbon fixation. The resulting organic molecules can be used to synthesize the precursors of macromolecules (nucleic acids, fatty acids, amino acids and carbohydrates).

In addition, it is not necessary that glucose will be synthesized and then it will be used for respiration. The triose (3C carbohydrate) can directly enter into glycolytic pathway.


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Why heart beats increase when we are in a state of tension even though it is a disadvantage?
Suppose a poisonous snake bites you; this will likely cause hypertension, and it will result in your heart rate increasing dramatically.
Because of the high rate of heart beats, your body will make the snake poison circulate throughout the whole body even faster. This will likely bring about death even faster. (definitely 100% disadvantage)
Why do heart beats increase when we are in a state of tension even though it is to our disadvantage?

Do autonomic nervous system differentiates a snake bite and a dog bite?

What research have you done before asking it here?

Hypertension and increased heart rate are not necessarily the immediate effect of ANY snake venom. In fact, Captopril is a drug for treatment of high blood pressure, which was derived from the venom of a Brazilian pit viper (see here and here for more information). So it really depends on the snake.
Also consider the fact that snake's and potential prey's evolution may not have each other's best interest in mind...

The heart rate increases due to any acute stress, it is part of the flight or fight response. This is part of the responses that readies the body for rapid extreme effort.
The body is not selective about it, any acute stress causes it. One idea why is that a hormone response is slower than a direct nervous response so the preparing the body needs to happen as fast as possible since it takes longer to complete, compared to an actual identification, decision and movement.
Also remember that only for a small number of snake bites is this counter-productive, for others it does no additional harm but helps get you away from the snake. Snake venoms vary greatly in their effects.

Because it's a poison so it has to do it's work which is making as much harm as it's possible.
Also, I'm not sure if heart beats faster because of poison or because of how you react for being in danger.
If it's because of the danger then it works with all dangers. Of course some situations could be better handled without this adrenaline rush but evolution shaped us to increase adrenaline so in most cases it helps - and the same reactions is visible in other animals.

Welcome to Biology.SE! Please add some references to your answer.

It has to do with the fact that blood needs to circulate faster when your body is in stress. Blood pressure tends to rise, and blood tends to pump faster to the brain, to compensate with the stress factor.
Even so, If you are bitten by a poisonous snake, your body has no choice. It is basically programmed to do what it does.

Welcome to Biology.SE and thanks for your contribution. Biology.SE is a scientific stack and we therefore ask users to mention their sources, and preferably references to articles in credible journals in their answers to allow other users to background read on the topics covered.

I disagree that your body has no choice.  If you panic as the result of a snake bite (or even just seeing a snake), your body will release adrenaline (& perhaps other hormones?) that causes increased heart rate &c.  If you don't panic, it won't - or at least not nearly as much.  If you've ever had allergy tests, where adrenaline is injected to counter the allergens, you've experienced the reverse of this: you get the increased heart rate & other physical fight/flight responses, without experiencing the mental state.

Your heart rate elevation is part of the body's fight or flight response, to essentially prepare your body to either fight the danger or to flee from it. Now, it doesn't matter if a snake is threatening you or you are in a stressful situation, the body reacts to it the same way. This is a basic response in almost all animals. So yes, the increased heart rate does help in getting more blood to your muscles which basically need all the energy they can get in tense situations. It's actually the same mechanism for any sort of stress, including fear (you might have noticed during a horror movie!). So while it is a disadvantage if you get bitten, most of the times it is serving to get you away from the snake ASAP.
https://en.wikipedia.org/wiki/Fight-or-flight_response

Please add some more details to your answer.


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Is a microspore diploid?
In  gymnosperms the plant body is predominantly sporophytic. It produces microspores or megaspores my textbook says that these undergo reduction division in order to form male gametophytes pollen grains and female gametophytes that is egg.
The thought of a spore being diploid is revolting, as I have learned in the case of bryophytes and pteridophytes that it's haploid. Can anyone help me asap.

Sadly I don't have a lot of time to study gymnosperms in details again, but my book (Campbell's "Biology", 11th edition) says that "Microsporocytes divide by meiosis, producing haploid microspores. A microspore develops into a pollen grain (a male gametophyte enclosed within the pollen wall)."
It says as well: "While the pollen tube develops, the megasporocyte undergoes meiosis, producing four haploid cells. One survives as a megaspore."
So microspores and megaspores seem to be haploid.

Hi Susan. If either of the answers you received are acceptable and useful, please consider upvoting them (by clicking the up arrow to the left of the answer) and/or "accepting" them (by selecting the check mark below the vote triangles). Thanks.

The spores (microspores or megaspores) in gymnosperms are haploid. The microspores came from the microsporocytes which are diploids cells of the sporophyte, divided via meiosis. So the haploid microspores do mitosis and form the male gametophytes (pollen grains), containing two male gametes (sperm cell) and a generative cell which will form the pollen tube.
The process conducting to female gametes in the ovule is very similar. A megasporocyte (diploid cell of the sporophyte) via two meiosis form four megaspores (haploid). Only one megaspore is functional (the others will degenerate) and do 3 consecutive mitosis to form eight nucleus with different functions, one of them is the egg cell (female gamete).
So the meiosis happens before the formation of the spores (actually it forms the spores) so they are haploid.
Source: R. F. Evert & S. E. Eichhorn "Raven Biology of Plants"

Hi Maso and welcome to Bio.SE. Rather than commenting on your sources, it would be better to include them in the answer by using the edit function.

Short answer:
A microspore is haploid.

Long Answer:
Gymnosperms are heterosporous, and therefore create two types of spores: male and female -- microspores and megaspores, respectively. These spores will develop into gametophytes which then undergo fertilization (i.e., the male/female gametophytes combine their chromosomes). To avoid constantly increasing the chromosome number of these plants, these gametophytes (and therefore the male/female spores), must only contain half of the "proper" number of chromosomes. In other words, these male/female structures must be haploid (1n). Haploid cells develop via meiosis, a process in which cells essentially split twice even though their chromosomes have only been duplicated (replicated) once. In a diploid cell, this means that the resulting cells (4 of them per parent) have only 1/2 the chromosomes as the mature organism.


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Why people don't harvest Locusts when infestation happeds?
We've heard about tremendous amount of money losses even leading to famine due to crop destruction from locust infestation over and over again, but all these grasshoppers are a valuable protein, probably way more valuable than the destroyed crops. Although most people from many cultures won't eat such insects, these can be ground to flour and stored to be fed to omnivore livestock like pigs or sold for profit or exchanged for grains.
Is there edible energy in the insect swarms? Can this be made into livestock feed? If not, is the reason this isn't common practice biological or economical?

The problem, Nigel, is that crops can be stored for months, whereas locusts are a mostly perishable food.

I don't think so. Dry proteins for commercial use can be stored for quite some time. Also after some research, it turns out that Meat and bone meal (MBM) has a shelf life of 12 months. Furthermore, there is a ton of consumable insects sold online vacuum-packed and cooked. And to top all this we live in a global economy where it won't matter anyway.

You have made my point for me. What you propose is much costlier than harvesting wheat, which needs very little by way of processing after harvesting. :) A global economy might not be an inconvenience to you, but to the farmers whose crops are consumed by locusts, I imagine they could hardly care less about global economies.

Locusts have been harvested in Thailand and Australia they call them sky-prawns. They deep-fry them and consume them happily.
http://www.bugsfeed.com/locust
http://www.fao.org/docrep/017/i3246e/i3246e.pdf
In Thailand Orthoptera or
grasshoppers include Patanga succincta,
Locusta migratoria, Acrida sp.,
Cyrtacanthacris tatarica and Oxya
japonica japonica (Thunb.)
(Hanboonsong et al. 2001; RaƩ anapan
2000). All of them are pests of
economic crops such as maize and
rice. Grasshopper species, parƟ cularly
Patanga succincta and Locusta
migratoria, used to be one of the
major pests of maize and rice. Today
they have become one of the most
popular edible insects since they were
introduced for human consumpƟ on
by entomologists − a campaign to eat
grasshoppers had been launched
because control efforts had been
unsuccessful. For example, in 1983
this was launched by local offi cials and
villagers in Prachin Buri Province
collected more than 10 tonnes for use
as food (Lewvanich et al. 1999).*


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Why do both the mango and the bee have "Indica" in their binomial name?
In my textbook, it is written that the binomial name of mango is Mangifera indica and the binomial name of a bee is Apis indica. Now in the name the second part is the name of species. But mango and bee are not the same species. One is a tree and the o,ther is an animal. Then why is their second name the same?

In short, we do not think about the uniqueness of the second part of the binomial (the species epithet) but about the uniqueness of the binomial itself (the genus and the species epithet). Thus, the unique binomial of mango is Mangifera indica and the unique binomial of bee is Apis indica. For more detail, see this question.
To complicate matters  slightly, plants and animals are governed by different nomenclatural codes. So it is possible for a plant to have the exact same binomial as an animal. These are called "hemihomonyms." For more detail, see this question. However, a plant cannot have the same binomial as another plant, and an animal cannot have the same binomial as another animal.
In this specific case, the authors probably chose to give both species the epithet indica because they are associated with the Indian subcontinent, which is the root of that word.

That is the species name it is often the same for unrelated organisms, that is why we use a two name system. Binomial nomenclature (literally, two term naming system) goes Genus species respectively.
The first part of the binomial identifies the genus (which should not be the same unless they are closely related) and the second is the species name which is often little more than a descriptor, you would be amazed how many species names translate to simple concepts like colors or one of the most common, familiaris which just means household or common. In dinosaurs many many end with carnegii because Andrew Carnegie funded so much paleontology and scientists knew who buttered their bread. In your case indica literally means "from India" in latin so it is not surprising many things carry it.
Mangifera indica means 'mango from India', Apis indica means 'honeybee from India;' guess where they were first discovered.
In short, the second name really doesn't matter as long as it does not match anything else with the same genus name. As long as the combination of the two names is different and unique. The first name, the Genus name, however should not be the same unless they are related.

Think of a binomial as a first and last name. Both the genus (first name) and specific epithet (second name) can vary, but both together indicate an individual [species]. Additionally, like most names at some point in their origins, the specific epithet (and often times the genus) "names" can have meanings (and so, in a way, act as adjectives). In your case, indica simply means that each taxa originated (or at least was first described) in India.
See here for further [easy to understand] explanation.

Just like namespaces in programming

Indica in binomial nomenclature means "of India" - from classical Greek and Latin.
Apis indica is more specifically the binomial name of the Indian honey bee, one of the predominant bees (most common bees) found and domesticated in India - differing from the western honey bees (Apis mellifera - mellifera is the Latin word for "honey-bearing") one of the first domesticated insects and most common honey bees around the world.
Mangifera indica or "Indian mango", has been so widely distributed around the world that it has become known as "common mango" and remains one of the most widely cultivated fruits within tropic regions.


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What does lymph actually look like?
I have scoured Google and a number of my anatomy textbooks for a picture of lymph. However, I cannot find any such photo (or video) showing its actual appearance.
Can someone provide a reputable image or source where a photograph of lymph can be seen?
What I do know:

Tortora & Derrickson (14th) A&P textbook mentions it consists of a "clear liquid extracellular matrix that is similar to blood plasma but with much less protein."

A photo purporting to be lymph does exist on Wikipedia, but lacking any further corroboration leads me to remain uncertain of the photo's authenticity.

Context:
I'm preparing a lecture for my 100 level college A&P course, and I was hoping to include a photo for my students to see and compare.
NOTE: I am hoping for a photo of lymph that is not classified as lipid-containing Chyle, for which I can find photos. However, a comparison photo would be ok :)

http://www.ijcasereportsandimages.com/archive/2014/012-2014-ijcri/CR-10458-12-2014-osman/ijcri-1045812201458-osman-full-text.php

This seems to be one of rare actual photos of lymph online (suggested in the comment above):

Image: Lymph (source: IJCRI - Case Reports Journal)
This particular lymph (or "lymph fluid" or "lymphatic fluid") was aspirated from a "lymphocele", which is an abnormal collection of lymph in the body (appearing outside of the normal lymphatic system).
While a lymphocele is not normal, the lymph in it, such as in this photo, looks quite normal: it is a clear (translucent) and yellowish liquid.

The lymphatic (lim-FAT-ik) system is a network of tubes that collects
  lymph (LIMF). This clear, pale yellow fluid drains out of blood
  vessels all over the body. (KidsHealth.org)

The froth is from proteins as they normally appear in the lymph.
The image of lymph in Wikipedia is not a clear lymph, but obviously a chyle (a milky fluid containing the lymph and chylomicrons due to thoracic duct injury).

Thanks for this! I'm not familiar with the International Journal of Case Reports and Images, but this is certainly better than I found (and, if I determine it to be reputable -- which I don't doubt -- it's a great new source for clinical images to infuse into my course lectures!)

@theforestecologist, if you need more medical images: https://biology.stackexchange.com/questions/38774/open-database-of-medical-images/79533#79533

Now this is the type of Q&A/discussion that this site is supposed to emphasize! I love learning new resources. Thanks again for your informational responses and help :).


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What is the reason behind the subphylum name "Urochordata" for tunicates?
There are two major invertebrate subphyla of the chordates (phylum Chordata):

Cephalochordata (the lancelets)
Urochordata, aka Tunicata (the tunicates)

My understanding is that the cephalochordates are named as such (meaning “head chords”) because the notochord reaches into the head. From Wiktionary:

Any of the primitive fishlike creatures, of the subphylum Cephalochordata, including the lancelets, that lack a true spine but have a notochord which, in the case of cephalochordates, reaches into the head, contrary to the Urochordata.

Urochordata, by contrast, means "tail chord", though I cannot find a reputable source (or any, really) that describes or details why this is the case.
I can surmise it's simply because the notochord doesn't reach the head of a tunicate embryo -- as is corroborated by an image from Lemaire 20111 copied below.

 Image D' shows notochord in red. Credit: Lemaire 2011
However, I would prefer a quotable, reputable source that indicates explicitly that the Urochordates are in fact named as such due to their notochord not reaching their head.
If this is not the case, then my question more broadly stands at: Why are the Urochordates named the way they are?

 1: Lemaire, P., 2011. Evolutionary crossroads in developmental biology: the tunicates. Development, 138(11), pp.2143-2152.

In 1877, Lankester proposed in "Notes on the Embryology and Classification of the
Animal Kingdom" division of the group we now call Chordata into three parts:

Urochorda
Cephalochorda
Craniata

which is more or less the accepted division today, with Urochorda being called Urochordata now.
In this essay, Lankester says:

The evidence of degeneration is admitted as conclusive in the case of the parasitic Crustacea and Cirrhipedes. It is equally incontestable in that very large and varied group of non-parasitic organisms, the Tunicata (Urochordate Vertebrata).2

(in the above 'Vertebrata' is what we call 'Chordata').  He adds this footnote:

2The whole argument as to the Tunicates of course rests on the view- supported by many arguments, that the larval urochord, which many of
  them possess, is not a larval organ acquired by larval adaptation, but is hereditary and transmitted from adult ancestors.

The term 'urochord' seems to be established and used without comment there, and probably is taken as simple neo-Latin for 'tail chord', although that may be somewhat loose, perhaps meaning the notochord is present but does not extend into the head.  A 1913 Webster's Dictionary defines urochord as:

(Zool.) The central axis or cord in the tail of larval ascidians and of certain adult tunicates.

In 1882, Lankester futher discussed the anatomy of the tunicates in the context of the division of the chordata in a paper called "The Vertebration of the Tail of Appendiculariæ".  This paper includes an illustration of a larval tunicate with the "notochord (urochord)" indicated.