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How can P450 distinguish between foreign and native compounds?
It is my understanding that P450 enzymes are capable of selectively degrading compounds that enter the cell from the outside (e.g. synthetic drugs) without damaging compounds that are metabolic intermediates normally found in cells. What is the mechanism that provides these enzymes with the ability to distinguish the foreign compounds that are substrates from the normal metabolic intermediates that are not substrates, if they are structually similiar?

False Premise
The false premise in this question lies in the end of the last sentence:

…the ability to distinguish the foreign compounds that are substrates
  from the normal metabolic intermediates that are not substrates,
  if they are structurally similar

The assumption here would seem to be that the similarity between normal metabolic intermediates and foreign compounds is too great for discrimination to occur. There is no reason to assume this.
Explanation

The substrate specificity of those P450 enzymes that metabolise
  xenobiotics is such that they will not metabolize normal cellular
  constituents.

There is a wealth of evidence that enzymes can have substrate specificity that is either extremely narrow or relatively wide. This obviously depends on the structure of the substrate binding site — its shape and size and the chemical nature of the amino acid residues there. Thinking in these terms one can envisage an enzyme that will discriminate against substrates with a single substituent at a particular position, but metabolize a variety of similar compounds that lack this. The evolution of P450 enzymes can be imagined as a process whereby mutations that allowed metabolism of toxic environmental compounds would convey an advantage and be selected for, but mutations that disrupted normal metabolism would be lethal (or disadvantageous) and be selected against.
The Broader context of P450 Enzymes
The question is posed in terms that might suggest that the only function of P450 enzymes is in removal of xenobiotics, and perhaps that they are only a feature higher organisms. In fact neither of these are true. Details of their occurrence in bacteria can be found in the Wikipedia article. However, a paper which I, as a non-expert, found interesting in this respect was published by Kawashima and Satta in PLOS ONE in 2014. This makes the point that there are two classes of P450 genes — those involved in normal cellular biosynthesis (e.g. steroids, cholesterols, vitamin D3 and bile acids), and those active against xenobiotics (e.g. plant alkaloids, aromatic compounds and fatty acids). Comparison of the genes for these in a variety of (mainly) vertebrates implies those involved in the metabolism of xenobiotics evolved from those involved in normal cellular metabolism, and such detoxification genes have arisen not just once, but on several occasions.


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Are there studies on the effect of reduced CO2 levels on human cognition?
I see studies that indicate elevated CO2 levels (>>400ppm) can cause cognitive impairment.
Are there also studies that investigate the effects of cognition under low CO2 levels (<<400ppm)?

I can't think of any biological basis for such a study.
CO2 is produced as a waste product of metabolism and exists in the blood and lungs at levels far higher than atmospheric levels (~100X). Relative to the air in the lungs, the atmospheric concentration of CO2 might as well be zero.
Very high atmospheric CO2 (relative to normal atmospheric levels) can have cognitive effects (among others) because it prevents CO2 clearance from the lungs and therefore increases blood CO2 (hypercapnia) and can cause respiratory acidosis.

Here's another good reference that supports what Bryan says here: https://en.wikipedia.org/wiki/Breathing

I guess impaired gas exchange makes sense for very high concentrations. Also in some studies high CO2 might correlate with cognitive effects due to confounders.

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Is the reason why lipid-soluble molecules can pass through membrane because
I have been studying about cell membranes and how water molecules are able to pass through it. (https://www.wiley.com/college/boyer/0470003790/animations/membrane_transport/membrane_transport.htm)
It is clear that the water molecules can squeeze through openings in the bilayer. My questions are:
1) Do small, non-polar molecules also enter through these gaps?
2) It states that the whole structure moves when vibrating. Does that mean the hydrophobic tails also move? If so, how do the non-polar molecules dissolve?
3) The top of the membrane is hydrophilic. How do non-polar molecules get past these hydrophilic heads into the hydrophobic interior core where they can be dissolved?
Thanks a lot!

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Insect/cocoon ID?
Can anyone ID this? We’re in the Rocky Mountains, Western US. We found it stuck to the wall of our garage, a few feet up, hidden behind a snow sled. It seems to be covered, or surrounded, in what looks like mouse hair. Is it a moth? It’s hard to see scale, but altogether about the size of a thumb.

I would guess this is the cocoon of a moth in the subfamily Arctiina in the Erebidae family.
For example, see this example of an Isabella Tiger Moth cocoon in Kent Co., Maryland from The Maryland Biodiversity Project:

 Credit: Nancy Martin
You can find additional images of various species here, here, here, and here (seen without the cocoon).
According to here, Pyrrharctia isabella (or the Isabella Tiger Moth shown above) is sometimes found in the Rocky Mountain region of the US, but I am not knowledgeable enough about these pupae to definitively point toward a species.
Based on the experiences of many others, I would advise not touching this with bare hands or clothing.


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X linked traits expression in females
We all know that females have an inactivated X chromosome (Most of its genes are inactivated).
Consider a female who is a heterozygous carrier of an X linked abnormality,
If the inactivated X was that carrying the normal gene, shouldn't the abnormality be expressed in this female? Why is it not expressed even though the other X is inactivated?

Because in different cells different copies of the X chromosome might be inactivated.
So, in (approximately) 50% of the cells you will have the X carrying the normal gene activated, and in the remaining 50% you will have the other.
You might start reading something here, and then go in further detail to understand. A nice article is here


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If an ethnic group holds nearly 100% of a particular haplogroup, does it means that people who have this haplogroup are their descendants?
Let me give you a hypothetical example. If the Egyptians were 100% E3b1, and the Levantines 50%, and the Anatolians 25%. Does this indicate that the Levantines and Anatolians are descended from Egyptians?
But what if instead of Egyptians, it was a distant people like Vietnamites who were 100% E3b1?

Short answer:
No.
If populations A and B share a haplogroup it does not imply that population A is B's ancestor, or population B is A's ancestor. No present-day population is the descendant of any present-day population, though both populations may share common ancestors. The common haplogroup is probably inherited from common ancestors.
Long answer:
No.
When you say "Egyptians" or "Vietnamese", in genomic studies you generally mean present-day people. People living in present-day Egypt or Vietnam may be related to each other, but they cannot as groups be each others' descendants. It is more likely that there is some ancestral population that is the common ancestor of both groups that carried the genetic variant. The only exception I can imagine is a VERY recent colonization (assuming there were no indigenous people in the colonized country, which is effectively never the case).
To take this specific example, it would be most likely that at some point in ancient human history the expanding human population (from e.g. out of Africa) had people carrying a haplogroup that settled Egypt, Anatolia, and Vietnam in independent events.
Therefore none of those groups would be descended from one another. Each population was founded by the people who stayed in that region, not the related people who left and colonized other regions.
Sampling of ancient DNA makes the question more interesting, if you for example found 20,000 year old bones sharing the haplogroup. Maybe that is a descendant of one or both populations. But again the relationship of that ancient individual to present-day geopolitical borders would still be fairly meaningless without a lot of supporting data.
It is additionally possible that the haplogroup arose independently in two different populations. This is sometimes called parallel evolution or convergent evolution. In this case there is actually no relationship at all between the populations. While this is much less likely than common descent, it is nonetheless a hypothesis that you need to reject before you claim that one group are the descendants of another group.
I hope that this helps!


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Are microsatellites viable markers for GWAS?
I'm just reading some papers on genome-wide association studies and find that most of them use SNPs as a marker. I understand that they're the most polymorphic and thus the best for accurate correlations, but would microsatellites provide another viable method to check for genetic correlation?
They're highly polymorphic and small enough to showcase differences, while maybe allowing for more statistical significance.

Microsatellites could be used for GWAS. Actually they were the basis for linkage studies and were also used in the first association studies. The main reason why they have been replaced by SNPs is that in the human (or other organims') genome, there are by far more SNPs than microsatellites.
GWAS rely on linkage disequilibrium between the marker and the real causal variant. LD decreases quite fast with distance, thus, the more markers you use, the more likely you are to genotype a marker in LD with the causal variant. In the end, I would strongly recommend to use SNPs to perform GWAS.


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Air bubble in addled egg
I'm a complete novice in biology. This is just a question that arose during Saturday night warmup and there is no better place to get answers :)
So, as probably most of you know, if you want to decide whether an egg is rotten/gone bad/addled you just put it in a bowl filled up with cold water and some salt.
If the egg stays on the bottom of the bowl then it is good.
If it floats to the top of the water then it is rotten/addled.
I imagine the egg is floating because there is an air bubble in the rotten egg.
But how would that air bubble get in the egg?

Egg shells look as if they're solid, but in fact they're filled with tiny pores through which air can and does diffuse.

...up to the time when internal pipping takes place, when pulmonary ventilation is initiated, about 20 liters (O2 + CO2 + water vapor) have passed through 10,000 pores of an 80 gm egg.

--Pores and gas exchange of avian eggs: a review.

A typical 60-g chicken egg has about 10,000 pores, each with a functional cross section of 150–200 μm^2; therefore, the total pore area is about 1.5–2 mm^2.

--Gas exchange in avian embryos and hatchlings
You only asked about chicken eggs, but chickens have it pretty easy compared to many other avian species.  For example, ostrich eggs have a much larger volume-to-surface area, meaning that exchange is less effective. One way ostriches may compensate is by incubating eggs at lower temperatures, reducing oxygen requirements; more significantly and related, incubation time is relatively slower for birds with large eggs.   Birds at high altitudes have larger total pore size, adapting to the reduced O2 pressure.
Actually, a more serious problem than oxygen exchange is water exchange.  The egg needs to manage water loss (not too much, not too little), and the more gas exchange the more water loss.  Accordingly, birds adapted to different humidities lay eggs with different gas exchange capacities (changing pore densities for the most part); birds in very arid environments, like gulls in Chile's Atacama Desert, have very low gas and water exchange, to the point where their developing chicks are relatively hypoxic:
--Reduced oxygen diffusion across the shell of Gray gull (Larus modestus) eggs.

As an egg ages, it becomes progressively less dense and this is a natural consequence of the development of the embryo. If an egg becomes contaminated by bacteria, then it will also become less dense. The reason for this is that as the contents of the egg develop (or decompose, as the case may be) gases are produced. These gases dissolve into fluids of the egg and then migrate out of the egg into the surrounding environment.

I would not use the terms "rotten/addled". The test you describe is a simple kitchen test to determine if eggs are "old" vs "fresh" (before the days of refrigeration).  Fresh eggs will sink while old eggs will tend to float. This is because all eggs have a "bubble of air" at the blunt end (presumably for the chick to breath while hatching). As the egg gets older, this bubble will increase in size due to simple desiccation (moisture loss) over time.
You can try the test using fresh vs. expired eggs from the market.  You will find that many more of them will float when they are weeks past their expiration date, but they are definitely not rotten/addled and some people will still use them. It is more a test for the cautious person to avoid possible health risks from older eggs. A rotten/addled egg will give off the characteristic "rotten egg" smell due to bacterial growth.


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Learning industry skills for virology?
I am trying to learn more about virology for a tentative job I could be taking soon, as a quality control person in virology.
However, I have not taken a formal virology course, nor any course work in "quality control".
Googling showed me this website for learning more QC topics, however I was curious if anyone had better suggestions.
My question is if anyone had (ideally free) resources on learning virology (in the context of preventing cell culture contamination) and quality control in industry labs they thought would be ideal?

I work in human somatic cell therapies. For human administration I need to do, at a minimum, sterility and mycoplasma contamination testing (BacT/Alert culture bottles (Biomerieux), MycoTOOL RT-PCR (Roche)). For virally transfected lines I may need to QC the virus titer in the final product, and in some cases QC the transfection efficiency (qPCR, ELISA, flow cytometry). I also need to test viability, cell number, potency, purity and identity per protocol requirements. Perhaps first try to understand what the company you're applying to is doing for better direction.

@CKM.                I was speaking with a recruiter and they spoke on maybe placing me in a QC virology position because they saw I had some DNA extraction experience. They are going under a period of restructuring so I dont know if they have an official position open. From similar job listings of positions the sterility and Mycoplasma testing were listed as needed. The company is a mid sized bio tech that manufacturers; as they have / hire alot of production people for maintaining cell cultures ( I assume in large bio reactors).

I could probably recommend, then, an intro virology text at the undergrad-level if you're interested in the science. QC work is a lot of technical expertise. So not only should I know a bit about the test I'm running, but also the equipment, the results and how to analyze or report them. You learn none of it outside the job position, really. Important skill set will be wet lab experience, and being good with computers and recordkeeping (non-exhaustive list).

@CKM.                 I would like that very much. Thanks. And I am happy to take any other resource recommendations, maybe more info on the sterility and Mycoplasma testing?


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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 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!

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

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.


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Why is the ability to drink salt water so rare in land-animals?
Apparently, some species are capable of drinking salt water, like the sea lion and otter.
But given how rare fresh water is, and how abundant salt water is, why have more land animals not evolved to drink it? Why are kidneys capable of handling such a thing so uncommon?
I understand that evolution doesn't necessarily always do what's most efficient on a macro scale, but this drives me nuts.
So many animals live less than a five minute walk from the shores of an ocean, and such water is so abundant that they'd never be thirsty.

How can you state [...]how rare fresh water is, and how abundant salt water is[...] ?

What do you mean?

Salt water is abundant only if you live within easy walk/crawl/flying distance of an ocean.  Fresh water is common everywhere on land, except in the driest of deserts.

I mentioned (in my last "paragraph") that many animals indeed DO live within such ranges. Yet virtually none of these animals are able to drink the water.

@Sermo: But it is a useful ability only to the part of the population that lives within range of salt water.  Unless your entire population lives there AND finds it awkward to get to fresh water, as with sea lions and other marine mammals, there's really no pressure for it to evolve.

According to an answer here there is around 356,000 km of coastline on the planet. If we take an average human walking speed of say 5 km/h then our 5 minute walk takes us 0.417 km inland - giving approximately 150,000 km^2 of land conveniently supplied with sea water.
Now according to this page the total amount of land area is around 150,000,000 km^2 which according to this page is covered by somewhere in the vicinity of 117 million lakes [I'm certain a large portion of them are more accurately described as puddles but well go with that number for now], that gives on average a fresh water body every 1.3 km^2.
If we simplify things and imagine dividing the land area into 1.3 km^2 grid with ~1.14 km the distance separating each watering hole meaning the furthest distance to a watering hole across all the earths land area (ON AVERAGE) is around 0.570 km or just under 7 minutes walk (using our previous 5km/h)
So according to my very very rough calculations only around 0.1% of the land area is located within 5 minutes of sea water while 100% is located within 7 minutes of fresh water! I don't think that extra two minute walk is going to be that much of an evolutionary drive for any species.

apparently, not even the sea mammals are drinking salt water, if they can avoid it (obtaining water from food, ice or other fresh water sources): https://www.scientificamerican.com/article/how-can-sea-mammals-drink/

In addition, a great many mammals are smaller and/or slower than humans, reducing the land area close to salt water they have available.  Smaller creatures can survive on water from rain & dew, which in many places is readily available.


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Linked genes outcomes in offspring
This question is from a genetics session in my university:
The test cross between a plant with smooth and yellow seeds and a plant with wrinkled and green seeds gives the following results: 140 plants with smooth and green seeds, and 142 plants with wrinkled and yellow seeds.
These results are consistent with which case of the following?

Linked genes
Epistatic genes
Genes with intermediate dominance
Genes with complete dominance and independent assortment

In my answer key the correct choice is linked genes.
What I know is that in the case of linked genes, the outcomes are: either all parental (complete linkage) or the majority of offspring have parental traits and we have few recombinants(partial linkage).
But here it seems like all offspring are recombinants?! How can this be? Is there a mistake in the question, in the answer, or in my information?
Any help is appreciated. Thank you.

There is nothing wrong with the question and it can be explained with not much more than mendelian genetics + linkage.
What do you think are the genotypes of parents?
First hint: If there is more than one phenotype (for the trait) of the offspring at least one of parents must be heterozygote. So the idea of pure lineages goes out of the window here.
Ok, there is at least one heterozygote for each color and smoothness of seeds. What is the genotype of the other parent?
Hint 2: Test cross is a term for cross between recessive homozygote and individual of unknown genome (with dominant phenotype). The test cross reveals genotype of the parent with unknown genome.
Hint 3: 1:1 ratio of phenotypes is typical of cross between a heterozygote and recessive homozygote.
Ok so we have heterozygote and recessive homozygote for both traits. Which traits are dominant and which are recessive?
Hint 4: This question seems to be inspired by original Mendel work. Feel free to read it here to find out which traits are recessive and which are dominant. It is quite a good read, clear in its presentation of evidence and conclusions and I recommend it to everyone.
However, this knowledge is not necessary to answer the question. How are dominant genes organized in parents? Principally we have two options:
(AaBb x aabb) or (Aabb x aaBb)
If we consider organization on chromosomes it expands to basically 3 options:
Option 1:
chr ---A---B---
chr ---a---b---
         X
chr ---a---b---
chr ---a---b---

Option 2:
chr ---A---b---
chr ---a---B---
         X
chr ---a---b---
chr ---a---b---

Option 3:
chr ---A---b---
chr ---a---b---
         X
chr ---a---B---
chr ---a---b---

I leave it to you to figure out which of the tree options leads to result offspring described in the question.

I aggree with you. I think there is a mistake in the question.
Note that the question does not specify whether the parental lineages are pure lineages (fully homozygotes) or not. In all cases, answer 'B' would not explain the observed pattern for the reason you explained. Such pattern would be possible with some complex epistatic interactions if the parental lineages were pure and with complete linkage.


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How are Cytotoxic T cells transfered?
We learned that Cytotoxic T cells are MHC dependent, and if CMH matchup doesn't occur between the T cell and the cancer cell for example, the former won't attack the latter.
If this is the case then how are T cells given through vaccines and transfers?

T cells are not transferred. Vaccines induce the host to expand their own T cells that are responsive to the antigens that are given.

Adoptive cell transfer incl. TIL and CAR-T are forms of T cell transfers, though.

First, they're still almost invariably autologous, and second, given that the question seems to come from a fairly naive viewpoint it doesn't seem worth confusing the issue. If the OP would like expansion on these, they should clarify the question.

I thought the same thing, fair enough.


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Evolution question on speciation? Really confusing!
Okay, my teacher assigned this homework question, but nothing like this was ever given in our textbook.
Suppose that a type of tree tends to speciate over 10 million years and a species of fly tends to speciate over 1 million years. In the event of a mass extinction, which of the following predictions would LIKELY be true?

A) It is impossible to determine how many niches or species the trees and flies would lead to over time.
B) The trees would fill more niches and create more species than the flies.
C) The flies would fill more niches and create more species than the trees.
D) They would both lead to the same number of species.

I am stuck between A, B, and D because A would have merit, as speciation period may not always correlate to have many changes occur, B may have merit because it could be showing a Gradual model of speciation, and D may have merit because they might both just end up as the one species described? Any help, not even an answer but guidance would be really great.

I appreciate that you have given which answers you think are the best possible and are now asking for help. Homework questions here can be a slippery slope, but I believe you have shown your due diligence and why you need help with it. Welcome to Stack Exchange Biology, by the way! If you have any issues or questions, please visit the help center!

Given that this is a homework question, the answer is C.  It is true that there isn't enough information given to answer this question, but there rarely is for homework questions.  The point is to keep the number of variables small so that a single best answer can be determined, not to perfectly reflect reality.  The only information you are given is the time taken for speciation to occur, which means that you should assume that all other variables don't matter in this case.  All other things being equal, the one that speciates faster will fill more niches.

The answer is C
Because it explicitly tells you the fly speciates faster than the tree (1my vs 10my). That means after the extinction event, all things being equal, the fly will speciate into more niches/species in the same amount of time. While other outcomes could occur, with the information given C is by far the most likely outcome.
This is no different than a physics question asking you which of two object will reach some arbitrary marker first give two different known velocities.

It's a very strange question and hard to know for sure what they are trying to ask. My thoughts would be that they mean, given the opportunity to speciate following a mass extinction which would be expected to produce the most species after some time. The answer would then be C, that number of fly species > number of tree species because they speciate at a higher rate this would be the "likely" outcome - however, any of the three predictions could occur in reality.
I rule out A becuase it's not a prediction, B would be the expectation if the rate was higher in trees, and D would be the expectation if the rates were the same. As long as you can justify the answer I see no reason for them to complain - part of the issue is the odd question, that's the teacher's/author's fault.

The information in the question, as given, is insufficient to provide any answer about niche filling. If the speciation rates are known, and differ (which is, I assume, given above as average waiting time to speciation), and extinction intensity is assumed equal for both groups ("fly" and "tree"), then "fly" is likely to leave more species, and neither (B) nor (D) can be correct. That leaves (A) and (C). There is no information about the rate of filling niches, so (A) must be correct. Note that this is especially true, if the information I list as assumptions is also not given.


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Lobed Nuclei still count as One nucleus?
Do the Lobed Nuclei of immune cells (such as Megakaryocytes) still count as one nucleus?

Yes. Lobation is when a nucleus deforms, but it is still a single compartment. How the nucleus deforms can be helpful in roughly determining the cell type by visual inspection.


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What is this insect in winter?
I came across a bunch of these tiny ball-pen-sized insects that (to me) look like they belong to the beetle family. They are all dead but I do remember seeing it once flying in my apartment. They are as small as fruit flies.

I think you're right that it's a beetle, but the picture quality (which I realize you may not be able to improve) will likely forbid anyone going any deeper than that.

@user please put more effort into your posts regarding grammar, capitalization, and spelling. This is a site intended for professionals, not yahoo answers. They will get downvoted. Regarding your question: I agree with Arther -- looks like a beetle, but the photo quality makes an informed ID rather difficult

"This is a site intended for professionals..." Has Stack Exchange implemented a new policy recently? This site is not "intended" for any specific, named group of people. The site is open to everyone, and strives to be open and welcoming to all, especially new contributors.

@theforestecologist That wasn't very nice or welcoming. Not everyone here is a native English speaker. If you have an issue with someone's grammar/spelling/punctuation, feel free to edit it or ask for clarification (I see you did edit this one).

@L.B. misspelling (and not correcting) words while using a built-in spell-checker and not capitalizing words like "I" are not an ESL issue; they're indicative of a rushed post or a lack of professionalism. Grammar is less necessary, but I did not tell the OP to write perfectly -- rather, I requested politely that they put adequate time/effort into writing a more professional post (as is suggested by our help section).

@theforestecologist Not here to argue. However, issues like not capitalizing "I" actually can be ESL issues and especially with a phone's autocorrect, that is a very common issue. I'm not defending making lots of mistakes. I am defending the person because we don't know them personally and they are asking a legit question and simply made mistakes.

@uhoh it is intended for a specific group. From our tour page: "Biology Stack Exchange is a question and answer site for biology researchers, academics, and students". Of course, anyone is welcome to use this site & we strive to make that experience helpful as much as we can. However, we do have standards (see here & here), & posters are expected to meet those standards.Voting/commenting are our tools for promoting adherence.

@L.B. sure we don't know anybody personally, which is why we have a code of conduct. And that's why I asked politely (see the use of "please"), and then followed-up by editing to show them their mistakes. It's a learning process, but one which requires pointing out a misstep. We can't just pretend everything is ok.

@theforestecologist okay that works because anyone who wants to learn can be considered a student. So we can agree that "This is a site intended for professionals..." is probably not the right way to paraphrase?

@uhoh professional in regards to conduct and style, not in regards to level of expertise. In other words, I was referring to professionalism

@theforestecologist yep that works.


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How can we usually "trust a fart" not to be liquid or solid?
Jack Nicholson's character Edward Cole in the movie The Bucket List said ...and never trust a fart, and a search for Al Roker leakage White House will clear up any doubts what that's all about.
How is the adult human body usually able to sense the difference between solid, liquid, and gas and enable the brain to consciously decide on the proper course of action? (e.g stay put, walk, or run!)
Per @theforestecologist's request I'll restate the question using my best "science words": How are adult humans able to determine when pressure in the rectum is the result of solid waste, liquid waste, or flatulence?
A search for answers has turned up the following:
Source: https://www.sharecare.com/health/digestive-health/how-can-i-have-normal-bowel-movements

In a rapid "sampling reflex," these nerves inform the brain about whether the rectal contents are intestinal gas or liquid or solid stoo...

However I can't view this link further.
Searching further for "sampling reflex" I've found this

Sensing of the arrival of stool in the rectum with activation of the recto-anal inhibitory and sampling reflexes which allow stool to enter the anal canal and to be distinguished from flatus.

This provides an opportunity for sensation to take place, but does not describe how  stool is distinguished from flatus, and doesn't even mention liquid.
At this point I'm way out of my depth.

I actually think you've asked a valid scientific question here, but you've wrapped it in so much non-serious, non-scientific baggage that others are almost certainly to judge this question negatively. I don't think it should be closed (fyi it's not "opinion-based" as one close voter has suggested), but if you do not edit the question you'll have a tough time keeping it positive or getting an answer. Please update accordingly.

@theforestecologist thank you for recognizing the validity of the question, but I think the wording is quite positive! Nonetheless I've added a third sentence. fyi informal words like "fart" have been used in this SE site on many occasions without issue. Biologists are generally comfortable with discussing the human body and it's functions without hiding them unnecessarily behind clinical terminology, and I think in this case a clinical view is not necessary.

you've misunderstood me a bit. it's not the topic or even your choice of using the word "fart" -- these are ok in my opinion. Your entire 1st paragraph is unnecessary and distracting and sets the tone that your question is not serious but rather, it comes across as juvenile. I would delete the first paragraph & perhaps provide more biologically-focused background. We do ask that all question askers provide evidence that they researched their own question, so I recommend that you do some research on your own and then update the question by adding a bit more scientifically-relevant info.

@theforestecologist okay that's a more concrete suggestion, thanks. While I won't remove the levity or existing "research", I've "given it a go" so to speak and added some additional research.

"How is the adult human body usually able to sense the difference between solid, liquid, and gas and enable the brain to consciously decide on the proper course of action?" I think the question is incorrect; the nerves send the proper information to the brain, which then transmits the properties of the stimulus (solid/liquid/gas) to another part of our brain which informs our ability to control the tone of our rectal sphincter, if that makes any sense. It's not just semantics. It's neurology.

@anongoodnurse "...(e.g stay put, walk, or run!)" I don't know about yours, but my sphincter does none of the above. ;-)

Your sphincter is smarter and more athletic than you realize! :-)


text:
Is there random assortment in metaphase II?
First, a little notation. Call a the first chromosome from my mother and A its homologous partner from my father. b and B would be the second pair, c and C the third, and so on, down to w and W (the 23rd).
The tetrads in interphase would be expressed as aa AA...ww WW (so, for example, AA are sister chromatids). Finally, use the notation a' and A' to express that those two chromatids have crossed over via recombination.
Ok: I understand that in Metaphase I, there's a random assortment of chromosomes at the equator, so that we might end up with a division like so:
aA'    Aa'
bB'    b'B
CC'    c'C
...
wW'    Ww'

Which pair ends up on the right or left is random, and there are therefore $2^{23}$  possible arrangements.
My question is whether an analogous shuffle happens during metaphase II? I visualize metaphase II as taking one of the columns above and turning it on its side, so that for instance taking the right column you have:
a' B  C  ... w'
A  b' c'     W

These "rows" are then split to become 2 of the 4 gametes.
The question is whether at this stage, before this final split, there is an analogous shuffling possible whereby, say, the A and a' could switch sides?
My intuition is yes, of course, but in all the accounts of meiosis I can find online, the "random assortment" and shuffling is all described as happening in metaphase I.
(I think whether the shuffling between this particular A and a' happens in metaphase I or metaphase II is inconsequential in terms of which one ends up in which daughter cell... but I'd still like to have a sense for what's literally physically happening.)

Metaphase I
Your understanding of the metaphase I is not entirely correct. In normal (human) metaphase I homologous chromosomes separate. Therefore, sister chromatides go together. More precisely sister chromatides are kept together at centromere. You have only two possibilities for each chromosome:
<-AA   aa->

or
<-aa   AA->

If we multiply the two possibilities for all 23 chromosome pairs it leads to correct number  223 of possibilities.
There can be one or more crossovers between two or more chromatides but the fate of crossovered chromosome arms is determined by the fate of centromere they get connected to.
Your diagram of random assortment, if I understand it correctly, allows for more than 2 possibilities for chromosome pair:
<-Aa   Aa->
<-aa   AA->
<-AA   aa->
...

And it would lead to incorrect number of possibilities (more than 2)23
Metaphase II
In metaphase II sister chromatides separate as they would in mitose. Yes, there is random asortment of which chromatide goes left and which goes right. With your notation it could look like this:
<- A   A'->
<- b   b'->
<- C'  C ->
<- D   D'->
...
<- w'  w ->

However, as I said earlier, some chromosomes can crossover more than once, so you can have thinks like:
<- g''   g'->

or
<- F'''   F ->

or
<- h'    h'->

Inverse meiosis
For every rule in biology there is an exception. Some species have inverse meiosis. This means they do it in reverse order. In metaphase I they separate chromatides and in metaphase II they separate homologous chromosomes.


text:
Simple and inexpensive geobiochemical studies
I plan to write a research proposal for conducting a small experiment related to geobiochemistry. I aim to make the experiment:
1) Simple (middle school aged students could comprehend its main ideas),
2) Inexpensive (less than $500 of science equipment is needed),
3) Fast (can be done by one person within 2 weeks of full dedication).
As a side note, the station does have a microscope that I could use.
I would have access to the surrounding areas and can collect soil, rock, shell fossils, etc. Previous groups have discovered methanogens in the soil and endoliths in the rocks. However, without much background in astrobiology, I am uncertain how much expensive equipment and time was needed for these experiments.
I am mostly hoping for ideas on how I could conduct a simple and feasible  experiment that could be shared with middle school students. Such as searching for life, biosignatures, etc. As I do not have experience searching for life and biosignatures in the field, I am truly unsure of how to approach this in a reasonable manner. Any suggestions greatly appreciated!

+1 Methane generation is one possible signature, and natural gas sensors are cheap and commonplace. Since methane can be found everywhere people or other mammals can be found (as well as other forms of life) the problem would be trying to do an experiment that is sensitive to methanogenesis from soil samples but not anything else.

Please do not expect the internet to do your job for you. Have you tried at all to come up with a question/project? Come on! In addition, this post is both opinion-based and to broad. Three reasons to close. Please put some of your own effort into this and edit this question accordingly asking for clarification of a specific idea that you come up with. Our goal is not to simply be an answer site, but rather a site that promotes self-learning with some expert help along the way.


text:
Are spinal nerves myelinated and unmyelinated at the same time?
I was trying to answer this question when I remembered that the somatic axon is myelinated, while both sympathetic and parasympathetic preganglionic axons are also myelinated. Are they only myelinated or are they both myelinated and unmyelinated? Thanks
Edit:
This is a question from an old lecture quiz (previous year) and unfortunately I do not have the answers for the questions. The wording of the question was

Spinal Nerves are
a.) myelinated
b.) unmyelinated
c.) answers a and b
d) none of the above"

Welcome to Stack Exchange Biology! If you have any questions, please visit https://biology.stackexchange.com/help.   Perhaps I am missing something, but can you clarify what you are seeing that makes you think some of these nerves are unmyelinated?

I was answering a quiz on a lecture slideshow which was from a previous year course, which unfortunately lacks answers. The question was, 'Spinal Nerves are a)myelinated b)unmyelinated c) a and b d) none of the above."

I added those details in an edit to the question. Hopefully no one treats it as a homework question since that is not what it is intended as.

Spinal nerves are mixed nerves containing afferent and efferent neurons of various types. Anatomically, they protrude from the spinal column bilaterally at each vertebral level. They contain both myelinated fibers (e.g., A fibers) and unmyelinated fibers (e.g., C fibers).
The answer is (c): both myelinated and unmyelinated.
Please note that spinal nerves are NOT located in the spinal cord, despite the fact that neurons in each spinal nerve will either originate or terminate there. A spinal nerve is a peripheral structure. It starts at the point where the dorsal and ventral root converge (See April's Clinical Anatomy, Ch. 1). If you have the opportunity to observe back surgery or dissect a human cadaver, you can see and touch a spinal nerve. They are cable like structures containing bundles of many many many axons, but no neuron in its entirety. A nerve is not a neuron. This is a common misconception.
Just to add, the details here may seem like trivia, but they are not. Similar questions (and questions that require you to understand the distinction between a nerve and a neuron) are often asked on US medical licensing exams. This is because they are relevant to understanding and interpreting neurological symptoms and physical exam findings.

Yes, there is grey and white matter in the spinal chord and the parasympathetic nervous system, so they are both myelinated and unmyelinated:

Here is an image of parasympathetic nerves:

Primary afferent fibers of the dorsal roots are either myelinated or unmyelinated. In the rat, cat, and monkey, thin unmyelinated and thick myelinated fibers are located in the lateral and medial parts of the dorsal roots, respectively, in the dorsal root entry zone (Light and Perl, 1979a).

Nothing is false in this answer, but it doesn't answer the question. Spinal nerves are not in the spinal cord, they are the nerves leaving the spinal cord. The presence of gray or white matter in the spinal cord is not relevant to the question.

thanks. He said: are they both myelinated and unmyelinated? I see what you mean. I updated the information.

I think you have a misunderstanding about what a nerve is. The boundaries of a nerve (e.g., a spinal nerve), a gross structure, are not the same as the boundaries of the neurons, a microscopic structure. A spinal nerve, at any level you measure it, will have fibers of different conduction velocity. Some of these (e.g. A fibers) are fast
and heavily myelinated. Some of them (C fibers) are slow and unmyelinated. The gray matter in the spinal cord doesn't have anything to do with the question, which is about a spinal nerve, a PNS structure, not the spinal cord (a CNS structure).

Grey matter mostly isn't myelinated. Grey matter is distinguished from white matter in that it contains numerous cell bodies and relatively few myelinated axons. What are you talking about? you are overcomplicating it. The inside of the spine, the spinal roots, and the parasympathetic system all contain myelinated and unmyelinated nerves. By nerves I meant nerve cells. Where did I say that nerves are assemblages of nerves?

Gray matter is not present in any nerve. Gray matter is a central structure that has nothing to do with the question. Nerves are not cells, they are bundles of fibers (a part of many many cells, but no neuron in its entirety).  You can see an individual nerve, and distinguish it from surrounding structures (vessels, muscle, ganglia). You cannot see a neuron, or, as some may call it a "nerve cell". This is not over complicating it, but it is something that many students and neuroscientists who focus on cell biology miss.

It may be helpful to read the wikipedia entry for nerve

The type of fat in myelin makes it look white. The presence of white and grey matter demonstrates that it does. it is relevant. It answers an element of the question:  Are they both myelinated and unmyelinated? Grey and white matter are an obvious visual indicator of the presence of myelin. let's avoid turning your good initial criticism into a baseless confusion over detail.

Let us continue this discussion in chat.


text:
Would there be any particular reason to choose strawberries for this DNA extraction tutorial?
The NileRed video What is DNA and what does it taste like? | Edible Chem shows the extraction of a surprisingly large amount of DNA from some strawberries. At 02:22 the narrator says:

What I think is really cool, is that it’s actually possible to isolate DNA from pretty much any living thing. For this video though, I’ve decided to get it from strawberries, because it’s one of the easiest sources.

I'm wondering if DNA is inherently easier to extract from strawberries than other fruits, vegetables, or other foods in general, or if for some reason there is more DNA (or DNA plus other molecules bound to it) it in strawberries than other foods to begin with.

As he is mentioning later in the video a "major reason" why he used strawberries, is that it's easy to crush them. In order to extract DNA from the tissue you need to damage the cells. We used tomatoes once, but with a blender. Works just as well..

@Frieke I was hoping for something more profound ;-( I am vaguely aware that some plants have absurdly huge genomes, and I was hoping that there was some amazing factoid about the strawberry genome being particularly huge.

@Frieke do you think that's worth posting as an answer? It does seem to answer my question, though strawberries being easily crushable is not the most profound sort of biology. I guess my other option is to delete the question.

A one-line answer without citations will attract the mods and downvotes. But I am not feeling like writing an essay about genome-sizes and crushability of fruits and vegetables ;)

@Frieke yep! okay thanks for the help, maybe I'll vote to close as off-topic and should be migrated to Cooking SE ;-)

It's on topic here and certainly not on topic at Cooking.SE.

@theforestecologist thanks for the encouragement; the smile emoticon was meant to indicate a bit of humor.

I figured as much, but I just thought I'd clarify just in case :p


text:
Is there a chemical compound, element or something else that could color the eye lens in purple?
I hope this is a right place to ask this question. I'm writing scifi book, and looking for information whether it is possible for any element, chemical compound, radiation or something else to color the human eye lens (and or freckles) to purple.

slightly related: Could being exposed to excess UV in the arctic lead to a human eye color change? If so, what is the mechanism?

You meant the iris by writing the lens? Colored lens would lead to partial blindness in chosen part of the spectrum.

If it's for a sci-fi book, how about genetically engineered (designer baby kind of thing) humans where the humans have a genes inserted to express purple chromophores in their lens or on their skin in melanocytes? It wouldn't be awfully straightforward, but hey, if you can cause organized fibrillation of lysozyme (a protein normally found in bodily fluids), you can get purple pigment! Also, a purple lens would mean that your purple-lensed character would be impaired in seeing purple.


text:
What's inside the perinuclear space?
The cell proper contains the cytoplasm in general and the cytosol in particular when referring to the fluid/gel without notable organelle.
Once we move inside the nucleus there is the nucleoplasm and the nucleosol.
My question is in the intervening void of the perinuclear space (between the inner and outer membrane of the nuclear envelope) what if any is the terminology used to refer to the internal chemistry in that space - and what is known about it's makeup?

The outer nuclear membrane is connected to the endoplasmatic reticulum (ER), so the perinuclear space will share some characteristics with the ER as well. However, there are bound to be specific differences as well, which I don't know about.

Interesting so the perinucllear space could almost be thought of as the innermost sack of the endoplasmic reticulum.


text:
Does anybody knows name of this bird I found in my backyard in India?

I found this bird in my backyard in India. I checked several websites but wasn't able to identify it. Any help would be appreciated.

Open images.google.com drag and drop this image. It will says the answer

I am pretty sure that this is a  Indian Paradise-flycatcher (Terpsiphone paradisi). Since we cannot see the length of the tail feathers, we cannot distinguish between male and female, the later have a much shorter tail.
See the image (from here) for comparision:

More information can also be found here and here.


text:
What is this plant that spontaneously sprouted in my balcony?
I have a big pot on my balcony that has inhabited many kinds of plants over the years. One spring I got to unexpected sprouts from seeds the size of an apple or orange seed. One survived and grew to what is depicted in the pictures here, but then unfortunately I got an infestation of spider mites that killed it.
I had previously rented out the apartment, and I suspect that this is the result of a couple of seeds that they intentionally or unintentionally put here. My best guess is that this is some kind of berry or something else edible that you buy in a grocery store.
You can also see some sun damage on some of the leaves in the picture. The plant in question is the most visible in the pictures, the others in the packground are passion fruit.
There were no thorns, and the leaves felt a little bit hairy, kind of like a common nettle but shorter and a fussier feeling. The height in the pictures is about 30-40 cm and it was growing fast until the spider mite attack.
What could it be?

i saw a lamb eating a bramble leaf once so i tried one and they have a particular and defining taste and chewyness. if you can't wait until it flowers, i sugest that you try a raspberry and a bramble leaf sprout and compare it, it will probably be the same as one or the other.

It looks like a raspberry, or some other kind of similar berry plant (blackberry etc.). The triple leaves and the habit of the plant are characteristic. Birds will often eat them and "deposit" the seeds randomly around the Earth.
https://plantvillage.psu.edu/topics/blackberry/infos
Berry plants usually have thorns or develop them as they grow. If no thorns are present, then perhaps it is another type of interloping plant. Other plants do look similar. In which case, your photos are insufficient for more further identification.

Blackberry seems most likely as I commonly see them in random areas such as fencerows.


text:
What labs/companies provide comparative genomic analysis?
I’m looking for labs/companies that provide comparative genomic analysis between two different species, AND do so for the “paying” public.  I am looking to test a hypothesis regarding genetic expression and would appreciate any direction.  Thanks!

What's your starting material and your budget? e.g. animal tissue and $x.xx

Thanks for the reply.  Yes, tissue, and a budget of appx. $5000.00. But I honestly have no idea how much labs might charge.

Well first figure out what kind of work you need done. If you have tissue, you'll need extractions done. If you're doing NGS you also need the library prepared and a sequencer ran. Then multiply that cost by the number of samples. At Duke's NGS core, for example, RNA-seq with library prep on their MiSeq instrument for 10 samples will cost you around 15,000. Extractions will probably be extra. I've seen companies push QIAcube extractions for around $65 a sample.

@CKM  Understood. Thank you for your help!

Earlham Institute have the expertise for this work.  They primarily work in public-funded research but they carried out private-sector work in the past.


text:
Is reverse senescence/"anti-aging" actually scientifically possible among humans yet?
I have been very interested in this since I myself am interested in reversing my skin's aging/genes/damage/etc. I also am interested in volunteering any future genetic altering of skin quality.
Basically I've heard of experimental drugs called senoyltics that are believed to (and have actually done so) have the ability to truly reverse aging at the cellular level and/or aging damage of skin and etc.
I am very intrigued and want to know if this is feasible for humans yet -- or any such breakthroughs. I really want my skin's genetic quality to be enhanced, but reversing aging damage by genes will suffice.
So skin aside, in general, is reverse senescence (with or without senolytics) anywhere near possible to reach human success? I've heard of labs and etc. working on this for testing, but nothing more.
My question is basically: is it possible? Are we really in the near future to reversing aging in humans?
As a note: I don't mean "anti-aging" as in preventing death -- more so as in making yourself younger in a myriad of ways, such as by appearance and physical ability (like heart; brain; skin texture/youth; etc.)

 Short Answer
You might be interested in learning about telomeres, telomerase, and telomerase gene therapy.
For example, Boccardi & Herbig (2012): describe a mouse study in which they used telomerase gene therapy to improve the healthspan and lifespan of mice by up to 24%.
As far as I know, we have no successful human trials of similar therapies that have targeted and succeeded at "decreasing the age" of humans.

However, this source does claim that a woman attempted to do so. I cannot substantiate these claims in any way, so I'm skeptical at best...

 Long Answer:
Telomere 101:
Telomere: non-coding nucleotide sequences on the tips of chromosomal DNA strands.

Due to the inability for DNA polymerase to replace RNA primers on the end of linear strands of eukaryotic DNA during DNA replication, ~50-100 base pairs are removed from the daughter strand from each replication event.

The "junk" (i.e., non-coding) telomere sequences (which could repeat 1000s of times) provide buffers against losing more valuable DNA when this happens. Eventually though, the telomeres run out, and replication events could lead to loss of coding regions of DNA...
According to Boccardi & Herbig (2012):

As we age, telomeres in most of our tissues progressively become shorter and therefore likely contribute to the failure of our organs and tissues observed in old age. Supporting this are data demonstrating that healthy lifespan is positively correlated with longer telomeres in humans, and patients suffering from age‐related diseases and premature aging syndromes display shorter telomeres compared to healthy individuals (Zhu et al, 2011).

The enzyme, telomerase can replace these telomeres, but telomerase is really only active in stem cells and white blood cells, so most adult cells lack this regeneration ability.
This is where telomerase gene therapy  comes into play.

In the simplest sense, this approach attempts to artificially add telomerase to adult cells to essentially add back telomeres and potentially slow or even reverse the aging process.*

 *Note: As far as I know, we don't actually know whether short telomeres are simply an effect of aging or if they are actually the cause of aging (and ultimately death), so this gene therapy is running on a relatively unsupported hypothesis.
For example: Boccardi & Herbig (2012) "Telomerase gene therapy: a novel approach to combat aging".

They found that adding telomerase to 1 year old mice increased their lifespan by 24%.

 Credit: Boccardi & Herbig (2012):
As Boccardi & Herbig (2012) note, however, applied human studies are still a thing of the future.

While these studies provide a proof‐of‐principle that telomerase gene therapy is a feasible and generally safe approach to improve healthspan and treat disorders associated with short telomeres, a clinical application in humans is likely still some time away.

However, this source does claim that a woman (Elizabeth Parrish, CEO of Bioviva USA Inc. -- notice the website :p) attempted to do so -- I cannot substantiate these claims in any way, so I'm skeptical at best...

Citations and additional suggested reading:

Boccardi, V. and Herbig, U., 2012. Telomerase gene therapy: a novel approach to combat aging. EMBO molecular medicine, 4(8), pp.685-687. read here

Campisi, J., Kim, S.H., Lim, C.S. and Rubio, M., 2001. Cellular senescence, cancer and aging: the telomere connection. Experimental gerontology, 36(10), pp.1619-1637. read here

Zhu, H., Belcher, M. and Van Der Harst, P., 2011. Healthy aging and disease: role for telomere biology?. Clinical Science, 120(10), pp.427-440.

So wait. I'm confused. Is telomerase gene therapy the same concept as "skin age" as a separate component from skin appearance/quality? Because people can be young with shorter telomeres and have poor quality skin, and the reverse can be true as well. So how will telomerase therapy impact skin quality itself as a genetic component in the whole process? I'm asking because the rats shown appear to look younger/more youthful in these gene experiments. So I'm unsure if "reverse aging" by telomeres functions as the same idea of looking more youthful and/or the skin's quality and texture/form overall

Not within the next two decades, at least (assuming you meant nearly total reversal of the effects of physiological aging). Any further than that is impossible to predict, since we are likely only a few breakthroughs away at this point (however, with extremely bad luck, these could take centuries to achieve, since presumably no scientist knows the 'optimal route' to developing these types of therapies at this point). But it is certainly possible from a scientific point of view.
While this is slightly off-topic, since you seem particularly concerned with skin aging, I would suggest protecting the stem cells of the skin from mutagens. These include UV radiation (which comes not only from the sun, but also from blue sky), background radiation (which depends on altitude and geographic location (inc. North American examples)(similar maps for Europe)) as well as lipid-soluble volatile genotoxins such as benzene and PAHs, which arise from the combustion of organic matter (e.g. wood burning, smoking, conventional BBQ grills, car exhaust).
Other factors that affect aging of the skin are the factors that degrade collagen, including UV radiation (again) as well as high blood sugar, which in turn triggers the formation of advanced glycation end-products that reduce collagen elasticity. One more factor associated with skin aging is particulate air pollution (Ding et al. 2017), which damages the DNA as well as other cellular structures by inducing oxidative stress (Piao et al. 2018). Particulates also often have genotoxic compounds adsorbed onto their surface (see e.g. Jia et al. 2017)).
Currently, the most effective way to prevent skin aging is to minimize exposure to the factors mentioned above. Many of these factors also promote certain other processes associated with aging (the accumulation of DNA damage causes cancer and accelerates stem cell aging (Rossi et al. 2007), whereas exposure to particulates is expected to contribute to the development of brain diseases such as Alzheimer's (Maher et al. 2016))
I would expect DNA mutations of the skin to be relatively easy to fix, though. For example, the skin is relatively accessible, so stem cell therapy could certainly work, as could a Cas9-based therapy used to strategically fix specific key mutations to prevent senescence. Presumably research to this end will be conducted relatively soon, now that Cas9 has gained popularity in the scientific community.
References:
Ding, Anan, et al. "Indoor PM 2.5 exposure affects skin aging manifestation in a Chinese population." Scientific reports 7.1 (2017): 15329.
Jia, Yi-Yang, Qi Wang, and Te Liu. "Toxicity research of PM2. 5 compositions in vitro." International journal of environmental research and public health 14.3 (2017): 232.
Maher, Barbara A., et al. "Magnetite pollution nanoparticles in the human brain." Proceedings of the National Academy of Sciences 113.39 (2016): 10797-10801.
Piao, Mei Jing, et al. "Particulate matter 2.5 damages skin cells by inducing oxidative stress, subcellular organelle dysfunction, and apoptosis." Archives of toxicology (2018): 1-15.
Rossi, D.J., Bryder, D., Seita, J., Nussenzweig, A., Hoeijmakers, J. and Weissman, I.L., 2007. Deficiencies in DNA damage repair limit the function of haematopoietic stem cells with age. Nature, 447(7145), p.725.

Keeping in mind that this was a very small, not especially well-controlled preliminary/exploratory study. Because life expectancy was increased by ~2.5 years - or got ~2.5 years younger biologically, depending on how you look at - it is the reason that this study is being talked about at all.
In the TRIIM study 9 men, ages 51-65, first took hGH alone (0.015 mg/kg, or ~3 IU for a person weighing 70 kg) 3-4 times per week for one week and then added DHEA (50 mg) the next week, similar to Fahy’s n=1.  The week after that, the same doses of hGH and DHEA were combined with metformin (500 mg). At the start of the fourth week, the doses were individualized based on each participant’s particular responses. (To put the hGH dosing into context, while it’s individualized, athletes using it for performance enhancement may take 10-25 IU 3-4 times a week and “longevity” clinics may prescribe somewhere in the ballpark of 1-2 IU/day.) The goal of this titration approach was to maximize IGF-1 and minimize insulin by varying each of the hormones and drugs.
The investigators reported a mean “epigenetic age” approximately 1.5 years less than baseline after the 1-year intervention. In other words, their epigenetic age got 1.5 years younger while their chronological age obviously went up another year (total 2.5 years taken off).
On a side note, after 1-year of treatment, there was “highly significant” evidence of restoration of thymic functional mass along with improvements in age-related immunological parameters, based on MRI imaging and favorable changes in monocytes and T-cell changes.
Reference: https://www.nature.com/articles/d41586-019-02638-w
Also, reversal of epigenetic changes with OSK (part of Yamanaka factors) is very promising. This paper is worth reading - https://www.biorxiv.org/content/10.1101/710210v1


text:
Are These Oyster Crabs?
I found these crabs at the end of September, 2018. My family was vacationing on the coast of Lopez Island in the Pacific Ocean off of Washington State. I have been trying to figure out what they are ever since.
I found two crabs, one that was orange and black, and another crab that was off-white and black. They are both about an inch and a half across and an inch from front to back. I did some research and the closest match I could find are oyster crabs, which are found inside oysters on the East Coast of North America (I found my information on oyster crabs here).
However, I found these inside clams on the West Coast. Also, the pictures of oyster crabs I can find online (figure 1) do not look like my oyster crabs. I was wondering if anyone can identify these crabs. Sorry about the picture quality and thanks in advance!

[Figure 1: A picture of an oyster crab that I found online. There are not very many pictures of oyster crabs online, and they all look similar to this one.]

[Figure 2: The back of the two supposed oyster crabs I found. They are not fighting, I just put them close together for the picture.]

[Figure 3: The front of the off-white supposed oyster crab. In the picture, you can see its tiny eyes and small mouth, along with the claws.]

[Figure 4: The front of the orange supposed oyster crab. In the picture, you can see its tiny eyes, small mouth, and claws.]

[Figure 5: The back of the orange supposed oyster crab.]

[Figure 6: The back of the off-white supposed oyster crab.]

[Figure 7: The undersides of the two supposed oyster crabs. As you can see, they both have eight legs and two claws, making them crabs and part of the crustacean family.]

What you have found are pea crabs, which have a fascinating life history of parasitism. https://www.whitestoneoysters.com/blogs/an-oyster-life/what-the-shuck-is-a-pea-crab

Thanks for answering this question! We appreciate when new users with expert knowledge begin answering questions! Please update your post, however, to include more information about why your ID is correct. Given the propensity for external links to go defunct, we ask that your answer here can adequately stand on its own in explaining both the correct answer and your rationale. Support as a link is fine (and citing/linking sources is preferred/required), but please capture some of the relevant detail from your external source in your post itself. Thanks!


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Can someone help me to identify what kind of pear is this?
I went to my local groceries supermarket (in Lima, Peru) and found this cheerful looking pear named locally as "pera canela". But I found it weird as the only variety which I'm aware of is Packham's pears. I tried to do some research on different cultivars and species known of pears. So far the only ones which I found were in this wikipedia's entry but it didn't help me much.
Below is a set of pictures I took of the pear referred to as "pera canela"

Figure 1. Picture of packed Pera canela, the printed label shows its local name.

Figure 2. Picture of Pera canela's as they are on a basket in groceries stand. Seen in the background.

Figure 3. Picture of Pera canela seen closer for identification.
I've tasted it and it is a little bit more sweeter than the Packham's variety, on the juicier factor I would say that it is pretty much the same as Packham's
So far by comparing it with different entries on Wikipedia. I'm not very sure if it's a local name given to either Abate fetel or perhaps to Bosc
 varieties, or could it be a D'Anjou?
Since I'm not good at identifying plants, can somebody help me identify which kind of pear it is? It would also greatly help me if the answer could include its scientific name so I could do more research into it.

Plu Code 4413 is a bosc pear (a cultivar of Pyrus communis).

From the PLU search tool available via the International Federation for Produce Standards

FYI: take a close look at the pear you're holding in your picture:

Pera canela, meaning "cinnamon pear" in English, is in reference to its color. From Wikipedia:

Famous for its warm cinnamon color

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


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Why does the seed of the coconut tree have a liquid in it?
What is the purpose of water in the coconut seed?  The reason I ask this is that I was reading about coconut water and all the benefits it has for us Humans.  But why does the tree put a liquid in the seed?  I read a lot more and learned that the liquid becomes a solid and is called endosperm, which is food for the coconut tree.  I'm still not happy with that answer because all seeds are food for the plant they become.  They are also a lot more.
I have come up with a very good explanation for the existence of coconut water and I want see if anyone else has any ideas.  Remember, I am not trying to find out why there is food in the shell.  That's obvious.

Hi! "I have come up with a very good explanation" -- you should post it here, members will be able to tell you what biology prevents your explanation or supports it

I think it's because the coconut is hollow and designed to travel on the sea for more than 100 days and 3000km. At sea, the sunshine and the salt has a strong drying effect on the coconut, so fresh water helps it resist sun and the osmotic force of the seawater.

I like your thinking.  I agree with your points on the design allowing the coconut to survive for 100 day and 3000 km.  But if you think about it, all the nutrition, including the liquid is inside the endocarp. Protected from those environmental dangers.  The Exocarp is very thick and robust and the endocarp is made of a hard woody material, which is why I am not convinced that your answer is correct.  Thank you for your comment.  I really appreciate it.

I will give my explanation after I feel that enough time has been given to this community of thinkers.  I really respect other people's points of view and am sincerely interested in seeing if anyone else can come up with my solution.

Since we talk about travelling on sea, maybe it is simply a reserve of freshwater for when the tree will start to grow if rain is absent in the first days. As you said most seeds have a reserve of food for the newborn plant, this one just has a reserve of freshwater as well in case the coconut ends up on an island surrounded by saltwater. It might also matter the way water affects how the cononut rolls, moves or falls from the tree. or maybe it helps the coconut resist impacts ?

I like your ideas about helping it roll and move once it falls from the tree.

It is a transitory state.
During coconut development the "milk" actually starts as a spongy solid a multinucleate endosperm. As the coconut develops it absorbs this tissue. Because of a coconuts hard structure this leaves a cavity since the coconut cannot change shape as the tissue density changes, some fluids including oils are left behind as hte tissue is broken down and reabsorbed. But this fluid will be reabsorbed as the the developing cotyledon fills in the cavity. The fluid is a by product of the cavity but the the cavity is needed due to the unusual development of the coconut.
As a side note most comercial coconut milk is actually squeezed out of the solid endosperm.

That is the milk part, not the water part.

@Coconut They are the same part, commercial coconut milk is made in a different way, but then commercial cheese is one step away for plastic that does not mean much.

Here are two things that I have not see anywhere else in my research on the subject.
First, I will explain why coconut trees at the edge of the beach seem to "reach" toward the sea, but usually go straight up when planted away from the beach.  Then I will get to why the coconut tree puts a liquid in its seed.
The main purpose of many seeds is to to take themselves away from the parent to start a new life somewhere else (hopefully better).  Just like us humans the coconut tree wants it's offspring to migrate.  It uses the sea as the medium on which it travels.   The coconut is too heavy to move toward the sea using wind or animals. It's also too tough for most animals to be able to get the nutrition locked inside it.  So the tree, which in nature would most likely find itself on a beach, contorts itself so that it's "head" is above the sea and then it drops is seed in the ocean to travel and find a new place to grow and propagate.  That would be my reasoning for explaining the commonly seen phenomenon of coconut trees leaning over the ocean.
So now that the coconut has started it's travels into the unknown, it needs to find a place to grow.  The seed bobs up and down on the ocean until it lands somewhere.  It could land on the same island or travel thousands of kilometers and land on another island or coral atoll or a sandbar.  This is where the liquid comes in to play.  The liquid which has been moving inside the coconut suddenly stops.  After a certain amount of time the next step in it's growth is triggered because of the still liquid.  Also, the cavity in the coconut keeps it from drowning.
That's it.  The "water" is a "level" that tells the coconut when to "drop a root and send a shoot"
Let me know what you think.

I've edited your post to remove the bit at the top about being back and ready to talk about this. Thank you for contributing. We can see that you're back and have something to share because you posted!

It looks like this post is mostly from your introspection about possible reasons. This is a great method for developing hypotheses, and can sometimes be a great place to start when a lot is known generally but not specifically, but in this case I suspect this is already better studied. Can you provide some references that support your conclusions?

you are right to say that the post is based on introspection.  I wanted to post this hypothesis on this medium because there are a lot of scientists that have knowledge pertaining to this subject.  My research is not going to be as well founded as many of the people on here.  I don't have any references to what I have hypothesized but would like to know if there is a better explanation.  If you know anyone that has studied the subject extensively please make them aware of this post and let me know what they think.  The thought came to me and I wanted to share it with the universe.

Then post it as a question not an answer.

I have never heard a good explanation on why coconut water exists.  My explanation is simple and makes sense.  If you can reference a better explanation, please do so.


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E.O. Wilson on sociobiology and the origin of morality
Somewhere in E.O Wilson's writing, he discusses how human values are rooted in our nature as a specific kind of animal. He argues that we have an identifiable optimal living place -- a grove at the top of a hill, with surrounding grassland give an area of clear view, overlooking a body of water. He then goes on to further make this case by imagining that naked mole rats have risen to intelligence. He pens a speech that such a being might give on some patriotic holiday. And boy howdy, it sure does not sound like any epideictic speech you could imagine a human giving. The use of shit as a metaphor for sustenance alone is sufficiently jarring, but there were a bunch more, all firmly anchored in aspects of mole rat biology and social structure that differ from ours.
I would like to cite and quote this passage. I thought this was either in Biophilia or Consilience, but I have not been able to find it in either book, or in a bunch of other searches via google scholar, and through my own books and ebooks of his.
Does this sound familiar to anyone? Can you point me toward where I would find it?

@com.prehensible If andrewH could quote the section verbatim, I'm sure it would be easy for him to find the relevant text.
To andrewH: I have not actually read any of EO Wilson's work, although I'm familiar with it from secondary sources. Have you looked in 'Sociobiology: The New Synthesis' or 'On Human Nature'?

It could also be from 'The Biophilia Hypothesis.' But I don't know at all for sure.

If human values are rooted in our nature, why don't we all have the same values?

@Eff it would be good to state the source of the information and the logic of the metaphor, not confuse readers with garden-fence English: we can't hear the vocal tone of the theatrically phrased question, without confusion. Indian, Australian and 2nd language english people don't understand Boy Howdy and epideictic! most of us have to fetch a dictionary. E O Wilson doesn't start his written phrases with And! E O Wilson is kind and if you address him a written request, he will respond to you in writing through is secretary or by mail / email. My friend wrote to him and had a signed letter.

@com.prehensible That's fair. And I think it's a good idea to email EO Wilson.

1930's professors are happy with handwritten mail, they may be diligent with email, it's hit and miss.

I think its from "Genesis, the deep origin of societies"

@jamesqf Humans are a complicated mix of instinct and reflection.  Wilson isn't trying to claim that everything you think and believe is rooted solely in your evolutionary history.  What he states in this arena is actually rather non-controversial, that human values are founded on evolutionary contingencies that would differ if we had emerged via a different natural history.  Let's take, for example, a taboo against killing small children.  You could claim that certain societies do kill small children but they always have to justify the act, implying that this is something that naturally makes

@jamesqf Humans uncomfortable.  This would not necessarily be the case in a society of intelligent pelicans, who always lay more eggs than they support and kill at least one child from almost every litter.  Such a society might consider it natural to have a minimum age to be worthy of moral consideration, whereas we would find such a thing abhorrent.  While our beliefs and social structures are heavily culturally influenced, even those cultural influences are ultimately contingent on our biology.

@Jeremiah: "...whereas we would find such a thing abhorrent." But not all humans do, or have historically.  E.g. the classical practice of exposing unwanted infants, or Victorian foundling homes.  And at the other extreme, we have the "pro-life" types who want to push that minimum age to before birth, even to conception, and others who find that abhorrent.

@jamesqf the thing about that is that we are aware of these practice because of justifications put in writing by the cultures that did these things because they were aware of the need for justification. This is something that is a moral hazard for us at all points in history. Things that have no moral dimension need no justification. What we even decide to pay attention to in the first place is driven by evolutionary contingencies. Human birth rates and reproductive strategies prime us to raise the killing of offspring as a moral issue in the first place.

@Jeremiah: Granted, I'm not an expert in the writings of ancient cultures (or even of Victorian England), but I don't know of them because of attempts to justify them, but simply because they were mentioned in passing as ordinary aspects of the culture.  I could also, given room enough and time, cite many more examples of things considered moral by one group, highly immoral by another.  For a current example, consider marijuana use in the US today.

@jamesfq but it wasn’t just a normal and accepted part of these societies. In Ancient Greece and Rome the practice of infanticide was seen as evil and barbarous, which is why they did it through exposure, to allay their own guilt by “putting it in the hands of the gods”. The same reason was behind infanticide by exposure in the Christian Middle Ages. In Victorian England infanticide was an unfortunate consequence of support being torn away from poor women, forcing them to do what they had to to survive but women were put on trial for this and could only escape litigation by claiming insanity.

@Jeremiah: Nope, not in Genesis.


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qPCR: Accounting for different sample mass when interpreting and comparing Ct
I'm trying to use qPCR to quantify the amount of a specific bacteria species in patient sputum, but I don't really have the option to use consistent quantities of sputum to elute DNA from. The qPCR works fine, but once I have the Ct results, what is the best way to account for the fact that I'm using different masses of sputum?

Are you always using a specific amount of DNA from your samples (i.e. 10 ng) or a relative amount (i.e. 10% of yield from one sample)? This make an important difference in how you can/have to normalise your results.

Relative amount, like 10% of the yield from a sample. We expect human DNA and DNA from other bacteria to be in the sample, so diluting all samples to the same quantity of DNA may not be useful to us.

If you are always using a relativ amount of your input yield for each sample, then you'll need to correct your Ct values for the absolute DNA yield of each sample. If you can't measure the DNA yield of each sample, then you'll just have to assume it is directly dependent on the sputum input mass. This assumption is pretty faulty though, since direct DNA measurements are much more exact and are not affected by biases from DNA extraction efficiency differences or batch effects.
Since Ct values represent a single qPCR cycle in the linear phase in which the target DNA is doubled, you need to adjust the CT values by +1 for samples with half DNA input and by -1 for samples with double input (or generally $Ct_{adjusted} = Ct - log_2(inputfactor)$ ). Of course this method of normalising assumes that the relative content of your target DNA in the sample is independent of the total sample yield (which may or may not be true; if your specific bacteria species is proliferating a lot more in one patient compared to the other this might affect both relative and absolute DNA amounts).


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Where does the energy required to turn ADP into ATP come from?
My teacher states that in order to convert ADP into ATP, energy from respiration is required.
However, I watched a video which states that energy from the son is used to turn ADP into ATP.
Which is correct?

Both are technically correct, and both of these claims are happening in different organisms

This is a site for "biology researchers, academics, and students" where questions are expected to be accompanied by demonstration of one's own efforts to solve a problem. This is the sort of very basic question that is best addressed to your school teacher. @SonicSplasher  hinted at the answer, but you should flesh that out for yourself, and in future consider that two apparently different statements might both be correct in different contexts. So you will need to  ask yourself what contexts they were made in.

@SonicSplasher actually both can be true in the same organism...

@theforestecologist yup in the case of photorespiration

This is a common problem when asking about the explanations for things that happen in a biological context.  When you ask for why something happens in biology, the answer to that question depends on what, specifically, you want to know.  For example, the same question, "Why can humans see more colors than dogs?" can be answered using a physiological mechanism (Humans can see more colors than dogs because we have an additional cone type in our eyes), or an evolutionary explanation (Humans can see more colors than dogs because our ancestors were under selective pressure to be able to identify ripe fruit).  Both of these responses would be correct but they are answering from different perspectives.
The question of where the energy comes from to phosphorylate ADP is another one of these questions that can be answered in a couple of different ways.  The immediate mechanism for providing this energy is the proton gradient between the intermembrane space of the mitochondria and the mitochondrial matrix in the case of Cellular Respiration and the proton gradient between the Thylakoid Lumen and the Stroma in the case of Photosynthesis.  But where did the energy ultimately come from?  The sun.  In the case of Photosynthesis, it is energy from the sun that drives the photosystems that generate that proton gradient in the first place.  In the case of your own body, you either eat a plant or eat an animal that ate a plant that got its energy from the sun in the same way, and then use the chemical energy contained in that food to sustain your own proton gradient.  Either way, the energy ultimately came from the sun.  It's just that the proximate (immediate) explanation is a chemical one driven by a chemiosmotic gradient maintained either by sunlight and water in the case of photosynthesis or sugar and oxygen in the case of cellular respiration.


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Why doesn't HIV spread through vectors?
HIV spreads only through body fluids. If a mosquito bites an HIV infected individual and then an uninfected individual, will the virus spread  to the new individual?

This doesn't take much effort to answer!  Googling "HIV mosquito" brings us straight to this blog post, which gives three main reasons (along with more details, links to other resources, etc.):

Only saliva is injected into humans when a mosquito bites and thus HIV positive blood that a mosquito may have previously ingested is never transmitted to other humans.
Unlike mosquito borne diseases, HIV is unable to replicate within the mosquito's gut and therefore is broken down.
HIV circulates in human blood at a far lower level than would be necessary to create a new infection.


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Can organ-accumulated iron get shed again?
Hemochromatosis can lead to an accumulation of iron in some organs. If the accumulated amount is not too high, will it go down again upon correction of blood iron levels?

What research, if any, did you do to answer your own question? I believe this is very easy to answer with a quick search.

@anongoodnurse I did quite a bit of googling, and reading articles. I might not be using the right keywords.

Please cite an article on the treatment of  hemochromatosis which you read that didn't answer the question. Then I'd be happy to share what I know.

@anongoodnurse https://hemochromatosishelp.com/iron-overload/

I'm sorry to be so picky, but that is not a reputable source; it's a for profit blogsite that sells supplements. The Mayo clinic is reliable and easy to understand.

@anongoodnurse sure, there you go: https://www.mayoclinic.org/diseases-conditions/hemochromatosis/symptoms-causes/syc-20351443 (it still doesn't answer my question)

Did you read the second page? The answer is there.

@anongoodnurse It doesn't. Nowhere does it say specifically whether iron accumulated in organs gets eliminated. It only talks about outcomes (e.g. "Phlebotomy will not reverse cirrhosis", which of course it won't since cirrhosis is about tissue scarring). And to me, "reduce your iron levels to normal", sounds like blood levels, although it's unclear. Maybe some organs shed the excess iron much more slowly, just like they would with e.g. lead. This is my last reply to you, as your comments are starting to border on trolling. If you don't want to or can't answer, that's fine.


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Is this a type of fruit fly?
I live in Taipei, and these flying insects are about 2-4 millimeters long (body length). They are very active when it's over roughly 24C indoors, and will fly, land and run around randomly on interesting surfaces then fly again, all in one continuous motion.
Some have moved into my apartment again.
They are attracted to food, especially coffee grounds!, vinegar, bread, and dark, moist areas. I can use these attractants to catch them inside bottles or plastic bags, but can't ever seem to get the last one.
I see them fly around while mating end-to-end (twice as long as a single fly) and they often go right past my face while doing so as if to say "ha! there's more of us on the way!"
The heads seem smaller than in images of common fruit flies that I've seen.
Are these likely to be fruit flies, or something else? I don't need an exact species identification, I'd just like have some kind of classification to describe them with besides "little flies".
In this answer to a related but different question, it was proposed that they were something very different, but I don't think that's the case.

Photos: the best I cold do with my cell phone plus a magnifying lens.

Didn't the last answer say it was a baby cockroach

@SonicSplasher That was an answer to a question about pesticides, not a species identification question, so even though it was suggested, I'm pretty sure these are not baby cockroaches. See my comment there. I can't help it that that answer's formatting makes it look like it's answering a species id question.

Search for drosophila buzzati and drosophila buskcii and drosophila simulans

This has been recently bumped by community; I add this comment for closure. This is a six-legged (hexapod) two winged (dipteran) fly. It is a female drosophilid, and identifying the species and subspecies from such a photo is impossible; typically, correct identification requires careful morphological assessment using a microscope, by a specialist/insect taxonomist. I don't think this fly is shaped like a Drosophilia melanogaster member. It seems a bit too long. Source: personal daily experience with manipulating fruit flies on a CO2 pad.

@SPr Thanks for your comment! The "ultimate closure" in Stack Exchange is of course acceptance. If you'd consider writing up something along the lines of "...without the possibility of genetic analysis... correct identification requires careful morphological assessment using a microscope, by a specialist/insect taxonomist." I could probably accept it.

I can't pinpoint on the species name but a quick common fruit fly should give you a image which look very similar to the one in your photos.

these Bois are around 1/8 in inches long
-striated abdomen

Hope this is the one

I mentioned that, but: "The heads seem smaller than in images of common fruit flies that I've seen." Your guys have a big head with a tiny neck, my guys seem to have a "unibody"

The thing is baby roaches cannot fly and the ones you mentioned are flying so this is the most similar one I can come up with or maybe some sort of Taipei variant

Thanks, I didn't think they did, I'm glad to know for sure now. I really appreciate the confirmation on the "no fly" baby roaches.

What kind of insect is a Bois?

"bois" here was another word for boys and i used boys informally to you know call them that without addressing them with their scientific name