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What property of water explains how sweating helps the runner continue running?
My question I have to answer is: A runner picks up pace on a warm day and starts sweating profusely. What property of water explains how sweating helps the runner continue running?
The following are four options I have to choose from to answer this question, and below that is the uncertain answer I chose.
A. Since water molecules are polar, they adhere to the surface of the skin, which allows cooling. The skin’s outer layer of dead cells enables the adhesion.
B. At elevated body temperature, the hydrogen bonds in water break, which allows water to escape as vapor. This causes heat loss in the body, which lowers body temperature.
C. Hydrogen bonds rearrange at higher temperatures and form a lattice structure that requires energy. This energy use lowers the heat in the body.
D. Sweating is due to the high heat capacity of water. When sweating increases, heat is released and the body temperature is lowered.
I chose (B), as (A) and (C) do not make sense and that (D) I think requires too much amount of time since water has a high heat capacity. Sweating, especially during running, is more immediate than (D). Would (B) be the correct answer?

I think the answer will be B and D. B explains the process of evaporation and D explains why water is a good choice of a liquid to evaporate.

@Oosaka No, I understand the detailed explanation of how water evaporating leads to cooling. I didn't want a simple answer with no explanation, no. I suppose I was trying to ask why an answer such as A or D wouldn't work, because I feel these answers could have some merit unless I'm wrong. Finding only one correct answer choice was unclear. Do you think they have some merit, or is it definitely clear that B is correct?

@Roni Saiba: No, water is the only choice for a liquid to evaporate because there's a lot of it in humans (and other animals).  Other liquids, for instance alcohol, would actually provide better cooling since they evaporate at lower temperatures, but they don't exist in the body in significant quantities.

@jamesqf But wont same volume of water carry more heat after evaporation than alcohol because of higher heat capacity? I apologize for my shortcomings in understanding physics.

@RoniSaiba yes, water has a higher heat capacity than, say, ethanol. The point is that our bodies contain absolutely miniscule amounts of alcohols, but we are ~70% water, so the "choice" of which fluid to use for cooling is obvious.

@RoniSaiba: Also, even though water has a higher heat capacity, it cools less effectively than things like alcohol for two reasons.  First, it evaporates at a lower temperature, so it will carry away heat when water just forms beads of sweat.  Second, there's a lot of water in the environment, so in places with high humidity, it doesn't evaporate all that well.  Compare Miami to Phoenix, or a steam room to a sauna.

@Renée Thank you for clarifying. I agree with you that D sounds technically correct (as I said), and assuming the teacher sees it as incorrect for some reason, I am curious as to what that reason is. A strikes me as incorrect because the water adhering to the skin isn't useful, it is in fact its evaporation is what helps, and I don't know of dead cells helping with evaporative cooling at all. Maybe the idea is that water needs to be in contact with the skin to draw heat from the body as it evaporates, but how much does that play? IIRC skin is hydrophobic to begin with. So, seems clearly wrong.


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Determine similarity in percentages between species A and B, A and C, and B and C

The chart above is a graphic that shows the amino acid sequence differences between different organisms for a protein keratin.
The question I am required to answer begins as, "Keratin is made up of about 450 amino acids. Determine the similarity in percentages between species A and B, A and C, and B and C. Explain how amino acid sequences can be used in determining how closely related two species are."
My initial solution to finding the percentages is dividing the respective differences in the chart above by 450. Then, subtract that number by 100, and hence, find the similarity percentage. For example, for species A and B, I would divide 4 by 450, resulting in 0.89%. I would next subtract this percentage from 100%, resulting in 99.11% similarity. Is this the correct procedure?
My initial solution to explaining how amino acid sequences can be used to determine how closely related two species are is as follows: The larger the difference in amino acid sequences between two species, the less closely related two species are. Is this explanation correct as well?

Step number one is correct, but note that there are several similarity (or alternatively distance) measures. What you choose is the simplest and most intuitive one and it a good one without any other assumption or explanation given.
Step number two is also correct, if the similarity is a good proxy for when the last common ancestor between two species is in time, which in this case should be.

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Making sense of infinite-sites mutation but finite-sites recombination coalescent simulator
Hudson (1983) introduced a coalescent simulator with infinite-sites mutations and finite-sites recombination. This seems paradoxical because the documentation of the simulator (section on crossing over) states that "one should think of nsites as the number of base pairs in the locus."
To reconcile this tension, I've been thinking of the haplotype as comprising an infinite number of base pairs (to support infinite-site mutations) but that there are a finite number of initiation sites at which the sequence can cross over during meiosis (to support finite-site recombination). I.e. the sequence is "unbreakable" except at the initiation sites, and each segment between initiation sites still contains an infinite number of base pairs.
Is that a sensible interpretation or am I way off base?

I hope you get an answer to your question, although I suspect it will not be understood by many on this list (myself included). If you are unsuccessful, you might try SE Bioinformatics.

Thank you for the pointer! Will repost on SE Bioinformatics if this post doesn't prove fruitful.

The first sentence of the abstract of the Hudson paper states: "An infinite-site neutral allele model with crossing-over possible at any of an infinite number of sites is studied." (I don't have access to the full paper.) The documentation that you point to does say finite for recombination, FWIW. See also: https://en.wikipedia.org/wiki/Infinite_sites_model

Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.

@MaximilianPress, sorry, frustrating paywalls. They start with a finite-site crossing-over model but then take the limit to infinite sites. As you point out, the linked simulator sticks to the finite regime.

Caveat: never personally used ms, I might be missing a subtlety of how this model is intended to be used.
I think it's useful to see how Hudson himself writes about the utility of the infinite-sites model in the context of finite recombination. Recall, infinite sites is a simplifying assumption to make math easier. Tajima (1996) boils this down as follows:

...the infinite-site model proposed by Kimura (1969) assumes that the total number of sites in each gene is so large and the mutation rate per site is so small that whenever a mutant appears it occurs at a previously homoallelic site.

Thus, infinite sites just says (among other things) that any given mutation is at a new site where no new mutation has occurred previously. This is an assumption that is handy for doing population genetics, which Hudson employs. In one paper he (and a colleague) write:

HUDSON (1983b) has also developed an efficient method for simulating samples from the neutral infinite-site model with finite recombination. His method generates the "history" of a sample. The history of a sample is a collection of correlated family trees, one for each site (for DNA sequence data, each nucleotide is considered a site). The family tree for a site traces the genealogy of a site back to its most recent common ancestor indicating which sampled gametes are most closely related and when the most recent common ancestors occurred.

If the rate of recombination is zero, then each site has the same family tree and therefore the history of the sample consists of just one tree. The method for generating this tree depends on results of WATTERSON (1975) (for details see HUDSON 1983; TAJIMA 1983). On the other hand, if the recombination rate is infinite, then all of the family trees are independent of each other, and each family tree is generated in the same way as when the recombination rate is zero. If the recombination rate is finite, then the topologies and lengths of the branches of the Family trees are correlated because of linkage, and generating them is more complex but still possible (HUDSON 1983b).

In other words, infinite sites is an assumption that helps us study the behavior of recombination (which is, of course, finite). We could alternately consider models in which we make zero or infinite assumptions about recombination, to study the behavior of finite mutating sites.
Elsewhere in the documentation for ms, Hudson writes:

In this model, the number of sites between which recombination can
occur is finite and specified by the user (with the parameter nsites). Despite the finite number of sites between which recombination can occur, the mutation process is still assumed to occur according to the ”infinite-sites” model, in that no recurrent mutation occurs, and the positions of the mutations are specified on a continuous scale from zero to one, as in the no-recombination case.

So it seems that he is using the property of no recurrent mutations laid out by Tajima, but also the feature of assuming that coordinates of the region of interest are continuous rather than discrete. One can imagine that this is convenient to make computation simple.
I think that the mental model that you've laid out is not bad in terms of an intuition about behavior, but to emphasize the main properties that I think are useful, one might say that 1) every mutation/allele is in a different (continuous) coordinate (no recurrent mutation), and 2) the number of possible recombination sites is discrete (nsites). So there are nsites recombining regions, each without recurrent mutation (and possibly infinite continuous sites, though I don't see how this is actually implemented so it may simply be that each of a finite set of sites doesn't recurrently mutate).

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Habitat requirements of black ant Lasius niger
Does anyone know of any published information on the maximum slope angle and/or minimum soil depth on which the black ant Lasius niger will build its nests? I have read that they won't nest on "a slope that is too steep", but what does this constitute in numerical terms?


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What is the average age of my flesh and my bone?
A study reported in the New York Times on August 2, 2005, claims that the average age of all cells in a middle age human is 7-10 years. This was based on new techniques at the time that allowed for very precise measurements of carbon-14 in human DNA.
My question is partly regarding whether or not this claim has been confirmed, changed or improved upon in the 12-odd years since the original study.
Mainly however, my question is simply: What is the average age of the flesh, bone and body as a whole of a middle-aged human?

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Do plants take in the same amount of CO2 as they release?
There are many claims in the media that trees remove more carbon dioxide form the atmosphere than they release back into the atmosphere. By what chemical pathway can this occur?
The law that matter is neither created nor destroyed surely applies as shown by the chemical pathway in the photosynthesis and respiration process.
6CO2 + 6H2O + sunlight energy.  -----> C6H12O6 + 6O2
C6H12O6 + 6O2.                  -----> 6H2O + ATP (energy) + 6CO2
Thus the SAME amount of 6CO2 taken in is released, in order for the plant to have formation of the ATP usable energy for plant tissue creation, so photosynthesis cannot happen at a  more rapid rate than respiration. If that happened, then yes, more CO2 is removed then released, but that would leave an unbalanced equation.
I am not arguing the story further down the road of tree tissue and carbon sequestration/storage.

The road to hell is paved with chemical equations.

Alan, check if there is some scientific research which proves that coal actually exists and comes from plants.

Doesn't an oak tree have more mass than an acorn?  Where did that mass come from?

You've made one faulty assumption: that the second reaction is occuring at the same rate as the first.  In fact, plants only burn enough glucose to fuel their activities. Much of the formed glucose is converted into storage forms like cellulose and starch.  In fact, the vast majority of a plant's carbon mass comes ultimately from CO2 which has been converted photosynthetically into carbohydrate forms. (Further reading)
Ultimately, when plants die, those carbon molecules are used as food for other species, such as animal and bacteria.  Ultimately, whether in composted plant material or fecal mater, the carbon is deposited on the ground.  So ultimately it is correct that trees & plants are removing CO2 permanently from the atmosphere.  Although some is being released to the atmosphere catabolically, more is re-absorbed for anabolic processes, and ultimately, that CO2 gets deposited on the ground in more complex carbon forms.

The amount of carbon stored in plants can be measured by carbon mass in it's dry weight. Trees are known for carbon sequestration ability, because they're long-lived, improve local microclimate and water retention and provide a habitat for many species. There are many positive consequences of having more trees, but soil is a much more efficient biological vehicle for carbon sequestration (still trees required).


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Base-stacking interactions versus hydrogen bonds
Is it correct that the hyperchromic shift in DNA is a result of the disruption of the base-pairing hydrogen bonds, but the actual denaturation of dsDNA has more to do with the base-stacking interactions? Why does separating the strands have any effect on the stacking of the bases? Why wouldn't the bases in ssDNA still experience stacking interactions?
I really appreciate any help with this. Thanks!

Related: https://biology.stackexchange.com/questions/89614/why-does-absorption-at-260nm-of-ssdna-increase-with-temperature

For a direct reference on the contribution of these two forces see here.
If it helps, think of the double helix of dsDNA as a more rigid structure than ssDNA, which flops around and generally is capable of a lot of steric freedom that dsDNA doesn't have. This freedom means that the bases of the ssDNA backbone may not always be in the correct orientation for stacking, because the two strands of the helix aren't forcing the bases together into that orientation. "Usually the DNA double helix is considered to be a relatively rigid structure. Certainly it is much more rigid than its component single strands." (see the review for a much more detailed discussion of this issue)
It's true that base stacking still occurs in ssDNA, it's just not enforced in the same way. It also appears to be somewhat sequence-specific, occurring more in polypurines than polypyrimidines, possibly because purines are bulkier molecules with more steric hindrance.
For a related conversation see here.


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Tiny worms found inside my house
I noticed spider cob hanging of my light bulb. That spider web was full of moving creatures. I quickly removed them and threw in the big. Wanted to find out what could that possibly be. I opened up light bulb and no traces to the ceiling. I found hundreds of them fallen on the floor, some where still moving. I do not have a good quality picture, but I have taken a video of it. Would anyone be able to identify? I live in Australia QLD, i think this could have been seeded by some fly?


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4DGenome or another comprehensive database of chromatin interactions
I'm searching for the most comprehensive source of chromatin interactions to support enhancer targets (data such like Hi-C, ChIA-PET, IM-PET, 5C, 4C, 3C, etc.) and my question according that could be split into two following parts:

On page http://epigenie.com/epigenetic-tools-and-databases/ I've found out links to two databases, but the reference to 4D Genome doesn't work. Does anybody know whether this database
http://4dgenome.int-med.uiowa.edu was moved somewhere else or maybe its only internally available for U Iowa community? (I'm asking about probably exclusive access, because on Tan's lab page http://www.healthcare.uiowa.edu/labs/tan/software.html only the 4DGenome has the trailing part of the link int-med.uiowa.edu (presumably this int-med strands for internal/general medicine or maybe in the sense of internal/intranet access), whereas all other services like IM-PET has its link starting with http://www.healthcare.uiowa.edu/labs/tan/.
Maybe you know even better database for chromatin interactions covering as much as possible cell lines/tissue types for GRCh38 assembly or any other whose coordinates could be easily converted, e.g. by liftOver? I need data only for human and mouse, but I would be grateful also for solely human data.

Thank you in advance for your answer.

All the sequencing data can be found in SRA. You just have to use the keyword to get the data. However, these would be raw data. This seems to be another database on long range chromatin interactions.

This problem has been finally solved with help from prof. Kai Tan.
It occurred that his lab has been moved from University of Iowa to Children's Hopspital of Philadelphia, so has been this service.
Now, the working link is:
http://4dgenome.research.chop.edu

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What is the difference between myoblasts, myotubes and myocytes
I am struggling to grasp the difference between myoblasts, myotubes and myocytes.
If I am right, myoblasts are mononucleated and differentiate into myotubes which are muscle fibers.
Are myocytes the mature muscle cell? I can't find a good definition for this.
Thank you for your help!

Please share what prior research you've done here?

On request I'm providing helpful explanation of the picture i have added for those who are new in learning
Myoblasts - focus on 'blast' which means related to early stage of cell which has not yet differentiated such cells are also called stem cells, once differentiated their fate is decided very much what they are going to be.
Myocyte - [cyte:cell] they are already differentiated, hence are fully specific about themselves what constituent they are going to become.
Myotubes - myocytes condense as a mass, also besides that they undergo elongation as well, which ultimately results into formation of bundle like structure. Now at this stage idea of a singular cell is lost, we can't pick up a part of it and say this is one cell.
May myotubes coalese and form few myofibril (imagine 1000 myotubes make 100 myofibril)
And bundle of 100 myofibril makes one myofibre/muscle fibre which has sneath covering called sarcolemma. Many such muscle fibres together (with the help of endomysium as connective tissue/glue) make muscle fascia which in turn with the help of perimysium(connective tissue/glue) and covering called epimysium makes up Muscle.

Source:
https://www.researchgate.net/publication/347023906_Effects_of_External_Stimulators_on_Engineered_Skeletal_Muscle_Tissue_Maturation
Mueller, Claudia & Trujillo Miranda, Mairon & Maier, Michael & Heath, Daniel & O'Connor, Andrea & Salehi-Müller, Sahar. (2020). Effects of External Stimulators on Engineered Skeletal Muscle Tissue Maturation. Advanced Materials Interfaces. 8. 2001167. 10.1002/admi.202001167.


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How to separate two plasmids from E coli with the same backbone?
I'm using transformation-associated recombination (TAR) in yeast to capture a biosynthetic gene cluster (32 kb) by transforming gDNA and a capture vector (11 kb) with homology arms. I identified a region-positive clone and moved the plasmid into E. coli. I did a midiprep and ran the plasmid extract on a DNA gel with the empty capture vector (no insert, 11 kb).
By size comparison, the midiprep extract appears to contain the empty capture vector, and there are some more faint bands near the top of the ladder at 15 and 20 kb. However, when I run a PCR on the plasmid DNA to screen for a 500 bp region in the middle of the biosynthetic operon, I get a clear band, which suggests I also have my plasmid of interest, since that DNA does not exist in E coli. I made sure the primers were orthogonal to the E. coli genome (a common source of contamination in plasmid extracts).
I guess where I'm stuck is how would I separate these seemingly cotransformed plasmids out from the E coli? I was thinking of doing a gel extraction of the higher MW band on the gel, but our kit caps the size limit at 23 kb, and my plasmid of interest is 44 kb... Any suggestions or advice would be appreciated.
I'm also thinking of transforming a very small amount of my midiprep extract and hoping that single colonies will have only picked up on plasmid. The issue is that they both have the exact same backbone, and I presume the smaller plasmid will replicate much faster than the plasmid of interest, but I'm not certain.

Do you have any selection marker available for your engineered plasmid?

The empty capture vector has both SpecR and AmpR, which also means the engineered plasmid has the exact same selection markers. The only difference between the capture vector and the recombinant plasmid is the gDNA insertion, which is just an operon, not other things are inserted.

I'd recommend trying for the single-colony screening. It should be pretty fast: transform into cells and plate today, colony PCR tomorrow. I think the fitness cost of the big plasmid shouldn't be too high to show up on a plate. Give it a shot and let us know how it goes!

There's a couple of options here - it could be that your plasmid extract isn't very pure, so some genomic DNA has come over and the ROI is in that. The PCR would detect this even if you don't have any captured DNA in the plasmid giving you a false positive.
You are also using two very large bits of DNA there. 32 Kb is a massive fragment to try to clone into a plasmid, most people would try to take it out in chunks of a few Kb at a time and then reconstruct. In my experience the general rule is that the insert should be about the same size or smaller than the plasmid. It's not a hard and fast rule, you can definitely do it the other way around, but it tends to be more challenging for some reason. A YAC (yeast artificial chromosome) or similar might be a better option to capture the full length.
A classic gel extraction should work. This is not a kit extraction, but rather done by eluting the DNA in the gel into solution and then performing precipitation on the DNA. However, for this to work you need quite a lot of DNA as the efficiency of the extraction is very low; usually much less than 10%, more in the 1-2% range.
Basically the protocol is to get the liquid containing DNA out of the gel chunk. I used to do this (>20 years ago) with a 0.5 ml tube - poke a small hole through the bottom with a heated paperclip and add your gel chunk. Place 0.5 ml tube with gel inside a 1.5 ml eppendorf tube and spin the hell out of it in a higher speed microcentrifuge - you need one that goes above about 20K RCF. You may need to place a small piece of filter paper in the hole to prevent the gel getting squeezed through if it is a low percentage gel. Collect any liquid that ends up in the bottom of the 1.5 ml tube and precipitate. There are also less DIY protocols at Current Protocols in Molecular Biology, I can vouch for the NA-45 paper one as working very well, but these still require some refinement of technique and things you are unlikely to have.
You might be better off just amplifying your whole fragment of interest from your extraction and then re-inserting it into a plasmid of your choice. This allows you to choose which plasmid to put it into and gives you some control over the method of insertion. This is easily achievable with a high fidelity polymerase such as Phusion, Q5, or LA polymerases.


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What is the optimal method to resuspend competent cells during wash steps?
I've recently moved on to making my own competent cells instead of buying commercially. I'm currently making electrocompetent cells. I was taught to swirl the pellets (in 500 mL conical tubes) in the ice buckets to resuspend, but they don't seem to resuspend very well. How important is the exact method of resuspension? Would a serological pipette resuspension be too harsh? I know vortexing would be an no-go, so I'm stuck between those two methods.
Thanks!

Electrocompetent cells are a bit more finicky than chemically competent in this respect.
Generally you do need to be gentle during the preparation - swirling is fine, but vortexing is not. Too vigorous a resuspension results in foaming of the medium and damage to the cells, which results in lower competency. However, in my experience, resuspension with a pipette is fine, so long as you don't cause a lot of bubbling in the solution. For small volumes a Pasteur pipette with a rubber bulb works well for this, or a pipettor set on about 50% for bigger volumes.
How much competency you lose by being too vigorous is up for debate, but in my experience you might lose about a log10 by being too rough. For competencies over about 107, I don't find that this is too big an issue, but it does depend on what you are trying to do (e.g. BAC vs plasmid) and the size of the DNA you are trying to add. The larger the DNA, the harder it is to transform the bacteria and the higher you need your competency to be.

I am trying to transform 30-50 kb constructs from yeast into E. coli. Yeast minipreps are notoriously low-yielding (low copy number construct), so I do need particularly high competency to overcome the limitations of the yeast minipreps. Thank you for your insights.

@OmarAntonioOcegueda check the protocols at Openwetware under Escherichia coli, particularly the Knight lab ones. Also have a look at Current Protocols in Molecular Biology - they usually have a section on considerations and background that is quite helpful in understanding the critical steps.

Thank you for the protoccol resources. I appreciate it. I haven't heard of openwetware before. I just found recipes for the Qiagen buffers which is neat lol


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Entry of particulate pollutants into the nasal cavity
NCERT Chemistry of Grade XII (India) writes

Particulate pollutants bigger than 5 microns are likely to lodge into the nasal passage, whereas particles about 10 microns enter the lungs easily.

I'm primarily a Mathematics student, and my experience in Biology has been fairly limited to high school Biology, so excuse any factual errors that I make during my argument.
From what I know of the respiratory system, the trachea divides further and further getting narrower (into Bronchi, Bronchioles), so how does this happen that particles smaller are getting lodged into the nasal passage, whereas larger particles are getting into the lungs? Shouldn't it have been the other way around?

Welcome to Biology.SE. This is not simply an answer site, but instead a site that promotes self-learning with some expert help. Consequently, questions that show little or no prior research effort are off-topic on this site as are "homework" questions unless you have shown your attempt at an answer. Please [edit] your question and tell us where you've looked for answers, what you do know about the topic, and where exactly you still have questions. Please take the [tour] and consult the [help] starting with [ask] for details.

Yes indeed, your quote has things backwards. Here is an image and a link to further information:
ref

If you follow the dotted line with your eyes - - - - - through the 1Micron grading... On the right side, the majority is absorbed by the head. On the left side, it's mostly the lungs.

other references


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Portal hypertension
"Portal hypertension is more frequent and manifests in more complex ways in chronic liver failure than in acute liver failure (Fig. 14.7). It stems from increased vascular resistance coupled with increased portal blood flow. The increased resistance to portal flow is at the level of the sinusoids and is caused by contraction of vascular smooth muscle cells and myofibroblasts, and disruption of blood flow by scarring and the formation of parenchymal nodules. Increase in portal venous blood flow is due to arterial vasodilation. The increased splanchnic arterial blood flow in turn leads to increased venous efflux into the portal venous system." Robbins & Kumar Basic Pathology.
In liver cirrhosis, the blood neither from the hepatic artery nor from the portal vein are able to enter the liver normally, hence blood backs up in both, right? With the following: "Increase in portal venous blood flow is due to arterial vasodilation", how does the arterial vasodilation cause an increase in portal venous blood flow? Which arteries is it talking about? If for example the hepatic arteries are in vasodilation, more blood fits them hence less blood would go into the portal venous system, so how would there be an increase in the portal venous blood flow? Am I simply missing the picture of the circulatory system around the liver?
Moreover, with "The increased splanchnic arterial blood flow in turn leads to increased venous efflux into the portal venous system", why did the splanchnic arterial blood flow increase? Venous efflux from where and why into the portal venous system?
Many thanks for any help!

Splanchnic refers to all the abdominal cavity organs, not just the liver.
The portal vein system carries blood from these organs to the liver instead of directly back to the heart. The more blood flows to these organs, the more goes through the portal system. Vasodilation increases blood flow because there is less resistance when the vessels are wider.
This is all a compensatory mechanism gone a bit wild; there's not enough flow through the portal system. Normally, arterial tone sets flow, so normally if there's not enough flow it's because the arteries need to relax. As they relax it does increase flow, but because it isn't actually the arteries that are the problem (the problem is the pathology in the liver) there is even more hypertension in the portal system.
Remember, too, that veins are low-pressure vessels. Hypertension in the veins is a problem at much lower pressures than normal pressure in the arteries.

thanks so much for your answer! What causes the relaxation of the arteries? Something released by the cirrhotic liver? And which arteries are in question?

@DritaRaci The splanchnic arterioles: small vessels throughout the organs of the gut. I don't know what specific vasodilators cause the relaxation, I don't think it's any one specific molecule; it's not from the liver directly it's part of the compensation for reduced blood flow.

You want to take a whole-systems approach here. When blood isn't flowing well through the liver, that affects blood flow everywhere upstream too. The total flow in a cross-section through the vasculature is equal. So if you aren't getting flow through the portal system, you're also not getting flow through the veins feeding it, through the capillaries in the other organs that the portal flow comes from, through the arterioles that feed them, etc. This creates local signals that say "hey, I'm not getting enough oxygen/blood" and that makes the arterioles dilate to let more flow in.

Same thing that happens when, say, muscles are active and using more oxygen.


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light hitting the center of the retinal receptive field
In my teachers slides, it says "light hitting the center of the retinal receptive field can either increase or decrease the number of impulses fired"
Is this "or" because it depends on whether the light hits a photoreceptor connected to an on or an off bipolar cell? So does that mean when light hits a certain place, it hits only one photoreceptor? How are these two types of bipolar cells arranged? I thought that if some light hits the center, there is an equal number of on and off bipolar cells.

Your teacher's slides should include which cell in the retina they are talking about. If they don't, the slides are very incomplete.

They do not. But what do you mean? What cell are you thinking of and why would that make a difference? Thanks!

Because there's no such thing as a "retinal receptive field". The retina doesn't have a receptive field any more than a school has a kidney. There are neurons in the retina, though; those have receptive fields. But there are a lot of different kinds of neurons in the retina. The statement would not be true if, for example, you applied it to a rod or cone photoreceptor cell.


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Next Generation Sequencing False Negative
In Variant Detection, RNA-sequencing, and ChIP-sequencing, we showed how we matching, or aligning, short NGS reads to the genome, and then make inference using the reads which aggregate or "pile up" at a given region: either to find a SNP, to quantify the amount of mRNA, or the quantify the amount of a protein which is bound to DNA. Define a "true positive" as detecting a SNP, detecting mRNA expression, or detecting a protein which is bound to DNA. Which of the following (you can pick more than one) could possibly lead to a false negative, e.g. we do not detect a true SNP, mRNA expression, or a bound protein at a location/region?
which one is the correct answer? why? (we can pick more than one)
1.The region we care about is not in the reference genome
2.The region we care about occurs 1000s of times in the genome, and we are ignoring reads which align to so many places
3.For the region we care about, the organism's genome is so different to the reference genome that the aligning program can't find a match
4.There are never false positives

Homework questions are received well when the asker shows an attempt to answer and explains their confusion.  Which answer(s) do you think is (are) correct, and why?

I think that the second and third ones are correct. because when the region occurs 1000s of times, the amount of aligning reads to each part results in decreasing numbers of possible aligning reads to only one specific region. and in addition, when the organism's genome is so different from the reference genome it could lead to a false conclusion of the alignments of the reads. I am not sure what is the difference between the first and third options!!? could you please help me with that? if my answers are incorrect ?

An example of 1) might be if you were looking for a mutation on the Y chromosome, but your reference sequence had only autosomes.
Read #2 a bit more carefully.  If there is a region repeated 1000 times in the genome, a lot of aligners are just throwing those reads away, on the grounds that you can't learn anything useful from them, and they will uselessly bloat the output files.  Diluting the coverage by splitting the read coverage will happen with some aligners if there are just a few places for the read to go, but not 1000.
Edit.  Let me try and make a better example.
You have a sample of an antibiotic resistant strain of some nasty bacteria.  This bacteria has some genes located on a plasmid.  Some other lab sequenced this bacteria and its plasmid; that's your reference.
You align your reads to your reference strain of bacteria, but oops, you accidently omitted the plasmid.  So your variant caller spotted no differences located in the plasmid.  If you were hasty and didn't check to see read coverage on the plasmid, you might assume that your sample's plasmid matched the reference, but you accidently didn't check that.
Next you get another antibiotic resistant sample.  You align it to your reference, and see no variants.  Okay, then, that's that...except that the reason you see no variants is because the people who gave you the sample misclassified it; it's really a different sub-species, and some regions of your reference are too different from your sample for the reads to align.
In general, you just have to remember that if your variant caller says there's no variant somewhere...that could also means there are no reads there.  In real life, people will do some QC on the read alignments stats to try and catch that.

so in your opinion, the first and the second one are the correct answers?

would you please explain about the third one? I cannot recognize the difference between this and the first one.

The first three choices can and do occur in genomics. For examples of each: genomes of cancerous cells involve translocations, which can create regions of the genome which do not occur in the reference genome. There are regions which occur 1000s of times in a genome, called transposons. Many software pipelines discard reads which map to many locations, and then true biology (e.g. a bound protein) which can occur at those regions is ignored. Also, in sequencing RNA or DNA from cancer cells, there can be so many mutations that the aligning programs have difficulty finding the match in the reference genome. Or, this can happen if we align reads from one species to the genome of another species (which does not yet have a reference genome constructed).


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Advice on type of database and software for research on genetic diversity of crops
for a research project I am evaluating the potential of Robusta coffee genetic resources in the tropic region of Africa. Different ex-situ genetic lines will be mapped as well as chemical, morphological and organoleptic analysis of the coffee beans.
I am looking for a type of database and software that would be well suited for this type of dataset. Are there any genetic database programs out there that allow you to merge other datasets (like plant descriptors or cupping profiles)? Or should I look the other way around and use a database that easily links with genetic fingerprint software?
Thank you,
Robrecht

This question is more likely to be considered on-topic in SE Bioinformatics as it seems mainly about the choice of software. I suggest deleting and reposting, but in your repost you should specify what you think a database program is — i.e. what data you wish to store and what processing of the data you are hoping external programs to do. Your computation skills will also be of relevance. You need to be more concrete.

ok thank you David, I will do that.

I don't know whether this is relevant for you, but I see here an example of tropical crops database that says it is made using the generalist mySQL system: https://tropgenedb.cirad.fr/tropgene/JSP/presentation.jsp

Also, much coffee research is published in Portuguese

Thank you for the advice.


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In this aquponic tank, what are these three plants and could they be killing my beta fish?
I have a small aquaponic fish tank. In the tank there are two unknown types of water plants from a local pet store and the top there are three air plants from a local garden center. This tank was setup ~2 months ago and at this point tests low for ammonia, nitrate, and nitrite it also is within limits (as set by the aquarium water test strips) for PH (~7.9), hardness, and alkalinity. As far as I understand it, the nitrogen cycle and bacteria bed of this tank is alive and well. Both the water and air plants grow voraciously.

Here are the plants themselves along with their root systems. The best I remember the left was labeled as "Decorative Pepper (Hot)" and after eating one the first day I can confirm they are extremely spicy.

The second day after setting up this tank I added a single male beta to the tank. Provided it is a hardy air breathing fish I assumed it would do well while the bacteria bed setup. Though, after ~1 week the fish had died. I assumed it (Bubble Bob) was just a sickly fish from the local pet store. I wanted a few more weeks just to ensure the bacteria bed had set up and recently added another beta (Beta Bernie). I bought Bernie from a local tropical fish store and made sure to select the most lively one I could find. I assume this store takes much better care of their fish than the local big chain pet store.
A day after adding Bernie to this tank he became very sluggish and layed on the bottom, only moving to get air, not wanting to feed. This went one for a second day. Two days ago I got a small cut, added some tap water (the same water used to fill the tank), some dechlorinator, and put Bernie in it and floated the cup in the tank (which is heated). After a day Bernie popped back to life.

From this (same water, only difference being the plants) my assumption is that one of the air plants I purchased is potentially poisoning my betas. Can you identify these three air plants? Are there any species of air plants which are known to release chemicals that hurt fish?

Consider posting this to https://pets.stackexchange.com/

I went back and fourth between here and pets. I figured if anything I could identify the plants here. Then ask pets if the types of plants are known to hurt fish.

this is a good fit over at pets but you will need to give a lot more information about your water and tank setup.like the results of your last water test, PH-AMMONIA-NITRITE.i will need information about how long you cycled your tank before adding fish.if anybody here can identify the plants you have it will help diagnose your problem.a better plant to use in your filter is watercress it is one of the best plants for removal of exess nutrients and it is eddible.

you say in your question"The second day after setting up this tank"does this mean you did not cycle the tank at all? please take a look here https://www.fishlore.com/NitrogenCycle.htm

If I'm right, the middle plant looks like some kind of croton plant. Every part of a croton is poisonous, including the roots. Capsaicin (from pepper) is a strong topical irritant, but I have no clue how much is released by the roots. If it is, I don't doubt it could kill a fish. The remaining plant is a begonia, which is (iirc) edible and pretty tasty, but does contain oxalic acid in flowers and stem. Don't know about roots. So, you have two definitely suspicious plants and a maybe. Not good.


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Bilirubin metabolism and UGT1A1 inhibition in human vs. monkey?
In human UGT1A1 seems to be the only relevant enzyme to glucuronidate unconjugated bilirubin into excreted forms. Is the pathway the same for e.g. the Cynomolgus monkey (Macaca fascicularis) in vivo? In case UGT1A1 is potently inhibited are there any other potential enzyme to metabolise/glucuronidate unconjugated bilirubin in monkey? Furthermore, bilirubin is analytically challenging in UGT1A1 inhibition studies in vitro. Estradiol (3-glucuronidation) has been used as a specific substrate for human UGT1A1. Do you know any substrates known to be specific for monkey UGT1A1?  Any reference would be highly appreciated.

UGT1A1 is common among most mammals that produce bilirubin (rats too). I haven't seen any evidence to suggest an alternate pathway in mammals of bilirubin metabolism. Look into gilbert's syndrome patients (they have a SNP which is a mutuation that causes UGT1A1 to be less efficient and thus a rise in plasma unconjugated bilirubin).
Also, bilirubin analysis from plasma/tissues is fairly straight forward with HPLC or LCMS assays. UGT1A1 inhibition in vitro however, is still a challenge. I think the trick will be to use CRISPR to knock it out.

It would be great if you could add some references.


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Bilirubin metabolism pathway in non-human primates (NHP)?
In human UGT1A1 seems to be the only relevant enzyme to glucuronidate unconjugated bilirubin into excreted forms. Is the pathway the same for e.g. the Cynomolgus monkey (Macaca fascicularis) in vivo? In case UGT1A1 is potently inhibited are there any other potential enzyme to glucuronidate/metabolise unconjugated bilirubin in NHP? Any reference would be highly appreciated.


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How to identify a coiled coil from the amino acid sequence?
I was wondering, when we have an amino acid sequence, is it enough to check whether the positions a-d correspond to hydrophobic amino acids in order to say whether it can form a coiled coil structure? Or would we need to make sure the other positions are not hydrophobic too?
All help greatly appreciated.

The heptad repeat, denoted [abcdefg]n, typically has hydrophobic residues at a and d, and polar/charged residues at e and g.

From here.
There is a prediction tool with useful images here.


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How is ligand binding modeled?
I have the following exercise to solve:

To be honest, for both parts, my only idea so far would be to divide the rate expression by the sphere area and multiply by the new available areas (that of a circle for part a and that of many circles for part b). But if I do this, I will have an "a" parameter always, which makes no sense because it is representative only of the sphere.
Any ideas on how to approach this?
All help is greatly appreciated.

Consider expressing that rate in terms of surface area. For the sphere presented, adsorption rate = surface area * (DL) /a. Then extrapolate to the 2d systems.

don't use the perfect square model. You will keep getting Pi but it's not a real life formulae only used for theory. Try to use a Cartesian graph but three dimensions to take into account curve flexibility. Integral calculus is similar too or better.


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Finding protein motifs by running sequence analysis in protein BLAST
I've run the following sequence (bottom of page) in NCBI protein BLAST and its been identified as Zn-dependent alcohol dehydrogenase. Next I want to see what protein motifs are in this protein. Where in the programme is it possible to see the motifs?
Thanks in advance!
Sequence:
MDRNRLAIVFPIFARCISAADFSTDLYLSEIYQQKVVTMKAAVITKDHTIDVKDTKLRPLNYGEALLEIE
YCGVCHTDLHVKNGDFGDETGRISGHEGIGIVKQDGEGVTSLNAGDRASVAWFFKGCGHCEYCVSGNETL
CRNVENAGYTVDGAIAEECIVVAEYSVRVPDGLDPAVASRITCAGVTTYKAVKVSQLQPGQWLAIYGYGR
FRQSSPSICQDMYFNAKDEQLAYYAKELGGADMVINPKNEAAKIIQEKLGGAHATVVTAVAKSAFNSAVE
AIRAGGRVVVVVAVGLPPPEKMDLSIPPRLVLVGIEVLGSLVGTREKEAFQFAAEGKVKPKVTKRKVEEI
NQIFDEMEHGKFTGRMILPTHHIWIVIGWQSFSLYSQDVSQPQIFRLTSISPRYINKRSPKQPSLLKIIR
STKTPNYALITGKRFWKSNIAGYVIPISMKTGISAMKPAEFQGMKVVSSSRTGKGLLLMPVTAPVLHGSS
KAAAIANIVSAGMKRFAATLKMPVIRLTALQKNASSSPNTRSACQMVLILRLPAGSLARVPPIKQRFLSY
SPDNGWPSMATGGLGNLALRYAKTCISTPKMNSSHTTPKSWAAQIWSSIRKTKLPKSFRKSSGEHTRRWR
LLPNPPLTRLLRLSARVAVLLLLSPLVCLLLKKWIAFLLVWCLSVSKSVPWSERGKRRPSSLQPKVRSSR
KLPSVKSKKSTKSLTKWNMVNSQAVYYQPITYGSSAGNRFPYIRKMYLSRRFFDPLSLRDISTKGSHHES
SRHYRSYDRRERHQITPSELRGSASGNRILRGMSYRSPCEKRGFRRNRQNFRARYRYRQAGRGRGYFSEC
RPRQCCMVLQRLRPLRILCQRENALPQRKCRLYGRRYSRRMHRRRRILGPRARWSSCGCQQDHLRGCNHL
SSKGFSATARTMAGHLWLRAVAIPFDMETPRHVFQRQRTARILRQRVGRRRYGHQSEKRSCQNHSGKARG
STRDGGDGCCQIRLLGCGYPRGWPCCCCCRRWSASSKNGFEHSSSFGACRYRSPRFLGRNAGKGGLPVCS
RRGQAESYQASRRNQPNLRNGTWIHRPYDITNPSHILYVMGWYHTACEFTMFHFVKDLVDFFDFTLGNFR
LDLTFGCKLEGLLFPRSDQGTDFDTDKHQTRRNAQIHFFRRRQTNGDNNNNTATRADSLNSRVKGGFGNS
RHHRRVCSPELFLNDFGSFVFRIDDHICAAQLFGVVCELFIFGVEIHVLAYRRARLPKPPVAIDGQPLSG
LLRNLYCFIGGYTRASDPAGNRRIKTIWHADRVFGDDDAFFCYSAVNRITGIFNVAAKRFIPADTIFAMA
AAFEEPCNTGAVTGIQRSNPFPVLLDDTYTFMPNSAGFIAEIPVFHMEIGMTYPAIFDFQKRFPVIQRAF
GVFHVDRMIFSNDGCFHGDYLLLIYLGEIEVSRKICGDTSCEYRENDCQPITIHYMWVGNIIRPVNLPCS
ISSKIWLISSTLRLVTFGLTLPSAANWKASFSRVPTKEPRTSIPTSTKRGGMLKSIFSGGGRPTATTTTT
RPPARIASTAELKADLATAVTTVACAPPSFSMILAASFFGLMTISAPPNSLAYASCSSLALKYMSWHIEG
LDCLNRPPMASHCPGCSETFTALVVTPAQVILLATAGSRPSGTRTEYSATTMHSSAIAPSTVPAFSTLRQ
SVSFPLTQYSQWPQPLKNHATLARSPAFREVTPSPSCLTIPIPSCPEILPVSSPKSPFFTWRSVHTPQYS
ISRSASPFRGRNLVSFTSIVSLVMTAAFMVTTFCYISERRSVEKSAAEIHLANIGKTIASRLRSICDGLV
ISYGLIYHVPFRQRFGFLRLYAWLSAPYLRLQTGRPPFPAFRPRNLGLRYRQAPNEEECSNPFFQEEADQ
RRQQQQHGHPRGPQQPSRRIWQQPSPPSRVLPRAFPEFWQLRFSDPYLRRPTLWRSMRAVHLWRNTCLGI
SKGIATARSHRWPAIVRAVAEKPLLLYRWLHPRKSCWQPQDQDHLARGPSIRRRRCILLLRRQPYNRHFQ
RCGKAFHSRHNIRNGRSLRTMQHWRGHRHSEKPLPRPARYLYLHALKFCRFHRRNPRFSHGDRYDIPRNI
RFPEALPRNSEGVIWCLSRRSYDLRLLSWLPFVDISRRDRGQSKNLRLRYILRIGKRLPADYDP

MOTIF search
First of all this is not possbile in BLAST (at least nog direclty).
There are a lot of tools to search for motifs in your sequence. I think a good way to start is to use MOTIF search. This searches for motifs in your sequence based on infomration in: Pfam, NCBI-CDD, PROSTIE PATTERN and PROSITE PROFILE (you can select which of these you want to use). Further you can also use INTERPRO (which also searches through serveral database, note that INTERPO searching can take a while but will give a nice graphical view). If you want to find new motifs you can use MEME (as suggest by @mxwsn). However to do this you have to find (or have) a set of sequences which resemble your seqence to find motifs. Because off course the algorithm is not able to find motifs in one sequence because it needs to compare a set of sequences to find some frequently occuring motifs, which could be of your interest.
So to summarize you can use MOTIF search (or INTERPRO etc...) to find motifs in your sequence which are already known. Or gather a set of sequences and find new motifs in them using MEME or a similair tool.

However, how did you conclude that your sequence is a Zn-dependent alcohol dehydrogenase? Because BLASTing the sequence you provided will give matches with this enzyme but only covering ~17%. Nonetheless a good way to find information about your sequence is indeed to find motifs and compare the sequence with HMM's or PSSM's of known proteins.
For example MOTIF search will give these results:
PROSITE:
    Zinc-containing alcohol dehydrogenases signature.
PFAM:
    Zinc-binding dehydrogenase
    Alcohol dehydrogenase GroES-like domain
AND A LOT MORE>>>

Searching PFAM will give you this:

Notice that the second domain (Zinc-binding dehydrogenase) is not completely present, more information can be seen in the detail overview:

I would advice to also take a look at how important these "missing" residu's are (e.g. using a MSA and look at conservation). Because your sequence could contain these domains but that does not necessarily mean that this IS A Zn-dependent alcohol dehydrogenase. It could be non-functional for example.

To find de novo motifs present in your protein sequences, you should use MEME or some other motif-finding tool instead of BLAST.

MEME discovers novel, ungapped motifs (recurring, fixed-length
  patterns) in your sequences.


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Limitations of Gibson Assembly method
Why is the Gibson assembly method limited to ~8 fragments and what can be done to raise this limit?
Why is the method called "seamless" and what are the advantages compared to annealing complementary fragments and using polymerase and ligase?
Thank you

The technique isn't limited to 8 per se, it's just for every additional fragment you want to add, you require an additional joining event to occur. Eventually, your cloning efficiency will just bottom out, and you'll get no positives. Assembly of >8 fragments is possible though - I know a few people who have managed up to 15 or so, though the efficiency again is hugely fragment-length dependent (small fragments are easier than large ones).
To increase the number of fragments, you can try step-wise assembly, sticking subsets of fragments together to make progressively larger ones, or optimise your fragment ratios and overlap lengths. This is a bit of a 'dark art' though - it would be a lot of trial and error with lots of potential variables.

The technique is called 'seamless' as it, in theory, leaves no scars (deleted or inserted bases). NEB has a great page explaining it, but this figure basically summarises:

There would be nothing stopping you going and annealing fragments and then extending them, but this is more like a "joining PCR", and Gibson assembly is designed to mitigate the need to do this. Joining PCRs are very tricky to get working, especially if your fragment sizes differ significantly. The Gibson mastermix contains enzymes in compatible buffers with all the necessary cofactors to allow them to work together.


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Fold Coverage of sequence read?
What does it mean when N-Fold coverage of read of sequence? Details will be much appreciated if a link provider with brief explanation.

What you're asking is a little unclear to me...I don't know if this is what you're looking for, but typically, the fold coverage of a read represents the number of times that particular read was sequenced in a given run.

Fold coverage is often derived with respect to a genomic locus, not a read. In sequencing experiments, fold coverage of a genomic loci (coordinate along a reference assembly) will be the number of aligned reads that overlap the position.

It could also be the average coverage of a genome based on number of reads, read length and expected genome size.

Thank you for the additional detail. Absolutely, on a genome level the fold coverage is computed as: number of reads * read length / genome size, and genome size here be either the true genome size or the size of the fraction of genome that is captured for sequencing.

N-fold coverage usually refer to the average number of reads spanning across a particular region of interest. For example, if you are interested in a gene and would like to know how confident your data is, you may look for the coverage.
There is no absolute definition on how N-fold coverage is calculated. The most common method is to get the arithmetic average per base.


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For fish, does a bony skeleton have any advantages over a cartilage skeleton?
I have learned that two important lineages of fish are the bony fishes (Osteichthyes) and the cartilaginous fishes (Chondrichthyes). Many websites mention an advantage of the cartilaginous skeletons of sharks and other chondrichthyans: they're lighter than bony skeletons.
But it has been harder for me to find out if we know of any things bony skeletons do for fish that cartilage skeletons can't do, or don't do as well.
My research and hypotheses
I found an old Manual of Geology by Samuel Haughton (1865) that says

[a bony] skeleton only affords an advantage over a cartilaginous skeleton by allowing a greater variety of points of attachment for the muscles of the Fish, and so admits of more powerful motions.

But maybe other people have discovered more things since this was written. Also, I'm curious if this is just a theoretical argument, or if we have actual evidence that bony fish are capable of using their muscles more effectively than cartilaginous fish.
I have three main hypotheses at present:

Haughton was right, and a bony skeleton is just more effective at serving as an attachment point for muscles.
Bony skeletons are more effective at protecting the fish.
There are no advantages to bony skeletons; bony fish just happened to evolve this way. (As far as I can tell, the early evolutionary history of fish has been a bit unclear and I haven't been able to determine if there is current consensus about whether bone or cartilage skeletons came first, and whether chondrichthyan cartilage skeletons are an inherited primitive feature or an innovation.)

As a fish morphologist, here's my best attempt. I really like the first reference I listed at the bottom, too.
1) Ancestral Condition:: The cartilaginous skeleton of chondrichthyes (sharks, skates, rays, chimaeras) is almost certainly a derived feature--a synapomorphy-- defining the clade. There are a few lines of evidence for this. First, the cartilage in a shark skeleton is a very specialized form of calcified cartilage,  unique to the group. Second, in other gnathostome and pre-gnathostome ancestors (Osteostracans,  other armored jawless fishes) had big bony head shields. The groups most closely associated with sharks (Placoderms, paraphyletic acanthodians) has both bone and cartilage in their skeletons. Basically I guess my point is that, while cartilaginous skeletons were ancestral for gnathostomes, that cartilage was very different from chondrichthyan cartilage, and bone turned up in many stem fishes before chondrichthyan cartilage. So the ancestor for sharks and bony fishes probably had both cartilage and bone but not the specialized calcified cartilage of sharks
2) Bone as a Plesiomorphic (ancestral feature), but not the entire skeleton: If we take what I've said above, it certainly suggests that your point 3 is in the right direction w.r.t. split between chondrichthyes and osteichthyes. The chondrichthyan skeleton is light...But the osteichthyes definitely took endochondral bone and ran with it--which brings us back to your original question: why did they replace their entire skeleton with bone? Why is always a tricky question in evolution, but we can speculate:
3) Potential adaptive value of a bony skeleton:

bone is better at transmitting muscle force than cartilage, so in that sense, you are correct
when fish were coming into prominence and diversifying, there were a lot of big, terrifying, predatory arthropods. Many early fishes have big bony armor plates-- which may have served to project them from their chitonous predators
More evidence for that -- when big scary predators went extinct, fishes began to pare down their bony armor (most teleosts have highly reduced skeletons).

Without a time machine we can't be certain of these things, but I'm pretty sure what I've laid out is fairly close to the common consensus.
Relevant lit:

https://academic.oup.com/nsr/article/1/4/490/1512529
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3237026/

Thanks for the edits, @kmm . I am not good at markdown. Or spelling, apparently!


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Are immunosuppressors necessary after a bone marrow transplant for Bubble Boy Syndrome?
I know that under normal circumstances, immunosuppressors are needed to mitigate the host body's immune reaction to the graft. However, people suffering Bubble Boy Syndrome have pretty much no immune system to begin with. Graft versus host disease does occur in some cases, but not all. So, in these other cases, are immunosupressors required?
Thanks to all!


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What is the rationale for the complex eye structure?
The eye is a lens that focuses rays of light from a limited spectrum, after which the the image is turned over to the brain receptors that interpret it (beginning with turning it the right side up first, I think).
It is a complex and fragile instrument whose sole purpose is to pre-process the image "mechanically" (rather than "electronically") before turning it over to the "CPU." Please bear with me.
Most creatures who have one eye usually have another one as well. This second equally complex piece of hardware has, it would seem, two purposes: one, it serves as a spare; two, it allows its owner to see depth a bit better. (You can still see depth if you cover up one eye: your brain has to make a few adjustments, and a few more assumptions, but it's not like depth perception is completely gone, right?)
Now think of the original camera obscura (the one that had no lens, just a hole). By adjusting the size of the hole (aperture) one could make the resulting upside-down image on the opposite wall a bit sharper. The image is still a bit pale, but the subtle differences in color values would still be enough for a powerful computer (such as our brain) to work out the nuances.
Why would then God (or Evolution, for those who still believe in it) opt for making an infinitely complex piece of hardware (the eye) and then furnishing a backup as well, instead of just adding a few lines of code to the operating system?
Please don't take any of this too seriously.

Note that in addition to having two eyes, vertebrates have two of almost everything, down to brain lobes.  So it might be more informative to ask why a) they're bilaterally symmetric; and b) why there are a few organs, like the heart and liver, that don't come in pairs.

Nothing an organism has is "infinitely complex"...

to start with @Ricky you could define "infinitely complex"... but it may be better to offer your definition of evolution, I imagine that's pretty flawed and would explain your stance.

@Ricky If you care about getting an answer to your questions (whether they regard evolutionary processes or not) you should try to clarify it in response to what I found unclear (see my answer/comment).

@Ricky: Actually, I was giving you what I thought was an obvious answer, which is that vertebrates have two eyes because they're bilaterally symmetric, and so almost every organ comes in pairs.  The mechanism for that is probably buried deep in the HOX genes (but I am not an expert on this).  Also, not every creature has two eyes: most spiders have 8, starfish have 5 (at the end of their arms!), scallops can have 100 or so...

@ricky Jamesqf was only giving some input which may have been useful or interesting to others reading your post, there's no need to be so confrontational (the same can be said about your statement "God (or Evolution, for those who still believe in it)" - given that this is a Biology site that is clearly meant to be an incendiary statement).

Welcome to Biology.SE. Here are just a few comments rather than an answer...
Clarification of the question
Can you please clarify how "just adding a few lines of code" could replace a second eye? The question is unclear for the moment.
Perception of depth
A simple amusing exercise you can do to explore how much depth perception you lose by having one eye is to try to catch object with both eyes open and then with one eye open only.
A single eye has much poorer ability to perceive depth than two eyes. However, it can still do so. You will learn much more on depth perception on wikipedia > depth perception.
Believe in evolution
You say [..] Evolution, for those who still believe in it [..]. Evolution is not a thing one believe or does not believe in, it is a thing one understand or does not. You might want to have a look at a very introductory course to evolutionary biology such as Understanding Evolution for example. That will help you to understand what evolution is about.
Mythology and Science
You mention "God". Please, mythical creatures are not welcome on science websites except eventually to make a metaphor. Note, on a slightly philosophical matter (which is not my domain of expertise), there is no contradiction between the existence of a God and Evolution. There is contradiction with the many of the false believes of creationism as often described in the Christian culture

I will probably not react to further comments and am just inviting you again to learn about what the science of evolutionary biology is about through introductory source of information such as Understanding Evolution by UC Berkeley for example.

Stack thrusts this closed question into my reading list. therefore I offer Richard Dawkins VIDEO demonstration of the evolution of the eye which is great and useful for the guy who asked the confused query: https://www.youtube.com/watch?v=eA1rR6ZCxMY


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Is the 5% of the oxygen used in the breathing process fully transformed into CO2?
More specific, I found out that the amount of oxygen we inspire is 21% from the total amount, with 0.04% CO2. The expired amount is 16% oxygen, with 4% CO2. Where does the remaining 1% oxygen go? Or are these only approximations?

When you write the number "21%", it represents equally all numbers rounded to 21%; that is, 21% is the same number as 20.5% and 21.49% under the most common rounding convention.
When you subtract two rounded numbers, you can easily get a number that is not zero. For example, 10.500 - 10.499 = 0.001 before you round, but if you round first, 11 - 10 = 1. 10.501 - 10.500 has the same difference, but if you round first and subtract you'll get 0. In other words, 16 + 4 = 21 is completely reasonable math in the world of rounding, the value of "1" is not meaningfully different from zero on that scale.

Got it. So it was just an approximation. Thanks!

@me1234 I wouldn't call it an "approximation" per se; it could be that the numbers were measured very very precisely, but if they've been reported to you as a number like "16%" you should know by looking at that number that it's clearly been rounded to an integer percentage value.


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What organism is this? Repetitive, long thread, double spikes, ... (from a human sputum sample)
Link to video

Collected in Portugal.

Welcome  André. Please take our [tour] and refer to the [help] for guidance as to our ways. Enjoy the site. I don't know about anyone else, but I'm not convinced that it's an organism. Did you ask the person what they'd eaten recently? Could you give us some idea of scale (how big)?

Thank you! The small cells you see next to it are neutrophils. So, it's thin but quite long. Goes on and on, coils, etc. And the double spikes repeat along the way. And it has that darker, nucleus-like, area near the level of the spikes. It must be a living organism or something made by one.

Why's this off-topic?


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Is this a Northern Black Widow?
I’m in Florida and my 5 year old spotted a spider on an old watering pale toy. It looks like a widow in shape and color, and has red spots down it’s back. Most black widows here don’t have anything on their backs, so I took to the web to try and be safe, and found that the Northern variant has spots, but all the pictures I found have the spots blended towards the back end and they don’t seem to have the outline around the spots like this spider.

Also, I didn’t flip it over to check for the typical hourglass on the abdomen as I didn’t feel confident that I could do so without harming the spider or potentially myself.

A jar would have be handy. Honestly, if a black widow can have a grey velvety abdomen with no red spots? I'd wager 200 it isn't.

Your spider has red circles outlined in white (it is visible if you zoom in). This, indeed, looks like a dusty Latrodectus variolus

@LifeInTheTrees it was covered in dirt so that would explain the velvety grey color, and the red spots are surely there, you'll need to view the full image and zoom in a bit, apologies for the poor quality. Also, didn't have a jar available.

@JimN just glad my 5 year old didn't disturb it enough to cause any issues! Thanks for the help!

Yes it appears to be a male Norther black widow covered in dust. Here's an image using different color balance:

These species of black widow are found in Florida: Latrodectus mactans (Southern black widow), Latrodectus geometricus (brown widow), Latrodectus bishopi (red widow), and Latrodectus variolus (Northern black widow) (Edwards 2002).
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Only the bites of the females are dangerous to humans. Despite their notoriety, Latrodectus bites rarely cause death or produce serious complications.(wiki)
male
https://upload.wikimedia.org/wikipedia/commons/c/cd/Black_widow_post_dorsal_1370.jpg
female:
https://upload.wikimedia.org/wikipedia/commons/thumb/a/a5/Latrodectus_variolus_%28Northern_Black_Widow%29%2C_F_Theridiidae.jpg/580px-Latrodectus_variolus_%28Northern_Black_Widow%29%2C_F_Theridiidae.jpg


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How should I measure the oxygen dispersed during photosynthesis in pondweeds?
I am to conduct a lab investigating how different wavelengths of light affects photosynthesis in Egeria pondweeds.
The idea is to put color filters on light bulbs and shine them on the pondweed in a sodium hydrogen carbonate solution. Then to measure the oxygen, I have an oxygen sensor which measures dissolved oxygen (mg/L).
Now, what I have a trouble with is if measuring the dissolved oxygen is the right way to measure the rate of photosynthesis depending on color of light? Will it work?

One experiment I saw online, was that during 5 minutes you measure the oxygen dispersed, and it will show you the mg/L depending on time.

That solution might just kill the plants.

Why not do it in a standardised pondwater, unless you don't mind the results being for only that sodium bicarb solution?

A couple thoughts.  The plant is undergoing cellular respiration too, so I am not sure that there will be a net oxygen out.  I assume that the sodium hudrogen carbonate is going to provide a source of carbon dioxide to a closed system, but even then the plant will release carbon dioxide from respiration from sugar that it has made and burned.

Is the atmosphere sealed and airtight?  You could possibly have Sodium Hydrogen Carbonate in a water reservoir in the container, but not in the water that the pondweeds are growing in.

what margin of error is acceptable in the result of your tests,light bulbs and filters might not be the best way to produce the different parts of the electromagnetic spectrum you want(i guess you want to keep the energy level fixed so only the color changes).different LED`s might be a better solution for your experiment.

Bubble formation might be easier to measure than oxygen concentration. Bubbles can be measured optically Or acoustically.
A sealed container with a little carbon dioxide gas might work.
See below article.
“Acoustic effects during photosynthesis of aquatic plants enable new research opportunities”
Helmut G. Kratochvil and Michael Pollirer
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5349586/

You can also work out via displacement - pondweed underneath an inverted container, traps bubbles that escape (gentle agitation might help) and measure volume .

The experiment means anything only if different "colors" (wavelengths of light) affect the rate of photosynthesis. A good experiment requires that you "keep everything same/identical*, to the extent possible, save the color of the light the plants are exposed to. If you detect any changes in the concentration of oxygen, you can plot the color of light to the oxygen concentration.
Photosynthesis is a chemical reaction:
$6CO_2 + 6H_2O \rightarrow C_6H_{12}O_6 + 6O_2$
At the very least, the concentration of $CO_2$ and amount of $H_2O$ must be constant for different colors, as they can alter the rate of photosynthesis, and are therefore confounding factors.


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Difference/similarity between adaptive radiation and species divergence?
I've been reading various answers on different sites but I still don't know whether adaptive radiation and species divergence are different or similar.
My questions:
1) On some sites, it says that adaptive radiation is a form of species divergence, while on others it says that they are different. Which one is correct?
2) Is the main difference that adaptive radiation occurs relatively rapidly and species divergence takes longer?
3) Darwin's finches is used as an example for adaptive radiation, but is it also an example of species divergence?
4) Are the finches on the galapagos islands all difference species (one species diverged into many)? Or are they all the same species, just with different characteristics (e.g size of beak)?

Adaptive Radiation
A radiation refers to the process by which one species rapidly speciate into a number of different species. A radiation can be adaptive or non-adaptive. An adaptive radiation is a type of radiation when new species are formed through selection into new ecological niches. Such adaptive radiation typically occurs after the raise of a key mutation that allows for further specialization such as a mutation causing a change in the Pharyngeal jaw as observed in cichlids (Albertson et al. 1998).
You can learn much more on adaptive radiation in the book The Ecology of Adaptive Radiation by D. Schluter
Species divergence
Species divergence refers to the process by which two existing species diverge through time, either through the accumulation of neutral (or non-neutral but equally selected) mutations or by selection on different trait values.
Species Divergence and Adaptive Radiation
Because of the semantic difficulties behind the concept of species (see here), it is unclear from which point can we talk about species divergence and by which point the observed process of divergence is only divergence within a metapopulation.
Ignoring the eventual detail of the definition of species, and considering species divergence as referring to the divergence between any two lineage (whether or not in reproductive isolation), then it is clear that species divergence is part of the process of adaptive radiation.

To answer your multiple questions directly
1) On some sites, it says that adaptive radiation is a form of species divergence, while on others it says that they are different. Which one is correct?
Adaptive radiation is a little more than a form of species divergence as it includes also the event by which divergences starts.
2) Is the main difference that adaptive radiation occurs relatively rapidly and species divergence takes longer?
mmhhh... not exactly as the concept of radiation also refers to the event allowing the divergence to happen
3) Darwin's finches is used as an example for adaptive radiation, but is it also an example of species divergence?
Yes, indeed! No radiation, without species divergence. On the other hand species divergence will occur between any two existing species regardless of whether they speciated through a radiation
4) Are the finches on the galapagos islands all difference species (one species diverged into many)? Or are they all the same species, just with different characteristics (e.g size of beak)?
The Darwin's finches refers to about 15 (different) species. The different species of Darwin's finches do NOT refer to intra-species variation but to different species. In other words, there is some reproductive isolation between these different species. Again, you might want to make sure you understand the concept of species and you might want to read this post (same as the one linked above) on the subject.

When you talk about species divergence, you mentioned that..."two existing species diverge"...Can this also occur from a single species? (e.g variation within one species population results into species divergence?)

Yes, you can have two population within a species that diverge (yielding eventually to speciation). Then if speciation occurred, then the species will keep diverging. Does that answer your comment? Take good care to realize how poorly defined is the concept of species though.


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Are there worms/snake traveling by rolling? (see youtube video)
Someone obtained this from a nature simulator :  https://youtu.be/l-qOBi2tAnI
Is there any animals travelling like this?

There is a spider that rolls but I am not sure if that counts.

yes I have already seen those sand spider, but it's far less impressive...


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Is DNA transcription inactive during mitosis ie no proteins are made? How does the cell survive?
I've read that during mitosis, DNA exists as heterochromatin, a form that is unable to be accessed for transcription.
Does this mean no new proteins are made during what can be 20% of a cell's life?  How does the cell survive?

To make proteins you  just need mRNAs. And most of the synthesis (transcription) is done in the S-phase, including the mRNAs required for later stages.

Consider two values, the average half-life of an mRNA, and the average half-life of a protein.  A cell may not need to transcribe it's essential genes non-stop.


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Why don't antibodies generally bind to food and drugs?
Are these excluded thru central tolerance?  What if you ingested something with a unique molecular structure that you hadn't ingested before?

Maybe my answer to your other question answers somehow this one?

B cells containing receptors against food's or drug's molecular structures may exists. However if the naive B cell binds the molecule without a second signal coming simultaneously from CD4 Tfh cells (linked recognition) the B cells recognizing this antigen will become anergic or will die by apoptosis. This occurs with antigens to which we are chronically exposed, like food.
Reference: Janeway's Immunobiology, 8th edition. Chapter 8 (The development and survival of lymphocytes). In particular section 8-26, p320-321.

I would add that many food allergy structures are recognized in hypersensitivity reactions because they oddly enough resemble helminthic peptide antigens. Furthermore, lipid/CHO-type antigens which aren't peptide can't be handled in the same way as peptide antigens, hence we have gamma-delta T cells and surface receptors like TLR-4 that have to do this job. Since antibodies get generated generally due to peptide antigen presentation by APCs, there's a lack of robust antibody production to non-peptide antigens.

I’m not an immunologist, but I think it fair to say that antibodies may well be able to bind to certain food or drugs. However there are several reasons that this may not cause their removal or trigger an immune response. These include:

Location. If the food is in the stomach I imagine that the digestive environment favours breakdown to sugars, amino acids etc and exposure to antibodies is minimal.
Chemistry. Certain substances such as fat, nucleic acids, are weakly antigenic.
Size. Small molecules are not immunogenic unless attached to a larger one.

Why are small molecules not immunogenic?
I think this is probably the key point here, so I'll expand on it a little in general terms.
If an antibody binds a foreign protein, this is large enough that other antibody molecules can bind it too. And the antibody is bivalent, so it may bind a second foreign protein. This leads to a cross-linked matrix that can be recognized by macrophages and engulfed. If a small molecule binds to an antibody this cannot happen and the molecule may well diffuse off again.
As well as binding those soluble antibodies (IgG) already present, antigens cause the antibody-producing cells (B-cells) to divide to produce more of the particular antibody. This happens because the B-cells have a membrane bound variant (IgM) with the same specificity on their surface. When a molecule binds to two of these membrane antibodies a signal is triggered to the cell. This can happen with a large molecule, but a small molecule can bind only one IgM on the surface and this expansion of antibody-producing cells will not happen.
This size requirement for immunogenicity can be understood in the context of the size of the bacteria and viruses which one presumes the immune system evolved to combat.
More Information
As I mentioned, I deliberately answering the question in general terms. If you wish to know more detail (and about cellular immunity) the following on-line book chapters (although a little out of date) may be of interest.

Berg et al. Ch. 33
Alberts et al. Ch. 24

hypersensitivity (allergy) is an autoimmune response, and it is caused by ingestion (peanuts) or inhalation (pollen)

@FoldedChromatin — You should critcize the question, not my answer, as you are criticizing its premise. And perhaps you would care to elaborate and explain how this occurs in molecular terms and why most people do not suffer from such allergies. As I said, I'm no immunologist, but your comments have contributed nothing to my understanding. If, as I assume, you have down-voted my question, you could point out to everyone which particular parts of my answer are incorrect.


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To what extent does the distribution of nerual transmiters in the brain vary human to human?
Suppose $x$ is a position in the brain, and $n_i(x)$ is the density of neuro recepter $i$ around that point. Any given human will have some distribution of neruo recepters $n_i(x)$ through out there brain.
I am wondering what do we know about the statistics of these densities, or how they vary from person to person?
For example, is there a variance in the amount of serotonin receptors in the brain between healthy or unhealthy people?
How does one go about measuring this?


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What would happen if blood flow wasn't periodic?
Blood pressure has its systolic and diastolic parts due to the beating heart and the body's used to that kind of thing.
What would happen to a person supported by a blood-pumping machine that applies steady blood pressure?
What would happen short term?
What would happen long term?

Actually the artificial hearts do maintain a steady pressure. I think the pulsating pumping of heart has got to do with how the organ evolved. Most movements of body fluids are because of a pulsating muscular movement.

In fact, we see our blood pressure as periodic, and feel our arteries pulsating. But our tissues don't see that. What I mean by that, is that tissues get their blood supply ultimately through their capillaries, where the blood pressure and flow is essentially constant throughout the cardiac cycle, as you can see on this chart:

Image from OpenStax. Article on Blood flow and pressure
As for the second part of your question, what would be the consequences of having constant/non-pulsatile pressure? We can only speculate, I don't think it would have any palpable consequences in principle.
The only "real-life" examples include people who are, for instance: on a Cardiopulmonary Bypass during a cardiac surgery, on Extracorporeal membrane oxygenation (ECMO) in the ICU or have a left ventricular assist device (LVAD) for severe heart failure. It's very difficult to infer anything from these situations, because any on these patients are already very sick, and consequences following these procedures are usually due to insufficient oxygenation, thromboembolism and such, which have nothing to do with the constant pressure.


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What are in common between transcription factors?
In terms of their structures (primary to tertiary) and locations?
Why do they have these commonalities? Or are any of these commonalities critical to their functions?

Transcription factors are a very heterogeneous group of proteins. Their two main objectives are to bind DNA & to recruit polymerase to that site. There are a of ways for them to accomplish these tasks.
To bind DNA, all they need is a pocket of positive charge, which are found in several structural motifs across many proteins. The wikipedia page actually provides a good sample of this diversity: https://en.wikipedia.org/wiki/Transcription_factor#Structural
The other co-factors that transcription factors recruit to get polymerase to the DNA strand also vary pretty widely. They link together through structurally complementary pockets of opposite charge, but beyond that, the details get pretty messy and there are a lot of details. Even reviews of transcription factors tend to focus on a specific class. If you want more than that very simplified explanation, I would actually recommend reading some reviews on the subject. Here are a couple:
http://www.ncbi.nlm.nih.gov/pubmed/25755661
http://www.ncbi.nlm.nih.gov/pubmed/25640595

Thank you very much for the answers. That is very clear.


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Why is an excess number of eosinophils consistent with a violent allergic reaction?
What roles do eosinophils play in allergic reaction?

The primary function of Eosinophils is to releas digestive enzymes and destroy extracellular parasites, but they also contain pro-inflammatory molecules and cytokines in their granules.
Eosinophils play an important role in late response inflammation. The primary inflammation is caused by degranulation of improper hyperactivation of mast cells when they encounter antigen/allergen (They have IgE bound to their receptors on a membrane). They release cytokines as IL-4 and IL-13 which recruit Th2 lymphocytes. Th2 lymphocytes release i.e. IL-5 which attract eosinophils.
Eosinophils release the content of their granules, which can degrade the tissue on an organism. Their cytokines attract more WBC - eosinophils (macrophages, TH2 lymphocytes and mast cells) and since this process is not controlled, they accumulate in tissues and it can lead to allergic reaction.
Good book contemplating this topic


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How can dopamine modulate synaptic strength?
Does dopamine act on G protein coupled receptor, leading to more Ca2+ channels on the postsynaptic knob?
Also, how is the specificity of the location (of the brain) that dopamine acts on controlled? Or is it controlled at all? Is this chemical associated with addiction?

Yes, dopamine receptors (D1-D5) are G protein coupled receptors,  which act primarily on adenylatecyclase (changing cAMP concentration, which activate proteinkinase A, which phosphorylates other proteins in turn such as CREB... you can find the pathway in the following article). D1 receptors activate adenylatecyclase, D2 inhibit its activity.
I wouldn't say it directly alters the Ca2+ channel concentration per se, the article says however it can modify their state.
According to this article, G proteins of these receptors could also have different effects (alternative effects through G-proteins such as activating phospholipase C, which results in IP3 formation which results in Ca2+ influx to cytoplasm from ER which acts on proteinkinase C) or new research suggest that it could also act through G protein-independent mechanisms via interactions with ion channels.

specificity of the location (of the brain) that dopamine acts on controlled?

The idea is that cells with certain neurotransmitter may induce growth of cells with same transmitter, thus forming specific circuits. I don't know however how specifically this happens and how the cells communicate to form specific connections (like dopaminergic connection from substantia nigra to basal ganglia) during development. I'd bet on some morphogenes. Someone else might know better :) .
Yes, dopamine is associated with addiction, as it's part of the reward system in brain. Many drugs inhibit its transport from synaptic cleft into the cells, which means prolonged activity, brain senses positive effects you can see when you've done something good (reward).

Thx that is an excellent detailed answer


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Determining the Accuracy of DNA Testing
The DNA Testing firm in the below article claims that its tests were "99.99 per cent" accurate.
http://www.telegraph.co.uk/news/uknews/1322077/False-DNA-test-led-father-to-reject-daughter.html
Googling "dna test accuracy" has led to numerous websites many of which claim an accuracy of their DNA testing to be 99.9%, with some even 100%!
How does a firm calculate this percentage accuracy? It seems to me that experimental data would not be useful in determining this percentage accuracy as there is no way to really confirm the fact that Bob is the son of John and vice versa as that is what we're trying to find out. Do they do so by factoring in slight inaccuracies in the laboratory procedure?
Acquiring experimental data would not be useful as I described above for paternity testing, a useful application of DNA testing, but could, to my knowledge, be used to determine the percentage accuracy of DNA testing in the recognition sense. By DNA testing various cells of the same person, and then seeing how many of them result to be from the same individual according to the DNA test (understanding that scientifically every cell should have the same DNA but then experimentally acquiring results that show that 999 in every 1000 cells show to link back to the same person) seems to be a working method...Is this how it works? Is this the notion conveyed with the idea of the percentage accuracy of DNA testing?

Essentially, yes. These tests are usually based on enzymes that replicate DNA, and they have a certain (small) probability of getting a base wrong now and then. You can estimate the error frequency by doing many repetitions of sequencing of the same DNA sample and counting the number of discrepancies. Of course, this assumes that there are no systematic errors, only random variation, which may not be entirely true.
The Sanger sequencing technique is estimated to have error rates on the order of 0.001% (or, is 99.999% correct). I don't know exactly how these firms calculate their numbers, but I would guess it is similar.


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Why eyes don't get heated while converging sunlight into retina?
It is a common observation that a magnifying glass when used to converge rays of sun to a fine point in paper, the paper burns due to intense heat.
Why doesn't this happen in our eyes? Our eyes are also doing the same, they are converging the sunlight into our retina but our eyes don't get burned, or to say get heated.
Is viterous or aqueous humor absorbing heat? If so, then the tiny amount of fluid present in the eye shouldn't be enough to cool the eye for a longer period of time, but we can spend the entire day at sunlight without any eye stress or pain.
Size of eye lens small compared to magnifying glass? However a magnifying glass of the size of eye lens should also be able to produce significant heating by converging sunlight.
As far as I know, the heating effect is due to Infrared rays not because of UV rays so we can safely ignore them in this case, right?

If you look straight at the sun, you do burn your retina, in the same sense as you get burnt by contact to a hot surface: living tissue is full of water, so the burning process does not look the same as for dry paper e.g., and the harm will be done long before combustion.
To go a  little further, the first layer of retina in vertebrates is made of so-called Muller cells, which conduct the light as optical fibres do to the photoreceptor cells, but it has also been argued that they can in some measure filter too strong light in order to protect photoreceptors. See http://www.pnas.org/content/104/20/8287.full
These cells are also strongly vascularised, which allows to regulate its temperature. You can read http://creation.com/mueller-cells-backwardly-wired-retina-v-dawkins

Converging sun rays at my hand (tissue, as you said) produces enough heat to draw back my hand spontaneously. But with our eyes, we can look at sun for a slightly longer period of time without noticing any change except extreme brightness.
Even when we aren't looking directly at the sun, the sunlight is still entering our eyes. Why this indirect sunlight (For a long period of time) doesn't produce any heat (Which should, as we are exposed to a longer period of time)?

Light converges on your retina only when looking at an object at an infinite distance. The ambient light is not converged to a single focal point on the retina, so the heating is not more than on your skin. I advise strongly against performing this experiment of comparing for how long you can hold your hand in focalised sun light and look at the sun. See also my edit.

I didn't read those articles you linked to as they are too scientific for me to understand but your ambient light description seems to solve my question to the finest. Thanks.
Btw, I didn't performed any such experiments for the sake of this question because I know it's harmful, I was just narrating my previous experience, we all've done these, once at least.


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Can our body adapt to periodic fluctuations in sleep?
Suppose that if I've to attend a morning class then I must wake at 5 AM in morning. Next, if I don't (attend the class) then I wake up at 7-8 AM.
I've experienced that, since I do attend those classes almost regularly, my body has adjusted itself (sleep cycle) to wake at 5 AM almost precisely without a alarm set and has also decided when to sleep (it seems to demand 7-8 hour of sleep). This, I think, is common to most of us.
Now suppose that I attend classes only on alternate days. Put simply, I wake up at 5 on first and at 8 on the next day and so on. This implies that I am constantly switching my sleep cycle every day. Would my body, now, be able to adapt to this continuously varying cycle (which is but periodic).
I suppose no, and that is just a guess based on my experience. But provided I give my body enough time, I think that it may really adjust to this scenario.
On a side note, assume that (in case it matters) I take a sleep of 7 hours during class days and a sleep of 8.5 hours during holidays to make this data realistic. .

There's a time bias after which it is less healthy and good sleep to be very clear mentally. the circadian rhythm works on a 24 hour basis and also a 4 hour basis, which is why we have meals every 4 hours. It also depends on age and how robust the person is. 7 hours sleep on week days and 9 hours at the weekends isn't stressful for some young people. I know a russian who works 24 hour shifts as a receptionist twice a week and she never got used to the sleep deprivation.

Oh that's interesting, this example perhaps proves that alternating sleep cycles is inpossible. Thanks for the real life example.

In the same way that it takes time to fully adjust to jet lag (~ 1 timezone/day), it is unlikely that the body can adjust to alternating patterns of 3hr gaps on wake time on a daily basis [Ref. 1].  We simply have not evolved to jump timezones.  The most healthy thing to do is to have one time to get up each day (5am) so that your body is in sync.
[Ref. 1]: Review about circadian rhythms

Definitely your body will adjust. All you have to do is make it a thinking point that you have to wake up early at 5 and trust me you will, if you don't think hard about it then you will wake up later than 5.

Perhaps you haven't read my full question I suppose. Since the answer doesn't, in any way, relate to it.


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Problem during DNA extraction from blood using automated magnetic beads extraction protocol
We've been using the Perkin Elmer Prepito D instrument + the Blood 250 associated kit for DNA isolation from blood for the last couple of years. It's been working well, however, lately the resulting extracts all show a null concentration. We've tried changing the kit and working with fresh blood with no results. We've also observed that the DNA seems to stay in the disposable deep wells plate bonded to the magnetic beads and it does not get transferred to the final tubes.
Does anyone have experience working with the Prepito instrument or have experienced a similar problem with any magnetic beads DNA isolation protocols ? Does anyone have any suggestion to what might be causing this problem or how we may solve it ?

Have you tried contacting the customer service about the issue?

I agree with @Chris, but there a few things to test first - ensure that the kit is prepared correctly using fresh reagents - don't let a newbie do it!


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Is it possible to use a fluorometer such as Qubit or Denovix DS-11 FX to detect DNA integrity/fragmentation?
I remember someone saying that the Thermo Fisher Qubit can be used to assess DNA integrity, is this true?
Our lab recently acquired a different fluorometer, the Denovix DS-11 FX. I'm wondering if it can be used to detect DNA integrity. I couldn't find any info about it in the manual.

In general, methods like Qubit rely on specific interactions between a fluorescent dye and the target molecules, be they dsDNA, ssDNA, RNA, or whatever. These are sensitive to the overall amounts of targets, not their size distributions (within reason, of course). For DNA, you will need to use an electrophoretic method like a Bioanalyzer or an agarose gel to quantify integrity.

The Qubit has an RNA integrity kit. They call it RNA IQ which works off binding of two different molecules. I haven't used it, so can't say if it is comparable to bioanalyzer, but they claim it is as good as electrophoresis (presumably visual inspection for integrity on this one). Bioanalyzer is the gold standard for RNA AFAIK, don't know about DNA.

There isn't an equivalent fluorescent method for DNA. Bioanalyzer orTapestation is the way to go.


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Why are foster mothers used in creating genetically modified organisms?
In every source I have seen regarding creation of transgenic mammals, a foster mother is used for the womb instead of the mammal who produced the egg cell. See these sources: Jax Mouse Genome Informatics ScienceDirect LibreTexts
Therefore, my question is: Why is another animal used instead of simply using the biological mother as the foster mother? Is it some kind of immune reaction to the transgenic embryo? If so, wouldn't the foster mother have the same reaction?

Mortality during egg harvesting perhaps...? Please be aware of our requirement to show your research (into the question) when posting.

For humans, retrieving mature oocytes is a costly procedure involving anesthesia, a laparoscope, and other equipment. As unpleasant as it may be, it's much more cost effective to just euthanize the female then surgically collect her oocytes via laparotomy. Imagine a tiny anesthesized mouse on an operating table with an anatomist/surgeon(?) using the world's smallest laparoscope collecting oocytes with the most delicate suction equipment, supporting the mouse post-surgery and reimplanting the embryos after her recovery? That's almost science fiction!