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Can DNA be flattened?
DNA is always shaped like a double helix. But could you flatten the double helix (which is essentially just a twisted ladder) and would DNA still be able to duplicate and control cells?

The double helix is the thermodynamically favourable conformation. You can possibly flatten it but it would consume energy. In general, the DNA does get unwound during translation and replication. As a part of the site policy, we insist that users put in some research effort from their side before asking. Provide a reasonable background and rationale for your question.

What precisely do you mean by “could you”? Being too large to crawl into a cell, I certainly couldn’t. And what do you mean by “flatten”. In the literal English meaning of the word this would violate the laws of chemistry, and if you don’t appreciate this you shouldn’t be posting here. If you mean unwind the helix, keeping the strands parallel, say so. But please take the trouble to express and explain yourself clearly.

And DNA is not always shaped like a double helix, as you say. There bacteriophages with single-stranded DNA genomes.

Flattening the double helix, i.e. making it look like a ladder (like in the usual diagrams of DNA, shown in the first figure below), would not be possible because of bond angles.

Figure 1

Figure 2
The only way for everything to be flattened out completely (as in Figure 1), is for all the bonds to be planar. However, we know that this is not true, as the C1 (carbon 1) is sp3 hybridised, not sp2, which means that the bond from the sugar to the nitrogenous base is not planar. The bond with the phosphates is also not planar. Hence it would be impossible to flatten DNA out like paper.
Moreover, there are relatively strong London dispersion forces between the layers of bases in the 3D structure (helical form). You can see on Figure 2 that the bases lie parallel to each other in each "step" of the helix. This adds to the stability of the molecule.
To answer your second question about whether DNA would be functional if flattened out, the answer would be no. The helical shape of DNA means that there is a minor groove and major groove, which is a property of its 3D shape. This is where proteins bind, which will help the process of replication (duplication) and transcription ("controlling" cells).

Figure 3

would DNA still be able to duplicate and control cells

The structure of DNA in a cell is more complicated than a double helix and its structure determines its function. DNA gets bundled up into chromatin, made up of units of nucleosomes: DNA wrapped around histone proteins.
Specific histones are chemically modified to allow the DNA inside to be unpacked, to "open up" the DNA to transcriptional machinery to generate specific proteins. The segments of DNA that open up are dependent on the type of cell — heart, brain, kidney, etc.
While an input of energy might allow DNA to be stretched out flat, it would almost certainly prevent cell-type specific proteins from being made, which rely on the condensed, three-dimensional structure of chromatin to regulate gene expression.

This only applies to eukaryotes and is therefore irrelevant to the question, which is badly thought out and is best ignored.


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Why does affinity of Hemoglobin increases for Oxygen in carbon monoxide poisoning?
I have studied this in almost every physiology book but I just can't understand how carbon monoxide can affect oxygen's affinity to Hemoglobin. I know that there is left shift in oxygen dissociation curve but  why?

Affinity for any ligand to a protein is a function of the shape of the protein which provides some place for the ligand to bind/interact.
Hemoglobin typically exists in tetrameric form: it is a collection of 4 subunits that each bind 1 molecule of oxygen.
The shape of hemoglobin is affected by CO2/pH, which is important for having high affinity for oxygen in the lungs and lower affinity for oxygen in tissues where a lot of CO2 is released (i.e., where there is a high rate of metabolism).
The shape is also affected by binding oxygen itself: binding oxygen to one subunit causes conformational change in the other subunits of the tetramer, increasing their affinity for oxygen. This is called "cooperative binding."
So, how does any of this relate to CO? Well, it turns out that not only does CO bind very tightly to hemoglobin in the place oxygen would normally bind, taking up space and reducing the capacity for oxygen, it also very strongly increases the affinity of the other subunits for oxygen. It increases the affinity enough that even in the low-oxygen high-CO2 environment of the capillaries, carboxyhemoglobin (hemoglobin bound to CO) continues to hang on to rather than release oxygen. This is represented by a shift in the dissociation curve to the left: oxygen stays bound even when the concentration is low.
This means that fewer CO molecules are necessary to cause deficits in oxygen transport than would be needed if it was only taking up space: one CO molecule binding to a hemoglobin tetramer effectively prevents transport of up to 4 molecules of oxygen.
As a quick caveat, I believe some of the biophysics here are still incompletely understood, so please consider this answer to be an approximation and an explanation of experimental findings to a level of precision sufficient to understand the pathophysiology of CO poisoning. More depth is necessary for a biophysical approach.

Roughton, F. J. W., & Darling, R. C. (1944). The effect of carbon monoxide on the oxyhemoglobin dissociation curve. American Journal of Physiology-Legacy Content, 141(1), 17-31.
Eaton, W. A., Henry, E. R., Hofrichter, J., & Mozzarelli, A. (1999). Is cooperative oxygen binding by hemoglobin really understood?. Nature Structural & Molecular Biology, 6(4), 351.

Genuine question, as this is one aspect of Hb I never loved at in my teaching. On the tense/relaxed equilibrium model, can CO be considered as affecting the equilibrium in the opposite direction to hydrogen ions? If so it might be helpful to show that in a diagram.

@David Very generally speaking yes that's accurate, but I'm not sure how the other contributors to the TR equilibrium are affected by CO, or how similar or different the states are in terms of actual structure as opposed to O2 affinity. Not really my area of research but my loose understanding is that the TR model is a good but simplified model, similar to other models I'm more familiar with like the HH gating constants for voltage gated channels.

@David This paper says that CO stabilizes the R-state and thereby increasing oxygen affinity. However, it would be interesting to see if this shift is simply because of less oxygen per Hb i.e. reduced co-operativity or some active mechanism of R-state stabilization by CO. I could not find any structural biology articles on this topic.

@WYSIWYG That makes sense. If CO binds well to the same site as oxygen it would be expected to shift the equilibrium to the R form that binds oxygen (as the poster said, although annoyingly without citation). However the oxygenated Hb is no use to the organism as the effect of CO on the equilibrium prevents or decrease its release. I suppose the point to emphasize is that this occurs where there is a greater concentration of oxygen than CO.

@David I think the Eaton paper would be of interest to you.

It doesn’t. Carbon monoxide has a higher affinity to hemoglobin (as in, binds better to the protein), that’s why it prevents oxygen from binding to hemoglobin.

I would also think this is the case, but could you add sources?

This is part of the toxicity of CO but does not answer the OPs question about oxygen dissociation.

To be precise CO binds to Fe atom. It is almost a very well known fact in co-ordination chemistry that CO (carbonyl) is a very strong ligand. It can therefore "poison" the metalloproteins by binding to the metal. CO can also poison the mitochondrial enzymes but I guess the toxic effects due to Hb poisoning start acting faster.

source: Stack Exchange

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

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How does a neutral allele change relative to a nearby allele under selection?
Suppose I'm looking at a gene being selected against (A) that's decreasing at a rate ($\Delta$P). If there's a nearby allele that is neutral (B) am I correct to assume that B will decrease with A at a rate of $\Delta$P*cM?
So for instance, if A and B are .5 cM from each other and A decreases from .8 to .4, will B decrease from .8 to .6 because there is only a 50% crossover rate between the two?

Depends if your trait is dominant, recessive or additive. You should talk entirely in terms of alleles and not as genes as you have to consider the heterozygote case. Your calculation would be correct for a dominant allele with deleterious effects but not necessarily for a recessive or additive trait.

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


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Where can I find DNA decryption research?
What is the name of the science that studies the mathematics of DNA?
Where can I learn about maths, statistics, types of code, numbers, patterns and graphs for genes and information found in DNA?

There isn't one, because I've never seen it regarded as a science per se, but you are free to invent one. In the meantime you could look up articles in what has been termed "Theoretical Biology", although this encompasses other areas. "Bioinformatics" analyses DNA (and other things) in the way you may be thinking, and appropriate books in that field may give you a start. Try browsing in your university library or bookshop (if you have access to these).

Are you asking about DNA in biology or DNA as a data store for non-biological data? "DNA decryption" mostly returns results for what I would see as a presently silly use of DNA in cryptography.

Yes, to know about all the codes and maths that have been found in Biological DNA, gene lengths, variations, duplicates, randomness of loci, types of markers, to see many graphs that represent what DNA is in numbers, lots of statistics and functional maths... I also only found silly pages about data security keys using  DNA.

You are probably looking for mathematical biology as a whole. Your question is very broad because it is unclear to me if you are talking about genetics in general or if you just want summary statistics for genes in particular organisms. From a mathematical perspective, there is also DNA topology (structural features of the DNA), the field of quantitative genetics (linking phenotypes and genotypes) and the entire field of population genetics (inheritance within populations).

Also "DNA decryption" isn't descriptive enough. There is an emerging field called DNA computing (or nucleic acid computing when including RNA as well) that uses DNA or RNA to perform computation tasks, as well as ongoing efforts to use DNA as a storage medium for information (DNA digital data storage).

I can think of several possible terms for what you could mean (with my interpretation of what people in those fields do):

Computational biology (the study of biological topics using computation)
Bioinformatics (the study of biological topics using computation)
Mathematical biology (the study of biological topics using mathematics)
Sequence analysis (the study of patterns in nucleotide [DNA] and protein sequences)
Genomics (the study of genomes or more generally large quantities of nucleotide sequence)

These all bleed into each other and doubtless other people have different interpretations.
There has been a ton of work in these areas, so they probably cover what you mean, but without some more concrete examples it's a little hard to say which is most appropriate.
As an aside, "DNA decryption" will be interpreted by most people in light of attempts to encode non-biological data in DNA and then decode it (see e.g. george church's stunts). However, based on what you say I think this is not really what you are interested in.
If you are looking for the technical literature for such fields, you could see the following journals, which are some of the better-known peer-reviewed journals focusing on these areas:

Bioinformatics
PLOS Computational Biology
Genome Research
BMC Bioinformatics
Molecular Biology and Evolution

Thanks! awesome answer. When I check what kinds of hackers and computer scientists have used numeric science knowledge to research, decode and classify DNA, only find dna being used for non-biological codes. I want to know, if you gave the DNA code to an elite hacker, who can get into the pentagon... What would he find?

@com.prehensible Just to be clear, this "DNA code" being given to a hacker is a naturally occurring DNA sequence, e.g. human genome or E. coli genome or whatever? Or a random DNA sequence, or something else? Naturally occurring sequences are usually assessed on the basis of deviations from random or comparisons between biological genomes, which have somewhat different "rules", so I'm just trying to understand what your baseline is here.


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Why do protein solutions have to be alkalised in biuret test?
I’ve read that CuSO4 solution reacts with peptide bonds that connect amino acids to create a violet colour, but the instructions always tell me to add NaOH solution to the protein solution before I add CuSO4. How is alkalising the protein solution before adding CuSO4 solution an aid to this process?

The directions explicitly state to add the sodium hydroxide before the copper sulfate? I've never done the biuret test myself, but I can't imagine it would make a difference. Commercially available biuret reagents are sold as premixed solutions.

Can you link the recipe you are talking about?

This is probably to prevent precipitation of copper hydroxide (see Itzhaki & Gill, 1964 - they suggest adding dilute copper sulfate slowly to the NaOH solution to avoid this). If you have the protein already alkalized and ready to react you'll get the color reaction before precipitate forms.
Commercial premixed solutions, like @canadianer mentioned in a comment, have tartrate present to prevent this (Geiger & Bessman, 1972 mention this).
It doesn't seem like it's strictly necessary to add NaOH first, but that's probably the most reliable way to do the assay without using an additional stabilizing agent.

Itzhaki, R. F., & Gill, D. M. (1964). A micro-biuret method for estimating proteins. Analytical biochemistry, 9(4), 401-410.
Geiger, P. J., & Bessman, S. P. (1972). Protein determination by Lowry's method in the presence of sulfhydryl reagents. Analytical biochemistry, 49(2), 467-473.

Wouldn’t adding sodium hydroxide solution to copper sulfate solution encourage the formation of copper hydroxide? https://en.m.wikipedia.org/wiki/Copper(II)_hydroxide

@UbaidHassan Yes exactly, which is why the OPs recipe tells them to add the hydroxide solution to the protein sample first. Might be confusing since my first reference also suggested adding copper sulfate slowly to sodium hydroxide, but that's only because the worst approach would be to add copper sulfate quickly or adding hydroxide to a concentrated copper solution. You use the same procedure with, for example calcium containing solutions that tend to form precipitate: precipitate is minimized when you keep the metal concentration low.

You mix those two chemicals to get a Cu(OH) 2 colloid, if you mixed them earlier it would settle down and not form a colorful complex (as efficiently). Base is added first because (i presume) it denaturates the protein which partly unfolds it, allowing copper ions to form complexes along a greater surface, giving clearer results.


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What's the difference between reaction norms and phenotypic plasticity?
I'm trying to understand better these two concepts, but I cannot see a clear difference yet.
Reaction norm: "set of phenotypes that can be produced by an individual genotype when exposed to different environmental conditions"
Phenotypic plasticity: "ability of individual genotypes to produce different phenotypes when exposed to different environmental conditions"
Are phenotypic plasticity changes temporary changes in genes; are they an extension of the reaction norm?

You should cite the sources from which you are quoting these definitions.

I think it's a little simpler than what you describe- phenotypic plasticity is the abstract property of phenotypes differing with respect to environment, whereas a reaction norm is a particular environmental response.
So you might make an argument like this:
"Daphnia show extensive phenotypic plasticity in their morphology. For example, see the attached figure showing head morphology norms of reaction (y axis) of two Daphnia strains with respect to food richness (x axis)."

This is figure 9 from Woltereck's original publication on reaction norms. It shows that as you grow Daphnia with denser cultures of algae (their food), more individuals in the population show a distinctive head morphology. It shows further that the shape of the curve is similar between two Daphnia strains (solid and dotted lines). Each curve is what Woltereck called a norm of reaction.
Hope that helps.

Phenotypic plasticity, as you define in your question, is an ability or a property of the organism (a given genotype) to manifest different phenotypes in different environments (Pigliucci et al., 2006).
Reaction norm is an analysis of the pattern of phenotypes exhibited in different environments. In other words it is an analysis of the phenotypic plasticity.

I'd pick on this a little. A norm of reaction (at least as originally defined by Woltereck 1909) is the pattern. It is the specific biological phenomenon expressed as differences in phenotype with respect to some environmental variable.

@MaximilianPress usually people represent these patterns as graphs/curves etc and that's what I meant by analysis. Some sources just defined it as a "curve". So I just used the term "analysis" because it appears like a post experiment analysis.

I agree that the representation is normally in the form of some quantitative visualization - but I think it's important to separate the phenomenon (a particular phenotypic response) from the analysis or visualization of the phenomenon (e.g. an ANOVA plot). See also my answer.


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Why has the human eye evolved to become sensitive only to the visible light?
The human eye has evolved to become sensitive only to visible part of the electromagnetic spectrum. Why? Why is infrared vision disfavoured for us by evolution but not for some other animals? I am not an expert of biology but curious.

First hit on google. There are some complete answers there and elsewhere!

I searched google. I found this answer on quora https://www.quora.com/Why-does-the-human-eye-only-see-the-visible-spectrum-Does-the-fact-that-yellow-is-in-the-middle-of-the-spectrum-have-to-do-with-the-sun It says that "because that’s what we evolved to use to find food and mates, and to identify threats to survival. ". But it doesn't make sense to me. Humans also have survival threats at nights.

99% of all the photons in the universe are from the cosmic background radiation, echoes from the big bang, the rest is infrared, save for 0.001% of the photons which are visible. We can sense IR with our skin, UV requires small eyeballs, and yes i want IR vision.

Actually, it's got nothing to do with evolution or even human biology.
Why?

What’s in a name? That which we call a rose,
  By any other name would still smell as sweet. William Shakespeare.

First, try to define visible yourself. Next look at the definition of it in various respected dictionaries; in our context it means

that can be seen

Consider the case of Goffin's cuckatoo, they can see as far up to as ultra-violet spectrum. They don't speak English (or Portuguese for that matter) but for them visible would mean "what they can see".
So, coming back to your question, even if we had capability to see, say, infrared spectrum, visible would have meant: VIBGYOR + infra. And then we'd have complained about not being able to see bacteria with naked eye :P

I think it's pretty clear the OP is not asking for the pedantic answer, nor does the pedantic answer have anything to do with biology.

@BryanKaruse sorry for that. But OP didn't show effort on their part and the question text lacked necessary specifications. Also, OP admits lack of expertise, a bio-physics answer would be pedantic for OP.

shall I find a cockatoo speaking portuguese on YT? :D


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Why is HPV vaccines targeted for preteens?
Why is human papillomavirus products targeted to children before sexual activeness? Could all ages benefit from this vaccine even if they may have or have not contracted a form of HPV to prevent other forms of HPV?
https://okinawa.stripes.com/community-news/preteens-teens-target-audience-hpv-vaccine
I could not find anything where it says it is more effective on younger people vs older people.

What has your research told you? The Biology.SE community has agreed that questions that show little or no prior research effort are off-topic on this site unless you have shown your attempt at an answer. Please [edit] your question and tell us where you've looked for answers, what you do know about the topic, and where exactly you still have questions. Unresearched questions may be subject to down-voting and closure.

@BryanKrause I did could not find if there were a reason other than just to get it before you have HPV.

Well, if you have to get vaccinated before you get infected, why isn't that a good enough reason?

A lot of sexually active adults carry one or another strain of HPV but most do not develop cancer. You can carry HPV — and spread it to others — without showing any symptoms yourself:

HPV infections are so common that nearly all men and women will get at least one type of HPV at some point in their lives. Most people never know that they have been infected and may give HPV to a sex partner without knowing it. Nearly 80 million Americans are currently infected with some type of HPV. About 14 million people in the United States become newly infected each year.

There is less reason to give a vaccine to someone older, generally, who is almost certain to be infected with some form of HPV. A vaccination is not a broad cure, though it can provide some protection against infection from strains of HPV that someone is not already infected with:

But the vaccine also offers some protection for HPV-positive women, reducing cervical lesions by 17% and genital warts by 35%. HPV-positive women usually aren't infected with all four of the targeted strains. In clinical trials, those infected with one or more of these strains before vaccination were protected against the remaining ones.

Pre-teens are unlikely to be infected with any forms of HPV, having no or much less sexual contact, and so they are the best candidates for being administered the vaccine.
This cohort will get the most protection from those strains that the vaccine protects against, strains which are most likely to cause relevant cancers.

From presentations made by oncologists at a cancer survivors support group at MDAnderson ; chances are very high the young people will get some HPV by age 20. The upside is that of the 50+ strains of HPV only a few cause cancers : but why take any chance on cancer ?  Another upside is there is now data that the vaccine works : It took time to show results because the HPV cancers don't develop until over age 40 and usually older ( I was 70). Unfortunately the vaccine was only given to girls at first , it is now recommended for boys and girls . The support group is for Dysphagia/swallow problems which are basically" head and neck  cancers" so mostly from HPV which is why it has been discussed. As these are informal oral presentations I can't site sources but I am certain the information can be found in medical journals.


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Microscope Recommendations
I am a Engineering University student, in my last year of completion of my degree. I had interests in biochemistry and biology since I was a kid, and been learning about that side by side in my spare time.
I want to get into biomedical research and buy a suitable microscope for that purpose.
After following various guides and info I could find, I have decided to go for a well manufactured compound microscope of high quality. But these fishy companies majorly Chinese are troubling me, with top companies like Leica, Nikon, Zeiss etc having quite same reviews.
I haven't yet decided the Manufacturer I want to buy from. I am willing to go for around $1000 for a well reputed manufacturer. There are numerous choices even within the top companies.
What are some best suggestions and recommendations for Compound Microscope according to my needs?

all suggestions are welcomed.
edit 1: Many Indian manufacturers called me, but I want some reliable global manufacturer, well known by its quality. I also need some expandable scope for future upgradations. Am I going the right way or should I buy from Indian manufacturers? and which manufacturer if well known one?
edit 2: The price I am going into is $1000.

What do you actually want to accomplish? A compound microscope isn't going to get you very far in biomedical research.

I am currently going for entry level one. Probably I will invest more later but for now, I want to get the basics clear.

Buy a microscope if you want to pursue a fascination with observing microscopic things as a hobby. But it will be of no use in biochemistry or molecular biology, where your hard skills are most likely to be applicable. The biochemistry labs in my university do not sport a single microscope, and I personally have only ever used one to check cell growth or virus infection (when I have to ask someone else how to use it).

Then I guess, currently I wish to do the basic things(not complex though). Thanks for clearing that out. But where should I start for getting one.

@David: And for a hobby-level microscope, $1500 is way overkill.  (I think I paid under $300 for mine, a few years ago.)  I think you would be better served by spending the extra money on things like a USB camera, polarizing filters, stains, &c.  Plus if you get a job in microbiology or some other field that requires microscope use, your employer will buy your equipment.

I used microscopes my whole adult life: provided by school or employers . I would look for a different job if  microscopes were not provided. Also , considerable support infrastructure is required for microscope  work.

@David Thanks for suggesting that. Maybe I should see the big picture instead of directly going for a high end one.

Can you suggest which manufacturer would be the best for that price range and quality?


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Is it possible to Clone a Dinosaur with a full strand of their DNA?
If you have a full strand of Dinosaur DNA would it be possible to make it living and hatch a dinosaur? Or would it be a failure? Could you use a bird or alligator, for replacein

“A full strand”? Spot the mistake.


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Why are dolphins born tail first?
I heard most dolphins are born tail first. I have read many explanations from books and internet articles and they said that dolphins are born tail first to prevent them from drowning.
But now I don't get this explanation. There must be no air in the mother's womb, so the baby dolphin can't breathe either way. I think they get oxygen from the umbilical cord until it's disconnected.
If this is true, why would they drown if they are born head first? Why are dolphins born tail first unlike most mammals?

Searching on youtube you find videos of head-first births of whales. So, even though tail-first seems to be more common, head-first does work. Since tail-first is otherwise uncommon in mammals, there is probably an evolutionary advantage to it. Maybe drowning becomes a problem in the head-first situation if the process is taking too long.

Cetaceans are born tail first for two reasons:

Avoid drowning
Being in the same direction of the mother.

As you already wrote, they developed this particular way of giving birth to avoid drowning of the calve. As they are mammals like us, they need to breathe immediately after the birth (think about us: we come out in a world of air and we are forced to breathe immediately). So, many complications can occur while giving birth and it may take long time. If calves go out by head first, they can drown easily. On the other hand, as soon as they are totally out, they swim and are forced to go to the surface by the mother in order to have their first breath.
The second reason is that, in this way, they are already in the same direction of the mother, so they can easily swim and recognise her. Imagine being born in a dark pool, where you can't see nothing. A bit confusing right? But they just come out and see the mother, that can guide them easily where to swim, instead of turning back, spend energy and precious time. They have to be quick, because they need to breathe and also need to swim away! A calf is an easy prey!
This adaption came with the evolution of the cetaceans. In fact, some of the ancestors were supposed to give birth head-first just as land mammals. But, as other adaptations to the environment, also this trait was found to be evolutionary successful. Also other mammals were found to give birth in this way (e.g. Manatees and reported cases for pinnipeds. For more references see: Gol’din, P. E. (2011). Case of Cephalic Presentation of a Foetus in a Harbour Porpoise Phocoena phocoena (Cetacea, Phocoenidae), with Notes on Other Aquatic Mammals. Вестник зоологии, (45,№ 5), 473-477. DOI:10.2478/v10058-011-0030-5).
You can find the info I shared here with references: North American Nature (2020). Why Are Whales Mammals? [https://northamericannature.com/why-are-whales-mammals/][1]

Thanks!! I have read in a book that Manatees give birth head or tail first in about fifty-fifty. And hippo, giving birth in the water, seems mostly head-first. I think the head-first would more efficiently resolve breathe issue when they faced problems at umbilical cord during the birth because mothers could lie with her belly up at the surface. But the tail-first has no chance. So I doubted it might not be the breathe problem. The direction problem gave me insight. Now I got interested in birth of Dugongs. They lives far out at ocean, where the direction might be more important in birth.

Of course, cetaceans are really different, as they usually live out in the ocean, so harder in any case than being around the coast:) We also have to consider that we still have a lack of knowledge regarding cetaceans, as they are quite hard to study. But, from what I know and I found, experts agree with those two reasons. Always good to have some discussion too:) And nice to see some interest in a "wired" creature like Dugong!


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What type of moth is this?
 What type of moth is this that was on my wall in Spain

please provide the approximate size of your moth. Also, indicating a bit more info about your location (urban, suburban, rural, etc.) and time (of day; of year) can be helpful in getting an accurate ID

It looks very much like Manulea palliatella, Family Erebidae, Subfamily Arctiinae.
https://commons.wikimedia.org/wiki/Category:Eilema_palliatella
These are present in Spain.


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What's the subpatellar tendon?
I read in Thomas Myers book Anatomy Trains:

Although the muscles themselves have attachments within the anterior
  compartment to the tibia, fibula, and interosseous membrane, the next
  station for the SFL [Superficial Front Line] is at the top of both the medial and lateral side
  of this track, the tibial tuberosity
Continuing in a straight line upward is no problem: the quadriceps
  begin their upward sweep here with the
  subpatellar tendon. The SFL  includes the patella, the large sesamoid bone designed to hold the SFL away from the knee joint
  fulcrum so that the tissues of the quadriceps have more leverage for
  extending the knee.

I can't find the term subpatellar tendon in my anatomy book. What does it refer to? Is it the patella ligament?

Can you add the text before "Continuing in a straight line upward is no problem" and the definition for SFL?

@kmm : I did so.

I suspect that you are correct, "subpatellar tendon" is referring to the patellar ligament. Although it is small, in the image below, (3) is the tibial tuberosity and (5) is the patella. (4) which is labeled "subpatellar tendon" is between the two. The only structure between them is the patellar ligament. So, I think this is what it meant (though in 20 years of teaching, I haven't heard that terminology).


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What did Francis Crick and James Watson discover that Rosalind Franklin didn't?
I've recently been introduced to the history of DNA research from Miescher to Franklin, Crick, and Watson, and I've found that Franklin had figured out a great many number of things out that Crick and Watson are popularly credited for when they 'acquired' her photo, including that:

DNA has a helical shape
The distance between two base pairs is 0.34nm, and each helical turn is made up of 10 bases at 3.4nm
Nitrogenous bases protrude inwards and the sugar-phosphate backbone is on the outside

On that note, did the paper written by Crick and Watson in 1953 result in any information that Franklin herself hadn't figured out? Or were Crick and Watson redundant when it comes to the current model of DNA?

Please do some research before posting. Franklin drew no conclusions from her photo and did no model building. Her x-ray photos do/did not prove the Crick/Watson model of DNA, they were only consistent with it. If you know of evidence or claims that Franklin had deduced one iota of what was in the C&W paper, please cite it. Where did you “find that Franklin had figured out a great number of things …”? Twitter?

Check out the story of "photo 51" one of the first photos of DNA taken under the supervision of Franklin. There is the background information there: https://en.wikipedia.org/wiki/Photo_51 ... you can say that there were some staff migrations, and personality issues. Antibiotics were discovered in France may years previously in a chance experiment, and the thesis was handed in 10 days before christmas and not followed up. Hunger for recognition and for a fight is something males have more of.

There were staff migrations and personality issues, information leaks between researchers and other factors. Her boss annoyed her. Watson and Crick used her geometry of a helix with previously known DNA nucleotides and phosphate from other researchers. She actually had discovered and photographed the helices.
Franklin had obtained the basic structure, shape and measurements of DNA.
Franklin:
She used careful hydration from 75-90% in order to obtain her best pictures. Hydration makes the DNA expand into a visible helical configuration. She used cylindrical Patterson map calculations to determing DNA's density, unit cell size and water content. From this she deduced the basic dimensions of DNA strands, and that the phosphates were on the outside of what was probably a helical structure. Her research was briefed/presented in an internal meeting/seminar at the college and was published officially in 1953 in support of Watson and Crick's presentation.
Watson and Crick:
Watson and Crick suggested a basic framework of a helical molecule for DNA,  Without elaborating precisely. Watson and Crick combine all the findings of other scientists, for the bases and acids of DNA, with Franklin's helix into a synopsis into a correct helical molecular structure. The phosphate and CAGT were already known, and they arranged it into a helix.
Judge for yourself if their research was brilliant research, if it is a discovery, or if it is laying the last pieces of a puzzle assembled by other researchers.
Watson and Crick stayed friends with Franklin after 1954 and shared friendly correspondence and some road trips, and helped with her health issue.
full pdf at .edu source here

If you check that publication, what may seem dishonest is that they iamge a photo by Franklin in support of their work, but only as a blurred photo, when they actually had access to all of her best photos. I haven't been able to find if Franklin published her photos independently in Nature or another magazine.

It was obviously not her best work.
Franklin obtained undenatured DNA gel from a Swiss researcher at Berne university, Rudolf Signer.
She used careful hydration from 75-90% in order to obtain her best pictures. Hydration makes the DNA expand into a visible helical configuration. She used cylindrical Patterson map calculations to determing DNA's density, unit cell size and water content. From this she deduced the basic dimensions of DNA strands, and that the phosphates were on the outside of what was probably a helical structure.
Her research was briefed/presented in an internal meeting/seminar at the college and was published officially in 1953 in support of Watson and Crick's presentation.

The Nobel Prize in Physiology or Medicine was awarded to Watson, Crick and Wilkins in 1962. The prize was not awarded to Franklin; she had died in 1958, and although there was not yet a rule against posthumous awards, the Nobel Committee generally does not make posthumous nominations. Watson suggested that she should have won the nobel prize for chemistry in his book, and Franklin is known through his distorting lenses. Ideally it would be interesting to know what Franklins personal letters and documents told of her research. Perhaps there is an autobiography of franklin? if not there should be one! She had differences with the lab director, professional or personal, we don't know, so she changed labs after only 2 years, leaving Watson and Creek and the research at King's. In july 25,2020 it will be the centenarian of her birth... She is older than Watson and Crick and would be 99 today. Perhaps she was not fond of helices?

This is a statement, but I'm not sure it is an answer to the well-articulated question asked.

Hey thanks, when I read the title to that paper I thought it was about sodium thymonucleate, I failed to add it to the answer information.

"Watson and Crick used her geometry of a helix with previously known DNA amino-acids and phosphate from other researchers." What are 'DNA amino-acids'?

sorry, corrected to nucleic acids.

Please could you correct/clarify two points in your answer. 1. The link http://www.sns.ias.edu/~tlusty/courses/landmark/WatsonCrick1953.pdf is dead. Could you replace it by a permanent link to the paper in the journal. I am not clear what it refers to. The May 30th 1953 paper shown? 2. You seem to imply that the X-ray fibre image entitled "Fig. 1 Fibre diagram..." is of Franklin's work presented in a W&C paper (the one shown?). It is in fact Wilkins' X-ray photo from Nature 171 p.738 (1953). W&C could not and did not publish Franklin's photos, so remarks on that score need removing.

The astounding takeaway from the Watson-Crick paper was their understated recognition that the structure of DNA suggested a scheme for making copies of itself.  This had not been stated before by anyone.  Whether they were in the right place at the right time or had actively prevented Franklin from sharing in the discovery can be debated, but their brilliant deduction clearly contributed a new idea to our understanding of molecular genetics.

Some of the information contained in this post requires additional references. Please [edit] to add citations to reliable sources that support the assertions made here. Unsourced material may be disputed or deleted.

Well, they did win a Nobel Prize.


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Black caterpillar

What kind of caterpillar is this please?

https://owlcation.com/stem/Black-Caterpillar-Identification

It would be good if you can give some context to the location of the animal (country/region/city) where it was found.


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conversion of distance matrices to pdb/coordinates
I am currently facing two transformational issues. Suppose I am given a protein's residue sequence and calpha distance matrix; is there a way to generate the 3d coordinates of the protein's residues from this information(I think there theoretically should be since it is a bijection up to rotation/translation).
The second issue I am faced with is generating pdb files. How does one make a pdb file given the coordinates of the protein's residues along with the sequence? Is this enough information?

We have two questions here: the first one is geometrical rather than biological, the second one would be perhaps better to ask on bioinformatics.SE, but shortly, if you have only coordinates of Cα atoms you can only write a PDB file with coordinates of Cα atoms only.

Concerning the second issue, an easy way is described here. By the way, it is a quite common manipulation under Python, but finding a library can present few difficulties. Concerning the first issue, some advanced features library (such as PyRosetta) shall help you.

@ElieKerArno - Welcome. A link-only answer is not considered an answer. An answer should be self-containing and self-explanatory. Mentioning a source however is great practice. I'm converting this to a comment, but feel free to expand on your comment and post a new improved answer. Check out the help center on answering questions.


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How could pharmaceutical metabolizing bacteria be used to synthesize them?
Lets say I have a pharmaceutical "P". It can be broken down by enzymes of one strain of bacteria into two molecules one of which can be further metabolized enzymatically by a different strain of bacteria. Both strains as a result can decompose "P" to the simplest metabolites.
Could one hope to reverse the reaction using the same enzymes and have the two bacteria produce "P" from basic nutrients and if so, how would the conditions have to be altered? Or perhaps would it be possible ex vivo?

Why are you complicating your question with two bacterial strains. As far as I can see, your question is whether a series of reactions that degrade a xenobiotic could be used to synthesize it, presumably on the premise that all reactions are reversible. Or do I misunderstand you?

You're quite right, however i will clarify that the core of the question is whether enzymes could too strongly affect the reversibility/equillibrium of the reactions, and if not, could this be done with living organisms or perhaps ex vivo? Also since i read about a pharmaceutical decomposed only by a certain two strain coculture i wonder if it would affect the answer in that case.

After posting I realized that you must have a particular situation in mind. My immediate reaction is that it won’t work because of the thermodynamics of synthesis and degradation pathways and the different enzyme specificity required. However I never answer questions in comments. If you need this explaining I’ll do so if nobody else does. But it may be a few days as I have other fish to fry at the moment.

In principle yes, because almost all reactions exist in an equilibrium and enzymes are catalysts (meaning they affect mainly the activation energy for a specific reaction).
The best approach is to purify the enzymes in question (probably not even from their original species, but from another transgenic bacterium), since this reduces your total systems from two different organisms and all their enzymes and metabolites to a very specific set of two enzymes and a handful of metabolites.
But ...

The natural equilibrium of the reaction might favor the more basic metabolites.
Even if you speed up the generation of "P", that won't help much if only a fraction is converted in the first place. Many biological systems deal with this problem by coupling unfavourable steps with hydrolysis of high energy molecules (like ATP), but linking to this to a given enzyme would be a very challenging process.
The enzyme(s) might not be overly specific for "P".
Many enzymes that remove or break down 'unwanted' products can act on multiple similar molecules. This make sense for cells, since its much more efficient to have one enzyme taking care of multiple 'bad things'. However, this makes reversing the process tricky since your reaction will yield multiple products of which only one is interesting. Optimising the enzyme to be more specific is relatively straight forward using in vitro evolution though.
'Basic metabolites' is not a clearly defined thing.
Many pharmaceuticals are pretty complex, and enzymes that break them down likely literally chop it into two pieces. Whether these pieces are actually easy to obtain chemicals that can be used as input for an enzymatic reaction is a different question. Depending on the complexity of 'P' you might have to use a pretty large number of enzymes (all of which may come with the above mentioned problems) to be able to start from reasonably basic molecules.


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Why does centipede keep running into my hair and bite me?
After I moved into a new house in the suburban area, I was bitten by an unknown creature near my spine at mid-night. I felt painful and dizzy. However, after 15 mins, I no longer felt dizzy and the pain faded, so I did not see a doctor.
Serveral months later, the same thing happened again at mid-night, the creature ran into my hair (I have long hair) and bit the back of my neck. This time we figured out that it was probably a centipede, as it was red, had many legs, and ran fast.
Yesterday, a centipede ran into my hair again in the morning. Luckily, I felt something was in my hair and I manged to shake off the centipede, so it did not bite me.
Why does centipede keep running into my hair and bite me and what should I do?

It could be useful to first identify the centipede. Did you catch it? The more common centipede in houses is [https://en.wikipedia.org/wiki/Scutigera_coleoptrata], I have seen it in my house but it never tried to bite us.

@heracho Yes, we caught it but sadly we didn't take any photo of it. It looks like https://en.wikipedia.org/wiki/Geophilus_flavus (brownish red & long)


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Immune response to IgA positive bacteria
If certain bacteria can be coated with IgA in vitro, does that mean they are likely to elicit an IgA immune response?
Edit
I'm working on a project that involves IgA-Seq analysis. Bacteria are coated with IgA and then sorted for how much IgA they actually ended up having on them. I'm a biostatistician, so I don't know the biochemical details. But I'm assuming that the IgA binds to receptors on the surface of some bacterial more than others. I was wondering if that was related to immune response. I tried googling, but couldn't find much.

Can you clarify what you mean by "coated with IgA"? Do you mean the bacteria bind to the constant region of the IgA heavy chain, or the variable region (which would presumably be shared with other isotopes during class switching)?

Hi @iayork. I added some information to the question.

Depending on the precise details of the experiment, I don't see a particular reason to suppose that being coated with IgA should mean that they'll elicit an IgA response.
I'm assuming that the "coating with IgA" means that the IgA is binding like an antibody, through the variable region binding site on the antibody to some epitope(s) on the bacteria. The way antibody class switching works is that the epitope binding region of the antibody remains the same while the constant regions switch from IgM to IgG or IgA, etc. That means that the ability to bind to the bacteria appeared in a non-IgA antibody, so the ability to bind, per se, is more or less separate from the isotype of the antibody.
The factors that drive a response toward IgA are heavily influenced by location - a response on a mucosal surface is much more likely to drive IgA than one that's systemic (simplistically, because the cytokines and cell types involved are different in the different locations).
An alternate possibility is that the IgA is binding the bacteria through its constant (Fc) region, analogous to Protein A.  If the bacteria have evolved an IgA-binding capability in this way, one might guess that they did so because they need it as a defense, and if it's specific to IgA one might guess that it's because they tend to have an IgA-dominant response. But that's an inference, not a strong argument. As a counterargument to that, Protein A does (sometimes) bind to IgA and that's likely more of a side effect than a primary thing.
So I think the answer is "probably not, but you'd need more information to have a good answer."


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After SRS, does the tissue that was previously the penis develop into actual, differentiated vaginal tissue?
I keep being told othereise, that the redulting "neo-vagina" isn't 'proper' vagina. This site is the only one that gave me a definitive explanation but I would like too see if there are more.

What is SRS, for those who don't know?

@kmm, SRS is 'sexual reassignment surgery.'

It's true that the microbiome and microscopic structure of the neovagina are not the same as those of a natal vagina, although explicating this outside of circumstances relating to post-surgical dysfunction or pathology seems unnecessary and a potential source of discrimination. Whether post-surgical outcomes are "proper," as you put it, should be evaluated on the basis of patient satisfaction and nothing else, especially not appraisals of minute features.

The medical care of the neovagina of transgender women: a review, Cornelisse et al. Sexual Health. 2017. Emphasis mine.
Microbiology of the neovagina
When assessing a troublesome discharge or bleeding from a neovagina, it is important to keep in mind that the histology and microflora of the neovagina is different from that found in the natal vagina, and hence the aetiology of vaginal discharge in trans women is different from that of cis women. Premenopausal cis women have a vaginal epithelium constructed of glycogen-rich epithelial cells that support the growth of lactobacilli, these produce lactic acid to maintain an acidic vaginal pH and so help to curb the growth of other commensal bacteria. When this mechanism fails, the resultant bacterial vaginosis is characterised by an overgrowth of Gardnerella vaginalis and other anaerobic vaginal bacteria. Neovaginas are not lined by a glycogen-rich epithelium. The microbiology of neovaginas created by penile infibulation and those created by intestinal grafts are discussed separately below.

These more in-depth discussions of the various microbiomes imparted by different approaches to constructing a neovagina begin on the third page (444) of the linked PDF.

I was talking about tissue differentiation. https://web.archive.org/web/20031125030637/http://www.gendercare.com/library/italiano_paper1.html

“Microscopic structure” and “histology” are synonyms for what you’re referring to as tissue differentiation. The cellular phenotypes in the neovagina are not the same as in a natal vagina — ”Neovaginas are not lined by a glycogen-rich epithelium.”

According to my link "They are only partially correct, since the normal female vaginal tissue is not truly mucosa either. It is called mucosa only because it lines a body passageway. It contains no mucous-secreting glands (Fawcett, et. al., 1995). That is why lubrication is a transudate phenomenon, the source being dilation of the capillaries that surround the barrel and the subsequent squeezing out of fluid through the vaginal walls, which in normal and artificially constructed vaginas have been shown to be a functioning two-way membrane"  Is this true?

You're asking about mucus production, then, and not tissue differentiation. It's true that lubrication is a transudative phenomenon, but the basal fluid in the neovagina is not the same as in a natal vagina: "The basal fluid in the vagina is in fact not produced from a single source but is a mixture of fluids from...the fallopian tubes, the uterus, the cervix and...the vestibular glands (Bartholin's glands)..."


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What species would this be?
A common way to define species can be found on Wikipedia:

A species is often defined as the largest group of organisms in which any two individuals of the appropriate sexes or mating types can produce fertile offspring

This got me thinking. Imagine the case where we have three "groups": A, B and C, where A and B cannot produce fertile offspring together (different species) but C can produce fertile offspring with both A and B.
Have this ever been observed? And how would you classify C?

This is a good example of why reproduction is an exceedingly poor defining characteristic of species. Evolutionary biologists, and taxonomists (the people who describe species) do not use the biological species concept (based on reproduction), but rather, the evolutionary species concept, based on fixed characters.

What you describe is called a ring species. From wikipedia:

In biology, a ring species is a connected series of neighbouring populations, each of which can interbreed with closely sited related populations, but for which there exist at least two "end" populations in the series, which are too distantly related to interbreed, though there is a potential gene flow between each "linked" population.1 Such non-breeding, though genetically connected, "end" populations may co-exist in the same region (sympatry) thus closing a "ring".

Have this ever been observed?

While ring species is a classical theoretical concept, the cases of ring species is often open to some interpretation and limit case of what we want to call a ring species.
The question has been asked at Do ring species exist?, however the post is still left unanswered.

And how would you classify C?

There is no obvious simple way to answer that question. The concept of ring species just shed light into the fact that the concept of species is an outdated concept and does not have a good formal definition. For much more discussion about the concept of species you should definitely have a look at the post How could humans have interbred with Neanderthals if we're a different species?.


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Can a person survive on blood in place of water?
This question: Can you get enough water by eating only fish? asks if a person could survive on fish alone. Can a person survive on fish and/ or blood alone of any species if stuck at sea or animal blood as a last resort where there is no water or fire?
Obviously if it was a fresh water fish there is water, but there are fresh water mud skippers that can breathe air and the water to tainted to drink in that case a fresh water fish blood maybe safer than the water. https://chemistry.stackexchange.com/questions/115901/what-can-i-eat-that-will-help-metabolize-blood
Desalination would be the best way to process the blood but this is in emergency situation scenario.
From @PTwr Comment's Link: If you drink blood regularly, over a long period of time the buildup of iron in your system can cause iron overload. This syndrome, which sometimes affects people who have repeated blood transfusions, is one of the few conditions for which the correct treatment is bloodletting. https://what-if.xkcd.com/98/

What level of processing is allowed?

Obligatory XKCD reference.

@PTwr good find . I have included some of it into the question. Thanks

Note fish blood contains a lot less hemoglobin. some fish lack it entirely.

You'd have no problem substituting blood for water, provided:

You allowed it to coagulate first, and
You prevented it from evaporating

Fresh blood has a high concentration of protein, certainly, but it's not a homogeneous fluid.  If you decanted the blood into a container and let it sit, it would soon coagulate, causing the majority of the cellular and protein components to precipitate and stratify.
The plasma fraction (approximately 55% in healthy mammals, and not radically different in most species with hemoglobin) forms a supernatant (the top, easily accessible layer) which is 95% pure water by volume and about 5% protein.
The sodium salt concentration of plasma is about 140 mEq/L, or 3.2 g per L (mEq = mg / atomic weight * valence, Online Calculator).  Since healthy kidneys can concentrate salt to 4-5X osmolality (and since the source material is physiologic blood), you'd have no problem drinking the top, liquid portion.  You would also avoid most of the long term iron issues as the hemoglobin is found in the erythrocyte (deposited) fraction.
Thirsty vampires will be disappointed that plasma appears amber, not "blood red"

@Jan, total osmolality for blood plasma is 275-300 mOsm/kg - see https://www.sciencedirect.com/topics/medicine-and-dentistry/plasma-osmolality for a reference.  This encompasses salts, glucose and soluble proteins.

@Jan, not clear what you mean by net water.  If you take a 1 L blood volume, 55% of that (the plasma) is 550 mL.  Is that what you mean?

@Jan - I'm not sure the back and forth is helpful, but I think you're missing that the kidneys serve to actively concentrate fluid.  Remember, your kidneys are actively concentrating your entire blood plasma volume about 60 times per day (which just like the orally consumed plasma is about 300 mOsm/L).  Kidney input is 300 mOsm/L, and output can go to 1500 mOsm/L.  For example, the original WHO Oral Rehydration Solution was 311 mOsm/L WHO ORS and rehydrates.  Also the "protein" in plasma is predominantly urea already.

@Kvohte, urea needs to be removed from the blood by urine. Consumption of 25 g protein (5% of protein in 500 mL of plasma) will result in 25 x 8 = 200 mL of urine, because 1 gram of protein results in the amount of urea that needs 8 mL of water to be excreted  ( nap.edu/read/10925/chapter/6#135 ). This means that by drinking 500 mL of water from plasma, you get only 300 mL of net water because the urea will force 200 mL of it out into the urine. Do you agree with this? So, plasma would be still hydrating, but not as much as it seems. I need to think about sodium effect a bit more.

Can't believe this question was accepted, blood literally kills you if you drink it...

Blood is not a good source of water.
1 liter of blood contains about 800 mL of water, 170 grams of protein and 2 grams of sodium (calculated from the composition of lamb blood).
When metabolized, 170 grams of protein yields the amount of urea that requires 1,360 mL of water to be excreted in urine (calculated from here); 2 grams of sodium requires about 140 mL of water to be excreted (from here).
This means that drinking 1 liter of blood, which contains 800 mL of water, will result in 1,500 mL of water loss through the kidneys, which will leave you with 700 mL of negative water balance.
Fish blood can contain less protein, for example, trout (check Table 1) contains about 120 g of protein (plasma protein + hemoglobin) per liter of blood. Using the same calculation as above (1 g protein results in the excretion of 8 mL of urine), drinking of 1 liter of trout blood, which contains about 880 mL of water, will result in 960 mL of urine, so in 80 mL of negative water balance.
Turtle blood can contain about 80 g of protein (plasma protein + hemoglobin) and 3.4 g of sodium per liter. Drinking 1 liter of turtle blood, which contains about 920 mL of water, will result in 80 x 8 mL = 640 mL loss of urine due to protein, and ~240 mL due to sodium, which is 880 mL of urine in total. This leaves you with 40 mL of positive water balance (to get 2 liters of water per day you would need to drink 50 liters of turtle blood, which isn't realistic.
In various stories (The Atlantic, The Diplomat, The Telegraph), according to which people have survived by drinking turtle blood, they have also drunk rainwater, so we can't conclude it was turtle blood that helped them. I'm not aware of any story that would provide a convincing evidence that the blood of turtle or any other animal is hydrating.

I think this answer addresses the main reasons. The iron issue may be a long term problem but most single foods will cause long term problems if one tries to feed on them exclusivley.

Assuming a sufficient supply, could you drink a lot of blood and eventually get to a point where the protein is no longer metabolized?

Normally, protein does not accumulate in your body, so it is metabolized even if you consume it in excess. Excessive protein is mainly converted to body fat.

Wouldn't a dehydrated body stop even picking up the protein from the small intestine and only absorb water? (just a guess) This also doesn't get rid of the sodium problem, but that is not so severe..

Protein absorption would stop only in severe dehydration. As long the water is absorbed, the protein will likely be absorbed too.

Question revised.

Blood of what, not all blood is the same. fish blood can vary quite a lot in protein composition.however it is true that all the reported cases of drinking fish blood for survival also included capturing rain water, fish blood being used to stretch water not as a complete replacement.

You can drink blood of course to a minimalistic amount (eg- a few teaspoons ) and also if blood is free from pathogens. But it should always be in very small amounts and from suitable donor. Here's why

The strange fact is, blood, when drank, is toxic. When confined to places where blood is supposed to be — such as the heart, vessels, and so on — it is essential for life. But when ingested it's a very different story.

Now why is it even harmful?

Haemochromatosis- this is a disease where your body has excess iron/ iron overdose which gets deposited in organs such as heart, liver , pancreas etc. This happens because blood is very much rich in iron but our body doesn't have any suitable mechanism to excrete the excess iron.
(There is some doubt with the actual cause of Haemochromatosis. It is a disease related to iron overdose but its not sure whether the main cause is genetic or it can be anything related to diet as well.)
Blood related disorders, eg :- AIDS, Hepatitis B etc - If blood is not taken from a suitable donor or the equipments you use to take it in are not sterilised properly, you'll probably contract one of these disorders, which are absolutely life threatening.
Malnutrition- Although blood contains 93% proteins and 1% carbs , blood is terribly low in minerals and vitamins.

So basically blood taken in small amounts will have no harm on you, but you surely can't survive on blood.
For the sources, visit - https://www.livescience.com/15899-drinking-blood-safe.html
https://www.sciencefocus.com/the-human-body/could-i-live-as-a-vampire-by-just-drinking-blood/
https://medicalxpress.com/news/2018-04-bad-blood.html

Could you please cite your references? Who made the  statement you're quoting?

@Arsak This whole answer has been taken from multiple sources, but the one i quoted is from https://www.livescience.com/15899-drinking-blood-safe.html

You should add this and the other sources to your post. It would surely improve your answer.

@Arsak thankyou so much for the suggestion, I have added the sources.

Haemochromatosis is a genetic disorder found in those of European descent, and common among those with Irish descent. It has nothing to do with drinking blood, but involves a variant chemistry for white blood cells.

@PieterGeerkens Please check out this link https://www.livescience.com/15899-drinking-blood-safe.html  I also checked onto this, and the defination is coming the same you are referring to. But maybe there are two sides to this, or maybe I am wrong. Anyways, please check onto this link and let me know about what's right.

@Ishi: The author is a writer and editor, not a scientist: "Benjamin Radford is deputy editor of Skeptical Inquirer science magazine and author of six books including Scientific Paranormal Investigation: How to Solve Unexplained Mysteries." Absence actual scientific evidence, this article is not worth the paper it was written on.

@PieterGeerkens thankyou so much for giving me the correct information, I'll immediately remove it from the answer as I don't want any ambiguity in the OP's mind.

@PieterGeerkens I'm pretty sure haemochromatosis is too much iron, regardless of the cause.  The genetic disorder is just the common cause, but it's still called haemochromatosis if it's dietary.

@JMac: Haemochromatosis is specifically too much ferritin, a particular iron compound used by the body to dispose of iron. This disposition is done through elimination of the white blood cells that create ferritin. Thinking that haemochromatosis is too much iron kills people - like my dad, whose physician refused to listen to experts such as Paul Adams: Honorary Fellowship for Distinction - Royal College of Physicians of Ireland 2013. You are thinking of iron overload, the generic syndrome.

@PieterGeerkens It seems like the definitions are themselves highly inconsistent.  Some places refer to hereditary haemochromatosis as just haemochromatosis, where you will find other sources which consider iron overload to be a form of haemochromatosis that is non-hereditary.

It's very difficult to be infected by HIV orally.

#2 and #3 don't seem particularly relevant. Yes, you can contract blood-borne diseases by drinking blood, but you can also contract water-borne diseases by drinking water. The fact that some blood is infected with disease doesn't make it an unsuitable replacement for water. And water contains no vitamins, and single-digit %DV of many minerals, depending on the source - I don't see how you could become malnourished by replacing part of your diet that has marginal nutritional value to begin with.

@PieterGeerkens Seems like they're not much of an editor, either, saying "when drank" rather than "when drunk".

@forest And usually more fun than drinking blood. Well. Depends on one's inclinations, I suppose.

sorry to -1, but the few teaspoons are too far off the mark. Upper Daily Intake, i.e. daily iron intake that is tolerable long term for healthy people without being likely to lead to health issues according to NIH (https://ods.od.nih.gov/factsheets/Iron-HealthProfessional/) is about 45 mg. Calculating with 500 mg Fe/l blood (http://www.jbc.org/content/104/1/157.full.pdf - that's human, didn't find fish info) and 15 - 35 % absorption (https://academic.oup.com/ajcn/article/91/5/1461S/4597424) means that UDI is reached somewhere between 250 and 600 ml blood per day. That's 50 - 120 teaspoons.

Acute trouble from too much iron occurs at > 20 mg/kg body weight (NIH). That would be around 8 l blood. And then, that trouble is mainly gastro-instestinal, not iron-storage/ferritin related. (I'm assuming that anyone with hereditary hematochromatosis will immediately discard the "solution" in OPs question. Just as anyone with fish allergy would.)

Also, note that (cow/zebu) blood is a major part of traditional Maasai diet (https://en.wikipedia.org/wiki/Maasai_people#Diet) - which is just one ethnicity among many who eat blood (and liver) sausages (https://en.wikipedia.org/wiki/Blood_sausage). Coming from a blood and liver sausage region, I can say that a serving blood sausage in a hot main meal (lunch/dinner) may be ≈ 150 - 200 g or 50 - 130 g blood ≈ 25 - 60 mg Fe (liver: 15 mg/serving). Main health concern here is usually not iron intake but lipids. (Anyways these traditional meals that are not eaten daily)

@cbeleites don't they drink water and have any other food? Because i'm here exclusively talking about "surviving on blood"

Ishi: of course they do (so do the "vampires" in your links). As @Jan's answer points out everyone has to: the protein content alone means that humans (and many carnivores) need additional water. Any amount of blood does increase thirst instead of quenching it. I should have been more precise and stated that my comments are concerned with your point 1 (2 and 3 already being taken care of by Nuclear Wang). Thus, I consider your answer to give 3 bad reasons against drinking blood while omitting the relevant one.

@cbeleites some fish lack hemoglobin entirely so iron levels are very low.

Bonus question?

Here is a specific account of a person surviving at sea drinking turtle blood, while eating some fish and drinking some rain water.
Several peoples have a habit of drinking raw animal blood, at least for ritual purposes; here is a recent account. They probably drink more than a few spoons full so that the Lifescience article quoted by Ishi appears alarmist.

It is very unlikely that blood from any animal, including turtles, will be hydrating and we can't just rely on a story.

@Jan Well, obviously it depends on how much water you ingest from other sources, and perhaps even on the food (because there is metabolic water). The body will also adapt to not having enough water (perhaps even by using stress metabolic pathways, like excreting uric acid?); the numbers found are surely the optimal, healthy ones. Apparently, blood is a net water drain under normal conditions, but whether that holds if there is little water overall is not immediately clear to me.

@Jan I also find refuting concrete evidence with "we can't just rely on a story" unsatisfying. What is science if not the collection and interpretation of stories? Of course ideally stories which have been intentionally and carefully produced, but stories nonetheless.

The first source you linked says that "We're not sure just how long you can survive off turtle blood, but Ivan did say that he was also drinking rainwater." We do not know the amount of rainwater he drank, so we cannot conclude that drinking turtle's blood helped. We can rely on stories and learn from them, when they clearly say what exactly happened, but we do not know this here.

Very informative and the answer could then be yes indefinitely.

@Muze Careful (that's why I didn't agree with your edit): I think Jan has a point. While blood is nutritious (which may have helped the survivor) it may indeed remove water from the body when it metabolizes the protein. That water must be ingested in addition to the minimum amount without blood. But it's also possible that when dehydrated the body can metabolize the protein through different pathways, or with less water, or simply excretes excess protein, but I could not find anything about it.

In the intestine, macronutrients (carbohydrates, fats and proteins) are usually completely or nearly completely absorbed. You can't hope your intestine will filter out protein and absorb only water. It is possible that intestine does not absorb all the protein when ingested in great amounts - in this case it will trigger diarrhea with a great loss of water.

@Jan That makes sense; but perhaps it could be removed from the blood (and be excreted) without metabolizing it? I read that it is a sign of kidney desease to have protein in the urine, but that would make sense under dehydration which stresses the kidneys. It could even be a sign for damage (due to dehydration) but still lead to more available water.

Excessive protein (amino acids) enters the cells, where it is converted mainly to fat - this process yields nitrogen, which is removed from the body via urine in the form of urea, which drags some water with it. So, it is exactly this "protein removal" that causes dehydration. In healthy people, unmetabolized protein is not excreted into the urine or otherwise and, in short-term, cannot be stored somewhere in the body in great amounts.

@Jan comments are temporary and these comments would be relevant in your answer.


text:
Why is beta- D fructofuranose two different structures when in free form and as part of sucrose?
This is the structure of fructose in free form:

The right moiety is the fructose as part of sucrose. The left one being glucose:

Both of the fructose are beta-D fructofuranose. But as it can be seen they both are clearly completely different structures. The anomeric hydroxyl group seems to be in an opposite position while the rest of the structure hasn't even changed shape.
Where am I getting this wrong. Thanks.

In sucrose, the two saccharides are linked by their anomeric carbons.

I'll try to explain this to you, but you should really look it up here: https://pubchem.ncbi.nlm.nih.gov/compound/beta-Levulose#section=3D-Conformer&fullscreen=true
This is the structure of beta-D-fructofuranose, as a 3D conformer. On paper, or as a 2D figure, we cannot visualize the -OH groups at positions 3 and 4.

They appear to be inside/outside the ring, but in reality, they're not really positioned that way. Both the -OH groups are oriented in an opposite manner, but in a plane perpendicular to that of the furan ring.
So when we flip it over to represent it in sucrose, the orientation of the -OH groups in the molecule flips too.
Think of it this way: if you have a piece of cardboard  (representing the ring) with a pin pierced into it (representing the -OH), and you flip the board over, the pointy side of the pin will face down too.
Moreover, if we represent it this way, the absolute configuration of the side chains at each of the carbons of fructose remain the same.
You could check that using their RS configurations.
For more on RS configurations, check out : https://chem.libretexts.org/Bookshelves/Organic_Chemistry/Supplemental_Modules_(Organic_Chemistry)/Chirality/Absolute_Configuration%2C_R-S_Sequence_Rules


text:
does anyone know what snake is this? found on my other family home
pic might be a little dark because it was on night

thank you very much for your answer

welcome. For species ID we need the geographical location (country, state) where you found it, and possibly also what time of year it was, temperature and what kind of habitat it might have coming from (is there forest around your home, ore are you way up in the mountains etc)

Looks like a constrictor, many of which are kept (and released) as pets. So the location my not be an indicator. In any case, it is not venomous.

It is a Boa constrictor. Like the comment mentioned, the geographic location helps. If you are in southern Central America or South America, it's probably native; elsewhere, it's probably someone's escaped pet. They are non-venomous, but will defend themselves if they are threatened or harassed by hissing and striking. They have many, small, very sharp teeth that could easily lacerate your skin, but not deeply.
These snakes populations are very, very reduced, so please do not harm it since it does not want to interact with you at all. They eat rodents and other pests, so it's good to keep their numbers up. They are also magnificently beautiful and have very interesting biology (for example, they give live birth and have pits on their faces that help them sense infrared!).


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Dna based question
We know that dna is an acid which is elaborated by deoxyribo nucleic acid.It has 4 nucleo bases.Now,the question arises, why dna has no uracil base?

this question has been already answered on SE. The link is given below:- https://biology.stackexchange.com/questions/171/why-is-thymine-rather-than-uracil-used-in-dna

First of all, uracil can be in DNA.
Cytosine can spontaneously convert to uracil by a process called hydrolytic desamination. This causes guanine, which was originally bound to this cytosine, to be bound to uracil instead (remember: uracil normally binds to adenine). The next time the cell replicates its DNA, the place opposite this uracil would be occupied by adenine instead of guanine, correctly changing the information on this DNA section. This process of cytosine deamination is one of the most common DNA damage, but it is usually effectively corrected.
In DNA, thymine replaces uracil. Uracil can be produced relatively easily from cytosine by deamination and hydrolysis, which then alters (mutates) the base sequence and possibly alters the information genetically encoded in the nucleotide sequence.
Desamination of cytosine to uracil
Thymine, on the other hand, differs from uracil in that it has an additional methyl group and thus cannot easily be formed from cytosine. Uracil present in the DNA can thus be recognized as a mutation and exchanged for cytosine by base excision repair.

This question is a duplicate (as well as badly written); so your answer here would not be very useful. You can post an answer to the linked question if you think it addresses an issue not covered by other answers.


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Are epigenetic modifications the most stable mechanisms for cell differentiation?
Wondering what the general take is on what are the molecular mechanisms that are mostly responsible for cell type differentiation stability; ie, for a cell's identity to actually become 'locked in' and progressively less susceptible to extracellular cues (for example, in heterotopic transplantation experiments such as Sue McConnell's).
I'm pretty convinced it really comes down to DNA methylation / chromatin remodelling / histone modifications in order to reach those truly stable, self-perpetuating, differentiated cell identities, but haven't been able to find a paper or review that actually discusses this. Your suggestions and opinions are welcome.
Also posted on reddit/labrats
Edit: I suppose another way to ask this is: Are Waddington's stable "attractor cell states" most likely or most easily explained by epigenetic modifications such as DNA methylation?

Epigenetic marks are reversible (you might be aware of induced pluripotent cells). Many animals can regenerate organs with high tissue complexity (such as a limb) and this involves de-differentiation in some species (Sandoval-Guzman et al., 2014). Even otherwise, cells can respond to extracellular/environmental cues to modify their epigenetic state (for e.g. EMT involved in wound healing). I would still consider epigenetic marks to be more "stable" than simple regulatory mechanisms.
Only way for a cell's identity to actually become 'locked in' is by genetic changes. The maturation of lymphocytes (especially the B-cells), would be a good example. These genetic changes happen via V(D)J recombination, class-switching recombination and somatic hypermutation.
L1 retrotransposons are also known to contribute to somatic heterogeneity in the brain neurons. However, the frequency of insertions is not very high (Evrony et al., 2012).


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Are there any non-pathogenic gram-positive bacteria in human gut?
I wish to know if there are any non-pathogenic (not even opportunistic pathogen) gram-positive bacteria in the human gut? Is there any reference that shows there exists a non-pathogenic gram-positive bacterium in the human gut?
I searched the internet but was unable to find anything conclusive.

A recent Nature article, entitled A new genomic blueprint of the human gut microbiota, contains the following Figure:

[Fig. 3 Phylogeny of reference and uncultured human gut bacterial genomes]
I don’t know much about bacteria, but, according to their entries in Wikipedia, Actinobacteria, and most Firmicutes are gram-positive and, as these appear to be present in abundance in the human gut of healthy individuals, one assumes that they are not pathogenic to humans.

Link to wiki: https://en.m.wikipedia.org/wiki/Gut_flora
Found this under Composition -> Intestines:
The small intestine contains a trace amount of microorganisms due to the proximity and influence of the stomach. Gram-positive cocci and rod-shaped bacteria are the predominant microorganisms found in the small intestine.


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What proportion of the people who lived 1000 years ago have genetic descendants alive today?
For context, I've been wondering about this for a paper I'm writing (in philosophy). Really, I want to figure out the chances that someone alive today will end up still having descendants 1000 years in the future. But people from 1000 years ago should be a good approximation.
So, any ideas? And are there any published papers which talk about this?

This related question would be a place to start https://biology.stackexchange.com/questions/36715/what-is-the-percentage-of-people-living-in-england-in-1500-ad-whose-lineage-is-s?rq=1

This is not a full answer, but I post it as one because the reasoning is too long to post it as a comment.
You can make a rough estimation using a few assumptions.
1) Let's say 1 generation = 25 years, so 1000 years are 40 generations.
2) Let's say that half of the population is able to leave offspring, so the probability of one individual having descendants = 0.5
3) Supposing that the average number of siblings is 3.

The probability of not having descendants in the 2nd generation  = 0.5
The probability of not having descendants in the 3rd generation is 0.5*(1-0.5^3) = 0.4375

After the 3rd generation, it becomes a combinatorial problem that is too hard for me. I can tell that the probability of not having offsprings, giving that it already has, is going to 0 because of the number of offspring > 2
If this approach appears useful, I suggest you ask for a more complete solution on https://math.stackexchange.com/

Expanding on @heracho's answer and Wikipedia, assume pi denotes the probability of having (exactly) i children, and that dm denotes the probability of extinction by the mth generation (note that this includes extinctions by all generations n with n < m). Then dm can be expressed as:
$\displaystyle d_m = p_0 + p_1 d_{m-1} + p_2 d_{m-1}^2 + p_3 d_{m-1}^3 + \dots = \sum_{i=0}^\infty p_i d_{m-1}^i$
with d0 = 0.
In other words, the probability of going extinct by the mth generation is equal to the probability of i children going extinct in m – 1 generations, summed over i. (The child lineages are assumed independent.) This recurrence relation allows you to calculate the extinction (and, by extension, survival) probability at any desired number of generations, if the values of pi are known. In simple cases it is also possible to work out the asymptotic value of dm by solving the fixed point equation dm = dm – 1 (see the Wikipedia page for an example).
In relation to your specific application, we can assume roughly 40 generations and use some empirical estimates of pi. The parity distribution of Denmark is given by Frejka (2008) as p0 = 0.127, p1 = 0.179, p2 = 0.443, p3 = 0.251 (where I simplify by assuming that people who have strictly more than 3 children actually have only 3 children). Plugging these parameters into the recurrence relation and iterating for 40 generations (see R code below), we get d40 = 0.17. Thus some 83% of the population can be assumed to have descendants in 1000 years.
I have taken Denmark as an example simply because it is the first country mentioned in Table 2 of Frejka (2008). However, to illustrate the dependence of the asymptotic value of dm on the parity parameters consider the case of Italy. From the same publication, we find p0 = 0.240, p1 = 0.235, p2 = 0.369, p3 = 0.156. With these values, we compute d40 = 0.41, obviously a very different situation.
I am not a mathematician, nor a biologist (nor a demographer), and the above logic obviously employs many ridiculous simplifications. It would be very interesting to know how all this pans out in a more realistic model.
Reference
Frejka, Tomas (2008) Parity distribution and completed family size in Europe: Incipient decline of the two-child family model? Demographic Research, 19(4): 47–72. https://www.demographic-research.org/volumes/vol19/4/19-4.pdf
R code
# get extinction probability (d) in generation m, given extinction
# probability in generation m-1, conditioned on probabilities
# of having 0, 1, 2, ... children (vector p)
extinctionprob <- function(d, p) {
  d <- d^(0:(length(p)-1))
  sum(d*p)
}

# iterate for 'ngen' generations
iterate <- function(ngen, p) {
  d <- 0
  for (i in 1:ngen) d <- extinctionprob(d, p)
  d
}

# usage example:
# iterate(ngen=40, p=c(0.240, 0.235, 0.369, 0.156))


text:
Do snails like water?
Simply question, do snail show when it's raining because they like it or/and need hydration and food or are they showing up just to escape somewhere, because they're scared of drowning?

Most types of snails survive droughts (that would kill otherwise through Dehydratation) by producing much mucos around themselves. This mucos will dry out if the sun comes up, so they hide under leaves or in the ground. If it's raining, those rings of mucos hydralise or "melt" and the snail begins to crawl. Like most amphibians snail take their oxygen by their skin furthermore they have lungs. By raninning they start moving for searching food, cause they dry out in sun.


text:
What does it mean for a gametocyte to "reprogram" the genes inside of it?
I am aware that frequently clones have genetic defects not present in the donor organism, even though the two are genetically identical. The reason for this is that apparently the enclosing gametocyte "reprograms" the genes inside of itself and during the cloning process, this reprogramming is not completed because the novel DNA is in the host gametocyte for too brief a period. Here is a quote from an article on the subject:

In cloning, scientists slip a cell from an adult into an egg with its
  genetic material removed. The egg then reprograms the adult cell's
  genes so that they are ready to direct the development of an embryo,
  then a fetus, then a newborn that is genetically identical to the
  adult whose cell was used to start the process.

What do they mean by "reprogram" the cell's genes? How can a germ cell modify its own nucleus in a way that would not affect the base pair sequencing?

More detail please. Clones of what? And the source of your quotation.

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


text:
Killer whale color
What purpose does the B/W killer whale color scheme serve? And what evolutionary pressure could possibly force all of them to go B/W in such a peculiar way ie with weird patches in the black. Also why not deep blue rather than black? And their diets are mostly near sea surface so I don't see how it helps them hunt, as stated in wiki

Interesting question. Can you please link to the wikipedia article and clarify where in the wikipedia article they claim that it their color pattern help them hunt (I think this the claim you are making when referring to wikipedia but I am not sure, so clarification would be welcome if I got this wrong).

https://en.wikipedia.org/wiki/Killer_whale#Feeding

You can edit your question to add this link in your question and clearly quote the passage that makes the claim that their color pattern help them hunt.

Although I'm not much into animal science, but let me try my hands on it.
The entire dorsal (top) surface and pectoral flippers are black except for the gray saddle.

The ventral (bottom) surface, lower jaw, and undersides of the tail flukes are mostly white. The undersides of the tail flukes are fringed with black.

Now let's come up to the main point, why does this happen?
The source I have referred to says there are two reasons :-

The distinctive coloration of killer whales is a type of disruptive coloration, a pattern that obscures the outline of an animal by contradicting the animal's body shape. In the flickering, filtered sunlight of the sea, other animals may not recognize a killer whale as a potential predator.
When you see the ocean from above, you see complete darkness. This helps the countershaded whale to actually blend with the darkness.

And when you see from underneath, you see light/brightness. The white ventral side again helps them to blend with it.
Source :- https://seaworld.org/animals/all-about/killer-whale/characteristics/
For the part of evolutionary pressure, it has already been answered on SE, visit
Selection Pressure on Orca Whale Coloration

Just one more question tho. Why didn't any other dolphins or well generally marine predators become as black as orcas did?

@nevertookcoursesbutwhy Because every animal has their own way of defense and their own unique way of dealing with predators or preying someone. Not all the animals (preys/predators) believe in camouflaging. For eg most of the dolphins protect themselves by having a social organisation and strong bonds b/w them.

Other dolphins do have the same counter shading! The orca is just the most extreme example. Additionally, the white patches behind their eyes is designed to a) make them look like a larger predator than they are, b) confuse prey as they are attacking from below.


text:
Starting to learn biology
Well, I've not any biological background but I feel interested towards it. Can you biologists suggest me how to start? Like, from where I can start learning it, from the basic level.
I'm from engineering and physics background.
Edit- I was advised to add the fields of biology that interest me.
I would like to learn microbiology, genetics and plant biology. I should mention that I've very little to no knowledge in biology. So, advise me how to get started from basics. I really have no idea how and from where to start.

Biology is a broad field. What exactly is interesting to you? Identification of plants or animals? Genetics? Ecology?...

Things like microbiology, genetics, biology of plants and such things.


text:
Which database has the ready made 16S rRNA Multiple Sequence Alignment File that I can download directly from?
In my case, I need the ready made 16S rRNA Multiple Sequence Alignment File for E.coli and use it to generate the phylogenetic tree file in Newick format. I've tried using the one from utexas website, but I get too many errors when using the alignment file for tree generation, either the file size is too big or the input file is not a fasta file, so I tried to read the alignment file in R using read.alignment() function and it reads fine. Still I get this error when I used it to generate the tree.
So, can someone tell me where do I get a ready made Multiple Sequence Alignment File for 16S rRNA of E.coli being the reference sequence?
Thank you.

Try to use the MEGA software. You download in this website: https://www.megasoftware.net/

What format is your alignment file in? Have you considered NCBI MSA Viewer or the Genome Workbench

It is in fasta format and the file size is 27 MB (too big for NCBI MSA viewer).

How about using Genome Workbench then? It probably does not have size limits.


text:
Are there any examples of information compression in nature?
As the title suggests, I am looking for any examples of naturally occurring information compression. Initially, I thought protein synthesis was such a form of compression, creating larger entities (proteins) from a small subset of chemicals (A,C,G,T(U) in DNA) via ribosomal translation. However, I was quickly disillusioned as the amount of information contained in DNA is not increased within proteins after their formation.
So are there any natural processes, whether in animal, plant or otherwise that exhibit information compression?

Can you give some example that, by your criteria, qualifies as information compression? Are seeds, sperms and ova not what you are searching for?

@Jan I think the OP is talking about compression as in typical compression algorithms (like .jpg compression), not just for replicated DNA from germline cells. So something along the lines of a genome consisting of many base pairs being concisely expressed by one of few base pairs, as opposed to a genome within one cell representing the genomes of many cells.

Preliminary Remarks
Many of the posts to this list about biological information (usually equated to DNA) from mathematical and informatics scientists start from what I regard as false premises, especially that the genome is similar to that man-made artefact, the computer. This post does not explicitly make that assumption, but I think it important to address the difference between computer systems and biological systems before considering possible examples of what is requested.
Do biological systems need to compress information?
Although one can argue that not all biological information resides in DNA (or RNA, in the case of organisms with an RNA genome) I suspect the poster was thinking of that, and that is what I shall restrict myself to — i.e. to genetic information. (Other answers may quite validly address other types of information.)
The point, at least historically, of compressing digital information on computers is space limitation. Lossless compression involves re-coding the information in a more compact form. For example, instructions in the PostScript language can substitute ‘d’ for draw, ‘s’ for stroke. Gif or tiff image compression can substitute 20x(256,0,0) for repeating (256,0,0) — a red pixel — twenty times. Such compressed information must generally be decompressed when it is used (e.g. when the gif file is displayed in a web browser).
I find it difficult to think of any compression/decompression of this type in biological systems, and I would point out that genome ‘space’ is generally (but see below) not a limiting consideration in biological systems. One example of this is the fact that many organisms (especially plants) are polyploid — that is they have multiple (apparently unnecessary) copies of the complete genome. Another example is that the genomes of mammals contain at least some DNA that can be regarded as unnecessary. Although there are arguments about ‘junk’ DNA having a function, it is difficult to argue that processed pseudogenes and SINES and LINES are necessary. However genome ‘space’ has not eliminated them.
Where space or size is a problem, there Nature often uses other solutions than compression. For example the genomes of RNA viruses are thought to be restricted in size because of the occurrence of slow non-enzymic alkaline hydrolysis of RNA. Influenza virus, for example, has a genome consisting of several shorter (less vulnerable) RNA segments, which may be considered as a solution to this problem.
However, here are a couple of possible examples, although not with the sort of compression used in computers.
Possible example 1: Antibody Genes
To put it in simple terms, the genome has the potential for expressing millions of different antibodies, but the immune system requires that antibody-producing cells only produce one type. Instead of having millions of antibody-producing genes, only one of which is expressed, there is a much smaller number of segments of the genes, from which each of the two antibody chains are combined in a process called recombination. This is illustrated below for the heavy-chain genes where combination of one of 250 V-regions with one  of 20 D-regions with one of 4 J-regions, giving 20,000 possibilities. The resulting heavy chain can combine with one of 1000 different light chains, giving twenty million possibilities. (The diagram and data are old, but the principle holds. See, e.g. the Wikipedia entry.)

Of course, there is an alternative, and converse, way of thinking about this. Rather than the existence of 500–600 genes being a way to compress 20 million, one can regard the existence of 500–600 being a wasteful way to encode only protein.
Possible Example 2: Alternative splicing of pre-mRNA
This is similar in principle to the first example, although the mechanism is different. Most of the protein-coding genes of higher eukaryotes are built up of two components — exons, which encode sections of the protein product — separated by introns, which do not. Both these components are present in the initial RNA transcript, but the introns are removed from this (spliced out) to produce the mature mRNA, which is translated into protein. An advantage of this arrangement is that there are alternative ways for the splicing to occur, involving removing some of the exons (as well as the introns). This can lead to different protein products, in some cases just two, in others dozens.

So one could regard this similarly as a compression mechanism — or alternatively as an example of wasted space in the genome occupied by the introns.
Possible Example 3: Read-through and frame shift proteins
Certain mature mRNAs have the potential to encode more than one codon by the processes of read-through or frame shift. In brief, a protein of 100 amino acids will have a mRNA with a stop-codon 300 nucleotides after the signal for the start of translation. However in a few cases (and most notably with small bacterial RNA viruses) the structure of the mRNA near the stop codon is such that in a certain percentage of cases a tRNA will misread the stop-codon, resulting in continued translation, producing a longer protein of different function.
Similarly, certain mRNAs have a structure at a certain point that encourages the tRNAs to continue reading in the wrong phase (missing a base or starting a base too early — I forget) so that the continuation of the protein has a completely different amino acid sequence.
There is an old review of this topic in Current Opinion in Cell Biology.
Although this is technically a way of compressing two proteins into one, its rarity makes it difficult to regard its biological rationale as being compression.
&c.
No doubt there are more examples. I had toyed with considering Wobble as a way of saving space for tRNA genes, but have probably written enough.


text:
Are there autotrophic fungi?
Are there any completely autotrophic species of fungus?
If so, what species are they? What ecosystem do they live in? Some answers from Quora state that a fungus can never be autotrophic, but why is that?
Thanks for your time!

There are some radiotrophic fungi in Chernobyl. Not sure if you would consider that as an example of autotrophy.

no none of the fungi in the nature is  autotrophic.
they are dependent mostly upon dead and decayed matter.
the reason that they are not autotrophic is that they lack any type of photopigment to carry out photosynthesis.
photopigments are necessary because the are the only components that can trap the solar energy and use it to extract the electrons from the inorganic source such as h2s or h2o by splitting them which are further used to prepare ATP and NADPHH+. these 2 are the assimilatory powers for the further dark reaction. so if these are not there then the processes of photosynthesis would not be there and therefore the organism will not be able to produce its own food in turn it would depend on other autotorphs for food (in case of fungi dead and decade matter).