text:
How many base codes are in DNA? Two or four?
We know there are four bases found in a DNA: adenine (A), cytosine (C), guanine (G), and thymine (T). We also know that A always pairs with T and G always pairs with C. Can we say that the DNA is coded binary with two options: AT and GC?

Your question is not about either genes or the genetic code, so I have removed these tags.

Please explain what you mean by “base code”. It is not a term that means anything to me as a molecular biologist. And then how such a thing (or apparently things are “in DNA”. I have answered your question from what seems a fair interpretation of it. But I really don’t know. And what do you mean by “coded binary”? Does this have a meaning in informatics or have you invented it by analogy with its use in terms of sexual relationships? Please rewrite your question, clarifying these points.

Can we say that the DNA is coded binary with two options: AT and GC?

Sort of, but really in one aspect. DNA is double stranded. It is replicated by splitting the strands apart and generating two new molecules using the existing strands as a template. The binary pairing you point out guarantees that the two new DNA molecules will be faithful copies of the original molecule.
However, replication is only one aspect of DNA. Translation is the conversion of DNA -> mRNA -> protein. Generation of the mRNA from DNA is also governed by the binary pairing, (except that mRNA uses Uracil, so an A in the DNA will be paired with a U in the corresponding mRNA). However, when it comes to generating a protein from the mRNA, each possible triplet of mRNA bases (which corresponds to a triplet of DNA bases) codes to one particular amino acid in the protein. It's this correspondence between triplets of mRNA bases (and the underlying DNA bases) and amino acids that's referred to as the genetic code.

This does not appear to be a question about biology but a semantic question in the realm of information technology. However, the answer is NO.
First, linguistically I would never use the word “coded” to describe or specify the sequence of DNA — which is what the poster appears to wish to do — any more than I would use the word to do likewise for proteins (I would not say that “a protein is coded by 20 amino acids”). The use of the word is poor — you can say “RNA is coded by DNA”. (I prefer to say “DNA encodes RNA”, as it is a single word that only exists as a verb.) But “DNA is composed of four different bases”. Keep the two ideas (template and composition) separate.
From a computational standpoint one can say that a DNA sequence can be described or specified using four characters and hence represented most compactly as a number to the base 4 — a quaternary number. NOT a binary number.
The fact that the poster’s logic is incorrect is simply demonstrated: the single strand of a DNA with the sequence ATGC is not the same as AAGC, TAGC, TTGC, ATGG, ATCG, ATCG etc.
The logical flaw is in an implicit assumption that because the sequence of the second strand is specified unambiguously by that of the first strand this somehow influences the numerical complexity of the first strand. It does not.

Thanks David. Quote: the single strand of a DNA with the sequence ATGC is not the same as AAGC, TAGC, TTGC, ATGG, ATCG, ATCG etc. My question is exactly how is it even possible to have AAGC sequence when we know that A always pairs with T.

Unless it is the case that when talk about ATGC sequence, we are actually talking about the bases on the one side of the DNA, that is complimentary to the TACG sequence on the other side of the DNA. I'm sorry about my poor terminology, I'm quite a stranger in this field.

I saw this and everything is clear now: https://www.youtube.com/watch?v=dijqYyFY1GM


text:
How does the shape of a protein determine its function?
There is currently much interest in protein folding and the problems in predicting how the sequence of amino acids determines how proteins fold into specific shapes. Accounts of this generally mention in passing that the shape of a protein determines its function.
How, in fact, does the shape of a protein determine its function?
And, looking at the other side of the coin, is it possible to predict how a protein will behave and function merely from its structure? If so, how?

Welcome to SE Biology. Unfortunately your question is very basic and shows no effort of having researched the question yourself as required here. There are whole books written on this topic, but you can find many sources by Googling.

@David Tahnk you. maybe you could give me an example of an article or book which explains HOW the shape of a protein determine its function. I Have been googling for hours. Asking here is my last resort. Also I am using the phone which is a bit limiting or slow. Looking forward for an answer if you have time?

OK, the problem is that there are detailed chapters in texts on different proteins with various functions from which students gain an appreciation of how composition determines structure and structure determines function. Perhaps I can come up with a brief summary with references to examples, but you need to understand the basic chemical properties of amino acids to get anywhere.

Perhaps review this to start? https://www.khanacademy.org/science/biology/macromolecules/proteins-and-amino-acids/v/introduction-to-amino-acids

@David That sounds great! Looking forward to read it. I am sure it will be beneficial, not only for me but for the community :)

Determining function and predicting function are two separate things. For example, a screwdriver's shape determines its function, but it might be hard to predict that function unless you also see some screws.
There are obviously a zillion different other molecules a protein might interact with, so just from its shape one probably couldn't tell much. However, we normally also have other information about the protein.  To start with, the amino acid sequence gives us information about what other proteins are related by evolution; smaller parts of the sequence may include known functional motifs.
Also, experimental work may indicate other molecules that physically interact with the protein, and we may then be able to identify if a part of the protein "matches up" with part of another known molecule (this is the "lock and key" idea). Genetic analysis may show that changes in the protein tend to affect a certain function, and so forth.

+1 Thanks for your answer!

Scope of this answer
As with any machine or useful artefact, the structures (including shape and surface chemo-electrical properties) of proteins determine their ability to fulfil the functions they perform. This relationship (and the way in which the structure arises from the amino acid composition and sequence) is illustrated in any textbook on biochemistry, which typically devote whole chapters to individual proteins. That, paradoxically, makes it difficult for the naïve student to obtain an overall perspective of the topic before going into more detail. This is the purpose of my answer, which is illustrative rather than exhaustive, and merely provides links to detailed accounts of different proteins. I shall use Berg et al. Biochemistry at NCBI Bookshelf for all my examples.
I shall not deal with prediction of function from structure. That is covered in another answer.
DIFFERENT FUNCTIONS
It seems to me best to start with functions and then indicate the general structural aspects, followed by detailed structural features that can accomplish such functions.
1. Acting as fibres
The spider’s web, the maiden’s flowing locks, the athlete’s muscles all constitute and depend on the properties of fibres which are protein in nature. All share the shape of having an extended chain. Each differs in how the chains are constituted, and with what other proteins it might interact (e.g. to give muscle its contractile properties).
Berg et al. include Fibrinogen as an example of fibre formation.
2. Binding of small molecules in an aqueous environment
Many proteins have a function that involves binding small molecules in an aqueous cellular environment. To do this they need to be folded into a roughly globular shape with a surface that renders them soluble in water, and they need to have a specific binding site for the molecule — an indentation in the surface of the correct shape and electrical charge. Examples of such proteins are those that bind oxygen (e.g. myoglobin and haemoglobin), antigens (immunoglobulins) and steroid hormones (soluble receptors). These proteins differ in which molecules they can bind (the binding site is specific) and differ in what events follow (are triggered or are possible) following binding. These latter are determined in a more or less obvious way by other aspects of the proteins structure. For example in the case of immunoglobulins which have two arms, the possibility of cross-linking to form larger aggregates occurs.
Berg et al. have a short introductory section on myoglobin and extensive treatment of haemoglobin, which shows how its subunit structure allows its function to be fine-tuned.
3. Binding of small molecules at the membrane
This is analogous to 2, above, but here the overall structure is partly hydrophobic, so that part of the protein can interact with and be embedded in the membrane. In this case the binding of a molecule (hormone, agonist) generally causes a change in shape, allowing interactions with other molecules or catalytic function, transmitting a signal across the membrane.
Berg et al. have quite an extensive section on an abundant class of membrane receptors.
4. Transporting molecules across membranes
Cell membranes are impermeable to polar molecules and special channels are needed to allow their passage. For a protein to be able to act as a membrane channel it needs to fold so that it has hydrophobic exterior interacting with the membrane, and (simplistically) a polar ‘hole’ through the middle, tailored to the specific molecule it will transport. The types of channel vary, but there are a set of common designs, some of which (such as porin channels) are more easily recognized visually than others (e.g. calcium ion channels).
Berg et al. consider the system involved in pumping calcium across membranes.
5. Catalysis
The largest category of proteins is enzymes — the proteins that catalyse the chemical reactions that allow life to occur. Although these are generally globular in shape, they have specific binding sites for the reacting molecules (substrates) — like the binding proteins. However, in addition, there are generally strategically positioned specific amino acid side-chains that actually participate in the reaction, often providing a pathway with a lower energy barrier. Families of enzymes exist with such similar reaction mechanisms, but working on different molecules (e.g. the digestive enzymes trypsin and chymotrypsin).
Berg et al. section 9.1 considers structure–function aspects of serine proteases such as trypsin.

source: Stack Exchange

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

sort: votes


text:
Can a polymer coated with antibodies have enough attraction to wrap around a virus?

Archived source for image
Please ignore the signal release. Does anyone know if it’s possible for polymer to wrap around a virus?

Please cite the sources of content like images in your questions.

Yes, we can concentrate viruses and other objects of interest onto beads using antibody conjugated beads (such as these ones from New England Biolabs - I have no affiliation to any company linked in this post, but do occasionally use their products).  This is a process called immuno-precipitation and has been around for a very long time.
This is also the principle behind lateral flow assays, where an antigen (it can be a virus, they are available for e.g. influenza and SARS-CoV-2) is suspended and placed onto the strip, where it crosses an antibody panel and binds to it. This then travels with the liquid front to a second antibody that detects the first and causes a signal of some sort to be released.

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


text:
Does an N1-methyl-pseudouridine substitution in the first codon position (in mRNA) result in a different amino acid?
Because of the possibility of ‘wobble’ in the base-pair made between the third (5’) position of the anticodon and the third (3’) base of the the mRNA codon , single tRNAs with appropriate bases in this position are often employed by the cell to decode more than one codon specifying the same amino acid (synonymous codons). This is not possible and does not occur in the first or second positions of the codon.
N1-methyl-pseudouridine has been used to replace uracil in the preparation of mRNA for vaccines because it renders the mRNA less immunogenic. It has the same potential for base–pairing as uracil, so that even if its orientation in space is not absolutely identical, one would expect it to be able to form a base-pair with the wobble position of the appropriate anticodon.
But what is the situation with N1-methyl-pseudouridine at the first or second codon positions, where base-pairing is more stringent? Is there a potential for miscoding there, producing a proteins with incorrect amino acids?

Welcome to SE Biology. It is the practice here to allow editing of questions (and answers), although the poster can revert them, in order to improve them. I have done this to your question to make the chemistry and logic more precise. Please do not regard this in a negative fashion. On another quite different point I would ask you to think about how these modified mRNAs are made and whether they work or not. That may help you to answer your own question.

Have you looked at any space filled models for this? You can start to see how the wobble works, and then I think you can start to answer your question yourself as others have stated.

@AtlLED — How are you suggesting this be modelled exactly — onto what published structure using what software? And why spacefilling — one seldom sees spacefilling models of nucleic acid hybrids, except to give an overall impression of the shape of a molecule? Distances and angles are what is important, but to measure these one has to know whether and to what extent the bonding atoms in N1-methyl-pseudouridine are displaced from those in U. Not quite so simple.

Possible terminology confusion? "The first base of the anticodon binds the third base of the codon in the mRNA." "the same tRNA can base pair with different nucleotides in the third position (3′ base) of the codon, corresponding to the first position of the anticodon (5′ base)." https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/anticodon  (I'm no biologist)

Summary
The answer would seem to be NO, from the very fact that the vaccine works. My answer discusses why this should be so. It takes a somewhat different tack to well-documented, but different, answer from @endolith.
Answer
The term ‘wobble’ was originally introduced by Crick to describe and predict instances of non-Watson–Crick base-pairing between the  3′- base of a mRNA codon and the 5′-base of a tRNA anticodon. This was provoked by the finding of the base, inosine, at the 5′-anticodon position of some of the first sequenced tRNAs, and other examples (such as a 5′-anticodon G being used to decode both 3′- codon C or U) were found in situations where the pair of codons involved specified the same amino acid. (See also this SE answer)
The term ‘wobble’ was specifically applied the base pairing at this position as it did not occur at the other positions, where it would generally cause the incorporation of the wrong amino acid. Moreover, when the three-dimensional structure of tRNA was elucidated an explanation for this was found in the strong base-stacking at the 3′- and preceding anticodon position, but not at the 5′-anticodon position (see G34 below — explanation in answer cited above).

Nevertheless, the term ‘wobble’ is sometimes used to mean any sort of non-Watson-Crick base-pairing, which can be the cause of ambiguity in cases where the context does not clarify the situation. I shall try to be clear in this answer.

The question is concerned with the possibility of non-Watson–Crick base-pairing — and consequent mistranslation — between tRNA and m1Ψ (N1-Methylpseudouridine — above) at codon positions 1 or 2 in the artificial Covid spike protein mRNA used in the Pfizer and Moderna vaccines. I would suggest that this does not happen to an appreciable extent otherwise very little spike protein would be produced and the vaccine would be ineffective, which is certainly not the case. The developers of these vaccines were clearly aware of the possibility that m1Ψ in the mRNA might have a greater mispairing potential than the unmodified U it replaced, as they changed a number of codons in consequence. However these changes were specifically U→C at the 3′-codon position (red shading, below), as the tRNA that decodes cognate pairs of codons ending in U or C always has a 5′-anticodon G. Of course, it would have been very difficult to do anything if there were miscoding of m1Ψ at the first two codon positions, but one can assume that the developers either checked that this did not occur or guessed correctly that it would not occur there to an appreciable extent.

A possible objection to the above argument is that readthrough of termination codons (UAG, UAA, UGA) occurs to an increased extent in mRNA in which m1Ψ has replaced U at the 5′-codon position. (This may be one reason for the use of multiple termination codons in the artificial mRNA — see this answer to the SE question on that topic.) However the situation here is different from the miscoding of, say, tyrosine codon UAC. In that case miscoding would involve competition between the tRNA for tyr and those for his, asn and asp (see green shading, below). However termination involves competition for the codon between tyr-tRNA and the termination factors. The modification of the codon U may conceivable decrease its affinity for the termination factor, which depends on RNA–protein interactions, not base-pairing.

"although it was not mentioned in any answer to the SE question on that topic." It was mentioned in mine: https://biology.stackexchange.com/a/107186/3126

Apologies. Your quotation did include that, but the general tenure of the quote was so negative that I did not take it as a suggestion of an explanation of why the developers did it. I'll edit my answer. (also upvoted yours)

Detailed Dissection and Critical Evaluation of the Pfizer/BioNTech and Moderna mRNA Vaccines says that this can happen:

all U nucleotides were replaced by N1-methylpseudouridine (Ψ) [14,15]. However, Ψ wobbles more in base-pairing than U and can pair not only with A and G, but also, to a lesser extent, with C and U [16]. This is likely to increase misreading of a codon by a near-cognate tRNA. When nucleotide U in stop codons was replaced by Ψ, the rate of misreading of a stop codon by a near-cognate tRNAs increased [17]. Such readthrough events would not only decrease the number of immunogenic proteins, but also produce a longer protein of unknown fate with potentially deleterious effects.
…
There is another reason for recoding U-ending codons to C-ending codons. All U nucleotides in the two mRNA vaccines were replaced by N1-methylpseudouridines (Ψ) which can wobble with all [four] nucleotides and, therefore, should not be used in 2-fold codon families.

However, citation 16 is Kierzek 2014, which is about Ψ, not m1Ψ, and two others seem to contradict this:
The Critical Contribution of Pseudouridine to mRNA COVID-19 Vaccines says:

However, Ψ contains an extra hydrogen bond donor group (N1H) that contributes to a universal base character, i.e., it can not only pair A but also wobble base-pair with G, U, or C in the context of a duplex (Kierzek et al., 2014). On the other hand, N1-methyl-Ψ has a methyl group instead in the N1-position (Figure 1), thus eliminating the extra hydrogen bond donor. Consequently, N1-methyl-Ψ can only use its Watson-Crick face to base-pair with another nucleoside, thus preventing it from wobble-pairing with other nucleotides (G, U, and C).

It cites the same Kierzek source for wobble-pairing of Ψ, but doesn't cite anything for lack of wobble-pairing in m1Ψ.
N1-Methylpseudouridine substitution enhances the performance of synthetic mRNA switches in cells seems to say the same thing?

Interestingly, Ψ oligonucleotides showed two Tm  values, suggesting the existence of an additional unstable binding  pattern. This observation, together with the fact that Ψ has an extra N1 imino proton (26,27) for hydrogen bonding (Supplementary Figure S5), agrees with previous research, which concluded that Ψ can act as a  universal base to form wobble base-pairing with multiple bases (28) and may alter structural stability (29). Thus, together with the results above, we conclude that m1Ψ-containing  miRNA-sensing switches outperform other switches because m1Ψ allows  higher basal protein expression and enhanced miRNA sensitivity.

Since m1Ψ only has one Tm value, this implies that it doesn't act as a universal base?

This is a very interesting and well-researched answer, but unfortunately it only addresses the question of misreading in the 'wobble' (third-codon) position, whereas the question, despite its introductory reference to wobble, specifically asks about the first position. Much as your contribution deserves credit, at the moment it is not an answer to the question. Admittedly the logic of the question seems flawed — greater stringency should only affect alternative base pairing, not that to A — but perhaps you could finish your answer by pointing that out. Then it could be upvoted.

@David I'm no biologist, but if I understand correctly, my references are talking about about the possibility of wobble pairing of any base, irrelevant of position within the codon.

Having looked at the references, I felt it would be better to explain my reasons in a separate answer, even if the punch line is just "No, because it works."  I find the  arguments in the "critical evaluation" paper that they did almost everything wrong most unconvincing. Pfizer's product beats Xia's speculation in my book. And the question is base-pairing between mRNA and tRNA anticodon, so that the third paper on mRNA switches is irrelevant. It is change of mRNA conformation by intra-RNA bonds and not wobble by even the loosest definition. It just shows m1Ψ is different from U.


text:
Understanding the names of microorganisms of the normal body flora
I'm taking an introductory course to microbiology and immunology, and i have been required to memorise the following microorganisms of the normal flora.
I'm trying to understand before I memorise, and I need your kind help because no textbook or any resource on google had helped me. I am trying to link the etymology and/or characteristics of the microorganism to its anatomical locale, for example: Heliobacter pylori --> helical bacteria, pylorus region of the stomach, or enterococci --> Entero = small intestine, cocci = circular. Some can be found out via a simple google search but the others cannot, can you help me link/understand it? It doesn't have to be anything so jargonic, just clever ways to facilitate memorisation, for example: lactobacilli --> lacto --> lactic acid --> acidic environment of the vagina and bacillus = rod shaped.
Many many many thanks in advance!

While the name of a microorganism sometimes reflects its shape, that is not always true. Additionally, the name doesn't necessarily reflect its location in the body.

There isn't any clever way to memorize where (everything/whatever) lives, e.g the ubiquitous Candida albicans which basically means white white. Sometimes it's just the hard work of memorizing that gets you through, if that's what you're required to do.

As mentioned in the comments to the question, binomial names for species are odd ones and don't necessarily relate to anything to do with either common location or a function of the species. However, a lot of the common bacteria were named fairly early on in the process of classifying species at a time when it was fashionable to name them based on a function or a characteristic of the species, much in the manner that Carl Linne did, when he set up the binomial system.
Here's my table of the meanings of the names for the in the list above:

First part
definition
second part
definition

Strepto
twisted chain
coccus
ball

Haemo
blood
philus
loving

Neisseria
after Albert Neisser

Candida
white

Actino
ray (of light)
myces
fungus

Staphylo
bunch of grapes
coccus
ball

Coryne
club shaped
bacterium
bacterium

Propioni
synthesizes propionic acid
bacterium
bacterium

Entero
relating to the intestine
bacteriaceae
family of bacteria

Entero
as above
cocci
ball

Bacter
representing bacterium
oides
like

Bifido
divided in two
bacterium
bacteria

Clostrid
spindle shaped
ium
suffix

Pepto
cook
streptococcus
see strepto...

Lacto
milk
bacilli
rod shaped

Myco
related to fungi
bacterium
bacteria

As you can see the names sometimes make sense in an immediate manner (e.g. Streptococcus = "twisted chain of balls" and Staphylococcus = "balls in a shape like a bunch of grapes"), but don't always - for example Bacteroides means "bacterium that is representative of bacteria" - which only makes sense if you know that this is probably the most abundant species found in the gut. Also note that for  Actinomyces; at the time it was named it was thought to be a fungus - hence the "myces" part. The colonies are fuzzy, like a fungus and form corrugations that, with a bit of imagination, look like rays/beams - hence the "Actino" part; so you kind of need to also know a little of the history to understand some of the names.
As far as I know there is no system from the names to work out the location of the organisms in terms of their names, the closest you might come is to know whether they are anaerobes or aerobes, and that will give you at least a hint of their location(s). However, this won't work for all species, and some are not bacteria, but yeasts, which are eukaryotic rather than prokaryotic.

this is so beautiful, I can't thank you enough! highly appreciated!


text:
How can ingesting a prion "infect" someone?
That's something that's been bugging me for a while...
Our gastrointestinal tract produces proteases that degrade proteins. Prions are proteins. Shouldn't they be broken by proteases?
Also, how can a prion pass the gastrointestinal barrier? Shouldn't the intestine be able to absorb aminoacids only (instead of full proteins)?

Prions are misfolded proteins with abnormal tertiary or quaternary structures. That grants them resistance (to some extent, at least) to proteases (1).
Also researchers believe that prions are able to replicate (2), by changing the structure of other proteins.
Regarding the gastrointestinal barrier, that isn't exactly true. It has been shown that small quantities of intact proteins do cross the gastrointestinal tract in animals and adult humans (3), and that this is a physiologically normal process required for antigen sampling by subepithelial immune tissue in the gut

So, the resistance to the proteases and the ability to replicate in certain conditions might explain the odds of a prion crossing the gastrointestinal tract and infecting an individual.

References:

http://www.ncbi.nlm.nih.gov/pubmed/24338008
http://www.nejm.org/doi/full/10.1056/NEJM199609193351218
http://www.ncbi.nlm.nih.gov/pubmed/3060169

I think explaining the replication process here is worth including for a more complete answer.

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/


text:
identification of this flower
I saw this flower in Pulau Ubin in Singapore. Can anyone identify the species of this flower?

Looks like some type of oleander.

It is indeed the Nerium oleander.. For more info refer to this link and also this

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/


text:
identification of species of snake
Can anyone identify this colorful snake found at Pulau Ubin in Singapore?

It is the paradise tree snake (Chrysopelea paradisi). It is a colubrid snake and is common in south-east asia. See this site for a better image.

And great flying snake movies at http://www.flyingsnake.org/


text:
Mechanism for switch of embryonic stem cells from "fast" cell cycle to "normal" cell cycle?
It is well-known that embryonic stem cells have a fast cell cycle (very roughly about 12 hours), while typically normal cells have a much longer cell cycle (very roughly about 24 hours).
Of course, it is not only the duration that is different, but there are many papers describing  differences between cell cycle regulation for normal and stem cells.
Question: What is known about "switch" mechanisms from the the fast cell cycle?
For some cancer cell lines in our research we see that certain drugs can switch from "fast" to "normal" cell cycle patterns - we also want to understand the mechanisms by that can happen.

This review (doi: 10.1534/genetics.118.301643) states that:

Cell cycle progression in the early embryo is likely driven by a single CDK (CDK-1) in association with B-type cyclins. In support of this, the alternating S and M phases of the early cleavage-type embryonic cell divisions do not require CDK-4/cyclin D or CDK-2/cyclin E kinase activity (Boxem et al. 1999; Boxem and van den Heuvel 2001)

It makes sense that the absence of a regulatory checkpoint (CDK2 and CDK4) accelerates cell cycle. It's like skipping security at the airport to get to the airplane faster.
So maybe that switch that you're looking for is connected to CDK2 and CDK4 taking control over cell cycle checkpoints.
Please note that this work was done in Caenorhabditis elegans, but it seems that cell cycle regulation is conserved in eukaryotes, since studies in mice (doi: 10.1073/pnas.1115201109) have shown that "Knockouts of Cdk2, Cdk3, Cdk4, or Cdk6 have resulted in viable mice", while cdk1 leads to embryonic arrest.
I know from my own research that myelomas dysregulate cyclins like crazy. So you might want to start there.

Welcome to Biology.SE. This looks like it might be a good answer and you've done a nice job of providing some supporting references. However, please include the complete reference information since links can break. One easy way to get that information is to search for the paper on Google Scholar and click on the ‟ symbol to get reference information. This is a good example of how to format references. ——— Also, can you please clarify what the "it" is referring to in "This confirms it, since ..."?

Thanks for the edit and the tip! Is providing the doi enough? That solves the 'link-might-break' problem, doesn't it?

You're welcome and thank you for editing — that is much clearer! Using a doi is certainly good, but my personal (possibly old fashioned) preference is for complete citations as they: 1) contain useful "meta" information that allows users to make a quick check for plausibility/reliability (e.g.s: Is this a recent publication? Was it in a journal with a good reputation?) and 2) can only be "broken" by destruction of both the internet and all the paper copies of the sources ...

Would you be so kind to give refrences to your research on: "myelomas dysregulate cyclins like crazy " ?


text:
Is there a minimum load below which an infectious agent will not cause disease?
Suppose a single smallpox virus is injected in an human adult's body. Will it cause disease in the host? Is there a minimum microbial load below which it will not cause disease?

It depends on the pathogen, delivery method, environment, etc. In most cases, a single pathogen is not enough to cause disease -- it may need many millions or billions -- but there are some cases where it does seem that a single pathogen can consistently cause infection. For example

The minimum infectious dose of ASFV in liquid was 100 [i.e 1] 50% tissue culture infectious dose (TCID50), compared with 104 TCID50 in feed. The median infectious dose was 101.0 TCID50 for liquid and 106.8 TCID50 for feed.

--Infectious Dose of African Swine Fever Virus When Consumed Naturally in Liquid or Feed
If you're asking specifically about smallpox, I don't think anyone has done the experiment (the natural and most susceptible host being humans, I think you'd have some trouble finding volunteers to find to lethal dose). A single virus of the related ectromelia (mouse pox) virus can cause death in particularly susceptible mouse strains:

The intranasal lethal mousepox model employing the A/Ncr mouse strain is used to evaluate anti-orthopoxvirus therapies. These infections mimic large droplet transmission and result in 100% mortality within 7-10 days with as little as 1 PFU [plaque-forming unit] of ectromelia virus.

--Mousepox in the C57BL/6 strain provides an improved model for evaluating anti-poxvirus therapies
As a side note, the notion of what a "single virus" actually is, is more fuzzy than you might think, but that's a more complicated question; to a rough approximation a single TCID50 or PFU can be considered to be a single virus.

According to these sources ( A, B, C, D ), infective dose varies widely among the diseases which are caused by pathogens. It is reported that as few as 10 enterohemorrhagic strains of Escherichia coli cells can cause an infection .
For an infection to occur, the pathogen must overcome and pass the physical, physiological, immunological and environmental barriers. Higher number of cells or viruses increases the possibility of overcoming these barriers. But, you should't forget that a pathogen cell or a virus particle doesn't need another one in order to infect the host, reproduce and cause a disease as a result. One single pathogen has all the necessary properties to do so.
So, in regard to the possibility of an infection, we can't say that one single pathogen can not infect a host and cause a disease. But, it is apparent that as a result of the biological properties of the pathogen and the characteristics of the infection mechanism, a particular pathogen has an observed infective dose that is different from other pathogens.
In addition to this consideration, don't confuse the number of pathogen in the environment (outside the host's body) with the number of pathogen injected into the host's body. Via the injection, the pathogen has already been transported behind some of the barriers.


text:
Are hormones antigenic?
I have been asked whether hormones are antigenic.
I would have to think that the answer is no because they are used as various drugs such as FSH in infertility treatments without the need of immunosupressants.

Welcome to Biology.SE! Please take the [tour] and then go through the help pages starting with [Ask] questions effectively on this site and [edit] your question accordingly. In particular, you would benefit from reading up about antigens.  ——— In general, we encourage you to do some research on your own and then, informed by what you have learned, ask any questions you still have (ideally with references to reliable sources). Thanks!

Where did your question come from? Are you sure you are quoting it correctly? Both testosterone and insulin are hormones, but they are very different in size, which influences their antigenicity. And my phrasing of the last sentence was deliberate, we don’t talk about molecules having antigens, but being antigens or having epitopes, and the question is generally whether they are recognized as foreign antigens by species other from those in which they originate. So you need to try to get the question clear, before you or anyone else can attempt to answer it.

Hormones have antigens.  Usually they are antigens our immune systems recognize as self.
Pretty much any big biological molecule will have antigens.  FSH is no exception.  The binding of FSH to anti-FSH antibodies (in a laboratory system) is one way to measure FSH levels in a human.
 Definition and Measurement of Follicle Stimulating Hormone

B. High-affinity binding assays
  1. Immunoassays. Immunoassays are widely used for clinical determination of FSH for diagnosis and in physiological studies
  because they are rapid, readily available, relatively cheap, and
  sensitive... Most commercially available assays are now based on
  sandwiches of monoclonal or monoclonal-polyclonal antibodies with a
  variety of detection modes and are generally more sensitive and
  precise than one-site assays. The latter assays are highly specific
  and may exclude some forms of the hormone of interest (e.g., Ref.
  176).

The antibodies used to measure FSH are from other species of mammals - usually mice but sometimes other animals. People (and other animals) normally do not form antibodies to molecules that have been present in their bodies since development.  The immune system is educated early on about what is self and so exempt from attack.  Mouse FSH is antigenically different enough from human FSH that mice can be induced to form antibodies against human FSH and then those mouse antibodies are used to make the lab test.   You can find out how those tests work with a little googling because they are for sale and their owners will brag about them.
It is possible to form antibodies against your own FSH or any other biomolecule in your body.  That is autoimmunity and usually that is not good.  The woman in the linked article was infertile because of antibodies against FSH.  Her FSH level was very high because her pituitary was cranking it out.  Her immune system bound it up as fast as it came out and so the FSH did not work.
Abnormally Elevated Follicle-Stimulating Hormone (FSH) Level in an Infertile Woman

We describe here a case of anti-FSH autoantibodies leading to
  persisting very high FSH serum levels in an infertile woman.

Bullet points

Any biological macromolecule has antigens.
The immune system may tolerate antigens it has been educated to recognize as self.
Sometimes the immune system becomes intolerant of an antigen it should recognize as self and attacks that antigen.  This is autoimmune disease.

As I mentioned in my comment on the question, we don't usually refer to molecules having antigens, but being antigens. We do refer to cells having antigens as they have macromolecules on their surfaces. You can easily check this by doing a Google search for "have antigens". It would be helpful to the poster and others to edit has question and your answer in this respect.

Antigenic sites are generally referred to as epitopes. They are not the same as antigens, which term is used to refer to the macromolecule with such site(s). Argue all you like, but scientific communication involves using, and introducing people to standard terminology that allows them to express ideas with precision in a way that is understandable to others. Not correcting novices for fear of offending them is selling them short


text:
How could an aquatic animal’s organ evolve so it could live outside water?
How could a fish’s organs evolve so that it could one day live outside of water.
I mean did it one day fully evolve then stick its head out of the water. That would mean that all the evolution of that fish would have needed to happen while it was essentially under water. But I can't see how that it is possible to convert from aquatic to semi-aquatic while living in the water.
Surely its organs would fail while only living in the water but having dual-function lungs and other organs.

Welcome to Biology Stack Exchange. Please take the [tour] and visit the [help] for more information on this site and how it works. In particular, note the homework rule - So, what do you know about evolution of the lung? As a hint, you might want to investigate respiratory systems in fish, particularly Lungfish.

look at fish that live in swamps they breath air because the water is so low in oxygen. we think lungs and legs both evolved in the water.

Which organs? the skin is watertight in most fish to prevent dehydration to saltwater. the only organs exposed to air are the eyes, skin, and whatever they breath with. if you look at US one of those is watertight and the other two constantly lose water.

It may surprise you to learn that most bony fish are capable of breathing air, not just the lungfish and mudskipper.  If you have ever seen a fish in a muddy lake looking like it's blowing bubbles on the surface, that is what was happening.  It was breathing.  Oxygen levels in the water can be super inconsistent, and many fish species need to be able to supplement that oxygen with oxygen from the air in order to survive.  If you ever get a betta, make sure it can make it to the surface because it will straight up drown if you don't.  The way they tend to do this is via the swim bladder.  The swim bladder is already almost a simple lung.  It can hold gas and exchange it with the blood.  All you need to make it a basic lung is a tube that connects it to the mouth.  Throw in some branches and ridges for surface area and you have a full on lung right there.  Some fish can fill the air bladder directly by gulping air.  Others gulp it into the stomach and then diffuse it into the air bladder, but most fish can breath air to some degree, even if they never come out of the water.  Fish that do come out of the water, like lungfish, do so using a modified swim bladder, one with a tube and some nifty ridges that lets it function as a full lung so the fish can go for a walk when its pool dries up.  From there, it's just more ridges, more pockets, more surface area, better tubes, basic optimization that evolution is real good at.  The line from swim bladder to lung is actually one of the straighter ones when it comes to evolutionary history.  There are definitely some winding roads but this isn't one of them.


text:
What is this spider?
I took the following picture of this spider in northern Switzerland (alt: ~700m) with macro flash (then it is not so big: probably around 2-3 cm, including the legs)

This spider made its web on the house and it goes out only during night.
In this region we have many Araneus diadematus, but this one looks totally different.
Is it the same family or another? Does anybody have a clue for the real name?
UPDATE: I saw it this afternoon (gave a fly to the web to make it go out), the body is probably around 7-8 mm wide and 9-11 mm long). And now I am sure the colors are more or less right.

My guess is that it is a spider from the Tegenaria genus. There are a lot of spiders in this genus, a lot of them are only active at night. And they are common in europe.

We also have this tegenaria species here but they all look thinner than this one. This one have a big fat body like the Araneus genus (even I guess it can be probably another genus)

Maybe Badumna longinqua (grey house spider)

@TheLastWord Is it not Australian species? do you think it can live in Europe? I have to mention it was taken in a natural environment.

@ruffp According to this article (http://publikationen.ub.uni-frankfurt.de/frontdoor/index/index/docId/26406) it is capable of establishing itself in Europe but I would not go as far as to say that this is Badumna longinqua. I went through pictures of some native spiders in Switzerland but could not find a match. Just venturing a guess based on some morphological features like the colour.

I'd guess it's Nuctenea umbratica, or otherwise similar in appearance and coloration pattern, but less frequent Nuctenea silvicultrix.
At least Nuctenea umbratica was recorded in Switzerland.

It look it was a Nuctenea umbratica by all the pictures on Google.
And according to the Bern university site, the distribution of Nuctenea silvicultix does not include Switzerland,
but Nuctenea umbratica does.

@ruffp: I also tend to think it's Nuctenea umbratica. It could be that Nuctenea silvicultrix avoids high altitudes, but it's presence in Germany and Italy makes it very possible to occur in Switzerland as well, so I'd not rule it out completely, but the chances are much lower.

authors: Сергей Лобанов


text:
What is this bird of prey with white belly?
This bird was around the house in northern Switzerland (alt: ~700 m) on January 17th 2016, and I am just wondering what kind of species it is.

The legs are yellow and the under (I do not have picture while flying, but saw it just before) is almost all white with just a black (or dark) stripe on the end of the tail.
For me it looks like a nordic species of Buteo buteo but can any specialist confirm it?

Common Buzzard, Buteo buteo
Belonging to the Accipitridae family, which consists of ~32 birds of prey in Europe, Buteo buteo is a fairly common bird of prey through much of Europe. Resident up to Northern limits of approximately Britain, Denmark, southern Sweden, Northern Germany, Poland, Belarus, and Ukraine, and through to the Southern limits of Europe. Also found in summer in Eastern Europe, Western Russia, Finland, and most of Sweden. Therefore, your location is within the typical range. Often seen in farmland, marshes, etc. which it uses as hunting grounds for small rodents, rabbits, birds, frogs, lizards etc. and seen perching on poles, posts, and other man made structures, just like in your picture.
Identifying features
The wingspan is between 1.1 and 1.4 metres, making it medium-large relative to many European birds of prey. It has a short neck and medium length of tail which is fan shaped when the bird is in flight, and the tail is about as long as the wings are wide (distance between front and back edge of wings). In these pictures you can see an adult first, and a juvenile. The juvenile has a much lighter colour, and has distinctive black markings on the leading edges of the wings, shaped like commas or speech-marks. Common Buzzards also have dark tips to the tails and wings, becoming much more prominent in the adult, and yellow legs and beak.

Images from RSPB. See also, Collins Bird Guide, ISBN: 978-0007267262.

See the image in Chris' answer for a picture of juvenile in a similar pose to the one you saw. This answer is here to provide more general and in-depth tips for identifying the Common Buzzard made in complement to Chris' answer.

I think your identification is correct - this is a juvenile Common buzzard (Buteo buteo), which have a lighter coat than the grown-up birds. See this image (from here), which also shows a juvenile bird:


text:
Reporting observation of a bird outside its seasonal presence
Last summer I saw this bird in the countryside of Bulgaria (Dobrich area) and I think this is a specimen of Great Grey Shrike (Lanius excubitor).

By looking more in detail the distribution of that bird (I checked in few books including the Collins Bird Guide in French edition), I noticed it is present in Bulgaria but only in winter season. However I took this pictures in August 2017.
First, is it really a specimen of Lanius excubitor?
And if yes, should it be reported in some way?
I know some other countries have reporting tool on Internet but I have no clue about observations in Bulgaria.

You can report any observation worldwide on www.observado.org If you add a picture your observations will usually be corrected if wrong.

It is NOT a Great Grey Shrike (Lanius excubitor).
It is a young Lanius minor Lesser Grey Shrike (which breeds in Bulgaria).
I say young (born the same year) because of the white tips of the feathers (they are new) and not so extended black mask (which probably induced you into the ID mistake).
I attach a picture of young Lesser Grey Shrike for comparison.
Generally you can report your observation on ebird.
There is a team checking the unusual observations (although for Europe at least many mistakes are not picked up).

Interesting answer, in fact I elimiate this specimen because they show it most of the time with rose coloring on the side (adults), and the young one were more brownish on the back, but I think you're right.

I have seen both species many times and thanks to your good pictures I have absolutely no doubt on the identification

Accepting the answer as I also found evidence for the white stripes on the back for the juvenile in another book.

it's a characteristic common to the juveniles of many bird species

The wiki article for the great grey shrike is very good and it says:
Females are more prone to migration than males; they do not appear to migrate, on average, longer or shorter distances than males, and consequently are the dominant sex in many parts of the winter range. Birds leave for winter quarters a more or less short time after breeding – July to October, with most birds staying to September – and return to nest mainly in March/April, but some only arrive in May.
So perhaps it was not out of season. https://en.wikipedia.org/wiki/Great_grey_shrike#Distribution_and_habitat

What is confusing in the wikipedia is the end of the paragraph you mentions: "In recent decades, the number of birds remaining on the breeding grounds all year has been noted to increase e.g. in Fennoscandia, whereas for example borealis seems to be as rare a winter visitor in northern Ohio as it was a century ago". That means they stay more often in the north (breeding grounds) than going down to south (central /east europe for winter). But I agree both statement can be true.

yes as wiki is written by multiple and it sometimes has ambiguities for that reason. best to check google scholar to have a real study.


text:
Why do proteins targeted for chloroplasts require two signal peptides?
Question #11 of the GRE Biology Practice Test says that proteins targeted for chloroplasts require two signal peptides:

Targeting of a newly synthesized protein is most likely to require two different signal peptides for which of the following destinations?
(A) Plasma membrane
(B) Lysosome
(C) Cytosol
(D) Chloroplast (Correct Answer)
(E) Endoplasmic reticulum

I can't find a reference for this.
I understand that a ribosome starts the synthesis of a protein in the cytosol and a signal peptide takes that to the endoplasmic reticulum (ER) which finishes protein synthesis in the ER lumen and then the protein is secreted in a vesicle to its destination (if it doesn't become an ER membrane protein). What's the purpose of the second signal peptide to enter a chloroplast?

Welcome to SE Biology. Please update the tags on your question to include the homework tag. Goodluck getting an answer.

@Michael_A Thanks for the welcome! I'm glad to tag properly, but I'm not currently in school, so this isn't homework. Is homework a broader tag for any test-based question?

Yes, exactly. Renaming it has been debated but it seems like we're stuck with it. Your question is a model of how to ask this kind of question and I think the tag is a minor issue but including the tag should reduce the odds of people downvoting the question.

@Michael_A Makes sense, thanks. I've added the homework tag.

Protein import to chloroplasts (and also mitochondria) can still have multiple destinations, because these structures themselves have sub-compartments:

both have an inter-membrane space as well as an 'inner space' (the stroma in chloroplasts, matrix in mitochondria).
proteins can also be targeted towards either of the two membranes
additionally chloroplasts have the Thylakoid stacks in the stroma which are separated by another membrane layer.

Due to this complex structure you need multiple signal peptides to properly target proteins to their destination.
I don't remember (or can find) all the details now but basically you (can) have:

a 'main' signal peptide that targets proteins directly towards the stroma (which will be removed there by the stromal processing peptidase (SPP)).
an additional signal peptide for import to the the thylakoid stacks (which will be 'made avaibalble' by cleavage of the first peptide)
there should be other signal peptides or at least variants that allow import to the intermembrande space and the inner membrane (via the TIC23 complex). [I couldn't find any sources for this right now]

Sources I could find:

TIC/TOC complex in wikipedia
in-depth scientific review


text:
How would one go about isolating a specific mRNA out of a pool of others?
I'm writing an essay about DNA recombinant techniques where the question asks to outline all the steps to arrive at having a colony of bacteria expressing a  gene of interest.The question makes you start with a pool of mRNAs, which I assume is for making cDNA. However, how do you go from having thousands of different mRNAs to just one kind?

Your cDNA approach is correct - you use poly-A primers to make cDNA for all mRNAs in the mix, resulting in a mix of cDNAs. Now how do you isolate the one you want from the mix?

Would you use Southern Blotting on the cDNA? would Northern blotting on the mRNAs bring you to the same end point?

Try reading this product insert (downloads a PDF) from Miltenyi GmbH. Half the battle is knowing what techniques or products exist, and when/how to use them. Granted there are other things you could do.

First of all you need to figure out what your goal is: an expression vector (i.e. plasmid) which will drive expression of a gene in bacteria (let's say E.coli), and your gene's coding sequence needs to be downstream of the promoter in that construct.
Your task is asking for a pretty routine lab task known as cloning (https://en.wikipedia.org/wiki/Molecular_cloning). Your mRNA pool might be the result of an RNA extraction from a tissue sample and your goal is to get bacteria that produce lots of the desired protein.
As this is homework, I will only give a broad overview and leave you to figure out the details.
Indeed one way you could approach this is actually some method to specifically extract the desired mRNA, then generating cDNA from it and pasting that into the vector. This is unlikely to give you good success rates, and in practice nobody purifies a specific mRNA unless they are interested in other molecules naturally bound to that mRNA.
Since this is a procedure with a very practical purpose without a scientific question behind it, there's a much more efficient way to achieve it.

Generate cDNA for all mRNAs in the mix ("first-strand cDNA synthesis").
Instead of removing unwanted RNAs, simply amplify the desired one using specific primers you designed and PCR. This gives you what is called the "insert".
Most likely if you ordered the expression vector online, you actually receive bacteria containing it, so you first have to culture those and extract DNA from the culture ("miniprep").
Next step is to paste the DNA into the expression vector. For this you need to digest both the vector and your insert using the same restriction enzymes ("restriction digest"). (Your insert will not have restriction sites on it, so you will need to introduce them by designing the primers for the PCR in step 2 appropriately.)
Run the restriction digest mixes on a gel (electrophoresis), identify the bands corresponding to the insert in one lane and the vector in the other, and extract them (gel extraction).
Ligate the insert and vector
Transform the finished product into competent E.coli


text:
sweet receptor's affect on insulin release
So I understand the basics of how the body releases insulin to keep blood glucose levels in check and (loosely) that higher insulin levels can lead to more (or at a faster rate) glucose being stored as fat rather than being made readily available for energy. For this reason, I try hard to keep a good balance of carbs/protein/fat with each meal... operating on the principle that the protein and fat will slow the breakdown of carbs into glucose and eventual absorption into the bloodstream.
Recently, I have heard some chatter suggesting that in addition to the absorption of glucose into the blood stream, the mere activation of our sweet receptors can/does cause the release of insulin as well.
If this is the case, when I have a snack of say an orange and some cheese, while I think I'm avoiding the insulin spike (by adding the protein and fat of the cheese) that an orange ingested by itself may cause, it's actually still occurring due to, not the high glycemic index of the orange, but it's sweet taste.
Does anyone know if there is any truth to this? And if so, what does the data say... are the spikes elicited by activation of the sweet receptors of similar levels to those from actual high glucose levels in the blood?
In Googling cephalic phase insulin release, I've read abstracts for a few studies that seemed to be more focused on the effects of artificial sweeteners... which isn't really what I'm looking for. But one study seemed to indicate that solutions of sucrose tended to elicit higher insulin levels (than other solutions tested), but not being from the bio/physiology world, it quickly became over my head. I know some fruits (such as my aforementioned orange) are quite high in sucrose.
In practical terms, I'm trying to figure out what other foods, if any, may cause this response and if it is significant enough that one concerned with maintaining consistent, low insulin levels should stay away from such foods.
Can anyone help shed some light on this for a curious layperson? Thanks!


text:
Why is glycerol the backbone of fat?
Fats are fatty acids joined onto the backbone of a glyercol (propane-1,2,3-triol).
Why was glycerol seemingly chosen by nature to be the backbone of fats? Why can't it have been a butane -1,2,3,4- tetraol or pentane with 5 alcohol groups or almost any other molecule?
So my question boils down to, is it just pure chance that glycerol is the backbone of fats or is there a deeper underlying reason?

Chance should always be high on our list of explanations of why the history of life turned out in some specific way. As James A. Coffman has described, there are a couple of different notions of chance. Evolutionary biochemistry is quite difficult because today's diversity of biochemical genotypes and phenotypes are a biased representation of the ancient past.
However, I think a case can be made that it was not 'pure' chance.
As your question itself suggests, the chemistry requires alcohols for the esterification with fatty acids to form acyl glycerols. I think that is 'sufficient' to say it is not 'pure' chance that among molecules that it was glycerol, but since you're also questioning "why glycerol?" over other alcohols, let's look at what glycerol has going for it compared to other alcohols.

Glycerol is relatively small. All else being equal, fulfilling a biological function with a smaller molecule requires less energy than larger ones. Compared to polyphenols, for example, this is a no-brainer because (1) building polyphenol would be expensive energetically, and (2) would be difficult to transport.
Glycerol is flexible. The two outer alcohols have the ability to move with respect to the central carbon so that as we go from glycerol to mono-acylglycerol, di-acylglycerol, and finally triacylglycerol, the outer groups' motion can reduce steric hinderance.
Glycerol can be converted into a lot of other things that form a part of metabolism. While it is conceivable that an extremely different metabolism without glycerol could have come to be, the fact that glycerol is directly and indirectly convertable into a large number of molecules with structural and energetic functions does give it better candidacy than molecules that are relatively unreactive or require large numbers of reactions to build anything useful biologically.
While glycerol doesn't have the greatest number of alcohol groups for its size (size in terms of carbon backbone, not necessarily molecular weight), it doesn't have the least number either. Steric hinderance or difficulty to synthesize of alcohols with the same size would make glycerol a better choice.

Hopefully that convinces you that glycerol was not completely random with respect to all other molecules or even all other alcohols. That is, not all the possibilities in those sets are equally good for the biochemical role that we now see glycerol fulfilling, and glycerol is defintely not the worst. However, there may have been other subsets of alcohols/molecules in existence at that time for which we don't have specific reasons for glycerol being better.
In conclusion, no, not 'purely' random.

UPDATE
Reading my answer above, I can see why someone reading my list of glycerol traits may think I am making a just so story on why it is specifically glycerol that we have today fulfilling a biochemical role of joining together fatty acids via acylation. To be clear, I am not addressing 'why' glycerol is the molecule fulfilling this role but rather whether it is purely random that glycerol is the molecule fulfilling this role. In my vernacular, 'purely random' implies a uniform probability distribution, which is to say that in this context each molecule was as likely as any other to fulfill the role that we see glycerol fulfilling in biochemical systems today. By citing reasons why some molecules are better suited in their properties, we show that the distribution cannot be uniform. We don't need to even place where glycerol sits on this distribution to determine that it is not purely random. We only need non-uniformity. The fact that glycerol has traits that make it more likely than others is an additional suggestion that among the molecules under consideration, glycerol was not the least likely.

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

Summary
To attempt to explain why organisms evolved with a particular molecule performing a particular function it is not sufficient to consider the suitability of the molecule for that function and to compare it in abstract with other possible molecules. It is also necessary to consider the metabolism in existence at the time the function arose, and hence the molecules available as precursors. It is argued that membrane phospholipids, which use the same precursor (phosphatidate) as triglycerides, arose early in evolution, so that the ‘choice’ of phospholipid backbone probably determined that of triglyceride. One ancient pathway that is known to have existed at the time of the emergence of membrane phospholipids is anaerobic glycolysis, which includes only hexoses and trioses. It is argued that a three-carbon compound could provide a simple backbone that a six-carbon ring could not, and emphasized that the glycerol phosphate precursor is formed in a single step from the  dihydroxyacetone phosphate intermediate of glycolysis. The separate evolution of a glycerol-phosphate backbone for membrane phospholipids on two occasions in the form of the different stereo-isomers glycerol-3 phosphate and glycerol-1 phosphate in bacteria and archaea is consistent with the view that the availability of a glycolytic intermediate influenced the “choice by Nature” of the backbone of phospholipids and triglyceride fats.
Molecular Evolution: Problems and Pitfalls
Before addressing this question I would once again emphasize some of the difficulties with questions on molecular evolution, often seen on posts to this site.
   One type of question asks why something that the poster believes would be advantageous has not evolved. As I have discussed in an answer to a question of this sort, the poster often only thinks of this in abstract, rather in terms of the actual selective pressures that drive evolution.
   The second and more frequent type, typified by this question, asks “Why did such and such evolve in this way?”. The common pitfall here is to assume that because it evolution did produce this result, the molecule in question must be the best suited to this function, and hence answers tend to list the way the structure of the molecule allows it to fulfil that function. The answers tend, in fact, to be to a different question “Why is this molecule suited to this biological function?” — a perfectly good question, but one of structural chemistry rather than evolutionary biology.

To even approach an answer such questions I think one needs also to consider the evolution of metabolism, and hope Nature may have left some clues to help. I shall adopt this approach to the present question. Another example related to nucleic acid bases can be found here.
Glycolysis as the source of precursors to the backbone
My premise is that the glycerol backbone of triglycerides arose early in evolution because it was first used for the membrane phospholipids. As shown in the schema below (adapted from Berg et al.), both fatty acids and triglycerides are formed from a common precursor, phosphatidate, a  monoglyceride built upon L-glycerol 3-phosphate (G3P). (In addition, the conversion to triacylglycerol utilizes the same type of acyl-CoA derivatives used in the formation of phosphatidate.)

Even if one does not accept that argument that what holds for phospholipids holds for triglycerides, the evolution of the glycerol backbone of phospholipids illustrates the general approach that I think should be employed.

The synthesis of the phospholipid backbone requires an abundant source of a carbohydrate precursor. Clearly membrane phospholipids evolved at early stage and before oxidative metabolism that uses membranes for the chemiosmotic synthesis of ATP. Comparison of pathways in many different bacteria and archaea suggests that the enzymes for glycolysis and gluconeogenesis (which latter may have arisen first) were present in the last universal common ancestor (LUCA), so it is not unreasonable to look there for the precursor.

Examination of my schematic of glycolysis, above, reveals that the pathway includes only hexoses and trioses. These, therefore, represent the initial choice of precursors to the backbone. The particular hexose rings contain hydroxyl groups (to which a fatty acid might be attached) with different orientations, making them unsuitable for a membrane component without further metabolism. The triose, dihydroxyacetone phosphate (DHAP), can be converted to G3P in a single step, and this provides a suitable backbone for phospholipids and triglycerides. (Of course hexoses are used for carbohydrate storage, but as polymers such as glycogen and amylose.)

Perhaps, in theory, there is a better backbone than a triose, but as trioses ‘work’ (as explained in the answer from @Galen), once membranes had developed it would require a very strong selective pressure for a change to occur even if metabolism had expanded and other precursors had become available. That is my postulate.
The significance of membrane phospholipids in archaea
An interesting phenomenon that throws light — and darkness — on the forgoing postulate is the structure of the membrane phospholipids in archaea. These differ from those in bacteria and eukaryotes in being ether phospholipids, rather than ester phospholipids, as shown in the diagram below (from Coleman et al.).

The ether phospholipids are thought to be more suitable for extreme environments, but their existence raises difficult evolutionary questions regarding the relative time of appearance of the two types and how eukaryote membranes could have evolved from an archaeal cell, as is thought by many. These are discussed in several reviews listed in the bibliography, but what is more relevant to this question is the fact that the backbone differs stereochemically between the two. In the bacterial (and eukaryotic) case it is D-glycerol, derived from sn-glycerol 3-phospate, whereas in the archaeal case it is L-glycerol, derived from sn-glycerol 1-phospate. However in both cases these are derived from dihydroxyacetone phosphate in a single step, as shown in this diagram from Pereto ́ et al.:

There are two conclusions to be drawn from this. The first is that the phospholipid backbone arose on two different occasions, but in both cases from the same glycolytic/glucogenic precursor — it was not chance. However “chance” would seem to have played a part in the stereochemical conformation of the backbone glycerol, which has no influence on the structural properties of the molecule.
Bibliography
The following articles discuss the origins of membrane phospholipids:
J. Pereto ́ et al. (2004) Trends in Biochemical Sciences 29, 469–477
J. Lombard et al. (2012) Nature Reviews : Microbiology 10, 507–514
S. Jain et al. (2014) Frontiers in Microbiology 5, 1–16
G. A. Coleman et al.(2019) Genome Biol. Evol. 11 883–898


text:
How would one track a mineral nutrient in a plant in order to determine if the nutrient has been remobilized?
Before abscission, senescence of a plant’s structural components that contain mineral nutrients (E.g. Magnesium, Potassium...) are re-mobilized from the senescent tissue and used in other plant tissue for anabolic activities.
How could an experiment to demonstrate this?
I was told that a radioisotope method would work. We can detect the presence of the radioactive particle in one part at a time-point, but how would we know whether it is the very same particle that shows up elsewhere after abscission?

You can't do it on a single-molecule level, but I'm in agreement with whoever told you to use radioisotopes. As to it being the same molecules, I would suspect that under most growing circumstances your plant isn't going to be exposed to neutron radiation or uptake radioisotopes from the environment to any significant degree., so the radioactive molecules would be the same ones you started with.

This looks like it was a homework question. Was it?

There are a variety of methods for visualizing elements in plants. Here is a review discussing various such methods.

As suggested by other answers, radioisotopes are one such means (works in vivo?).
One may also use X-ray spectroscopy: "With x-ray fluorescence-based approaches, elements are detected based upon their characteristic fluorescent x-rays. These fluorescent x-rays are generated by passing the specimen through a focused beam of high-energy x-rays (XFM), electrons (SEM- and TEM-EDS), or protons (PIXE)."
Various electron microscopy methods, sometimes in combination with X-ray or radiography methods.
Fluorescent tagging of elements with high-affinity fluorophores (works in vivo?).
X-ray fluorescence microscopy (XFM).
etc., go look at the paper.

Here is a helpful graphic summarizing strengths and weaknesses of various approaches:

If you are interested in non-destructive sampling for tracking over time, there are several methods available from that list.

Magnesium isotopes would allow you to track the movement of magnesium.
Injection of the radioisotope 28Mg (half-life of 20.915 hours) into senescent cells may allow you to observe the direct effect of magnesium movement from senescent cells to other cells. If abscission were to occur, you could check abscised plant tissue. If you wanted to check if anabolism was also occurring, this may take more thought.
This is assuming senescents and abscission in the plant model takes under ~20 hours. Which I think is unlikely, however there are plenty of other 'mineral nutrient' and magnesium radioisotopes available.
Note
Radioactive isotopes have the ability to emit radiation allowing them to be imaged. This is great when they are inorganic molecules, because plant tissue is (mostly) organic. These variables allow imaging to be highly effective at particular emissions.
A similar approach was done here (Pay-wall(another here with-out paywall)).  However these studies added another step 'fractionation'. This may be a helpful idea, fractionation is a separation process to measure the abundance of Magnesium (they refer to it as Magnesium Purification). This is another reason to use an isotope, instead of imaging it may be useful for purification.

I suspect injection into already-senescent tissue is too late in the process to answer the OP's question.  Perhaps a much earlier injection of a longer-lived isotope, then periodic testing over time to see if migration of the isotope occurs only/mostly with the onset of senescence.


text:
How can facultative anaerobes exist without catalase?

Catalase-negative bacteria may be anaerobes, or they may be facultative anaerobes that only ferment and do not respire using oxygen as a terminal electron acceptor

A facultative anaerobe is an organism that makes ATP by aerobic respiration if oxygen is present, but is capable of switching to fermentation or anaerobic respiration if oxygen is absent

But if facultative anaerobes can be present in oxygen rich environments, don't they have to have catalase in order not to die?

There is another class of peroxide decomposing enzymes called peroxidases. These enzymes can catalyze the reduction of $\ce{H2O2}$ to water using an electron donor. However, unlike in the catalase reaction, the electron donor is not another $\ce{H2O2}$ molecule and no molecular oxygen is produced. Thus their presence would not be detected by the typical spot catalase test (which looks for gaseous oxygen generation). For example, NADH peroxidase catalyzes the following reaction to protect cells from oxidative damage:
$$\ce{NADH + H+ + H2O2 -> NAD+ + 2H2O}$$
Thus catalase negative organisms can still have a means of protection against $\ce{H2O2}$. You can read more in this textbook, specifically the section titled "Oxygen Toxicity".


text:
Why does vinegar made from wine contain only about half as much acid as the original alcohol?
It is my understanding that the fermenting bacteria process the alcohol into acetic acid. But why is it about half the percentage of volume? For example table wine is often 12% ethanol, but vinegar is generally about 5% acetic acid.

Can you add sources to your claims? As a hunch, enzymes help to swiftly establish equilibria. Enzymes don't push the equalibrium to an end product. Further, the end product may be toxic. Take the fermentation processing during beer brewing - there's a substantial amount of sugar left after the beer is ready. Alcohol is toxic to yeast.

Not really; i take this claim as a fact of everyday life. Both alcohol and acedic acid contents are indicated on the bottles. German language Wikipedia has a list of aciditys for various types of wine (those alkohol contents are not indicated), but i guess that is no scientific source:  https://de.wikipedia.org/wiki/Essig#G%C3%A4rungsessige

Yep, makes sense. +1

What evidence have you that the wine used for wine vinegar contains 12% alcohol? I would have thought it would more likely be lower alcohol wine made from poorer grapes with a lower must weight (content of natural grape sugar). It is unlikely to bear much relationship to commercial table wines, which are often chaptalized in order to reach the EU minimum alcohol level.

That the acetic acid always has 5% has the simple reason that it is diluted to this concentration.

@Chris — Actually it's generally 6% in the EU, but you're right. I found an interesting paper on sherry vinegar production, which starts with 13% ethanol and ends up as over 11% acetic acid + 1.5% ethanol. Also a general article about industrial production of vinegar which explicitly states that it is diluted to 5-6%.

I'm voting to close this question as off-topic because it turns out this question has a trivial answer that is nothing to do with biology.

@Chris: And further, that it is diluted to that concentration because that's what tastes good.  Though vinegars do vary in acetic acid concentration.  To high a concentration can be hazardous, though.

@David That article states that it is diluted in case the "The generator method" is used, which does'nt start with wine.  Do you have any reference for wine vinegar -not vinegar 'essence'-  usually being diluted?

@HannesH — No, but people don't usually advertise that they water their beer (or whisky, unless you buy cask strength and then water it yourself). I leave you to join the dots.

As regards Sherry vinegar (which I mentioned is from sherry at 13% ethanol (less than normal sherry, incidentally), an internet search suggests 7% acetic acid is a more normal final concentration. That would suggest to me that it is watered down from 11%.

Would it? Would'nt it suggest that my question is still valid? - pending any reference to watering as the standart practice, ofcourse.

@Chris Besides that it isn't always 5%, could you reference why you think that vinagar from wine -not "essence"- is diluted?


text:
What function does a mane serve in animals that possess it?
Horses, Donkeys, Antilopes and Bovines grow masses of hair on top (and sometimes below) the neck. What function does it serve? Is that to hinder predators biting?

Keep in mind there is not much to the mane in wild equids it is only the human bred populations that have large manes. Also since you are talking about very different groups with very different mane structure the answer may be different for each. I suggest moving antelope and bovids to a seperate question.

Perhaps it can prevent predators from wrapping the claw over the top of the neck while biting the throat, except that predators often bite anywhere on the side and hind and ears and whatever they can catch to ground the zebra first. Perhaps it's to do with amplifying the size to make them look taller and stronger. strong animals have very strong necks.

@John Todays Eqids have dense standing manes, as had undomesticated wild horses (see https://en.wikipedia.org/wiki/Chauvet_Cave#/media/File:Chauvethorses.jpg ). Similaritys with those of e.g. sable antelopes look like convergent evolution and may well be the point.

@HannesH except you don't know if it is convergent evolution. manes vary a lot in size, placement, and stiffness across all those groups while equid manes are all almost identical outside domestication. .

I am not aware of the evolutionary advantage of the mane in the animals that you mention. In fact, the only reference I could find talks about a predator, not a prey, and thus it might indicate that mane is not mainly an adaptation against predation. I also want to mention that not every trait in every animal is advantageous at the current moment, many traits are 'vestiges' from previous adaptations (or maladaptations). In this case, however, the widespread appearance of the trait in different animal groups might indicate that it is in fact adaptive.
The evolution of mane in the lion seems to be related to sexual selection, as only male lions have mane, but there are competing hypothesis too, in that it appears that the ancestor of the lion was mane-less, and thus the appearance of mane only in lions (and not in other felines) might have been a product of drift (maybe through a bottleneck).
The evolution of mane in other groups of animals might have also been relevant for sexual selection, as it seems that the ancestors of horses had no mane, and thus something that most 'maned' animals have in common is the selective pressure to reproduce and have the mane perhaps as a secondary sexual character indicative of sexual maturation -as it occurs with lions- (I clarify that this is only my own speculation).

I believe the reason male lions have a mane is to protect their neck from damaging bites from other males (males fight over territory and females). Given that the manes of other animals, such as horses are also on the neck, a region that large predators often seem to target, I wouldn't be surprised if they are for the same purpose - i.e. - to protect against bites.

@TimFoster except the horses mane is the least useful place for stopping bite damage to the neck.

@John, not sure what you mean, a dorsal neck bite is a common predator strategy, you see it on nature programs all the time

@TimFoster a "dorsal" neck bite is not biting through the top of the neck, it is biting the sides of the neck.

@John based on a bit of Googling, it looks like biting the back of the neck in order to break or damage the spine is pretty common.

@TimFoster for small prey sure, not horses.

@TimFoster, when you say "I believe...", what is your source? I provided some sources in my answer, but I think you are just going with a 'gut feeling' with no supporting evidence, at least not one I can find.

@ lions are suffocation killers not bone breakers, they bite the front of the neck in large prey. a horse mane is pointless to defend against lions. https://www.sciencedirect.com/science/article/pii/S0003347205809078

Do not horses nip each other on the neck? Could it be a social adaptation?

The horses mane main purpose is to be braided by equestrianists.. ;)


text:
Correlation of Meselson and Stahl with “multifork” replication in E.coli
Because of the limiting value of the rate of DNA replication, rapidly dividing E.coli use multiple replication forks [1][2]. Thus, DNA replication of one generation has already begun in the previous generation.
To me, this poses a problem in understanding the results of the Meselson and Stahl experiment[3]:

Source Biology, Textbook for Class XII National Council of Educational Research and Training (https://ncert.nic.in), NCERT Publications (version: November 2021 Agrahayana 1943) https://ncert.nic.in/textbook/pdf/lebo105.pdf
Shouldn’t the DNA from generation I have somewhat more of 15N DNA, as its replication started when the E.coli was still in the 15N medium? Is that the case or is there another mechanism?

J. Mol. Biol. (1968) 31, 519–540

The EMBO Journal (2007) 26, 4514–4522

Proc. Nat. Acad. Sci. (1958) 44, 671–682

It is sometimes considered that the result was an artifact for a reason similar to that which you mention. However, it happened to be correct in its conceptual outcome, and was not rejected by subsequent better-controlled experimental tests.  This is pretty standard for experimental science. The result would not have been so widely believed if it were not that everyone else's data agreed.

Interesting the paper you reference. However it is not clear to me what you mean by "everyone else's data agreed"? "Subsequent results confirmed or were consistent with"?

@David yes, more or less that. If we are getting into the philosophy of science, we could say that their results were paradigmatic, or that the results were subjected to confirmation by various other experiments. But I think that going into epistemology of science is probably more than we require to say that the scientific community is more likely to accept results that are consistent with everyone's own private data.

What evidence is there that such private data existed?

I voted for this answer on the basis that it linked to an article (actually a book review) that suggests that the result is an artifact of shearing when the DNA was forced through a syringe before ultracentrifugation. However I disagree with the social/historical remarks. 1. There was no reason to disbelieve the results on the basis of multiple replication forks because this was 1958 and nothing was known about them and certainly not the rate of DNA replication. 2. They were certainly  not consistent with conservative replication. 3. They fitted with the Watson/Crick model.


text:
Would my hands sweat this much if I wasn't wearing gloves?
I've wondered about this for a long time, and hopefully someone here has a reasonable answer. I'm a cell and molecular biologist, and much of my time at the bench is spent wearing (usually nitrile) gloves. I've noticed that if I wear them for longer than 10 or 15 minutes they start accumulating sweat. However, my hands aren't clammy or damp when I'm not wearing gloves, so my question is whether my hands are always sweating at approximately the same rate, and the impermeable barrier of the gloves just traps the moisture, or does the enclosed environment inside the gloves promote sweating? My hands don't seem particularly hot when I have the gloves on, and the gloves themselves are pretty thin, although they do have some insulating properties, as I can handle items taken from a -80°C more easily gloved than bare-handed. What causes this diaphoresis?

Skin produces a basal level of sweat all the time, so as far as makes sense to me, they simply prevent evaporation.

To the (potential) close-voters: This is not a medical question (I'm not asking for medical advice, I'm simply describing a phenotype). This isn't (or shouldn't be) primarily opinion-based, because I'm not asking for opinions, I'm asking if there is a clear, biological explanation for this. If you happen to disagree, please leave a comment and I'll try and clean up the wording.

Hand sweating has been fairly well-studied, both because sweating from the hands is one of the main mechanisms of heat dissipation at higher temperatures and because there is a significant effect on palmar sweating by the autonomic nervous system (the main cause of hyperhydrosis of the palms).
Disregarding autonomic effects (stress response), the single most important determinant of hand and foot blood flow is the thermal status of the body core. Heat dissipation is more marked in the hands than feet, and remains so as temperature increases.
Studies have been done of palmar sweating in extremes of temperatures, palmar sweating changes with aging (decreases), palmar sweating in disease, etc. But what has not been studied is the effect of localized heat on sweating of the palms, which would be of interest to you if sweating was a result of the insulating capacity of the gloves.
What is known about palmar sweating is that it is an ongoing and important process in both genders, at all temperatures, and at all ages. The most reasonable assumption then, given the limits of the literature, is that your hands sweat continuously and steadily at a given temperature, and it is highly likely that you are noticing it when wearing gloves only because the vapor barrier caused by the gloves prohibits evaporation.
The roles of hands and feet in temperature regulation in hot and cold environments
OBSERVATIONS ON THE ACTIVITY OF SWEAT GLANDS WITH SPECIAL REFERENCE TO THE INFLUENCE OF AGEING
Why do I get sweaty palms?

But then - If sweating reduces temperature, would the increased temperature not facilitate sweating? That was the reason for me not answering this, apparently, but actually not quite obvious question (+1 for the excellent answer btw :-)

@ChrisStronks - That's a real possibility! Palm sweating is a response to core temperature. Hand temperature isn't reflective of core temp (it varies much more), and there were no studies where the hands alone were warmed to measure it's impact on core temp or sweat production or evaporation was prevented. I have to guess, then. I think it's unlikely that the small heat gain from the hands would affect the core temperature, but I could be wrong. I wished I had found more on that (it was frustrating not to be able to say definitively). :-/

@ChrisStronks Sweating does reduce the temperature - you are right. But the glove prevents evaporation and thereby the cooling effect.

@Chris - yes! And therefore without the evap-cooling effect (I thought) the hands would start to sweat more because of the local temperature increase (sorry I wasn't clear). But as (@)anongoodnurse indicates: it's core temperature that drives sweating so my reasoning isn't valid I guess :) Interesting question after all :-)

Thanks for the answer, I had kind of forgotten about this question. It's too bad there hasn't been any work done on local temps, because I suspect that's why this happens - the gloves are somewhat insulating and there's no opportunity for evaporation, therefore raising the local temperature and causing a positive feedback loop. I guess I'll have to read up more on sweating disorders, as I tend to be rather... shall we say... damp frequently, but that's OT for here unless I anonymize it :)


text:
What are the branches of system ecology?
What are the branches of system ecology that scientists research in nowadays? Or what can system ecology can applied to, or be used?
I have read its Wikipedia page, but sadly it doesn't answer my question. The most relevant section of it is the "Closely related fields", but again, it doesn't answer my question directly.
From what I understand, system ecology is a sub-field of theoretical ecology. It uses thermodynamic in physics to explain a biological system, with the help of network thinking and some technique of visualization. I have presented this in detail what I understand on my website.

Related: How is the Energy Systems Language used in ecology?

The new keyword yields more results, but they still aren't satisfied me. Thanks for your compliment, may I see your site?

What are the branches of system ecology that scientists research in nowadays? Or what can system ecology can applied to, or be used?

This field is often referred to as systems ecology or ecosystem ecology. It is the study of ecosystems. Thermodynamic principles are often used to construct food/system webs (networks) to understand cause and effect within the system. But I think systems ecology can be considered beyond just a numerical approach to include social (human) dynamics.
A great primer for systems ecology is that by Howard T. Odum:
Odum, Howard T. "Systems Ecology; an introduction." (1983).

I have presented this in detail what I understand on my website.

After reading the post on your website I have some recommendations for complex systems science groups/hubs in which you can look for potential mentors/collaborators/ideas:

International Institute for Applied Systems Analysis (IIASA; Austria)
Santa Fe Insitute (US)
National Socio-Environmental Synthesis Center (SESYNC; US)

so if the question is "what are the branches of system ecology?", then the answer is "food web with application of thermodynamic is the only branch"? Is that correct?

I don't know how to answer how many branches there are, since Systems Ecology comprises theories from all over the place. There are groups which focus on ecological interactions only, and those that attempt to incorporate social-ecological interactions.


text:
Is it possible to conduct scientific research without actually getting close to the sample/specimen?
For example, I have never get closed to a whale. The only source I have is research from who has get close to it. If I read their research and find a new thing, would my "discovery" be scientific? If yes, can you give some example of such research?
There is a related question in Philosophy SE: “Dinosaurs did exist once”. Is it knowledge or is it only justified belief? However this question is more about the knowledge directly produced by field researchers, while in this question I focus more on researchers who can only access secondary research. Plus that dinosaurs extincted, so in a sense I and a paleontologist are equal: neither of us can have direct experience to a living dinosaur. But whales are still living, and that equality is gone. So maybe the threshold for scientific research between a living organism and an extinct one is different?
Follow up questions:
• Is it possible to have a scientific review of a method if the author doesn't have direct experience of it? on Philosophy SE
• Can one have good understanding on a method without having direct experience with it? on Data Science SE
Meta question: Why are questions about whether research without direct experience is scientific or not subjective?

While interesting, I feel this question is not well suited for Biology.SE.  Any answers you receive will be necessarily subjective; re: What constitutes a scientific discovery? Is research conducted from second-hand data truly research?

@acvill I've considered asking on Philosophy or Academia, but I would like to have insight specifically from biologists. I suppose there are good subjective questions?

@user1136 does that discovery produce any falsifiable theory?

Would you consider the following scenario "close to"? If so, I can turn it into an answer and cite examples.  Say a data scientist reads a paper and contacts the authors for a collaboration. They collaborate to extract further insights from the data and eventually publish.

@Punintended yes, that can work. But if you have examples of having no contact or exchange with the one who has direct experience with it (perhaps they are dead), then it would be more convincing

To build on @Punintended's comment: you have immense amounts of publicly available data (see for example GEO Datasets) that anyone can download and analyze without any necessary interaction with the original authors.

Hard to answer but you can look into meta-analysis and see if that's appropriate or even feasible for whatever you're trying to do.

How close do you think astronomers get to the subjects of their studies?

@swbarnes2 one can argue that telescope is no difference to microscope

It depends on one's field - whether what you study actually requires first-hand knowledge of the experimental subject and the methods of dealing with or not. Moreover, one could invert the question and ask, whether a field, based solely on the knowledge of the experimental subject, can be considered science?
Theoretical physics/chemistry/etc.
In some sciences, such as physics, there is traditional division into experimentalists and theoreticians - the former are people who actually work in a lab, but who limit themselves to very basic statistical analysis of the phenomena observed. The latter are providing deeper, model-based, analysis of the data and description of the phenomena. Very often their work is not tied to any particular experiment, bordering on very abstract math. Looking at the list of the Nobel prize winners in physics one can easily convince oneself that this work is no less valuable than the experimental work.
Similar division exists in other fields, e.g., one can freely talk about quantum/theoretical/computational chemistry.
Computational biology, bioinformatics, biostatistics, epidemiology, population genetics
Although biology is relatively young science, the times when it was frowned upon by physicists as mere stamp collecting have long been gone: evolutionary theory and epidemiology have been put on a firm mathematical footing, and the explosion of genomic data in the last couple of decades has ushered in the professions of bioinformatician and computational biologist - all complete with designated job descriptions and advanced university programs. Less noticeable, but no else widespread is the observation using modern technology - such as video and sound recording - every conference features a few talks like this, related to swarms of insects, flocks of birds, or behavior of whales (incidentally, whales have been extensively studied in connection to tracing enemy submarines. The analysis of the data is often done very far away from the sea.)

All science is either physics or stamp collecting. - a quote attributed to Ernest Rutherford, but likely of even earlier origin.

Is it possible to have a scientific review of a method if the author doesn't have direct experience of it?

@Ooker could you clarify your point?