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Pyruvate dehydrogenase: Apparently anomalous NAD/FAD redox reaction
Below is the mechanism for the reactions of the pyruvate dehydrogen complex, which oxidatively decarboxylates pyruvate and transfers the acetyl group to coenyzme A for further metabolism in the Krebs cycle.

The key point is that after $\ce{FAD}$ has reoxidized the dihydrolipoamide, the resulting  $\ce{FADH2}$  is reoxidized by $\ce{NAD+}$, which is reduced to $\ce{NADH}$.
I find the chemical energetics of this difficult to understand. According to standard tables of redox-potential for half reactions, $\ce{FAD}$ is a stronger oxidising agent, and a weaker reducing agent, than $\ce{NAD+}$, which is why it used in the succinate dehydrogenase reaction, for example. How, then, can it reduce $\ce{NAD+}$?
If $\ce{FADH2}$ is really able to reduce $\ce{NAD+}$ it should generate as much ATP in oxidative phosphorylation after oxidation of succinate to fumarate, despite the relatively low free energy change for that reaction. But that is absurd.

This is the most perceptive question on a biochemical topic that I have seen in the last twelve months, and deserves far more votes than it has received. A student, apparently new to biochemistry, has brought his chemical knowledge to bear and pointed to an apparent anomaly which most text-books ignore. The beauty of this question to me is that the explanation for this apparent anomaly illustrates the application of chemistry in a biological context. I have learnt from finding the answer to the question, and I hope the poster's interest in biological chemistry has been stimulated by it.

[1-2] IMO, and as I pointed out (politely) in the comments to the accepted answer, there is no thermodynamic problem here whatsoever. Why shouldn't FADH2 reduce NAD(+)? The reaction is reversible. It may be inferred from the standard redox potentials that the position of equilibrium greatly favours FAD reduction by NADH, but this does not mean that the reaction cannot (thermodynamically) proceed in the opposite direction. All that is required is a negative delta G. The position of equilibrium in ethanol dehydrogenase reaction,for example, greatly favours acetaldehyde reduction, and NADH ...

[2-2] can reduce acetaldehyde (to produce ethanol, as happens in yeast), BUT NAD(+) can oxidize ethanol (to give acetaldehyde, as happens in liver). When dealing with redox potentials and Gibbs free energy, one needs to sharply distinguish between standard conditions and actual conditions. For a reaction to proceed spontaneously (only) requires a negative delta G (or a positive redox potential), not a negative standard delta G (or a positive standard redox potential)

IMO a great reference to this problem is Calculating apparent equilibrium constants of enzyme-catalyzed reactions at pH 7 by RA Alberty. The pdf is freely available

Summary
The redox potential widely quoted in text books for the half-reaction reduction of FAD to FADH2 is indeed inconsistent with the observed direction of several reactions involving this coenzyme, including its reduction of NAD+ in the dihydrolipoamide dehydrogenase reaction. The reason for this is that the value quoted is determined for free FAD in aqueous solution, which does not equate to the situation within the enzyme. In its tightly bound state in flavoproteins, the immediate environment (and, in some cases, covalent linkage) alters the affinity of the flavin ring for electrons, hence causing the redox potential to deviate from that in solution. The extent and direcction of this deviation differs in different flavoproteins.
Restating the problem
The basic idea of chemical theromodynamics is that reactions are energetic favourable if the (Gibbs) free energy change is negative (see e.g. Section 14.1.1 of Berg et al.). Although the actual free energy change, ΔG, is influenced by the relative concentration of the reactants, the usual starting point for assessing this in biochemistry is the ‘standard’ free energy change at pH7 and 25˚C — ΔG0′. In the case of oxidation/reduction reactions the standard oxidation–reduction potentials E0′ of each of the two half reactions are usually known (as they can be measured in solution), and one calculates the ΔG0′ from the oxidation–reduction potentials of the two half reactions, using the formula:

ΔG0′ = –nFΔE0′

What is important for this discussion is not so much calculation of actual values, but determining their sign, as for a negative ΔG (reaction energetically favourable) a positive ΔE is required.
Let us consider an example using the much abbreviated version of Table 18.1 of Berg et al. Biochemistry, below:
Oxidant     Reductant       n     E´o (V)
Succinate   α-Ketoglutarate 2   – 0.67
NAD+        NADH            2   – 0.32
FAD         FADH2           2   – 0.22
Fumarate    Succinate       2   – 0.03

Consider one of the energy-generating oxidation reactions of the Krebs tricarboxylic acid cycle:
α-ketoglutarate + NAD+ → succinate + CO2 + NADH
This is made up of two half reactions:
(+ 0.67 V) α-ketoglutarate  → succinate
(– 0.32 V) NAD+ → NADH
which gives an overall ΔE0′ of  + 0.35 V, i.e. a negative ΔG0′, which is consistent with the actual direction of the reaction and the production of energy. (Actual worked numeric examples can be found in Berg et al.)
Now if we consider the dihydrolipoamide dehydrogenase reaction
NAD+ + FADH2 → NADH + FAD
The two half reactions are:
(+ 0.22 V) FADH2 → FAD
(– 0.32 V) NAD+ → NADH
This gives an overall ΔE0′ of – 0.1V, i.e. a positive ΔG0′, which, as the poster astutely points out, is not consistent with the direction of the reaction.
Resolving the apparent anomaly
Berg et al. do, actually, remark on this in section 17.1.1 on the pyruvate dehydrogenase complex:

This electron transfer to FAD is unusual, because the common role for
FAD is to receive electrons from NADH. The electron transfer potential
of FAD is altered by its association with the enzyme and enables it to
transfer electrons to NAD+.

So, how is “the electron transfer potential of FAD altered by its association with the enzyme”? The quotation from Ghia and Massey1 provides a general summary:

The pyrimidine nucleus of the three-membered ring system is electron-deficient and can be viewed as an ‘electron sink’. In thermodynamic terms, any interaction which tends to lower its electron or negative charge density will increase the redox potential. The reduced flavin consists roughly of an electron-rich phenylenediamine moiety fused with a (4,5-diamino)-uracil. The latter is the moiety in which the negative charge (i.e. two electrons taken up by the oxidized flavin) is localized and, most importantly, stabilized. The degree to which this negative charge is stabilized or destabilized is an important factor governing the redox potential. Thus while a positive charge in the protein around the pyrimidine ring will contribute to increase the redox potential, the presence of negative charge or of a hydrophobic environment will lower it.

In the specific case under consideration — dihydrolipoamide dehydrogenase — it has been established2 that a positively charged lysine-57 sidechain (numbering for the A. Vinelandi enzyme) that increases the redox potential (with, perhaps, a small contribution from the backbone N of alanine-326):

[FAD environment in dihydrolipoamide dehydrogenase from A. Vinelandi. NAD is shown in light blue, except for the O and N atoms at the end of the flavin ring interacting with the protein. A section of the latter is shown as a wireframe in salmon pink without sidechains, except for lys57 and ala326. (Own diagram from 3LAD.pdb)]
A second apparent anomaly and its resolution
In drawing attention to the apparent anomaly in the reduction of NAD+ by FADH2, the poster suggested that this would imply one should by able to obtain enough energy to produce 3ATPs from reducing FADH2. The problem with this is that one actually needs FAD to have a lower redox potential to perform the reduction of fumarate that occurs in the Krebs cycle:

This can be seen by considering the redox potentials in the table above:
succinate + FAD + → fumarate + FADH2
The two half reactions are
(–0.22 V) FAD → FADH2
(+0.03 V) succinate → fumarate
Thus, there is an overall ΔE0′ of – 0.19V, i.e. a positive ΔG0′ — another anomaly!
Berg et al. are rather coy on this one. They do not comment, but in their Table 17.2 of free energy changes in the steps of the TCA cycle — where all the other values are given as exact figures — they quote  “~0” for this step.
This implies a higher (more positive) redox potential for FAD than the –0.22 quoted in the table — certainly not the lower one of dihydrolipoamide dehydrogenase.
I turns out that this is, in fact, the case. In succinate dehydrogenase (aka as fumarate reductase) FAD is covalently attached to a histidine residue (his44 in E. coli) at the other side (position 8) of the flavin ring3.

[FAD environment in succinate dehydrogenase from E. coli. NAD is represented as previously. A section of the latter is shown as a wireframe in salmon pink without sidechains, except for his44 and a backbone N. (Own diagram from 1L0V.pdb)]
An extensive review4 of the redox potentials of covalently and non-covalently bound flavoproteins shows that covalent attachment increases the redox potential.
Final observations

Chemistry is a powerful tool for understanding biology at the
molecular level. Biology is subject to the laws of chemistry, but the
chemistry of the special environments encountered (protein interiors,
spaces compartmented by membranes) need taking into consideration,
something that the classically trained chemist, new to the subject,
may not fully realized.
Elementary textbooks often have to walk a fine line between
comprehensibility and truth. The student of biological chemistry
should realize that the initial simplifications that enabled him to
get an overall grasp may mask greater complexities. One of the
intellectual satisfactions in science can be found by resolving these
complexities in a rationale manner.

References
1Ghisla and Massey (1989) Mechanisms of flavoprotein-catalysed reactions
2Maeda-Yorita et al. Biochemistry (1994) 33, 6213–6220
3Kim and Winge (2013) BBA 1827, 627–636
4Heuts et al. (2009) FEBS Journal 276, 3405–3427

Your answer is gold! I really enjoyed it. The concept you used is called symphoria or Neighbouring group participation or anchimeric assistance in organic chemistry texts. I was familiar with this concept in the field of organic chemistry and how it was used to determine the mechanism of reactions But I'd never seen the actual use of this in biochemical studies. Great job!

(+1) [1-3] Although I don't like criticizing such an excellent answer, I think the following point is relevant: to the sentence "... which, as the poster astutely points out, is not consistent with the direction of the reaction." must be added the qualification "when the reactants are in the standard state". But what determines spontaneity is the actual reduction potential (or Gibbs free energy), not the standard reduction potential (unless standard conditions happen to apply). ...

[2-3]  That is, the conditions within the active site may well favour oxidation FADH(2)  by NAD(+) without the need to postulate any change in oxidation/reduction potential of cofactor by binding to the enzyme. To take an example given by Berg: the LDH reaction.  When reactants are in the standard states (1M), the reaction greatly favours pyruvate reduction. But in the Cori cycle, depending on in vivo conditions, the enzyme may act either as a pyruvate reductase OR as a lactate dehydrogenase.

[3-3] If we were to consider only standard reduction potentials we would conclude that the enzyme always acts a pyruvate reductase.  Similarly, although the point about isocitrate dehydrogenase is a good one, but MDH is surely a counter-example? The position of equilibrium of the MDH reaction greatly favours oxaloacetate reduction (when reactants are in the standard state, oxaloacetate reduction is the 'spontaneous' reaction), but in the TCA cycle MDH functions as a malate dehydogenase, contrary to the above analysis.

@Sam Thank you for your kind words. This sort of effect is fundamental to other aspects of protein chemistry, especially catalysis, where the environment of an amino acid residue can alter its properties.

@user338907 — I agree that an unfavourable ΔGo can be 'overcome' by, e.g. the removal of products producing a favourable ΔG. In a metabolic pathways, this may be especially relevant. In approaching this question I was aware of this possibility. However this does not seem to be the case for dihydrolipoamide dehydrogenase, as there is no "pull" on the NADH produced. I personally was surprised at the extensive literature on the redox properties of FAD, and somewhat ashamed at my ignorance. For me the difference between the diffusible NAD and tightly-bound FAD has acquired another dimension.

In the example of dihydrolipoamide dehydrogenase from A. vinelandi, the interaction of the FADH2 with the protein should ideally decrease the reduction potential, (not increase it). If the reduction potential is decreased, then the protein-bound FADH2 will be better able to donate e- to NAD+. Thus, it doesn't make sense to position positively charged aa residues next to the FADH2 in this particular example provided from A. vinelandi.


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How can I clone a gene into a plasmid vector with an N-terminal his tag and TEV cleavage site between the tag and the start of the sequence?
I'm a scientist who has significant experience in chemistry but am relatively new to molecular biology and biochemical techniques. I'm trying to make an isolated domain of a protein (166 residues, 19.5 kDa) with an N-terminal His tag and a TEV cleavage site between the His tag and the N-terminus of the domain. The purpose is to study the properties of the domain in isolation, but without any tags that might interfere with its function. Using the His-tag will make for easy purification, after which the tag can be removed with TEV protease, leaving only a glycine at the N-terminus of the domain, which will not affect my experiments in an appreciable way.
The way I've gone about doing this is to use a forward primer that, after the restriction site and start codon, contains the sequence which codes for the his tag followed by the TEV cleavage sequence, followed by the first 6 codons of the domain sequence. The reverse primer contains the final 6 codons of the domain sequence followed by a stop codon and restriction site. These primers are used to amplify the target domain sequence from a plasmid that contains the full protein sequence, but with the N-terminal cleavable tag attached. The plan is then to clone this DNA insert into a pET21b vector to transform into DH5alpha / BL21 cells.
However, it seems like I'm having problems during PCR amplifying the sequence of the domain from the template DNA. After cloning my purified PCR product into the pET21b vector, and successfully transforming into DH5a cells, sequencing the section of the cloned plasmid with the insert revealed that the insert DNA consisted of only the forward and reverse primer sequences on the ends, sandwiching a single alanine codon. Put another way, the inserted sequence reads as (His-tag)-(TEV cleavage site)-(First 6 codons of domain)-(Single Ala Codon)-(Last 6 codons of domain). This would mean all my cloning steps were fine, but the insert DNA was copied incorrectly during PCR. If it were just the primer ends, I'd think there was some sort of overlap between the primer sequences, but there is that one alanine from the domain template DNA (alanine is the next residue after the first 6 in the domain sequence). A weird result, and I'm not sure where to begin troubleshooting.
My question is, is there anything that I'm doing in this procedure that might stand out as particularly problematic that would cause this issue? Or more generally, is there a better way to put a TEV protease-cleavable his tag on the N-terminus of a protein? Any advice would help, even if it's just to point in the direction of useful references or protocols, and I'm happy to clarify as needed. Thanks!

I don't think your approach is problematic, I think it's just a  PCR technical issue. Have you run your PCR product on an agarose gel to check it ? How have you purified you PCR product : column, gel extract ? Can you add the primers sequences ? What I can envision so far is that your primers may have Tm to far apart.

I hadn't run a gel on it, but I used a Qiagen pcr cleanup kit (mini eppendorf column). The primer sequences are: Fwd: TAAGCAGAATTCATGCACCACCACCACCACCACGAAAACCTGTATTTTCAAGGCCTGGATTATAGACCAGTG
Rev (reverse complement, 5'->3'):TGCTTACTCGAGTTATACTGTTTTTGTGAAGTACAG

Welcome to Biology.SE! Please [edit] the above information into your post (comments are ephemeral and often overlooked — as such they should not be used to convey information important to understanding the question). ——— Note that you should always run a gel to check the size of PCR products — knowing the size (and number) of bands produced could be key to answering your question. In addition, it could be helpful for you to post the target (template) sequence — a (cryptic) primer binding site is one of many possible explanations for your result. Thanks!

Ok, so if you haven't run a gel I would do that first and as mention by @tyersome you should always do it so you know what you're working with. In the meantime if you could share the target sequence it would help us check if there is something happening there. Thanks.

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What is the life of cell-free genetic circuits?
Can genetic circuits be tested in a cell-free environment? What would be their life if we keep them at room temperature?
The circuits which are composed of DNA-based components are commonly referred to as genetic circuits. By testing, I meant to say to test its behavior i.e. applying input signals (perhaps proteins) to see if it generates an output signal (another protein, may be fluorescent protein).
By life, I meant to say, for how long such a circuit (containing strings of dna) can survive at normal room temperature.

Welcome to Biology.SE! What do you mean by a "genetic circuit" and what kind of testing are you interested in doing? What do you mean by "life"? Are you sure these are biological questions? Please note that questions should be clear and demonstrate prior research. In addition, separate questions should be posted separately. ——— Please take the [tour] and then go through the [help] pages starting with [Ask] questions effectively on this site and [edit] your question accordingly. Thanks!

Quick search for "cell-free genetic circuit" gets this article as first result. They give time for which the transcription and translation reactions run. I wouldn't call the reactions life.

Thanks for your responses.
@tyersome: The circuits which are composed of DNA-based components are commonly referred to as genetic circuits. By testing, I meant to say to test its behavior i.e. applying input signals (perhaps proteins) to see if it generates an output signal (another protein, may be fluorescent protein).
By life, I meant to say, for how long such a circuit (containing strings of dna) can survive at normal room temperature.

@BagiM: Thanks for reaching out. I am not calling the reactions a "life". As I said in previous comment, I meant to say for how long such a system can be usable.

@HasanBaig Comments are meant for suggesting clarifications and such; it's better to edit your question in response rather than replying as a comment. Questions and answers are meant to be long-lived, comments are not.

Also it's up to you to write clearly, not to expect others to interpret your writing to discover your intent.

I just edited the question.

And I thought people are already aware of genetic circuits. This is the reason why I did not explain it in details. Next time I will try to explain in more details.

The word "survive" does not really clarify the previous word "life". The reaction mix is not living at any point in time. Are you asking at what time does the production of fluorescent protein stop? Are you asking how long it takes for reactants (ATP) to be consumed? Are you asking how long it takes for the individual components of reaction to degrade (eg. RNA-polymerases to loose function)? For the first two questions, If you have read the article I linked in my previous coment you could have find the answer yourself.

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text:
What is the water content of avian blood?
I'm doing a work about heavy metal contamination in seabirds. I have found that the toxic threshold for Cu in blood is 1,15 μg/g wet weight. That number refers to an average between some seabirds. I need to convert that value from wet weight to dry weight.

You're going to have to be a good deal more specific than that.  "What percent water" - does that include the water inside erythrocytes & WBCs?  And what species?  Some birds increase their hematocrit in preparation for migration, which could throw levels off; some birds live in the desert wheras others live in the water, which could effect normal "percentage of water."  Please [edit] your question to specify what research you have done so far and what information specifically you are after.  Thanks!

@Ifer May i ask you why do you even want to know this information?

Sorry, I'm new in the blog and I don't know how it works yet, but thank you for the advice :)


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How does flow rate of Ion channels depend on the length of the selectivity filter?
The length of the selectivity filter of ion channels such as the potassium channel commonly is only half of the thickness of the membrane. Some book such as MBoC says this can benefit the transfer, so I wonder how will the flow rate of the channel depend on the length of the selectivity filter.
Intuitively, the longer it is, the lower the flow rate will be. But consider the following factor this may not be true:
There is no "resistance" in the selectivity filter. The ions in the channel are basically in thermal balance with the selectivity filter wall and bounce forth and back randomly all the time. The driving force of the flow is not kinetic energy, but the ion density difference at both side just as normal diffusion process. From this point of view, the flow rate should not be depend on the length of the selectivity filter, at least not very much.
If so, then the fact that the length of the selectivity filter is only half of the thickness of the membrane maybe only a coincidence in evolution history and doesn't bring much benefits.
Considering most ion channel have very similar selectivity filter length and synthesis of new ion channel proteins with longer selectivity filter is not possible with today's techs, this can't be decided by experiments. Is there some molecular dynamnics simulation about how the flow rate depend on the length of the selectivity filter?

Would you please include a more specific citation, please? (page numbers / journal article)  Thanks!

@rotaredom Figure 11-24 of MBoC "The pore vestibule facilitates transport by allowing the K + ions to remain hydrated even though they are more than halfway across the membrane"


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Can Western Blots be used to quantify the activity of a protein?
I am new to Western Blot analysis and I have recently done my first two. I am studying a phosphoprotein (a protein kinase) that can be both activated and inactivated via phosphorylation at a specific amino acid residue. I have labelled my membrane against the active and inactive forms of my protein of interest (using phosphospecific antibodies), as well as the total protein (using pan-specific antibodies).
I know that Western Blots are used to quantify the expression of a protein (i.e. how much of a specific protein there is in a sample). But I was wondering how they can be used to quantify the activity (e.g. how functional the protein is) of a protein, e.g. how can I measure/determine whether my protein is more active/inactive in my treatment samples vs. control?
For example, I have normalised the integrated density values for my active protein bands against the integrated density values for my total protein bands. Then I have calculated the fold change in protein level for my active protein in treatment samples relative to control.
If I have observed that the fold change for my active protein is reduced by 40% (as an example) in treatment samples relative to controls, would this be sufficient data to say that the activity of my protein of interest is reduced in treatment samples compared to control?

You may need to optimise your question here: 'How functional is the protein?'. Too broad, what does functional mean? Also, more importantly what are the differences between your control and treatment groups? Are you asking: Because there is more protein expression, is there more protein activity? If so, you do not have sufficient evidence yet. More protein does not prove more activity, especially since the activity is undefined.

The protein I am studying is constitutively active, so by functional I mean what proportion of the protein is in its active form compared to total protein (active + inactive forms of the protein) in my samples. The difference between my control and treatment groups is that I am comparing knockout and wild-type brain lysate samples. I am investigating whether knocking out a protein affects the activity of my protein of interest.

Thank you for your response, it adds clarity.

I see 3 parts to a complete answer:

If you define the phosphorylated protein as active, and non-phosphorylated protein as inactive, and you have a total protein blot (as you say, via pan-specific antibodies) as you describe, then you have done everything correctly.

It's simple math from there on based on radioactivity or fluorescence or mass or whatever you use to quantify your band intensity. The 3 components should match up with the inactive protein amount (active + inactive = total). If this is consistent, you have additional evidence that you have done it correctly.

However, here come the hidden assumptions: this is all assuming that (i) you are not experiencing significant protein loss during your preparation steps, that (ii) your antibodies are good (specific and yield the complete protein extract), that (iii) the blotting procedure is performed correctly, and most importantly, that (iv) your initial definition is valid, that the phosphorylated protein is truly the active form of the protein, and that the unphosphorylated counterpart is the inactive form. You see, this is not always the case, though with some (most?) kinases, it is. If it has not previously been demonstrated, one may raise the reasonable objection that your assumption is wrong. However, I take it that in your specific case, the kinase activation by phosphorylation is well understood.


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If the IAVI G001 HIV vaccine proves itself, why would it work?
The IAVI G001 HIV vaccine trial looks promising.
If it works, will it work by preventing a single cell from being infected, or by allowing the body to attack infected cells?
What I'm trying to understand is if a person living with HIV for years can't develop immunity, why might the vaccine succeed?

There are a lot of sources of information about the vaccine that include information about how it works. Have you read those explanations, and if so, what are you not understanding?

Yes, I've read them but they either didn't answer my question or were too technical to be understood by a layman.

Can you please add more background to include specifics about what you've learned and how that doesn't answer your question?


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Impact of Terminator Efficiency in Genetic Constructs
I was looking at the iGEM Bioregistry of Terminator parts which offer varying degrees of termination efficiency. I am wondering why studies into combinatorial synthesis of genetic circuits for metabolic engineering include terminators as a variable component within their designs, such as this paper by Woodruff et al., 2017? This must come at great complexity cost to overall library size, where I would of assumed one would take the most efficient terminator and fix it within the design. How could terminator strength or sequence effect optimisation of a metabolic pathway in an impactful manner such that this extra complexity becomes worthwhile?

My guess is that they used different terminators to ensure sequence variability. Cloning several copies of an identical sequence into a plasmid can lead to spontaneous loop-outs, causing the additional copies to get lost over time. And for why less efficient terminators are kept in Parts Registry: why would you remove well-characterized parts and thereby lose potentially valuable data? You can only appreciate the efficiency of one part by comparing it to another.

@gaspanic Interesting, thank you for your thoughts!

To add to gaspanic's answer, not all terminators work equally well under all conditions. So if terminators weren't characterized in the organism or tissue you are working in the efficiency might be different. Additionally, though rarely people might be looking to design with a leaky terminator mimicking bacterial use of leaky terminators to use one DNA sequence to create two mRNAs of different length.
[Edit] Sources for further reading
Example of terminator efficacy differences between different species
Example of terminator differences between tissues
Terminator Attenuation - stopping of termination only sometimes
Leaky stop codons as a molecular tool

Your answer may or may not be correct, but we have no way of knowing because it is just an assertion, with no supporting evidence. Please read the Help on Answering Questions.

Sorry, I thought this was widely accepted enough that it didn't need specific references for the assertions.

@PlantPromoter This is very true that part behaviour can vary not only strain to strain but system to system (metabolically engineered system). I guess if you have the ability to implement such complexity nothing is to be lost. I don't think in this case of Woodruff et al., that readthrough would create any benefit to their system because all transcriptional units have their own promoters.


text:
What is this very small black bug?
I saw a very tiny black bug crawling over my computer screen the other day. Having recently acquired a "fingertip microscope" for smartphone, I started investigating.
On a white paper it seemed like a small black dot. I think its in the 0.3 - 0.8 millimeter range.
It would have been fairly unnoticeable if it weren't for it to crawl over my screen.
What could it be? I was thinking about dust mites, but they say it should appear as white. So I'm not entirely sure.
I live in Western Europe.
Note: don't look at the scale. It is wrong.

Also related: Bug Identification: Tiny Bugs


text:
What exactly makes red meat (probably) unhealthy?
It seems generally agreed that (even fresh, unprocessed) red meat is at least somewhat bad for human health.  But why exactly is this the case?  It's difficult to find any attempt at an explanation, especially for anyone not too familiar with diving deep into the medical literature.
Is it because the myoglobin in red meat is carcinogenic or otherwise harmful? That would seem to be the most direct explanation, and there are a few studies on this, but they don't seem to be widely cited in discussions on health effects of red meat.  If that is true, would it mean that one should avoid dark, myoglobin-rich fish and poultry such as tuna and ostrich just as much as mammal meat?
Is it only because red meat tends to be more fatty?  In that case, would leaner cuts of red meat have the same health effects as white meat?
Or is it possible that there is some deep genetic reason why the flesh of mammals is more harmful than the flesh of birds and fish for human consumption?  (I had wrongly assumed this was a strange idea, but acvill's answer gives a plausible explanation.)

The gut microbiome is partly to blame, at least for the associations of red meat consumption with heart disease.  Red meat has a high concentration of L-carnitine, which is metabolized by bacteria in the gut to produce trimethylamine, which is further metabolized by FMO3 in the liver to produce trimethylamine-N-oxide (TMAO). High blood levels of TMAO are associated with higher risk for both cardiovascular disease and early death from any cause.
Sources on the relationship between the gut microbiome, L-carnitine, and heart health:
New study links L-carnitine in red meat to heart disease
Red meat, TMAO, and your heart

Or is it possible that there is some deep genetic reason why the flesh of mammals is more harmful than the flesh of birds and fish for human consumption?

The NIH gives the following values for the carnitine content of different foods:

Food
Milligrams (mg)

Beef steak, cooked, 4 ounces
56–162

Ground beef, cooked, 4 ounces
87–99

Milk, whole, 1 cup
8

Codfish, cooked, 4 ounces
4–7

Chicken breast, cooked, 4 ounces
3–5

Ice cream, ½ cup
3

Cheese, cheddar, 2 ounces
2

Whole–wheat bread, 2 slices
0.2

Asparagus, cooked, ½ cup
0.1


text:
Caloric Mimicry
I was thinking about natural "zero calorie" sweetners and how these compounds could come to be via evolution. I was specifically thinking about monk fruit. While artificial selection likely played a role in the life history of the modern cultivated variety, this plant still needed to initially possess sweetness traits for humans to select. It seems to me to be an interesting case of mimicry — copy the palatability signal of caloric value of other fruits while not devoting valuable resources to creating equivalent amounts of sugars —because it depends on those other fruits/foods being consumed often enough to sustain the propagating organism. This makes it hard to classify the nature to the relationship in the propagator-mimick-mimicked triangle: the propagator-mimick relationship may be read as parasitic, commensal or mutualistic depending how we consider the value of non-caloric nutritional factors for (reproductive) success. Same can be said for the mimick-mimicked relationship, as both benefit from the strengthening of the sweetness signal, but the true signal might in fact benefit more under complete knowledge on the part of the propagator. As a strategy, it is also very interesting because it requires a generalist propagator in an ecosystem with a certain amount of biodiversity, so it seems more likely for this relationship to emerge in nutrient rich environments than poorer ones.
Can anyone think of other examples and are there any existing examinations of similar relationships in the literature?

Nice idea. Plants generally can afford to be energetically wasteful, so I doubt we will see examples of such a high risk / low reward strategy

Interesting proposition. Mogroside appears to have a very complex chemical structure which I would of thought to be very metabolically expensive to create. Although it is 250 times sweeter than sucrose is there any way to quantify if it is > 250 times less expensive to create, I am sure there are many ways to quantify metabolic expense beyond carbon to carbon comparisons etc?

Synsepalum Dulcificum's fruit contains miraculin which makes acids taste sweet. A small amount of citric acid combined with a tiny amount of miraculin will taste like a lot of sugar.

@KaPy3141: Proteins are expensive (nitrogen) for plants and valuable to animals. Even Drosophila can have sugar/calorie hunger and/or protein hunger. So a plant that mimics a lot of protein using a much smaller quantity of some compound (which could also be a peptide) maybe. But the main parts of the plant that are "designed" to be eaten (the fruit and nectar) aren't very proteinaceous.

@JEJS So it could just be a energetically more expensive strategy that becomes successful in a environment where the propagator, here humans, has evolved receptiveness to sweetness. But since mogrosides can act as antioxidants, maybe the benefits outweigh the costs and the sweetness mimicry is an additional bonus?

@KevinKostlan Interesting. Is that the same as "miracle berry"?

@KevinKostlan: Nice point about Nitrogen. I fully agree: Basically, fruits can be assumed to be nutritiously cost-optimized, while ample access to CO2 and sunlight allow higher 'generosity', in terms of calories (sugars).

Yes, carrion flowers for example mimic the scent of rotting flesh to attract flies which will then carry their pollen to other carrion plants.  With sugar specifically though, I'm not sure it would work as well because I believe the fake sugar in drinks like zero calorie soda are actually just as energetically expensive as natural sugar to produce.  So while a plant producing artificial sweetener might not give us any calories, it still has to expend a bunch of calories to produce it.


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Can GFP reporting be used to track localization of peptides in the ER, Golgi, and plasma membrane?
Suppose I want to study the trafficking of a peptide throughout the ER, Golgi, and plasma membrane. An idea I had was labeling a secreted or plasma membrane integral protein with GFP and using time-series live cell microscopy to track it through the secretory pathway.
However, I am concerned that by the time everything is set up, the cell will be at steady state, which means GFP signal would be present throughout the secretory pathway, preventing me from doing this tracking.
How might I overcome this, without changing the fundamental technology (GFP reporting)?

There are several well-established techniques for this kind of experiment ...

Historically speaking, the use of VSVG (Vesicular Stomatitis Virus G protein) labeled with GFP was indeed a practical method to define the secretory pathway. (@tyersome comment)

However, I am concerned that by the time everything is set up, the cell will be at steady state, which means GFP signal would be present throughout the secretory pathway, preventing me from doing this tracking.

Sec mutations in S.cerevisiae: Many biochemical pathways are initially identified owing to a particular mutation in the synthesis process. Recall Beadle and Tatum experiment and the logic they used to clarify the existence of 3 enzymes used in arginine metabolism.

(Image taken From https://www.chegg.com/homework-help/questions-and-answers/following-experiments-beadle-tatum-searching-mutations-disrupt-arginine-biosynthesis-pathw-q41797559)
A similar approach was taken back then to identify the distinct parts of the secretory pathway. Five different mutations in S.cerevisiae were identified named from A to E. Culturing all A to E mutated strains plus VSVG-GFP assay would clearly demonstrate the entire route.

(Image taken from https://slideplayer.com/slide/4382105/)
For example, even if the mutated class B, reaches the steady/equilibrated state, transport vesicles, Golgi, and the rest will not show the fluorescence activity (characteristic of VSVG-GFP) because all of the proteins have accumulated in the previous step(i.e budding from Rough ER)
Further Readings :
https://pubmed.ncbi.nlm.nih.gov/2188733/
https://www.sciencedirect.com/science/article/abs/pii/0092867481900647
MCB Lodish et al 8th edition chapter 14 section 14.1
https://www.nature.com/articles/35073068

Is this to say that it is indeed impossible to monitor localization without knocking out parts of the pathway and comparing?

@actinidia  Knocking out and comparing is usually the easiest way but, now that we know the basic fundamentals and characteristic features of each step in this pathway, other methods can also be employed but I haven't searched or seen any researches, to be honest. You can search for it on your own. Theoretically, we can use 1) Förster resonance energy transfer (FRET) Biosensors: As you know, there is a pH gradient from ER to cis Golgi and later to trans Golgi. (Later sections are more acidic) So one can use this feature to build a molecular environmental biosensor that assumes different ---

@actinidia ---conformations in the presence of different pHs, which in this case would colorize the pathway with 2 different colors(for example Yellow/Green if GFP and YFP are used in the construction of the biosensor protein.)
2)Pulse-Chase methods definitely could be used but it doesn’t use the fluorescence as you’ve asked, so it is off the table.


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Does the mRNA of the covid19 spike protein contain any nuclear localization signals
Does the covid19 spike protein amino acid sequence, as used in the covid19 vaccines, contain a nuclear localization signal. Because if they do, isn't there a chance that the RNA can find its way to the cell's nucleus?
In the case of the AZ and J&J vaccines, which use adenovirus vector DNA to encode for the spike protein. Is there a chance that the DNA of the vaccine could get incorporated into the genome, as described here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2570152/ ?
There is a further discussion of this potential problem here
https://cassandravoices.com/science-environment/science/healthy-people-do-not-require-genetic-vaccination/

And what should happen there?

Avoid degradation, change the genome? HIV does this and has sequence motif similarity with covid.

You would need a reverse transcriptase, which is not present in the nucleus.

My understanding is that all of the sequence similarity with HIV is purely coincidental nonsense, and that the similarity is no stronger than similarity with completely separate genomes. It's like wondering if the mailman is your real father because you noticed he has a nose and by golly you have a nose too.

Well, there is the LiNE-1 RT which is localised in the nucleus.

Bryan, Whether you believe in coincidences or not is neither here nor there.

I kind of expected the question would be downvoted, but is no one really interested in the answer, have we all gone political now?

@ejectamenta I don't think this is a question of politics, but the fact that your question makes it appear that you have a significant lack of understanding about the underlying biology here. Perhaps you could try to explain the context of your question in more detail, illustrating what you know about the processes that leads to to be concerned about this in the first place.

"significant lack of understanding about the underlying biology here" I really don't see the need to cast aspersions or patronise. I also don't think this is the place to present a thesis. If back ground knowledge is required there is always Wikipedia. eg. https://en.wikipedia.org/wiki/Nuclear_localization_sequence I also don't see that my question is particularly out of place given the other questions being asked on stack biology.

I think OP's question is valid and the reasons people are suggesting to close the question are complete bogus. OP might come off as abrasive but that is no reason to vote close. The quality of the question is okay. I tried an attempt to answer it, but I still think that the largest obstacle here is that @ejectamenta may not appreciate the difference between DNA (human genome), the viral RNA genome, the viral proteome, and the spike proteins specifically, which are just a few specific proteins. And also that integrating into the genome and localizing to it are two completely different things!

The term nuclear localization signal is not to be found in your reference. How come you refer to protein, not to DNA/RNA?
Quote from your reference: "Some (...) requirements for targeted integration have been elucidated. The AAV components that are required have been identified. These include the ITRs (in cis), Rep78 or Rep68 (in trans), and a 138-bp sequence termed the integration efficiency element (IEE), located within the P5 promoter in cis..."
What you refer to is "integration efficiency element" or the like, it is not "nuclear localization element?

Does the mRNA of the covid19 spike protein contain any nuclear
localization signals?

I take it you are talking about the coronavirus SARS-CoV-2, and asking whether its RNA genome contains any nuclear localization signals that act post-translationally as signals to specifically import the spike proteins into the nucleus. I cannot find any reports where any of the spike proteins are nucleus-imported, i.e. the spike proteins do not have any (working) nuclear localization signal as far as we can tell.
Some of the proteins coded within its RNA genome are however imported into the nucleus. These are not the spike proteins though.
If you are interested in where the proteins localize within the infected cell, I suggest the following article as a very excellent starting place:
A systemic and molecular study of subcellular localization of SARS-CoV-2 proteins
As for the mRNA, I cannot find any evidence that it localizes to the nucleus. However, there have been reports that other coronavirus' mRNA can localize to the nucleus, that CoV-1 contains a nuclear export motif, and that other coronavirus RNA can localize at the nuclear pore complex to interfere with trafficking between cytoplasm and nucleus space (i.e. at the gateway into the nucleus, but not inside!). This has been shown at least once more. However, these are not the spike proteins, but rather proteins like Nsp1 (non-structural protein 1) that are not categorized as spike proteins.
There has also been an interesting pre-print floating around since 2020 about the possibility of SARS-CoV-2 integrating into the human genome if we were to ectopically add a reverse transcriptase (RNA -> DNA writing enzyme) to the equation. Please read it with a grain of salt, I don't know that the paper has been peer-reviewed and unfortunately I cannot comment right now on the veracity of the research. It is also an in vitro experiment performed under circumstances that do not exist in humans, so the conclusions do not apply to discussions on the COVID-19 pandemic; it is only a proof of concept of integration-ability of the virus, rather that a demonstration that that occurs in vivo.
Here comes the cognate question:
Will we ever find the spike protein-coding sequences integrated into our genome?
A protein being inside the nucleus cannot integrate into the DNA genome though. With RNA, you would also require a reverse transcriptase to integrate it into DNA, which humans do not have. Therefore the odds of finding a spike protein-coding sequence in the genome, especially in the germline, if you are concerned with cross-generational effects, is virtually and practically zero.
EDIT:
You additionally ask in your edit whether DNA in the AZ and J&J vaccines could get incorporated into the genome (integration events). This is a known concern as it leads to carcinogenesis. You specifically ask about adeno-associated virus vectors. Below I quote an excerpt from  Ura et al. (2014) Developments in Viral Vector-Based Vaccines from part 3.3. Adeno-Associated Virus Vectors:

Generally, recombinant AAV vectors are generated by deletion of the
Rep and Cap coding regions between the ITRs. These regions are used
for endogenous transgene expression. Owing to the deletion of these
regions, AAV vectors cannot integrate into the host genome, and their
DNA also persists in an episomal form. This preferable feature in the
AAV vectors boosts their safety profile, by preventing the onset of
tumorigenesis.

In other words, the virus is recombined and its ability to perform genome integration is taken away prior to any considerations of use as vector for the deliver of genes or immunogenic particles, such as the ones you would see in CoV-2 vaccines.

The first clinical trial of a therapeutic retroviral vector took place
in 1990. Subsequent clinical studies have raised serious concerns
regarding genotoxicity, mainly due to possible viral genome
integration. The AAV vector has the ability to express episomal genes
without integrating itself into the host genome, and has hence been
approved by the EMA for clinical use.

As you can see, this has been in top consideration for a couple decades now, it is of course not an issue likely to be overlooked by regulatory bodies nor researchers or vaccine-producing companies.

Thanks for the detailed answer. I just would like to comment that the LINE1 provides a RT pathway that could be used with RNA (mentioned in the pre-print) and that the AZ vaccine being based on DNA would not require RT and could just use the existing DNA replicating machinery to incorporate into the genome, that is, if it were to gain entry to the nucleus, which apparently Adenoviruses are able to do.

You are right, I later read up on LINE1, I was not aware of those mechanisms at play. I plead some ignorance on the topic. I'm hoping that a better answer crops up, as I'm not a virologist and I don't follow the newest news about CoV-2 very much. Hope the brief answer was of some use. And luckily for us, CoV-2 is no adenovirus nor retrovirus!

I am more concerned about the vaccines, covid is difficult to avoid now that it is out in the enviroment, the vaccines however are (pseudo) optional.
The following article mentions "For the latest trial, the components of the gene-editing system – encoded in the genome of a #virus — are injected directly into the eye" https://www.nature.com/articles/d41586-020-00655-8
IMO, AZ, J&J and other DNA vaccines are a risk for genome takeup. The mRNA vaccines less so, but we are playing with unknowns here. Please consider upvoting the question so that it doesn't get deleted.

I hope you can admit and reasonably plead some ignorance about some of this too, since I think you may be connecting unrelated dots. If you want to integrate a sequence into the genome, say with gene-therapies based on CRISPR/C9, you can use strategies originally discovered in retroviruses... But that is not what is going on in the vaccine. The vaccine comes in 2 main variants: mRNA that codes for the harmless spike protein, and the spike protein itself. Both raise an immune response. Neither can be integrated into our genomes as they are. So absolutely no need for concern.

You're quite right that was the wrong reference to give, because, as you point out, the paper itself used a different technique. But to talk again about the vaccines, the AZ is a viral vector vaccine containing its spike encoding in a chimpanzee adenoviral vector as DNA. Isn't there the possibility that this could end up in the nucleus and inadvertently perform 'gene therapy'. Here's a better reference to what I'm talking about. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2570152/

See edit in response to your edit.


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Does stronger reaction to vaccine (fever, days of nausea) mean that an immune system would have reacted the same to the virus?
I have heard that the real danger of Covid-19 is the strong immune response. Is it more likely that a person's immune system would have reacted dangerously to the virus?

Please give a source for the claim rather than ‘I have heard’. Thank you.

These studies suggest that young people have stronger reactions to the vaccines than older people. So your hypothesis is contradictory to the studies that we have for the moment:
img 1
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How to get white bioluminescence?
So I was wondering if it is possible to get white bioluminescence. Actually, I have heard dinoflagellates that produce blue light when there is some disturbance in the water. So I was wondering how to make this blue as white. If it works inside a flask, that is also fine because it should officially work.
So there are a few certain species of dinoflagellates that produce blue light when there is a disturbance in the oceans they live in. It is something like this:

Now, they regularly live in calm seas, and when there are small disturbances like waves or a person walking through them, they start glowing. This is one of the most stunning examples of bioluminescence.
I was planning to make use of these dinoflagellates. I was planning to put them in a black box, with a glass pane at the bottom. In the black box, there would be a tiny and slow motor to simulate the disturbances. Now, my only question is how to make these dinoflagellates glow white instead of blue. Are there any certain species of dinoflagellates that glow white that I am not aware of, or do I have to add any certain chemicals to the water to make them glow white (Please give a chemical that won't hurt the dinoflagellates), or is there any certain food to make them glow white, or should I add any changes to the glass pane to make the blue light look like white light?
BTW here is an image of the model I am talking about:

It's not perfect but is just a base model. Thanks in advance. If you need any other information, please comment.

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


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Production of plant derivatives using genetic engineered micro-organisms
I saw a Thought Emporium video where spider silk was produced by genetically modifying yeast. I have also read about companies making vanillin (vanilla flavour) using this technique.
I am curious to know if plant derivatives like saffron (or its flavour), rubber, or even substances like quinine, tetrahydrocannabinol and cocaine, can also be produced by this same technique. From the information I have found, it seems that some plant derivatives are being manufactured in genetic engineered micro-organisms, but most are not.
Some of these derivatives are very expensive, so I would imagine such techniques could be used to mass-produce them more cheaply. If so, what is stopping industry from doing it? If not, what is the problem?

@tyersome While this question is high-level, I think it's entirely reasonable and readily answerable.

Are you asking what we can theoretically do or what is we can currently capable of?

@tyersome I have very little knowledge of advanced biology and I come from an electrical engineering background. So to 'show an attempt' or to research would mean reading all the basic biology books, which defeats the purpose of having a site like stackexchange.

@John I am mainly concerned about what we are capable of today.

@electronikor You don't need an advanced degree in biology to show you have researched a question before asking it here. The model here is to help people who have shown prior effort at understanding a relevant question - the purpose of SE.biology isn't to spoon-feed people who don't fancy spending time researching a question for themselves.

@user438383 'Research' is a broad term and what qualifies as 'prior research' and what isnt is some esoteric subjective knowledge that only the mods can lay claim to. Also, I would like to point out I have put in enough prior effort to search and even reach out to some PhD scholar on twitter and I didn't get convincing answers anywhere. It would be helpful if the terms could also mention the procedure to 'show' this prior effort. Perhaps attach screenshots of all the searches and results?

@electronikor if you've done your prior research then that's great - just say what you did in the original question (i.e. - I read these papers / articles / asked these people / did whatever and still couldn't find the answer). You don't have to write a whole essay detailing everything you did, but just show enough to signal to the community that you have spent some time trying to find an answer before posting and you'll find people here are very receptive.

@jakebeal — The question is vague and as written the answer is "yes", but that is trivial. The OP has "no knowledge of biology or genetics" and so is unlikely to be able to understand your (or any) non-trivial answer without taking the time to gain some background. If they take that time, the answer should become obvious — if they don't I expect that your answer is wasted effort. ——— That being said, since you spent the time to write a good answer maybe you could edit the OP's post so that it is a good question for this site?

@tyersome I've attempted some minor cleanup and improvement; I actually found it a pretty cogent question to begin with.

@jakebeal thanks a lot!

General Considerations
The question asks specifically why certain plant products are not produced commercially in genetically modified micro-organisms. There are some general reasons, illustrated in some of the examples mentioned:

The product is actually a complex mixture, rather than a single compound. This is the case for saffron, preparations of which contain protein, fat, fibre, sugars and gums, in addition to the the bioactive components — thought to be crocin, crocetin, picrocrocin and safranal (see this review).
It is much easier and cheaper to obtain the product by growing the plant. Although saffron is expensive because it is obtained by hand from crocus blossoms, other plant products do not have this problem, e.g. cotton, mentioned in another answer.
The overall market may not justify the effort. Ignoring other considerations the worldwide consumption of saffron, for example, is small, whereas that for vanillin is huge.
Highly developed chemical production methods may already exist. This is the case for rubber, the chemical production of varieties of which was stimulated by the development of tyred vehicles, and subsequently by war-time demands. Natural rubber is actually a mixed polymer, and specific polymers have been used to develop types of synthetic rubber with individual desirable properties.

Production of Secondary Metabolites
The question mentions “quinine, tetrahydrocannabinol and cocaine” — specific secondary metabolites of plant metabolism which may be of value in medicine, but the complex structure of which renders them difficult to synthesize chemically, much less on a commercial scale. This seems the most pertinent area to consider, especially as the question mentions the successful production in bacteria of another secondary metabolite, vanillin.
I shall take a single example of the successful synthesis in yeast of a pair of secondary metabolites — tropane alkaloids — hyoscyamine and scopolamine. These two compounds (hyoscyamine is shown) have much more complex structures than vanillin:

This is reflected in the fact that their synthesis entails 26 enzymes, compared to the 15 use in the engineered synthesis of vanillin. The synthesis of these more complex secondary metabolites illustrates some problems encountered in the production of such compounds from plant genes cloned into micro-organisms not encountered with vanillin, and not fully covered in other answers thus far:

Identifying the genes for all the enzymes involved in a uncommon biosynthetic pathway
Modularizating the pathway between different organelles to mimic the separation that occurs in plants
Maintaining concentrations of precursors and intermediates that might be removed by the yeast cell’s own metabolism

The example to be described was published in an article in Nature in 2020 by Srinivasan and Smolke, and reports the synthesis of the medicinal alkaloids hyoscyamine and scopolamine starting from simple sugars and amino acids. These compounds occurs in plants of the families nightshade (Solanaceae), coca (Erythroxylaceae) and bindweed (Convolvulaceae), and currently they are produced commercially by extraction from crops grown in tropical and sub-tropical countries.
Identifying the Genes
In many biosynthetic pathways the genes responsible for individual steps can be identified by homology of the predicted protein products to those of known genes. In addition, the genes for biosynthetic pathways are often clustered. However, plants which produce useful products may be relatively obscure and their genomes poorly characterized. In the case of the synthesis of hyoscyamine in the nightshades, Solanaceae, the enzyme responsible for catalysing the final step of the 26 step pathway was unknown. Srinivasan and Smolke had to identify candidate genes from gene-expression patterns under different conditions and then, for the 12 candidates identified, express their gene products and assay for the required hyoscyamine dehydrogenase that catalyses this step.
Modularizing the Pathway
In plants the synthetic pathway does not take place in a single location, but is compartmented between different organelles and, indeed, different tissues. The latter is, of course, not possible in yeast, but was mimicked by directing the products of these 26 genes to six different subcellular locations by engineering appropriate targeting signals onto them. These were the cytosolic fluid, the mitochondrion, the peroxisome, the vacuole, the endoplasmic reticulum, and the vacuolar membranes. This is one reason why yeast rather than bacteria (which lack subcellular organelles) were used in this work.

The purpose of this is explained in a Nature News & Views piece from which the diagram above is taken:

“Subcellular compartmentalization of enzymes can improve product
biosynthesis by enabling proper enzymatic activity and isolating
metabolic intermediates to reduce their toxicity and loss to competing
pathways. By restricting space, compartmentalization also increases
local interactions between the enzymes and their targets. …so each
step can be separately optimized to maximize productivity.”

Maintaining concentrations of precursors and intermediates
Expression (in fact over-expression) of the enzymes of a pathway is not enough to ensure adequate production of the end-product. The precursors for the pathway (here glucose and phenylalanine) must be continually available at a suitable concentration, and reactions which consume key intermediates must be supressed. To this end eight other genes were disrupted in the work in question.
Coda
The example described is a major tour de force, showing the power of recombinant molecular genetics to express genes in micro-organisms for production of secondary metabolites. Possible it is, but routine it certainly is not. In addition to overcoming the types of problems described, there remains the task of obtaining an efficiency of production that it commercially viable. The authors of this work write:

“Process improvements to increase productivities from titres reported
here (around 30 to 80 μg per litre)… to commercial production
(approximately 5 g per litre)…we anticipate would take 1–2 years of
focused effort by a professional team.”

In principle, any biological product should be able to be developed through microbial synthesis, with the appropriate choice of chassis. Indeed, this was the goal of the DARPA "1000 Molecules" program, which did indeed demonstrate it was possible to rapidly engineer new pathways for production of new biomolecules.
In practice, however, some products are far more difficult to achieve than others.
A (very) rough sorting from easiest to hardest:

Small-molecule chemicals that are "near" to an existing metabolite already being produced by the organism, requiring only small number of modifications to the organism.
Proteins, polymers, and small molecules requiring more extensive or difficult synthesis
Materials with a homogeneous structure
Materials with a highly heterogeneous structure

Basically, the more you have to manipulate the cells, the harder it is, and if you need the cells to coordinate with each other to make a material it gets much harder yet. Even some simple everyday materials, such as cotton, are actually fantastically complex and would be extremely difficult to synthetically generate, since even a single cotton fiber has a carefully controlled multilayer structure far larger than any microbe.
Finally, just because something can be produced doesn't mean it will be produced efficiently. Getting from a proof-of-principle to something that operated effectively at industrial scale is a massive challenge, and while this is likely to become easier in the future we just aren't there yet.
Something to keep an eye on, however, is BioMADE, a major government funded venture just kicking off with the aim of making such production much more feasible.
In short: in the near term, expect to see mostly high-value products with relatively simple routes to synthesis, but over the long term a much broader range of materials can in principle be produced.

Thanks a lot.Its a very lucid answer. I was mainly awestruck by The Thought Emporium's video on making spider silk with yeast. I thought if something that is produced by a complex organism like a spider can be made by yeast modification. Then why not something the ester(s) that gives saffron its fragrance?

@electronikor It's a good thought; it just happens that some things, like silk, happen to be much more accessible than others due to the nature of the substance being fabricated.

@electronikor  — saffron is not a good example as it is a mixture of substances, the bioactive components of which are thought to be crocin, crocetin, picrocrocin and safranal, although the preparations used contain protein, fat, fibre, sugars and gums. The synthesis of the bioactive components is hardly likely to be the limiting factor in the lack of a replacement for preparation of saffron from flowers.

Not all can be produced.
Getting the correct glycosylation on proteins hasn't been systematically worked out. For example, to make human-compatible antibodies.
Many of the proteins are modified by multiple enzymes after production - this could require massive amounts of research to replicate.
Some biological products are just unknown mixtures.

Is glycosylation an issue for any current plant products?

@jakebeal — the compartmentalization of the steps of secondary metabolism in the example I consider in my answer suggests it, or some other post-translational modification, might be, but I have not researched the details. The case of human-compatible antibodies is, of course, irrelevant to the question which asks about products of plant metabolism.


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HPV. How do viruses persist outside the body?
The main route of transmission of human papillomavirus (HPV) is generally believed to be sexual. While fomites have been postulated for inexplicable infections, sexual health professionals regularly counter that lying respondents are the more likely explanation.
Research into HPV seems to have mostly stalled and there are few in depth in-vitro studies into viability of the virus outside the body, the infectivity of fomites or their infective dose that I could find.
There are some footnotes and references to animal models, with claims that HPV can remain infective at least 7 days after desiccation but no upper limits. There is some more precise research but understanding the significance is difficult for layman.
For example research published in Nature stated HPV-16 "can remain viable and capable of transducing the reporter construct upon stimulation of cell cycle re-entry for at least 2 weeks, but most likely for no longer than 4 weeks."
How can one understand the viability and limits of viruses, and HPV in particular, outside the body?
To clarify: Despite the fanciful language of the bounty I'm not looking for certainty, but general principles of environmental virology and an overview of statistical observations in regards to HPV in particular.
Note: The various aspects which influence the persistence of viruses in the environment spoken of below are summarized with some additional detail in a literature review published in 2010 in Food and Environmental Virology.

Good question - but I think it could be improved by including some links to the studies you mention. Thanks

Please [edit] your post to include references documenting the persistence of infectious HPV outside of the body. Without that evidence you may very well be asking about a phenomenon that doesn't actually occur. In the future please also make sure to write out abbreviations in full at least once. Thanks!

Refined the question as suggested.

As far as I can tell this topic, specifically for human papillomavirus (HPV), hasn't been fully investigated. There is some literature on it (as cited by OP), but it is sparse, making this an open field for someone to investigate. As such there is no certainty about how long a sample can persist in the environment as a huge number of factors come into it.
However, this is a difficult topic to investigate - how do you mimic in the laboratory the conditions under which you would find the virus in a natural shedding? In terms of HPV, no-one seems to have fully investigated just how the virus is deposited in terms of how it is shed in a natural manner from warts. It is assumed in the literature that it is in the form of keratinised squamous epithelial cells with virus inside, and probably naked virus too. These will have different profiles of decay in the various environments because of the natures of the different forms.
In terms of environments for persistence, there are a huge number of factors that might play into it. Here are a few of the known significant ones: heat (max temperature and min temperature as well as freeze/thaw cycles), light (particularly UV from sun), humidity (overall in environment and local to the place were the virions are), salinity (beach?), chemical (e.g. chlorine at a pool), how the virus is deposited, and last but not least, what the virus is in (a skin cell? mucus? naked virion?)
HPV is a non-enveloped virion containing double-stranded DNA. The virion is composed of 72 capsomers each consisting of 5 copies of the structural protein L1 and forms a strucutre with icosahedral symmetry. The capsid is capable of self-assembly under the right conditions, which means that it is likely quite stable (relative to some other viruses), as it can potentially re-form if damaged by heat or something similar.
The virus enters the cell through abrasions or micro-traumas of the skin surface, where it invades the squamous epithelium and only grows in those keratinized cells. It can also invade and grow in epithelial tissues of some mucosa such as the nasal passages, throat and vagina. Some of these tissues are shed containing virus through abrasion and natural shedding of the epithelial surfaces.
Now that we have a bit of the biology out of the way:
How do we test for persistence of a virus in the laboratory? Actually it is quite simple, generally you grow and purify the virus (or a surrogate similar virus) and then place some as droplets on the surface you wish to test. You then subject it to the conditions that you want to mimic and see how long you can detect it for.
The methods of detection vary depending on the virus and study. Some will use molecular detection methods like the ability to PCR amplify genetic material from the virus as a surrogate for genetic damage making the virus incapable of replication. The other most commonly used is to try to propagate the virus from swabs taken from the surface it was applied to. This doesn't work for all viruses, as some are not culturable, or are very difficult to culture (e.g. for SARS-CoV-2, only about 30% of positive samples can be cultured, but for measles virus very close to 100% can be cultured). If the virus is not culturable, it may be that it can get into the cell and either replicate but not escape the cell, or that replication is incomplete, so genes are expressed, but no virions formed. If either of those two options are go then the presence/viability of the virus on the surface can be determined by looking for activity of one or more viral genes.
I can't give you landmarks for HPV, and the exact sequence of events is unknown for any of the viruses I know anything about, but in general viruses tend to be non-viable before you can no-longer detect genetic material. Exactly how long each of these takes depends highly on the virus. For instance, take two quite topical viruses - SARS-CoV-2 and influenza, both enveloped (less stable) RNA viruses with similar size and structures and similar routes of transmission. Viable influenza persists for about 2 weeks on stainless steel, but only 1 week on cotton, but you can detect the RNA for up to 17 weeks, while CoV-2 only persisted for 1 week on steel, but RNA could be detected for the full duration of the study (though I can tell you personally from my CoV-2 as yet unpublished results >14 days on some surfaces under some conditions at room temp).

That was quite an elaborate answer. This discussion of HPVs in water environment could be a great addition - recent discovery of HPV's presence in urban wastewaters and surface waters has led to hypotheses of water-borne transmission. Although it claims there is little data reg the fate/stability or waterborne transmission of HPVs - waterpathogens.org

Thank you for a very elaborate answer indeed. Does the quote from the research published in Nature, cited above, establish any sense of an upper boundary for HPV-16 in the environment?

@PrashantBharadwaj I noticed the article you mention while looking into this subject. It would be a rather frightening vector for the disease but hopefully one that may be mitigated in the standard water treatment process if it turns out to be viable.

'The virion is composed of 72 copies of the structural protein L1' it's 72 capsomers, each of which has 5 copies of L1. So 360 copies total: https://link.springer.com/content/pdf/10.1007/s00705-006-0798-8.pdf

@timeskull - you are quite right I will edit to correct.

bob1's answer is good, but I was already working on this one so I'll go ahead and post the parts that aren't redundant:
What does it mean for a virion to lose infectiousness?
To be 'infectious' a  virus particle perform a set of tasks that result in more virus particles. A simplified list for HPV could be: attach to receptor on host cell > enter cytoplasm > enter nucleus > make proteins > copy DNA > assemble new virions from protein and DNA > exit cell. The first four tasks must be performed by proteins in the virion; if enough of these are degraded, the corresponding task cannot be completed, and the virion cannot infect a cell. This means that there are many different routes by which any particular virus might be inactivated. One of the references in the question suggests HPV can be inactivated by gunk from dead cells sticking to the otherwise-viable virions:

The greater inactivation of the virions in the extracts at 56 C may be due to denatured cellular protein, which visibly aggregated at 56 C and above, interfering with infection.

Viruses are not metabolically active on their own!
This means that damage cannot be repaired, and also that a functional protein cannot be 'reset' after it changes shape. To use the SARS-2 spike protein as an example, the spikes have energy stored in them like a mousetrap. If the transition from open to closed is triggered while the spike is bound to ACE2 on a host cell's membrane, the motion of the spike protein changing shape will bring the viral membrane in contact with the host membrane, fusion occurs, and the virion contents enter the host cytoplasm. If the transition is triggered before the spike is bound to a host receptor, that spike is 'dead'. SARS-2 virions have many spikes, but if all of them trigger prematurely, the virion as a whole becomes uninfectious. The transition from the high energy 'prefusion' state to the lower energy 'dead' or 'postfusion' state has to be energetically accessible in order to be triggered by the new host cell. This means that the risk of premature triggering is inescapable. Therefore, damage or premature transition of all copies of some viral protein that changes shape to allow cell entry is a likely candidate for inactivation for any viral species. This hasn't been investigated systematically, though, so there's no reference I can cite for this.
In papillomaviruses:
Unlike coronaviruses, HPV doesn't have a membrane that can fuse with the host's for cytoplasm entry. Instead, it is absorbed by endocytosis, then the capsid disassembles, and L2 disrupts the endosome membrane. The details of how this happens aren't known, but it's likely that L2, which is protected inside the capsid most of the time, becomes exposed by structural changes to L1 which occur in the endosomes. This suggests to me that degradation of L1 is the main cause of viral inactivation outside of the cell. That hypothetical structural change of L1 would need to be identified before you could start to investigate if it's present in inactivated particles.

Thank you for contributing to an already full answer with additional technical detail and in an accessible manner. Do either of you have any perspective to share on the process of decay of viruses outside the body, and a sense of  their "life expectancy"?

there's no data on that as far as I know. The proteins are probably degraded fastest by UV rays, then chemical attack by oxygen. 'Life expectancy' can't be predicted yet. Even fairly similar viruses might have different rates of survival. Viruses that transmit through a fecal-oral route are usually tough, and blood-transmitted viruses are usually fragile. Viruses with a lipid envelope usually degrade faster than ones without. But there are a lot of exceptions.


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Amount of carbon captured in photosynthesis by a plant
Is it more proportional to the mass or the volume of the plant? I thought it might be helpful to think on the cellular level here. Even a reference to an external explanation would be useful.

Welcome to Biology.SE! Unfortunately, I'm having some difficulty understanding the context of your question. Can you please elaborate on the background of this question and why the standard description of carbon capture hasn't solved this problem for you?

I guess I'd loved a unified explanation on the level of cell biology. I mean I've phrased the question in what I thought was a pretty good way. Why can't I find it? Even a link to your favorite technical resource would be lovely. Search engine optimization is not doing it for me

The effective carbon capture of a plant involves not just the plant itself but the system that it is part of. Perhaps start by reading up on carbon farming and see if what you find either answers the question behind your question or else allows you to refine it to be more answerable? https://en.wikipedia.org/wiki/Carbon_farming

Welcome to Biology.SE! I am not entirely sure what your are asking but here are some places you might want to start:
Photosynthesis Molecular Biology
If you want to know about the number of sugar molecules created 'per photon' by photosynthesis you can explore the light-dependent and light-independent reactions used in photosynthesis. In particular you might want to look at the Calvin Cycle and how NADPH is used there and how NADP is reduced to NADPH in the light-dependent reactions.
Carbon Capture Efficiency
You might be interested in the variation between plants in carbon capture efficiency, i.e. not all plants are equally 'good' at photosynthesis. To think about this you might want to look at different photosynthesis mechanisms (C3 vs C4 and CAM; different forms or amounts of Rubisco enzyme) or you might want to look at sunlight 'capture' mechanisms (photosystem I and II and the accessory pigments like chlorophyll and carotenoids) or even at adaptations to different light environments (trichomes, leaf shape, etc).


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Bacterial endosymbiosis of bacteria
Endosymbiosis was crucial to the development of complex life and it continues to happen to this day. The origin of mitochondria see bacterial guests in archaea hosts, some of which later took in cyanobacteria which became chloroplasts. Modern "eukaryotes" have varying ranges of ancestry from these two domains with animals being about 50-50. More recent endosymbiosis examples include bacterial or protist guests in eukaryotic hosts.
But are there any examples of a bacterial guest endosymbiosis in a bacterial host? Bdellovibrio bacteriovorus enters other bacteria but it destroys them much like the lytic phage cycle. Bacteria inside bacteria inside mealybug cells have been found. However, this isn't an example of a bacterial symbiosis of another free-living bacterium or even of an extracellular animal-associated bacterium. Are there any examples of bacterial endiosymbiosis of bacteria that aren't intimately associated with the intracellular machinery of a eukaryote?


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Is covid vaccine helpful for a covid patient?
I am not a biology student and this question came in my mind out of nowhere.
I read somewhere that the vaccines contain some denatured or almost dead corona viruses and when these are injected in our body , our immune system remembers them and if the actual (killer) corona virus enters our body , our body recognises it and quickly attacks it.
But if we have a  corona patient his body has already identified the corona virus and so if the vaccine is given the body will not have much changes to do and simply refuses it .
So is it okay to give the covid vaccines to a covid patient ? Can it make the infection even worse ?

This is a site about specific problems in biology, not one for general medical questions. Your question may be acceptable on SE Medical Sciences, but I regard it as off-topic here.

In short, no. It's not harmful but it won't do anything to prevent or mitigate the current infection.
How vaccines work in general is that they train the immune system to respond to an infection so that they are prepared for it. Generally protein component of the virus or an inactivated form of the pathogen is used as a vaccine. The immune system recognises the proteins as 'foreign' and develops anti-bodies to fight them. Then you are immunised to the virus without having to suffer the symptoms of infection. Vaccines work before you are infected as a preventative measure. Then when you are infected, the immune system is prepared and can fight of the virus with the antibodies already developed since the virus has the same "antigen" proteins as you immune cells have already been exposed to from the vaccine.
So what happens when you are vaccinated when you are already infected? Basically nothing.
The benefit of a vaccine is a head-start to train your immune system how to fight it to prepare for the early stages of infection. If you are vaccinated, your immune system will destroy the virus before the it multiplies or gives you symptoms. If you've already been infected then the active virus has already infected many of your cells and multiplied into many copies. Adding inactivated viral particles or spike protein antigen won't help your immune system, it's already been exposed to them by the ongoing infection. Your immune cells are just playing catch up to the infection that's already taken hold. The virus has already stormed the beaches and the immune cells were not prepared. Vaccination now is arguably pointless. They will eventually produce antibodies against the virus already in your system even if you weren't vaccinated.
Lasting immunity after recovering from infection is not guaranteed and a vaccine could give immunity to other strains. For these reasons, it could still be recommended by medical professionals if you've already been infected. However, you need to be vaccinated before exposure to the virus for it to be effective. A vaccine is not a treatment.
Note: the currently available AstraZeneca, Pfizer, Moderna, and Johnson & Johnson vaccines for SARS-CoV-2 do not contain live or inactivated coronavirus. They trick the host system into producing the spike protein from instructions carried by the vaccine.
Citation for clinical application: Jenner, E (1798) An Inquiry into the Causes and Effects of the Variolae Vaccinae.


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What will happen if one keeps the photosynthesis plant active 24x7?
While reading this article online something said on it made me wonder.

Also, there have been suggestions and a Dawn / Dusk type of ramp up and down to simulate the slow changes in the sun have value, but we have not seen solid universal data in this regard to date...

It made me wonder if we are simulating the sun in a dark room for growing the plants with the help of red, blue, and a little bit of far-red light, what will happen to the plants if we keep the ideal conditions for which the plants carry out photosynthesis whole day? Does it affect its yield or the plants die out quick?
I am an engineering student working on indoor farming, my knowledge of botany is the same as a high school student. So if I am wrong please tell me.

Do plants 'stay awake' or fall asleep?

During the night they are mostly inactive.

Welcome to Biology SE! I'm afraid that your question as currently posed is a bit confusing. Can you please try to explain more of the context of your question and what you understand about the mechanisms at play?

@Gurkirat perhaps edit your question to say 'active' (and maybe specify what kind of activity), since plants don't go asleep or stay awake.

You might read about gardening/farming in Alaska, or other areas in the north, where even if you don't get actual midnight sun, there's no actual darkness, just a period of twilight.

this depends a lot on the plant, look at CAM plants for instance.

@John they have different metabolism, but I am talking about normal phosinthesis. If you keep the conditions ideal (maintain proper LED wavelengths throughout the day), and pump CO2 to the environment (the place you are using for indoor farming), and water, etc. Is there any possibility that the health of the plant can be hindered or they are overworked? Is such thing (overwork, health, hindrance, etc.) present in botany?

I don't know the "correct" answer (I don't think one answer covers all plants) but I have lost plants under lights when I have forgotten to cycle (on/off). They had water, food and fresh air, but some need darkness to perform optimally. Certainly blooming is often day-length related; some plants need short days, some need long.

@anongoodnurse  your answer certainly add more to my knowledge, but now I wonder what is the point of using LED if you have to maintain a cycle. Sure we can manipulate many variables now, but I always thought that this advancement would reduce the growth period by half.

This question depends on the plant. The have varied hormonal responses to light to program their lifecycle. For many plants, you can keep the light on 24/7, they will grow faster. For plants that interpret it as a sign of midsummer aridity, they may flower and seed as a response.

Ideal conditions for photosynthesis
You mention ideal conditions to carry out photosynthesis, I would just like to point out that this includes carbondioxide levels, temperature, and nutrients as well as light.
Flowering
As anongoodnurse mentions performance might be measured by blooming which, in most flowering plants, has a day-light related component. However, for general growth increasing daylight over the 'natural' day length can often increase yield.
Daylight Cycles
The important point to note is that plants do 'ramp up' at dawn getting ready to start photosynthesizing (for some plants with temporal photosynthesis mechanisms (see CAM photosynthesis) this can be even more important). The reason plants do this is because plants can suffer from 'photobleaching' which can be considered similar to sunburn in humans, if they are not ready for sunlight. Getting 'ready' can involve lots of things including opening stomata (pores) to let CO2 in, changing which metabolic pathways are active,  and moving about chloroplasts inside cells. Plants 'figure out' how and when to ramp up based on circadian rhythms which work well on 24 hour clocks and slight changes over time. Thus 12 hrs to 16 hrs can be a big change, particularly if the change happens by lights coming on earlier. Additionally, the 24 hour 'clock' means that plants will do better with 18hr light then 6hrs dark cycles than 36hrs light 6 hrs dark, because the total cycle length should be about 24hrs.
Photosynthesis Side Effects
Finally, constant photosynthesis does take its toll on plants as photorespiration accompanies photosynthesis. In C3 plants (most crops) this can reduce photosynthetic output by 25% whilst creating ammonia as a byproduct. The ammonia needs to be detoxified as a build up in the cell can cause cell death. Thus plants need enough 'respite' from photosynthesis to deal with photorespiration byproducts or they will suffer.

Thanks a lot, I was looking for an answer like this

Adding my thanks, too. +1. (Only had a vague idea of the need for darkness, but not the consequence of its absence.)


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By selecting sex cells after meiosis, would it be possible to create two offspring with inverse parental DNA of one another?
Would it theoretically be possible to select two sex cells after a male meiosis (filtering out the two where crossover had taken place) and combine each with two sex from a female meiosis (imagining they were all egg cells, even though only one would be) to create offspring with inverse inherited parental DNA of one another?
For example: If the mother's DNA is AB and father's is CD then the offspring could have AC and BD - inherited from both parents but completely different from one another.

Theoretically? Yes. Very theoretically possible.
In practice? It's difficult to isolate the exact daughter cells (sperm) from the same meiotic event, have these cells complete maturation, and only then have them fertilize an egg. Normally you need quite a lot of sperm cells even with in vitro fertilization, but also in principle all you need would be a single sperm cell to make a zygote!
To address some misconception: when you say "inherited from both parents but completely different", that applies also for regular sex cells and fertilized eggs. You don't need to fish for the precise 2 daughter cells following meiosis to get this outcome. Mitosis produces 2 genetic copies, while meiosis in humans produces 4 unique daughter cells. All individuals, as diploid as we are as humans, are products of genomes that have been very well shuffled (recombined).
Reality: the real-life reasons to perform such a procedure would be taken as very dubious, so I don't think realistically anyone would perform this. But in the designer baby era of the future, who knows!

Sure it would be bery dubious. Was just a silly idea i had. I did have a misconception about crossover where i thought only 2 daughter cells would recombine, when it seems they all do. Still, it seems the resulting children would have mutually exclusive DNA besides that which is shared by both parents. Would i be right in thinking that one child would recive an X chromosome and the other Y from the sperm making the children opposite sex too?

Correct! The ratio of Y and X chromosomes in the haploid sex cells (spermatozoa) is 50:50 as a result of meiotic distribution, and this originates from the X and Y chromosomes being separated between two daughter cells during meiosis.

Here there be monsters
The biggest problem with your scenario as presented is that the complementary genes in the female do not go into the "secondary oocyte" but into the "first polar body" ("2" below).

The first polar body remains in the perivitelline space beside the oocyte, but it is a tiny thing, generally considered too small to potentially make a zygote.  It is emitted as a diploid during the first division of meiosis, and divides again afterward.  I think the one below has already divided.
Now, because it's impossible, we should naturally expect to find such a case, and I will not disappoint:  Bieber, 1981.  In that case the polar body had not divided yet, and the resulting twin, within the chorion, was a triploid and severely deformed "acardiac monster".  A 2015 review mentions polar body twinning without describing the possibility of diploids, so I'll assume this hasn't actually been demonstrated.  I know the first polar body is a bit half-hearted about its division.

It should be relatively straightforward to obtain immature sperm while they are still linked by cytoplasmic bridges as illustrated above, do in vitro sperm maturation to obtain complementary sperm, and attempt some sort of fertilization of egg and a daughter of the first polar body.  The resulting twins would share a chorion but monochorionic and diamniotic.  Such a procedure would still be very likely to produce a malformed embryo due to the development of a very tiny zygote.  I was concerned about epigenetic differences, but after a helpful comment, I did find a reference that the methylome is similar to that of the secondary oocyte, and a paper reporting that it is possible to transfer polar body nuclei to oocytes with 42% viability.  Given remaining uncertainty and a lack of apparent medical necessity, it might still be more advisable to stick to routine human cloning with germline genetic modification. :)

I knew there'd be a problem with female meiosis producing only one egg, but I guessed maybe DNA could maybe be transplanted from a polar body into another egg. I hadn't considered that epigenetic information could make this infeasible, so thanks for the additional information.

You are right!  I'd seen one thing about epigenetic changes and polar body extrusion which I may have misinterpreted, given other sources I found.  I'll update the answer accordingly.


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Soil microbiology reference
I am after some good reference on Soil Microbe Ecology and Biology. I am a biophysicist, and have read the very gentle approach of "Life in the Soil" (James Nardi). Another book I have been recommended is "Soil Microorganisms and Higher Plants: The Classic Text on Living Soils" by Krasil'nikov. This I found very hard going and I was wondering if there was anything more modern on the same subject.

Unfortunately, looking for books tends to be very opinion-based, and thus is typically not a good match for this site.

what would a good site/platform be for this?

Research Gate  might be a good place to post a question like this. It might also help if you provided a little more context about your specific interests re: soil microbiology. It's a broad, interdisciplinary field that has many overlapping themes with agricultural applications, biotechnology, conservation, bioremediation, environmental toxicology, epidemiology and public health, theoretical ecology and evolution, and even astrobiology. It's good to build a broad knowledge base when starting to learn a new subject, but it can still help to narrow your focus just a bit.


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What is the criterion for genetic similarity among siblings and humans in general?
I just started reading Blueprint by Robert Plomin. He makes some well-known statements about genetic similarity which we all have read somewhere but I would like to know what the criteria for genetic similarity actually are:
He writes that all humans are the same for 99% of the 3 billions base pairs of our DNA. I take that to mean something like this: If our DNA had only 100 base pairs and we compare two individuals, those two individuals' DNA would differ in only one place out of the 100 base pairs.
But he also writes that siblings are (on average) 50% similar genetically. I know the rudimentary story of two chromosome pairs, one from mother, one from father, etc. My question is simply how this can be spelled out precisely. I mean, if any two humans are 99% similar in terms of their DNA, how can two siblings be only 50% similar genetically?
I have a slight suspicion: 99% similarity between the DNAs of any two human beings leaves out 30 million base pairs where they are different. Two siblings then are, in addition to the 99& similarity in base pairs, also 50% similar regarding the remaining 30 million base pairs. Thus, two siblings differ from each other in only 15 million base pairs. SO the 99% shared DNA is what makes us human, as opposed to apes, and the rest constitutes the arena in which individual differences take place?

You seem to have the right idea — 99.5% identical base-pairs rather than 90% — but precision is the key here. X% similar means nothing. X% identical likewise unless it is stated precisely what is being compared. What does the author say precisely, or does he not?

you may be interested in these related answers: https://biology.stackexchange.com/questions/1981/how-many-genes-do-we-share-with-our-mother https://biology.stackexchange.com/questions/61147/neanderthal-human-genetics https://biology.stackexchange.com/questions/61206/how-can-someone-share-50-of-their-dna-with-their-parents-yet-all-humans-share-9?noredirect=1&lq=1

Your slight suspicion is close to correct. There are two different ways to discuss 'proportions of shared DNA' (identity by state, versus identity by descent). If two individuals share an allele that is identical by descent, it must by identical by state, but the reverse isn't true.
The 99% figure comes from comparing all of the base pairs and follows the concept of 'identity by state', where 'state' is A, T, C, or G. If individual 1 and individual 2 both have an A at position 39, they match. Average over all positions in the genome, and there's your 99% figure.
The second part of your suspicion is not quite correct, largely because of assortative mating and drift within local populations. The 50% figure comes from classical theory of Fisher, Haldane, and so on. They were trying to solve the mathematics starting from pedigrees and Punnett squares. They didn't have access to the high-throughput DNA sequence data that is common today, but you can follow a rare allele through a pedigree if it causes some observable outcome in its carriers. As a consequence, the classical theory is defined in terms of 'rare' alleles and follows the concept of 'identity by descent', and is tightly linked to the sorts of things you can observe in a pedigree. Having examined many pedigrees, you can generalise the patterns to derive classical population genetics theory. The key thing to remember here is that this branch of theory is expressed in terms of limit formulae: 'as variant A becomes rare, statement Y becomes closer to true'. In that context, the 50% figure is approximately the probability that your full-sibling has a rare allele, given that you have it.
That 50% is a direct consequence of the mechanics of meiosis: you have two copies of each allele. One copy of each allele was inherited from your mother, and the other from your father, at random. As a result, offspring have an exact 50% chance of inheriting any rare allele carried by one of their parents, and so are exactly 50% identical by descent to each of their parents. By the same reasoning, individuals are 50% identical by descent to their full-siblings, on average. In contrast, all humans are 99% identical by state, because a large portion of the genome is shared by all humans.

I think that your formulation in terms of IBS and IBD is probably the most useful for asker, e.g. "All humans are 99.9% identical by state in terms of aligned DNA sequence, whereas sibs are on average ~50% identical by descent from their parents, in terms of inheriting the same chunk of DNA." I think it's worth emphasizing the motivations between those 2 numbers. Otherwise I very much agree with you, I would just weight it differently.

Thanks! I've just edited to try to highlight that contrast.