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Is the Common Cold an Immune Overreaction?
It's my understanding that the majority of symptoms associated with the common cold (runny nose, inflamed sinus, slight fever) are essentially the result of the immune system's response.
I've never heard of someone dying of the common cold (unlike influenza), even in immune compromised people. As such, what damage would the cold virus inflict if there was no immune response? Would it be catastrophic?

Related

Generally, you need some immune response. For the particularly bad immunodeficiencies, even something as seemingly benign as a rhinovirus will extend beyond it's preferred niche in the nose, infect the lower respiratory tract and cause death. Perhaps if I get some time I'll write an answer about this.

Can someone die of the common cold?
No.
The common cold is a clinical syndrome restricted to upper respiratory tract involvement. By clinical syndrome, I mean it is the constellation of symptoms (rather than the consequence of a specific pathogen). As you mention, these symptoms are the result of the immune response, rather than tissue damage or compromised function as a direct effect of a pathogen or its toxin (e.g., the watery diarrhea in cholera).
As defined (see, e.g., Cecil Medicine Ch. 369), this clinical syndrome cannot lead to death.

The common cold is an upper respiratory syndrome of rhinorrhea and nasal obstruction, frequently accompanied by sore throat, sneezing, and cough.

Can the viruses that cause the common cold cause death?
Yes. Many viruses that cause the common cold also cause other clinical syndromes that can cause death. This occurs when viral replication moves to the lower respiratory tract. As an example, influenza viruses are responsible for 25 - 30% of common colds (see Bennett, Principles and Practice of Infectious Disease, Ch.58). When it moves beyond the upper respiratory tract, influenza is responsible for substantial mortality. Other virus families that are responsible for both a common cold syndrome and lower respiratory tract syndrome in immunocompetent individuals (e.g., bronchiolitis, pneumonia) include parainfluenza virus, metapneumovirus, adenovirus, and (rarely) coronavirus. Rhinovirus, responsible for 40-50% of common cold cases, is uniquely unsuited to lower respiratory tract involvement, because of its preference for the cooler environment of the nasal mucosa, replicating best at 33 C (Murray Medical Microbiology, Ch 56). However, in individuals with Severe Combined Immunodeficiency (SCID), lower respiratory tract involvement does occur. There are a number of case series reporting death due to lower respiratory rhinovirus. This is an example.
Can the common cold lead to serious illnesses other than lower respiratory tract involvement?
Yes. Other morbidity can occur as a result of the immune response that produces the common cold syndrome. Rhinorrhea and congestion can progress to a viral rhinosinusitis, a separate syndrome with its own complications, or a secondary bacterial infection, which can lead to bacterial sinus involvement and/or bacterial lower respiratory tract infection. Otitis media is another common complication, especially in children, and has its own potential complications. Asthma (and, generally speaking, most lung diseases) can also be exacerbated by what would otherwise be a simple common cold and predisposes to lower respiratory tract involvement. Asthma does deserve special mention, because rhinovirus associated exacerbations can be fatal, but this is a consequence of asthma rather than a common cold syndrome. Further discussion of these syndromes are beyond the scope of the question, but are discussed briefly in the chapters referenced above.

I don't think coronavirus is that rare as a cause for LRTI. "Coronavirus Causes Lower Respiratory Tract Infections Less Frequently Than RSV in Hospitalized Norwegian Children" shows that coronavirus (in particular, HCoV-OC43 and HCoV-NL63) was in 44% of the LRTI patients in the sample (of coronavirus or RSV), RSV was in 71%, and 15% had both. So RSV is more common, but not overwhelmingly so.

@Charles look at the methods section. Those are nasopharyngeal samples, upper respiratory tract samples. Members of the coronavirus family are not typically isolated from lower respiratory tract samples. It occurs in some specific important syndromes, e.g., SARS, but the common viral families responsible for both upper and lower respiratory tract syndromes are influenza, parainfluenza, metapnuemovirus, and adenovirus. Rhinovirus are even less likely to be isolated from the lower respiratory, but, again, it does occur, especially in severely immunocompromised children.

@Charles Generally, be skeptical of any study that says: "look, i isolated this very common virus from the site where it typically lives. It must be responsible for this particular thing". Rhinovirus and coronavirus are also quite commonly isolated from the nasopharynx of healthy individuals.

Yes, the samples are collected from the upper respiratory tract, and every patient has an URTI. That's the context we're working in here: colds, which are URTIs. But some URTIs progress to LRTIs, and I gave the numbers for LRTIs. The numbers of URTIs are larger and have a higher fraction of HCoVs.

@Charles as discussed,URI predisposes to LRI, but if rhinovirus or coronavirus cause the URI, it's typically a secondary infection by some other virus or bacteria that causes the LRI. Isolating a very common virus from the upper respiratory tract is not useful for determining the cause of a lower respiratory tract infection.

You think that you'd have a URTI progress to a LRTI without leaving any virions in the nasopharynx? I mean, the study authors clearly disagree with you, given the causatives (e.g., "Nevertheless, it should not be forgotten that HCoV-OC43 or HCoV-NL63 may also cause severe lower respiratory tract infections.") throughout the paper and in other cited papers.

Let us continue this discussion in chat.

The common cold is not the result of a single virus. Over 200 viruses can cause a cold, so specific symptoms could vary depending on the virus in question. However, in the absence of an immune response, the virus is may destroy bodily tissues as it completes its life cycle of infecting a cell, using the host cell machinery to replicate its genome, and causing the cell burst open and release the next generation of viruses. This destructive effect could lead to catastrophic symptoms. Especially since the infection is in your respiratory tract, severe tissue destruction could be fatal. It should be noted, though, that the infection generally subsides in a week even with a compromised adaptive immune system (like in HIV/AIDS). This is probably why you've never heard of people dying from the common cold, since it is likely that if their immune system is that compromised as to make such a thing possible, the cold would be the least of their problems.
Sources: https://www.cdc.gov/antibiotic-use/community/for-patients/common-illnesses/colds.html
The most common virus that causes the cold is the rhinovirus, which undergoes the lytic cycle: https://en.wikipedia.org/wiki/Lytic_cycle
clarification: as kindly pointed out by De Novo (thank you!), Rhinovirus itself does not lead to tissue destruction in respiratory epithelia. The Rhinovirus was mentioned simply as an example of the lytic cycle of viral replication, which results in the destruction (lysis) of infected cells and could result in tissue destruction.

So would it be fair to say that because a lesser immune response would suffice for many common colds, e.g. those caused by Rhinovirus, the symptoms are often "unnecessarily" strong? So the immune system essentially says "better safe than sorry"?


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How does the dopamine spike from drugs compare quantitatively to pleasurable non-drug activities?
I did find this popular press article that quotes a researcher offering the following quantification: "in lab experiments done on animals, sex causes dopamine levels to jump from 100 to 200 units, and cocaine causes them to spike to 350 units. '[With] methamphetamine you get a release from the base level to about 1,250 units...'" [1]
However, I haven't found any research study supporting this claim or providing any details?
[1] http://www.pbs.org/wgbh/pages/frontline/meth/body/

This review article [1] gives dopamine responses for rats (similar to the BBC article above) and includes references to the underlying studies:

Sex/Food:  150% - 300%
Alcohol/Ethanol:  190%  (1g/kg) *
Morphine: 200% (1mg/kg) *
Nicotine:  220%   (0.6mg/kg) *
Cocaine:  350%  (5mg/kg)
Methamphetamine:  1000%  (1mg/kg)

These are percentages of the baseline dopamine level (not percentage increases), so 100% would be no effect.  They correspond to dopamine levels in the Nucleus Accumbens, which is a brain region involved in processing reward.
Also, the drug effects are dose dependent, so the above values show the dosage with the largest effect among the dosages tested in this study [2], which was referenced from the review article.  The values marked with asterisks were estimated visually from the graphs.
[1] Allerton M, Blake W. The "Party Drug" Crystal Methamphetamine: Risk Factor for the Acquisition of HIV. Perm J. 2008;12(1):56–58.
 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3042341/
[2] Di Chiara G, Imperato A. Drugs abused by humans preferentially increase synaptic dopamine concentrations in the mesolimbic system of freely moving rats. Proc Natl Acad Sci U S A. 1988;85(14):5274–5278.
 https://www.ncbi.nlm.nih.gov/pubmed/2899326

Hi Andy, nice answer. We like answers to be able to stand on their own, however. A link to a source is good but please also provide a full citation. And if the articles provide more info like dosages it would also be better to include those directly.

I added a more detailed citation.  However, the review article I cited does not include dosages, though results for various dosages are included in some of the studies that they reference.  If I find time, I may track them down.

source: Stack Exchange

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

sort: votes


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Hardy–Weinberg equilibrium for SNPs
I have a SNP stats file structure, which contains all information about genotypes and imputed SNP/INDEL imputation qualities, allele frequencies and minor allele assignment.
SNPID   RSID    chromosome  position    A_allele    B_allele    minor_allele    major_allele    AA  AB  BB  AA_calls    AB_calls    BB_calls    MAF HWE missing missing_calls   information
--- rs200405949 NA  10023   CCAA    C   C   CCAA    923.32  16.662  0.012   911 6   0   0.0088756   4.8216e-17  1.0638e-05  0.024468    0.47987
--- rs201803828 NA  10097   CCA C   C   CCA 930.29  9.711   0   924 4   0   0.0051654   -0  1.0638e-06  0.012766    0.50802
--- rs185444096 NA  10177   C   T   T   C   291.03  45.234  0.712   216 12  0   0.069231    9.6433e-17  0.64152 0.75638 0.80608
--- rs200882690 NA  10299   TA  T   T   TA  292.62  43.613  0.744   219 12  0   0.066921    4.8216e-17  0.64152 0.75426 0.79622
--- rs56377469  NA  10469   G   C   C   G   239.25  474.83  225.9   38  69  20  0.4929  0.10014 2.234e-05   0.86489 0.42593
--- rs7341907   NA  10869   C   G   G   C   239.29  474.8   225.89  38  69  20  0.49287 0.10014 2.234e-05   0.86489 0.42597
--- rs149305563 NA  14665   G   A   A   G   267.44  66.53   2.973   144 16  0   0.10755 0.10741 0.64155 0.82872 0.79468
--- rs149079262 NA  14690   C   G   G   C   207.26  115.51  14.189  56  25  1   0.2135  0.12672 0.64153 0.9117  0.79388
--- rs141156662 NA  15883   A   G   G   A   259.05  71.908  6.001   131 13  1   0.12451 0.20633 0.64154 0.84468 0.80157
--- rs202192731 NA  17614   CT  C   CT  C   7.893   142.55  789.45  1   39  581 0.084231    0.27659 0.0001117   0.33511 0.47425

I managed to assume/figure out the meaning of all columns but two - HWE and information.
HWE:
I assume HWE means Hardy–Weinberg equilibrium, and is actually a chi-square value obtained via Pearson's chi-squared test, and using only samples from the same dataset (and not compared to some general dataset, e.g. GWAS). Using HWE , we can then calculate the p-value using the degrees of freedom (one in this case) via the gamma function (e.g. via p-value calculator), and if the result is significant, this means that the specific SNP is not in HWE, hence this SNP is either in linkage disequilibrium, or needs to be rejected/ignored because of genotyping (i.e. data obtaining) errors. If so, what significance level is mostly used/best for such cases? In the Hapmap II paper, SNPs are removed if they are not in HWE with a p-value < 0.001.
information:
I have no clue what it means or how it's calculated.

Regarding "information": specifying the software used for analysis could be of help. As of now, I have no idea of what it is.
Regarding "HWE":

Not knowing the software I am not sure, but I can guess that In the column you already have the pvalue.
There is no clear agreement on the threshold, and not even if SNPs outside of HWE should be removed or not. You can give a look to this paper (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2796342/) to start understanding. The choice depends a lot on the study sample and the questions you are trying to answer.

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


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What makes iodine an effective antiseptic?
I'm thinking about tincture of iodine, potassium iodide (Lugol's), and povidone-iodine (PVP-I) specifically, which, as is my understanding, work by solubilizing elemental iodine in an aqueous solution. These solutions slowly release free iodine, and it is ultimately the free iodine that does the biochemical damage that kills microorganisms.
But how, specifically, does free iodine cause this damage? The Wikipedia page on povidone-iodine says that free iodine:

kills eukaryotic or prokaryotic cells through iodination of lipids and oxidation of cytoplasmic and membrane compounds.

and that:

Slow release of iodine from the PVP-I complex in solution minimizes iodine toxicity towards mammalian cells.

I understand that elemental iodine strips electrons from all kinds of stuff because it is such a strong oxidizing agent, being so close to neutral valency, and obviously that's bad for important macromolecules, but I guess I'm looking for a bit more detail on how it works (or doesn't work) in other respects, with answers to questions such as:

Why does iodination of lipids cause the lipid membrane to fail?
Why does "slow release" make a difference for mammalian cells - are eukaryotic cells somehow better able to handle the damage caused by low concentrations of free iodine than prokaryotic cells?
What makes bacterial spores and protozoan parasites such as Giardia resistant to iodine's antiseptic properties?

Sorry that that's more than one question. But if anyone is able to elaborate on any of these concepts, I'd greatly appreciate it!

Welcome to Biology.SE! This seems like an interesting series of questions, but please take the [tour] and then go through the help pages starting with [Ask] questions effectively on this site and [edit] your question accordingly. ——— In particular, please separate your questions — each post should be focused on one question. This helps you get answers to all of your questions and makes those answers more accessible to searching by other users. (You can provide links to the related questions in your text.) Thanks!

The most recent review I could find on this subject was from 1999 — maybe you can use that as a starting point to find out more ...


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Help me identify this animal from Bangladesh
I have come across this animal in a facebook group. After one group member identified it as Asian palm civet, I looked at some google images, I am not convinced. Judging from google images, this animal doesn't look like any of the common civet species found in Bangladesh.
Location: Noakhali, Bangladesh

Looks like the Large Indian civet. Notice the size and the fur coloration pattern on the neck.
From wikipedia:

The large Indian civet ranges from Nepal, northeast India, Bhutan,
  Bangladesh to Myanmar, Thailand, the Malay peninsula and Singapore to
  Cambodia, Laos, Vietnam and China.[1]

Looks like it is found in eastern parts of Bangladesh including Noakhali district – the place where the picture was taken.

Is it a Small Indian Civet?

From Wikipedia: The small Indian civet has a rather coarse fur that is brownish grey to pale yellowish brown, with usually several longitudinal black or brown bands on the back and longitudinal rows of spots on the sides. Usually there are five or six distinct bands on the back and four or five rows of spots on each side. Some have indistinct lines and spots, with the dorsal bands wanting. Generally there are two dark stripes from behind the ear to the shoulders, and often a third in front, crossing the throat. Its underfur is brown or grey, often grey on the upper parts of the body and brown on the lower. The grey hairs on the upper parts are often tipped with black. The head is grey or brownish grey, the chin often brown. The ears are short and rounded with a dusky mark behind each ear, and one in front of each eye. The feet are brown or black. Its tail has alternating black and whitish rings, seven to nine of each colour. It is 21–23 in (53–58 cm) from head to body with a 15–17 in (38–43 cm) long tapering tail.

The fur pattern on the neck is entirely wrong, and the coloration doesn't match: the Small Indian Civet is two-colored (typically light and dark brown), while the mystery animal appears to be three-colored (black, white, and brown).


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Does natural selection still increase biological complexity?
I recently read The Selfish Gene by Richard Dawkins, which I found very interesting. In one of the last chapters, he gives multiple possible explanations to the question "Why did natural selection give rise to complicated lifeforms?".
Since complex (say: multi celled) life exists, that means natural selection at some point did increase complexity, as we went from the primal soup to multi celled organisms (with many steps in between). My question is whether this trend of increasing complexity is still going on? Is natural selection a never-ending arms race, tending towards increasingly complicated genomes? Or did natural selection reach some plateau, local optimum, of biological complexity, after which the only evolution taking place is "on the same level".
I have thought a bit about a metric for complexity, but since I have no background in biology I am not at all certain. At first thought, the length of the genome sounds like a promising candidate, but the phenomenon of freeloading, not-functioning DNA (conveniently described in The Selfish Gene too) undermines this. I hope it is clear what I mean by "complexity".
Thanks for answers in advance, it has been fun speculating.

Hi Lourens & welcome to Bio.SE! This is an interesting topic. To make your question more answerable, try to focus in on a specific question. If you could start with your definition of "complex-life" and ask a question on what you don't understand about the definition. For example, your current definition is simply how "multicellular" an organism is. Is a blue whale more complex than a human?

On a side note, the Selfish gene is >40 years old. We understand far more about genes now than we did then. For example, even the definition of "non-functioning" DNA is problematic; wikipedia describes this evidence of functional "junk" DNA.

@James yes specifically the definition of complexity is difficult, as I mentioned too. But we can agree that a human is more complex, then, say a microbe. So at some point, natural selection gave rise to more complexity. What my question boils down to is whether this is still happening.

Answering that last question depends intimately on a definition of complexity. I'm not quite sure where people get so interested in complexity and evolution, but questions similar to this have been asked numerous times here and they have all failed (as far as I recall) to give any operational definition of complexity that can help answer the question.

People seem to forget that bacteria and archaea have been evolving for just as long and they largely remain unicellular.

Possible duplicate  Is variation a result of Evolution? or https://biology.stackexchange.com/questions/42050/if-evolution-is-not-about-increased-complexity-why-does-so-much-complexity-evol

Sure, a human seems to be more complex than E.coli. We would start answering this question by trying to measure & quantify the complexity of these organisms. Is the complexity the number of cells, something anatomical like the number of appendages, environmental adaptability, variety of hats, number of coding genes, or sequence complexity? Only then can we discuss if that specific feature appears to be rising, falling, or plateauing in the biosphere. Without these specific exact definitions, this question cannot be answered completely.

There are multiple definitions of complexity, ranging from algorithmic complexity to computational complexity.  In biology, I'd say that algorithmic complexity (Kolmogorov complexity) is most relevant.  Unfortunately, we don't yet know enough about genetic circuits and all the other things that go on at the subcellular level even to make plausible estimates of an organism's complexity.
If the complexity of a human being were analyzed all the way from physiology down to the subcellular & molecular level, I think it would be apparent that most of the complexity is present at the subcellular & molecular level.  In fact, essentially all of the complexity of a multicellular organism is encoded at the subcellular level, so it's appropriate to say that's where the complexity resides.
It is not entirely clear that a human being, whose genome contains ~3 billion base pairs, is more complex than a protozoan Amoeba Proteus whose genome is ~34-43 billion base pairs.
All of the processes that have been active in evolution since the beginning are still active, and changes in complexity - regardless of the definition of complexity - are still going on.
The closest things there is to a "plateau" is a relatively static distribution of genotypes that can last only as long as the adaptive landscape is unchanged.  However, the adaptive landscape is always changing because of climate changes, plate tectonics, invasive species, disease, intra-species iteractions, and even because of chance fluctuations in the distribution of genotypes.

thank you for your answer. As @James also pointed out in a comment, my question fails by the definition of complexity. Not only that, the abstract idea of complexity I had in mind seems flawed after reading your answer, since I was clearly biased towards the human scale. Your fact about the amoeba dubia's genome seems to be outdated, although your point still stands. Correcting for the measurement error gives the indirect estimate of 67 billion base pairs. https://bionumbers.hms.harvard.edu/bionumber.aspx?id=104470&ver=6


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Parts of the brain pivotal for maintaining consciousness
From an answer to another question (on conscious experiences by coma patients) I have learned that

no conscious experiences, complex thoughts, or complex emotions can
  occur when one is in coma (clinically unresponsive, with absent or
  minimal brainstem reflexes, and with severely abnormal EEG)

This means that proper modes of activity of the cortex and the brainstem are necessary conditions for conscious experiences.
Two questions arise:

Has it been shown that proper activity of the brainstem and the cortex is also a sufficient condition for conscious experiences, i.e. all other parts of the brain might be mute or otherwise improperly active? Or are there other parts of the brain whose proper activity is also necessary for conscious experiences?
Why is it that next to the newest parts of the brain (cortex and neocortex) also its oldest part (the brainstem) is pivotal in maintaining consciousness? What about other parts that evolved later?

Note that with "necessary" I don't mean causally necessary but merely logically or observationally necessary, i.e. "not observed without".

The minimal neural mechanisms that are jointly sufficient for consciousness (conscious percept, thought, memory, etc.) to occur, under constant background conditions, are called the neural correlates of consciousness (NCC) [1]. The background conditions are enabling factors that must be present for the NCC to be able to function (e.g., the heart must beat and the lung must exchange air to supply the brain with oxygenated blood, the blood levels of sugar and other blood constituents must be in normal ranges, the ascending reticular activating system (ARAS) must be functioning, etc.), but they are not the NCC.
The ARAS is the neural network in the core of the brain extending from the rostral pons to both thalami and the basal forebrain, and from there it sends extensive axonal projections to the cerebral cortex, including the consciousness neural network (which is the anatomical part of the NCC). The ARAS is responsible for the alertness of consciousness, but it is not responsible for the content of consciousness. So, it is not part of the NCC proper. However, there can be no consciousness if there is no stimulation from the ARAS, even if the consciousness neural network is intact and able to function, such as in the case of extensive brainstem hemorrhage, infarct, and trauma. And the level of conscious alertness depends on the activation from the ARAS – the more activation, the higher level of alertness. This results in various conscious level’s states, such as (from lower to higher level of alertness) coma, stupor, drowsiness, normal alertness, and heightened alertness [2]. So, the answer to question #2 – why this oldest part (the brainstem) is pivotal in maintaining consciousness – is that it is the way the consciousness neural process has evolved to be dependent on the ARAS for its level of function (i.e. its alertness).
On the contrary, if the ARAS is working normally but the consciousness neural process is not, there can be alertness without, with minimal, or with some awareness. The degree of impairment of awareness depends on how much the consciousness neural process is dysfunctional. For example, in the case of damages to the consciousness neural process from diffuse cerebral hypoxia, extensive bilateral cerebral infarcts, or diffuse cerebral cortical injury, the results can be various abnormal conscious awareness’s states that range in severity of abnormal conscious awareness, depending on how much the consciousness neural process is impaired, such as (from mild to severe) acute confusional state, akinetic mutism, minimally conscious state (MCS), and vegetative state (VS). In the latter two categories, which are severe conditions, the patients can open eyes and have some reflex responses, such as blinking, chewing, and yawning, but show no (in VS) or minimal (in MCS) signs of conscious awareness of self and the environment (by clinical testing or by special investigations such as EEG, evoked potentials, and fMRI) [2].
Regarding the neural circuits of consciousness, as far as one can conclude from the evidence at present, it seems very likely that the Default Mode Network or Resting State Network [3], which includes the medial prefrontal cortex, posterior cingulate cortex, precuneus, hippocampal and parahippocampal cortex, retrosplenial cortex, and some parietal and temporal cortices, is the network of the consciousness neural process when the mind is in the state of passive internal mentation, not performing cognitively demanding tasks, and not attending to outside stimuli. This network overlaps with the network that functions for access consciousness (consciousness of episodic stimuli, not consciousness of continuous stimuli as in the former case). At present, evidence shows that the network of Global Workspace theory proposed by Baars [4] or the network of Global Neuronal Workspace hypothesis of Dehaene [5], which includes the cortico-thalamic (C-T) core and a network of neurons with long-range axons densely distributed in the prefrontal, fronto-parietal, parieto-temporal, and cingulate cortices, is the network of access consciousness. So, the complete neural network of consciousness that functions to be conscious of continuous events and episodic events is likely to be some form of combination of these networks, such as the neural network in the extended theory of global workspace of consciousness proposed by Song [6].
The complete neural circuit of consciousness, whatever it is finally found to be composed of, and the way it functions will constitute the complete NCC. The complete NCC is necessary and sufficient for consciousness to occur. Even if we do not have the complete NCC now, the above current models that we have are fairly well supported by experiments. I hope this answers question #1.
References.

Tononi G, Koch C. Consciousness: Here, there and everywhere? Philos Trans R Soc Lond B Biol Sci. 2015 May 19;370(1668):20140167. DOI: 10.1098/rstb.2014.0167.
Ukachoke C. Chapter 6 – Consciousness. In: The Basic Theory of the Mind. 1st ed. Bangkok, Thailand; Charansanitwong Printing Co. 2018.
Andrews-Hanna JR. [The brain’s default network and its adaptive role in internal mentation.(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3553600/) Neuroscientist. 2012 Jun;18(3):251–270. DOI: 10.1177/1073858411403316.
Baars BJ, Franklin S, Ramsoy TZ. Global workspace dynamics: Cortical “Binding and propagation” enables conscious contents. Front Psychol. 2013;4:200. DOI: 10.3389/fpsyg.2013.00200.
Dehaene S, Charles L, King JR, Marti S. Toward a computational theory of conscious processing. Curr Opin Neurobiol. 2014 Apr;25:76–84. doi: 10.1016/j.conb.2013.12.005.
Song X, Tang X. An extended theory of global workspace of consciousness. Progress in Natural Science. 2008 Jul 10;18(7):789–793. DOI: https://doi.org/10.1016/j.pnsc.2008.02.003.

Thanks for this comprehensive answer!

You don't mention the claustrum which is according to Crick and Koch one of the seats of consciousness in the brain. Would you consider it as part of the NCC or as an enabling factor like the ARAS?

I think the case for claustrum is still controversial. For example, “… another case report describes a patient who was conscious despite the fact that the claustrum and … had been destroyed bilaterally as a consequence of herpes simplex encephalitis” Koch C, 2016 and please search discussion about claustrum in this paper.

However, because claustrum is higher up in anatomical level than the thalamus and basal forebrain, which are the terminal nuclei in the current ARAS network model, it shouldn’t be part of the ARAS. Also, studies have shown that it has extensive connections to cortical and subcortical regions and its functions are complex integration of various cortical inputs (ex. color, sound and touch) into one experience, not just simple stimulation of consciousness. So, if it’s one essential part of consciousness network, I believe it’s part of the NCC, not the ARAS.


text:
Is PrEP used for anything other than HIV?
In the field of HIV prevention, PrEP is an abbreviation of pre-exposure prophylaxis. This is a very generic term. Are any diseases other than HIV prevented using a similar approach? Do they use the same name?

Prophylaxis is typically prior to exposure. Condoms, for example, were historically referred to as prophylactics, in that they prevent pregnancy and many STIs. The reason the pre-exposure bit is given special attention in this context is that it refers to use of drugs with substantial risk of harm. Because of their associated risk, these drugs were previously only used for post exposure prophylaxis. Similar to rabies vaccination after an animal bite, this strategy involves preventative treatment given after exposure but before a critical point in the progress of an infection.
To more directly answer your questions

Are any diseases other than HIV prevented using pre-exposure prophylaxis?

Many, many, many diseases. Vaccines are a good example of prophylactic treatment, typically given prior to exposure. Malaria prophylaxis is another example, where a medication (with non insignificant risk of harm) is given to healthy people traveling to an endemic area.

Do they use a different term?

In most cases, as you can see by searching for the words used in the linked references, the term is simply prophylaxis, rather than pre-exposure prophylaxis.

Yes, I'd wondered about the semantics. I assume vaccines aren't classed as PrEP because of the different mechanism by which they work?

@ChrisW vaccines are treatment prior to exposure, intended to prevent infection. And so they are pre exposure prophylaxis*, but they are typically just referred to as prophylaxis. The special terminology for HIV PrEP is, as I indicated, to distinguish use of ARV prior to exposure from use of ARV post exposure, which has been done for about 25 years.

Sorry, I meant the difference in that vaccines are typically an injection of the virus, (immune response) rather than a continual drug to prevent the disease if you come into contact with it (pharmacological response) - I hadn't realised that both were technically PrEP.

@ChrisW condoms are technically pre-exposure prophylaxis as well.


text:
Why is dimethylmercury so poisonous?
According to the Wikipedia article Karen Wetterhahn, Karen Wetterhahn died after only a very small amount of dimethylmercury got absorbed through the gloves. What is it about the way the body works that makes dimethylmercury so poisionous. I don't know very much about biology. I know a few things like how proteins act like a catalyst. I would like an answer that starts all over from scratch giving me the right basics after which I will understand the answer of why dimethylmercury is so poisonous and then explains why it's so poisonous.

I think this question needs some focus. Why do you ask an answer that starts from scratch?

@James Because I don't have all the information I need to understand an answer suited for experts in biology.

@Timothy "From scratch" is indicative that a question needs some more research. Asking about "why code X does Y from scratch" on SO would result in swift closure. It's hard to tell what you are actually asking.

For a very disturbing article on dimethyl-mercury and Karen Wetterhahn, see The dangers of dimethylmercury, published in Chemistry World in 2019

Organic mercury compounds like Methylmercury or Dimethylmercury act as toxins by binding to thiol or sulfhydryl groups of
proteins. These Mercury compounds cause oxidative stress, lipid
peroxidation, mitochondrial dysfunction, and changes in heme
metabolism.
Dimetylmercury is absorbed via gastrointestinal tract and later it
enters bloodstream and is circulated to whole body. It binds
with essential proteins like haemoglobin through the sulfhydryl groups present in
cysteine. These complexes resemble the structure of methionine, therefore it easily circulates throughout the body and could cross the blood-brain barrier.
Mercury can bind to mitochondrial enzymes which can lead to cell
injury and death. It is reported that mercury can inhibit aquaporins
which prevents water transport across cell membrane.
Mercury also inhibits the kinase activity of protein LCK, which
decreases the level of T-cells and weakens the immune system.
Mercury also act as neurotoxin by inhibiting the neuronal membrane
excitability by effecting postsynaptic activity. It  inhibits Protein
kinase C and Alkaline phosphatase, which damages brain formation and
functioning even at blood-brain barrier.
Organic mercury mainly causes developmental effects by binding with
the tubulin  protein,  which prevents microtubule assembly and
inhibits the process of mitosis.
Mercury also results in  autoimmune response by effecting Major
histocompatibility complex (MHC) class II molecules, self peptides,
T-cell receptors, or cell-surface adhesion molecules.

(Via:  http://www.t3db.ca/toxins/T3D0361
https://www.sciencedirect.com/topics/neuroscience/dimethylmercury )

Is it exactly the same reason why dimethylcadmium is also so very poisonous?

Yes..but it enters the body through inhalation.

Check out this link:  https://www.google.com/amp/s/www.medicaldaily.com/most-dangerous-chemical-world-why-chemists-steer-clear-one-substance-394764%3famp=1

A good succinct answer to a vague question. +1


text:
Is this a bed bug
I'm moving into a new house. We have pretty much thrown out all of the bed furniture's and have not seen any bugs in the sheets or anything like that.  But, while preparing for painting, I saw this little guy on the wall and I've never seen one of those before.  Know what it is?  Is it a bed bug?
The plastic thing you see here is an electrical outlet wall plate. I would say the insect is about 2 mm. I live in Quebec, Canada
(Edit: i understand there is another post like mine but his pictures show an adult bed bug while my pictures show what I think is either a nymph or a book lice or something else). Thanks!

Does this answer your question? Insect identification - Is this a bedbug?

Size, shape, and coloration make me thing psocid (or book louse), but your pictures aren't too great. If you can, try uploading a better photo and you'll likely get a more definitive answer. If that's not possible, then I would recommend searching our site for other posts about psocids which will result in quite a few hits for you to compare images to. Good luck!

Thanks, I'll look for that, never heard of those!


text:
Typical firing patterns of neurons in the default mode network in resting state
Inspired by the Wikipedia article on the default mode network where I read:

Hans Berger, the inventor of the electroencephalogram, was the first
  to propose the idea that the brain is constantly busy. In a series of
  papers published in 1929 he showed that the electrical oscillations
  detected by his device do not cease even when the subject is at rest.

I came up with the following question:

Are there data available for typical firing patterns of single neurons
  (of a given type, in a given region or functional unit) in the
  default mode network in resting state  over some significant
  period of time, say a minute?

By "typical firing pattern" I mean:

the overall number of spikes (per minute)
the number of isolated spikes
the number and duration of tonic bursts
the number and duration of other firing patterns as proposed e.g. by Eugene Izhikevich
and the mean distances between them

Or are such data not available, maybe because they are too hard to gather or cannot be summarized in a sensible way.
I ask just to get an idea, and because I would like to know if - for example - the maximal, mean, or median number of spikes per minute has an order of magnitude of 10, 100, 1,000 or 10,000 - or even more?

The DMN is composed of many different cortical brain areas each containing many cell types; I think it would be difficult to define anything as 'typical' among them. There are also no hard borders to the DMN; you could define some for a given purpose, but it would be hard to find agreement.

Both classifying neurons into proper subtypes and recording firing patterns of neurons (in their natural environment) are not very easy tasks. This review (not sure if freely available) is mostly about the classification but also contains a good introduction & some examples on different electro-physiology.

@Nicolai, thanks for the link, unfortunately not freely available. (What to do?)


text:
What happens when a human ingests a large meal, and after a short time follows it up with a large amount of indigestible carbs?
A human eats a large meal and indigestible carbs (IC) with such a timing that the IC arrive to the small intestine when it is already full and busy breaking down and absorbing the meal. What would happen to the IC? Would they stay there until the digestible meal is digested, or would they somehow be moved along? Would they start fermenting if they are stuck there for some time? Would they push the unabsorbed remnants of the meal out as the body tries to excrete IC? Would they hamper absorption or aid it?

Indigestible carbs are known as dietary fiber. They slow down gastric emptying, which results in slower absorption of the absorbable nutrients in the small intestine.

Early research regarding soluble fiber demonstrated delayed gastric
  emptying and decreased absorption of macronutrients, resulting in
  lower postprandial blood glucose and insulin levels [44]. This is
  most likely due to the viscosity of soluble fibers inside the GI
  tract. Interestingly, different types of soluble fiber had varying
  effects on viscosity and nutrient absorption. Guar had the highest
  viscosity as well as the greatest effect at decreasing postprandial
  blood glucose. Therefore, it would be assumed that an increased level
  of soluble fiber would be associated with a decreased risk of
  diabetes. However, several recent studies have demonstrated the
  opposite showing no correlation between soluble fiber and a reduced
  risk of diabetes (Nutrients, 2010).

So, dietary fiber can slow down the absorption of macronutrients (carbohydrates, proteins, fats), but does not reduce the amount of macronutrients absorbed (at least not significantly).
Dietary fiber can be soluble (for example, stachyose and raffinose in legumes) or insoluble (for example, cellulose in fruit skins or grain hulls) (Linus Pauling Institute).
They are microbes, mainly in the large intestine (not in the healthy small intestine), that ferment soluble, but not insoluble fiber. Fermentation of a large amount of soluble fiber produces a lot of gas (flatulence), which typically occurs several hours after a meal.
Insoluble fiber can stimulate intestinal motility and thus help in constipation, but large amounts can be laxative, which could result in decreased absorption of nutrients; soluble fiber can trap some bile secreted by the gallbladder and may thus reduce the synthesis of cholesterol (Linus Pauling Institute).
Dietary fiber probably does not interfere significantly with the absorption of minerals and vitamins (Nutrients Review).


text:
How are the images of both eyes combined to form one image?
When you see an object by one eye, ex.right eye, you see it from the right direction and the opposite if you see it by your left eye, but when you open both eyes, the image appears somehow centric in between.

How does the brain combine both images to form the final image?

You might also ask "how does the image on the retina become inverted ?"

@blacksmith37 - that is a very different question, and for that matter a question based on an invalid premise, assuming the image gets flipped back again in the brain; it is not, as there is no retinotopic ground truth necessary in the brain. The merging of two retinal projections, however, is the very basis of the most important cue for depth vision, i,e., retinal disparity.

well to start the brain does not form an image, there is no homunculus.

The visual system contain several stages in which the information from both eyes is progressively mixed and analyzed, starting in the lateral geniculate nucleus.
Even if you feel seeing just one merged object with both eyes, your brain is using both images to calculate the 3D position of that object.
One fun fact: The image that you feel centric, it is actually bias towards one of your eyes, the called "dominant eye". You can check what is yours by a simple experiment


text:
Can it always be determined if an animal is a carnivore, omnivore, or herbivore by its teeth or are there exceptions?
Take the panda, for instance, it has canines but it's an herbivore. However, are there are other aspects of its teeth where one could still tell that it's an herbivore? Do the teeth always relay the information about whether an animal is a carnivore, omnivore, or herbivore?

Welcome to Biology.SE! With the panda example you seem to have answered your own question. You also might find the answers to this question to be of interest.  ——— Please also take the [tour] and then go through the help pages starting with [Ask] questions effectively on this site and edit your question accordingly. Thanks!

@tyersome I didn't actually answer the question, there may be other aspects to a panda's teeth that tell what its diet is, rather than just are there big canines or not. That was just an example where maybe more investigation is needed, or maybe one couldn't tell just by the teeth, I don't know,  hence the question.


text:
About the mechanism of coupled reaction/metabolism with ATP
I am not in the field of biochemistry so this may be a rookie question or misconception.
I heard occasionally about the energy "released" from ATP hydrolysis fueling (endergonic) biological reactions. I am concerned about how does the energy "released" actually "fuel" another reaction mechanistically. In chemistry and physics, you can say that the fact that energy is released is a sign that the process (ATP hydrolysis) is energetically favorable (more stable bonds are formed as some weaker ones are broken). Subsequently, when the released energy is heat for instance, this heat can be used to do (or "fuel") mechanical work (like in a car engine). This is intuitive to me but the same cannot be said with ATP hydrolysis. How does the release of energy from ATP-hydrolysis actually "fuel" other reactions? or is it a misuse?
Thank you so much.

This is a basic, although not simple, question which has been asked here before. It is best researched in a biochemistry text book rather than in an answer on this list. You will find a good account in Berg et al. of how the overall free energy change is regarded as determining whether a chemical conversion is thermodynamically favourable, and how an unfavourable reaction can be coupled to a favourable one.  After reading that, please repost here or on Chemistry for clarification.


text:
What is the need of mucilagenous coating in pollen grains of aquatic plants?
I'm a high school student from India and here in our prescribed biology book(NCERT), it is written that pollen grains of aquatic plants have a mucilagenous coating to protect them from wetting.
My doubt is that they already have the most resistant chemical, the sporopollenin, on their exine to protect them. It cannot be degraded by acids, enzymes, high temperature, alkalis. Then what is the need of another layer of mucus to protect even the most resistant of nature's chemical? Or is it that sporopollenin is absent in aquatic plants? I cannot find anything good to satisfy my doubt out there on Google.


text:
Identify an animal (Japan, urban area)
I met this animal yesterday while walking along a small river in Yokohama, Japan. It came out of the bushes some 5 meters away from me, but while I was launching the camera app on my smartphone, it already went away into a fenced area where I couldn't follow and was quite far, so these are the best pictures I could take. It seemed to have something wrong with it's fur (either molting or sick). Could be a japanese raccoon dog (a.k.a. tanuki), although the images I found on Google don't look much like it to my untrained eye (maybe because of the fur), or some kind of a fox (looked even less likely). Tried asking locals, but they tend not to know anything about animals, unless those animals are either dogs, cats or foods. So, what is this?

EDIT: the size is hard to describe, I would say, it was a bit bigger than a big domestic cat, and also had different proportions - longer body, neck and legs.

Welcome to Biology.SE! For identification questions please [edit] your post to include an estimate for the size of this mammal. A description of what you could observe about its coat/skin might also help. ——— You may also want to take the [tour] and then go through the help pages starting with [Ask] questions effectively on this site. Thanks!

I've been able to narrow it down to 3 species in Musteloidea, the weasel superfamily, but I think you observed a Tanuki that was suffering from scabies.
1) Tanuki / Japanese raccoon dog - 'Tanuki' - (Nyctereutes procyonoides viverrinus).
Visually similar to what you observed. The feet and face in particular seems to fit with a tanuki. Tanuki are often observed in urban areas in Japan and have been increasing in recent years. There are frequent reports of tanuki with scabies that have missing fur and a similar appearance:
(Google search for "tanuki" and "scabies":
https://www.google.com/search?q=%E7%96%A5%E7%99%AC%E3%82%BF%E3%83%8C%E3%82%AD
2) Common raccoon - 'Araiguma' - (Procyon lotor)
Since they were introduced in 1962 as pets, there are some wild populations in Japan, including in Kanagawa prefecture where you observed the animal.
3) Japanese badger - 'Anaguma' - (Meles anakuma)
Another possibility but I think it does not fit your observation.
There are a few other species in this superfamily but I think it is safe to exclude them due to a lack of visual similarity.


text:
How are newly synthesised proteins targeted to the plasma membrane?
There does not seem to be a definitive answer to how proteins destined to be intrinsic plasma membrane proteins are directed there. Presumably, assuming starting at a cytosolic ribosome, the pathway is via the SRP/Sec61 translocon system into the ER co-translationally, followed by COPII vesicular transport to the Golgi for modifications.
From here, is the system that of COPI transport back to the ER? I think I read that if sitting in the ER membrane, proteins can 'slide' into the PM via some vague endomembrane system juggling. Or, packaging into vesicles which can then fuse with the PM?


text:
Could Cyanobacteria farms help dilute pollutants in the atmosphere
If I understand correctly, roughly ~2.8 billion years ago cyanobacteria started pumping large amounts of oxygen into the atmosphere.
Using modern industrial processes could this be emulated by making cyanobacteria farms to help slow down the climate problem?
I also read somewhere that someone was able to genetically (or through other means) turn off the ability of a specific bacteria to reproduce causing it to produce a byproduct much more efficiently. Could this also help these "farms"?
Alternatively could we genetically strip the bacteria of all other functions other than procreating and photosynthesis? Making this bacteria live in a "bubble" would mean it wouldn't need a lot of defense mechanisms. This could make a single purpose bacteria that would be super efficient at doing this single task.

How about just planting trees?

Good question. My gut says that bacteria would be easier to mass produce, to genetically mold into what we would want and are more efficient at doing photosynthesis. To my knowledge cyanobacteria are the only other organism other than humans to have impacted the environment on a global scale.

Plants and algae (including blue green algae, aka Cyanobacteria) sequester CO2 when they grow. But in terms of growing more Cyanobacteria, look up iron fertilisation: the oceans aren't green like a pond because there is not enough iron or phosphate or both. However this means creating new ecosystems as opposed to saving them

Also note that the 'great oxygenation' event was an even more drastic climate change than what we are seeing currently. While it paved the way for most modern lifeforms (who depend on a somewhat narrow O2 concentration) it killed probably more than 90% of what was living back the  (since they couldn't deal with O2 at all).

@Matteo Ferla instead of creating ecosystems could industrialization not just treat them as part of a process in a factory. They wouldn't be introduce into the wild but used in self contained bubbles. Mostly so that all their processes requiring energy to be spent on protecting themselves from the environment and predators could be genetically removed (More efficient and less likely to become an invasive bacteria).

Iron fertilisation (wiki) is at a larger scale and cheaper (a ship releasing a container size of nutrients across an oceanic crossing is sufficient to make a substatial planktonic boom, which when it dies sinks and thus buries the carbon it converted into biomass. If you had a algal farm you would sequester CO2 as biomass, which you would need to bury.

In terms of pollutants, there are several ventures, such as LanzaTech to mention one, who use bioreactors attached to an industrial process to bioremediate it. In their case they use a thermophile who uses carbon monoxyde to make CO2 and biomass (no idea what they do with biomass).

@Matteo Ferla [Joke] Soylent Pink? [/Joke] Thanks for the info, I'll be looking them up.

You have various questions here.

If I understand correctly, roughly ~2.8 billion years ago cyanobacteria started pumping large amounts of oxygen into the atmosphere.

The great oxygenation event was not an instantaneous process and represents a change from one equilibrium (low oxygen) to another (20% oxygen). This abundance of oxygen and organic carbon means that there is "niche" for organisms that burn up pre-existing organic carbon and use oxygen as terminal electron accept. Fermenting organisms use the organic carbon as a feedstock, but don't have oxygen so the use highly reduced organic molecules as terminal electron acceptors (less energetic), making mixed acids (sweat bacteria) or ethanol (yeast).

Using modern industrial processes could this be emulated by making cyanobacteria farms to help slow down the climate problem?

Cyanobacteria and other aerobic phototrophs convert carbon dioxide to oxygen and organic carbon they can use to make biomass. So if you had enough of these you'd need to get rid of the biomass. Responsible forestry for housing actually ticks this box (cf. vs. a mature forest, which is nearly at equilibrium where the biomass gets consumed by other organisms, else you'd had a faster growing topsoil).

I also read somewhere that someone was able to genetically (or through other means) turn off the ability of a specific bacteria to reproduce causing it to produce a byproduct much more efficiently. Could this also help these "farms"?

It is a grand challenge of synthetic biology to stop growth. It is really hard to do as "cheat" (i.e. variant that can grow faster) will dominate. Biofuel research suffers from this as the fatty acid biosynthesis pathway is highly expensive energetically and cheats eventually win despite the most complicated safeguards.

Alternatively could we genetically strip the bacteria of all other functions other than procreating and photosynthesis? Making this bacteria live in a "bubble" would mean it wouldn't need a lot of defense mechanisms. This could make a single purpose bacteria that would be super efficient at doing this single task.

The carbon will be a problem, so you'd need to make biomass or some value added compound.
Three additional points:
Green biotech
There are many "green biotech" companies out there and there is an increasing number of green chemistry awards going to biocatalysis (enzymes for a reaction) and in some cases synthetic biology processes (whole enginereered organisms for a product or intermediate). But the former field is slow at growing because it needs to compete against a century of homo/heterocatalyis (normal chemistry), while the latter needs a lot more technological innovation to improve the production chassis (e.g. cheats, slow reactions, iron-sulfur cluster over-expression and electron balance are common issues: hydrogenase is a classically cited example of a hard target with great potential).
Note that most green biotech uncouple the process and use the biomass from regular algae or plants to feed their engineered organisms, as it is easier and there are less containment issues.
Algal blooms
In the comments I mention, iron fertilisation of the oceans (a ship releasing a container size of nutrients across an oceanic crossing is make a substatial planktonic boom, which either increases fish levels or sinks and thus buries the carbon it converted into biomass). This is a curious case of huge scale and cheap algal farming. But we don't know all the details, yes we'd be turbocharging the oceans (which are barren relative to say a jungle), but we may favour toxin-releasing algae, jellyfish and imbalance fisheries and actually send to extinction others.
Bioreactor in the ISS
The Internation space station splits water to make oxygen, dumps all carbon waste outside (CO2 and ...) and has water and food shipped up. This is odd as you'd expect they would be the first to use algae to scrub CO2! However, things are changing: they are trialing an algal bioreactor, which on a larger scale will result in a near-closed loop system. However, there are many engineering and some biological issues that need to be faced.


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What are the constraints on an operon?
From what I understand, the term operon is loosely defined to be a collection of genes that are found to be in the same proximity in a genome.
Some definitions enforce that an operon is only regulated by a single promoter and all of the genes are transcribed together.
If the above definition is strict, that would imply a couple of things

Genes are opposite strands cannot be in the same operon (since they cannot be transcribed together)
Overlapping genes cannot be in the same operon for the same reason.

I realize that part of the issue with these definitions stems from an ongoing investigation behind this phenomenon.  But are there strict standards surrounding the definition an operon? What is the minimal definition of an operon?
Relevant links

What is an operon?
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4161906/pdf/12864_2013_Article_6422.pdf
https://en.wikipedia.org/wiki/Operon

From Henderson's Dictionary of Biology 14 ed. An operon is: a type of gene organization in bacteria, in which the genes coding for the enzymes of a metabolic pathway are clustered together in the DNA and transcribed together into a single mRNA. This mRNA is then translated to give the individual proteins. The expression of all the genes in an operon is controlled by a single promoter.
I'm not sure what an overlapping gene is, but according to this definition, yes genes on opposite directions of a promoter or different loci cannot be a part of an operon because they wouldn't be on the same mRNA.


text:
In vivo, does it take energy to move double bonds from cis to trans in long chain unsaturated fatty acids
In vivo, I understood that because all polyunsaturated fatty acids bonds are -cis they are crowded, kinking the molecule, and because of that, the oxidative enzymes cannot initially access them. They first have to be moved to the -trans side to allow the enzymes to act on the double bonds. So my first question: is ATP needed to move double bonds from -cis to -trans? And also, when the long-chain FA like EPA & DHA are oxidized, because of this energy expenditure to move them, wouldn't they yield less total bond energy when oxidized than if they were just oxidized in vitro, e.g. by heating?
If this is true, then how much ATP is used to first get those double bond groups into the -trans position so the oxidation enzymes can reach them? And … thus could I state that in vivo breaking of long chain polyunsaturated fatty acids would not yield as much energy as would in vitro breaking of these bonds?

As I understand it the question refers to mammalian oxidative degradation of dietary polyunsaturated fatty acids, as the diet is the major source of such fatty acids. Its concern is with two different aspects of this process neither of which involve the use of ATP. The proposition in the final paragraph is therefore incorrect.
The first aspect is not explicitly stated, but seems evident in the mention of the crowding of fatty acids with cis double bonds and the repetition of “in vivo”. I would rephrase it as:

How is the agglomeration of lipids disrupted so as to be available to
  the enzymes that degrade it?

This is as much physiology (not my field) as biochemistry, but there are many accounts available (e.g. this I found at random) regarding the emulsification of lipids by bile salts in the small intestine and their conversion to chylomicrons in the lymph and blood. The latter are either processed and stored in the adipose tissue and later oxidized when needed, or oxidized directly, in the mitochondria, especially of the liver.
The disruption of fatty acid aggregates is purely a physical process facilitated by the chemical environment in which they find themselves. This alone allows oxidative enzymes access. (In passing, I would say that it is difficult to conceive of a mechanism by which ATP could be used to disrupt a hydrophobic aggregate — see Appendix.)
The only stage at which ATP is required is the conversion of free fatty acids to fatty-acyl CoA by fatty acid thiokinase before reaction with carnitine and entry into the mitochondria in the form of acyl carnitine. In relation to the handling of hydrophobic molecules in a hydrophilic environment (or vice versa for membrane transport) it may be worth mentioning in passing that carnitine is a zwitterion.
The second aspect of the question is more straightforward. In chemical terms what the question refers to as “moving double bonds” is called isomerisation. So the question is:

Does cis-trans isomerisation of unsaturated fatty acids require ATP?

This is described in standard biochemistry texts such as Berg et al., from which the diagram below is taken.

No ATP is involved.
Of course a reductase is required to catalyse the reduction of double bonds using NADPH as a reducing agent, regardless of whether they are cis or trans. As the related NADH can be oxidised in the electron transport chain to produce ATP by oxidative phosphorylation, this could be regarded as equivalent to using ATP. However this has nothing to do with the isomerisation.
Appendix: ATP and energy — concepts and  misconceptions
Although this question includes some chemically correct references (the need for cis-trans isomerisation for unsaturated fatty acids to act as a substrate for acyl CoA dehydrogenase), it does raises some suspicions of an incomplete grasp of the factors affecting the viability of biochemical reactions and the role of ATP. If this is correct — and shared by others — I suggest reading an account of how the concept that the Gibbs free energy change of a chemical reaction determines whether or not it proceeds, and how the negative free energy change in the hydrolysis of ATP can be coupled to reactions that have an (otherwise unfavourable) positive free energy change.
Two points relevant to the question are worth mentioning in this regard. Although ATP can be used to cause motion, this involves motor proteins like myosin, kinesin and dynein interacting with large molecular structures. Thermal vibration and thermodynamics are the normal drivers of motion in a cell. The second is that many biochemical isomerisation reactions have standard free energy changes close to zero as, in isolation, the alternative structures have similar energies. What normally prevents the reaction proceeding is the activation energy barrier for the interconversion reaction of one isomer to the other, which is where enzymatic catalysis is comes in. The actual free energy change depends on the concentration of reactants and products, so if the cis isomer builds up and the trans product is removed by reaction then the reaction will proceed in the cis-to-trans direction.


text:
Differences between neurotransmitters and neuromodulators
According to the Wikipedia article on neuromodulation

a neuromodulator can be conceptualized as a neurotransmitter that is
  not reabsorbed by the pre-synaptic neuron or broken down into a
  metabolite.

In another Biology SE answer I read that

neurotransmitters can be considered neuromodulators when their action
  is on channels outside of the synaptic cleft.

Trying to bring these two conceptualizations together I come up with the following more specific differences between neurotransmitters and neuromodulators:

Neurotransmitters have typical short delay times (until they reach a receptor). Neurohormones may have arbitrary long delay times (the time they need to diffuse through the extracellular fluid). As a slogan: "Neurotransmitters work at once, neurohormones with a distance-dependent delay."
Neurotransmitters have specific target neurons (via the receptors of the synapse where they are released). The number of target neurons of a neuron (affected by the neurotransmitters it releases at its synapses) is rather well-defined (and goes into the thousands). The number of target neurons affected by the neurohormones a neuron releases is not so well-defined (and I'm missing an idea of the order of magnitude).
Neurotransmitters are effective only once and for a short time (due to fast reabsorption or break down into metabolites). Neurohormones can be effective for a long period of time.
This is due to different biochemical mechanisms by which specific neurotransmitters and neuromodulators affect specific receptors.

I wonder if this list is somehow correct and complete. (This is my question.)
Next to this list a list of commonalities would be interesting:

The same molecules can be neurotransmitters and neuromodulators.
Both are stored in and released from vesicles by similar mechanisms.
Both get effective by interacting with receptors and affect if a ligand-gated ion channel opens or not.

Key points:

Neurotransmitters directly stimulate or inhibit ionotropic receptors (the receptors of ion channels) in the postsynaptic membrane within a single synapse.
Neuromodulators act on metabotropic receptors within or outside the synapses of many neurons at the same time; they modulate the release of neurotransmitters and excitability of ionotropic receptors; the signaling between metaboreceptors and ionoreceptors usually involves a cascade of secondary messengers.

Neurotransmitters
"Classical neurotransmitters" stimulate or inhibit the fast-acting ionotropic receptors of ion channels. Their actions last few milliseconds and are limited to a single synapse, which means they are released from a presynaptic membrane of one neuron and they target the postsynaptic membrane of one (or, sometimes two or maybe more) postsynaptic membranes of the neurons involved in the same synapse, or a single muscle cell or other target cell (Oxford Scholarship, The Revisionist).
Examples of neurotransmitters: noradrenaline, acetylcholine, dopamine.
Neuromodulators
Neuromodulators act on the slow-acting metabotropic receptors inside or outside the synapse of "thousands" of neurons at the same time. In long-term (minutes), they modulate the release of neurotransmitters and excitability of ionotropic receptors. They are usually (but not necessary) released from presynaptic membranes into the synapse by the same mechanisms as classical neurotransmitters but can then leave the synapse through "spillover" and act on the neurons other than those involved in the synapse. So, their action is diffuse, but usually still limited to to certain neural pathways. (International Encyclopedia of the Social & Behavioral Sciences, 2001, Encyclopaedia Britannica, Wikipedia, Current Opinion in Neurobiology)
Examples of neuromodulators: dopamine (D receptors), serotonin (5HT receptors), acetylcholine (M and nicotinic receptors), noradrenaline (alpha and beta receptors), histamine (H receptors), endorphins and neuropeptides (Wikipedia, Journal of Chemical Neuroanatomy, 2011.)
Neurohormones are released from neurons into the bloodstream and have a systemic effect, for example:

Oxytocin and vasopressin, which are produced in the hypothalamus travel to neurohypophysis from where they are secreted into the blood and act on the mammary glands and uterus.
Adrenaline, which is secreted from adrenal medulla acts, via sympathetic nervous system on various tissues, usually on the smooth muscles of the blood vessels, heart, gut, etc.

Can a certain molecule can be a neurotransmitter, neuoromodulator and neurohormone at the same time?
Yes, for example:
Noradrenaline acts as a classical neurotransmitter and neuromodulator in the postganglionic neurons of the sympathetic nervous system and as a neurohormone secreted from the adrenal medulla (International Encyclopedia of the Social & Behavioral Sciences, 2015)
Dopamine acts as a classical neurotransmitter and neuromodulator in the dopaminergic pathways in the deep areas of the brain, such as thalamus and pituitary gland (picture); as a hormone, it inhibits the secretion of prolactin from the pituitary gland.
Are both neurotransmitters and neuromodulators stored in and released from vesicles by similar mechanisms?
Yes or no. Neurotransmitters are always released into the synapse, while neuromodulators may or may not be released into the synapse (Oxford Scholarship).
Do both neurotransmitters and neuromodulators get effective by interacting with receptors and affect if a ligand-gated ion channel opens or not?
Neurotransmitters can be effective if the ligand-gated ion channel are open and neuromodulators can open or close the ion channels.

Since the same molecule can be both a neurotransmitter and neuromodulator, it may not be that important to define the differences between the both in detail:

It could, therefore, be concluded that the aspect of defining
  neurotransmitters has taken a back seat to the investigation of the
  actions of individual signaling molecules. (International Encyclopedia of the Social & Behavioral Sciences, 2015)

Your key points suggest: neurotransmitters and neuromodulators act on completely different receptors. If this is the case, my question becomes somehow obsolete, because this would be the main differentiating issue. But to be honest: my impression was another one: that they act in a significant manner on the same receptors (but possibly more or less directly?)

@Hans-PeterStricker  Yes, the whole point is in different receptors. Here's a PhD who strictly emphasizes this: https://www.quora.com/What-is-the-difference-between-neurotransmitters-and-neuromodulators. Neurotransmitters act directly and neuromodulators indirectly, but neuromodulators do not stimulate ionoreceptors; they just make them more or less excitable. But the same substance can act both as neurotransmitter and neuromodulator. Many substances have both roles, actually.

But the last point is essential: "they make them more or less excitable". This means: they act on them.

@Hans-PeterStricker neurotransmitters directly stimulate/inhibit ionoreceptors. Neuromodulators only change the "plasticity" of ionoreceptors, which makes them more or less excitable. It's like they make the door harder or easier to open. Or if you want, a neurotransmitter is like a bowling ball, and a neuromodulator can make the pins more or less hard to fall.

I know that, but it remains the same: they act on them, only differently (somehow more indirectly, less specifically and less strongly,  and somehow delayed or whatever - but they act on them). So what does it mean that they "only" change the plasticity: they change it.

@Hans-PeterStricker OK; I didn't mention in the answer but, neurotransmitters act on ionoreceptors directly, while neuromodulators first act on metaboreceptors, which usually trigger a cascade of secondary messengers, one of which will then act on ionoreceptors. So, a neuromodulator may not act directly on the ionoreceptors, but I can't exclude that.

To put it differently: they are enabling factors.

Now we get into the tedious details of secondary messengers (which I am aware of but only start to learn about).

For my excuse: I didn't know of metaboreceptors until now, but now I know. Thanks a lot.

@Hans-PeterStricker I added this: "The signaling between metaboreceptors and ionoreceptors usually involves a cascade of secondary messengers."

One last question: How do the metaboreceptors communicate with the presynaptic neuron (because you say "they modulate the release of neurotransmitters")?

@Hans-PeterStricker, via G-protein and, additionally via secondary messengers, such as ATP.

I ntentionally put a quote at the end of my answer, which suggests that, after understanding basic differences, it may be better to concentrate on individual messengers, like dopamine, etc.

There are so many details to be known! It's really complicated. What I only learned now: that metaboreceptors may be located in vesicles.


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What is the threshold of significance when measuring difference in proteins' radii of gyration?
In molecular dynamics simulations of proteins, the radius of gyration is often used to assess protein compactness. Given two proteins, what difference in radii of gyration can be considered significant? 1 angstrom, 5 angstroms, 10 angstroms? Significant meaning: yes it is definitely more compact or no it is definitely not more compact. I have been searching but can't find any reference related to that.

Welcome to Biology.SE! I think this is actually a statistics question in disguise — whether a difference is significant will depend on the degree of variance in the two values you are comparing! Also note that these answers will always be probabilistic rather than Boolean (yes or no) ... ——— Please also take the [tour] and then go through the help pages starting with [Ask] questions effectively on this site. Thanks!

If you need an introduction to statistics, I have found starting with a relatively accessible and reliable source like Khan Academy to be very helpful.

@tyersome The question is more about the threshold one should use to apply a statistical test. The test will tell wheater there is a significant difference or not at a given threshold (1 angstrom, 5 angstroms, 10 angstroms). I think a simple t-test is enough. But a which threshold to use is more biology-related.

Given only the difference of two values, you can make no claims about whether those values are significantly different. In order to determine if two proteins have significantly different radii of gyration (Rg), you will need repeated measures and a statistical test. To demonstrate the kind of analysis you need to do, consider the following examples.
Example 1 -- proteins A and B, 12 measurements each, 0.1 Å resolution
H0: there is no difference in mean Rg between protein A and protein B.
Data

Rg protein A (Å)
Rg protein B (Å)

10.1
11.1

10.2
11.2

10.1
11.1

10.3
11

10.9
11.7

9.8
10.8

9.9
10.9

10
11

10.3
11.2

10.1
10.8

10
11.5

9.5
11.1

Summary Statistics

-----
Protein A
Protein B

Mean
10.1
11.1

Variance
0.113
0.0706

Results
For two independent samples, we can perform an unequal variance t-test. With α = 0.05, we calculate a two-tailed p value of 5.26 × 10-8, so the null hypothesis can be rejected. Despite having a difference between means of only 1 Å, proteins A and B have a significantly different mean Rg.

Example 2 -- proteins C and D, 12 measurements each, 0.1 Å resolution
H0: there is no difference in mean Rg between protein C and protein D.
Data

Rg protein C (Å)
Rg protein D (Å)

15
5.5

11.5
2.4

12.2
13.3

20.6
14.2

20.2
17.2

11.2
12.6

15.2
17.8

9.3
9.9

10.8
10.1

14.9
8.4

14.2
10.4

8.2
4.8

Summary Statistics

-----
Protein C
Protein D

Mean
13.6
10.6

Variance
15.2
22.9

Results
Applying the same test as in Example 1, we calculate a two-tailed p value of 0.100, and the null hypothesis cannot be rejected. Despite having a difference in means that is 3 times larger than the observed difference for proteins A and B, the large variance in the measured values means that there is no significant difference in the mean Rg for proteins C and D.


text:
Ion-gated ion channels
Today I've heard for the first time of calcium-gated ion channels but find it hard to get an idea how they work, where they are located, and which role they play.
I assume calcium-gated ion channels are just a special form of ion-gated ion channels, which would be a fourth group of ion channels next to voltage-, lipid-, and ligand-gated ion channels (with ligands being some larger molecules). But on ion-gated ion channels even less is to be found on the internet.
One specific paper that mentions ion-gated ion channels is this (Experimental Neurology, 2001)
One paper that mentions calcium-gated ion channels is this (New England Journal of Medicine, 2015)
Where do I find a general introduction into ion-gated ion channels - if they exist?

KIR could be considered as a ion gated ion channel. In this case Mg+2 blocks the channel from the inside preventing the "outward" conduction of ions.

The main families of calcium-gated channels I am aware of are the calcium-gated potassium channels and the internal ryanodine receptors involved in calcium-induced calcium release - you could start from those linked Wikipedia articles.
I wouldn't really make these a fourth category, they should either be thought of as voltage-gated channels that are modulated by intracellular calcium, or as ligand-gated channels - the ligand just happens to be a calcium ion.
Some channels in this category are not influenced by calcium directly but via calmodulin, which is a common mediator of calcium-driven intracellular influences.

Ryanodine receptor is also a good example.

@WYSIWYG Thanks - added.


text:
Identify this South African spider
A family member saw this spider in her garden in the Cape Town area of South Africa. It's very attractive and I wondered what species it was?

Approx size is that it would fit roughly on a 3cm diameter circle.

Welcome to Biology.SE! For identification questions please [edit] your post to include the size this spider. This can be helpful for narrowing down possible species.  Thanks!

Based on the location and image you provided, I suspect this spider to be Garden Orb-Weaver, belonging to the spider family Araneidae.
Just a side note: I used an app called iNaturalist to identify this spider. It is a helpful app to identify insects and plants.
Here is a similar image I found online:


text:
Nitrogen deficiency and chloroplast function
Q. The formation of which of the following in the chloroplast is affected by a deficiency in nitrogen?
(a) Glyceraldehyde 3-phosphate
(b) Starch
(c) Enzymes
(d) Carbohydrates
My thoughts:
Nitrogen is used in both of chlorophyll and in converting carbohydrates into proteins so I am puzzled between glyceraldehyde 3-phosphate and enzymes.
However, glyceraldehyde 3-phosphate, starch and carbohydrates are nearly identical in this context and enzymes aren’t produced in the chloroplast either.

This site doesn’t provide a service for people to cheat on their homework.

This question was asked in a national Biology exam in my country and the majority are split between PGAL (nitrogen is used in chloroplast) and Enzymes (nitrogen is used to convert carbohydrates to proteins) so I wanted to hear other opinions. I’m still new here so I don’t know how this opposes the point of this page?

Please read the Help on answering Homework questions, of which this is an example. You are required to demonstrate that you have attempted to answer such questions yourself.

Does my recent edit make it acceptable?

Yes, except that the English of the question is incorrect. I assume it should be ( even though a little clumsy) “The formation of which of the following is affected…”.

Fixed, so, what do you think the answer is?

No idea. I don’t know what PGAL is. Does it contain N? Also, your title is sure to collect down votes. Change it to something like “Nitrogen deficiency and chloroplast function”.

phosphoglyceraldehyde

Ok. If only one is correct, the answer should be evident from my previous comment, assuming that they are all made in the chloroplast, which I cannot be certain about as I’m not a plant biochemist.

Chloroplasts, like mitochondria, contain DNA (in a circular chromosome) and the machinery for reading that DNA to produce RNA and protein. This chromosome encodes many enzymes involved in transcription and translation and also RUBISCO, which is one of the most important enzymes for life on earth!

so just to be sure, you're saying it's Enzymes?

I'm not saying anything about the answer. I have no idea what the question writer wants and think this is a badly written question. A nitrogen deficient plant will be be limited in the ability to make proteins and chlorophyll. I would expect that everything would be affected eventually ...


text:
Does the Human Eye White Balance?
OK, this may be a stupid question…but here goes.
Does the human eye “white balance” itself?
I assume that each human perceives colour slightly differently according to the peculiarities of their own eye, but within parameters (notwithstanding colour-blindness).
But does our eye (or brain) white balance? Or do we simply all see our own personal colour balance?
If the eye can white balance in real life, can it also colour balance a photograph that has been taken at the wrong colour temperature.
So, say I shoot and print an image shot at 2000K. The image printed will have its luminance information intact, but colour-wise, it will be very, very orange.
If I could somehow exclude all other vision from my eye and fill my entire viewing capacity with that single image, would my eye balance the colour back to a true white?
If it does not, why not? What goes on in our brain to say “this is an image at a fixed colour temperature, so you will see it as an orange hue”
Please excuse me if this is an eye-roller of a question. I’m not a Biologist, so I am well aware I may be demonstrating my own ignorance in asking the question!

I'm pretty sure any sort of color (or orientation / image / ...) correction happens in the brain. Anecdotally you can test this i.e. by wearing tinted glasses for a while (your vision should adapt to a more normal color up to the point where you take them off and get an opposite color shift for a while). Similar effects happen with other vision distortion effects (i.e. top-down mirroring glasses), which is why I'm pretty sure this happens in the brain & not the eyes.

Hi Nicolai - Thanks for responding! I see your point. And I can get my head round the brain making adjustments to what we see - white balancing on the fly. But are there limits? If the tint is such that, for example, no green information gets through to your eye, does your brain then "invent" the green information in order to render white? So, as per my example, if I was to look at a picture shot at 2000K, to the exclusion of everything else, could my brain invent the colour information missing and render it a "true" white balanced image?

I don't know how this works in detail, so I can't really answer these specific points of the question (which is also why I only wrote a comment and not an answer)

Welcome to Biology.SE! This phenomenon is known as color constancy. Please note that we encourage you to do some research on your own and then, informed by what you have learned, ask any questions you still have (ideally with references to reliable sources). ——— Please also take the [tour] and then go through the help pages starting with [Ask] questions effectively on this site and edit your question accordingly. Thanks!

The human brain white balances, the eyes do not, but the process is not instantaneous.
the easiest way to see this is to make a person wear colored lenses they will soon see colors normally again, but will need to readjust, taking a similar length of time,  once the glasses are removed.
Your eyes will balance an image back to white , but it takes time, and may happen faster in a landscape image.
https://www.sciencedaily.com/releases/2005/10/051026082313.htm
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820566/
there is a great ted talk showing a major aspect of this visually.
https://www.ted.com/talks/beau_lotto_optical_illusions_show_how_we_see?language=en
you can also see it with common photo negative color illusions.
Stare at the center dot on this for a minute then look at the second image.

you will see that the as the brain adjusts color balance you can use the lag as the eye readjusts to see false color in black and white images.

There's an easier, or at least less contrived, way to see the white balancing in action.  Go skiing late in the afternoon when there's a gaudy orange sunset.  Take a picture of the snow that you are perceiving as white.  It'll be orange.

@jamesqf not everyone lives where it snows ;)

Yes, some people are deprived.  But they can do the same experiment with any sort of white or light-colored object.


text:
How can I propagate a community of anaerobic bacteria sampled from mud in a bog?
I'm doing research on anaerobic bacteria. In the fall I took mud samples from a bog and have been working with them but I didn't take enough. Now winter has rolled around (Im in Canada) and all the bogs are frozen over. I need more material to work with — is it possible to make a mud mixture myself and carry over the bacteria?  If so could anyone help me out with the mixture ratios? Is contamination a concern here (I would assume not)? And how long would the propagation take?

Welcome to Biology.SE! Please take the [tour] and then go through the help pages starting with [Ask] questions effectively on this site and [edit] your question accordingly. I've made edits to your question that I think make it a better fit for this site — please check to make sure I haven't broken anything! We also encourage you to do some research on your own and then, informed by what you have learned, ask any questions you still have (ideally with references to reliable sources). For example, could you use a Winogradsky column? Thanks!

I suggest getting an augur or whatever it used to make ice holes for fishing , and cut  down into the bog and get more samples.


text:
Why doesn't evolution converge on perfection?
I got to know about an organism called "Tardigrade(water bear)" which is an extremely hardy organism and can survive in most conditions.
My question is that if the aim of life in general is to ensure the continuity of the species, why have we not simply stayed as tardigrades? it seems like they are the perfect candidates for survival purposes- ensuring(to a degree) that the species does not get wiped out as easily as dinosaurs.
Does that mean that life has  a more different incentive--not to just only survive? or it doesn't have any? Could this be the reason of our incapability to make a superhuman intelligence, because our imitation of learning is to reach a certain objective when life does not have any distinct goal? Or am I missing a key point here?

BTW I am an amateur in Machine Learning where we basically try to mimic the learning of phenomenon of nature through 'evolution'. So I would appreciate answers with minimum of abbreviations and as simple as possible :)

Edit:
I am overwhelmed by the response I have received but seeing the answers and communincations, I have inferred that my question may be very basic and vague to biologists. The person who can answer would be the one who has studied both subjects(Deep learning and Evolution). But even then I thank you all for devoting you precious time to attend to my question. Cheers! :)
Also I wonder if there is some paradox somewhere here - in Machine Learning when we simulate some environment the agent, just like evolution figures how to survive it. But when more factors are present, the intelligence doesn't increase after a certain point. Could this Thus be that there is something ethereal unexplainable by science (like soul) which actually gives us a more-than-enough complex brain to further increase our intelligence? Or is this a baseless thought?

Welcome to Biology.SE! Please take the [tour] and then go through the help pages starting with [Ask] questions effectively on this site. ——— As pointed out by @WYSIWYG this has a strong overlap with an existing question. Furthermore, as currently written this question doesn't really make sense since what counts as "perfection" changes depending on circumstances. Thanks!

I encourage you to check out some of the online resources available for learning more about evolution. For example, this a useful introduction to evolutionary theory from UC Berkeley. ——— I have also found a relatively accessible and reliable source like Khan Academy is great for starting to learn about a new area. In addition, many textbooks with a good level of detail are also freely available online e.g. from NCBI.

Just like neural networks are at most analogous to biological brains, evolutionary algorithms are only analogous to biological evolution. Be careful when using one to try to understand the other.

@BryanKrause I think you might be the one who has experience in both fields. Neural networks mimic a human brain and their function as they are reasonably intelligent (If you follow-up to the breakthroughs in AI). By simple incentivising them we can develop primitive intelligence.  My question inquires into that - Maybe humans don't have an incentive. This maybe the reason we have such complex thought processes

@neelg I do have experience in both fields. I disagree that neural networks mimic a human brain and disagree that they are reasonably intelligent. At best you can make some analogies. Animals definitely have incentives.

@neel g: No, neural networks don't really mimic a human brain, or even a very simple animal one.  They're based on some old and not very accurate ideas of how a brain was thought to work, and proved useful for some limited problems.  They could be called intelligent only if you use a circular redefinition of the word as being "what artificial neural networks do".

@jamesqf "Proved useful for for some limited problems". I highly disagree with that. ML is literally everywhere. It can solve some of the most humanly-challenging tasks. if you just maybe browse it's breakthroughs, you find that they can do from things like reading minds to writing articles almost similar like humans to deepfakes. True they do not have their own thought processes, but for a bunch of numbers they exhibit a Suprising level of intelligence. Also, I would like to know what is the 'modern' idea of how our brain works. I had the basic assumption that our brain also has neurons.....

The key point you're missing is that perfection is a variable, or perhaps more accurately, a function of many variables that depend on environmental factors and the actions of other species.  Even tardigrades have evolved a multitude of different species*, suited to different environments and lifestyles. And apparently they don't do all that well in hot water: https://www.nature.com/articles/s41598-019-56965-z
A creature that evolves to be close to perfection for one set of environmental variables can be seriously mal-adapted to a different set.  An albatross, for instance, is very close to perfection - that is, well adapted - to its niche as a creature that flies over oceans, while a dolphin is likewise close to perfection** for an air-breathing creature that lives in that ocean.  But either would die in short order in the other's environment, and neither is as well-suited to desert life as a camel.
As for the really unrelated question of why we don't know how to make a "super-intelligence", we don't even know how intelligence actually works, as you should know if you've studied the field.  On current evidence, intelligence, at least of the tool-making sort that some humans display, doesn't really seem to be a trait suited to long-term survival.
*About 1150, per Wikipedia: https://en.wikipedia.org/wiki/Tardigrade
**So much so that their basic body plans have been repeated throughout evolution: e.g. ichthyosaurs and marine pterosaurs. There are numerous other examples of such convergent evolution: https://en.wikipedia.org/wiki/Convergent_evolution

My question is that if the aim of life in general is to ensure the continuity of the species

That is not the aim of either life or evolution. Rather individuals have the goal of surviving and genes have the aim of replicating themselves. Individuals that survive get a chance to replicate their genes.
As for why all other organisms that are not ceased existing to make room for more Tardigrades, see above points.

I'm sure you understand natural selection. But there are many different forms of evolution (well 4 main ones). One is based on absolute chance. For example dinosaurs were just unlucky when the asteroid struck; it wasn't as if they weren't adapted. This is called gene drift. What I'm trying to get at is that there is less than one variable that affects evolution, leading to variety.
Another example within natural selection; the food chain. We start off with all producers. One producer becomes a consumer by a genetic mutation. The producers aren't reacting to this because they never needed to, so they get picked off one by one until more adapt to either defend or become secondary consumers (consumers that eat the original). There you go; multiple different types of insects, reacting in response to each other. Assuming an unchanging environment and only natural selection is at play, one could predict that they'll end up in an endless loop of evolving from one state to another to react to each other and going back to their original state (though in real life the environment will change preventing this).
As a side note for your coding; you may want to consider changing the environment at random every so often.
In short: you can't reach a single organism due to interference with other animals and other methods of evolution.
Technically; the aim of a being biologically isn't to survive, but for them to reproduce and pass on their genes, hence natural selection; a small but important discrepancy to make, Our incapability to make a superhuman intelligence has got nothing to do with our biology. Humans are able to cast aside anything to do with their natural emotions, hence a computer doesn't take these into account. The reason we can't have a superhuman intelligence is because we simply don't have the knowledge of human psychology, and the technical ability to make one.

I agree with all you statements, but you didn't answer my question on the super-intelligence part....was my assumption a correct one?

allow me to edit

Why evolution do not converge on perfection? I see two main reasons:
First: the "life problem" configuration change in time, so the perfect living being (let's called it global minima) should change over time too.
Second: As the "life problem" have several dimensions and the level of complexity is huge, there's no guarantee for the existence of that global minima. All the living organisms then represents near local minima solutions, that evolve over time, like solutions in a evolutionary optimization algorithm.
Why we don't evolve to a superhuman intelligence? I can tell: Who said it doesn't? Maybe in a future there will be super-intelligent-human-like living beings.
One key point is that the intelligence that allow us as a specie to survive and modified our environment do not play against us.


text:
Is the frequency at which a species mutate affected by natural selection?
As per natural selection, is it safe to assume that some species will have it genetically encoded so that they produce a certain 'perfect' rate of mutation so that they can adapt to an environment that changes quickly?
Another way to put this; does every type of organisms have  roughly the same amount of mutations each time they reproduce (relative to the size of their DNA)? If so, is/can/could this be governed by natural selection?

Does this answer your question? Has there been any observation of species adapting the evolution process?

Drake's rule
Let $L$ be the size of the genome. Let $\mu$ be the average per nucleotide mutation rate, then the genome-wide mutation rate $U$ is $U=L \mu$. There is a general relationship between the genome size of an organism and the nucleotide mutation rate that makes that the genome-wide mutation rate is often approximatively 1. There is of course several orders of magnitude of variation around this value of 1 among organisms.
This rule is called Drake's rule after the name of the author who first discovered it (Drake, 1991).
To my knowledge, this relationship is not fully well understood. Because you are looking for an adapted mutation rate in your question, I would like to highlight that I would not go about assuming this is adaptive. I could imagine that some molecular genetic constraint of the replication process could be causing this type of relationship between $L$ and $\mu$.
You will probably want to read this post about Drake's rule.
Mutation rate in humans
In humans, the average mutation rate is estimated to be around $\mu=2.5 \cdot 10^{-8}$ (Nachman and Crowell, 2000; see also this post), with a genome size of about $L=3 \cdot 10^9$, leading to an estimate of the genome-wide mutation rate of 80.
Interestingly, the mutation rate is in fathers is age-dependent. See the post Gender and age-specific mutation rate in plants.


text:
How are proteins reused in the body?
Part of what we eat are proteins,
and our body is in part build of proteins.
Are the proteins of the body build based on proteins in food at all?
Are proteins in food directly reused in the body,
or are proteins first disassembled?
How far are they disassembled, randomly in various pieces, or systematically to keep what can optimally be used to build new proteins, while nothing is wasted for energy?
(The question Can proteins/peptides pass through the intestine? and it's answers are related, and provide some context and relevant parts, but is not a duplicate.)

Does this answer your question? Can proteins/peptides pass through the intestine?

@tyersome Not sure that's the best dupe, since it doesn't cover the "normal" way of business. I know variations of this question have come up before, though.

@tyersome It gives some insight about part of the answer, so it is good that it is linked.

It's not a duplicate of " Can proteins/peptides pass through the intestine?"

Short answer: Indeed the proteins in our body are based on amino acids from external food sources. BUT, proteins up-taken from food are ALWAYS disassembled first into amino acids, through specialized enzymes, proteases, (for instance Pepsin in the stomach's gastric juices and Tripsin in the pancreatic juices), during digestion, in the alimentary canal, (gut). This enables the body's liver to build the proteins most needed by the organism itself, through the processes of transamination, that allows conversion betwixt amino acids, and deamination, that removes N2 from the amino acid, (let's say the "amino" part is removed, and then expelled as urea), to excrete amino acids in excess. In addition this breaking down of external proteins is necessary, since they can act as labels for pathogens, and external organisms in general, and thus would soon be destroyed by the immune system if reused straight away.