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Why does monoculture cause lower microbiome diversity and health in bees and how can we fix it?
How can you be sure certain microbes only grow on limited plants, so bees can only swallow limited microbes in a monoculture environment? Why can't bees just evolve to eat or lick dirtier places such as toliets or huamn feces as when wolves evolved to dogs, why can't or humans spread diverse microbes on a monoculture crop and give special growing spray on the plants and the beehives?
Could we just engineer genetically modified bees that can adapt to monoculture?

Welcome Coo. When posting we're required to show evidence of our own researches into the topic. The best thing to look up is the bee's immune-system  - and how they rely on a variety of phytochemicals in order for it to function. Where would they get those. You should edit that in and link to your source.

You're saying some plants can't have all phytochemicals, and bees eat the phytochemicals, and phytochemicals are necessary for health?

No I'm saying that you need to edit the question to show your research. Answering questions in comments is forbidden, but I gave you a hint as to how to look to find the necessary material to find suitable links for your references.

"Why can't bees just eat or lick dirtier places as wolves evolved to dogs...(?)" This is very confusing to me, as one doesn't follow the other. We can't force bees to act in unnatural ways; many past attempts to genetically modify something (even some through selection, e.g. holsteins) have had unanticipated negative consequences. Genetic modification isn't the answer to the enormous problems humans have caused the insect world. If a problem has a human cause, it would benefit from a change in human behavior, not our tinkering with the genomes of our victims.

As far I understand the problem the main cause of decrease in bacteria in monoculture is using pesticides. Onwona-Kwakye M, et al. Pesticides Decrease Bacterial Diversity and Abundance of Irrigated Rice Fields. Microorganisms. 2020 Feb 25;8(3):318. doi: 10.3390/microorganisms8030318. PMID: 32106524; PMCID: PMC7142973.
Also anongoodnurse has good point that you can't force some species act against its' nature.

Technocratic view on the problem solutions are quite common these days. If you look into history then most of the technological solutions has created much bigger problems. Eg. we can say that solving food production problem didn't solve starvation if you look bigger picture and looking into future then we are facing famine unseen because of human population size, climate change and soil degradation.

Also, monoculture isn't about the biome in the monoculture; it's about the nutritional deficiencies associated with being exposed to only one kind of pollen and nectar for long periods of time. Bees don't live for very long; it would be as if you were only allowed to eat oranges your entire life. It's just not a good enough diet.

Domestic honeybees aren't really in trouble. Colony collapse alarms were somewhat overblown. Commercial beehives are trucked around the country to pollinate various crops and orchards during different growing seasons, so monoculture isn't necessarily the concern for honeybees. However, the diversity of wild bee populations suffer when native habitats are converted for other uses. Around 25% of wild bee species are specialist pollinators that might only collect pollen and nectar from one or a few different wild flowers. Take away those wild flowers and the bees die with them.

@MikeyC - Your comment is entirely untrue. It appears you have a lot of reading to catch up on. Honeybees live 5-7 weeks. If they are transported to an orchard (for all intents and purposes a monoculture) or a lavender field, those flowers are almost the entirety of their diet. If in a lavender field, it is the only source of nectar they have for their entire lifespan. That is very bad for honeybees.

This is a good, big but complex question. One issue honey bees face are viral and bacterial pathogen attacks and the low diversity in their microbiome is believed to be a contributory factor. Viral attacks are particularly problematic.
For example Assis de Silva et al 2023 raises exactly the same question that the OP does. It's a huge problem and widely known.
Crop rotation is a strategy to increase the microbiome in the soil and presumably in the plant, thereafter (waving my hands about a bit) in the bee.
The number of soil microbiome studies demonstrating crop rotation are beneficial to the soil microbiome which are in the public sector is very limited (I'm not aware of any). This work has certainly been done in the private sector, but its against employee contracts to report the findings.
Most published rotations concern legumes to increase nitrogen that increases the growth of the cash crop (USDA did a large number of studies in the 1990s on this). Basically here the rhizobia populations in the soil are increasing, albeit not empirically demonstrated via metagenomics.
Ultimately monocultures are about revenue for the crop rather than the bee, so whilst your question is a good one, economically I can not see a farmer rotating their crops on a hypothesis it might give the bee a more diverse microbiome and halt the decline of their populations through pathogens.
Also viruses are, I think, the major pathogen of honey bees and I'm not certain the microbiome of the bee will provide resistance to viral attacks.
Viral attacks were associated with vector-borne infections in bees (mites I think) and targeting the mite is probably the best strategy, but I have no expertise here. How a mite can be differentially targeted in a bee colony is way outside my expertise, I suspect it can't be done.

Nice answer, +1. I think, though, that it's safe to say that monocultures cause malnutrition in bees, which in turn causes decreased immunity to disease of all kinds, so planting a diversity of pollen sources wherever bees are kept/moved to is a reasonable place to start.


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Base Substitution Probabilities Derivation
In Felsenstein's 1981 Paper Evolutionary Trees from DNA Sequences: A Maximum Likelihood Approach, he describes (in equations (6) and (7)) a derivation of the equation of the probability of a particular base substitution.  I am having trouble making the connection between equations 6 and 7.  That is, going from
$$P_{ij}(dt) = (1- u\  dt)\ \delta_{ij} + u\ dt \ \pi_j \quad\quad [6]$$
to
$$P_{ij}(t) = e^{-ut}\ \delta_{ij} + (1- e^{-ut}) \pi_j \quad\quad [7]$$
where $u$ is the rate of base substitution per unit time, $\pi_j$ is the probabiltiy of observing a particular base and $\delta_{ij}$ is the Kronecker delta function (1 if i=j, 0 if i != j).
In the paragraph that follows these equations there is an explanation as to why the exponential term makes sense (if you already know thats what it is), but I'm not understanding how to get from the first equation to the second. Any insights?
In case anyone is ever interested (or perhaps if I eventually forget), it appears that Felsenstein is using a Poisson Process approximation for equation [7], although even with this new information I still do no see the connection between equations [6] and [7].
Page 9 of this thesis had a pretty good explanation of this.

(1) There are two cases. For the first equation (6), the case $i \neq j,$
$$(1) \hspace{13mm} P_{ij}(dt) = u~dt ~\pi_j $$ if we have a transition from one base to another (for example G to C). In the case $i = j,$
$$(2)\hspace{10mm} P_{jj}(dt) = (1 - u~dt) + u~dt~\pi_j $$ holds for a same-base transition (G to G) or a non-transition (say, G and no change). Intuitively, we expect that, all things being equal, the probability of a base to same-base situation is slightly higher: it is the sum of probability that the base changes to itself plus the probability the base sits and does nothing in time $dt$ (with the same net result).

(2) Now we look at the equation(s) (7). Again there are two cases.
$$(1a) \hspace{10mm} P_{ij}(t) = (1 - e^{-ut})\pi_j $$
For case 2 (base to same base transition, $i = j$):
$$(2a)\hspace{13mm} P_{jj}(t) = e^{-ut} + (1 - e^{-ut})\pi_j. $$

(3) The author uses  $P(dt),$ $P$ at a very small (infinitesimal) quantity $dt.$ He tells us the leap from (1) to (1a) follows "almost immediately" when we see that $e^{-ut}$ is the probability that no base transition occurs. Well, then $(1 - e^{-ut})$ is the probability that a transition occurs.
Now $e^{-ut} \approx (1 - ut) $ (a truncated Taylor series) or $ut\approx (1 - e^{ut}).$ So for short times $dt$ we have $u~dt \approx (1 - e^{-u dt})$ and this explains his first equality $P(dt) = u~dt~\pi_j.$
So we have to recognize when he tells us about $e^{-ut}$ that $u t$ is the [truncated] Taylor series representation of $(1-e^{-ut})$ for $t$ very near 0. That is how he gets from 1 to 1a and (6) to (7).

(4) $(1 - u)$ is the probability that no transition from one base to another occurs in some short time $t_i.$ The probability that this happens over n consecutive time intervals is $(1 - u)^{(nt_i)}.$ Let $nt_i = T.$
Note that  $u \ll 1.$ We can write $(1 - u)^T = (1 - \frac{uT}{T})^T $ and
$$\lim_{T \to \infty} (1 - \frac{uT}{T})^T= e^{-uT}.  $$ This reasoning comes directly from that used to derive the Poisson distribution which is used to study rare events. See, for example, Deonier, Computational Genome Analysis, p.74.

It seems that you are giving a description of why equation [7] refers to the same probability in equation [6].  But this is only possible because you are given equation [7] already.  How would one arrive at equation [7] given only equation [6].  Is there a mathematical trick short of reversing the process you showed at the end of your post?

@fermats_last_nerve: The bottom line is that he only includes (6) because he begins with the probability $u$ and the statement of (6) is an intuitive re-statement of the English. He (or Kaplan before him) already modeled the substitution as a rare event, so he is just trying to justify (7) in the simplest way possible. The power series for $e^{-ut}$ is $1 - ut + \frac{(ut)^2}{2!}-\frac{(ut)^3}{3!}+...$ Someone working in this setting is probably expecting this trick. When I see $dt$ I think integration but his hint is generous enough.

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Do macrophages engulf mtDNA?
Let us assume that in a human body, a mitochondrial DNA is released to extracellular environment.
We know that mtDNA inheritance is solely matrilineal.
So the question is, If your mitochondrial DNA is released to the extracellular environment (or into
cell cytoplasm) due to cellular and/or mitochondrial damage, what could be the
ramification of this released DNA if your immune system cells (such as macrophages,
dendritic cells or B cells) pick up and sense these DNA as a danger signal?
Is there any chance for mtDNA to survive by establishing a new mtDNA ?
I am thinking, macrophages engulf and destroy them but cannot provide sufficient evidence.

Macrophages ingest and are activated by bacterial DNA

EDITS - I appreciate the comments and have incorporated them here.  Thanks to    @Superbest and @user22406 for raising them.  I hope this makes a better answer for the community.
Under normal circumstances, genomic (self) or mtDNA released into your cell or body cause absolutely no (known) problems.   I'll explain why that is, how the body can detect bacterial DNA, and finally the circumstances in which DNA can cause problems.
Self-DNA generally causes no problems
Almost from conception, cells in your body die.  Sometimes as part of pre-programmed sequence (eg inter-digital cells of the fetal limb paddle die and form fingers) or normal replenishment of cells such as the white blood cell (hundreds of millions of neutrophils die each day) or your gut epithelium.
Macrophages consume liberated DNA, and the reticulo-endothelial system in the spleen, liver and lungs filters the blood for cellular fragments.  This paper (from @Superbest) shows that bacterial DNA, and not normal human genomic DNA, can activate macrophages.
So your immune system develops, and is constantly being exposed to, virtually every cell type and cell component (proteins, lipids, DNA and RNA etc).  If self-DNA could spark an immune reaction, normal life would be difficult.  We don't make antibodies (from B-cells) or T-cells that react with self-components due to a process called anergy in which any developing T- or B- cells that could react to self-components during their maturation are instructed to shut down and/or die.   Yes, mitochondrial are inherited matrilinearly, but they still lyse and cause anergy, preventing an auto-immune response.
(Not all cell death is harmless- @Superbest's comment reminds us that apoptosis (involved in finger formation and other tissue remodelling and cell turnover) can package cellular components into self-contained vesicles.  On the other hand, damaged or lysed cells can liberate cytoplasmic components that can be pro-inflammatory or pro-coagulant.)
Macrophages' vacuoles contain DNAse II, an enzyme that degrades DNA it encounters following phagocytosing/endocytosing fragments of dead cells.  More about that later....
Our bodies can detect bacterial DNA.  Same DNA, different decoration
However, invaders (bacterial, viruses, worms etc) may activate a family of receptors called Toll-like receptors (TLRs).   TLRs have evolved to have specificity for antigens not seen in mammals e.g cell walls, bacterial flagella and so on.  Some TLRs do recognise DNA or RNA.  You may know that DNA contains 4 nucleotide bases, A,T,G and C.  In mammals, special sequences of two bases, C-G, (called "CpG"s) can be enzymatically modified by a methyl group.  In bacterial CpGs are not typically methylated and so a TLR (e.g TLR-9) that detects un-methylated CpGs is generally detecting bacterial DNA.
Mitochondria are different
Mitochondria have features that resemble bacteria: a cell wall, a genome and the production of proteins that begin with the amino acid N-formyl-Methionine (f-Met).  Mammalian proteins don't have f-Met at the start ("N-terminus").  Macrophages have a receptor that can recognize f-Met sequences (especially f-Met-Leu-Phe, fMLP) and activation of the fMLP receptor stimulates phagocytosis.
This 2013 paper describes the controversy whether mammalian  mtDNA is methylated (at CpGs) and offers strong evidence that it is methylated.    In contrast, the Oka paper  gives 5 citations where mtDNA is not CpG-methylated.
So..do mitochondria look like bacteria to our innate immune system?
@user22406 flagged this paper by Oka et al which cites this paper by Zhang et al as evidence that mtDNA can be pro-inflammatory.  The Zhang paper provides evidence that mitochondria can stimulate the immune system's receptors for (1) f-Met-peptides (i.e detecting mitochondrial proteins that look 'bacterial") and (2) receptors for un-methylated CpGs, the TLR-9 receptor.  The Commentary on the article has a great figure of how mito components might promote inflammation which copyright prevents me adding.
The Oka paper uses 2 key techniques: (1) surgical constriction of the aorta to cause heart enlargement (cardiac hypertrophy) and (2) a mouse strain with the gene for DNAse II deleted (noted as -/-, two minuses, both alleles gone).  In the hearts of DNAse II -/- mice, they observe higher levels of deposition of mtDNA in the damaged heart (Supplemental Fig 2), greater heart damage and many animals die.  This suggests that excessive levels of DNA (not degraded in these DNAse -/-  mice) may be driving the damage. (The general phenotype of DNAse -/- mice was studied by Kawane et al  and the mice get an arthritis).  In Oka's DNAse II -/- mice, the degree of heart damage can be reduced by blocking TLR-9 (using an inhibitory oligo).  In aortic constricted mice where the DNAse II gene is intact (+/+), adding the TLR-9 blocking oligo gave some improvement, suggesting that the level of unmethylated DNA liberated in tissue damage may stimulate TLR-9 in normal animals.
The authors also examined aortic constriction in TLR-9 -/- mice and found they had less lung and heart damage compared to controls.
In summary, the Oka paper suggests something is signalling  via TLR-9 to drive inflammation and damage in this model and implies (but does not prove) that the 'something' is mtDNA.
mtDNA in the plasma
Another Zhang paper  detects up to 1ug/ml of mtDNA in the blood following major trauma (car and motorcycle crashes, falling 4 stories etc).  Their paper shows that this level of liberated mitochondria could stimulate immune cells (via TLR-9 and f-Met receptor).
mtDNA won't get back inside the cell
Extracellular DNA and RNA is generally broken down and cleared rapidly.  DNA, being a large, negatively charged molecule, will have extreme difficulty passing through an intact cell membrane.  In the laboratory, cells need to be exposed to high voltage electric shocks to make transient 'pores' in the cell membrane to allow DNA to enter or have the DNA formulated in liposomes.  Even if endocytosed, there is no known pathway to direct endocytosed DNA to the nucleus or an new mitochondrial 'host'.  So mtDNA would be extremely unlikely to re-seed into a new cell or a mitochondria.
But self-DNA can be harmful if released in large quantities
During successful cancer chemotherapy, large numbers of tumor cells lyse and may give rise to tumor lysis syndrome.  Among the products released when a tumor is killed is DNA. A and G - the 'purine bases' - can be further metabolized into uric acid.    Uric acid can crystallize in the kidney and cause damage.
Summary
Mitochondria may be the remnants of endosymbiotic bacteria but, absent major trauma or mutations in both of your DNAse II genes, mitochondria come (and stay) in peace.

You are wrong in your reasoning about cells dying. Apoptosis specifically involves digestion of all DNA, and packaging of the cytoplasm of the vesicles, so none of it spills. In fact, spilling of the cytoplasm from necrosis is detected by the immune system, and causes inflammation.

@Superbest. Fair point re some cytoplasmic contents being pro-inflammatory or even pro-coagaulant.  Yes, cells die by a number of means including by apoptosis, autophagy and necrosis.  My point was host DNA doesn't drive meaningful immune responses.  Macrophages/RES consuming apoptotic bodies mean lots of DNA enters immune system pathways.  I'd be happy to edit the answer if you can point to data for genomic or mtDNA driving an immune response, like OP asked.

"Macrophages/RES consuming apoptitic bodies mean lots of DNA enters immune system pathways." - No, it doesn't. All the DNA in those apoptotic cells is chopped up. They are only consuming single nucleotides or small oligonucleotides. Own DNA does not appear to be inflammatory, according to the paper I linked to in my other comment.

@Superbest.  Apoptosis experiments show it generates a DNA ladder - by relatively infrequent endonuclease cuts, and not complete digestion.  Other than that, we seem to be in agreement, no?

@Superbest. Would you mind if I included your reference in my answer?  You found a nice, early and clean experiment.

Mitochondrial DNA that escapes from autophagy causes inflammation and heart failure http://www.nature.com/nature/journal/v485/n7397/full/nature10992.html

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Why are flies not scared when landing on a monitor with changing graphics?
I have been wondering why would insects in general, not be scared when important changes happen on your monitor where they have landed...
If you move even just a finger, they are scared to death and fly away, but anything on my monitor and they remain completely placid.

Ha ha interesting question. Maybe 0.5 second of no change in graphics on your monitor is enough for a fly/mosquito/other to infer that the thing is not moving. And once they landed they may not see what under their feet and can't detect further movement. Or they might just understand that the thing they're walking on is not moving and therefore whatever they see, they grasp there is no danger. Also are you sure that the insects that land on your monitor are those that are really scared of movement such as mosquitoes for example.

Today it was a large fly. I've mainly got flies, but saw some other insects there too. Note that I, on purpose, would say... move a window under the insect and saw absolutely no reaction. So I can say that there was rather heavy movement.

Hypothesis: Flies can resolve each individual frame and recognize that the screen is just changing color/don't notice that some of the flashing is changing colors. Hypothesis 2: The fly isn't looking at your finger but feeling your finger move with pressure senses.

Hmmm... my finger is on the mouse, the fly is on the screen, so I'm not too sure about hypothesis 2...

My guess: A fly's eyes are probably half a centimeter away from the screen, which means that they see pretty much all of the screen from a 90 degree angle. Try looking at your screen in a 90 degree angle and you wont see any changes either.

Flies see motion. When the monitor screen changes, the visible spectrum of the pixel is changing and nothing is moving.

Flies have limited color vision. Each color has its own wave frequency, but flies have only two kinds of color receptor cells. This means they have trouble distinguishing between colors, for instance discerning between yellow and white. Insects cannot see the color red, which is the lowest color frequency humans can see. However, houseflies have the ability to see polarized light, but humans cannot differentiate between polarized and unpolarized light. Polarized light is light in which the waves travel only in one plane. [1]

Monitors have polarized film on them so you could test the color hypothesis by taking an old monitor you are willing to sacrifice and removing the polarized film. Then you could test if the flies jump when the screen changes. See here for removing the polarized film on the monitor, or if you have access, this article on A behavioural study of polarization vision in the fly, Musca domestica may hold the answer without needing to ruining a monitor.

I can't reconcile your answer with the well-studied optomotor response of fruit flies (e.g., http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2846117/), where in flies are tethered in place and their visual field is changed via LED screens, simulating movement. Photo here: http://depts.washington.edu/flyarama/

@kmm here it discussed the flicker affect. That is, insects with compound eyes respond better to moving stimuli then stationary. I am about to eat a cupcake so I will read your link in a bit.

That's what I can't figure out. The OP describes things moving on the screen, which should activate the flicker effect.

@kmm movement on the screen isn't 3D movement since nothing actually moves. What is happening is the pixels are changing colors. Since flies cannot distinguish nearly as many colors, they won't perceive the change. However, if I wrapped my hand in red (which is hardest for them to see) and moved it towards them, the movement will be picked up since their is depth perception amongst other characteristics in play as well as background colors being removed from view by my movement.

@kmm did you read LED Arena and Visual Behavior Assay section at the end? They used UV, blue, and green light. Flies can see UV light. Your computer screen has polarizating film blocking UV. So the experiment seems to be geared to benefit the limited visual ability of the fly. Also, they were started by vibration before each experiment to heighten their visual senses.

As indicated by @kmm there is little reason to believe that a difference in polarization or color would cause a differential escape response. - Which also is not claimed by the paper cited in the answer. Flies do not like a darkening: http://link.springer.com/article/10.1007/BF00197657  ;  also note that flies have little reason to visually monitor the platform on which they stand (and that the movement of the pixels poses no danger to them) - whereas they sense dangers from above (such as a finger) - also you can still scare them to death by hitting your monitor and inducing vibrations

Flies monitor the space above them:
Flies have a very strong innervation of the back of the head, which contacts the surface ( http://flybase.org/reports/FBim0000875.html ). While working in a fly lab, which studied behavior, I was told that these nerves sense changes in the light intensity above a fly - and it is this "third eye", which usually triggers the escape response of flies.


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Are snake capable of love? (social bond in a male/female couple)
I'm wondering whether it has been noticed that some species of snake form male/female couples for life (or at least multiple reproduction cycles) like other types of animals do (penguins come to mind).
I understand that there is no such thing as chemical love, so that is out of the question.
I also know that most reptiles are loners or even attack/eat each others when they happen to meet. At the same time, there are snake pits with at times over 100 snakes living together.
So have we observed social bonding ("love") between a male and a female snake?

Could you please split this question up? Ideally, you'd ask these two separate questions in two separate posts. As a matter of personal preference, I would like this question better if you didn't bother with the term "love" - just ask "do any snakes form long-term pair bonds"?

@BenBolker I made an edit to restructure the point about the pit. It was not really a question only an example of possible socializing between snakes.

Not as far as I can tell. The closest example I can find is within-season pair bonding in copperhead snakes (defined as a male-female pair remaining together for some time, in this case defined as longer than a quarter of the breeding season).
Smith and Schuett (2015)'s abstract says:

Pair-bonding between sexes is common in vertebrate taxa, yet it has been noted far less frequently in some groups such as reptiles, and snakes in particular. Evidence to date indicates that many snake mating-systems are polyandrous, with both males and females having multiple partners in a single breeding season, and thus unlikely to exhibit lengthy pair-bonds. Wittenberger and Tilson (1980) suggested that pair-bonding exists when pairs remain intact for a consecutive period equaling at least 25% of the breeding season. Using this criterion, we present evidence of pair-bond formation in a North American pitviper, Agkistrodon contortrix (Copperhead), a species with a polyandrous mating system.

They observed one male-female pair that were found together over the course of 26 days out of a mating season of 70 days.
Uller and Olson (2018) say "in fact, multiple paternity in lizards and snakes is extraordinarily  common  and  reach (sic) higher  levels  than  that documented for any other vertebrate group": in their Table 1, the minimum level of multiple paternity observed in studies in snakes is 1/6. (Multiple paternity implies that females are mating with multiple males over the time scale associated with producing a single set of offspring. Genetic non-monogamy does not necessarily imply social non-monogamy — social monogamy + genetic non-monogamy is called extra-pair copulation — but it does suggest it ...)

Smith, Charles F., and Gordon W. Schuett. “Putative Pair-Bonding in Agkistrodon Contortrix (Copperhead).” Northeastern Naturalist 22, no. 1 (March 2015). https://doi.org/10.1656/045.022.0104.
Uller, Tobias, and Mats Olsson. “Multiple Paternity in Reptiles: Patterns and Processes.” Molecular Ecology 17, no. 11 (2008): 2566–80. https://doi.org/10.1111/j.1365-294X.2008.03772.x.

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Does exhalation help us speak, and if so, how?
Everyone knows that we breathe in oxygen and breathe out carbon dioxide. That's how the respiratory system works. But we also use the respiratory system to produce sound and language. When we speak or emit sound, our glottis opens up, and depending on whether the sound is vocalized, our vocal chords vibrate. We then use articulators (tongue, lips, teeth) to shape the sound we produce.
But what kind of air is emitted in the first place? When our glottis opens up, what kind of air is passing through, and why does it pass through? The most obvious answer, which is my first guess, is that carbon dioxide is passing through our glottis and our trachea, and that we use this to create sound. In this way we would be using the product of respiration for a separate purpose: to create sound and communicate.
This is only a guess. But a logical one. The question, to put it most simply, would be, do we utilize our natural cycle of exhalation to produce sound and speak? Or is something else going on?

Exhaled air is not changed drastically from inhaled air; it is still mostly nitrogen and oxygen.

@canadianer I see. But would you agree that the air which helps us produce sound is exhaled air? I.e. We take advantage of exhalation in order to speak? It's almost a stupid question, but I would like to get a solid understanding of the mechanism.

Yes, I would agree.

There is a very minimal increase (and I do mean minimal) in the CO2 concentration depending on how fast we speak, how often we stop to take breaths, etc. compared to plain, expired breath. This is because the inhaled air is being held back in the lungs and released more slowly as we speak, giving more time for O2/CO2 exchange to occur. However, it will mostly occur in what's called "dead space" and the %CO2 will be changed for a few breaths thereafter as well.

Not including water vapor, argon and trace elements, inhaled air at sea level: ~79% nitrogen, ~21% O2, ~0.04% CO2. Exhaled air: ~79% nitrogen (the body doesn't "use" inhaled nitrogen), ~16% O2, ~4% CO2
It is this exhaled air we use to speak. However, there is a very minimal increase (and I do mean minimal) in the CO2 concentration and decrease in the O2 depending on how fast we speak, how often we stop to take breaths, etc. compared to plain, expired breath. This is because the inhaled air is being held back in the lungs and released more slowly as we speak, giving more time for O2/CO2 exchange to occur. However, it will mostly occur in what's called "dead space" and the %CO2 will be changed for a few breaths thereafter as well.
To demonstrate this, speaking until we're "out of air" should make us slightly dizzy because maximal exchange will have taken place at a certain point, after which our blood CO2% will rise, and our blood O2% will fall.
After that, the higher serum CO2 will cause us to take a deeper breath, a 'cleansing breath' if you will, to jump start the return to normalcy in blood gasses. It is very, very hard to resist this deep breath (which is why breathing has a voluntary and an involuntary component, i.e. you can't hold your breath until you die.)
Breathing

If an average of 5% of your expired gas changes from 1.45 grams per liter to 1.95 g/L as it goes from O2 to CO2, the total change of mass of expired air is about 1.5 percent. That's countered by warm air which expands so it becomes lighter.
So the fluid physics of the expired air doesn't make a marked octave difference compared to raising the vocal chords.
Air at 0'C is about 5 percent heavier than air at 20 degrees, 20'C incoming air would be 1-2 percent heavier than the same air 30'C.
Another physics thing is that dry air is lighter than moist air.
Oxygen absorption has no major role to play in sound generation, as Nitrogen constitutes 78% of the volume.
why does it pass through? Exhalation contributes to control the volume of the sound output. Air pressure is necessary to cause the vocal chords to vibrate as taught chords that can oscillate continuously when displaced by a constant flow of air.
Quite complex muscle actions of the thorax, rib cage, diaphragm, and abdomen occur during utterances, here are some measurements.
The vocal chords are also known as vocal folds. They narrow during sound production, and are open during respiration. They narrow very thin and vibrate as a direct cause of exhalation. There is a video of vocal folds vibrating, and you can see them vibrate. https://en.wikibooks.org/wiki/Acoustics/Human_Vocal_Fold
http://www.entusa.com/larynx_videos_flash/normal_larynx/normal_larynx_mp4-0.htm
Above them is an air chamber that guides the sound waves into vowels, like A E I O U.
Other mammals don't have a developed air chamber above their vocal chords, and mostly can make screech sounds rather than vowels, however mammals can drink and breathe at the same time, which humans can't. You can study evolution of the voice box on other threads.
It's the same as with a trumpet, if the guy doesnt breathe outwards, sound is not produced, and stronger breathing changes the sound.


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How do mutations come to be shared by all cells?
It's my understanding that various hazards can damage the DNA in our cells, causing mutations.
But whenever I picture this, I see the damage being done to one of our tissues (for example, our lungs due to smoking, or our skin due to UV rays).
When I think about this, I see that... many cells in a smoker's lungs, or many cells on the back of a beach-goer's neck, may have mutations in their DNA. But only the cells in that tissue have these mutations... the other cells in our body would not have the same mutations.
In particular, sperm and egg cells would not have the same mutations, so the mutations due to smoking and UV rays shouldn't pass on to children.
Are there instances where mutations that occur over the course of our life are spread to every cell, including sperm and egg cells, so that every cell reflects the mutation, and the mutation is passed onto our offspring?

This usually happens when the mutations occur at an early stage of development, such that a precursor cell with the mutation gives rise to all other cells in the body.  Are you asking about cell-to-cell "transmission" of mutations?

Sperm/egg can be affected by the general body physiology, such as in case of starvation etc, by epigenetic mechanisms. These epigenetic changes that can be passed to next generation. See Transgenerational Epigenetic Inheritance

Goods question! Only mutations that occurred when we were in the early stages of development will affect all cells. That's why pregnant mothers shouldn't smoke. The reason for this is that one cell goes on to divide and become all our cells so any mutations in that cell are passed on to cells formed when it divides. That same principle explains your smoker example. In the lung we have two types of cells which are called Type 1 and Type 2. Type 1 cells are constantly dying as they get old and they get replaced by type 2 cells whose job it is to divide continuously to replace Type 1 cells. So we have lots of type 1 and few type 2. When type 2 divide they make one type 1 cell and one type 2 cell, so type 2 cells never run out. If smoke causes a mutation in type 1 cells generally they're okay because they'll die before enough mutations occur. Of course something that causes lots of mutations could make it cancerous before it dies but that's rare. Now if it occurs in Type 2 cells every subsequent type 1 or type 2 cell that cell makes is mutated.
The last thing you mentioned are mutations that occur to eggs and sperm. When making sperm you have the same as above. One cell makes sperm and a sperm maker cell. The sperm is like type 1 cells and the sperm maker cell is like type 2. So mutations affect them as they do above, where a mutation in a sperm maker cell is way worse. As for eggs women are born with all the eggs they'll ever have and there's no egg maker cells. So mutations just occur, and the older women are the more mutations. That's why the older a mother is the much higher risk of genetic diseases like downs. But an older man only has a slight increase in risk.
Mutations that affect eggs and sperm tend to be really harmful, as they affect every cell, so these cells or "babies" die before the mother even realises she's pregnant or as a miscarriage. I've not given the scientific names for things but if you request them, I'll give you the real names, but hope you enjoy the principles.

Hi AndroidPenguin, thank you for the explanation. I really appreciate your examples with Type I and Type II cells in the lung, as well as the analogous sperm and sperm maker cells. I didn't know that some cells were designated to be the producers of others, kind of like the factory pattern in software design.

I wonder whether these 'factory' cells always replicate through meiosis? I know that sperm maker cells do, since they produce haploid cells, but not sure about type II cells in the lung. A more general question would be, if cell A replicates to produce cells A and B, does it always do so through meiosis? As far as I understand, it's not possible to achieve this with mitosis.

Type 2 cells replicate through mitosis: one of the daughter cells differentiates into a type 1, the other stays undifferentiated as a type 2. Type 1 cells can't divide because they're so far down the maturity process, also I imagine its a protective mechanism. As for sperm maker cells, as I call them here, they divide mitotically into one sperm maker and one cell that's a pre-sperm cell (still diploid). This divides again as per meiosis to give rise to 4 haploid sperm cells. You need it to divide again for crossover (when the genes swap around so you get a random selection from your dad)

Yes, all cell division in the body is through mitosis. Meiosis is a very special form that occurs only in the ovaries and testes to produce egg and sperm cells - absolutely nowhere else!
Do note that mitosis can be asymmetrical, i.e. producing two different kinds of daughter cells rather than simply multiplying the parent (as in the example with type II cells).


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Why does protein folding not depend on the order in which it is synthesized?
I read an article recently, written by researcher from Department of Biochemistry, University of Washington, which stated that:

Similarly, success in de novo protein design bears on the question I get after every talk about the importance of the order of chain synthesis on the ribosome to protein folding; computational protein design calculations completely ignore the order of synthesis which hence cannot be critical to protein folding.

I was wondering, how could it be that the form that the protein is folded to, does not have anything to do with the amino-acid sequence that constitute this protein? What I mean, is in case I look at mirror image of a protein, would it fold the same? if I consider for example the sequencers: ser-gly-ala-glu-pro-asp and asp-pro-glu-ala-gly-ser, will they both fold the same? (I think those are d-protein and it's l-protein counterpart)
Can anyone provide evidence that this is, in fact, so. Or do I misunderstand the section quoted?
link to the paper: sci-hub.tw/10.1002/pro.3588

Welcome to SE Biology. I've tidied your question a little. Some tips on using the site. First, please finish the Tour. It  would be useful also to read the Help on asking good questions. One way your question could be improved is to cite the article you quote from, preferably with a link, so we can double-check it. Second, I am not clear what  you mean by "the order of amino acids". Do you mean that you would expect those synthesized first to fold first and independently of those later in the chain?

@David thank you for your remarks. I've edited the question, I hope Iv'e managed to better explain what I mean.

how could it be that the form that the protein is folded to, does not have anything to do with the amino-acid sequence that constitute this protein?

The quote by the researcher says that the form is unrelated to the direction of synthesis (N->C rather than C->N). It implies that all that matters is the amino-acid sequence that constitutes the protein, and that protein folding is driven by thermodynamic stability rather than by kinetics.

in case I look at mirror image of a protein, would it fold the same?

Yes, if you had an exact mirror image of a protein alone in solution it would adopt the same fold but mirrored. The N and C-temini would be on the same amino acids but all amino acids would be D rather than L chirality. This molecule would not generally be found in biology, since typically life uses L-amino acids. It would have different enzymatic behaviour on chiral molecules.

if I consider for example the sequences: ser-gly-ala-glu-pro-asp and asp-pro-glu-ala-gly-ser, will they both fold the same? (I think those are d-protein and it's l-protein counterpart)

These are not mirror images, they are entirely different molecules. They are not chiral counterparts (L and D). In general they would not fold to the same structure as the CO and N groups in the backbone are flipped, see more on reddit. However this is a topic of research and some reversible sequences have been found, see Zhang2016 and Mittl2000.
On a deeper level, the researcher's claim that synthesis direction (and hence synthesis broadly) is unimportant is not clear cut. For designed proteins it may be true but these are small and hyperstable. For larger proteins and protein complexes kinetics play more of a role, and chaperones may be used to protect a growing chain as it comes off the ribosome. See for example discussion in Sorokina2018 and Deane2007.

Thank you for your reply. could you please further explain what's the difference between mirror image and reversed order of the protein? I thought that the two sequences I mentioned were mirrored.

Sure. A protein is just a molecule, and it is a molecule with chirality: https://en.wikipedia.org/wiki/Chirality_(chemistry). This means that the mirror image of the molecule is a different molecule, but the connection between everything is the same. You can also, separately, reverse a protein sequence, though calling this "mirroring" is a bit confusing as you are not reflecting anything in 3D space. In this case you get a molecule that actually has different connections: the termini are in different places and the C and N in the backbone are flipped when you reverse the sequence.

In addition to what is already said, I want to mention something more subtle. What other people have commented here is about an old 'dogma' due to Christian Anfinsen, which postulates that all that matters is the sequence of aminoacids + the microenvironment (pH, temperature, etc).
However, I think you might be confounding two other layers of biochemical complexity. One, L versus D aminoacids. If all the machinery of protein synthesis (including the ribosome and the messenger RNA!) was perfectly specular (i.e. D-amino acids and L- sugars, and the corresponding RNA sequence), everything else being the same, then the folding would be expected to be the same (although in practice, this is a new field of molecular engineering that is not that advanced). In fact, it is not clear why we have a particular chiral form of sugars and amino acids, and might as well be an accident of evolution.
The second thing that might be confounded in your question is the order in which a particular amino acid is added to a newly synthetized protein. Even though the previous answers seems to dismiss this as unimportant; it is in fact very important. Amino acids at the beginning of a protein chain are being folded as soon as they exit the ribosome. Thus this is quite an important process, as proteins aren't just 'waiting' to be completely synthetized for the folding to start: they are continously interacting with the environment (including chaperones!), so the folding does depend also in the order of synthesis.

You're probably right that the order in which amino acids are added is important. It's just that the article quoted in the question seems to says that it isn't (in most cases).

Except aren’t there chaperones to PREVENT such initial inappropriate folding?

The question is asking if the order of the protein affects the native structure of the protein. Amino acids do begin to interact and form structures as soon as they are incorporated into the growing peptide, but as the paper you referenced states "in no case has a protein domain been shown to be able to fold into its native structure while still inside the ribosome", this is because although the amino acids fold, they form kinetically trapped intermediates and not the native structure. The native state is generally formed once all amino acids are present, so it it independent of order.

I suspect the author meant something a little different. It's not just that it doesn't matter if a protein is synthesized from N- or C-terminus it's also not important for the end result of folding that the synthesis is gradual at all.
When designing proteins de novo they model the folding on a computer. The gradual addition of amino acid residues to the protein is not part of these models, the computations are made on the entire sequence at once. Still, when the designed proteins are synthesized on ribosomes they fold correctly. So the fact that the proteins are built step by step shouldn't influence how they are folded very much. As long as there is a sufficiently low free energy state it will be achieved.
Also, N-ser-gly-ala-glu-pro-asp-C and N-asp-pro-glu-ala-gly-ser-C are not exactly the mirrored images of each other. They just have terminal amino and carboxyl groups swapped. I imagine this can influence folding a bit.

The quote is getting at protein structure is generally thermodynamically driven and not kinetically driven. The structures would be different if you took a mirror image of the sequence that you showed as the amino acid at the n and c terminus are different as is the orientation of all the other amino acids. However, if the ribosome were to be able to translate in the direction of c to n terminus rather than n to c terminus then the structure of the protein formed would be the same, that is what the quote is getting at. This is because like I say protein folding is typically thermodynamically driven, even though some amino acids come out of the ribosome first and form a structure (the kinetic structure as these amino acids came first) the structure with the lowest free energy is formed. This occurs because typically there is not a large energetic barrier for the protein to overcome to refold to find it's minimum free energy structure and so the thermal energy is sufficient to allow for the activation energy to be overcome and hence the process is thermodynamically driven to minimise the free energy of the protein.

Thank you for your reply! I guess my problem is that I don't quite understand the difference between thermodynamically driven process and kinetically driven one. I'll make sure to read into that.

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What kind of spider is this? From New Zealand
Found this spider in my bin, sorry for poor quality photo, has a massive red bum, haven't seen one like it, can anyone identify it?, around the size of my finger or thumbnail. I am from New Zealand

Welcome to Biology.SE! Please [edit] your post to include as much of the following essential information to improve your chances of getting a good answer: 1) one or more clear closeup photos of the organism (photos from multiple angles if possible)); 2) the location (e.g. country and region — the more specific the better) where you observed this organism; 3) habitat information; and 4) an estimate of the size of the organism (human nails vary significantly). ——— Please also take the [tour] and then go through the [help] pages starting with [Ask] questions effectively on this site. Thanks!

This appears to be the False Widow Spider (Steatoda grossa), which is a cosmopolitan species found over much of the world.

The female S. grossa is 6-10.5 mm in length and dark coloured with a round, bulbous abdomen. Typical colouration ranges from reddish brown to black, with light-coloured markings.


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Where does the silica found on grass and other plants come from?
Grass has tiny silica "teeth" on it called phytoliths:

I have trouble understanding how can a plant possibly extract silica from soil and form anything out of it. Silicon dioxide is used for chemistry glassware and can survive nearly anything.
I found that what the plants use is actually monosilicic acid in the form of $Si(OH)_4$, but I have not been able to find how that comes to be in the soil in the first place. Clearly, silicon dioxide does not hydrate in water readily the way potassium oxide does, for example, otherwise glassware would not be a thing.
And even if I knew how does the hydrated form of the oxide form, I still do not understand how do the plants manage to dehydrate it in order to prevent it from being water soluble.
Can someone explain the whole chain from $SiO_2$ through $Si(OH)_4$ back to $SiO_2$ that can be seen in the picture above?

Does this help? https://besjournals.onlinelibrary.wiley.com/doi/10.1111/1365-2435.12704 Keyword to parse the paper: "dissolved Si (DSI),"

The solubility of silica is low but non zero

Most glassware isn’t pure silica anyways

Silica $\neq$ silicon dioxide! So the chain is: silicon dioxide $\left(SiO_2\right)$ to orthosilicic/monosilicic acid $\left(Si(OH)_4\right)$, which can then polymerize to form silica particles, see image below.
The first step in the chain occurs via reaction with a basic solution (e.g. aqueous sodium hydroxide, $NaOH$). The resulting $Si(OH)_4$ is water-soluble, and thus can be taken up by organisms. Enzymes such as silicatein can then catalyzes the reaction to form silicate particles. These particles can then be deposited in specific parts of the organism. See Otzen's 2012 review in Scientifica for more information.

Could you clarify the difference between silica and silicon dioxide please? It seems that it's crucial part of the problem.


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Is this a carpenter bee?
This bee visits our balcony every day multiple times, but only for a brief time, making it hard to take a good picture:

Here's another picture, I finally got lucky so I'm adding it to the question:

It does not look like a typical honeybee. It does not make noise as bumblebees do. It also looks a lot like it's really the same creature every day. It always comes and leaves on the exact same path. The face looks a lot like carpenter bee, but I also couldn't find one like this on the internet.
This is in central Europe.


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Best method to cure cancer as of now?
I am not talking about chemotherapy or radiotherapy. So, if it exists, what is the best biological technique to cure cancer as of now?

why rule out chemo/radiotherapies... they may be the "best". Also what is the meaning of best in this context; something may cure cancer excellently, but cause heart attacks as a side effect, be ridiculously expensive and involve unethical methods to develop and manufacture it, while something else might cure 2% of cancers and have no side effects and minimal financial and ethical costs.

@rg255 I don't know why chemo, but radiotherapy is ruled out because the OP wants to know only biological methods. And best might mean, of course, something that cures cancer most effectively, has least side effects, be ridiculously cheap, follows ethics to develop & manufacture i.e. more utopian in scientific terms :)

Oncolytic viruses are a potential cure as of this ted talk I came across

There is no general therapy for cancer - as there is no general cancer. Cancer is the umbrella term for a disease where you have body cells growing without control, leading eventually to death. But since there is a wide variety of cells in the body, there is also a very wide variety of different cancers.
To treat these, surgery is often the first line of therapy. For some cancers this is already sufficient to cure the patient, examples are skin cancers (not only melanoma but the other forms as well) where you can cure a very high potion of the patients. This only works for early forms of the cancers when there are no metatases present.
Besides this, additional therapies are used - as you said yourself chemotherapy in the different forms as well as radiation therapy. Chemotherapy is given systemically and targets fast growing cells (cancer cells have these properties) and causes mutations or other problems which let the cancer cells eventually die. Radiation works with the same principle, but is more focussed.
Relatively new therapies are the targeted therapies where the treatment uses the occurance of certain common mutations. An example would be the mutated BRAF kinase in melanoma (and also in a number of other cancers) which can be specifically inhibited with an inhibitor. This avoids a lot of problems general adverse effects of the drugs. Additionally immune therapies are also new which use antibodies against surface receptors of T cells to prevent their inactivation. These T cells then attack the tumor.
These are all non-biological treatments. More biological ones are modified oncolytic viruses. In this therapy you inject genetically modified viruses which preferrably infect the tumor and then destroy it. These are relatively new, but an interesting option. See references 1 and 2.
An old method is the usage of bacteria to treat tumors - the first obervations on this where done in the late 19th century, see reference 3 for more information and a lot of further references.
A number of the chemotherapeutic drugs used today are originated from nature, but are today synthesized and used in a pure form and not isolated from their origin anymore. Examples would be vincristine, irinotecan, etoposide, and paclitaxel. See references 4 and 5 for details.
Besides this, there are no effective "natural" cancer cures, despite the claims of several "alternative medicine people". These are either based on wrong assumptions of biology or wrong ideas like Homeopathy.
References:

Advertisement Oncolytic Viruses and Their Application to Cancer
Immunotherapy
Oncolytic viruses: a new class of immunotherapy drugs
Strategies using bacteria to target tumors
Anti-inflammatory and anticancer drugs from nature.
Drugs From Nature, Then and Now

I'd like to vouch for adoptive cell transfer therapy, ACT, using tumor-infiltrating lymphocytes, TIL (Lee & Margolin, 2012). While the therapy is currently geared largely for metastatic melanoma, there are investigative studies involving TIL ACT in other cancers such as head/neck, cervical, ovarian, breast, etc. I want to note immediately that this is not a cure but rather a promising treatment.
The idea is that T cells have recognized a tumor antigen and become activated toward the tumor. They extravasate to the tumor and attempt to kill it, but they become overwhelmed by evasive tumor mechanisms and the tumor environment. So they're just kind of there, with the tumor, ready to fight but too tired to finish the job. Hence, tumor-infiltrating lymphocytes.
The patient will have an accessible tumor excised by a surgeon, where a technician will cut the tumor into small fragments. The fragments are incubated with media and IL-2 in a way that skews the growth toward lymphocytes. And so from the same patient we'll take some blood, and separate the PBMCs, and then irradiate them. The irradiated "feeder" cells provide to the lymphocytes co-stimulatory signals that promote their growth. We also incubate the T cells with an agonistic monoclonal antibody OKT-3 that activates CD3 on the T cells. And so with this, the T cells rapidly expand over the course of a couple of weeks to several billion cells. Importantly, we should have a good population of CD8+ T cells that are tumor-reactive.
The patient, before re-infusion of their own T cells, undergoes lymphodepletion with the drugs cyclophosphamide and fludarabine. The point is that immune responses are heavily regulated, and so you want to get rid of T-regs, and other immune regulatory cells that might blunt the effectiveness of the TIL. You also figure, you're infusing several billion cells, you need to make room for these extra immune cells. The T cells should then in theory find every tumor with the antigen they were programmed for initially and kill them with granzymes, perforins, etc.
There are some barriers to the treatment, the first being that it's largely exploratory and thus not widely available. Due to the complexity of the treatment, it's also very expensive (at the NIH, $500,000 USD perhaps?). You must also consider that while we're growing these TIL, there's a patient dying on the other end that may not make it to the treatment phase. There are stochastic issues that also prevent the treatment from reaching it's maximum potential.
The first is the tumor: they exhaust the T cells quite a bit, and in T cell exhaustion you get an abrogation of the T cell mechanisms, and so our fight becomes bringing these TIL back from the dead:

Source: T Cell Exhaustion
For example: The presence of the T cells also sometimes cause the tumor to begin expressing PD-1L, ligand to a programmed death receptor PD-1 that T cells up-regulate in exhaustion. Through SHP-2, PD-1 blocks stimulatory signal 1 to T cell activation at ZAP70. The tumor microenvironment is also very acidic, and the T cells take issue with this and it blunts development. Because of this, when you're growing T cells out of the tumor fragments, sometimes you get a bad yield, and the way you actually cut the fragments, or how the surgeon excised the original tumor play a part in manufacturing the cancer treatment. You can have a patient that might respond well to TIL, but end up they just don't grow out of the tumor.
And so research is focused on getting the T cells to grow better, making the tumor less stubborn, and reducing the noise caused by these stochastic effects that aren't at the moment in much control of the scientist. You can also make note that while TIL ACT is largely a biological therapy, you still need chemo as a crutch to achieve optimum efficacy, hence the cyclophosphamide/fludarabine immunodepletion.
PS I tried to cover everything but we can go deeper and deeper with this therapy so I wanted to keep it brief, but this means I may also miss some critical notes, so I'm available to clarify things if need be.


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Evolutionary support for parenting book "The happiest baby on the block"
The book by Dr Harvey Karp (MD) The Happiest Baby on the Block proposes that the duration of human gestation has evolved as a tradeoff between cranial size and development of the infant.  He hypothesizes that from an overall developmental perspective human babies are all premature and would benefit from additional time in their mother's womb; however, because humans have such big brains, and therefore our babies have big brains, the infant needs to be born earlier than would be developmentally ideal so that it doesn't get stuck in the birth canal.  The result is babies that have big brains but are highly vulnerable and dependent on their parents until their development progresses further.
I discussed this with some students in class as an example of the use of ideas from human evolutionary ecology and life history theory in the popular press, but with the disclaimer that I had no idea if any of Karp's ideas are backed up by any evolutionary or anthropological data.  Could anyone point me towards literature that support or contradicts Karp's claims?  For example, are human infants more dependent than those of other primates?
[The upshot of Karp's theories are that the best way to have a "happy" newborn is to mimic conditions that it would experience in the womb, such as swaddling.  Works for my child!]

How many more weeks in utero does Karp think would be ideal? I don't know Karp at all, but a quick search indicates he's known for soothing babies by swaddling. Great. My mother swaddled all her infants many decades ago.
If he is comparing human neonates to  primate neonates, he's correct. Baby primates are born pretty much knowing how to cling onto the mother with four extremities, necessary because primates are quadripedal, and need their arms to walk as well, meaning baby needs to hold on, aided by opposable toes. (Chimps and gorillas do support the baby with one hand longer, though.
But what evolutionary advantage would it serve for our infants to come out grasping? humans are bipedal, meaning we have arms that can be used to carry an infant. If we need our arms, we have the intelligence to fashion slings or carriers.
The same goes for any ability: sight, motor skills, etc. They don't need to be born with these skills, because they are cared for.
Antelopes drop a newborn which is up in minutes and able to see and run. Cats drop a newborn which can wiggle, crawl some, is blind and as helpless as a human.
Babies, through evolution, are able to live outside the womb (assuming no complications) without extraordinary maternal assistance from about 36 weeks on. A look at growth charts show steep rises in both cranial size and weight gain.

But you can see that a baby's head at the 10%ile takes at least six weeks to catch up to a baby the size of one born at 90%ile. Why doesn't that baby just gestate for 6 more weeks?
There is much more than head size going on here. There is the placental size, the amount of amniotic fluid, the possibility of meconium aspiration, etc.
Stillbirths are twice as common at 42 weeks and 4 times as common at 43 weeks.

Approximately 20% of postterm (41 weeks gestation) fetuses have fetal postmaturity syndrome, with chronic intrauterine growth restriction from uteroplacental insufficiency. These pregnancies are at increased risk of umbilical cord compression from oligohydramnios, [low Apgar scores], intrauterine passage of meconium, and short-term neonatal complications (such as hypoglycemia, seizures, and respiratory insufficiency). ...[T]he 4-fold decrease in the incidence of the meconium aspiration syndrome in the United States from 1990-1998 has been attributed primarily to a reduction in the postterm delivery rate [(induced delivery at 41.5 weeks)]. Postterm pregnancy is also an independent risk factor for neonatal encephalopathy and for death in the first year of life.[17, 18]

Maternal complications and death also increase with post-term deliveries.
Are term babies actually evolutionary preemies? I haven't read Dr. Karp's book or heard his reasoning, but it seems superficial to me. Medically, from an infant and maternal standpoint, a 38 week delivery is ideal. Over hundreds of thousands of years, the female uterus and pelvis, and the fetal placenta and amniotic fluid found the most favorable time for delivery into a human environment.
If we gestated for two years, like elephants, yes, our babies would be more capable at birth, but we aren't elephants, and mothers and babies would die.
Postterm Pregnancy (Medscape)
Elephant birthing and calves (Wikipedia)


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A number of questions regarding chemotaxis assay using PBMCs
In our lab we would like to study the chemotaxis of PBMCs towards conditioned medium obtained following treatment of cancer cells with different compounds.
My questions are regarding the method of purification of PBMCs from whole blood:

I have read a number of protocols saying that during the isolation process the buffers used should not contain calcium or magnesium ions, as these can cause the activation of the PBMCs. Is that so? From my knowledge Ca+2 is a second messenger only in TCR signaling. I am not sure reegarding the other cells present, and how magnesium is relevant at all.
Even if I use PBS (without any calcium or magnesium ions) to isolate the PBMCs from blood, in the end I resuspend the isolated PBMCs in medium which does contain these ions. Is there any rationale to use calcium and magnesium-free buffers for the isolation when  the final medium contains these ions anyway?
When I begin the assay, should the PBMCs be activated or not? In other words, do chemokines also activate the PBMCs or are chemotaxis and activation two totally independent processes? How should activation/no activation affect my results?

Thank you in advance.


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Why does the ovum prefers to be arrested at metaphase 2 of meosis before fertilization? What is the possible advantage of this process?
Why does the human  ovum prefers to be arrested at metaphase 2 of meosis before fertilization? What is the possible advantage of this process??Please help me with it.

In different animals meiosis is arrested at different points: it's not always metaphase 2.


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Mass Spectrometry Terminology
I began reading this paper (http://www.biomedcentral.com/1471-2105/14/56) and had a few questions about mass spectrometry terminology that I couldn't find answers to elsewhere.  Consider the following line:
"The resulting peptide signals in the LC-MS map are referred to as features while the selection of features for fragmentation with MS/MS is called precursor ion selection."
I'm not sure what an LC-MS map is, so I can't properly understand what features or precursor ion selection are: can someone define these terms for me with examples?

LC-MS stands for Liquid chromatography–mass spectrometry. The LC-MS map shows the separation of samples by polarity and mass.

As I understand precursor ion refers to the tryptic peptide ions prior to fragmentation after the first round of MS.

LC-MS map they refer to is the projection of two separation method (Liquid Chromatography - Mass Spectroscopy) results into an imaginary plane. It's a conceptual map. From this map, peptide signals referred to as "features" (article uses this term) are selected for the next level of fragmentation and then MS again.
Figure 1 of the article you cite simulates a small fraction of this larger map.

In a liquid chromatography coupled to mass spectrometry (LC-MS) analysis, as analytes elute from the chromatographic column they are sprayed through a hypodermic needle maintained at a high potential difference relative to the mass spectrometer. Combination of this potential difference and the pH of the LC buffers causes the analyte molecules to pick charge. Analyte ions are then pulled into the MS and guided using lenses. Then these ions are separated based on their m/z (mass-to-charge) ratios inside an analyser and then detected using a detector.
At any given time, detected signals are typically represented on a 2-D map/graph between m/z on the x-axis and ion intensity/relative abundance on the y-axis. This is called as MS1 scan or precursor ion scan. Now, depending on the mode in which LC-MS analysis is being carried out, precursors are selected for fragmentation and further MS measurements, which is called as MS/MS or MS2 or product ion scan. Several of these MS1 or MS2 snap-shots can be used to construct a elution time profile for every ion. For an ion having a specific m/z ratio, this can be represented as a 2-D map between retention time on the x-axis and ion intensity on the y-axis. Area under this profile can be used to estimate the ion current of an analyte and under the given conditions it is proportional to the abundance of the analyte in the sample.


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Can the eye determine which type of defocus is presented to it?
I have a question regarding myopic and hyperopic defocus.
My question is, is the eye able to determine which type of defocus is presented to it and if so what mechanisms allow it to distinguish between the two types of defocus. This question was thought of after reading a study which showed that the eye's AL could change temporality based on which type of defocus was presented to it and I was unable to find a definitive answer on to why this happens.
As well as this, I saw numerous reports on how different lenses can slow the progression of myopia by presenting peripheral myopic defocus onto the retina without an explanation on why this occurs.
Thank you for taking the time to read my question and I look forward to your response!


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Do babies have a fight or flight response?
Do babies react in the same way as young children and adults in regards to the fight or flight response? If they do not respond in a similar way or don't have a fight or flight response at all then at what age is this developed. My teacher said that babies don't have a fight or flight response and we are unsure of when this develops but I'd like more information if there is any.
Thank you!!

I think it is 6 months of age, however I found minimal supporting information.


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Why do we get tunnel vision during fight or flight response?
I have a question regarding tunnel vision during the fight or flight response. I believe that during fight or flight high levels of adrenaline are released which causes the pupils to dilate allowing more light to enter which allows us to be more aware of our surroundings. Why is it that sometimes we suffer from tunnel vision then? I know it allows us to focus on the main threat but if our pupils are dilated and more light is entering and hitting our retina how is it that we have tunnel vision? Shouldn't we see more now with a dilated pupil?
Thank you for reading my question!


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Vitamin A Deficiency
I have a quick question regarding Vitamin A deficiency.
The photoreceptor molecules in both rods and cones have the same general structure which is retinal which is bound to a protein called opsin and depending on the photoreceptor opsin changes but the retinal is always the same. And it is the retinal that makes the opsin light sensitive and so it is highly important.
My question is, why is it that when researching the symptoms of vitamin A deficiency one of the most common ones is night blindness. I understand that if not enough retinal is formed not enough rhodopsin is formed and so the patient would suffer from night blindness but wouldn't it also mean that the patient wouldn't be able to produce enough of the other photoreceptors as well and so doesn't only suffer from night blindness but from complete blindness?

Good question! As you write Vitamin A is quite important vision as it is an integral part of the light sensitive rhodopsin protein. Rhodopsin is necessary for a type of photoreceptor, the rod. It is located in outer segment of the photoreceptor. Vitamin A is also required to other opsins that are needed for the cones to function.
When someone has Vitamin A deficiency it does not mean that they have no Vitamin A. For example instead of having i.e. 100 Vitamin A you only have 30 (arbitrary numbers!).
In the retina, you have the very light sensitive rods and the less light sensitive cones. Rods need a lot of rhodopsin (and hence Vitamin A) as they have to detect small levels of lights (it is thought that a rod can detect a single photon!).
Cones, on the other hand are not so sensitive to light. During the day there are tons of photons*. Since you need less Vitamin A for cones to function, you will see the symptoms of Vitamin A deficiency later compared to rods.
Hence, when you still have a bit of Vitamin A but not enough (e.g. 30 instead of 100) you will first notice it in systems that need Vitamin A the most. It turns out that this are the rods. And yes, if you had 0 Vitamin A you would be blind. But since Vitamin A is needed for many other processes, you will probably be dead at that point.
*Personally, I find it hard to grasp just how large the difference in Illuminance (and hence photon numbers) is for example between day and night. See here for a comparison. As you can see, our visual system has to deal with an enormous dynamical range of illuminance. The fact that we usually don't even think about these differences in light intensities in everday live is testament to how fantastic our visual system is in dynamically adapting to the huge differences in input.

Thank you for your answer! You explained it perfectly, sometimes people explain things in a really complicated way and I need a dictionary just to go through the answer but yours was really easy to understand and I appreciate that.


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Reusable microarray chips
Microarray chips allow us to conduct many expression experiments in parallel to each other but they can be used only once as far as i know. Are there reusable microarray chips? Have people ever tried it? If there are, are they becoming more common? If people do not choose to use them even though they are in the market, what can be the reasons?

As far as I am aware, there are no commercially available re-usable microarrays. The reason for this is most likely that the arrays are really sensitive and you run into the trouble with false positive signals. I have once seen a microarray which has been stripped and still delivered quite some signals in areas which had a strong signal before.
You have to make sure to strip all the hybridized samples from the chip without damaging the probes which are bound on the surface. I think the trade-off between "everything is off" and "some sample is still bound" is not good enough. Who wants to risk false positive signals and possibly retract publications on this basis? You may also loose weak signals which are hidden under false-positive signals.


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Why does not the host produce any immune response to antiserum antibodies?
When an antiserum is injected to a person to protect oneself from a certain disease, the antibodies in the antiserum come from another organism. The question is:
Why don't the injected antibodies cause an immune response in the individual?

If an antiserum derived from another animal was used then it would be active immediately, whereas the patient would take 10-14 days (this figure from memory) to mount an immune response against the foreign antibodies. So the antiserum would have plenty of time to 'cure' the patient.

That's a good question - because its certainly possible to get antisera against antibodies.
Sometimes antisera is actually human antisera, so there would be no rejection at all.  But that is for extreme cases, e.g. serum transfusions from convalescent Ebola survivors to current Ebola patients.
One would expect that you could only give an antiserum once and then it would be less effective each time you get it.  Since antisera to snakebites is the most common application, where its quite possible to be exposed to multiple bites over one's lifetime.
I found one reference to a horse antiserum treatment that's being used. It makes reference to a source of antiserum which sounds like its been designed to reduce the antibody antibody immune reaction:

Horse-serum antivenin has been available since 1956; a purer antivenin with improved properties was released in 2000 (see Medication). With the reduced side-effect profile of antigen-binding fragment antivenom (FabAV) and the improvement in tissue injury with antivenin administration, the threshold for dosing is lower.

Even before the availability of these new treatments, its probable that most patients can endure multiple anti serum treatments from the same source animal.  Even goat, horse and rabbit antibodies are pretty similar to ours and the reaction will not be as strong, in addition to which, the immune system will tend to clear out the antigen-xenoantibody complexes from the blood.
I can't find references, but my guess is there must have been some cases of rejection and reaction otherwise they would not have bothered to improve the serum treatment.
Update: just read this little blurb in scientific american, that describes how venom antisera will occasionally cause deadly reactions, while most of the time simply disarming the venom.  The new generations of antivenoms described have the Fc portion of the antibodies removed.  This eliminates the adverse immune reaction but I also think also eliminates any immune resistance the patient might get out of the antisera.  The Fc portion of the antibody is the part which our immune cells bind to.  In this case the new antivenoms aren't anti sera exactly, but they do use the antibodies to deactivate the venom toxins and crosslink them to make them less effective.


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Modern alternatives of DNA footprinting
Since DNA footprinting is an old method I thought there may be some more recent and effective methods to identify a DNA sequence, do you know any of them?

You could look into ChIP-Seq

Identify it as what? Guess the species of origin? Guess the individual it came from? Guess its function?

Since he is talking about footprinting, I assume he wants to identify what motif a particular protein binds.

@canadianer ah! DNAse footprinting, OK.

DNAse-seq is the most obvious choice. It uses the same idea as DNAse footprinting but measures output using high-throughput sequencing, so it can be done on a whole genome in one shot.

DNA sequencing, RFLP, IHC, In Situ Hybridization, Southern Blotting.
I think the technique you are looking for (what you are talking about), is an Electro Mobility Shift Assay or EMSA


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Why do nattokinase and serratiopeptidase remain effective when given orally, but not insulin?
Why do nattokinase and serratiopeptidase not break down in the stomach and intestines?
Article says that serratiopeptidase is absorbed in rats intestines after oral intake - https://iubmb.onlinelibrary.wiley.com/doi/abs/10.1111/j.1470-8744.1994.tb00308.x

Added reference to the body of the question, thanks


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I would like help Identifying this insect
We found this in our house after coming in from outside but we are unsure if it came in on one of us (riding our coat) or was in our house before. We live in Massachusetts if that helps. We would like to know if anyone can ID these poor quality images.

Please [edit] your post to include an approximate size and any other contextual info you can think of. Additional better photos are also always useful for future visitors to comapre to. Thanks.


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Why do colors clash in your brain?
Wen pairing two or more colors together, some "clash" or cause a effect visually where the two colors meet. To me it appears to be a black line between the colors or shading when in fact there is not. I grey scaled the picture to confirm. In dogs, they would just see different shades of grey and this effect would not affect them. So, what is this that which make this effect in the brain?

Could you explain what you mean by "clash"?  I don't see any real difference between the colored image and the grayscale one.  Maybe it's something specific to YOUR brain - or maybe I'm the odd one :-)

@jamesqf there is an optical illusion of a very thin black line between the red and the blue sections in the top image. There is less contrast between the two gray tones in the bottom image, so this illusion doesn't appear as evident (at least to me). Do you know if you have some version of color blindness?

@MattDMo: No, I don't have color blindness, and I see that "illusion" on the gray scale image as well, though not as strongly.  If it is an illusion, and not an artifact of whatever created the image,  But I haven't tried blowing up either image myself.  I would suspect, from having done some work with computer feature recognition, that it's an artifact of higher processing levels segmenting the image into recognicable features, but I don't actually know.

@jamesqf it is indeed an artifact https://i.sstatic.net/3E7PO.png

Magnify your image.
I just put it in GIMP and it is clear that there are several pixels in the red and the blue near the border which are a darker color than those adjacent - the drawing program must be responsible.
Lateral geniculate nucleus
That said, differences of red and green hue are handled more in the parvocellular layers of the LGN, while grayscale differences are handled more in the magnocellular layers, with blue cones contributing to the koniocellular layers the most.  In your images, all three are involved.  There are some individual differences reported between these regions and their timing of activation in regard to dyslexia - it's a hot topic, and these variations seem to be the explanation for that perplexing condition.  I'm not going to point to any specific paper because I'm not sure how to interpret the "clashing", but there's some interesting reading there!

Your first paragraph about magnification is not, I think, relevant. What you are observing is something called “anti-aliasing, which is a way in which a smooth, rather than a jagged, border is produced (in the brain). The visual effects need not be generated by computer — they were and are a staple of certain printed publications for centuries.

@David: I can't say that I've ever noticed them in print images, but are you sure the ones you see aren't an artifact of the inks mixing at the border?

Actually my comment is not quite right. In high quality printed images a smooth interface between two inks of different colours occurs because the individual dots of ink are so small. On a computer screen there is a limit (traditionally 72 dots per inch, now generally 120 dpi or higher, but still enough to give a visible jagged edge between two adjacent colours. This is called aliasing. Computer programs can trick the eye into seeing a smooth edge  by making a transition between the colours of the pixels at the interface — anti-aliasing. cont.

cont. Looking closely at the example and generating one of my own in Photoshop with the same colours I notice that the anti-aliasing in the example is different from that produced automatically by Photoshop in having darker colours at the interface. As you say, it must have been produced by the program that generated the image, although quite why I am not sure. Perhaps a compression effect. Highly compressed jpegs can do this, although the image is currently in png format. I could add a composite illustration to your answer if you don't object.

cont. Got it wrong again. It's not a jpeg compression artifact, which is different, but a sharpening artifact. It's the way that Photoshop's "unsharp mask" filter produces its effect. I can reproduce its generation in a series of images. So as far as I can see the question is concerned, the poster is seeing what is actually there, so it is not an optical illusion. The general area of how these image manipulations trick the brain is interesting enough, but not particularly new or subject to detailed biological analysis. They just know how to do it.


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What is this insect species? It lives in damp places in a cocoon like structure and can protrude its head from both ends
Lives in damp places and can protrude head from both directions, 1 cm long approximately

Yeah its a case bearing moth.. Thanks for responding! I was looking for it since long..


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What type of jellyfish is this
I have been swimming in the seas around Minorca and saw a jellyfish I had not seen before.
I have tried to find it and have (eventually) found 1 single picture of the jellyfish.

The problem I have is, the image is from one of these "buy our picture" website and offers no information about the creature.
What type of Jellyfish is this and can I assume from the picture that it does not actually sting humans?
I have researched, and viewed sites like (As well as Google/Bing images)
http://www.holidays-majorca.co.uk/trips/beaches/types-jellyfish-around-majorca
http://www.seafriends.org.nz/indepth/jellyfish.htm (I know, it's NZ but I'm looking everywhere I can)
http://www.glaucus.org.uk/Moonjell.htm
http://www.whatsthatfish.com/browse/tags/limit/Jellyfish
http://www.imenorca.com/en/entrada-de-blog/jellyfish-minorca
http://www.menorca-tips.com/EN-jellyfish.html
http://www.mcsuk.org/downloads/wildlife/Jellyfishguide.pdf

https://jellywatch.org/

Eventually, I've stumbled upon an article which calls it a cigar jellyfish.
Further research even shows a very empty entry on Wiki about it, which consists of the single line entry:

The cigar jellyfish (Olindias phosphorica) is a species of jellyfish from the Central and East Atlantic, and the Mediterranean Sea, including off Malta.[2]

Also an interesting article about it being 'rare' in Malta (despite the above information)


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What bird makes this sound?
It sounds like some kind of crow but not really. Here is my recording: https://www.youtube.com/watch?v=4TsKFUugot8&feature=youtu.be#t=06s
This bird always wakes me up at 04:00 and this started in late June. I live in a village in Hungary.
I really need to know and don't know where to ask.

Please [edit] your question and mention 1) where you heard this 2) what time of day 3) what period of the year.

It can't be confirmed but it sounds like a pelican.


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Are the 5 digits of all land vertebrates an accidental number?
All land verterbrates except some frogs have 5 fingers on hands and feet.
The first vertebrate lizards came out of the water and had 7 fingers ( -370mn yrs), and then 6 fingers, and after 30 million years, all their descendents had 5 fingers on both limbs.
someone told me "5 is much more of an accidental number", so if all land vertebrates had 7, then 6 fingers, why did that get selected to 5?

Related (if not duplicate): Why don't mammals have more than 4 limbs? and Why do some bad traits evolve, and good ones don't?

There are more exceptions than frogs. It depends a bit upon what you call a finger, but typically snakes don't have fingers, ungulates don't have fingers, cats have 4 toes at each hind paw, ....

Note also that the first vertebrate coming out of the water was not a lizard (not a squamata).

By the question why did that get selected to 5 there is a potential false assumption that make it clear that your question is a duplicate of Why do some bad traits evolve, and good ones don't?. I'm voting to close as duplicate. Please have a look at this post and if you think it did not answer your answer, please clearly explain why.

The general question is a duplicate. Articles here, here, and here emphasize the contingent nature of the five-finger tetrapod.


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Why are there few tetrapod dinosaur carnivores?
Today, most big carnivores are quadrupeds. Bears, Tigers, wolves.
During the Jurassic and the Cretaceous, carnivores were mostly bipedal, dinosaurs mostly from the Therapod family.
Why was bipedalism previously a very efficient predator mode for dinosaurs, when evolution could have made some quadruped familes, at least for the 10-400 kilo carnivores? For the Paleogene, there were briefly terror birds, and since then all the major carnivore families have been quadrupeds, and mammals have not evolved dinosaur convergeant evolution towards Therapod body formats. Why not?

A lot of bipedal birds eat fish and many eat rodents and other things.

birds are not parralel evolution of therapods. why is there no parrallel evolution of therapods in the paleogene, and no parellel evolution of wolves, tigers and fast quadrupeds in the cretaceous-jurassic?

This is actually a really good question.  Several large groups of dinosaurs (theropods, most famously) were bipedal, and highly successful at it; while today, very few mammals are bipedal.  What was it about dinosaurs that made bipedalism a successful solution, while mammals typically prefer quadrupedalism?
There were two important differences between the immediate ancestors of dinosaurs and of mammals that made bipedalism more likely in the former, and both are related to lizard tails.
The classic lizard shape puts the center of gravity relatively far back: They have smallish heads, their front limbs don't have much musculature, and they tend to have long, heavy tails. So as soon as they start to accelerate -- which moves the center of gravity further back -- they automatically rear up, like a race-car starting up. In fact, as modern lizards run faster and faster, it's not unusual for them to raise up and basically become temporarily bipedal.  For example, around the 45-second mark in this YouTube video. For a detailed analysis see Why go bipedal? Locomotion and morphology in Australian agamid lizards.
So as a consequence of basic lizard anatomy, they're prone to become bipedal when they accelerate. This could work out relatively well for lizards, because dinosaur ancestors started off with bigger, more powerful tail muscles that could be coopted into muscles for hind limbs.

Bipedalism, when combined with a caudofemoralis musculature, has cursorial advantages because the caudofemoralis provides a greater source of propulsion to the hindlimbs than is generally available to the forelimbs. That cursorial advantage explains the relative abundance of cursorial facultative bipeds and obligate bipeds among fossil diapsids and the relative scarcity of either among mammals. Having lost their caudofemoralis in the Permian, perhaps in the context of adapting to a fossorial lifestyle, the mammalian line has been disinclined towards bipedalism, but, having never lost the caudofemoralis of their ancestors, cursorial avemetatarsalians (bird-line archosaurs) were naturally inclined towards bipedalism.

--The functional origin of dinosaur bipedalism: Cumulative evidence from bipedally inclined reptiles and disinclined mammals
Another argument that has been made is that bipedalism freed up the forelimbs for other uses, but that last reference pooh-poohs that notion in favor of the better transportation concept - though of course they're not mutually exclusive, early dinosaurs could have mainly gone bipedal for transport but have had some impetus from forelimb use that became less important in later species.

Most of the dinosaur predators were derived from a common ancestor. The body plan was efficient, and the theropod predators speciated widely (including birds). But statistically, the number of therapod predators are not independent observations, but linked to each other through ancestry. Similarly, most mammalian predators (Carnivora) are linked to a common ancestor. Both forms worked, but there is not evolutionary pressure to evolve toward a particular form; only pressure to favor successful accidents. So it is an interesting question, but it could be that the predator niche was filled by bipeds in dinosaurs and quadrapeds in mammals.

Because most dinosaurs evolved from bipedal ancestors. Your evolutionary baggage has a huge impact on what adaptations you can develop. Usually organisms only change their form of locomotion drastically when there is very unusual circumstances or a strong and more importantly consistent pressure. The ancestral form for dinosaurs is bipedal, this is lost in several groups but the earliest forms in each group is bipedal. Bipedal is the default. The groups that did go quadrupedal also developed many specializations for herbivory, like chewing teeth, herbivory requires some specialization including a much larger gut so becoming quadrupedal can be an advantage, although even among the herbivores many stay bipedal or hybrid bipedal unless they are very front heavy.  If you are already bipedal there are not many advantages to becoming quadrupedal.
You can look at a large version of illustration here.

Mammals on the other hand have lost several key adaptation that make evolving bipedalism difficult, Mostly the drastic reduction of the tail which shifts mass and muscle forward, but also a weaker ankle and hip structure. The lumbar region of the spine is also a serious weakness for a biped. Most of these features are either holdovers form mammals long evolutionary history as tiny insectivores, during which we lost many features, or in the case of our lumbar region due to our breathing mechanism so they cannot be easily changed either.