gene expression - which exact mechanism triggers the first cell differentiation after n divisions?

The first differentiation in human embryogenesis is from early blastomeres into trophoblast, which forms the outer layer of the blastocyst, and inner cell mass (ICM). It may be unsurprising then that cells on the inside of the 8-16 cell stage morula
differentiate into ICM whereas those on the outside differentiate into trophoblast. However it is currently unclear whether this is a causal relationship (the inside-outside model) or whether blastocyst patterning is set-up earlier in cleavage (such as in the apicobasal polarity model) or if it is some combination of the two.

You were correct in imagining that tissue patterning is determined by chemical substances: a very broad class called morphogens. Cells don't necessarily count how many times they have divided but cell division can certainly affect morphogen concentration and localisation. I suppose in some sense you could describe this as a clock. I wouldn't though, especially because mammalian cleavage is asynchronous.

One line of studies showed that a transcription factor called Tead4 specifies trophoblast$^{ref}$. It was then shown that Tead4 can be regulated by cell-cell contact (mediated by Hippo signalling) $^{ref}$. They hypothesised that the magnitude of cell-cell contact could provide a mechanism by which Tead4 localisation could be controlled in presumptive trophoblast and ICM. This could explain why the cells have different fates because inner cells are completely surrounded (more cell junctions) whereas outer cells are largely exposed to the medium. Note that I only provided that as an example of a possible mechanism. It is not confirmed and, as with any model, the real picture is incredibly more complex and likely involves many factors.

I'm reluctant to go into too much detail on this because you're asking about a complex process that is still under active study and I'm unclear as to how much information you actually want. A book could be written on this subject alone, and many review papers have been published. Here's a recent one:

Development: Do Mouse Embryos Play Dice?

I suggest you read that and then if you have further, more specific questions, we can try and answer them for you.

biochemistry - Humidity for wood rotting

I'm afraid this is not a topic of chemistry, the main degradation process in wood decay is a matter of biological attack, of course life needs water so if the ambient is very humid the wood decompose very well if the ambient is dry the wood can be conserved easier.
However wood is not a substance but a complex material, you have to investigate the degradation process for all the components. Chemically holocellulose is the most degradable part of wood, his microcrystalline structure improve the resistance but cycle of imbibitions can blow up the structure leading to a larger surface more suitable for degradation. The hydrolysis of cellulose however doesn't occur at normal temperature only peeling off can occur under 100 °C.
Lignin is more and more durable if a little bunch of micro and macro organism wouldn't decompose it we would be sub-merged by a large quantity of lignin.

dna - How much natural genetic variation is there between bacteria of the same species?

I'm sure the answer will depend on the specific species, but I'm looking for a ballpark figure for bacteria.

Yes indeed it will. Bacteria are a huge domain of life; you might as well ask for variability between all plants or between all animals. Bacteria can live in very different environments, and the whole things is made more complex by widespread horizontal transfer.

Still, for bacteria, you can't do much better than E. coli, and boy are they a mess. Here's a paper from 2010 that blew my mind. The authors sequenced 61 E. coli genomes and found:

...that any given E. coli genome sequenced will have only roughly 20% of its genes part of the E. coli core, and the remaining 80% are not found in all other E. coli genomes.

20% variability within a species. 20%, one species. E.coli is an extreme example, but still, species is a stupid concept. Here's a 2006 paper finding that plenty of unique Campylobacter proteins simply aren't in plenty of Campylobacter species.

On a more broad scale, here's an excellent (and free) paper you should look at. It examines islands of "microdiversity" among various species, finding that some species are easily 50%-75% different. A simple way to estimate this is too look at gene number for bacterial species, which should make it clear that some of these bugs vary by up to an order of magnitude.

In short: A lot.

pharmacology - Can Opioids Attenuate some of the symptoms of Psychosis?

9 Substance-Induced Disorders says...

Withdrawal results in agitation, severe body aches, gastrointestinal symptoms, dysphoria, and craving to use more opioids. Symptoms during withdrawal vary—some will become acutely anxious and agitated, while others will experience depression and anhedonia.

It adds that even with complete abstinence that these symptoms can last for weeks.

The paper sites Levinson et al. 1995 and Zukin and Zukin (1992) under the Opioid section, and also talks about PCP and it's effects such as an acute psychotic state.

PCP may have been included there as Drugs.com states:

PCP is a noncompetitive NMDA/glutamate receptor
antagonist, but also interacts with other receptor sites, and may have
effects with dopamine, opioid and nicotinic receptors.

Opioids and the Treatment of Chronic Pain: Controversies, Current Status, and Future Directions also explores opioid usage. They say that there are some people on opioids who have problematic behaviour that isn't related to the drugs. They do say that people who actually need the opioids act differently than people who are abusing the opioids, but it's not mutually exclusive. "[...] some patients who are treated for pain do develop severe behavioral disturbances indicative of a comorbid addictive disorder."

• Levinson I, Galynker II, Rosenthal RN. Methadone withdrawal
  psychosis. Journal of Clinical Psychiatry. 1995;56:73–76. PubMed


• Zukin, S.R., and Zukin, R.S. Phencyclidine. In: Lowinson, J.H., Ruiz,
  P., Millman, R.B., and Langrod, J.G., eds. Substance Abuse: A
  Comprehensive Textbook. Baltimore: Williams & Wilkins, 1992. pp.
  290–302.

Continued research suggests that the only psychological effect that opioids have are psychological addiction. Although it can act as a sedative according to Benyamin et al. (but it is listed as a side effect).

In this study, they concluded that long-term use actually reduced functional connectivity in the brain. Although the patients that they were compared against had to be of clear health physically and mentally.

I was unable to find anything that suggested that it would help with psychosis. Most data suggests that it should only be used on a short term basis and long term use actually can cause detrimental effects mentally and physical dependance.

According to Treatment4Addiction.com withdraw actually causes psychosis and other detrimental effects, most of the research has been focused on getting away from opioids. It would probably be a bad idea to treat psychosis with a drug whose withdraw symptoms include psychosis.

evolution - What is the evolutionary rationale for palm sweating?

As @Ben states, every theory of 'why' we evolve a trait is just a guess and never more than part of the story. But there are theories.

The palms of our hands are a major source of heat transfer out of our body. For bears it is the nose and pads of their feet, for dogs it is their toungue, for us a major portal for heat out of our body is the palms of the hands.

Black bears are extremely well-insulated animals, equipped with a heavy coat of fur and a thick layer of subcutaneous fat that help them maintain their body temperature as they hibernate through winter. But once spring arrives and temperatures rise, these same bears face a greater risk of overheating than of hypothermia. How do they dump heat without changing insulation layers?

Heller and Grahn discovered that bears and, in fact, nearly all mammals have built-in radiators: hairless areas of the body that feature extensive networks of veins very close to the surface of the skin.

Rabbits have them in their ears, rats have them in their tails, dogs have them in their tongues. Heat transfer with the environment overwhelmingly occurs on these relatively small patches of skin. When you look at a thermal scan of a bear, the animal is mostly indistinguishable from the background. But the pads of the bear's feet and the tip of the nose look like they're on fire.

These networks of veins, known as AVAs (arteriovenous anastomoses) seem exclusively devoted to rapid temperature management. They don't supply nutrition to the skin, and they have highly variable blood flow, ranging from negligible in cold weather to as much as 60 percent of total cardiac output during hot weather or exercise.

Given this, one could see how the palms of our hands are more likely to react to emotional situations where the heart rate elevates and sometimes we get hot under the collar. The AVAs will

I am not physiologist, but the quote above comes from an article I stumbled upon a few months ago. They use the AVAs to reduce the swelling associated with exercise and got some amazing results. I guess that's another story though.

biochemistry - Does DNA react in all of the ways most other acids do?

It may seem counterintuitive that deoxyribonucleic acid has nitrogenous bases. Nonetheless, nucleic acids (thus including RNA) were called that way because the phosphate backbone (linked by phosphodiester groups) is a derivative of phosphoric acid.

Phosphoric acid

Image Source

Phosphodiester group

Image Source

Note that the only difference between these two groups is that in the case of the phosphodiester, two O-H bonds are replaced by O-C bonds. This make the last remaining hydrogen atom quite acidic (can quickly be identified by how the conjugate base exhibits resonance). In fact, it is so acidic that at physiological pH, the phosphodiester group is deprotonated, giving that nucleotide a negative charge. This property is does have a profound effect on DNA's structure and "behavior" in a cell, and is often exploited in genetics, such as in gel electrophoresis.

An interesting fact is that this acidity of the phosphodiester group actually competes with the basicity of the nitrogenous bases. However, since most often DNA is double-stranded, individuals bases will hydrogen-bond with its partner to make base pairs, which stabilizes and thus reduces this basicity.

TLDR: Although different acids of different molecular composition can act in very different ways, the overall acid-base chemistry is seen in nucleic acids.

human biology - Axial skeletal system

Because your textbook is probably worded poorly.

It appears that the Japanese (and several other ethnic groups) apparently have a higher proclivity for the 10th rib to be a true floating rib, but every ethnic group has the chance of having a floating 10th rib.

With that said, the one McGraw-Hill book cited in the Wiki article is the only source I've seen for this higher morphology rate. I, personally, wouldn't trust just one source, and (if true) the rate may not be much higher.

human biology - What prevents a pregnant woman's immune system from recognizing her fetus as nonself (and attacking)?

I'm familiar with the scenario of Rh- mother with Rh+ fetus having complications (more so after her first child), but that's not what I'm curious about. I want to know mechanistically why a pregnant woman's body does not display a reaction similar to what we see with rejection from a mismatched organ transplant. On the most basic level, I feel as though the fetus should be recognized as "nonself" due to paternal genetic contribution.

I feel as though if this mechanism could be understood, it could be harnessed for other situations (e.g., organ transplants).

zoology - Aside from cockroaches and other insects, which species (of all kinds) are 'immune' to ionizing radiation?

According to Paul Stamets, Gomphidius glutinosus is especially well suited to collecting Cesium-137:

G. glutinosus has been reported to absorb – via the mycelium – and
concentrate radioactive Cesium 137 more than 10,000-fold over ambient
background levels.

That article and Stamets' book Mycelium Running have more details on other species.

evolution - What is the Edward O. Wilson fuss about?

After reading the article, the fuss is about this:

In currently accepted theory Eusociality or "kin selection" explains altruistic behavior (the sacrifice of yourself or resources you control for the betterment of something else besides you) by relating the act to the amount of genetic information passed on.

The relevant equation is Hamilton's rule:

                                                              $rB > C$

C is the cost to the actor (the person giving up resources). B is the number of others involved, and r is the relationship value to the actor in terms of genetic similarity.

So if you and two full-siblings (who each share on-average 50% of your genome) and a bus comes straight at the group, and you have the capability to push them out of the way while dying yourself, kin selection suggests you shouldn't because the genetic cost is equivalent. You eliminate yourself from the gene pool, and save the equivalent of yourself for future generations (2 x 1/2 = 1).

However, if you and three siblings were in the situation, then it's evolutionarily advantageous to be altruistic. You would die (a cost of 1), but you would save the equivalent of 1.5x your genome (3 x 1/2 = 1.5) to pass on to future generations.

Thus, communal and social behaviors like those of ants basically boil down to: Everybody is so closely related that spending resources to help your kin is essentially spending resources to ensure the majority of your genome survives (which is the big point of evolution, after all).

Wilson's argument, what I can glean from the small brief of the study and the article, is that you don't need the relatedness equation to explain altruistic behavior in social situations (basically the row is he's saying the currently accepted theory is wrong). All you need to start with is a genetic mutation somewhere along the line that causes the offspring to stick close to home. Once you have a few generations that don't leave the nest, you start to develop social behavior that results in altruism because you've gone from selfish individuals to a group setting.

The article and Wilson don't give any more insight other than altruism apparently develops spontaneously from the formation of groups. Simply being social is the explanation for why some individuals will give resources to others to ensure the success of the others.

Whether or not Wilson is correct isn't really discussed. He openly admits to needing a lot of research, some of which is being performed.

cell biology - "Acellular" designation for organisms

From Wikipedia:

Some biologists refer to wholly syncytial organisms as "acellular" because their bodies contain multiple nuclei which are not separated by cell walls.

As Albano pointed out, "cell walls" should probably be "cell membranes".

Paramecium and some types of amoeba like the Chaos genus have multiple nuclei so they fall under this definition.

zoology - Is it possible to pet/groom birds?

I know first hand that Diamond, a tame Pionus chalcopterus, will sometimes respond to having his head and neck scratched in an interesting manner: he may make "panting" or "huffing" noises unique to this activity, lean his forehead or beak against my hand, and half-close his eyes.

I'll add to Ryan's answer by pointing out another use of preening: peeling the cover from newly-grown pin feathers.

How to (safely) pet

It's important to read body language correctly. Just as in Manderan it's funny to call your mother-in-law a mountain horse, you must learn the distinction between "scratch my neck" and "stay back or I'll bite". The ruff is raised normally as a signal of aggression.

Bring your hand up to his level wrist up and fingers trailing down in a relaxed posture. Make sure he sees it, without startling him. Human hands are not "natural" to non-domesticated species, so give him a few seconds to process. Higher thinking is slow and an optional "mode" so to speak. If he wants to be petted, he'll engage or remain neutral and undisturbed.

Diamond has learned through consistancy that a natural but superficial agressive signal is understood as "give me space", so a horizontal body position with beak in-line like an arrow (the "T-Rex position") and a slight (symbolic) darting motion means you should withdraw. But he may change his mind in a few minutes now that the subject has been raised.

---

The general points are:

• understand his body language


• be consistent in your own actions and associated meanings. They're learning a pidgeon with you (pun intended), not like dogs that intuitively know humans,


• give hime time to "think".


• develop a routine

How does hemoglobin-free blood transport oxygen?

Snails, like most molluscs, have a protein called hemocyanin dissolved directly in the hemolymph ("blood"). Hemocyanins are copper-containing metalloproteins: the binding site for a single O₂ molecule contains two copper atoms. Unlike hemoglobin, where reversible oxygen binding is accomplished without a change in the oxidation state of the Fe(II) atoms in the heme prosthetic groups, in hemocyanin the copper undergoes a transition from colourless Cu(I) in the deoxygenated state to blue Cu(II) when oxygenated.

Incidentally, there are certain species of fish that manage with little or no hemoglobin - icefish.