Genuine Puzzles In Biology?

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How does consciousness work, and why did it evolve?

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I don't know how, but, as for why: because it apparently helps survival immensely. I'd say it is probably a function of having a relatively complex brain.

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Why haven't plants closed the green gap?

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Either it is unnecessary or having black plants would lead to problems via heat dissipation.

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Why hasn't a version of Rubisco without the oxidase activity evolved?

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My guess is that the molecule simply cannot be improved anymore just due to molecular conformation. That is to say, the molecule has improved since the past, but it has reached a point where there can be no improvements upon the current molecule and it would take a completely alternate molecule to have better function.

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What, exactly, is the evolutionary relationship of viruses to the rest of life and to each other?

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Having read Parasite Rex by Carl Zimmer, it seems that viruses might be unusual anti-immune system products from parasites. For instance, a parasitic wasp produces endogenous viruses from its own genetic code to attack the immune system of caterpillars so that its eggs/larvae aren't killed by the host's immune system. So, I think it is likely, given that some ~80% of eukaryotic organisms are parasites, that such endogenous viruses simply 'escaped' and became independent, rather than a tool of parasites for performing some function.

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What is the nature of the link between Archaea and Eukarya?
Why do Archaea have such different membrane lipids to the other two domains of life?

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I can't really answer the first, but the second seems to be related to their extremophile natures. As such, a classic phospholipid bilayer breaks apart rather easy in hot, alkaline environments, like they favor. Any archaea that didn't have a membrane to withstand such a habitat wouldn't live to pass on offspring with more traditional membranes.

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How did life get started anyway?

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Well, if the following article is accurate, pyrophosphite might be responsible: http://news.yahoo.com/.../newtheoryforlifesfirstenergysource

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Not on the inside, we're not, and in particular the kidneys aren't quite symmetrically placed --- the left kidney is somewhat higher in the abdomen.

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However, we're completely symmetrical during development, especially during organogenesis. It is only after about 10 weeks of development (for humans) that the heart stops being a symmetrical organ and assumes a lopsided shape and moves toward the left side of the body, with the lungs moving to accomodate it. The GI-tract is initially just a straight tube, only later lengthening and coiling about all throughout the gut. Similar stories for all the other organs. Originally, everything developed on the midline or on the sides in pairs, and only later on in development does everything shift around to fit in our torsos.

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I tried to post this as a new topic. Because it is sitting idle in the proposed topics category, I thought may be I should post it here.
1. How does thought originate?

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2. How do you recall something from your memory?

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Probably these two questions are similar. But I think they are different. May be their mechanism of origin is similar.

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If you believe in mind body dualism, then, they may have an easy answer. But is the mind different from brain? Or is it a 'metaphor' used to signify the collective out put of the brain?

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I recommend reading "How the Mind Works" by Stephen Pinker. I don't think he's 100% right on everything in that book, but I think he's right about the vast majority (75%). I can't even really summarize it well, because it is over 600 pages long and details a lot of function and form of the brain.

Dogmafood What is the prevailing theory about how this fungus evolved the characteristic of controlling it's hosts behaviour in such a specific manner?Ants have very simple brains and, as such, the fungus only has to utilize a few neurotransmitters of its own manufacture to produce a certain behavior in the ants, such as a compulsion to climb to the highest point nearby. The exact mechanism may not be known at this time (I'm not certain myself; it could be known but I am unaware of it), but it rests on simple neurotransmittor usage on the part of the fungus to get the desired behavior in the ant.There are other virus that effect rats in such a way as to increase it's chances of being eaten by a cat. I think there is another that effects fish in such a way that they will be eaten by a bird. Could rabies be said to be doing the same type of thing to it's hosts?First, it's not a virus, it's a parasite, and they do much the same thing as the fungus: affect hormone cascades in the brain. By reducing the emotion of fear in an organism (or by increasing the likelihood of other behaviors), it increases that organism's likelihood of being eaten by the final host of the parasite.Another question is how does genetic memory or instinct occur?Alleles that control for the structure of the brain and the release of certain neurotransmittors.Why am I instinctively afraid of spiders and snakes and heights?Because your ancestors' relatives who weren't died before they could reproduce. I see how being afraid of dangerous things is helpful but how do my genes remember that from previous encounters in other generations?The thing is that they don't remember previous encounters: certain behaviors are "hardwired" into brains by hormone cascades from certain stimuli (think of hunger or how you pull your hand away from a hot stove or a sharp object). Those ancestors of yours who happened to be afraid of snakes and spiders were more likely to survive than their relatives who did not feel such a fear.

Dogmafood Thanks for the reply Akhlut.No problem.I realize that most of my questions are only a genuine puzzle to me. I think what bewilders me the most is trying to imagine the circuitous evolutionary route that this fungus has taken. Without the time to do the research, my main hypothesis is that it was once a surface parasite (their equivalent to athlete's food), that eventually started releasing poisons into the ant to try to eliminate its immune response and happened to hit upon several neurotransmittor analogues that altered its behavior. I don't know if that is what, in fact, occurred, but it seems likely to me.Is there evidence that we actually have instinctive fears? I recall a study that showed children are naturally wary of heights but I wonder if fear of snakes and spiders are not a learned behavior. I have taught my kids not to be afraid of the little critters but I can't remember what their initial reaction to them was. Well, there's evidence that other animals have instinctive fears. For instance, you can condition rats to be fearful of brightly-lit areas (mild electric shocks in a brightly-lit cage) and you can condition monkeys to be fearful of snake-like objects (flexible tubing, for instance, by showing a video of a monkey eliciting a fear response in proximity to the tubing). However, you cannot make a rat fearful of dark places or monkeys fearful of arbitrary objects (rocks or trees). This is because certain things are naturally hardwired as being "always good" for certain animals: rats typically don't like bright areas anyway because they're small, nocturnal prey animals, but they conversely like dark areas for that same reason. Monkeys don't like snakes because they can eat them, but they like trees because they live there.I imagine it is similar for humans: it isn't an automatic phobia, but a predisposition for becoming fearful in response to stimuli that leads to phobia (being bitten by a snake or being told how dangerous they are).A little off topic perhaps but if our behavior and choices are a result of hormone floods and chemical reaction to stimuli what room does this leave for the concept of 'free will'? Why do I like vanilla ice cream? Why do I find my wife attractive? It's a tricky question that I honestly don't have any ideas about. While it's easy to say that a mosquito has little in the way of free will, for large-brained, complex animals like mammals, birds, some reptiles, and cephalopods, it is entirely different and perhaps unknowable. While some simple preferences (food) are easy to say why we like them (fatty foods were great when we didn't have such reliable agriculture to keep us fed at all times), and even some more complex ones are relatively easy to answer (we find our mates attractive because of a combination of physical attraction and attitudes compatible with our own, which means optimal reproduction and survival of offspring), there is still the problem of trying to figure out how much is within our conscious control versus instinctual or environmentally produced phenomena.So, to that end, I'm not sure how much I'd worry about how much of my preferences are determined by hormone cascades and genetic influence.

herebedragons First, although the ant does have a fairly simple brain, it still has over 250,000 brain cells - no small feat to hyjack and manipulate in such a way to get the desired behavior. It would take a tremendous amount of trial and error.Fungi tend to have really small generation times, so they'd have plenty of time to engage in such "trial and error."The ant don't just "climb to the highest point" but climb to just the height the fungus likes to be at to release its spores and on the proper side of the plant. The fungus then disolves the ant innards but leaves the muscles holding the mandibles intact and thus preventing the ant carcass from dropping to the forest floor and failing to release its spores.Okay, I oversimplified a bit and was basing things off of memory. Mea culpa.I don't believe fungi have neurotranmitters of their own, but release chemicals that bind to host neurotranmitters effectively short circuiting them. Not as simple to get a very specific behavior - and this behavior is very specific not just general wandering around and clamping onto a plant leaf. Its not like they have eaten a "magic mushroom" and are going crazy with halucinations.It's still rather simple behavior, though: climb to a certain height, clamp on, and then sit there. Most of this can be achieved through changing photopreference on behalf of the ant and then forcing a bite reaction once a preferred height is reached.I realize you are probably just simplifing for the sake of space and explaination time, but come on, a one sentence explaination for memory and instinct? How do these alleles code for a specific memory? How does the genetic code specify a particular image implant or an instinctive behavior?They don't code for memory, but for instinct: two distinctly different things.Anyway, because instincts are hundreds/thousands of discrete behaviors, it is difficult to generalize beyond "alleles control brain structure, hormones, and neurotransmittors," however, I can use some examples. For instance, in most mammals, being monogamous or polygamous is a very instinctual behavior, insofar as if a species follows one strategy, it is unlikely to follow the other all that much. Apparently, at least in rodents, vasopressin mediates monogamy to a large extent; thus, if you introduce a gene that strongly expresses vasopressin in a vole species that are normally polygamous, they'll be much more likely to be monogamous after the introduction of that gene. ( http://www.sciencedaily.com/...ases/2001/09/010917075347.htm )To speak about phobias: I, personally, am unsure how phobias to certain stimuli would be more genetically prevalent (i.e. how fear of snakes in specific would function from a genetic perspective), however, fear in mice has at least a partial genetic component: Genetic relationship between anxiety-related and fear-related behaviors in BXD recombinant inbred mice - PubMed From this, we can conclude that there are genetic components to fear in general, and it can probably create susceptability to more specific fears (snakes, spiders, heights, whatever).Do you really believe that snakes and spiders presented that great of a selective pressure on our ancestors? Perhaps in certain parts of the world there is greater pressure, but overall, I can't imagine there is enough selective pressure to drive adaptive phobias.Snakes: definitely. Our primate ancestors lived in Asia and Africa for tens of millions of years alongside very dangerous snakes (large constrictors and highly venomous snakes), thus making a fear of snakes a very rational trait to evolve. Hence, phobias of snakes existing in numerous other primate species. Arachnophobia has probably been much less selective since our ancestors became larger, but it may also not have been selected against, and thus remained semi-fixed in the population.