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What evolutionary pressures pushed Galápagos tortoises to mature so slowly and live so long?
I read that they take up to 40 years (in the wild) to reach the age of reproduction and are thought to live over 100 years, with one in captivity reaching over 170 years.
Can someone explain in layman's terms how taking longer (especially spending years as a small tortoise) to reproduce was a winning trait, and how their biology delays the processes of senescence to the extent that it does compared to most other species?

This isn't so precisely focused on tortoises, but a general theory in evolutionary biology for why some animals live longer is K vs r selection theory.
The idea here is that animals will make a sort of evolutionary 'choice' and configure themselves to breed as numerously and quickly as they can.  This is called 'r' selection, named after the constant that is proportional to the rate or speed of breeding.  r selected animals adapt quickly to a rapidly changing environment and their lives are pretty cheap.  Many insects that lay hundreds or thousands of eggs every few weeks are examples of r selection. They do not care for their offspring (and may even eat them!).
K selected animals breed to be highly competitive in the environment.  They tend to be highly optimized for success and this often means they are larger, they live longer and require more investment as newborns.
By this theory the galapagos tortioises live longer because their environment changes very slowly and the tortoises are so optimized for that particular way of life that they have no predation or any competition at all.  Islands like the Galapagos are studied in fact because they are so isolated by the water that new species rarely ever arrive.  Such new arrivals may cause drastic changes in their ecosystems because islands are stable environments because migration happens so rarely.
There are other theories that emphasize other factors in the evolution of larger, longer lived animals, but I think r/K selection may describe the environmental pressure on the Galapagos tortoise.


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How many species did Carl Linnaeus classify?
How many species did Carl Linnaeus (senior) classify?

Welcome to biology SE.  I think that while it is answerable, this is a rather narrowly defined question.  You might get a number, but why is this number interesting to you? Is there a larger question you are interested in?

@dd3, I am interested in taxonomy in general, but I'm also curious about this specific question.

More than 13,000.
Plants: >9,000 names.
In Systema Naturae 10th edition, commonly taken as the starting point of modern taxonomy, Linnaeus is reported to have published around 6,000 plant names (I haven't counted, but Müller-Wille gives 5,900 and Stearn says "almost 6,000". The Wikipedia figure of 7,700 may come from a different edition of Systema Naturae).
However, that's just SN10. Luckily, a wonderful source has compiled the names from all of Linnaeus's work:
The Linnaean Plant Name Typification Project of the Natural History Museum says that Linnaeus published more than 9,000 valid plant names in his life (names that are still valid under current nomenclatural conventions), and they have many of them in a searchable database with references to where Linnaeus published them.
Animals: >4,200 names.
For SN10, different authors give 4,236 or 4,378 animal names. Stearn says "nearly 4,400", so perhaps he too was unsure. The total number Linnaues described in his life is probably higher, as he did write separate zoological publications like Fauna Svevica, but I couldn't find a source like the project bringing together all of his animal names.

 Müller-Wille S. 2006. Linnaeus' herbarium cabinet: a piece of furniture and its function. Endeavour 30: 60–64.
Stearn WT. 1959. The Background of Linnaeus's Contributions to the Nomenclature and Methods of Systematic Biology.)

SN10 is the (official) starting point only for zoological taxonomy. In botany Species Planatrum (1753) is accepted as the beginning instead.

Indeed this is a bit of interesting history.  Linnaeus was not a modest man, but he was also a prodigious contributor to biology.  He made many editions of his two major works Species Plantarum (1753) and Systema Naturae published in 1759.  Systema Naturae covered both plants and animals and had 12 editions, eventually with 3 volumes in several parts.
Linnaeus' sampling of species was not broad - he traveled to Lapland France, and England.  His main experience was in botany and was able to look at samples in gardens which were a popular pursuit amongst wealthy hobbyists of the day and visited botanists in England and had samples from other continents.  He had heard about chimpanzees, but it doesn't seem as if he ever saw one.
Wikipedia gives a final count of nearly 10,000 species including over 7000 plants, from the entries in his works.  Linnaeus felt that there would be very few more to be discovered; he estimated 10,000 species of plants which turned out to be completely wrong.  The Encyclopedia of Life has 1,316,775 entries today.  This was probably perpetuated by the influence of Aristotelian thought, which persisted through Darwin's life, that species were only the result a higher reality creating animals attuned to a local climate and geography and so the same species would in the mountains of Scandinavia would be the same as the alpine regions of India say.  But even Aristotelianism, which stood  for over a millenium the 19th Century and Darwin's work, was probably more the result of confirmation bias than any real proof.

Thanks for the detailed answer.  However, you may not know, but Amazing Discoveries is actually a Christian site that makes dubious arguments about evolution elsewhere.  See e.g. http://amazingdiscoveries.org/C-deception-Creation_evolution_theory_compromise

@MatthewFlaschen whoops I guess I could use a different reference - it was unintentional.  I added the wikipedia reference.  I decided to keep the amazing discoveries link because in fairness, the page is pretty fair and credit is due for their good homework.

What's your source for Linnaeus thinking there would be only 10,000 species? Wikipedia (quoting Stearn) says 10,000 plant species. For comparison, EOL lists 250,000-380,000 plant entries.

Quite right - I changed my response.  I think the point still holds that Linneaus had no idea how diverse the biological world was, or really how species worked.

Complete agreement!

One comment on the dates for Systema Naturae: the first edition was published actually in 1935, while the first volume of the 10th edition (which is taken as the starting point for animal taxonomy) was issued in 1758.

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Do bacteria die of old age?
I know that the cells of mammals at least stop dividing when they are old, and then die a programmed cell death. Then other cells have to replace them.
But in a bacterial colony, each cell replicates for itself. Obviously, if a division of a bacterial cell of generation N were to produce two new cells of generation N+1, and all bacteria died of old age at generation M, there would be no bacteria left around.
So how is it regulated in bacteria? Are their divisions simply unlimited? Does a cell never die and just divide forever?

This is yeast, not bacteria, but very related to your question: http://www.pnas.org/content/109/13/4916.full

This is a interesting question and for a long time it was thought that they do not age. In the meantime there are some new papers which say that bacteria do indeed age.
Aging can be defined as the accumulation of non-genetic damages (for example oxidative damage to proteins) over time. If too much of these damages are accumulated, the cell will eventually die.
For bacteria there seems to be an interesting way around this. The second paper cited below found that bacteria do not divide symmetrically into two daughter cells, but seem to split into one cell which receives more damage and one which receives less. The latter one can be called rejuvenated and seems to make sure that the bacteria can seemingly divide forever. Using this strategy limits the non-genetic damage to relatively few cells (if you consider the doubling mechanism) which could eventually die to save the others.
Have a look at the following publications which go into detail (the first is a summary of the second but worth reading):

Do bacteria age? Biologists discover the answer follows simple
economics
Temporal Dynamics of Bacterial Aging and Rejuvenation
Aging and death in an organism that reproduces by morphologically
symmetric division.

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Is there a biological basis for different accents?
How did accents first develop? Was it climate dependent? or was it a social behavioural issue?
Is there any biological reason for the development of accents?

Your question is (badly) based on the assumption that there is something out there with no accent. EVERYONE has an accent, just like everyone has a fingerprint.

It has to do partly with brain wiring and partly with the mouth musculature, as nicely examplified by this: http://en.wikipedia.org/wiki/Foreign_accent_syndrome

A better question: "Is there a genetic basis for different accents?" Almost everything in biology has a biological reason.

Surely the evidence indicates that it is unlikely and that this is strictly nurture rather than nature? Take a kid from anywhere and raise them while they learn to speak and they will have the accent of those around them with exceptions being rare.

No. Accent is purely environmental. The ability to pick up the unique sounds of a language or variation of a language ceases around puberty: http://en.wikipedia.org/wiki/Language_acquisition
This is why adults learning a second language have trouble distinguishing the unique sounds of the second language. For learners of English, the "th" sounds and the difference between "l" and "r" can be difficult. For languages based on Sanskrit, there are a variety of aspirated/unaspirated consonants somewhere between "b" and "v" that English-speakers have a hard time distinguishing, much less imitating.


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What mechanisms tell temperate trees when to drop leaves?
I've been looking around and cannot find a definite answer on what it is that tells trees to change their metabolism and drop leaves. I see that such activity is called Deciduous.
What interests me are the specific mechanisms by which a tree knows that it's time to drop leaves. Is it photoperiod shortening (day duration?) Is it temperature changing metabolism? Is it build up of some toxic compound?
Thank you for your input!

For answers, also see the duplicate what is the mechanism behind plants losing their leaves?.

FYI: "Deciduous" is not the activity itself of losing leaves.  (The activity is called "abscission.")  Rather, "deciduous" is an adjective that describes the types of trees that display abscission.

Here is a good USDA link:
http://www.usna.usda.gov/PhotoGallery/FallFoliage/ScienceFallColor.html
It would appear that the shortening days are a main trigger, and there are other factors. I did a basic search using Google for "what triggers leaf fall in deciduous trees?", since I always thought temperature and changing seasons were major triggers and wanted to double check.


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Is there an instinct-driven body language for birds?
Over the last year or so, I've been observing house sparrows, because they are so prevalent in the northeast US cities. I noticed that a lot of sparrows, even in different cities seem to have very similar body language for communicating. I learned 3 expressions
Here's an example of a sparrow feeding their young. The young bird opens month and flickers its wings in what I can only describe as impatiently.
A sparrow swipes its beak along a surface at its feet - something food related?
A sparrow fluffs its feathers, turning into something like a tennis ball made of feathers.
I'm looking at this video of a sparrow raised in captivity, and it does 2 out of 3 expressions described here.
What interests me is if expressions like these are "local dialects" or universal, thus found across different geographies and times? for example, do sparrows in northeast US use the same expressions as sparrows in Australia? What about sparrows in the United Kingdom in the 1950s?

Cf this question: http://biology.stackexchange.com/questions/2463/is-there-such-thing-as-animal-non-verbal-body-language/2464#2464

In general, animal communication contains both "cultural" aspects and genetic components.
As you suggest, the cultural aspects vary more across geographies and times. The genetic components might vary as well, with genetic differences among different populations, but you'd expect them to be more conservative than the cultural aspects. To make the matter even more complex, if the communication behaviors affect mating; they could in turn have an effect on the genetic components!
This article describes birds raised in captivity that had "maladjusted" songs (which would support both genetic and cultural components), and North Carolina cowbirds raised by Texas parents who grew up with a Texas birdsong dialect (evidence for cultural components). Although the piece is mostly focused on song, I imagine the mechanisms would be similar for body language.

Full disclosure – the author of that linked article is my father.


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Do primates other than humans have a consistent sleep schedule?
I'm doing some sleep research and would like to compare a human sleep pattern as recorded by a wrist-based actigraph with a "natural" sleep pattern, such as from apes. In an experiment like that, a human wears an activity monitor on a non-dominant arm over multiple days. The monitor analyzes activity pattern and can detect when the user is asleep versus active.
Can someone suggest a research article or a website that did a sleep study of primates (monkeys/apes) either in captivity or natural habitat over multiple days?
I'm particularly interested in how consistent their bedtimes are - do primates go to sleep in the evening whenever they feel like, or do they stick to a more consistent sleep schedule?

Check out Sleep Architecture in Unrestrained Rhesus Monkeys (Macaca mulatta) Synchronized to 24-Hour Light-Dark Cycles.  From the abstract: "With minor exceptions, most notably a delay in peak delta activity, sleep-wake architecture, regulation, and consolidation in rhesus monkeys strongly resembles that of humans."


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Have there been attempts to identify Chomsky's "language mutation" in humans?
I'm not versed in either biology or linguistics so please forgive any naiveties I may commit.
I've learned that Noam Chomsky thinks that language is a result of a single genetic mutation in humans. It would be a mutation allowing the human brain to conceive of natural numbers as I understand. Have there been any (even speculative) attempts by biologists to locate that mutation in the human genome and/or in time? Is it even feasible?

It seems a very simplistic view. After all, spoken language relies on vocalization, which plenty of species have. On the other hand, sign language can be used for communication. There are also other types of non-verbal signaling in humans and other species. So what exactly is language?

@Lubo As far as I know, most linguists agree that no animal apart from humans has been observed to use language. Animal communication lacks certain characteristics they require in a language. I understand that what Chomsky considers the constituent characteristic of language is what he calls recursion.

Please add a link to source your statement of Chomsky's theory. I very much doubt he claimed it was a single mutation. That is very unlikely.

@terdon http://en.wikipedia.org/wiki/Origin_of_language#Approaches That's all I've got. I understand that Chomsky's view is not shared by most scholars.

@ymar Chomsky's linguistic theories are rather mainstream, and have biological implications, as I discuss in my answer. The claim about a single mutation or gene is however a rather singular one, devoid of serious scientific support.

may be helpful https://www.pnas.org/content/104/19/8184

The anthropologist Svante Pääbo is more recently famous for trying to track down the 'language gene'.  There isn't a lot of reference to Chomsky in his work as I've noticed, but it is to me the same intriguing idea.
That being that the chimpanzee and the bonobo have 99+% identical to human genome sequences and we also have data from human variations as well from a few thousand individuals.  Using this data you could try to evaluate a small list of differences which might have led to the inborn trait human beings have to acquire language.
Pääbo's work focused on FOXP2, which leads to language disorders in humans when it is damaged in human beings.  On the other hand its also known that primates can learn to speak rather well if they are trained their entire lives by the right people.  They can even reflect on abstract ideas such as life after death.  This is a typical result when looking for a single gene that causes something- it rarely leads to a conclusive result as a phenotype like verbality, or even height or body mass is the result of the action and fine tuning of many genes acting in concert.
That is, if you introduced human FoxP2 into transgenic chimps its unlikely that they would be as verbal as human beings.  This current reference for instance talks about how important the slower development rate for human children is.  This is one of the most unusual thing about human beings - it takes 1/3 to 1/5 of the human lifetime before we are fully mature.  This phenotype is incredibly unlikely to be the result of FoxP2 alone, or any single gene.
There has been recent work published (2012) where the unique human FOXP2 gene was put into transgenic mice.  They seem to have different sort of personality tendencies and are said to vocalize differently - brain activity profiles are also different.  Kinda exciting, but not the Secret of NIMH yet....

Thanks a lot! As for "rather well", that strongly depends on the expectations. If you watch Koko on Youtube (and there are plenty of videos), you can indeed see many surprisingly human-like behaviors, but I was disappointed but her "language" personally. Her trainer was very clearly not objective. When Koko said the wrong thing, she'd say things like, "Why are you joking Koko?" and repeat that until Koko said what she was expected to say. Koko was largely unaware of syntax -- word order was random.

@ymar yes well - Koko and any other animal (including parrots) trained to cognate can't seem to get past 3-5 year old level.  Another question that never seems to resolve.

To my knowledge, Chomsky does not claim that there is a specific gene or mutation responsible for the human linguistic abilities - at least not in strictly biological sense. The claims of Chomsky and his followers, known as generative grammar, are more general: the study and the comparison of many human languages have shown that all the languages are structured according to the same principles (as opposed to the earlier Sapir-Whorf hypothesis that languages are products of purely random evolution). This similarity is the basis for the Chomsky's claim that this language structure is likely hard-coded in the human brain. This is further supported by mathematical complexity arguments, showing that the language rules are too complex, and the variety of the possible phrases that one can produce is too large to be learned within a reasonable time, without having a prior model of how the langauge is structured.
Thus, the linguistic ability, like many other traits, is likely a result of many mutations and action (and interaction) of many genes. Note that this involves not only the mental abilities, but also purely physical capacity to produce wide range of sounds that many animals do not possess.
Remark: Noam Chomsky is a renowned mathematical linguist, chose theories of generative/transformational grammar are pretty much the basis of the modern mainstream linguistics, and play an important role in the modern computer science. Thus, these are not to be dismissed, unlike his more controversial political views, which are anything but mainstream.

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Is there such thing as Animal non-verbal body language?
Have there been any studies done on the animal use of their bodies to signal, communicate or express their emotions, particularly to members of other species (ex: humans)?
I've been observing a very intelligent indoor-outdoor cat who has been doing the same sideways stretching posture every day he met me. There has been a number of other postures that the cat has been using - tearing at a carpet with claws, or dragging himself against the carpet by using claws that I've repeatedly observed.

Another cat was thumping her head against a door to "knock" and indicate that the cat is outside.
To me, these gestures appeared as clear expressions of intent or emotional state.
Other experiment involved "trained" geese at a local pond who would indirectly approach humans to ask for food. Their body, neck and head position appear to indicate intent (is the animal grazing towards the human or away from the human).
Yet another experiment involves nesting birds who start to clearly express their displeasure at me located near their nesting area. They repeatedly produce high pitched screech until I move away.
For example I repeatedly see geese assume this gesture to intimidate other geese.

As a human, I'm very conditioned to vocal and eye related coordination, and this "non-verbal" language is fascinating to me.
Have there been any studies in how indoor/outdoor - partially domesticated animals communicate with humans?
Is it true that this communication uses their entire body and not just the vocal cords?
Is there some "foundation" language that would be similar among members of the same species, or is it entirely a learned skill that has nothing to do with evolutionary adaptation?
Finally, is there some sort of a brain complexity cut off at which level the animals can no longer understand if they are being communicated with?

My understanding (at least in dogs and cats) is: in absence of human contact, little of their communication is sound-based/verbal.  To this point, most dog-training programs I've seen use visual commands, and then once the dog starts to respond to them, voice commands are added simultaneously with visual command.  Getting the animal to respond solely to the voice command (in absence of any visual indicator) is the very last step in training.

Maybe this question could benefit from focussing a bit. As general as it is now, is there any doubt that the answer is “yes”?

The closest reason that I know of for such behaviour is simple conditioning!
B. F. Skinner conducted some fairly famous experiments with pigeons, where he put hungry pigeons in cages, and randomly administered the food. The pigeons associated the foods arrival with whatever they happened to be doing at the time (be it looking to the right, or bobbing their heads). They would then keep trying this until more food came out (randomly), and the pigeons 'superstition' was confirmed. See the wiki.
I realize this is not concrete, but it seems to me that they are not 'communicating' as such, they are simply repeating what has worked before. It is your anthropomorphication that has meant this seems like deliberate communication in my opinion. Although I'm sure it could be argued that all communication is having been 'conditioned' to use words/gestures to get your meaning across.

Update (14.6.12)
Just read the abstract for this paper (published yesterday) that finds that experts in dog behaviour can interpret the ('socially relevant') posture of a dog in a similar way to that of a human. We can therefore interpret the body language of an animal (in this case, dog), if we are familiar (you do not even have to have owned a dog necessarily) with the kinds of postures adopted. So the dog does not have to consciously 'communicate' for us to interpret their emotional state (happy/sad/angry/...).
In terms of human-pet communication then, there seems to be more emphasis on the human interpretation of the natural postures adopted by animals, than the animals themselves. Pets may behave very differently to animals in the wild, but it comes back to what the specific human is used to. If you have had a lot of contact with pet dogs you are in a better position to associate the current behaviour of a pet dog with the correct emotional state. No doubt the animal with subconsciously adjust their behaviour to achieve the 'correct' human interpretation, and thus get fed, or whatever.

Ah, so there's a cognitive bias on my part to see these gestures as an expression of language rather than simply repeating what has worked before. This makes a lot of sense!

Darwin wrote a classical book on the subject, The Expression of the Emotions in Man and [other] Animals. Among other things, he showed how opposite emotions cause opposite movements. For instance, when angry/about to attack, a dog will lower its tail, erect the hair close to the neck, move the ears back, etc. The ears back serve the purpose of protecting the ears from an adversary bite, the hair erected serve the purpose of scaring the adversary, making the animal look bigger than it really is. When happy/pleased, all signs are in the opposite direction: a dog will raise its tail, lower the hair close to the neck, move the ears to the front, etc.
Anolis and other lizards are also known for communicating visually. Anolis repeatedly extend and retract their colorful dewlaps in order to send messages to other members of the same species.
Apis bees, one of the most studied organisms, makes its famous waggle dance, where the distance, inclination and waggle intensity is proportional to the distance, direction and abundance of the food source informed to the other bees in the hive.
Some behaviors may be cultural, i.e., learned by an animal and passed through generations in its population. There's a great book on the subject, The Evolution of Culture in Animals, by John Tyler Bonner.
I think it was Jane Goodall, the woman who spent decades among the chimpanzees in Gombe, Tanzania, who told the story of a female chimpanzee who learned human sign language (not sure if that's on her marvelous book Through a Window). Not only she was able to create new words mixing what she already knew, but she also taught the language to her child, without the researchers telling her to do it.
So yes, there are LOTS of animal non-verbal body language, both innate and learned.
Talking about verbal language, I remember the two great groups of passerine birds: Oscines (or "Passeri") and Suboscines (or "Tyranni"). In the first, singing ability is mostly learned, while it seems to be mostly innate in the second. Here are some references.

Animals most definitely can communicate through body language! It sounds like you have a good idea of some methods through which they communicate easily noticeable to humans. To give you an interesting example I've been looking at recently is the idea of 'vigilance' in wild species such as impala, elephants and giraffe.
Mammals and birds are known to reduce the risk of predation by actively modifying behaviour to spend less time in vulnerable states that permit capture (Powell, 1974). The ‘group size effect’ is a well-documented phenomenon, whereby species in groups experience an improved predator detection rate, despite individually scanning less. This is more efficient as it allows more time for activities such as foraging and mating.
The problem here I've been looking at is how animals tell others in their groups whether a predator is approaching. So far from reading literature the key seems to be less with vocal cues, and more with 'posture' of the organism. Thus, the 'posture' of an animal in a group is a key way of communicating whether danger is approaching and the group members will respond appropriately.
It is important to remember is, like humans, few animals rely on one sense to communicate. This makes sense as certain conditions - such at night or when located far from others in the groups - they may still need to express information to others. These behaviour are largely innate (as far as I know), so they are not learned but rather 'automatically' engage in them.
I know this doesn't answer all your question but I hope it gives a bit of insight into communication in wild animals.

Welcome 2Bio.  References and sources are needed on a scientific stack. This looks more like an opinion.

Apologies, references will be added!


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Laying eggs vs giving birth: is there a connection with internal vs. external ears?
I have heard that "The animals who have their 'EARS' outside their body give birth to their young ones and the animals who have their 'EARS' inside their body lay eggs." Is this true? Are there counterexamples?

Just to expand on @rg255's very good answer, you could make the same sort of claim using just about any characteristic that is more commonly found in mammals.
Giving birth to live young is a characteristic of most (see the platypus below), if not all, mammals. Therefore, you could make the statement about external ears (also more common to mammals) using any other mammal specific body plan. For example:

"The animals who have their 'TESTICLES' outside their body give birth to their young ones and the animals who have their 'TESTICLES' inside their body lay eggs."

I am pretty sure you will find that this is as true as the statement about ears.
As in all other debates about this kind of thing, the platypus comes along and complicates things. This beastie has no external ears (or external testicles for that matter), it has tiny ear slits instead and it lays eggs. So, even this extreme weirdo seems to follow the ears (or testicles) on the inside means eggs rule. However, it is a mammal, it produces milk that it will feed to its newly hatched young like all mammals (well, almost, it doesn't have teats and instead the young suck up their mother's milk through her spongy belly).
A more straightforward and well known example that directly contradicts the ears claim is the dolphin. Dolphin ears are small holes on the sides of their heads but they give birth to live young as do all sea mammals. In fact, I am pretty sure that all sea mammals lack external ears (and cetaceans at least also lack external testicles) but give birth to live young. So seals, sea lions, walruses etc also contradict the ears rule.
In conclusion, no it is not true that all animals with internal ears lay eggs.

Actually there is a lot of variation in testes among mammals (descended vs. undescended, scrotal vs. astrotal): http://biology.stackexchange.com/questions/559/why-do-some-mammals-not-have-testes-in-a-scrotum

@kmm ah, but can you name an animal with external testes that lays eggs :) ? Anyway, that was just a tongue in cheek example to highlight the arbitrary nature of the distinction mentioned by the OP.

on a similar tongue in cheek note... I can't think of any animals with testes that lay eggs or have a pregnancy ;)

@GriffinEvo stretching the definition of having testes, the male angler fish will attach itself to the female and wither away leaving, essentially, only its gonads attached which the female will use to fertilize her eggs. Strictly speaking, at that point she has both testes of a sort and lays eggs :).

You are quoting from Imam Ali,

"The animals who have their 'EARS' outside their body give birth to
  their young ones and the animals who have their 'EARS' inside their
  body lay eggs."

And in short the answer is that is wrong. Giving birth to live young is called vivipary. When a species lays eggs it is called oviparity. There are other mechanisms too.

Ovuliparity: fecundation is external (in arthropods and fishes, most
  of frogs)
Oviparity: fecundation is internal, the female lays zygotes
  as eggs with important vitellus (typically birds)
Ovo-viviparity: or
  oviparity with retention of zygotes in the female’s body or in the
  male’s body, but there are no trophic interactions between zygote and
  parents. (Anguis fragilis is an example of ovo-viviparity.) In the sea
  horse, zygotes are retained in the male’s ventral "marsupium". In the
  frog Rhinoderma darwinii, the zygotes developed in the vocal sac. In
  the frog Rheobatrachus, zygotes developed in the stomach.
Histotrophic
  viviparity: the zygotes developed in the female’s oviducts, but find
  their nutriments by oophagy or adelphophagy (intra-uterine cannibalism
  in some sharks or in the black salamander Salamandra atra).
Hemotrophic viviparity: nutriments are provided by the female, often
  through placenta. In the frog Gastrotheca ovifera, embryos are fed by
  the mother through specialized gills. The lizard Pseudomoia
  pagenstecheri and most mammals exhibit a hemotrophic viviparity.

Though it is true that most typically we would associate egg laying with animals with ears "inside" such as birds and snakes, there are some examples that are not this way. Boa constrictors are one species which gives birth to live young rather than laying an egg and being a snake their ears are 'inside their body'. However I should point out that this is Ovoviviparity, not viviparity. For an example of a lizard with viviparity see the Pseudomoia lizard genus.

Good answer +1. Although there are some counterexamples, there is still quite a high correlation between having ears inside/outside and being oviparous or viviparous. So why is there a correlation? It is certainly only due to phylogenetic correlation. If one make a study and decorrelate the effect of phylogeny, he would, I guess, find out that there is no significant correlation between ears position and viviparity/oviparity.

@Remi.b I agree, it is likely just a correlational relationship, rather than causal, but perhaps environments/lifestyles where external ears are less useful (e.g. underwater for reduced drag) are also typically less favourable to the birth of live young. I can imagine a bird doesn't want ears because they cause drag and wants to lay eggs to reduce the time it spends carrying the weight of a chick(s) - I'd imagine a pregnant bird would suffer from the extra weight when trying to fly.

@GriffinEvo Kindly excuse me for though people liked your answer more than that of anyone else but may be because of my lack of knowledge, I found terdon answer rather good and easy to understand be to accepted.

Internal or external ears is Not Relavent to an animal giving birth or laying eggs...
Examples
Sea Lions - External Ears - Live Birth
Seal - Internal Ears - Live Birth
Sharks - Internal Ear - Eggs (Oviparous), Live Birth (Viviparious), and Egg cases in mothers womb hatch producing young that feed on siblings before a live birth (Ovoviviparious)
Dolphins - Internal Ears - Live Birth
Frogs - Have an external ear drum - Lay Eggs
Exhidna (mammal) - Internal Ears - Lay Eggs
There is no relation to animal ears being internal(inside)/external(outside) to laying eggs or giving live birth.
I am a Biologist having worked at with a large variety of animals (egg layers and live birth) for 14 years. Feel free to ask any questions you may have. And by all means please do your own research to see the information I've provided is accurate.
Great Inquary, I hear of lots of fun facts to remember things...some true,  some not
True Fact...
You can SEE a SEA Lions ears but
A SEALS ears are SEALED up


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Raphide toxicity in Pothos plant
Recently I found out that the common houseplant Pothos (Epipremnum aureum) is toxic to cats and dogs due to the presence of "insoluble raphides." I have a lot of these plants around my house and my cat drinks water from the vase that they are in (I put drinking water into the vase that he always drinks from). He doesn't chew the Pothos leaves, he only drinks the water, is it still dangerous? I tried several times to give him water in an ordinary bowl, but he prefers the water that's associated with the Pothos plant, so I thought that maybe the roots of the plant excrete something nutritious (but I guess that's not the case, apparently...).
Is it harmful for an animal (cat) to drink water that has a Pothos plant immersed in it?
Also, my other cat does chew on the Pothos leaves (he goes crazy for them). Is it possible to have immunity and not be affected by the toxic chemicals? I read that chewing is supposed to provoke stomach irritation, but I would think that if the cat that chews the leaves suffered from irritation he wouldn't keep getting excited about chewing the leaves...
So what is going on? Many thanks!

Perhaps someone else can answer this with more certainty, but I'd guess that because raphides are essentially sharp crystals that cause irritation-related symptoms, rather than toxic chemicals in the way one might usually think of them, that drinking the water wouldn't pose a problem (actually, I suppose the word "insoluble" might be a clue here). Raphides are defence against herbivory, and chewing raphide-containing leaves is what you want not to do (or not let your pets do).
Veterinary Toxicology p. 889 has more info.

"insoluble" is a big clue, I'm dense today. Thanks for the input and link.

I wasn't being sarcastic! I'm still trying to work out the whole soluble/insoluble fiber thing, myself.


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Online resources for entomology?
I'm going to teach a c ollege-level introductory entomology course soon, and I'm looking for free online entomology resources. Does anyone have any recommendations?
In particular I'm looking for phylogenetic resources, experiment ideas, images, topics, etc.
Ideally, I'd love to find a discussion forum consisting of other entomology instructors sharing their ideas.
Thank you!

The Entomological Society of America has dedicated page called Entomology Resources for Teachers, which might answer many of your questions. It compiles curated links to resources, universities,
Here are a couple of other entomological links/resources that I have saved from before:

Bugguide.net
Pictures, simple keys and taxonomical info. Also has a forum.
The Entomological Foundation: Education
Links, project ideas etc.
Kerbtier.de
Webpage on beetles found in Germny, but relevant for many European countries. Also has general pages on e.g. beetle morphology and a glossary that might be useful.


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Is chlorophyll living or non living?
Is chlorophyll living or non living, and after boiling the water out of a chlorophyll extract would it still live, as in would it still maintain its properties after re-adding liquid to the dried chlorophyll?
Thank you for any help.

Do you want to know about chlorophyl or about plants? Chlorophyl is just a chemical contained for instance in plant cells.

If you meant "chloroplasts" rather than "chlorophyl", there might be an interesting debate, cf. Richard Smith's answer here about cyanobacteria as being almost "free-living chloroplasts" http://biology.stackexchange.com/questions/2848/photosynthetic-pigments-vs-chloroplasts/2850#2850


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How to learn biomathematics?
I'm currently an undergraduate math student and researching on the internet I discover that exists an area called "biomathematics". Looks so interesting. They use the graph theory and topology to describe the cells and DNA structure. Was love at first sight, because I really love maths and biology.
I'm reading the book "Clinically Oriented Anatomy" of Keith L. Moore and "Essential Cells Biology" of Bruce Alberts, but I don't know if I'm doing right. If anyone know how to start to learn this science I would really appreciate it.

Moore is a human anatomy text and is unlikely to be helpful for Mathematical Biology (but a great book for human anatomy).

@kmm I don't know if is necessary to have some anatomy knowledge, because I think that is important to know where are located the parts of human body...

This is highly relevant: http://biology.stackexchange.com/questions/9102/suitable-introductory-book-on-bioinformatics-for-a-computer-scientist

MathsBio is quite a large field. It is an interdisciplinary branch having utility in a lot of branches in biology like biophysics, biomedical, genetics and molecular biology. Applied  Mathematics is generally used in modelling and understanding biological phenomena where we have to deal with large amount of data, for example the use of graph theory for analysing biochemical networks. Systems biology is an emerging field which uses a lot of mathematics.
You should pick a book depending on the field in which you want to use mathematics, though having knowledge of elementary biology is necessary. I am suggesting some books which cover wide application of mathematics in biology.
Mathematical Biology: I. An Introduction by JD Murray
For systems biology:
Mathematical Modelling in Systems Biology: An Introduction by Brian Ingalls

I have taken Brian Ingalls class.  It is largely mass action kinetics with some dynamical systems considerations as far as the mathematics goes.
In other words, it's largely systems of differential equations.

I took the General Chemistry class, because I want to have Biochemistry (have pre-requisites, Organic Chemistry I and II).

I second the suggestion of Murray's Mathematical biology - great introduction with large coverage.

I really like "A Biologist's Guide to Mathematical Modeling in Ecology and Evolution" by
Sarah P. Otto & Troy Day, although it's more specific to Biology and Evolution - which may have been the first field in biology to use mathematics.


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Lactose Intolerance
What nutrition is given to infants who are lactose intolerant? I understand, in today's day and that age we have non-lactose formula milk, but what happened, before lactose-free milk was created, to those who suffered from lactose intolerance (Native Americans, Asians, etc.)?

The lactose intolerance Wikipedia page explains the problem fairly well, so I'll refer you to that for a more detailed explanation.
Briefly, the most common cause of lactose intolerance is primary lactase deficiency, which affects the majority of the world's population. This only affects adults: the majority of people do not produce lactase as adults.

Congenital lactase deficiency, instead is a very rare, autosomal recessive genetic disorder that prevents lactase expression from birth.
  [...]
  Congenital lactase deficiency (CLD), where the production of lactase is inhibited from birth, can be dangerous in any society because of infants' nutritional reliance on human breast milk during their first months. Before the 20th century, babies born with CLD often did not survive, but death rates decreased with soybean-derived infant formulas and manufactured lactose-free dairy products. Beyond infancy, individuals affected by CLD usually have the same nutritional concerns as any lactose-intolerant adult.

A couple of good references:
Lactose intolerance in infants, children, and adolescents. - Heyman, Pediatrics 2006
Genetics of lactase persistence and lactose intolerance. - Swallow, Annu Rev Genet. 2003

To expand on the infant thing: lactose is present in most mammalian milk but mammals usually only consume milk as infants so there is no need to preserve functioning into adulthood. It's only our weird fondness for milking other animals that has led to selective pressure on retaining the necessary enzyme into adulthood.

In fact, being lactose tolerant is the mutation. Adult mammals are normally not lactose tolerant, only the still milk drinking babies have the lactose gene activated. Humans developed this mutation earliest in the Neolithic.

Lactase persistence (LP), the dominant Mendelian trait conferring the ability to digest the milk sugar lactose in adults, has risen to high frequency in central and northern Europeans in the last 20,000 years. This trait is likely to have conferred a selective advantage in individuals who consume appreciable amounts of unfermented milk.

(citation from Burger et al., PNAS, 2006)
So in fact, people who are lactose intolerant are just plain normal. There is normally no reason to feed babies lactose-free milk. The rare cases where you need to do this are very well described in the post of nico.


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What makes an animal/species suitable for domestication/training?
Humans have domesticated all manner of creatures during the course of their civilization - dogs, horses, several types of cattle, varieties of birds, and perhaps others too.
A prerequisite for an animal to be domesticated, obviously, is that there be some return from the animal voluntarily, or otherwise. For instance, milk from cows/buffalos.
What I'm looking for is an answer to the question what ... characteristics must an animal fulfil to be domesticated/trained. Docile is, perhaps, one characterstic. Amenable to training may be another. What other characteristics must be fulfilled before one would venture to consider training/domestication of another species?

The ability of an animal to be trained or domesticated appears to be genetic. A quick Google search revealed this Review: http://rspb.royalsocietypublishing.org/content/278/1722/3161.full.pdf


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How does Artificial Selection work?
As far as I know for evolution to work mutations  are necessary. Mutations are the raw material on which natural selection works.
But mutations are always completely random and human beings have no control over it.Then my question is how artificial selection works? Would it have been possible to domesticate dogs from wolves, if there would have been no mutations in wolves to begin with?

artificial selection != evolution.

I would even say evolution > selection

Both natural selection and artificial selection require genetic variation in the underlying population to work.  The exact source of this genetic variation is not particularly important theoretically.  In reality this genetic variation originally comes from mutations of various sorts (not just point mutations, but also duplications, recombinations, etc.).  If you had no genetic variation then artificial selection would not be effective.
You might be interested in Stephen Jay Gould's essay "A Dog's Life in Galton's Polyhedron" (found in the collection "Eight Little Piggies"), where he explains that domestic dogs have very little variation in skull length (relative to body size), but large variation in skull width.  It seems that it is very difficult to artificially select for dogs whose skull and body don't have the correct ratio, even though you can wildly change the sizes of dogs, the width of their skulls, the length of their legs, etc.

You seem to have a few different concepts in there...

But mutations are always completely random and human beings have no control over it.

Aside from the fact that mutations are not completely random (not always, at least), it is not true that humans have no control over them. Imagine you grow plants, and you start to cross those plants that have a larger stalk, allowing them to be more resistent to wind: you are effectively selecting a certain mutation. Surely, you cannot choose which specific sequence you want to mutate, but still you are enriching your population of plants with a specific mutation.
Nowadays of course you can specifically mutate the genome in the lab, but that is a different matter.

Would it have been possible to domesticate dogs from wolves, if there would have been no mutations in wolves to begin with?

Note that artificial selection has been used to generate the different breeds of dogs, by breeding animals with specific characters.
However, domestication is a different matter. Wolves and dogs are the same species (Canis lupus) and domestication is not strictly dependent on selective breeding. You can domesticate an adult animal without inducing mutations in its DNA. Probably epigenetics plays an important role there, and epigenetic patterns could possibly be transmitted to the offspring.
Of course, then you will use selective breeding to expand the domesticated population, and to select those traits you are interersted into. With artificial selection you are just selecting the mutations you want, the way you generate them is irrelevant to the matter: for instance you can irradiate plants to enhance mutation rate, and consequently the appearance of new favorable traits.

But imagine a hypothetical situation, where there is no mutation at all. Then can artificial selection work?

@user774025: well, no, but natural selection would not work either then...

even if there is no mutation, as long as there is variation within the population, selection (artificial or natural) will work

@Richard Smith: and how would you have variation without mutation?

Sex, recombination, viral introgression, etc. I interpreted the 'hypothetical situation' as there being no mutation happening now. In a hypothetical system where there was never any mutation, there could only be variation if you started with variation.

@Richard Smith: well, technically speaking those are examples of mutations, as you are changing the genome. Replication without some mutation would be some sort cloning. Anyway, it is not only an hypothetical situation, but an absurd one :) Point is: whether you are selecting mutations by natural selection, by looking at the phenotype or by inducing them in a lab, more or less specifically, the output is always the same.

@nico good point, I was thinking of a very narrow definition of mutation.

Accumulated mutations over generations will make up the genetic variation present in a population for a species. For example, wolves naturally had a certain amount of genetic variation, or diversity, before humans started domesticating wolves. They still do, but to a lesser extend now since their populations have decreased.
Artificial selection is different from natural selection in that is forced artificially by us, humans, upon a species, like wolves, to change the traits to our liking. The first few traits that were artificially selected from wolves were probably related to their behavior: being more submissive and less erratic in their behavior. Then different people started crossing different breeds with interesting traits to try and combine the desired traits into new breeds.
One of the consequences of such dramatic breeding efforts is a decrease in haplotype diversity in dog breeds and higher incidence of undesired diseases. That is, during the crossing of breeds, part of the natural variability in the original populations was lost, and the resulting breeds only had one identical haplotype (in both copies) for many areas of the genome where there used to be two distinct ones, and if that haplotype was bearing an allele for a recessive disease, it showed up in homozygosis. This is the reason why for many important species of plants and animals, there are efforts to try and keep the original wild populations alive, in case we need to draw from the genetic diversity when the domesticated breeds need more.


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Is there a name for this principle in biological contexts?
This is mostly a question about usage.
There is a probability-related idea that has been used in at least two biological contexts. The idea is that if something happened, it was probably likely to do so.
This has been used in discussions about evolution, in which it is said that while we have trouble imagining circumstances in which self-replicating forms arise, the odds were probably in favor of their emergence when it actually occurred. And in discussions of the existence of intelligent life--it may be prevalent if we make the somewhat natural assumption (among others) that our own emergence was not highly improbable, given the existence of a suitable planet and so on.
Is there a name for this principle? I am familiar with the idea in the context of probability but have thought of it as an 'argument from likelihood' in biology. Also if there is a good description of the idea in a biological context a reference would be appreciated.
The tag is a little arbitrary. Thanks for any suggestions.

conditional probability?

@memming: Almost, except that it's a fallacy. To say that condition X existed because if it did then conditional probability would give a simple explanation for Y is backwards. So the idea is related.

It may also be called as Idea of maximum parsimony. It is used in phylogenetics to construct phylogenetic trees which require the least number of evolutionary events.

Max. parsimony is essentially Occam's razor. Maybe that's the best we can do.

@daniel Yes. I just wanted to give a specific example

@memming's comment above is also right. Occam's razor would work if we could assume anything about initial conditions. Then conditional probability gives the simplest explanation.

The principle of least effort / path of least resistance fit pretty well: animals, people, and systems (like evolution or a mechanical system like a machine) will naturally choose the path of least resistance or effort. The principal applies to chemistry (low energy states) and physics (the path an electrical current takes) as well. Occam's Razor fits somewhat too in an abstract sense in that nature favors simple solutions over complex ones. You may find something in thermodynamics as well.


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How common is bacterial mediated transformation? In plants? In animal cells?
The most common method to transform plants is by soaking plant tissue in cultures of agrobacteria (this is not their current classification) which transfer DNA into the plants.
Is lateral gene transfer ability like this found a lot in nature?  Is agrobacterium tumificans especially good at this or is its use in plant genetics only because this strain is well studied?
Is a method like this used for animal cells at all?

An early report of conjugative transfer into mammalian cells (CHO cells) is:

Waters, VL (2001) Conjugation between bacterial and mammalian cells, Nat. Genet. 29: 375–376.

This work used the broad host range plasmid RK2 to mobilise shuttle vectors carrying selectable markers. To rule out transfection DNAse I was added (and in controls this was shown to block transfection by a large amount of vector DNA). In any case, the fact that the transfer of the vector required the presence of the mobilising plasmid is pretty strong evidence for a conjugative mechanism.
There is also more recent evidence for transfer into human cells via Type IV secretion systems: here is a recent example:

Fernandez-Gonzalez et al. (2011),Transfer of R388 Derivatives by a Pathogenesis-Associated Type IV Secretion System into both Bacteria and Human Cells. J Bacteriol 193: 6257-6265

And here is a recent review of the topic:

Llosa et al. (2012) New perspectives into bacterial DNA transfer to human cells Trends in Microbiology 20: 355-359.

In animal cells the process is called transfection, to differentiate from transformation which is the process by which cells become immortalized (cancerous). I'm mainly familiar with mammalian cells, and in these systems some reaction is required to open pores of some sort in the cell membrane to allow the genetic material to enter. Viruses can mediate cellular entry on their own, but I am unaware of any method that uses live bacteria (although this doesn't mean that some specialized method doesn't exist).


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How does plant grafting work?
Plant grafting is a process whereby a piece of one plant is inserted into another and results in a change of the original plant. For example, grafting a piece of a lemon tree into a bitter orange tree will cause that tree to produce lemons instead of oranges for the rest of its life.
How does this work? I mean, at the genetic level. I guess the grafted plant is now a chimera of some sort but if so

How does the grafted DNA affect the host cells?
Are all of the host's cells affected?
If we were to sequence the grafted tree which genome would we find?
Is it perhaps that the host DNA is not affected at all and the effects come via a change in expression levels? If that is the case I would assume grafting will only work between very closely related species. Is that so?

Basically I know very little about plant genetics and physiology. I remember from my undergraduate days that plant genetics are just plain weird. Most, if not all, have various levels of polyploidy. Is that relevant?

Surely the grafted part retains its genetic identity and grows normally (as "lemon" in your example) while the rest of the tree retains its "orange" identity. It is a chimaeric plant. You could think of it like an organ transplant in a mammal.

@AlanBoyd, yes I imagine it is chimerism of some sort. Yet you can take a normal bitter orange tree, cut off most of its branches (not even sure that is necessary) and graft a piece of lemon tree bark onto it. From that day on, the entire tree produces lemons, not oranges. So, somehow the grafted tissue is suppressing the original plant. Not what happens in an organ transplant.

This article analyses the exchange of DNA during the process of grafting
Exchange of Genetic Material Between Cells in Plant Tissue Grafts - Stegemann and Bock, Science 2009
Quoting from the article:

Although the grafted tissues fuse and establish vascular connections,
  the stock (the lower part of the graft) and scion (the upper part,
  usually supplying solely aerial parts to the graft) are thought not to
  exchange their genetic materials. But grafting (whether natural or
  assisted) provides a path for horizontal gene transfer. Gene transfer
  is confined to the graft site and no long-distance transfer may occur.
  Analyzes indicating that large DNA pieces or even entire plastid
  genomes are transferred. Only plastid genes may be transferred, no
  transfer of nuclear genes occur. Plant cells are connected via
  plasmatic bridges called plasmodesmata, but the passage of large
  macromolecules requires the action of specific plasmodesmata-widening
  proteins. Whether large DNA pieces or even entire organelles can
  travel through plasmodesmata requires further investigation.
Finally, although our data demonstrate the exchange of genetic
  material between grafted plants, they do not lend support to the tenet
  of Lysenkoism that “graft hybridization” would be analogous to sexual
  hybridization. Instead, our finding that gene transfer is restricted
  to the contact zone between scion and stock indicates that the changes
  can become heritable only via lateral shoot formation from the graft
  site. However, there is some reported evidence for heritable
  alterations induced by grafting and, in light of our findings,
  these cases certainly warrant detailed molecular investigation.

Wow, so you're teling me that the genes controlling fruiting are in the plastid genome?

NO. The stock and scion are not to exchange their genetic materials. Only in graft site and only in the plastid genome exchange are possible.

I'll read the article and get back to you, thanks.


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Why does the stomach ache if you take a brisk walk after lunch or dinner
After eating your lunch or dinner, if you take a brisk walk, most of the time your stomach aches. Why does that happen? What happens with respect to the body metabolism?

Maybe the acid can go to places through the sphincters (because you move) where the epithel is not accustomed to that kind of acids and then it hurts. And also there is more blood while you are digesting in the stomach and the inervation is more sensitive at that time. But I don't have any proof at my hands right now, so only a comment ;)

The reasons for Exercise-related Transient Abdominal Pain are unknown. The current theories are:

Irritation of the parietal peritoneum, a structure lining the abdominal wall as it rubs against the visceral peritoneum, which lies against it and over the top of the abdominal organs
Strain on the ligaments that suspend the abdominal organs (however somewhat unlikely as it occurs during swimming

It used to be thought that blood was diverted away from the diaphragm during exercise causing pain however that has been found to be incorrect.
See this link: http://www.ausport.gov.au/ais/nutrition/factsheets/hydration/cramps_and_stitch


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Does cooking or ripening reduce the concentration of solanine in nightshade?
I recall a story from one of my Botany professors where he encountered a woman picking Solanum dulcamara (nightshade) berries. When he asked her what she was doing with them, she responded that her husband had her make a pie from them every year.
As her husband was presumably still alive, and since I regard this particular professor as reliable, what would have removed enough solanine from the berries to avoid ill effects? Does the concentration decrease upon ripening, or would cooking destroy the toxin? Would that also be why we fry green tomatoes?
(As a disclaimer, no-one should eat plants that are known to be poisonous. Even though some people don't react to poison ivy, it is still a bad idea to rub it all over your body.)

Did you mean Solanum viride or Solanum viridifolium?

The common name is green nightshade. I am guessing viridi, but I will check in Flora of the Pacific Northwest.

Actually, it doesn't show either of those in my area. I don't have one to key out, but the illustration for S. dulcamara looks like the correct one.

If you ask Dr. Duke's phytochemical database, by far the most solanine is found in green potatoe fruits (their skin), with much less in leaves and tissues. Similar values are seen in green tomatoes, with dozens of mg per 100g fruit. There is no value for Solanum dulcamara (doesn't mean there is nothing in it) but it appears to have small quantities of atropine. Furthermore, Wikipedia gives for solanine a minimum toxically effective dose for humans of 200 mg---that's where dizzyness and dispnoe starts---, and gives for children a lethal amount of S. dulcamara of 30-40 unripe berries or less. The amount of solanine increases (in potato) when temperature goes up, because it is produced by plants as an antifungal against rot. Ripening in S. dulcamara and, as we know all ourselves, potato and tomato, destroys solanine, so fully ripe berries seem to be okay. Solanine does not degrade when cooked but is lost with the cooking water. For an account of solanine poisoning from potatoes see e.g. this free paper. Newer potato varieties have much less solanine than those from former times.
http://www.ars-grin.gov/duke/
http://de.wikipedia.org/wiki/Solanin
Know your databases!

The database link is good. My background is in taxonomy and phylogenetics, so I am at a loss for knowing where to look up things that are not gene/protein sequences or species identification. It is unfortunate that the evidence in the answer for reduced levels in nightshade after ripening is all implicit. I would have thought there would be some information about levels, or lack thereof in the ripe berries.

First of all there is no solanine in green tomato, there wasn't, and there never will be.

Steroidal glycoalkaloids (SGAs) extracted from tomato leaves and
  berries (Lycopersicon esculentum Mill.) were separated and identified
  using optimized reversed-phase liquid chromatography with electrospray
  ionization (ESI) and ion trap mass spectrometry (ITMS). The ESI source
  polarity and chromatographic conditions were evaluated. The ESI
  spectra contain valuable information, which includes the mass of SGAs,
  the mass of the aglycones, and several characteristic fragment ions.
  Cleavage at the interglycosidic bonds proximal to the aglycones is the
  most prominent process in the ESI process. A protonated molecule,
  [M+H]+, accompanied by a mixed adduct ion, [M+H+Na]2+, was observed
  for α-tomatine (i.e., m/z 1034.7 and 528.9) and dehydrotomatine (i.e.,
  m/z 1032.6 and 527.9) in positive ion mode spectra. The structures of
  these tomato glycoalkaloids were confirmed using tandem mass
  spectrometry. The identification of a new α-tomatine isomer
  glycoalkaloid, named filotomatine (MW 1033), which shares a common
  tetrasaccharide structure (i.e., lycotretraose) with α-tomatine and
  dehydrotomatine, and soladulcidine as an aglycone, is described for
  the first time. It occurs in significant amounts in the extracts of
  wild tomato foliage. Multistage mass spectrometry both of the
  protonated molecules and of the doubly charged ions was used for
  detailed structural elucidation of SGAs. Key fragmentations and
  regularities in fragmentation pathways are described and the
  fragmentation mechanisms involved are proposed.

2005 - Analysis of tomato glycoalkaloids by liquid chromatography coupled with electrospray ionization tandem mass spectrometry

Your bitter nightshade really has solanine content:

Alkaloids are well known for their antimicrobial activity. Though all
  natural alkaloids come from plants, not all plants produce alkaloids.
  Plants of the Solanaceae family are known for their high alkaloid
  content. Alkaloids are found in all plant parts like roots, stems,
  leaves, flowers, fruits and seeds. In the present study, those plant
  parts of Solanum dulcamara were selected which have been reported to
  produce a high content of a specific alkaloid: solanine (from unripe
  fruits), solasodine (from flowers) and β-solamarine (from roots).
  These alkaloids were extracted from various parts of S. dulcamara by
  well-established methods and were screened for their antibacterial
  activity. Human pathogenic bacteria, viz., Enterobacter aerogenes,
  Escherichia coli, Staphylococcus aureus, were selected for the study.
  All three alkaloids inhibited the growth of E. coli and S. aureus.
  However, no significant activity was observed against E. aerogenes.
  Minimum inhibitory concentration and minimum bactericidal
  concentration were also evaluated.

2009 - Biological activity of alkaloids from Solanum dulcamara L.

The glycoalkaloid content usually decrease by ripening, so that the animals can eat them safely and deliver the seeds. At least that's my observation. So there is a good chance that the ripe fruits are edible...
If they are not, it is hard to get rid of the solanine. Solanine is heat stable it decomposes over 200°C (about 240-260°C afaik) and it is not (poorly) water soluble. So cooking in hot water does not help.

Reduction in concentration of α-chaconine (CHA) and α-solanine (SOL),
  toxic glycoalkaloids in potatoes, during cooking by 3 procedures was
  investigated. Raw or cooked potato samples (2 g) were extracted twice
  with 5% acetic acid solution. The extract was purified on Sep-Pak C18
  and CHA and SOL contents were determined by HPLC. Recoveries of CHA
  and SOL from raw potatoes were 96.5 and 98.2%, respectively, vs. 96.2
  and 96.7% from cooked potatoes. >93.9% of CHA and 95.9% of SOL
  remained in potatoes after boiling. Contents of both were reduced by
  15% on microwave treatment. On deep-frying alkaloid contents varied
  according to temperature. At 157°C, both alkaloids were unaffected; at
  170°, potatoes showed a large variation in residual alkaloids. At
  210°, alkaloids were partially decomposed; after 10 min heating, 64.9%
  of CHA and 59.7% of SOL remained. It is suggested that the critical
  temperature for decomposition of both alkaloids in potatoes may be
  around 170°. Results confirmed the relatively high stability of CHA
  and SOL in potatoes under normal home cooking conditions.

1990 - Effect of cooking on contents of α-chaconine and α-solanine in potatoes.

Deep frying over 200 °C might help, because it degrades the glycoalkaloids and probably moves them from the fruits to the oil, but be aware that this is an old article... Teflon will burn over 270°C afaik, and you should check the smoke point of the oil, because most of them have in a range of 150°C to 250°C. I guess there are other methods which I don't know of, but I think you don't want to eat that pie... ;-)


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Goats are so fearless but sheep are not. Is there any genetic difference responsible?

As you see in the picture goats (not only wild goats) are so fearless, but I never saw any sheep do this. What is the source of this difference in behavior?

How is this getting so many up-votes?  No offense to the OP but do we really feel that this question shows research effort?

Perspective update: Are they fearless, though? Or just desperate to escape from a predator (i.e. fearful)? Perhaps they are not so brave as they are naive; having never experienced, or witnessed, the perils of a fall? Perhaps they are just following the brave/naive "leader goat" (to the right). I would be cautious in using the word "fearless"... some background reading, as recommended by @KennyPeanuts, would be nice.

Obviously there are genetic differences. What other possible explanation could there be? If you're asking what genes are involved in the differences, no one has any idea which thousand of the tens of thousands of genetic differences are responsible for this complex behavior.

But there must be some previous scientific attempts to answer this or part of this question

1. Sheep are fearless

2. English common names are misleading when it comes to the genetic differences between goats and sheep
You posted a picture of Mountain Goats (Oreamnos americanus), which are a different genus than Domestic Goats (Capra aegagrus). Both Capra and Oreamnos are members of the Subfamily Caprinae, as are Domestic Sheep (Ovis aries).
Within Caprinae, Capra and Ovis are actually more related to each other than either one is to Oreamnos, despite the confusing way that we parcel out English common names. Oreamnos is, in fact, more closely related to the Musk Ox! (Here's the Tree of Life page that shows the phylogeny of Caprinae).
The Domestic Sheep genus Ovis also includes mountain species such as the Bighorn Sheep Ovis canadensis, which is plenty fearless. See the Bighorn Sheep above, and in this incredible photo. For what it's worth, the Domestic Goat genus Capra also includes cool mountain species, such as the Ibex.
Edit: the differences in behaviour between the domestic goat and sheep would be a combination of the initial differences between wild Ovis and Capra and the coevolutionary process of domestication; where humans shape niches to fit animals and animals to fit niches. It's possible that there has been more neotenization in the domestication of sheep, in which individuals who show immature characteristics are successfully selected for. See also this other question on apple and pear domestication.

(Bighorn Sheep photo by TwelveX, used under CC BY-NC-SA license.)

@MySky the fearless and awesome Urial Sheep (Ovis orientalis vignei) should be near you! At least, Wikipedia says it lives in the mountains of NE Iran.

Beautiful answer.

You are right. what about differences between domestic goat and sheep. Which genetic difference leads to difference in behaviors (not abilities).

@MySky I've added a paragraph about the differences between domestic goats and sheep.

You should also bear in mind that the fact that they are great climbers does not make them fearless. For example, if I were to find myself floating 500 meters above the ground, I would be terrified. The fact that birds do not appear to be scared in the same situation does not make them fearless, it just makes them fliers.
Similarly, I am sure a fish would be terrified if forced to spend half an hour in a beach bar. I, on the other hand, would find it enjoyable and not scary at all. It does not mean I am fearless or brave. You can only be brave when you ignore your fears not when you have none. Since mountain goats are exquisitely suited to jumping around on sheer mountain cliffs, it probably causes them no more fear than visiting a beach bar would cause me.


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What are the physiological effects of wine?
I have read that alcohol in general and wine in particular can have advantageous as well as detrimental effects on human health. Is this true? What are the physiological effects of consuming wine in moderate quantities?

Are you asking for physiological benefits of alcohol? If so, then it's probably worth editing your question to reflect that. I doubt biology has anything to say about gambling or sin.

Hello Kevin, I am Asking benefits and Disadvantages of Wine (Not only its alcohol, maybe it have some thing else, I dont Know)

I think you should limit your question to the wine aspect. There are certainly answers for that part of the question.

So please edit it. maybe you do better

In it's current shape I'm downvoting this due to lack of research effort and the inclusion of a, to be honest, entirely irrelevant religious verse detracting from your question.

@MySky It's your question, not mine.

I think maybe you can edit it better. I am not native

Dear Rory, I am abiologist and also a beliver. I like Know more in both directions. it is not a relegious question, it is really a biological concern for me.

I have completely rewritten the question to focus on the biological aspects alone. @MySky, I hope you don't take offense but as written your question would soon have been closed.

It is maybe better

There are two components to wine: 1) alcohol, 2) the remains of grape. And regarding these two, there exist pretty definite answers: 1) alcohol brings destruction to body system on multiple levels 2) the residue that's left from the source grape (particularly, its seeds) is what grants wine its useful properties. The same and even more useful effect can be acheived by simply eating raw grape with seeds, crunching them, without any alcohol.

It is undisputed that heavy alcohol consumption (of any variety) leads to many deleterious effects on health.
It has also been claimed, however, that low to moderate alcohol intake can in fact be protective against some medical conditions (in particular, cardiovascular and cerebrovascular events). That is, there is often said to be a 'j-shaped' curve relating alcohol consumption to mortality and morbidity: low to moderate intake actually slightly reduces risk of adverse events relative to people who abstain completely from alcohol, but the risk increases markedly as consumption becomes heavy. See Plunk et al (2014): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3872245/
Sometimes the protective association is attributed to the alcohol content itself (i.e. the ethanol), and sometimes to non-alcohol compounds (often specifically those found in red wine). The existence of such a possible protective effect at moderate doses is not a controversial position but it is also not settled science as yet. You should make up your own mind by reading reviews and ideally meta-analyses in the area. As a starting point, this 2013 review by Chiva-Blanch et al. in the journal Alcohol & Alcoholism has been well-cited by other researchers and is available to read in full here: https://academic.oup.com/alcalc/article/48/3/270/244770


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Interdependency between organsims on our planet and its relation to ecosystem?
I am not a biologist but I just wonder if all species are interdependent. I mean if the tiger becomes extinct does it affect the ecosystem? If the mosquito or mouse become extinct does it affect the environment and us?
I am asking because this question was raised by one of my friends when I was in favor of protecting tigers, lions but I had no answer to "tiger extinction will not affect humans".
So, is it true that the extinction of any species will affect all other species?

The problem is not really that we don't understand some stuff (lthough this is certainly true) but that an ecosystem, or the biosphere is a highly complex network of interactions. This network is continuously displaying some chaotic (determinist but not foreseeable) behavior. In such a system it becomes very hard or practically impossible to predict what the impact of a change (even a minor one) might be. To illustrate, one could say that killing half of the world's lions might cause the population of rabbits in Norway (!) to increase but killing two thirds might cause the same population of rabbits to decrease. Note: Stuart Kauffman wrote some articles where he argues that life is a system which is always balancing between chaotic dynamic and non-chaotic dynamic. Today, many conservation biologists use the tools of graph theory (network analysis) in order to get a better understanding of how things are influenced by a minor change.
But defending an endangered species like the pandas or elephants is certainly much more a matter of ethics than of human security faced with environmental shifts. I would guess (a reference on how the world's money is spent on conservation action would be interesting) that an important part of the money  spent on programs for the defense of endangered species are for ethical reasons, just because these species are big, clever, sing well or display nice colors.
There are many false reasons in ecology (in the political sense of the word) where people act for their ethics rather than to defend humans from environmental change. (I don't mean that ethics is stupid, or that only defending the environment for the benefit of the human species should be considered). You may already have heard "the amazonian forest is the lung of our planet" suggesting that this forest produces lots of $O_2$. This is completely wrong! Cutting down this forest would not change much in terms of either $O_2$ or $CO_2$ levels (except if the wood is burned!).
So to summarize I would say:

We spend quite a lot of money defending species for ethical reasons rather than to protect humans from environmental shifts.
Changing a little thing might affect the world-wide biosphere in a way that is practically impossible to predict.

Could you elaborate on your point about the amazon? While it is probably true that little of the world's oxygen comes from the Amazon, your sentence seems to be equating O2 to CO2.

@terdon I have no reference for the following! The amazon forest is an ecosystem that reached its climax, meaning that trees are not growing more that what they're dying. Or in other words, trees don't fix more CO2 than what they free up to the atmosphere. So yes, $V_{CO2}=V_{O2}$ in the amazon. Therefore, in terms of CO2 there is no cost of cutting down this forest (except for the fuel to be consumed for the work and except if the wood got burnt). And globally speaking, indeed most of the oxygen is produced of several species of plankton.

I know, my point is that your phrasing is confusing: "Cutting forest != decrease in $O_2$, therefore no difference in $CO_2$ production. I have edited to show what I mean.

Remi.b's answer is spot on - predicting the effects of losing a given species is nigh on impossible. However, I do think that there are some general trends that can give us some intuition, and make the campaign to protect certain species more than just an ethical issue.
Biodiversity (i.e. having a wide range of different organisms (and genetically diverse organisms)) has a number of potential benefits (for references see the work of David Tilman, among others):

Improved resilience to catastrophic events.
Improved temporal stability of populations within an ecosystem (which kind of dovetails with (1))
Improved ecosystem productivity (this has mostly been studied in terms of the amount of biomass grown by plants in an ecosystem, but may generalize to other kinds of ecosystem functioning)

Ecosystem services are effects that various ecosystems have on the world that makes it more hospitable to humans. While some may be, as Remi.b suggested, overhyped, some are very real, such as bioremediation (the removal of compounds toxic to humans from the air and water), the continued presence of pollinators and nutrient-rich soil in which to grow crops, and carbon sequestration. Given that the continuation of these ecosystem services is necessary for our long-term survival as a species, it is in our interest to ensure that ecosystems remain intact to provide them. Increasing resilience and temporal stability of ecosystems reduces the chance that we will lose ecosystems and the services they provide. Increasing the productivity of an ecosystem in many cases increases the extent to which it can perform that service (this is most obvious in the case of carbon sequestration). (NOTE: I'm phrasing this all in terms of human survival because I think that's the most clear cut argument. I think there are other arguments, but they're murkier)
Of course, this raises the question of how much of an impact the loss of a single species (such as a tiger) is likely to have on the benefits associated with biodiversity. There are a few hypotheses here, but in any specific case the impacts will be fairly dependent on the role of the extinct species in the ecosystem. The loss of some species (keystone species) will have a disproportionate impact on the rest of the environment. While it is hard to predict which species will turn out to be keystone species until it is too late, apex predators (like tigers) are more likely than average to be keystone species, or to have an important but not disproportionate role in the ecosystem. This makes sense, because such predators are fairly often the only species at their trophic level in an ecosystem, and having more trophic levels dramatically increases the biodiversity possible in an ecosystem.
Even if there isn't reason to think that a certain species is relatively important to an environment, there can sometimes be benefit in trying to save it via what's called "the umbrella effect." This boils down to the idea that saving one species generally involves saving the rest of the ecosystem that it lives in. So sometimes, from a funding perspective, it makes the most sense to choose the most charismatic species from a given ecosystem and attempt to get public investment in saving that species. An attempt to save this species can then result in preserving a great deal of biodiversity in the rest of the ecosystem.
So, ultimately, no, we cannot know how important a given organism is to an ecosystem or to human well-being. But we can make some fairly well-informed guesses.

+1 Indeed the notion of resilience is important to add to this discussion. The danger does not only come from in unpredictable ways which is what my answer suggested.


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Can an insect poison itself with food?
Is it possible that an insect poisons itself while eating "wrong" plants/fruits/... and have symptoms like pain (may hard to measure or detect) or orientation disorder?
Background:
I observed a physically apparently healthy caterpillar moving in circles (or rather changing its direction constantly and end up at the same point again) on the street and falling over in middle of moving or standing. My first and a bit naive thought was, that it may have eaten something wrong...

this sounds like a parasite.  http://en.wikipedia.org/wiki/Behavior-altering_parasites_and_parasitoids

Indeed, many plants produce molecules which are poisonous to things that eat that plant (insect, mammal, bird) in the "hopes" of preventing that animal from eating them. In this sense, even eating the "right" fruit may be dangerous (if that individual plant happens to be an exceptionally vigorous producer of the poison, or because the eater is weakened for some other reason, or simply ate too much). I doubt insects would eat the wrong fruit that much, because evolution favors insects that can precisely recognize correct prey plants, at least in indigenous surroundings.
Indeed, many plant "flavors" that we humans enjoy (such as garlic and peppers) are likely such herbivore poisons that we happen to be immune to. In fact, almost every plant is actually poisonous - the question is, poisonous to which species?
Plant defense is a very actively researched topic these days, since it relates to things like agricultural efficiency and global food shortages (and besides, it's a very interesting phenomenon). Here is a review discussing what you ask about in more detail: http://www.plantphysiology.org/content/121/2/325.full
An addendum upon reading this question many months later: While evolution has perfected the ability of insects to recognize correct food, this has not been the case for man-made pesticides. I would guess that the caterpillar you saw is more likely to have eaten an artificial chemical (either pesticide or pollutant) than a "wrong fruit".

The article is really interesting, but explains more the plants point of view. I was a bit more interested on the actual affect of poison on insects.

@Zwie Here's another one: http://www.ncbi.nlm.nih.gov/pubmed/12179963

Caffeine is also one such toxin. A neurotoxin in insects...


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Resource plant anatomy/lifecycle vocabulary
I've been curious about a lot of vocabulary words in the world of botany. I've had quite a bit  of trouble finding somewhere online to help me out, but I'm having some trouble finding a resource like that.
Optimally, I'm looking for something with diagrams of anatomy, over the course of time, maybe some photo examples, and some sort of dictionary to accompany. Is there anything like this, online or offline that anyone knows about?

Re-reading your question, I realize my answers below may be too general. Are you looking for a resource specifically about ontogeny, for example seed>seedling>adult anatomy?

I mostly wanted to know what parts of the plant are being affected by different things. For example, I have some apple seedlings that had a problem up to the ridge where the cotyledon stopped and the rest of the plant started, is there a name for that, if so, what is it?

I imagine there are resources targeted specifically to growers, and that the folks in the Gardening SE would be better positioned to tell you about them. However, I've also added one more resource to my answer below that may help.

I find that the folks at Gardening SE are incredibly knowledgeable, but aren't exactly botanists... I like both sides and was curious what to ask perhaps a botany professor. Thank you for your answer! I think that book looks good.

specifically development-focused
An Introduction to Plant Structure and Development by Beck looks comprehensive and has been well-reviewed. It has both photos and diagrams, and sections certainly deal specifically with growth/lifecycle. It's available to preview or purchase as an ebook on Google Play.
more general plant anatomy vocabulary resources
In print, Plant Identification Terminology: an illustrated glossary by Harris and Harris is a fairly standard reference, and I've found it very useful both for looking up terms and for just flipping through.
Online, but with fewer diagrams, you could try the Glossary page on the Angiosperm Phylogeny Website.
This might sound silly, but if you're looking for more of a course on the fundamentals rather than a dictionary of the specifics, the Botany Coloring Book is actually a great, seriously useful work.


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Does artificial high intensity light damage permanently dark ecosystems?
Popular science features on wildlife typically capture camera images using natural light, or high-speed exposures. This is not possible where the ambient light is extremely poor.
E.g. Caves, Undersea
For beings accustomed to the stygian dark, the high illumination for a video camera and/or the flash of a still camera could both be the equivalent of a 1" spanner wallop on the head or worse. Do we, inadvertently, injure the local ecosystem this way?

Yes, it's possible to damage dark-adapted ecosystems this way, and there are at least a few examples of it happening:

Deep sea Norwegian Lobsters were blinded by being brought to the surface as bycatch by fishermen (or by scientists tagging them). The original paper is Loew 1976, a more recent paper (Chapman et al. 2000) suggests that even a <1 minute light exposure could cause significant harm, which suggests a camera flash could certainly have an effect.
There is evidence that shrimp that live by deep-sea hydrothermal vents have been blinded by the floodlights of exploratory vehicles (Herring et al. 1999).

Chapman, CJ et al. (2000). Survival and growth of the Norway lobster Nephrops norvegicus in relation to light-induced eye damage. Marine Biology 136:233-241 doi:10.1007/s002270050681
Herring, PJ et al. (1999). Are vent shrimps blinded by science? Nature 398:116 doi:10.1038/18142
Loew, ER (1976). Light, and Photoreceptor Degeneration in the Norway Lobster, Nephrops norvegicus (L.) Proceedings of the Royal Society of London. Series B, Biological Sciences 193:31-44

(turned comments by me and @KennyPeanuts into an answer)

Is it known if the blinding is permanent?

Interestingly enough, Chapman et al. 2000 say that for the lobsters, the blinding is permanent, but doesn't seem to be related to growth/survival!

I don't know how harmful the exposure to a camera flash could be to organisms that live in complete darkness. However, since the animals that live in this conditions are usually blind, and the time of exposure is quite short, it's reasonable to assume that the damage produced should be minimal.
In the case of caves, permanent artificial illumination is very destructive to the environment, but the effect is due mainly to temperature changes and the introduction of organisms coming from more illuminated parts of the cave (cave organisms are usually slow and react poorly to light, so they are an easy prey if they're under light). In fact, for tourist activity, the use of lanterns or miner helmets is highly recommended.
In the case of abyssal ecosystems, ecological invasions are less likely, since there still exist a vertical barrier based in temperature, oxygen and carbon dioxide concentration and pressure. However, in this ecosystems there exist many animals which are very sensitive to light, due to the prominence of bioluminescence. Some of this animals could be damaged by the kind of light you describe. However, it's very unlikely that the main functioning of this ecosystems could be affected because of its extensive size. Moreover, the low population densities it has implies that even very long submersions would encounter only a few samples (with the exception of volcanic vents and some other geological curiosities which, in fact, are even more isolated from the rest of the biosphere by physical and chemical barriers), so the global effect should be negligible.


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Is territoriality only the domain of the male of a species?
Is territoriality (recognizing a geographic location, and challenging another member of the same species and gender) only in the domain of the male of a species? Are there any species out there where the female of the species identifies, defines, and protects her territory? What about any species where territoriality is gender neutral (tic humans excluded!)?
I thought of bees, but that is a community affair - even if it is a matriarchial society.

From personal observation: house sparrows "stake a claim" at a bird feeder, and both males and females chase away competitors

Absolutely not.  In many spiders and insects, the female holds the territory.  Many spiders for instance have much larger females than males - in these species the female can be > 10x bigger than the male and the male may not even eat during its lifetime.
Ordinary garden orb weaving spiders are this sort of animal.  Only the females even spin webs.
Another example is the Australian red back spider.
Quite often males are the 'disposable sex'.

Both sexes of red squirrels defend exclusive year round territories.
See Smith 1968 or Steele 1998.

The elephant matriarch (in Africa) leads her followers where they go for food and water.


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Can the body of any organism on Earth live without impairment both in vacuum, and within Earth's atmosphere?
I know from reading that a human in vacuum needs a space-suit to survive.
Is the body of any organism on Earth capable of living equally in vacuum, and on/below Earth's surface within the atmosphere?

I think this is more of a physics question than biology.

Any body?  As in you're looking for an organism that is capable of surviving in a vacuum and with an atmosphere or you're looking for Chuck Norris?  Assuming not the latter , google suggests this but it's an unreferenced Wiki point :/

On what's surface?

Yeah, what do you mean by 'on its surface'?

Why the negative vote?

I didn't downvote, but people did because your question in its original formulation made no sense.

I'd like to add that most of the answers here have the organisms in hibernated forms.  I think there is a fungus that was growing in the space station, but I'm not sure anything on earth is functional in the vacuum of space, only hibernating... anyone?

Remarkably, Tardigrades are multi-cellular animals which can survive the vacuum of space.

I even think NASA sent a few of them up to space, brought them back to earth and awakened them...

"Tardigrades" are basically the answer to every biology question which begins with "can any animal...", aren't they?

And they're so cute too! http://cdn.zmescience.com/wp-content/uploads/2013/12/tardigrades-electronmiscroppe.jpg

Adding to Noah's answer, some lichens can survive the vacuum of space too. In an experiment led by Leopoldo Sancho from the Complutense University of Madrid, two species of lichen - Rhizocarpon geographicum and Xanthoria elegans - were sealed in a capsule and launched on a Russian Soyuz rocket on 31 May 2005. The lichens were in perfect condition when observed after the return to earth.


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Scientific name for the union point of a plant stem and root
Is there a word that describes the meeting point of a plants growing stem and its root?
Is this the same term for aerial roots above soil level?

From Basconsuelo et al 2002:
"The zone of the plant axis where the arrangement of vascular systems changes from root- to stem-structure is often called “transition region”" (see also the refs they cite).
The idea behind it is that the organization of the vascular tissues is radically different in the root in comparison to the stem, such that the switch cannot occur in one point. This transition region (in general case) crosses the air-ground interface.


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Measuring fitness / lifetime reproductive success (LRS) in Drosophila
I am planning a fitness assay of Drosophila melanogaster. I'd like to get a good measure of lifetime reproductive success (lrs) but I don't want to count all the offspring produced over a lifetime by 100's of focal flies. The solution I am toying with is to count offspring production over the first few days or weeks. But before I commit to this I need to know if there is existing research material on the following:
Does early reproductive output correlate well with lrs? (this could be a low correlation if a fly trades early-life offspring production for late-life offspring production)
How much of a fly's reproductive output does one need to count before they have a good estimator of lrs? (does counting the offspring produced in the first day of life correlate well to overall lrs or do I need to count more - 5 days, 10 days, 50 days...)

Just finished an experiment (yesterday) where I measured lifetime reproductive success (LRS) of a few hundred flies, with measures taken from 24 hours of production every 7 days over the entire life of the fly. From this I can now answer the question.
Correlations of time interval to total offspring production (reproductive success [RS]):

Correlation of Week 1 RS         with Total LRS:    $\rho $ ~ 0.7
Correlation of Week 1 + 2 RS     with Total LRS:    $\rho $ ~ 0.9
Correlation of Week 1,2 +3 RS    with Total LRS:    $\rho $ > 0.9
Correlation of Week 1,2,3 + 4 RS with Total LRS:    $\rho $ > 0.95

Approximate conclusion (at least from my data - it may vary depending on experimental conditions and specific flies) is that LRS can be well estimated by measuring three to four weekly intervals.

I haven't done LRS but I don't see a reason why you couldn't make that measurement over only a few days, if you keep this method consistent through out all your populations. Just as a control you might have to do a complete LRS to see if you get any patterns in their egg laying behaviour, which I assume/believe is a decreasing pattern over time but just check the pattern of your WT and make sure your food is the same throughout all your experiments as changes in yeast % can completely distort your results as fly lay eggs like crazy when given yeast!! so use the same batch of fly food.
Although I'm no expert at this, if you look at female ovaries and do some molecular/phenotypic characterisations, you might get some interesting data if you are already observing a huge difference between your populations although you would have to look at the literature for this but having played around with these stuff a little, you find a surprising amount of data! This is in a way nice since you take the males out of the equation as the reproductive fitness could be compromised by either males or females in a population. To determine this you need to cross the males and females of your population of interest to WT flies and count the embryos (although this is slightly dangerous since if males are not performing well, females can lay lots of unfertilised eggs, blanks, and they are indistinguishable from fertilised egg so maybe count the hatched offspring and immediately discard them although that presents its own set of challenges and variables and to be honest its not likely to happen since you usually get this blanks in virgin females that have not yet courtshiped). If you observe lets say no changes in embryo numbers when your male populations are crossed to WT females but significant changes when females are crossed to the WT males, you would know the problem is with the males in your population.
Hope this helps!
EDIT: So I looked a bit further into this and came across this paper (http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0024560). If you look at Fig 6, I think it answers your question. I'm basically quoting the paper here. They measured the correlations between adult LRS and cumulative and short-time measures of fecundity and offspring production. Correlations of the short-time measures of fecundity and offspring production with adult LRS were highly dependent on the time of measurement. For young females the correlations were low, but when measured from older females, the correlations were much higher (up to 0.67 for short-time fecundity and 0.83 for short-time offspring production). For both short-time fecundity and short-time offspring production the highest correlations with adult LRS were reached when the female age was about 50 to 80 days. The length of the time frame had only a minor effect: the correlation of the 10-day measure with adult LRS was generally only slightly higher than that of the 2-day measure. The short-time measures performed well in comparison to the cumulative measures of fecundity and offspring production. So in short if you let your females age a bit and measure their fecundity, then it should be representative of their LRS.

Just edited the answer so hopefully thats more helpful.