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X chromosome "weight"?
According to Wikipedia, the X chromosome has approximately 153 million base pairs, while the Y chromosome has only 60 million base pairs. Thus, the difference is roughly 93 million base pairs.
My question is: Could this "extra" 93 million base pairs in virtually every single female cell of the human body slightly contribute to the "extra" relative weight of the female as a whole, in comparison to a male (of course) with a similar amount of cells? Or would this weight be so small that we can consider it negligible?

Theoretically...
93 million bp/cell x 650 daltons/bp x 10^13 cells/body x 1.66 * 10^-27 kg/dalton = 0.001 kg
So I would say it's not too much of a difference :P
however this ignores the rest of the chromosomal material: histones

Not too much of a difference, but it's something! Thanks.

Girls take note, this is not a valid excuse. Seriously though, this difference is exploited in some (albeit minimally effective)  techniques to sort sperm for gender selection.

Yep. Believe it or not, X sperm swim slower than Y sperm.

So, what is the difference in weight between X and Y sperm?

Very small. Using the same method as above yields an answer of around 0.1 picograms.

@ bobtheowl2, @ jp89: Could you provide some reference for the sorting procedure?

Is that difference due to the weight or rather the metabolism of the sperm due to having a different sized genome?

Hmmm, is it really true that Y sperm swim faster? If that were the case, you would expect that there be more men than women.

And indeed we do see such an imbalance. There are more male conception to female conception. Estimated 160 male conceptions to 100 female. There are 107 male birth to 100 female birth. But you can see males are losing individuals due to spontaneous abortions. This comes from males have only one X chromosome. A bad copy of a ChrX gene and you die if you are male.


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Is there a cheap and easy way to check for potentially unsafe UV exposure?
My lab has an older large Fotodyne tabletop UV transilluminator for visualizing gels.  It has a UV blocking cover that hopefully reduces UV that passes through, but I've always been suspcious as to how effective it is.  Obviously this part can be replaced with a new one, but short of guessing on the recommended 50 hr lifetime, how would one know the level of UV passsing through?  I considered simply placing a gel on top, but that is far from quantitative.  I am really just curious if there is an easy to make and/or obtain sensor that could be used to know when UV expose could be considered dangerous.

Is there a more appropriate tag than DNA?

Agreed, I'm still below the threshold for creating tags.  Safety or visualization would have been remotely closer.

I'm not sure this is on topic in its present state.  It's more about safety procedures than the formulating or running of gels.

@jonsca safety procedures should surely be included within experimental design?

@bobtheowl2 sorry about that, didn't even consider your rep!

@RoryM This seems more of an laboratory equipment maintenance issue rather than something directly involved with the process of experimental biology.  Perhaps a meta post is in order.

@jonsca sure sounds like a plan =)

The instrument you are looking for is probably an UV-meter.

That does seem obvious after looking at products available in a google search.  Maybe one the reusable ~6 level color changing sensors would be adequate or even one of the ~$30 handheld digital models. Spending several hundred dollars is out of the question though. I was just hoping someone would say, oh yea all labs in the world use this cheap x sensor to warn us of excessive exposure (analogous to radiation badges).

@bobtheowl2 I did try and find a radiation badge style dosimeter for you but it seems the only ones they have at present are for 24/7 exposure studies and tend to be quantitative rather than a qualitative red light approach

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How many mice are on the Earth?
We are 7 billion human beings on the Earth. But how many mice are there? How would you estimate such a number?

There are many rats and mice in the world.
From the recent number factors, in some LEDC's the population of mice are slowly rising at 1 mice every 15 seconds being born but in higly developed countries with great ecological systems, there is a complete difference with an unknown amount of rats and mice being born.

Mark-recapture is the most frequently used method for small mammals. It's best when combined with uncertainty estimates and population dynamics models (e.g. projection matrix).
The fluctuations of small rodent populations have long fascinated scientists, and various models have been developed. Logistic regression models can be used to estimate likelihood of mice outbreak based on local rainfall data.
Estimates vary.
Rat population in New York city, for example, was thought to be 1 rat to 15 humans in the mid 40s, 1:36 in the late 40s (Davis ratio), 12:1 in 2002.
The population of mice is often estimated per hectare - 0.25-60/ha in buildings and 1-200 in the field, over 1000/ha during outbreaks. 10^9-10^10 hectares of habitable land means
that populations of mice and men are, probably, of the same order of magnitude.

"Rat population in New York city, for example, was thought to be 1 rat to 15 humans in the mid 40s, 1:36 in the late 40s (Davis ratio), 12:1 in 2002. " - why the reverse?

Can you try to extrapolate a very approximate world population from these numbers?

Good answer! Citations would be nice - eg. who's Davis?

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How can you improve solubility of colloidally dispersed substances?
If you solve collidally dispersed substances then the particles can form large colloids. This may block narrow passages and diffusion into dense structures may become completely impossible.
What can you do to improve the solubility of such substances?

This sounds pretty inorganic chemistry-ish. Any way to phrase it more towards biochemistry (i.e. relationship to proteins, biological systems, etc...)?

In my case, three-four rounds of sonication greatly helps in having smaller and more homogeneous hydrophobic particles dispersed in water.


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How to set up a slow cooling on an AB Veriti thermal cycler?
I want to incubate my sample at 50ºC and then slowly cool it down to 4ºC at a rate of 0.1ºC/s. I am using  AB Veriti thermal cycler. Does anyone know how to set up the rate of cooling? It has to do something with the ramp rate, which is given in % but I don't know how to convert this into a real rate.

If I recall correctly (from when I interned at ABI), you can't directly set this in the Veriti interface.  However, (again, I'm not 100% certain -- I couldn't find anything to confirm this after 30 minutes of googling,) the ramp rate percent refers to the percent of maximum ramp rate for the heating block.
According to the product website, the max heating block ramp rate is 5 °C/s while the max sample ramp rate is 4.25 °C/s, so you need a ramp rate between 2% and 2.4%.

As a side note, the people at ABI are very proud of their instruments. If you'd like, (if the web contact forms aren't very helpful), I can put you in touch with someone from the Foster City office to help you squeeze the most out of your machine.  (I'm not sure how to say that without sounding like an advertisement — I'm just trying to be helpful.)

It would be great if you give me a contact. Can you email it to me please? Thanks a lot.

You've successfully hidden your email address from the internet, and I wouldn't want to ruin that for you, so if you'd like, you could email me with your address.  My email's in my profile.

apparently they are hidden to the world!

As Thomas pointed out, there is a maximum ramp rate which you can set up on the thermocycler. Its value can go from 0% to 100%. I can then assume that a 100% ramp rate will corespond to the maximum ramp rate of 4.25°C/s for the heating block or 5°C/s for the sample. which means that a ramp rate of ~2.4%. Subsequently, I set up my reaction at a 2% ramp rate, as I started a timer at the time the ramp cycle started. To my surprise, the temperature was cooling down too slowly. Thus, I empirically found out that a ramp rate of 5% corresponds to ~0.1°C/s cooling speed.
I wished there was more precise way to calculate it. Perhaps the slope of the line changed at different temperature intervals. It would be great if I can talk to the AB people so that they could justify my finding.

The maximum rates change with the product version, by the way.  The Veriti "Fast", 96-well has a ramp rate of 5 °C/s while the Veriti "normal", 96-well's max. sample ramp rate is 3.35 °C/s.  But still, this would be a 3% ramp rate, not 5% like you found.


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Do insects with compound eyes have depth perception?
Do insects with compound eyes have depth perception? They fly as if they do, but their eyes are so close together it seems like the image would be 2 dimensional.

"1001 questions answered about insects" by Alexander Barrett and Elsie Broughton Klots includes the following passage:

Do insects have depth perception? Depth perception of some sort is important to an animal who has to catch its prey; fortunately most
  insects have it to a degree.  Although they do not have binocular
  vision that can be compared with man's, it is true that when one eye
  is covered their depth perception is markedly affected.  The criterion
  of depth seems to depend on the angle of simultaneous stimulation of
  two corresponding points of the retina of the two eyes.

However it does not mention compound eyes specifically.
There may be other methods of obtaining a perception of distance rather than the binocular vision seen in humans.  This paper suggests that there is 'clear evidence' that  some insects perceive depth by moving their head to artificially create parallax, which they can then recognise and interpret as depth and distance.  They cite the Praying Mantis as an example, which does have compound eyes.

keep in mind they do this the same way we do, by having two different eyes, a single compound eye will not have depth perception.

Short Answer:
Yes.
Nityananda et al. (2018) confirmed a novel form of stereo vision by putting tiny colored glasses on praying mantises.

 (Newcastle University, England) [source]
 Long Answer
Background
Stereopsis = the perception of depth and 3D structure obtained from visual info from 2 eyes.
Vertebrates (including humans and all primates) use stereoscopic vision to perceive depth. Each eye sees slightly different images based on their side-by-side orientation, which allows the brain to "calculate" the difference and generate our perception of depth. This is typically accomplished in organisms with 1+ billion neurons in the brain.
Nityananda et al. (2018) have confirmed for the first time that an invertebrate (with only ~1 million neurons) also is capable of stereopsis.

Work by S. Rossel (and others) as early as 1983 had previously suggested this was the case.

Specifically, their work showed that instead of using correlations of image contrast for stereopsis...

Mantis stereopsis...relies on detecting luminance change at positions corresponding to appropriate disparities.

In other words, they propose that mantids are looking for changes in the light patterns over time -- basically, they're only looking for movement.
You can read their paper here.
Sources

Nityananda, V., Tarawneh, G., Henriksen, S., Umeton, D., Simmons, A. and Read, J.C., 2018. A Novel Form of Stereo Vision in the Praying Mantis. Current Biology.

Khan, Amina. 2018. What do you see when you put miniature glasses on praying mantises? A new method for robot vision. Los Angeles Times. Accessed Feb 2018. http://www.latimes.com/science/sciencenow/la-sci-sn-praying-mantis-vision-20180209-story.html.

Wikipedia. "Stereopsis." Accessed Feb 2018. https://en.wikipedia.org/wiki/Stereopsis.

The sense of depth is required to us to orient ourselves in a 3D world. Insects do orient themselves in the exterior 3D world, thanks to the ability to detect the plane of sunlight polarization, that is used as a navigation compass in foraging expeditions and when coming back home.
You can find a good review on Current Biology (Krapp 2007) and a lecture about insect vision from Cornell University.

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How do porcupines keep from pricking each other while mating?
How do porcupines keep from pricking each other while mating? It seems like they would constantly be scratching each other.

The female stood with the tail held sharply to one side, and the quills on
  the back lying very flat.  The male stood on his hind legs, while the
  front legs grasped the sides of the female. There was no repetition  of the act.

The male's urethra is 115-120 mm long, and his penis is 75 mm, so the he doesn't need to be as close to the female as one might think.  The retractor muscles are attached to the lower portion of the pelvis, which is likely well below the level at which the male's quills end.
Apparently, a dozen or so porcupines will den up in close quarters for the winter, so one can probably guess they have a good sense of whether their spines are hurting another, but that's only conjecture.
I suppose the take-home message is, nature will find a way.
Struthers, P.H. (1928) Breeding Habits of the Canadian Porcupine (Erethizon dorsatum).  Journal of Mammalogy, 9(4), 300-308. http://www.jstor.org/pss/1374084
Mirand,E.A., Shadle,A.R.(1953).  Gross anatomy of the male reproductive system of the porcupine
Journal of Mammalogy, 34(2), 210-220. http://www.jstor.org/pss/1375622

I love the "There was no repetition of the act." The male learned his lesson the first time!

There are several other publications that describe the mating behavior of porcupines in detail.

@AndersonGreen Definitely add another answer, then.  This was by no means exhaustive! :)


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Is the minicolumn the unit of the neocortex?
There are many arguments for what the unit of the neocortex is. "Columns" seem to be the standard, but what exactly those are is extremely contradictory between individuals, cortical regions, and species. Often times, when a column is referred to, it's actually a functional column without any anatomical borders (such as Hubel and Wiesels ocular dominance columns). Sometimes, the "column" is semi anatomical, such as the rat barrel cortex. Other times, these functional columns are confabulated into anatomical units, without any evidence for a border.
So my question is, could Mountcastle's "minicolumns" be the actual anatomical unit of the cortex? I've heard arguments that they are mere developmental relics. But they seem like the only reliable and consistent unit in the cortex.

I am skipping the background information (I will amend my question later) for now.
So, what is known about minicolumn?

The term was coined by Ramon y Cajal who saw narrow stripes, running from white matter to the surface (reference) in his preparation with Nissl staining.
The hypothesis about minicolumns to be anatomical units was proposed by Mountcastle in 1957, known as "columnar hypothesis" in neuroscience (reference).
It has been shown that minicolumns grow from progenitor cells within the embryo (reference), and don't require brain functions to emerge.
Minicolumns  contain neurons within multiple layers of the cortex (reference).
One of the latest review on the topic (Buxhoeveden & Casanova, 2001) contains 121 references to experimental papers on this topic.

I wouldn't say that these columns are developmental relic, for there is a known heterogenity among these structures (like hypercolumns, macrocolumns and segregates) and it is rather improbable that all these types are relics.
So, as long as we stick to the term "anatomical unit", I see no problems why columns (with all possible types and sizes of them) should not be it.

Thanks for the reply! Unfortunately it succumbs to the terminology confusion I mention in the question. The columns of Ramon y Cajal were the "minicolumns" of Mountcastle. Mountcastle's "column" was described as a bundle of minicolumns fused with dense horizontal projections., But evidence for actual anatomical borders on these "columns" is lacking. Same for ocular dominance columns, hypercolumns, macrocolumns, etc... Specifically, I am curious if the minicolumns, not columns, are developmental relics. In other words, is there evidence that minicolumns carry distinct functional significance?

@Preece I will amend my answer soon to address your question, sorry for a delay!


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Sequencing the genomes of polyploid organisms
I've done some transcriptomics work in the past with a polyploid organism, and this presented some unique challenges in the data processing and analysis. Since then, I have been brainstorming about the technical challenges one may face when sequencing and assembling the genomes of a polyploid organism. As far as I am aware, there are no polyploids whose genomes have been sequenced.
If one wanted to sequence, for example, a tetraploid organism, one approach would be to prepare and sequence all of the DNA together and then rely on post-sequencing analysis to tease apart the two co-resident genomes. However, it would be difficult, if not impossible, with this approach to distinguish inter-genome variation from intra-genome variation.
An alternative approach would be to isolate DNA from both co-resident genomes separately, and then sequence and assemble the genomes separately, so that inter-genome variation and homology need not be considered. However, I'm thinking at a very high level and have little intuition as to the technical feasibility of this approach. When there are two or more co-resident genomes, is it be possible to isolate DNA from only one of those genomes? What would this rely on (for example, would thorough cytogenetic/cytogenomic characterization help)? If this task is not possible, what types of limitations must be overcome to enable it?

I'm interested in the issues related to transcriptomics on polyploid organisms (I'll be doing some comparative transcriptomics between related but different ploidy organisms). If I ask this as a separate question, could you elaborate on the issues involved and how you solved them?

I'm not sure, as the material is yet unpublished. I guess it would depend on the question.

@jmusser I reverted your title edit since it didn't really capture the question. The title "How are the genomes of polyploid organisms sequenced?" isn't really appropriate--it seems like you're asking how it is currently done (it's not). I'm asking how it should or could be done. If you have any more suggestions about improving the title, I'd be happy to consider these.

@DanielStandage, sorry, I just like to turn the title into a question. :)

@jmusser No worries, I have no problem with that assuming question adequately captures what is being asked.

Take a look at the strategies used to sequence the wheat genome. Wheat is hexaploid. The project is described at http://www.wheatgenome.org/.
For early work on the maize genome, we employed methyl filtration in order to reduce genome complexity and size - transposons are filtered out and genes + promoters and such remain. The gene sequences are different from the two genomes, so says the theory, and those can be distinguished. See http://www.ncbi.nlm.nih.gov/pubmed/10545948 for the reference.

As I know wheat (both 4n and 6n) is allpolyploid (it came into being by hybrydization of different species). Isn't it harder to sequence genome of autopolyploid species?

I'm not sure. Sequencing is not the real problem - it is accurate genome assembly.


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How often can you reuse coomassie stain?
I usually heat to boil in the microwave, and stain for 12 minutes. How often can I reuse this buffer?

Since there's a lot of methanol in Coomassie stain, a significant amount would probably evaporate off each time you microwave it. Therefore, it'd be probably a good idea not to reuse it because (1) you're losing methanol, and (2) the concentration of everything else is thrown off.
Why do you boil the stain? I just pour mine at RT right on the gel and it works fine.

Doesn't heating it up make it stain faster?   Also, labs I've worked in have done both: reuse and not.  My impression is that you can reuse some of it, but it's best if mixed 50/50 with fresh stain.  But of course, this is all lab folklore.  I'd be curious to know if there has ever been a systematic study of whether/how much re-use affects results.

I've never boiled it and it always stained my gels fine in 10-15 minutes. (Plus it takes a few minutes to boil anyways... and sniffing those methanol vapours isn't exactly good for you...)

And after I've stained the gel, I just pour it back into the container. I've used the same bottle of stain for 2+ years. Works like a charm.


text:
How is the number of mitochondria in a cell regulated?
How does the cell regulate the number of mitochondria in a cell? What happens when there are too many or too few?

The concept you refer is recognized as mitochondrial biogenesis and it is regulated by AMPK which senses the cellular energy demand. If you have few mitochondria in the cell, the electron transport chain works suboptminally generating less ATP. When the AMP/ATP ratio is high (low ATP) AMPK is activated, and turns on the catabolic pathways required to produce more ATP, included mitochondrial biogenesis.


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What is the advantage of circular DNA in bacteria?
From what I understand, bacteria have circular DNA. What advantages does it have over linear strands like for eukaryotes?
Do there exist bacteria with more than one ring of DNA?

Interesting question!

Streptomyces species are Gram+ bacteria which appear to have linear chromosomes.

closely related question: Is there an advantage to linear chromosomes?

Vibrio cholerae is known to have two circular chromosomes.
Bacteria cell division is a lot simpler and efficient as compared to eukaryotic cell division, partly due in part to the nature of their chromosomes. They don't have to undergo mitosis -- condensation of chromosomes, segregation, spindle fibre formation, attachment et al aren't involved in bacterial cell division.
Circular DNA also circumvents the Hayflick limit (thus allowing it to be "immortal"), which is the number of times a cell population can divide before it stops, presumably due to the shortening of telomeres, the sequences at the end of the chromosomes. Since circular DNA lacks telomeres, it does not get shorter with each replication cycle.
Circular DNA can also facilitate horizontal gene transfer such as Hfr mediated conjugation. Remember, conjugation is analogous to a "rolling-circle" type replication which is of course, only possible on circular pieces of DNA.

I made a minor edit to your answer, hope you don't mind.

interesting, but aren't fission yeast also immortal?

Yes- but they need telomerase to maintain their telomeric ends. Bacteria avoids this problem altogether by using a circular chromosome.

To expand a little bit the other answer, I would also add that bacteria can have other (usually circular) DNA segments aside from their main chromosome. These are called plasmids and are double stranded molecules of DNA that can replicate autonomously.
Plasmids often carry genes that allow an organism to survive in certain conditions, for instance they could carry the resistance to an antibiotic, or the gene that encodes for a specific nutrient that may be absent in the environment and so on.
As the other answer says, plasmids can be transferred horizontally between bacteria in a process called bacterial conjugation, and that is made possible by the presence of a specific plasmid, called the F-plasmid in the donor. The F-plasmid encodes, amongst other things, for the F-pilus protein pilin, that allows the formation of the pilus necessary for DNA transfer.
Because of their properties, plasmids are widely used in laboratory as vectors, to transfer genetic material to cells in order to give them specific "abilities" (e.g. you could insert a gene that encodes for a certain receptor normally not expressed by the cells to allow its expression and test its function).
Finally, it is worth remembering that plasmids can also be found in eukaryotes (e.g. in yeast).


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Do cows produce milk excessively?
Do cows produce more milk than it is required for their calves? It seems like cows are able to provide milk all the time (all year around). Is it so? Or do they, like other mammals, produce milk only in ammounts requeired by their offspring?

milk cows have millenium of selective breeding for milk production. they produce 2-3 times more than normal cows and have crazy sized udders. In the wild, can baby animals risk drinking too much milk? not really! Mammal milk production is normally decided by A/birth and B/the babies appetite and then weaning.

Dairy cows are bred, or selected to give milk.  So they do produce excessively.  The normal bovine wild type, like other mammals, not only produce less milk, but also will tend to stop lactating when the calf is not nursing.
I would be interested to know if dairy cows stop giving milk if they are not milked every day.  I understand they can get very uncomfortable if they are not milked, but i don't know if they stop giving milk or if they are injured in some way.

Can you please provide a reference for the fact that if you milk a wild cow (good luck with that) every day, after removing its calf, it will stop producing milk at some point? Alo, if they are selected to produce more milk they do not produce it excessively. If you select a plant to have bigger fruits, its fruits are bigger, sure, but they do not grow excessively, they just grow the right size for that particular plant, which happens to be bigger than other plants.

@nico "The calf is not nursing" I think he means after the calf is weaned. Also, 'excessive' is a relative term. A cow producing 4 1/2 gallons per day would be considered poor by the farmer, but is excessive in terms of her calf's needs.

@jmusser: that is what I am saying. If you get a wild cow and continue to milk it after weaning its calf it will most certainly continue to produce milk.

The average domesticated dairy cow produces far more milk than would be required to feed their calf. All cows, wild and domesticated, will only lactate in the period between their calf's birth and weaning. Milk is calf-food, and when there's no calf, there's no evolutionary advantage in producing milk.
On dairy farms, cows are milked twice daily, from spring (when they give birth) until late autumn. This mechanical milking 'fools' the cow into continuing to lactate. When a cow has stopped lactating, they will only start again after giving birth. This means that you can't just start milking a cow and expect to get milk.
Generally farmers milk their cows from spring (birth) until late autumn. The reason for stopping in autumn is simply because the grass grows much slower in winter, so there isn't enough food to support lactating cows. However, it is entirely possible to milk longer than a year; I know of farmers who milk their cows continuously for two years. These farmers will have to purchase a lot of supplimental food (like hay or silage) during winter. The advantage of milking for longer than one season is that the cows do not have to give birth every spring, but instead only every second spring.
I believe (but can't guarantee) that in winter, most milk purchased in a shop comes from the opposite hemisphere. I do know that here in New Zealand, we export a lot of milk to northern-hemisphere countries.
If you were to suddenly stop milking a cow, they might get sick but generally they will survive. It's still something to avoid!
Although if the calf is left with their mother then the cow would be relieved.
I do not have an 'official' source for these facts. However, I grew up on a dairy farm, so this was my life.

Thank you very much. This answer seems most informative and real-life applicable.

I was under the impression that certain breeds (holsteins for one) have been so over bred for the milk producing trait that there are periods where there milk production is so high, not being milked can actually cause the udder to tear allowing them to die from sepis.  Note: that's anecdotal I don't have information confirming or denying it.

Cows only produce milk after a calf is born and their lactation period lasts approximately 10 months. In many instances, farmers have given growth hormone (GH)¹ to cows in order for them to produce more milk. It must be noted that there are many side effects associated with this, not to mention the residual effects it may have on us humans as consumers. Primarily though, the cows would have decreased immune efficiency and this would leave them vulnerable to all types of parasitic infections or disease.

Welcome to Bio.SE. Can you give a reference to the GH use? The calf-bit is pretty much common sense So reference not needed there :) Thanks for your contribution!

Thank you for the welcome ^ ^ (is there a specific format for references) this is a scholarly article on the subject: http://goo.gl/MDvaDL ..also the wiki is found here: http://goo.gl/thQnmE

If you click the link icon (the chain shaped icon) in the question window, it allows you to insert web links to articles etc. However - the wiki page you refer to is about sex hormones (estradiol, progesterone etc) and the article link is on antibiotics. I have downvoted your answer as it needs work since your claims about GH may be unsupported in the literature. After edits I am happy to upvote, don't worry.

Thank you for explaining this AliceD, I have added a GH reference now.


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How does water move throughout plants?
I haven't yet found a decent explanation for how water moves throughout plants. It does seem to travel more efficiently upward than out or down. Why is that?  How does it travel through the plant?

Most water moves up through the xylem by capillary action. Imagine dipping a pipette into a small pool of water; the water would rush up into the pipette. Or, imagine dipping the edge of a paper towel in water. The water "runs" up the paper towel. This is capillary action.
As water evaporates out of the leaves and such in higher regions of the plant, a capillary force pulls up more water. If for instance, you were to dry the top of your saturated paper towel, more water would be pulled up from the pool below to wet that top section.
As for a molecular explanation, Wikipedia has a good explanation of Cohesion-tension theory.

Indeed it does. There is tension between the weight of the water and the force of the capillary action, which they think is what limits the height of trees (http://www.nature.com/nature/journal/v428/n6985/abs/nature02417.html). Remember that the xylem is like a very, very skinny tube, so it isn't like there is a single massive column of water flowing up.  With a narrow tube like that, the weight of the water builds pretty slowly.


text:
Why can you graft two unrelated cacti successfully, but you cannot do this on garden trees?
Any cactus can be grafted onto any other cactus, and even the most unlike of them grow together. My latest graft was a Schlumbergera truncata scion on an Opuntia microdasys rootstock. This kind of graft is always successful. Why can't garden trees be grafted in a similar way, between genera?

Firstly, different genera of trees can occasionally be successfully grafted. For example, quince, genus Cydonia, may be used as a dwarfing rootstock for pear, genus Pyrus.
However, it is true to say that this is the exception rather than the rule.
In the case of plants in the family Cactaceae, I would suggest that grafting is usually successful for two main reasons:

Genetic similarity. Plants in the family Cactaceae while known to be morphologically often very different, have relatively little genetic diversity. This will increase the likelyhood of a successful graft.
Ease of aligning vascular cambium. This is required for a successful graft, and in Cacti this is quite easy to achieve since the cambium is clearly visible when you prepare the scion and stock.

It is also possible that Cacti readily form callus tissue, which would also aid in the grafting process.
Nyffeler, R., 2002, doi: 10.3732/ajb.89.2.312 Am. J. Bot. 1 February 2002 vol. 89 no. 2 312-326

just to add my link.  This guy has patiently grafted 11 fruit to a single tree.  http://inventorspot.com/articles/lemon_tree_japan_bears_eleven_ki_9572

Interesting. However, it looks like they are all from the same Genus - Citrus.


text:
Would a plant need light if the chemicals gained by photosynthesis were given through the roots or as a foliar spray?
If you took the chemicals a plant gains through photosynthesis and put it through the plants' roots or by injection, or used as a foliar application for intake through the stomata, would the plant need light? If not, how would it respond to the treatment?

Are you suggesting that someone would artificially supply a plant with sugar, proteins, lipids, etc. via the roots?  Isn't that sort of like putting a plant on a feeding tube?

Yes. Would it work?

This approach can be used to culture mycorrhizae http://www.jstor.org/stable/3760183

There are a couple autotrophic plants that parasitize other plants that kind of do this already. But you probably couldn't do it to any plant. But you could do it to some

Not exactly the same thing, but a species of algae has been genetically altered to allow it to  uptake glucose, bypassing the need for photosynthesis: http://www.unisci.com/stories/20012/0615013.htm

I doubt this would work for the vast majority of plants.  I think it would cause root rot as the microorganisms in the soil would out-compete the plant.  Also the transport systems of the plant might not be efficient in this direction.
I mean might there be a plant somewhere where this might work?  Sure.  Fungi that grow in the dark would be a lot like such plants, so its biologically possible.  There might be a primitive plant that doesn't need its chloroplast to be active to live.  I've never heard of one and wikipedia is not helping here...

http://en.wikipedia.org/wiki/Monotropa_uniflora


text:
How would a plant sprout and grow in a zero gravity environment?
Have any experiments been carried out involving sprouting and growing plants in a zero gravity environment? If so, what was the outcome? How did the plants sprout out of the soil without gravity? Did they grow outward or toward light sources?

There have been several experiments in growing plants in microgravity (strictly speaking, we do not achieve "zero-g" since astronauts remain in orbit about the Earth).
Changes in plant growth due to the influence of a gravity field is sometimes called gravimorphogenesis. More specifically, gravitropism is a differential growth response of plant organs to gravity. For example, roots grow downwards (positive gravitropism) and shoots grow upwards (negative gravitropism) on Earth.
Studies (e.g. 1) suggest that in micro-g, there is no preferred direction; roots may grow "up" and shoots "down".
It is thought that this growth response is due to the relative distribution of auxin in the plant. On Earth, auxin will preferentially move down into the root-tips due to the location of amyloplasts in the root-cap cells. In micro-g, amyloplasts do not settle at the "bottom" of the plant, therefore there is a more generalized distribution of auxin, and therefore there will be no preferred growth direction.
In addition, changes in plant gene expression as a response to micro-g environments are also being investigated (2) and suggest that auxin transport inhibitors may block the activation of the auxin responsive promoters in Nicotiana spp. (tabacco).
(1) Mechanisms in the Early Phases of plant Gravitropism CRC Crit Rev Plant Sci. 2000 ;19 (6):551-73  11806421  Cit:65
(2) Transcription Profiling of the Early Gravitropic Response in Arabidopsis Using High-Density Oligonucleotide Probe Microarrays, Plant Physiol. 2002 October; 130(2): 720–728.
doi:  10.1104/pp.009688

I find over 100 articles returned by a PubMed query for "Arabidopsis microgravity." Arabidopsis was taken aboard at least one if not more Space Shuttle missions to answer this and other similar questions. A couple recent papers from this search are:
Spaceflight transcriptomes: unique responses to a novel environment.
Paul AL, Zupanska AK, Ostrow DT, Zhang Y, Sun Y, Li JL, Shanker S, Farmerie WG, Amalfitano CE, Ferl RJ.
Astrobiology. 2012 Jan;12(1):40-56.
PMID: 22221117
An endogenous growth pattern of roots is revealed in seedlings grown in microgravity.
Millar KD, Johnson CM, Edelmann RE, Kiss JZ.
Astrobiology. 2011 Oct;11(8):787-97. doi: 10.1089/ast.2011.0699.
PMID: 21970704
Parabolic flight induces changes in gene expression patterns in Arabidopsis thaliana.
Paul AL, Manak MS, Mayfield JD, Reyes MF, Gurley WB, Ferl RJ.
Astrobiology. 2011 Oct;11(8):743-58. doi: 10.1089/ast.2011.0659.
PMID: 21970703
Gene expression changes in Arabidopsis seedlings during short- to long-term exposure to 3-D clinorotation.
Soh H, Auh C, Soh WY, Han K, Kim D, Lee S, Rhee Y.
Planta. 2011 Aug;234(2):255-70.
PMID: 21416242
A novel phototropic response to red light is revealed in microgravity.
Millar KD, Kumar P, Correll MJ, Mullen JL, Hangarter RP, Edelmann RE, Kiss JZ.
New Phytol. 2010 May;186(3):648-56.
PMID: 20298479

It might be helpful to include clickable links to your answers =) n.b. I realise that your rep might be prohibitive in doing this for the time being =D

Agreed, links are helpful, but someone may wish to refine or rerun my query, rendering links less useful. There's enough info in my response to be helpful to this audience and I think that is the main point.


text:
What is the most heat-tolerant organism?
What is the most heat-tolerant (or heat loving - hyperthermophile) organism so far identified? What adaptations does this organism have in order to endure such high temperatures?

Methanopyrus kandleri has been able to grow and proliferate at temperatures of up to 122°C when under around 20atm (Takai et. al. 2008).  This was achieved in the lab but the theory should hold true for deep sea thermal vents.  Another strain of M. kandleri survived incubation to 130°C however was unable to reproduce at this temperature.
One of the key adaptions for thermophiles is the selection towards an extremely thermo-stable copy of the enzyme DNA polymerase.  This allows DNA replication at high temperatures and is similar to the 'Taq' polymerase used in the polymer chain reaction in labs, derived from another thermophile, Thermus aquaticus.

References

 Takai K, Nakamura K, Toki T, Tsunogai U, Miyazaki M, Miyazaki J, Hirayama H, Nakagawa S, Nunoura T, Horikoshi K. 2008. Cell Proliferation at 122°C and Isotopically Heavy CH4 Production by a Hyperthermophilic Methanogen Under High-Pressure Cultivation. PNAS 105: 10949–10954.

+1 although Taq is the specific polymerase of T. aquaticus, I am not sure whether there are specific names for M. kandleri polymerase...

I'd add that biochemically speaking, animals and microorganisms from thermal vents tend to have a higher GC content in their genomes, which makes it more thermostable.
All of the proteins are adapted to work at higher temperature.  There are a higher number of salt bridges and specific hydrogen bonds in the proteins to stabilize them - more arginines, more glutamic acids, etc. While this reference says that Cysteine is less common, I imagine anything which is not in a reducing environment will have more disulfide bonds - e.g. for proteins on the cell surface.
Sulferous deep sea vents would tend to be reducing as is the inside of the cell, but maybe in the case of fresh hot water spring extemophiles this may be the case.
Reference:
http://peds.oxfordjournals.org/content/13/3/179.full

What about fire? A grass fire across the prairie or a forest fire generates temperatures in excess of those mentioned here and yet many organisms, mostly plants, need fire to allow for seeds to open and germinate. I know fire is a short-lived situation, but is extreme nonetheless. The bark of the burr oak, for example, is rather resistant to fire.

I was thinking more of organisms which thrive (survive, multiply) in conditions of sustained high temperature. However, you make a good point here!


text:
Does extracted DNA degrade after a certain time period?
For direct use as template in PCR runs. Chelex 100 5-10% w/v extraction. Without listing the whole protocol, in the end the supernate is decanted off and then stored at 4°C. I was under the impression that this could be stored and later used almost indefinately but two of four samples extracted several months back failed to produce a product (when it was known they should have).
Assuming no mistakes were made and the reactions were the same, is there a technical reason the template would degrade to an unusable point?
Is there a rule of thumb about how long it can reasonably be expected to last?

Related: http://biology.stackexchange.com/questions/973/how-long-can-i-store-extracted-rna

My rule of thumb for DNA samples (in TE or water) - if I have plans to use it that week, I store at 4C. If I plan on using it within a month, I store at -20C. If I'm not sure when I will use it, I keep multiple aliquots at -80C. DNA can degrade by acid hydrolysis in water, because of contaminating nucleases in the sample, and by multiple freeze/thaw cycles.

Is there any long term storage option at room temperature? http://biology.stackexchange.com/questions/2231/how-to-diy-preserve-pet-dna-today-so-that-it-can-be-used-in-20-years
-Thanks!

DNA has a half-life of over 500 years under perfect circumstances. However, DNA degrades over time, and when kept in solution, it is difficult for there to be exactly 0 microbes, DNases or chemicals present which can hydrolyze the helix. It degrades over time and old DNA samples kept even at -20C very frequently show poorer results, especially when it is thawed repeatedly. Primers can also degrade gradually at room temperature, etc.


text:
How do plants 'tell time' for circadian rhythms based on a ~24 cycle?
I've read that many plants have some sort of circadian rhythm where they perform a certain action on a cycle of about 24 hours, like the mimosa plant opening and closing its leaves. Obviously, this is done in order to synchronize with the sun, but many such plants continue to perform these actions even when left in constant darkness or light. It follows that this is the result of some sort of biochemical pathway, but whatever internal 'clock' is used is also independent of temperature.
How can these plants perform certain actions every 24 hours at different temperatures when the chemical reactions most biochemical pathways use are temperature dependent?
It would seem like the length of the cycle should vary widely according to the temperature as it affected the reactions involved, but instead it stays at a very constant length very close to 24 hours. How can this be?
(This is in my textbook, but unfortunately the book doesn't cite any studies. I would greatly appreciate it if anyone could help me find one to link to so I can improve the  question. :)

The short answer is that it is because the reaction chains dispensing time and enzymes doing those reactions have evolved to negate the impact of environmental factors.
The true answer is that the plant clocks do gradually lose sync with 24h cycle when put in stable lighting conditions and move to some more-less random characteristic frequency of their  molecular clock which is quite likely dependent on environment (still it is obviously close to 24h) -- the sad truth is that every clock needs syncing to work properly.


text:
Can DNA produce ribozyme-like structures?
RNA is known to act as an enzyme via its ability to fold itself in specific ways.
Is DNA capable of such structures? Or is it some biochemical reason stopping the folding?
Have they been observed in nature?

There are no known natural DNA enzymes (deoxyribozymes), but there are various synthetic DNA enzymes. The first deoxyribozyme that has been reported (Breaker and Joyce, 1994) catalyzed the Pb2+-dependant cleavage of RNA.
Various deoxyribozymes have been synthesized, they can catalyze RNA cleavage, RNA ligation and many other reactions like DNA phosphorylation or Thymine dimer photoreversion, and even a Diels-Alder reaction (see Baum and Silverman, 2008 for a review).
DNA lacks the 2'-hydroxyl group that RNA posesses, but there is some evidence that this doesn't significantly decrease the potential of deoxyribozymes compared to ribozymes. In one experiment DNA and RNA enzymes that catalyze a Carbon-Carbon bond formation were compared and both achieved comparable catalytic rates (Chandra and Silverman, 2008).
For more information about DNA enzymes you can look at the publications from the Silverman lab, they're probably the most active research group in this field.

Baum, D. A. & Silverman, S. K. Deoxyribozymes: useful DNA catalysts in vitro and in vivo. Cell. Mol. Life Sci. 65, 2156-2174 (2008).
Breaker, R. R. & Joyce, G. F. A DNA enzyme that cleaves RNA. Chem. Biol. 1, 223-229 (1994).
Chandra, M. & Silverman, S. K. DNA and RNA Can Be Equally Efficient Catalysts for Carbon−Carbon Bond Formation. J. Am. Chem. Soc. 130, 2936-2937 (2008).

DNA has recently been designed to act as a targeted drug-delivery agent at George Church's lab.  This doesn't involve catalyzing a reaction between two substrates, but it does involve significant internal conformational changes based on binding to highly specific substrates.
http://www.sciencemag.org/content/335/6070/831.abstract

This isn't a ribozyme at all.

@bobthejoe It's not a ribozyme, but it does demonstrate a parallel flexibility of conformation and function to ribozymes.  Part of the question addresses whether there is a biochemical reason "stopping the folding".

In that regard, you should really cite Ned Seeman's work. The DNA in the box and the DNA origami work better reflect the conformational flexibility of higher ordered DNA structure. I would believe that the alternative discussion in http://biology.stackexchange.com/questions/287/what-implications-has-the-missing-2-oh-on-the-capability-of-dna-to-form-3d-stru better describes the limitations of DNA in achieving these non-canonical structures.


text:
Evolutionary origin and exogenous cues of ~28 day infradian rhythm?
The most obvious example of an approximately monthly biological cycle is the human menstrual cycle. My questions are the following:

Is it known when and where this cycle or one like it arose?
What exogenous cue(s) (if any) is/are this cycle based on? The moon's
orbit around the earth is seemingly obvious however the only cue that
I can think of that would be easily sensed by organisms is variance
in night-time illumination, which seems like a very weak phenomenon
when compared to day/night and seasonal cycles. King and neap tides may be a suitable cue however they have a half-monthly modulation.
The moon has been steadily retreating from the earth over the course
of its history, which means that months have been slowly getting
longer. Is there any fossil (e.g. biogeochemical) evidence of
organisms with biological cycles in synchrony with a 'short month'?

I don't know whether the length of the Moon's orbit is such a good explanation: the menstrual/estral cycle varies a lot amongst species. For instance, mice and rats have a 4/6 days estral cycle, chimpanzees have a 37 days menstrual cycle. Also, many animals go in anestrus (they don't cycle during certain periods of the year).

@nico - Ah, that shows what I know about estrus: I was under the impression that the estral cycle was a single seasonally-modulated cycle rather than a 'cycle within a cycle'. Also didn't know that the chimpanzee menstrual cycle was different. I suspected the periodicity of coral spawning might be an example of an evolutionarily early 28-day clock but wiki seems to suggest that that's a case of an exogenous trigger rather than entrainment.

the difference between estrous cycle and menstrual cycle is essentially that in the estrous cycle there is reabsorption of the endometrium if the animal is not fertilized. The wikipedia article explains it quite well.

A double-blind, prospective study during the fall of 1979 investigated
  the association between the menstrual cycles of 305 Brooklyn College
  undergraduates and their associates and the lunar cycles.
.... Approximately 1/3 of the subjects had lunar period cycles, i.e.
  a mean cycle length of 29.5 ± 1 day. Almost 2/3 of the subjects
  started their October cycle in the light 1/2 of the lunar cycle,
  significantly more than would be expected by random distribution. The
  author concludes that there is a lunar influence on ovulation.

(Menstrual and Lunar Cycles, Friedmann E., American Journal of Obstetrics and Gynecology, 1981)
Another source supports this conclusion, finding that "a large proportion of menstruations occurred around the new moon."
Somewhat related, this study found that light exposure shortened menstruation cycles.
In summary, there seems to be a good amount of data suggesting that lunar cycles do in fact calibrate the length of human menstrual cycles to some degree.

There seems to be some data suggesting that the two are correlated. As to causation I think we're not even close to prove that.

@nico Well, if they are correlated but lunar cycles do not affect menstrual cycles, then there are two other possibilities. Either menstrual cycles affect lunar cycles, or a confounding factor affects both lunar cycles and menstrual cycles. Neither of these seem very likely. Additionally, we know that light exposure seems to have some effect on cycle length.

then why would it only work for humans and not for other primates?

@MatthewPiziak: correct me if I'm wrong, but isn't there a third possibility as well - that the lunar cycle affects something which is the causation of the human menstrual cycle.
nico - I have no idea about the cycles of other relative close ancestors to us (ie primates), but do you know if they deviate substantially from the human cycle?


text:
Why did the sensitive plant (Mimosa pudica) evolve its leaf-closing mechanism?
Why did the sensitive plant, Mimosa pudica, evolve its leaf closing mechanism? Does it help in a heavy storm? Does it scare off whatever animals might think it a good meal?

By the way, I am not an evolutionist.

Are you sure you mean evolutionist? An evolutionist is someone who thinks the theory of evolution by natural selection is largely accurate. Are you saying you don't think evolution by natural selection is likely?

There are many reasons why Mimosa pudica (More commonly now referred to as the TickleMe Plant) may have evolved it's leave- closing mechanism. I have observed the movement when insects have landed on my plants. The insects apprear to be frightened by the movement as they do move on rather quickly when the plant collapses. The movement of the TickleMe Plant also occurs when the sun sets or if I place the plant in a dark room. This may be a way to reduce water loss by transpiration as the leaves fold down upon each other. Another reason for the leave movement may be to expose the few thorns found on adult plants. This could be another warning for herbivores to stay away. In cold weather TickleMe Plants will close their leaves as well, could this be a way to maintain its body temperature. All in all, this is the most amazing house plant and I am always learning new things about this plant and its beautiful cotton candy like TickleMe Plant pink flowers.


text:
If I graft two trees together while young, will they grow as one plant?
If I were to graft two apple saplings together --  by bending the tops toward each other and lashing them together --  will the plants grow as one and benefit from one another, or will they be fighting each other for root space and light? If they would grow with each other, then I could theoretically grow a line of closely spaced fruit trees to any length, and they would be strengthened by each other in bad conditions.

check this out

That is not grafting, if they are not sharing vascular tissue all you are doing is making a weird topiary. apple trees are very often grafted (to prevent inbreeding infertility) so if you want to do it you can find plenty of information.

@John: That's really not why apples (and many other fruit trees) are grafted.  Grafting allows particular varieties to be propagated quickly (varieties don't come true from seed), you can select rootstocks to control height (dwarfing or semi-dwarfing), add hardiness & disease resistance, &c.  You can even graft several varieties of a fruit on a single tree.  See any commercial fruit tree catalog.

@jamesqf I was talking about apples specifically not all fruit. Apple often have a singe branch from a crabapple grafted on to the tree because apples will not fruit with pollen from a similar apple (a gala apple tree will not fertilize with pollen from another gala apple tree for instance) by grafting a very different breed it insures that each tree will fruit as much as it can.

@John that is uncommon, and in commercial orchards it’s pretty much unheard of. Grafting is basically used to propagate cultivars, which don’t come true from seed,   As well as get consistent anchorage, mature height, disease resistance, etc.. Source: worked in nursery for many years, grafting trees, and also had a personal orchard, and maintained several others for many years.

@John: OK, makes more sense when you explain it, though I've never seen or read about it before.  But I tend to prefer heirloom varieties, where it's not so much of a problem.  Or if it is, the nursery says "plant two varieties" :-)  But grafting onto various rootstocks is absolutely the norm.

It is common is apple trees sold for domestic use and I am well aware of the many uses for grafting, I was giving an example a layman might be familiar with. Apple don't come true from seeds for the same reason the grafting I mentioned is done they exhibit strong inbreeding infertility so fruiting apples need constant outbreeding. Cultivars can be bred true from seeds however it is extremely time consuming (15 years +) and very labor intensive, grafting is just faster. Legacy nurseryman myself ;)

There are a couple of answers to this question.  Especially where trees are concerned, you can graft two or more trees onto the same rootstock, or even a single limb into a tree.
But if the graft takes, it won't behave too much more differently than just more branches of the same tree.  Structurally intertwining them will not be different than if you had just taken a single tree's branches to support each other.  The graft will usually only have a single set of roots, from the host tree.  They will not compete.  The tendency will be for the branches to grow apart so that they can independently get their own light.  This is very much like any other single tree.  Not sure about fusing two halves of a tree together - exposing the roots would tend to kill the tree or unsettle it.

What you describe is not grafting it is called inosculation and can prodice some truly impressive results.
Inosculation can sometimes lead to natural grafting but it just as often does not. Apples are a good candidate for this to form grafting but it is not guaranteed. More importantly said trees are often competing for light so you end up having to plant more trees for the same amount of fruit, plus it is extremely time consuming.
As for strengthening that depends a lot on what you call strengthening, they may help each other structurally but joining becomes a liability for say something like drought conditions because you have a smaller root mass per tree.


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Why is it that cats can jump so high for their size, compared with humans?
My cat is about 1' high at the shoulder, and I am a little over 6', but my cat can easily jump onto something as high as I am. That is 6x it's height. If a cat can do this, then Why can't I jump up onto my barn roof? That is a little less than 36' up. I have a hard time jumping onto even a 4' platform. Now if my cat had trouble jumping onto an 8" platform, I would think that pathetic. Do cats have muscles 20x stronger than humans, for their mass?
Is it just their skeleton providing leverage?

Why are Cheetahs so fast?

Cheetahs are strong.

Square-cube law. In fact it predicts that jump height (absolute height, not in terms of size) is the same for all animals. In reality it varies of course, but it isn't a simple rule.

Cats have different body structure than human beings. Its body-kinetics are quite different from us. Yes, muscles are quite strong, but this not the only reason. To know in-depth about the reasons behind the cats’ extreme jumping abilities, you can just refer this online article - "The Glory of the Cat – adidarwinian" at http://adidarwinian.com/the-glory-of-the-cat  Along with the flexible spine, strong muscles, flexible joints, they have a peculiar trait known as righting reflex. The same article has information on this peculiar trait. Due to the righting reflex instinct, cats can even survive falls from the high rise buildings.

There is not a linear relationship between the size of a muscle and its power. The cat weighs significantly less, but the decline in muscle power is not identical. If he weighs 20x less than you, but his muscle generate 1/5 as much force, he will still be able to jump way higher than you.

Part of this difference comes from strength being proportional to the cross-sectional area of the muscle (increasing as the square of linear dimension/height) while mass is proportional to volume (cubic with linear dimension/height).  The rest (probably a majority) might be leverage and perhaps proportion of fast-twitch muscle.

Here is another answer talking about this non-linear relationship between size and muscle strength.

Both the mass of an animal and the amount of energy their muscle can release rapidly are proportional to their volume. The height to which they can jump is proportional to the ratio of the two, so most animals can jump as high as any other to within a small factor. The remaining difference between those who can who can jump about 6' such as your cat or Javier Sotomayor, and yourself, is practice.

Shortwinded answer:
Cats are not exceptional jumpers.
Their mystique fits a pattern defined by physics and illusion.
Medium-winded answer for cat lovers:
I care for cats who began feral
and now come and go as they please.
My territory-marked (tattered) curtains show exactly
how high these cats can reach without jumping.
They are amazing, with marvelous agility, senses, personalities and wits.
These acrobats cannot, however, jump as high as it looks.
Longwinded . . .
To compare the jumping abilities of humans and cats,
and countless other animals,
requires more than measuring the altitude of a platform.
Two pertinent factors easy to overlook are:
 A. How much did the center of mass rise?
B. Did the maneuver include climbing as well as jumping?
A misleading factor is:
C. How does jump height compare to body size?
Considered in reverse order,
comparing a human who can reach 7 feet without jumping
to a cat who can reach 3 feet:

C.   How does jump height compare to body size?
              This is surprisingly irrelevant.
Physics alone determines that
jump height is generally independent of body size,
down to smaller than a mouse,
where limiting factors become
the fluid properties of air resistance and viscosity,
not the
kinetic factors
of gravity and musculoskeletal physiology.
Under the neutral assumptions of
power laws,
a 7/3-as-long human is expected to produce roughly
49/9 ≈ 5.4 times the jumping force
of a 3/7-as-long cat.
This force acts over a muscle contraction
approximately 7/3 as long,
delivering ∼343/27 ≈ 13 times the jumping energy.
The weights of this human and cat
likewise have somewhere near a 13 :1 ratio,
which happens to cancel out the difference in energy,
and that is not a coincidence.
It is physics.
[Somewhat ugly mathematical formulas to be added if requested.]

B.   Did the maneuver include climbing as well as jumping?
              The cat is quicker than the eye.
A human’s jumping onto a meter-tall platform
typically ends with a footed landing.
No climbing involved.
When a human gains a three-meters-above-ground tree branch, though,
that branch is first grabbed by the hands,
followed by a lot of pulling and climbing
before the feat is complete.
When a cat bounds upon a two-meter-tall fence,
the same sequence of pulling and scrambling occurs, only quicker.
Here are two slow-motion videos.
One shows a cat climbing more than jumping.
The other shows a cat reaching a high target purely by springing.
https://www.youtube.com/watch?v=705OzYq7cXU
https://www.youtube.com/watch?v=UYEeJEYMDwI
Beautiful!
And note that the highest leap
reaches perhaps 7 feet.
Which leads to . . .

A.   How much did the center of mass rise?
              Cats have an edge on humans, but not by much.
Cats who can reach
3 feet
without jumping and
7 feet on the fly
raise their centers of mass by
7−3 = 4 feet.
This is impressively comparable to the best human athletes,
but this does not reach a separate realm of ability.

Ps. Yes every feral cat who comes close enough receives a veterinary visit. Cheers to county funding! (Nonetheless these wondercats still exhibit territorial behavior and occasionally receive patch-up visits. Perhaps material for a future question.)

I mean, I've had my cats clear jump over 6'. Assuming a cat is 2 1/2 feet tall, like you said, if it was standing like a human, that's jumping over twice it's height. I've seen them do this without 'climbing', but even if we say that the cat scrambled up the last foot, that's still at least a 5 foot jump. Now I am 6' 3" tall. I've never come close to jumping twice my height (around 12 feet). And then if you're going to look at weight, a cougar would be close to me (I'm 205 lbs). Cougars have been measured at 18' vertical jumps in one bound (some say well over 20').

I love this question, @J.Musser. If a cougar can raise its center of mass 10 feet or more, that is beyond astounding!  That you have leapt upon a platform 4 feet tall is believably impressive. Not easy, coming from someone who has tried. Nonetheless, our familiar felines are amazing in other ways.

I have done a 52" box jump, max. My original question was why cats (specifically house cats, but I guess any cat) can jump so much higher compared to their size than humans can

Size is an attractive diversion. I'm still looking for the right question at this site to go on and on about that.

I wouldn't mind reading if you have something to write... yeah I was into fitness. 640lb deadlift, 350lb bench, 80lb curl, 160lb weighted squats... I've gone somewhat softer in recent years would be interesting to see how I can jump now

There is no way to lift that much without developing a fast twitch.

I don't have a twitch other than normal random twitches. I failed to land a 25 foot jump while (trying to) demonstrate tuck and roll techniques, suffered a lot of damage, and never really came back from that. Loose skin now

We humans have overgrown our safe performance boundaries. Another answer in search of a question.

Sorry to have deleted the comment that rejoiced an over-4-foot-and-then-some spring, J. Musser. By "fast twitch," I referred to muscle fibre and you probably understood that, but saying so now just for the record . . .

There's also a scale effect.  For instance, my 70 lb (~30 kg) dog can easily jump the 4 ft (~1.2 m) panels around the corral.  I can vault them too, using hands to go over,  My 1200 lb (~500 kg) horses either can't or don't want to jump that fence.

@jamesqf a horse is not a cat. I talked about scale earlier, going up to human size (cougar). They can clear 18 feet in one bound.

@homnid  I wasn't familiar with the term. Hahaha.


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Do eye muscles relax when you close your eyes?
I wonder whether the eyes muscle relax when you close them. Common knowledge told us the eyes muscle get tense when you stare at nearby object. If you close your eyes, you eye lids have 0 distance with you eyes. Would the eyes muscle relax in this case?

Related: http://biology.stackexchange.com/questions/968/what-is-the-eye-muscle-status-when-you-stare-at-distant-view-through-a-glass-wal

I would guess that the eye muscle relaxes when the eye is closed. After having the eyes closed, just in the moment after opening them, it seems that the focus is in the distance. It takes a fraction of a second before you can read some text on your computer screen for example . This focusing-duration seems to be shorter when looking into the distance after opening the eyes.
Another effect is when you look at an object in short range for quite a moment and then close your eyes. You can feel the relaxation.

Certainly noticed what you mean when closing eyes and then attempting to immediately focus on a near-to object.  I wonder if it could be due to it being dark when the eye is closed - this could I suppose result in the relaxation (as there is nothing to "see" if you do this in a pitch black room).

I can confirm the eye muscles relax. Not just intraocular muscles, but also the extraocular muscles. I've recovered from chronic eye strain. I know.


text:
Questions to ask to a panel of people that will be sequenced
Some genes have been shown to be associated with left-handedness.
Working with some clinicians, I've recommend them to ask their patients (whose genome will be sequenced) if they are "right or left-handed".
It's a simple phenotype (without any ethical issue) that will be later fun/interesting to analyze through the sequencing data outside of the main study.
Do you know any other such kind of simple phenotype that we could ask to our patients ? :-)

I've heard wet/dry earwax is a very simple and genetically identifiable phenotype.

23andMe is a company that provides sequencing. Before they sequence your genome, they ask you to fill in a couple of surveys, one of which is about your physical features. Here is a list of some of the questions they ask:

How much hair do you have on your upper/lower back?
When you walk, in what direction do your feet naturally face?
Do you have a line or indentation (dimple) in the middle of your chin?
Excluding any hair loss, does your natural hairline have a widow's peak (a V-shaped peak of hair at the front of the hairline)?
Can you flip your tongue over so that the underside is on top?
Can you lift one eyebrow while keeping the other eyebrow in place?
Which is longer, your big toe or the toe next to your big toe?
On your left hand, which finger is longer, your index finger or your ring finger?
What is your shoe size in U.S. shoe sizes?
How would you describe the arches of your feet?
Can you bend down and place your entire palms on the floor while keeping your legs straight (see above image)?
Which image best matches the natural shape of your face (with your hair pulled back)?
  ...

That's a small list of phenotype questions you can ask ;-)

The full version of this list is long and that can bring about interview or questionnaire fatigue. Do not forget to factor in the length of time for a subject to answer all questions nor the cost of entering and analyzing those responses. Frankly, if 23andMe is asking these types of questions, you shouldn't because they will beat you to a report on the association. Deep phenotyping is critical, but direct that effort to collecting lifestyle data - like diet, sleep, exercise - which all influence the genotype-phenotype association

I think that if 23andMe ask these questions, there is a strong reason for their selection. And if you pay the money for your genome to be sequenced, you would want to answer as many questions as they ask you.

Just a small nitpick, 23andMe does not offer what is generally considered genome sequencing (which at current market prices would be northward of $8k). Their product is SNP genotyping via microarray analysis (at $10s-$100 / chip depending on the company). The array currently repported in use by the company is the Illumina OmniExpress.

Yeah, the strong reason for the selection of these traits/questions is 23andMe's desire to engage a customer base with curiosity questions - like smelling asparagus metabolites in the urine. Their (business) model is quite different from a researcher trying to convince a review panel to fund their proposal, hence my call to focus on more medically oriented phenotypes. At the same time, 23andMe has an obstacle in obtaining reliable data on one's lifestyle. I have nothing against these questions when asked via the secure 23andMe site, but better questions can be asked by Pierre's colleagues.

Another list of simple human traits can be found on the Western Kentucky University site.
I will ask also AB0 and Rh Blood Groups, you can use this also to check associations with other genotypes/phenotypes, see this stackexchange question
If you are going to sequence also the mitochondrial DNA, you may want to reflect on questions to ask also about their mother phenotypes.
Finally you may want to find also the windows, mac or linux preference gene.

I trust that the linux gene is recessive? ;-)

I hope that the Linux gene is dominant! More likely that it is rare, and in combination with certain deletions ;)

Please people, don't talk about dominant/recessive traits! Best case scenario, there are some associations ;-) Besides, the 'linux gene' would have more environmental effect.

+1 Gergana! It is definitely a gene-by-environment interaction!. As GxEs are our forte, we'd take keen interest in the study.

One that I wish we asked the subjects in our studies is: When do you normally go to sleep each evening and when do you normally wake up? This can get more detailed, but these 2 basic questions can allow segregation into morning or evening types (or both).
Deep phenotyping is critical to a better understanding of the genetic influence on disease risk phenotypes, and so one should collect lifestyle data - like diet, sleep, exercise - which all influence the genotype-phenotype association (these are called gene-environment interactions). If you can come up with phenotypes that distinguish different paths to the "same" disease outcome, that would be relevant to ask. In other words, there are often many paths to a very similar disease outcome, but as those paths are different, the disease may be slightly different. This requires sub-classification of disease - think of the different types of breast cancer. So, collecting these phenotypes, if you know them, in conjunction with diet, exercise, etc, will give you some very interesting possibilities.

Some other ones:

Are you a Singer? :-)  AVPR1A and SLC6A4 Polymorphisms in Choral Singers and Non-Musicians: A Gene Association Study http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0031763
Do you have sunbed sessions?
Do you dance?  (via C.Dina. ) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1239939


text:
Do the majority of fish lack scales on their heads?
Based on pictures, it seems to me that a vast majority of fish species that have scales do NOT have scales on their heads.
Is that fact true?
To make this properly answerable:

lets' define a "majority" as >70% of fish species. But frankly, I'm more interested in actual numerical answer than whether it passes some arbitrary threshold or not.
The universe which I'm interested in measuring the percentage are fish species that have "normal" (Cycloid and ctenoid is the technical term, I believe?) scales on their bodies.
If that's not specific enough, you can restrict the universe to species in Actinopterygii (ray-finned) that have scales.

Shouldn't a majority be 50% + 1? Also are you referring to species or to total numbers?

@Kevin - species, as the first bullet point notes. As far as 70% vs 50%+, the question came out of an argument, for which mere 50%+ would not be a convincing enough number, whereas 70% would. And without a specific number, this would be a bad SE question (too vague)

@DVK: there is really no argument that 50%+1 > 50%-1, hence it is the majority. But I'm just nitpicking.

(Should be comment, but rep=1.) This might be helpful (from Wikipedia): "The same genes involved in tooth and hair development in mammals are also involved in scale development." Mammals tend to have less hair on their face than on their bodies. If you can track down the reason for that, then you might have the same reason for fish, and then could use that to reason out your estimate.

Would also be nice to know (or at least think about) whether if this is the case it's because of synapomorphy (i.e. shared heritage) or convergence.

aren't they just much smaller and softer so harder to see clearly as scales?

A lot of fishes have scales on the opercle ("cheek"), and sometimes inferior to the orbit of the eye--but they are often very small. I'm not sure about overall patterns, or how common they might be. I could see a hydrodynamic reason for not having scales rostrally to avoid inducing drag, but not sure the literature agrees with the answer.

The only Actinopterygii that I know of which do not have scales on their head are of the order Cypriniformes, which includes fish such as minnows and carp, as well as of the order Anguilliformes, which includes various Eels. There are ~4000 species of order cypriniformes, and ~900 species of order anguilliformes.
As mentioned by @Ell, most fish have scales on their heads, they're just really small/fine. Example actinopterygii that exhibit this are salmon and trout.
Source: F.H. Pough, C.M. Janis, & J.B. Heiser 2013. Vertebrate Life, 9th ed. Prentice Hall., Chapters: 5-6, 8-9.

@nico The description of majority you just presented is in fact erroneous. https://en.wikipedia.org/wiki/Majority#Erroneous_definitions

@Charles I was not the one who defined majority, just said that 50%+1 > 50%-1 , which is purely a math statement :)

Ah, my mistake. I suppose that clarification should be directed towards @kmm.

I know Chondrichthyes (sharks and rays) have scales on hte head, their entire body is covered in tiny placoid scales. Don't know about other fish with different scale types.

I certainly agree with your general observation, but not being an ichthyologist, I can only offer a partial answer, based on a particular family of fish. Within the family Tripterygiidae, most species lack scales on their head, or have highly modified types of scales. A comparative study of 48 species showed that only 2 have "normal" scales of their head (Jawad, 2005).

The squamation pattern of the bases of the fins
  varies among species. The head is usually devoid of scales
  except for two species that have squamation with body-
  type scales (Matanui bathytaton (Hardy, 1989) and
  Norfolkia clarkei). Several species have head ctenoid scales
  modified into tiny spicules of different shapes (Acantha-
  nectes rufus Holleman & Buxton, 1993, Apopterygion
  oculus Fricke & Roberts, 1994, Axoclinus carminalis,
  Ceratobregma acanthops, Cremnochorites capensis, Ennea-
  nectes boehlkei Rosenblatt, 1960, Forsterygion malcolmi
  Hardy, 1987, Forsterygion varium (Forster, 1801), Karalepis
  stewarti, Matanui bathytaton, Norfolkia clarkei, Notoclinops
  caerulepunctus Hardy, 1989).

So far, I haven't found a broader comparative study, to support your general question. Someone more knowledge in the area and the literature can perhaps offer a more general answer. This is at least an indication that your observation might be correct.
Reference
Jawad. 2005. Comparative scale morphology and squamation patterns in triplefins (Pisces: Teleostei: Perciformes: Tripterygiidae). Tuhinga 16 (1), 137-168

Based on a lack of written evidence, in searching Google and Google Scholar, I believe fish have scales on their heads, where I'm defining 'scales' as 'solid, protective bony scales' [see below], and I'm assuming the fish heads are covered with solid protective bony Big scales.  I think a lack of scales on fish heads would be a fish fact that wouldn't be too difficult to find.

Some fish lack scales altogether, such as gobies and toadfish:
https://www.slideshare.net/gurya87/types-of-scales-in-fishes-44959366
This wikipedia article mentions scales repeatedly [examples below] but says nothing about a lack of scales on fish heads -https://en.wikipedia.org/wiki/Fish_anatomy

a.  The dermis is covered with overlapping scales.
b.  The dermis of bony fish typically contains relatively little of the connective tissue found in tetrapods. Instead, in most species, it is largely replaced by solid, protective bony scales.
c.  The outer body of many fish is covered with scales,

I can't find reference to it is not good justification.


text:
Are prions an important driver in evolution?
I understand that prions have been implicated in the passing on of epigentic information[1]. Are prions thought to play a significant role in the evolution of organisms?

 Alberti S, Halfmann R, King O, Kapila A, Lindquist S. 2009. A systematic survey identifies prions and illuminates sequence features of prionogenic proteins. Cell 137: 146–58.

@aland Thanks for your effort to improve the quality of citations in the questions and answers on this site. You may be interested in this thread in the meta regarding the best location for complete/verbose references.

It is proposed that prions are a good mechanism for "testing" phenotypic variation.
There are many identified proteins with prion-determining domains (PrD) in the yeast genome that can spontaneously switch between conformations with some low probability (eg: check SUP35 for one example, and [1] for a good overview of more). The theory is that:

the low probability of switching from non-prion to prion state allows for many more mutations and variations to accumulate -- generating greater genetic diversity than in standard expressed gene variability where most mutations are silent or detrimental
the prions provide a ready form of non-permanent inheritability that can be "trialed" by offspring and others in a colony of organisms -- this can be especially beneficial during say temporary changes in environment
if the prion phenotype is widely successful, selective pressure can easily mutate it into a more permanent fixture in the genome.

Check out the excellent paper published just last week in Nature exploring this this topic [2]. To give a sense of just how evolutionarily-advantageous prions can be, in the author's experiments and analysis they note that 40% of the prion traits they analyzed were beneficial to growth (eg:  in the paper strain UCD939 gains additional resistance to acidic conditions from the prion [PSI+]).
Assuming these hypothesis, prions would thus play a significant role in the evolution and variability of organisms.
[1] Crow, et. al. 2011. doi:10.1016/j.semcdb.2011.03.003
[2] Halfmann, et. al. 2012. doi:10.1038/nature10875


text:
Can a cell culture insert plate be used with a vacuum manifold?
There exists 96 well plate setups for use with vacuum manifolds. Is it possible to use 6/12/24 plate inserts with the same setup?

This company sells a vacuum manifold for 24, 48 and 96 well plate formats.


text:
Can any other animal choke on food?
I read somewhere (I think it was Bill Bryson's book on the origins of the English language) that of all animals, we are the only ones that can choke on food (having something to do with how our larynx is positioned).  I'm unable to find reference to this fact online, however, and am curious if this is just my having misunderstood something (or Bill having led me astray!).

Choking fish and other animals are not cogent to the question. Fish breathe through gills (interaction with oxygenated water), dolphins have blow-holes in the top of their heads, etc. ?do horses and others have a breathing tract that does not intersect with their method of eating , especially drinking ? R.M.

In response to the answer, I add only that lizards and birds DO suffocate upon regurgitated food. Talk to herpetologists and bird keepers for ample, and sad experience with this.

Bill Bryson mentions this in 'The Body', chapter 6 "[...] uniquely among mammals we send our air and food down the same tunnel, only a small structure called the epiglottis [...]" That's what brought me here, but I listen to the audiobook so I can't tell if he gave a reference.

From the Smithsonian website:
Humans are the only mammal that cannot breathe and swallow at the same time, and we are the only species that can choke on its own food. The reason? The lowering of the voice box in our throats (during infancy) enables us to create the enormous range of sounds used in producing language; but this lowering of the voice box comes at a big cost in adulthood.
http://newsdesk.si.edu/factsheets/did-you-know-human-origins-facts

This is incorrect, any vertebrate that can breath through its mouth can choke on food. Not all animals can breathe through their mouths but many can. The shared portion of the esophagus and trachea called a pharynx and the pharynx varies quite a bit across vertebrates. a continuous pharynx is not exclusive to humans, humans just have a very large complex pharynx making much much easier for us to choke on our food.

The veterinarian in our group offers this: For humans, who choke much more frequently than other mammals, it is likely to be a cognitive problem. We talk and eat at the same time and so give ample opportunity to allow food passed the epiglottis and choking. Animals do choke - dogs can, cats can. Not all animals can vomit and this is particularly a problem for horses, whose stomachs will rupture instead of releasing contents through the mouth.

YIKES, didn't know that about the horses. Interesting

This is rather late, but would it be possible to add some citations?

Horses also cannot breathe through their mouths.

I don't agree with the accepted answer which seem to assume that food is chewed. I don't think that can be assumed if generally talking about animals and choking.
So in addition to Larry's statement of dogs and cats:
Fish regularly chokes on prey.

Birds can choke.

Even dolphins choke:

Can it be called choking if it isn't in the wind pipe, and if the animal doesnt breathe air? Perhaps the human is the only animal that can get food in their breathing apparatus.

There are different kinds of choking on food. All non-gilled animals also choke when they fall in the water. Drowning is choking. insects asphyxiate and fish asphyxiate in air but technically insects don't have any obstructed passages. Perhaps you can say fish choke when their mouth is obstructed with air, choking also means gulping because of asphyxiation of any kind.

An animal gets food in their wind-pipe, which is death from choking.
An animal gets food stuck in their eusophagus, which is perhaps indigestion, not directly choking.

Yes! Humans are the only known animals whos recent evolution has dgiven them one of the worst throat control of all throated animals, and who can easily get food inside their breathing apparatus and die from it, who can choke on vomit and who can't regurgitate as efficiently, and who can't breathe and drink. The valve used for dividing the air and food channels has changed and is used by the humans for speaking.

In other mammals the eusophagus is different: The larynx is fixed at the top of the throat and can make a valve at the back of the nose to form a breathing tube parallel to the esophagus.
Humans are speaking through the valve that is normally used to drink and breathe at the same time. When they drink, the Adams apple raises to form a valve at the top but it doesn't form a continuous airway to breathe while drinking.
For other animals such as birds and fish, it is especially important to breathe and eat simultaneously because
A/ they can drink large volumes at waterholes in competitions with other animals and as potential quarry
B/ Herbivores can spend much larger amounts of time than humans eating, ruminating, and if they have less breath for running then it's a disadvantage
C/ Carnivores can eat much larger chunks than humans, they regurgitate it to their children, they get larger things stuck in their throat, so they have much more performant and controlled throat functions
D/ Birds and Lizards regurgitate foods and get them stuck in their throat and it would be a problem for them if the suffocated or got regurgitated food stuck in their windpipe because they didn't have an adequate valve there.
E/Fish dont have as constricted a junction between their breathing and eating functions.
Here is an excerpt from a book:
In most Animals the larynx sits high in the throat and serves as a valve. As the animal drinks, the larynx forms a continuous tube with the space at the back of the nose, thus the airway -trachea to nose- forms a continuous hose that runs up through through the space of the mouth and throat into the esophagus. in other words the animal can drink and breathe at the same time. The larynx of the human being has been repositioned half way down the throat as the Adam's apple of the male makes clear. So the human being cant drink and breathe at the same time without choking. That seems like a disadvantage- except that the descent of the larynx leaves a large space above it which acts as an echo chamber.
If a human makes a siren sound while touching the adams apple he will see what the space is used for, it sounds same as a monkey when the adams apple is high at the top of a note. If a human also swallows and monitors his larynx he can imagine that other animals are the same except that their larynx performs better as a valve and doesn't have many octaves of controllable voice range.

How does this answer the question?

It explains the mechanical difference in the throat which means that humans are the only documented animals who can get food in their windpipe due to the recent evolution of speech which has displaced the valve they use to block their lungs while eating. i will write more of a yes no approach to it if you want.


text:
How crowded is the bacterial cell?
I was wondering what is the protein concentration in an E. coli cell. When studying enzyme kinetics and activity in vitro, I would argue that the substrate and enzyme concentrations resemble those in vivo. As a result, conclusions made by such assays do not apply 100% to the naturally occurring reactions. Are there any examples in literature that address this issue?
Along those lines, what is the concentration of fatty acids/nucleic acids in the cell?

The macromolecule concentration within E Coli is estimated to be around 0.3-0.4 g/ml [1]
The concentrations of your substrate in respect to your enzyme are generally fairly analogous to in vitro studies compared to in vivo studies. However, this is heavily based on the assumption that the diffusion constants for both molecules stay consistent. In many cases that is true and errors can be corrected for using PEG to imitate the crowding effect. And yes, people have begun to look at the question [2]
However, for larger macromolecules like DNA and chromosomes that do see effects from subdiffusive transport, the molecules don't obey diffusive random-wal behavior [3]. The classic model system is the lac repressor which exhibits non-diffusive kinetics due to its interactions with DNA.

http://www.ncbi.nlm.nih.gov/pubmed/1748995
http://www.ncbi.nlm.nih.gov/pubmed/21237136
http://prl.aps.org/abstract/PRL/v104/i23/e238102
http://www.ncbi.nlm.nih.gov/pubmed/7317363

Composition of E. coli (dry weight): 55% protein, 20% RNA, 10% lipid, 15% other
Protein concentration is about 100 mg/ml or 3 mM. From the size of an E. coli cell, 1 nM is about 1 molecule/cell. This is ~1000 molecules/cell for HeLa cells.
Diffusion coefficient for an "average" protein: D ~ 5-15 microns^2/s, or ~10 ms to traverse an E. coli. For reference, a small metabolite in water diffuses about 30-100x faster.
Reference: Cell 141:1262, Key Numbers in Biology

For a great visualization of the macromolecules inside the cell, check out David Goodsell's illustrations.  He tries to reproduce the protein and DNA density within the cell to show how things might be in vivo.  Really great stuff.
The answer is - its very concentrated.  Compare the density of the cell to that of a typical crystallized protein, which is I believe 0.8 g/ml of protein.
http://mgl.scripps.edu/people/goodsell/


text:
Is there a term for tool use in animals?
Is there a technical/scientific term that scientists use to refer to tool making abilities found in certain types of animals?
Reference http://en.wikipedia.org/wiki/Animal_cognition#Tool_and_weapon_use

Note that you actually ask two different questions here - 'tool use' and 'tool making' are two different behaviours. Although, to the best of my knowledge, the correct terms for them (whatever the species) are 'tool use' and 'tool making' respectively.

Having read this article on tool use in Chimpanzees in full, I am inclined to say that if such a term existed then either the article itself or the titles of any of the 30 articles referenced would have included it.
Searching a couple of online biological dictionaries and ethology sites hasn't yielded anything either, therefore until someone else points out that I'm missing the obvious I'd say you're free to coin the term yourself!

Yeah, I've never seen anything more formal than just plain "tool use". For instance, see the article "The Ecological Significance of Tool Use in New Caledonian Crows"

Ok. Thanks for the answer. Appreciate it. Was hoping for a "scientific term" if such a thing exists. Thanks anyway!

I think "tool use" could serve as a good term on it's own, don't you think?

Yea... But I am looking for a phrase which confuses the layman. :-p haha.

:-) All these years I've wondered why an "ophthalmologist" couldn't just be called "eye doctor"... Let's please just call "tool use" as "tool use". No more Latin, Greek. Let's just stick to the current state of English.