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What are the effects of sleep deprivation?
Having recently pulled an "all-nighter" while trying to fix a fatal bug in our release code, I started thinking of any health risks that I might have.
What are the adverse effects of staying up for staying up for 42 hours, considering I took no caffeine or other stimulants, as well as no depressants such as alcohol?
Upon googling I found a lack of facts, what would be good is a list of effects and rough times that they start happening.  And any significant problems I would face, but moreover I would like to know what causes them?  Unfortunately I only studied Biology until GCSE (UK - SAT/TAKS Alternative) and might need some simplified explanations or links to help understand more complex tasks.
I'm not even sure if this question is grammatically correct, and my brain power has slowly dwindled, should I be worried?  I have read this and understand it to a vague extend.

Something that I know is that it affects memory negatively. If you search google scholar then you'll get a lot of articles on sleep deprivation experiments.

I've never heard of google scholar before.  Thanks for pointing me in that direction!  It seems a cool google sub-site.  Also thanks for the information on more sleep deprivation experiments.

Personally, I notice that most cognitive effects of sleep deprivation become very strong during times in which I would be habitually asleep, and minimal when I would awake normally. Arousal also seems to minimize perception of sleepiness, while being idle/bored makes it worse. You don't seem to have experienced this, your symptoms just get worse and worse.

You seemed to have answered your own question with your edit.

I noticed it worst when I was actually having a shower Superbest - Not sure if it was the heat that made be drowsy or what.  I guess I did Eastman, however why this is caused was not answered, and whether there are any lasting effects.

I recommend watching this youtube video by Hank Green (SciShow): https://www.youtube.com/watch/?v=pwNMvUXTgDY

24 Hour Mark
The consequences of sleep deprivation at 24 hours is comparable to the cognitive impairment of someone with a blood-alcohol content of 0.10 percent, according to a 2010 study in the International Journal of Occupational Medicine and Environmental Health.
36 Hours
Now your health begins to be at risk. High levels of inflammatory markers are in the bloodstream, said Cralle, which can eventually lead to cardiovascular disease and high blood pressure. Additionally, hormones are affected — your emotions can be all over the place.
48 Hours
After two days of no sleep, the body begins compensating by shutting down for microsleeps, episodes that last from half a second to half a minute and are usually followed by a period of disorientation. “The person experiencing a microsleep falls asleep regardless of the activity they are engaged in,” she said. Microsleeps are similar to blackouts, and a person experiencing them is not consciously aware that they're occurring.
72 Hours
Expect significant deficits in concentration, motivation, perception, and other higher mental processes after many sleepless hours, Cralle said. “Even simple conversations can be a chore,” noted Kelley. This is when the mind is ripe for hallucinations. Kelley recalled a time he was on guard duty and repeatedly saw someone standing with a rifle in the woods, ready to sneak into camp. Upon closer inspection, he determined he was actually looking at a branch and shadows.
Sleep: Why We Need It and What Happens Without It - SciShow from Humza Zaidi's comment
.

According to healthysleep.med.harvard.edu:
Sleep and Disease Risk
The price of insufficient sleep may be poor health. Study after study has revealed that people who sleep poorly are at greater risk for a number of diseases and health problems. And now the search is on to discover why this might be. more
Sleep, Performance, and Public Safety
Lack of sleep exacts a toll on perception and judgment. In the workplace, its effects can be seen in reduced efficiency and productivity, errors, and accidents. Sometimes the effects can even be deadly, as in the case of drowsy driving fatalities. more

Little more specific citation/reference will be better.

Edited :) @Dexter


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What is the mechanism of oxygen uptake in E. coli?
How does E. coli uptake oxygen? Most of the literature I found is concerned with response to oxygen level supplied in the medium, as opposed to how much is actually transported inside. Can they shut down the oxygen uptake if required? For example, to avoid damaging effects of reactive oxygen species.
There exist bacteria which die in presence of oxygen (strict anaerobe), while some use oxygen when available but also can survive in absence of it (facultative anaerobes, like E. coli). Are there bacteria which cannot consume oxygen for metabolism, but when exposed to oxygen they don't die, rather simply discard the oxygen and carry out fermentation? In a sense, they are strict anaerobe (their mode of metabolism is anaerobic), but they can still survive in presence of oxygen in environment.

Have a look at this related post too

This question got me thinking about what are the metabolic enzymes that take oxygen up in E.coli. I searched the metacyc database for reactions that consume molecular oxygen and there are only 3 that take in oxygen and one that produces oxygen.
All three consumers of oxygen in E.coli are the oxidation of ubiquinone by at two sites in cytochrome-bcl or by cytochrome-bo.  All of these export protons to create the gradient that drives ATP formation by F₀F₁ ATPase in the periplasm (the region between E.coli 's inner and outer membrane).

On the production side, superoxide dismutase reduces superoxide to oxygen to control oxidation damage.  Apparently the innards of E.coli are somewhat oxygen tolerant.

Thank you, is diffusion alone the mechanism of uptake?

yes, as @canadianer describes. I'd only wanted to add a description of how oxygen is taken into the system and consumed, which seemed like part of your question as well :)

I would be grateful if you could provide me some  references on how oxygen uptake capacity ( diffusion capacity) changes over growth rate or other variables, if any.

The plasma membrane is quite permeable to oxygen and thus oxygen enters the cell simply by diffusion. Reactive oxygen species can be reduced enzymatically in aerobic organisms. Obligate anaerobes lack or don't produce sufficient quantities of these enzymes. An organism that doesn't use oxygen for metabolism but is also not relatively harmed by it can be classified as aerotolerant.

Image from: http://en.m.wikipedia.org/wiki/Anaerobic_organism
Original Caption: Aerobic and anaerobic bacteria can be identified by growing them in test tubes of thioglycollate broth:
1: Obligate aerobes need oxygen because they cannot ferment or respire anaerobically. They gather at the top of the tube where the oxygen concentration is highest.
2: Obligate anaerobes are poisoned by oxygen, so they gather at the bottom of the tube where the oxygen concentration is lowest.
3: Facultative anaerobes can grow with or without oxygen because they can metabolise energy aerobically or anaerobically. They gather mostly at the top because aerobic respiration generates more ATP than either fermentation or anaerobic respiration.
4: Microaerophiles need oxygen because they cannot ferment or respire anaerobically. However, they are poisoned by high concentrations of oxygen. They gather in the upper part of the test tube but not the very top.
5: Aerotolerant organisms do not require oxygen as they metabolise energy anaerobically. Unlike obligate anaerobes however, they are not poisoned by oxygen. They can be found evenly spread throughout the test tube.

Can you please give me an example of aerotolerant bacteria?

I think some Streptococcus and Lactobacillus spp.

Clostridium intestinale has been described as aerotolerant.

E. coli is a facultative anaerobe…

I would like to get example of aerotolerant but strictly anaerobic bacteria.

I am adding a supplement/concluding remarks to the existing answers.
Some points to be considered:

Electron transport chain can work without oxygen and can use other chemical species as electron acceptors.
E.coli is capable of aerobic respiration, anaerobic (anoxic) respiration and fermentation (substrate level phosphorylation).

How does E. coli uptake oxygen?

Short answer as already mentioned by canadianer: Passive diffusion

Can they shut down the oxygen uptake if required?

Oxygen is the primary electron acceptor and E.coli would prefer oxygen to other electron acceptors. Only in the absence of oxygen is the FNR regulon switched on. Other bacteria can show negative aerotaxis i.e. running away from oxygen (they obviously have to be motile) [ref]. This paper also comments that positive and negative aerotaxis happens via a common mechanism- sensitivity of proton motive force to O₂. However, ROS has no role to play in it. It is most likely that at high oxygen levels E.coli will try to jack up anti-oxidant response. To conclude- they cannot regulate oxygen uptake.
Aerotolerant anaerobes: Clostridium perfringens, Clostridium intestinale.

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Where I can find information about the study of animal vision?
I read a lot of articles on the internet about how dog see the the world. But I can't find the source of these study. I want to know how did scientist setup the experiment to find out animal vision. I don't know which keyword should I use to search for the information on the internet. Can anybody please send me some research paper about the problem?

A few days back I watched a documentary called Your Inner Fish. In it, there was a small segment about animal vision studies. Basically they had monkeys in a lab, looking at a screen which showed e.g. mostly blue bubbles, but then at some specific spot also red bubbles (sort of like those red-green color blindness tests). Every time the monkey poked the correct spot on the screen, it got a reward. So then they had added a third opsin gene (e.g. humans have three) to this monkey and it could separate colors that other monkeys couldn't.

While their work was in the cat rather than the dog, your starting point should be the work of Hubel and Wiesel.  They are the indisputable pioneers for vision research in general.  They won the Nobel Prize in 1981 for Physiology and Medicine.
See their Wikipedia entries (Hubel and Wiesel), the original 1962 paper, their popular press book, the Nobel Prize speech about their work and Roger Sperry's, and Wurtz's review (cited below).

Hubel, D.H. and Wiesel, T.N. (1962). Receptive fields, binocular interaction and functional architecture in the cat's visual cortex, The Journal of Physiology, 160(1), 106-154.
Wurtz, R.H. (2009). Recounting the impact of Hubel and Wiesel. The Journal of Physiology, 587, 2817-2823. DOI

Color vision was shown to be dichromatic (sensitivity to two color peaks) by Neitz et al. (1989). For a broader review of color vision of mammals, see Jacobs (1993).
Literature Cited
Jacobs, G.H. 1993. The distribution and nature of colour vision among the mammals. Biological Reviews 68: 413-471.
Neitz, J. et al. 1989. Color vision in the dog. Visual Neuroscience 3: 119-125.

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What does the term 'epitope mapping' mean?
Epitope mapping means identifying the binding site of antibodies on the target antigen. This means that the site to be identified is part of the antigen and not antibody, am I right?

yes.. you are right. Why the confusion :)

No, just wanted to make sure, actually I am reading immunoinformatics for my phd, and hence i should have crystal clear idea about the things i study. So thats y asked this question. It is not homework. its discussion

i know it is not a "homework" homework.. by homework we mean something that can easily be looked up.

yes,, things can be looked up, but sometimes understanding is a bit difficult more so becoz i havnt touched biology in the past 7 years


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Pollinator mating system in orchids
I came across three terms in an article on pseudocopulation. However I don't quite understand what it means.
They are:
1) solitary and haplodiploid
2) social and haplodiploid
3) diploid
These are mentioned in reference to pollinator mating systems in orchids. Could anyone please explain the above mentioned terms?

Can you provide a link to the article you read so I have context. I assume from the terms that the terms refer to the insect pollinators but I would like to be certain before I answer.

As 3cat already stated, the terms actually refer to the pollinators. While solitary and social describe the behavioural traits (see this wikipedia article), diploid and haplodiploid give information about the chromosome number of the pollinators (see here and here).
The descriptions in the article depict different combinations of both characteristics.


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What can myelination tell you about the evolution of sensory receptors?
I am reading Avi Chaudhuri's Fundamentals of Sensory Perception and wondering if the information given about the somatosensory system could tell us anything about the way it evolved.
It seems (at least naively) reasonable to assume that nerves became larger and more myelinated as time went on. The types of somatosensory nerve fibre are (in order from least to most myelinated):
C < A-delta < A-beta < A-alpha
This gives an ordering on receptors of:
warm receptors < cold receptors < nociceptors < tactile mechanoreceptors < proprioceptors
My question is then: was this the order in which these receptors evolved? If not, can myelination still give us useful information about the evolutionary history of the nervous system?
P.S. Meta question: is this question better suited for the Bio or Cog Sci stack exchange? I asked it here since it seemed to be more about evolution than neurons.

I think it's definitely on-topic here and would be welcomed on CogSci as well.  The evolution aspect is probably better addressed here, as you have already observed.

Interesting question. I will dissect your question into its assumptions before giving my view on the overall question.
1) ..that nerves became larger.. : Why should there be a general tendency for nerves to increase in size during the course of evolution when there is no need to?
2) ...that nerves became more myelinated...: A general tendency towards more myelination is not the case. Myelination is definitely a trait that has been acquired later in evolution, but "the more the better" does not apply. Imagine an electrical conductor - to insulate it a bit of plastic is enough. Adding more after that doesn't make a substantial difference.
3) ...the order in which these receptors evolved...: myleine sheaths are made up of glial cells that wrap themselves around axons of neurons. Myeline makes neural transduction more efficient and faster. Hence, the amount of myelination tells you something about the efficiency and speed of transduction of the nerve (Hartline (2007)). For example, longer axons tend to be myelinated, short ones not. That, in turn, will have certain evolutionary benefits for the host, as more efficient communications means less energy required, lesser loss of information, and increased processing speeds. The amount of myelin hence tells you something about the importance of efficient communication of that sensory system. However, it does not tell you anything about when this receptor evolved.
Hence, the relation between myelination and receptor evolution is remote at best. In terms of evolution, amounts of myelination may tell you something about the evolutionary pressure placed on faster and more efficient workings of the receptor systems.


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Is severe but short-term pain worse than moderate but prolonged pain for the body?
I'm wondering about the effects of different durations and intensities of pain on the body. So the two can be compared, let's say that the cause of pain is the same in both cases, but in one the duration is shorter although the pain is more severe, and vice versa. Also, by effects, I mean biological but also psychological (which is probably more interesting), but the latter might be out of the scope of this site, so forgive me if it is.
For the sake of a (rather grim) example, if someone is exposed to a painful stimulus such as a mid-voltage shock for a long duration, and if someone else is exposed to a much higher voltage shock for a much shorter duration of time, which would produce worse effects on the body's normal functioning? (Somewhat morbidly, I should say to assume that they both live and do not die on the spot.) Since the answer very well might depend on the type of harmful stimulus, I'll give another example of a burn. If one is repeatedly subjected to a first-degree burn for a while and another is subjected to a third-degree burn only once, which is worse?
Upon pondering the question, it seems that the psychological effects would be more interesting since they should be roughly the same regardless of the type of stimulus, but biologically the effects obviously differ.
Thank you for your time, and any responses or thoughts on this would be greatly appreciated.
Edit: Obviously most experiments to test this would be subjective and unethical, especially in the case of psychological effects, so just an opinion from someone more knowledgeable in biology is more than fine.

The psychological answer will very much depend on how the individual copes with pain and not be the same for all individuals. This said, I think you should use a more abstract example, because the ways you are right now causing the different types of pain are also harmful in other ways than just causing pain and so also influence the biological answer with the fact that for example a high voltage shock is more damaging.

The biological part of the answer to your question depends on the thing causing the pain. Burning for example, a large burn can be very life threatening biologically but small burns are not as harmful comparatively. But the psychological harm they would cause is phenomenal. This is because large burns open up the body to infections, dehydration and a lot of other harm.
Let's take stabbing as another cause of pain. One stab in a less dangerous place missing all important structures may be not that harmful but may be painful. However multiple small stabs into important structures like arteries or spinal cord could be horribly destructive.
Then let's look at headaches or nerve pain. Here it is only the pain and usually there isn't any destructive or harmful process. Most individuals would take one really, really bad headache followed by never having a headache then chronic daily "tension" headaches.
Psychologically though usually the chronic daily pain is the worst. Particularly as without adequate pain management from the start, it is less responsive to painkillers (analgesia). It frequently adds to depression if it does not cause it itself and can lead to suicide. Also painkillers themselves may cause chronic pain which does not help.
In summary, acute severe pain suggests something is seriously wrong and needs to be dealt with immediately biologically as there is likely a damaging process underlying it. However if this event is survived, it may be linked with high disability from any biological process that underpinned the pain. Chronic daily pain suggests a long continuing process. The cause of this may be life threatening, such as cancers, but is usually less dangerous at least compared to acute severe pain biologically. However the psychological aspects of this pain are seriously important as they can be particularly detrimental.

Frankly, I don't see how this answers the question. "The biological part of the answer to your question depends on the thing causing the pain." I would have interpreted the question as to mean exactly the opposite => what long-term bodily harm does the pain itself cause? It is clear that whatever causes the pain can be inherently harmful (or not, as in your headache example). But what additonal harm does the pain itself cause? It clearly makes the sufferer unhappy, unless they learn to ignore it through meditation etc.; but does it, e.g., restructure neurons in the brain, etc.?


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How can oxygen production during photosynthesis be measured?
I'm curious how people measure quantitatively photosynthetic rate in labs.
I've seen many qualitative examples with direct observations of bubbles forming in water due to photosynthetic output of aquatic plants.
The ways I have come up with are:

to measure the CO2 intake.
to measure the O2 output.
to measure the amount of sugar produced.

The 3rd option seems most trivial, but I don't know how to measure the amount of CO2 present in a container. With a reaction? Or with a measuring machine of some sort? What about O2?

Similar post


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What is a protective epitope?
What is a protective epitope? An epitope is basically a part of antigen. So does it mean that when the epitope combines with an antibody, it helps in the functioning of the antibody instead of going against it?

Lets define the nomenclature first: An antigen is a large structure (protein, virus, bacteria and so an) which is recognized by the immune system as foreign. The word antigen derives from the abbreviation ANTIbody GENerator. Exposure of our immune system to an antigen results in an immune response and the generation of many antibodies.
An epitope is a small part of an antigen - typically these are small structural elements or small peptides (8-11 amino acids in length) which are recognized by the binding site of an antibody. See the picture below (from here):

Here the antigen is the albumin protein. On the surface you can see 8 different epitopes which lead to the generation of 8 highly specific antibodies against the epitopes (antikörper is the german word for antibody). Every antibodies is highly specific for its epitope and will recognize no other epitope and helps raising an immune response against it. What happens after an antibody bound to its epitope can be read here.
Antibodies directed against a protective epitope are directed against (highly) conserved structures of the antigen. For example the recognize a highly conserved structure of a virus which means that even when this virus mutates (like influenza does) it will still recognize the conserved epitope and give protection against this virus (or better: antigen).

understood. But what does  a protective epitope mean?

Ah, sorry, forgot to answer that. I will updated the answer, better now?

what is a protective epitope? I still dont find the answer of y question. what exactly is a protective epitope?

It is a normal epitope. But one which is widely distributed between different strains of a virus/bacteria etc. and gives you a very good protection against these antigens.

The word protective is an adjective which describes the function of the noun epitope. It is an effective protector against infection. Like @Chris said its protectiveness is derived from recognizing a conserved region of a molecule. Recognizing a conserved region of a molecule is what merits the special adjective 'protective'.

so, we can say that all antigens have a protective epitope?

antigen receptor is epitope, am I correct??

Nope, this is the paratope. The epitope is the part of the antigen which is recognized by the antibody.


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sex limited genome transmission
In general, for dioecious species, a large portion of the genome passed from parents to offspring of both sexes - in mammals the X-chromosomes and autosomes are passed from a mother to both daughters and sons, and autosomes from the father to both sons and daughters. Only the small amount of genes present in the Y-chromosome and mitochondria are inherited solely within one sex.
Is there any species (not just mammals) where most, or even all, of the genome is inherited in a sex-specific trajectory? What is the most sex-limited genome known to researchers?

In birds and reptiles females are the heterogametic sex with allosome configuration ZW. However it has been reported that a homogametic WW female boa was born by parthenogenesis. So it means that although W is shorter than Z, it can still support life. So I guess that ZW system in general exchanges more sex-limited genetic material than XY system.
Platypus has 5 pairs of sex chromosomes. See here. This can qualify as the top case of sex-limited transmission.

Platypus just HAS to be utterly weird on every level ...

Is there any species (not just mammals) where most, or even all, of the genome is inherited in a sex-specific trajectory?

Here are a bunch of cases and specific examples that may interest you

There is a species of ants where both genders evolve to be able to reproduce by parthenogenesis (which means that males might be call females as well). In this species, the two genders mate together to create workers that do not reproduce! Therefore, when you look at the phylogenetic tree you can see that males and females are on two totally separate branches as there is reproductive isolation between the sexes in terms of fertile offspring. There is an article by L. Keller on the subject.
In the amazon molly, there are no males. But it is interesting because females need sperm to start the development of their ovules although they don't even use the genetic material of the sperm. Therefore, the amazon mollies need to find mates in sister species. In consequence, they imitate the females of the other species. There is a recent article from Hanna Kokko that investigate with a mathematical model how such system may be able (not cause the extinction of the amazon molly or of the sister species).
Sex-specific segregation distorter. Nasonia sp. may be an interesting case study
Haplo-diploidy. In ants for example, sons receive genetic material from their mother only. They are haploid.
if the rate of sexual reproduction is different from 1 then, females are responsible for more than half of the inherited genes in the next generation.

I apologize for the lack of references $\ddot \smile$

The new mexico whiptail reproduces purely through parthenogenesis. The species itself originates as a hybrid of two other species of whiptail, but the hybridization can't make fertile males. The females can reproduce through parthenogenesis so that's how the species continues to exist. So 100% of the genome is passed mother to daughter for many generations, very few new mexico whiptails are made through a fresh hybridization of the parental species.
http://en.wikipedia.org/wiki/Cnemidophorus_neomexicanus


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What are the atmospheric requirements for large dinosaurs?
What are the atmospheric requirements for large dinosaurs? and are the atmospheric constituents for supporting large dinosaurs any different from the atmosphere today?

nice question! worth looking at the atmospheric composition of earth at that time but whether that was the optimal atmosphere for large dinosaurs is much harder to tell I would imagine!

@Bez i think this question is drawn from creationism rather than evolution....i dont remember any atmospheric requirements for animal sizes...

@caseyr547 good point! but it would still be interesting to know about the atmospheric composition of earth at that time and whether that was in anyway more suitable to species back then compared to now if they switched environments. I suppose species back then either had to adapt or die based on the particular atmospheric conditions they were in although it is more likely that they evolved slowly over time as with any other evolutionary processes. I agree with you but thought provoking still.

A mineralogical from sufficiently old and correctly dense rock and dirt might give an idea of the state of the atmosphere from that time @Bez but I do not know if mass spect is that advanced yet

In general large animals would need more oxygen. This would be especially true for animals with less efficient oxygen transport, such as insects. There was more oxygen in the atmosphere in the distant past due to an imbalance in cellulose creation and digestion. This is also where coal comes from. It's explained in more detail in some episode of Cosmos ( the new one ). If I find more details I'll come back with an answer.

Thanks for this info! From that data, I wonder if something besides oxygen levels may have been involved 350,000 years ago. Isn't the real issue the partial pressure of oxygen and not just the amount of it? Is there any reason to believe that partial pressures of oxygen varied? Can that be detected in the rock record?

Oxygen levels have changed greatly throughout Earths's history starting with very little atmospheric oxygen and gradually increasing as photosynthetic activity appeared until all the oxygen sinks such as minerals had been filled, then taking off, reaching as high as 35% of the atmosphere during the carboniferous period 3. The reasons behind this sudden increase in O₂ has to do with the development of bark covered wooden plants, a feature made possible by the molecule lignin, which strengthens the trunks of trees and makes tall plants possible. However, lignin was hard for microbes to digest, and the dead trees built up, never returning their carbon to the atmosphere as CO₂. So the oxygen they had made while alive stayed in the air 4.

The plot shows the upper (red) and lower (green) estimates for O₂ concentration over time. The data for this plot was taken from a review of analysis of sulfur, carbon, iron, and manganese deposits 2. If you're interested in how isotopic analysis can give information about atmospheric oxygen, read that paper, it's detailed.
That spike in the plot is the carboniferous. This period in history is interesting because of the appearance of large invertebrates, such as 3 foot wide dragonflies and 6 foot long centipedes 5. Since these animals move oxygen through a series of tubes called trachea, where air just moves through by diffusion, it was speculated that the higher concentration of oxygen allowed this growth. Recent research indicates that insects can force air through their trachea, and that competition between predators and prey could have explained most of the size 6.
So how does this affect dinosaurs? The carboniferous period was about 350-300 million years ago, which corresponds with the spike on the graph. Dinosaurs appeared in the Triassic, which was about 250-200 million years ago, but oxygen levels were at 16% of the atmosphere at the time 7 ( current O₂ levels are about 20% ) If we move into the Jurassic, about 200-150 million years ago, oxygen levels rise to about 26% 8. In the Cretaceous, about 150-65 million years ago, O₂ was at about 30% 9. The O₂ percentages are taken from the infoboxes on the right side of the wikipedia articles, which in turn take the number from a plot very similar to the plot I posted here, despite being in German 10.
I compiled lists of heaviest and lightest dinosaurs by going through the wikipedia article on dinosaur size 11 and going to the article on each dinosaur and checking if it was Triassic, Jurassic, or Cretaceous.
If we look at the heaviest dinosaurs, most of them appeared during the Cretaceous:
Heaviest Dinosaurs
Theropods                           Metric Tons     Period
Spinosaurus aegyptiacus             7-20.9          Cretaceous
Carcharodontosaurus saharicus       6.1-15.1        Cretaceous
Giganotosaurus carolinii            6.1-13.8        Cretaceous
Tyrannosaurus rex                   6-9.5           Cretaceous
Oxalaia quilombensis                5-7             Cretaceous
Acrocanthosaurus atokensis          5.6-6.2         Cretaceous
Tyrannotitan chubutensis            4.9-5.6         Cretaceous
Suchomimus tenerensis               2.7-5.2         Cretaceous
Therizinosaurus cheloniformis       5               Cretaceous
Tarbosaurus bataar                  4-5             Cretaceous

Sauropods                           Metric Tons     Period
Amphicoelias fragillimus            122.4           Jurassic
Argentinosaurus huinculensis        60-90           Cretaceous
Antarctosaurus giganteus            69-80           Cretaceous
Mamenchisaurus sinocanadorum        75              Jurassic
Sauroposeidon proteles              40-60           Cretaceous
Paralititan stromeri                59              Cretaceous
Brachiosaurus altithorax            28.7-56.3       Jurassic
Puertasaurus reuili                 50              Cretaceous
Ruyangosaurus giganteus             50              Cretaceous
Alamosaurus sanjuanensis            50-60           Cretaceous
Futalognkosaurus dukei              38.1-50+        Cretaceous
Turiasaurus riodevensis             40-50.9         Jurassic/Cretaceous
Camarasaurus supremus               47              Jurassic
Diplodocus hallorum                 30-42.5         Jurassic
Supersaurus vivianae                32-40.2         Jurassic
Elaltitan lilloi                    42.9            Cretaceous
Tehuelchesaurus benitezii           41.3            Jurassic
Apatosaurus louisae                 18-41.3         Jurassic

Ornithopods                         Metric Tons     Period
Shantungosaurus giganteus           9.9-22.5        Cretaceous
Iguanodon seeleyi                   15              Cretaceous
Saurolophus angustirostris          6.6-9           Cretaceous
Iguanodon bernissartensis           8.3-8.6         Cretaceous
Edmontosaurus annectens             3.2-7.6         Cretaceous
Brachylophosaurus canadensis        4.5-7           Cretaceous
Saurolophus osborni                 6.6             Cretaceous
Lanzhousaurus magnidens             6               Cretaceous
Parasaurolophus walkeri             3-5.1           Cretaceous
Charonosaurus  jiayinensis          5               Cretaceous
Barsboldia sicinskii                5               Cretaceous

Ceratopsians                        Metric Tons     Period
Triceratops horridus                5-14            Cretaceous
Triceratops prorsus                 6.5-11          Cretaceous
Titanoceratops ouranos              6.5-11          Cretaceous
Eotriceratops xerinsularis          10              Cretaceous
Pentaceratops sternbergii           3-4.8           Cretaceous
Pachyrhinosaurus canadensis         3-4.4           Cretaceous
Styracosaurus albertensis           4.2             Cretaceous
Agujaceratops mariscalensis         2.6             Cretaceous
Centrosaurus apertus                1.1-2.5         Cretaceous
Coronosaurus brinkmani              2               Cretaceous
Rubeosaurus ovatus                  2               Cretaceous
Achelousaurus horneri               2               Cretaceous
Pachyrhinosaurus lakustai           2               Cretaceous
Chasmosaurus belli                  2               Cretaceous

Thyreophorans                       Metric Tons     Period
Dacentrurus armatus                 5-7.4           Jurassic
Ankylosaurus magniventris           1.7-6           Cretaceous
Stegosaurus stenops                 2.6-5.3         Jurassic
Cedarpelta bilbeyhallorum           5               Cretaceous
Hesperosaurus mjosi                 3.5-5           Jurassic
Tuojiangosaurus multispinus         4.8             Jurassic
Wuerhosaurus homheni                4               Cretaceous
Niobrarasaurus coleii               4               Cretaceous
Stegosaurus ungulatus               3.5             Jurassic
Gobisaurus domoculus                3.5             Cretaceous
Nodosaurus textilis                 3.5             Cretaceous
Palaeoscincus costatus              3.5             Cretaceous
Sauropelta edwardsi                 3               Cretaceous
Edmontonia rugosidens               3               Cretaceous
Edmontonia schlessmani              3               Cretaceous
Edmontonia longiceps                2.3-3           Cretaceous
Tuojiangosaurus multispinus         2.8             Jurassic
Euoplocephalus tutus                2-2.7           Cretaceous
Jiangjunosaurus junggarensis        2.5             Jurassic

This isn't exactly a fair way to do it, but I didn't want to calculate average dinosaur mass over time. I know that some groups, such as the ceratopsians didn't appear until the late Jurassic, skewing the results, and I didn't make any attempt to differentiate between late or early periods. However I also noticed that many of the smallest dinosaurs appeared in the Cretaceous as well. Pay attention to the units, even the smallest sauropods are measured in metric tons.
Lightest Dinosaurs
Theropods                           kg              Period
Parvicursor remotus                 0.137           Cretaceous
Epidexipteryx hui                   .164-.391       Jurassic
Compsognathus longipes              0.26            Jurassic
Ceratonykus oculatus                0.3             Cretaceous
Juravenator starki                  0.34-0.41       Jurassic
Ligabueino andesi                   0.35            Cretaceous
Microraptor zhaoianus               0.4             Cretaceous
Sinosauropteryx prima               0.55-0.99       Cretaceous
Rahonavis ostromi                   0.58            Cretaceous
Mahakala omnogovae                  0.76-0.79       Cretaceous
Xiaotingia zhengi                   0.79            Jurassic
Mei long                            0.85            Cretaceous
Microraptor gui                     0.95-1.50       Cretaceous

Sauropods                           Metric Tons     Period
Pleurocoelus nanus                  0.5             Cretaceous
Magyarosaurus dacus                 0.75            Cretaceous
Europasaurus holgeri                0.8-1           Jurassic
Bonatitan reigi                     1               Cretaceous
Lapparentosaurus madagascariensis   1.4             Jurassic
Lessemsaurus sauropoides            1.8             Triassic
Lirainosaurus astibiae              1.8-4           Cretaceous
Shunosaurus lii                     2.2-6.7         Jurassic
Ampelosaurus atacis                 2.5             Cretaceous
Amargasaurus cazaui                 2.6-3.8         Cretaceous
Hypselosaurus priscus               2.7-8           Cretaceous
Euhelopus zdanskyi                  3.4             Cretaceous
Neuquensaurus australis             3.5-6.1         Cretaceous
Rinconsaurus caudamirus             4.1             Cretaceous
Atacamatitan chilensis              4.3             Cretaceous
Dicraeosaurus hansemanni            4.4-5           Jurassic

Ornithopods                         kg              Period
Gasparinisaura cincosaltensis       1-13            Cretaceous
Yueosaurus tiantaiensis             3.9             Cretaceous
Fulgurotherium australe             6               Cretaceous
Notohypsilophodon comodorensis      6               Jurassic
Yandusaurus hongheensis             6.6-7.5         Jurassic
Hypsilophodon foxii                 7-21            Cretaceous
Thescelosaurus sp.                  7.9-86          Cretaceous
Valdosaurus canaliculatus           10              Cretaceous
Haya griva                          11              Cretaceous
Agilisaurus louderbacki             12              Jurassic
Drinker nisti                       20              Jurassic
Changchunsaurus parvus              20              Cretaceous
Qantassaurus intrepidus             20              Cretaceous
Zephyrosaurus schaffi               20              Cretaceous
Oryctodromeus cubicularis           20              Cretaceous
Orodromeus makelai                  20              Cretaceous

Ceratopsians                              kg        Period
Liaoceratops yanzigouensis                2         Cretaceous
Yamaceratops dorngobiensis                2         Cretaceous
Psittacosaurus sinensis                   4.1       Cretaceous
Psittacosaurus lujiatunensis              5         Jurassic
Yinlong downsi                            5.5       Cretaceous
Micropachycephalosaurus hongtuyanensis    5.9       Jurassic
Chaoyangsaurus youngi                     6         Jurassic
Xuanhuaceratops niei                      6         Jurassic
Bagaceratops rozhdestvenskyi              7         Cretaceous
Psittacosaurus meileyingensis             8         Cretaceous
Psittacosaurus neimongoliensis            8-8.4     Cretaceous
Archaeoceratops oshimai                   10        Cretaceous
Psittacosaurus mongoliensis               12.1-20   Cretaceous
Psittacosaurus sibiricus                  15        Cretaceous

Thyreophorans                       kg              Period
Scutellosaurus lawleri              3               Jurassic
Emausaurus ernsti                   50              Jurassic
Scelidosaurus harrisonii            64.5-270        Jurassic
Animantarx ramaljonesi              300             Cretaceous
Struthiosaurus transylvanicus       300             Cretaceous
Struthiosaurus austriacus           300             Cretaceous
Gargoyleosaurus parkpinorum         300             Jurassic
Mymoorapelta maysi                  300             Jurassic
Minmi paravertebra                  300             Cretaceous

So what does this mean for the relationship between oxygen levels and dinosaur size? Higher oxygen levels in the Jurassic and Cretaceous probably allowed for larger animals to exist, however as time went on Dinosaurs became more diverse in general, including size. Many of them evolved to become smaller, despite being allowed to become larger by higher levels of oxygen. We should also note that even though oxygen levels were still lower than they were during the carboniferous, the animals were much larger, most likely due to their more efficient oxygen transport systems (lungs, 3(4?) chambered hearts, sealed circulatory systems, hemoglobin).
If we think about what could drive species to become larger, competition for food and protection from predators comes to mind. Sauropods that could reach the leaves in taller trees had distinct advantages over those who could not. Prey animals stood a better chance at fighting off predators if they were bigger. Likewise, predators could kill larger prey if they became larger too. Oxygen didn't drive them to become larger, it simply allowed them to.
To actually answer the question, could the modern atmosphere support animals as large as dinosaurs? It probably could. The heaviest living animal today is the blue whale, at an average mass of 110 metric tons, is heavier than all but 1 of the sauropods on the list I compiled. The heaviest land animal living today is the African Elephant, with average mass of 4.9 metric tons and as high as 10 metric tons, would be a respectable competitor with many of the dinosaur groups I listed 12.
Another interesting question is not how oxygen affected the size of organisms, but how it affects it their metabolism. Cold blooded animals don't need as much oxygen because they don't spend as much energy. Warm blooded animals must constantly expend energy to maintain body heat, and this requires greater consumption of oxygen. Obviously being large and warm blooded would force you to need even greater levels of oxygen than 1 or the other. It may be that the advantages of being warm blooded outweighed the advantages of large size, but I don't want to dig into that question right now.

How can I make those lists look better? I wrote them in a spreadsheet, and I'd like to make them look like a spreadsheet here too. I know how to make a table in HTML, but I don't want to write that much HTML by hand.

take a screenshot from excel or whatever post as picture

inline citations are also better than links at the bottom in my opion

and you need to say how those %O were gathered

Tables are cleaned up, citations are inlined, and added some information about how the % O2 was determined, with a link to an article with much more detail than I could post here.

I'm not so sure that larger land animals require that much more oxygen.  The problem is metabolism's waste heat.
Anyone remember the square-cube law?  All other things being equal, double an object's size, and its area quadruples, while its volume octuples.
Broadly speaking, an object loses heat in proportion to surface area, while an animal produces heat in proportion to volume.  For our double-sized creature, heat production per unit area would double.
Other things being equal, to reduce overheating, metabolic rates would have to go down, thus reducing the oxygen demand.
Conversely, consider the opposite: a creature half the size of the original.  It now produces half the heat per unit area.  If it needs to maintain a minimum body temperature, then (other things being equal) its metabolic rate will need to go up.  This will certainly be easier if the oxygen concentration is higher.
Of course, other things are never equal, so this is only one piece of the puzzle.  But it seems that, for land animals that are already large, increased oxygen levels alone should push size downward.
Or am I missing something?

Also, why would land animals necessarily require more oxygen than aquatic ones?  The largest whales today weigh more than the largest known dinosaurs, and they do perfectly well on the current atmosphere.

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


text:
Can humans survive without consuming life?
Some people say that it's awful that humans eat animals.  They feel that it's barbaric, because you're killing life and then on top of that, you're eating it, and that you should eat vegetation instead.
But isn't vegetation life too?  Personally, I see no difference between animals and veg as all life has cells, dna etc
So my question is, is it possible for humans to live healthy long lives without eating any type of life, i.e no animals, no plants, no cells (dead or alive) etc? If it is possible, how would it be done?

you might be able to survive on animal products such as milk (protein source) or an egg (although whether egg is life or not is up for debates) but I would imagine it would be pretty touch so I would say no if you can't use any plant/veg although you might be able to use rice (source of carbohydrates) from rice grains but then whether a grain is living or not is debatable (grains are quiescent) so the question is quite opinion based!

@Bez, In my view, milk, eggs, rice are all life or part of life. So there is no clear cut nutrition a human can consume which has no link to something living?  Basically, humans must consume life to live... ?

based on your definition of life, yes!

You mean on a strictly vegan based diet? No, that is not possible as we are not able to synthesize many important factors as Vitamin B12. There is no vegetable source for it.

What about eating things that have died without you directly or indirectly having killed them? E.g. a fruit on its own is not alive and if you remove the seeds and plant them you are in no way killing anything.

It would require the ability to synthesize all the sugars, fats, amino acids, vitamins, etc necessary for life totally from chemical sources. It would be very expensive and burn a lot of energy. You might be able to engineer bacteria or yeast to make them, but then you'd still be eating living things.

@oshirowanen just remembered this (http://www.bbc.co.uk/news/science-environment-16972761) but I do not know if that falls in your definition of life and killing the living.

"any type of life" asks for the most inclusive reasonable definition of life, and that would include any type of cell or cellular material as alive.

It's possible since 1972:  https://en.wikipedia.org/wiki/Vitamin_B12_total_synthesis

Clarification, please? Consuming "life" seems too ambiguous as many answers/comments point out. Various seeds, and many other similar plant parts, are intended (by evolutionary tendencies) by the plant to be eaten and somewhat spread by animals. Some number of plant species would become extinct if parts of them were not eaten/spread by animals. By not eating them, is that contributing to the extinction of a species? (Probably wouldn't happen due to other animals, but it might have philosophical implications for the question.)

Also, food synthesis technology is progressing rapidly: Breakthrough reveals how vitamin B12 is made is from a full year ago.

The vague definition of life and intangible solutions presented makes the question and any solution offered highly speculative and philosophical in nature, deviating from any practical solutions or biology.

Hi all - I've removed a lot of the comments on this question that were not requesting clarification etc. - please remember to use Chat for extended discussions

@oshirowanen In the question you have "without eating any type of life, i.e no animals, no plants, no cells (dead or alive)..." Dead cells and life are in the conflict here and may cause confusion.

Long ago I read a post elsewhere about a hypothetical diet (with supplements) such that it only contains things that are intended to be food - milk, honey, eggs, fruit.

@MichaelT are eggs intended to be eaten?

@Anixx the yolk of the egg is nutrients for a developing embryo. This is an issue in non-placental animals. Speaking of placenta, look up placentophagy (warning - not for the squeamish) and consider what diets this would be acceptable in (you're not killing anything to obtain it - it's a byproduct of life).

A related question I asked on Hinduism - Why can we eat 'living' plants but not 'living' animals?

The answer to your question is yes it is certainly possible.
At one time it was thought that there was something special about "organic" chemicals which meant that they could not be artificially synthesised out of fundamental elements. In 1828 Frederick Wöhler synthesised urea (CO(NH2)2) which is often taken as the first demonstration that the organic v inorganic distinction was not a sound one (for more on this see the Wikipedia article on Wöhler synthesis.
As far as we know all essential human nutrients can be synthesised from inorganic ingredients, even complex molecules such as Vitamin B12.
Other contributors have pointed out that organic pathways for synthesising our food have evolved over long periods to be very efficient - at least in the conditions prevailing on Earth. You haven't ruled out copying biochemical pathways using chemicals that are entirely of inorganic origin. Anyone trying to do this seriously could create glucose (for example) by artificially creating enzymes (perhaps via artificial DNA) to do the job. The thing is that we already have self-replicating and repairing machines to do that already (plants).
There might be circumstances when we needed to use artificial synthesis. I can think of two science-fiction stories that deal with this question, the first of which goes into some detail:

The Moon is Hell by John W. Campbell, in which astronauts are stranded on the moon and forced to make food from what they find there.
Technical Error by Arthur C. Clarke, in which a man is accidentally rotated through the fourth dimension. His employers contemplate the difficulty caused by the "handedness" of many biological molecules meaning they would have to artificially synthesise many of his foods.

It may be that a future expedition to Mars (say) might have to think about these things.
A little searching fails to come up with standard inorganic syntheses of glucose and similar substances. The reason for this is almost certainly because it is so easy to use organic inputs. Glucose is easily made by the hydrolysis of starch. Starch is very common and cheap. Even l-glucose is usually made out of organically derived precursors (or sometimes even using d-glucose).
UPDATE: sources etc
One problematic question is: where do you get your input for making nutrients? As others have pointed out, exactly where to draw the line is difficult.
This problem starts in defining what is alive in the first place. Do you count viruses (which can go down to a few thousand base pairs of RNA) or satellite viruses (STobRV has only 359 base pairs) or prions? In a sense these are "just" very large molecules. But then really simple bacteria are not many orders of magnitude more complex. As an aside most systems of ethics that do not permit eating meat do not make an alive/non-alive distinction, choosing some other aspect such as sentience, though Jainism comes close to doing so.
The second problem is, if we reject living things as sources of food, how far removed from those living things are we allowed to get? You say no cells in any state including "dead". That would exclude (say) fruit even though most fruits are expressly created by plants in order to be eaten (and in some cases must be eaten) - something that vegans, jains, fruitarians and others would be happy with eating. If we could use dead material things would be much easier.
But would you also include hydrocarbons (coal, oil, gas) which were once living organisms? If you do, then you are in difficulty because terrestrial carbon is recycled through the biosphere. All CO2 was (to a close approximation) once a part of a living thing. If you take that position then of course you are going to have to go off-planet to find your source chemicals and your problem becomes very much harder.
I was assuming that you were restricting yourself to consuming cells that retain some of their cell structure but had not completely degraded. If that is where you draw the line then there are ample sources of raw materials on earth.
Genetic modification is much more science fiction though not entirely impossible. Some nutrients could be made by humans without much difficulty. Our inability to manufacture vitamin C is down to one missing enzyme (L-gulono-gamma-lactone oxidase) which is present in most vertebrates (I think of mammals only guinea pigs, humans and some bats are unable to synthesise it). You could certainly imagine some very careful genetic modification changing humans so they no longer need to consume vitamin C.
But photosynthesis would be much harder. Chloroplasts (which do the job in most plants) are really a very primitive form of life living in plant cells which may independently reproduce  (and for that reason might be excluded by you - they aren't "cells" but they have membranes). They could easily end up in conflict with our mitochondria (since intracellular conflict between organelles is possible) and you would need to do enormous amounts of work to make human cells co-operate with them properly.
More in keeping with your theme would be adding photosynthetic systems directly to human cells along with a suite of enzymes to manufacture all the things we cannot. That is of course in principle scientifically possible (since plants do it) but much harder than it looks. Living systems are very complicated and small changes can have unexpected consequences. Even very minor genetic modifications are problematic. The human autotroph is likely to be some way off.

+1 for the Asimov story! It is possible to survive on poisons only if one can rotate oneself through a fourth spatial dimension. I must also mention "Technical Error" (aka "The Reversed Man") by Clarke.

A "yes" would indicate that it would be possible right now. Do we have readily available technology for it available now? I guess not. Wouldn't that make a "No, but theoretically possible in the future"?

I had a go at finding pricing for artificial synthesis of things like glucose but got nowhere (for reasons that are obvious). We know how to do it (i.e. we have the technology). Doing it might be insanely expensive, but humans are well known for doing insanely expensive things :-).

Just to understand better: say we have set up a laboratory to inorganically synthesise every necessary nutrient. What would we use as raw materials? Where would we get carbon and the other elements? Would we able to obtain them without violating the OP's provisos?

All organic components can be found in air and it is certainly possible to make them useful (plants do it too). Inorganic nutrients would need to be drawn from the ground but no live organism would need to be used or killed for that.

FWIW, the summary of Left to Right is quite inaccurate. Here's the full text: http://www.scribd.com/doc/209177509/Asimov-Isaac-Gold-02-Left-to-Right

@TimS. Well spotted. My mistake, I had in mind Technical Error and a hurried search found me the wrong story. The reference to chirality in amino acids made me think Asimov for obvious reasons.

Did you mean to say, "most fruits are expressly created in order to be eaten ... by the plant", or did you actually mean "most fruits are created by the plant expressly in order to be eaten"? +1 for considering the variety of angles.

Ooops, yes, "by the plant" got a way from its antecedent.

Interestingly the GM to restore Vitamin C production has already been tried: http://www.sciencedirect.com/science/article/pii/S0888754303002714

If you count coal or CO2 as "life", why not water? In that case you're boned as it was all once in a dinosaur: https://what-if.xkcd.com/74/  Granted, most wasn't molecularly incorporated and liberated (via dehydration/hydration reactions).

@NickT - that's exactly my point. How difficult this is depends very critically on exactly where the line is drawn. If you are allowed to use dead leaves/wood etc then it is much easier. If you aren't, it is unclear why CO2 and as you say H20 is OK.

It would be helpful to consider photosynthetic efficiency, en.wikipedia.org/wiki/Photosynthetic_efficiency since plants can be thought of as biological solar panels. If we wanted to replace all food with abiotic sources, we'd have to burn a lot of energy to do it. Thankfully, artificial solar panels are already more efficient than plants at energy capture, it would still require methods to use that electricity to fix carbon and nitrogen and produce nutrients. But it's at least possible to estimate the energy cost.

An excellent answer, but I don't think it satisfies the parameters, given from http://what-if.xkcd.com/74/ that "This means that while the chances are that most of the water in your soda has never been in another soda, almost all of it has been drunk by at least one dinosaur" so that even the inorganic compounds (say, water) you're using for synthesis have at one point been part been part of a living organism. It's possible, but not guaranteed. We could collect hydrogen and oxygen from Jupiter to make water avoiding this issue, assuming Jupiter is lifeless and formed from lifeless origins.

@DonBranson: I think we can distinguish between chemicals that were once part of a living organism and chemicals that were actually produced in a living organism. If you take my blood to make heme, that's very different from making it using an iron splinter that had previously been stuck in my hand.

@ruakh Your point is that the chemical would exist regardless of whether it was one part of creature? That's a good point.

Living organisms can be divided into hetrotrophs and autotrophs. Autotrophs like plants and algae are able to produce complex organic compounds from relatively simple inorganic components. They are satisfied with sunlight, water and other abiotic stuff and do not need to consume "life".
We -- along with all other animals -- are not autotrophs, but heterotrophs. This means that we cannot produce organic compounds by ourselves but need to 'reuse' the ones that are produced by autotrophic organisms. That's why no human will ever be able to live without consuming other life.

Ever? Are you sure about that?

As user137 pointed out, you would need to synthesize ALL nutrients from anorganic sources. No one will ever do this because plants have had hundreds of millions years time to become really really good in that. Why would you want to compete with them? In so far: Yep...never ever.

@N0ir OP defines milk as life if you look at the comment threads so it becomes difficult to offer any solutions apart from synthesis or food.

@antonone key word probably being possible for a "human"...possible for something a human evolves into? I don't see why not. But it'd be different enough that it probably wouldn't be classified as a human any longer.

organic != life. vultures? bacteria that decay matter? organisms consuming milk, eggs, fruit, pollen?

The question was whether it was possible, not whether we would. Also "never" is a long time.

This answer is wrong. As explained by @FrancisDavey, it is certainly possible for us to synthesise every single nutrient we need from inorganic substances, at the expense of energy which we can gain non-organically too for example through solar or nuclear sources. That is, by all ways of understanding it, "without eating any type of life".

Following this logic, you would have to answer almost every question with "yes, it's possible". Can we travel between solar systems at warp speed? No, but some people imagine it to be possible at some point far, far in the future. But based on our current knowledge that's fiction and does not mean anything. My answer is based our current knowledge, too. At the moment and in all foreseeable future it will not be possible to live without consuming 'life' (as defined by oshirowanen). I doubt it ever will...

At the very least current technology would allow you to build bacteria to synthesise all nutrients you need, in which case you would then not need to consume any live organisms but only chemical products they're not using themselves. It is true that you could consider everything within physical boundaries as possible, but what this question asks is either within or not far off available technology. Of course you are correct that the chance of it happening anytime soon is zilch due to lack of demand, but that's not what's being asked.

It has neither been asked if there is some way imaginable. Apart from the fact that in the OP's sense there is no difference between bacteria- or plant-synthesized substances, I interpreted the question in a more practical way than you. It seemed to me that the OP wanted to know if there is some way how he/she can live without harming or exploiting any living creature.

There is no known technology that would allow interstellar travel at warp speed (indeed there's no scientifically known process that would allow it - the Alcubierre "drive" doesn't allow it in the conventionally understood way) whereas all vitamins, amino acids etc have known inorganic syntheses (and obviously so with artificial enzymes) so it isn't the same thing.

i dont like this answer but i'm not going to downvote...i watch dr who and farscape so i am opposed to the idea that plants cannot evolve into sentient lifeforms.

I'm sorry to hear. Perhaps this site suits you better: http://scifi.stackexchange.com/

re. your second comment, have you BEEN to a grocery store. what is a vitamin pill in the first place. have you seen how animals are raised on a factory farm. as far as competing with nature, mankind's stance has always been "bring it on."

Even on a purely synthetic diet, your body would still use living cells as an energy source. Our bodies contain more bacterial cells than human, mostly contained in our gut. These microbes process any nutrients we ingest and when they die, we absorb their cellular components as nutrition.
The lining of the gut is the most rapidly dividing population of cells in the body. Unlike skin cells, when these die, our intestines recycle much of this as nutrition. Throughout the rest of our bodies, when a cell dies, its components are recycled: red and white blood cells, mucosal membranes, invading microbes, etc.
When you kiss, engage in intercourse, there's also an exchange of living cells which die in the process.
Abstaining from organic food, human contact will not stop the fundamental processes of autophagy, apoptosis, digestion, cell turnover of both our own and microbial cells.

The most beautiful answer.

Human solid body waste is as much as 50% dead bacteria from the gut.

Your question is phrased somewhat ambiguously as to whether you're asking about the theoretical possibility, the feasibility, or the practical ability in everyday life.
1) Theoretically, yes. It is chemically possible to produce all substances that humans need to survive without the use of living organisms in the process. In the end, biological systems use chemical processes, so at the very least it would be possible to isolate the biological (enzymatic) machinery and use it without the live organism around it. The latter is within current biotechnological capabilities.
2) Feasibly, no. Going through the hassle of making all those substances in that way would probably be less efficient than simply using the biological (live) systems that already exist and are very efficient at it - in particular, plants.
3) Practically, no. Using only currently commercially available products (i.e. things you could buy right now), you will probably not be able to source a full human diet without relying on some live organism at some point in its production exactly because of number (2) above.

So now we agree.

I don't think we ever disagreed XD I felt like number 1) in my answer was what the question asked and so that would be the correct answer - but it's true that the question is sort of ambiguous and hence I decided to post this general answer.

mattkaeo's answer provides an interesting additional consideration for (1), though. I don't know whether it's clear what happens when you stop "eating" your symbiotic gut flora. One might suppose that if all the necessary nutrients get into the bloodstream somehow then you're good to go, but there's probably more to deal with than just synthesizing the nutrients, since various systems in and around the digestive tract will be perturbed and need sorting. People fed entirely IV tend to be fairly unhealthy, admittedly they're usually unhealthy to start with, that's why they're fed by IV.

As long as the necessary nutrients are consumed orally and go through digestion, your gut flora and your own health should be fine. You could synthesise and consume indigestible carbohydrates (i.e. fibre) to support that additionally. His answer is an interesting thought though and does answer the question "Can humans survive without consuming life?" in a different angle.

@SteveJessop there have been experiments on animals, rising them in a bacteria-free environment and thus without gut flora. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1500832/ for example. The current verdict seems to be that this is possible, but unhealthy; if we ever would raise humans in sterile environment (interplanetary colonisation by growing people from fertilized cells and local resources?) then we should 'infect' them with the common gut bacteria.

Depends on how you define "life"? Is unfertilized chicken eggs alive?
What about cow milk? Well there are bacteria in it. What if you get rid of that bacteria? Then some people would not be able to utilize lactose...
Also as Bez mentioned rice grains are quiescent, meaning they are in a dormant state and not really "alive" but again depends on how you define "life". Even top biologist have trouble defining "life" and there exist many competing definitions of "life". All of them have their advantages and disadvantages, but there is no universal definition of life on which all biologists would agree.
If you consider everything above as "life" then it is not really possible for humans to survive without consuming other life.
If only we could sustain chloroplasts in our epidermis layer we would be able to synthesize sugars for ourselves. But then we would become little green men...
So it is much better to respect your meat. Whenever you eat meat just be conscious that something had to die to produce that meat. Be grateful for that lost life and realize that part of it will live in you.

Ask you asked, my definition of life is something has cells/dna in any form (dead, dormant, or alive).

Viruses have DNA/RNA in them yet they are not living, they are more like containers. So not everything that has DNA is actually life. You can have a bunch of DNA in a tube, you wouldn't consider it life would you?

Question: Is it possible for humans to live healthy long lives without eating any type of life, i.e no animals, no plants?
First, according to a definition of a living organism(biology-online), milk is not live, because it does not have an ability to reproduce itself, among other...
My claim: If you consider milk and honey non-live (no DNA), then, yes, humans can survive for some time by consuming only these, and water. An example are infants, who can live exclusively on human breast milk and water for more than 1 year.
This is human milk composition (Nutritiondata), from which you can see it contains all essential nutrients (Nutrientsreview) (essential amino acids, fatty acids, vitamins and probably all essential minerals - not all essential minerals are listed in Nutritiondata milk composition, though).
But to actually prove that humans can or cannot "live healthy long lives" by consuming only milk and honey, one would need to do a human trial...and I'm not aware of any.

I think if you live off the by-product of a creature that consumes life, it would be cheating to claim that you don't.

You do not need to kill or harm a living being to use its milk. I believe, from what is obvious to me, this is how things are meant to be, at least for infants.

And how will the cow produce its milk? It has to graze, therefore killing thousands of organisms.

No.
It is possible but extraordinarily impractical to nourish yourself without killing animals, plants or even bacteria, as many have explained in detail.
However, your immune system constantly kills pathogens that infect your body. What's worse, the macrophages literally catch and eat these bacteria alive, so you are very much "consuming" them.
You could live in a bubble, but even then there are bacteria in your gut. In your gut, they are not attacked by your immune system, but they can sometimes get through the gut lining into the body, where they are attacked. They could also escape from you anus into the environment, and then end up elsewhere in your body.
Even if you had a magic force field keeping the gut flora inside the space of your intestinal lumen, they could still mutate and become immunogenic, then get consumed by your macrophages. Anyhow, collectively, your gut flora has more cells than your body, so is it really fair to say "you" did not consume any life when this symbiotic bacterial mass living inside you (more like you are the parasite living outside it) consumes some of its own cells?
But let's say you get rid of your gut flora, too. It's a hell of a life, and you wouldn't wish it on your enemy, but it solves that problem. Now only human cells are present inside your bubble. What happens when eventually your cells mutate and you get cancer? There are natural killer cells that will try to consume the cancer. So you have still consumed life.
Let's say you made yourself immune to cancer. That's impossible, but let's say you made your DNA polymerase so high fidelity that it takes millions of years for even a single mutation to occur (this is also almost impossible). Your body still has to kill cells through apoptosis as part of maintaining its own function. Again, to conserve resources, these cells are literally swallowed. It's debatable whether an apoptotic cell is alive, but it is made to die by influence of other cells, so this is very analogous to killing a chicken and eating it. In principle.
The answer is no, but your question becomes meaningless if you define "life" scientifically. It is only possible to live without consuming life if "life" means only plantae, metazoa and fungi. But that is not what it means, because at least some Eastern religions do consider eating microbes to be "consuming life".

Lame, boring answer
The Universe has a finite reserve of (dis)entropy. When that runs out, no more life can exist, because all life must increase entropy. Even on Earth, by simply being alive you are taking up space that could be used by other organisms. To be alive you require some form of energy; even if this energy is solar, you would still be using up energy that could have been used by a plant.
By simply existing, you are irreversibly destroying vital resources necessary for other life. Thanks to you, at least some life somewhere will be left without resources and starve. Therefore you cannot exist without harming life.

It may be feasible to live without consuming anything that was alive, but it would be incredible difficult.
For example, all humans need to consume glucose to survive. Glucose is the only food source used by cells in the brain. Plants are the easiest source of food source for glucose. If we can't get glucose from plants, then we would need to synthesize it without the aid of enzymes or any sort of organism. A quick google search does not yield any hits for how this synthesis could be performed. Probably because it is so easy to get a plant to make the sugars for us.
Now think about all the amino acids, vitamins, fats, and minerals that we would also need to synthesize or extract without any organism intervention.
You have gone from the good intention of not harming another organism to the creation of a whole chemical industry dedicated to the production of nutrients for people.
Think about this as well. When you poop, a lot of the poop is actually dead bacteria that was living in your gut.

Can you please improve your answer and add some references? If you want to know about glucose synthsis in the human body, look up gluconeogenesis.

It would be great if you could add references to your answer specially regarding the last line!

@Chris Gluconeogenesis is how your body generates glucose as a last resort. It is a lot easier just to eat glucose. It requires the use of enzymes. I suppose you could synthesize the enzymes in vitro.

@alex But what about glycogen? Doesn't the breakdown and synthesis of glycogen not require enzymes? And doesn't glycoysis, the TCA cycle and the Respiratory Redox Chain make extensive use of enzymes in turning glucose into "energy"? IMO Chris makes a very good point (to which we may add that no net synthesis of glucose can occur from fatty acids).

"When you poop, a lot of the poop is actually dead bacteria that was living in your gut." Some of them are still alive... imagine their horror... Now all vegetarians are gonna stop pooping

@N0ir As John Lennon put it "Imagine there's no heaven..."

Sounds surprisingly, but neither glucose or any other carbohydrate is essential for human life. Humans can produce all carbohydrates, including glucose, they need. Also, human brain, when no glucose is available (prolonged fasting), can use ketones as a fuel.

Well, technically if you are eating something from a plant or animal without killing that plant or animal, then technically you would not be "consuming life" as nothing as been killed. Fruits, for example, can be removed from the tree without harming it and in fact are meant to be removed as that is how the tree reproduces. Ditto with berries, melons, squash, cucumbers, peppers, beans, seeds, nuts, etc.
As for animal products I think only milk and honey would qualify as technically an egg is a future animal.
So yes, I would say that it is completely possible to live a healthy life without once killing another living thing.

As far as I understand, fruits are alive, they have cells and dna just like animals and humans.  A single cell is a simple form of life.  So if you're eating fruit, technically, you're consuming life.  Therefore, no different from eating an animal.  If you think about it on a larger scale, you could say that animals are the fruit of the earth...

There is no way you could go through life without EVER consuming something with cells. Even while you are sleeping several hundred ants, insects, spiders, etc WILL crawl into your mouth and be swallowed over your lifetime. Why the problem with consuming cells, anyway? Fruits and the like will fall off and decompose anyway and they are not sentient, so why the moral dilemma?

Ah, I see. Then I suppose it's theoretically possible to survive without INTENTIONALLY consuming living cells, but great scientific effort would have to go into making the synthetic products available

@oshirowanen if you count even single cells as alive, then that includes bacteria and other single-celled organisms that aren't even plants. Such a diet isn't currently feasible, for some key nutrients the only vegan options are obtained by killing bacteria.

Honey is produced from nectar that does not contain any living cells and carefull beekeeper should be able to take at least some from the hive without killing any bees. However bees themselves will also consume pollen that is alive.
It also may be possible to feed on fruits; while cells there are still alive, they are about to die soon without any prospects of future surviving. If you really do not want to harm the plant in any way, take the seed from the fruit and plant it somewhere. Fruits are for seed propagation only and the plant should really not have any pretensions to you afterwards.
Dead leaves in the autumn may contain the needed materials; unfortunately they are not edible directly and would need some pre-processing technology.

It is entirely possible to live without consuming life using only current technology.  In fact, there is a company called Soylent which has developed a food substituent designed to replace all eating, entirely.  The philosophy of that company is that – food is just a collection of chemicals for the body to process, and that as long as the body gets all of the necessary chemicals, it will survive fine. That is exactly what soylent aims to do – the powdered mix they produced has all the chemicals necessary for human life.

The ingredients in Soylent get its calorific value from rice, oats, soy and other plant products.  As such it doesn't fulfil the criteria of the question asker

Soylent Green is People!


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Is there a known minimal stretch of DNA that can distinguish any two people in the world?
I imagine this could be used as a universal Identifier.

I guess it depends on the particular stretch of DNA. Some sections of DNA are conserved and under heavy selection pressure (such as p53) whereas others can vary.

Here is what the data says. UK government must have had some scientific evidence when it settled on a 10 variable-length sections of genome for their database, SGM+. In one such variable sections, some people have 10 repeats of CTTT, others have 11, others have 12 etc. The largest of those fragments, at its maximum length, are about 350 base pairs. The US government uses 13 such variable-length sequences for its CIA database, called CODIS. On both sides of the Atlantic, roughly 3-4 thousand base pairs were judged to be enough, with some safety margin, by the most advanced geneticists in the world, working on public money.
The catch is that these variable length sequences are disjoint, so you end up requiring far more than 4,000 bp. If you need these markers on the same DNA strand (chromosome), you should space them by 50 centimorgans, at which distance they recombine independently. But according to http://www.sciencemag.org/site/feature/data/genomes/265-5181-2094.pdf , the longest chromosome only has 350-400 centimorgan. It means you cannot get 10 independent DNA sequences on a human chromosome, be it the longest.
I predict there is no such continuous DNA stretch, that would tell apart any two non-twins. Since it is much better to use multiple chromosomes in DNA fingerprinting, I doubt you will find more relevant experimental data.

When designing PCR primers we typically use a minimum length of 20 bases, because the probability of a sequence of N bases appearing by random is $\frac{1}{4^N}$, and $\frac{1}{4^{20}}$ is about 9x$10^{-13}$, or about 1 in a trillion. Since the human genome is a little over 3 billion bases long, a 20 base sequence should appear only once. However, most of an individual's DNA isn't random, it's inherited from their parents, and they got their's from their parents, etc. Long story short, there isn't a lot of unique DNA in any given person. The uniqueness is only visible on the large scale, you have half of your DNA from your father, and half from your mother. So would any of your siblings, but the specific DNA they got from each parent would be different from yours.
I think we can calculate the odds of getting a specific set of chromosomes from a parent. If there are 23 pairs of chromosomes, then the probability of getting any given set should be $\frac{1}{2^{23}}$, since we have 2 parents, the odds of getting your specific set of DNA is $(\frac{1}{2^{23}})^2$, which is about 1 in 70 trillion. So the odds of you having a non-identical twin that has the same DNA as you is very low. But any given 20 base sequence should have a 50% probability of appearing in you and the sibling.
But if we look at 2 20 base sequences of DNA in you and your sibling, and each had a 50% chance of appearing, then the probability of both sequences appearing in the both of you is 25%. If we add a third, it goes to 12.5%, and so on. If there are 7 billion humans on earth, we need a probability of less than 1 in 7 billion, and $2^{33}$ is about 8.6 billion, so if you looked at 33 different sites on the genome it should be able to differentiate you from every human on the planet
By the way, did I do the math right? I'm not a mathmagician and I could have made a mistake in my probability calculations. I have also assumed that the spontaneous mutation rate and crossing over rates are low enough to ignore, but both would serve to make your DNA a little more unique.


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When did CRISPR/Cas9 evolve and what is the likelihood that a superior system for live cell genome editing has already evolved on earth since then?
I've read that CRISPR/Cas9 is currently being implemented and tested for its ability to edit genomes in live cells, and that it is supplanting other genome editing tools in labs, such as TALENs and Zinc finger nucleases.
I understand that there may be a few metrics used for analyzing any genome editing system.  One is the efficiency, which could be measured perhaps in edits per time or edits per molecule.  Another metric might be error-rate.  What is the probability that a genome is altered in something other than the intended way?  Another metric might be the length of the genome that may be edited at once.
I've also read that CRISPR/Cas9 evolved in bacteria.  When did CRISPR/Cas9 evolve in the history of life on earth?
If CRISPR/Cas9 evolved in bacteria, and before other evolutionary advances, including some of those that may have enabled certain multiceullar forms of life, I have to wonder if other systems like CRISPR/Cas9 but superior to it in some metric evolved as well.
How does recombination in sexual reproduction work?  Might it involve biomolecular machinery like that of CRISPR/Cas9?
How does the adaptive immune system work?  How does VDJ recombination work?  Does it involve an advanced (relative to CRISPR/Cas9) genome editing system?
How might one estimate the probability that a system superior to CRISPR/Cas9 exists already?

could you further expand on the question and set out some parameters or perhaps share your thoughts or work on the matter so that any input is constructive.

Lots of interesting questions! Let me try to address a few of them as I don't think I am qualified to answer them all but hopefully I can get this thread started. I am a graduate student in the biophysical chemistry field and have been following a little bit of the Crispr Cas9 craze in the last couple of years. So I am not an expert on Cas9 by any means but I do find it interesting.
Many speculate that as long as their have been cellular life, viruses or some obligate parasites have existed as well. This stems from the idea that viruses perhaps are not "non-self" but rather are parts of the host that happen to become inanimate particles that escape the cell and then find another suitable host. Some viruses have co-evolved with the host, perhaps to prevent other viruses from invading its "home/birth mother". Again, much of this paragraph is just speculation, but it is likely that CRISPR systems, or an adaptive immune systems like it have existed as long as viruses/obligate parasites have.
Error rates, you can look at some of the papers that have come out recently but the idea is that there are a lot of error rates, especially if the RNA is constitutively transcribed from a plasmid. Some people have suggested delivering, not the plasmids for the guide RNAs and the Cas9 protein, but instead, the Cas9 protein complexed to the RNA itself. Other ways to control the amount you deliver to a cell include delivering the RNA for the Cas9 protein so it is eventually degraded. This avoids the complication of delivering DNA which can be transcribed multiple times potentially flooding your cell with cas9 protein or guide RNAs, increasing the likelihood of off target effects. Or you can have the cas9 protein and the guide RNA plasmids under inducible promoters, so you only get expression say if you introduce a small molecule to your cultured organism and limit the amount you deliver of it.
As to if there are other systems "superior" to it, and by superior you mean more efficient, and has less off targeting effects? Sure those things may very well exist, since we haven't sequenced the entire planet yet! All joking aside, maybe start looking around at research groups that do adaptive immunity in prokaryotes, you might find some interesting ideas...
VDJ is a very cool system that I know only a little about but this review might be worth checking out:
"Mechanism and Control of V(D)J Recombination versus ClassSwitch Recombination: Similarities and Differences", which can be found here.
Also recombination in meiotic versus mitotic replication is covered in this review: "Meiotic versus Mitotic Recombination: Two Different Routes for Double-Strand Break Repair", which is available here.
So to answer your question, I will have to defer to someone else!
My question to you is what is "advanced"? Life as we understand it has been evolving for about 3-4 billion years. "Advanced" suggests that one organism has evolved better or faster. I don't know if I would call anything more advanced per se, but maybe more complicated and more capable of rapidly adapting to new environmental pressures? Bacteria have us trumped if there were rapid changes to the environment, global warming, asteroids careening into the planet etc.
Estimating this probability requires knowing how large the entire sequence space of the Earth is, some have estimated 5-50 million eukaryotic species but depends on what metric you would use to define a new species. It is unknown for prokaryotes. My guess is that you have 100's of millions of different organisms that are capable of having some type of adaptive immune system that may be inherently different from CRISPR/Cas9 system but still use some similar elements, like nucleic acid complementation, as a mode of defending against obligate parasites. Then the questions are how many of those organisms have we sequenced and how many proteins do we have any idea how they function based on sequence similarities to other proteins? Or if we have directly characterized their 3D structure based on Cryogenic Transmission Electron Microscopy (Cryo EM), NMR or X-ray crystallography. So, I imagine we have just hit the tip of the iceberg in finding natural enzymes that can function as gene editing and gene locating tools. Plus, we may start designing our own enzymes like what Professor David Baker at UW works on. Huge ocean to go exploring, bring a molecular fishing pole :-)

Thank you for getting the thread started with this interesting response.  To respond to your question about what I mean by "advanced," I suppose I've conflated two separate meanings in the term.  On one hand I am interested in whether a substantially different genome altering system evolved (I suppose that is true with VDJ?) after CRISPR/Cas9, and on the other I am interested in whether any such system provides a measurably "superior" genome editing system.  So I conflated "advanced" in evolutionary time with some practical and measurable superiority for intentional genome editing by humans.

Well you could look at systems like the RISC complex in eukaryotes (RNA interference), or the other Cas9 based systems that function using different PAM recognition motifs or the Cas6 Endonuclease complex which supposedly cuts foreign RNA. Not sure what else may be available, obviously the TALENs systems and Zinc finger nucleases may still be useful tools as they become more high throughput in design.
I think at the moment the type II cas9 system from Streptococcus pyogenes is pretty robust and decently well characterized. So far its a good platform to modify and optimize for exogenous hosts.


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Null distribution of Blomberg's K
I've noticed different functions in different R libraries have different ways of assessing significance for Blomberg's K. For instance, picante's phylosignal looks at a distribution of PIC variance values from shuffled trait values to assess significance; when phytool's phylosig calculates a null distribution of Blomberg K values for shuffled traits.
What is the interpretative difference between the two and when should one approach be used over another? And what does it mean if the observed Blomberg's K is greater than 1 (traits less similar than expected under Brownian Motion model of evolution), but significantly greater (or less) than the null distribution of Blomberg's K-values?

The methods should be equivalent, given the same data. Using phylosignal's demo:
library("picante")
library("phytools")

set.seed(5)
randtree <- rcoal(20)
randtraits <- rTraitCont(randtree)

phylosignal(randtraits[randtree$tip.label],randtree)

phylosig(randtree, randtraits[randtree$tip.label], method="K",test=TRUE)

phylosignal returns:
         K PIC.variance.obs PIC.variance.rnd.mean PIC.variance.P PIC.variance.Z
1 1.430635          0.01147             0.4631411          0.001      -2.662701

and phylosig:
$K
[1] 1.430635

$P
[1] 0.001

Both give K = 1.430635 and an identical P-value.
Mathematically, it shouldn't matter if you shuffle the trait values or generate a null distribution of K. To get a null distribution for K, you have to shuffle something, and the tip values are probably being shuffled. You could check the code to be sure. An analogy is that, when doing a randomization for an ANOVA-like test, you can either shuffle the observed values or the group membership. Either way will give the same answer.
As for interpretation, Brownian motion is the simplest model for trait evolution, implying no direction, optima, rate changes, etc. K = 1 when the observed variation equals the expected variation. If K is greater than 1 then neighboring tips tend to resemble each other more than you would expect, suggesting a deviation from Brownian motion.


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Is oxidative phosphorylation less efficient in gram positive bacteria?
Gram negative bacteria perform oxidative phosphorylation in their periplasmic regions, between the inner and outer membrane where a proton gradient is maintained and used by the ATP synthase to make ATP.
Gram positive bacteria do not have a second membrane, but only a porous polysaccharide capsule.  Oxidative phosphorylation then would on try to pump protons to the outside of the bacterium and it could diffuse out into the surrounding environment.  Does this cause gram positive bacteria to operate less efficiency?  does it make them more vulnerable to a basic pH in their environment?

A similar question was already answered at How do Gram + bacteria use a proton gradient for F-type ATPase? . In those answers, there is a general belief that Gram negative bacteria do not have much control over their intermembrane space pH, because their outer membranes have many porins, such as OmpC, which allows free passage both ways for protons and other molecules smaller than 600 daltons. If that is true, there is not much of a difference between Gram positive and Gram negative ability to control pH just outside the inner membrane.
There is a long review at DOI: 10.1016/j.bbamem.2005.09.010 . The first two examples of pH sensitivity are E. coli (divides more slowly when pH goes from 7 to 8.7) and B. subtilis (divides more slowly when pH goes from 7 to 8.5). The first is Gram-negative, the second is Gram-positive. B. subtilis undergoes growth arrested at pH 9, suggesting it might be more sensitive, but again, the difference is just subtle.


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How do Type I restriction enzymes work?
According to NCBI, type I REases have a specific target sequence but randomly make cuts at sites far from the target sequence.
How does the restriction enzyme travel from the target sequence to the distant site of restriction, and what is the point of having a target sequence if the cuts are random and far away from the target sequence?

The enzymes don't need to travel down the DNA to get from their binding site to their cut site, if the sites are far enough apart the DNA can bend back around and the protein could touch both sites at once. I'm not familiar enough with this class of enzymes to be sure.

To answer your last question first: as long as a restriction enzyme recognises a specific sequence then goes on to cut the DNA it really doesn't matter where the cut takes place, as long as the invading DNA is destroyed.
The WP page on restriction enzymes provides a useful summary of the various classes of restriction enzyme, and led me to a review about Type I enzymes here.
Unlike the familiar Type II enzymes, Type I enzymes require ATP, which they use to power their movement along the DNA, once they have been activated by binding their recognition sequence. The HsdR subunit of the enzyme (R, M and S subunits) contains sequence motifs which mark it out as being related to DNA helicases, which, of course, are able to translocate along a duplex and unwind the duplex.
One particularly striking demonstration of the DNA translocation ability of EcoK1 (a Type I enzyme) is described in

Davies et al. (1999) The DNA translocation and ATPase activities of restriction-deficient mutants of EcoKI. J. Molec. Biol. 292: 787-796 doi:10.1006/jmbi.1999.3081

The experiments are based upon the mechanism by which phage T7 injects DNA into E. coli cells.  The phage ejects about 850 bp of the 40 kb genome into the host; the entry of the bulk of the DNA is coupled to transcription, first by host  RNA polymerase, and subsequently by the phage-specific RNA polymerase, once the corresponding gene has entered the cell. If the drug rifampin is used to block transcription then the whole process stalls. This block is overcome if the initial leader of 850 bp is engineered to contain a recognition sequence for EcoK1 whereupon the restriction enzyme is able to translocate the entire genome into the cell at 100 - 200 bp per second. Mutations in the helicase motifs of the HsdR subunit abolish this activity.


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What is the name of this big plant with a purple trunk and green to purple berries?
I have photographed the following plant in our garden in Pittsburgh, PA.
Do you know the name of the plant?

cf http://gardening.stackexchange.com/questions/2609/what-is-this-fast-growing-plant-with-blue-black-berries/2610#2610

also cf http://biology.stackexchange.com/questions/19612/what-is-the-name-of-this-plant

So clearly we need to start pokeweedID.stackexchange.com, where the only correct answer to any question will be "Phytolacca"...

The plant looks like Pokeweed (Phytolacca americana) to me, a common "weed" in the U.S.

3cat looks like you're right. I have to dig this up all the time, and it's not fun. Of course, being a professional horticulturist/arborist/landscaper means you want to never see this plant again, al least in beds. This is the fouth SE question asking for the id of this weed.


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What is this beetle?
During a pit stop on the road from North Carolina to New York (somewhere in Delaware) I found the following (dead) insect in the car park:

As you can see from the quarter next to it (25 mm diameter) it is rather large - maybe six centimeters, including the "horns".
What was it?

Looks like it must be a male Dynastes tityus (Linnaeus, 1763).
There are photos for comparison, and a full description with maps and some interesting notes on habitat and behavior, on the University of Nebraska State Museum Generic Guide to New World Scarab Beetles

FWIW, my searchpath on this was 1) "huh, that looks like a scarab", 2) google image search for scarabaeidae+delaware

Looks like you are exactly right. Thanks a lot for your "searchpath" information as well.

Thanks for posting the lovely photo! The scale is a nice touch, too.

It was an iPhone 5, and the light was fading. I was quite surprised just how good it came out... you can see my reflection in the carapace (do you use that word for beetles?). I am a physicist, not a biologist - I would never think of taking a picture like this without some way to determine the size...

Having learnt the correct name, I googled some more. The common name is Eastern Hercules Beetle, it can grow up to 60 mm in length (so this was a big one), and it is "among the largest and heaviest beetles in the US". It even made it onto a US postage stamp in 1999