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Deinococcus Radiodurans
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"A lethal level of radiation for humans is about 700 rads. The bacterium deinococcus radiodurans can withstand 1.5 million... There’s never been anything like this level of natural radioactivity on earth in its 4.6 billion year history, so how can we explain the evolution of such a capability?"
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The picture opposite is an electron micrograph of the extraordinary bacterium Deinococcus radiodurans, which can not only withstand devastating levels of radiation (both ionising and ultraviolet), but can also resist horribly genotoxic chemicals such as concentrated acids, and oxidative damage (those free radicals you hear about...)
[Some strains are able to withstand up to 5 million rads of gamma radiation, higher than quoted on the card.]
Its astonishing resistance to the destructive powers of radiation is explained when we understand the damage caused to a cell when it's irradiated: the DNA strands are split into countless fragments (many of the breaks being double-stranded, so that there's no direct way to know how to stitch the ends together). And exactly the same thing happens when the cell is massively dehydrated...
Most bacteria respond to adverse external conditions by turning themselves into spores (strictly speaking endospores): tough little casings in which the cell mechanisms grind to a halt while the organism waits for things outside to improve. Spores are extremely tough, and have proved to be a successful way for many types of bacteria to survive.
Somewhere in the distant past, however, the ancestor to Deinococcus took another route, best summarised in the phrase "bring it on...". It gritted its metaphorical little teeth, took a deep bacterial breath, and let its DNA be torn asunder as it dehydrated. The reason? It had evolved a DNA repair mechanism second to none, which could reassemble the strands, when water was once again available.
It's this mechanism which D.radiodurans has inherited. In terms of its resistance to radiation, this is an exaptation: the mechanism had evolved for other purposes, but turned out to be useful here.
Although it's not entirely certain how the repair system functions, we do know that Deinococcus genes are packaged in four identical circular chromosomal loops, allowing the bacterium to align copies of identical genes next to each other, so that intact sequences on one gene copy can be used by enzymes to repair the blasted sequences on another. (This of course gives it a means of fixing double-strand breaks.)
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| Andromeda and the Night Sky |
"As shown on the front of the card, the Andromeda galaxy is actually six times larger in the sky than the full moon! All the other images show the relative sizes of other objects, including Jupiter’s magnetosphere, the largest structure in the solar system. Why don’t we see such a wonderful night sky?"
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First, the objects on the front page are that size in the sky; it isn't a trick. For example: since Andromeda is about 2.9 million light years away, and it's about 150,000 light years across (though it's hard to say where the edge of a fuzzy object actually is...), a wee bit of trig tells you that it subtends an angle of:
which is six times the Moon's 0.5° width.
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These objects are very faint, and not many photons per second reach us. People often believe that we can't see distant galaxies because our eyes aren't as sensitive as photographic film. In fact, the opposite is true: the human eye is much more sensitive to light than either film or digital sensors. In terms of film speeds, the ISO rating of the eye for photopic vision (in bright illumination) is between 10 and 1600, but for scotopic (low light) vision, the rating is between 10,000 and 50,000! Indeed, we now know that the rods in the retina (which respond to low level illumination) can in fact detect individual photons of light. (See this page for more information (scroll down to section 8, "Rods and Night Vision"), part of the enormous University of Utah site "Webvision: the organisation of the retina and visual system".) (Note that, although the rods can detect individual photons, it takes about ten such impact signals to trigger the associated neurons to fire, so our visual system can't directly observe the quantum nature of light...)
The problem is not one of sensitivity, therefore, but exposure. Whereas film (or CCDs) can be exposed to the sky for seconds to hours to capture photons, the human eye has a maximum exposure of around 100 milliseconds (a tenth of a second), so even staring at the same spot for a long time wouldn't work. (To be fair, it has evolved to work as a moving image device; staring at an approaching lion for tens of seconds to form an image wouldn't have much survival merit...)
Jupiter's magnetosphere (the spatial volume of its enormous magnetic field) is of course the exception: it isn't visible at all. The diagram on the card shows what it would look like if a) the boundaries where it interacts with the solar wind were visible, and b) if we were seeing it sideways on. (Because the Earth is a lot nearer the Sun, we always see Jupiter fully illuminated, so its magnetosphere would be circular from our point of view. (But less visually appealing for the card... :-)
On a slightly more romantic note, find the Andromeda Galaxy in the sky, one dark night. If you have good eyesight you'll see it as a tiny blur. But just consider for a moment... The photons of light now streaming into your pupil and onto your retina started out their journey from the surface of one of Andromeda's hundreds of billions of stars when your remote ancestors were plains apes in Africa, and those photons have spent the last three million years winging their way silently across the vastness of intergalactic space, just at that moment to land and deposit their tiny quanta of energy in the rod cells of your eye.
(And another thought: given that, no matter where you move around on the ground you still see the galaxy in the sky, there is at that very instant a six million light-year diameter sphere, the surface of which is entirely filled with photons from Andromeda, of which your pupil is intercepting an infinitesimal fraction...)
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| For completeness, the full list of objects (left to right) on the card is: |
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Bodes Galaxy (M81), The Pinwheel Galaxy (M101), The Moon, The Andromeda Galaxy (M31), The Sunflower Galaxy (M63), The Sombrero Galaxy (M104), Jupiter's Magnetosphere, The Triangulum Galaxy (M33). |
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| The Messier catalogue numbers of all the galaxies are given above. You can see them all from the UK, easily with binoculars. (It's possible to see all 109 Messier objects in a single night, with clear skies and a good view to the horizon.) |
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| Question: The placement of the objects on the card was governed solely by aesthetics. Does the Moon ever come that close to Andromeda, however? |
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The Deep Biosphere
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"If every single animal and plant, down to the smallest bacterium, was erased from the entire land surface, the sky and all of the ocean, from the surface to the deepest abyss, we would still not have removed the majority of living things on the planet. Where are they?"
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This is perhaps the most controversial of all the "facts", since there's some dispute as to the actual numbers... First, however, what we do know.
Micro-organisms live in the tiny, liquid-filled spaces between grains in rock. (Even under pressure such spaces persist, down to a depth of many kilometres.) Unusal organisms, part of a group known as extremophiles for their ability to exist under severe conditions, have been recovered from deep drilling operations on land and at sea (in Sweden, for example, where deep drilling in granitic rock has been taking place as part of a study for nuclear waste disposal). It seems as if there is bacterial life existing at depths of up to at least a kilometre, and possibly deeper...
Traces have been discovered of what seem to be microbial tracks in samples of volcanic rock recovered from beneath the sea floors of the Atlantic and the Pacific by the Ocean Drilling Program, at depths of up to six kilometres.
Sub-surface marine sediment estimates go from 10 to 30% of the land biomass. If we include the estimates of material in the oceanic and continental crust, we begin to approach (and in fact, many believe, to exceed) the total biomass on the surface.
Perhaps the best known proponent of the deep biosphere theory was Thomas Gold, the controversial astronomer and geoscientist. Taking an extreme position, he postulated the existence of large numbers of organisms down to depths of many kilometres, as well as offering alternative views of the formation and scope of oil deposits. (See his biography page above for more details.)
There are conflicting views on the sub-surface biomass, however, particularly regarding the ability of deep organisms to derive sufficient nutrients for survival. (And many of the growth processes seem to be taking place very slowly.) It may be more hostile than first believed, at depth. But the deep biosphere may have more importance than sheer mass...
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| The Origins of Life – A Safer Environment? |
| Although we might think of the living conditions at depth as being unreasonably harsh (with high temperatures and pressures, and low nutrient content), they do offer an environment which is unchanging over hundreds of millions of years (or longer), for delicate chemical and evolutionary processes to occur. The early Earth's surface was a hostile place: in particular the radiation flux in a reducing atmosphere unprotected by an ozone layer (no oxygen, of course) would be devastating to early (and presumably fragile) self-replicating systems. Deep beneath the surface this wouldn't be a problem. |
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| In addition, chemosynthesis (whereby energy is obtained by the breaking and reforming of chemical bonds in compounds) is a much simpler – if less efficient – mechanism than photosynthesis, and it's been suggested that early forms of life could have developed using chemical energy processes (as well as being protected from the disruptive surface environment) before the more complex photosynthetic structures and pathways evolved in hardier organisms, better fitted to withstand surface conditions. |
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| Interestingly, these deep-living bacteria and archaea may well be the last survivors on the planet. It's been calculated that, if the Sun were to go out suddenly, or if the Earth were to be moved out to the orbit of Pluto, everything on the surface and oceans would of course freeze solid. But the deep dwellers wouldn't even notice that anything had happened, for tens to hundreds of millions of years... |
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| Snowballs and Coal |
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"In a room lit normally by electric light, look at a clean, white snowball. Then, outdoors on a bright summer’s day, look at a dark lump of coal. The coal is actually brighter than the snowball. Why don’t we see it that way?"
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A simplistic (and incorrect) description of the eye tells us that it receives photons of light, focuses them onto the retina where an image is formed, then the different colour-sensitive cones (ignoring the rods for now) detect the amount of red, green and blue light, and the information goes back to the brain, where we 'see' the objects...
In fact, a huge amount of processing is carried out in the thirty or so different parts of the brain which comprise the visual system. The eye (wonderful as it is), is only the first step.
The retina can respond to very low light levels using the rod cells, which are not colour sensitive (scotopic vision). We're concerned here with bright light and only the cone cells (photopic vision), by which colours are perceived. In particular, we're interested in what's called the psychophysical impact of the light on a human observer.
A bright, sunlit day is about one hundred times brighter than a room lit by electric light. If we use a light meter to measure the absolute number of photons being reflected, the outdoor coal registers a higher value than the indoor snowball. The coal is brighter, and more photons are hitting your retina, sending a stronger signal to your brain.
But your visual system is concerned with the entire scene, not just an individual component. Once your pupils have adapted to the brighter outdoor light, the brain registers the relative brightness of objects. Although the coal is reflecting lots of photons, it's reflecting fewer than most of the surrounding objects, and it's the relative score which counts.
And when you go indoors, your eyes register a hundred-fold drop-off in intensity, but the relative brightness of the snowball is still a lot higher than almost anything else in the room, so your brain decides that it's bright.
Of course, it's not reflecting white light at all, but your brain even manages to cope with that, as we see below...
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What would happen if each eye was presented with a different illumination scene? (If you could arrange things so that one eye was looking into a room with electric lights and a snowball, while the other was seeing only a daylight scene, with a piece of coal.) Which of the images would dominate? Which of the two objects would look brighter this time? Or would the brain superimpose some averaging effect, given the overlap, and accept the brighter of the two images...?
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| When is Yellow White? |
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You may have once used daylight film to take a picture in electric light, and been horrified to see just how orange the prints appeared. Your camera isn't faulty, however, and neither is the film. It's recording the scene exactly as it was. It's your visual system which compensates for the indoor illumination, saying (in effect) "I know what's meant to be white, so I'll alter my perception of all the colours to take that into account." (Click here, or on the image opposite, for a brief description.) |
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| You can easily test out a similar way in which our visual system is fooled, without waiting for it to snow. With your TV set turned off, look at the screen; it's dark grey, rather than black. (If you have any really black fabric, hold it up next to the screen to be convinced.) Now turn on the TV, and watch a programme in which there are images with many dark shadows. The shadows look really black, much blacker than the actual screen colour. Now, the TV isn't emitting special black photons; instead, your visual system leaps into action, exploiting the same circuitry as it does for the coal above, and decides that the shadows really are black... |
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| * Our literally-minded SCI-FUN technician Mark, on reading the card, said: "Hold on... one minute I'm looking at a snowball; the next, I'm outdoors on a bright summer's day?" So I should have written: "On a cold winter's day, bring in a crisp white snowball. Store it in the freezer until the summer. Then do the test." :-) |
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Breathing Everyone's Air
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"Breathe out, then wait for a second. Now breathe in. In that single breath, you have just inhaled molecules that have been breathed out by almost every person who has ever lived. In fact, that breath contains molecules exhaled by every single organism that has ever breathed, right back to the first bacterium. (Why would it not include the breath of most people who were born in the last ten years or so?)"
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This is the extension of the "every time you breathe, you inhale a molecule from Julius Caesar's last breath" problem. Which means that we inhale a molecule from everyone's last breath. Which means every creature's last breath.
We can arrive at this extraordinary conclusion with just a few lines of simple calculation (and some assumptions, of course).
First, we look up the total mass of the Earth's atmosphere. (We could work this out by taking an equation for the density profile with respect to height (in actual fact a fairly complex formula), then integrating over a series of thin spherical shells, and finally factoring in the relative masses of the constituent gases... but we don't have time. (If anyone out there has such a calculation, let me know!))
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We know that nitrogen and oxygen are the principle constituent elements in the atmosphere (78% and 21% respectively), and we can use their molar mass (0.028 kg and 0.032 kg, rounding for isotopes) to work out the average mass of a molecule in the atmosphere (ignoring all the trace bits and bobs). The large denominator below is Avogadro's Number, the number of molecules in a mole. (Not the garden-digging variety...)
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Then we divide this mass by the mass of the entire atmosphere to get the total number of molecules:
This gives us an approximate number of molecules for the entire Earth.
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| Now, the amount of air in one average breath is known as the tidal volume, and is around 0.5 litres in a healthy adult. (The largest exhaled breath is 3 to 6 litres – your vital capacity – and there's also a residual volume of air which is not exhaled.)
By the Ideal Gas law, one mole of any gas at 25°C will occupy 24.5 litres (not 22.4, which is the value for 0°C), so our half litre of breath has the following number of molecules:
Almost there...
Assuming (see below) that the molecules in Caesar's last breath (or any other breath) are evenly distributed throughout the atmosphere, we have a simple probability calculation:
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For the above calculations to be true we need to consider how long it takes for molecules to disperse in the atmosphere. (We're ignoring here all the ways in which the gases can be locked up in the ocean, or in surface compounds, but we'll assume that, over time, as many molecules are released back into the atmosphere as are absorbed. This is the wobbliest part of the calculation, especially for the dispersion value, but, hey, it's Christmas.)
Much work has been done in examining the dispersal of molecules in the atmosphere, from the gases erupted from volcanoes to the spread of radioactive fallout after major accidents. (Strictly speaking, we have to separate out the spread of particulates from gaseous molecules.) Assuming that you've just breathed out, here are some rough rules of thumb: it takes tens of days for the molecules in your breath to be evenly distributed in an area, say, of a hundred square kilometres; a year is needed for the molecules to travel to the opposite hemisphere; and ten years or so for their distribution in the stratosphere (the 20 km thick region of the atmosphere, starting about 10 km up, above the troposphere, where mixing is reasonably rapid).
So.... if we set a figure of ten years, we can reasonably expect your breath to have spread out evenly over the entire world. (In fewer than ten years, diffusion won't have spread the molecules far enough.)
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| We can therefore extrapolate to all living organisms, although some waving of hands has to be done here, given the varying lung capacities and rates of respiration of various creatures. Certainly, since the calculations above are for one breath only, it's a solid certainty if we include all the breaths throughout their lives of creatures from the past.
[Just to bring us all down to earth a bit, and lower the tone, these calculations also apply to farts...]
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| Question: What are the three main gases in the Earth's atmosphere? |
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| You aren't really all You... or are You? |
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"Ninety percent of the cells in your body are bacteria and other parasites; only ten percent of you is you! Does this mean that your arms, legs and body are all made of bacteria?"
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"90% of your cells are bacteria..." This is true; indeed, it may even be an understatement: several sources state that your intestinal flora alone outnumber your body cells by ten to one.
But of course, sheer numbers aren't the whole story. Bacteria are tiny in comparison with most of your cells. Roughly speaking (and there are variations, of course, according to type), human cells mostly lie within the range of 10 to 150 microns (thousandths of a millimetre), mostly at the upper end of the range. Bacteria are about 1 to 10 microns (most are at the smaller end), and viruses are 0.005 to 0.3 microns. So in terms of volume, your body cells vastly outweigh the rest.
Even so, another estimate has it that we each carry around several kilos of bacteria, by dry weight; still a fair old chunk.
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There's a wonderful way to see these differences in size, on the How Big is a...? page at the Cells alive! site. Just start the animation, then use the magnifying glass slider to zoom in on the pinhead... (You might want to turn the sound off, as it makes an annoying 'boop boop' noise, every time you change magnification...)
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Most of the bacteria in our bodies are either harmless or positively necessary (your gut e.coli, for example). Some are usually fairly harmless, such as the group A streptococci, which cause no more than a sore throat. Occasionally, however (and we don't know why) these strep bacteria can run riot in the body, the most gruesome example being (put down whatever you're eating...) the flesh-eating disease, necrotising fasciitis. Yum yum. (Do your own Google search for pictures.)
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On a more jolly note, the website www.giantmicrobes.com offers cuddly soft-toy versions of various bacteria and viruses; the flesh-eating version is shown opposite.
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The smallest infectious things are prions, snippets of protein which can interfere with cellular processes; they aren't strictly speaking living things, however (though I'm not sure whether a sheep with scrapie would be particularly impressed, if you told it...)
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| (Research is ongoing into the existence of nanobacteria, proposed organisms with a diameter well below the lowest size traditionally accepted for bacteria. (Viruses aren't included here, since they can only reproduce using the mechanisms of a host cell.) Evidence is claimed in several areas, but many are still sceptical that all the needed cellular machinery can fit into such a small space.) |
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The idea of nanobacteria hit the world headlines a few years ago when some researchers claimed to have discovered fossilised organisms of nanoscale size in a meteorite known to have been blasted off Mars. Alas, it now seems increasingly likely that these were simply artifacts of the coating process used to produce samples for electron microscopy. The possibility of deep sub-surface organisms is interesting, however, since we now know from the recent NASA Mars Rovers that large quantities of water did exist in the past. Could there still be bacteria, hundreds of metres deep in the Martian crust?
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| Question 1: What's the largest human cell? (It's so large that it's visible with the naked eye, though you'd have to be in a fairly unusual position to be looking at one...) |
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| Question 2: Some of the largest (strictly speaking, longest) cells in nature are about 3 metres long? Which animal's neck do you think these might come from, and what type of cell might they be? |
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