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Prof. A's Science Fix- Aug 10 2012 Edition

There is no denying that the biggest news in science this week comes from NASA. Something very exciting has just happened:


NASA Curiosity Rover landed safely on Mars! Michel was the first one to sound the alarm at our site on August 5th: “Something very exciting is going to happen tonight. The SUV-sized NASA rover Curiosity is to touch down on Mars at 1:30 AM (Florida time.) If it makes it in one piece to the surface - an incredible feat in itself - a set of fascinating experiments will begin with the robotic chemical lab that's on board” And then on August 6th, the fantastic news, as described by Michel: “Curiosity is now open for business on Mars. Humanity has successfully put a semi-autonomous robot jam-packed with high-res sensors and fancy software on a tiny rock fourteen light-minutes away. That's an impressive demonstration of the power of scientific predictions. I don't know how long is the NASA list of things that could go wrong but I bet it is astronomical. Now the coming weeks will be critical. Before going anywhere Curiosity will test its subsystems and deploy its paraphernalia. That's another gazillion things that could go wrong. But these people are good - think the Voyagers, Cassini, Apollo 11 - pretty much the best that we have”.

Check out how the NASA scientists and technicians celebrated:

And do not miss the BBC special on the Curiosity Rover, here on our site. Courtesy of Mohamed.

And now that Curiosity is going to give us so much data, perhaps we should start thinking about the future of Mars: colonization? Some scientists have already started thinking about colonizing microbes.


Engineering life to survive on Mars and aid human colonization. Curiosity has landed safely on Mars and is ready to start exploring for possible signs of past life on the Red Planet. As for life on Mars in the present tense, it is not a very life-friendly environment, even for microbes. It is very cold (average temperature is minus 80 degrees Fahrenheit, though there is water in its ice caps) and the atmosphere is 95% carbon dioxide. Even for extremophile microbes, it would be a challenge. But right here on Earth there are scientists working to engineer bacteria that could potentially live on Mars, and even help humans to colonize Mars, by producing food or extract minerals. Their work is carried out under the International Genetically Engineered Machines (iGEM) challenge, a synthetic biology competition for students. The goal is to engineer microbes to perform new tasks. A collaborative team from Stanford and Brown universities have created a “Hell Cell”, that Ben Geilich, the student team captain from Brown University, defines as “a genetic box of crayons for extremophile conditions.” The Hell Cell is a collection of genetic modules, that the students call “BioBricks”, engineered from DNA from a variety of organisms, including a radiation-resistant bacterium capable sequesters large amounts of manganese, a special strain of E. coli, capable of resisting to cold and droughts, and even a cold-resistant species of Siberian beetle that makes proteins that can serve as “antifreeze”. The BioBricks are currently being introduced into E. coli, which is a favorite model in microbiology labs, but it can be used in other bacterial species as well. In addition to the Hell Cell, the team is developing bacteria that could extract rare metals from the silica that coats most electronic devices. Releasing life on Mars would be problematic if Curiosity finds some living microbes there, because there is no telling what engineered bacteria could do to the local microbiota, but if there isn’t any life there, it would be a bit easier to make the argument for releasing engineered microbes on Mars.


Meanwhile, on our own Blue Planet, the evidence for the huge impact that our presence is having on the globe we share with so many other creatures keeps mounting.


Caffeine pollution in the Pacific Ocean coast off the US Northwest. Maybe we humans do drink too much coffee; maybe there are too many Starbucks around the globe. Or perhaps we just need to be much more careful about how we dispose of our waste. The waters off the coast of Oregon are now caffeinated, and we have no idea what effect caffeinated seas can have on aquatic wildlife. Interestingly, caffeine levels off potentially polluted areas, that is near sewage-treatment plants and larger communities were below the detectable limit (9 nanograms per liter) but the wilder coastlines in more remote areas were comparatively highly caffeinated, at about 45 nanograms per liter. The possible explanation is that monitoring is more stringent near developed areas, and in more remote areas, the contamination could be coming from on-site waste disposal systems, like septic systems, that are not monitored as much as waste coming from sewage systems. Also, Oregon cities are relatively small so the sewage plants don’t process a huge volume of waste. Bigger cities such as Boston have been found to be pumping fairly high levels of caffeine in the harbor, from its sewage plants. Caffeine has been documented in waters around the world, including the Puget Sound, the North Sea, and the Mediterranean (all those espressos and Turkish coffees!). Caffeine is thought of as a good tracer for the presence of other human contaminants, such as pharmaceuticals, fragrances, detergents, hormones, etc. Aquatic plants and animals are getting hit with a whole slew of substances whose effects on the ecosystem are totally unknown. Marine biologists have found that in the lab, caffeine levels similar to the ones found offshore affect intertidal mussels, causing them to produce specialized proteins in response to environmental stress. This could in theory result in a change in growth rate, or less offspring, and these changes may end up affecting the whole food chain.  Other human contaminants have been shown to have drastic effects already: at a remote Ontario Lake, estrogen from birth control pills has caused fish populations to collapse.


And while we are on the subject of sea water, I just learned something amazing about our oceans that I have never hear of before: the presence of huge internal waves.


The largest waves in the sea are vertical! The only waves I knew existed are superficial, horizontally moving waves, like the ones we admire and sometimes surf, and tsunami waves who are huge but move horizontally. I’m not an oceanographer, but if I was one, I’d be enthralled too, with the biggest waves in the ocean: internal waves. These occur deep below the surface. They can’t be seen from shore, but they are so HUGE that they can be seen from space! (See satellite photo of the Strait of Gibraltar; the crests are the internal wave surface signature; this internal wave is caused by the tides forcing water to flow back and forth over the Gibraltar sill). Internal waves are similar to shore waves: they undulate, have crests and troughs, and break. Surface waves and internal waves are both caused by the meeting of two fluids of different densities. For surface waves, the two fluids are very different, because they are air and water. For internal waves, the two fluids are water of different densities: the deeper the seawater, the denser it is. There are many density layers therefore many chances for internal waves to occur. The almost infinite number of density layers at different depths means that they can move vertically. Internal waves can move water up and down over 200 meters (~600 feet); they have been hypothesized to be capable of sinking submarines. Internal waves can travel thousands of miles; for example, internal waves generated in Hawaii have been tracked by satellite propagating all the way to Alaska. Internal waves (of air) also occur in the atmosphere, they are ones that cause a choppy flight over mountains).  They occur at the Sun too. 


And thinking about the water and organisms that live there permanently or temporarily, here is a fascinating little adaptation that allows a terrestrial organism to walk underwater.


Beetle walks underwater on dry feet. This story reminds us of the astonishing adaptations that make animals so nicely fitted to their habitats. We are all familiar with the ability that insects have to walk on totally flat surfaces, such as a flying walking up your living room window. It's so mundane that we don't even bother thinking about why they can do that. It's the thousands of hairs (setae) on an insects's feet or claws that allow them to be so "sticky". Some insects have oily hairs on their feet too. The European green dock beetle (Gastrophysa viridula), like most beetles, can walk on flat surfaces, but it can also walk underwater, on the bottom of a body of water, with the same ease as in dry land. It's not that the beetle is not heavy; it floats, like all beetles, so how does it manage to walk underwater? Scientists at the University of Kiel (Germany) and the National Institute for Material Science in Tuskuba (Japan), just had to find out.  So they got a couple dozen beetles and let them walk off a stick onto the bottom of a lab water bath, where the metallic green beautiful insects just kept on walking. duo captured 29 wild beetles, and allowed them to walk off a stick onto the bottom of a water bath. Once there, they kept on walking. They took pictures of the beetles' footsteps, and they realized that their oily hairs trapped tiny bubbles that displaced water and created a minuscule patch of dry land under each step, so that the sticky hairs could operate normally, by capillary adhesion. They confirmed it was the bubbles that did the trick, because if they added a tiny amount of detergent to the water, the surfactant action disrupted the bubbles and the hapless beetles immediately floated to the surface. Air cushions inspired by the beetle's feet could one day be used to improve locomotion underwater for man-made machines. 


But, in contrast to the beetle, another notoriously sticky creature does not fare so well when walking on water.


How to unstick a gecko. We have discussed the astonishing stickiness of gecko’s feet, which allows the little lizard to scurry up a glass surface with no difficulty whatsoever.  The secret is that the charismatic reptiles (I hear they even do TV commercials!) can exploit van der Waal’s forces. These molecular attractions are very weak, but the soles of geckos’ feet are covered with tiny, branched hairs that end in flattened pads. The hairs result produce a huge surface area, and the piling up of many weak van der Waal’s forces end up creating an extremely strong adhesive power. But geckos don’t normally live on glass, they live in tropical or sub-tropical areas. And they are likely to encounter rain and wet surfaces. So scientists set out to find out how they do on wet surfaces or if their feet were submerged in water.  They measure the force of adhesion by finding out what force it took to unstick a gecko from a wet surface, in the lab.  They used little harnesses on the geckos to gently tug on them with a device that applied measurable forces and record when the lizards let go of the surface. If they wetted their footpads, or if they submerged their legs, their adhesive force decreased ~20-30 times. They did better on misted glass, but after a few steps their toepads got saturated with water and they slipped. Knowing that water is like kryptonite fir their super adhesive powers is important because scientists are trying to develop super-adhesives for human use based on the gecko model. There are already “gecko tape” synthetics: University of Berkeley scientists have built a gecko-modeled adhesive that permits a car to drive up a very steep incline but only on a perfectly smooth, dry road.  Researchers at the University of Kiel (Germany) created a 20 X 20 cm square gecko tape that can hold the weight of an adult human.


And speaking of humans and sticky stuff, have you ever considered that tartar could end up being a boon and not only for hygienists?


Dental tartar in archaeology. The media glamorize what archaeologists do in the field: they travel to exotic places usually with beautiful whether and they excavate for artifacts and skeletons surrounded by throngs of adoring very young graduate students that do all the menial work. Of course, fieldwork is extremely important in archaeology but many people do not realize that labs and museums are full of drawers and drawers with skeletons and artifacts waiting to be studied. A lot of interesting stuff goes on in the lab, and technology helps dig out a lot of information from unsuspected places, for example tartar in ancient teeth. Christina Warinner, a geneticist at the Centre for Evolutionary Medicine at the University of Zurich, has been sampling and analyzing the dental calculus (tartar) that coats the teeth in fossil and ancient skull collections. Ancient humans accumulated as much as 600 milligrams of calculus on their teeth, a lot more than modern humans who brush their teeth and visit the dentist regularly, and typically have only about 30 milligrams. Tartar is a mineralized biofilm with food remnants and bacteria, and DNA can be extracted from it. Warinner in fact found that ~ 1000 times more DNA can be obtained from tartar than from the bones themselves. Of course, the DNA is not just human but also bacterial. She identified DNA from 2,000-4000 species of bacteria, including pathogens.  Analysis of DNA from ancient specimens will allow us to uncover the evolutionary history of human health and disease, and we could reconstruct a very detailed picture of the diet, infection and immunity from thousands of years ago, and figure out how these parameters interplayed.  Tartar now looks very appealing, and the bacteria in the biofilm certainly look very pretty under the microscope (see photo).


And here is a neat story that combines archeology with genetics, a perfect marriage when we want to study our forebears.

Corn cultivation and recent human evolution. The best known examples of recent human evolution is the adaptation to heights in certain populations (Tibet and the Andes) and lactase (the enzyme that digests lactose, or milk sugar) persistence in adulthood which allowed some European and African groups to consume dairy without unpleasant side effects, well past infancy. These adaptations happened in the last few tens of thousands of years. The lactase persistence mutations are especially intriguing, because their fixation into the population likely occurred as a consequence of a cultural change, in this case keeping herds. Now there is another example of culture-gene co-evolution, the first one from Native American populations, and it appears to be linked to maize cultivation. An article in PLoS One, describes an allele (a variant) of the ABCA1 gene, named Arg230Cys (meaning an arginine, which is an amino acid at position 230 is substituted by a cysteine (another amino acid), for those of you who are curious regarding nomenclature).  This allele has been found in 19 different Native American populations, from North, Central and South America, and it's no present on any other groups. It is associated with abnormally low production of HDL cholesterol (the "good" cholesterol) and with increased risk for obesity, diabetes, and heart disease. The area of DNA sequence around the Arg230Cys shows the typical reduced diversity which is the hallmark of what geneticists call a "selective sweep", indicating the variant was favored by selection. The researchers pinpoint the appearance of this polymorphism to between 19,000 years ago to 7,000 years ago. This is coincident with the domestication of Zea mays (maize or corn), as measured by the age of maize pollen found at archaeological sites. A staple crop can provide a more predictable food source compared to hunter-gatherer lifestyle but when the crop fails, it means famine. Scientists speculate that the allele makes carriers better at storing fat, which would be a sort of insurance against bad harvest years. Since DNA sequencing got faster and cheaper, new development in population genetics will sure show a few more interesting cases of culture-gene co-evolution

And going further back in time: it seems like every week we get news of a new ancestor.


Homo rudolfensis? Our tree keeps getting bushier. The earliest known human species is Homo habilis (that lived 2.3-1.4 million years ago).  It is the first species recognized to use tools and to begin looking human, compared to the australopthecines (“Lucy”).  H. habilis is not considered to be directly on our line, so there must be other Homo species out there who were our direct ancestors. One such species could be Homo rudolfensis, who lived ~1.9 million years ago and is known from a single skull, very similar to H. habilis. Throughout the years, paleoanthropologists have debated whether it is a separate species or just a variant of H. habilis.  Now three new fossils from Koobi Fora in Kenya may shed some light on the issue.  One of the specimens is represented by the upper jaw and part of the face from a juvenile (adolescent) from ~1.9 million years ago; it is definitively in the genus Homo and looks more like H. rudolfensis than H. habilis. The second fossil is a lower jaw, between 1.87 and 1.78 million years ago, and it is similar to the juvenile, which in turn is most similar to the original H. rudolfensis skull. The third fossil to be found is a fragment of lower jaw fragment, ~1.9 million years ago, and it is also similar to the juvenile and thus, to H. rudolfensis. These new fossils appear to confirm the existence of a species separate from H. habilis, and H. rudolfensis is a good bet for a classification, instead of designating a totally new species.  This does not “re-write the history of our soecies” as some newspapers have reported, but they are very important finding and have just been published in Nature. The leading authors are second and third generation Leakeys, what an incredible family! The leaders of the project are Meave and Louise Leakey, a mother-and-daughter team.  They are not assigning a fixed species to the fossils for now, as they prefer to wait for further discoveries. But their findings suggest that East Africa was teaming with hominin species, which presumably occupied different niches. One thing appears certain: human evolution was far from a straight line.


Highlighted VIDEO: A minute and a half science. Why is music so rewarding to us humans?

Is music humanity's drug of choice? What is the mysterious power behind its ability to captivate, stimulate and keep us coming back for more? Find out the scientific explanation of how a simple mixture of sound frequencies can affect your brain and body, and why it's not all that different than a drug like cocaine. Written and created by Mitchell Moffit (twitter @mitchellmoffit) and Gregory Brown (twitter @whalewatchmeplz).

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Comment was by Chris on August 16, 2012 at 11:26pm

Here's more on human caused water pollution:

Are Urinating Swimmers Killing Fish?

German officials have banned swimmers from Eichbaum Lake while studying the link between fish death and public urination.

There’s an old joke about the silent ‘p’ in swimming pools (think about it), but it turns out that urinating in a lake may be far from funny. German researches have come to believe that a significant amount of human urine may be responsible for an algae bloom that poisoned over 500 fish at Eichbaum Lake in northern Germany.

“Swimmers who urinate in the lake are introducing a lot of phosphate” that can contribute to algae blooms, a spokesman for the Hamburger Angling Association told Bild newspaper. “We’re calculating half a liter of urine per swimmer per day.” The Angling Association has been in a long-standing feud with the lake’s swimmers, according to The Local, so that number may be suspiciously high. Bathers are currently banned from the lake due to the high levels of algae, but the city’s Urban Development and Environment Authority (BSU) is working to re-open the lake for swimmers before the summer season starts.

To help resolve the whodunit, the BSU is calling in the local university to test the pee-death theory. According to The Local, the BSU believes that the fish deaths were caused by a combination of natural causes and something far less taboo than public urination: ice skating.  “The ice-skaters make a noise that wakes the fish out of hibernation,” BSU spokeswoman Kerstin Graupner told the Local. “Then they can’t breathe and freeze. That’s a very common phenomenon.” Their bodies are only now being found.

For those questioning whether or not human urine could be responsible for fish death, the answer is yes.  According to i09, the phosphates in human urine act like a fertilizer that can promote algae growth. Algae blooms deplete the oxygen available to fish, causing them to suffocate. Additionally, the scientists in Hamburg believe the algae that has bloomed in the lake is particularly aggressive, releasing a toxin that changes the lakes natural ammonium to the far more deadly ammonia, which restricts the fish’s breathing.

Eichbaum Lake is not the first natural wonder to receive a pee ban. Ecologists warn visitors not to pee when they visit Australia’s Great Barrier Reef for fear that algae blooms will kill the coral.


Comment was by Davy on August 16, 2012 at 5:52pm

Awww! Thor's at it again throwing that bloody hammer of his around again!

Good Pic though.

Comment was by Doone on August 16, 2012 at 5:50pm

Lightning Over The Caspian Sea

Comment was by Davy on August 16, 2012 at 4:27pm

On rainbows - When you are in the air and the conditions are right for a rainbow you actually get rain-ring not a bow. 

Comment was by Doone on August 16, 2012 at 1:47pm

Not a Rainbow but intensely interesting anyway

Comment was by Michel on August 16, 2012 at 1:43pm

@archaeopteryx -

Mind if I add something?

Never =)

I have added the link HERE and under the Pages 3 menu.

Comment was by archaeopteryx on August 16, 2012 at 12:39pm

Mind if I add something?

    This was blatantly purloined from the How Stuff Works website - - that I would strongly recommend you visit for all of your knowledge needs.

    When white sunlight hits a collection of raindrops at a fairly low angle, you can see the component colors red, orange, yellow, green, blue, indigo and violet - a rainbow. For simplicity's sake, we'll only look at red and violet, the colors of light on the ends of the visible light spectrum.
    The diagram below shows what happens when the sunlight hits one individual raindrop.

    When the white light passes from air into the drop of water, the component colors of light slow down to different speeds depending on their frequency. The violet light bends at a relatively sharp angle when it enters the raindrop. At the right-hand side of the drop, some of the light passes back out into the air, and the rest is reflected backward. Some of the reflected light passes out of the left side of the drop, bending as it moves into the air again.
    In this way, each individual raindrop disperses white sunlight into its component colors. So why do we see wide bands of color, as if different rainy areas were dispersing a different single color? Because we only see one color from each raindrop. You can see how this works in the diagram below.

    When raindrop A disperses light, only the red light exits at the correct angle to travel to the observer's eyes. The other colored beams exit at a lower angle, so the observer doesn't see them. The sunlight will hit all the surrounding raindrops in the same way, so they will all bounce red light onto the observer.
    Raindrop B is much lower in the sky, so it doesn't bounce red light to the observer. At its height, the violet light exits at the correct angle to travel to the observer's eye. All the drops surrounding raindrop B bounce light in the same way. The raindrops in between A and B all bounce different colors of light to the observer, so the observer sees the full color spectrum. If you were up above the rain, you would see the rainbow as a full circle, because the light would bounce back from all around you. On the ground, we see the arc of the rainbow that is visible above the horizon.
    Sometimes you see a double rainbow - a sharp rainbow with a fainter rainbow on top of it. The fainter rainbow is produced in the same way as the sharper rainbow, but instead of the light reflecting once inside the raindrop, it's reflected twice. As a result of this double reflection, the light exits the raindrop at a different angle, so we see it higher up. If you look carefully, you'll see that the colors in the second rainbow are in the reverse order of the primary rainbow.
    And that's really all there is to rainbows. Light and water happen to combine in just the right way to paint a beautiful natural picture.
Comment was by Adriana on August 16, 2012 at 10:00am

This rainbow post is so good, it needs its own discussion.

Comment was by Doone on August 15, 2012 at 7:35pm

How many colors are really in a rainbow?

“The colors of a rainbow so pretty in the sky.
Are also on the faces of people going by.” -Louis Armstrong

It’s no secret that white light is the light that we see when all the colors shine together and are seen at once. This has been known for over 400 years, when Isaac Newton demonstrated that white light could be broken up into all the known colors by dispersing it through a prism.

White light through a prism

Image credit: Adam Hart-Davis.

All that we’re doing is breaking white light — in this case, sunlight — up into all of its component colors. This can be done artificially (such as by configuring a prism) or naturally (in the case of a rainbow), and covers wavelengths both inside and outside what our eyes can perceive.

The Electromagnetic Spectrum

Image credit: Antonine Education, retrieved from Kerry Clavadetscher.

While the Universe contains wavelengths of light that range from many meters long (radio waves) down to ultra-energetic, high frequency gamma-rays (with wavelengths as small as a single proton), it’s only light ranging from about 400 nanometers to a little over 700 nanometers that provides us with the light visible to our human eyes.

Lucky for us, that’s where a good deal of the Sun’s light falls, especially after atmospheric absorption is taken into account.

The Solar Spectrum

Image credit: Robert A. Rohde, as part of the Global Warming Art project.

But I was recently asked a question (that was also posted here) that I hadn’t been asked before:How many colors are there really in the rainbow? In more technical terms: How many distinct frequencies can a photon have in the frequency range visible to humans?

You might think — off the top of your head — that the answer is infinity; why wouldn’t you be able to just have an infinite number of frequencies that occur in that range?

Harmonic nodes

Image credit: © 2012 Russell Rolen.

If light were a continuous, classical wave, that’s exactly how it would work. But light, remember, is an intrinsically quantum phenomenon, and so if the energy of the photons coming from a source are finite and discrete, then so must be the frequencies (and, interchangeably, the wavelengths) coming from them.

After all, this is how atoms work.

Spectra of different atoms

Image credit: Marcel Patek.

Atoms can only emit and absorb light of very specific frequencies, and hence we can observe absorption and emission lines unique to individual atoms. Not only that, but atoms can be combined in extraordinarily intricate patterns to create a myriad of molecules. Many different types of molecules with many different wavelengths of absorption/emission, to be sure, but a finite number nonetheless.

But the Sun is not made of neutral atoms.

The Sun through the 171-wavelength filter

Image credit: NASA's Solar Dynamics Observatory (SDO).

The Sun is a miasma of incandescent plasma, and the rules that govern atoms and the specific wavelengths that they can emit and absorb light at do not apply to plasmas. Instead, they can emit at an arbitrarily large number of frequencies, dependent on the temperature of the plasma. For the Sun at just under 6000 K, with some regions slightly hotter and others slightly cooler, it emits about 40% of its energy in the form of photons that fall in the part of the light spectrum visible to our eyes. And oh, are there a lot of them: somewhere on the order of 1045 visible-light photons come from the Sun every second. While this number isn’t infinite, it means you’d have to go to a sub-Planckian precision to discern a frequency difference between two photons that were very close in energy.

On the other hand, your eyes are very much made up of neutral molecules that are highly restricted with respect to the wavelengths of light they can respond to.

Layout of the Human Retina

Image credit: Benjamin Cummings / Pearson Education, Inc.

While the rods cannot discern color at all, they are sensitive to as little light as a single photon, hence they are most useful under extremely low-light conditions. But under brighter conditions, the cones move forward in the eye, with each cone cell sensitive to a particular set of wavelengths of visible light, capable of discerning about 100 different shades of that color.

Cone Cell anatomy

Image credit: Ivo Kruusamägi from Wikipedia.

Since most humans have three separate types of cones (making us trichromats), a total of (100)3= 1 million colors are discernable to a typical human. Some humans are born without one of the three types of cones, creating a condition known as color blindness; color blind (dichromat) humans can only see (100)2 = 10,000 distinct colors. On the other hand, some humans havefour distinct types of cones, making them tetrachromats and allowing them to distinguish up to (100)4 = 100 million separate colors!

Visible Spectrum

Image credit: Encyclopædia Britannica, Inc.

So going off of unique frequencies, there are more colors in a rainbow than there are stars in the Universe or atoms in your body, but that goes far beyond what we can perceive. Your imperfect eye can (probably) only discern about a million distinct colors when you view a rainbow, or anything else, for that matter.

But oh, what a spectacular view it is to be able to see all that our eyes permit.

Double Rainbow

Image credit: Shanana Rocks.

It may just be a tiny fraction of the information actually encoded in the light of the Universe, but now that I’ve been asked, I’ve got to conclude that what we can see is pretty amazing for a simple trichromat!

Comment was by Davy on August 12, 2012 at 6:50pm

Going on the rate at which their accuracy is going the next science bot will land in a area of about 12 square miles or bang on target!!

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