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Prof. A’s Science Fix- April 6 2012 Edition

NOTE: Those who read to the very end of this blog will be rewarded with a surprise.


Science at Atheist Universe


FEATURED VIDEO: Perpetual Ocean (mesmerizing!)

A team of data visualizers at Nasa's Goddard Space Flight Centre has put together this hypnotic animation of sea surface currents around the world. Watch it in HD if you can. Their model maps ocean and sea ice data across the world. The patterns under the ocean represent the bathymetry of the depths below the surface, exaggerated 40x. The topography of the land has been exaggerated 20x. The model simulates flow at all depths, though the visualization only shows surface flows. There is 20 minute version of this video on the Nasa website.


ASTRONOMY:Two very interesting posts in this category!


Many billions of rocky planets in the habitable zones around red dwarfs in the Milky Way. The chance that our planet is the only one where life exists keeps diminishing with each new discovery.  A new result from the European Southern Observatory’s High Accuracy Radial velocity Planet Searcher (HARPS) in the La Silla site in Chile shows that rocky planets not much bigger than Earth are very common in the habitable zones, where liquid water can exist on the surface, around faint red stars called red dwarfs. There seems to be are tens of billions of such planets in the Milky Way galaxy alone, and probably about one hundred in the Sun’s immediate neighborhood. Red dwarfs account for 80% of the stars in the Milky Way. The international team has been able to recently estimate how common different sorts of planets are around red dwarfs. The frequency of occurrence of super-Earths in the habitable zone is 41% with a range from 28% to 95%.  Some of these planets will pass in front of their parent star as they orbit, and at this point the planet's atmosphere can be studied, and we can begin to look for signs of life, according to  a HARPS team member, Xavier Delfosse.


Neil deGrasse Tyson on surviving a killer asteroid. Neil deGrasse tyson wrote a very good opinion article for Wired Science, about killer asteroids, and what we should do as a species to survive or rather, deflect, a potentially annihilating impact. He points out that roughly 1,000 asteroids are classified as “potentially hazardous,” based on their size and trajectory. Usually the hazardous asteroids would be those with a diameter of 1 kilometer of > 1 Km. An impact of this sort could put the entire human species at risk of extinction. deGrasse Tyson says it is possible to develop an early-warning system and also to devise some defense strategies to avoid the impact and its consequences. This type of impact occurs more or less once in about a hundred million years. the last time it happens, the dinosaurs died out, and many other large life forms as well. For example, Apophis, one of these potentially killer asteroids, will dip below the range of our communication satellites on April 13th, 2029 (it will be a Friday the 13th, ha!), and if its trajectory on that day passes within a narrow range of altitudes which astronomists call a “keyhole,” then our planet's gravity will influence its orbit and the asteroid will hit Earth directly in 2036, likely slamming into the Pacific Ocean, creating a massive tsunami that will destroy the entire Pacific Rim. He concludes by saying that if we don't our act together to devise a strategy to avoid the collision, should Apophis pass through the "keyhole" in 2029, we will not be much better than the dinosaurs who could do nothing but watch in amazing and die when their asteroid impacted Earth.


HUMAN EVOLUTION:It seems that exciting news come in pairs lately. There were two very interesting pieces of news in the field of human evolution in the past couple of weeks:


Were humans cooking 1 million years ago? Fascinating new evidence of 1 million year old plant and animal ash in a South African cave suggests that our ancestors were already cooking their food. Judging from the age of the ash, it is likely that the cooks were Homo erectus. Paleontologists ruled out a spontaneous fire started by, for example, lightening, because the cave is very deep, and one of the earliest sites of known human habitation. They also ruled out a fire ignited by bat feces, or guano, that is known to spontaneously combust occasionally; they found no traces of guano in the cave. Since cooking makes food easier to digest and therefore more energy containing, it is important to know when humans have actually realized the advantages of cooking and used it in a regular basis. The earliest proven evidence of regular cooking is currently ~ 400,000 years old, from a site in England and another in Germany. More evidence is needed to be sure that humans were cooking their food already 1 million years ago, but this South African ash is a great start. This however, does not mean the humans had already figured out how to light a fire, but that they could have used it when available.


Newfound fossil foot bones identify new tree-dwelling prehuman species. Eight newly-found fossil foot bones suggest that our ancestor Lucy (Australopithecus afarensis) had company 3.4 million years in Ethiopia. But while Lucy was already committed to walking upright, this other hominid probably walked awkwardly upright while on ground, but had retained the ability to grasp with its big toe, so it was very adept at tree-climbing. The toe is unmistakably opposable, just like that of Ardipithecus ramidus or like that of modern chimps. More fossils will need to be found before this animal can be named a new species, but the discovery points to the diversity of hominid species found in Ethiopa between 4 and 3 million years ago. Brian Switek wrote a great news article in Nature about this discovery.


NEUROSCIENCE and GENETICS: Autism genes: it's complicated.This week's edition of Nature has 3 back-to-back articles from 3 different groups who have sequenced the "exomes" (the part of the genome that codes for proteins) of a huge number (almost 600) of autism trios (in genetics, a trio is parents and affected child), as well as almost 1,000 additional autistic people. This massive effort yielded 3 new genes related to autism, CHD8, KATNAL2 and SCN2A. The other interesting bit of information is that fathers older than 35 years old are much more likely to pass on these mutations. . But the most important result is that these studies conform that autism is an extremely heterogeneous group of disorders, with >1,000 genes contributing to the risk of developing the condition. Although it is not clear how mutations or variants of these genes contribute to the disease, CHD8 is very intriguing because it is a chromatin remodeling factor. Chromatin refers to the packaging and "wrapping" of genes, it has to do with gene expression, it is part of epigenetics, a very hot new field. Recent papers have identified germline mutations in chromatin remodeling factors in syndromes that include intellectual disability and epilepsy, pointing to a role of chromatin remodeling in disorders of the central nervous system. For a very detailed blog describing these 3 articles (very technical), go here: Autism exomes arrive. This NYT article is more readable although less detailed: Scientists Link Gene Mutation to Autism Risk.


BONUS FEATUREUgly Pictures of Animals. Doone started out this discussion by posting really ugly pictures of animal body parts, such as ox penises, that people consume as foods. I exhort all members to counterbalance the gross effect by posting pictures of ugly, unusual, but LIVE beasties that people aren’t really filling up their stomachs with. Such as this super cute-ugly California condor.



Science bits and news from other sites:


Great site to test your brain: testmybrain.orgWarning: looking around that site can be highly addictive. The site contains a whole bunch of internet-based experiments, as well as science education.  You can get lost into self-discovery by clicking around the site. You can learn about how your brain works, what your personal aptitudes are, etc.  For example, check the spinning woman illusion. How does it turn for you? Can you reverse it?



This is the weave of your brain. The position of nerve fibers in the living human brain has been mapped using a new technique called diffusion spectrum imaging. The methodology allows the determination of the position of nerve fibers from the way water flows through and around them.  Interestingly, the wiring mostly looks like an orderly lattice of nerve fibers that cross each other at right angles. The work was published in Science last week.  Hereis the abstract of the original publication. The nerve fiber pathways formed a rectilinear three-dimensional grid that was continuous within 3 principal axes of development. This reflects a much simpler organization than many scientists would have suspected. Brain scans using the same technique revealed a very similar pattern in 4 monkey species. Scientists are speculating that this grid-like organization could be advantageous during brain development, providing a map for growing nerve fibers so that they find their way to the appropriate destination. In addition, this type of architecture supports functional spatio-temporal coherence, and incremental rewiring for cerebral plasticity and brain evolution.



Viruses Controlling Mosquito Blood-Feeding Behavior. Many viral diseases are spread through vectors, such as ticks, mosquitoes, etc. One great question in biology is: what happens to the vector when it carries the virus. Does it itself get sick? A group at Johns Hopkins University has studied the effects of the Dengue virus (formally named DENV) on its main vector, the mosquito Aedes aegypti. Dengue is a tropical and subtropical disease, which affects over 100 million people yearly!  And 2.5 billion people live in areas at risk for transmission. Mosquitos become infected by biting infected humans; the virus replicates in the mosquito midgut epithelium and then spreads to the salivary glands. When the infected mosquito bites another human, it transmits the virus. Since the mosquito’s salivary gland acts as a potent immune system site, what happens to infected salivary glands? Scientists looked at gene expression in non-infected mosquito salivary glands and DENV-infected salivary glands and identified genes affected by DENV infection. Infection has a broad effect on salivary gland functions, including immunity, host-seeking, and mosquito behavior. There were two genes, coding odorant-binding proteins (OBP), which were over-expressed by DENV infection in the salivary glands! OBPs affect host-seeking and blood-feeding behavior. The virus controls the insect’s behavior by regulating these chemosensory genes. When the researchers specifically silenced these two genes, they found that the mosquitos probed the host for longer times; in other words, their feeding behavior was less efficient. In summary, overexpression of these two proteins, induced by viral infection, turn the mosquito into a more efficient blood-seeking, bloodthirsty machine!  This more efficient feeding behavior enhances the chances that the virus will be transmitted to a new host. What a beautifully tuned host-parasite system!


Male pygmy hippos control sex ratio with their sperm. In mammals, the number of female and male progeny averages out to be equal, but in captivity, pygmy hippo (Choeropsis liberiensis) births are skewed towards having more females than males. Out of 1,089 births in zoos in the 100 years, < 43% of baby pygmy hippos were boys. But what is the cause of the skewed ratio? In mammals, males are the heterogametic sex, meaning that sperm will carry either an X chromosome or a Y chromosome, while eggs all carry an X chromosome. In other words, fathers determine the sex of the baby. Usually there is an equal number of sperm with X and Y chromosomes, and an equal probability of fathering a daughter or son. Since the male is in control of the offspring sex ratio, to see if daddy pygmy hippos are responsible for the skewed sex ratio, scientists collected sperm from several males living in zoos (by a procedure called electroejaculation) and counted how many sperm had a Y chromosome and how many an X chromosome. This can be done by “painting” the X and Y chromosomes with specific dyes. 2,000 sperm cells from each male were counted. And the numbers of X and Y chromosomes were not equal. In fact, the Y to X ratio (43.4%) was almost exactly the same as the ratio of sons to daughters in the population (42.5%). How males selectively get rid of 7% of Y chromosomes-bearing sperm is not known. Since in the wild, males need to control relatively large territories for breeding purposes, scientists speculate in a zoo environment, it could be in the father’s best interest to produce fewer sons, because they would compete for territory, while investing more in daughters would increases his chance to pass on genes to the next generation. Unfortunately, there’s no data on wild pygmy hippopotamus populations or breeding behavior in the wild, and they are critically endangered, with only 3,000 specimens left. (OK, I confess, this post was exclusively an excuse to post a picture of this impossibly cute baby pygmy hippo).


3000 pound feathered dinosaur discovered in China. As Darwin said, “endless forms most beautiful and most wonderful have been, and are being evolved." China is yielding amazing fossil creatures, the latest is this gigantic feathered ancestor of T. rex, named Yutyrannus huali, that lived 60 million years before T. rex.  It was 30 feet long and 3,000 pounds, the largest feathered tyrannosaur ever found.   Its name is a combination of Latin and Mandarin and it means “beautiful feathered tyrant.”  If your idea of beautiful is a mean looking, 3,000 lbs toothed gigantic downy-feathered rooster, I guess it’s an appropriate name.  The discovery has been published in this week’s edition of Nature. Since the creature was an ancestor to T.rex, it suggests that perhaps our favorite giant tyrant lizard was also feathered.  Y. huali’s skeleton is so finely preserved, that downy feathers are clearly visible. The beast was covered in feathers from head to toe. Small tyrannosaurus-like creatures were known to be feathered, but it was speculated that perhaps only the small varieties would be feathered, to provide insulation. Since Y. hualiwas so big, it is tantalizing to think that the feathers may have served other purposes, perhaps for courtship in addition to insulation. At this point there is no data on the coloration of the plumage, but if other fossils yield that information, brightly colored feathers would be a sign of sexual selection.  Now close your eyes and imagine a gigantic fearsome tyrannosaurus, stomping the ground and displaying a luscious plumage, like that of a parrot or peacock, to impress a prospective mate. Now that must have been a sight to behold!


Ice Age saber-toothed lemmings. What is it about Ice age mammals that even the humblest of rodents was a real badass? A new fossil was found in Norway, of a really strange little creature: a saber-toothed lemming, as big as a guinea pig. Paleontologists named the species Lemmus scimitardontii (“scimitar teeth”). It had sharp, robust fangs, twice as long as its own skull. The creature was found in glacial sediments on the floor of a fjord. The fossils were described by Dr. Avril Poisson (a distant relative of our very own Michel, perhaps?), from the High-Arctic Institute of the Museum of Montreal (HI-MOM). Radiocarbon dating suggests that all of the fossil big-toothed lemmings at the site died in a single event. Did they fall off a cliff like their modern relatives sometimes do? Their fur had trapped a large amount of pollen, from Arctic mango, indicating that they died on a warm Arctic spring day. The teeth seem out of place in a tiny vegetarian rodent.  Did male saber-toothed lemmings use their teeth in combat when competing with other males? Or was it a “defense” against predators? Swallowing one of these little guys would result in massive bleeding. It would be of no help to the eaten rodent, but perhaps served as a deterrent for other predators. We may never know why evolution gave such enormous teeth to such little creatures, but it sure does not look like intelligent design.  It looks like, well…it is actually…this. Congrats to those who figured it out from the start.

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Comment by Adriana on April 8, 2012 at 9:24am

Wow, I had missed the fact that the Antarctic Bottom Water has been drastically reduced since the 80s. Scary stuff.

Yes, the saber tooth lemming is a fantastic little creature :-)

Comment by Neal on April 8, 2012 at 6:53am

Excellent post, I did keep reading. I missed the perpetual ocean vid when first posted, and after going to the site I see that this was put together with climate change in mind. 

That saber-toothed lemming is awesome.

Comment by Neal on April 7, 2012 at 7:54pm

Amount of Coldest Antarctic Water Near Ocean Floor Decreasing for Decades

ScienceDaily (Apr. 3, 2012) — Scientists have found a large reduction in the amount of the coldest deep ocean water, called Antarctic Bottom Water, all around the Southern Ocean using data collected from 1980 to 2011. These findings, in a study now online, will likely stimulate new research on the causes of this change.

Two oceanographers from NOAA and the University of Washington find that Antarctic Bottom Water has been disappearing at an average rate of about eight million metric tons per second over the past few decades, equivalent to about fifty times the average flow of the Mississippi River or about a quarter of the flow of the Gulf Stream in the Florida Straits.
"Because of its high density, Antarctic Bottom Water fills most of the deep ocean basins around the world, but we found that the amount of this water has been decreasing at a surprisingly fast rate over the last few decades," said lead author Sarah Purkey, graduate student at the School of Oceanography at the University of Washington in Seattle, Wash. "In every oceanographic survey repeated around the Southern Ocean since about the 1980s, Antarctic Bottom Water has been shrinking at a similar mean rate, giving us confidence that this surprisingly large contraction is robust."

Antarctic Bottom Water is formed in a few distinct locations around Antarctica, where seawater is cooled by the overlying air and made saltier by ice formation. The dense water then sinks to the sea floor and spreads northward, filling most of the deep ocean around the world as it slowly mixes with warmer waters above it.

The world's deep ocean currents play a critical role in transporting heat and carbon around the planet, thus regulating our climate.

Science Daily

Comment by Neal on April 7, 2012 at 7:48pm

The perpetual ocean is excellent. Ocean currents can have a major impact on climate, is that updated regularly? 

Still reading.

Comment by Michel on April 7, 2012 at 11:58am

Yes, a great web site - I've added it as a page in the animal-vegetal-mineral group.

The animated images of the beasts are very cool. Lots of data and amazing animals! My favorite is theMegatherium, a 6-meter long 3.8 tons sloth!

Comment by Hope on April 7, 2012 at 11:13am

Beautiful :)

Comment by Adriana on April 7, 2012 at 11:10am

That is a good site, Hope! I found one of my favorite beasts there, Macrauchenia! I've seen the actual skeleton in La Plata, Argentina, in a beautiful Natural history Museum in that very pleasant city! Charles Darwin himself was the first person to have described the fossil llama-like creature during his Beagle voyage!

Comment by Hope on April 7, 2012 at 10:50am

Yutyrannus huali was interesting! I love it!.. I think they should add it here it's about prehistoric animals!

Comment by A Former Member on April 6, 2012 at 11:34pm

That baby hippo is too cute.

Comment by Davy on April 6, 2012 at 5:47pm

No excuse required for the pygmy hippo as the article was interesting in its own right. 

Yeah! It is a bit hard to imagine a T-Rex sporting luscious plumage at that.

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