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Prof. A's Science Fix- September 14 2012

THE COLOR BLUE IN LIVING ORGANISMS

 

Blue has always been my favorite color, ever since early childhood (no pink for me, no thanks!). I still own a lot of blue clothing (blue jeans, anyone? Best article of clothing invented by humanity!). So, naturally, I was fascinated by a ScienceShot post on the bluest fruit, a little berry-looking thing that does not even have a single blue pigment! The almost unreal iridescent blue of the fruit of Pollia condensata, an African shrub, is caused by the way light interacts with the layers of cellulose fibers in the fruit’s skin. The cellulose fibers are stacked like spiral staircases, but spaced at slightly different intervals from one another.  The distance between the rods determines which colors the spirals reflect when light hits them. Most of them reflect blue light, but others reflect different hues, producing in the end an astonishing metallic blue that has never been previously described in any biological material. Animals are known to produce iridescent colors using layers of chitin (butterflies) or keratin (peacock feathers), but this is the first time it is seen in layers of cellulose. This is a remarkable example of convergent evolution between plants and animals,. Evolution always builds on existing stuff. Perhaps the fruit’s coloration evolved to attract birds, which love sparkling things, tricking them into eating something that looks delicious. The actual fruit is neither tasty, juicy nor nutritious. Inspired by this blue fruit awesomeness, Michel posted these gorgeous pictures of two blue creatures: the blue dragon (a sea slug) and a jellyfish. Check our discussion Beautiful Photographs of Animals & Nature for more gorgeous images and information about our natural world. Who needs supernatural beings when we have such extraordinary fellow earthlings all around us?

And to continue with the blue theme:

 

 

 

 

 

 

 

 

Martian 'blueberries' could be clues to presence of life. Spherical concretions of iron oxide are found on our blue planet, for example in the Jurassic Navajo Sandstone near the Colorado River, Utah, where these structures consist of a hard shell of iron oxide surrounding a softer interior of sand. The formation of the concretions was previously thought to arise purely by chemical reactions, but now an Australian team of geologists found that bacteria contributed to the shaping of these unusual round structures.  Using special microscopy techniques, the scientists demonstrated the presence of microbial-like fossils as well as the presence of elements of biological importance, such as carbon and nitrogen in concretions from Utah (in the photo). This is very exciting because the Opportunity Rover (a NASA robotic probe older than Curiosity) found iron oxide concretions, called "Martian blueberries" on the red planet in 2004. This raises the possibility that microbes on Mars contributed to the formation of the “blueberries”.  As I’m sure you recall, the new Mars Rover, Curiosity, touched down on Mars about a month ago, art a site called the Gale Crater, considered geologically significant for its potential to reveal signs of water or past bacterial life. Hopefully Curiosity will find "Martian blueberries", since this robot has the capacity to identify minerals and organic material, and perhaps it will lead to the identification of traces of ancient microbes in iron oxide structures.

 

And from blue, to GREEN:

 

THE PLANT WORLD AND US

 

The anticonvulsant properties of a marijuana chemical. Many plants have pharmacological properties that are beneficial to treat human or animal diseases. Other plants give us pleasure because we love their flavor or texture. Other plants give us pleasure for other reasons, their beauty, or the sense of well being they provoke.  Many people say cannabis makes them happy. But besides this fun property, it has other interesting characteristics: very often in our site we have highlighted the current or potential medicinal uses of marijuana. Here is a new one: anti-epileptic seizures. English pharmacologists are investigating the anticonvulsant properties of cannabidivarin (CDBV), one of the least studied compounds found in cannabis. The interest was sparked by many instances of anecdotal evidence that marijuana can be used to control seizures in people suffering from epilepsy. To investigate the effect of CDBV, the researchers induced seizures in lab rodents. The CDVB-treated animals had seizures that were less severe than those treated with placebo, and their mortality was lower. CBVB had fewer side effects than three of the most widely prescribed anticonvulsants.  This is an encouraging result, although in the animal model, the seizures were induced on purpose, so it is an artificial model and it may not translate to humans. Still, with 20-30% epileptics who are refractory to current treatments, the need for new drugs is great. The scientists will make a decision soon whether the data warrants a clinical trial. It would be great if it does, and if it helps people with intractable epilepsy.  The abstract of the original publication can be found here.

 

Soapy taste of cilantro linked to genetic variants. Do you, like me, love cilantro (coriander to the British)? Many people adore its taste, but others can’t stomach it. I think we discussed it previously on our site and there were some members who loathed cilantro. Surveys show that 21% of East Asians, 17% of people of European ancestry and 14% of people of African descent say that cilantro tastes like soap; only 3–7% of south Asians, Latin Americans and Middle Eastern subjects found it distasteful, which is interesting, since cilantro is used pretty heavily in all these cuisines, possibly suggesting that part of the perception is genetic and part is cultural (like so much of human behavior and preferences, so nothing to write home about here). The recent data comes from the direct-to-consumer DNA typing California-based company, 23andMe. Two common gene variants were linked to people's perception of cilantro taste as “soapy”. One of the variants is found in a cluster of olfactory receptor genes. One of those genes, OR6A2, encodes a protein that is highly sensitive to aldehydes, a type of chemicals known to contribute to the flavor of cilantro. But the contribution of this variant to perception of the distasteful flavor is subtle, since nearly 50% Europeans are homozygous for the 'soapy' variant (that is, have 2 copies if this gene variant), and only 15.3% of these said cilantro tasted like soap; and from the 13% of Europeans who had no copies of this variant (homozygous for the “minor” variant), only 11.5% of them reported the soapy taste. The estimate is that roughly 10% of the like or dislike of cilantro is due to common genetic variants. If you go to the post, you’ll find a recipe for cilantro pesto sauce: since crushing the herb accelerates the rate of aldehyde breakdown, this sauce should be agreeable even to cilantro haters.  

 

But there is still much we need to learn about HUMAN GENETICS AND GENOMICS, and a fairly big step was accomplished last week by the publication of 13 simultaneous articles in the journal Nature, describing project ENCODE.

 

The ENCODE project: no more "junk" DNA. The Human Genome Project, completed a decade ago, was only the beginning or trying to understand our genome: we still have to understand what all the bits and pieces do. For all of us in the field, it is no surprise that most of our genome is not "junk" or useless DNA. That was just a name coined in the 1970s to call DNA that did not appear at the time to be part of genes, or to have a function. A huge project called ENCODE (Encyclopedia Of DNA Elements), involving 32 labs around the world, has undertaken the task to annotate the bits of the genome and what they do? Are they regulatory elements? Or do they make RNA? The results have just been published in several papers in Nature and there is a website, free for all to use, to navigate the annotations in the genome. There is too much to talk about, but basically the take home message is that we now know that at least 80% of our genome has a function, in other words, it's not "junk", and also that regulatory switches are a big part of our genome, and understanding these switches will be a big part of understanding how our genome relates to disease risks and diseases. Here is the link to the ENCODE website in case you want to play around. Also, Ed Yong wrote a very extensive article on the ENCODE project, I recommend bookmarking it for future reference: ENCODE: the rough guide to the human genome. And none other than Tim Minchin narrates this great Nature video illustrating why the project ENCODE is important:  

 

And just to illustrate how much fun one can have with genomics, consider how much we can learn about our prehistory and history. Hat tip to Davy for posting this fascinating story about human migration.

 

DNA confirms and dates South Asian coastal trek to Australia. A year ago, a multinational team of geneticists and anthropologists sequenced the genomic DNA extracted from a lock of hair of an Australian aborigine man from the early 20th century revealed that Aboriginal Australians are the current human population that have had the longest continuous association with the land they inhabit than any other human group outside of Africa: 70,000 years! The reason to use the DNA from a man who lived a century ago was to avoid confusing results due to possible admixing with people of European origin.  Comparing the man’s DNA to DNA from other human populations suggests that his ancestors parted ways with the ancestors of other human populations at some point between 64,000 to 75,000 years ago. These data also confirm that human migrations have occurred in more than one wave out of Africa. Modern Asians, for example, originated from a dispersal event that took place 25,000 to 38,000 years ago. This means than when the ancestors of the Aboriginal Australians started their journey out of Africa, the ancestors of Asians and Europeans were still in Africa or the Middle East and were not differentiated from each other. No doubt, the ancestors of Aboriginal Australians were remarkable people who undertook a very difficult trip from Indonesia to the Australian continent, about 50,000 years ago.  Impressive, if you ask me. It always moves me to think of our ancestors dispersing just about everywhere in the globe such a long time ago. At the same time, I then remember that these time frames are nothing but a few thousand generations, in other words, the blink of an eye in evolutionary terms.

 

Anthropologist Barbara King posted a great article on the National Public Radio (NPR) blogs that goes very well with the subject of human migrations.

 

For How Long Have We Been Human?. As a professor of biological anthropology, Barbara King decided to start the school semester with this time line of highlights of human evolution:

6-7 million years ago: Start of the human lineage, following a split with the lineage containing chimpanzees and gorillas 

2.6 mya: Onset of large-scale making and use of stone tool technology 

2.5 mya: First human ancestors in our own genus, Homo

200,000 years ago: First modern humans, Homo sapiens

30,000 years ago: Cave paintings and rock paintings begin to emerge on multiple continents

~12,000 years ago: Onset of agriculture and human settlements. 

The question is: is the date for becoming human 200,000 years ago, when you first see anatomically modern H. sapiens? Prof. King rightly says that very few people would say that “becoming human” is a matter of anatomy. I agree with her. It is all about our behavior, our minds, in my opinion. For example, Neanderthals may not have looked like us anatomically, but they seem to have behaved like us, making sophisticated tools and burying their dead, for example. Would we not call them “human”? I think they definitively were human. So perhaps the question is: when did modern behavior started? The earliest date so far is 100,000 years ago. The evidence is a “paint factory” found at Blombos Cave in South Africa, where people used tools to grind ocher, combine oils and charcoal, to make dyes. Unfortunately, the paint was not used on rocks; did these people use it to decorate their bodies? We may never know. But paint making is a modern behavior and an indication that those people were us. Check out the artifacts they were making in that cave! (photo): engraved ochre, arrow heads, etc. And 40,000 years ago in Germany, people were making flutes out of bones. Making musical instruments is pretty unquestionably modern behavior. Whether it was 100,000 years ago, or 40,000 years ago, it still gives me vertigo to think that people were acting like people such a long time ago (not in evolutionary terms, but in human generation time), that their minds functioned pretty much like ours.

  

But enough paying attention to stuff that relates to us. We are just one of the species on this planet. Here is some science news on fascinating animals.

 

ENDLESS FORMS MOST BEAUTIFUL

 

Pit vipers reproducing by parthenogenesis (virgin birth)Parthenogenesis is a phenomenon where females can reproduce without any male intervention, that is, in the absence of fertilization. The mother basically clones herself. It is a relatively rare phenomenon, and in vertebrates, it is found in fish, amphibian and reptiles. Boas and several lizard species, including Komodo dragons, have been observed to occasionally reproduce asexually in captivity. In the wild, there is a lizard species, the New Mexico whiptail, which reproduces exclusively by parthenogenesis: all the members of its species are female; their way of reproduction is obligate parthenogenesis, meaning they cannot reproduce by another process. Now scientists have discovered that copperheads and cottonmouths, venomous snakes known as pit vipers, also reproduce asexually in the wild. In their case, parthenogenesis is facultative, meaning optional. The discovery was made in already pregnant females captured in the wild. Zoologists suspected parthenogenesis because the litters of previously observed parthenogenesis in snakes (boas) have a high proportion of stillborn offspring, and the entire litter consists of males. Yes, males. This is possibly because in snakes, unlike mammals, the females are the heterogametic sex, meaning they have two different sex chromosomes, which in reptiles and birds are called Z and W (in mammals, it is X and Y). The researchers confirmed the offspring was the product of parthenogenesis by DNA sequencing: the babies' genotype was basically identical to that of the mother. The finding is significant because it is the first time that facultative parthenogenesis in a reptile has been recorded to occur in the wild. What made the snakes decide to reproduce asexually is not known, and it is not the absence of males in the area. Brian Switek wrote a very good article on this research.  

 

New Species of Cercopithecus monkey found in the Democratic Republi.... Finding a new species of African Monkeys is a rare event; it had not happened for almost 30 years. The new species is called lesula monkey in vernacular (Cercopithecus lomamiensis is the scientific name) was found in 2007 as a juvenile at the residence of the primary school director in the town of Opala. Before describing it as a new species, a whole bunch of genetics, morphology, ecology was done to confirm that it is indeed not a variant of a previously known species. The article describing the lesulas as a new species, has just been published in PLoS One. The new species lives in the forests of the middle Lomami Basin in central DRC, confined to the lowland rain forests between the middle Lomami and the upper Tshuapa Rivers. You may remember that geographic isolation is key to speciation, that is, the formation of new species. The nearest cousin is Cercopithecus hamlyni, a black-furred monkey, separated from the lesulas by both the Congo and the Lomami rivers. The geographical distribution is important to direct conservation efforts to this area of central Congo, known as interfluvial (between rivers) TL2 region, because it contain a high diversity of primates.

 

Hopefully conservation efforts will preserve this new monkey species. Other mammals have not been so lucky.

 

Japanese River Otter Declared Extinct. The Japanese river otter (Lutra lutra whiteleyi) has been officially declared extinct last week. The last sighting was in 1979. This otter was a subspecies of the European river otter. I absolutely like otters, whether they are river or sea otters. They are such intelligent, active creatures. The Japanese river otter did not have to disappear from the face of the Earth. It went extinct because of human action. What a crying shame. It was hunted to extinction for its fur, and in addition to that the rivers were polluted as well. Japanese river otters used to number in the millions. They were a successful species. Almost 3 feet in length, they lived on fish and shrimp. The otter is still the official animal symbol of Japan’s Ehime Prefecture. Yoshihiko Machida, a professor emeritus at Kochi University, has devoted many hours to try to find some otters still alive. He says that in 1999, the presence of otter droppings was confirmed. He plans to keep looking for them I hope his optimism pays off.

 

And not to end the blog on a sad note, and to see if you’re still awake, check out this great video showing you how to estimate large numbers even if you have very little additional information. It’s all about orders of magnitude and the power of ten.  Try it out!

 

GREAT MATH VIDEO: The Power of 10

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Comment by archaeopteryx on September 18, 2012 at 2:03am

Fascinating, Chris - thank you for that detailed explanation. We truly are the caretakers of our planet, and should have been actively participating in that endeavor for at least the past 70 years.

Comment by Chris on September 18, 2012 at 1:37am

@ Davey & Archaeopteryx,

Fish habitat would improve with the improved kelp forests that act as carbon sinks as terrestrial forests do. Adriana is correct about photosynthesis but the study was about carbon sequestering not oxygen generation and it didn’t take fish into account. The otters are to kelp as wolves are to trees in their relative forests. I never thought of oceans that way and wondered if Japan could have used similar studies to fund rehabilitating the river otters they just listed as extinct.

I must somehow have an account setup on my other computer to open the  Frontiers in Ecology and the Environment link. This computer needs a password. I'm going to have to figure out how the other computer opens it automatically. In the mean time I copied sections of the report and pasted it below. 

Here we ask, how do sea otters impact C standing stocks and flux through their indirect effects on kelp populations? We provide an initial answer to this question by combining data collected over the past 40 years on differences in kelp abundance between systems with and without sea otters, the chemical composition of kelp, the net primary productivity (NPP) of kelp forests, and the areal extent of habitat suitable for kelp forest development across 5400 km of the sea otter’s range in the North Pacific Ocean. We then discuss the implications of these results for atmospheric C sequestration.

When sea otters are present, urchins seek refuge in rock crevices and subsist on kelp detritus. In the absence of sea otters, urchins often adopt a mobile feeding strategy of grazing on living kelp, thus reducing kelp density and kelp bed distribution.

Four facts point to the potential utility of using altered food web dynamics to reduce atmospheric CO2 concentration. First, C is the elemental backbone of the living biosphere, comprising >50% by mass of all organic matter globally. Second, the abundance and distribution of autotrophs, which hold much of the world’s non-fossilized organic C in their tissues and transform inorganic to organic C through photosynthesis, are strongly influenced by species interactions, especially herbivory. Third, food web dynamics worldwide have been extensively altered, especially through the loss of large vertebrate consumers. And fourth, despite extensive global habitat destruction and fragmentation, large tracts of land and water remain in which food web structure and dynamics could be restored or altered with appropriate conservation and management.

We combine data collected from the past 40 years to estimate the indirect effects of sea otters (Enhydra lutris) on ecosystem carbon (C) production and storage across their North American range, from Vancouver Island to the western edge of Alaska’s Aleutian Islands. We find that sea otters, by suppressing sea urchin (Strongylocentrotus spp) populations, allow kelp (Order Laminariales) ecosystems to develop with a net primary productivity (NPP) of 313–900 grams C per square meter per year (g C m–2 yr–1) and biomass density of 101–180 grams C per square meter (g C m–2). In the absence of sea otters, these areas would have an NPP of 25–70 g C m–2 yr–1 and biomass density of 8–14 g C m–2. Over an ecosystem area of approximately 5.1 °— 1010 m2, the effect of sea otter predation on living kelp biomass alone represents a 4.4- to 8.7-teragram increase in C storage. At 2012 prices (US$47 per ton of C), this stored C would be valued at US$205 million–$408 million on the European Carbon Exchange. Although questions remain concerning the pathways and compartments of kelp C flux and storage, sea otters undoubtedly have a strong influence on these elements of the C cycle. Predator-induced trophic cascades likely influence the rates of C flux and storage in many other species and ecosystems.

Comment by James M. Martin on September 17, 2012 at 9:58pm

There is no reason to believe the Bible cannot be interpreted on a symbollic level, seeing it as metaphor.  But why would one waste the time?

Comment by archaeopteryx on September 17, 2012 at 3:06pm

@doone - RE: "...why Santorum would feel compelled to utter such a brutally quotable statement."

Don't you suspect that it was for the same reason that Yeshua was reported to have said, "Except ye be as a child, thou shalt not enter into the kingdom of heaven"? Intelligent, adult minds tend to reject fairy tales.

Comment by Davy on September 17, 2012 at 2:13pm

Reconstructing the face of model who posed for Leonardo's "Mona Lisa" will show us just how well Leonardo captured the face of the model but it will also help the facial reconstructers fine tune their art. 

Comment by Doone on September 17, 2012 at 1:17pm

An anti science explanation 

Doug Mataconis has a good sense of why Santorum would feel compelled to utter such a brutally quotable statement.

What Santorum said today is emblematic of rhetoric you hear quite frequently from people on the right such as Sarah Palin, Michele Bachmann, Rush Limbaugh, and Sean Hannity. Generally, they idea seems to be that there’s something about being intelligent, or curious about the world, or interested in something beyond the orthodox interpretations of history and the law that conservatives insist upon. You see it manifest itself in the rejection of even the rather obvious fact that humanity can have an influence on the environment around it and, most irrationally, in the very rejection of everything that biology, anthropology, physics, and cosmology teach us. For many on the right, it’s easier to believe in the stories written in a 6,000 year old book than it is in the evidence of just how amazing the universe around them actually is. They can believe whatever they want, of course, but the fact that they constantly try to force these beliefs on others, most especially through the public school system, makes their disdain for knowledge a matter of public concern.

Comment by Adriana on September 17, 2012 at 1:02pm

Hey, do you guys remember a couple of months ago in the Science fix I reported about the discovery of a skeleton which was supposed to be that of Mona Lisa? UPDATE: It's not her skeleton, it belongs to another wealthy woman, but the researchers think they are getting closer.

An archaeology team has been on the hunt for the supposed model of Leonardo's 1506 masterpiece, yet according to Vinceti "the ledgers kept by the nuns of this convent tell us that, presumably, the remains exhumed today are those of Maria Del Riccio, a wealthy woman who (died) in 1609." (Lisa del Giocondo died in 1542.) Nonetheless, Vinceti expressed hope that their hunt was getting warmer, and, since the convent's graves are buried atop each other, finding Mona Lisa's remains could be a matter of digging deeper. Once her body is extracted, scientists could attempt to reconstruct her face and compare it to the painting, although facial reconstruction is debatable in terms of accuracy. Even if the skeleton is proved to have been Leonardo's muse 500 years ago, we are confused as to the benefits of such a discovery.

Comment by Neal on September 17, 2012 at 12:56pm

Great article. I likes me some turtles. =)

An easy explanation for those who don't have the educational background to understand the difference between discovery and make believe.

Comment by Adriana on September 17, 2012 at 12:39pm

Is that tortoise really BLUE?? What species is it?

Comment by Michel on September 17, 2012 at 12:32pm

In reality it all happens within this one turtle. 

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