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	<title>SciTechStory</title>
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	<link>http://scitechstory.com</link>
	<description>Tracking the impact of science and technology</description>
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		<item>
		<title>Getting your head around huge brain projects</title>
		<link>http://scitechstory.com/2013/03/24/getting-your-head-around-huge-brain-projects/</link>
		<comments>http://scitechstory.com/2013/03/24/getting-your-head-around-huge-brain-projects/#comments</comments>
		<pubDate>Sun, 24 Mar 2013 13:03:39 +0000</pubDate>
		<dc:creator>storchlein</dc:creator>
				<category><![CDATA[Commentable]]></category>
		<category><![CDATA[BAM]]></category>
		<category><![CDATA[Big Science]]></category>
		<category><![CDATA[Brain Activity Map]]></category>
		<category><![CDATA[epigenetics]]></category>
		<category><![CDATA[Human Brain Project]]></category>
		<category><![CDATA[Human Genome Project]]></category>
		<category><![CDATA[intelligence]]></category>
		<category><![CDATA[Large Hadron Collider]]></category>
		<category><![CDATA[LHC]]></category>
		<category><![CDATA[memory]]></category>
		<category><![CDATA[neuron activity]]></category>
		<category><![CDATA[neuroscience]]></category>
		<category><![CDATA[thinking]]></category>

		<guid isPermaLink="false">http://scitechstory.com/?p=2981</guid>
		<description><![CDATA[As the ‘thinking’ goes &#8211; a billion here, a few billions there and eventually we’ll know how the brain works. The billions are Euros and dollars. The “there” are two projects aimed at learning how the human brain works. Even President Obama got into the act a while ago to mention in the State of [...]]]></description>
				<content:encoded><![CDATA[<p>As the ‘thinking’ goes &#8211; a billion here, a few billions there and eventually we’ll know how the brain works. The billions are Euros and dollars. The “there” are two projects aimed at learning how the human brain works. Even President Obama got into the act a while ago to mention in the State of the Union address about U.S. government funding for the Brain Activity Map project. Though at the moment this project is hardly more than an interesting article in the journal <em>Neuron</em>. The underlying assumption is that neuroscience is ready for big breakthroughs, if only there is enough money to coordinate and fund a massive research project – sort of like the all-out effort of putting man on the moon. Only in this case, substitute “explaining mental activity” for the “getting to the moon.”</p>
<p>If that sounds like an odd juxtaposition, it should. The Moon is a very real, measureable, and as we’ve seen, reachable object. Mental activity – with such useful but nebulous concepts like ‘thinking,’ ‘intelligence,’ ‘rationality,’ ‘memory,’ ‘cognition,’ or even (shudder) the soul – is elusive, controversial and vastly complex. </p>
<p>There is a similarity in the brain projects to the Human Genome Project of the 1990s. At the time the human genome project began, it seemed like mapping all of the genes in human DNA would provide a road map to cure thousands of diseases, unlock the secrets of human development and generally bring about a new level of understanding of the ‘blueprint’ of life. At the time, biochemists were just beginning to understand the chemical pathways by which DNA is created and goes about its work. As it turns out, this research led to the discovery of an entire field of study – epigenetics – that seeks to explain how genes are expressed and regulated. The knowledge of epigenetics vastly complicates the interpretation of DNA. For example, where medical researchers once thought that reading the human genome would lead to explaining and curing thousands of diseases, they now believe that perhaps 1 to 3 percent of diseases have a purely genetic cause. Otherwise, most diseases including cancer, heart and neurological disease are a complicated mixture of genetic, epigenetic and environmental causes. In short, the Human Genome Project was important, influential and worth the effort – but it was hardly the answer to all the mysteries of DNA or of human development. <span id="more-2981"></span></p>
<p>The Brain Activity Map project seeks to explain how the brain works. Its primary assumption is that all significant cognitive activity is the result of connections and transmissions between neurons. Even now, this is a precarious assumption. Neuroscientists do not know how the brain works or what constitutes intelligence. They know about pieces of the many brain processes, but for the most part the fundamental biochemical explanations for how the brain produces ‘thinking’ and ‘memory’ are in the early stages of exploration. Moreover, scientists already know that neurons share at least some of their activity with another type of brain cell, the astrocytes. Once thought of as one of the lowly glia (white matter), providing structural support and housekeeping for the neurons, it’s becoming apparent that astrocytes participate in the coordinating and regulation of brain processes. That means mapping the activity of all the neurons in the brain is unlikely to reveal the full picture of intelligence. The knowledge will probably be useful, but by itself won’t explain the great mysteries of the human brain. </p>
<p>Conceptually, the Brain Activity Map project has many potential problems. It isn’t enough to map all brain activity in isolation from what stimulates the activity – interpretation requires knowing all sides of the process, a daunting and complex challenge. The human brain is, of course, different than most if not all animals, but we don’t yet know exactly ‘where’ and ‘how’ that is, much less how it got that way. This makes it very difficult to interpret human brain activity, because we may be confounding unique and universal processes. There is also the problem of separating what the brain is capable of doing, the so-called dynamics of its potential, from what the brain usually does in specific instances. Mapping neuronal activity will have great difficulty in separating the laws of brain dynamics from what it records as the details of brain activity. </p>
<p>I’ve touched on just a few of the problems that neuroscientists already can see about the Brain Activity Map. There are also worries in the community about the shifting of significant money into this project and away from many other worthy projects, or the effect this much emphasis on only one aspect of brain research will have on the all the other research tracks. Many will point out that “Big Science” rarely produces up to expectations. Besides there is already another massive brain research project underway, the European Human Brain Project that seeks to simulate the human brain through computational (computerized) means. </p>
<p>One way to look at this is that both the Brain Activity Map and the Human Brain Project are short on knowledge for the fundamental processes that underlie brain activity (much less higher activity such as cognition, memory, and emotional or rational intelligence). Both also lack the technological sophistication necessary to carry them to full extension. The Brain Activity Map lacks the techniques to gain a coordinated picture of brain activity. The Human Brain Project lacks the model and the raw computational horsepower to simulate an entire human brain. Neither project has the theoretical and engineering underpinning of another Big Science project – the Large Hadron Collider.</p>
<p>And yet…as science attempts these over-ambitious projects there is much to be learned by pushing the state of knowledge. One thing most neuroscientists agree upon is the need for ‘getting the big picture’ about how the brain works. Big projects are nothing if not an attempt to coordinate the research efforts of many neuroscientists. Perhaps they will stimulate the development of new technologies. Perhaps they will reveal a useful evaluation of how much we don’t know.</p>
<p>Perhaps. The aggravating prospect is not knowing whether these large projects will ultimately provide useful insight, or whether they are barking so far up the wrong tree that they will mislead rather than forge ahead.  </p>
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		<item>
		<title>Planck’s Universe</title>
		<link>http://scitechstory.com/2013/03/24/plancks-universe/</link>
		<comments>http://scitechstory.com/2013/03/24/plancks-universe/#comments</comments>
		<pubDate>Sun, 24 Mar 2013 08:35:01 +0000</pubDate>
		<dc:creator>storchlein</dc:creator>
				<category><![CDATA[News]]></category>
		<category><![CDATA[age of Universe]]></category>
		<category><![CDATA[Big Bang]]></category>
		<category><![CDATA[CMB]]></category>
		<category><![CDATA[cosmology]]></category>
		<category><![CDATA[ESA]]></category>
		<category><![CDATA[Hubble constant]]></category>
		<category><![CDATA[inflation]]></category>
		<category><![CDATA[NASA]]></category>
		<category><![CDATA[observatory]]></category>
		<category><![CDATA[Planck]]></category>
		<category><![CDATA[Standard Model]]></category>
		<category><![CDATA[universe]]></category>
		<category><![CDATA[WMP]]></category>

		<guid isPermaLink="false">http://scitechstory.com/?p=2975</guid>
		<description><![CDATA[Cosmic Microwave Background radiation map of the Universe&#8230;Credit: ESA, Planck Collaboration The big news for this week and I do mean big as in as big as the whole Universe, is a new collation and analysis of data from the European Space Agency’s (ESA) Planck observatory mission. The new analysis reveals several things about the [...]]]></description>
				<content:encoded><![CDATA[<p><img src="http://www.scitechstory.com/images/planckmap.jpg" alt="Planck map of the CMB Universe" /><br />
Cosmic Microwave Background radiation map of the Universe&#8230;Credit: ESA, Planck Collaboration</p>
<p>The big news for this week and I do mean big as in as big as the whole Universe, is a new collation and analysis of data from the European Space Agency’s (ESA) Planck observatory mission. The new analysis reveals several things about the observable Universe that revise astronomer’s thinking.</p>
<p>The Planck observatory is a satellite, the flagship mission of ESA launched with the assistance of the U.S. space agency NASA, that sits in a location over a million kilometers from Earth. It scans the observable Universe for tiny differences in the Cosmic Microwave Background (CMB), the faint traces of radiation (photons, light particles) that are remnants from the Big Bang. The Planck microwave receivers are the most sensitive and technically sophisticated yet assembled and they have made it possible to map the fluctuations (“hot or cold”) in the Universe to an unprecedented degree of resolution. It is providing astronomers with a picture of the Universe only 380,000 years after its formation in the Big Bang (which in cosmic time is only trillionths of a second). From this information, a great deal can be deduced about the nature of the Universe: <span id="more-2975"></span></p>
<ul>1. The Universe is a bit older than previously believed. Planck observations place the age of the Universe at 13.82 billion years. The old estimate, from the WMAP studies was 13.73 billion, give or take 120 billion. Actually, the new estimate is within that range at the upper end of the old estimate but the Planck estimate is considered more accurate. </ul>
<ul>2. The rate of expansion for the Universe is a bit less than in the standard model of inflation after the Big Bang. The Planck data put the expansion at 67.3 kilometers per second per megaparsec (a megaparsec, 3.26 million light years, is a frame of reference for the speed of expansion. If you look at a galaxy one megaparsec away, it appears to be moving away at 67.3 km/sec. A galaxy two megaparsecs away appears to recede at twice that speed, and so on.) Previously the speed of expansion was thought to be 74.2 km/sec/Mpc, so according to Planck data the Universe is expanding more slowly, which accounts for the greater age as well. The speed of expansion is known as the Hubble constant. Since the old and new estimates don’t agree, neither will astronomers. There will be much debate about what it means.</ul>
<ul>3. The composition of the Universe is a bit different than scientists thought. According to the Planck data (with the old estimates in parentheses), the Universe is 4.9 percent normal matter (4.6 percent), 26.8 percent dark matter (24 percent) and 68.3 percent dark energy (71.4 percent). Changing the amount of dark energy by 3.1 percent may not seem like much – but on the scale of the Universe! Cosmological models will need revision.</ul>
<ul>4. The Universe is (apparently) lopsided. Of course, this isn’t exactly what you may think it means. The light coming in (into Planck and other observatories) is randomly fluctuating (between some and no light) and evenly distributed (see the map image above). This is expected. However, the new data show that while the fluctuations are random, their amplitude (brightness/temperature) isn’t, quite. The distribution of brighter and less bright light is uneven, just slightly brighter on one side of the Universe than the other. How? Why? This will have cosmologists and astronomers at their wit’s end for a while. If verified (and so far the WMAP data confirms it), it might mean that dark energy is changing over time, or that the Big Bang imprinted some kind of form onto the Universe that existed <em>before the Big Bang</em>. Et cetera.</ul>
<ul>5. There is a cold spot in the new map of the Universe that is much bigger than previously thought. This may mean it is more important, although at this point scientists don’t know why it exists at all.</ul>
<p>For astronomers and the field of cosmology, this is a big package to unwrap. The results are much like previous results, but slightly different – different enough to suggest revisiting some cherished ideas in cosmology. Of course, the information and analysis is subject to much further refinement. The implications, which are on a scale difficult for the human mind to comprehend, are subject to a lot of interesting speculation that will be very difficult to verify. However, for astronomers the payoff from years of work at the Planck data, the payoff, the reason to celebrate – are a lot of new questions. </p>
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		<title>Micro-endoscope: A visual probe as thin as hair</title>
		<link>http://scitechstory.com/2013/03/18/micro-endoscope-a-visual-probe-as-thin-as-hair/</link>
		<comments>http://scitechstory.com/2013/03/18/micro-endoscope-a-visual-probe-as-thin-as-hair/#comments</comments>
		<pubDate>Mon, 18 Mar 2013 10:52:45 +0000</pubDate>
		<dc:creator>storchlein</dc:creator>
				<category><![CDATA[News]]></category>
		<category><![CDATA[endoscope]]></category>
		<category><![CDATA[endoscopy]]></category>
		<category><![CDATA[fiber-optic]]></category>
		<category><![CDATA[Joseph Kahn]]></category>
		<category><![CDATA[micro-endoscope]]></category>
		<category><![CDATA[MMF]]></category>
		<category><![CDATA[modes]]></category>
		<category><![CDATA[photonics]]></category>
		<category><![CDATA[random intensity light]]></category>
		<category><![CDATA[scientific instruments]]></category>

		<guid isPermaLink="false">http://scitechstory.com/?p=2965</guid>
		<description><![CDATA[A schematic of the micro-endoscope&#8230;.Credit: Joseph Kahn, Stanford University The endoscope, a thinish, flexible tube with a light and image sensor or lenses at the probe end, is an indispensable tool of medicine, especially surgery. Endoscopy, the technique of using the endoscope, is the driving force behind minimally invasive surgery, which is radically changing the [...]]]></description>
				<content:encoded><![CDATA[<p><img src="http://www.scitechstory.com/images/kahn_endoscope.jpg" alt="Micro-endoscope diagram" /><br />
A schematic of the micro-endoscope&#8230;.Credit: Joseph Kahn, Stanford University</p>
<p>The endoscope, a thinish, flexible tube with a light and image sensor or lenses at the probe end, is an indispensable tool of medicine, especially surgery. Endoscopy, the technique of using the endoscope, is the driving force behind <em>minimally invasive surgery</em>, which is radically changing the way modern surgery is progressing. The minimally invasive approach seeks to reduce the amount of tissue damage caused by the surgical procedure. In older, traditional methods large incisions are cut through the flesh to access underlying organs. In many cases, the amount of cutting for access far exceeds the cutting at the actual target of the surgery. With minimally invasive surgery, only three to five ‘ports’ are cut through to the target, one specifically for the endoscope. </p>
<p>Since the cut must be big enough to accommodate the diameter of the endoscope, the smaller the endoscope, the smaller the incision. This obvious correlation led to a research effort to decrease the size and complexity of the endoscope. The best result to-date, published in the journal <em>Optics Express</em> [24 February 2013, paywalled, <a href="http://www.opticsinfobase.org/oe/abstract.cfm?URI=oe-21-2-1656&#038;origin=search">Resolution limits for imaging through multi-mode fiber</a>] and developed by a team of engineers at Stanford University (Berkeley, California USA) uses a single fiber-optic strand to achieve resolution of 2.5 microns in size, with 0.3 microns resolution a goal for the near future. The human eye is able to resolve about as small as 125 microns, that’s in thousands of an inch – a tiny grain of sand or a thin hair. The best current endoscope can resolve about 10 microns, so the new “micro-endoscope” represents a major step in terms of both endoscope size and resolution. <span id="more-2965"></span></p>
<p>Other designs of single fiber endoscopes have been under development for some time, but the Stanford micro-endoscope brings to the work something new – a combination of <em>random intensity light</em> and special software algorithms (programming) to unscramble the light to produce an image. The random intensity light creates of pattern of light rather than a steady beam, which reflects from the target into the fiber-optic thread and carries back through the fiber. The light coming through the optic-fiber travels in multiple paths, or “modes” as they are known in optics, a <em>multimode fiber</em> or MMF. </p>
<p>The returning light becomes scrambled during transmission and must be ‘interpreted’ by special software to piece it back into a coherent image. It was here that the Stanford researchers discovered something they did not expect. Their unique algorithm to interpret the light created an image with four times the resolution than the number of modes in the fiber. All prior research had only been able to achieve resolution equal to the number of modes. They discovered that in the MMF fiber the modes become ‘mixed,’ in practice actually increasing the number of modes in the fiber. This accounted for the increased resolution. </p>
<p>The significance of the improvement created by the micro-endoscope means that endoscopy will become practical to observe the function of cells and small tissues, penetrate and observe the functioning brain, and a myriad other applications where the high resolution and very small diameter of the endoscope is practical. The only limitation of the micro-endoscope is a requirement for the optic fiber to be rigid. This means the endoscope itself is delivered through an ultrafine needle, which must be thick enough to remain rigid when inserted into tissue. </p>
<p><img src="http://www.scitechstory.com/images/sts-sciPublication.gif" alt="Research Spectrum" /></p>
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		<title>Big Telescopes: ALMA already on the job</title>
		<link>http://scitechstory.com/2013/03/14/big-telescopes-alma-already-on-the-job/</link>
		<comments>http://scitechstory.com/2013/03/14/big-telescopes-alma-already-on-the-job/#comments</comments>
		<pubDate>Thu, 14 Mar 2013 12:10:26 +0000</pubDate>
		<dc:creator>storchlein</dc:creator>
				<category><![CDATA[News]]></category>
		<category><![CDATA[ALMA]]></category>
		<category><![CDATA[array]]></category>
		<category><![CDATA[Atacama]]></category>
		<category><![CDATA[cosmos]]></category>
		<category><![CDATA[infrared]]></category>
		<category><![CDATA[radio astronomy]]></category>
		<category><![CDATA[radio telescope]]></category>
		<category><![CDATA[scientific instruments]]></category>
		<category><![CDATA[universe]]></category>

		<guid isPermaLink="false">http://scitechstory.com/?p=2952</guid>
		<description><![CDATA[Some of the ALMA antenna array at Atacama….Credit: ESO Today, March 13, 2013 marks the official ‘opening’ of the world’s largest telescope, ALMA (Atacama Large Millimeter-submillimeter Array). As the biggest and most complex telescope project in history, astronomers hope it will open a new chapter in the observations of the cosmos. Located near San Pedro [...]]]></description>
				<content:encoded><![CDATA[<p><img src="http://www.scitechstory.com/images/alma.jpg" alt="ALMA Telescope" /><br />
Some of the ALMA antenna array at Atacama….Credit: ESO</p>
<p>Today, March 13, 2013 marks the official ‘opening’ of the world’s largest telescope, ALMA (Atacama Large Millimeter-submillimeter Array). As the biggest and most complex telescope project in history, astronomers hope it will open a new chapter in the observations of the cosmos. Located near San Pedro de Atacama in Chile, it is the crowning achievement of those who believed that with modern technology a ground-based telescope array can perform as well as those in space. It’s also a lot easier to visit.</p>
<p>ALMA underwent ten years of construction, 1.4 billion dollars in cost and pushed the world’s radio astronomy technology to the max. A total of 19 countries have contributed to ALMA, through three primary partners: the European Southern Observatory (ESO); the National Astronomical Observatory of Japan; and the US National Radio Astronomy Observatory (NRAO) in Charlottesville, Virginia, funded by the US National Science Foundation (NSF). The United States alone contributed about $500 million to the project, the largest such outlay for any such facility in the world.</p>
<p>Consisting of 66 antennas, the last to be installed later this year, the array is brimming with the latest breakthroughs in radio and infrared receiver technology, much of which concentrates on focusing and refining the faintest signals in the universe. </p>
<p>The inaugural week includes the usual hoopla and ALMA is reporting results. In other words, this week is ceremonial, as the array has been in operation with a reduced number of antennas since 2011. The website: http://www.almaobservatory.org/ is well stocked with information and the first reports of ALMA observations.</p>
<p>A good overview of the project, warts and all, is available (free) at the journal <em>Nature</em> [14 March 2013, <a href="http://www.nature.com/news/radio-astronomy-the-patchwork-array-1.12591">Radio astronomy: The patchwork array</a>]</p>
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		<title>“Gray Mars” and the stuff of life</title>
		<link>http://scitechstory.com/2013/03/13/gray-mars-and-the-stuff-of-life/</link>
		<comments>http://scitechstory.com/2013/03/13/gray-mars-and-the-stuff-of-life/#comments</comments>
		<pubDate>Wed, 13 Mar 2013 07:34:56 +0000</pubDate>
		<dc:creator>storchlein</dc:creator>
				<category><![CDATA[Commentable]]></category>
		<category><![CDATA[Curiosity]]></category>
		<category><![CDATA[drill sample]]></category>
		<category><![CDATA[environment]]></category>
		<category><![CDATA[evidence of life]]></category>
		<category><![CDATA[Gale Crater]]></category>
		<category><![CDATA[gray soil]]></category>
		<category><![CDATA[life]]></category>
		<category><![CDATA[Mars]]></category>
		<category><![CDATA[water]]></category>

		<guid isPermaLink="false">http://scitechstory.com/?p=2947</guid>
		<description><![CDATA[Rover Curiosity’s bore hole in Mars rock, note color change from reddish to gray Scientific knowledge requires a process of confirmation, for example, scientists have believed for decades that Mars had water and may still have it either in ice form or in the underground. This belief started with observations drawn from Mars photographs from [...]]]></description>
				<content:encoded><![CDATA[<p><img src="http://www.scitechstory.com/images/curiosity-bore-hole.jpg" alt="Bore hole in Mars rock" /><br />
Rover Curiosity’s bore hole in Mars rock, note color change from reddish to gray</p>
<p>Scientific knowledge requires a process of confirmation, for example, scientists have believed for decades that Mars <em>had</em> water and may still have it either in ice form or in the underground. This belief started with observations drawn from Mars photographs from the earlier orbital missions in the 1960’s. Several decades later, the amount of confirmatory evidence is overwhelming. There’s no doubt Mars had water, probably lots of it and an entirely different climate. There’s still water on Mars, we know of the ice form; there remains a possibility of underground water. </p>
<p>Based on our Earth experience, where there’s water (liquid form), there’s life. Consequently, scientists have long speculated that at one time, or possibly even now, life existed on Mars. The evidence for that is not yet conclusive, one way or another; but pieces of the story continue to accumulate. The latest, and in many ways the most promising (short of actually finding something alive or remnants of something that was alive) are reports from a sample drilling made by Curiosity, the latest U.S. Mars rover. <span id="more-2947"></span></p>
<p>Working in what is believed to be an ancient streambed in the Gale Crater; Curiosity drilled out a sample from sedimentary (water deposited) rock and then analyzed the sample in its on-board laboratory. One thing, visible immediately (see picture above), was a previously unseen transition from red rock/soil, which indicates an extreme level of oxidation (very life unfriendly), to a gray material only partially oxidized (life friendly). From the results of sample chemical analysis, scientists identified sulfur, nitrogen, hydrogen, oxygen, phosphorus and carbon – in quantities and combinations that are the key chemical ingredients for life (at least as we know it). </p>
<p>This is not evidence of life, past or present – only that life <em>could</em> have used these ingredients to develop and survive. They represent a rather typical and benign environment, similar to those found on Earth (minus available liquid water). This new information is a bit like the discoveries of amino acids and similar compounds in the rocks of meteorites. They are ‘indicative’ of life – found wherever life exists – but not evidence of life. </p>
<p>The current Mars in a very inhospitable environment – mostly it’s too cold, too dry and too bombarded with UV light to support any kind of life we know. The evidence suggests, ever more strongly, that this was not always the case. The Mars environment was quite different – however, that was probably a billion or more years ago. Conditions have radically changed, and if there once was life, where did it go? We have, as yet, no evidence about that – only supposition that if evidence of life still exists (alive or fossilized), it’s probably underground. </p>
<p>Another way to look at the new evidence is to speculate that since enough is known about the possible favorable conditions for life (water and appropriate chemistry) – if no life is found the huge question will be why? Or to flip the expression, if we find life on Mars (living or fossil), it won’t be that big of a surprise. </p>
<p>Now all we have to do is wait for confirmation…</p>
<p>[SciTechStory: <a href="http://scitechstory.com/2010/03/04/life-on-mars-if-it-exists-is-below-the-surface/">Life on Mars: If it exists is below the surface</a>]<br />
[SciTechStory: <a href="http://scitechstory.com/2011/02/24/mars-water-what%e2%80%99s-all-the-fuss/">Mars water: What’s all the fuss?</a>]</p>
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		<title>Epigenetics ‘leaks’ into trans-generational inheritance</title>
		<link>http://scitechstory.com/2013/03/11/epigenetics-leaks-into-trans-generational-inheritance/</link>
		<comments>http://scitechstory.com/2013/03/11/epigenetics-leaks-into-trans-generational-inheritance/#comments</comments>
		<pubDate>Mon, 11 Mar 2013 11:59:24 +0000</pubDate>
		<dc:creator>storchlein</dc:creator>
				<category><![CDATA[News]]></category>
		<category><![CDATA[chromatin dynamics]]></category>
		<category><![CDATA[demethylation]]></category>
		<category><![CDATA[DNA]]></category>
		<category><![CDATA[epigenetics]]></category>
		<category><![CDATA[genetics]]></category>
		<category><![CDATA[histones]]></category>
		<category><![CDATA[inheritance]]></category>
		<category><![CDATA[methylation]]></category>
		<category><![CDATA[PGC]]></category>
		<category><![CDATA[primordial germ cell]]></category>
		<category><![CDATA[trans-generation]]></category>

		<guid isPermaLink="false">http://scitechstory.com/?p=2942</guid>
		<description><![CDATA[One of the bigger and most important ‘debates’ in biology – both now and in the past – is whether adaptations made for the environment of a single individual can be inherited by its offspring. This is not about genetic inheritance, mutation, and the reproduction of the genes in DNA. This is about epigenetics, the [...]]]></description>
				<content:encoded><![CDATA[<p>One of the bigger and most important ‘debates’ in biology – both now and in the past – is whether adaptations made for the environment of a single individual can be inherited by its offspring. This is not about genetic inheritance, mutation, and the reproduction of the genes in DNA. This is about <em>epigenetics</em>, the way in which the genes are regulated. It is an article of central biological dogma that all trans-generational inheritance (parent to children) is the result of DNA and genetic action. While over the last decade or two, it is apparent that epigenetics is abundantly active within dividing cells (mitosis); it is supposed to be non-existent for procreative cells (sex cell meiosis). Evidence for this comes from a number of studies demonstrating how <em>primordial germ cells</em>, cells that are the precursors to the egg and sperm, are routinely and efficiently stripped of their epigenetic markers.</p>
<p>Now comes a study from the University of Cambridge (UK) and reported in the journal <em>Science</em> [25 January 2013, paywalled, <a href=" http://www.sciencemag.org/content/339/6118/448"> Germline DNA Demethylation Dynamics and Imprint Erasure Through 5-Hydroxymethylcytosine</a>] showing that while most epigenetic markers are indeed efficiently and systematically removed – the process is imperfect; some of the epigenetic markers are transmitted to the next generation. One way of putting it, epigenetic markers leak into genetic trans-generational inheritance.  <span id="more-2942"></span></p>
<p>While the biochemical explanation behind the Cambridge study is complex, the basic discovery is that one form of epigenetic control of the genes – methylation (a biochemical marker attached to genes that turns them off) – is incompletely washed from the primordial germ cells. </p>
<p>In their study with mice, the Cambridge researchers observed that primordial germ cells (PGCs) have a cellular environment rich in two enzymes (TET1 and TET2) that are responsible for removing markers from the cytosine of genes (demethylation). For the most part, this ‘wash’ given the DNA in PGCs is effective.</p>
<p>However, and here’s where the study get interesting, the researchers found numerous areas of DNA where the methylation markers did not get erased. They found areas both on repetitive DNA elements and on single copy genes. The key, they believe, is that the two other major elements of epigenetics – histone configuration of DNA and chromatin dynamics – protect areas of DNA from demethylation. How, exactly, is still unknown. Why, is not even speculative. How much – quite a bit – but the ‘residual’ epigenetic markers have yet to be quantified, much less evaluated.</p>
<p>In short, it appears that while most epigenetic methylation markers are erased for each new generation – not all of them are erased. This means that a certain amount of single individual adaptation to the environment (such as for famine or temperature change) may be passed on through the parents to the children. This inheritance is somehow influenced or guided by the other two functions of epigenetics, which affect how DNA is folded to present specific genes during the process of development.</p>
<p>There are more questions than answers raised by this research, but it is another piece of evidence that epigenetics can be part of trans-generational inheritance. Now it will take a few more years to work out the biochemical details of how this happens. A great deal of work needs to be done to determine if there are significant differences among species for trans-generational epigenetics. Eventually, there may be a useful evaluation of its significance.</p>
<p><img src="http://www.scitechstory.com/images/sts-sciPublication.gif" alt="Research Spectrum" /></p>
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		<title>Glia brain cells: Not just infrastructure</title>
		<link>http://scitechstory.com/2013/03/08/glia-brain-cells-not-just-infrastructure/</link>
		<comments>http://scitechstory.com/2013/03/08/glia-brain-cells-not-just-infrastructure/#comments</comments>
		<pubDate>Fri, 08 Mar 2013 11:05:58 +0000</pubDate>
		<dc:creator>storchlein</dc:creator>
				<category><![CDATA[Impact]]></category>
		<category><![CDATA[astrocytes]]></category>
		<category><![CDATA[brain cells]]></category>
		<category><![CDATA[glia]]></category>
		<category><![CDATA[Goldman]]></category>
		<category><![CDATA[intelligence]]></category>
		<category><![CDATA[mice]]></category>
		<category><![CDATA[mouse model]]></category>
		<category><![CDATA[Nedergaard]]></category>
		<category><![CDATA[neurons]]></category>
		<category><![CDATA[neuroscience]]></category>
		<category><![CDATA[smarter mice]]></category>
		<category><![CDATA[synapses]]></category>
		<category><![CDATA[white matter]]></category>

		<guid isPermaLink="false">http://scitechstory.com/?p=2927</guid>
		<description><![CDATA[So many stories about this recent neuroscience research begin with – “human brain cells make mice smarter” – and miss the point of the research almost entirely. It’s not about mice. It’s about a type of human brain cells, glia, which are just now coming into focus for neuroscience. For those that understand the prolog, [...]]]></description>
				<content:encoded><![CDATA[<p>So many stories about this recent neuroscience research begin with – “human brain cells make mice smarter” – and miss the point of the research almost entirely. It’s not about mice. It’s about a type of human brain cells, glia, which are just now coming into focus for neuroscience. For those that understand the prolog, this research is, ahem, revolutionary.</p>
<p>To be fair, the paper itself, by Goldman and Nedergaard and published in <em>Cell, Stem Cell</em> [07 March 2013, <a href="http://www.cell.com/cell-stem-cell/abstract/S1934-5909(13)00058-1">Forebrain Engraftment by Human Glial Progenitor Cells Enhances Synaptic Plasticity and Learning in Adult Mice</a>] sounds like it’s about mice. Of course, mice are involved, but what the research did – put human glial (white matter brain cells) into mice brains – sheds far more light on what glial cells do in humans than on the fact that the mice became a tad bit smarter. The research demonstrated that glial cells most likely have a significant role in human intelligence.</p>
<p>Why this should be considered important, even revolutionary, goes back to the “Neuron Doctrine” developed by Ramon y Cajal more than a century ago, which states that all information processing and communications in the nervous system takes place between neurons. Since glia do not have any of the hallmarks of neurons (dendrites, synapses, axons), they were considered unimportant to information processing and cognition. The general attitude, which is still probably the majority opinion today, was “there are neurons,” where all the mental action begins and ends, and then there’s “the white stuff,” the glial cells that sort of hold the brain together and do housekeeping – basically infrastructure material. </p>
<p><span id="more-2927"></span><br />
One of the 101 level neuroscience textbooks on which I cut my frontal lobes has this bit about glial cells: </p>
<blockquote style="background-color:#EAF4FF;"><p>
We have devoted most of our attention in this chapter to the neurons. While this decision is justified by the current state of knowledge, some neuroscientists consider glia to be “the sleeping giants” of neuroscience. One day, they suppose, it will be shown that glia contribute much more importantly to information processing in the brain than is currently appreciated. At present, however, the evidence indicates that glia contribute to brain function mainly by supporting neuronal functions. Although their role may be subordinate, without glia, the brain could not function.</p>
<p>[Source: <a href="http://books.google.com/books/about/Neuroscience.html?id=75NgwLzueikC">Neuroscience, Exploring the Brain – Bear, Connors and Paradiso, Second Edition, 2001</a>]
</p></blockquote>
<p>This is an admirable scientific position. Since then, the state of knowledge in neuroscience has obviously changed along many fronts, and the knowledge of glia is among them. Here, for example is a related reference in SciTechStory about the participation of glia in the synapses:</p>
<p>[SciTechStory: <a href="http://scitechstory.com/2012/04/03/rethink-the-brain-more-evidence-for-the-tripartite-synapse/">Rethink the brain: More evidence for the tripartite synapse</a>]</p>
<p>The work by husband and wife team cell biologist Steven Goldman and neurobiologist Maiken Nedergaard, both at the University of Rochester Medical Center (New York, NY USA) began with their previous experiments treating mice that had a genetic disorder similar to human multiple sclerosis. They implanted human glial <em>progenitor</em> cells (something like stem cells but with more specific development paths, in this case, glial brain cells) in the cortex of newborn mice. The human glial progenitor cells apparently healed the mice, which went on to live a normal life span. At the same time, the researchers noticed something unexpected – the human glial cells had completely replaced the mouse glial progenitor cells. They wondered if this would have any impact on normal mice. </p>
<p>Goldman and Nedergaard knew that, in particular, one type of glial cell, the <em>astrocyte</em> is different in human beings than most other animals (perhaps all other animals). For one thing, they are much bigger. In this case, the human astrocytes are 20 times larger than mouse astrocytes. Where a mouse astrocyte may span about 100,000 neurons and synapses, the human astrocyte spans about 2 million. </p>
<p>The vast neuron coverage by glial astrocytes may be important to coordinating human intelligence. That’s because it is now known that astrocytes do have a way to participate in the processing and transmission of information. Unlike neurons, which primarily use a chemical/electrical signaling system, astrocytes communicate using neurotransmitters – chemicals that pass signals through ion exchange, for example, at the synapses between neurons. The astrocytes use calcium-based neurotransmitters, communicating through rapid waves of calcium ions. Nedergaard and her associates found that human astrocytes transmit signals 3 times faster than mouse astrocytes.</p>
<p>To test whether the unique properties of human astrocytes would, first, survive in a normal mouse brain and, second, have some beneficial effect, the researchers isolated human glial progenitor cells and labeled them with a fluorescent protein so they could be identified after transplantation. They injected these cells into the forebrain of mice and examined the results from 2 weeks to 20 months later. They found that mature human astrocytes grew and inserted themselves into the mouse brain, by six months replacing most of the mouse astrocytes. They maintained their unique human size and sent long twisted cellular processes (filaments) through layers of cortical gray (neuron) matter just as they do in the human brain.</p>
<p>Just as in humans, the astrocytes participate in the transmission of signals in the gap junctions (synapses) between neurons and, surprisingly, they increased the speed and strength of the signal transmission in mice. This is how the mice became ‘smarter.’</p>
<p>The researchers put the mice through a battery of tests, mazes, object selection, shock reaction – the mice treated with human astrocytes were often many times quicker to learn and react than untreated ‘normal’ mice. For example, in learning a maze route, the normal mice required four or five attempts. The treated mice learned it on the second try.</p>
<p>While this ‘enhanced mouse’ is of dubious value (ethically and practically) for the mice, its value is another demonstration of how human glial cells are different than other animals and may well be the basis of what distinguishes our intelligence. Glial cells make up about half the total volume of the human brain. In terms of numbers of cells, 90% of a human brain is glial cells. In elephants, it is 97%. It could be said that glial cells may well be the proverbial “elephant in the room,” the decisive but unmentioned factor in human intelligence. </p>
<p>Research into the role of glial cells, especially astrocytes, in the processes of memory and mental coordination may be of great impact on neuroscience.</p>
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		<title>CRE: A killer coming to a critical care facility near you</title>
		<link>http://scitechstory.com/2013/03/07/cre-a-killer-coming-to-a-critical-care-facility-near-you/</link>
		<comments>http://scitechstory.com/2013/03/07/cre-a-killer-coming-to-a-critical-care-facility-near-you/#comments</comments>
		<pubDate>Thu, 07 Mar 2013 13:09:27 +0000</pubDate>
		<dc:creator>storchlein</dc:creator>
				<category><![CDATA[News]]></category>
		<category><![CDATA[carbapenem]]></category>
		<category><![CDATA[CDC]]></category>
		<category><![CDATA[CRE]]></category>
		<category><![CDATA[drug resistance]]></category>
		<category><![CDATA[E. coli]]></category>
		<category><![CDATA[Enterobacteriaceae]]></category>
		<category><![CDATA[lethal infection]]></category>
		<category><![CDATA[pandemic]]></category>
		<category><![CDATA[warning]]></category>

		<guid isPermaLink="false">http://scitechstory.com/?p=2918</guid>
		<description><![CDATA[It is not pandemic, not yet, but the spread of a particular form of drug resistant bacteria is serious enough to warrant this March 6 statement from Dr. Thomas Frieden the head of the United States Centers for Disease Control and Prevention (CDC): CRE poses a triple threat. First, they’re resistant to all or nearly [...]]]></description>
				<content:encoded><![CDATA[<p>It is not pandemic, not yet, but the spread of a particular form of drug resistant bacteria is serious enough to warrant this March 6 statement from Dr. Thomas Frieden the head of the United States Centers for Disease Control and Prevention (CDC):</p>
<blockquote style="background-color: #F4EAEA;"><p>
CRE poses a triple threat. First, they’re resistant to all or nearly all antibiotics. Even some of our last-resort drugs. Second, they have high mortality rates. They kill up to half of the people who get serious infections with them. And third, they can spread resistance to other bacteria. So one form of bacteria, for example, carbapenem-resistant <em>Klebsiella</em>, can spread the genes that destroy our last antibiotics to other bacteria, such as E. coli, and make E. coli resistant to those antibiotics also… We only have a limited window of opportunity.</p>
<p>[Source: <a href="http://www.cdc.gov/media/releases/2013/p0305_deadly_bacteria.html">CDC: Action needed now to halt spread of deadly bacteria</a>]
</p></blockquote>
<p>CRE is the acronym for the tongue twisting <em>carbapenem-resistant Enterobacteriaceae</em>, where carbapenem is one of the major antibiotic groups of last resort and Enterobacteriaceae is a large family of seventy gut-dwelling bacteria (including the ever present forms of Escherichia coli – E. coli, Klebsiella, Salmonella and Shigella). These are bacteria generally present in the human digestive system, often kept at low and relatively harmless levels by natural defenses. However, for people whose immune systems are weakened or in situations where more virulent forms of the bacteria are present – these bacteria can become killers. <span id="more-2918"></span></p>
<p>Unfortunately, one of the places where this is most likely to happen is in hospitals, particularly in intensive care units (ICU). These drug resistant bacteria like the ‘sterile’ plastics, tiles and metals of the hospital environment. It’s also where they are routinely exposed to a variety of antibiotics, all the better for their adaptation to resist them.</p>
<p>The CRE bacteria also thrive in many critical care institutions – nursing homes, rehab units – where patients are weakened, immunologically compromised, exposed to many outsiders and where they often contract diarrhea, the most potent mode of distribution for bacteria. Given these characteristics CRE spread easily. So far, they have been diagnosed in 42 of the United States and in many countries around the world. The numbers are increasing with 4.6 percent of U.S. hospitals and 17.8 percent of long-term care facilities reporting cases in 2012. </p>
<p>This is not epidemic or pandemic level – not yet. But given the way this particular drug resistance spreads, it seems like only a matter of a few years before it becomes common and epidemic. Remember, IT CANNOT BE TREATED with drugs and IT KILLS. These words are in capitals, not because typed shouting is cool, but because the danger is real and, for the most part, not much is being done about it. The CDC is pushing a non-funded, voluntary reporting system for CRE in the United States. Among other countries, only Israel has an all-out national program against CRE.</p>
<p>So it can’t be that bad, can it? We’ll see.   </p>
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		<title>ePSC: A new type of pluripotent stem cell</title>
		<link>http://scitechstory.com/2013/03/06/epsc-a-new-type-of-pluripotent-stem-cell/</link>
		<comments>http://scitechstory.com/2013/03/06/epsc-a-new-type-of-pluripotent-stem-cell/#comments</comments>
		<pubDate>Wed, 06 Mar 2013 09:54:20 +0000</pubDate>
		<dc:creator>storchlein</dc:creator>
				<category><![CDATA[News]]></category>
		<category><![CDATA[embryonic]]></category>
		<category><![CDATA[endogenous]]></category>
		<category><![CDATA[ePSC]]></category>
		<category><![CDATA[genetically stable]]></category>
		<category><![CDATA[immortal]]></category>
		<category><![CDATA[induced]]></category>
		<category><![CDATA[iPSC]]></category>
		<category><![CDATA[mortal]]></category>
		<category><![CDATA[new stem cell]]></category>
		<category><![CDATA[pluripotent]]></category>
		<category><![CDATA[stem cells]]></category>

		<guid isPermaLink="false">http://scitechstory.com/?p=2906</guid>
		<description><![CDATA[Researchers at the University of California San Francisco have discovered a new type of stem cell. This does not happen every day, guaranteed. In fact, this discovery is potentially very important. Called an endogenous pluripotent stem cell (ePSC), it has much the same characteristics as embryonic stem cells, the ability to become almost any other [...]]]></description>
				<content:encoded><![CDATA[<p>Researchers at the University of California San Francisco have discovered a new type of stem cell. This does not happen every day, guaranteed. In fact, this discovery is potentially very important. Called an <em>endogenous pluripotent stem cell</em> (ePSC), it has much the same characteristics as embryonic stem cells, the ability to become almost any other kind of cell. However, the ePSC was found in human breast tissue. It’s relatively rare, but still a viable source of pluripotent stem cells that ought to avoid the controversies associated with anything embryonic.  <span id="more-2906"></span></p>
<p>As described in the online edition of the <em>Proceedings of the National Academy of Sciences (PNAS)</em> [28  February 2013, <a href="http://www.pnas.org/content/early/2013/02/27/1218682110.full.pdf+html?sid=a341d50f-c478-418c-841a-643f06206047">Rare somatic cells from human breast tissue exhibit extensive lineage plasticity</a>] the characteristics of the ‘new’ stem cells are not identical to embryonic stem cells or “induced” (i.e. human engineered) pluripotent stem cells (iPSC) and the differences are significant. For one thing, the ePSC is ‘mortal,’ meaning that unlike embryonic or induced stem cells it can make a finite number of reproductions, it can’t go on reproducing forever. For another, an ePSC is genetically stable, that is, unlike the other stem cells; it doesn’t have a tendency to produce as many mutations or to create other genomic errors. </p>
<p>Both the mortality and genetic stability properties of ePSCs could be of research or clinical significance. Potentially ePSCs can be programmed to reproduce a specific number of times, for example, in an organ repair procedure, and then stop reproducing to let the ‘normal’ cells continue the process. The genetic stability might be a factor in using ePSCs to combat cancer, where genetic instability is often at work. This sort of application for ePSCs is, for now, speculation. </p>
<p>What is most immediately important about ePSCs, and already tested in-vitro within the lab, is the ability to successfully become a wide range of adult (that is, specialized) cells. This includes cartilage, bone, gut, brain, pancreas and heart cells. Research had already identified types of stem cells used to generate one (or so) specialized cells with an organ or tissue, but ePSCs are far more versatile – acting, as the researchers put it, like a “patch kit” for body tissue of many kinds. This aspect of ePSCs will generate a great deal of follow-up research by scientists looking at the application of stem cells in organ growth and repair.</p>
<p>UCSF researchers, Thea Tisty and Somdutta Roy and their colleagues, will continue to pursue ePSCs in other parts of the body. They believe that similar (or identical) pluripotent stem cells may be found in other tissue, which would help increase the supply of the rather rare cell. </p>
<p><img src="http://www.scitechstory.com/images/sts-sciPublication.gif" alt="Research Spectrum" /></p>
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		<title>Mapping commercial sea routes in the Arctic Sea</title>
		<link>http://scitechstory.com/2013/03/05/mapping-commercial-sea-routes-in-the-arctic-sea/</link>
		<comments>http://scitechstory.com/2013/03/05/mapping-commercial-sea-routes-in-the-arctic-sea/#comments</comments>
		<pubDate>Tue, 05 Mar 2013 11:08:44 +0000</pubDate>
		<dc:creator>storchlein</dc:creator>
				<category><![CDATA[Commentable]]></category>
		<category><![CDATA[Arctic Sea]]></category>
		<category><![CDATA[climate change]]></category>
		<category><![CDATA[commercial shipping]]></category>
		<category><![CDATA[global warming]]></category>
		<category><![CDATA[north pole route]]></category>
		<category><![CDATA[shipping routes]]></category>

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		<description><![CDATA[Map of potential Arctic Sea shipping routes…..Credit: UCLA Last year (2012) 46 ships made the journey over what used to be considered the mythical “Northwest Passage” – they sailed through the Arctic Sea from Hudson’s Bay to Alaska and beyond. They had to wait until late summer and voyage in the company of icebreakers for [...]]]></description>
				<content:encoded><![CDATA[<p><img src="http://www.scitechstory.com/images/arcticsea-routes.jpg" alt="Arctic Sea Routes" /><br />
Map of potential Arctic Sea shipping routes…..Credit: UCLA</p>
<p>Last year (2012) 46 ships made the journey over what used to be considered the mythical “Northwest Passage” – they sailed through the Arctic Sea from Hudson’s Bay to Alaska and beyond. They had to wait until late summer and voyage in the company of icebreakers for safety – nevertheless, think about it: For the first time in recorded history, a continuous sea-voyage from the Atlantic to the Pacific via the Arctic Sea is possible – commercially possible. Why is that?</p>
<p>Global warming. </p>
<p>The map above, drawn by researchers at the University of California Los Angeles and published in the online journal <em>Proceedings of the National Academy of Sciences</em> [25 January 2013, <a href="http://www.pnas.org/content/early/2013/02/27/1214212110.abstract?sid=220845de-a5ba-4c15-a18f-f534b64a72eb">New Trans-Arctic shipping routes navigable by midcentury</a>] outlines the potential commercial sea routes over the Arctic by the period 2040-2059. By that time sea transport in the Artic will be more or less routine and the ships will not need ice breaker escorts. How is this possible?</p>
<p>Global warming.</p>
<p>In fact, the projections are for the polar ice to thin so much that a <em>direct route over the pole</em> with icebreaker support may be possible. This will cut the trip from Europe to Asia by at least 20%. Even though the Arctic routes will probably never be available year-round, the commercial appeal to shippers is obvious. With it will come a great push to open up the routes, establish supply lines, communications support, new towns, new port facilities and there’s the distinct likelihood of shipping oil and gas from wells in that region. As more land area opens from melting snow and permafrost, the exploration for resources grows with it. All because of…</p>
<p>Global warming.</p>
<p>Of course, none of this including the 46 ships and record low ice-pack in the Arctic Sea could possibly be real….</p>
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