<?xml version="1.0" encoding="utf-8"?>
<rss version="2.0" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:wfw="http://wellformedweb.org/CommentAPI/">
	<channel>
		<title><![CDATA[io9: ask a biogeek]]></title>
		<image>
			<url>http://tags.lifehacker.com/assets/base/img/thumbs140x140/io9.com.png</url>
			<title><![CDATA[io9: ask a biogeek]]></title>
			<link>http://io9.com/tag/ask a biogeek</link>
		</image>
		<link>http://io9.com/tag/ask a biogeek</link>
		<description><![CDATA[io9 posts tagged 'ask a biogeek']]></description>
			
		<item>
			<title><![CDATA[iGEM, or How to Build a Biological Organism in a Single Summer]]></title>
			<description><![CDATA[
<p><img src="http://cache.gawker.com/assets/images/io9/2008/11/iGEMteams.jpg" class="left image500" width="500" />The <a href="http://en.wikipedia.org/wiki/IGEM">International Genetically Engineered Machine</a> competition brings undergraduates from around the world to MIT's campus to share the results of a summer's worth of synthetic biology research. Each team tries to create the best synthetic organism. Here you can see the iGEM participants (photo courtesy of David Appleyard and iGEM). I'm one of the folks in black up in front. (No, the other one.) Find out what these students cooked up over the summer, and who won.</p>

<p>Congratulations to <a href="http://2008.igem.org/Team:Slovenia">Slovenia</a> , who took the grand prize BioBrick trophy home with them with their project, which was designed to create a vaccine for <a href="http://en.wikipedia.org/wiki/Helicobacter_pylori">H. pylori</a>, infection with which is associated with ulcers and gastric cancer. H. pylori possesses <a href="http://2008.igem.org/Team:Slovenia/Project/Engineered_flagellin_vaccine">"stealth flagella"</a>, which manage to avoid an important immune receptor. Slovenia attempted to combine bits of other bacterial proteins (that aren't capable of avoiding that receptor) with bits of H. pylori proteins in an attempt to hand-feed H. pylori antigen targets to the immune system, with promising results.</p>
<p><a href="http://2008.igem.org/Team:Freiburg">Frieburg</a> took second place by combining DNA origami (the animation is borrowed from <a href="http://2008.igem.org/Team:Freiburg">their wiki</a>) with a clever receptor scheme in order to attempt nanoscale control of cellular signaling.</p>
<p><img src="http://cache.gawker.com/assets/images/io9/2008/11/Freiburg2008.png" width="350" height="218"></p>
<p>This DNA origami basically takes a long piece of DNA and, by adding many short carefully chosen DNA tethers designed to bind to the longer DNA in specific places, fold it into a particular shape.</p>
<p>Third place went to Caltech's <a href="http://2008.igem.org/Team:Caltech">multifunctional probiotic bacteria</a> by adding functions to a commercially available, non-pathogenic <a href="http://en.wikipedia.org/wiki/Probiotic">probiotic</a> strain of E. coli - functions including pathogen defense, vitamin production, and a treatment for lactose intolerance. (Bioengineered bacteria - digesting lactose so you don't have to.) Probiotics <a href="http://www.technologyreview.com/biomedicine/21654/">were big at iGEM this year</a>, with MIT <a href="http://2008.igem.org/Team:MIT">taking a probiotic approach to dental care</a> and finalist <a href="http://2008.igem.org/Team:NYMU-Taipei">NYMU-Taipei's BactoKidney</a> - a bacteria that attaches to the wall of your small intestine, then munches on waste products before abandoning ship before it overstays its welcome.</p>
<p><img src="http://cache.gawker.com/assets/images/io9/2008/11/NYMU_main_pic.png" height="440" width="600"></p>
<p>The image is from <a href="http://2008.igem.org/Team:NYMU-Taipei">NYMU-Taipei's wiki</a>, where you can see its full-resolution glory. Trust me, dialysis isn't nearly so adorable.</p>
<p>UC Berkeley didn't do so bad either - we had two teams, one devoted to a wet lab project <a href="http://2008.igem.org/Team:UC%20Berkeley">to combine engineered bacteria with robots</a>, making large-scale synthetic biology projects possible, and the other working on computational tools <a href="http://2008.igem.org/Team:UC%20Berkeley%20Tools">to keep better track and make better use of collections of genetic parts</a>. Our wet team, CloneBots, <a href="http://sanfrancisco.about.com/b/2008/11/12/uc-berkeley-team-a-finalist-at-igem-2008.htm">made it to the finals</a>, and our comp team, Clotho, won for best software tool.</p>
<p><object type="application/x-shockwave-flash" width="400" height="225" data="http://www.flickr.com/apps/video/stewart.swf?v=63881" classid="clsid:D27CDB6E-AE6D-11cf-96B8-444553540000"><param name="flashvars" value="intl_lang=en-us&amp;photo_secret=4db4df4de0&amp;photo_id=3027531153">
<param name="movie" value="http://www.flickr.com/apps/video/stewart.swf?v=63881">
<param name="bgcolor" value="#000000">
<param name="allowFullScreen" value="true">
<embed type="application/x-shockwave-flash" src="http://www.flickr.com/apps/video/stewart.swf?v=63881" bgcolor="#000000" allowfullscreen="true" flashvars="intl_lang=en-us&amp;photo_secret=4db4df4de0&amp;photo_id=3027531153" height="225" width="400"></object></p>
<p>This year was my first jamboree, and I was gobsmacked at the collective hard work and ingenuity on display. Anyone who does research knows how difficult it is to accomplish a significant amount of work in a single semester, but these teams went at their projects with energy and intensity, and it shows.</p>
<p>Congratulations, everyone! We hope to see you in 2009. If iGEM or our <a href="http://io9.com/5049810/announcing-the-winners-of-the-io9-mad-science-contest">mad science contest</a> sound like your idea of a good time, see if your university has an iGEM team. If not, it's time to start one.</p>
<p>On a more somber note, this is going to be my last Ask a Biogeek - professional obligations abound. If I didn't have a chance to get to your question yet, apologies. A few of those obligations may be of interest to y'all, so keep an ear to the ground and you may be hearing from me again soon. Take care!</p>
]]></description>
			<link><![CDATA[http://io9.com/5091615/igem-or-how-to-build-a-biological-organism-in-a-single-summer]]></link>			<guid isPermaLink="false"><![CDATA[io9-5091615]]></guid>
			<category><![CDATA[ask a biogeek]]></category>
			<category><![CDATA[biology]]></category>
			<category><![CDATA[feature]]></category>
			<category><![CDATA[igem]]></category>
			<category><![CDATA[science]]></category>
			<category><![CDATA[synthetic biology]]></category>
			<pubDate><![CDATA[Thu, 20 Nov 2008 09:00:00 PST]]></pubDate>
			<dc:creator><![CDATA[Terry Johnson]]></dc:creator>
			<wfw:commentRss>http://io9.com/index.php?op=postcommentfeed&amp;postId=5091615&amp;view=rss&amp;microfeed=true</wfw:commentRss>
		</item>
				
		<item>
			<title><![CDATA[Three Horror Movies That Even a Scientist Could Love]]></title>
			<description><![CDATA[
<p><img src="http://cache.gawker.com/assets/images/io9/2008/11/reanimator_01.jpg" class="left image500" width="500" /> As a scientist I have mixed feelings about SF-oriented horror, which tends to show my lab coat-wearing brethren as myopic, obsessive, morally challenged individuals or as humorless skeptics. When <em>Fringe</em> needed a scientist for its team of white hats, the best they could come up with was a former, vaguely repentant mad scientist. Kind of unfair, considering how many plot ideas they've stolen from our journals. But there are a few bio-inspired scary movies out there that I would recommend.</p>

<p><strong><a href="http://en.wikipedia.org/wiki/Re-Animator">Re-Animator</a></strong></p>
<p>This adaption of Lovecraft's short story stars SF-favorite <a href="http://en.wikipedia.org/wiki/Jeffrey_Combs">Jeffrey Combs</a> as Dr. Herbert West, a <a href="http://en.wikipedia.org/wiki/Miskatonic_University">Miskatonic University</a> medical student obsessed with curing death. Classic mad scientist territory. When his radical theories are met with resistance by the dean, he does what every good scientist would do - a series of secret experiments in his basement. After bringing his roomie's girlfriend's dead cat back to some semblance of life, clinical trials begin at the local morgue (with predictably gruesome results).</p>
<p>With the exception of one particularly disturbing scene (you'll know it when you see it), the film is gleefully gory. West dispatching a faculty member bent on stealing his work with a shovel to the head is par for the genre. Venomously hissing "plagiarist!" as he swings? Comedy gold.</p>
<p>While the dead aren't likely to shamble from their graves anytime soon, advances in resuscitation including <a href="http://en.wikipedia.org/wiki/Therapeutic_hypothermia">therapeutic hypothermia</a> have pushed back the medical point of no return, and recent evidence shows that perhaps much of the damage done to oxygen-starved brain cells <a href="http://www.damninteresting.com/?p=860">is caused more by the sudden reintroduction of oxygen during a medical intervention than its deprivation</a>. Rather than <a href="http://www.sciencedaily.com/releases/2008/07/080701083506.htm">jump start an oxygen-starved brain with pure oxygen</a>, we may instead want to more gently awaken the cells with gradual oxygenation. It'll have to do until West's glowing serum is perfected - "mindless homocidal madness" is one of those side effects that the FDA really frowns upon.</p>
<p><strong><a href="http://en.wikipedia.org/wiki/Judas_Breed">Mimic</a></strong></p>
<p>Disease-fighting bioengineered insects that rapidly evolve into human-sized superbugs capable of mimicking humans. What's not to like? Mimickry is a survival mechanism<a href="http://en.wikipedia.org/wiki/Mimicry">relatively common in nature</a>. While it's extremely doubtful that such rapid changes could occur, I have to give them points for originality.</p>
<p><strong><a href="http://en.wikipedia.org/wiki/Alien_(franchise)">Alien</a></strong></p>
<p><img src="http://cache.gawker.com/assets/images/io9/2008/11/Alien-eggs.JPG" height="225" width="395"></p>
<p>The life cycle of a xenomorph - egg, facehugger, chestburster, and fully-grown alien warrior - might seem needlessly complex, but there are parasites here on earth that make exploding out of John Hurt's chest look easy by comparison. <a href="http://en.wikipedia.org/wiki/Clonorchis_sinensis">Clonorchis sinensis</a>, the liver fluke, passes through a snail and a fish before ending up inside one of us.</p>
<p>As unpleasant as an egg-implanting facehugger might be, at least it puts you to sleep. When the wasp <a href="http://scienceblogs.com/loom/2006/08/04/an_old_fave_the_wisdom_of_para.php">Ampulex compressa</a> finds its chosen prey, a cockroach, it uses its specially-designed stinger to perform a gruesome bit of brain surgery after an initial sting. The roach ends up with a dose of venom delivered directly into the part of its brain responsible for flight reflex. Once this is done, the roach is as docile as a lamb - the wasp grabs hold of its antenna and guides it home, where the roach gets a fatal wasp larva implantation. Facehuggers may be rather forward, but at least they don't ride you around like a sacrificial pony.</p>
<p><img src="http://cache.gawker.com/assets/images/io9/2008/11/Ampulex_stinging.jpg" height="164" width="249"></p>
<p>If you think that sort of behavior-tweaking couldn't happen in humans, keep in mind that quarter of Americans are infected with <em>Toxoplasma gondii</em>, <a href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=11007336">a parasite capable of making rats think that seeking out cats is a good idea</a>. The parasite wants to get into the cat's stomach and doesn't much care how it gets there. Some research <a href="http://www.news.com.au/story/0,10117,20975555-29277,00.html">suggests that toxoplasma-infected humans are also affected</a> - men become less intelligent and more withdrawn, while women become more outgoing and promiscuous.</p>
<p>It might also explain why Chekhov seemed so mopey after Khan stuck that worm in his ear.</p>
]]></description>
			<link><![CDATA[http://io9.com/5075611/three-horror-movies-that-even-a-scientist-could-love]]></link>			<guid isPermaLink="false"><![CDATA[io9-5075611]]></guid>
			<category><![CDATA[ask a biogeek]]></category>
			<category><![CDATA[alien]]></category>
			<category><![CDATA[feature]]></category>
			<category><![CDATA[horror]]></category>
			<category><![CDATA[mimic]]></category>
			<category><![CDATA[re-animator]]></category>
			<category><![CDATA[top]]></category>
			<pubDate><![CDATA[Thu, 06 Nov 2008 09:00:00 PST]]></pubDate>
			<dc:creator><![CDATA[Terry Johnson]]></dc:creator>
			<wfw:commentRss>http://io9.com/index.php?op=postcommentfeed&amp;postId=5075611&amp;view=rss&amp;microfeed=true</wfw:commentRss>
		</item>
				
		<item>
			<title><![CDATA[Where Are My Medical Nanobots?]]></title>
			<description><![CDATA[
<p><img src="http://cache.gawker.com/assets/images/io9/2008/10/nanotech-05_01.jpg" class="left image500" width="500" /> Reader Wendy asks: <strong>When will nanobots clean out my arteries?</strong> While medical molecular machines are not likely to appear in the clinic soon, there's a decent amount of research going into the development of <a href="http://en.wikipedia.org/wiki/Nanobot">nanoscale robotics</a>, and not only for therapeutic use. One could easily imagine these widgets appearing in diagnostic assays and nano-scale manufacturing. Before we can hope to command tiny robots to crawl or swim to a damaged or <a href="http://en.wikipedia.org/wiki/Stenosis">stenotic</a> artery to effect repairs, we first need to build tiny robots capable of crawling or swimming.</p>

<p>Luckily, molecules that can crawl already exist in nature. <a href="http://en.wikipedia.org/wiki/Kinesin">Kinesin</a>, for example, is a protein that crawls along microtubules in our cells - hitch a bit of cellular cargo to it, and it'll go along for the ride.</p>
<p><object width="425" height="344"><param name="movie" value="http://www.youtube.com/v/686qX5yzksU&hl=en&fs=1">
<param name="allowFullScreen" value="true">
<embed src="http://www.youtube.com/v/686qX5yzksU&hl=en&fs=1" type="application/x-shockwave-flash" allowfullscreen="true" width="425" height="344"></object></p>
<p>Molecules with "legs" made of DNA <a href="http://www.newscientist.com/article.ns?id=dn4958">can be coaxed into a vaguely similar "walk"</a> on a surface also composed of DNA, while <a href="http://newsroom.ucr.edu/cgi-bin/display.cgi?id=1166">less biological variations</a> could be useful in the computing industry. There are a number of <a href="http://en.wikipedia.org/wiki/Synthetic_molecular_motors">molecular motors</a> that can convert chemical or light energy into motion - getting useful work out of that motion, however, can be tricky.</p>
<p>Not all tiny robots are nano, of course. <a href="http://www.dartmouth.edu/~news/releases/2005/09/14.html">Dartmouth's "inchworm"</a> is relatively huge at over a hundred microns in length, and this six-legged crab-bot is even larger - the chassis is made of polymer with an engine composed of rat heart tissue. When the tissue contracts, it provides power to crawl the 'bot <a href="http://discovermagazine.com/2008/feb/tiny-robot-walks-using-rat-heart-muscle">at about 0.002 miles per hour</a>. Not bad for a ride less than a millimeter long.</p>
<p><object width="425" height="350"><param name="movie" value="http://www.youtube.com/v/XJZ_jejWDfc">
<embed src="http://www.youtube.com/v/XJZ_jejWDfc" type="application/x-shockwave-flash" width="425" height="350"></object></p>
<p>When nature provides a convenient source of motility, like heart tissue or <a href="http://en.wikipedia.org/wiki/Bacterial_gliding">bacterial gliding</a>, harnessing it can be a lot easier than building a molecular machine from scratch. The <a href="http://www.pnas.org/content/103/37/13618.short">micromotor below</a> harnesses bacteria to turn its rotors.</p>
<p><img src="http://cache.gawker.com/assets/images/io9/2008/10/0011q46d.jpg" width="702" height="407"></p>
<p>The bacteria move from the center of A into the channels. When they meet the circle at the end (B, C) , they tend to be going in one direction (D). The rotor (E, F) fits into the circle and is coated with sialic protein which the bacteria stick to and push. It's like the beginning of <em>Conan: The Barbarian</em>, except microscopic, and with better acting.</p>
<p>While true nanobots would have to be even smaller than the crab or this rotor, they do show an interest in producing useful locomotion in increasingly smaller packages. Besides, to produce a useful bot may require a collection of various nanoscale parts that assembled together produce a larger-than-nanoscale 'bot.</p>
<p>If you can't crawl, you're going to have to swim. Again, nature is ahead of us with the <a href="http://en.wikipedia.org/wiki/Flagella">flagellum</a> - basically, a propeller for microbes.</p>
<p><img src="http://cache.gawker.com/assets/images/io9/2008/10/350px-Ecoli_flagellum_01.jpg" width="350" height="200"></p>
<p>The adaptability and motility of these bacteria are a few of the reasons why researchers are using them <a href="http://edition.cnn.com/2007/TECH/science/02/08/ft.nanobots/index.html">as inspiration for their own devices</a> and working to modify them <a href="http://www.news-medical.net/?id=739">to deliver drugs to cancer cells</a>, and perhaps heart disease follow. If it's not bacterial in origin, don't be surprised if the world's first medical nanobot is <a href="http://discovermagazine.com/2008/jun/29-3-ideas-that-are-pushing-the-edge-of-science">sperm-propelled</a>.</p>
<p>Building nanoscale machines from scratch that can swim is harder than it sounds (and it ought to sound pretty hard). For one thing, our physical intuition about swimming breaks down at the nanoscale. If you were to shrink, <em>Fantastic Voyage</em>-style and find yourself swimming in water, <a href="http://spectrum.ieee.org/jun08/6271/2">you'd think the water had turned into a highly viscous liquid like molasses</a>. This has to do with the dynamics of fluids at different length scales, as E.M. Purcell discussed in his <a href="http://brodylab.eng.uci.edu/~jpbrody/reynolds/lowpurcell.html">Life at Low Reynold's Number</a> talk. Simply shrinking a design that swims well at the macroscale is no guarantee that it'll zoom along at the micro- or nanoscale.</p>
<p>Once you have a nanoswimmer or nanocrawler (or have appropriated one from nature), you're going to have to figure out how to guide it towards your target and either release its payload or do whatever repairs need to be done. As far as heart disease is concerned, it's going to be a race between the nanobots and extensive genetic tinkering to prevent the problem in the first place.</p>
]]></description>
			<link><![CDATA[http://io9.com/5066893/where-are-my-medical-nanobots]]></link>			<guid isPermaLink="false"><![CDATA[io9-5066893]]></guid>
			<category><![CDATA[ask a biogeek]]></category>
			<category><![CDATA[fantastic voyage]]></category>
			<category><![CDATA[feature]]></category>
			<category><![CDATA[medicine]]></category>
			<category><![CDATA[nanotech]]></category>
			<category><![CDATA[top]]></category>
			<pubDate><![CDATA[Thu, 23 Oct 2008 09:00:00 PDT]]></pubDate>
			<dc:creator><![CDATA[Terry Johnson]]></dc:creator>
			<wfw:commentRss>http://io9.com/index.php?op=postcommentfeed&amp;postId=5066893&amp;view=rss&amp;microfeed=true</wfw:commentRss>
		</item>
				
		<item>
			<title><![CDATA[What's the Future of Cancer Diagnosis?]]></title>
			<description><![CDATA[
<p><img src="http://cache.gawker.com/assets/images/io9/2008/10/vlcsnap-3825966.png" class="left image500" width="500" /> I talked about the importance of early cancer diagnosis in <a href="http://io9.com/5044076/where-is-my-cure-for-cancer">a previous post</a>, and reader Ian wrote back to ask for more detail. Early detection can be life-saving, but accuracy in these tests is also a serious problem - a test that misses existing cancers is obviously bad, but one that detects cancers that <em>aren't</em> there or <a href="http://scienceblogs.com/insolence/2007/04/detecting_cancer_early_part_1_more_compl.php">suggests a future cancer that will never develop</a> can expose patients to unnecessary procedures, some of them invasive. I'm not knocking cancer screening &mdash; just noting that, for a given test, the potential for early detection is not the whole story. Early <em>unambiguous</em> detection is the goal. Let's take a look at a few of the methods we can apply to improve cancer diagnosis.</p>

<p><strong>Genetic screening: find out which people are likely to develop certain cancers in the future.</strong></p>
<p><a href="http://en.wikipedia.org/wiki/Cancer#Genetic_testing">Certain genetic mutations</a> predispose a person to developing various cancers. While no mutation is a guarantee that cancer is in a patient's future, in a few cases the tendency is so strong that pre-emptive treatment is indicated, though earlier and more frequent screening is more common. It's estimated that <a href="http://www.nytimes.com/2008/05/27/health/27brod.html?_r=1&oref=slogin">5-10 percent of cancers are strongly hereditary, along with another 20-30 percent that are weakly hereditary</a>. Certain mutations of the <a href="http://www.cancer.gov/cancertopics/factsheet/risk/brca">BRCA1 and BRCA2 genes</a> , for example, increase the lifetime chance of a woman developing breast cancer from around 13 percent to somewhere between 36 and 85 percent.</p>
<p>Research for other risky versions of genes continues, and will eventually branch out into risky <em>combinations</em> of genes that appear in single nucleotide polymorphism genotyping (for <a href="https://www.23andme.com/">a few hundred dollars</a>) and complete genome sequences (<a href="http://www.nytimes.com/2008/10/06/business/06gene.html">soon to be a few thousand dollars</a>).</p>
<p><a href="https://www.23andme.com/more/genotyping/"><img src="http://cache.gawker.com/assets/images/io9/2008/10/beadchip.png" width="200" height="238"></a></p>
<p>When <a href="http://en.wikipedia.org/wiki/Personal_genomics">personal genomics</a> and medical histories (finally) come together, with a little luck we'll be able to find new correlations between genes and cancers. Family history is a good but imprecise indicator of risk; a better understanding of the specific genetic factors behind it will improve a physician's ability to assess an individual and design a regimen of treatment or prevention appropriate to the patient.</p>
<p><strong>Tumor markers: search for indirect signs of an existing or developing tumor.</strong></p>
<p>Usually this refers to a blood or urine test, though <a href="http://www.eurekalert.org/pub_releases/2008-10/aafc-spc092308.php">saliva</a> or even <a href="http://www.technologyreview.com/Biotech/21296/">smell are also options</a>. If you can find a substance that increases or decreases in abundance when a certain kind of tumor is present, assays that look for these <a href="http://en.wikipedia.org/wiki/Tumor_markers">tumor markers</a> can be used for routine evaluation. One of the most common markers is the <a href="http://en.wikipedia.org/wiki/Prostate_specific_antigen">prostate specific antigen (PSA)<br></a> - elevated levels of PSA in the blood are often (but not always) associated with prostate cancer. Because the test is prone to false positives, a worrisome blood test result is usually followed by ultrasound imaging. Looking for <a href="http://www.eurekalert.org/pub_releases/2008-02/aafc-nnp013008.php">multiple tumor markers at the same time can potentially be more accurate</a>, while <a href="http://www.leeds.ac.uk/media/press_releases/current/15minutes.htm">new technologies</a> decrease the time and expense of the necessary assays.</p>
<p>For tumors caused by infections, the presence of the infection itself can be used to determine at least risk - while a high-risk <a href="mailto:http://en.wikipedia.org/wiki/Hpv">human papillomavirus</a> infection certainly doesn't guarantee a cervical cancer, it does suggest that more frequent screening may be in order.</p>
<p>Similar <a href="http://www.technologyreview.com/Biotech/20822/">profiling of the tumors themselves</a> <a href="http://www.nature.com/nature/journal/v452/n7187/full/nature06913.html">could indicate what sorts of drugs would be effective against an individual's particular tumor</a>.</p>
<p><strong>Imaging: look for the damn things.</strong></p>
<p>This is a tricky business, because the difference between a benign and a cancerous (or pre-cancerous) mass can be difficult to tell without going in, taking out a sample, and subjecting it to various tests. In a colonoscopy, many suspicious lesions turn out to be harmless, but they still require a biopsy, which is even less fun than a colonoscopy without a biopsy. If you want to avoid bringing the cells to the microscope, bring the microscope to the cells - the <a href="http://www.eurekalert.org/pub_releases/2008-10/mc-mce100708.php">pCLE system</a> is effectively a fiberoptic microscope that can examine lesions in the colon without a biopsy.</p>
<p>If possible, avoid the colonoscopy entirely - take a series of radiographs of the colon and turn them over to the computer <a href="http://www.medgadget.com/archives/2008/09/virtual_colonography_vs_standard_colonoscopy.html">to reconstruct its 3D structure</a>. Examination of a virtual colon is far more comfortable than the alternative.</p>
<p><img src="http://cache.gawker.com/assets/images/io9/2008/10/vc_collage_01.jpg" width="315" height="278"></p>
<p>If a computer can be used to verify a doctor's "eyeball spectroscopy" (as in <a href="http://www.medgadget.com/archives/2008/10/computer_assisted_mammography_shows_promise_in_a_clinical_trial.html">computer-assisted mammography</a>, currently in clinical trials), the visual analysis of an expert can be combined with digital image analysis to separate the healthy from the suspicious.</p>
<p><img src="http://cache.gawker.com/assets/images/io9/2008/10/D42A90B8-E7F2-99DF-392F5C5C65BAF454_1.jpg" width="320" height="320"></p>
<p><a href="http://www.sciam.com/article.cfm?id=3-d-mammography-breast-cancer">Displaying mammography results in 3D</a> is also potentially useful in helping physicians to find suspicious masses, while <a href="http://www.eurekalert.org/pub_releases/2008-09/uocm-msd093008.php">improvements in MRI technology</a> work to increase the resolution of images generated by the technique.</p>
<p>Imaging can also be combined with treatment to increase its effectiveness. <a href="http://www.medgadget.com/archives/2008/10/nanoparticle_detecttion_in_vivo_minus_side_effects.html">Cancer-seeking nanoparticles</a> can also be detected using various imaginge techniques - a build-up of the particles is desired at the cancer site, but not elsewhere, and being able to detect where the treatment is collecting is a partial measure of its efficacy.</p>
<p>Finally, technologies like the <a href="http://www.medgadget.com/archives/2008/09/cyberknife_focuses_in_on_moving_targets.html">CyberKnife</a> combine imaging and robotics to guide radiation delivery to the patient by zeroing in on its target and following it as the patient moves.</p>
<p><img src="http://cache.gawker.com/assets/images/io9/2008/10/CyberKnife_System_Beauty_Sh.jpg" width="300" height="379"></p>
<p>A good technique catches cancer early and is as unambiguous as possible. Unfortunately, early <em>and</em> unambiguous is a tall order.</p>
<p><strong>Do you have questions you've always wanted to ask a biogeek? You can <a href="mailto:tdj@io9.com">email me</a>.</strong></p>
]]></description>
			<link><![CDATA[http://io9.com/5059257/whats-the-future-of-cancer-diagnosis]]></link>			<guid isPermaLink="false"><![CDATA[io9-5059257]]></guid>
			<category><![CDATA[ask a biogeek]]></category>
			<category><![CDATA[biology]]></category>
			<category><![CDATA[cancer]]></category>
			<category><![CDATA[feature]]></category>
			<category><![CDATA[medicine]]></category>
			<category><![CDATA[mri]]></category>
			<category><![CDATA[science]]></category>
			<category><![CDATA[top]]></category>
			<pubDate><![CDATA[Thu, 09 Oct 2008 09:00:00 PDT]]></pubDate>
			<dc:creator><![CDATA[Terry Johnson]]></dc:creator>
			<wfw:commentRss>http://io9.com/index.php?op=postcommentfeed&amp;postId=5059257&amp;view=rss&amp;microfeed=true</wfw:commentRss>
		</item>
				
		<item>
			<title><![CDATA[Will I Evolve Into a Being of Pure Energy?]]></title>
			<description><![CDATA[
<p><img src="http://cache.gawker.com/assets/images/8/2008/09/thumb160x_180px-Dukat_releasing_pah-wraith.jpg" class="left image158" width="158" /> <em>Welcome back to <strong>Ask a Biogeek</strong>, a column where biology researcher Terry Johnson answers questions about biology &mdash; no matter how weird.</em> Back when I discussed our <a href="http://io9.com/5036316/what-are-the-unlikeliest-futures-for-the-human-species">unlikeliest futures</a> as a species, one commenter added to the list of improbabilities our eventual transcendence into a non-corporeal form. That's hardly the only evolutionary myth propagated by science fiction. Misunderstandings of basic evolutionary theory are often so egregious they make "hearing explosions in space" seem mild in comparison. Warning: In discussing a few of the worst and most common offenses against evolutionary common sense, I'm going to spoil the hell out of a lot of old science fiction.</p>

<p>Let's get this out of the way - <strong>evolution does not have a destination in mind</strong>. There is no end boss, no level of development after which evolution retires and takes up shuffleboard. Evolution works via <a href="http://en.wikipedia.org/wiki/Natural_selection">natural selection</a> - organisms that are well-suited to their environment are more likely to have offspring, passing along those heritable traits that give rise to success. Traits that are favorable in one environment may be neutral or even disadvantageous in another.</p>
<p>A variant of one of the genes that produces hemoglobin <a href="https://www.23andme.com/health/sicklecell/">grants protection against malaria</a> to anyone possessing a single copy of that variant. Possess two copies, and you're stuck with <a href="http://en.wikipedia.org/wiki/Sickle-cell_disease">sickle cell anemia</a>. In an environment rife with malaria, the advantages of having a single copy of the variant may outweigh the risk that you'll shack up with someone who likewise carries the variant, occasionally producing a child with sickle-cell anemia. In a malaria-free environment, there's no advantage to the variant at all (that we know of). Evolution has no "master plan" for hemoglobin - natural selection simply favors what works in a given situation. Change the situation, and you'll very likely change the result.</p>
<p>Even a trait as useful as intelligence is not universally favorable. Take the humble fruit fly (<em>Drosophila melanogaster</em>), and select for a breed that more quickly learns to avoid foods spiked with bitter quinine. Pit these flies against normal flies in an environment where food is scarce, <a href="http://carlzimmer.com/articles/index.php?subaction=showfull&id=1210252305&archive=&start_from=&ucat=11&">and the normal flies will out-compete them, hands down</a>. We aren't exactly sure why - it could be that learning is energetically and biologically expensive. Too expensive, under some conditions - sometimes, maybe, it pays to be dumb.</p>
<p><img src="http://io9.com/assets/images/io9/2008/09/Drosophila_Kopf_140x.jpg" width="280" height="280"></p>
<p><strong><a href="http://en.wikipedia.org/wiki/Drosophila_melanogaster"><br>
Not smart enough</a> to resent the insinuation.</strong></p>
<p>Even if evolution <em>did</em> favor what we would consider a progression to a more "advanced" state (and it doesn't), there isn't a snowball's chance in hell that we'd end up clouds of pure energy, despite numerous fictional examples to the contrary. From the <a href="http://en.wikipedia.org/wiki/Vorlon">Vorlons</a> in <em>Babylon 5</em> to the <a href="http://en.wikipedia.org/wiki/Lensman">Arisians</a> in the <em>Lensman</em> series, SF loves its non-corporeal beings, most of whom evolved to shed their physical bodies in favor of floaty glowy bits. <em>Star Trek</em> alone has <a href="http://memory-alpha.org/en/wiki/Non-corporeal_species">so many non-corporeal races</a>, they could hold tea parties together (if they had mouths).</p>
<p><img src="http://io9.com/assets/images/io9/2008/09/Organian_Dikionium_Beta_XII-A.jpg" width="600" height="136"></p>
<p><strong><a href="http://memory-alpha.org/en/wiki/Organian">Organians</a>, <a href="http://memory-alpha.org/en/wiki/Dikironium_cloud_creature">a Dikironium cloud creature</a> (which technically contains some matter), and <a href="http://memory-alpha.org/en/wiki/Beta_XII-A_entity">the Beta XII-a entity</a>. Together they form the lava lamp brigade.</strong></p>
<p>The fact of the matter is - matter. The information that defines or influences our traits is stored by matter (specifically, by molecules of <a href="http://en.wikipedia.org/wiki/DNA">DNA</a>), and that information is put to use inside the cell to rearrange matter into other forms. Setting aside the difficulty of conceiving of a non-corporeal lifeform in the first place - and that's no mean feat - trying to get to that lifeform starting with a considerably corporeal organism like us via evolution requires a staggering suspension of disbelief. Despite this, some of the <a href="http://en.wikipedia.org/wiki/Ascension_(Stargate)">Ascended</a> in <em>Stargate</em> switch back and forth between energy and matter more frequently than I take vacations.</p>
<p>Similarly, evolution does not favor remorseless logic, nor does our evolutionary past suggest any noble savages in our ancestry. Easily <a href="http://www.farscapeworld.com/episodes/synopsis/10212.php">my least favorite episode</a> of <em>Farscape</em>has the lead character messed with by an alien probe, producing a hyperintelligent "evolved" Crichton (who's also a bit of a bastard) and a beastly yet admirable "devolved" Crichton. SF is full of races that have evolved into powerful but amoral, calculating beings - despite evidence that much our recent evolution has seemingly been devoted to <a href="http://www.sciencenews.org/view/feature/id/35249/title/Evolutions_Ear">communication and language</a>.</p>
<p><img src="http://io9.com/assets/images/io9/2008/09/my_three_crichtons.jpg" width="672" height="336"></p>
<p><strong>In the future, humanity will have no use for compassion. Nor, evidently, a skull.</strong></p>
<p>Lastly, tinkering with evolution's work is not necessarily a bad thing. (Full disclosure: that's kind of my day job.) Personally, if I were an alien species contacted by a <a href="http://memory-alpha.org/en/wiki/United_Federation_of_Planets">United Federation of Planets</a> so freaked out by their <a href="http://memory-alpha.org/en/wiki/Eugenics_Wars">Eugenics Wars</a> and <a href="http://memory-alpha.org/en/wiki/Klingon_augment_virus">Forehead Plagues</a> that they'd outlawed <a href="http://memory-alpha.org/en/wiki/Genetic_engineering">genetic engineering</a> for anything other than eliminating genetic diseases - I wouldn't be terribly impressed. A more advanced culture would probably look askance at Starfleet's <a href="http://memory-alpha.org/en/wiki/Julian_Bashir">"don't sequence, don't tell" policy</a> towards genetically enhanced organisms serving in the military. It seems like every week or so someone's being regenerated by a transporter accident, but I have to satisfy myself with my race's natural lifespan? Like hell!</p>
]]></description>
			<link><![CDATA[http://io9.com/5050374/will-i-evolve-into-a-being-of-pure-energy]]></link>			<guid isPermaLink="false"><![CDATA[io9-5050374]]></guid>
			<category><![CDATA[ask a biogeek]]></category>
			<category><![CDATA[babylon 5]]></category>
			<category><![CDATA[evolution]]></category>
			<category><![CDATA[feature]]></category>
			<category><![CDATA[lensman]]></category>
			<category><![CDATA[star trek]]></category>
			<category><![CDATA[stargate]]></category>
			<category><![CDATA[top]]></category>
			<pubDate><![CDATA[Thu, 18 Sep 2008 09:00:00 PDT]]></pubDate>
			<dc:creator><![CDATA[Terry Johnson]]></dc:creator>
			<wfw:commentRss>http://io9.com/index.php?op=postcommentfeed&amp;postId=5050374&amp;view=rss&amp;microfeed=true</wfw:commentRss>
		</item>
				
		<item>
			<title><![CDATA[Where Is My Cure for Cancer?]]></title>
			<description><![CDATA[
<p><a href="http://www.labnews.co.uk/news_archive.php/761/5/visions-of-science-winners-chosen/"><a rel="lytebox" href="http://io9.com/assets/images/io9/2008/09/cancer_cell_migrating.jpg"><img src="http://io9.com/assets/images/io9/2008/09/cancer_cell_migrating.jpg" class="left image500" width="500" /></a></a><iframe src="http://digg.com/api/diggthis.php?u=http://digg.com/health/Where_Is_My_Cure_for_Cancer" align="right" frameborder="0" height="82" scrolling="no" width="55"></iframe><em>Welcome back to <strong>Ask a Biogeek</strong>, a column where you ask biology researcher Terry Johnson any question you want — no matter how weird.</em> Reader Charlie writes:<br></p>
<blockquote>How about an article on the current cutting edge cancer research/treatments? Is there anything out there that is promising? Will there be a cure in our lifetimes?</blockquote>
<p>Sadly, cancer is not a single disease, but a class of diseases - while we may effectively cure some forms of cancer, it's doubtful that we'll be able to cure them all, and unlikely that a single form of treatment will be effective against all or even a wide range of cancers. The cells in our bodies are tightly regulated, but over time entropy has its way, and some lose their original genetic programming. Often these breakdowns are harmless and strictly local, but in the case of <a href="http://en.wikipedia.org/wiki/Cancer">cancer</a>, they can be catastrophic.</p>

<p>If you look at the human body as an ecosystem, it's remarkably well-behaved. Various types of cells fulfill their proper roles in their proper places. The rapid cellular growth that is appropriate in the lining of our guts, for example, would be hazardous in the adult brain. Cells are regulated by their microenvironment (hormones, the surrounding tissue, etc.), with healthy cells reacting as you would expect. Cells with DNA damage resulting from viral infections, exposure to carcinogenic chemicals or radiation, or simple error during division are not so predictable.</p>
<p>The body is not entirely unprepared for damaged cells. Our immune system seeks them out, and there are mechanisms within the cell designed to sense damage and cause <a href="http://en.wikipedia.org/wiki/Apoptosis">apoptosis</a> - programmed self-termination. These systems catch many dangerous cells, but not all.<br>
<a href="http://en.wikipedia.org/wiki/Carcinogenesis"><br>
<img src="http://io9.com/assets/images/io9/2008/09/Cancer_requires_multiple_mutations_from_NIH.png" width="156" height="459"></a><br>
If a damaged cell escapes the immune system and its own self-destruct devices, it will often grow more damaged with time, accumulating mutations. A "successful" cancer will acquire additional mutations that allow it to grow uncontrollably into a tumor, feed itself via the formation of blood vessels, and <a href="http://en.wikipedia.org/wiki/Metastatic">metastasize</a> - break away from the original tumor to form new colonies elsewhere in the body. Not every cell in the tumor needs to be the same for this to happen; if even <a href="http://en.wikipedia.org/wiki/Cancer_stem_cell">a small population of cells</a> hits a combination of errors that allows it to break away and take root elsewhere, the prognosis can be bleak.</p>
<p>I'm talking about cancer in a very general sense, but it's important to remember that not all cancers are the same. The types of cellular breakdown that lead to an aggressive breast cancer are not necessarily the same as the damage that would give you leukemia (though there may be a few gross similarities), and they originated with different kinds of cells in the first place, housed in different tissue niches. Nor are all cancers of the same general type the same - for example, some breast cancers overexpress a protein called <a href="http://en.wikipedia.org/wiki/HER2">HER2</a>, but not all. So, a tumor is composed of a mixture of cells which share some (but not all) of the same kinds of breakage with their immediate neighbors, cancers of the same type in other patients, and cancers of a different type entirely. It's hard to come up with a generalized cure when there are so many different ways for cells to flip out.</p>
<p>Early detection of a treatable cancer is critical. If you can catch the tumor before it metastasizes, you have only a single tumor to deal with. Imaging techniques like mammograms, X-rays, and MRIs can be used to detect tumors, though more exotic techniques for detection are on the way. Dogs have been shown to be capable of <a href="http://news.nationalgeographic.com/news/2006/01/0112_060112_dog_cancer.html">smelling cancer,</a> and research into the compounds they detect could lead to an <a href="http://www.technologyreview.com/Biotech/21296/">artificial diagnostic nose</a>.</p>
<p><img src="http://io9.com/assets/images/io9/2008/09/skincancer_x220.jpg" width="220" height="188"></p>
<p>Cellular therapies are another option. If your immune system is full of fail, perhaps it's time to send in the cavalry? <a href="http://technology.newscientist.com/article.ns?id=dn9138">Immune cells from cancer-resistant mice can be used to kill advanced tumors in normal mice</a> (well, "normal" for lab mice, anyway). Cells can also be used to target existing treatments to the site of the cancer, by using genetically modified cells that <a href="http://www.eurekalert.org/pub_releases/2006-12/sjcr-gmc122106.php">home in on a tumor and, once there, activate an anti-cancer drug</a>, reducing the wear and tear of side-effects on your healthy tissue. Since viruses are already quite good at homing in on cells, <a href="http://www.eurekalert.org/pub_releases/2008-08/uoaa-gta082208.php">they're another potential cancer-busting option</a>.</p>
<p>Nanotechnology has a few tricks up its sleeve if cells and viruses don't do the trick. <a href="http://www.technologyreview.com/Nanotech/21316/?a=f">Nanotubes can be loaded with drugs</a> <a href="http://www.medgadget.com/archives/2006/05/nanotubes_get_n.html">and "capped"</a>, potentially capable of releasing an anti-cancer payload on demand (though the "demand" part is still under construction). Once localized to a cancer cell, light at an appropriate wavelength zaps the nanotube, which absorbs it and heats up, effectively <a href="http://io9.com/5017054/carbon-nanotubes-cook-cancer">cooking the tumor</a>.</p>
<p><img src="http://io9.com/assets/images/io9/2008/09/rd-nanotube.jpg" width="197" height="153"></p>
<p><a href="http://discovermagazine.com/2005/nov/killing-cancer-with-nanotubes">Nanotubes in green, cancer cell nuclei in red.</a></p>
<p>Similar results have been achieved <a href="http://www.technologyreview.com/read_article.aspx?id=17956&a=f">using gold-plated nanoparticles</a>, while bundles of nanorods form <a href="http://www.medgadget.com/archives/2005/10/the_cancer_nano.html">light-activated cancer-shredding cluster bombs</a>.</p>
<p><a href="http://www.medgadget.com/archives/2005/10/the_cancer_nano.html">"As if billions of cancer cells cried out...and were suddenly silenced."</a></p>
<p><img src="http://io9.com/assets/images/io9/2008/09/Panchapakesan-NanoBomb-03lg.jpg" width="600" height="407"></p>
<p>It's likely that not all of these approaches will bear fruit - if every cancer cure that worked on rats also worked on humans, I probably wouldn't have to answer this question. With a disease as diverse as cancer, however, it makes sense to approach a wide variety of possible treatments.</p>
<p><strong>Do you have questions you've always wanted to ask a biogeek? You can <a href="mailto:tdj@io9.com">email Terry Johnson</a>.</strong></p>
]]></description>
			<link><![CDATA[http://io9.com/5044076/where-is-my-cure-for-cancer]]></link>			<guid isPermaLink="false"><![CDATA[io9-5044076]]></guid>
			<category><![CDATA[ask a biogeek]]></category>
			<category><![CDATA[cancer]]></category>
			<category><![CDATA[feature]]></category>
			<category><![CDATA[nanotechnology]]></category>
			<category><![CDATA[science]]></category>
			<category><![CDATA[top]]></category>
			<pubDate><![CDATA[Thu, 04 Sep 2008 09:00:00 PDT]]></pubDate>
			<dc:creator><![CDATA[Terry Johnson]]></dc:creator>
			<wfw:commentRss>http://io9.com/index.php?op=postcommentfeed&amp;postId=5044076&amp;view=rss&amp;microfeed=true</wfw:commentRss>
		</item>
				
		<item>
			<title><![CDATA[What Are the Unlikeliest Futures for the Human Species?]]></title>
			<description><![CDATA[
<p><img src="http://cache.gawker.com/assets/images/8/2008/08/340x_Smoky_The_Nanobot.jpg" class="left image340" width="340" /><em>Welcome to Ask a Biogeek, a column where you ask UC Berkeley researcher Terry Johnson any question you want — no matter how weird.</em> Reader Matthew asks:<br></p>
<blockquote>This is an odd question, but is there anything we're certain <i>isn't</i> coming? Most of my friends are all starry-eyed optimistic sci-fi readers, and they continually bombard me with what will be the "future of the human species" . . . from "meat vats" for growing cruelty free meat to clone armies. Anyway, is there anything that is solidly stymied at this point? Any futurist direction we know is blocked?</blockquote>
<p>"Blocked" is perhaps too rigorous a standard, but there are certainly some futures far less likely than others. I can't <a href="http://en.wikipedia.org/wiki/Negative_proof">prove a negative</a>, but perhaps I can convince you that a few common science fiction or futurist tropes are, shall we say, favored poorly by probability.</p>

<p><strong><a href="http://en.wikipedia.org/wiki/Grey_goo">Grey Goo</a> Eats the Planet</strong></p>
<p>Self-replicating molecular machines run amok, proving so capable of turning other molecules into copies of themselves that Earth's ecosystem is completely taken over by an amorphous mass of presumably-grey nanotechnology. Futurists and science fiction writers have imagined nanotech ecophages that originate on our planet, through nanoweapons research or mutations in beneficial nanotechnology, along with alien nanotech - whether star-faring remnants of some other species' lab accident or a deliberate attempt at genocide. These vivid visions of a nanotechnological apocalypse caught on with the public, despite <a href="http://www.iop.org/EJ/news/-topic=763/journal/0957-4484">much evidence to the contrary</a>. Nanotechnologist <a href="http://en.wikipedia.org/wiki/K._Eric_Drexler">Eric Drexler</a> originally coined the term "grey goo", and now rather wishes he'd hadn't. No one is working on self-assembling nanomachines that even hint at the abilities a true ecophage would require, and concerns over the catastrophic (though enormously unlikely) grey goo scenario turn attention away to <a href="http://en.wikipedia.org/wiki/Nanotoxicology">more pedestrian health concerns</a>, like toxicology.</p>
<p><img src="http://io9.com/assets/images/io9/2008/08/greygoo.jpg"></p>
<p><a href="http://www.lolsingularity.com/lolsingularities.html">Oh noes!</a></p>
<p>Considering biology, I'm fairly confident that if grey goo were possible, we'd be living in it. Single-celled organisms have been doing chemical experimentation for billions of years via mutation and natural selection, and if there was a magic, self-catalyzing molecule out there, I expect they'd have found it. It wouldn't be for lack of trying - protein enzymes perform chemistry all the time, and <a href="http://en.wikipedia.org/wiki/RNA_world_hypothesis">RNA can both catalyze reactions and store genetic information</a>. I don't discount the possibility that killer grey goo molecules could merely be difficult or impossible to synthesize using the amino acids, nucleotides, and raw materials that life on earth manipulate and depend upon - but life has been pretty clever about applying those resources so far, and the closest nature has come to a self-replicating nanomachine would probably be a <a href="http://en.wikipedia.org/wiki/Prion">prion</a>. Though disease-causing prions are notoriously difficult to destroy, they have yet to convert the Earth's biomass into mad cows.</p>
<p>An amazingly successful organism - not a single molecule replicating itself, but a more complex collection of molecules, like a cell - could potentially lead us into a <a href="http://www.wired.com/medtech/health/news/2004/07/64235">Green Goo</a> Ragnarök. On Earth, however, it would find an already-existing ecosystem full of the survivors of a molecular arms race that began in the <a href="http://en.wikipedia.org/wiki/Abiogenesis">primordial soup</a>. A newbie might be able to find a niche or even flourish, but to displace all other life on Earth is asking a bit much - though the results of a partial takeover and significant shift in Earth's ecosystem could still be disastrous to humanity.</p>
<p><strong>A Meal in a Pill</strong></p>
<p>Your body requires a certain amount of carbohydrates, protein, and fats. Add in the necessary fiber, and an "average" human being needs at in the ballpark of 250 grams of food. Assuming a density of around 1.0 gram per cubic centimeter, my back of the envelope calculation suggests that a pill taken three times daily would be a few inches in diameter.</p>
<p><img src="http://io9.com/assets/images/io9/2008/08/250px-Anti-Pressure_Pill.jpg"></p>
<p><a href="http://futurama.wikia.com/wiki/Anti-Pressure_Pill">Fry: "I cant swallow that." Professor Hubert Farnsworth: "Well, then, good news! It's a suppository."</a></p>
<p>Even neglecting essential vitamins and minerals, that's not easy to swallow. The military, long interested in convenient, non-perishable foodstuffs, is considering a <a href="http://www.defenselink.mil/news/newsarticle.aspx?id=44529">transdermal nutrient delivery system</a> instead.</p>
<p><strong>A <a href="http://memory-alpha.org/en/wiki/Universal_translator">Universal Translator</a></strong></p>
<p>The prevalence of universal translation devices in science fiction has more to do with avoidance of subtitles than scientific plausibility. It's difficult enough to wrap up the "A" plot in a 42-minute television episode if every line requires manual translation by non-native speakers. Mysteriously English-speaking aliens may strain credulity, but without them, crackling dialogue is a challenge.</p>
<p>Linguistics posits a basic <a href="http://en.wikipedia.org/wiki/Universal_grammar">universal grammar</a> shared by all known languages, though in typical anthrocentrism this grammar is universal only to humans. Alien grammar needn't share much of anything with ours, and the language itself could be composed of sounds, smells, flashing lights, posture, magnetic fields, spurts of superheated plasma, or some complex combination of these or other phenomena. Real-time translation of known alien languages would be complicated enough - the device would have to detect every possible phenomena that an alien could use to communicate with on top of the translation task. Translation of <em>new</em> languages would require enough exposure to learn the vocabulary.</p>
<p><img src="http://io9.com/assets/images/io9/2008/08/180px-UniversalTranslator2267.jpg" width="180" height="135"></p>
<p><em>Star Trek</em>'s universal translator posits universal concepts shared by all intelligent beings - a pretty big "if" - and associates brainwaves with these concepts. Imagine a pocket-sized functional MRI machine that sees the patterns associated with a certain universal concept and translates it into your language. Sounds great - but it assumes a central nervous system suspiciously similar to our own. That's reasonable when your galaxy is filled with beings who resemble you (with bumpier foreheads) - for us, probably not so much.</p>
<p><strong>Do you have questions you've always wanted to ask a biogeek? You can <a href="mailto:tdj@io9.com">email me</a>.</strong></p>
]]></description>
			<link><![CDATA[http://io9.com/5036316/what-are-the-unlikeliest-futures-for-the-human-species]]></link>			<guid isPermaLink="false"><![CDATA[io9-5036316]]></guid>
			<category><![CDATA[ask a biogeek]]></category>
			<category><![CDATA[feature]]></category>
			<category><![CDATA[grey goo]]></category>
			<category><![CDATA[meal in a pill]]></category>
			<category><![CDATA[nanotechnology]]></category>
			<category><![CDATA[top]]></category>
			<category><![CDATA[universal translator]]></category>
			<pubDate><![CDATA[Thu, 21 Aug 2008 09:00:00 PDT]]></pubDate>
			<dc:creator><![CDATA[Terry Johnson]]></dc:creator>
			<wfw:commentRss>http://io9.com/index.php?op=postcommentfeed&amp;postId=5036316&amp;view=rss&amp;microfeed=true</wfw:commentRss>
		</item>
				
		<item>
			<title><![CDATA[Son Of "Where Are My Cybernetic Implants?"]]></title>
			<description><![CDATA[
<p><img src="http://cache.gawker.com/assets/images/8/2008/08/thumb160x_bleex.jpg" class="left image158" width="158" /><em>Welcome to Ask a Biogeek, a column where you ask UC Berkeley researcher Terry Johnson any question you want — no matter how weird.</em> There seems to be a strong correlation between my posting an article on a subject, and my RSS feeds filling up with exciting new research, which I then wish I'd been able to include. The usual post-article deluge of goodness, combined with <a href="http://io9.com/5031826/first-look-at-the-poster-for-the-movie-version-of-neuromancer">the poster for a Neuromancer movie</a> practically forced me to revisit the burning question: <a href="http://io9.com/391064/where-are-my-cybernetic-implants">Where are my cybernetic implants?</a></p>

<p>Japan's <a href="http://www.sciam.com/article.cfm?id=real-life-iron-man-exoskeleton">HAL exoskeleton</a> is joined by the <a href="http://www.argomedtec.com/products.asp">ReWalk</a> system - a partial exoskelton designed to allow users with mobility issues to walk with the help of crutches.</p>
<p><object width="425" height="344"><param name="movie" value="http://www.youtube.com/v/gQRQs-N-ZIM&hl=en&fs=1">
<param name="allowFullScreen" value="true">
<embed src="http://www.youtube.com/v/gQRQs-N-ZIM&hl=en&fs=1" type="application/x-shockwave-flash" allowfullscreen="true" width="425" height="344"></object></p>
<p><a href="http://bleex.me.berkeley.edu/bleex.htm">Berkeley's Lower Extremity Exoskeleton (BLEEX)</a> is designed to assist soldiers, firefighters, or rescue personnel by supporting heavy equipment with the exoskeleton instead of the wearer's back. The 100-pound BLEEX rig plus a 70-pound backpack <a href="http://www.berkeley.edu/news/media/releases/2004/03/03_exo.shtml">feel like a 5-pound load to the wearer</a>.</p>
<p><object width="425" height="344"><param name="movie" value="http://www.youtube.com/v/fRkg6H0ZP8A&hl=en&fs=1">
<param name="allowFullScreen" value="true">
<embed src="http://www.youtube.com/v/fRkg6H0ZP8A&hl=en&fs=1" type="application/x-shockwave-flash" allowfullscreen="true" width="425" height="344"></object></p>
<p><a href="http://www.berkeleybionics.com/">Berkeley Bionics</a> demonstrates the latest version, which is easier to move in than without.</p>
<p><object width="425" height="344"><param name="movie" value="http://www.youtube.com/v/EdK2y3lphmE&hl=en&fs=1">
<param name="allowFullScreen" value="true">
<embed src="http://www.youtube.com/v/EdK2y3lphmE&hl=en&fs=1" type="application/x-shockwave-flash" allowfullscreen="true" width="425" height="344"></object></p>
<p>Amputees can look forward to advances like the <a href="http://www.popsci.com/scitech/article/2008-05/natural-artificial-foot">K3 Promoter</a>, a prosthetic foot with tensioned steel cables designed to mimic the action of tendons and ligaments, or <a href="http://blog.wired.com/gadgets/2008/05/dean-kamens-rob.html">Dean Kamen's "Luke" arm</a>. The following video shows the arm in action as its creators discuss its engineering versatility.</p>
<p><object width="425" height="344"><param name="movie" value="http://www.youtube.com/v/R0_mLumx-6Y&hl=en&fs=1">
<param name="allowFullScreen" value="true">
<embed src="http://www.youtube.com/v/R0_mLumx-6Y&hl=en&fs=1" type="application/x-shockwave-flash" allowfullscreen="true" width="425" height="344"></object></p>
<p>When a prothesis cannot <a href="http://www.spectrum.ieee.org/feb08/5957/2">be completely controlled via the user's nervous impulses</a> — or a completely robotic arm with human-like control is desired — a biomimetic arm may serve. SENOPAC's robot hand combines a sensory "skin" with a controller inspired by the human cerebellum, <a href="http://www.medgadget.com/archives/2008/07/copying_nature_for_more_convincing_prosthesis.html">capable of a quick snap of its fingers or the delicate handling of a chicken's egg</a>.</p>
<p><img src="http://io9.com/assets/images/io9/2008/08/robotic-hand-from-eu.jpg" class="center"></p>
<p><a href="http://www.physorg.com/news136039196.html">SENOPAC's biomimetic arm — 'cause evolution is hard to beat.</a></p>
<p>Intel's working on a robotic hand <a href="http://blog.wired.com/wiredscience/2008/06/video-robotic-h.html">that can feel objects before it touches them</a> — relying on <a href="http://en.wikipedia.org/wiki/Electrolocation">electrolocation</a> to give the hand a "Pre Touch" sense.</p>
<p><object width="425" height="344"><param name="movie" value="http://www.youtube.com/v/DB3pNtZvlRA&hl=en&fs=1">
<param name="allowFullScreen" value="true">
<embed src="http://www.youtube.com/v/DB3pNtZvlRA&hl=en&fs=1" type="application/x-shockwave-flash" allowfullscreen="true" width="425" height="344"></object></p>
<p>The rest of the body has much to look forward to. Patients experiencing renal failure typically require <a href="http://en.wikipedia.org/wiki/Dialysis">dialysis</a> — their kidneys are no longer able to filter wastes from the blood, allowing them to build up and throwing off the body's ability to regulate waste, acid, electrolytes — you name it. Dialysis artificially filters dangerous levels of wastes out of the blood, but it is an expensive, time-consuming procedure during which the patient is effectively bedridden. AWAK, <a href="http://www.newsroom.ucla.edu/portal/ucla/ucla-and-va-researchers-design-52444.aspx">the automated, wearable artificial kidney</a>, would replace dialysis with a wearable device that operates continuously. It's not quite implantable, but a kidney that you wear is potentially much better than a kidney that you rent time on three times a week.</p>
<p><img src="http://io9.com/assets/images/io9/2008/08/kidney_gura.jpg" class="center"></p>
<p><a href="http://current.com/items/89141484_wearable_kidney_could_help_millions_of_people">AWAK - "dialysis on the go".</a></p>
<p>In an attempt to make mind-machine interfaces work more smoothly, <a href="http://www.spectrum.ieee.org/may08/6269/2">this micro-mechanical electrosensory robot</a> wouldn't rely on the usual surgical technique for implanting electrodes in the brain, which is "stick an electrode into the brain and hope it ends up somewhere useful". This device is designed to make minute adjustments automatically to individual electrodes, nestling them firmly in the signaling "sweet spot" — and, if necessary, keeping them there as the architecture of the brain changes. It'll zero in on neurons using software similar to airplane-tracking software currently in use by the U.S. military.</p>
<p><img src="http://io9.com/assets/images/io9/2008/08/robot_as_brain_computer_interface.jpg" class="center"></p>
<p><a href="http://www.primidi.com/2008/05/21.html#a2192">A better brain-computer interface?</a></p>
<p>Advances such as these could serve to improve devices such as Neuro_Pace, <a href="http://www.medgadget.com/archives/2008/08/neuropace_maybe_first_since_jesus_to_treat_epilepsy.html">an implant which detects oncoming seizures and short-circuits them</a>, or <a href="http://www.medgadget.com/archives/2008/05/i_for_one_welcome_our_robotarm_controlling_monkey_overlords.html">the brain-controlled robotic arm that even a monkey can use</a>:</p>
<p><object width="425" height="344"><param name="movie" value="http://www.youtube.com/v/jOkpn0BN2HE&hl=en&fs=1">
<param name="allowFullScreen" value="true">
<embed src="http://www.youtube.com/v/jOkpn0BN2HE&hl=en&fs=1" type="application/x-shockwave-flash" allowfullscreen="true" width="425" height="344"></object></p>
<p>Oh, and that artificial retina we mentioned last time? Now there's <a href="http://www.eurekalert.org/pub_releases/2008-05/f-wvi052908.php">a wireless version</a>. No word yet on what sort of security the wireless signal has. I rather like the idea of a future where you can wander around searching for public point-of-view feeds, though heaven only knows what the marketing people would do with that data.</p>
]]></description>
			<link><![CDATA[http://io9.com/5033080/son-of-where-are-my-cybernetic-implants]]></link>			<guid isPermaLink="false"><![CDATA[io9-5033080]]></guid>
			<category><![CDATA[ask a biogeek]]></category>
			<category><![CDATA[cybernetics]]></category>
			<category><![CDATA[cyborgs]]></category>
			<category><![CDATA[feature]]></category>
			<category><![CDATA[implants]]></category>
			<category><![CDATA[neuromancer]]></category>
			<category><![CDATA[top]]></category>
			<pubDate><![CDATA[Thu, 07 Aug 2008 09:00:00 PDT]]></pubDate>
			<dc:creator><![CDATA[Terry Johnson]]></dc:creator>
			<wfw:commentRss>http://io9.com/index.php?op=postcommentfeed&amp;postId=5033080&amp;view=rss&amp;microfeed=true</wfw:commentRss>
		</item>
				
		<item>
			<title><![CDATA[Where Is My Hypospray?]]></title>
			<description><![CDATA[
<p><img src="http://cache.gawker.com/assets/images/8/2008/07/thumb160x_hypospray.jpg" class="left image158" width="158" /><em>Welcome to <strong>Ask a Biogeek</strong>, a column where you ask UC Berkeley researcher Terry Johnson any question you want &mdash; no matter how weird.</em><br>
Reader Mairi proxies the following question: <strong>My mom wants to know when we're going to get needle-less, <em>painless</em> injections.</strong><br>
While I personally covet the <a href="http://io9.com/380780/where-is-my-medical-tricorder">medical tricorder</a>, I would almost prefer that my doctor have a <a href="http://memory-alpha.org/en/wiki/Hypospray">hypospray</a> - Starfleet's painless, needle-free injection system. The concept of a high-pressure alternative to a syringe dates back to <i>The Shadow</i>'s radio show, and medical devices that function accordingly exist today. These, however, are not the only potential alternatives to a painful jab.</p>

<p>The syringe has been around since the 9th century, thanks to the Iraqi/Egyptian physician Ammar ibn 'Ali al-Mawsili', though he used it exclusively <a href="http://en.wikipedia.org/wiki/Syringe">to remove cataracts from the eyes of his patients</a>. Intravenous injection using syringes didn't come into vogue until the mid 1700s. Likewise, the first high-pressure <a href="http://en.wikipedia.org/wiki/Jet_injector">jet injectors</a> were not intended to deliver drugs - they were grease guns or components of diesel engines, and their accidental application to human bodies was anything but painless.</p>
<p><img src="http://io9.com/assets/images/io9/2008/07/ped_01.jpg" class="center"></p>
<p>The <a href="http://www.medicalhealthcareinfo.com/content/This_version_of_the_Ped-O-Jet_.php">Ped-O-Jet</a>, a foot-powered jet injection vaccinator.</p>
<p>In 1960 the medical jet-injector, the <a href="http://www.nlm.nih.gov/exhibition/smallpox/sp_eradicate.html">Ped-O-Jet</a>, was developed for vaccination against smallpox - predating Star Trek's hypospray by several years. Not exactly painless, but invaluable for quick, mass-injections or vaccinations. The "Ped" referred to the power supply - a foot-powered pump. Its reusable tip made is less expensive, but led to concerns that infections could be passed from one patient to subsequent patients. More compact improvements like the <a href="http://www.jtip.com/componen.htm">Jtip</a>, <a href="http://www.bioject.com/biojector2000.html">Biojector</a>, or <a href="http://findarticles.com/p/articles/mi_m0EIN/is_2001_Oct_18/ai_79224129">PenJet</a> make it possible to <a href="http://www.medgadget.com/archives/2008/02/self_administered_avian_flu_vaccine_set_for_trial.html">self-administer flu vaccines</a> and <a href="http://www.medgadget.com/archives/2006/08/the_intraject_s.html">migraine medication</a>.</p>
<p>Needle or no, shooting liquids into your flesh at high speed is not guaranteed to be painless, and some users complain of bruising and soreness. The <a href="http://berkeley.edu/news/media/releases/2005/03/16_microjet.shtml">MicroJet</a> uses a <a href="http://sciencereview.berkeley.edu/articles.php?issue=13&article=briefs_1">piezoelectric actuator</a> to repeatedly deliver more precisely controlled volumes of liquid. The very thin streams of liquid produced by the MicroJet reduce the area of skin affected by the injection and (with a little luck and the right settings) <a href="http://www.engineering.ucsb.edu/news/132">reduce pain</a>.</p>
<p><script type="text/javascript">
newVideoPlayer("/microjet.flv", 506, 99,"");
</script><img src="http://cache.gawker.com/assets/stills/microjet.flv.jpg" style="display: none;"></p>
<p>A MicroJet <a href="http://berkeley.edu/news/media/releases/2005/03/16_microjet.shtml">in action</a>.</p>
<p>When a drug can penetrate the skin or mucous membranes on its lonesome, an <a href="http://en.wikipedia.org/wiki/Inhaler">inhaler</a> or <a href="http://en.wikipedia.org/wiki/Topical">topical</a> application of the drug in a cream or a <a href="http://en.wikipedia.org/wiki/Transdermal_patch">transdermal patch</a> will do. Topical applications are painless, but not every pharmaceutical can penetrate the skin without help. The <a href="http://gizmodo.com/archives/life-imitates-star-trek-sonoprep-needleless-injection-022206.php">SonoPrep</a> uses ultrasound to permeabilize an area of skin, making it temporarily possible for drugs to seep through skin that would typically block it from entry.</p>
<p><a href="http://en.wikipedia.org/wiki/MEMS">Microelectricalmechanical systems</a> (MEMS) devices are another alternative. Instead of one big injection, why not lots of tiny ones? <a href="http://news.bbc.co.uk/2/hi/health/7002482.stm">Microneedle devices</a> look and feel like a patch, but they actually consist of hundreds of microneedles that can be programmed to deliver drugs steadily and painlessly.</p>
<p><img src="http://io9.com/assets/images/io9/2008/07/microneedles.gif" class="center"></p>
<p>Lilliputian <a href="http://news.bbc.co.uk/2/hi/health/7002482.stm">microneedle</a> jabs.</p>
<p>NanoPumps deliver insulin slowly enough that large-scale injections are unnecessary, regulating blood insulin levels with steady, constant flow.</p>
<p><img src="http://io9.com/assets/images/io9/2008/07/nanopump.jpg" class="center"></p>
<p>An insulin <a href="http://www.medgadget.com/archives/2008/06/insulin_nanopump_prototype_from_debiotech.html">NanoPump</a>.</p>
<p>While many of these drug delivery methods are far less painful than a needle stick, I love a challenge - how about a <em>pleasurable</em> drug delivery method? Look no further than <a href="http://www.dailymail.co.uk/health/article-1033750/The-tomato-vaccine-prevent-Alzheimers.html">edible vaccines produced by genetically modified food</a>. No matter how picky an eater you are, it's preferable to an injection.</p>
<p><strong>Do you have questions you've always wanted to ask a biogeek? You can <a href="mailto:tdj@io9.com">email me</a>.</strong></p>
]]></description>
			<link><![CDATA[http://io9.com/5025663/where-is-my-hypospray]]></link>			<guid isPermaLink="false"><![CDATA[io9-5025663]]></guid>
			<category><![CDATA[ask a biogeek]]></category>
			<category><![CDATA[drugs]]></category>
			<category><![CDATA[feature]]></category>
			<category><![CDATA[hypospray]]></category>
			<category><![CDATA[star trek]]></category>
			<category><![CDATA[top]]></category>
			<pubDate><![CDATA[Thu, 17 Jul 2008 09:00:00 PDT]]></pubDate>
			<dc:creator><![CDATA[Terry Johnson]]></dc:creator>
			<wfw:commentRss>http://io9.com/index.php?op=postcommentfeed&amp;postId=5025663&amp;view=rss&amp;microfeed=true</wfw:commentRss>
		</item>
				
		<item>
			<title><![CDATA[Where Is My Silicon-Based Life?]]></title>
			<description><![CDATA[
<p><img src="http://cache.gawker.com/assets/images/8/2008/07/9c/5c/thumb160x_9c5c0d3d30d9e132c6a9bbe4d035e29e.jpg" class="left image158" width="158" /><iframe src="http://digg.com/api/diggthis.php?u=http://digg.com/general_sciences/Ask_A_Biogeek_Where_Is_My_Silicon_Based_Life" align="right" frameborder="0" height="82" scrolling="no" width="55"></iframe><em>Welcome back to <strong>Ask a Biogeek</strong>, a biweekly column where UC Berkeley biology researcher Terry Johnson answers your questions, no matter how weird.</em> Reader Mike asks:<br></p>
<blockquote>Can you speculate on what a silicon based lifeform might look like? What would an "organic chemistry" look like for silicon, instead of carbon?</blockquote>
<p>Life on earth is (so far as we know) exclusively <a href="http://en.wikipedia.org/wiki/Carbon">carbon</a>-based. Thanks to its <a href="http://en.wikipedia.org/wiki/Valence_(chemistry)">position on the periodic table</a>, carbon can comfortably form bonds with up to four other elements - including other carbon atoms - allowing it to form a wide variety of complicated molecules necessary for terrestrial life. <a href="http://en.wikipedia.org/wiki/Silicon">Silicon</a>, being right below carbon on the periodic table, is chemically similar in many ways, leading science fiction authors to consider the possibility of life with a biochemistry that switches out carbon in favor of silicon.</p>

<p>In 1894 <a href="http://www.daviddarling.info/encyclopedia/S/siliconlife.html">H. G. Wells wrote</a>:</p>
<blockquote>
<p>One is startled towards fantastic imaginings by such a suggestion: visions of silicon-aluminium organisms – why not silicon-aluminium men at once? – wandering through an atmosphere of gaseous sulphur, let us say, by the shores of a sea of liquid iron some thousand degrees or so above the temperature of a blast furnace.</p>
</blockquote>
<p>Since then writers have imagined silicon-based creatures as diverse as Star Trek's <a href="http://www.memory-alpha.org/en/wiki/Horta">Horta</a> and the <a href="http://en.wikipedia.org/wiki/Xenomorph_(Alien)">Xenomorph</a> (though I may be cheating here, since it's unclear how rigidly the xenomorph adheres to silicon-only biochemistry).</p>
<p><img src="http://io9.com/assets/images/io9/2008/06/tmhorta.jpg" style="display:block;display:block;display:block;display:block;"></p>
<p>"I'm a doctor, not a bricklayer!" - a clear example of <a href="http://en.wikipedia.org/wiki/Carbon_chauvinism">carbon chauvinism</a>.</p>
<p>Silicon is also a major component in <a href="http://en.wikipedia.org/wiki/Integrated_circuit">microchips</a>, so one can make a case that an <a href="http://en.wikipedia.org/wiki/Artificial_intelligence">artificial intelligence</a> would be a silicon-based lifeform. So, which is more likely - stumbling upon silicon-based biochemistry out there amongst the stars, or creating life that thinks with silicon-based microchips here on earth?</p>
<p>Silicon is the most abundant element (barring oxygen) in the earth's crust. If silicon is so chemically similar to carbon and it's so readily available, why aren't <em>we</em> silicon-based? Silicon is routinely used by carbon-based lifeforms, but while (for example) <a href="http://en.wikipedia.org/wiki/Diatom">diatoms</a> (a type of algae) make their cell walls out of silica, carbon in is the backbone of their DNA, their proteins, and the basis of their biochemistry. Silicon is just along for the ride.</p>
<p>The answer involves subtle differences between carbon and silicon chemistry. While carbon and silicon can theoretically form very similar kinds of structures, complicated carbon-based molecules tend to the stable, while <a href="http://en.wikipedia.org/wiki/Alternative_biochemistry">complicated silicon-based molecules tend to fall apart</a> (especially in water).</p>
<p>There's a major waste disposal issue as well - carbon dioxide is a gas, and silicon dioxide (sand) is a solid. When we metabolize oxygen, we produce carbon dioxide as a waste product, but it dissolves easily in our blood for rapid waste management. If, on the other hand, we produced sand internally with every breath, chaffing would be the least of our worries. Most silicon molecules <a href="http://nai.arc.nasa.gov/astrobio/feat_questions/silicon_life.cfm">also lack chirality</a> (or "handedness"), which is a hallmark of terrestrial carbon-based life, but not necessarily a deal-breaker.</p>
<p>I won't go so far as to say that there's no such thing as a silicon-based biochemistry. As Arthur C. Clarke said, "When [a distinguished and elderly] states that something is impossible, he is very probably wrong." Being relatively young and almost completely undistinguished, my odds would be even worse. I will say that, if a silicon-based biochemistry exists, it probably doesn't use silicon the way we use carbon, and we might even have a difficult time recognizing it as life (unless it mind-melds with Spock).</p>
<p>Though silicon would be the basis for a chancy biochemistry, it makes (in part) a fine integrated circuit. As computation and storage become less expensive, our knowledge of how living things think has expanded, thanks mostly to increasingly powerful experimental techniques. Our brains are <a href="http://en.wikipedia.org/wiki/Gordian_knot">Gordian Knots</a> of neurons; a tangle of cunningly interconnected cells from which consciousness arises. If we'd like to replicate that consciousness <a href="http://en.wikipedia.org/wiki/In_silico">in silico</a>, we need to do more than untie the Gordian knot - we need to somehow ascertain which strands of the <i>intact</i> knot interact to understand and reproduce the brain's wiring.</p>
<p>Alexander the Great's solution is pretty close to the mark, though he'd have needed a thinner sword. First, you section the brain into microscopically thin slices, then you image the slices. Reconstruct the images into a 3D model and you might be able to tease out which neurons communicated with each other.</p>
<p><img src="http://io9.com/assets/images/io9/2008/06/001k08z2.jpg"></p>
<p><a href="http://www.spectrum.ieee.org/print/6268">A fruit fly brain - an image that took 10 months to produce.</a></p>
<p>It's also possible to help distinguish individual neurons by coaxing neurons to fluoresce different colors, a technique aptly called a <a href="http://www.livescience.com/animals/071031-brainbow.html">brainbow</a>.</p>
<p><img src="http://io9.com/assets/images/io9/2008/06/001eyxqc.png"></p>
<p><a href="http://www.wired.com/science/discoveries/multimedia/2007/10/gallery_fluorescentneurons">The amazing technicolor brainbow.</a></p>
<p>Once you have a wiring diagram for the neurons in a brain, you can run a computational model of how they'd interact. Today it takes a supercomputer like <a href="http://bluebrain.epfl.ch">Blue Brain</a> to simulate even part of a rat's brain, but that part (the neocortal column) looks to be reacting much like a real rat's would.</p>
<p><img src="http://io9.com/assets/images/io9/2008/06/001hwz43.jpg"></p>
<p><a href="http://www.seedmagazine.com/news/2008/03/out_of_the_blue.php">A virtual rat neocortal column, according to Blue Brain.</a></p>
<p>I expect that the first silicon-based life will be a simulation of carbon-based life. While our brains rely on their three dimensional structure, ion channels, and neurotransmitters to do the grunt work of consciousness, a simulated brain could achieve the same end result without the benefit of carbon. With a little luck these exacting imaging studies will become become possible <a href="http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371%2Fjournal.pbio.0060164&ct=1">without having to chop a brain into thousands of thin slices</a>.</p>
<p>When that day arrives, you'll see me stocking up on hard drives.</p>
<p><strong>Want to ask Terry a question? <a href="mailto:tdj@io9.com">Email him</a>!</strong></p>
]]></description>
			<link><![CDATA[http://io9.com/5020921/where-is-my-silicon+based-life]]></link>			<guid isPermaLink="false"><![CDATA[io9-5020921]]></guid>
			<category><![CDATA[ask a biogeek]]></category>
			<category><![CDATA[alien]]></category>
			<category><![CDATA[consciousness]]></category>
			<category><![CDATA[feature]]></category>
			<category><![CDATA[Silicon-based Life]]></category>
			<category><![CDATA[star trek]]></category>
			<category><![CDATA[top]]></category>
			<pubDate><![CDATA[Thu, 03 Jul 2008 09:00:00 PDT]]></pubDate>
			<dc:creator><![CDATA[Terry Johnson]]></dc:creator>
			<wfw:commentRss>http://io9.com/index.php?op=postcommentfeed&amp;postId=5020921&amp;view=rss&amp;microfeed=true</wfw:commentRss>
		</item>
				
		<item>
			<title><![CDATA[Where Are My Bioengineered Ecologies?]]></title>
			<description><![CDATA[
<p><img src="http://cache.gawker.com/assets/images/8/2008/06/thumb160x_terraform_mars.jpg" class="left image158" width="158" /> <em>It's another installment of <a href="http://io9.com/tag/ask-a-biogeek/">Ask a Biogeek</a>, a column where UC Berkeley biology researcher Terry Johnson answers all your questions &mdash; especially the weird ones.</em><br>
<br>
Reader Daniel wonders:</p>
<blockquote>As a biologist who studies whole organisms and populations, I find that more and more of biology (in terms of funding, positions and emphasis) is going to the sub-organismal level. We now have lots of cell biologists, geneticists, neurologists, biochemists, biomechanics, bioengineers and so on, but not a lot of behaviorists, population ecologists, biodemographers and others who study the emergent properties that arise at the higher levels of organization. What role, if any, do you foresee for understanding of these higher level biological phenomena in the future sci-fi-ish stuff?</blockquote>
I believe we're rapidly reaching the point where scientists will be both ready and able to consider artificially-induced emergent biological properties &mdash; in other words, terraforming. Let me take you on a tour of today's state-of-the-art in this emerging field.
<p>As far as emerging biotechnology goes, science fiction grapples more frequently (if not always very seriously) with issues of organismal or ecological impact than the scientific establishment. There are good reasons for this. Ecological ruminations are a tradition for the authors, and the scientists have - until quite recently - been limited by technical considerations. As a scientist, I hope the title Planetary Ecologist will go on someone's tax return someday.</p>
<p><img alt="GW193H292.jpg" src="http://io9.com/assets/resources/2008/06/GW193H292.jpg" width="193" height="292" align="left" hspace="4" vspace="2"><br>
<a href="http://dunepedia.wetpaint.com/page/Sandworm">A Sandworm of Arrakis, from Frank Herbert's <i>Dune</i>.</a></p>

<p>Some would say that Frank Herbert's <i>Dune</i> was the beginning of ecological science fiction, but its roots go much deeper than that. Every time an author has imagined an alien world and then tried to fill it with beings capable of surviving on it, that author is grappling with issues of ecology, and every time an author has decided how those aliens would act, they were engaging in a bit of recreational behaviorism. Herbert elevated the tone and raised the bar, no doubt, but there is a long-standing tradition of biological and behavioral what-if in SF. The rise of environmentalism coupled with another favorite SF theme - dystopianism - brought us the environmental disaster subgenre, from the ridiculous <i>The Day After Tomorrow</i> to more thoughtful treatments like <a href="http://en.wikipedia.org/wiki/Kim_Stanley_Robinson">David Brin</a>'s <i>Earth</i> or the works of <a href="http://en.wikipedia.org/wiki/Kim_Stanley_Robinson">Kim Stanley Robinson</a>.</p>
<p><img alt="275px-TerraformedMarsGlobeRealistic.jpg" src="http://io9.com/assets/resources/2008/06/275px-TerraformedMarsGlobeRealistic.jpg" width="275" height="275" class="left"></p>
<p><a href="http://en.wikipedia.org/wiki/Colonization_of_Mars">Mars (with a little terraforming and a lot of luck).</a></p>
<p>While there are (of course) ecologists in the scientific community, there are very few thus far that bridge the gap between research at the molecular level and ecologies larger than a tissue culture dish. This is not to imply that ecologists are ignorant of molecular biology; the field has generated far too many useful tools for that. The bioengineers and cell biologists who are designing new organisms at the molecular level, on the other hand, are not always well versed in the basics of ecology and evolution. They are necessarily focused on what one scientist has called <a href="http://www.nature.com/nature/journal/v450/n7172/abs/nature06523.html">the molecular sociology of the cell</a>.</p>
<p>Up until quite recently it would have been ludicrous to expect a molecular biologist to consider the higher-level environmental interactions of, for example, a particular gene, because he or she was still trying to figure out (at a molecular level) what the damn gene did to the cell itself. Take a peek at <a href="http://www.studiodaily.com/main/technique/tprojects/6850.html">the inner life of a cell</a> (if you haven't seen if before). A single cell is a giant bag of confusion. Trying to sort out web of interactions between the thousands of molecules present in hundreds of compartments using the technology at hand has been compared to figuring out the rules for a game of football using only pictures of the field (that only show certain players) at various times. This is why many researchers like to work with single cells instead of a cell in its natural environment, whatever that is - the cell alone is complicated enough. Experimental limitations or therapeutic concerns often require an intimate knowledge of a single organism's physiology, effectively tying a researcher to a single animal. Heinlein said, "Specialization is for insects". I would add grad students to the list.</p>
<p>Take <i>E. coli</i> as an example. We've had its genome sequenced for over a decade. Type its name into <a href="http://scholar.google.com/scholar?q=e%20coli">Google Scholar</a> and you'll find over 1.5 million hits. Yet programming this bacteria - <a href="http://en.wikipedia.org/wiki/Synthetic_biology">synthetic biology</a> - is still a difficult and time-consuming process. When The University of Texas at Austin's entered their <a href="http://www.utexas.edu/features/2005/bacteria/">light-sensitive pigment-producing bacteria biofilm</a> in the intercollegiate Genetically Engineered Machine (iGEM) contest, they realized that their achievement barely scratched the surface - that the "program" they'd written into the bacteria was relatively simple compared to the programming it already used to survive. In recognition of this fact, they produced perhaps my favorite <a href="http://en.wikipedia.org/wiki/Hello_world_program">"Hello world"</a> program ever.</p>
<p><img alt="UT_HelloWorld.jpg" src="http://io9.com/assets/resources/2008/06/UT_HelloWorld.jpg" width="300" height="295" class="left"><br>
<a href="http://en.wikipedia.org/wiki/Image:UT_HelloWorld.jpg">10 GOTO e. coli 20 Hack it genetically to turn it into a light-sensitive film</a></p>
<p>It's also important to note that almost all of the engineered cells and organisms made today are never meant to be released in the environment (and wouldn't be likely to survive in it if they did). Those that aren't created purely for research purposes are typically meant to live in small, artificial, and easily replaceable ecologies, like bioreactors in a pharmaceutical company or fermenters in a winery.</p>
<p><img alt="bacteria4.jpg" src="http://io9.com/assets/resources/2008/06/bacteria4.jpg" width="350" height="233" class="left"><br>
<a href="http://www.utexas.edu/features/2005/bacteria/">Either the bacteria are doing what they've been programmed to or we have a serious Cthulhu problem.</a></p>
<p>Genetically modified foods are a special case, but as a special case they've already received the most attention by ecologists. GM organisms that are designed to move outside of the lab enter the purview of the ecologists.</p>
<p>While disciplines like <a href="http://en.wikipedia.org/wiki/Bioinformatics">bioinformatics</a> combine computational and molecular biology with evolutionary studies, increasingly complicated bioengineered organisms designed for the wild will require the ability to effectively model the ecologies they were designed for. In brief, once we're good enough at figuring out how to make a cell jump or play dead, the next frontier of design will be figuring out <i>when</i> we want a cell to jump or play dead, considering its surroundings. <em>Top image via <a href="http://www.tranism.com/weblog/">Electro-Plankton</a>.</em></p>
<p><strong>Do you have questions you've always wanted to ask a biogeek? You can email me at tdj@io9.com.</strong></p>
]]></description>
			<link><![CDATA[http://io9.com/394481/where-are-my-bioengineered-ecologies]]></link>			<guid isPermaLink="false"><![CDATA[io9-394481]]></guid>
			<category><![CDATA[ask a biogeek]]></category>
			<category><![CDATA[dune]]></category>
			<category><![CDATA[ecology]]></category>
			<category><![CDATA[environmentalism]]></category>
			<category><![CDATA[feature]]></category>
			<category><![CDATA[mars]]></category>
			<category><![CDATA[synthetic biology]]></category>
			<category><![CDATA[top]]></category>
			<pubDate><![CDATA[Thu, 05 Jun 2008 09:00:00 PDT]]></pubDate>
			<dc:creator><![CDATA[Terry Johnson]]></dc:creator>
			<wfw:commentRss>http://io9.com/index.php?op=postcommentfeed&amp;postId=394481&amp;view=rss&amp;microfeed=true</wfw:commentRss>
		</item>
				
		<item>
			<title><![CDATA[Where Are My Cybernetic Implants?]]></title>
			<description><![CDATA[
<p><img src="http://cache.gawker.com/assets/images/8/2008/05/thumb160x_cyberarm10.jpg" class="left image158" width="158" /> A reader who would like to remain anonymous asks:</p>
<blockquote>As a disabled person whose body is basically falling apart (details too gross to go into), I've been wondering for a long time when I can get my cyborg transformation underway. What's the status of materials that are compatible with being implanted in the body?</blockquote>
First of all, Anonymous, my best wishes. I hope that the next advance coming 'round the bend is a comfort to you. There are two fundamental approaches to organ-level repair: the biological approach, which includes transplants and <a href="http://io9.com/375688/forget-the-jetpack-+-where-are-my-replacement-organs">tissue engineered organs</a>, or what we'll call the cybernetic approach, which creates replacements out of artificial materials capable of appropriately interacting with the body. Keeping this in mind, let's take a look at the cutting edge of human-machine interfaces.
<p><br>
The use of the term "cybernetic" hints at where the difficulty lies - traditionally, cybernetics is the study of the interactions within complex systems with an emphasis on feedback and control. The body is a terrifically complex system, which can be maddening to meddle with - surprisingly forgiving in some respects, infuriatingly recalcitrant in others.</p>
<p>Full disclosure - I'm a cyborg. I wear corrective lenses and shoes that modify my feet appropriately for an urban environment. It's not exactly Robocop, true, but according to the loosest definition, most of us already have a complicated relationship with technology blurring the line between "me" and "stuff." It's not a relationship that's going to get simpler. The relatively simple implants and prosthetics of today will soon give way to devices that interface more completely and naturally with the body. We have a number of <a href="http://en.wikipedia.org/wiki/Biocompatibility">biocompatible</a> materials available to us already, from titanium to various polymers. They aren't perfect by any means, but the body can be surprisingly accommodating.</p>
<p>Sometimes you can avoid implantation altogether with an exoskeletal assist. A weakened body can recover some of its strength via an exoskeleton that senses an intended motion of the wearer and reinforces it.</p>
<p><img alt="A070BA0E-9DA1-A982-E2844D04DDC05DC6_1.jpg" src="http://io9.com/assets/resources/2008/05/A070BA0E-9DA1-A982-E2844D04DDC05DC6_1.jpg" width="320" height="320" class="left"></p>
<p><a href="http://www.sciam.com/article.cfm?id=real-life-iron-man-exoskeleton">Stark Enterprises and Apple present: the Iron Man.</a></p>
<p>For organs no longer present, there are robotic limbs that obey commands given by the mind. The bionic limb below senses commands from the wearer and (with a lot of practice) obeys. Obviously the connection between nerve and the robot limb is unusual, but the brain is pretty good at making unfamiliar signals familiar with use.</p>
<p><img alt="070719-bionic-hand_big.jpg" src="http://io9.com/assets/resources/2008/05/070719-bionic-hand_big.jpg" width="461" height="281" class="left"></p>
<p><a href="http://news.nationalgeographic.com/news/2007/07/070719-bionic-hand.html">"They tell you to try and think as if you have two hands."</a></p>
<p>Even entire arms can be replaced, by rerouting the motor nerves that control the arm to the chest where they can be read by the robotic arm's shoulder mount.</p>
<p><img alt="Picture4.jpg" src="http://io9.com/assets/resources/2008/05/Picture4.jpg" width="600" height="468" class="left"></p>
<p><a href="http://news.bbc.co.uk/2/hi/health/5348458.stm">A not-so-phantom limb.</a></p>
<p>Having a cybernetic limb sounds great until you consider how much you depend upon your sense of touch. Walking with a leg that's asleep is no mean feat, and have you ever tried to eat a meal fresh from the dentist before the novocane wears off? Sure, your shiny robot hand is sturdy, but the wineglass you want to pick up with it isn't - and just because the hand won't be damaged by that hot stove doesn't mean the flesh attached to your extremely conductive prosthesis won't be. The first thing they did after fitting Luke Skywalker with a replacement was test to see that he could feel with it.</p>
<p><img alt="LukeHand.jpg" src="http://io9.com/assets/resources/2008/05/LukeHand.jpg" width="500" height="267" class="left"></p>
<p><a href="http://www.iratemds.com/?p=42">"I will become a jedi, bite off more than I can chew, and get my hand lopped off...like my father before me."</a></p>
<p>When the sensory nerves connecting the brain to the missing limb are also rerouted to the chest, a touch on the patient's chest <a href="http://www.technologyreview.com/Biotech/19759/?a=f">can feel like someone's brushing against fingers that are no longer there, or stretching skin that no longer exists</a>. While the recovered sensations are currently somewhat random, further research into the phenomena along with a robot arm including sensors that feed back to the sensory nerves in the chest could give us cybernetic replacements capable of being tickled.</p>
<p>Astounding as these interfaces are, the devices themselves are still wearable - that is to say, removable. We won't neglect the truly implantable devices. For example, Matt Nagel, though quadriplegic, can use the 96 electrodes implanted into his motor cortex to move a cursor on a computer screen or command a robot arm by thought alone.</p>
<p><img alt="Picture2.jpg" src="http://io9.com/assets/resources/2008/05/Picture2.jpg" width="420" height="296" class="left"></p>
<p><a href="http://www.nature.com/nature/journal/v442/n7099/full/442125a.html">Matt Nagel wills his computer into action.</a></p>
<p>The senses have not been neglected, either. Though the resolution of existing bionic eye implants is as of yet only in the tens of pixels, these devices allow the wearers enough vision to dramatically improve their quality of life. No word yet on whether they'll come in <a href="http://en.wikipedia.org/wiki/Molly_Millions">mirrorshades</a>.</p>
<p><img alt="_42581541_bionic_eye2_416.gif" src="http://io9.com/assets/resources/2008/05/_42581541_bionic_eye2_416.gif" width="416" height="215" class="left"></p>
<p><a href="http://news.bbc.co.uk/2/6368089.stm">A bionic retinal implant.</a></p>
<p>Finally, there is the <a href="http://en.wikipedia.org/wiki/Cochlear_implants">cochlear implant</a>, used regularly by over 100,000 people worldwide to directly stimulate the auditory nerves of the deaf or extremely hard of hearing. These have been around since the late '70s, but only recently has the technology become advanced and popular enough to encourage <a href="http://www.wired.com/wired/archive/13.11/bolero_pr.html">users to hack their own implants</a>.</p>
<p>You'll know that the human-machine interface has truly arrived when the first thing you do post-implantation is replace the standard firmware with an open-source alternative.</p>
<p><em>Terry Johnson is a biology researcher at UC Berkeley and io9's resident biogeek. If you have a question you'd like Terry to answer, email him at: tdj@io9.com.</em></p>
]]></description>
			<link><![CDATA[http://io9.com/391064/where-are-my-cybernetic-implants]]></link>			<guid isPermaLink="false"><![CDATA[io9-391064]]></guid>
			<category><![CDATA[ask a biogeek]]></category>
			<category><![CDATA[bionics]]></category>
			<category><![CDATA[cybernetics]]></category>
			<category><![CDATA[feature]]></category>
			<category><![CDATA[neuromancer]]></category>
			<category><![CDATA[star wars]]></category>
			<category><![CDATA[top]]></category>
			<pubDate><![CDATA[Thu, 22 May 2008 09:00:00 PDT]]></pubDate>
			<dc:creator><![CDATA[Terry Johnson]]></dc:creator>
			<wfw:commentRss>http://io9.com/index.php?op=postcommentfeed&amp;postId=391064&amp;view=rss&amp;microfeed=true</wfw:commentRss>
		</item>
				
		<item>
			<title><![CDATA[Where Is My Uterine Replicator (AKA Artificial Womb)?]]></title>
			<description><![CDATA[
<p><img src="http://cache.gawker.com/assets/images/8/2008/05/340x_artificial-womb.jpg" class="left image340" width="340" /> Reader Karen asks:</p>
<blockquote>One of my favourite sci-fi conceits in the Vorkosigan works of Lois McMaster Bujold is the uterine replicator. Sticking a fetus in a regulated jar until it's come full term and I can get my new baby boy, girl or hermaphrodite without all the vomiting, constant peeing, strenuous pushing, pooping on the operating table, and possible endangerment to life, reproductive organs and blood sugar levels sounds like fucking bliss. When can you get that to me?</blockquote>
Given the risk - and many months of what can charitably be termed "inconvenience" - what are the alternatives to signing up for nine months of incubator duty? Let's find out.
<p>The design (and I use the term very loosely) of the female reproductive system <a href="http://scienceblogs.com/denialism/2007/11/ask_a_scienceblogger_which_par.php">leaves a lot</a> <a href="http://en.wikipedia.org/wiki/Puerperal_fever">to be desired</a>. Having a baby has been <a href="http://en.wikipedia.org/wiki/Maternal_death">a dangerous proposition</a> for most of human history. Historically one out of every hundred births resulted in the death of the mother. Modern health care can reduce that mortality ratio to nearly 1 out of every 10,000 births, but it is not (and never will be) entirely safe.</p>
<p>While our large craniums and upright posture have their advantages, <a href="http://www.newscientist.com/channel/being-human/human-evolution/mg13818742.900.html">they make traveling the birth canal an ordeal</a>. If you don't believe me, compare the size of the infant cranium (black rectangle) to the pelvic inlet (white rectangles) for humans and a few of our primate cousins.</p>
<p><img alt="pelvis.jpg" src="http://io9.com/assets/resources/2008/04/pelvis.jpg" width="629" height="217" class="left"></p>
<p><a href="http://www3.interscience.wiley.com/journal/110541076/abstract">This is why they call it "labor".</a></p>
<p>The geometry does more to engender sympathy than confidence. Artificial wombs have appeared variously in science fiction, from Aldous Huxley's <a href="http://en.wikipedia.org/wiki/Brave_New_World"><em>Brave New World</em></a> to <a href="http://www.imdb.com/title/tt0121765/"><em>Star Wars</em></a> and <a href="http://www.imdb.com/title/tt0133093/"><em>The Matrix</em></a>.</p>
<p><img alt="matrix04.jpg" src="http://io9.com/assets/resources/2008/04/matrix04.jpg" width="650" height="390" class="left"></p>
<p><a href="http://www.cyberpunkreview.com/movie/essays/understanding-the-matrix-trilogy-from-a-man-machine-interface-perspective/">Adorable and energy-effective!</a></p>
<p>The Force may have a strong effect on the weak minded, but good luck trying to convince a few million surrogate mothers that bringing a Stormtrooper to term would be a joy.</p>
<p><img alt="hatchery.jpg" src="http://io9.com/assets/resources/2008/04/hatchery.jpg" width="267" height="150" class="left"></p>
<p><a href="http://www.starwars.com/databank/location/tipocacity/?id=eu">These are not the wombs you're looking for.</a></p>
<p>Iain M. Banks' <i>Culture</i> novels, on the other hand, tend more towards "natural" births, though the mother's body has been extensively bioengineered for safety and choice. Culture citizens have conscious control over their own fertility, and can store a fertilized egg in stasis for years - their pregnancies have a snooze button.</p>
<p>Whether you'd prefer a new and improved reproductive system installed as a replacement for your own or external to yourself (say, next to the washing machine), there are a few recent advancements bringing it a step closer to reality. An emulsified liquid blood substitute called <a href="http://en.wikipedia.org/wiki/Perflubron#Medical_treatment">perflubron</a> has had some success used as a replacement for amniotic fluid for premature babies in respiratory distress. It's not a complete replacement for the complex stew of hormones, lipids, and proteins normally present in the amniotic fluid, it is at least a promising way to get oxygen into developing lungs.</p>
<p><img alt="b604923k-f3.gif" src="http://io9.com/assets/resources/2008/04/b604923k-f3.gif" width="354" height="503" class="left"></p>
<p><a href="http://www.rsc.org/delivery/_ArticleLinking/DisplayHTMLArticleforfree.cfm?JournalCode=JM&Year=2006&ManuscriptID=b604923k&Iss=43">Believe me, the mouse is as surprised as you are.</a></p>
<p>Even if we had a tank filled with a healthy, fully-functional amniotic replacement, we'd need an organ to make use of it. Researchers at Cornell University's Center for Reproductive Medicine and Infertility have built <a href="http://www.popsci.com/scitech/article/2005-08/artificial-wombs?page=1">primitive tissue engineered uteruses</a> using cells donated by infertile patients. Human embryos (left over from in vitro fertilizations) successfully implanted upon these multilayered constructs and gestated for 10 days. After that the experiments were ended - full-term experiments with mice have had very mixed results, but even being able to implant upon such a device is a serious achievement.</p>
<p>Once these engineered uteruses are perfected, we'll presumably have the option of surgically implanting them. Uterus transplants in animals as large as ewes have demonstrated that they can, at least, <a href="http://www.newscientist.com/article.ns?id=dn11501">be removed and re-implanted without loss of function</a>. Attempts to do the same in humans have <a href="http://query.nytimes.com/gst/fullpage.html?sec=health&res=9F01EFDC1230F934A35750C0A9649C8B63">thus far failed</a>, but <a href="http://query.nytimes.com/gst/fullpage.html?sec=health&res=9F01EFDC1230F934A35750C0A9649C8B63http://www.washingtonpost.com/wp-dyn/content/article/2007/01/14/AR2007011401091.html">we haven't stopped trying</a>.</p>
<p>Combine a fully-functioning uterus with a setup like Tokyo's Juntendo University's and instead of transplantation you could achieve ectogenesis - fetal development outside of the human body. Their bioreactor <a href="http://www.newscientist.com/article/mg15520924.400-heres-looking-at-you-kid.html">could bring goats to term</a> (not always successfully) by pumping in nutrients and removing waste. Of course, the goats still needed to do most of their developing in a natural womb, but combine this apparatus with a uterus engineered from your own tissue, and maybe you'd have initial implantation and the tail-end of pregnancy covered.</p>
<p>As surprising and weird as this all is, we're still many decades away from a safe, human uterine replicator that can bring an embryo from conception to zeroeth birthday party. Even once we've sorted out the technical aspects of the womb itself, we'll have to deal with what the rest of the mother's body contributes to development. Hormones have already been mentioned, but baby also borrows mommy's disease-fighting machinery. Our replicator will require nearly complete endocrine and immune systems, too.</p>
<p>All in all, I'd take a serious look at adoption.</p>
<p><em>Terry Johnson is a biology researcher at UC Berkeley and io9's resident biogeek. If you have a question you'd like Terry to answer, email him at: tdj@io9.com.</em></p>
]]></description>
			<link><![CDATA[http://io9.com/385976/where-is-my-uterine-replicator-aka-artificial-womb]]></link>			<guid isPermaLink="false"><![CDATA[io9-385976]]></guid>
			<category><![CDATA[ask a biogeek]]></category>
			<category><![CDATA[bujold]]></category>
			<category><![CDATA[feature]]></category>
			<category><![CDATA[star wars]]></category>
			<category><![CDATA[the matrix]]></category>
			<category><![CDATA[top]]></category>
			<category><![CDATA[uterine replicator]]></category>
			<pubDate><![CDATA[Thu, 08 May 2008 09:00:00 PDT]]></pubDate>
			<dc:creator><![CDATA[Terry Johnson]]></dc:creator>
			<wfw:commentRss>http://io9.com/index.php?op=postcommentfeed&amp;postId=385976&amp;view=rss&amp;microfeed=true</wfw:commentRss>
		</item>
				
		<item>
			<title><![CDATA[Where Is My Medical Tricorder?]]></title>
			<description><![CDATA[
<p><img src="http://io9.com/assets/resources/2008/04/dfxw3jg8_129hspv2kgc_b.jpg" class="left image500" width="500" /> Reader Juan asks:</p>
<blockquote>If not the medical tricorder from Star Trek, when could we possibly see diagnostic equipment capable of scanning for infections, viruses or impending heart attacks, attached to wrist watches or other portable devices?</blockquote>
Nothing against the phaser, but for many of us the most coveted piece of away team equipment is the <a href="http://memory-alpha.org/en/wiki/Starfleet_tricorder">tricorder</a>, the <a href="http://memory-alpha.org/en/wiki/Medical_tricorder">medical version</a> of which can perform a complex examination in a single whistling pass over a patient. If you've ever tried to lie perfectly still in a thumping MRI machine or sat in a doctor's office waiting for lab results, you've longed for faster, more portable diagnostic devices.
<p><img alt="aliveekg.jpg" src="http://io9.com/assets/resources/2008/04/aliveekg.jpg" width="200" height="253" align="left" hspace="4" vspace="2"> If you're interested in your EKG or your glucose level, you may have to find a tricorder ringtone for your iPhone. <a href="http://www.foxnews.com/story/0,2933,289898,00.html">Wearable heart monitors with Bluetooth</a> are well on their way to market. Not only could a doctor remotely monitor a patient using a PocketPC such as the <a href="http://www.alivetec.com/products.htm">Alive EKG</a> (at left), there's no reason why a patient's bluetooth-enabled cell phone couldn't be used to automatically alert a physician in case of emergency, too.</p>
<p>Impressive as that is, I'm a firm supporter of devices with lasers over devices without lasers. This <a href="http://www.medgadget.com/archives/2007/08/portable_digitizer_for_wound_monitoring.html">laser digitizer</a> (below), when attached to a PDA, can be used to record the width and depth of a healing wound - helping doctors and nurses better track patient progress. The PDA, called the <a href="http://www.aranzmedical.com/products.htm">ARANZ Medical Silhouette</a>, can then be used to upload measurements and images into a patient file. I challenge anyone to use this device without feeling like you are living in the future.<br>
<img alt="aranzmedicalsilhouette.jpg" src="http://io9.com/assets/resources/2008/04/aranzmedicalsilhouette.jpg" width="500" height="356" align="left" hspace="4" vspace="2"></p>
<p><img alt="cellscope.jpg" src="http://io9.com/assets/resources/2008/04/cellscope.jpg" width="250" height="219" align="left" hspace="4" vspace="2"> Not every portable monitoring device needs to be quite so high tech. Patients in rural areas and the third world often do not have physical access to doctors - but for many applications, they might be able to do without. The <a href="http://medgadget.com/archives/2008/03/cellscope_for_rural_microscopy_on_the_go.html">CellScope</a> (at left) aims to turn an ordinary cell phone camera into a "telemicroscope" capable of sending high-magnification images of skin or blood samples to a doctor for remote diagnosis. An inexpensive alternative to a long trip for a routine diagnosis, and the speed at which the information can reach a physician makes this a potentially valuable tool for keeping real-time track of disease outbreaks.</p>
<p>The gold standard for infectious disease monitoring in patients is usually a blood test for a biomarker molecule of some sort. While we can't yet wave a device over someone and know that much about the contents of their blood, we may be soon be able to miniaturize the equipment necessary to perform the analysis. Electronic noses, for example, may soon be able to diagnose diseases by smell (with a little help from <a href="http://news.bbc.co.uk/2/hi/technology/6614567.stm">a layer of artificial mucus</a>) - if <a href="http://www.newscientist.com/article.ns?id=dn8549">a dog can be trained to smell cancer on a patient's breath</a>, why not?</p>
<p>Microfluidic lab-on-a-chip technologies (pictured below) can already be used to determine <a href="http://www.sandia.gov/news/resources/releases/2007/saliva.html">the presence and extent of gum disease</a> by testing for biomarkers present in a few microliters of saliva. Researchers aim to pack everything the device requires <a href="http://www.sciencedaily.com/releases/2005/02/050210005401.htm">into a 5-pound package</a>, and to develop similar chips for other diseases. If you'd like to avoid getting the disease in the first place, real-time infectious disease monitors can be used as an early-warning system, with prototypes currently capable of detecting the presence of <a href="http://www.mtbeurope.info/news/2006/606008.htm">the avian flu virus</a>. While there's plenty of tweaking to do before these silicon chip-based sensors are installed in hospital air vents or worn by soldiers in the battlefield, the alternatives to early detection range from a mild fever to coughing up blood - followed by extensive tests to reveal why you have a mild fever or are coughing up blood. Far better to know what's coming so that we can limit exposure and treat the disease as early as possible.</p>
<p><img alt="microfluidichips.jpg" src="http://io9.com/assets/resources/2008/04/microfluidichips.jpg" width="500" height="403" align="left" hspace="4" vspace="2"><br>
If these possibilities aren't tantalizing enough to interest you in medical miniaturization, keep in mind that Gene Roddenberry inserted a clause into his contract stating that <a href="http://memory-alpha.org/en/wiki/Tricorder">anyone who can build a tricorder can use that name to describe the device</a>. One company has <a href="http://www.stim.com/Stim-x/0996September/Sparky/tricorder.html">already combined</a> an EMF meter, light and colorimeter, barometer, thermometer, and clock into a tricorder, but the medical version is as of yet unrealized. If you succeed, a warning - reversing the polarity on any of these devices is more likely to bugger its electronics than allow it, like most technologies on Star Trek, to perform impossible feats critical to the plot.</p>
<p><em>Terry Johnson is a biology researcher at UC Berkeley and io9's resident biogeek. If you have a question you'd like Terry to answer, email him at: tdj@io9.com.</em></p>
]]></description>
			<link><![CDATA[http://io9.com/380780/where-is-my-medical-tricorder]]></link>			<guid isPermaLink="false"><![CDATA[io9-380780]]></guid>
			<category><![CDATA[ask a biogeek]]></category>
			<category><![CDATA[biology]]></category>
			<category><![CDATA[feature]]></category>
			<category><![CDATA[medicine]]></category>
			<category><![CDATA[science]]></category>
			<category><![CDATA[star trek]]></category>
			<category><![CDATA[top]]></category>
			<category><![CDATA[tricorder]]></category>
			<pubDate><![CDATA[Thu, 17 Apr 2008 09:00:00 PDT]]></pubDate>
			<dc:creator><![CDATA[Terry Johnson]]></dc:creator>
			<wfw:commentRss>http://io9.com/index.php?op=postcommentfeed&amp;postId=380780&amp;view=rss&amp;microfeed=true</wfw:commentRss>
		</item>
				
		<item>
			<title><![CDATA[Forget the Jetpack - Where Are My Replacement Organs?]]></title>
			<description><![CDATA[
<p><img src="http://io9.com/assets/resources/2008/04/whole_heartB_x220.jpg" class="left image500" width="500" /><em>Welcome to <strong>Ask a Biogeek</strong>, a column about cutting-edge biology by UC Berkeley researcher Terry Johnson.</em> Knowing <a href="http://io9.com/356738/how-many-of-your-internal-organs-can-you-live-without">which organs you can live without</a> is all well and good, but wouldn't you rather have replacement organs? Tissue engineers already have some pretty good ones if you happen to lose your skin or severely damage your bones. And there are some other organs we're cooking up for you too, as long as you can hold out for a few more years.</p>

<p>Tissue engineered skin has been used on humans since 2001, though initially <a href="http://ithaca.rice.edu/kz/USAToday/SkinArticle.htm">it was merely a replacement for cadaver skin</a> as a temporary solution for burn patients whose skin was damaged too extensively to consider skin grafts. More permanent solutions designed to more closely mimic the structure of skin are on the way, with several different designs currently under research or in the clinic. We're a long way from a tissue engineered donor-free <a href="http://news.bbc.co.uk/1/hi/health/4484728.stm">face transplant</a>, but we'll get there. There are non-medical benefits to this work as well - a variation on tissue engineered skin called <a href="http://www.newscientist.com/article.ns?id=mg19526144.100">Episkin</a> is being marketed in Europe as an alternative to animal testing of cosmetics.</p>
<p>One of the advantages of skin from an engineer's point of view is that it's easy to feed. Thin sheets do not require a system of blood vessels to supply the cells inside the sheet with adequate oxygen and fuel. Cartilage is another tissue that can do pretty well without a vasculature, and has a tendency to heal poorly - a combination that sends clinical researchers off to write grants. If you're looking at total knee replacement in the future, keep in mind that there's already <a href="http://www.carticel.com/default.aspx">one therapeutic alternative</a> and <a href="http://www.eurekalert.org/pub_releases/2007-05/bpl-tes050907.php">several others in the works.</a></p>
<p>If you're a sports fan, at one time or another you've probably had your team's season imperiled by a player's torn ligament. While these lingering injuries may be a boon to broadcasters and sports writers, for athletes they can be career-ending events. A biodegradable polyester combined with cells from undamaged ligament may be the solution - in rabbit knees, <a href="http://environment.newscientist.com/article.ns?id=dn11214">these engineered ligament replacements already rival transplants</a>. The thing about a transplant is, that transplant tissue has to come from somewhere. If from another body, you've got tissue rejection to look forward to. If from you, getting there requires a scalpel and seriously good painkillers. These engineered alternatives, using cells from the patient cultured outside of the body, do a lot less hurting to get to the healing.</p>
<p><img alt="ctcscanjaw270804.jpg" src="http://io9.com/assets/resources/2008/04/ctcscanjaw270804.jpg" width="200" height="176" class="left">Most bone breaks heal on their own with a little immobilization, but not all, and fractures aren't the only problem one can have with bone. A man in Finland lost his upper jaw to a tumor, <a href="http://www.reuters.com/article/scienceNews/idUSL012172320080201">but doctors were able to create a replacement.</a> A biomaterial scaffold was created in the shape of the missing part, then seeded with mesenchymal stem cells from a culture of the cells in a sample of the patient's fat. The whole device was then implanted in the man's abdomen, where it was given nine months to develop before being removed and implanted into the jaw. That may sound a little roundabout, but considering the only other option was hacking enough bone out of the man's leg to rebuild the jaw, you can see the attraction. Similar work has been done in Germany <a href="http://www.abc.net.au/science/articles/2004/08/27/1186625.htm">using the patient's back as an incubator</a> instead of the abdomen, giving you a potential choice of scars as well.</p>
<p>If that same fellow ended up a few teeth shy, or you're worried about encroaching denturehood, engineered <a href="http://www.newscientist.com/article.ns?id=dn11204">teeth</a> are possible as well - in mice. Until it's working in humans, I strongly suggest you floss regularly.</p>
<p>There's a lot of exciting work in kidneys, but if you know any potential donors try and stay on their good side. There are already a few <a href="http://www.washingtonpost.com/wp-dyn/content/article/2006/04/03/AR2006040301387.html">tissue engineered bladders</a> engaged in their usual duties inside patients.</p>
<p>Heart disease is a leading cause of death in the United States, and to some, the holy grail of tissue engineering. <a href="http://web.mit.edu/newsoffice/2007/vascular-1217.html">Replacing clogged blood vessels</a> or valves with healthy engineered tissue would save lives and wear and tear on the parts of the body where we usually go scrounging for healthy vessels to replace the damaged bits with. It doesn't get much tricker than a complete engineered heart transplant - a machine that requires incredible timing, physical power, a highly specific vasculature, and most importantly, a vanishingly small failure rate. One approach is to cheat - that is, <a href="http://www.technologyreview.com/Biotech/20058/">take an existing donor heart and remove all of the cells, leaving the structure intact.</a> The deheartinated hearts are then seeded with heart cells from the would-be patient. Rat hearts treated in this manner can be <a href="http://www.stemcell.umn.edu/stemcell/faculty/Taylor_D/home.html">coaxed into beginning to beat anew</a>, though as of yet not hard enough to replace an ailing ticker.</p>
<p>Do you have questions you've always wanted to ask a biogeek? You can email me at tdj@io9.com.</p>
]]></description>
			<link><![CDATA[http://io9.com/375688/forget-the-jetpack-+-where-are-my-replacement-organs]]></link>			<guid isPermaLink="false"><![CDATA[io9-375688]]></guid>
			<category><![CDATA[ask a biogeek]]></category>
			<category><![CDATA[biology]]></category>
			<category><![CDATA[feature]]></category>
			<category><![CDATA[tissue engineering]]></category>
			<category><![CDATA[top]]></category>
			<pubDate><![CDATA[Thu, 03 Apr 2008 09:45:57 PDT]]></pubDate>
			<dc:creator><![CDATA[Terry Johnson]]></dc:creator>
			<wfw:commentRss>http://io9.com/index.php?op=postcommentfeed&amp;postId=375688&amp;view=rss&amp;microfeed=true</wfw:commentRss>
		</item>
		</channel>
</rss>
