The DNA Network |
| Stephen Colbert, Microbe Fan [The Daily Transcript] Posted: 29 May 2008 08:42 PM CDT |
| Programming and science education [business|bytes|genes|molecules] Posted: 29 May 2008 07:58 PM CDT From a discussion on /.
As a computational scientist (and with both a physical and a life science background), that such arguments still happen is appalling. IMO, all scientists, especially those remotely connected to theory and/or computational science should be given the opportunity to learn some formal software engineering and computer science principles (for physical chemists, bioinformaticians, etc is should be mandatory to do some courses). Everything I know, which is not much, is self taught. It’s the princples and practices that are important, not the specifics. Have seen way too much noodly, unmaintainable code and bad hacks over the years (including my own). Perhaps things have changed, but apparently not that much, and given attitudes towards software engineering in academia, I seriously doubt it. Technorati Tags: Software Engineering, Programming, Science, Education  |
| Chicken Development - Sunny-side up [Bayblab] Posted: 29 May 2008 07:04 PM CDT  Check out a series of photos of a chicken developing. The very early ones are especially interesting. Now I know what to look for if I think that my breakfast has been fertilized. |
| Genetic Variation II: What is a RFLP? [Discovering Biology in a Digital World] Posted: 29 May 2008 06:52 PM CDT RFLP is an acronym that stands for "Restriction Fragment Length Polymorphism." That's quite a mouthful and once you've said this phrase a few times, you realize why we use the initials instead. I know a Restriction Fragment Length Polymorphism sounds like something that must be impossibly complicated to understand, but if we take the name apart, it's really not so bad. Read the rest of this post... | Read the comments on this post... |
| The Future of Cell Biology - Part I - Organellar Shape [The Daily Transcript] Posted: 29 May 2008 06:18 PM CDT OK this is an attempt to revive the blog. This entry is inspired by a talk given about a month ago by my mentor, Tom Rapoport. I hope that it will be the first of a series of posts where I ramble on about what we don't know. In each post I'll discuss a topic that remains mysterious. I'll try to point out what we don't fully comprehend and add my two cents. Today's topic will be organelle shape. Look inside any eukaryotic cell and you'll lots of little membranous organelles whizzing around. These membranous structures play crucial roles in various cellular activities. Very often their shape contributes to their function. Why? Think about surface area - the more membrane an organelle has, the more/less efficient certain processes are. Think about organelle contacts. Mitochondrial membranes may need to be close to certain portions of the endoplasmic reticulum (ER) in order to exchange molecules. Think about the movement of vesicles between different compartments. The Golgi is constantly losing and gaining membrane vessicles which pinch off and fuse with each Golgi stack. These vessicles travel between the Golgi and other organelles such as the ER and the endosomes. All this vesicle exchange is dictated in large part by organelle morphology and distribution. Think about transport. It may be helpful that an organelle is a rod in order for it to be translocated up and down neuronal projections. And think about other functions. For example, the nucleus shape may influence the spatial arrangement of chromosomes and thus affect gene expression. Many cells have bizarre looking nuclei, and almost nothing is know as to how the nuclear shape is altered and how this contributes to proper cellular function . So the central questions of how and why organelles are shaped are relatively fertile ground within cell biology. Read the rest of this post... | Read the comments on this post... |
| Colbert is now obsessed with Microbes [The Tree of Life] Posted: 29 May 2008 04:10 PM CDT Yes that is right, Colbert is now obsessed with Microbes. He has started a new report ... "The Microbe Beat". On this first one, Colbert discusses Martian Microbes, Penicillin and other microbial things. This is perhaps the greatest coup for getting microbes the recognition they deserve since, well, since ever. Please make this the most watched Colbert video ever. Thanks to my PhD student/employee Jenna Morgan for pointing this out. |
| Detection of Colorectal Cancer Using a Blood-based, Six-Gene Biomarker Set [Highlight HEALTH] Posted: 29 May 2008 03:13 PM CDT At the annual meeting of the American Association for Cancer Research (AACR) last month, researchers from GeneNews Corp. reported that the probability of colorectal cancer (CRC) in asymptomatic patients can be accurately stratified by RNA expression profiling of six genes in whole blood [1]. The company focuses on developing blood-based biomarker tests for the early detection of diseases and personalized health management. Stratification is a statistical method of sampling from a population, whereby members are grouped into subgroups that display a consistent feature. In the current study, the six-gene panel was able to stratify a population with average risk for CRC into three groups:
The study comes after publication of their approach to detecting blood biomarker sets earlier this year in the journal Clinical Cancer Research [2]. The study evaluated blood RNA samples from an Asian population and identified five genes in patients with CRC that could be differentiated from controls. In the study, researchers screened 31 whole blood samples from patients without CRC (n = 15) or patients with CRC (n = 16) by DNA microarray, a technology that enables scientists to examine how active thousands of genes are at a given time. They identified 37 genes unrelated to age or gender that were significantly different between controls and patients with CRC. The 37 genes were then tested with a large training set of 115 samples (57 controls, 58 CRC) using real-time PCR. 17 of the 37 genes were validated as differentially expressed. Five of the 37 validated genes were selected for logistic regression analysis. Logistic regression is a statistical model used for prediction of the probability of occurrence of an event, using predictor variables that may be either numerical or categorical. The predictive power of the five genes was then validated with a third independent set of 92 samples (49 controls, 43 CRC). The validation correctly identified 88% of CRC samples and 64% of non-CRC samples. In their most recent study, GeneNews examined more samples than previously analyzed, this time in a heterogeneous North American population. Researchers screened a training set of 243 whole blood samples from patients without CRC (n = 127) or patients with CRC (n = 116) by DNA microarray. Six genes whose expression could meaningfully discriminate between the two groups were identified [3]:
The predictive power of the six genes was then validated in a blinded, independent set of 337 samples (171 controls, 166 CRC). The combined training/blind set had an average accuracy of 70.8%. GeneNews has announced plans to develop a laboratory test later this year based on the six-gene panel called ColonSentry [4]. Similar blood screening tests are under investigation by the GeneNews for prostate, breast and ovarian cancer. Why is this important? Colorectal cancer (CRC) is the third most common cancer in both men and women with an estimated 49,960 deaths expected to occur in 2008, accounting for 9% of all cancer deaths [5]. A simple, noninvasive test that can classify average risk patients into more defined groups would help to assess an individual’s risk for CRC. Since CRC can often be treated if caught early enough, those having an increased probability could be screened more frequently. Screening can result in the detection and removal of colorectal polyps before they become cancerous. Additionally, screening can help to detect CRC that is at an early stage. Consider these statistics: when CRC is detected early, the 5-year survival rate is 90%. If the cancer has spread locally, the 5-year survival rate decreases to 68%. For patients with advanced CRC that has metastasized, the 5-year survival rate is 10% [5]. The American Cancer Society (ACS) has published guidelines for the early detection of cancer. Beginning at age 50, men and women at average risk for developing CRC should be screened with one of the following tests: Tests that find polyps and cancer
Tests that mainly find cancer
Don’t underestimate the importance of regular cancer screening. One of the reasons for a decline in CRC incidence rates since 1998 is increased surveillance. If you’re at risk, get checked. References
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| Health News in Second Life: Counseling Center [ScienceRoll] Posted: 29 May 2008 01:42 PM CDT As I have several projects in Second Life, the virtual world, I come across plenty of interesting news focusing on the health/medical aspect of virtuality.
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| Mind your P's and Q's [The Gene Sherpa: Personalized Medicine and You] Posted: 29 May 2008 01:23 PM CDT In another Hairbrained "We're not doing medicine" scheme I point your attention towards Q-Trait From the site Who shops for genetic tests? Genetic tests are not just for people with concern about... [[ This is a content summary only. Visit my website for full links, other content, and more! ]] |
| 23andMe Unveils 23andWe [BUZZYEAH » My Genome] Posted: 29 May 2008 01:16 PM CDT 23andMe just sent out an email announcing the launch of 23andWe. Awwwww another cute name.
The concept behind 23andWe is pretty simple: They provide me with easy, fun questions in survey form and I get to see how my answers compare to the rest of the 23andMe community. At the same time, 23andMe is correlating my answers to my genetic data (which they think will lead to a new way of doing genetic research). Here is a question from one of the surveys:
Here is one of my answers compared to results from the rest of the 23andMe community:
All in all, the surveys are a breeze and I can see myself doing plenty more of them in the future. Plus, there's the added bonus that I might be helping progress genetic research in some tiny way. Update: I guess 23andWe was launched at D6 today. You can read about the demo over at the D6 blog or watch the video below: |
| GINA, The Bad News: Adverse Selection [PredictER Blog] Posted: 29 May 2008 12:59 PM CDT This is the second post in a series of posts in which I share what I see as the ups and downs of the Genetic Information Nondiscrimination Act of 2008 (GINA or H.R. 493). Although the legislation will hopefully do much to encourage research and protect predictive health patients, GINA is not all roses. The legislation has numerous critics who have good reasons to be critical. For starters, it sets the stage for adverse selection to occur in the health insurance industry. Adverse selection happens when an information gap emerges between the beneficiary and the insurer; if the beneficiary knows much more than the insurer, then the insurer is unable to accurately assess the beneficiary's risk. This information imbalance results in more claims being made than the insurer reasonably predicted. GINA facilitates this phenomenon by allowing beneficiaries access to genetic information, but denying it to insurers. If, for example, a beneficiary finds out from a genetic test that he has a significantly increased risk of developing prostate cancer, he would use that information in deciding whether or not to purchase insurance, but the insurer would be unaware of that increased risk in deciding in which group the individual should be placed, what rate he should be charged, etc. This is potentially a big problem in the insurance industry, because insurers need to be able to accurately determine risk in order to prevent claims exceeding predicted levels. In the long run, inaccurate risk predictions in the industry will result in rate hikes, and rate hikes will drive healthier participants out of groups. In a the worst case scenario, this could start a downward spiral in the direction of group or insurer insolvency. - Sam Beasley |
| Be Efficient Online with RescueTime [ScienceRoll] Posted: 29 May 2008 12:58 PM CDT I have dozens of online projects (Second Life, two medical blogs, two blog carnivals, Wikipedia, etc.) so I spend quite a lot of time on the web. That’s why it’s so important to be efficient while being online. And the best tool in our hands is RescueTime.
Give it a try and let me know your feedback.         |
| Another view on the PI vs postdoc POW [Mailund on the Internet] Posted: 29 May 2008 12:16 PM CDT A little while back, I posted a few thoughts about the differences about post doc life and PI life. A different perspective is posted here: Mentorship styles. The point of view is of a grad student just starting out. It is very optimistic. I like that, but find it a bit naive, but go read it just for the different perspective! (Just so I don’t insult anyone: by naive I only mean less experienced and perhaps too optimistic. I am not saying that the post is simplistic or anything… please don’t take it the wrong way!) |
| Posted: 29 May 2008 11:52 AM CDT |
| Life science Ph.D.s as industrial strength technicians? [Discovering Biology in a Digital World] Posted: 29 May 2008 11:32 AM CDT "Why won't biotech companies hire people with Ph.D.s to be technicians?" "I already have a Ph.D., how do I find a job?" These were some of the questions that commenters left after my earlier posts (here, here and here) on biotechnology workforce shortages. Unfortunately, for these students and post-docs, the shortfall of employees in the biotech industry is largely a shortfall of technicians. It is a sad thing that promoting science careers can have the unintended consequence of creating a surplus of unhappy post-docs and even more unhappy graduate students. Perversely, many of the efforts to expand and improve science education often don't reach the students who'd be happy to be technicians. Both groups get misled by the incorrect notion that science jobs require a Ph.D. I'll tackle the job searching question in a later post, for now, let's focus on why it is that having a Ph.D. could make job searching harder. Read the rest of this post... | Read the comments on this post... |
| Oh the things we do for science… [Mailund on the Internet] Posted: 29 May 2008 11:05 AM CDT I have to get up at 4am tomorrow to get on the train for this symposium in Copenhagen. I so do not want to get up that early… It looks like a very interesting meeting, judging from the program, and I do not want to miss it. I even had to cancel a talk I was going to give at CLC Bio myself to get there, but when I saw how early I had to get up to get there, I considered staying away… I hate getting up early. I’ve gotten used to getting up around 6 am — otherwise I simply cannot manage to do all the things I plan for the day — but since I never manage to get to bed before midnight, four in the morning is a bit scary. I wonder if my alarm clock will even allow me to set such an early time for the wake up time? |
| Bayblab has more Science than Pharyngula! [Bayblab] Posted: 29 May 2008 09:20 AM CDT Kinda. Sorta. And only if you go by percentage of content. In the wake of AC's State of Science Blogging post, Stephanie Z has done some data mining. She examined the content of 5 blogs over a month of posting - Pharyngula, Greg Laden's Blog, Tetrapod Zoology, Cognitive Daily and ourselves. The results can be found in a guest post at Greg Laden's place. |
| Breakthrough: Scientists Encode Genome [Eye on DNA] Posted: 29 May 2008 03:55 AM CDT
Wow! They’ve encoded an entire genome! NOT. Usually, the reference is to a genome being decoded although there is debate surrounding the use of that terminology as well. RPM at evolgen says:
Photo credit: Walking female form, Wellcome Images via Creative Commons |
| A Study of Journalist Coverage of Research Studies [DNA and You] Posted: 29 May 2008 02:49 AM CDT The Wall Street Journal Health Blog has a very interesting post on a report card of sorts for journalist coverage of medical topics and research. The independent group performing the study, which was published in PLOS Medicine, was not particularly complementary. |
| Wiki’fied Proteins. Do You Trust Them? [] Posted: 29 May 2008 02:28 AM CDT
Wikipedia’s Jimmy Wales (most. self-referential. hyperlink. ever.) is struggling to stay relevant by trying to get a toe-hold in biotech. Boing Boing reports on WikiProteins: a collaborative space for biologists to annotate proteins.
While it’s theoretically a great idea, we’re wondering about whether – given the amount of mis-, dis- and non-information on Wikipedia (as well as tons and tons of cyber-vandalism) — the whole Open Source, Wiki collaboration model translates effectively to something as important as, say, the source code for humanity. Aren’t there enough Xtian Fundies and BioLuddites out there who’d love to monkey-wrench BioWikis as part of their ongoing efforts to keep things just like they used to be? Discuss. |
| Novel Imaging Technique in Preclinical Development: MRI Imaging of pH [Cancer and Your Genes] Posted: 29 May 2008 02:18 AM CDT A report in the journal Nature details preclinical studies of a novel imaging technique that might have relevance to cancer diagnostics or therapeutic monitoring in the future (abstract available here). Dr. Kevin Brindle and colleagues showed that by using a modified form of bicarbonate detectable by magnetic resonance imaging (MRI), pH (the degree to which a particular tissue is acidic or basic) can be imaged in vivo. Although it is still a long way from the clinic, this technology could have important future implications in oncology and other areas of medicine. |
| Interview Series II - Megan Smolenyak Smolenyak [The Genetic Genealogist] Posted: 29 May 2008 02:00 AM CDT Megan blogs about genetic genealogy and other genealogical topics at Megan’s Roots World (which I highly recommend adding to your feed reader or daily reading list). In the following interview, Megan talks about her introduction to genetic genealogy, about the field as it stands today, and about some of the possible future directions of DNA testing. The Genetic Genealogist: How long have you been actively involved in genetic genealogy, and how did you become interested in the field? Megan Smolenyak Smolenyak: I’ve been an almost lifelong genealogist, but the genetic component entered the picture for me around 1999-2000 thanks to some work I was doing with the U.S. Army. I track down families of soldiers still unaccounted for — mostly from Korea, but also Southeast Asia, WWII and even WWI. It’s my responsibility to locate the next of kin and three mtDNA candidates — in other words, three relatives of the soldier who share the same mtDNA (maternal) line. Because of this, when the first couple of companies launched in 2000, I was one of the first in line simply because I had already had the opportunity to learn the fundamentals of how DNA testing could be used for genealogical purposes. TGG: Has genetic genealogy helped you break through any of your brick walls or solve a family mystery? MSS: Definitely. My first experience with genetic genealogy was the Smolenyak tale featured in the “Did She Marry Her Cousin? episode of DNA Stories in the video player on your blog. It turned out my hypothesis was wrong, and although I was initially disappointed, I realized that I had just saved myself years of effort and who knows how much money trying to prove something that was completely false. That’s what made me an early proponent. I realized right out of the gate that DNA can sometimes resolve mysteries that the paper trail never will. TGG: Lately the news has been filled with stories about the ethical issues associated with genetic testing, largely as a result of the launch of new companies like 23andMe, deCODEme, and Navigenics. How does genetic genealogy factor into this discussion? MSS: As much as I'd like to claim that we're a different animal, the fact is that these new companies provide some ancestral information. In fact, there already seems to be slightly greater emphasis on this aspect than when they first launched, perhaps because they've realized there's an existing market. So going forward, it's virtually inevitable that the general public will intermingle genetic genealogy companies and offerings with these new tests and companies. Overall, I'm delighted with these new possibilities, but I confess there's a small part of me that's mourning a loss of innocence of sorts. Strictly genealogical tests didn't give away your secrets (well, except for the occasional NPE!), so folks could feel quite comfortable taking them. Now, with the addition of medical and other information, people will likely think twice. Having said that, I think we all knew this time was coming and I'm glad to see the field moving forward. TGG: What do you think the future holds for genetic genealogy?
MSS: My poor little brain can't fathom all the possibilities, but I believe we're entering the genomics age. The genetic genie is out of the bottle, so it's time to buckle our seatbelts and hang on (how's that for a mixed metaphor?)! I've always thought it would be the medical aspects of genetics that would drive things forward in a big way and that's clearly happening. I can't even begin to imagine all the ethical issues we'll all wrestle with, but because of the medical benefits, I think it's inevitable that genetics will become a routine part of our everyday lives. Just as we have a generation or so that's grown up taking computers and the internet for granted, I think the same will be true of genetics for those being born now. What's especially interesting to me is the public's involvement in all this. I recently interviewed with a journalist from Le Monde, and remarked that this is the first scientific revolution that will at least be partly driven by public participation. An obvious example of this is impatient genealogists applying pressure on scientists to uncover more ancestrally-informative SNPs. We do this because we want to know more about our roots. Imagine the amplification of this phenomenon when the mass public starts campaigning for specific genetic research for medical conditions that affect their families. And I suspect that the existence of companies like 23andMe will only encourage this kind of (to me, positive!) behavior. Because genetic genealogy has been around since 2000, I think anyone trying to get a handle on this interplay between the scientific community and the general public would be smart to study us. And yes, genetic genealogists will definitely benefit from all the advances. Remember, it was just circa 2000-2001 that a 4-marker Y-DNA test sold to the public was considered amazing, and now, none of us would waste our time with such a test. We ain't seen nothing yet! TGG: Aside from genetic genealogy, what other genealogy-related projects are you involved with? MSS: Phew! A lot! I already mentioned my work with the U.S. Army, but I'm also the Chief Family Historian and North American spokesperson for Ancestry.com and co-founder of RootsTelevision.com, a free, online channel of genealogical programming. And I write and speak and consult for television programs. Basically, I'm all about getting the g-word out there! TGG: Thank you, Megan, for this interesting and very enjoyable interview! Other posts in the TGG Interview Series: |
| Avoiding the lure of the internet [Bitesize Bio] Posted: 29 May 2008 12:39 AM CDT There is no doubt that the internet has revolutionised science by making information freely available. But when it comes to actually getting work done, the internet can be a problem. With all of that lovely information available right at your fingertips it’s easy to get sucked into surfing when you are trying to work. Here are 5 ways to avoid the lure of the internet and stay efficient 1. Leechblock is a Firefox extension that will block access to any website for any period you specify. So you can block all of those sites that suck up your time, or schedule a set time each day where you can view them. You could allow access to your favorite news sites only during your lunch hour, for example. 2. Temptation blocker is a bit more of a blunt instrument than Leechblock. It allows you to lock yourself out of applications for a set amount of time - so you could use it to block your browser, games, email or whatever is distracting you. If you need to get back into the application before the time is up you can, but the program makes you type in a 32-digit alphanumeric code as a disincentive before unblocking the program. 3. Deleting all bookmarks to websites that eat up your time is a simple way to make it more difficult to navigate to your favorite time-consuming site. But that can be a bit drastic as sometimes you might just want to surf. Alternatively you could use Firefox’s multiple profile capabilities to create one profile for work and one for play. 4. Mozilla’s Prism, is an intriguing piece of software that allows you to run web applications you use/need often as if they were on your desktop. So there is no need to actually open a browser, meaning less opportunity for distractions. 5. Lo-tech options.. these include unplugging/switching your wireless off while working, using pen and paper instead of a computer and exercising some self discipline(!) How do you avoid online distractions? Let us know in the comments. |
| Mice mothers devote energies to offspring when life is threatened [Think Gene] Posted: 29 May 2008 12:23 AM CDT An Iowa State University researcher has found that sick female deer mice devote their energy to producing healthier offspring. Lisa Schwanz, a researcher in the department of ecology, evolution and organismal biology, studied the size of offspring for both infected and healthy mice and found that females that had been infected with a parasite produced larger offspring than healthy females. This finding was unexpected because most mammals tend to focus on their own survival when they are threatened with sickness or infection. Schwanz’s research findings have been published in New Scientist magazine. She writes, “Organisms are predicted to decrease investment in current reproduction when parasitism has the greatest impact on current reproductive ability.” In other words, “infection in animals typically leads to responses that invest in the survival, not offspring,” Schwanz said. In deer mice, however, the opposite was happening. In the study, Schwanz infected 30 female deer mice with a parasite that lowers the future reproductive ability and eventually kills the mice. By producing larger babies now, the mice are probably compensating for this loss in future reproduction, she said. She also kept 21 deer mice healthy as a control. After several weeks, all the mice were paired with mates. When the baby mice were born to both infected and healthy mothers, the offspring were tagged and weighed. The results show that the offspring of the infected mothers were bigger. In deer mice, larger offspring are more likely to survive and reproduce. “This shows there is a lot of diversity in the ways animals deal with infection,” she said. As the results of this study are not what she was expecting, and Schwanz feels that makes the results were noteworthy. “It is really striking to find such strong results,” she said. The type of parasite used in the study was an indirect parasite, meaning that it cannot be passed from one mouse to another. A deer mouse can only get infected from a source other than deer mice. That way Schwanz was able to ensure that mothers did not infect their offspring. Source: Iowa State University Sick mice put their babies’ health first. 04 April 2008. NewScientist.com Josh says: This is such an interesting study. It makes evolutionary sense, where if the mother “knows” it won’t survive to reproduce more, it invests all the energy it can into making the current offspring as strong and likely to survive as possible. |
| How do you calibrate the molecular clock? [Mailund on the Internet] Posted: 29 May 2008 12:22 AM CDT How do you calibrate the molecular clock — where you need a few known sequence divergence times — when you only know a few speciation times? Yesterday at a meeting (I’m not sure I can tell you which meeting; I’m not sure how open it is supposed to be :-/) we discussed the divergence time of human-orangutan and human-macaque. We need the sequence divergence time to calibrate a CoalHMM model for figuring out some speciation and population genetics parameters of ancestral species. No definitive answer came up at the meeting, but there was a short discussion by email after the meeting. This paper was sent around, where the divergence times were estimated to 25MYA and 13MYA, respectively, although the last of those numbers is actually the calibration point used in the analysis, so it is an assumption more than an estimate. The problem is, the 13MYA used for the calibration is based on fossil evidence, and as far as I can see, that would make it an estimate for the speciation time between human and orangutan. We need the sequence divergence time. Speciation time and divergence time can vary with millions of years (if the effective population size is large enough). If 13MYA is the divergence time between human and orangutan, we get a speciation time that is unrealistically recent. If the divergence time is 18MYA instead, as we assumed in this paper, we would get a speciation time around 12MYA which would match the MBE paper. But how do you figure out the divergence time needed to calibrate the clock? Is there any way to get it, rather than the speciation time, from fossil evidence? For our purposes, I suppose we can just as well work with speciation times for our calibration, but not everyone is using CoalHMMs for their analysis, so how do you deal with this problem? |
| Monkey controls prosthetic limb using its brain and feeds itself [Think Gene] Posted: 29 May 2008 12:20 AM CDT A monkey has successfully fed itself with fluid, well-controlled movements of a human-like robotic arm by using only signals from its brain, researchers from the University of Pittsburgh School of Medicine report in the journal Nature. This significant advance could benefit development of prosthetics for people with spinal cord injuries and those with "locked-in" conditions such as Lou Gehrig's disease, or amyotrophic lateral sclerosis. "Our immediate goal is to make a prosthetic device for people with total paralysis," said Andrew Schwartz, Ph.D., senior author and professor of neurobiology at the University of Pittsburgh School of Medicine. "Ultimately, our goal is to better understand brain complexity." Previously, work has focused on using brain-machine interfaces to control cursor movements displayed on a computer screen. Monkeys in the Schwartz lab have been trained to command cursor movements with the power of their thoughts. "Now we are beginning to understand how the brain works using brain-machine interface technology," said Dr. Schwartz. "The more we understand about the brain, the better we'll be able to treat a wide range of brain disorders, everything from Parkinson's disease and paralysis to, eventually, Alzheimer's disease and perhaps even mental illness." Using this technology, monkeys in the Schwartz lab are able to move a robotic arm to feed themselves marshmallows and chunks of fruit while their own arms are restrained. Computer software interprets signals picked up by probes the width of a human hair. The probes are inserted into neuronal pathways in the monkey's motor cortex, a brain region where voluntary movement originates as electrical impulses. The neurons' collective activity is then evaluated using software programmed with a mathematic algorithm and then sent to the arm, which carries out the actions the monkey intended to perform with its own limb. Movements are fluid and natural, and evidence shows that the monkeys come to regard the robotic device as part of their own bodies. The primary motor cortex, a part of the brain that controls movement, has thousands of nerve cells, called neurons, which fire together as they contribute to the generation of movement. Because of the massive number of neurons that fire at the same time to control even the simplest of actions, it would be impossible to create probes that capture the firing pattern of each. Pitt researchers developed a special algorithm that uses limited information from about 100 neurons to fill in the missing signals. "In our research, we've demonstrated a higher level of precision, skill and learning," explained Dr. Schwartz. "The monkey learns by first observing the movement, which activates his brain cells as if he were doing it. It's a lot like sports training, where trainers have athletes first imagine that they are performing the movements they desire." Source: University of Pittsburgh Schools of the Health Sciences Josh says: I’m excited not only about the possibility of true prosthetic limbs, but also about the implications for neural-computer interactions on a larger scale. |
| Patent for A Pig: The Privatization of Genetic Information [Think Gene] Posted: 28 May 2008 09:42 PM CDT This video has the tone of a polemic but this is an area where a strong call to action is needed. Is there anyone out there even willing to defend big corporations that are patenting naturally occurring genes and then aggressively “protecting” their IP? This is indicative of the broader problem with the US patent system which doesn’t encourage innovation in the way it was meant to. |
| Directed Evolution: The Biological Engineer's Lathe [adaptivecomplexity's column] Posted: 28 May 2008 09:16 PM CDT A lathe may be a critical machine shop tool for a manufacturing plants, but what tools go into an industrial biological machine shop? Biological tools are in common use in many manufacturing processes, especially nature's best chemists - enzymes that perform highly specific reactions better than even the most ingenious chemical synthesis reactions. Natural enzymes, however, are sensitive creatures, and they are often unable to withstand the harsh environment necessary for an efficient industrial process. To overcome this deficiency, biological engineers often resort to one of the most effective tools in the biologist's machine shop: evolution. A group of scientists at the University of Toulouse, writing in Protein Science, have used directed evolution to engineer a hardier polymer-making enzyme, demonstrating how we can use evolution to engineer biological tools for manufacturing processes. |
From MSNBC:
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