http://bjoern.brembs.net/ This is the personal blog of biologist Björn Brembs. It features neuroscientific research, sports and various political or personal topics. en-gb 2010-09-09T09:30:23-04:00 bjoern@nospam.com hourly 1 2000-01-01T12:00+00:00 http://bjoern.brembs.net/news.php?item.650.3 2010-09-09T09:30:23-04:00 bjoern This is preparation number seven in my attempts to establish operant learning in isolated leech ganglia and it's a control preparation, which means I'm just stimulating it every three minutes at ganglion 18 for an hour and a half.Controls are important, because they tell you what baseline(s) your manipulations should be measured against. In this case, I didn't do anything to the preparation other than observing its responses to the 30 stimulations. For the first ten trials, it responded with a swim/crawl ratio of 7-3. It increased this ratio to 8-1 (one trial was not responded to) in the next ten trials, only to go down to 3-5 (two no-response trials) in the final ten trials. Together with the data from the first no-shock control, this may mean that there is a tendency to bias the decisions away from swimming and towards crawling in these preps. I'll definitely have to do more of these preps and find a way to graph the data properly.Tomorrow, however, will be the first control where I stimulate the anterior ganglion, but not contingent to any behavior. Instead, the prep will be stimulated according to the stimulation sequence of one of the preceeding preps (a so-called yoked control). http://bjoern.brembs.net/news.php?item.649.3 2010-09-09T09:30:23-04:00 bjoern In my attempts to establish operant learning in isolated leech ganglia I'm now at preparation number 6. In my last post, I promised to show some screenshots of the software I'm using, WinEDR. Here's a screenshot of the preparation generating swimming patterns after a stimulation of ganglion 18 (click for fullsize image):And here is one showing crawling patterns in response to the same stimulation in the same preparation:The first channel is the recording from the DP nerve of ganglion 10 and the second channel is the recording of the anterior ganglion (2 or 3), which I stimulate contingently during training. The window spans 40s of recording, in case that isn't quite clear from the screenshots. This little program works really well and I enjoy doing my experiments with it a lot. Very easy, fast and it does what it needs to do.This preparation started out to only generate crawling behavior in all ten pre-test trials. Not unexpectedly, during training, the animal started to generate swimming patterns, when crawling patterns were paired with stimulation of the anterior (2/3) ganglion, and I got a 4-6 swim/crawl ratio. Similar to the last two preps, it reverted to its pre-test behavior in the final test (s/c ratio of 1-9), showing that the anterior stimulation can bias decision-making towards swimming, but only transiently. The next two preps will have to be control preps: in the first, I'll omit the anterior stimulation completely, to see what the unstimulated development of the patterns looks like. In the second, the stimulation will be 'yoked' to one of the previous preps, such that the anterior stimulations are not related to any of the animals decisions. This way I'll be able to find out if the anterior stimulation has to be contingent to bias the network towards swimming.After these two preps, I'll have to think about what the next steps will be. Hopefully, I'll get some insight from these experiments. Maybe I should increase the intensity of the anterior stimulation to make it really aversive?Sticking with the Open Science mantra, I've now also plugged all the data from the first 6 preps into a Google Spreadsheet for the two persons following this blog, or anyone else with good ideas. Over the coming weekend I'll be attending the annual GAIN (German Academic International Network) meeting in Boston and won't be able to do any experiments. I'll try to blog from there, but as usual, there is no way to foresee the availability of WiFi and the time I'll have. http://bjoern.brembs.net/news.php?item.648.5 2010-09-09T09:30:23-04:00 bjoern WTF is ORCID, you ask? It's something scientific publishing should have had 20 years ago. It's meant to become a system that disambiguates authorship and attributions. For instance, go to PubMed and search for author 'J. Smith', and you will find out that this person has authored 17435 papers. Obviously, it is almost impossible to find or follow authors with common names. 'Open Researcher and Contributor ID', ORCID is one of the initiatives that are trying to solve this problem.Today, ORCID announced that they are launching a non-profit organization, "dedicated to solving the name ambiguity problem in the scholarly research community". Given the backing of this organization by a large number of significant players in the field, from publishers such as Elsevier or NPG, to other non-profits such as CrossRef all the way to Thomson-Reuters of IF-infamy, I'm optimistic as to the potential of this long overdue initiative.It is good to hear that Martin Fenner is on the board of the new non-profit, as I know him personally and think very highly of him. At least one competent and enthusiastic member on that board This makes me even more optimistic that something finally will come out of this that solves this problem that has become somewhat of an embarrassment: the supposedly most advanced segment of modern society (scientists) cannot figure out a way to disambiguate the names of its contributors! http://bjoern.brembs.net/news.php?item.647.5 2010-09-09T09:30:23-04:00 bjoern It's a classic canard to argue that all chaos would break loose in a secular or atheistic society, because the only way you could possibly have morals is from religion. A recent example may well be this post at Pharyngula with comments. Obviously, moral codes change over time, different religions have different morals and philosophers have discussed morals without religion ever since Plato. One clearly doesn't need religion to create morals or ethical behavior.However, as Jesse Bering recounts on NPR's "All Things Considered", imaginary beings are just as good for preventing cheating in children as are adults who are actually present in the room. Maybe gods initially were good for policing a continuously tempted populace in times before police were actually invented? Gods knew everything and saw everything and no bad deed could go unnoticed. The effectiveness of this constant surveillance is exemplified convincingly in the experiment referenced in the NPR story, where they also speculate on how this might have helped religious tribes gain evolutionary advantages over non-religious tribes in early human evolution. I find this argument to be rather intriguing, even though I think there are many more facets to the evolution of religion than just policing.In secular societies this surveillance is missing. Maybe it is not a coincidence that a country which by several measures is among the least religious in Europe and hence probably the world, the UK, is also among those countries with the largest per capita number of surveillance cameras? Cynically speaking, is it possible that the UK is just among the first to realize that the surveillance vacuum that has been created by finally freeing ourselves from the shackles of religion has to be replaced with real-world surveillance?As more crimes and misdemeanors are publicized as being caught on camera, like the recent incidence in the UK of a woman throwing a cat into a trash can:or in Germany, where violent beatings have also been caught on surveillance cameras placed in subways and other public transportation systems:as these images become more engrained in people's minds, they will feel just as surveilled as they felt when they used to be religious.Consequently, religious people should welcome these cameras as they hold non-religious people to the same high moral standards as their religion holds them Alternatively, secular societies have to work hard: not only to educate and train the public in all manners of self-control, be it anger management, or simple restraint when the urge to shoplift overcomes you. In addition to these psychological factors, secular societies also have to to reduce the socioeconomic factors influencing crime.Religion, cameras, conditioning or welfare - which is the golden road to a civil and peaceful society?P.S.: Obviously, some people, especially in the USA, are going to argue that arming the public is yet another way to a civil and peaceful society... http://bjoern.brembs.net/news.php?item.646.3 2010-09-09T09:30:23-04:00 bjoern Let's see how long I can manage to blog each day about each preparation Slowly but steadily I'm making progress in my attempts to find out if one can get isolated leech nervous systems to learn. Here are the problems I've been able to solve in the first two weeks:Dissection/HardwareRecordings with sucktion electrodesModifying MatLab script for digital storageStimulation parametersSpontaneous activityThis has allowed me to actually do four full experiments last week, all the while I was still trying out various things and the effect they have on decision-making in the isolated leech nervous system. Now I think I have most of the details down and will start collecting some data to see what the statistics say, beyond the individual variability.Today, just in time for the fifth preparation, I've been able to install new recording software since the more than provisional MatLab script I was using was less than even bare bones and had various bugs and deficiencies. I'm now using WinEDR (Windows Electrophysiology Disk Recorder), a very capable freeware program from the University of Stratthclyde. Will post a video of the recording screen soon. It's absolutely perfect for the straightforward physiology I'm doing. If you're doing electrophysiology, you should definitely have a look into it! It is this software which has enabled me to automate the experiment enough to ba able to live-blog from the experiment, so to speak. Cutely enough, the first three hits on Google if you search for "Windows Electrophysiology Disk Recorder" are three electrophysiology papers Today's prep started off like the picture-book example: in the first 10 trials, it generated swimming 6 times and crawling 4 times. I decided to stimulate the anterior ganglion whenever it generated swimming for the next 10 trials. This resulted in a 9-1 S/C ratio for these 10 trials interestingly enough. The final 10 test trials yielded a S/C ratio of 6-3 (the very last stimulation didn't generate any patterned activity at all) which was right back to where it was in the beginning.This is the second prep that did that and the first one was stimulated upon crawling (and it transiently increased swimming during the training phase as well). I'm starting to get a hunch that the anterior stimulation is transiently biasing decision-making towards swimming, no matter if I stimulate the prep when it generates crawling or when it generates swimming. Or is this anterior stimulation actually rewarding? We'll find out what the data says when I have measured more preps.Let's see what tomorrow's prep will do. Isn't science exciting? I hope to have a Google spreadsheet filled in some time during this week, for all of you who want to have a look at the raw data (like the two people reading this are actually going to care, lol ). http://bjoern.brembs.net/news.php?item.645.3 2010-09-09T09:30:23-04:00 bjoern For the last two weeks I've been trying to develop an operant learning paradigm for isolated leech nervous systems. To do these experiments I traveled to visit Bill Kristan's lab at UCSD. After he showed me how to dissect the animal, I went and did some pilot studies on where to stimulate the animals and how. The plan was to first get the animals to generate swimming or crawling behavior in response to stimulation of a nerve at ganglion 15, just as described in Kevin Briggman's Science paper. The initial problem was that the animals all swam spontaneously, as shown in this video:This spontaneous swimming behavior makes it impossible to decide which activity was spontaneous and which was triggered by the stimulation. Moreover, it seemed that this spontaneous swimming was an indication that the preparations were very prone to respond with swimming to any kind of stimulation, anywhere. I think I have the problem of spontaneous swimming solved now by removing some of the connective tissue around the ganglia (it's actually a blood sinus called the 'stocking'). This should prevent the accumulation of serotonin in the blood sinus, which biases the system to swimming activity. I also had to move the stimulation from the published ganglion 15 down to ganglion 17 or even 18 in order to get any crawling at all (apparently some weird seasonal thing). Still, it doesn't seem I'm getting a 50-50 distribution of swimming vs. crawling, yet. I need to play around with the duration and intensity of the stimulation it seems. The last prep today almost exclusively crawled, sigh. Anyway, I seem to be making headway.Progress is slow, though. The dissection takes about 3 hours, then the nervous system gets 1h of rest (aka lunch) and then the trying out, testing, recording and stimulating takes about another 3-4 hours, which makes it too long to get two decent preps into a single day. I need to somehow shave off a few hours from this schedule, I only have three weeks left.Why am I doing all this, you ask? Well, if the nervous system is making a decision upon each stimulation whether it should generate crawling or swimming activity, maybe I can find a nerve to stimulate which would bias this decision one way or another. So I've started to stimulate a nerve in the very front of the nervous system, ganglion 2 or 3. When I do that during a swim I can usually switch it off. If I do so during a crawl, they usually stop crawling, too. However, the method is not as reliable as I would want it, yet. The idea behind this is that eventually I should be able to get preps where in a pre-test phase they exhibit (ideally) a 50-50 ratio between swimming and crawling in response to the stimulation at ganglion 17/18, Then, during training, I choose one of the patterns and shut them off with the ganglion 2/3 stimulation. After training, I hope to see a shift in the ratio, away from the initial one, becasue the nervous system has learned that the pattern in question is always followed by some unpleasant stimulation.I've done similar operant conditioning experiments in the marine snail Aplysia, so these kinds of things can work in principle. But which nerve to use and which stimulation parameters is always tricky. It may well be that I can't get the nerve chords to modulate their decision-making. http://bjoern.brembs.net/news.php?item.644.5 2010-09-09T09:30:23-04:00 bjoern As you may know from my previous posts, I'm currently working (for a few weeks) at the University of California in San Diego, more precisely in La Jolla, California:View Larger MapThe university is so close to the beach that it is possible to go surfing for an hour and still be in the lab in time for the experiments (if you get up early enough that is). So here's a picture of what I've been doing between seven and eight each morning for the last week and a half:Not that I'm in the water more than on the board, but hey, I'm a total newb - and enjoying it anyway! I'm so stoked, dude http://bjoern.brembs.net/news.php?item.643.11 2010-09-09T09:30:23-04:00 bjoern ReaderMeter looks in the database of reference manager Mendeley and checks how many people have bookmarked which papers for later referencing in their scientific papers. So, for example, you can go and check out the statistics of yours truly. It's not all that impressive, compared with my citation statistics, but given the userbase of Mendeley and compared with my peers, it seems about right. This data show you how many people have probably read your papers and might be planning to cite them in a later manuscript.ReaderMeter depends critically on the number of Mendeley users generating the data, of course. This means that every biologist user on Mendeley will be more likely to bookmark any of my papers, while engineers or social scientists will be less likely. This is how the userbase skews these statistics, just like citations cannot be compared accross disciplines. These sorts of statistics once again show how absurd it is to have different providers offering different services:You have Faculty of 1000 (disclaimer: I'm a faculty member), who provide expert reviews on research publications, but their logo only shows up on evaluated papers in PubMed and not on any of the other search portals (yes, we have 4-6 of these in the sciences). To find evaluations and/or the evaluated papers, you need to subscribe to them.You have PLoS One (disclaimer: I'm an Academic Editor), where every published paper can be commented on, downloads and citations are tracked and your search for papers can be filtered/sorted by some of these criteria. However, this functionality exists only on their site and no user profiles on PLoS reveal anything about the user: no number of papers published or handled as editor, no citations or downloads, nothing.You have Frontiers in Neuroscience (disclaimer: I'm an Associate Editor) where some, how shall I put it, technically rather obscure process also evaluates readership and leads to the 'promotion' of papers through a journal hierarchy such that the most widely read papers end up in a very general journal eventually. None of this can be seen outside of the Frontiers website and so one can only compare papers within the frontiers system.You have CiteUlike, another reference manager, where you can get Amazon-like suggestions à la "users who have also read the paper you just bookmarked, have also bookmarked this paper:" Alas, you need to visit their website in order to get these suggestions.Most if not all of these bits and pieces of information are important to scientists and administrators. Yet, there is no way to get all these statistics from one source (or for one researcher, for that matter). Thus, all of these great efforts are, at least for now, useless, because they're either skewed by a small userbase, or locked into a subscription or plain impractical. These limitations mean that they're impossible to use for any sort of comparisons other than proofs of principle, that they're impossible to use as filter, sorting or discovery system other than for a very limited number of fields and an even more limited number of papers.In brief, these great innovations are doomed to fail, because they'll die out before even a double digit fraction of scientists knows about them. In the end, the beta-max vs. VHS battle will play out before our eyes again: superior technology will loose against the deeper pockets. In our case, it will mean that the Thomson-Reuters and the Elseviers will come up with some form of easy to understand  "Impact Factor 2.0" with which we'll be stuck for another 50 years.If we want to get a grip of the current pace at which science progresses, there needs to be a movement which unifies these great efforts to create standards. These standards will attract a lot of attention, because of their usefulness, and hence will lead to adoption. Right now, what we have are fragments, each of which makes us sigh: oh, if only we would have this for all publications!Why don't we have this for all publications already? Because the widespread frustration with the current publishing system leads to ever new circles of people coming up with always new and brilliant ideas. But the opposition is splintered and the People's Front of Judea doesn't talk to the Popular Front:So what are these organizations/people waiting for? Get your heads together and develop standards, to make all these really important technologies available to everybody. I want one place where I find, sort, discover and store the scientific literature for my daily work. I want this place to poffer the latest technology to assist me in the stupendous task of doing that with 2.5 million scholarly papers published every year. Obviously, I'm more than willing to pay for a place where I can get that. I've estimated before that a place like that will probably save me 5-10 hours of boring title-sifting every week.Alternatively, you could just sell these goodies all to Thomson Reuters or Elsevier of course... http://bjoern.brembs.net/news.php?item.642.3 2010-09-09T09:30:23-04:00 bjoern As reported earlier, I've now been working for a couple of days in Bill Kristan's lab at UCSD in La Jolla, California. The first few days I was practicing the dissection of the leech nervous system. I need to take the entire nervous system out of the animal, place it in a petri dish and then attach electrodes to the prepration to record the nervous activity as well as stimulate the nervous system electrically. Here's a video showing the reuslts of my first dissection  (actually, Bill did most of it, showing me the ropes):By the middle of last week I had learned the dissection as well as how to record and stimulate using sucktion electrodes. This video shows one of the first recordings I made:The to me really interesting and exciting thing was the spontaneous activity in this preparation (and with most others since then). With absolutely no stimulation whatsoever (remember, this is a completely isolated nervous system) the nervous system started initiating swimming activity just so! This is a really convincing example of the capacity of nervous systems to be active and initiate actions in the absence of any releasing stimuli. Besides responding to external stimuli, brains always actively initiate activity, regardless of the environment. I would even make the claim that responding to the environment is a secondary trait that evolved as a means to channel spontaneous activity into adaptive states. The video above provides some very nice anecdotal evidence supporting the published, peer-reviewed data. http://bjoern.brembs.net/news.php?item.641.3 2010-09-09T09:30:23-04:00 bjoern After much to little time spent writing, a first draft of the article for the Proceedings of the Royal Society is online. There was no way to get this article in the sort of shape I had initially planned, but given the deadline of September first, this will have to do. The main points are in there, that's what counts. I still could use some more references, for instance and I'm sure I'm much to brief and dense in many places.Anyway, some of you have expressed interest in reading and commenting on this version. The document I linked to above should be editable by anyone, please let me know if you want to comment but are having trouble. Just use some sort of color in your comments or edits, so I can easily track them. I'm sure there are plenty of things which could be improved upon...Thanks in advance for any suggestions and edits, of course, if they make it into the article, you will be mentioned in the acknowledgements (goes without saying). http://bjoern.brembs.net/news.php?item.640.1 2010-09-09T09:30:23-04:00 bjoern We now have two new additions to the brembs.net blogging family. Please welcome my nephew Ben and my daughter Freya. Ben is now almost two years old and Freya is close to three months old, so their blogging style or language may not be fully developed, yet. Still, head on over and give them a holler, I'm sure they'll get a thrill out of it http://bjoern.brembs.net/news.php?item.639.3 2010-09-09T09:30:23-04:00 bjoern I'm currently in sunny southern California for some experiments at UCSD. This is the place where one can find the marine snail Aplysia in its natural habitat. As I've been working with Aplysia for about ten years now, I felt it was about time to see Aplysia in the wild and observe what these animals do when they're not in a tank waiting to be experimented upon. Just this morning, before heading out to UCSD, I went snorkeling in La Jolla Cove in the hope of seeing some specimens. All these years working on Aplysia and I had never seen one in the wild. What do they do? Why can they learn? Do they only learn about how to handle their food? I always imagined these snails as sort of the cows of the sea, living happily on their food and, being hermaphrodites, not really having any trouble finding mates, either. Any other forms of learning are probably purely coincidental of neurons in general being plastic. Unfortunately, I didn't find any Aplysia at all today. However, when I checked the table of contents of thelatest issue of the Journal of Neuroscience later in the evening, I found this great paper that was so long overdue: "Lobster Attack Induces Sensitization in the Sea Hare, Aplysia californica".Sensitization leads to a form of non-associative memory that leads to the animals to respond more strongly to a weak stimulus after having experienced a very strong, often noxious stimulus, compared to animals that did not experience the strong stimulus. Sensitization is also one of the most intensively studied and best understood forms of learning. Finally, after roughly 40 years of research on sensitization in the marine snail Aplysia using electric shock in the laboratory, the new paper by Watkins et al. provides evidence that Aplysia sensitizes to natural, ecologically relevant stimuli: lobster attacks.Sensitization of sensori-motor synapses in Aplysia is one of the first and most basic models for the cellular and molecular basis of memory. The Nobel Prize for physiology or medicine in 2000 was awarded, in part, for work using this preparation. For more than four decades, laboratory work has unraveled the neurobiological processes underlying this simple form of memory. These studies were done either in intact animals using electric shock as sensitizing stimulus, in reduced preparations with either shock or the biogenic amine serotonin leading to sensitization (serotonin is thought to be released in response to electric shock), in isolated ganglia or even in cell culture with individual sensory and motor neurons. For all this time, the researchers studying these processes have had to speculate what the ecological relevance of the processes that they were studying was, if they had any. The paper by Watkins et al. provides first evidence suggesting that sensitization may be an adaptive response to attacks by lobsters.The authors put individual Aplysia in the same tanks as starved spiny lobsters and compared the head withdrawal and the siphon and mantle withdrawal reflexes of animals who were attacked with the reflexes of those who weren't. They found that 30 and 60 minutes after the attack, the duration of the withdrawals was increased in both reflexes in the animals that were attacked compared to the non-attacked animals, constituting compelling evidence for sensitization. Granted, Watkins et al. used tank experiments with starved lobsters attacking the slugs. However, both species are sympatric and the authors cite observations that these attacks do occur in the wild. Also granted, the fitness effect of sensitization on future predator attacks is rather speculative, but at least there is a testable prediction now: sensitized animals should be a tougher prey than naive animals.Be that as it may, at the very least, as of today, neurobiologists finally have a plausible story to tell when they are asked, as I have often been asked and been asking myself, why Aplysia needs to learn anything.Small aside: It is amusing to note that the authors report the carapace length of the lobsters they used to have been between 80-90cm. Animals with an overall body length of that dimension would be regarded trophy size. Lobsters with a carapace length of 80-90cm would probably have a body size of around 180cm, a rather average height for a human male and a lobster size worthy of its own publication. Now I'd love to have the tail of a 6 foot lobster for dinner! Watkins, A., Goldstein, D., Lee, L., Pepino, C., Tillett, S., Ross, F., Wilder, E., Zachary, V., & Wright, W. (2010). Lobster Attack Induces Sensitization in the Sea Hare, Aplysia californica Journal of Neuroscience, 30 (33), 11028-11031 DOI: 10.1523/JNEUROSCI.1317-10.2010