Journal of unfinished projects science | email to someone | printer friendly
The other day, we've discussed a new idea among colleagues. We thought there should be something like a "Journal of unfinished projects", where people could post data and some text about any unfinished projects they have lying around. Personally, I have a bunch of projects I can't persue right now (for various reasons) but I would hate to see them just die and sink into oblivion. Mostly, I have some interesting preliminary data, but nothing publishable. Wouldn't it be great if there was a place to advertise these projects, share the data and have someone else finish it, or collaborate on finishing it?
I don't know of any place where one could do that...

Tuesday 06 January 2009 - 12:35:39 ----- comments: 0

projects   journal   


EvolutionGems@Nature science | email to someone | printer friendly
Nature magazine has a nice little collection of evolution gems up on their website, freely accessible without subscription. What's it all about? Read yourself (PDF):
Most biologists take for granted the idea that all life evolved by natural selection over billions of years. They get on with researching and teaching in disciplines that rest squarely on that foundation, secure in the knowledge that natural selection is a fact, in the same way that the Earth orbits the Sun is a fact.
Given that the concepts and realities of Darwinian evolution are still challenged, albeit rarely by biologists, a succinct briefing on why evolution by natural selection is an empirically validated principle is useful for people to have to hand. We offer here 15 examples published by Nature over the past decade or so to illustrate the breadth, depth and power of evolutionary thinking. We are happy to offer this resource freely and encourage its free dissemination.

15 EVOLUTIONARY GEMS
Henry Gee, Rory Howlett and Philip Campbell*

Gems from the fossil record
1 Land-living ancestors of whales
2 From water to land
3 The origin of feathers
4 The evolutionary history of teeth
5 The origin of the vertebrate skeleton
Gems from habitats
6 Natural selection in speciation
7 Natural selection in lizards
8 A case of co- evolution
9 Differential dispersal in wild birds
10 Selective survival in wild guppies
11 Evolutionary history matters
Gems from molecular processes
12 Darwin’s Galapagos finches
13 Microevolution meets macroevolution
14 Toxin resistance in snakes and clams
15 Variation versus stability

*Henry Gee is a senior editor for Nature; Rory Howlett is a consultant editor for Nature; Philip Campbell is editor-in-chief of Nature.
Each gem is a page long and based on a Nature publication. Great stuff!


Thursday 01 January 2009 - 12:26:18 ----- comments: 0

evolution   Nature   


New Year's Eve in Germany is Dinner for One time Random Science Video | email to someone | printer friendly
Ok, no science content this time. In Germany, most stations are showing this clip on New Year's Eve. Yes, every year.



Wednesday 31 December 2008 - 11:02:02 ----- comments: 0

fun   video   


Geekiest night out ever news | email to someone | printer friendly
Last night was a memorable night. It didn't really start off very geeky at all. We had roasted duck for dinner at a friend's place. It was a fabulous meal with a 2005 Beaumes de Venise with the bird and a 2005 Podio Alto with the cheese. Stuffed, a little tipsy and in a party mood, we went to the Alte Kantine in Berlin Prenzlauer Berg. And this was when the geeky part started. The new version of Shazam had come out and I wanted to try of this version could handle the volumes in clubs. Unlike previous versions, the new version had no problems at all and detected many of the songs they played. So for most of the night (when I wasn't getting drinks, basically) I was dancing with a drink in one hand and the iPhone tagging songs in the other. And to top the whole thing off, around 1am there comes this hot young lady up to me: "Excuse me, but I just can't help it. You look so familiar, I think we've met before." As I open my mouth to chastise her for using the cheekiest pick-up line ever on me, she continues: "you're not working at a Max-Planck Institute by any chance, are you?" Not being entirely sober anymore, that threw me off, so I wondered whether we had met at one of Yoshan's parties? Nope, she didn't know him. But then she said she studied Bioinformatics at my university and it was clear: I teach the neurobiology course for bioinformatics students and must have been her teacher last year or so. Then I lost track of her somewhere in the crowd. Tagging songs with Shazam and getting propositioned by one of your students in a nightclub - can it get any worse? Mmmkay, it would have been worse if I hadn't alrady been dancing with two girls as she aproached me
Anyway, here are some of the songs they apparently played last night: Stop the Clocks (Donots), Hot N Cold (Katy Prry), Disturbia (Rihanna), Rck this Party (Bob Sinclar), Infinity 2008 (Guru Josh Project), Cobrastyle (Teddybears), Jerk it out (Caesars), Temperature (Sean Paul), Seven Nation Army (The White Stripes), Song 2 (Blur), Put your hands up for Detroit (Fedde le Grand), Do it Again (The Chemical Brothers), Allein Alene (Nephew & Polarkreis 18), Don't stop the music (Rihanna), So what (Pink), Foundations (Kate Nash), This is the life (Katy MacDonald), Sex on Fire (Kings of Leon), Mr. Brightside (The Killers), Never be alone (Justice vs. Simian), That's not my name (The Ting Tings).Did I mention Shazam is a very, very cool app?

Tuesday 30 December 2008 - 10:05:46 ----- comments: 1

Shazam   Alte Kantine   students   fun   party   


Speaking in Hawaii news | email to someone | printer friendly
This has been very busy 2 weeks! Paper re-submitted, answered questions for my grant, grading and handing back students' lab reports, experiments and so on, leaving no time for blogging. Now finally an item I must blog about: I'll be flying to Hawaii in the end of April! Whoohooo! As mentioned earlier, together with Jonathan Wolpaw, I applied for a symposium at the 19th Annual Conference of the Society for the Neural Control of Movement, taking place April 28 – May 3, 2009 at the Waikoloa Beach Marriott Resort and Spa on the “Big Island” of Hawaii. And guess what, our session got accepted! We will now speak on April 30, 2009 at 4.30-6pm on the topic "Spontaneous behaviors and evoked responses: two sides of the same coin?". Here's the abstract we submitted:
Spontaneous behaviors and evoked responses are traditionally viewed as separate and distinctly different phenomena. This distinction underlies the standard dichotomies between reflex and voluntary behaviors, and between evoked responses and the behavioral states or contexts in which they occur. In the typical tightly controlled laboratory environment, it is convenient to focus on stimulus-evoked behaviors and to treat spontaneous behaviors as simply nuisances to be minimized or averaged out. This focus ignores the critical role of spontaneous activity in creating the behaviors evoked by specific stimuli.
Drs. Wolpaw and Brembs will discuss recent vertebrate and invertebrate research indicating that spontaneous and evoked behaviors are not only inextricably linked but are, in important respects, no longer distinguishable from each other. This erosion of the traditional distinction is driven by the recognition that spontaneous variability is a necessary feature of all adaptive behaviors, and that even the simplest reflexes and stereotypic responses are controlled by sensory feedback. In contrast to the standard stimulus-response concept, the central thesis is that spontaneous behaviors provide a substrate that interacts with the environment so as to produce and maintain adaptive (i.e., appropriate) behaviors.
Dr. Wolpaw will discuss evidence that the quintessential evoked behaviors of vertebrates – reflexes mediated by spinal pathways – are highly plastic and display dependencies on past experience like those of spontaneous behaviors. The stimuli that evoke these reflexes are basically probes that assess ongoing spontaneous activity, and the resultant sensory feedback modifies that activity. Furthermore, the high variability of these reflexes underlies their adaptive capacities. He will also consider how the artificial behaviors created by brain-computer interfaces (BCIs) – behaviors produced by brain signals rather than muscles – arise largely from the interaction of spontaneous brain activity with sensory feedback. By connecting spontaneous activity to external consequences, BCIs create another situation in which spontaneous activity is shaped into adaptive behavior.
Dr. Brembs will discuss studies in several invertebrate species indicating that evoked behaviors are derived traits with reduced features, and have evolved from initially spontaneous behaviors. For example, in the fruit fly Drosophila, mathematical analyses of the temporal structure of spontaneous behavioral variability and genetic dissection of several feedback-based learning systems indicate that behavioral variability is not noise, but rather is essential to the brain’s capacity to use sensory feedback to create and maintain effective forward models for behavioral control. This function is implemented by a hierarchical interaction of learning systems (partially mediated by the mushroom-bodies) that shapes spontaneous actions into habitual responses.
In sum, converging evidence from disparate taxa and seemingly unrelated preparations indicates that spontaneous behaviors and evoked responses are opposite ends of the same spectrum. The data suggest that behavioral flexibility arises from an interaction of spontaneous and evoked behaviors that reflects individual history and genetic endowment and is continuously updated. This interaction maintains a balance between flexible exploration and efficient exploitation and ensures adaptive behavioral choice.


Tuesday 23 December 2008 - 09:06:50 ----- comments: 0

Limiting the impact of the impact factor science politics | email to someone | printer friendly
Jeremy Green from King's College London writes in this week's issue of Science, in response to Kai Simons' editorial:
K. Simons's Editorial "The misused impact factor" (10 October, p. 165) reminded me of the Tolstoy story in which his brother tells him not to think about a white bear: When you say, "Don't think about it," it becomes hard to think of anything else. Instead, AAAS and Science should take the lead by defining some declarative "bibliometric postulates" that specify a code of conduct for the use of simplified indices. Postulates might include "numerical factors applied to journals should not be used to evaluate individuals" or "numerical journal factors should never be quoted without disclaimers explaining that they include falsified papers." Only an organization like Science with the backing of the non-commercially beholden AAAS has the profile to defend itself and scientists from enslavement to the impact factor's absurdly one-dimensional parameterization of achievement.
The sad thing is that especially the use of a journal-level metric such as Thomson's Impact Factor to evaluate individual scientists is so obviously wrong on so many levels that a statement to this extent should be about as necessary as a disclaimer "not for consumption" on a package of fishing hooks. This still holds even if the BIF were a valid metric, which, of course, it is not. Apparently, now the situation has gotten so out of hand in some places that scientists feel compelled to ask Science for help to encourage the dissemination of statements of the obvious even among scientists. How much worse will it get, before things start to change?

Friday 05 December 2008 - 10:21:51 ----- comments: 0

Interview@McGill! news | email to someone | printer friendly
I just received a phonecall from Rüdiger Krahe from McGill University in Montreal, Canada. He invited me to interview for a tenure-track position offered at their Biology department (neurobiology). Of course I'm really excited to interview at such a prestigious university and am really looking forward to having a look around there. A lot of great work is coming from this place and it would be an honor to join this institution.

Wednesday 03 December 2008 - 12:12:40 ----- comments: 4

interview   McGill   


Experiments are now reproducible Random Science Video | email to someone | printer friendly
The peer-reviewed, open-access and PubMed-listed Journal of Visualized Experiments ( JoVE) is here to stay:



Wednesday 03 December 2008 - 05:07:49 ----- comments: 1

JoVE   


...and now for some R-E-S-P-E-C-T news | email to someone | printer friendly
R-E-S-P-E-C-T
Find out what it means to me
R-E-S-P-E-C-T
Take care ... TCB
respectcartoon.jpg
via Pharyngula.

Friday 28 November 2008 - 08:03:29 ----- comments: 0

atheism   religion   


Research dollars per paper science politics | email to someone | printer friendly
In this week's Science, Rui Sousa from UT San Antonio points out, how absurd it is to evaluate researchers by the amount of money they spend, rather than on their productivity, in other words, the research dollars they spend per publication:
No prestige should be attached to the level of funding that an investigator has managed to secure. The most basic of truths must be emphasized: Money is a means, not an end. We do not do science to get money. We get money to do science. Funding cannot be a measure of productivity, because scientists do not produce research dollars. Research dollars are produced by taxpayers [...]. The amount of money spent by a researcher is not a measure of his productivity, but of his consumption, and might even be counted on the negative side of the ledger when he is evaluated.
One of the easiest ways to measure productivity is to count the dollars spent for a research paper (more complicated measures may include the type, scope, impact and/or length of paper etc.). I have received approx. 35k Euros in research funding since Jan. 2004. Since then, I have published 8 research papers, with two more in the pipeline. For the sake of simplicity, let's say I have published ten papers with 40k, which makes roughly 4 grand for an average of my research papers. Is that good or bad? I have no idea, since so far, nobody ever really evaluated research like that.

Friday 28 November 2008 - 03:09:58 ----- comments: 4

Darwin relative at Gatsby workshop news | email to someone | printer friendly
Last night, at the workshop dinner in the Trattoria Verdi, I got to know Horace Barlow, 86-year old great-grandson of Charles Darwin. As the most experienced researcher at the workshop, he is very noticably revered by the other participants and captivates with his sharp mind and wit. At the same time, Horace's scientific family tree shows one of the problems in science today: it's a snowball system where only very few trained scientists get to find a job in the profession they learned. So it was very exciting to meet such a famous man from such a great family, but his long and successful career is also a reminder of this general problem in science.

Wednesday 26 November 2008 - 05:37:59 ----- comments: 0

Second day at Gatsby workshop on simpler cognition science | email to someone | printer friendly
This day started with the talk by Alex Kacelnik on choice and decision-making in starlings. This was again a very interesting talk and contained a lot of theoretical considerations about decision-making after showing a series of very cleverly designed experiments. For instance, he told us that choice may be a computation of behavioral actions with different latencies (when the choice is forced by a stimulus). These theoretical considerations were derived from modelling the experimental data. Interestingly, in their experiments, starling respond more quickly when faced with a simultaneous choice than with a sequential choice. In total, Kacelnik compared his sequential choice model with about 5-6 different choice experiments and his model fitted the data better than more complex models.
The second talk rang from home in a way as it was by Mandyam Srinivasan on honeybees (our department works largely on honeybees). After some introductory history on pattern recognition in bees, he told us about how bees an generalize certain features of patterns, such as orientation or symmatry, even up to the extent that they can learn to solve a delayed matching-to-sample test with a set of entirely new patterns, an experiment famously published in Nature. I just found that a very similar talk, together with many of the slides he showed here is posted here. He also showed us data indicating that bees can count up to about 4. Finally he showed some very intersting experiment in which it became clear how bees use the polarized light pattern on the sky for orientation.
The final talk before lunch was by Nigel Franks on House Rock Ants. These ants make decisions as to which area is best suited for a new nest. The main criterion for this choice is the size (area) of the nest. The go into potential sites, lay down scent trails and then re-visit the sites for comparison. Other contributing features are brightness and headspace. The data suggest that these ants use a weighted additive strategy for their choice. Similar to the results from Alex Kacelnik in starlings, the ant data suggest that this nest choice is done sequentially and involves mainly thresholds and timing. If the ants are forced to choose a nest quickly, they make more erros, i.e., choose a nest which is inferior to the other option, indicating a speed/accuracy trade-off. Nigel next went to the topic of teaching in ants, also famously published in Nature. In tis paper he and his student argued that the tandem runs of these ants from the old nest to the new nest constitutes all important criteria for teaching. Nigel's final section was about tracking individual ants using RFID tags glued to their tergites. He used this technique to investigate the way the ants decide between a near but bad nest and a far away but better nest. It turned out they first recruit to the worse, close nest and then switch to searching for the far away, better nest. Individual ants are able to make a decision for the better nest and break the colony consensus for the worse nest. This means that a portion of ants is continuously looking for better nests, even if a nest is being or has already been established.


Tuesday 25 November 2008 - 08:10:13 ----- comments: 4

LabTimes article online news | email to someone | printer friendly
I just noticed that my LabTimes article about new innovations in science communication in general and JoVE in particular has just come out:

JoVE.jpg

Go and read it and let me know what you think (PDF download).


Monday 24 November 2008 - 17:11:38 ----- comments: 2

JoVE   LabTimes   LaborJournal   


First morning of the Gatsby workshop on smaller cognitive systems science | email to someone | printer friendly
This meeting started off with a very interesting and entertaining morning. Great speakers throughout with engaging topics and captivating personalities. It started off with what the speaker, Gasper Jekely, called 'the proto-eye'. He studies phototaxis of the larvae of a simple marine polychaete (Platynereis dumerilii). They only have two eyes (well maybe four, but that would take too far here) and these eyes modulate the ongoing behavior of a ring of cilia which propels the animal. Each eye (which is basically only able to sense if there is light on its side of the animal or not) slows the beating of the cilia when it received light in the adjecent areas of the ciliary ring. The ring and eyes are placed such that this simple modulation leads to reliable phototaxis (i.e. movement towards the light). I thought this was an extremely interesting very simple example of how even simple animals first, spontaneously generate behavior and then the environment acts on this behavior and modulates it.
The second talk was about phonotxis in crickets, by Berthold Hedwig. He presented a lot of interesting data, the most interesting piece for me was how male chirping could entrain female crickets to turn towards non-cricket sounds (they usually ignore non-cricket sounds). Play female crickets alternating chrips left and right and they will turn to each chirp. After a few turns, you play an artificial test sound, which usually doesn't lead to turning, right at the time when the next chirp would come, and the animals turned as if they had heard male chirping for quite some iterations.
The final talk of this session was by Holger Krapp, about multimodal gaze control. He uses the blowfly (Calliphora vicina) to study how visual and mechanical stimuli are perceived and help the animal control its direction of gaze. In particular, he records from neurons in the lobula plate of the fly's visual system. He find that the neurons there are particularly well-tuned to detect visual stimuli which correspond to the main movements of the animal, namely translation and rotation along it's main body axes.

Monday 24 November 2008 - 11:33:28 ----- comments: 0

Of course school kids need to know about creationism before evolution! science | email to someone | printer friendly
The fuss in Texas reminds me of how silly the 150 year-old refusal of religious nutcases to accept reality actually is. They want creationism to be taught in US schools. Of course creationism needs to be taught in schools. It should even be taught before evolution. You know, just like in Geology class, kids get taught that before Columbus, people thought the earth was flat. Just like in Physics class, before Galilei, people thought the earth was in the center of the solar system. Just like in these two examples, before Darwin, people thought we were created by some guy in the sky. And just like Columbusism and Galileism, it makes perfect sense to teach evolutionary biology as 'Darwinism'  smoking.png

I just don't understand what the problem is?


Saturday 22 November 2008 - 08:05:15 ----- comments: 2

"Smaller cognitive systems" in London news | email to someone | printer friendly
I'll be off on Sunday to a workshop about "Smaller cognitive systems" by the Gatsby Charitable Foundation in London. I've been invted to give a talk there and I thought I'd talk about "Learning the Consequences: State-dependent Modulation of Spontaneous Decisions in Flies". I'm still working on the slides, but I'll post them here as soon as they're done - maybe even during the meeting.

Friday 21 November 2008 - 12:40:08 ----- comments: 4

SfN annual meeting over news | email to someone | printer friendly
The night before the last day of this year's annual SfN meeting marked a first in my 5 year blogging experience: I met a person who actually reads this blog regularly! Mary Petrosko, undegraduate student at Dominican University confessed and proved she actually reads a lot of what I post here. This means I now know 50% of my readership. A memorable evening indeed. Read the abstract of her poster here.
The last day at the meeting itself was even more memorable. My poster session was in the morning and it was a 4h non-stop presentation marathon. A ot of people showed up and some also asked very good questions. People were very enthusiastic, it was awesome! After the poster session, Jonathan Wolpaw came to me and asked me if I was interested in co-hosting a session at a workshop on motor control in Hawaii next year! The topic would be centered around behavior as spontaneous actions vs. responses to stimuli. I told him I'd be delighted to attend such a session if it were on the northpole or the Sahara desert. And Hawaii ain't no cold desert elated.png
After the meeting I teamed up with Steve de Belle (UNLV) and David Glanzman (of bullfight/paper writing fame) for a few post-meeting beverages in David's hotel bar. We were enjoying our great wine and cheese, when a few men in expensive suits sat down at a table next to us. We all agreed that one of them must be Kofi Annan. I didn't get a good look at the others, but according to David, they were "oozing political power".
After drinks, we met Michael Stebbins (of Sex, Drugs and DNA fame) for a Chinese dinner, which also was fantastic, especially when the appetizer was a flaming volcano for three. A few beers in the Rocket Bar rounded off the evening, so we went back to Steve's place for a night cap (excellent Portwine!). Thanks, Steve, for a legendary evening! (I'm at his house writing this about an hour before I have to get to the airport for the flight back to Berlin)

Thursday 20 November 2008 - 12:58:00 ----- comments: 2

SfN2008   petrosko   stebbins   deBelle   wolpaw   glanzman   


Operant conditioning of a reflex? science | email to someone | printer friendly
Ever since I got into operant conditioning now over a good dozen years ago, I was aware that there was a researcher in New York studying operant learning in rats in a very unusual experimental setup. His lab triggers the well-known stretch reflex (the one you know from your doctor when he hits your knee with a rubber hammer) and then rewards animals which react either with a higher than average (up-conditioning) or lower than average (down conditioning) muscle contraction. After a number of trials, the animals consistently produce large or small contractions, where before training they varied widely.
For all these years I've been aware of this work and at the various SfN meetings have been walking by his posters hoping to spot his name on one of the badges around the posters. Well, yesterday I finally got to meet Dr. Wolpaw. It was a short but very exciting meeting where we immediately realized to how similar conclusions and interpretations our vastly different research studies had led us. He finds that the variability in the stretch reflex comes from cortical control centers injecting the variability via the cortico-spinal tract. This was very reminiscent of the way we interpreted our finding that there is always the same mathematical signature in the temporal structure of fly turning behavior, irrespective of whether the behavior was spontaneous or elicited. So despite the behavior being triggered and executed by the spinal cord, the cortex is critically involved in the conditioning process and so far it seems as if the way this is happening may indeed follow the same basic principles found in many other vertebrate and invertebrate preparations.
This was a very memorable first day at this year's conference for me! Hopefully, we'll stay in touch and keep exchanging ideas in the future.

Sunday 16 November 2008 - 10:25:59 ----- comments: 0

SfN2008   operant   H-reflex   wolpaw   


Arrived at SfN in Washington, DC news | email to someone | printer friendly
Just got to the convention center and it's already teeming with people! They expect around 32,000 attendees and you could definitely see plenty of people with poster-rolls at the airport. The Wi-Fi connection here so far is decent, we'll see how it holds up once 32,000 people are checking their email at the same time - we all know scientists use the internet only for email, and not for blogging, twittering or friendfeeding
I have quite a stuffed itinerary this year so I better get going. Unfortunately, I have not found a way to make the itinarary public, which would have been a nice feature: being able to see which posters and sessions your friends have flagged as important.
Just a suggestion for the future "facebook for scientists"...

Saturday 15 November 2008 - 12:11:37 ----- comments: 0

SfN2008   


SfN poster uploaded science | email to someone | printer friendly
Phew! It's been a frantic last 2-3 weeks. Massive teaching schedule, then grading the protocols of the students' experiments and simultaneously preparing the poster for the SfN meeting in Washington DC and the talk I have to give at the Gatsby Charitable Foundation Workshop on "small cognitive systems" the week right after SfN. I'm so glad when I'm finally in the plane over the Atlantic! As usual, I've already uploaded the poster in PDF format for download (1.8MB):

sfn_2008.png

Here's all the info:
Program#/Poster#: 792.12/TT60
Title: Adenylyl cyclase and PKC differentiate operant and classical learning in Drosophila
Location: Washington Convention Center: Hall A-C
Presentation Time: Wednesday, Nov 19, 2008, 11:00 AM -12:00 PM



Thursday 13 November 2008 - 10:53:42 ----- comments: 0

poster   SfN2008   meeting   


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