[Comp-neuro] Discussion - Kuhn - and brief comments

Asim Roy ASIM.ROY at asu.edu
Thu Sep 4 21:38:55 CEST 2008

Here's something from Wikipedia on adult neurogenesis. The references are below.
"Some authors (particularly  <http://en.wikipedia.org/wiki/Elizabeth_Gould_(psychologist)> Elizabeth Gould) have suggested that adult neurogenesis may also occur in other areas including primate neocortex (e.g., Shankle et al. 1999, Gould et al., 1999b; Zhao et al., 2003), although others, including Rakic (2002), have questioned the  <http://en.wikipedia.org/wiki/Scientific_method> scientific evidence of these findings; in the broad sense, they suggest that the new  <http://en.wikipedia.org/wiki/Cell_(biology)> cells may be  <http://en.wikipedia.org/wiki/Glia> glia. A recent paper by Ponti, Peretto, and Bonfanti found evidence of neuronal neurogenesis in the cerebellum of adult rabbits. [1] <http://en.wikipedia.org/wiki/#cite_note-0> <?xml:namespace prefix = o ns = "urn:schemas-microsoft-com:office:office" />"
Therefore adult neurogenesis may not be restricted to the dentate gyrus. The broader argument here is that the brains of humans and other animals have mechanisms and processes in place to use these new cells, when they occur, to either construct new networks or enhance existing networks. And so adult neurogenesis not only provides the most concrete biological evidence for the "blank slate" idea of ANN, but also the evidence that there are mechanisms and processes in place to utilize it. Given the fact that the brain goes through changes all the time (reconfiguration in terms of new connections, synaptic adjustments), the "blank slate" for learning need not always be from neurogenesis. Learning does take place even when neurogenesis is restricted, but it becomes harder, as shown by many studies, one of which is quoted below. To reiterate the broader point: the brain indeed has mechanisms and processes to work with "blank slates," but the "blank slate" need not always be from neurogenesis. Here's something from a study linking learning and neurogenesis in crickets, from Cayr, Scotto-Lomassese, Malaterre, Strambi and Strambi [2007]:
 "Since the discovery of adult neurogenesis, a major issue is the role of newborn neurons and the function-dependent regulation of adult neurogenesis. We decided to use an animal model with a relatively simple brain to address these questions. In the adult cricket brain as in mammals, new neurons are produced throughout life. This neurogenesis occurs in the main integrative centers of the insect brain, the mushroom bodies (MBs), where the neuroblasts responsible for their formation persist after the imaginal molt. The rate of production of new neurons is controlled not only by internal cues such as morphogenetic hormones but also by external environmental cues.....In search of a functional role for the new cells, we specifically ablated MB neuroblasts in young adults using brain-focused gamma ray irradiation. We developed a learning paradigm adapted to the cricket, which we call the "escape paradigm." Using this operant associative learning test, we showed that crickets lacking neurogenesis exhibited delayed learning and reduced memory retention of the task when olfactory cues were used. Our results suggest that environmental cues are able to influence adult neurogenesis and that, in turn, newly generated neurons participate in olfactory integration, optimizing learning abilities of the animal, and thus its adaptation to its environment." 



        M. Cayr, S. Scotto-Lomassese, J. Malaterre, C. Strambi and A. Strambi, "Understanding the Regulation and Function of Adult Neurogenesis: Contribution from an Insect Model, the House Cricket," Chemical Senses Advance Access, DOI 10.1093/chemse/bjm010, April 2, 2007. 


*	Gould E, Reeves AJ, Graziano MS, Gross CG. (1999b). Neurogenesis in the neocortex of adult primates. Science. Oct 15;286(5439):548-52. PMID 10521353 <http://www.ncbi.nlm.nih.gov/pubmed/10521353>  
*	Ponti G, Peretto B, Bonfanti L (2008). "Genesis of neuronal and glial progenitors in the cerebellar cortex of peripuberal and adult rabbits". PLoS ONE 3 (6): e2366. PMID  <http://www.ncbi.nlm.nih.gov/pubmed/18523645> 18523645. 

*	Rakic P. Neurogenesis in adult primate neocortex: an evaluation of the evidence. (2002). Nat Rev Neurosci. Jan;3(1):65-71. PMID 11823806 <http://www.ncbi.nlm.nih.gov/pubmed/11823806>  

*	Shankle, WR, Rafii, MS, Landing, BH, and Fallon, JH (1999) Approximate doubling of the numbers of neurons in the postnatal human cortex and in 35 specific cytoarchitectonic areas from birth to 72 months. Pediatric and Developmental Pathology 2:244-259. 
*	Zhao M, Momma S, Delfani K, Carlen M, Cassidy RM, Johansson CB, Brismar H, Shupliakov O, Frisen J, Janson AM (2003). Evidence for neurogenesis in the adult mammalian substantia nigra. Proc Natl Acad Sci U S A. Jun 24;100(13):7925-30. PMID 12792021 <http://www.ncbi.nlm.nih.gov/pubmed/12792021>  

-----Original Message-----
From: comp-neuro-bounces at neuroinf.org [mailto:comp-neuro-bounces at neuroinf.org]On Behalf Of Garrison Cottrell
Sent: Wednesday, September 03, 2008 8:30 AM
To: Asim Roy
Cc: CompNeuro List
Subject: Re: [Comp-neuro] Discussion - Kuhn - and brief comments

I hate to jump into this, but... 

Speaking as a true novice, I would like to point out that the neurogenesis that occurs on a daily basis is very specific to the dentate gyrus; if someone knows of "daily neurogenesis" elsewhere, I would like to hear about it. 

This is not the same as learning in an ANN - these new neurons have a specific function, which some of the best minds in our field are currently trying to figure out (see Aimone, J., Wiles, J., & Gage, F. (2006). Potential role for adult neurogenesis in the encoding of time in new memories. Nature Neuroscience, 9(6), 723-727. for one example).

It is only if you don't have a good weight change rule (e.g., STDP) and/or you believe in localist encodings that you need neurogenesis to learn.

(shields up! ;-))


On Sep 2, 2008, at 12:50 PM, Asim Roy wrote:

Asim Roy:  "a "blank slate" simply implies a network whose connection weights and other parameters have not been set yet -"
Jim Bower's response: And, no such thing in biology, where development doesn't end and learning begins - it is continuous, and development probably recapitulating evolutionary history.  Another reason why the mainstream ANN models make no sense.
Jim, would love to get some references for your statement:- "development probably recapitulating evolutionary history." This really is the kind of process in the brain that I am looking for. Just a few references would suffice.
By the way, learning takes place during development too. Just ask anyone in cognitive science. Development is not disassociated from learning. And ANN never implied learning begins after development. That's a misconception. 
On the "blank slate" idea in ANN, just look at the phenomenon of adult neurogenesis. Our adult brains generate new cells in the thousands on a daily basis and they are part of the "blank slate" because they don't come with ready-made connections or anything. The process that you refer to as "development probably recapitulating evolutionary history" is called "learning" in ANN. It's that process that constructs networks out of these new cells and makes them operational.
Asim  Roy
Arizona State University 


-----Original Message-----
From: comp-neuro-bounces at neuroinf.org [ mailto:comp-neuro-bounces at neuroinf.org]On Behalf Of james bower
Sent: Wednesday, August 27, 2008 9:05 AM
To: CompNeuro List
Subject: [Comp-neuro] Discussion - Kuhn - and brief comments

A few brief comments -- given that school has started, and I now have to prepare to "influence" the latest next generation.

First a BIG POINT:

Klaus Stiefel:  pre-paradigmatic " What he meant by that is a disagreement about the basic explainanda"

No, Kuhn was focused on process to quote:  "the early developmental stages of most sciences (are) characterized by continual competition between a number of distinct views of nature, each partially derived from, and all roughly compatible with, the dictates of scientific observation and method,  (In pre-paradigmatic science) what differentiates these various schools (is) not one or another failure of method - they are all "scientific" - but what we shall come to call their incommensurable ways of seeing the world and practicing science within it"  (pg 4 The Structure of Scientific Revolution.)   If this discussion over the last two months doesn't make it clear that, as a field, we currently have "incommensurate ways of seeing the world and practicing science within it"  I don't know what does.  Kuhn goes on to say:  "Men (sic) whose research is based on shared paradigms are committed to the same rules and standards for scientific practice."  Again, this discussion makes it pretty clear to me that we have not yet reached that point. In fact,  (and I would say reflecting this fact) the kind of discussion we have been having here seldom ever happens as we are content (and being pre-paradigmatic can get away with) agreeing to not discuss what we don't agree on, another characteristic of pre-paradigmatic science -- and the reason I don't mind starting these discussions.

Bryan Bishop:  "There's a few too many layers of folk psychology here,"

I agree, and have characterized all of biology as fundamentally folkloric in nature -- based on story telling, with few real definitions of anything.  Something comp bio (neuro) will, I hope, eventually fix.

And on to the approaches we don't agree on:

Bryan Bishop:  "I bet it  becomes clear that trying to do "natural language processing" from statistical inferences doesn't get us as much hard science as the brain could provide."

Of course, I agree -- and also agree that this field continues to be distorted by what is essential snake oil we sell to the Department of Defense about how studying the brain will help win wars.  This rather self serving commitment to "neuro-morphic engineering" as it is now called, has been distorting our science for a while.  In the last 8 years even more dramatically.  

Mario Negrello:  "I'd say instead that some approaches gather more acolytes, and then overflow others in sheer voluminous quantity,"

Unfortunately, as just noted, very often related to who you are selling the science to (funders) and also, unfortunately, how 'easy' the methods are and therefore how many can jump on the bandwagon without much preparation (or even knowledge of the brain in this case)   -- 20 years studying the realistic model of the Purkinje cell and counting.  

Bard Ermentrout:  " I suspect that it would be too hard to adjust parameters for realistic models "

Is hard bad?  Or is the brain, in fact, hard?

Igor Carron: "The groundwork of theory as you put it has, in nuclear technology, always been a way to acquire and use experimental findings." 

And this, in fact, is the value of theory -- not to capture 'truth' as many in comp neuro seem be believe, but to organize experimental studies -- the more the theory is removed from the actual structure of the brain - the more it exists by itself, disconnected from the ability to improve, or more importantly to refute it.

Asim Roy:  "a "blank slate" simply implies a network whose connection weights and other parameters have not been set yet -"

And, no such thing in biology, where development doesn't end and learning begins - it is continuous, and development probably recapitulating evolutionary history.  Another reason why the mainstream ANN models make no sense.

Asim Roy: "Is there a way in computational neuroscience to verify any of these theories of learning? "

Wrong question.

Axel Hutt:  " can (neuro)biology really treat a population of some thousand elements ? "

We will need to figure out how - numerous groups are working on it.

Anibalmastobiza:  "cerebellum, usually considered as a center for motor processing and coordination just  as it was for the basal ganglia that now we know that is also involve in cognition"

While I appreciate the support, I have another question for cognitive neuroscientists, how come anything that lights up in a brain scan becomes a "cognitive center"  seems weird to me.  



Dr. James M. Bower Ph.D.

Professor of Computational Neuroscience

Research Imaging Center
University of Texas Health Science Center - 
-  San Antonio
8403 Floyd Curl Drive
San Antonio Texas  78284-6240

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