On Jan 29, 2012 at 11:05 AM, Evgenii Rudnyi wrote:
I have started reading the paper on a cell as a semiotic system.
It is nice:
“Genes and proteins, in short, are assembled by molecular robots on the basis of outside instructions. They are manufactured molecules, as different from ordinary molecules as artificial objects are from natural ones. Indeed, if we accept the commonsense view that molecules are natural when their structure is determined from within, and artificial when it is determined from without, then genes and proteins can truly be referred to as artificial molecules, as artifacts made by molecular machines. This in turn implies that all biological objects are artifacts, and we arrive at the general conclusion that life is artifact-making.”
I like it. Well, I would say that “from without” should be “from outside”.
while searching on what biosemiotics is, I have found
“I started my career as an entomologist and ecologist, but soon realized that I have to answer more fundamental questions: what is life, how it evolves, learns, and functions.”
It could be a good candidate for the course.
On Jan 30, 2012 at 4:55 PM, Liz Swan wrote:
I’m glad you liked the paper. Barbieri is a very innovative thinker in my opinion. You might want to join the biosemiotics community list-serv.
On Jan 30, 2012 at 6:57 PM, Dick Gordon wrote:
Dear Liz & Evgenii,
Okay, I’ve invited both Barbieri and Sharov to give us talks. By the way, Marcello was my guest at both SUNY/Buffalo and NIH in 1974.
On Jan 30, 2012 at 7:15 PM, Liz Swan wrote:
Great, I think they’d both be great guest lecturers.
On Feb 1, 2012 at 4:03 AM, Dick Gordon wrote:
Alexei Sharov, who runs the Biosemiotics Listserve, has agreed to give us 4 lectures, so I guess we’re covered on it for now. He just has to choose dates. Thanks.
On 2012-02-01, at 11:07 AM, Alexei Sharov wrote:
I have not checked this [Biosemiotics] listserver recently, apparently it is dead. As far as I know there is no active listserver on biosemiotics. The main way of communication so far is attending annual meetings, the next one will be in Tartu, Estonia:
Also we have an e-mail list of about 50 people and this list some times becomes active for a couple of weeks (usually initiated by posting some interesting paper or topic).
There is little unity in the biosemiotics movement. Most recognized leaders (Hoffmeyer, Favareau, Kull etc.) follow closely Peirce and Sebeok. Barbieri builds his own mechanistic version of biosemiotics labeled “organic codes”. I don’t like both approaches and follow the methodology of pragmatism / constructivism / instrumentalism. Most biosemiotic activity is in Europe, and here in US I am rather isolated.
I will schedule my talks in a couple of days, and will certainly include biosemiotics issues into my talks.
How many people usually attend these meetings? Is there a simple way to record them and replay later?
On Feb 1, 2012 at 1:29 PM, Dick Gordon wrote:
Thanks for this lesson in sociology of science! But why is it not catching on in the USA?
On Feb 1, 2012 at 10:23 PM, Liz Swan wrote:
Hi. I don’t know why it is slow to catch on with US biologists (Alexei is right, I was one of the few from the US at the June meeting in NYC) but I think US philosophers are slow to embrace biosemiotics because it sounds continental (philosophy from the continent of Europe) which is much less popular here than mainstream analytic philosophy.
On 2012-02-02, at 9:52 AM, Alexei Sharov wrote:
Liz and Dick,
Yes, it is very difficult to break cultural traditions for Americans! Analytical philosophy may be Ok for physics and engineering (although it seems to fail in cosmology) but it does not work well in biology. But we should not complain because biosemiotics is still in its infancy, and a lot should be done to make it more acceptable for people. We need a better terminology which is not esoteric and can be understood by scientists and common people. Also we need convincing examples of successful practical applications.
On Feb 3, 2012 at 12:34 PM, Liz Swan wrote:
Hi. I was initially attracted to philosophy of biology when in graduate school, probably because I was searching for something like biosemiotics, and was very disappointed by the field. It is mainly just philosophical analysis of terms used in biology, so questions like “what is a gene?” and “what is a species?” motivate tons of literature that engages with the biology from the sidelines but doesn’t make any useful advances in either philosophy or biology (in my humble opinion).
It is hard for me to imagine what ‘successful practical applications’ would look like in biosemiotics. Can you offer an example?
On 2012-02-03, at 1:57 PM, Alexei Sharov wrote:
That’s a good question about ‘practical applications’. I would like to see biosemiotics not just a philosophy, but more like a “systems method” in biology. I agree that good terminology is an important potential output or “product” of biosemiotics. But I hope that biosemiotics can do more than to redesign terms.
So far in science we deal mostly with two levels of reality: (1) human level which deals with the world as we perceive and use it, and (2) “disassembled” level where we partition the world into reasonable independent objects (molecules, particles, planets, organisms) and try to reconstruct the human level-reality from the behavior of these objects. Biosemiotics offers a possibility of using additional levels of reality that correspond to the world as perceived by non-humans (infusoria, ants, cats). As a result, each object becomes multidimensional because it has different meanings for different organisms.
As an example, consider the problem of life origin. Most people think of life origin in structural terms: what is the probability that some simple proto-organism gets assembled by chance in some best possible conditions? You don’t need to be a mathematician to tell that such probability is zero. Now let’s take another approach: try to imagine a simplest system where we can identify signs that encode some heritable properties of that system? It appears that catalytically active molecules can “encode” surface properties of oil microsphere in water, as I explained in attached paper. Moreover, these catalytically active molecules can make evolving functional networks that eventually leads to more complex systems. In contrast to the structural approach, I use a functional method (which most US scientists do not appreciate). First proto- organisms were not “frankensteins” assembled from parts but they were fully functional and autonomous from the beginning (however the functions were very simple at the start).
I hope that biosemiotic thinking will help to understand the functions of genes, which are definitely more complex that most people think. Gene is like a butterfly, which goes through several “life stages”: DNA, mRNA, protein. And the protein may directly or indirectly take care of earlier stages to help them survive and reproduce. Each gene persists for millions of years in organisms who change their environments and habits. Genes persist thanks to their advanced “survival strategies”: diversifying or monopolizing their functions, establishing networks with other genes. So far we know very little about genes. Most of this knowledge comes from knockouts or mutations. However, we detect only those few phenotypes that do not get compensated by other genes. The bulk portion of gene’s functions remains unknown. Biosemiotics helps to make meaningful associations between cellular life and human life. For example, very few people know that the nucleus is a “brain” of a cell, that ribosome is a programmed robot, and mitochondria are like domesticated plants or animals. To understand the function of genes we need to learn how to think in terms of a cell or a gene. Eventually, this may lead to “really practical” applications like regeneration medicine and pharmacology.