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Nick Thompson

Daphnia's jeans

Message: 2
From: National Science Foundation Update <[hidden email]>
Date: Thu, 3 Feb 2011 14:47:36 -0600 (CST)
Subject: The Most Genes in an Animal? Tiny Crustacean Holds the Record

The Most Genes in an Animal? Tiny Crustacean Holds the Record
Thu, 03 Feb 2011 13:12:00 -0600

Description: Image of a Daphnia or water flea. Scientists have discovered that the animal with the most genes--about 31,000--is the near-microscopic freshwater crustacean Daphnia pulex, or water flea.

By comparison, humans have about 23,000 genes. Daphnia is the first crustacean to have its genome sequenced.

The water flea's genome is described in a Science paper published this week by members of the Daphnia Genomics Consortium, an international network of scientists led by the Center for Genomics ...

More at http://www.nsf.gov/news/news_summ.jsp?cntn_id=118530&WT.mc_id=USNSF_51&WT.mc_ev=click

Nicholas S. Thompson

Emeritus Professor of Psychology and Biology

Clark University

http://home.earthlink.net/~nickthompson/naturaldesigns/

http://www.cusf.org

============================================================
FRIAM Applied Complexity Group listserv
Meets Fridays 9a-11:30 at cafe at St. John's College
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Eric Charles

Re: Daphnia's jeans

Fascinating! Does this take us arrogant human's down a notch?

I must object though to the conclusion that the water flee has the most genes, followed almost immediately by the admission that we don't know much about the genome of most organisms. Why can't they just say "The most gene of any known species"? (or "species we know about the genes of")

Eric

On Fri, Feb 4, 2011 10:33 AM, "Nicholas Thompson" <[hidden email]> wrote:

Message: 2
From: National Science Foundation Update <nsf-update@...>
Date: Thu, 3 Feb 2011 14:47:36 -0600 (CST)
Subject: The Most Genes in an Animal? Tiny Crustacean Holds the Record

<a href="http://www.nsf.gov/news/news_summ.jsp?cntn_id=118530&WT.mc_id=USNSF_51&WT.mc_ev=click" onclick="window.open('http://www.nsf.gov/news/news_summ.jsp?cntn_id=118530&WT.mc_id=USNSF_51&WT.mc_ev=click');return false;">The Most Genes in an Animal? Tiny Crustacean Holds the Record
Thu, 03 Feb 2011 13:12:00 -0600

Scientists have discovered that the animal with the most genes--about 31,000--is the near-microscopic freshwater crustacean Daphnia pulex, or water flea.

By comparison, humans have about 23,000 genes. Daphnia is the first crustacean to have its genome sequenced.

The water flea's genome is described in a Science paper published this week by members of the Daphnia Genomics Consortium, an international network of scientists led by the Center for Genomics ...

More at <a href="http://www.nsf.gov/news/news_summ.jsp?cntn_id=118530&WT.mc_id=USNSF_51&WT.mc_ev=click" onclick="window.open('http://www.nsf.gov/news/news_summ.jsp?cntn_id=118530&WT.mc_id=USNSF_51&WT.mc_ev=click');return false;">http://www.nsf.gov/news/news_summ.jsp?cntn_id=118530&WT.mc_id=USNSF_51&WT.mc_ev=click

Nicholas S. Thompson

Emeritus Professor of Psychology and Biology

Clark University

<a href="http://home.earthlink.net/%7Enickthompson/naturaldesigns/" onclick="window.open('http://home.earthlink.net/~nickthompson/naturaldesigns/');return false;">http://home.earthlink.net/~nickthompson/naturaldesigns/

<a href="http://www.cusf.org/" onclick="window.open('http://www.cusf.org/');return false;">http://www.cusf.org
============================================================
FRIAM Applied Complexity Group listserv
Meets Fridays 9a-11:30 at cafe at St. John's College
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Eric Charles

Professional Student and
Assistant Professor of Psychology
Penn State University
Altoona, PA 16601

Jochen Fromm-5

Re: Daphnia's jeans

In reply to this post by Nick Thompson

How many memes does a mind have?
What would be needed to reconstruct a mind?

-J.

============================================================
FRIAM Applied Complexity Group listserv
Meets Fridays 9a-11:30 at cafe at St. John's College
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Nick Thompson

Re: Daphnia's jeans

In reply to this post by Nick Thompson

I bet you somebody will post something in the next day claiming that humans have fewer genes because they have a larger brain “instead”.

I will pre-perjoratize that idea as crap.

Nick

From: [hidden email] [mailto:[hidden email]] On Behalf Of Parks, Raymond
Sent: Friday, February 04, 2011 10:18 AM
To: '[hidden email]'
Subject: Re: [FRIAM] Daphnia's jeans

That raises a number of interesting questions.

1. Is there more survival advantage in a higher number of genes or in a lower number of genes? On the one hand Daphnia has a 50% greater chance of random mutation from external factors - on the other hand, Daphnia has a 50% greater chance of absorbing damage without mutation.

2. Since Daphnia is a non-vertebrate I'm going to assume it's ancestors evolved long before man. Does this mean life has evolved from more genes to less?

3. I believe that good engineering is as much about removing what is unnecessary as adding to a design. Is this proof of good engineering in evolution?

4. Alternately (and this gets into complexity), is the expression of genes in the living creature an emergent process? Does the number of genes have an effect on that emergence?

Ray Parks

From: Nicholas Thompson [mailto:[hidden email]]
Sent: Friday, February 04, 2011 08:33 AM
To: The Friday Morning Applied Complexity Coffee Group <[hidden email]>
Subject: [FRIAM] Daphnia's jeans

Message: 2
From: National Science Foundation Update <[hidden email]>
Date: Thu, 3 Feb 2011 14:47:36 -0600 (CST)
Subject: The Most Genes in an Animal? Tiny Crustacean Holds the Record

The Most Genes in an Animal? Tiny Crustacean Holds the Record
Thu, 03 Feb 2011 13:12:00 -0600

By comparison, humans have about 23,000 genes. Daphnia is the first crustacean to have its genome sequenced.

The water flea's genome is described in a Science paper published this week by members of the Daphnia Genomics Consortium, an international network of scientists led by the Center for Genomics ...

More at http://www.nsf.gov/news/news_summ.jsp?cntn_id=118530&WT.mc_id=USNSF_51&WT.mc_ev=click

Nicholas S. Thompson

Emeritus Professor of Psychology and Biology

Clark University

http://home.earthlink.net/~nickthompson/naturaldesigns/

http://www.cusf.org

David Eric Smith

Re: Daphnia's jeans

I should be quiet because this is not my area.

But the evo-devo people around me seem very often to say that, in the
domain of large multicellular organisms, much of the change between
species comes from altering regulatory pathways and systems, not
generally from altering (numbers of) genes, or the overt things that
genes code for.

I assume that a valid way to put some of these questions would be to
suppose that adaptation to environments, filtered through the
complexity and pre-commitments that constitute development, can be
carried on structures of many kinds. The algorithmic complexity of
regulation or response may not be easily tracked by numbers of genes,
to the extent that more "structural" adaptations such as catalysts or
transporters are.

We then wonder what determines the apportioning of the information
representations that constitute adaptation, or of control functions.
Why some adaptations through duplication, divergence, and
specialization of genes. Why other adaptation through changing the
combinatorics with which regulatory proteins respond to signals or
determine expression levels? Why some controls through protein
regulators, other controls through small RNA regulators? Perhaps
other controls through epigenetic modifications of either DNA or its
structuring proteins. Why some adaptation through changing
"hard-wired" internal representations of the environment, and other
adaptation implicit in algorithms for responding to environmental
states as signals?

I think these are ways of putting the questions that allow us to look
for characteristics of the environment and of the material an organism
has available to build with, which can acknowledge evidence like gene
counts, but not pre-interpret it (?).

Eric

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Meets Fridays 9a-11:30 at cafe at St. John's College
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lrudolph

Re: Daphnia's jeans

In reply to this post by Nick Thompson

On 4 Feb 2011 at 14:33, Nicholas Thompson wrote:

> I bet you somebody will post something in the next day claiming that humans have fewer genes because they have a larger brain "instead".

As the saying goes, what counts isn't the size of your
genome, it's how you use it.

To a first order approximation, if you (a species)
are making a living, you're using your genome just fine.

To second order, perhaps, how *long* (in years? generations?)
you've been makiung a living might come in.

But to first order, humans and Daphnia are tied (along
with a bunch of other stuff).

============================================================
FRIAM Applied Complexity Group listserv
Meets Fridays 9a-11:30 at cafe at St. John's College
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Vladimyr Burachynsky

Re: Daphnia's jeans

In reply to this post by Jochen Fromm-5

Jochen Fromm " What would be needed to reconstruct a mind?"

I had to respond, I suspect a kind of Koan content to the question.
Reconstruct or Construct?? Since the latter does not seem to have occurred
historically I am not sure the former is possible at this time.

Then I bumped into one of Hume's references. "The mind is a theatre.."
Basically a picture show of unrelated images played out and given a meaning
from some arbitrary emotional reservoir. If the mind is basically
irrational and built upon a set of compulsions for emotional gratification
then perhaps it is not unlike a flock. Each picture wishes to be the center
of attention providing links to emotional rewards.

Lucien Goldmann, being very clever and linguistically obtuse seems to
suspect that the class consciousness of Heidegger, Lukacs and Marx is not
actually real and some how still depends on the acts and thoughts of
individuals(he does not actually come out and deny group consciousness but
he certainly goes a long way toward dismantling the concept) . If a class
consciousness while apparently real to us is an emergent phenomena defying
easy explanation( or even proof of existing) perhaps our minds are also an
assembly of individual emotional entities the whole of which is equally
elusive of definition. I am Only thinking out loud.

I have been struggling to understand 20th century European philosophers and
the complex language, is a problem for me . But My intuition suggests that
they were struggling to define a Mind from a perspective that kept shifting.
Flocks are not sentient so they are simple by comparison to Minds but they
may be usefully analogous. The thread of the moderns is that two distinct
realities seem to exist for the mind, the one fabricated from the senses and
the other outside and beyond immediate perception.

So is a mind a machine flipping through random images attempting to
construct a self gratifying Narrative to explain away each and every obvious
contradiction introduced by flawed perception? Perhaps literature gives us a
window into the way we construct individual realities, if each mind finds
difficult contradictions then perhaps literature provides temporary
solutions in favour of simple magical explanations. Is it possible to build
a mind on such simplistic foundations and then perhaps we can reconstruct a
mind that is less dependent on self gratification. Funny that in some way
the addiction to emotional rewards is every bit as crippling as a drug
addiction which simply intensifies the effects of the original.

It is interesting that philosophers from prior to the French revolution have
been focused on Group and Individual properties and attempting to
rationalize these unknowns. We have often attributed to the Group a mind as
if it were an individual, Hobbe's Leviathan is perhaps the first clear
presentation of the idea. We seem to suspect that examination of groups
will produce insight into individual minds.

As for the question regarding the number of memes, I will back off not being
certain that even Dawkins knew for certain what he had exposed. If class
consciousness does not exist except in some action then perhaps emergent
behaviour requires some more discussion and clarification. Especially when
dealing with living sentients.

Miraculously I made it through years of education without any exposure to
philosophy or humanities and only in old age do I have the patience to
persevere. I must admit I once arrogantly mocked such pursuits. I now
regret my past in large part.

So shall we begin by Building a Theatre (akin to Hume's) and supplying it
with images(Props) and then allow the director and stage manager to appear
then a script writer to make sure each performance is consistent(A number of
agents coupled to form a single entity akin to Hobbe's Leviathan)? . It
looks like a number of Auto Agents forced to cooperate, however we can not
distinguish if it is mindlike until it produces something. That seems to be
a problem, what would it have to produce before we accept that some Mind
even exists.? That evidence we need would seem in some way a little like
Praxis, an effect upon the world akin to Lucien Goldmann and Georg Lukacs'
use of the ideas. Further more the programming of the Agent constituents
would now seem to qualify in some way as equivalent to Dawkin's memes. The
meme does not appear to be an established concept within the recent
philosophical theses. That is not the only oddity I have noticed, the other
is a slow acceptance of feedback loops creating complexity. Marx seems to
venture into such ideas only marginally but considering the time in which he
wrote he must have been seriously handicapped in the available language
tools. ( I am not a Marxist, just curious) However with careful reading I
think there has always been passages alluding to complexity before the idea
was given full acknowledgment. Complexity lurks deep in philosophy. There
were references to Lukacs in Goldmann's work that sound as if he knew
exactly how to arrange various Agents to achieve social transformations.
There is a curious mention of Groups requiring an external member loosely
associated for the purpose of a global perspective while the majority are
focused on tasks at hand. The loosely associated agent can steer the group
and deliver it new knowledge(Memes) which the group can rapidly assimilate
and manifest as concrete reality through action. There is some
acknowledgement about the instability and lifespan perhaps someone has more
insight into these issues. I am not a philosopher and venture to say that
nothing I say could be trusted in the least. But if others in this group
poke around a bit perhaps we can build some understanding( I hope deeply).

I appreciate your tolerance of my musings, I would prefer sitting beneath a
Linden tree and drinking German beer. Bertrand Russell never quite knew how
to regard the Heidegger line of thinking and mentions them almost
dismissivly and quickly moves on to beating upon Existentialists, but that
was a different era. I suspect that if Complexity Theory had been around
earlier the entire line of Western Philosophy would have changed.

-----Original Message-----
From: [hidden email] [mailto:[hidden email]] On Behalf
Of Jochen Fromm
Sent: February-04-11 3:25 PM
To: The Friday Morning Applied Complexity Coffee Group
Subject: Re: [FRIAM] Daphnia's jeans

How many memes does a mind have?
What would be needed to reconstruct a mind?

-J.

============================================================
FRIAM Applied Complexity Group listserv
Meets Fridays 9a-11:30 at cafe at St. John's College lectures, archives,
unsubscribe, maps at http://www.friam.org

============================================================
FRIAM Applied Complexity Group listserv
Meets Fridays 9a-11:30 at cafe at St. John's College
lectures, archives, unsubscribe, maps at http://www.friam.org

Jochen Fromm-5

Re: Reconstructing Minds and Soul Dust (was: Daphnia's jeans)

As Eric said I should be quiet because this
is not my area, but I cannot resist :-)
I think these questions are interesting.
Can we (re-)construct minds from different
parts or pieces ? Is there a blueprint for
a soul (whatever that is)? If genes construct
bodies, then maybe memes construct minds.

An autobiography is maybe the thing which
is perhaps the most similar to such a
blueprint. One difference to genetic blueprints
is the temporal relationship: genetic blueprints
exist before the life of the individual, whereas
autobiographies exist only after the life of
the individual. During our life, our personality
is reinforced and we become more like ourselves.

Yet autobiographies of other people and
ancestors can be used to "build new souls".
"Holy books" are often autobiographies of
famous prophets or represent the history of
whole countries and cultures. Maybe stories,
fairy tales, myths, "holy books" and belief systems
in general (or all set of rules and ideas which specify
the right kind of behavior) can be considered
as "memetic blueprints" to build souls? Are
they the scripts which contain the rules that
direct our plays?

If a body is a 3-dimensional entity, how much
dimensions does a mind or a soul have? How many
memes are needed to "make a mind"? I would
say it depends. Maybe at least as many dimensions
as roles which a person plays. A person plays
many roles, related to nationality, language, family,
work, etc. Each role is associated with a bundle
of behavior patterns or a set of memes. Do you
agree?

By the way has anyone read "Soul Dust" from
Nicholas Humphrey http://www.humphrey.org.uk/ ?
Is it worth reading?

-J.

============================================================
FRIAM Applied Complexity Group listserv
Meets Fridays 9a-11:30 at cafe at St. John's College
lectures, archives, unsubscribe, maps at http://www.friam.org

Carl Tollander

Re: Daphnia's jeans

In reply to this post by Nick Thompson

Perhaps it is the other way around. That more complex structures and processes evolve as a consequence of some developmental ability to do ever more with less (where 'less' may mean less pre-specification). While it may be an understatement that that would be kind of cool if it were so in general, it's also somewhat pejorative-worthy and it posits a mechanism for the emergence of such linkage, the explanation of which may lie beyond my pay grade, in one direction or another.

Notice that framing things this way might change the questions at hand away from how I get some selection-advantage at a lower-level form of algorithmic complexity from having a smaller (or more compressed) genome.

Carl

On 2/4/11 2:33 PM, Nicholas Thompson wrote:

I bet you somebody will post something in the next day claiming that humans have fewer genes because they have a larger brain “instead”.

I will pre-perjoratize that idea as crap.

Nick

From: [hidden email] [[hidden email]] On Behalf Of Parks, Raymond
Sent: Friday, February 04, 2011 10:18 AM
To: '[hidden email]'
Subject: Re: [FRIAM] Daphnia's jeans

That raises a number of interesting questions.

1. Is there more survival advantage in a higher number of genes or in a lower number of genes? On the one hand Daphnia has a 50% greater chance of random mutation from external factors - on the other hand, Daphnia has a 50% greater chance of absorbing damage without mutation.

2. Since Daphnia is a non-vertebrate I'm going to assume it's ancestors evolved long before man. Does this mean life has evolved from more genes to less?

3. I believe that good engineering is as much about removing what is unnecessary as adding to a design. Is this proof of good engineering in evolution?

4. Alternately (and this gets into complexity), is the expression of genes in the living creature an emergent process? Does the number of genes have an effect on that emergence?

Ray Parks

From: Nicholas Thompson [[hidden email]]
Sent: Friday, February 04, 2011 08:33 AM
To: The Friday Morning Applied Complexity Coffee Group [hidden email]
Subject: [FRIAM] Daphnia's jeans

Message: 2
From: National Science Foundation Update <[hidden email]>
Date: Thu, 3 Feb 2011 14:47:36 -0600 (CST)
Subject: The Most Genes in an Animal? Tiny Crustacean Holds the Record

The Most Genes in an Animal? Tiny Crustacean Holds the Record
Thu, 03 Feb 2011 13:12:00 -0600

Scientists have discovered that the animal with the most genes--about 31,000--is the near-microscopic freshwater crustacean Daphnia pulex, or water flea.

By comparison, humans have about 23,000 genes. Daphnia is the first crustacean to have its genome sequenced.

The water flea's genome is described in a Science paper published this week by members of the Daphnia Genomics Consortium, an international network of scientists led by the Center for Genomics ...

More at http://www.nsf.gov/news/news_summ.jsp?cntn_id=118530&WT.mc_id=USNSF_51&WT.mc_ev=click

Nicholas S. Thompson

Emeritus Professor of Psychology and Biology

Clark University

http://home.earthlink.net/~nickthompson/naturaldesigns/

http://www.cusf.org
============================================================
FRIAM Applied Complexity Group listserv
Meets Fridays 9a-11:30 at cafe at St. John's College
lectures, archives, unsubscribe, maps at http://www.friam.org