Is DNA the Blueprint of Intelligence?

[apeiron]

Further examples of actual papers that some cannot be bothered to read because their views are already decided...

http://bib.oxfordjournals.org/cgi/reprint/2/3/258

With the availability of quantitative data on the transcriptome and proteome level, there is an increasing interest in formal mathematical models of gene expression and regulation. International conferences, research institutes and research groups concerned with systems biology have appeared in recent years and systems theory, the study of organisation and behaviour per se, is indeed a natural conceptual framework for such a task. This is, however, not the first time that systems theory has been applied in modelling cellular processes. Notably in the 1960s systems theory and biology enjoyed considerable interest among eminent scientists, mathematicians and engineers. Why did these early attempts vanish from research agendas? Here we shall review the domain of systems theory, its application to biology and the lessons that can be learned from the work of Robert Rosen.

The work of Robert Rosen is important in that he not only identified
the weaknesses of our common approach to represent natural systems but he also
outlined a possible way to transcend the reactive paradigm in order to obtain
representations of anticipatory systems.

One of Rosen's achievements is that he introduced a formalism rich enough in entailment to allow final causation without implying teleology. The conceptual framework in which he developed his relational biology is category theory.

His conceptual framework arose from a criticism of the transfer of principles of Newtonian physics to biology. It is in this context that his work deserves renewed interest in the postgenome era of biology and bionformatics. One of the challenges for the emerging field of systems biology is then to link abstract mathematical models, like for example (M,R)-systems, to specific current problems of genomics. An important difference from the 1960s is the availability of three types of gene expression data at different levels: genome level (sequences), transcriptome level (microarrays) and proteome level (mass spectroscopy, gel techniques).

 

[apeiron]

http://www.zbi.ee/~kalevi/textorg.htm

Signs appear as a result of the categorisation process which takes place with the interaction of texts. This can be interpreted as a primary form of anticipation learning. The behaviour of the sequential organic molecules with a high combinatorial potential gives rise to several features which are isomorphic with those of semiotic systems, and text. Organism is a text to itself since it requires reading and re-presentation of its own structures for its existence, e.g., for growth and reparation; it also uses reading of its memory when functioning. This defines an organism as a self-reading text. Anticipation is a property which primarily appears in autocatalytic cycles. For textual autocatalytic systems, anticipation could be represented as a sign.

 

[JoeDawg]

http://www.zbi.ee/~kalevi/textorg.htm

Well of course there is a teleology to biological replication.
But evolution is more than just replication.

Genomes don't select for two legs, all they do is implement a selection. The 'selection' for two legs, happens because of a random mutation, and then enviromental pressure, within populations(not genomes).

Its only after the selection process, that you get a coherent implementation of genomic 'text'.

I don't think your refs are saying what you seem to think they are.
And if those other refs are, I think they are wrong.

 

[binbots]

Is it not possible to see oursleves as AI instead of intellegent. I mean if we create a robot with AI would he not ask and seek all the questions and answers we do. WHo create me? Where did I come from? etc. I see us as amazing biological machines designed by our cells for our cells. The machine became so advanced that it started to question its own existence and thought of itself as a single being. Even though we know we are made up of cells and even more bacteria. Just like evolution gave us legs and eyes, we with this AI survived and began to know things that our cells could not comprehend. We are not smarter just have better tools to observe. Just like if we create AI machines they will start to understand things bigger than us. Intellegence is not something that can be measured. It just is survival of the WHOLE SYSTEM of evolution.

 

[apeiron]

Well of course there is a teleology to biological replication.
But evolution is more than just replication.

You are mixing up development and evolution. Modern biology is learning how to make that distinction. That is the point of Rosen's MR systems for example.

If you are to generalise psychological notions like intelligence to DNA - which was the OP - then intelligence is displaying adaptive behaviour. Adaptation of mental states involves the two aspects of ideas and impressions, anticipations and learning. There is a cycle of activity, an interaction between expectations and what happens.

To apply this to DNA, we would have to shift scale from individuals to the species level of adaptation of course. So the genome is that generalised scale of intelligent and responsive knowing.

Anticipation then relates to the developmental aspects. Learning would be selection - across many individuals and many generations.

You perhaps still want to say the selection, the learning based on "random" mutations come first. But it is really the anticipations that provide the context for any learnings. The output precedes the input - which is what non-systems thinkers feel is so "wrong".

And I say "random" as randomness is always the product of constraint. Genetic variety is gaussian - constrained to a single scale. Unbounded variety is more likely to show a geometric mean. So again, a prediction is being made via anticipatory constraint.

An excellent paper on the patterns of nature is...
http://stevefrank.org/reprints-pdf/09JEBmaxent.pdf

 

[apeiron]

Is it not possible to see oursleves as AI instead of intellegent. I mean if we create a robot with AI would he not ask and seek all the questions and answers we do.

The desire to see all reality in terms of machines continues to be science's biggest philosophical error.

Machine models can be useful - for making machines for example. But the problem displayed over and over in these forums is the inability to think about nature in any other terms.

 

[JoeDawg]

You perhaps still want to say the selection, the learning based on "random" mutations come first.

Yup. Because evolution may have feedback loops, but it progresses linearly.

 

[apeiron]

Yup. Because evolution may have feedback loops, but it progresses linearly.

Which invalidates the idea that anticipation precedes learning how?

 

[JoeDawg]

Which invalidates the idea that anticipation precedes learning how?

Sigh.

 

[apeiron]

Sigh.

Sigh away. Beats having to support your quick assertions with arguments and citations. At least you are aware now there is a rather large literature on these issues.

 

[JoeDawg]

Sigh away. Beats having to support your quick assertions with arguments and citations. At least you are aware now there is a rather large literature on these issues.

Your 'citations' don't seem to support your claims...
All you did is regurgitate half-digested ideas and then repeat them.

Do you really expect anyone to take that seriously?

 

[apeiron]

Your 'citations' don't seem to support your claims...

That is a serious accusation. I think you should either retract it or demonstrate how they fail to demonstrate the fact there is a move to generalise psychological notions such as anticipation to a systems biology approach.

 

[JoeDawg]

That is a serious accusation. I think you should either retract it or demonstrate how they fail to demonstrate the fact there is a move to generalise psychological notions such as anticipation to a systems biology approach.

I've already responded to your claim and your citations.
This is the part where you explain its all based on a dichotomy.

 

[apeiron]

I've already responded to your claim and your citations.
This is the part where you explain its all based on a dichotomy.

Another cop out reply. A series of unsupported smart arse one liners do not make a "response".

And yes of course it is all based on dichotomies. Haven't you noticed that already?

Evo-devo. Category theory. M-R systems. Anticipation and learning. What else are the cited sources talking about?

And also triadics. Peircean semiotics and hierarchy theory.

A symmetry is monadic. Breaking a symmetry is dyadic. Mixing the broken symmetry is triadic. It really is as simple (and complex) as 1,2,3.

As I say, your problem is that you are stuck in a materialist discourse. Only monadic models compute. The sound of one hand imagining it is clapping.

 

[Klockan3]

Apeiron, just because they use a model which treats genome as intelligent do not mean that it is by the standard definition. Saying that genome is intelligent since it produces viable species is like saying that water is intelligent since it always bunches up in such a way as to minimize its potential energy! Clearly since water can solve such hard problems it must be intelligent! And even if you change the attributes of the system water have anticipated this sort of behavior and thus always adapts to any new configuration you might imagine in an instant!

 

[apeiron]

Apeiron, just because they use a model which treats genome as intelligent do not mean that it is by the standard definition. Saying that genome is intelligent since it produces viable species is like saying that water is intelligent since it always bunches up in such a way as to minimize its potential energy! Clearly since water can solve such hard problems it must be intelligent! And even if you change the attributes of the system water have anticipated this sort of behavior and thus always adapts to any new configuration you might imagine in an instant!

Correct. That is what pansemiosis would be. You start at the other end of the problem for a change. Instead of trying to build upwards from dead materials, you go the other way from mental terminology. You take a term like intelligence, or better yet anticipation, and see how it applies to psychology, then biology, then chemistry and physics.

A system with scale does anticipate its future states in some meaningful sense. Once water has formed up into a droplet bound by surface tension, it will carry that state forward into the future, resisting perturbations (up to a point). It becomes a system with a memory.

We could call it something different so that we not accused of some kind of spooky mentalism - hysteresis for instance.

Or we can actually work backwards from complexity to discover simplicity.

A flexible mind has no trouble working in either direction and gets used to modelling in both.

 

[binbots]

Why don't we look at intelligence from a bigger perspective. If we all agree of the rules of evolution then survival and reproduction are the guide lines for defining intellegence. By those standerds we are actually pretty dumb. Humans have not been around very long and we seem to believe that we are on the brink of extiction. If you take reproduction then insects win the battle.

 

[binbots]

If you say that we are smart becuase of say math you forget that math is something we made. You can not judge something you created for it will be bias. If ants could make large machines and weapons and then they blew themselves up would we consider them smart?

 

[apeiron]

Why don't we look at intelligence from a bigger perspective. If we all agree of the rules of evolution then survival and reproduction are the guide lines for defining intellegence. By those standerds we are actually pretty dumb. Humans have not been around very long and we seem to believe that we are on the brink of extiction. If you take reproduction then insects win the battle.

I think you have to separate out the notions of adapted and complex still. One is a measure of the system's equilibrium balance, the other of its sheer intricacy and variety.

So the big question about humans is how much we are an out-of-equilbrium fluctuation, soon to be corrected (whereas insects as part of ecosystems are more "intelligently" adapted - they would score higher on the in-equilibrium measure, and the question then is that what you really mean by intelligence?)

Then there is the separate notion of complexity. This can be measured by the number of different states an anticipatory system can access. Clearly, the human mind can access many more states of memory, imagination, expectation, planning, than even a co-ordinated insect colony, a group mind like an ant or bee colony.

We could also count neural complexity as a surrogate measure of mental complexity. The human brain has something like 1000 trillion connections all shaped by personal history. It is the densest occurence of systems complexity in the known universe.

So if intelligence is measured in terms of anticipatory complexity, humans win hands down.

Putting it all together, we can say that hominids were both at the top of the tree in anticipation terms and also in equilbrium with their environment up until about 100,000 years ago.

Then we broke free of a balanced biological situation with the invention of grammatical speech and the new thing of cultural evolution. Something only humans have.

So we became log/normal. On an exponential growth path against a linear environment. Out of equilibrium. We can see this in terms of population growth, oil consumption, rare Earth consumption, any measure of entropification really.

Our invention of language (memes on top of genes) was a phase change for Earth ecology. It took the biosphere into a new space. The question is what will be left when the new system, a combination of genes and memes, settles to its eventual equilbrium balance, as it must.

Some dream of Kurzweil's singularity. Others would be less optimistic.

 

[Kajahtava]

Most people here seem to work on the assumption that intelligence exists (whatever that means). That human beings who simplify and abstract reality to better cope with it experience such a concept is no guarantee to its existence, and I am sceptical towards its supposed existence.

I believe that if you experience a certain concept but cannot come to a definition of it in hard terms that can be objectively tested and verified you most likely deal with a concept that has no place in serious naturalistic science and instead deal with a concept that human beings subconsciously invent to better deal with the complexity of the world around them, you know, like 'chair' or 'evil'.

It also seems that human narcissism seems to make us hold ourselves as the one 'sentient', some linguistics think that 'human', 'man', 'manus' and 'mind' ultimately come from from one and the same origin I believe. Then there's also stuff like the mirror test which is really nazi science and as shaky as Hitler's attempts to prove the superiority of the German people. If people being able to recognise themselves in the mirror is a proof of their 'self awareness' then likewise it's a proof that humans are not self aware but dogs are because they can recognise themselves from the scent of their piss while humans can't.

 

[apeiron]

I believe that if you experience a certain concept but cannot come to a definition of it in hard terms that can be objectively tested and verified you most likely deal with a concept that has no place in serious naturalistic science and instead deal with a concept that human beings subconsciously invent to better deal with the complexity of the world around them, you know, like 'chair' or 'evil'.
.

The problem is that a word like intelligence seems like a thing rather than a process. Like consciousness, goodness and other troublesome word, it makes the mistake of "entification" - turning processes (which operate in contexts) into entities (which simply exist, entire unto themselves).

Which is why I suggested shifting the discussion to words like anticipation which are clearly processes. Intelligence leaves an ambiguity over what should be measured, in a way that anticipation doesn't.

Then there's also stuff like the mirror test which is really nazi science and as shaky as Hitler's attempts to prove the superiority of the German people. If people being able to recognise themselves in the mirror is a proof of their 'self awareness' then likewise it's a proof that humans are not self aware but dogs are because they can recognise themselves from the scent of their piss while humans can't.

The mirror test actually involves animals noticing a red dot or something similar marked on brow and ear. So it is not about recognising self, it is recognising that something has changed about their appearance.

Nothing shaky about the test itself. How it should be intepreted is another matter. But it does produce repeatable data.

For your dog example, what would happen if they were fed asparagus? Humans often notice something has changed.

 

[Kajahtava]

The problem is that a word like intelligence seems like a thing rather than a process. Like consciousness, goodness and other troublesome word, it makes the mistake of "entification" - turning processes (which operate in contexts) into entities (which simply exist, entire unto themselves).

I'm sceptical towards the existence of 'consciousness', either, most people believe that the interaction of neurons breeds consciousness or 'introspection' or 'self awareness', I shall be bolder and claim that I don't know what they are and that they don't exist, and that human beings in fact do not experience consciousness, they just claim they do, including myself, counter intuitive I suppose.

Which is why I suggested shifting the discussion to words like anticipation which are clearly processes. Intelligence leaves an ambiguity over what should be measured, in a way that anticipation doesn't.

In an empirical sense? One should define when anticipations are not met of course.

The mirror test actually involves animals noticing a red dot or something similar marked on brow and ear. So it is not about recognising self, it is recognising that something has changed about their appearance.

Nothing shaky about the test itself. How it should be intepreted is another matter. But it does produce repeatable data.

Fair enough, but you can say that about any test. If I drop water in a bowl and see it fall and then thereby have claimed to prove that ghosts exist? I mean, it's reproducible all right, a lot of things are. I just think very little conclusions can be drawn from this, and the test is politically laden and invented primarily around human beings, first they decided upon a thing that human beings share, then they tried to see if other animals also did. No one would make such a a test and observe from it that humans fail it and thus conclude that humans lack sentience, but dogs have it aplenty.

Also, Wikipedia makes no mention of the dot, and as unreliable you may find wikipedia, I find it more reliable than most sites, and certainly than a random user on a forum if I may be so bold to say so.

Also, it's not as reproducible as one might think, various individuals of species passed it with not extremely similar degrees, then again 'species', is guilty of the principle, it doesn't truly exist, it's just an abstraction the human mind makes to categorized and thus reserve brainpower.

Of course, most animals' primary senses is their nose, not their eyes.

For your dog example, what would happen if they were fed asparagus? Humans often notice something has changed.

Dogs however do so a lot sooner. I doubt a human being would smell from a dog that she's ready for it, male dogs have no trouble whatsoever.

Which is also why I find 'sexually dimorphic' an awkward category for species, it's at max 'sexually dimorphic' to the perception of humans. Fruit flies have no trouble seeing the difference between their sexes, and I doubt they'd notice the difference between a human being and a chimp, let alone a male and female human.

 

[apeiron]

I shall be bolder and claim that I don't know what they are and that they don't exist, and that human beings in fact do not experience consciousness, they just claim they do, including myself, counter intuitive I suppose.
.

Well, that trumps Descartes I guess.

the test is politically laden and invented primarily around human beings, first they decided upon a thing that human beings share, then they tried to see if other animals also did. No one would make such a a test and observe from it that humans fail it and thus conclude that humans lack sentience, but dogs have it aplenty.
.

I think what the researchers were trying to show, and did indeed show, was that there was a gradation in this regard from animals to humans.

Also, Wikipedia makes no mention of the dot, and as unreliable you may find wikipedia, I find it more reliable than most sites, and certainly than a random user on a forum if I may be so bold to say so.
.

I agree. Wiki is reliable. See http://en.wikipedia.org/wiki/Mirror_test and read the second paragraph.

Gordon Gallup built on these observations by devising a test that attempts to gauge self-awareness by determining whether an animal can recognize its own reflection in a mirror as an image of itself. This is accomplished by surreptitiously marking the animal with two odourless dye spots. The test spot is on a part of the animal that would be visible in front of a mirror, while the control spot is in an accessible but hidden part of the animal's body. Scientists observe if the animal reacts in a manner consistent with it being aware that the test dye is located on its own body while ignoring the control dye. Such behaviour might include turning and adjusting of the body in order to better view the marking in the mirror, or poking at the marking on its own body with a limb while viewing the mirror.

 

[Kajahtava]

Well, that trumps Descartes I guess.

Je dis que je pense donc je dis que je suis.

Of course, that I think suffices as proof for me that I think, but that I think is not a given, it is a naïve assumption. I find the hypothesis that all humans have no more or less feeling than a random rock and just process signals by the laws of physics and have evolved to become a sophisticated and adaptive swarm-intelligence based computer to be a lot simpler. With respect to the lethal weapon of Mr. Ockam, it explains all the observed data, that humans claim they are self-aware can easily be attributed to that doing so of course enhances their chances of survival. And it removes the complicated and vague issues like 'where does consciousness come from?', 'do other people have a mind?', 'what is consciousness?', by just not making the axiom that human beings are conscious, which is different than making the axiom that they are not, just leaving it out of the whole schlump, we can answer all quaestions, and needn't raise any new ones.

I think what the researchers were trying to show, and did indeed show, was that there was a gradation in this regard from animals to humans.

Sure, but we can show a gradation in many things, we can probably show that humans have one of the best senses of balance on the planet. However, does that bring us to any meaningful data on 'self awareness'?

I agree. Wiki is reliable.

Ahh, good, I was afraid the wiki card would be pulled. Wiki system isn't perfect, but it's a hell more reliable than for instance a newspaper or just a random site on the web made by one person with Ph.D. behind his or her name. A million people that can edit also means that a million people can check for errors, and the sourcing policy is quite okay.

See http://en.wikipedia.org/wiki/Mirror_test and read the second paragraph.

Indeed, I just read it, and I agree that the test is flawed in its usual context. We can us it to some extend to see what animals realize visually that another animal copies their every move, but that's about it. It's not really self awareness, and for all we know it just tests egocentricity, ahaha.

Also, I find 'self awareness' far too vague to be tested. If I make a computer program that prints "I know that I am a computer program and that I my only capability is informing you of what I am." then surely I have just programmed a very simple intelligence that does some computation and accurately is able to describe what it is, is it then self-aware?