Thoughts on Biological Chemistry and Emergence

My dog was licking my face this morning – as he often does in the morning. Many people refuse to let dogs lick their faces. Understandable. I am one of the apparently few people who allow it. There are a few exceptions when I don’t like it, such as right after my dog has eaten stinky dog food. Otherwise, he is a very healthy, tidy and gentle (and smallish) dog. His breath is barely noticeable.

Dog’s lick people’s faces for a number of possible reasons; these are nicely explained in several articles, such as:

https://pets.thenest.com/dogs-lick-humans-faces-5892.html

https://shopus.furbo.com/blogs/knowledge/why-does-dog-lick-my-face

But the proposed reason that most intrigues me is that it is a form of chemical communication. Dogs have such a sophisticated sense of smell that they can actually gather information (dog-like information) about people they are licking. Licking can also have a calming effect on licker and lickee (if you are not a fan of dogs licking your face you may disagree, so just pretend that you’re a dog for a moment).

According to this article:

“Scientists believe that the major source of people’s positive reactions to pets comes from oxytocin, a hormone whose many functions include stimulating social bonding, relaxation and trust, and easing stress. Research has shown that when humans interact with dogsoxytocin levels increase in both species.”

Even more fascinating is a study that indicates that interacting with dogs can have health benefits for humans:

Beneficial Dog Bacteria Up-Regulate Oxytocin and Lower Risk of Obesity

So, having a dog can reduce obesity? That is certainly new to me!

Chemical Ecology

While my dog was licking my face and kicking up his oxytocin, and consequently making me release the same chemical into my bloodstream, I was thinking about how social animals regulate chemistry within their pack. (Similar with the visible/audible dimension: when my dog sends growling signals, I will sometimes get up and check out the window for intruders. He is modulating my behavior). So, I began to see more clearly how chemical exchange might be important for the cohesion of a group of social animals. I suspect there are many more chemicals involved in regulating the behaviors of pack animals – including humans.

And I realized that the orchestration of chemicals – not only in a single animal body – but among a group of animals – is largely invisible to us. But of course: chemicals are too small to see. They are molecules made of atoms. We experience their signaling effects as behaviors and notions. And we humans may have evolved such complex societal structures that we can hardly even recognize the chemical foundations of so much of our social behavior. This is the nature of emergence.

When a new level of emergence takes shape (for instance, when chemistry becomes complex enough to enable replication and variation and therefore genetic-based biology), new, larger structures take on their own agency and begin to regulate their sub-components in turn. Ancient chemistry didn’t just allow an apparatus to emerge that conveys information for replication (genetics); it also allowed a complex network of signaling between organelles, cells, organs, organisms, ecosystems, and societies. Each level gives rise (and gives way) to larger structures.

Emergence and Top-Down Effects

Emergence is a fascinating subject – not only because of the beauty of imagining simple components coming together to make a whole that is larger than the sum of its parts – but because that whole can attain autonomy; it can actually reach down and regulate those components that allowed it to come into existence in the first place. It’s possible that this top-down influence is an innate and necessary property of emergence.

If you are a fan of emergence, like me, you enjoy spinning narratives about how various levels of reality came into existence:

physics
chemistry
biology
intelligence
technology
super intelligence

The name of this blog is “Nature->Brain->Technology” – which is a nod to three of the levels in that list.

Dawkins’ book, The Selfish Gene – triggered new insights on genetics – and some lively debates. Dawkins coined the term “meme”. And I suspect he may have had a sense that the title of the book itself could turn into a meme. It brought forth ideas about how genes are powerful agents that cause an upward cascade of effects, making us do what we do: from the perspective of the selfish gene, we humans are “lumbering robots” whose purpose is to simply ensure its replication. Everything else is an illusion of human purpose. But it may be more subtle than this. Are genes the only things that are “selfish”? Could there be a lower level of selfishness going on?

My new insight from building oxytocin with my dog is that there is another layer of emergence involved, which is more fundamental to genes, and which gave rise to genes. My insight was echoed by an article called “Forget the selfish gene — the evolution of life is driven by the selfish ribosome“, which states:

“The selfish ribosome model closes a big theoretical gap between, on the one hand, the simple biological molecules that can form on mud flats, oceanic thermal vents or via lightning, and on the other hand LUCA, or the Last Universal Common Ancestor, a single-celled organism.”

Anything that smells of Eve is suspect. It’s more likely that there was a sort of distributed “Eve Soup” with a lot of pseudo-replication happening over a very long period of time. It is possible that the origin of life cannot be pinpointed to a single time and space…specifically because it is emergent.

Besides face-licking, there are probably many more phenomena that we have low-dimensional explanations for. They may someday be revealed as the effects of various selfish agents operating on various levels. Emergence is a scientific tool – a conceptual framework – that helps reveal otherwise invisible forces in nature.

For instance: why do we yawn?

The physiological purpose of a yawn remains a mystery. “The real answer so far is we don’t really know why we yawn,”

It may be more productive to stop looking for “the purpose”, and to look at it through the wide lens of emergence.

Music is Language. Language is Improvisation

(This article is re-published and re-edited from a previous version written on December 2004)

People are often amazed by musicians who play by ear, such as pianists who can just pick up melodies and play them on the spot, adding chords, accompanying singers who pause or change keys in mid-tune, inventing harmonies, etc.

I have found that sometimes the people who are the most amazed by improvisation are actually professional musicians who are classically trained – very accomplished musicians in fact – but they rarely engage in the art of improvisation. Many classically-trained concert pianists who can sight-read Bach and Bartok with astonishing skill do not improvise. To them, the magic of inventing musical expression on the spot is curious, impressive – even alien.

Vasily Kandinsky (1866–1944): Komposition 8 (Guggenheim)

As a person who was figuring out Beatles tunes on the guitar with my brother at age nine, improvisation has always been natural – synonymous with the very idea of music. I never had the patience as a young man to interpret a bunch of tiny black dots on a page. Only later in life did I actually learn to read – and even to this day, I have to mumble under my breath: “every…good…boy…does…fine” before I can produce a single note.

Music is About Ears, Not Eyes
I believe that improvising music is no different than speaking – it is in fact the most natural form of music creation. This is because we are a language species, and therefore, we are improvisers by nature. It just so happens that we practice improvisational speaking a lot more than we practice improvisational music.

Reading A Script To Your Husband or Wife
Imagine coming home from work and walking up to your spouse, opening up a booklet and beginning to recite from page 134, third paragraph: “Good evening dear, and how was your day?” That would be ludicrous. Obviously one does not need a script to talk. We are able to construct sentences on the fly, to fit the situation, to express the mood of the moment, and to respond to what the other person had just said. We are improvisational creatures – and our brains have evolved to allow us to do this very well. Every day of a person’s life, a unique sentence – a combination of words – is generated which that person has never said, and will never say again. And of course, that is just the words – those symbolic units that dance around in abstract space. There is much more to natural language than mere words, operating on deeper levels of brain and society. There is intonation, timing, punctuation, body language – essentially, the musical dynamics of speech.

While I am referring to the musicality of speech as the basis for advocating improvised music, I am not making a negative statement about classically-trained musicians who sight-read and do not improvise. I’m just suggesting to those who are amazed by improvisation that… this is where it all started. It’s not amazing at all! It is the origin of music itself.

Playing Back an Improvisation Preserved for Eternity
It would be totally wrong for me to say that musicians who sight read are not creative, or are not engaged in the spiritual level of music. Classically-trained musicians, as well as conductors, are the ones who have allowed us to enter into the minds and souls of Vivaldi, Beethoven, Stravinsky, Satie. And they are certainly more than just technicians who scan manuscripts as if they were records in a juke box. They are interpreters of the original emotion and meaning that was present when the musical piece was composed. Many a tear shed from the eye of a violinist is the same tear that Tchaikovsky shed when he created the original melody. And the fact is, neither you nor I could ever actually hear Tchaikovsky composing. Because he has been dead for a long time. His music is brought to life by living souls. And each interpreter brings his or her mood, individuality, culture, and the technology of the times – into the experience.

Chopin and Monk Interpreters
I recall hearing a radio program about Chopin’s music in which a musical critic referred to “Chopin interpreters”, classical pianists who specialize in expressing the essence of Chopin (at least as far as critics and historians could tell). I’ve even come across the term, “Chopinist”. This is also used in reference to contemporary jazz pianists who play Thelonius Monk – “Monk interpreters”, as well as musical scribes who preserve Monk’s recordings into notation. Any interpreter of a late jazz composer deals with an extra level of interpretation due to the fact that a large part of the composers art was improvisation – performances of the same musical piece were played differently for each recording. In the case of Monk, with his unique manner of weaving syncopated rhythm and harmony and using silent pauses of “thought”, there is an individual cosmology to be understood – one must enter into his mind to see this musical machinery at work.

The Universality of Communicating with Sound
The history of music is probably as old as the history of human speech itself. Like the earliest examples of “art” we know of, created on the walls of caves, music may have had a functional aspect. It may have been a way for humans to communicate to each other in a more ritualistic and transcendent way than the average grunting of daily life.

The world has many materials which the human species has appropriated, all of which produce overtones when struck, plucked, or stroked. Some materials produce more coherent overtone spectra – in which the fundamental frequencies are easily heard: other materials produce complex overtone spectra, and serve a percussive purpose. These overtones are a part of the physical nature of our world, and they are echoed within the language-generating machinery of our brains. Why did dodecaphonic music not free music from the tyranny of harmony? Because the language of music is inherently hierarchical – and this is because of the way physical objects vibrate. And we are physical objects.

I believe that the logic of harmony emerged from two things:

1. physics
2. the need for humans to communicate.

Connect to Your Soul with Music
I would conclude that the joy of creating music is not for the privileged few who have gone through the rigor of seven years at the Conservatory. Music is the underlying sound of our speech. It happens all the time – every day of our lives. To improvise with sound is natural, whether it takes the form of beating rhythms on your knee or cooing to a newborn baby. It is also a way for us to connect to the harmonic logic that resides in the molecular structure of the world. And it’s a way for us to connect to each other with the sounds that lie beneath mere words.

The Information EVOLUTION

I remember several decades ago learning that we were at the beginning of an information revolution. The idea, as I understood it, was that many things are moving towards a digital economy; even wars will become information-based.

The information revolution takes over where the industrial revolution left off.

I am seeing an even bigger picture emerging – it is consistent with the evolution of the universe and Earth’s biosphere.

Screen Shot 2016-06-16 at 10.20.47 AM

At the moment, I can hear a bird of prey (I think it’s a falcon) that comes around this neighborhood every year about this time and makes its call from the tree tops. When I think about the amount of effort that birds make to produce mating calls, and other kinds of communication, I am reminded of how much importance information plays in the biological world. The variety and vigor of bird song is amazing. From an evolutionary point of view, one has to assume that there is great selective pressure to create such energy in organized sound.

money+gorilla+teeth+omg+weird+primatesThis is just a speck of dust in comparison to the evolution of communication in our own species, for whom information is a major driver in our activities. Our faces have evolved to give and receive a very high bandwidth of information between each other (Compare the faces of primates to those of less complex animals and notice the degree to which the face is optimized for giving and receiving information).

Our brains have grown to massive proportions (relatively-speaking) to account for the role that information plays in the way our species survives on the planet.

Now: onto the future of information…

Beaming New Parts to the Space Station

Screen Shot 2016-06-16 at 10.29.58 AM

Guess which is more expensive:

  1. Sending a rocket to the space station with a new part to repair an old one.
  2. Beaming up the instructions to build the part on an on-board 3D printer.

You guessed it.

And this is where some people see society going in general. 3D printing will revolutionize society in a big way. Less moving atoms, More moving bits.

To what degree will the manipulation of bits become more important than the manipulation of atoms?

Not Just a Revolution: Evolution

My sense is that the information revolution is not merely one in a series of human eras: it is the overall trend of life on Earth. We humans are the agents of the latest push in this overall trend.

Some futurists predict that nanotechnology will make it possible to infuse information processing into materials, giving rise to programmable matter. Ray Kurzweil predicts that the deep nano-mingling of matter and information will be the basis for a super-intelligence that can spread throughout the universe.

Okay, whatever.

For now, let’s ride this information wave and try to use the weightlessness of bits to make life better for all people (and all life-forms) on Earth – not just a powerful few.

No Rafi. The brain is not a computer.

Rafi Letzter wrote an article called “If you think your brain is more than a computer, you must accept this fringe idea in physics“.

Screen Shot 2016-06-11 at 12.50.53 PM

The article states the view of computer scientist Scott Aaronson: “…because the brain exists inside the universe, and because computers can simulate the entire universe given enough power, your entire brain can be simulated in a computer.”

Who the fuck said computers can simulate the entire universe?

That is a huge assumption. It’s also wrong.

We need to always look close at the assumptions that people use to build theories. If it can be proven that computers can simulate the entire universe, then this theory will be slightly easier to swallow.

By the way, a computer cannot simulate the entire universe because it would have to simulate itself simulating itself simulating itself.

The human brain is capable of computation, and that’s why humans are able to invent computers.

The very question as to whether the brain “is a computer” is wrong-headed. Does the brain use computation? Of course it does (among other things). Is the brain a computer? Of course it isn’t.

The Singularity is Just One in a Series

I’m reading Kurzweil’s The Singularity is Near.

It occurs to me that the transition that the human race is about to experience is similar to other major transitions that are often described as epochs – paradigm-shifts – in which a new structure emerges over a previous structure. There are six key epochs that Kurzweil describes. (The first four are not unlike epochal stages described by Terrance Deacon and others.)

  1. Physics and Chemistry
  2. Biology and DNA
  3. Brains
  4. Technology
  5. Human Intelligence Merges with Human Technology
  6. Cosmic Intelligence

When a new epoch comes into being, the agents of that new epoch don’t necessarily eradicate, overcome, usurp, reduce, or impede the agents of the previous epoch. Every epoch stands on the shoulders of the last epoch.This is one reason not to fear the Singularity…as if it is going to destroy us or render us un-human. In fact, epoch number 5 may allow us to become more human (a characterization that we could only truly make after the fact – not from our current vantage point).

I like to think of “human” as a verb: as a shift from animal to post-human, because it characterizes our nature of always striving for something more.

animal to posthuman

There are debates raging on whether the Singularity is good or bad for humanity. One way to avoid endless debate is to do the existential act: to make an attempt at determining the fate of humanity, rather than sit passively and make predictions.  As Alan Kay famously said, “the best way to predict the future is to invent it”. We should try to guide the direction of the next epoch as much as we can while we are still the ones in charge.

In a previous article I wrote that criticizes some predictions by Nick Bostrom, I compare our upcoming epochal shift to a shift that happened in the past, when multi-cellular beings evolved. Consider:

Maybe Our AI Will Evolve to Protect Us And the Planet

tree-of-lifeBillions of years ago, single cells decided to come together in order to make bodies, so they could do more using teamwork. Some of these cells were probably worried about the bodies “taking over”. And oh did they! But, these bodies also did their little cells a favor: they kept them alive and provided them with nutrition. Win-win baby!

I am not a full-fledged Singularitarian. I prefer to stay agnostic as long as I can. Its not just a human story. Our Singularity is just the one that is happening to us at the moment.

Similarly, the emergence of previous epochs may have been experienced as Singularities to those that came before.

Why is it a Color “Wheel” and Not a Color “Line”?

This blog post was published in May of 2012 on EyeMath. It is being migrated to this blog, with a few minor changes.

I’ve been discussing color algorithms recently with a colleague at Visual Music Systems.

We’ve been talking about the hue-saturation-value model, which represents color in a more intuitive way for artists and designers than the red-green-blue model. The “hue” component is easily explained in terms of a color wheel.

Ever since I learned about the color wheel in art class as a young boy, I had been under the impression that the colors are cyclical; periodic. In other words, as you move through the color series, it repeats itself: red, orange, yellow, green, blue, violet…and then back to red. You may be thinking, yes of course…that’s how colors work. But now I have a question…

Why?

Consider five domains that can be used as the basis for inventing a color theory:

(1) the physics of light, (2) the human retina, (3) the human brain, (4) the nature of pigment and paint, and (5) visual communication and cultural conventions.

(1) In terms of light physics, the electromagnetic spectrum has a band visible to the human eye with violet at one end and red at the other. Beyond violet is ultraviolet, and beyond red is infrared. Once you pass out of the visible spectrum, there aint no comin’ back. There are no wheels in the electromagnetic spectrum.

(2) In terms of the human retina, our eyes can detect various wavelengths of light. It appears that our color vision system incorporates two schemes: (1) trichromatic (red-green-blue), and (2) the opponent process (red vs. green, blue vs. yellow, black vs. white). I don’t see anything that would lead me to believe that the retina “understands” colors in a periodic fashion, as represented in a color wheel. However, it may be that the retina “encourages” this model to be invented in the human brain…

(3) In terms of the brain, our internal representations of color don’t appear to be based on the one-dimensional electromagnetic spectrum. Other factors are more likely to have influence, such as the physiology of the retina, and the way pigments can be physically mixed together (a human activity dating back thousands of years).

(4) Pigment and paint are very physical materials that we manipulate (using subtractive color), thereby constituting a strong influence on how we think about and categorize color.

(5) Finally: visual communication and culture. This is the domain in which the color wheel was invented, with encouragement from the mixing properties of pigment, the physiology of the retina, and the mathematical processes that are formulated in our brains. (I should mention another influence: technology…such as computergraphical displays).

Red-Green-Blue

Consider the red-green-blue model, which defines a 3D color space – often represented as a cube. This is a common form of the additive color model. Within the volume of the cube, one can trace a circle, or a hexagon, or any other cyclical path one wishes to draw. This cyclical path defines a periodic color representation (a color wheel). A volume yields 2D shapes, traced onto planes that slice through the volume. It’s a process of reducing dimensions.

But the electromagnet spectrum is ONE-DIMENSIONAL. The physical basis for colored light cannot yield a higher-dimensional color space. The red-green-blue model (or any multi-dimensional space) therefore could not originate from the physics of light.

DID HUMANS INVENT PURPLE IN ORDER TO GLUE RED AND VIOLET TOGETHER?

An alternate theory as to the origin of the color wheel is this: the color wheel was created by taking the two ends of the visible spectrum and connecting them to form a loop (and adding some purple to form a connective link). I just learned that Purple is NOT a spectral color (although “violet” is :) Purple can only be made by combining red and blue. Here’s an explanation by Deron Meranda, in a piece called…

PURPLE: THE FAKE COLOR – OR, WHAT REALLY LIES AT THE END OF A RAINBOW?

And here’s a page about how purple is constructed in the retina: HOW CAN PURPLE EXIST?

Did the human mind and human society impose circularity onto the color spectrum in order to contain it? Was this encouraged by the physiology of our eyes, in which various wavelengths are perceived, and mixed (mapping from a one-dimensional color space to a higher-dimensional color space)? Or might it be more a matter of the influence of pigments, and the age-old technology of mixing paints?

Might the color wheel be a metaphorical blend between the color spectrum and the mixing behavior of pigment?

Similar questions can be applied to many mathematical concepts that we take for granted. We understand number and dimensionality because of the ways our bodies, and their senses, map reality to internal representations. And this ultimately influences culture and language, and the ways we discuss things…like color…which influences the algorithms we design.

 

The Evolution of Mathematics on Planet Earth

tumblr_ncxcqixe9k1qzy92fo1_1280

math-heartMany people couldn’t imagine Math and Biology going out on a date. Flirting with each other from time to time…maybe. But a date? Never! Math is precise, abstract, cool, and distant. Biology is messy, unpredictable, prone to mood swings, and chemically dependent…as it were.

But this may be changing.

“The conversion of biology into a more quantifiable science will continue to the extent that it might even become the main driving force behind innovation and development in mathematics”

Philip Hunter

Let me explain why I think Math and Biology are ultimately compatible, and in fact, part of a Single Reality.

tumblr_my165xRv5f1swaxzgo1_250

I have written a few articles on the subject of math, and raised questions as to the universality, truth-status, and God-givenness of Math. Here is something to consider about Math and Biology:

Math Evolved in the Biosphere

Let’s start with numbers. Imagine a mother crow busily feeding her three chicks. She would become worried if she came back to her nest to suddenly find two chicks instead of three.

House_Crow_feeding_chicks

She would know there something is wrong with this picture…because crows can count (they can subitize small numbers, like about 2 or 3).

How did it come about that some animals, like crows and humans, can count? First of all, in order for intelligent beings to be able to count, they have to live in an environment where countable objects are found, and where counting has some evolutionary benefit. Consider a gaseous planet where fluids intermix and there is no way to detect a “thing” or “event” and to compare that with another “thing” or “event”. In this kind of world, there is nothing to count.

seahorseFor that matter, it is unlikely that an intelligent entity that can count could ever evolve on such a planet in the first place, because structure and differentiation at some physical level are required for living things to bootstrap themselves into existence.

Theories of autopoiesis, negentropy, and the emergence of mind from matter rely on the existence of a prior structure to the universe where it is possible for self-regulation, and self-creation to arise. One might say that the origins of life had a head start long before those first molecules started dancing together and accidentally reproducing. Maybe it wasn’t such an accident after all.

imgres

…which brings me to a core concept: since Earth’s biosphere gave rise to animals that can count, as well as those things that can be counted – at the same time, we must understand ourselves as in and of the biosphere – we and it all evolved together: one did not come before the other.

70212-1024x603Which came first: the chicken or the egg? Neither. They have both been in a continual state of becoming since egg-like things and chicken-like things have existed. And if you go back in time far enough, these things look less and less like chickens and eggs.

We animals have evolved to understand containment, and that is partly because hierarchy evolved within the fabric of physical biology. We know what it means for something to be “inside” or “outside” of something else. We clumpify, categorize, differentiate, compare, and identify. All animals need some degree of this compartmentalization of nature in order to operate within it.

We cannot separate our math from the environment from which it evolved. The very foundations of math evolved within the bodies and minds of animals as a part of evolution. At least this is what several recent scientists and philosophers are suggesting. (Mathematicians are more likely to claim that math is universal, constant, and unchanged by biology.)

OctoMath

In a previous article I consider what kind of math would have emerged if octopuses has evolved to become the complex and dominant species on earth, instead of humans. This is not so hard to imagine, considering how intelligent they are.

Screen Shot 2015-08-10 at 12.19.31 AM

Would an advanced octopus race have stumbled upon complex numbers? Would they have become as obsessed with the Cartesian coordinate system as we are? Since they have no skeletons, would they have formulated a geometry based on angles and lengths? Of course we can’t know, but it is likely that they would have created some math concepts that we may never achieve. And that would be because the long history of math that we have built and that we rely on to create new math has taken our brains and societies too far away from the place where an octopus-like math would naturally arise.

mouroborobius2Now consider aliens from a completely different kind of planet than Earth. What kind of math would originate in that world? Many people would argue that math is math and it doesn’t matter who or what discovers or articulates it. And there may be some truth to this. But we can only hope and imagine that this is the case.

Until we meet aliens from another planet and ask them if they understand and appreciate the fibonacci sequence, I have to assume that their math is different than ours.

What do you think?

(I would have consulted one of my octopus friends on the subject…but I don’t speak their language).