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:

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:

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.


Having sex with robots to save the planet

Long long ago, there was an accident in a warm puddle. A particular molecule – through some chance interaction with the soup of surrounding molecules – ended up with a copy of itself. Since the surrounding soup was similar to the original, the copy was more likely to replicate itself. And so it did. The rest is history. We call it evolution.

It is possible that similar accidents happened elsewhere around the same time – not just in one single puddle. One could also say that variations of this accident are still happening – only now at a massive scale.

Every act of every living thing can be seen as an elaboration of this original act. Self-replication is the original impetus of all life. We share a common ancestor with amoebas – who replicate asexually. The invention of sexual reproduction boosted genetic creativity. More recently in the scope of Earth’s history, creativity escaped the confines of genetics. We humans are the primary hosts of this creative engine.

Human beings have contrived all of the resulting aspects of survival to an art-form. This includes – not just the act of sex – but also the act of preparing food (cuisine), the act of making sounds and speaking (music and singing), and the act of altering the environment to create new structure (visual art). The abstractions and representations of the world that the brain generates via the body are derivations and deviations from the original acts of survival. It’s a form of self-replication.

The emergence of abstractions, mental models, and representations is increasing in complexity. This is an inevitable one-way blossoming accelerated by the emergence of the animal brain. The human experience is conflicted; we are oriented toward achieving escape velocity from Original Nature, but we also long for Original Nature. How can we resolve this conflict?

The original act of self-replication has powerful repercussions – billions of years after the original accident – it has taken on many forms. It is the reason we humans have strange phenomena like orgasm. And selfies.


We are at a crossroads in the history of life on Earth. The current era of global warming is almost certainly the result of the overpopulation and hyperactivity of humans, who have released – and continue to release – too much carbon into the atmosphere. One effective solution to global warming would be to reduce the primary agents of the fever…to reduce human population.

And so, converting that original act of replication into works of art is not just creative and exciting: it may be necessary. Humans must transcend the Earthly act of self-replication in order to preserve the health of the planet.

The future of sex will be…let’s just say…interesting. Every cell in our body contains the blueprint of a desire to replicate. Nature and society are structured around the elaborate machinery that has emerged to ensure self-replication – of human bodies and culture. This desire has made its mark on every aspect of society – even if we don’t recognize it as such. We cannot escape it. And so we need to virtualize it, because self-replication of human beings (physically) has become a threat to the planet that sustains us. It’s our duty to Mother Earth.

I am a living organism and so I have to contend with this crazy desire to replicate. Note: I am childless. I have never replicated my genes and have no intention to do so at this stage in my life. But I am passionate about replicating ideas, art, words, and software.

Now, what about the title of this blog post? Will people eventually start having sex with robots? It will certainly be more subtle than that. In fact, it has been said that by the time we get to that point, WE will be the robots.

Is this the kind of future I want? Strangely, yes. Because I will have long returned to the Earth – my molecules will have been handed down through generations of living things. I will be a part of Earth’s physiology. My tribe will be bigger than humanity.

One of my molecules may even end up in a warm puddle somewhere.

“The Gene” doesn’t exist. It’s always a tangled hierarchy of genes plus environment

Maybe I’m obsessing over a tiny bit of language here, but I really believe that the language we use has a large impact on the way we think about things, and thus, the way we go about solving problems. Take the concept of “gene” for example.

Everything I’ve leaned about genetics tells me that there is no clear obvious separation of genes and environment. It’s like the boundary of the Mandelbrot Set.

seepferdseepferdIf you try to untangle the source of something to determine whether it is from genes or environment (nature vs. nurture), you usually fail. And that’s because the interactions of genes with the environment is really like the boundary of the Mandelbrot Set. You can keep zooming in, but you’ll never find the boundary.

And this is fundamental to how nature operates.

Both Environment and Genetic Makeup Influence Behavior

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From Wikipedia:

Nature versus nurture debates assume that variation in a trait is primarily due to either genetic differences or environmental differences. However, the current scientific opinion holds that neither genetic differences nor environmental differences are solely responsible for producing phenotypic variation, and that virtually all traits are influenced by both genetic and environmental differences.


it is rarely productive to talk about a “gene” in the singular. “Genes” is almost always a plural concept. And the reason is because the interaction of genes and environment (the fundamental basis for evolution) goes all the way down to the level of the genes themselves. In other words:

At a Basic Level: Genes are the environment for genes

The way a gene is expressed is influenced by the other genes who take part in the choreography of expression.

I originally learned this from reading Richard Dawkins’ The Selfish Gene. From the point of view of the single gene, being the most atomic unit of selection, EVERYTHING other than itself…constitutes the environment. That includes other genes.

So, when you hear a science writer claiming that “Researchers determine that there is no ‘math gene’…”, you should conclude that the author is (1) correct, and (2) ignorant about biology.

Of course there is no math gene. Math skill (or any skill) grows out of a tangled interaction of inherited instinct (genetic makeup) and environmental factors (experience, learning, outside influences). The “nature vs. nurture” debate is counter-productive. The question should not be about determining which is the cause. It should be about determining the way these two factors come together to continually bring the natural world into being.

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Because it’s a tangled hierarchy of influences, people get uncomfortable. Science is supposed to untangle these things, right? Not always. Science can help us understand that tangled hierarchies are actually the norm. That’s nature.

This is not to say that there are no culprit genes for certain diseases or observable traits. They do in fact exist in certain cases. For instance: there do exist “single gene disorders“. But these are usually mutations – deviations of an otherwise natural situation.

John Oliver recently made a compelling rant against science journalism, and how perfectly valid science often gets trivialized, simplified, and even rendered false…for mass consumption.

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There is no single bullet theory in nature. Science writers should spend less time looking for a simple story to catch people’s eye with a punchy headline. Nature is complex…like the Mandelbrot Set. And that’s awesome.

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