Showing posts with label biology. Show all posts
Showing posts with label biology. Show all posts

Thursday, June 18, 2020

The Cosmic Reset


In an early episode of the original Star Trek, aliens put Kirk on a rugged planet to duel with the captain of a rival Gorn ship. Kirk wins as the dinosaur-like Gorn was intelligent but really slow.

On Earth, dinosaurs never became intelligent. Arising 240 million years ago, they survived some 175 million years and for 135 million of those were the dominant land animal. By the time they became extinct, dinosaurs had perfected two ways of living: eating plants or eating each other. The plant eaters were excellent at converting plant matter into animal bulk and could grow very large. The carnivores were very good at using tooth and claw to eat the vegetarians. Some carnivores – such as the raptors – may have hunted in pacts and perhaps had some wolf-like intelligence. But in general, brain power doesn’t seem to have been on the dinosaurs’ primary evolutionary path.

Mammals arose just 10-15 million years after the dinosaurs. But for most of their first 160 million years, they lived underfoot as squirrel-sized, nocturnal plant eaters and insectivores. For this life style, relatively larger brains gave an evolutionary advantage. So under the feet of the dinosaurs, mammals got smart. Still, even with their brains, they could not compete with tooth and claw.

Enter the six-mile wide asteroid that found the earth 66 million years ago. That asteroid – nudged out of its distant orbit by a chance encounter with another rock or after swinging too close to Jupiter or Saturn – had travelled silently on its way for perhaps a million years to arrive just seconds before the earth moved just beyond it in its own orbit. When it hit, it set the earth on fire and after it had burned away, caused a long dark winter that left most creatures dead and many extinct, including the non-avian dinosaurs. This disaster was, however, good news for the mammals. Perhaps because they were small, lived underground and could eat anything, some survived (along with birds, who are smart flying dinosaurs). Within a million years, the earth had recovered and mammals were the dominant large land animal. Some of those eventually evolved even further in reliance on brains, eventually producing us.

That asteroid wiped the slate clean, resetting the course of animal evolution in favor of the brain and intelligence. There is no reason to assume that an additional 66 million years would have led the dinosaurs towards the Gorn as in 175 million, it had not done so. It’s as if the universe has a bias in favor of intelligence and sent a “do-over” to set things right.

Monday, May 18, 2020

Humming along….


The human brain is able to store and retrieve memories spanning the decades of an individual life. This occurs despite the exchange, death and constant rearrangement of our neurons. Which raises the question of how? In the hard drives of modern computers – classical or quantum – data is stored in physical bytes (or qubits). Data is written to them and retrieved from them. They can be re-written but the bits themselves do not otherwise change. If one does change through damage or failure, that bit of information is – generally speaking and leaving aside backups – lost. Computer memory is hard. Ours is soft, organic. Amidst the constant comings and goings of millions of nerve cells, our memories – our very identity and sense of self – remains constant (within the margins of error associated with life and aging). It’s a marvel of evolution, really.

According to a recent study, we owe this happy state of affairs to the fact that “as individual neurons die, our neural networks readjust, fine-tuning their connections to sustain optimal data transmission.” It’s a matter of individual nerve cells and networks of same being both excited and inhibited from discharging, thus maintaining a dynamic balance. Through this process, the entire system (networks of networks) achieves “criticality’ – sustaining an overall state that apparently maintains the data structure despite changes affecting the underlying organic bits. What this means is something like this: our inbuilt self-regulating rhythm of neural activity at the individual nerve, synapse and network levels tends towards an optimal level of brain-wide activity. That allows us to remember stuff even as nerve connections change. It’s like the brain is constantly humming to itself the story of our lives. The humming is the basis of mind and memory.

While one might take the notion of this “humming” as simply a metaphor, the researchers suggest that the mechanism they hypothesize also may explain consciousness. But it seems to me this cannot be the case. Ever listen to a gurgling stream? It kinda hums too. But a stream – okay, as far as we know – is not conscious. But we are. I hum therefore I am.

Saturday, March 21, 2020

COVID-19: The Great Equalizer


By now, the human species has been altering the natural order for some 11000 years. It started with the advent of agriculture and went through urbanization and industrialization which transformed the surface of the earth and began changing a host of natural systems including the climate, animal life, forests and oceans. We humans have known about this for a while. But most of us – especially those of us in the advanced economies and not living too close to the rising waters – could see the impact of our disruption of natural systems as something that would affect other people – future generations, the poor, those living in low-lying island nations – and not so much us in the here and now. COVID-19 has altered that by bringing to all of us the results of our changes to the earth. It has equalized the impact of the destruction of natural environments (which stresses what lives in them thereby making them more prone to diseases that can jump to us), the way we use animals (including how close we live with them and the antibiotics we use to fatten them) and the close quarters (in large numbers) in which we live. Add to this the way we use hydrocarbons to travel and transport, the interconnectedness of our ways of life and economies and the varying shortcomings of our political systems. We should not have been surprised by the current bio-crisis. It’s not that any one of these caused the virus but that the total impact of what we have wrought was largely hidden until now though very much operative.

So COVID-19 shows us that the bill won’t wait to be delivered and that everyone must pay. The rich may be able to retreat to their enclaves and private transport. But their world will change as ours does. The species as a whole will survive. But this is the wake up call. The future disrupted world is upon us now. Returning to “normal” – whenever and whatever that turns out to be – may well be just a breather before the next episode. We need to take the next step in our evolution – remake our economies and politics, restoring nature even if gradually and treating each other more equally – and start now or the humanity that makes it to the 22nd Century may be unrecognizable.

Wednesday, September 25, 2019

Interlude: Unconscious Artificial Intelligence?


I’ve been considering the nature and role of consciousness for some years. Along the way, I’ve wondered about Artificial Intelligence (AI) and whether at some point it might become conscious. My conclusion has been that however complex and “intelligent” an AI would become, that would not produce consciousness. Consciousness requires life and – as at must include at least some degree of self-awareness – it could only be the property of an individual organism with some organized “self.” Machine intelligence might be constructed – coded – to simulate self (and thus pass the Turing Test) but this would nevertheless not be an awareness of self. (Even now, AIs and robots can be quite “clever.” A recent visitor to a Tokyo hotel asked the robot concierge how much it cost. It replied “I’m priceless.” Cute.) However elaborate the mind – in the case of the most advanced AI’s built with neural networks this might be quite sophisticated, even to the point that the human programmers might not be able to replicate its internal processes – consciousness is an additional property beyond mere complexity and processing power. In the first season of HBO’s Westworld, android “hosts” become conscious through the repeated experience of pain and loss. But of course, to feel such emotions, one must first experience them as such. Quantity (of coded processing operations) does not equal qualia. Qualitative experiences are only possible if one is already conscious.

But human beings not only possess a conscious mind but also an unconscious one. Most brain processes – even those that at some point enter consciousness – originate and work away unconsciously. We all have the experience of dreaming and also of doing things quite competently, without any awareness of having done them. (We may, for example, drive a familiar daily route and get to our destination without remembering details of the ride.) The brain processing of the unconscious mind may indeed be replicated by advanced machine intelligence. As AI becomes more complex, given the power of electronic circuits and the complexity of coded learning via neutral networks, the processing capacity of machine intelligence may well exceed human despite not becoming conscious. They would also, perhaps, exceed human ability to understand what they are “thinking” (or even “dreaming”). It was Stephen Hawking who most famously warned of the dangers of such AIs. He warned that we need to be attentive to their management.

So, though AIs may never become conscious or self-aware, they may nevertheless run autonomously along routes enabled by the algorithms coded into their machine DNA and come to “conclusions” we humans might find inconvenient or dangerous. (They might for example decide that human activity is injurious to the planet – which it seems it is – and seek to correct the disease.) Limits should be included in the most basic AI coding and algorithms. Isaac Asimov thought of this some time ago. His Three Laws of Robotics make a good start:

First Law – A robot may not injure a human being or, through inaction, allow a human being to come to harm.

Second Law – A robot must obey the orders given it by human beings except where such orders would conflict with the First Law.
Third Law – A robot must protect its own existence as long as such protection does not conflict with the First or Second Laws.

To these he later added a zeroith law: A robot may not harm humanity, or, by inaction, allow humanity to come to harm.
This last might be might turn out to be a doubled-edged sword.


Next week I will return to  Notes on "A History of Political Theory"

Tuesday, August 28, 2018

Dinosaurs and Intelligence

Dinosaurs arose some 240 million years ago. They became the dominant terrestrial vertebrates after the Triassic–Jurassic extinction event 201 million years ago. Their ascendancy lasted another 135 million years until the Cretaceous mass extinction 66 million years ago opened the world to the eventual rise of mammals and us. The first mammal-like forms appeared some 225 million years ago. But for the next 160 million years, mammals had to find their niches in the shadow of the dinosaurs, characteristically living a nocturnal lifestyle, emerging from burrows to feed only at night. This may have favored the evolution of better eye-sight, smell, touch and hearing to be able to navigate, find food and survive in the dark. But they still had to hide from the dinosaurs.

The question of why dinosaurs never developed cognitive intelligence, despite the many millions of years they were the top vertebrate clade, forms a rich WWW vein. (Search for the question and check it out.) Some dinosaurs did get quite intelligent in the form of birds. Some avian dinosaurs are even tool users. But there is no evidence that dinosaurs ever achieved anything like the human intelligence which has allowed us to alter our environment in ways both planned and unplanned. We human beings (the last surviving species of the homo genus) have been around for only some 200 thousand years. If one starts counting with the Australopithecus, then our progenitors go back around 3.6 million years. In either case, the fact that dinosaurs didn’t develop intelligence and complex technology even over a hundred million years while we did in just a few raises at least two questions: Is the rise of intelligence inevitable and does it have survival value over the long run?

The second question may be easier to answer. Dinosaurs and all other life on earth have done pretty well without human-style intelligence. Indeed, intelligence has not played a major role over the four billion years of life on earth. Some dinosaurs may have been clever hunters, as are wolves for example, and Jurassic Park has shown us a possible example. But they apparently found the use of claw, teeth, armor and size sufficient to last until a huge asteroid took them out with most other life. This leads to an answer to the first question, was the rise of intelligence inevitable. We can never know what might have happened with the clever dinosaurs if they were given the next 65 million years instead of mammals. Large brains need extra oxygen and are costly in energy. Maybe there would never have been any evolutionary advantage to making the investment. Human intelligence may be a cosmic accident, the result of a particular rock hitting at a particular moment allowing the burrowing underclass – mammals – to take their furtive ways into the sunlight.

So to return to the question of the long-term survival value of our big brains, the dinosaurs did really well without them and it is not clear that they will save us from ourselves.

Monday, July 9, 2018

Electrons & Salt

I have been working for the past two months within three degrees of the equator and re-watching The Ascent of Man (an excellent BBC series from the 1970s). Led thereby to consider:

1. the fact that a point on the surface of the earth at the equator spins faster than a point nearer the poles; thus

2. verified according to Einstein's theory of relativity – as speed increases, time must move slower to preserve the absolute limit of the speed of light – time must move a tiny bit slower for me than folks back home up north. 

This led me to wonder what the speed of an electron around an atomic nucleus might be, whether it would approach the speed of light and what that might mean about the nature of reality. The nature of reality is already very strange. Consider that what appears to us as solid matter – from the atom on up – is mostly just empty space. There is so much space inside ordinary matter that you could squeeze our sun down to the size of Manhattan Island (or something like that) and make it one big and very heavy neutron. Things seem solid to us because of electro-static forces that hold together and repel assemblages of atoms and molecules. This strangeness doesn't even include the weirdness of quantum physics. Anyway, what might be going on as an electron spins around inside an atom? 

Of course, electrons actually don't orbit the nucleus like little planets around a sun. Electrons exist in a kind of cloud of probabilities subject to certain allowed energy levels that can be thought of as shells. It is possible, mainly as a thought experiment, to estimate a kind of notional speed of an “orbiting” electron leading to a value of around five million MPH. That is fast but still only about 1% of the speed of light. So while time would certainly pass more slowly for an electron than for me, there would not be any profound relativistic effects. 

This then led me to consider the strangeness of salt. Salt is made from the ionic combination of a poisonous gas (chlorine) and a soft metal that burns in air (sodium). It is also vital to life. Perhaps because life evolved in the sea, sodium and chlorine ions are essential elements for the functioning of core biological systems. What rules of the universe led to the sixth most abundant element in the earth's crust (sodium) marrying so happily and fortuitously with the 21st (chlorine)? 

The sodium atom has a lone electron in its outer shell that it quite willingly donates to the chlorine making the sodium a negative ion and the chlorine a positive ion. That allows the two to remain together through that electro-static charge in a crystal lattice to make common salt. Electrons do not move at relativistic speeds because they are given mass through interaction with the Higgs Field. If they did move at the speed of light, as do massless photons, atoms would not exist and we would not be here.

Saturday, January 27, 2018

If There Was A Cosmological Design, What about the Designer?


I have been speculating about the origins of the universe and consciousness for some time now. Following St. Thomas’ finger, modern science points to an act of creation tightly constrained to produce the universe of matter and energy that we see around us (and in which conscious beings arose). If the fundamental constants of physics were not exactly what they are, if the Higgs boson did not manifest itself in a way to create the menagerie of particles that physics has discovered, the Big Bang would have produced some other kind of universe or perhaps none at all. We discover the laws of nature because they – the laws – appear to be there. They were there from the very first moment something “exploded” into spacetime. We exist in a universe that seems to have been designed according to these laws, or better, was created through using a particular set of fundamental constants and rules.

Of course, if there was a design, it suggests there was a designer. (I’m now reading Mind & Cosmos by Thomas Nagel. He suggests something like a design without a designer but more on that another time.) My question this time is why anything capable of designing a law governed creation on the order of the cosmos would have to use or obey law? The traditional notion of a Transcendental God is a being all-powerful and without constraints. As noted here before, I tend not to believe in such a god. And in fact, it seems that whatever set in motion the particular universe we find ourselves in was constrained to act through rules of the game we now discover as fundamental physics. Could an omnipotent god be constrained? Could not such a god simply call a universe that would look like ours into being by commanding or dreaming it? What kind of “god” would work with a rule book and where would that rule book have come from? Either that rule book precedes its use or for some unknowable reason the god created it in order to use it? What kind of god would do the later? And if the rules predate the god then we have not yet reached the First Cause.

I have no answers to these questions so let me have some fun. Let’s imagine a toolkit of cosmic software that allows the creation of universes. It contains menus of all sorts of starting conditions, rules and variables. A “player” – amateur or professional – plugs in, picks through the many choices available and runs the program. The “machine” cranks and out spews the result. Some might crash immediately, others just sit there shining or in the dark, others maybe moving forward in whatever way the rules encourage. A “successful” run might eventually contain things like stars, planets and people. If this program came on the market here, it would quickly outsell any of Sid Meier’s creations.

I said fun, but this is really a thought experiment for it raises the question of why any designer would create a universe and let it run without further ado. For it seems that the putative designer plays no further part in influencing outcomes. There is good and evil in our world and one must assume that it exists anywhere conscious beings exist. Lots of bad things have happened here on earth – to civilizations, societies, individuals – despite whatever prayers or entities were sent the gods’ way. One might argue that God showed its care for us by allowing us free will, by allowing us reason, by giving us the ability to tell right from wrong. There is scant evidence that that has worked out very well when one looks at the present state of the world, or as my historian friend would say, at any period of history. What possibly could be the intention of the possible designer who set our world in motion? Play, experiment or maybe child-rearing?

What if there was no designer but simply a design and the universe is an example of the eternal return?

Saturday, February 27, 2016

Deep Time: Take Two


It's hard to fully comprehend the depth of time past. The universe came into existence some 13.8 billion years ago (BYA). The earth was formed around 4.5 BYA. The first signs of life – simple microbes – appear about 3.5 BYA. But as presented in a wonderful book about just how complex and essential they are – Life's Engines: How Microbes Made Earth Habitable by Paul Falkowski – microbes are anything but simple. Microbes – bacteria and archaea – are prokaryotes, single cell life without a nucleus or organelles. Everything else – single cell or multi-cell plants and animals – are eukaryotes: cells containing a nucleus and organelles such as mitochondria. The prokaryotes developed the ability to extract energy from the chemical environment and, eventually, from the sun. It took another two billion years for them to evolve into complex cells: the eukaryotes.

Two billion years is a long time. Why did it take that long to go from bacteria and archaea to the first eukaryotes? The machinery to convert chemicals such as hydrogen sulfide or ammonia, and then the much harder task of using sunlight, to fuel life would have taken a long time to develop. But not just that. Extracting energy from the environment meant a complex process of freeing electrons from chemical bonds, transferring those electrons around within the cell and using them ultimately to create other chemicals that would store those electrons (i.e., serve as “food”) to provide energy for cellular processes. Photosynthesis is an even more complex process that uses sunlight to crack electrons from water and combine them – through intermediate steps – with carbon dioxide to produce carbohydrates and, as a waste product, oxygen. This complex machinery had to evolve step by step through the repeated random changes in DNA and RNA as winnowed through natural selection. (A good part of the first billion years after the formation of earth would have been used for the construction of the RNA/DNA mechanism itself.) As Falkowski argues, the processes for producing and consuming biologic energy work as tightly as a complex and precise system of interlocking gears: one out of place and the whole won't work. All the parts of the machinery had to come on line more or less at once or it would not function. Somehow, the machinery evolved anyway, implying that a lot of time was required for vastly more failures – in which the resulting organism from random mutation simply died – than successes.

That the machinery was there to be evolved – that the givens of the universe allowed such a thing to come into existence – is also worth pondering. As is the fact that we would not be here otherwise.

Sunday, June 22, 2014

Familiar Paths


I'm recently back from several months living in the Midwest. I liked it in Des Moines and developed some comfortable routines, including favorite bike rides. But now back home in DC, I've returned to the many paths and byways that I've used for the past 35 years. Being at home feels good for various reasons. It's nice to be back with family and friends. But I get a distinct pleasure from biking or walking along long familiar paths. In certain seasons, I'm drawn to particular greenways. Something about doing this plucks deep neural cords, satisfying an apparently primordial need to keep to the well-worn paths of home. Perhaps it harkens back to the time when we lived in small bands in a particular place where it was vital for survival to know the routes and places where we could find food and water through the changing seasons. Evolution might have favored development of behavior that anchored such knowledge through the release of endorphins when triggered by the right external markers. This might suggest the need for all of us to find ways to allow ourselves to be so anchored along familiar ways that bring us to be somehow in nature.

Just a thought.

Sunday, June 15, 2014

New Letters for the DNA Alphabet


Scientists recently created a life form – using a living bacteria as a starting point – with two extra letters in the DNA alphabet. The DNA of all living creatures on earth is made up of four such letters – the nucleotides A, C, G and T. They pair up – A with T and C with G – to form DNA “words” that direct protein construction and the development and maintenance of every living organism. These scientists added two synthetic nucleotides thus adding two new letters to the genetic code. They note that this opens up the possibility of creating new DNA-based “nanomaterials and proteins with exotic abilities.”

This discovery may be the hidden sleeper of recent scientific developments. When one considers that all of life as we know it – and which we have not even yet discovered all the forms – is built up of long strings of two-letter genetic words, adding a new letter – and why stop there – could open up vast vistas of new products and even new life forms. It may give brand new meaning to “genetically modified.” Cultures that grow rather than construct their technology is a common motif in science fiction. There may be careers out there for those who can write genetic code as we now write computer code.

Monday, March 10, 2014

Life as Striving Towards Self-awareness


The remake of Cosmos began airing last night. Featured a presentation of the time since the Big Bang scaled as a year-long calendar starting January 1 at 13.8 billion years ago (bya) and ending in the last few seconds of December 31 corresponding to the entire time of human recorded history. Been thinking about this immensity of time focusing on recent news of the earliest piece found of the earth’s crust and of the earliest signs of life.

The earth was formed some 4.5 bya. The moon was formed in a colossal collision between earth and a Mars-sized planet some 4.45 bya. That oldest piece of crust – a zircon – has been dated to 4.4 bya. It took some 50 million years after the collision for the earth to cool down enough to have a solid surface. But the earth was still in for further impacts during the Late Heavy Bombardment that lasted until around 3.9 bya. The first signs of life – monocellular bacteria and archaea – appear around 3.5 bya. But it takes almost another two billion years for complex single cell life – the first eukaryotes, cells with nuclei and DNA – to appear. Sexual reproduction follows at about 1.2 bya and the first multicellular life at 1.0 bya. The first fossils of multicellular animals date to around 550 million years ago (mya), fish to 500 mya, land plants to 475 mya, insects to 400 mya, reptiles to 300 mya, mammals to 200 mya and primates to 60 million. Humans are some 2 million years old.

Life was quick to emerge once the earth had a solid surface. It took only 400 million years for inert chemicals interacting somewhere on that surface to become life. To us, that is a long time. But given the leap from non-living to living, maybe not so much. During those 400 million years, the laws of physics and chemistry plus the raw conditions of earth and water somehow gradually led to small clumps of matter coming and staying together and reproducing themselves. The first such clumps that successfully kept out the environment, organized themselves internally and made copies of themselves may have been something like viruses. At what point they crossed from non-living examples of complex chemistry to living things is unknown. But it took another two billion years for those clumps to become the most simple form of single cell life we know and then another billion years years or so to become the simplest form of multicellular life.

Four hundred million years for life to get started, two thousand million to reach the level of bacteria, another one thousand million to reach jellyfish and then fish in 50 million years, plants on land in 25 million, 75 million more for land animals (insects). Some 170 million after the first land animals takes us to dinosaurs and then — clearing the board — their extinction 65 mya. In a blink of an eye, at 60 mya, the first primates appear and then in the past 200,000 years homo sapiens.

Life started quickly but took a long time to build the tool box for evolution by sexual reproduction. It then took off leading to complex life within a comparatively short time and exploded in the last 500 million years. What about the universe might account for the easy start to life, the steady progress of evolution and the relatively fast emergence of higher forms of life and ultimately human awareness?

With the confirmation of the Higgs field, it now seems that the universe beginning with the Big Bang had its properties imprinted from the start. The laws and constants of physics and chemistry seem to conspire to produce the material universe of which we find ourselves part. Atoms emerge from a primordial soup of particles, combine in stellar processes to form elements and eventually become planets. Stars themselves combine the simplest elements in such a way as to provide copious amounts of free energy. The Kepler program has confirmed that planets are common and most stars have them. Put together a planet like the early earth – and there probably are millions of them in our galaxy alone – and wait 400 million years or so and life may emerge. Given a degree of long term stability, it may become self-aware.

I've speculated here that consciousness is itself a property of the universe and may well be prior to it. But how might it be connected to life? What is “life” and how did it emerge from chemistry and physics? Suppose that consciousness pervades matter and the universe and drives – through the laws of physics – increasing levels of complexity beginning with atoms toward sufficiently elaborated organizations of matter to enable mind and thereby self-awareness. Life becomes a form of striving, a movement of consciousness toward a clumping of matter sufficiently complex to provide it with the biological substrate for perception and thought. Life is the process of individual striving within and against its environment. At various levels, we call this process physics, chemistry or biology. Within biology, it manifests as evolution. But it might be seen as “God thinking.” Hegel anyone?