Philosophy of Genetics

Nicholas Wade's Before the Dawn

Here are some excerpts from “Before the Dawn: Recovering the Lost History of our Ancestors” by New York Times reporter Nicholas Wade:

Out of Africa
It must have a required a … genetic revolution … to make possible the emergence of behaviorally modern humans [from Africa] (p. 31)  Religion, language and reciprocity ... all seem to have emerged [there] some 50,000 years ago. (p. 168) 

Between 60,000 and 40,000 years ago much of Africa was depopulated … The reason may have been a long period of dry climate … The ancestral population itself … shrank to as few as 5,000 people. (p. 50-51) Those departing, a group of perhaps just 150 people, planned to leave Africa altogether. (p. 12) [They] crossed over the Red Sea … traveled along the coasts of southeast Asia, arriving in Australia some 46,000 years ago. (p. 8)

Modern language probably evolved only 50,000 years ago [in Africa] … all languages are probably offshoots of a single mother tongue. (p. 226) The propensity for religious belief [also dating from that time] may be innate … wired into the human mind. (p. 164)

50,000 years ago – the evolution of behaviorally modern humans
After the dispersal of the ancient population from Africa 50,000 years ago, human evolution continued independently in each continent. (p. 9) For much of the period during which the exodus from Africa unfolded, from 50,000 to 30,000 years ago, people everywhere may have looked pretty much the same … It seems likely that the first modern humans who reached Europe 45,000 years ago would also have retained black skin and other African features. (p. 95)

It has long been assumed by historians, archeologists and social scientists that human evolution was completed in the distant past … It now appears the opposite is the case. The human genome has been in full flux all the time. (p. 267)  The genome evolves so fast that whenever any community starts to breed in isolation … within a few centuries its genetics assume a distinct signature. (p. 10)

[For example,] a new version of the microcephalin gene appeared around 37,000 years ago … and is now carried by most people in Europe and East Asia. [Another] gene, a new version of ASPM, emerged 6,000 years ago and is now carried by 44% of Caucasians. Both genes are thought to be involved in determining the number of neurons formed in the cerebral cortex [conferring some cognitive advantage]. (p. 271)

The human genome bears many marks of recent evolution, prompted by adaptation to events such as cultural changes or new diseases. (p. 9)  From a historical point of view, the most interesting class of evolutionary [genetic] changes are those that occurred in response to human culture. (p. 270)

The last 15,000 years – the evolution of less violent humans
Human societies have progressed through several major transitions in the last 15,000 years … accompanied by evolutionary [genetic] as well as cultural changes. (p. 178)  Each … major cultural transition … could have become genetically embedded as the individuals who best adapted to each new social stage left more children. (p. 179)

There is a 45,000-year delay between the time of the ancestral human population [who departed Africa 50,000 years ago] and the first great urban civilizations … A suite of genetic changes [may have led to less aggressive behavior] that made people readier to live together in larger groups, to coexist without constant fighting and to accept the imposition of chieftains and hierarchy. (p. 129) 

Warfare was a routine preoccupation of primitive societies. Some 65% were at war constantly … A typical tribal society lost about 0.5% of its population in combat each year. (p. 151) If warfare was the normal state of affairs, it would have shaped almost every aspect of early human societies. (p. 157)  A willingness to kill members of one’s own species is apparently correlated with high intelligence. (p. 148) When they grow beyond a certain size, of 150 or so people, disputes [in tribal societies] became more frequent, and with no chiefs or system of adjudication, a group would break up into smaller ones along lines of kinship. (p. 72) 

It required … a diminution of [innate] human aggression and probably the evolution of new cognitive faculties, for the first settlements to emerge, beginning 15,000 years ago, and it was in the context of settled societies that warfare, trade and religion attained new degrees of complexity and refinement. (p. 265)  With [innately] tamer people, the path was now set for larger and more complex societies … that would transcend the limited horizons of the hunter-gatherer band. (p. 177)

In the Near East, around 15,000 years ago, people at last accomplished a decisive social transition, the founding of the first settled communities. (p. 9) The first evidence of a successful and long term settled community comes from people called the Natufians, who lived in the Near East from about 15,000 to 11,500 years ago. (p. 126)  The first cities started springing up in southern Mesopotamia [Iraq] some 6,000 years ago … As societies became more intricate, their operations demanded … more specialized cognitive abilities.  The invention of writing around 3400 BC opened the way to the beginning of recorded history. (p. 234) 

Though they were probably egalitarian at first, they soon developed a hierarchical form, with elites, leaders and specialization of roles. (p. 178)  Without specialized roles and some kind of hierarchy, a human society cannot grow beyond a certain level of size or complexity. (p. 69) 

Genetics and race
Today’s races did not appear until about 12,000 to 10,000 years ago [after the glaciers began their final retreat 15,000 years ago.]. (p. 200)  People can be assigned to racial groups based on sampling just a few hundred sites in their genome. (p. 194)

Genghis Khan had nearly 500 wives and concubines … An astonishing 8% of males throughout the former lands of the Mongol empire carry the Y chromosome of Genghis Khan [which] raises the question whether grandiose procreation wasn’t just a perk of Genghis Khan’s power but a motivation for it. (p. 236-7)

Richard E. Nisbett, a social psychologist at the University of Michigan, believes there are “dramatic differences in the nature of Asian and European though processes” … Did rice farming encourage the conformity for which eastern societies are known and small-scale farming the rugged individualism of the west? (p 274)

The future of human evolution
For social species the most important feature of the environment is their own society. So to the extent that people have shaped their own society, they have determined the conditions of their own evolution. (p. 267)

The inhabitants of the far future are always portrayed as looking and behaving exactly like people today. [But] all that is certain about future evolution is that people will not remain the same as they are today. (p. 275)  Future evolution will differ from that of the past … new genes inserted into the human genome on a widescale basis to replace existing genes [may supplant] the quaint and hazardous method of conceiving at random. (p. 277)  When the first generation of [genetically modified] humans … turn out to be entirely normal and robustly healthy, various enhancements of desirable traits [like intelligence] are allowed … With germline modification … human intervention can reach a desired outcome much more quickly. (p. 278)

The genes that influence human social behavior are inscribed somewhere in the genome but have not yet been recognized. (p. 141) “The human mind evolved to believe in the gods. It did not evolve to believe in biology,” writes Edward O. Wilson.  (p. 266)

Evolution is accelerating

According to a recent article in US News & World Report:

Until recently, anthropologists thought that human evolution had slowed down. But last December, [John Hawks, a professor of anthropology at the University of Wisconsin] reported that it has actually accelerated 100-fold in the past 5,000 to 10,000 years [and] recent genetic changes account for about 7 percent of the human genome.

In the last 5,000 to 10,000 years, humans have invented writing, mathematics, the wheel, and written law. Perhaps our brain evolved to address these challenges? The article continues:

The human brain, which has evolved into a cognitive machine unique in the world, is likely to change even more in the future. Our niche in nature, says Stephen Pinker, an experimental psychologist at Harvard University who studies the evolution of language and the mind, is the "cognitive niche." In research published last year, [Gregory Wray, an evolutionary biologist at Duke University] identified genes that control glucose metabolism in the brain as among those most recently evolved. Those changes may have been essential to fueling the human brain's growth to a size twice that of our nearest cousin, the chimpanzee.

Intelligent Design (without God)

As I wrote previously, "intelligent design" does not require a God, nor does it prove that God exists.  Humans are "evolved entities", and we can certainly design new things.  Thus, one product of evolution (mankind) can design other products, and even purposely breed new species.  In other words, the process of evolution itself can design new forms of life, without the need for God.

How does intelligent design work, then, if it doesn't require God?  The same way that human innovation works.  Small, specialized subunits in our DNA (like startup companies or research labs) develop innovative ideas, then evangelize their discovery to a wider audience.  If the idea resonates with decision-makers, they make resources available to further develop and deploy the idea.

This assumes that the blueprints for such specialized "idea labs" exist in our DNA.  How would they work?  Just like any human "idea lab".  An observation function (perhaps cross-generational) is followed by a generative "brainstorming" function, drawing upon past experience, or by establishing new twists and combinations.  The DNA must draw upon a library of experiences, and must also have a blackboard to record ideas in progress.

Humans are intelligent designers.  I doubt we're the first ones.  My bet is that the "design function" was built into life's DNA long ago, perhaps hundreds of millions of years in the past.

Building virtual robots

When trying to devise artificially intelligent robots, scientists spend too much time constructing physical parts (robotic hands, servos, battery packs), and too little time developing the intelligent programming and algorithms.  This begs the question: Why build anything physical at all? Why not develop and simulate the robot body virtually, on a computer?

Lego, with its line of MindStorms robot kits, has done just that. Now you can experiment with new robot designs in silico, without the need for a soldering iron, or assembly of any physical pieces at all.  All the components are simulated in a virtual world on a computer. Hopefully, this technology is the wave of the future, and scientists can return to working on the hard problem, which is artificial intelligence!

One downside of the Lego offering is its lack of physics and interaction. There's no gravity and collision detection between objects.  These have been addressed in computer games ("physics engines"), and hopefully that technology gets absorbed into the experimental world of intelligent robot design.

Intelligent design, revisited

At some level, humans are merely matter.  We are simply part of that ball of material called "Earth" orbiting the Sun.  We consist of molecules and atoms, just like rocks and sand and flowers.  So, when thinking about evolution, we shouldn't consider humans as being special or "outside of the system", or any different from any other part of the Earth.  We must consider the whole planet, animate and inanimate, as merely matter, all part of Nature.

So what does this perspective tell us about evolution?  Let me give an example of "intelligent design" by human actors.  The VHS video tape that we rent in stores is being replaced by a completely new technology, the DVD.  There is no gradual evolution, from one technology to the next.  It is an abrupt change.  DVDs were invented in special laboratories by a small group of humans.  A complex marketing and distribution system allowed those inventors to spread the word, and make the new technology available.  The invention was popularized, early adopters gave way to mainstream acceptance, and DVDs have nearly replaced VHS tapes in just a few years.

The ability to invent new things is a human trait.  So, are we humans special?  No.  We are merely one form of matter, just part of the overall system (Earth or Nature).  Since one form of matter on Earth can plan and design things, then other types of matter can potentially do it too, by planning and executing strategies, and not just relying on happenstance and blind chance.  Furthermore, since humans and pre-humans have possessed this ability to plan and design for millions of years, perhaps this "intelligent design capability" of Nature has existed for billions of years!

Let me repeat this for clarity.  Usually, we humans tend to think of ourselves as "outside of Nature", not part of it.  So take a deep breath, and try to imagine that humans and Nature are really the same system.  Humans can invent and design entirely new things like DVDs.  Humans can also create new species (through planning and breeding).  Since we are merely part of Nature, this implies that part of Nature can create new species through planning and breeding.  This is not speculation; this is fact!  Some matter can design the form of other matter.

Perhaps the classical theory of evolution is still valid, but has long since been supplanted by intelligent design when new species arise.  If humans are intelligent designers, it follows that the Earth (or matter or Nature) is an intelligent designer as well (perhaps for billions of years), since we (as matter) are simply part of the Earth.  So whether or not you believe in God, intelligent design is certainly possible.  And we all know that the Earth is not the center of the universe!

God and Darwin

Recently, some pro-Darwinists have been attacking religious faith because it's not scientific and rational.  But it shouldn’t really matter (to someone who believes in evolution) whether humans are rational or not.  It’s the outcome (and effect) our faith has that matters, and how this aids our survival as a species.  The belief itself is not relevant to scientific debate.

I’m not a religious person (maybe I'm missing that gene), but you don’t have to be religious to see the effect of religion on human cultural evolution.

Where did God come from?  In the last 5,000 years, the human mind evolved to cherish abstractions as being as important as our own survival.  First, we invented abstract things like writing, the wheel, rule of law, and democracy.  These came about because humans started to see abstractions as being more important than self-preservation.  We became obsessed with “the principle of the thing” over practical concerns.  This can be seen most clearly in religious fanatics who blow themselves up “for the cause” or “for an idea”.  That is the raw inclination behind religion and invention and rule of law.

During the time of the Roman empire (2,000 years ago), life was miserable and short for the average person.  Many people began to embrace Christianity, not because it's rational, but because the church promised to support everyone as Christ did, especially the downtrodden and outcasts, who were given a level of care by the church they hadn’t known before.  Even when the early Christians were tortured and thrown to the lions for their beliefs, they bravely and willingly gave their lives for the idea of "God" and His grace.  Eventually, the Roman empire had to convert to Christianity, because they couldn't fight the faithful any longer.

Christianity, then, has a practical effect.  True, it can be open to abuse, because any time you start accepting the words of your leaders on faith (without questioning), they can become corrupt, or launch religious wars.  That’s why the Protestant reformation was so important, to remind people they have a direct path to God.  He can hear your prayers without the need for an intervening church hierarchy (priests, etc).  The Protestant revolution led directly to the humanist idea that every man and woman is an important and sacred individual, the foundation of democracy.

So religion has been very important to the development our modern notions of law, morality, and science and evolution.  Is there a God?  It doesn’t really matter, does it?

The evolution of psychology

Evolutionary psychologists believe the human brain evolved dozens of specialized "modules" (to perform specific tasks, like "liar detection" and "mate selection") that helped us to survive as a species.  Humans evolved a "language acquisition" module some 200,000 years ago, they say, since without it we would be unable to speak and learn complex grammar.

Later abilities, such as the ability to read, were built as side-effects on top of existing modules.  Since writing was only developed 5,000 years ago, that is too recent for the brain to have evolved a special module for reading.

Taking this argument one step further, do we really believe that language ability itself developed for the first time in humans some 200,000 years ago?  Or is it also a side-effect of other modules that evolved millions or even billions of years ago, before organisms even had neurons and brains and minds.  All they had then was their DNA, with viruses transferring some DNA back and forth between them.

The first cellular organisms evolved on earth some 3,600,000,000 years ago.  There were no multi-cellular organisms on earth for the first 3 billion years, only arriving a mere 600 million years ago.  Primates (monkeys) evolved only 55 million years ago, which is but a blink in time, compared to the history of life on earth.

So my theory is that many (if not all) mental modules are actually built upon abilities which evolved many millions (or billions) of years earlier, when we were still single or multi-cellular organisms.  Specifically, I think the ability to plan and design things (including our own evolution) may be billions of years old.  The interesting question will be figuring out how these DNA-based modules were able to transfer their capability to neuron-based modules in the brain.

A human is a virus's way of replicating itself

A recent article in Discover Magazine claims that viruses may have evolved well before other types of life on earth, and indeed may have "played a key role in inventing the very cells of which humans ... are made. ... Evolution's archvillain looks more and more like its vital and formative force."

When life first arose on Earth some 4 billion years ago, there is a possibility that a large virus entered a bacterium and "harmlessly persisted there", forming the world's first nucleated cell, similar to our own.  In this case, we may be "all decended from viruses".

More shocking, "most of the genetic material on this planet is viruses" and "the better part of the human genome is composed of viral DNA" and "the human genome, considered as a mass, contains more retroviral sequences than actual genes" (a retrovirus like HIV can insert its own genetic material into our own).

So, let's speculate on what this all means!  Instead of thinking of ourselves as being occasionally infected by viruses, we should consider that we are simply a collection of viral genes, cobbled together over billions of years.

Or, perhaps humans are constructed by and for viruses as their own personal playground, battleground, nursery and hospital.  Perhaps we are in the midst of a great war between viral factions, who design their own hosts (such as humans) to inhabit (and discard) for their own purposes.

HIV and Intelligent Design

Humans can design things.  Humans can make plans.  Therefore, a product of evolution (people) can plan and design.  Since humans are made of matter, it follows that certain types of matter can design and plan other types of matter.

The question is, did this ability originate with humans, or did it evolve earlier?  Indeed, is it an inherent part of the process of evolution itself?  In other words, can the "process of evolution" (the grand designer, if you will) plan and design future beings?

If it could, it would need a way to "stand outside" of the organism it was designing or modifying, and be able to step back and observe how well it was doing.  So, what type of DNA can be transferred from one organism to the next (and perhaps pass on a signal of some sort). 

Why, HIV, of course!  HIV can be transmitted from one person to another, and the genetic material becomes integrated with the DNA of the new host.  HIV has an exceptional knowledge of monkey (and now human) DNA, since it is able to exploit many other genes in the host to replicate itself.  So it could be thought of as extra-human DNA!

The process of evolution (as we currently understand it) involves an early death of the host (before he/she can bear children).  In other words, if you're not innately fast enough to evade a predator, you get eaten.  In the same way, the HIV virus could be bringing an early death to certain weakened individuals (such as those with tuberculosis), as part of an "intelligent design" scheme.  It gets treacherous to speculate, of course, because there is no proof for any of this, yet. 

Evolution, the Grand Designer

As I wrote previously, evolution doesn't have to be a process of random (genetic) change and natural selection.  There's no reason that the process of evolution couldn't have the ability to plan which changes to make, conduct experiments, and retain the best results.  After all, humans have the ability to design things, and we are merely matter, ourselves the product of evolution.

A recent scientific discovery sheds light on how this process might work.  Studies "revealed that during evolution, the chromosomes are rearranged by breaking typically in specific locations, rather than in a random fashion, as had been widely thought." (See also here for more details) 

Evolution is not incompatible with Design

Humans are self-conscious designers. We develop an idea, then act purposefully to plan, design and build whatever it was we imagined. A watchmaker, for example, can design a new type of watch. An artist can design a new work of art never seen before. A furniture designer can create an entirely new kind of chair. This ability to act with purpose is an important human trait.
   
But is it strictly a human trait? Most scientists will tell you so. The process of evolution, they might give as an example, has no ability to plan or design at all. Evolution proceeds blindly, they say, by random genetic mutations and then survival of the fittest.

But is the process of evolution really so random? After all, life on earth has been evolving for billions of years. It seems possible, even probable, that the collective DNA of society has evolved a self-consciousness of its own, to allow it to control the future direction and design of the species.
        
First, let's look at how humans design things. A furniture designer, for example, may want to create a new type of chair. She does not know ahead of time exactly how it will look, or what the final design will be. She proceeds by building a frame or making sketches, then changes things, here and there. At each step, she assesses the work in progress, then applies rules she has learned before; from her experience. Her rules sometimes apply well, and sometimes they don't, because past rules don't always apply to new situations. Perhaps at times she decides to add a random element to the work-in-progress. Then she sits back to reflect on what she has created. She uses her capacity for recognition to guide her.

So human designers mainly proceed by applying some known rules, which may or may not fit a specific case, then sitting back to reflect on what has transpired. Like an artist carving a bust from a solid block of stone, the blows of the chisel are similar to the rules we apply when designing: Each one is but a stab, or guess, at getting the design right. Then we must sit back to recognize if we are getting closer to the goal.

Our ability to recognize a good design is separate from any notion of knowing how to design. Humans technically don't know how to design anything new: We simply apply old rules, and some of them work, to bring us closer to a desired end, which we can recognize.

So, can evolution really design anything?    

If what humans do is called design, then it wouldn't be hard for the process of evolution to employ similar strategies. It's "goal" could be to reduce entropy, by creating more complex beings. Or it could have a "goal" of reducing tension between an organism and its environment.

So now we enter the world of speculation. Under what circumstances could a cross-generational mechanism be employed to "design" new creatures? It would require:    

• A feedback mechanism in the genes, to "recognize" how well an organism is doing; In other words, a cross-generational inner eye.
• Our genes must be parameterized, such that body size or shape, for example, could be adjusted by a cross-generational mechanism. In other words, if genes leave themselves open to be adjusted in standard ways, they could be employed to design creatures, given certain restrictions.
• A cross-generational "note pad," which could record which genetic parameters were altered, and how well the change worked. This information would be stored in the genes, to be transmitted on to later organisms. It is plausible that DNA has evolved an ability to record information into itself, perhaps employing retroviruses, which can alter human DNA.

Intelligent Design

Scholars and theologians have debated for centuries the question of "intelligent design".  Are humans designed by God for a purpose?  Or did we evolve over millions of years, as the Darwinists believe?

I think it's a false choice.  Clearly, humans can design things, and humans are merely made of matter.  So it's possible for some types of matter to design other types of matter.  It's certainly feasible that the process of evolution has a built-in design capability.

It's useful to look at Economics for an example of how this might work.  Businessmen and entrepreneurs devise new ideas, and raise capital (money) to make them happen.  In some cases (as with the FederalExpress package delivery system), an idea takes billions of dollars to implement, and needs to be fully operational from the first day.  It's impossible to evolve such a design slowly and incrementally.

In other words, certain types of matter (known as "humans") have devised a way to create radically new businesses, without having to evolve them incrementally.  Evolution is simply a process of matter reconfiguring itself over time into new combinations.

Therefore, I believe that evolution is compatible with intelligent design, and that we simply haven't uncovered the mechanism yet.