Biochemical Soul Musings on Nature, Science, Evolution, Biology, and Education


Doctrine: the Antithesis of Evolution and All Science

Dr. Jim West has implicitly claimed that because evolutionists often defend the theory of evolution so passionately and vociferously (or as he puts it, with "religious zeal"), then that must mean that evolution is "doctrine" [1. in this argument, I am only referring to the common usage of doctrine meaning "dogmatic system of beliefs" as opposed to the more innocuous "codified system of teachings". Of course evolution is a codified system of teachings. But it is a system that inherently acknowledges its own fallibility and tenuous nature]. (his post title: If It’s Not A Doctrine, Why Are People So Defensive?).

I hear this argument all the time, in multiple variations - claiming that because we defend evolution passionately, that means that evolution is "dogmatic" or "religious."

This is specious logic at best. I originally responded to his post in his own comment section, and I reproduce my thoughts here:

1) Just because someone is vociferous and passionate with any sort of claim, defense, proclamation, or simple statement, that does not have any bearing on its “religiosity”. Calling a passionate response “religious zeal” is simply an attempt to obfuscate the language and warp the debate.

2) Equating the passionate nature of a subject’s defense with anything concerning the nature of that subject is simple fallacious logic (i.e. what the hell does passion of a response have to do with whether or not it is doctrine?)

I will agree with the philosophical premise that ALL scientific knowledge is predicated on the prime assumption that sense relates to reality. Thankfully, simple pragmatism allows us to build science from the fact that it seems to work.

However, neither science nor evolution can be considered “doctrine” for the simple inherent acknowedgement within the scientific epistomology that it will always be possible that the prime assumption might be false. This is why science “fact” isn’t based on provability, but by falsifiability. Even the falsification of any scientific hypothesis is always considered inherently tentative. You cannot call something doctrine if that doctrine implicitly acknowledges its own fallibility.

(note: obviously in this argument, I am only referring to the common usage of doctrine meaning “dogmatic system of beliefs” as opposed to the more innocuous “codified system of teachings”. Of course evolution is a codified system of teachings. But it is a system that inherently acknowledges its own fallibility and tenuous nature.)

(Update: he has deleted my comments multiple times - maybe the word "hell" offended him? Or perhaps he couldn't argue?

Update 2: now they are online - apparently he doesn't like people to use pseudonyms. I guess I could have made up a name, but oh well - My name is easy enough to find.)


Carnival of the Godless #98

C. L. Hanson over at Letters From a Broad: The Adventures of a Friendly Ex-Mormon Atheist Mom Living in France Switzerland (I love that title) has composed the 98th biweekly edition of Carnival of the Godless, a blog carnival containing a myriad links to thoughts on atheism or tangentially related topics. This edition is particularly well done, and contains hours worth of edifying reading and links to make your brain cells hurt.

Graciously included in this latest edition is my own previous post, Hope in the Black Void of the Unknowable, in which I muse on whether we really want every human on earth to see the Universe and ourselves as science sees us, namely "no more than blips of energy in an inconsequential cosmic blink."

Check it out, and if you have your own musings on issues relating to an absence of God, go to Carnival of the Godless and find out which blog is hosting the latest edition and submit your stuff to them.


Building a Better Human

Transhumanism, to quote Wikipedia is

“a term often used as a synonym for "human enhancement", is an international, intellectual and cultural movement supporting the use of science and technology to enhance human mental and physical abilities and aptitudes, and overcome what it regards as undesirable and unnecessary aspects of the human condition, such as disability, suffering, disease, aging, and involuntary death.”

I often think about the eugenic possibilities of applied science (technology) that may arise in the coming years, decades, and longer. I have long considered myself a transhumanist. That is, I see no general philosophical or moral issues with human enhancement or even directed human evolution, in theory.In practice, however, I think there are several issues that may well prevent our race from ever even attempting such a project. (Don't even think about mentioning the Nazis to me. Though using a warped eugenics, they were NOT transhumanistic.)

Let me first state that I think that external technological enhancement is already in early bloom and will continue to be used to ever increasing degrees. By “external” I mean the use of robotics, artificial limbs and organs, cognitive enhancement, or extension of the senses. However, there is a fundamental difference between this type of enhancement verses the actual altering of the human genetic code and inherent function of human biology.This article will focus almost exclusively on biological modifications.

it's NOT all in the genes

The moral, social, cultural, and philosophical implications of biological transhumanism have been discussed ad nauseum by many thinkers much greater than I. Books have been written (e.g. Brave New World). Movies have been made (e.g. GATTACA). However, it is only now that we are truly entering an era in which it can be discussed and contemplated from a practical standpoint, and in which we may even begin to realize the transhumanist goals. Not only have we now sequenced the entire human genome, but we are developing tools for altering the genetic code in living human beings. (see question 10 from my previous post: 23 Things Science Can Tell Us about Life, the Universe, and Everything)

However, one thing that I find sorely lacking in most discussions of how we might enhance the human condition is a discussion of Developmental Biology. Before we tackle the main question at hand, I feel I must first take a short diversion into describing development.

Most of the public have heard our genomes described as “the DNA blueprint” of humankind. As any developmental biologist will tell you, DNA is not a blueprint for anything – this is a horrible metaphor for DNA’s true function. The closest metaphor we have for the relationship between DNA and a thinking, breathing human is the relationship between a recipe and a cake. DNA does not describe anything about what a human looks like or how it works. There is not a gene that contains the information on how to make an eye, for example, or what the eye looks like or works. All it tells you is which protein to make at which time and in which cell.

As the field of development now knows, the genes encode for RNAs that encode for proteins (vast oversimplification, but lets keep it manageable). In a single fertilized egg, there are an unknown hundreds or thousands of genes and proteins “turned on” and interacting with each other and with the cell, and even with the mother (in the case of humans).

As the cell divides, new genes are turned on, others are turned off, and a new level of complexity is added. The cells now exist in a growing, changing, dynamic network. This network includes genes, RNAs, proteins, different cells talking to each other, groups of these molecules forming modular, yet interdependent pathways, and all of these interactions are now occurring in discrete areas of space and time.

Yet at the reductionist level, all of these things work by more-or-less simple rules about their own behavior. For example, gene A is only turned on when protein B is present. Protein B is only present in cell type C. So in cell type C, gene A is turned on, to make Protein D. Based on its particular shape, Protein D can only interact with Proteins E and F…etc.

This is another vast oversimplification, and one can imagine this network growing to nearly unimaginable complexity, with some proteins turning genes on, others making stuff like muscle, others making neurotransmitters, and a million other effects ensuing. To go back to our eye example, all of these interactions result in subsets of cells growing and shaping themselves into the structure of the eye at specific times and places. The environment around the eye tells the cells where to go and what to become. Some cells produce tons of beta-crystallin and make the lens. Others grow long axons and connect to the brain, while also producing molecules that react to light. We currently know of about 200 distinct cell types that arise from these interactions of genes, proteins, and cells in space and time.

So, given all this amazing complexity, will we ever reach a point at which we can enhance or evolve ourselves? My own answer is: theoretically, yes – practically, no. (again - see Question 10 of 23 Things Science Can Tell Us about Life, the Universe, and Everything).

There is no doubt that we will eventually have all the pieces of the puzzle of our own development (assuming we last long enough). But there is one key element glossed over in discussions of how we apply our scientific knowledge to human enhancement: experimentation and research on developing embryos. I think that regardless of how much data and understanding we obtain from animal studies and studies of human disease and genetics, we will never be able to apply any directed changes without experimentation on humans. This is a simple fact.

"You're starting to look like your mother"

Let’s look at one example: animal cloning. Animal cloning involves the relatively simple activities of inserting a nucleus from one animal cell into the cell of another, and coercing that cell to become an animal. We now do this all the time. Heard about Booger the cloned puppies from Korea yet? But there is one problem – in order for us to get to this advanced (and retardedly stupid) point of being able to clone a long lost and beloved dog, we had to go through the production of thousands of utterly deformed animals of many different species (remember the breast-gland derived sheep, Dolly?). I once went to a great seminar by Dr. Ian Wilmut (the Scottish scientist who cloned Dolly). He showed us some data from some mouse or other rodent cloning he was doing – I don’t remember the specifics. But I do remember that out of something like 500 animals produces, only a fraction were viable.

So I ask, does anyone really think that we can alter human development without going through similar experimental growing pains? How many seriously deformed or deficient human embryos will need to be produced before we get it right? No matter what kind of fundamental change one wishes to accomplish in an adult human body, that change will have to occur at the developmental level, altering specific developmental pathways in specific cells. No matter how big the "cloud" of data, or how vast our computing power, we will always have to test any technique to make sure it works (despite the fact that some actually think that astronomical amounts of data make science unnecessary).

My guess is that such evolutionary enhancements would cause be far too many deformed babies for any even half-moral or ethical people to allow. There are people right now attempting to clone humans, and even this is morally reprehensible. Why? Despite the fact that I have no God, no absolute or cosmologically meaningful morals, I still have an in built belief that conscious-human destruction or harm is wrong. It is hardwired in humanity to place value on human life (with some exceptions and gray areas). Furthermore, there are no positive benefits of human cloning for reproduction, other than scientific knowledge itself, and it will unarguably cause deleterious effects on an unknown fraction of embryos, leading to suffering. And it will most certainly NOT bring loved ones back, though apparently there are thousands of gullible pet-owners who believe otherwise. But I digress. Granted, we may come very very - tantalizingly - close to achieving directed enhancement through work in animals, in human cell culture and tissue culture, but this will not quite be enough.

In essence, I think it is near impossible that we will be able to progress to a point where we can actual tinker with our own genomes (at least during or before developmental stages), due solely to cultural/ethical issues, though it will be technically possible. We will definitely attempt to change adult cells (e.g. gene therapy to give certain cells the ability to produce insulin, which is already underway), but this is a far cry from the types of changes to consciously evolve our form and function – a far cry from adding, subtracting, or changing pieces within the insanely complex developmental pathways that lead to our construction.

Despite my pessimism, there is one possible work around that I can foresee. It will take at least one mad scientist working in conditions that would never be considered ethical today, but it is at least conceivable. Imagine the creation of a human being without a brain – without a consciousness. This is, in fact, one goal of Regenerative Medicine today, though not explicitly stated. We will eventually at least be able to produce organs outside of the body – to grow them in a dish. Now if we had an entire human body devoid of a brain, one could easily see us performing experiments on such a life form without worrying about pain and suffering. (Note: I am ignoring moral qualms from anyone who believes in a soul, or believes that we are “as we were meant to be,” or anyone who thinks that the word “natural” actually means something). But for us to create such an entity, this will likely involve ethically questionable research on humans as well, and it may not even be possible to develop a human without a brain while maintaining the integrity of all other organs. Nonetheless, such a creature could at least give us a “model organism” on which to test our various enhancement techniques. Of course, none of these enhancements would involve cognitive function enhancement, for obvious reasons.

All of this type of research, should it ever occur in any form, will require a progressive revolution in the populace at large. We will have to overcome our archaic “playing God” ideas – (honestly, in what ways have we NOT been trying to play God since the discovery of fire, and the domestification of plants and animals). We will have to get over this idea that somehow “natural” things are bette
r than “unnatural” - the words have no meaning in reality. Accepting genetically-modified foods - a potential savior to world poverty, though it is admittedly rife with its own inherent issues that WILL be addressed - will be a necessary first step. It will also require computing power many magnitudes greater than what we have now, but I think this will inevitably come.

In summary, I have very little faith that our society and culture will allow such enhancements, despite the fact that this is the only way we will evolve, barring major cataclysm. I also think side-effects such as the class divisions between altered people seen in GATTACA, might prove to be too big of an issue. I’m not sure human nature will ever progress beyond dividing itself on whatever divisions are possible. Perhaps if we changed our brains…ahh Catch-22.

Then again, I am but a product of today. Who knows what cultural and societal changes may come? Perhaps our children, or great, great…grandchildren will embrace transhumanism.

I doubt it. As I’ve said before, multiple times, humans are no longer evolving at a macro scale, regardless of what cultural norms envelop us. I think that our animal natures will always grow to repress any escape we might attempt from them.

I hope not.

I really want my baby to have gills.


NPR This I Believe: Hope in the Black Void of the Unknowable

Update: This essay can now be found on the NPR "This I Believe" website.

Recently, I wrote an essay for This I Believe, an NPR radio series that asks Americans to answer this simple question. My essay has not yet been reviewed; however I doubt my chances of getting selected on the radio program. It is a bit too impersonal, too “what I don’t believe,” and not nearly as eloquent as many of the best essays (for the absolute best – see below mine). My essay is actually a shorter and reworked version of another essay I wrote on the same subject.

Note: If you find that you believe in something strongly and have a story to tell around that belief, I highly recommend you submit your own essay to NPR This I Believe.

This I Believe: Hope in the Black Void of the Unknowable

As a scientist studying the development of the brain and as a student of all scientific knowledge, I find it highly probable that all life and human experience is devoid of inherent meaning or purpose. The Universe seems nothing more than an enormous cosmic accident – an accident that will be corrected in due course as the Universe and its inhabitants are eventually destroyed in an equally pointless cataclysm. At least this is the view of my Universe as seen through the eyes of empiricism, the only eyes through which I know how to look. My morals, my accomplishments, my feelings and thoughts, and my connections to others and to the world in which I live are apparently no more than blips of energy in an inconsequential cosmic blink. However, underlying all of my knowledge and all of science I hold one major faith, one prime assumption. This is the assumption that my senses and experiences are relating real information about reality. That I am not merely in “The Matrix.” There is simply no philosophical workaround to this argument – it is impossible for me to absolutely know anything.

Thus, I cannot conclude anything definitively about my ultimate creator. I cannot absolutely believe in anything. I can only think from within the pragmatic view of science – that my senses work and my experiences along with the collected experiences of my brethren explain my reality better than any other means of purported knowledge. I can only decide to educate my future children about where we as a species come from, though I cannot guess where we may be going. I must make them understand that our science, our knowledge, is the closest thing to an explanation of our Universe we will likely ever have. However, just as importantly, I must admit where this knowledge can never reach, and allow that place to be inhabited with hope – a hope that maybe, just maybe, in that dark void of unknowability lies a meaning to my existence, a meaning I can never know or comprehend.

I must make them understand that although the fables passed down from our ancestors are no longer useful as a defining belief, the true possibilities of our meaning and our worth may be infinitely larger than I ever imagined. I believe that if we take into consideration the grandness of nature, the mind-boggling array of galaxies in our Universe, and the insanely complex biology and chemistry within ourselves, the unknowable creation of our Universe will seem only that much bigger and infinitely more awe-inspiring. I have seen but a glimpse of this awe in the intricate networks of neurons speaking to each other in unintelligible chemical languages, and I can almost fathom an entity setting it all in motion with a mere equation.


As the philosopher Karl Popper once said, “Our knowledge can only be finite, while our ignorance must necessarily be infinite.” I believe that it is in this infinite ignorance where my only hope for greater cosmic meaning may lie.

The Best "This I Believe" Essay Ever:
NPR This I Believe: I Am Evolution

by Holly Dunsworth, a physical anthropologist at Penn State.

I believe evolution. It's easy. It's my life. I'm a paleoanthropologist. I study fossils of humans, apes and monkeys, and I teach college students about their place in nature.

Of course I believe evolution.

But that is different from believing in evolution.

To believe in something takes faith, trust, effort, strength. I need none of these things to believe evolution. It just is. My health is better because of medical research based on evolution. My genetic code is practically the same as a chimpanzee's. My bipedal feet walk on an earth full of fossil missing links. And when my feet tire, those fossils fuel my car.

To believe in something also implies hope. Hope of happiness, reward, forgiveness, eternal life. There is no hope wrapped up in my belief. Unless you count the hope that one day I'll discover the most beautifully complete fossil human skeleton ever found, with a label attached saying exactly what species it belonged to, what food it ate, how much it hunted, if it could speak, if it could laugh, if it could love and if it could throw a curveball. But this fantasy is not why I believe evolution — as if evolution is something I hope comes true.

After all the backyard bone collecting I did as a child, I managed to carve out a career where I get to ask the ultimate question on a daily basis: "Where did I come from and how?"

If our beliefs are important enough, we live our lives in service to them. That's how I feel about evolution. My role as a female Homo sapiens is to return each summer to Kenya, dig up fossils, and piece together our evolutionary history. Scanning the ground for weeks, hoping to find a single molar, or gouging out the side of a hill, one bucket of dirt at a time, I'm always in search of answers to questions shared by the whole human species. The experience deepens my understanding not just about what drives my life, but all our lives, where we came from. And the deeper I go, the more I understand that everything is connected. A bullfrog to a gorilla, a hummingbird to me, to you.

My belief is not immutable. It is constantly evolving with accumulating evidence, new knowledge and breakthrough discoveries. For example, within my lifetime, our history has expanded from being rooted 3 million years ago with the famous Lucy skeleton, to actually beginning over 6 million years ago with a cranium from Chad. The metamorphic nature of my belief is not at all like a traditional religious one; it's more like seeing is believing.

So I believe evolution.

I feel it. I breathe it. I listen to evolution, I observe it and I do evolution. I write, study, analyze, scrutinize and collect evolution. I am evolution.

Amazing, no? If you enjoyed this beautiful and poignant essay, I highly recommend you read the interview with Holly Dunsworth on the excellent Forms Most Beautiful blog (one of my favorite blogs on the internets).


Science: the death of God or corroborative evidence for Him?

I've recently been reading "The Brothers Karamazov" by Fyodor Dostoyevsky, a nineteenth-century Russian novelist, and I came across the following quote:

"Remember always, young man… that science which has become a great power in the last century, has analyzed everything divine handed down to us in the holy books. After this cruel analysis the learned of this world have nothing left of all that was sacred. But they have only analyzed the parts and overlooked the whole, and indeed their blindness is marvelous. Yet the whole still stands steadfast before their eyes…" p. 171

It struck me as a statement in fitting with much of the sentiment of those who think that science is incompatible with religion. Many believe that science is simply trying to explain and thus take away many things and events that could previously only be attributed to God. Of course, science is completely incompatible with a literal interpretation of the bible, but if it is interpreted a little more loosely - keeping in mind that it HAS been altered through the centuries by translation - then NOTHING that has been learned by science is in direct contradiction with the bible. I should also note before I get going that I am not Christian myself, and I believe that if there is a God he is infinitely more complex and powerful than any God we have yet imagined. OK, that being said… back to the topic at hand.

The point of the quotation is that science analyzes only the individual aspects of physical reality, i.e. physics, astronomy, physiology, evolution, geology, etc. Science looks at all these parts and fails to look at the whole of reality and creation, and thus it is blinded to the divine nature of this reality. I think that I can safely say that I both agree and disagree with those sentiments. When I say that I agree, however, what I mean is that I can understand why one might say that, standing from a highly religious or spiritual position. Most science as seen from the public's eye, seems very cold and removed from any spiritual awareness of reality. In fact, virtually the only science that the public sees are those aspects of science that end up being applied in consumer technologies and medicine. We see on the news everyday articles dealing with some new genetic discovery that might save lives or some new property of some alloy that will make faster computers. Even the science in space, i.e. the International Space Station or Mars exploration, is reported to the public as something that will lead to new consumer products or give us another place to live in the coming centuries. There is no focus on the underlying meaning of any of these discoveries and thus very little in the way of religiosity, awe, wonder, or spirituality - that is from the perspective of the public and media.

However, when you look at the actual science being conducted through the eyes of the researchers you see the discoveries in a different light. This is where I disagree with the quote. Almost every major scientific discovery has shown one thing: reality is way more complex, ordered, and awe-inspiring than seems intuitively possible. Think about quantum physics (not that that is easy to do), or recent discoveries in genetics, or discoveries about the past of Mars, or some of the recent pictures of entire planetary nebulae taken by the Hubble Space Telescope. I promise you that when those researchers are sitting there thinking about the implications of their results, they are experiencing a kind of spiritual epiphany. Imagine being Robert Hooke in the 1600's and looking at a piece of cork through a microscope. There's no way of knowing what he expected, but when he saw that it was made of millions of smaller units, which he termed cells, he had to be overcome with excitement and awe. What I'm trying to say is that science does not offhandedly dispel the mysteries of life and reality and it does not try to make anything less sacred. On the contrary, for every question answered ten more arise. There is still plenty for God to do. We may be able to explain how a planet orbits or an apple falls based on gravity, but where did gravity come from, what causes it, why does gravity work with exactly the right force necessary to sustain an orbit at a precise distance from the sun, and why do the laws of nature allow for the exact chemical reactions necessary for thousands of process, which are themselves necessary for the existence of a living organism. Ask any physicist what gravity is or the strong and weak nuclear forces that hold atoms together. All he/she can do is explain what these forces do. No one on this earth has the faintest inkling of what gravity actually is. It's a force. But what does that mean. We have all these mathematical laws of physics, but no one understand why they are the way they are or what makes them like that. Did you know that if the gravity constant (force of gravity) was altered in the slightest bit, by something like 0.000000000000000000001 or many factors less, then matter would not be able to hold together like it does, stars wouldn't exist, planets wouldn't exist, and life would be impossible. There is much that God can still do in our scientific world and the powers science is leaving to him are much more elegant and complex than the powers that most current religions want to give him (not that we could ever prove or know there was a God involved - but this article should be taken to heart by those with "faith")

What seems more powerful and awe-inspiring to you: a God that says "poof" and has created the heavens and earth and living creatures in seven days, or a God who can slowly orchestrate the evolution of an entire universe, complete with trillions of galaxies, each filled with hundreds of billions of stars, many with hundreds of orbiting smaller bodies. He can orchestrate it for billions of years with stars dying out and giving rise to new stars all the time, obliterating all planets of the old star. He can control it so precisely that fifteen billion years after the first explosion of matter, on one of these ultramicroscopic grains of sand (probably millions more in the universe - but one for sure) actually evolves an extremely simple life form that evolves over the course of 4 billion years into a being that has the ability to look out from that grain of sand and wonder how the rest of the rocks got there? You can read my article on determinism that explains how a God could possibly orchestrate this entire existence of the universe by simply laying down the laws of physics, taking a ball of matter, and throwing it into the mix in a specific way. Now that is an all-powerful God!! All science does is show us how incredibly intricate and complex this "plan" is and how infinitely intelligent this God (should he exist) would have to be to accomplish it all.