The Human Onion

“I ain’t descended from no monkey.” The fact that humans are genetically related to the great apes by a distant common ancestor, seems to be the most distasteful aspect of evolution to a lot of people. Personally, I don’t know if we or the apes should be more offended.

I suppose when you look at a grinning chimp and stop to think that our genome differs only 2% it does give pause. It makes some people feel that there is nothing special about humans. More of that scientifically-induced loss of wonder that people carp about. But modern biology demonstrates that we are far more than a naked ape. Man doesn’t have to resort to mysticism to find that we are indeed remarkable creatures even though our origins are as natural as any other life form on this world. That is the real miracle. What follows is a very high level visual metaphor (very simplified) that tries to illustrate some basic forces that resulted in that most unique of Earth’s creatures, Man. This is a mere introduction to 4 intersecting (and somewhat arbitrary I admit) levels, all affected by genetics, that appear to have shaped us into something unique. These layers shouldn't be thought of as distinct domains particularly as there is interplay amongst these processes. But I find the separation useful in discussion of key attributes. Huge texts are dedicated to parts of each of these layers so nothing more than a passing mention can be made here. But at the end I hope you gain the following: 1) a desire to learn the details; 2) an appreciation of how humanity could have risen to its unique status through natural means; and 3) a recognition that we really are unique creatures despite our shared origins.

I think of the 4 layers as:
Classical genetics
Developmental regulation
If you want to learn more about these layers go over to Mors Dei where Jared will share details of the science. He does a much better job of that than I.

Classical genetics: How can we be so different from Chimps with so few seemingly small differences in basic building blocks? The probable answer is that there is a lot more to it than classical Mendelian genetics. If people know anything about genetics at all, this is what they learn. Autosomal dominance, recessive traits, sex linked genes, etc. Most of the ‘genetic’ conditions people are familiar with (or which they are aware have a genetic component) like hemophilia A, Sickle Cell disease, Huntington’s Disease, etc. involve this type of simple inheritance. I say simple because the causative defect or variation is relatively easy to understand. Some mutation in a gene that results in some readily apparent alteration. Missing factor 7, a missing enzyme, or an oddly folded hemoglobin molecule for example. These genes didn’t fall from the sky. They evolved from the genes of earlier creatures and form the basic building blocks of humanity as they do for all other life here on Earth. The fundamental importance of this facet of biology is represented by figure 1 below.

The fundamental laws governing the selection and building of peptides from translated DNA segments is the same for human as for amoeba. We can, in this age, run back the clock and identify key milestones in the evolution of peptides over the millennia. There is no evidence that anything mystical happened along the way. Our cells contain DNA consisting of the same 4 base pairs as any any other life form on Earth (let’s ignore viruses for the moment). Our genes consist of some sequence of these 4 base pairs (with some variability even within our species) just like a canary. Our genes are transcribed into mRNA strands just like a Chimp’s. Our mRNA is translated into peptide strands using ribosomes and tRNA that are pretty much the same as any other eukaryote. So far, not so much to account for our unique characteristics. That doesn't mean that the process isn't extraordinary. It is, but it's something we humans share with all life on Earth.

Developmental regulation: Figure 2 shows that there is believed to be a very important layer beyond what we think of as classic genetics. Not that these processes aren't governed by the same chemistry as the preceding one, it's just that the effects are a lot more complicated and cryptic. Finding the cause and effect isn't always straight forward.

This layer represents the interplay of the various peptides and proteins produced by classical genetic translation on each other. Genes allow for the production and expression of certain peptides but these peptides also help regulate not only the final expression of traits in the organism but the production of other gene products as well. Genes may contain information useful in the production of a certain peptide, but other peptides (enzymes, etc.) largely govern its final form and function. If I can be forgiven a metaphor here, the timing, presence, function and even quantity of peptides appears to provide an additional and extremely critical level of rich information beyond the genes themselves. As the 4 base pairs of DNA are used to determine peptide sequences, the peptides themselves appear to create an additional syntax that has profound importance to the form of the organism. Mixed and matched for development and regulation, variations on a theme of the various peptides can result in a very different animal.

It's important to note that nothing about this in any way negates the importance of genes. What it says (at a high level at least) is that the interplay of gene expression products is a critical set of traits that is as important a target of natural selection as more obvious structural traits.

Back to my poor metaphor. If genes can be thought of as the letters in an alphabet then consider that all the words in the English language can be created from mixing, matching and trimming strings of letters to form the words. Consider peptides as analogous to the words. But the words themselves (like the peptides in our biology) can provide further and far richer context and nuance to language by how they are strung together. Take the word red for example. Formed of three letters it has a well understood (albeit variable) meaning. But take red and put it into a sentence and everything changes. A red car; a red herring, a red letter day, etc. - all have very different meaning. If the metaphor is apt then the interplay of peptides would seem to offer tremendous opportunities for unique characteristics despite basic core similarities.

Plasticity: Presumably as a byproduct of some of that wondrous variety possible from these first two layers of humanity, a third emerged as represented by figure 3. Although not a mechanism limited to humans, our evolution seems to have taken it to a new level.

It now appears that some of the shenanigans going on in level 2 are not necessarily fixed in stone. Environment, experience, etc. can result in some variation in development and regulation. I'm not suggesting any kind of Lamarckism here but this ability to control at least some aspects of our own progression and/or direction within the limits of a single lifetime is a huge part of being human. This seems to be particularly true with regard to one facet that separates us from our biological kindred - the marvelous human brain. The human brain over time has developed a wondrous capacity for plasticity presumably due to various selection pressures on the first two layers discussed. Here environment, training, and experience can do more than just change the 'software' configuration of the brain. It appears to actually lead to structural changes in response to these factors. We can to a large extent become our own sculptors to some extent. This is a marvelous gift that is no less wondrous because it was the result of natural processes. This coupled with the remaining layer is what allows humans to transcend beyond any simple instinctive programming. We could invent art, science, philosophy, law, even theology.

Again this isn't to say that we are altering our genes in this way. But this ability to alter our personal stars (a product of our particular course of evolution) to some degree does appear to be a huge part of what distinguishes us from our closest cousins.

The human brain evolved better and better means (not volitional of course) to process and store information resulting in a better and better ability to retain and build upon experience. This might have been the story except somewhere along the way, humans took the great leap that forever separated them from all that came before...

Culture: Humans invented culture. They invented history. History and culture created a means to store and aggregate experience over the course of many lifetimes in a nonbiological form. It allowed humans to benefit further from neuroplasticity by allowing specialization of individuals for a collective purpose (figure 4). Culture in concert with the innate ability of the human brain to adapt within a single lifetime (not in a genetic inheritance sense) seems to have created a perfect storm of intellectual growth that resulted in many of the things that are unique about our species.

Memes, information and knowledge, the result of experience and analysis, became as important to what defines humanity as the basic biology. And sets us apart on this Earth.

Some might say that memes threaten our survival but that isn't necessarily so. Memes, made possible by the neuroplasticity from which we benefit and adapt, itself a gift of our developmental regulatory mechanisms, derived from the basic building blocks of all life, provides us a unique opportunity. The opportunity to break free of the cycle of adaptation and extinction that has been the story of all that came before. No longer simply defined by our own biology and able to actively alter our environment if we want. What we do with that ability remains to be seen. We may fall victim to our own base programming - biological determinism of a sort. Our we may think our way into finding the means to changing our own stars. If that isn’t uniquely human, and miraculous, what could be?


Michael Lockridge said...

Nicely designed system. ;-)

Pliny-the-in-Between said...

Nicely designed system. ;-)

It is amazing. So amazing it almost looks designed if you don't look too close... ;)

mac said...

If designed, we really should have a heart to heart with the designer!

pboyfloyd said...

Note from God to Michael Lockeridge:-

"If I'd designed this, there'd be some reason why radio-active metals couldn't explode, or just weren't on the Earth. There'd be some reason why cells couldn't become cancerous. There'd be some reason why everyone WOULD be precious to everyone else, no shallow beauty and such.", note from unGod to Michael Lockeridge.

Michael Lockridge said...

Hmmm. So, perceived flaws in the design cause you to exclude God (in any form) from the equation, Pboy? Or is it the logical inconsistency or lack of logical necessity of God that causes your rejection? Or, is it something more personal? Your intensity implies an underlying bitterness, the presence of an emotional reason behind your non-belief. What might it be?

Harvey said...


Michael Lockridge (with considerable respect from me for his demonstrated intellectual honesty) illustrates the problem with any non-theist trying to demonstrate the factual knowledge we now have about genetics, evolution, physics, etc., etc. to any Deist. In the end, no matter how well-supported or well explained, the majority fall back on such rejoinders as : "Hmmm. So, perceived flaws in the design cause you to exclude God (in any form) from the equation, Pboy? Or is it the logical inconsistency or lack of logical necessity of God that causes your rejection? Or, is it something more personal? Your intensity implies an underlying bitterness, the presence of an emotional reason behind your non-belief. What might it be?"
The implication is that even if you understand the science and recognize it as the best explanation (so far) for observed reality in our Universe, it doesn't rule out a "designer". If you want or need the comfort of belief in a creator/designer/God/...., it is extremely difficult to accept the overwhelming likelihood (based upon current knowledge) that this life is all there is, that our only "purpose" is to reproduce successfully and nurture our offspring until they, in turn, can reproduce, and that in the end, we cease to exist to any greater extent than we did before the moment of our individual conceptions. If one has trouble accepting these truisms that best available evidence so strongly supports, it is extremely difficult to let go of the hope that there is a Deity somewhere that notices each of us and that perhaps can be "worshipped" to the point that it will permit us to escape reality when we inevitably die. Excellent try, nonetheless!

Pliny-the-in-Between said...

Thanks Harvey,

I'm not really trying to get people to change their minds particularly. i just find it incredible that we seem to be unraveling more and more of the story of how we came to be. And it's fun to share that.

pboyfloyd said...

Yea, Mike, what Harvey said.

I'm not bitter that there aren't any gods. (sorry?)

pboyfloyd said...

I was thinking about that comment, wondering what, whether I had a happy childhood pertained in any way at all to 'design'.

I'm sure that your, "Nicely designed system. ;-)", was meant half-jokingly. Kind of a joke with a point?

Now I took your point to mean that you believe that there is a god(God), and HE designed this system(these systems?).

I think that you understood my 'counter-point' all too well, to feel the necessity to 'poo poo' them as (merely)'percieved'. Then you repeat 'logic' as if that somehow might taint my point.

Finally you feel the need to question my emotional stability.

So, we have me pointing out that if God designed this universe, he might have designed it better and you countering by painting my point 'trivial', 'lacking an emotional perspective' and implying that I myself am 'damaged goods'.

Well, Michael, I sure hope that that makes YOU feel better about you and your God. I must have touched a nerve?

Michael Lockridge said...

Pboy, I have much appreciated your sharply analytical responses, both to me and other bloggers as I have had opportunity to read them. Your arguments and observations are sharp, to the point, and often correct.

The very intensity in your response, the sense (as much as can be perceived in writing alone) that there is a lot of emotion there, caused me to consider the possibility of emotional issues. Some discount God and all that God implies on intellectual grounds. Others do so due to emotional issues.

Those were simply observations. Of all the atheists I read, follow, and interact with on the Internet, you have been the one to most often fall to personal attacks and occasional name calling.

I have no issue with such responses, in most cases. However, your fine analytical mind can be overshadowed by such responses. If I follow the instinct of simply ignoring you for those outbursts, I will deny myself access to an excellent mind.

It would delight me if you were to choose to believe in God and follow Jesus. However, that would be between you and God. As to you and me, I hope that we can exchange ideas, experiences, and even emotions in a manner that enhances both of our lives.

You have visited my blogs, and made comments. You are always welcome. I value you.


Pliny-the-in-Between said...

I grew up raised by a Catholic father, Protestant mother living in a southern baptist town. It gave me an interesting perspective growing up. I saw the catholics essentially practicing a religion based upon a merger of Roman culture with early Christianity, the UCC folks worshiping a kindly and loving and very '60's'version of Jesus, and the baptists running around pissed off at everything spewing fire and brimstone and promoting a highly unscientific world view. All coming from one book allegedly. The more I learned about all the conflicting and inconsistent doctrines the less logically based it became to me. The more I studies the more surreal it became until it crossed into the world of simply cultural lore. The converse was true of science. The more I learned about the science the more my own observations of the world around me fit into the larger framework. And strangely I suppose the more linked I felt to the universe and more in tune to its wonders.

Pliny-the-in-Between said...

PS I am not an atheist - I'm an amystic. ;)

Saint Brian the Godless said...

You are amystic and I am a mystic. Close.

At least, my BB scenarios lead to a mysticism of sorts, even if it's closer to 'quantum mysticism' than to traditional schools.

However, basically I am an atheist, with some mystic tendencies which I endeavor to not let get too far out of hand. This is because my core attitude is that I DO NOT KNOW and so I try to approach it all with an open mind, not eliminating anything but giving weight to options based on their liklihood. I have no idea if the BB thing (consciousness-based reality) is even close to real, or just something that appeals to me due to personal experiences. Science will tell, eventually, at any rate. I have great trust in science to eventually find the right answers in due time, even if said answers border on the mystical or the fantastic, or conversely if they are quite mundane and non-mystical in nature.

Religion can't wait for us to find answers, so it goes with it's best guess, which is always God of course. However, fervor and desire and wishful thinking do not a reality make.

pboyfloyd said...

Yea, sure, Michael. Hey, I thought you took a funny, sly dig at Pliny's systems, and I gave you a 'pat' back, is all.

Did you know that there's not 'loose neutrons' floating around all over the place? Matter of fact they're unstable and pop into a hydrogen atom within 15 minutes of escaping an unstable atom.

If we imagine God designing 'it all', I'm sure HE didn't design neutrons like that to give people the opportunity to blow the BEJEEZUS out of each other.(hey, what do I know?)

So, that seems like a (potentially) fatal flaw in the 'design' of sub-atomic particles.

Now, life itself! No doubt a 'shining example' to many theists, of the Godly design producing the shiniest of the shining examples, us.(we're SO egotistical, no?)

But there's a flaw. We sometimes self-destruct! Point being, if it's a 'design', it's a bad one.

Then there's society, largely on who is the handsomest, prettiest.(what a bunch of self-absorbed pricks/c*nts we all are)

And that was just off the top of my head, Michael.

Now, when you start vaguely alluding that I'm emotionally scarred, I understand that that is a standard religious response and all that crap, but I'm not, as you noticed, going to let THAT sit around as the 'elephant in the room' that you seemed to want it to be, just the same as if you'd called me a 'God-hater'.

You're basically saying, "Good emotions us, bad emotions you guys!.. We win!"

Well, no, no you don't, not on those grounds you don't. It was an obvious and easy 'road' you took there, and your second comment, while layering on the flattery, doesn't really 'take it back', it just lowers the tone considerably.

Pliny-the-in-Between said...

Ste B! You at least you appreciate my John Denver tribute below...;)

Michael Lockridge said...

Hmmm. You might be projecting the "you vs us" implications in my comments, or else I am communicating poorly. Most people have mental and emotional issues, or so I have observed. I sure do. In fact, I am convinced that it is such flaws that draw/drive many conversion experiences, and a great many other human decisions as well.

As to flattery, I have little inclination toward that. I rarely say what I do not mean, though I may couch what I say in the least offensive terms I can manage. Anger rarely contributes to communication.

As to the issue of winning, I am not trying to do so. This is a venue of exchange, at least in my view. I "win" when I take away new information or a new perspective. Hence, I win quite often.

pboyfloyd said...

Well Mike, Mikey-baby, Michael, you old sock.

You seem to have covered everything there except the one you brought up.

The 'design' thang.

(..and sure, I might be reading too much into the 'emotionally scarred' thing, but I've heard it before from people, and it seemed to me that they were, using that to dodge the issue(inadvertong-tly?)

Harvey said...


"As to the issue of winning, I am not trying to do so. This is a venue of exchange, at least in my view. I "win" when I take away new information or a new perspective. Hence, I win quite often."

This is precisely the attitude I have detected in your posts, both here and on your own blog. If more of your co-believers were able to truly engage without the need to "win" or get the affirmation that you "have it right" by convincing as many of us non-believers as possible to agree with you, the world (and blogspace) would be a much more pleasant place. It also has occurred to me that those believers who are actually at peace with their particular slant on things seem the least likely to need such affirmation.

Jared said...

Sorry that I arrived late to the party, I just have two cents to add. While these layers of "human" do seem to exist, it is very often incredibly difficult to determine precisely where one begins and another layer ends; this is the case for practically everything in biology if you investigate far enough. Although these descriptions are certainly useful in understanding our uniqueness, I could certainly apply these four layers to brown capuchins (an all hominine primates), orcas, common bottlenose dolphins, sea otters, and many other animals; particularly because they learn behaviors from observing other members of their group (culture, in a very broad sense) and have the other three layers fairly pegged as well. For my last point about the original post; the other hominines should be more offended.

As far as the "designed" point goes; only on a cursory external-only inspection of organisms could they possibly appear designed. As soon as you begin your dissection of an organism, you realize how much of a patchwork of fixes it is.

Pliny-the-in-Between said...

Good points all. There is a lot of overlap amongst these processes and certainly Man, as an animal, doesn't differ particularly in either biology or chemistry from other animals. But culture, and I suppose I should qualify that as history, would appear to be unique to us. No doubt other animals learn from experience and elders (the cetaceans as mentioned for example) but without history - i.e, writing, it can never go beyond lore.

Jared said...

But Pliny, written history is a relatively recent invention. Is that to say that we humans have only been around since the dawn of written history?

Pliny-the-in-Between said...
This comment has been removed by the author.
Pliny-the-in-Between said...

No not at all. But I think an argument could be made that written history (or writing in general) is what has allowed us to advance to a point culturally that makes it appear that we are separate from nature to many people. It's our cultural trappings and technology that make us seem so distinct. The point we've both been making in posts is that biologically speaking, it's harder to tease out the uniqueness than one might first imagine. It appears that our uniqueness is probably more a matter of degrees and good fortune than anything biologically distinct.

But I'm getting a bit ahead of myself here. The purpose of this post was just to start a discussion of some of the factors which have and do shape humanity. In later posts I'd like to look at these factors in more detail to see what we are when all the trappings of modernity are stripped away. More specifically, what factors provided the attributes that have allowed us to advance culture to such a degree. Your human model post is a great start to that discussion.

1208茹宣dinoreale said...
This comment has been removed by a blog administrator.
Jared said...

I am currently bogged down in all the things that can go wrong during embryonic development. It is quite the list which I shall need to prune, but I've found some rather interesting ones so far.

An unrelated question: why do you have so much asian porn spam?

Pliny-the-in-Between said...

Asian porn? I never checked the links to the spam sites. I've just ignored them. I guess it's time to add the spam guard stuff like some of the other sites.

Pliny-the-in-Between said...

Compiling a list of developmental faults? Man you are a glutton for punishment. After taking embryology I was amazed that any of us develop successfully. The unfolding of a living being from a single cell in a few months has got to be one of the wonders of the universe.

Jared said...

I've repeatedly said I tend to be masochistic when it comes to learning...

On a related note, sonic hedgehog does a whole lot of cool shit...