Week Three: Genetic Evolution

Random scramblings on a lot of complicated information...



1. “99.4% of the most critical DNA sites are identical in human and chimp genes” What do you make of this?

In order to be fair and not emotional about this, it would be interesting to know how well human DNA matches the other, now extinct, species that are currently classified as being part of the same genus "homo." That would resolve the question of the article in one way (or perhaps create additional arguments). But that is the not question here. It is simply to comment on the fact that we are genetically extremely close to chimpanzees.

First, I think it's exciting. It's a priviledge to see such a close, yet distant in so many ways, relative alive along with us. I wonder about Homo habilis, erectus, etc., and if their behavior would be more chimp like, or more human like. Also, I've worked with primates (gorillas) and have looked into their eyes and it is obvious to me there is a common understanding and connection. So, it's not that much of a surprise.

But we are significantly different from chimps in a lot of important ways -- the ability to "talk" (as in human speech) cannot happen with chimps because their vocal cord structure is different. While they can walk upright for short stretches, their physiology is different that ours so they are not officially bipedal. Their skull shape and size, and their teeth vary significantly.

I also found a website that says human and fruit fly DNA is 60% similar, which makes the 99.4% figure a little less impressive. Also, it was found that 80% of the proteins in the human and chimp genomes are different, which is important because the proteins are responsible for creating the physiological variation.

That said, I think comparative genomics is an extremely interesting field! And hopefully it will lead us toward accepting and respecting non-human animals more. The genetic closeness between living beings also means that we are all prone to the same environmental impacts and that we really should pay close attention to the fact that many species are going extinct, or are mutating in disadvantageous ways.

I wonder though why we would be more likely to grant "rights" only to those who are similar to us? This exact thinking -- the "other" isn't as worthy and I'll accept and respect you only so long as you are like I am -- is what is beneath racism, sexism, and other equally harmful belief systems.


2. Check out the Prokaryotes, Eukaryotes, & Viruses Tutorial
http://www.biology.arizona.edu/cell_bio/tutorials/pev/page2.html

I found the link a little thick with too many speciality words which made it a little hard to understand. I am glad that I read Fritjof Capra's words on the topic in "Web of Life" last week. From the tutorial I did learn, however, about viruses and how they are technically "not alive" (according to this website, but this is contested by others) but just strands of genetic code that require a host to copy and transport them. For some reason this is very interesting to me. They are awfully clever even if they are not considered to be alive. However, I would side with those who think viruses are alive.

3. Impressions on Human Genetic Evolution
http://www.cartage.org.lb/en/themes/Sciences/LifeScience/PhysicalAnthropology/
HumanGeneticEvolution/mainpage.htm

Something occurred to me as I read this:

"For example, populations that are better able to exploit resources may have greater biological fitness and therefore contribute disproportionately to the gene pool. This is illustrated by the development of agriculture, which can support more people than the hunter-gatherer cultures."

This statement could be regarded as unscientific and culturally-laden. Judging something as "better" or "worse" is tricky. Not only in terms of applying subjective values, but also in terms of scientific judgment. WIth a short-sighted view it might seem that the more people you can support, the better, but humans have survived a lot longer as small hunter-gatherer bands than we have survived so far as agriculturists. And agriculture leads to more sedentary living, populations expand, and then what? Well, disease rips through large sedintary bands of people more disastrously than it does small, mobile tribes. If a small group of people die from a disease, then they are gone, but that is just a small percentage of the whole human population. If a disease takes hold in a sedentary group of people, many more are at risk. Agriculture also, in my opinion, led us to hoarders mind set-- stockpiling -- and away from a nature-based mind set. Agriculture was the first step humans took in conquering nature. And where are we now? Nature seems to be getting the last laugh as our lifestyles are not working in conjunction with it. So what is "Better"? What is "Worse"? What, ultimately, would be the smartest route to survival?

4. Cybernetics
This topic is complicated! Intuitively I like this systems approach, though it seems much more complicated. Fractals also came to mind (for some reason, I'm not sure why), and then one of the web pages started talking fractals which made me think I was on the right track. It certainly will take more than a few minutes of visiting websites to get some kind of grasp of it. I found some definitions and explanations from a few different websites (in addition to those suggested) were helpful...

Cybernetics: How systems function

Autopoiesis: Self-generating system, like a cell. Remains stable despite matter and energy continually flowing through it.

Life: the ability to self-produce, rather than "reproduce" (you are still alive even if you don't reproduce)

Co-evolution example: "For example, the light entering our eye does not 'cause' the photochemical release that occurs, that mechanism must already exist, light just triggers it. This ties in with the complexity view that selection acts on systems whose structure has already self-organized."

From the evolutionary cybernetics page:

Yet, the Darwinian approach remains controversial. There are two main reasons:

most people find it difficult to imagine how the intrinsically "dumb" process of blind variation can give rise to intelligent, apparently purposeful systems, such as organisms, minds or societies.
some scientists (e.g. Kauffman, Margulis) claim that we need alternative mechanisms of evolution, such as self-organization and symbiosis, that complement variation and selection

I stumbled upon this guy (http://howardbloom.net/) whose book "Global Brain: The Evolution of Mass Mind from the Big Bang to the 21st Century" seems really interesting, equally complex, and somehow related to all of this... From the website description: "Global Brain tells scientific tales so vivid and so little-known they scintillate. The book zooms in on the birth of the first communal intelligence in colonies of cyanobacteria 3.5 billion years ago. A single bacterial society in those days of a spanking-new earth held trillions of members, all hyperlinked by a chemical communication code...and all working together to literally reengineer their genes. Each colony upped the level of microbial ingenuity by broadcasting data-laden macromolecules over the span of continents and seas. Using this global information-web, bacteria pioneered the first planet-straddling research and development system eons before the emergence of brains."

And this guy on youtube does an alright job explaining autopoiesis, but it is ten minutes long:



5. Can you catch cancer?

Week Two: Evolutionary and Developmental Biology

My thoughts on Evo-Devo and how Darwinism matters to me... (This is a pretty long post. I apologize. The topic made me a little obsessive and I had trouble stopping and went contrary to my better judgment.)

We live by story. And the story we are living by is driving our species to extinction. It is that the story we live by is shaped by the prevailing theory of who we are, what we are here for and where we are going. Thus if we change the theory, we can change the story, and thus the old pattern of our lives, opening the way to the better world.

-- David Loye


Theories of how we came to be here, right here, right now, and where we are going, are all stories. You have the Darwinists, the Creationists, the Neo-Darwinists, the Evolutionary Developmental Biologists...and the lay person, who may or may not consider the question at all.

Charles Darwin:


From a personal standpoint, my own biology and evolution is a mystery to me. From my heart, I can only thank my parents and my ancestors for surviving and reproducing. I feel like a biological concoction and continuation of their lives. I am the result -- as are my sisters and parents and cousins and aunts and uncles -- of a long chain of a family of survivors.

How did I get to this current point and am I appropriately adapted to my environment? Perhaps not -- I don’t have any children. Is reproduction essential to being considered successful in an evolutionary sense? Maybe on an individual level but at the level of the collective, perhaps *not* reproducing is even more essential to the survival of humanity (and the rest of the planet) at this point.

What I can say with certainty is that I don’t feel that my current environment is a very good match for my biology, and vice versa. The noisy world raises my cortisol levels and it frequently doesn’t make me feel good. Does happiness play a part in “evolutionary success”? I am attempting to go beyond my body’s dislike of crowds, noise, garbage, and bad manners through the use of culturally learned behaviors like meditation and energy work, etc., to adapt better to my environment. Other people are using a lot of drugs to ward off the onslaught of overwhelming sensory input. From the looks of our drug sales, particularly antidepressants and anti-anxiety medications, a lot of people are feeling they need some help, beyond what our biology offers, to adapt better to this crazy environment we have created.

In the early nineties as an anthropology student I received some good basic training in theories of evolution and genetics. What was presented was rather simple and straightforward and made sense--genes are passed down, and if they are suitable for the environment at hand you reproduce, passing those “fit” genes along. Occasionally mutations happen, randomly, creating variations. The story was that the environment drives biology. In recent years I have come to think that “evolution” is more complicated than what I had been taught.

The mapping of the genome produced surprising findings. There are fewer genes controlling our biology than we expected. Variations in the genetic makeup between species are smaller than what we assumed we would find. And there are holes in the paleontological record -- there are “missing links” and much is unexplained.

The evo-devo people discovered, through looking at DNA on the molecular level, that genes between species are not all that different, but they express themselves differently.

This New York Times snippet was a good basic summary of what exactly evolutionary developmental biology is:

http://video.on.nytimes.com/?fr_story=3ba8ecaed1cf130c1d0ea4baa3876356bea3bb58

Motivations for studying evolution have varied, but hopefully it will ultimately lead us to “finding our place” as Dr. Sean Carroll states in the New York Times video. And that, I think, is what the intense arguments regarding the genesis of life have been about. There is profound disagreement as to where the human place is. Above nature? A part of nature? At the “top” of the food chain? Better than the rest? Smarter?

I tend to think that the revolutionary thinkers on the subject have it right (please see below) -- it seems everything is pointing to the fact that we are interconnected with the planet as a living being, and all life on the planet is really not that much different, in essence, from other life forms...in other words, we are all one (the same thing that physics says). The hard part is getting mentally beyond these isolated bodies and seeing things within a deeper context and history. I also think the earth is trying to evolve with us, and trying to adapt to the changing circumstances of what the conditions of the planet have become. She (the earth) might feel the need for some antidepressants right now, too. And I think she's a little crabby -- hence all the tsunamis, earthquakes and such.

In the last thirty years or so there have been other revolutionary thinkers on the subject of evolution. There has also been a re-looking at what Darwin actually said. Here are some interesting thoughts and thinkers on the subject:

1. David Loye



At 83-years-old David Loye has had a wide ranging background, from being in the trenches of WW II to spending ten years on the faculties of Princeton and the UCLA School of Medicine. In later life, his thoughts turned to Darwin and evolutionary theory. He went back and re-read Darwin and made some surprising discoveries. He now believes that Darwinists and Neo-Darwinists have misinterpreted Darwin. His claim is that Darwin believed what primarily drives human evolution are "the moral qualities." And that the moral qualities are “advanced, either directly or indirectly, much more through the effects of habit, by our reasoning powers, by instruction, by religion, etc., than through natural selection.”

In the Descent of Man he searched for the following terms, to see how prominent they are in Darwin’s thinking.

Survival of the fittest = used 2 times in Descent
Competition = 9 times
Selfish and selfishness = 12 times

Love = 95 times
Moral sensitivity and morality = 92
Sympathy = 61
Mutual, mutuality, mutual aid = 24

Loye also writes that "The shift from the emphasis for the first half [The Origin of Species] to the full Darwinian theory [The Descent of Man] and story [Darwin's journals] — and your understanding and involvement — can not only help move us toward the better future. In the long run, it may help save ours and all other species."

Link to Loye’s work: http://thedarwinproject.com/about/about.html

2. Rupert Sheldrake, a controversial figure in science and former biochemist trained at Cambridge and Harvard, has presented the theory of “morphic resonance” to explain how genes could be so similar amongst species, but the expression of those genes so diverse (for example, the genes dictating the spots on a moth are basically the same as the genes dictating a mammal's limbs). Morphic Resonance is like a cloud of memory that exists around individuals, societies, cultures and species, that carries memory which informs everything from the shape of a limb to societal behavior patterns. This morphic resonance also evolves, and it carries with it much more of the story than just our genes do.

Rupert Sheldrake’s theory of morphic fields:

http://www.sheldrake.org/Articles&Papers/papers/morphic/morphic_intro.html



3. Lynn Margulis, a microbiologist and partner with James Lovelock in creating the “Gaia Theory,” revolutionized evolutionary thinking with her theory that symbiotic relationships--a co-evolution with the planet and other life forms -- are what have been the determining factors in the evolution of species. This is systems thinking. Margulis has found that significant portions of the human genome are either bacterial or viral in origin. Bacteria evolves very differently from other life forms, as they can share DNA during their lifetimes with other bacteria. Some of our human DNA does not reside in the cell nucleus, but outside of it -- this is the mitochondrial DNA. It is theorized that this mitochondrial DNA resulted from viruses that have become a permanent part of our DNA. The advent of microbiology greatly changed the view of evolution. According to Margulis, many scientists still approach evolution at a macro level, leading to great misunderstanding. From her Wikipedia entry:

“She also believes that proponents of the standard theory "wallow in their zoological, capitalistic, competitive, cost-benefit interpretation of Darwin - having mistaken him... Neo-Darwinism, which insists on (the slow accrual of mutations by gene-level natural selection), is a complete funk." She opposes such competition-oriented views of evolution, stressing the importance of symbiotic or cooperative relationships between species.”

Links about Margulis:



http://www.geo.umass.edu/faculty/margulis/

4. And finally Fritjof Capra sums up much of this systems-based evolutionary thinking in his 1996 book “The Web of Life.” He reviews Darwinists, Neo-Darwinists, Margulis and Lovelock, deep time, findings from microbiology, and then moves into evolution and human culture. In the end Capra writes "that a proper understanding of human evolution is impossible without understanding the evolution of language, art, and culture. In other words, we must now turn our attention to mind and consciousness, the third conceptual dimension of the systems view of life.”



Comments on the links:

Darwin's books are like the Bible -- many interpretations are possible. Though they definitely answer one question -- life forms have changed over time -- the exact path and way that happens is up for discussion. Depending on one's world view -- scientific, religious, or somewhere in between -- arguments can be constructed to support that world view. It's slightly troubling how so many different people can be so sure that they have the right answer as to what this all means. And kind of laughable that the mystery remains! The mystery remains! Buddhists will tell you you have to find the answers out for yourself and be your own teacher. I just cross my fingers and hope we can get ourselves to a place of greater peace and happiness, personally and collectively.

Week One: Our Biological Selves

1. Do we really understand our biological selves?



What a funny and complex question to think about. On a personal level my body remains a mystery. I am often surprised and sometimes confounded by my own biology. I created an art project once where I broke my body down into its various parts, drew pictures of each part--my foot, my leg, my ear, my nose, my belly, etc.-- and told the stories that belonged to each part. So many stories our bodies have to tell! The line between biology, culture, personal history, and societal beliefs begins to blur.

We have, as a human culture, many understandings of our biological selves and perhaps no understanding at all. As a graduate student in medical anthropology this very question was the leading question in all research related to the field. The answer to the question depends on who you talk to: a woman with "heart trouble" in Iran and a cardiologist in the United States will have very different explanations and treatment ideas for her symptoms. Arthur Kleinman, a medical anthropologist who wrote a groundbreaking book in 1980 called "Patients and Healers in the Context of Culture," provided the term "Explanatory Models" or EMs to describe this phenomenon. For Kleinman, it is vital to always ask a patient "what do you think is the cause of this problem?" And this question will lead to a greater understanding, for both patient and physician, of how to treat someone's symptoms, and of what the cause of the symptoms really is--especially when working with someone who comes from a different belief system.

In the West we might be led to believe that allopathic medicine possesses the REAL understanding of our biological selves. That the close scientific investigation of the body provides the correct answers. Yet really, surprisingly, through study of things like the placebo effect, alternative forms of healing, and turning an anthropological eye on Western medicine itself, we discover that this isn't exactly the case.

Cecil Helman, an anthropologist at the University of London, studied, among other things, culture and pharmacology. Helman writes: "In many cases, the effect of medication on human physiology and emotional state does not depend solely on its pharmacological properties. A number of other factors, such as personality, social or cultural backgrounds, can either enhance or reduce ths effect, and are responsible for the wide variability in people's response to medication." That statement is rather shocking for someone coming from a Western biomedical perspective. How can this be?

Helman reports that in study after study placebos have been shown to effectively "cure" practically any organ system in the body. He states:

"It is therefore the *belief* of those receiving (and/or administering) a placebo substance or procedure in the *efficacy* of that placebo which can have both psychological and physiological effects."

An important point here lies in the parenthetical phrase "and/or administering" -- it doesn't even have to be the patient that has the strong belief -- it can be only the physician's belief that impacts the efficacy of a treatment! A study was done on five treatments (specifically, in this case, five different drugs) for angina pectoris "all of which are now believed to have no specific physiologic efficacy, yet at one time all were found to be effective and were used extensively." How can it be true that at one time a drug cured on a number of people of angina pectoris and now the drug doesn't work? The only difference found between the time the drug worked and the time it did not is the collective belief of the physicians!

It is this study that comes to mind when people try to defend acupuncture as truly effective because it seems to work on non-human animals. What they are trying to say is that the effectiveness of acupuncture can not only be in the mind of patient because it works in animals who have no belief in acupuncture. What is missing here is the impact of the belief of the acupuncturist on the outcome.

Another case where this is true -- the impact of belief of a practioner on the biology of another being -- is with the effectiveness of prayer. Dr. Larry Dossey is a physician who reports on the effectiveness of prayer to heal in his book "Prayer is Good Medicine." Again, there are many scientific studies that validate his assertion.



In light of all these studies, a straightforward understanding of the physical parts of the human body (and the effect of chemical substances on the body to treat sickness) begins to hold a little less weight in offering a true understanding of biology. We are not machines. Nothing can be explained in simple biological terms...unless maybe that is your belief system.

The short way to answer this question then, do we really understand our biological selves, is no. What a fantasic mystery we are!

There is perhaps another way to speak about our "biology" our "life" that includes more than just looking at our internal organs...



2. Impressions on the links on evolution:

There's a lot of information in those links! I guess I never knew that the topic of evolution could span so far and wide. I looked into "Deep Time" which really provides some perspective on our own little lives. It's amazing to me that life as we know it took so long to evolve, and that we are capable of destroying a lot of it in the blink of an eye. I also looked at PBS's mate selection quiz which made me wonder if my lips were puffy enough and my chin small enough...never thought a site on evolution could make me feel so evolutionarily inadequate! And finally, I tend to believe that life forms can sort of "will into being" certain traits. Even with all that time for change involved, it still seems a little too weird that moths could develop spots that look like owl eyes. My world view would throw some consciousness into the mix there. I still stand by the belief that we are not machines!