Evolving systems course, week 4: biological evolution and change

    Our course has gone to the next step!

    I really enjoyed last week's discussion. I felt the whole course is closer and closer to the scientific perspective of looking at the universe. Paul told us last week that the revolution is really actually just a random process, and we discussed with Anne about wether it is the force of nature that made us to be the way we are now. I believed that the way creatures evolving does have a pattern. Though Darwin and other scientists wouldn't agree with me, I do believe that desire plays a role, a quite important rule in the past billions of years. Look at us, we seem to be using all of our organs pretty much every day. Why doesn't the nature just give us another pair of eyes or one less hand? We are good as what we are now. If we are just a "random product", why are we "ruling" the world now? We can accomplish much more tasks by the magnificent tools that we invented-not assembled by the earth itself, than any other species on this planet. Why is that? It has always bothers me to think about the concept of being a human and self. Even the question that why am I even thinking about this kind of abstract things. What is "me"? After taking off our names, who are we? Is each one of us unique? What about after life? Can I still feel "myself"? There are so many questions in my mind. I hope to discuss them with you and hear your opinions later on.

    Also, hope you guys have some more interesting questions for us to talk about! :)

Warning: this post rambles about something that might not even exist. Reader discretion is advised.

During the past three weeks, I have discussed evolution in a scientific context on three separate occasions. Biology, then anthropology, then ESEM. The discussion has been mind-numbing. We evolved. I get it. I do appreciate evolution - after all, it explains the tremendous diversity of life on Earth - but I want to take a step back and analyze who we are, not where we come from.

The human species is unique. I would not call us more "evolved" than other organisms, since all living creatures have evolved to survive in their current environment. However, humans are puny in both size and stamina, and we have grown to rely on intellect, not strength. I have heard our intelligence described in terms of ice cream - on the proverbial Cone of Life, we are a scoop above a rat, two scoops above a frog, and three scoops above an anemone. Our advanced tools, our languages, and our myriad emotions all suggest that human intelligence surpasses other species, but how does our brain power define us as people? Are we an expression of a hyper-talented cerebrum and an extra scoop of vanilla, or is there more to us? Is our intelligence the product of a soul?

When the theory of evolution was first acknowledged in the scientific world, religion responded with outcry. How could scientists have the nerve to insinuate that life originated from random mutations, instead of the deliberate action of God? Even as religion grew to accept the notion that a divine hand might guide evolution, merging scientific knowledge with religious beliefs, a major dilemma remained: when did God give us souls?

The soul is essential to the Catholic faith I grew up in. Present in every human being, the soul is tainted by the Original Sin of Adam and Eve, which dragged mankind into a fallen state of sinfulness and death. Catholics claim that Christ's death on the cross was the ultimate repentance for the resultant sins of the world, thus opening a pathway to everlasting life for all righteous believers. The soul is the seat of the conscience, a person's governing body of free will, allowing him/her to choose a Christlike life, sinless and pure, or to face the certainty of Hell. Thus, without an immortal soul, humans would not be humans, but animals incapable of choosing to follow the Messiah. 

If evolution is correct, as many believe, then we and chimpanzees diverged from a common ancestor, some 5+ million years ago. Where in this timeline of evolution did the soul arise? Even if the human population bottlenecked at some point in our evolution, humanity never consisted of one man and one woman, the Adam and Eve of the Bible. Without Adam and Eve, the drama of Original Sin could never had occurred, and the need for Christ would not have followed. Denying the existence of Adam and Eve seems to bring down the entire fortress of Catholic Christian thought. What's more, the loss of Adam and Eve denies humans a soul.

Without a soul, what is the purpose of music, and art, and literature? Why else would humans possess a sense of aesthetics, an altruistic streak, and a near-universal belief in a higher power? Did our powerful brains invent the soul to explain our uniqueness? Did the soul evolve through our invention? Questions to ponder...answers I don't know.

Sorry for the late-ish post!

I really liked this week's discussion. I loved talking about biological evolution because it felt like a biology class, which, as we know, I much prefer to "the philosophical crap" (to quote myself...). Though I know I need to be more open to the "crap", I was not completely closed off this week when we talked about the difference between a narrative and non-narrative story. Though I won't go so far as to say the non-narrative story with the "great chain of being" had any validity whatsoever in comparison to the narrative story presented by Darwin, Lyell, and Malthus- I will admit that I can appreciate the attempt to explain the unknown from a point of view that had some logic behind it. While I was totally turned off by the creation stories because I found them to be b.s., I thought the "Great Chain of Being" idea was interesting despite its lack of time and history.

By far the most interesting thing to think about was the idea that humans are still changing, and, as far as we can tell, will never stop evolving (until we all die in 2012, at least). What will we become??? I wish I would be alive to find out because I want to know!!! What is going to be the next mutation to propagate amongst humans? Perhaps a third eye or eleventh finger…? It’s actually pretty upsetting to think of the fact that we are “yesterday’s news”. Just like we investigate the way the homo genus use to be, we will be investigated. In a couple thousand years, our descendants may be saying “Wow! Can you believe people in the year 2010 had to waste 8 hours (or much, much less if you’re a Bryn Mawr student) of every day sleeping?! What a waste!” I feel so…un-evolved. To be honest, I’ve never been upset by the prospect of dying until now. I guess that’s part of being in the “information age”- with facebook and twitter and what not, we’ve become addicted to receiving and publishing information. Dying would really put a damper on receiving new information… including finding out what's in our future. Bleh. I guess as long as we didn’t just miss out on the “immortality” mutation, I guess I can live with this.  

I had some problems talking in class last week. I felt like I knew the answers to some of the questions that were asked but I couldn't explain the answers properly. So I just sat there and felt... like a useless sack of slightly old potatoes. It was very uncomfortable. 

On a completely different note, I am a hoarder. I am a pack rat of a ridiculous and potentially disastrous scale, so I think I might as well put my nature to good use and share some things I've collected about on the internet. Some of these are just general bio things, some are evolutionary-specific, but hopefully they'll be informative and maybe even help some people writing their papers (doubtful, but dream big eh?). I collect links for just about everything, so if you want anything from recipes to cute cat pictures to science/music/literature search engines ask me.

www.becominghuman.org/

www.stonepages.com/ <-- Probably more useful as we head into the cultural unit of our discussion

www.proteinatlas.org/

www.biology.arizona.edu/site.html

aether.lbl.gov/Images/resizenowmap.jpg <--- More suited to our previous excursions into space, but I suppose it's better late than never. Again, I have lots of these sorts of things, so if this interests anyone just ask.

www.chromoscope.net/ <--- Also slightly more suited to last unit.

evogeneao.com/images/Evolution_poster_lg.gif

www.eurekalert.org/pubnews.php <--- General good science source collector

www.guardian.co.uk/science/2010/jul/02/mutation-gene-tibetans-altitude <--- I believe this was the article we referenced in class

www.darwin.rcuk.ac.uk/581/all/1/Grow_your_own_plant.aspx <-- Educational game! Waste time in the name of science!

humanorigins.si.edu/evidence/human-evolution-timeline-interactive

www.mnh.si.edu/ <--- Yes, it's a museum. But it is an incredible museum with more interesting things than most museum websites.

www.utexas.edu/features/2007/ancestry/graphics/ancestry5_medium.jpg

archive.nlm.nih.gov/proj/ttp/flash/gesner/gesner.html <--- A look on how we used to percieve species.

www.ted.com/ <--- A general site with some things that are very science-y, others that are just interesting.

So those are some of my links. I have a billion and a half more, and if it turns out there is actually any use for me to post more of them I will.

I remember reading, “Humans did not evolve from chimpanzees.”  What.  A few humans told me we did.  “Humans are not ‘higher’ or ‘more evolved’ than other living lineages.” Oh, then we just have a really big ego to consider us slightly lower than God.  Okay. 

Something that bothered me in class was our order on The Great Chain of Being.
Dieties
People
Whales
Birds
Earthworms
Dirt

Maybe “bothered” isn’t the right word, but I felt uncomfortable that Whales was placed above Birds because that seems out of order.  To me, that was like 1, 2, 4, 3, 5, 6.  It’s just wrong.

I think that birds are valued more than whales.  They’re majestic, beautiful, and hold a lot of symbolism in some cultures.  I can’t think of any of those characteristics for a whale except MAYBE majestic if someone convinces me enough.  Many artists paint, sculpt, or write about birds.  There are even gods with bird heads! (Here’s a picture of Horus, the falcon headed Sky God [or as I secretly call Birdman].)

The introduction of non-narrative stories shocked me.  I wrote in my notebook to define it as, “That’s just the way it is” (*Cue 2Pac song).  I’m still in awe.  Non-narratives are awful!  They’re ignorant.  To me, that’s like a lazy excuse not to be curious and discover.  That’s like sitting there idly, being a waste of space.

I found the different kinds of stories explaining biological evolution interesting, particularly the part about how Darwin started off the idea of explaining why things (or animals) are the way they are with a narrative, rather than the unifying, universal pattern like the Chain of Being. The thing about explaining it through a hierarchy like that is that what if one of the links in the chain breaks? Or disappears? According to wikipedia, the Dodo bird (for example) went extinct in the 17th century. Did it not have a place in the chain of being? Shouldn't something have changed? I'm wondering why people didn't see too many flaws in their theory. I mean, obviously people did but this system lasted for a while, didn't it?

I just found it very interesting about the revolution in ways of thinking to change from the universal pattern to the narrative.  The universal pattern would be more optimistic because it would be stable and unshakable even by humans (ex. if global warming had occurred under this way of thinking, it would just be God's doing and not the fault of humans). The narrative takes away our ability to transfer our responsibility onto something else, saying "that's just how things are" instead of taking care of business like we should.  The narrative also takes away the hierarchy, so that we could rethink the ladder-like form and move about in it, so that we could, if circumstances provided, place ourselves closer on the spectrum to God and do things like genetics and cloning, while also widening the distance between humans and everything else, like animals and plants (justifying things like animal testing and experimentation etc.) A stray thought i had when contemplating this idea is contrasting it to (well, what we imagine would be) the way of thinking of some Native Americans, valuing animals and plants at the same level as humans.

A thought I had during class but didn't get an opening to say was that there's a difference when someone (like a scientist) tells what they believe based on fact and observation to be truth, even though it's incorrect, and when somebody makes something up that they know to be incorrect and tell it to be truth, but it works. For the first, I was thinking of somebody's (I can't remember who at the moment) heliocentric view of the galaxy. He believed it to be true, and told it to be true, but eventually it didn't work (because the planets were all moving on the same path around the sun or something like that). That doesn't discredit his explanation (story) just because it wasn't true. On the other hand, in this situation, the Church made up the geocentric theory and told it to be true, and it worked for a while, even though it wasn't correct.

I just watched Memento so my brain is kinda effed right now, but I won't bring up the reality question in this post. Anyway.

I'm talking about biological evolution in three of my four classes right now, which is cool because I'm getting three different sides. My bio class is talking about how evolution forms itself, in a vague round about way that is hard to explain. My anthropology class is pretty much giving me the nitty gritty historical stuff, and this class is using what we already know about biological evolution as a jumping off point for different types of evolution, and it is also using it as a story.

I like discussing biological evolution because it seems just as crazy a story as any of our creation stories. It just happens to have a ton of evidence behind it. I mean… what made the initial nucleotides decide to connect to each other and make the first RNA strand? Then after a while, what make the first cells come together to make sponges - which are the first animals? Genetic mutations made us the species we are today, and it was really all just random chance. In the instance of the giraffe, some freak giraffe back in the day was born with an abnormally long neck due to a random genetic mutation, and it just happened to be in a perfect environment for long necked things, and it had a ton of long necked giraffe babies because it was the best fit, and the rest is history. Biology. Both. This happened to us too! It all boils down to being in the right place at the right time, and having the right genetic mutation at the right time and place. One thing different in the genetic composition of the original cell and we could have blue skin and huge eyes and long bodies and glowing plants and pterodactyls and a neurological connection to the planet! It is a staggering thought. Ever since I read Your Inner Fish by Neil Shubin, I've been blown away by how much chance was involved in making us what we are today, especially our hands. They're so handy. I did not just make that pun.

 On that note, I'll say: if you have time, read Your Inner Fish, and goodnight.

One of the most exciting points I found in last week’s discussion was whether people want to explore in new environment or stay comfortably in familiar one. The discussion reminded me the period of time when I applied American universities. People couldn’t understand why I wanted to give up the chance to attend a great university in China, find a stable job after graduation and stay close with my family because it has always been considered as a as good standard way of living. Under the atmosphere of queries and criticisms, it was sometimes hard to tell why I was so busy doing American college application. If I had not chosen this way, I would definitely have more time to spend with my friends and family. And the reality was I experienced tough brainstorming, painstaking information gathering and comprehensive source researching every day. At the same time, I tried to be the same as my classmates, trying to know what they were talking about, pretending to be a normal one but mentally doing lessons alone with another system. I feel regretful about that. But every time when I ask myself, how about having something cool and beautiful and extraordinary but hard or tough? I was and am and will always be the first one to say YES and I hope that it stays that way.

Now, when I retrospect that experience, I found that I’m a person who don’t want to spend my life flatly, believing what other believe is a right, doing what other believe I should do. I am more than a person who smile when someone else smile. I do want to find a comfortable place for me in the world, both physically and spiritedly. And maybe there isn’t such a place, because everything I want is also always changing.

Now, Inspired by other students’ experience and took further consideration of mine, I amazingly found that if we apply this theory to the evolving universe, it makes a lot of sense. Say, people wanted to find themselves a comfortable position in the world so that they created creative myth. But as time passed by, people born with more comprehensive observation and knowledge didn’t feel comfortable of always believing in what the older generation said, so that they worked on their own and created more stories that seemed more reasonable in their position. Gradually, what we call scientific story is formed. At the same time, in this case, we can feel free to put scientific story, which is what we believe nowadays, between the position of true and false. People will never find the “real truth” because they keep evolving and continuously seek more answers that satisfy themselves.

In my AP biology class senior year we talked a lot about both Darwin and his work. Mostly we spoke of natural selection, and more specifically decent with modification. As Paul Grobstein said at the end of Thursday's class, we can explain evolution without using the phrase natural selection, because that's only part of the story. Also most people think to believe that natural selection and sruvival of the fittest are the same thing, when in fact they are not. Survival of the fittest implies that the strongest animal will pass on its genes and the weakest will die. Well in some circumstances the weaker, or smaller animal is the one to survive a change in environment and live to pass on its genes. Also some animals are just inherently able to withstand diseases or famines because of their genetic makeup, while not always being the leaders of the pack. Descent with modification means a random change in genes and physical structures over generations. These two concepts are both part of evolution and are not mutually exclusive, but do not mean the same thing.

I love that the biological part is coming. But the different perspective of thinking about it makes me ponder too.

I have already appreciated Paul’s model in my bio lab, when the class were discussing about diversity and evolution. From the model, we can tell one thing special from Darwinism which includes the intraspecies and interspecies competition, environmental pressure, and the claim that diversity exists at the beginning of the world and it is fixed. While in the model, we can see that the parental generation (not just one female and one male but a mix-gender group with comparatively similar characters) owns limited number of properties for the two characters in x and y axises. But when they start reproduction, the properties in this population tend to be diversified over time. And with random separations and combinations in genes (which is first studies by Mendel), or say pangens(the way Darwin tries to explain for genes ), the 2-dimentional graph in the certain area will be almost filled up. This difference shows that the change in properties occurs over time by free and random separations and combinations of genes, also by a loose environment which won’t be too tough to allow only one type of a species to survive. And the change of telling the biological story occurs when scientists have more observation and developed technology to prove their assumption.

The initial motivation, which I believe it exists, doesn’t come from an exclusive intelligence. We can say that different factors with tremendous amounts in environment, intraspecies and interspecies come to the big natural selection which decides the direction of evolution. We can also say that different story-telling with tremendous amounts in culture background, location, time makes the big human-made selection which decides the direction of creation stories.

There can hardly be an exact beginning, for no one could name the time when the first organic molecule came into being. There can hardly be an objective observer, who can stand out of any species in the world to judge or record everything.

But the eternity stands in a different way of living. For one life, it may couldn’t last forever, whether for an ephemeron or a sea turtle. But as one species still exist on earth, the genes, the records and proofs of their ancestors’ lives, are there. Just like what Henrietta cells means to some extent. This eternity is not worshiped by an individual, but it affects our recognition of long lasting. Esp. for those who believe in god and soul. When the life is gone, but the cells and genes are there, who generates/carries the soul?

After the class, I really have a lot to share about our great Esem Class. I felt that the role of instructor is to lead the direction of class discussion. When we were walking to another section of group which shared the same topic with u, the topics were completely different.

The model Professor Paul Grobstein showed gave me a visualized impact of the evolutions made on the environment. The answer we found for the drive changes over time is the environmental changes. On other hand, the model did tell us the reproduction with varies is the core force to provide the diversity in the ecological system. The natural selection, which I used to considered is a way to direct the pathways of evolution, is eliminating the possibilities is being created by all the biological reproductions. The remaining possibilities over time became the evolution we know today.

Typically, I found the questions I found interesting is that “Whether human beings are more evolved than other species?” Most people agreed on this statement that human are superior on the biological evolution level because the intelligence shown on human. The smartness which is the ability to overcome our weakness using tools and the technology we developed over generations of excellent pioneers is remarkable. However, I still believe that statement depends on the definition of intelligence. I believe every species are equal. All kinds of animals today are in the stage evolution which enables them to be “clever” enough to hind the fittest way to survive and reproduce in this world. Somehow, people are lucky enough to be the spice can use tools. This fact does not give us the authority to depreciate other amazing living things.

However, I still have some questions about the evolutions. What drive the change of the environment where the natural selections took place? Also, are the eliminated species or individuals really meaningless and useless?

The other thing I really want to mention is the confident attitude for your own writing. I was really dumfounded when I read the third passage of students’ writing. She wrote that “My story came from me, a layer of complexity in this universe. I am not small, nor am I big, but I am here.” I really want to thank her for letting me know or teaching this key point: Never depreciate your own work! There are so many stories in this world, and each of them has its own value, including mine. The feelings I have for my own work from my education background make me change my minds so easily. I am not a confident person for almost anything. For example, I won’t make my point until I am 90% sure of it. In my second essay, I basically overturned the whole story I wrote first time. I totally ignores the value my essay has. I was not confident enough to insist my viewpoint. When divergences appeared, I would usually choose to comprise for an agreement. And I always thought the problem is in my side. It’s OK to be different and disagreements are allowed in this society. So far, the LAC experience and our Esem have already taught me that to develop critical thinking and skeptical for all the information received from the surroundings. From now on, I will tell myself that even though I might not be good enough to be praised but I am unique and I deserved the right to speak out loud and I must be confident and proud of my own work. I have the right create my layer of complexity the way I want.

 What I have found interesting about this seminar so far is it's ability to connect all my classes. In history we have talked at length about how the subject is not about what happened, it is about interpreting the stories we have about what happened. My anthropology class has been talking all about biological evolution. I have never had any courses link up so perfectly before. It's a little un-nerving. 

I had a little trouble this week with paying attention in class or participating full heartedly in the discussions that we were having mostly because of this virus that is going around school and that I just so happened to catch. By the end of class on Thursday I  was not getting a grasp on anything we were discussing in Paul's class. I thought the simulation was very interesting but some of the topics and ideas brought up were a little confusing or hard to comprehend because I wasn't giving it my full attention. Not because I didn't like the topic, but just because I was feeling so sick that my mind was more focused on sleep and hot tea.

However, during our Thursday discussion I did grasp a new understanding on these essays that we write every week. The last two essays I've written so far I worried about them being "acceptable." I'm so use to someone handing me a prompt and saying "this is your prompt, this is how you're specifically going to write your essay." So, needless to say, it's caused me to feel a little bit of pressure on these essays because I'm constantly worrying about if I'm writing about the right idea or the right topic. During Thursday class though, while reading others essays, I realized that there really is no right or wrong in how we want to write these essays. It is our own responsibility to choose if we write them creatively or analytically, first person or third person. There is no set prompt or specific way to how we should write in this class. We choose the direction we want our essays to go and we will not be scolded at our marked down if we decide to take a more unique/untraditional approach towards them.

I'm really grateful to Paul, both for creating "Evolution as Reproduction with Variability, and for inviting our class section to join his today, to watch a demonstration of the model. There were a couple of points in the explication, though, where I got hung up. I'm wondering if others of you were similarly stuck in those same places (or in others), or if you might have explanations that could help me better understand what was being demonstrated.

So here's where I got confused:
* the demonstration began with the explanation that we were looking @ a model of organisms that would reproduce offspring, which were "sort of like them, but not identical." This was my initial--and so deepest--confusion: I thought we were there to see a demonstration of "why change occurs over time," and of what motivates that change. But change was built into the starting conditions of this demonstration.  Where from these initial variations? Where from the "changes" that distinguish parents from offspring?

* The real point of the demonstration seemed to be not "why change occurs," but rather where increasing diversity comes from: i.e., that diverse initial conditions lead to increased diversity. To make this point, Paul repeatedly said that the "space was getting bigger," but this explanation seemed to me to slide from a particular idea (that diversity increases with time: more hair colors, say, or more body types) and its VISUAL representation. But it isn't necessarily the case that more space is needed (or used) in that process of diversification. The idea and its representation were confusingly collapsed.

(Actually, now that I've started in questioning, I'm starting to doubt the claim that diversity always increases --though I'm also remembering, along these lines, the "disappearing blonde gene" hoax, based, evidently, on a misinterpretation of how recessive genes work....)

* I thought Paul ended his talk very effectively, by juxtaposing some excerpts from student papers, all of which showed creation as being motivated by  "desire" or aspiration. He said that, in sharp contrast, the changes in the population in the computer model were not "driven"--and he passed over the suggestion, made by several of you, that the "drive for reproduction" might be relevant here.

So I'd like to understand this distinction better: if we say that evolution has no "driver" (=no "architect," no "motivation," no "plan"), what then is the role of the sexual drive? Freud wrote compellingly of unconscious drives--but in his dismissal of such "drives," was Paul just emphasizing the fact that, in the process of evolution, no conscious intention is @ work? Was he denying the role of any biological imperative?

 Usually I like to figure out things by myself in my mind, and when I discuss/communicate with others I simply express my opinions. But today, through the discussion, my thoughts became clear. I often got inspired by conversations but had never got my mind organized by conversations. I felt excited about today's experience. 

About the certainty and uncertainty delivered by creation myths and scientific stories:

The scientific stories give us a sense of uncertainty, which makes me feel that it is almost impossible to know the real origin of the universe. It is really annoying for me that I will never know the truth, because I am curious and I want to know the truth so bad.

And I think the creation stories also give a sense of uncertainty, not to us, but to the ancient people who, with limited knowledge, could not proof their stories wrong.(but we can proof them wrong now)

However, when we now read those creation stories, we feel certain. We feel certain not because the stories are more believable, but because we know the stories are 100% wrong, not "either right or wrong" as the scientific stories.

Now I believe that creation stories evolve into scientific stories as human beings gain more and more knowledge. No boundary is between the creation and scientific stories. I believe that, in some day, science will be myth.  

As I gained more understanding of the evolving universe, a new question rose: what is my position in the universe? (when I looked back at the name of our ESEM: making sense of ourselves, I felt like I have now reached the door of that topic )