Friday, March 07, 2008

The Intellect of Man - A House Upon the Sand

Evolution is the gradual genetic change, or mutation, of a species over large amounts of time. Through the process of Natural Selection, the advantageous genetic mutations/traits are passed on to future generations, leading to the formation of more advanced and complex organism more highly adapted to their environment.

This theory, and I stress theory, makes a lot of sense. We see environmental adaptation happening all the time all around us, that means the theory as a whole must be true and proven scientific fact, right? Wrong.

The principle of adaptation and Natural Selection are considered to be pretty set in stone. If I creature cannot adapt to a change in its environment, then it becomes extinct, thus falling victim to Natural Selection. Not a very hard concept to understand, and it has been shown time and time again. However, just because the underlying principle of evolution has basis in fact, does not mean that the entire theory is true.

Let's start with the origins of Evolution. The theory was first transcribed and published before DNA and genetics were even truly discovered. The original theory doesn't even mention genetics, just the passing on of traits from one generation to the next. Now, you may look at that and say "That's genetics!", and you are right. Darwin didn't know that, though.

The traits about which Darwin spoke were physical traits and changes. Things about the animal that change during its life-span, not during its conception. By his logic, this is how a Giraffe would have evolved: a horse-like animal moves to an environment where it is forced, for one reason or another, to eat the leaves out of the trees rather than the grass on the ground. The animal that can reach the highest gets the most food and has an advantage over the others, so as the animals try to get the leaves, they stretch and strain their necks to get higher. The one that, literally, stretches its neck the farthest has the most advantage and will, therefore, be the most likely to pass that trait (the elongated neck, caused by stretch and strain) on to its offspring. In other words, as the creature changes itself physically, it is able to pass those physical changes to its offspring.

That is essentially about the same as saying: If someone cuts off their left hand when they're 20, and has children, those children have a chance of being born without a left hand. That, as we now know, is a preposterous idea.

As we have learned about genetics, however, the theory has adapted to incorporate the new knowledge. The modern theory now states that genetic mutations that happen at the time of, or before, conception can cause advantageous changes that will be more likely to be passed on to offspring. The theory now lines up with modern-day knowledge of the known workings of the genetic code.

Problem is: we know very little, all things considered, about the genetic code. We know what genes do, how DNA is replicated, what genes do what, but we don't know WHY they do it. DNA is used as the template for RNA, which, in turn, is used as the template to create proteins. These proteins, the building blocks of life, are what drive everything. One small chemical chain to one microscopic protein can kill an entire organism, just look at cancer. We don't know why they effect everything the way they do, we just know that they do, and that's that.

There are also massive gaps in the fossil record. Gaps which Darwin, himself, has stated were the largest problem for his theory as a whole. There are "missing links" a throughout the fossil record, where no common ancestors have ever been found, when, by Darwin's own theory, the fossil record should be rife with the fossils of transitional forms.

Problems also arise because of paraconformities. Paraconformities happen when the fossils records appear geologically backwards, and where no evidence of erosion (to displace the bones) or tectonic overthrusting can be found. This means that parent species is found to be younger than the child species. I have yet to find a decent explanation for this occurrence. Mostly, from what I have read, it is considered a "mystery" and just accepted as one of those things that will be explained by someone else some other time.

Thus we see that the foundation upon which evolution was initially created has crumbled to dust beneath the advancements of science, and the new modern theory of evolution, derived from the first, rests upon a foundation that is as equally unknown as genetics were when evolution first arose. Darwin knew traits were passed on somehow, he just didn't know why or how. Just as scientists today know that proteins drive the lifecycle, they just don't know why or how. He thought that, even though their were massive gaps in the fossil record, proof to fill these holes would show up eventually. None has yet been found. Lastly, and mostly caused by the drive of science to fill the fossil record gaps, fossils have been found in an order other than what the evolutionary cycle would dictate it must be. No theory has been conceived to explain this.

11 comments:

Bennion said...

I'm a friend of Erica's, and a big believer in evolution, so she sent me a link to your blog and recommended I read it. I hope you don't mind my commenting on it.

I appreciate that you're learning about evolution and are approaching it with an open mind, but I disagree with a few parts of your post.

I don't like how you "stress theory." It's a theory, but not for lack of evidence. Theory just means "way of interpreting data." No matter how much evidence is accumulated in favor of evolution, it will never become a law. Some people take "theory" to mean "unproven," which is certainly not what it means. A theory that has satisfied many, many tests of its validity becomes known as a successful theory, and as far as I know, science has never abandoned a successful theory.

You're correct that adaptation is a product of evolution, and evolution is not a product of adaptation. Evolution is a product of random genetic changes coupled with natural selection. I realize Darwin didn't know about genetics, but I've never seen any evidence that he thought traits acquired during one's lifetime would be passed down to one's children. If you could cite something for that, I'd appreciate it.

While I don't think that we have any really good theories on the origin of life (or at least any with strong evidence behind them), I think we do know WHY DNA does what it does. Because it's a product of natural selection as well, and has descended from other strands of DNA that created an environment in which they would be replicated and passed down. If that strand of DNA could not create an environment in which it would be replicated and passed down, it would shortly cease to exist.

I also think that gaps in the fossil record do not pose any problem for evolution. Fossils only form under very rare, and near perfect conditions. We're lucky that we have as many as we have, but the absence of a common ancestor of a species certainly isn't evidence against evolution. It just means its ancestors weren't in the right circumstances to be preserved in fossils.

For example, we have found many of our own ancestor's fossils in Africa, but never a chimpanzee's ancestors. This is almost certainly because chimpanzees largely lived in jungles, where the conditions are not right for a fossil for form.

Also, I never never heard of the problem of "paraconformities." Who are we to say which direction evolution ought to be going in? Sometimes evolution will shoot off in one direction, and then seem to change and almost reverse course. It isn't going in a specific direction, it will meander all over the place! So if a fossil is found that appears to be "backward" according to how we think evolution should have progressed, the problem is probably that we just don't know the circumstances under which that species was evolving.

Anyway, I hope you take that all well. Later I'll look up a good article about the issue of evolution meandering instead of moving in a specific direction. Cheers,

-Bennion

Beefy said...

I stress theory because the main point of evolution has not been proven. Adaptation and Natural Selection (to an extent) have been proven to exist, but nothing as extreme as evolving into a new genetically-unique individual. Evidence exists that it might, but just because it might doesn't mean that it does. I plan on covering most of these in later sections. This is, as yet, a very unfinished work.

Adaptation is, the way I see it, a minor form of evolution. A species moves into a new environment and those most fit to inhabit that environment will survive and reproduce. Evolution, while not relying wholly upon this, does use it as one of the major points by which evolution can start to occur.

Most large evolutionary changes usually happen because of some form of population bottle-necking. A mass extinction, starvation, etc. Usually without these events, by the theory, evolution would move very, very slowly.

But, back to topic, it remains a theory for lack of concrete proof. The only changes man has observed (and granted, very short time frame, etc, etc) have been simple adaptation. It is easiest to see these in bacterium. Nothing as extreme as evolving.

To split a very fine hair, just because fossils (and the only real "evidence" of evolution would have to be in fossils since nothing can be observed) show similar or slow adaptive/improving features in them does not prove that one species came from the other. All it really shows is that two similar species existed at one point. There is no hard link between them, just the assumption that what we think happened did. A very fine hair, but you can probably see that perspective if you have an open mind.

As for Darwin's belief that physical changes occurring during the individuals life-span were passed on to offspring, he talked about it in the first chapter of An Origin of Species. It was the entire premise of his theory. Like I stated, though, as science has gained more knowledge about genetics, the theory has been changed to fit that knowledge. Thus references were made to the "modern" theory of evolution.

I will talk about the DNA/RNA issues in a later section. Things such as the environmental conditions during which they were supposed to be produced, pairing, RNA to DNA transition, Replication, Protein Synthesis, etc.

Paraconformities, from what I have read, happen when, for example, three species are found. A simple form, an advanced form, and a perfected form, if you will. A paraconformity is when the advanced form (considered to be the middle link in the species) is dated and found to be older than the simple form. Thus, by dating, showing a devolution, then massive evolution, but lacking the time frame for the change from simple to perfected to occur. I'll talk about them more later on, too.

As for fossil formation. You make a good point. It does require the right circumstances to form a fossil. The missing link to which I am referring, however, are not those between different species, but to those missing between the different classes. I'll write a section on these too, you'll just have to wait :)

Bennion said...

The theory of evolution can never be "proven," just as the Theory of Relativity can never be proven. However, it's hard to understate the amount of evidence there is for it. I personally find the DNA evidence to be the most compelling, but there's a great deal of evidence out there. Out of curiosity, what books are you reading about evolution? How are you learning about the evidence for it?

Adaptation cannot cause random genetic change, which is what really drives evolution.

I agree that larger populations evolve more slowly than small ones, and that just because two fossils are similar, we cannot know for sure that they are closely related.

I definitely don't think that fossils are the only "real" evidence of evolution though! I think anatomical evidence and DNA evidence are also very powerful evidences of evolution. The only competing theory that I know of is design, so when animals have body parts that they don't need or that could have easily been designed better, then that's an indication that they've evolved. Also, there's a lot of our DNA that doesn't appear to do anything, called "junk DNA." Some of it we can tell used to do something, but because of a mutation has stopped functioning. When a simlar sequence of junk DNA is found in between the same genes in two different animals, that's an indication that those animals had a common ancestor. That should be considered evidence of evolution as well as fossils.

Also, there is no "perfected" form of an animal. It will surely continue changing in the future, and who are we to say that it's perfected now? Animals never completely stop changing, either.

Thanks for the bit about Darwin. I've read quite a bit about evolution, but never Origin of Species. I'll read the chapter if I ever get around to it, it sounds interesting. Thanks,

-Bennion

Beefy said...

You can find the entire published works of Darwin online. You just have to do a google search for them. I find it hard to read large amounts of small text on a computer screen, though.

The point of my writing is not really to say "Look, this disproves evolution!", but to simply point out that there are inconsistencies in the theory and the evidence supporting it. That doesn't mean it's not true, by any means, simply giving an objective view to the side of the theory less often seen from the public view.

The only book I'm in the process of reading on the subject of Evolution, currently, is Origin of Species. Most of my other research has been gathered and gleaned from individual researches online (both for and against), my college biology class, and personal opinion. I'm in the process of doing more research as I go, but I have a broad enough knowledge of the subject in general to make an objective argument one way or the other.

I will also say that most of what I write is these comments cannot, because of space requirements, be fully explained and have the reasoning fully presented, so they will be a bit lacking in most areas.

Adaptation happens because of genetic differences that either existed because of random genetic change, or result when a genetic change happens that make the animal more suited to live in that environment. I think we're probably defining the term differently.

I do realize there is no "perfected" form. That is why I added in "if you will" after the statement. It was simply used as a description to show a different point in evolution beyond "advanced". I wasn't arguing the point of perfection of species.

We assume that because two species have the same "junk" portion of DNA, they must have kept that chunk from a common ancestor. We could also say, however, that it has a function that we just don't know about: a function that both creatures have the potential of exhibiting, but the right external conditions do not exist to activate it.

It's kind of like co-evolution. We see two species that have evolved the same trait. Let's say a blubber layer to keep them warm. However, the two are genetically unrelated. The "junk" DNA may have a feature like "grow more hair if it's *really* cold" or "increase efficiency of sweat glands when dehydrated".

I will, however, admit that beyond an understand of what they are, I have not researched into "junk DNA", specifically. With no observable change, though, it can't truly be used as "hard" evidence. We can assume their is a relationship between the two, but it is just an assumption.

However, I do believe that many species have evolved from common ancestors with each other. These related species, though, are often genetically compatible-ish. Donkeys and Horses, Lion and Tigers, different breeds of Finches, etc. I plan on talking about that in more detail later on as well.

Bennion said...

I'm pretty sure that when "a genetic change happens that make[s] the animal more suited to live in that environment" isn't usually considered "adaptation." That's considered evolution. So, yes, it's a difference of definitions.

As for junk DNA having a possible function, I think that's possible for a lot of junk DNA, but not all of it. For example, chimpanzees have the same chromosomes as we do, except that they have chromosomes 2A and 2B instead of our chromosome 2. If you look at where the two are connected in our DNA, it's kind of "smashed together." I'm pretty sure that sequence of code where the two are connected is no longer functional. It's also connected in such a way that it appears to be some kind of a DNA duplication error that caused the two to be connected. I'm pretty sure if God had created us separately, and needed to connect the two chromosomes, He would have just connected the two, and not mashed them together like that. And why would God make it appear that the two chromosomes being connected is the result of a DNA duplication error if we didn't have a common ancestor with chimpanzees?

Also, sometimes DNA between two dissimilar animals is much more similar than the DNA between two similar animals. For example, the DNA of a hippopotamus is more similar to that of a whale than the hippopotamus's DNA is similar to any other animal. Scientists believe this means that the hippopotamus has a closer common ancestor with the whale than it does with any land-dwelling mammal. If DNA primarily reflected function instead of ancestry, why the DNA of two animals that are so different in function be so similar? Wouldn't the hippopotamus have DNA more similar to a cow or something if DNA reflected function?

There are also species who have evolved the same functionality separately. For example, there are bats that look quite similar, and do very similar things (though in different parts of the world), but have DNA that is extremely different. Scientists believe they are similar because they fit the same niche in the environment, but the DNA is different because they descended from different animals and are not closely related.

I think these pieces of evidence strongly show that the majority of our DNA reflects our ancestry, and probably doesn't really do anything else. Junk DNA.

Beefy said...

When a create has "evolved", per say, it changes into its own genetically-unique creator. From the definitions I have read. For a genetic change to be considered evolution, it either has to genetically isolate it from the rest of the species or allow it to survive through something the rest of the species cannot. Dark skin is an adaptation to protect humans from intense sun radiation, there is a genetic difference between those who have it and those who don't, that is not evolution, because the humans are still genetically compatible.

As for junk DNA, I haven't researched it enough, or the differences between our closely related species, to really make a definitive argument either for or against. I'll research more into it.

I will have to research into similarities and differences like you have described. I would assume, though, that the common ancestor sharing individuals would have similar structures, such as internal organ systems, etc, while niche-related organism shared common functionality but different structure. I don't know, though, I'll look into it.

I would argue, though, that it is not the majority of our DNA that indicates ancestry. I think the majority of our DNA has a function of some sort, and there are some small parts that are left over as junk.

Bennion said...

I know that mainstream scientific thought considers the majority of our DNA to be junk DNA. The specific examples come from "An Ancestor's Tale," which is one of the primary sources I've learned about evolution from. I believe the niche-related organisms have fairly similar internal structures.

Single species can "evolve." When it splits into two species, that's called "speciation." I think some humans having darker skin is a good example of having a different evolutionary history, or having evolved slightly differently, even though we're obviously the same species and genetically quite similar. Btw, some human populations have evolved lactose-tolerance, while others have not, as another example.

Good luck with your researching! Let me know if you'd like me to look anything up or provide sources,

-Bennion

Anonymous said...

Fascinating article and great discussion with Benion. I'll certainly keep reading as you continue to post. I to have always had a fascination with the orgin of this world and life on it. I respect the work which hard working scientists do and that which we have learned from it. I'm not nearly as well educated on this subject as Bennion or yourself but paraconformities have also confused me. I had to do a bilogy report around the same time they had just found homo sapien remains which actually predated what was previously believed to be its ancestor. (I can't find my report or else I would name it for you, I'll try to find it so I can give you the site) The scientist explained that it would be like saying your mom and your great grandma were sisters. These scientist believed in evolution and their explanation of what their finding meant was that the homo sapien simply had another ancestor and that we would find it eventually. Once again I'm not an expert, but something I've wondered, like when Benion used the theory of relativaty, that theory rewrote many theories of physics which had previously been accepted as the truth. An example is of course Newton's laws of physics. Newton's laws, though they work in our world, do not apply to the macro or micro objects. However, I wouldn't say that his discoveries were useless. I guess relating this to the acutual subject, as I have been reading up on theories about the orgin of life, the evidence aquired which backs these theories, some unknows in the data etc. I guess I ask that if a genius like Newton didn't figure everything out at once, than is it possible that life started in a different matter than we originally concieved? The problem is I'm not aware of any theory which better fits the data than evolution. That's why it's so widely taught is despite it's holes any biologist I've ever spoken to responds, "Hey it's not perfect but it's the best we got."

I guess what this is a long way for me to say is there a competing theory which also fits the scientific data which we do have?

Keep up the good work!

Beefy said...

The argument you bring up is exactly why I am writing these. Intellect. What one is able to believe is qualified as "scientific" data. My discussion so far has been from a religious viewpoint.

I'll quote my introduction: "They are those who have looked into evolution and know the holes in the theory, know the assumptions around which everything revolves. They see how chaotic the entire theory is, and the crumbling rock that is its foundations. Yet, because the idea of a God, a supreme being and Creator, seems more preposterous to them, they side with evolution because it makes the most sense."

That's the kind of idea. Their intellect, per say, is too restrained to see God as a viable alternative to evolution. Evolution makes more sense, from their perspective, so they stick with it.

Someone who can comprehend a God, who believes in a God, is not thus restricted. God created man, in His own image, He created all things that in this world are. God is not limited to random chance, God chooses and picks.

But to most, saying "Evolution doesn't make sense, therefore God must exist" is fallacy equivalent to saying "I don't see Dinosaurs today, therefore they must never have existed."

To each man his own beliefs, though. I'm not trying to say that evolution doesn't exist. Right now I'm just showing a side most people never experience, the side where evolution is unstable and incomplete. To open their eyes and make them think for themselves.

But, the scope of this work is incomplete. I'm not entirely sure where I want to take it. I'll figure it out sometime.

Thanks for commenting, I'll try not to let you down with my posts.

Bennion said...

There have been theoretical problems with evolution, and practical discoveries that have challenged it, since it was proposed. Most of these problems have been resolved as scientists have learned more and and the theory has been refined.

The only competing theories I know of are Creationism (which is scientifically ridiculous), and Intelligent Design. One scientist I respect, Francis Collins, wrote about Intelligent Design in "The Language of God." He said there's a fair bit of science behind it, but predicts that it will fail as a scientific theory. I personally don't know a whole lot about it, but I know that most biologists don't like it a whole lot. It will almost certainly be rejected by the scientific community. But it's still the only alternative theory with actual science behind it out there :)

Good luck with your research,

-Bennion

Beefy said...

There it is "scientifically ridiculous". What is and isn't considered scientifically ridiculous varies by time and date and societies.

I agree that Intelligent Design will most likely be rejected by the scientific community. That is because, in my experience, most of the scientific community is bent on try to prove that God doesn't exist, not acknowledging that He may have had a hand in something.

For all we know, the answer to all of the theoretical problems with evolution is staring us in the face and we are either too stubborn to admit it, or we keep trying to find ways around it because we are bent on proving something.

Just like any study can be designed and twisted to show any viewpoint and still pass peer reviews. If someone wants to "prove" something they usually can. If someone wants to "disprove" something, it is the same.

It's just a matter of who considers what a viable option. If you are trying to prove that God doesn't exist with science, you can find all sorts of ways to do it. On the same note, if someone is willing to accept God as an option, you can find all sorts of ways to do it.