Posted by Mike O on: 10.02.2008 /
Similar to last week, I’ll be using articles from www.howstuffworks.com as the basis for this post - in particular, their articles on How Evolution Works, and How Cells Work.
I’m on chapter three of How Evolution Works - DNA and Enzymes.
First, I should mention that I don’t have much trouble believing this aspect of the evolution topic. Why? Because we can see scientifically that this is how things work today. We can see it and reproduce it, and that is enough to satisfy the skeptic in me.
My questions regarding cells and DNA are not whether or not they work the way we think they do (unlike speciation, which we talked about some last week, and can only be assumed). My questions revolve around the origin of cells and DNA, the completeness required for the evolutionary process to work, and the spontaneous start of any of the processes involved.
1) Cell Structure - In their article on How Cells work, they give the parts of an E-Coli bacterium - the Cell wall, cytoplasm, DNA and Flagellum. Assuming a chemical origin to life, how could a chemical reaction produce a cell wall, filled with water, other elements and DNA, with flagellum to propel it? Even if a chemical reaction could produce the parts, I don’t see how it could produce the parts in that form. The flagellum is interesting because a chemical reaction doesn’t need to move - how or why would it develop things that make it move? NOTE - I know the E.Coli may not have come directly from a chemical reaction - but something did. And something was the first thing with a flagellum. So ultimately, for purely natural evolution to work, a chemical reaction produced a flagellum.
2) Enzymes - Again, my issue has nothing to do with how enzymes work. My issue(s) have to do with where they come from (origins) and how they work together. The E.Coli bacterium, for example, has 1000 enzymes in the cytoplasm. The article likens enzymes to “little chemical reaction machines,” and cells to “a little bag full of chemical reactions.” My difficulty with this is reactions need something to react with. That means that the 1000 enzymes within the E.Coli bacterium needed 1000 external things to react with, all coming about simultaneously. Either that, or E.Coli must have started with one enzyme (which had it’s reactant), and then another etc.
3) DNA - In the chapter called “Making Enzymes work,” the author makes this statement about DNA:
If a cell is just a collection of enzymes causing chemical reactions that make the cell do what it does, then how can a set of chemical reactions create the enzymes it needs, and how can the cell reproduce? Where does the miracle of life come from?
The answer to these questions lies in the DNA, or deoxyribonucleic acid
Once again, my question goes to the origin of DNA. In an E.Coli cell, the DNA strand is about 4 million blocks long and is a “wadded up ball” floating free in the cytoplasm. Where did that complicated structure come from so that it could be reproduced in it’s complete form.
The author says this about DNA in general (and of E.Coli in particular):
The amazing thing about DNA is this: DNA is nothing more than a pattern that tells the cell how to make its proteins! That is all that DNA does. The 4 million bases in an E. coli cell’s DNA tell the cell how to make the 1,000 or so enzymes that an E. coli cell needs to live its life.
Which leads me to believe that E.Coli had to have originally had all 1000 enzymes, and 1000 reactants had to be in existance for those enzymes to react with. I don’t know - it sure seems like “life” only works when all the parts are in place, and evolution doesn’t seem to require that - the parts evolved. Seems like a vicious, unstartable circle. Which came first, the parts required for evolution to work, or the evolution of the parts?
The author has this to say about Human DNA:
A human’s DNA is about 3 billion blocks long, or almost 1,000 times longer than an E. coli’s. Human DNA is so long that the wadded-up approach does not work. Instead, human DNA is tightly wrapped into 23 structures called chromosomes to pack it more tightly and fit it inside a cell.
Hmm. Lucky.
Let’s step back now from “How Cells Work” to “How Evolution Works”.
Enzymes do the work of cells. And to make the enzymes that the cell needs, (From How Life Works, DNA and Enzymes):
the chemical mechanisms inside an E. coli cell make a copy of a gene from the DNA strand and use this template to form the enzyme. The E. coli might have thousands of copies of some enzymes floating around inside it, and only a few copies of others. The collection of 1,000 or so different types of enzymes floating in the cell makes all of the cell’s chemistry possible. This chemistry makes the cell “alive” — it allows the E. coli to sense food, move around, eat and reproduce.
I don’t doubt that this is how it works. But how did this process get started? Where did the “chemical mechanisms” with the ability to make a copy of a gene as a template to form an enzyme come from? And why? If the “food” was there to move towards and eat, where did it come from? And if not, what good were the enzymes? Again, the process seems to require all of the parts to be in place - which they weren’t. Not if it all comes back to a single common ancestor.
Let me close by saying AGAIN that I am not trying to explain away evolution - I believe in God, and that he created what we have today. If he did that through evolution, fine with me. I just don’t see a purely natural process as sufficient to explain life. So far, my core sticking points with evolution are:
1) Origins - I don’t believe a spontaneous chemical reaction became a structured, biological, self-replicating cell - or group of cells.
2) Speciation - I don’t believe different species, let alone plants and animals, have common ancestors. I believe we can modify a species through breeding, but one species cannot produce another. We talked about this at length last week - I just need to learn more about that before I can accept it.
3) Completeness - The evolutionary process seems to require completeness to work. Chemical reactions all need their reactants, and cells need all of their chemical reactions to work.
Comment by: Raghu Mani
1Mike, first of all, the theory of evolution has nothing to do with how the whole process got started. Evolution starts with the first self-replicating entities and proceeds from there. So how did the first self replicating entities arise? Short answer - we don’t know … yet.
There is an entire field called abiogenesis (which has a lot more to do with chemistry than biology) which is studying this and people working in this area have come up with a few interesting hypotheses but there is no real consensus in this area. The field is waiting, right now, for its first big breakthrough.
As far as evolution is concerned, God could have created those first building blocks or space aliens could have - it doesn’t matter. We start with the first primitive self-replicating entities and proceed from there.
Regarding creation of enzymes, it isn’t anywhere as hard as you imagine it to be. There was a rather dramatic finding in Japan a couple of decades where bacteria had evolved the ability to digest nylon using brand new enzyme (which has been called “nylonase”). Given that nylon had been around at the time of the discovery, for only a little over 50 years, the bacteria have been able to evolve this enzyme in less than that period of time.
If bacteria could synthesize a new enzyme in 50 years it isn’t that hard to believe that a lot more could evolve in a few billion years.
I don’t have time to answer your questions in detail but let me give you one quick answer and make a couple of general comments. Regarding your lack of belief in one species arising from another - that is something even most creationists have been forced to give up. There have been tons of observed instances of speciation recorded - in which the final child species could not interbreed with the original parent species. This is why creationists talk of “kinds” between which evolution is impossible. They can’t say species are immutable anymore because there is a staggering amount of evidence for species change that even they cannot ignore.
A lot of your difficulties with evolution seem to arise out of your personal incredulity. I’m sorry but that isn’t an argument against evolution. The only way out of your difficulty here is reading some solid scientific material. The Cliff Notes- type summaries on howstuffworks is not going to cut it. Talk.Origins is a good start and then there are books written by biologists which do a good job laying the evidence out. What’s impressive isn’t any single piece of evidence. It is the way the evidence keeps piling up. The more you read, the more impressed you get. I am not a biologist, nor do I have the time to answer all of your questions. For the information you are looking for, you’re just going to have to read a lot of books.
Other difficulties of your seem to arise because of genuine holes in evolution. That’s right - we don’t have all the answers. The big unsolved problem is abiogenesis but there are numerous other smaller ones. The point is that we never have all the answers. That is why biologists do research in the area of evolution - to answer questions and plug gaps. The same is true for all of science - gaps in our knowledge exist. Trying to stuff God into the gaps in our knowledge, however, is not the answer. This whole “god of the gaps” argument has been long recognized by theologians as a terrible argument. Sooner or later, science is going to plug those gaps. What are you going to do then - find smaller and more obscure gaps to stuff him into?
I’ll try and take a stab at some of your issues in more detail later.
Raghu
Comment by: Dr. Arv Edgeworth
2So you believe in abiogenesis? Isn’t Biogenesis a Law of Science? Aren’t almost all mutations harmful? Don’t mutations almost always cause a net loss of useful genetic information? Wouldn’t mutated life forms be the least likely to survive? Why wouldn’t natural selection weed those out? Were Niles Eldridge and Stephen Jay Gould right when they said there is no evidence of slow change in the fossil record? I’m still waiting to see one case of observable evolution. I’m still waiting to hear an explanation for the beginning of the universe or the first cell without violating at least four known laws of science. I think people have been lying to you. You have been taught what to think, but not how to think. As was stated on X-Files: The truth is out there! I hope you find it.
Comment by: steve martin
3Hi Mike,
Some quick responses.
1. On speciation, this is something that has been observed & everyone agrees it happens. Even Answers In Genesis (probably the most popular YEC organization) admits this. In fact, they now see “rapid speciation” to explain how we could have so many species alive today & in the fossil record if all non-aquatic life once lived on Noah’s ark. (see: arguments creationists should not use and search for “No new species have been produced”).
2. Your key concern I think is that “I just don’t see a purely natural process as sufficient to explain life” (and I’m assuming you mean biological evolution, not chemical evolution). I’m not sure what the concern is here: even scripture asserts that “natural events” and “God guided” events are not in conflict. Eg. Psalm 139: 13, 14 talks about God “knitting us together in our mother’s womb” but no one believes this is in conflict with the “natural” process of embryo development.
Comment by: steve martin
4(Sorry if this comes through twice - thought I submitted it but it never appeared).
Hi Mike,
Some quick responses.
1. On speciation, this is something that has been observed & everyone agrees it happens. Even Answers In Genesis (probably the most popular YEC organization) admits this. In fact, they now see “rapid speciation” to explain how we could have so many species alive today & in the fossil record if all non-aquatic life once lived on Noah’s ark. (see: Aruguments Creationists should not use and search for “No new species have been produced”).
2. Your key concern I think is that:
I just don’t see a purely natural process as sufficient to explain life
I’m not sure what the concern is here: even scripture asserts that “natural events” and “God guided” events are not in conflict. Eg. Psalm 139: 13, 14 talks about God “knitting us together in our mother’s womb” but no one believes this is in conflict with the “natural” process of embryo development.
Comment by: Mike O
5Sorry, Dr. Edgeworth … your comment got caught in our spam-catcher. Here it is …
Comment by: Mike O
6Raghu, is it fair to say that evolution on the grand scale is an extrapolation of adaptation on the small scale? I wonder Adaptation plus time –> evolution? It seems like it.
Comment by: Raghu Mani
7It is more complicated than that. There are several possible mechanisms for evolution over the long term but adaptation is probably the most important.
Just a few answers for Dr. Edgeworth.
1. Abiogenesis has nothing to do with evolution and it is right now a highly speculative field. It remains to be seen if a robust theory will come out of it.
2. Biogenesis is merely the creation of life from life which is something you see happenning everyday. We can extend it to evolution by saying all life originated from a common ancestor. Abiogenesis is about how the first life emerged from entities that would not consider to be living.
3. Most mutations are neither harmful nor helpful - they are neutral. Harmful mutations do outnumber helpful ones but plenty of helpful ones have been documented. The example I give above about the evolution of nylonase has been tracked down, I believe, to a specific beneficial mutation in “junk” DNA.
4. Eldridge and Gould merely said that you have long periods of relative stasis followed by shorter periods of relatively quicker evolution. That would, according to them, lead to fewer changes seen in the fossil record at species level and a lot more changes seen between larger groups of animals. Not everyone accepts this view. Controversies are part of science.
5. There are plenty of observable cases of evolution - I documented one above about the evolution of an enzyme in bacteria to digest nylon and there are also tons of recorded examples of speciation. What you cannot observe is dramatic changes to an organism because such changes take tens or hundreds of thousands of years - at the very least.
6. The beginning of the universe and the origin of the first cell have nothing to do with evolution. As I mentioned, evolution starts with the first life and tries to explain how the diversity we see got here. The origin of the first cell is an issue for abiogenesis and the origin of the universe is an issue for cosmology. There are some answers and some speculation but not every hole has been filled. Science does not equal atheism. The only restriction is that you cannot make God part of a scientific theory. As far as ultimate origins is concerned you can choose to believe God did, you can choose to believe one of various hypotheses that scientists have proposed or you can, like me, accept that there is no answer yet and may never be one in our lifetimes.
Anyway, I’ve had it with this discussion. Looks like we are arguing in circles. I am not a biologist and all that I am doing is summarizing information from various online sources in these posts. There is no reason why I should continue to do this when the online sources are there for everyone to look at. Believe what you will - I have better things to do with my time.
Raghu
Comment by: Steve Martin
8Hi Mike,
Some quick responses.
1. On speciation, this is something that has been observed & everyone agrees it happens. Even Answers In Genesis (probably the most popular YEC organization) admits this. In fact, they now propose “rapid speciation” to explain how we could have so many species alive today & in the fossil record if all non-aquatic life once lived on Noah’s ark. (see: http://www.answersingenesis.org/home/area/faq/dont_use.asp and search for “No new species have been produced”).
2. Your key concern I think is that “I just don’t see a purely natural process as sufficient to explain life” (and I’m assuming you mean biological evolution, not chemical evolution). I’m not sure what the concern is here: even scripture asserts that “natural events” and “God guided” events are not in conflict. Eg. Psalm 139: 13, 14 talks about God “knitting us together in our mother’s womb” but no one believes this is in conflict with the “natural” process of embryo development.
Comment by: Mike O
9That’s an important distinction - when you read science magazines, however, evolution is thrown out there with the big bang theory. The “evolution” of the universe, etc. So it’s a reasonable misconception.
OK, that’s pretty cool. This is from Wikipedia
OK …
I admit that … as I’ve said before, it takes a long time to rebuild a paradigm. You can’t just toss out everything you’ve been told because someone else tells you something different … any good thinking person would weigh the evidence … and that takes time. You have to remember … I’m considering things I’ve rejected out-of-hand for my entire life. Please allow me a bit of incredulity (sp?)
It’s a good place to start. That would be like me asking you to consider Christianity by studying the whole Bible. It’s just too much to start with. Cliff notes may not get me there, but it is getting me started. Remember, I started as someone who didn’t believe this at all … why would I dedicate a ton of time studying something I didn’t believe? No, start with a primer, whet the appetite, and let it grow from there is a better approach.
That is true … I am moving along. If it’s any consolation, y’all are watching a paradigm shift - mine. That, in itself, should be interesting to watch.
Comment by: Mike O
10Raghu,
I went out to Dr. Edgeworth’s site, and it’s a good example of how reading about something you are convinced isn’t true, isn’t a very good approach to finding out if it’s true or not. Let’s say he’s right. You’re convinced he isn’t right, so how much time are you going to spend delving into his site, or sites like it, to find out if it’s true? How much do you care what cases he’s built for YEC? Even if he’s right, he has no credibility with you, so your first reaction will be to reject everything he says in favor of what you already know to be true. Heck, you’re losing patience here, and you’re in the majority!
That’s how it was with me and evolution … I was already convinced it wasn’t true, so reading the writings of people I don’t believe isn’t going to be effective in changing my view. But for me, starting with a source I did trust - howstuffworks and to some extent, the evolutionists here - has made it easier to consider the option I once knew was incorrect. Now I see that there’s more to it than I thought.
Have you ever really studied creationism and tried to put aside all you thought you knew about evolution? It’s harder than you think, yet you think people should be able to do that with creationism when considering evolution. It’s just not that easy.
Comment by: joe
11I wonder what Dr Edgeworth’s doctorate is in. I suspect from his writing that I have more qualifications in natural science than he does.
Comment by: Raghu Mani
12Mike,
No, I have not read Dr. Edgeworth’s site but I have read plenty of creationist literature. It’s all the same. A few points
1. Creationism is not science. Please find me a book or reference on creationism that does not mention evolution or mentions it only in passing. You won’t find one. The entire “science” of creationism is attempting to poke holes in evolution and hoping that creationism becomes true by default. I’m sorry, that does not work. You need to put forth a scientific theory of creationism that is completely independent of evolution. I could name you tons and tons of books on evolution which talk about the science without mentioning creationism or creationists.
2. Then there is the issue of the actual scientific work done by these creationists. Where are the peer reviewed papers, where is the actual field work? Has one of these people actually excavated for and found a fossil? Have they actually done any work in the lab sequencing DNA? It is an important point. There are a tens of thousands science books and websites out there. I have time to read only a small number of them. If the author has done something significant in his field, that is an indication to me that his opinions are worth spending the time to read. This is why I keep harping on Francis Collins - an evangelical Christian whose scientifc achievements are tremendous - his achievements alone make his book worth checking out.
3. For the most part (with a few rare exceptions) creationists don’t do science. They sit back in their armchairs and cherry pick things from scientists they would like to distort. Sometimes they simply make stuff up. Go to the talk.origins website. Chances are that every single argument you have read on any creationist website or book has been answered there.
Raghu
PS - Regarding reading the Bible, I actually have. I have read the King James Bible from cover to cover … and the Qur’an … and a lot of the Hindu holy books. On top of that, I have read apologetics of various kinds. When it comes to religion, I have gone to the original source. That’s the only way to find out about it. Even though religion and science are totally different entities, the above principle still applies. The closer you go to the original sources, the better you are going to understand it. My cutting and pasting from these place is no better than the Cliff Notes-type sources you’ve been getting your information from - it is not going to get any of us anywhere.
Comment by: How Evolution Works - Cells and DNA | All Reason
13 10/5/08 10:33 AM | Comment Link |[...] ..Real Full Article [...]
Comment by: Jason
14A cell membrane is essentially layers of protein protecting the cytoplasm of the cell, not water. The whole thing is on an unimaginably tiny scale. The flagellum doesn’t so much provide a means of movement through a fluid but a means of tunnelling through loosely packed molecules. Chemically speaking the flagellum is a rigid protein that only “moves” because it is excited by ions generated in the electrical field of the cell.
In a very real sense the life of a cell is about as alien an environment as we can imagine.
If it makes it easier an enzyme is more a catalyzer for a chemical reaction that a machine for making them. A cell or simpler organism may absorb several million enzymes and discard those that it cannot use, or inert in the environment. It makes sense to me that this must have first occurred naturally and the useless enzymes kept out by the cell membrane as the cells organisms became more complex. How? Useful enzymes catalyse chemical reactions that produce carbohydrates that are used in the cell membrane. Just don’t ask me which came first?
DNA is made from a less complex acid called rNA. I know I’m simplifying and missing key points. rNA are organic molecules that combine with other organic molecules. Scientists have detected organic molecules in comet trails as well as all over the globe. They occur naturally in our universe.
Yes. I think that’s fair to point out. However an almost unimaginably long time has occurred for these parts to come into place all by themselves. It is certainly unlikely but unlikely events occur very often when you wait long enough.
Ah, it didn’t. Not just like that. Organic molecules first formed, then combined, did a bit of jiggery pokery and formed amino acids, enzymes, rNA and all those cool things found in cells. These combined and formed cell membranes and other interesting stuff. This all happened in a way that we’re trying to understand. Have you read about the Miller-Urey experiment?
It’s good that you’re not put off and want to keep looking into it. It’s interesting stuff.
Good point. However you must consider that the elements that are not complete lead to death for the life form, leaving only those that “fit” in the environment. There’s also that pesky matter of an awful long time and a lot of chemicals to play with. Eventually something happened that we now refer to as the origin of life. We don’t know precisely what that was.
With abiogenesis, as with any scientific discipline, we first come up with an idea of how we think it might have happened. We collect evidence to support it. There might be several competing ideas. Then we devise an experiment to test the idea and try to come up with ways that it can be shown not to work. If we find that the theory isn’t robust we abandon it and try to think of a better idea. Sometimes we just have to shrug and say “I dunno” and keep looking.
Now creationism must be treated in exactly the same way as any other idea. How can we come up with an experiment to disprove a claim of creationism? First we have to examine the claims and the processes that are being explained.
What does creationism actually claim as an explanation for a process? Let’s take the eye as an example. According to creationism the eye is a sensory organ created in whole. Where is the evidence? Well we have eyes and so do many other creatures, these are good observable facts. However all eyes are not the same. Squid eyes lack the blindspot common to mammals which indicates a different origin. Snail eyes are very simple light and movement detectors incapable of seeing colours. Goldfish eyes see into the ultraviolet and infrared spectrums. Human eyes are terribly weak compared with other animals. Some animals have eyes but cannot see at all. These indicate that the eye is different in species because the animal has different needs in terms of visual detection. The range of eyes and the complexity that we can see support the idea of evolution. A created eye, one would think, would not have a blind spot. Why create a deliberate flaw?
There are others. All primates lack the ability to synthesis vitamin C. This is supporting evidence for a common ancestor who lacked the ability and passed it to his or her offspring long before we diverged to form gorillas, humans, chimps, etc. Again, why create this flaw and why share it with our ape cousins?
We look for evidence to discredit our ideas in the scientific method. Not, as Dr. Arv Edgeworth’s link indicates, because the scientific method is inherently negative but because we insist on testing the robustness of our ideas.