Darwinism

[LonePiper]

Man, I'm just too OCD to let this go. Sorry to all those others here who are sick of this discussion! And sorry for resurrecting it again. I haven't been here in a while.

Anyway:

SenseiOtho, firstly, yes. One of the points I wanted to see addressed was abiogenesis. But I also would have liked to see your interpretation of my comments on the Cambrian Explosion.
And I apologize for not reading the creationist paper. The way your post was worded I thought that your quote was the only part of it relevant to the discussion.

In regards to the rest of your post, I will try to respond to you as best I can, but there are some points I admit I will not be able to give a complete answer to. I am not a molecular biologist, nor an organic chemist. They are two areas of biology and evolution I haven't had the chance to properly study yet.
But I think the overarching answer I can give that could apply to most of what you have said is this:
When a theory consistently and reproducibly confirms the data, and especially predicted data, it's not going to be thrown completely out just because of a gap where no data is yet available or where a single piece of evidence does not fit within expectations.
And I'm not just talking specifically evolution. I don't even just mean subsets of science like geology, physics, - evolution - whatever. I mean the whole premise of science, which is that there is a naturalistic and observable cause to everything. When science consistently and repeatedly makes accurate predictions about the world we live in by observable and predictable evidence it makes no sense to give up and bring in a supernatural entity just because the evidence hasn't been found yet.

I disagree with a number of your statements and your unchecked and unreasoned bias is amazing (did you even look at the research paper?) but for the sake of time I'll just try to answer your question and I'll use non-creationist since you seem to throw them out without even considering their work. I'm becoming more and more convinced that your problem (not just you, but the other atheist here as well) with theism and devotion to evolution has very little to do with scientific evidence. but anyway....

I'm a little confused. You say I'm being biased and disregarding evidence. I was taking especial care to only post about things I have actually read from reputable sources (by the way, if you want references I'll gladly give them for any point you make, but it might take a while for me to find them which is why I didn't post them to begin with), and aside from my not reading your article (which I have now apologised for), I would like to know where I have been biased? All I've done is present the evidence as I have read it (or rather with rewording to suit the context).

1) The assumption that there was no free oxygen. This is the assumption of all the experiments that I have seen that simulating creating basic building blocks of life. O2 totally stops and destroys the production of organic compounds. There is strong geological evidence that significant amounts of oxygen was present in the earth's early atmosphere. For instance, many minerals react with oxygen (such as the rusting of iron), and the resulting oxides are found in rocks dated earlier than the origin of life. (J.H. Carver, "Prebiotic Atmosphere Oxygen Levels," Nature 292 (1981):136-38; & James F. Kasting, "Earth's Early Atmosphere," Science 259 (1993): 920-26.)

You say significant amounts of oxygen. How much is that? I have read that there may have been trace amounts, but nothing as significant as you imply

--The oceans have an equilibrium with the atmosphere, so the oceans would have had the same amount of O2 as the atmosphere. (this would destroy any organic compounds that moved out of anoxic conditions)

Overall, yes. But there are many many different environmental situations that can cause anoxic conditions in local areas.

-- if there was not oxygen in the Atmosphere, then there would have been no Ozone. Ozone forms a protective shield from the ultraviolet radiation from the sun. Without it life/organic compounds would be destroyed from the high levels, yet life clearly flourished on early earth. (which would also destroy organic compunds in anoxic environments)

But how much liquid water is needed to shield organis compounds? Keep in mind, life (as far as scientists generally predict) originated in the oceans. By some accounts in ver deep oceans.

--the Miller-Urey experiment is now dismissed by many origin-of-life researchers because "the early atmosphere looked nothing like the Miller-Urey simulation." (Jon Cohen, "Novel Center Seeks to Add Spark to Origin of Life," Science 270 (1995):1925-26.)

Fair enough. Perhaps disputable, but Miller-Urey is not the only source for abiogenesis hypotheses. Besides, as I said the main reason they are still useful is not to do with the conditions of early Earth, just to show (usually undergraduates and high school students) that complex organic compounds can be formed under natural conditions.

--to claim anaerobic conditions for the formation of life greatly limits the places and opportunity for these random processes to form and stay protected from being destroyed. This would mean that the first life also had to form in these conditions or else suffer the effects of O2. But that's fine if that claim gets around oxygen. I'll let you take it for the sake of argument, even though there is no empirical evidence for that claim.

But how many anaerobic conditions were there on the early Earth? And keep in mind that we have at least one billion years leeway here from the Earth's formation. The first signs of simple life on Earth come from I think about 3 billion years ago. The Earth is supposedly 4.5 billion years old. The amount of anaerobic conditions that may have existed on Earth for that time for simple life to evolve is staggering.

---organic chemicals from metiorites gets you around this O2 problem for their basic formation, but it doesn't stop their destruction once here on earth. It also doesn't solve the problem of the chemicals being stopped or destroyed form forming into life. So what if you have some chemicals slam into earth, you still have to deal with the O2 to get any more complex for life.

As the solar system has aged less and less debris has fallen onto Earth. The early solar system had a lot of random crud flying about which has become less and less as it has been absorbed by the planets. The early Earth would have had a huge amount of these kind of meteorites hitting it, and coupled with the point that there were a good billion years at least for life to form, it's hardly a stretch of the imagination that a reasonable amount of organic compounds managed to make it to environments where they weren't destroyed. (And I'm still sceptical about there being enough O2 to hinder abiogenesis)

2)Reactions are reversible. the creation of organic chemicals would take some form of energy. The sun, lightning, or heat from volcanic activity are the three big ones normally used. While some chemical reactions form easily under these conditions, they also break easily. Energy is a two-edged sword that can create and destroy just as readily. The simulated experiments normally take or collect the created compounds and get them away from the destructive forces used to create them. Taking this into account the "prebiotic soup" would favor simple molecules and work against complex ones. (this would affect anoxic environments)

Firstly let me say that the "prebiotic" or "primordial" soup is not a particularly favoured hypothesis of abiogenesis by scientists today. There are many many more theories, most of them far more sophisticated and elegant. Some of them even include completely inorganic molecules. Crystals and clay are a particularly fascinating example! (I can elaborate on that one if you're interested)
Anyway, I'm going to have to bring up the billion years again. Sure, the vast majority of organic compounds were probably destroyed before they got anywhere. But over one billion years and probably an uncountable amount of organic compounds (or even inorganic!) worldwide at any one given time, one could easily imagine even just one of them managing to self-replicate, and for that replication to last long enough to replicate again.

3)Interfering Cross-Reactions: While many reaction needed for biologically important compounds have been observed under artificial laboratory conditions. In nature many reactions that occur in nature work against the formation of biologically important compounds. Amino acids, for instance, do not readily react with each other. They do readily reach with other substances like sugars. But for life to form the amino acids would need to only reach with each other. They would not just float around in some type or soup and only react with other amino acids. They would react with anything they come in contact with making all sorts of cross-reactions. This would tie them up and make them useless for any type of biologically useful function, it would just make a useless tar. Even in the carefully planed primitive atmosphere experiments confirm this. Most of what they form is a tar with only some very small peptides. If the scientist in a controlled environment can't do it, it cast real doubt on it happening naturally. (this also covers your far-fetched self-replicating non-amino acid molecules theory even if in anoxic conditions) (Alan W. Schwarts, "Interactable Mixtures and the Origin of Life," Chemistry and Biodiversity 4(4) (2007):656. He is the editor of Origins of Life and Evolution of Biospheres;also Robert Shapiro, "A Simpler Origin of Life," Scientific American (Feb 12, 2007)

This is one area where I have to admit I don't have the credentials to make a comprehensive answer, but I will answer the points I can. As I have mentioned, the "prebiotic soup" is not even the favoured theory of abiogenesis at the moment, and the only argument you seem to have against all the other theories is saying they are "far-fetched". Some of them may seem far-fetched, but once again I have to say we are talking about an unbelievably huge testing-arena. Not only countless shallow lakes and sea-bottoms, but all of those recurring in different places (sometimes for thousands if not millions of years at a time) all over the planet far a billion years. A self replicator forming by pure chance now seems almost inevitable (maybe you disagree, but technically a self-replicator only has to be a very simple thing)
After that this self replicator would spread everywhere it possibly could - after all it would have had no rivals. Until it started meeting its own relatives. From the very start there would have been some kind of competition. And with possibilities abundant, who knows what could have been made of amino acids (amongst other things) to gain an advantage? The ultimate advantage of course would have been the superior copying fidelity that amino acids provide. Originally they may have had a completely different function, then a subsidy to self-replication, but they would have grown to something much more.
Or maybe there was a different chain of events. It's not known at this time, but I'm sure there's a bunch of theories by scientists (many of them better than mine I'm sure!)[/quote]

4)Racemic Mixtures: Amino acids, sugars, proteins, and DNA are not simply bundles of chemicals. they exhibit very specific 3-D structures. Even if they have all the right pieces, they don't always have the right structure. The problem is that that amino acids (and sugars) appear in two forms (chiralities). they can exists as mirror images of each other, sort of like a right and left handed glove, they are actually referred to as right handed or left handed amino acids. In simulated experiments(such as Miller and Urey) the "left" and "right" appear about 50/50 for both amino acids and sugars. Scientist have not been able to get concentrations of one or the other in "natural" simulations. The reason this is a problem is that only the Left handed amino acids are used in life. If even one of the right handed forms get involved in the structure of the protein, it diminished and often completely destroys the function of it. To add to this problem living things include only right-handed sugars in life(such as the sugar phosphate backbone in DNA). How did living things exclusively prefer one form to the other when there should have been an even mixture. Life shows characteristics that are alien to anything known to be produced under ordinary material conditions. (this would affect anoxic environments)

Again, a lot of this is outside my field of knowledge. Even so I could bring forth a fairly good hypothesis. It's pretty much the same as a lot of what I said about the Cambrian. It's a good chance that complex life as we know it (and even most, if not all, simple life) has evolved to become dependant on the complex structures that may have been originally circumstatial. Remember that evolution does support common ancestry. Perhaps by chance the right-handed preferring organisms managed to out-compete the left-hand preferring? Or maybe there is an inherent advantage in one over the other in the finer points of string theory (or whatever) that we haven't discovered yet?
My point is that it's not a major stumbling block. It's just another gap in data.

5)The synthesis of polymers problem: even if you had all the correct amino acids(Left handed) and sugars(right handed) you run into the staggering complexity of organizing them in the right sequence with only the correct bonds. Amino acids can chemically join together in a number of ways, but only the "peptide bond" is in functional proteins. You have to solve the problem of only the correct bond before you can even touch the problem of the correct order of amino acids. Living cells solve this problem using enzymes (which are proteins). In nature or a prebiotic soup you don't have this luxury. Things get even more complicated when we talk about the nucleotides found in DNA.

I don't think there's much here I can say that I haven't already said. Apart from bringing up that this is just another rehash of "irreducible complexity" which doesn't have much clout (and i will get to). I don't know how these things formed. As I said I'm not an organic chemist. There are theories out there - probably even well substantiated ones. I just haven't read them in detail. And even if there aren't any, that doesn't mean anything. Scientists could easily just make up some answer, but that's not the way science works. A made up answer will never gain approval of the rest of the scientific body. If there is no answer it is because they haven't found the right way to test the hypotheses yet,or they haven't found the right hypothesis.

In a small protein consisting of 100 subunits, and using only the 20 amino acid found in life. the number of different sequences (with only peptide bonds) is 20 raised to the 100. (or about 10 raised to the 130). MIT biochemist Robert Sauer applied a technique that took into account the variations that would be tolerated at a given protein site. His number that the probability of forming a 100-subunit functional protein is only 1 in 10 raised to the 65. While that is much better it is still an infinitesimally small probability. Just for reference it has been estimated that there are 10 raise to the 65 atoms in the universe. (if you want to claim amino acids from meteors helped form life, then you have even more problems because the Murchison meteorite had over 70 amino acids, which make the possible combinations significantly larger and even more improbable)[J. Bowie and R. Sauer, "Identifying Determinants of Folding and Actiity for a Protein of Unknown Sequences:Tolerance to Amino Acid Substitution," Proceedings of the National Academy of Science 86 (1989): 2152-56.; J. Bowie, J. reidhaar-Olson, W. Lim, and R. Sauer, "Deciphering the Message in Protein sequences: Tolerance to Amino Acid Substitution," Science 247 (1990):1306-10.; J. Reidhaar-Olson and R. Sauer, "Functionally Acceptable Solutiions in Two Alpha-Helical regions of Lambda Repressor," Proteins, Structure, Function, and Genetics 7 (1990): 306-10. see also Hubert Yockey, Information Theory and Molecular Biology (cambridge: Cambridge University Press, 1992) 246-58.]

Unfortunately I can't provide an answer to this as it's far outside my limited knowledge of organic chemistry and molecular biology. If I find some time I will try and research your points to form a discussion on them.

These are major problems that you cannot just wave off as if they don't matter or say well we just don't have enough information yet. These problems have arisen because of all the information we do have, This is not an ignorance problem. You can deny the evidence and still hold to the spontaneous generation (abiogeneis) that Darwin claimed out of ignorance to the true complexity of life, but you must realize and admit that you do so on grounds other than the scientific evidence. As I said before I think the true issue with theism is not a scientific one, but either emotionally based or philosophically based.

Even if I conveniently ignore your equating abiogenesis with evolution (they are two different things), I still have to disagree.
The "problems" you mention that arise from more information tend always to be smaller problems than their previous generation of problems. In Darwin's day he was criticised because he didn't knwo how characteristics were passed on from a parent to offspring. That is a fairly big gap in knowledge. Later chromosomes were discovered and the way in which they combine between the two parents to produce the offspring. Slightly smaller gap, but still missing knowlede. Then DNA was discovered - what chromosomes are made of, and the basic code for life. And so on. The gaps keep getting smaller. And yes, each time we reduce the gap more questions are raised. But they are always smaller questions because they only tend to be relevant to the newest set of answers we've acquired.

I just had to comment on this... It seems that we agree that Darwinian evolution fails to work linearly (at least in some cases). Behe's irreducible complexity only works against direct or linear evolution where the function is kept. So your forced to argue for indirect evolution with changing function that progressively gets more complex. But the question I have for you is where is the evidence to back up your theory? You mention the poison injector found in the flagellum (its called a type 3 secretory system or TTSS). There are two problems with claiming this as your reason for believing in indirect evolution. 1) it is like finding an island between Europe and North America and saying that that explains how you get from one point to the other. There is still a lot of difference between the two that is unexplained. Your claiming two much explanatory power from the actual evidence. 2) It doesn't make since from an evolutionary stand point. Which came first the flagellum or the TTSS. Well, you want to say the simpler TTSS came first because it fits with your preconceived theory, but from an evolutionary stand point it makes more since to say the flagellum was first. Water was abundant on early earth, it is assumed that live evolved in water of some type of soup. There was single cell life living in water many millions of years before any multicellular organism. The flagellum is useful for moving in water and finding food in water or other liquid environments. While the TTSS is useless in a open water environment. Not until there were multicellular organisms would the TTSS have any purpose or anything to poison. The flagellum would have been functionally useful long before the TTSS. It makes more since to say that the TTSS de-evolved from the flagellum. The opposite from what your claiming. I've fine with things de-evolving, we see it in animals like the cave fish and salamanders who lost their eye sight and color.

The flagellum is only an example. I used it because Behe used it. Perhaps early bacteria had a different way of getting around that wasn't quite as efficient as a flagellum (after all, they couldn't evolve something that complex and efficient in one go. They had to have something else. So no - it doesn't make sense that it was first from an evolutionary standpoint), or maybe they didn't have the same need to move around so fast. And besides (and correct me if I'm wrong), I'm pretty sure not every bacteria has a flagellum. Those without seem to manage quite well...
And as I take it, you are implying that a bacteria with a TTSS could not have evolved a flagellum because the two are useful in two mutually exclusive environments. Well, there are many many "halfway" zones in any habitat. The border between one environment and another. A bacteria hunting a mediocre living with a TTSS in a border zone may suddenly find enormous horizons by simply changing to a flagellum and moving to open water.
Or, as I keep saying, perhaps there's another explanation we haven't thought of.

And, backtracking a little bit, you ask where is the evidence for non-linear evolution? Oy-veh! (Just because I love the expression, not because I'm jewish ) - just look at the fossil record! Every transitional fossil (and believe me, there's tons despite what you might hear. I can give you a list if you want) shows evidence of this. Even most of the other fossils (which could arguably be considered transitional anyway, as there is no "end point" in evolution)
Just look at the fin bones of late devonian fish turning into digits in early carboniferous amphibians! Look at the jawbones of early synapsids turning into the earbones of later mammals!
I have more, but I'd have to consult some books which are not with me at the moment.