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Evolution is it a Fact or a Theory?

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quote:

Originally posted by $iLk:

quote:

Physical science is full of empirical evidence the evolution is a fact.

I guess the real disparity is that the definition of fact and the definition of scientific fact are two different things.

It's semantics, but it's also important to note.

As to the rest of your post, it's all well and good except that while those who are proponents of the Evolution theory tend to focus half their data attempting to cast doubt on Divine Creation as opposed to using real science to further understanding of true fact.


Scientists do not try and disprove creationism, creationists ATTACK science, so science defends itself. If creationists left Science alone, there would be no problems.

Cretionists are the ones that started this, and get very upset when science dashes their hypothesis to pieces.

Creation is the realm of religion, evolution science.

If creationists would quit attacking science because they are so afraid of, science wouldn't have to defend itself against such silliness.

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Guest Shingen

quote:

Originally posted by Eclipse:

That is not the issue here if I've read things correctly. No one will disagree that microevolution occurs, as your example pointed out, but where the issue lies is when one organism becomes a totally different organism.

I thought the discussion of the "theory of evolution" against the "theory of creationist", dealt with not when a species becomes a different species, but was life intentionally created or randomly generated.

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quote:

Originally posted by Shingen:

quote:

Originally posted by Eclipse:

That is not the issue here if I've read things correctly. No one will disagree that microevolution occurs, as your example pointed out, but where the issue lies is when one organism becomes a totally different organism.

I thought the discussion of the "theory of evolution" against the "theory of creationist", dealt with not when a species becomes a different species, but was life intentionally created or randomly generated.


Evolution has NOTHING to say about that, the creation of life has NOTHING to do with evolution, that is abiogenesis, and it is still so new that they are still in the hypothesis stage.

How life was created is not a question asked by Evolution, how life became what it is, is the question evolution asks. The fossil evidence shows us plainly that macroevolution takes place, it is HOW it takes place that is the question. Although we are getting closer to answering that question, Genetics is helping pin it down.

But how was life created? Evolution doesn't care....

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quote:

Originally posted by Jaguar:

The fossil evidence shows us plainly that macroevolution takes place, it is HOW it takes place that is the question. Although we are getting closer to answering that question, Genetics is helping pin it down.

But how was life created? Evolution doesn't care....

Though the fossil record may SEEM to support evolution, genetic evidence actually goes the other way. As an example, after the Genome Mapping project, they came up with a "code" of sorts of what comprises Human DNA, what's interesting is that, using the specified chemicals that make up DNA, they calculated that there are actually over a Billion Billion possible combinations. That is a 10 with 20 zero's. Out of all those combinations, we "Just Happen" to have the ONE perfect combination, you see, almost any other combination would have been disastrous for us and would either not have worked out or left us susceptible to disease and infertility. So I am supposed to believe that out of a chance of one in a Billion Billion, we just got lucky? Any mathematician will tell you that anything over a Million Million is almost impossible to EVER occur and anything over a Billion Million is absolutely certain to NEVER happen. Just to illustrate how far fetched this idea is, it is about the same probability of every person in the world flipping a coin all at the same time and every single one of them getting heads. I don't care if everyone in the world did this every minute of the day for 2 lifetimes, it will just NEVER happen, the odds are so far stacked against it, that it is just plain impossible. It's the same with Macro Evolution. The odds of a change in DNA occuring, that "somehow" matches up to be JUST the perfect balace to create a whole new species is just absurd.

I get a cut on my finger and white blood cells rush to the area and target and destroy any invading bacteria, my blood cells were designed to harden at the presence of the right combination of Oxygen and Nitrogen, to protect my skin as it heals. T-cells make enzymatic replications of the protien of any bacteria in the area and transmit throughout my nervouse system the protein signature of the invader so it is destroyed on sight by any white blood cells. I am supposed to believe that all this happened by accident? That my body and all it's incredible designs is somehow a cosmic mistake? I refuse to believe that. You may believe in luck, but I don't.

For you to sit there reading this screen with eyes that rival Supercomputers in computing power, refraction, light composition, and imaging connected to a brain that has Random Access Memory that could only be measured in the Billions of Terrabytes and say that you are a mistake, go ahead, I feel for you buddy, the evidence is all around you of God's creations, but if you want to keep denying him Go ahead, he gave you that free will of yours.

Say what you want. Build your house of cards, in then end if I'm wrong, no big deal, but if you are wrong well, you'll have some explaining to do.

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Guest $iLk

Of course for me it's as simple as sitting in the grass, breathing in the clean air and looking up at the sky... it all fits together in a way that looks a lot different and new when you are in the right spiritual frame of mind.

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quote:

Originally posted by Darkling:

quote:

Originally posted by Jaguar:

The fossil evidence shows us plainly that macroevolution takes place, it is HOW it takes place that is the question. Although we are getting closer to answering that question, Genetics is helping pin it down.

But how was life created? Evolution doesn't care....

Though the fossil record may SEEM to support evolution, genetic evidence actually goes the other way. As an example, after the Genome Mapping project, they came up with a "code" of sorts of what comprises Human DNA, what's interesting is that, using the specified chemicals that make up DNA, they calculated that there are actually over a Billion Billion possible combinations. That is a 10 with 20 zero's. Out of all those combinations, we "Just Happen" to have the ONE perfect combination, you see, almost any other combination would have been disastrous for us and would either not have worked out or left us susceptible to disease and infertility. So I am supposed to believe that out of a chance of one in a Billion Billion, we just got lucky? Any mathematician will tell you that anything over a Million Million is almost impossible to EVER occur and anything over a Billion Million is absolutely certain to NEVER happen. Just to illustrate how far fetched this idea is, it is about the same probability of every person in the world flipping a coin all at the same time and every single one of them getting heads. I don't care if everyone in the world did this every minute of the day for 2 lifetimes, it will just NEVER happen, the odds are so far stacked against it, that it is just plain impossible. It's the same with Macro Evolution. The odds of a change in DNA occuring, that "somehow" matches up to be JUST the perfect balace to create a whole new species is just absurd.

I get a cut on my finger and white blood cells rush to the area and target and destroy any invading bacteria, my blood cells were designed to harden at the presence of the right combination of Oxygen and Nitrogen, to protect my skin as it heals. T-cells make enzymatic replications of the protien of any bacteria in the area and transmit throughout my nervouse system the protein signature of the invader so it is destroyed on sight by any white blood cells. I am supposed to believe that all this happened by accident? That my body and all it's incredible designs is somehow a cosmic mistake? I refuse to believe that. You may believe in luck, but I don't.

For you to sit there reading this screen with eyes that rival Supercomputers in computing power, refraction, light composition, and imaging connected to a brain that has Random Access Memory that could only be measured in the Billions of Terrabytes and say that you are a mistake, go ahead, I feel for you buddy, the evidence is all around you of God's creations, but if you want to keep denying him Go ahead, he gave you that free will of yours.

Say what you want. Build your house of cards, in then end if I'm wrong, no big deal, but if you are wrong well, you'll have some explaining to do.


Ahh yes, the statistically impossible argument.

I have seen this one as well, and it is just as silly as the others that I have seen.

Again, straight out of the creationist Strawman handbook.

We'll take this one itsy bitsy step at a time.

And you are going back to abiogenesis again, BAD creationist, BAD.... I told you not to try and change the subject.

But I'll play....

My comments will be in italics and what I feel is important within it, will be in bold.

From this website

quote:

Every so often, someone comes up with the statement "the formation of any enzyme by chance is nearly impossible, therefore abiogenesis is impossible". Often they cite an impressive looking calculation from the astrophysicist Fred Hoyle, or trot out something called "Borel's Law" to prove that life is statistically impossible. These people, including Fred, have committed one or more of the following errors.

1) They calculate the probability of the formation of a "modern" protein, or even a complete bacterium with all "modern" proteins, by random events. This is not the abiogenesis theory at all.

2) They assume that there is a fixed number of proteins, with fixed sequences for each protein, that are required for life.

3) They calculate the probability of sequential trials, rather than simultaneous trials.

4) They misunderstand what is meant by a probability calculation.

5) They seriously underestimate the number of functional enzymes/ribozymes present in a group of random sequences.

I will try and walk people through these various errors, and show why it is not possible to do a "probability of abiogenesis" calculation in any meaningful way.

A primordial protoplasmic globule

So the calculation goes that the probability of forming a given 300 amino acid long protein (say an enzyme like carboxypeptidase) randomly is (1/20)300 or 1 chance in 2.04 x 10390, which is astoundingly, mind-beggaringly improbable. This is then cranked up by adding on the probabilities of generating 400 or so similar enzymes until a figure is reached that is so huge that merely contemplating it causes your brain to dribble out your ears. This gives the impression that the formation of even the smallest organism seems totally impossible. However, this is completely incorrect.

Firstly, the formation of biological polymers from monomers is a function of the laws of chemistry and biochemistry, and these are decidedly not random.

Secondly, the entire premise is incorrect to start off with, because in modern abiogenesis theories the first "living things" would be much simpler, not even a protobacteria, or a preprotobacteria (what Oparin called a protobiont [8] and Woese calls a progenote [4]), but one or more simple molecules probably not more than 30-40 subunits long. These simple molecules then slowly evolved into more cooperative self-replicating systems, then finally into simple organisms [2, 5, 10, 15, 28]. An illustration comparing a hypothetical protobiont and a modern bacteria is given below.

go to the site for the pictures

The first "living things" could have been a single self replicating molecule, similar to the "self-replicating" peptide from the Ghadiri group [7, 17], or the self replicating hexanucleotide [10], or possibly an RNA polymerase that acts on itself [12].

Another view is the first self-replicators were groups of catalysts, either protein enzymes or RNA ribozymes, that regenerated themselves as a catalytic cycle [3, 5, 15, 26, 28]. An example is the SunY three subunit self-replicator [24]. These catalytic cycles could be limited in a small pond or lagoon, or be a catalytic complex adsorbed to either clay or lipid material on clay. Given that there are many catalytic sequences in a group of random peptides or polynucleotides (see below) it's not unlikely that a small catalytic complex could be formed.

These two models are not mutually exclusive. The Ghadiri peptide can mutate and form catalytic cycles [9].

No matter whether the first self-replicators were single molecules, or complexes of small molecules, this model is nothing like Hoyle's "tornado in a junkyard making a 747". Just to hammer this home, here is a simple comparison of the theory criticised by creationists, and the actual theory of abiogenesis.

I will spell this out, just in case you decide NOT to go the website.

Creationist view of Abiogenesis.

Simple Chemicals-------------Bacteria

BOOM just like that, NOT quite

L theory of Abiogenesis

Simple Chemicals-----Polymers-----replicating polymers-----hypercycle------Protobiant-----Bacteria

Note that the real theory has a number of small steps, and in fact I've left out some steps (especially between the hypercycle-protobiont stage) for simplicity. Each step is associated with a small increase in organisation and complexity, and the chemicals slowly climb towards organism-hood, rather than making one big leap [4, 10, 15, 28].

Where the creationist idea that modern organisms form spontaneously comes from is not certain. The first modern abiogenesis formulation, the Oparin/Haldane hypothesis from the 20's, starts with simple proteins/proteinoids developing slowly into cells. Even the ideas circulating in the 1850's were not "spontaneous" theories. The nearest I can come to is Lamarck's original ideas from 1803! [8]

Given that the creationists are criticising a theory over 150 years out of date, and held by no modern evolutionary biologist, why go further? Because there are some fundamental problems in statistics and biochemistry that turn up in these mistaken "refutations".

The myth of the "life sequence"

Another claim often heard is that there is a "life sequence" of 400 proteins, and that the amino acid sequences of these proteins cannot be changed, for organisms to be alive.

This, however, is nonsense. The 400 protein claim seems to come from the protein coding genome of Mycobacterium genetalium, which has the smallest genome currently known of any modern organism [20]. However, inspection of the genome suggests that this could be reduced further to a minimal gene set of 256 proteins [20]. Note again that this is a modern organism. The first protobiont/progenote would have been smaller still [4], and preceded by even simpler chemical systems [3, 10, 11, 15].

As to the claim that the sequences of proteins cannot be changed, again this is nonsense. There are in most proteins regions where almost any amino acid can be substituted, and other regions where conservative substitutions (where charged amino acids can be swapped with other charged amino acids, neutral for other neutral amino acids and hydrophobic amino acids for other hydrophobic amino acids) can be made. Some functionally equivalent molecules can have between 30 - 50% of their amino acids different. In fact it is possible to substitute structurally non-identical bacterial proteins for yeast proteins, and worm proteins for human proteins, and the organisms live quite happily.

The "life sequence" is a myth.

Coin tossing for beginners and macromolecular assembly

So let's play the creationist game and look at forming a peptide by random addition of amino acids. This certainly is not the way peptides formed on the early Earth, but it will be instructive.

I will use as an example the "self-replicating" peptide from the Ghadiri group mentioned above [7]. I could use other examples, such as the hexanucleotide self-replicator [10], the SunY self-replicator [24] or the RNA polymerase described by the Eckland group [12], but for historical continuity with creationist claims a small peptide is ideal. This peptide is 32 amino acids long with a sequence of RMKQLEEKVYELLSKVACLEYEVARLKKVGE and is an enzyme, a peptide ligase that makes a copy of itself from two 16 amino acid long subunits. It is also of a size and composition that is ideally suited to be formed by abiotic peptide synthesis. The fact that it is a self replicator is an added irony.

The probability of generating this in successive random trials is (1/20)32 or 1 chance in 4.29 x 1040. This is much, much more probable than the 1 in 2.04 x 10390 of the standard creationist "generating carboxypeptidase by chance" scenario, but still seems absurdly low.

However, there is another side to these probability estimates, and it hinges on the fact that most of us don't have a feeling for statistics. When someone tells us that some event has a one in a million chance of occuring, many of us expect that one million trials must be undergone before the said event turns up, but this is wrong.

Here is a experiment you can do yourself: take a coin, flip it four times, write down the results, and then do it again. How many times would you think you had to repeat this procedure (trial) before you get 4 heads in a row?

Now the probability of 4 heads in a row is is (1/2)4 or 1 chance in 16: do we have to do 16 trials to get 4 heads (HHHH)? No, in successive experiments I got 11, 10, 6, 16, 1, 5, and 3 trials before HHHH turned up. The figure 1 in 16 (or 1 in a million or 1 in 1040) gives the likelihood of an event in a given trial, but doesn't say where it will occur in a series. You can flip HHHH on your very first trial (I did). Even at 1 chance in 4.29 x 1040, a self-replicator could have turned up surprisingly early. But there is more.

1 chance in 4.29 x 1040 is still orgulously, gobsmackingly unlikely; it's hard to cope with this number. Even with the argument above (you could get it on your very first trial) most people would say "surely it would still take more time than the Earth existed to make this replicator by random methods". Not really; in the above examples we were examining sequential trials, as if there was only one protein/DNA/proto-replicator being assembled per trial. In fact there would be billions of simultaneous trials as the billions of building block molecules interacted in the oceans, or on the thousands of kilometers of shorelines that could provide catalytic surfaces or templates [2,15].

Let's go back to our example with the coins. Say it takes a minute to toss the coins 4 times; to generate HHHH would take on average 8 minutes. Now get 16 friends, each with a coin, to all flip the coin simultaneously 4 times; the average time to generate HHHH is now 1 minute. Now try to flip 6 heads in a row; this has a probability of (1/2)6 or 1 in 64. This would take half an hour on average, but go out and recruit 64 people, and you can flip it in a minute. If you want to flip a sequence with a chance of 1 in a billion, just recruit the population of China to flip coins for you, you will have that sequence in no time flat.

So, if on our prebiotic earth we have a billion peptides growing simultaneously, that reduces the time taken to generate our replicator significantly.

Okay, you are looking at that number again, 1 chance in 4.29 x 1040, that's a big number, and although a billion starting molecules is a lot of molecules, could we ever get enough molecules to randomly assemble our first replicator in under half a billion years?

Yes, one kilogram of the amino acid arginine has 2.85 x 1024 molecules in it (that's well over a billion billion); a tonne of arginine has 2.85 x 1027 molecules. If you took a semi-trailer load of each amino acid and dumped it into a medium size lake, you would have enough molecules to generate our particular replicator in a few tens of years, given that you can make 55 amino acid long proteins in 1 to 2 weeks [14,16].

So how does this shape up with the prebiotic Earth? On the early Earth it is likely that the ocean had a volume of 1 x 1024 litres. Given an amino acid concentration of 1 x 10-6 M (a moderately dilute soup, see Chyba and Sagan 1992 [23]), then there are roughly 1 x 1050 potential starting chains, so that a fair number of efficent peptide ligases (about 1 x 1031) could be produced in a under a year, let alone a million years. The synthesis of primitive self-replicators could happen relatively rapidly, even given a probability of 1 chance in 4.29 x 1040 (and remember, our replicator could be synthesized on the very first trial).

Assume that it takes a week to generate a sequence [14,16]. Then the Ghadiri ligase could be generated in one week, and any cytochrome C sequence could be generated in a bit over a million years (along with about half of all possible 101 peptide sequences, a large proportion of which will be functional proteins of some sort).

Although I have used the Ghadiri ligase as an example, as I mentioned above the same calculations can be performed for the SunY self replicator, or the Ekland RNA polymerase. I leave this as an exercise for the reader, but the general conclusion (you can make scads of the things in a short time) is the same for these oligonucleotides.

Search spaces, or how many needles in the haystack?

I've shown that generating a given small enzyme is not as mind-bogglingly difficult as creationists (and Fred Hoyle) suggest. Another misunderstanding is that most people feel that the number of enzymes/ribozymes, let alone the ribozymal RNA polymerases or any form of self-replicator, represent a very unlikely configuration and that the chance of a single enzyme/ribozyme forming, let alone a number of them, from random addition of amino acids/nucleotides is very small.

However, an analysis by Ekland suggests that in the sequence space of 220 nucleotide long RNA sequences, a staggering 2.5 x 10112 sequences are efficent ligases [12]. Not bad for a compound previously thought to be only structural. Going back to our primitive ocean of 1 x 1024 litres and assuming a nucleotide concentration of 1 x 10-7 M [23], then there are roughly 1 x 1049 potential nucleotide chains, so that a fair number of efficent RNA ligases (about 1 x 1034) could be produced in a year, let alone a million years. The potential number of RNA polymerases is high also; about 1 in every 1020 sequences is an RNA polymerase [12]. Similar considerations apply for ribosomal acyl transferases (about 1 in every 1015 sequences), and ribozymal nucleotide synthesis [1, 6, 13].

Similarly, of the 1 x 10130 possible 100 unit proteins, 3.8 x 1061 represent cytochrome C alone! [29] There's lots of functional enyzmes in the peptide/nucleotide search space, so it would seem likely that a functioning ensemble of enzymes could be brewed up in an early Earth's prebiotic soup.

So, even with more realistic (if somewhat mind beggaring) figures, random assemblage of amino acids into "life-supporting" systems (whether you go for protein enzyme based hypercycles [10], RNA world systems [18], or RNA ribozyme-protein enzyme coevolution [11, 25]) would seem to be entirely feasible, even with pessimistic figures for the original monomer concentrations [23] and synthesis times.

Conclusions

The very premise of creationists' probability calculations is incorrect in the first place as it aims at the wrong theory. Furthermore, this argument is often buttressed with statistical and biological fallacies.

At the moment, since we have no idea how probable life is, it's virtually impossible to assign any meaningful probabilities to any of the steps to life except the first two (monomers to polymers p=1.0, formation of catalytic polymers p=1.0). For the replicating polymers to hypercycle transition, the probability may well be 1.0 if Kauffman is right about catalytic closure and his phase transition models, but this requires real chemistry and more detailed modelling to confirm. For the hypercycle->protobiont transition, the probability here is dependent on theoretical concepts still being developed, and is unknown.

However, in the end life's feasibility depends on chemistry and biochemistry that we are still studying, not coin flipping.


I thought you studied biology, ever taken a class in biochemistry? You should.

Put down the creationist handbook against evolution, because it is WRONG.

But we can keep going if you like.

NEXT.......

Oh and there are LOTS of other examples of the fallacie of this argument, but that would make a post at least 5 pages long, and I'm just not into that here.

Oh, and your last point, I will have some explaining to do if I'm wrong?

Well, guess what, I don't happen to believe that God is some omnipotent all powerful creature with delusions of grandeur and will get angry with me if I don't kiss his feet and pray to him every day.

I believe that if I use the brains that he gave me and educate myself to a point where I figure out how it all started and how it all happened, that he will be rather pleased that I went and used those brains to come to my own conclusions.

I live, and I use those gifts that I have to educate myself and use what I have been born with, that is enough.

[ 03-02-2004, 02:27 AM: Message edited by: Jaguar ]

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quote:


Originally posted by Chaoticmass:

I agree with this guy,
Ian Johnston
.


Oh, yeah!! Nice link!

It's amazing to me that people will have so much problem accepting that which is so plainly obvious, yet, so readily believe in the non-explanation, that everything just appeared from nothing.

I've had it suggested to me that all the fossils were burried all over the planet by God as a trick to test our faith in him.

ok...

My favorite Carl Sagan quote comes to mind...

"Those afraid of the universe as it really is, those who pretend to non-existent knowledge and envision a Cosmos centered on human beings will prefer the fleeting comforts of superstition. They avoid rather than confront the world. But those with the courage to explore the weave and structure of the Cosmos, even where it differs profoundly from their wishes and prejudices, will penetrate its deepest mysteries."

-Carl Sagan

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quote:

Originally posted by Andergum:

It's amazing to me that people will have so much problem accepting that which is so plainly obvious, yet, so readily believe in the non-explanation, that everything just appeared from nothing.

OK, isn't that what the Big Bang Theory says? So what's the difference?

I believe that God created the Universe out of nothing.

You believe that the Universe Created itself out of nothing.

Which sounds dumber to you?

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quote:

Originally posted by Jaguar:

quote:

Originally posted by Darkling:

quote:

Originally posted by Jaguar:

The fossil evidence shows us plainly that macroevolution takes place, it is HOW it takes place that is the question. Although we are getting closer to answering that question, Genetics is helping pin it down.

But how was life created? Evolution doesn't care....

Though the fossil record may SEEM to support evolution, genetic evidence actually goes the other way. As an example, after the Genome Mapping project, they came up with a "code" of sorts of what comprises Human DNA, what's interesting is that, using the specified chemicals that make up DNA, they calculated that there are actually over a Billion Billion possible combinations. That is a 10 with 20 zero's. Out of all those combinations, we "Just Happen" to have the ONE perfect combination, you see, almost any other combination would have been disastrous for us and would either not have worked out or left us susceptible to disease and infertility. So I am supposed to believe that out of a chance of one in a Billion Billion, we just got lucky? Any mathematician will tell you that anything over a Million Million is almost impossible to EVER occur and anything over a Billion Million is absolutely certain to NEVER happen. Just to illustrate how far fetched this idea is, it is about the same probability of every person in the world flipping a coin all at the same time and every single one of them getting heads. I don't care if everyone in the world did this every minute of the day for 2 lifetimes, it will just NEVER happen, the odds are so far stacked against it, that it is just plain impossible. It's the same with Macro Evolution. The odds of a change in DNA occuring, that "somehow" matches up to be JUST the perfect balace to create a whole new species is just absurd.

I get a cut on my finger and white blood cells rush to the area and target and destroy any invading bacteria, my blood cells were designed to harden at the presence of the right combination of Oxygen and Nitrogen, to protect my skin as it heals. T-cells make enzymatic replications of the protien of any bacteria in the area and transmit throughout my nervouse system the protein signature of the invader so it is destroyed on sight by any white blood cells. I am supposed to believe that all this happened by accident? That my body and all it's incredible designs is somehow a cosmic mistake? I refuse to believe that. You may believe in luck, but I don't.

For you to sit there reading this screen with eyes that rival Supercomputers in computing power, refraction, light composition, and imaging connected to a brain that has Random Access Memory that could only be measured in the Billions of Terrabytes and say that you are a mistake, go ahead, I feel for you buddy, the evidence is all around you of God's creations, but if you want to keep denying him Go ahead, he gave you that free will of yours.

Say what you want. Build your house of cards, in then end if I'm wrong, no big deal, but if you are wrong well, you'll have some explaining to do.


Ahh yes, the statistically impossible argument.

I have seen this one as well, and it is just as silly as the others that I have seen.

Again, straight out of the creationist Strawman handbook.

We'll take this one itsy bitsy step at a time.

And you are going back to abiogenesis again, BAD creationist, BAD.... I told you not to try and change the subject.

But I'll play....

My comments will be in italics and what I feel is important within it, will be in bold.

From this website

quote:

Every so often, someone comes up with the statement "the formation of any enzyme by chance is nearly impossible, therefore abiogenesis is impossible". Often they cite an impressive looking calculation from the astrophysicist Fred Hoyle, or trot out something called "Borel's Law" to prove that life is statistically impossible. These people, including Fred, have committed one or more of the following errors.

1) They calculate the probability of the formation of a "modern" protein, or even a complete bacterium with all "modern" proteins, by random events. This is not the abiogenesis theory at all.

2) They assume that there is a fixed number of proteins, with fixed sequences for each protein, that are required for life.

3) They calculate the probability of sequential trials, rather than simultaneous trials.

4) They misunderstand what is meant by a probability calculation.

5) They seriously underestimate the number of functional enzymes/ribozymes present in a group of random sequences.

I will try and walk people through these various errors, and show why it is not possible to do a "probability of abiogenesis" calculation in any meaningful way.

A primordial protoplasmic globule

So the calculation goes that the probability of forming a given 300 amino acid long protein (say an enzyme like carboxypeptidase) randomly is (1/20)300 or 1 chance in 2.04 x 10390, which is astoundingly, mind-beggaringly improbable. This is then cranked up by adding on the probabilities of generating 400 or so similar enzymes until a figure is reached that is so huge that merely contemplating it causes your brain to dribble out your ears. This gives the impression that the formation of even the smallest organism seems totally impossible. However, this is completely incorrect.

Firstly, the formation of biological polymers from monomers is a function of the laws of chemistry and biochemistry, and these are decidedly not random.

Secondly, the entire premise is incorrect to start off with, because in modern abiogenesis theories the first "living things" would be much simpler, not even a protobacteria, or a preprotobacteria (what Oparin called a protobiont [8] and Woese calls a progenote [4]), but one or more simple molecules probably not more than 30-40 subunits long. These simple molecules then slowly evolved into more cooperative self-replicating systems, then finally into simple organisms [2, 5, 10, 15, 28]. An illustration comparing a hypothetical protobiont and a modern bacteria is given below.

go to the site for the pictures

The first "living things" could have been a single self replicating molecule, similar to the "self-replicating" peptide from the Ghadiri group [7, 17], or the self replicating hexanucleotide [10], or possibly an RNA polymerase that acts on itself [12].

Another view is the first self-replicators were groups of catalysts, either protein enzymes or RNA ribozymes, that regenerated themselves as a catalytic cycle [3, 5, 15, 26, 28]. An example is the SunY three subunit self-replicator [24]. These catalytic cycles could be limited in a small pond or lagoon, or be a catalytic complex adsorbed to either clay or lipid material on clay. Given that there are many catalytic sequences in a group of random peptides or polynucleotides (see below) it's not unlikely that a small catalytic complex could be formed.

These two models are not mutually exclusive. The Ghadiri peptide can mutate and form catalytic cycles [9].

No matter whether the first self-replicators were single molecules, or complexes of small molecules, this model is nothing like Hoyle's "tornado in a junkyard making a 747". Just to hammer this home, here is a simple comparison of the theory criticised by creationists, and the actual theory of abiogenesis.

I will spell this out, just in case you decide NOT to go the website.

Creationist view of Abiogenesis.

Simple Chemicals-------------Bacteria

BOOM just like that, NOT quite

L theory of Abiogenesis

Simple Chemicals-----Polymers-----replicating polymers-----hypercycle------Protobiant-----Bacteria

Note that the real theory has a number of small steps, and in fact I've left out some steps (especially between the hypercycle-protobiont stage) for simplicity. Each step is associated with a small increase in organisation and complexity, and the chemicals slowly climb towards organism-hood, rather than making one big leap [4, 10, 15, 28].

Where the creationist idea that modern organisms form spontaneously comes from is not certain. The first modern abiogenesis formulation, the Oparin/Haldane hypothesis from the 20's, starts with simple proteins/proteinoids developing slowly into cells. Even the ideas circulating in the 1850's were not "spontaneous" theories. The nearest I can come to is Lamarck's original ideas from 1803! [8]

Given that the creationists are criticising a theory over 150 years out of date, and held by no modern evolutionary biologist, why go further? Because there are some fundamental problems in statistics and biochemistry that turn up in these mistaken "refutations".

The myth of the "life sequence"

Another claim often heard is that there is a "life sequence" of 400 proteins, and that the amino acid sequences of these proteins cannot be changed, for organisms to be alive.

This, however, is nonsense. The 400 protein claim seems to come from the protein coding genome of Mycobacterium genetalium, which has the smallest genome currently known of any modern organism [20]. However, inspection of the genome suggests that this could be reduced further to a minimal gene set of 256 proteins [20]. Note again that this is a modern organism. The first protobiont/progenote would have been smaller still [4], and preceded by even simpler chemical systems [3, 10, 11, 15].

As to the claim that the sequences of proteins cannot be changed, again this is nonsense. There are in most proteins regions where almost any amino acid can be substituted, and other regions where conservative substitutions (where charged amino acids can be swapped with other charged amino acids, neutral for other neutral amino acids and hydrophobic amino acids for other hydrophobic amino acids) can be made. Some functionally equivalent molecules can have between 30 - 50% of their amino acids different. In fact it is possible to substitute structurally non-identical bacterial proteins for yeast proteins, and worm proteins for human proteins, and the organisms live quite happily.

The "life sequence" is a myth.

Coin tossing for beginners and macromolecular assembly

So let's play the creationist game and look at forming a peptide by random addition of amino acids. This certainly is not the way peptides formed on the early Earth, but it will be instructive.

I will use as an example the "self-replicating" peptide from the Ghadiri group mentioned above [7]. I could use other examples, such as the hexanucleotide self-replicator [10], the SunY self-replicator [24] or the RNA polymerase described by the Eckland group [12], but for historical continuity with creationist claims a small peptide is ideal. This peptide is 32 amino acids long with a sequence of RMKQLEEKVYELLSKVACLEYEVARLKKVGE and is an enzyme, a peptide ligase that makes a copy of itself from two 16 amino acid long subunits. It is also of a size and composition that is ideally suited to be formed by abiotic peptide synthesis. The fact that it is a self replicator is an added irony.

The probability of generating this in successive random trials is (1/20)32 or 1 chance in 4.29 x 1040. This is much, much more probable than the 1 in 2.04 x 10390 of the standard creationist "generating carboxypeptidase by chance" scenario, but still seems absurdly low.

However, there is another side to these probability estimates, and it hinges on the fact that most of us don't have a feeling for statistics. When someone tells us that some event has a one in a million chance of occuring, many of us expect that one million trials must be undergone before the said event turns up, but this is wrong.

Here is a experiment you can do yourself: take a coin, flip it four times, write down the results, and then do it again. How many times would you think you had to repeat this procedure (trial) before you get 4 heads in a row?

Now the probability of 4 heads in a row is is (1/2)4 or 1 chance in 16: do we have to do 16 trials to get 4 heads (HHHH)? No, in successive experiments I got 11, 10, 6, 16, 1, 5, and 3 trials before HHHH turned up. The figure 1 in 16 (or 1 in a million or 1 in 1040) gives the likelihood of an event in a given trial, but doesn't say where it will occur in a series. You can flip HHHH on your very first trial (I did). Even at 1 chance in 4.29 x 1040, a self-replicator could have turned up surprisingly early. But there is more.

1 chance in 4.29 x 1040 is still orgulously, gobsmackingly unlikely; it's hard to cope with this number. Even with the argument above (you could get it on your very first trial) most people would say "surely it would still take more time than the Earth existed to make this replicator by random methods". Not really; in the above examples we were examining sequential trials, as if there was only one protein/DNA/proto-replicator being assembled per trial. In fact there would be billions of simultaneous trials as the billions of building block molecules interacted in the oceans, or on the thousands of kilometers of shorelines that could provide catalytic surfaces or templates [2,15].

Let's go back to our example with the coins. Say it takes a minute to toss the coins 4 times; to generate HHHH would take on average 8 minutes. Now get 16 friends, each with a coin, to all flip the coin simultaneously 4 times; the average time to generate HHHH is now 1 minute. Now try to flip 6 heads in a row; this has a probability of (1/2)6 or 1 in 64. This would take half an hour on average, but go out and recruit 64 people, and you can flip it in a minute. If you want to flip a sequence with a chance of 1 in a billion, just recruit the population of China to flip coins for you, you will have that sequence in no time flat.

So, if on our prebiotic earth we have a billion peptides growing simultaneously, that reduces the time taken to generate our replicator significantly.

Okay, you are looking at that number again, 1 chance in 4.29 x 1040, that's a big number, and although a billion starting molecules is a lot of molecules, could we ever get enough molecules to randomly assemble our first replicator in under half a billion years?

Yes, one kilogram of the amino acid arginine has 2.85 x 1024 molecules in it (that's well over a billion billion); a tonne of arginine has 2.85 x 1027 molecules. If you took a semi-trailer load of each amino acid and dumped it into a medium size lake, you would have enough molecules to generate our particular replicator in a few tens of years, given that you can make 55 amino acid long proteins in 1 to 2 weeks [14,16].

So how does this shape up with the prebiotic Earth? On the early Earth it is likely that the ocean had a volume of 1 x 1024 litres. Given an amino acid concentration of 1 x 10-6 M (a moderately dilute soup, see Chyba and Sagan 1992 [23]), then there are roughly 1 x 1050 potential starting chains, so that a fair number of efficent peptide ligases (about 1 x 1031) could be produced in a under a year, let alone a million years. The synthesis of primitive self-replicators could happen relatively rapidly, even given a probability of 1 chance in 4.29 x 1040 (and remember, our replicator could be synthesized on the very first trial).

Assume that it takes a week to generate a sequence [14,16]. Then the Ghadiri ligase could be generated in one week, and any cytochrome C sequence could be generated in a bit over a million years (along with about half of all possible 101 peptide sequences, a large proportion of which will be functional proteins of some sort).

Although I have used the Ghadiri ligase as an example, as I mentioned above the same calculations can be performed for the SunY self replicator, or the Ekland RNA polymerase. I leave this as an exercise for the reader, but the general conclusion (you can make scads of the things in a short time) is the same for these oligonucleotides.

Search spaces, or how many needles in the haystack?

I've shown that generating a given small enzyme is not as mind-bogglingly difficult as creationists (and Fred Hoyle) suggest. Another misunderstanding is that most people feel that the number of enzymes/ribozymes, let alone the ribozymal RNA polymerases or any form of self-replicator, represent a very unlikely configuration and that the chance of a single enzyme/ribozyme forming, let alone a number of them, from random addition of amino acids/nucleotides is very small.

However, an analysis by Ekland suggests that in the sequence space of 220 nucleotide long RNA sequences, a staggering 2.5 x 10112 sequences are efficent ligases [12]. Not bad for a compound previously thought to be only structural. Going back to our primitive ocean of 1 x 1024 litres and assuming a nucleotide concentration of 1 x 10-7 M [23], then there are roughly 1 x 1049 potential nucleotide chains, so that a fair number of efficent RNA ligases (about 1 x 1034) could be produced in a year, let alone a million years. The potential number of RNA polymerases is high also; about 1 in every 1020 sequences is an RNA polymerase [12]. Similar considerations apply for ribosomal acyl transferases (about 1 in every 1015 sequences), and ribozymal nucleotide synthesis [1, 6, 13].

Similarly, of the 1 x 10130 possible 100 unit proteins, 3.8 x 1061 represent cytochrome C alone! [29] There's lots of functional enyzmes in the peptide/nucleotide search space, so it would seem likely that a functioning ensemble of enzymes could be brewed up in an early Earth's prebiotic soup.

So, even with more realistic (if somewhat mind beggaring) figures, random assemblage of amino acids into "life-supporting" systems (whether you go for protein enzyme based hypercycles [10], RNA world systems [18], or RNA ribozyme-protein enzyme coevolution [11, 25]) would seem to be entirely feasible, even with pessimistic figures for the original monomer concentrations [23] and synthesis times.

Conclusions

The very premise of creationists' probability calculations is incorrect in the first place as it aims at the wrong theory. Furthermore, this argument is often buttressed with statistical and biological fallacies.

At the moment, since we have no idea how probable life is, it's virtually impossible to assign any meaningful probabilities to any of the steps to life except the first two (monomers to polymers p=1.0, formation of catalytic polymers p=1.0). For the replicating polymers to hypercycle transition, the probability may well be 1.0 if Kauffman is right about catalytic closure and his phase transition models, but this requires real chemistry and more detailed modelling to confirm. For the hypercycle->protobiont transition, the probability here is dependent on theoretical concepts still being developed, and is unknown.

However, in the end life's feasibility depends on chemistry and biochemistry that we are still studying, not coin flipping.


I thought you studied biology, ever taken a class in biochemistry? You should.

Put down the creationist handbook against evolution, because it is WRONG.

But we can keep going if you like.

NEXT.......

Oh and there are LOTS of other examples of the fallacie of this argument, but that would make a post at least 5 pages long, and I'm just not into that here.

Oh, and your last point, I will have some explaining to do if I'm wrong?

Well, guess what, I don't happen to believe that God is some omnipotent all powerful creature with delusions of grandeur and will get angry with me if I don't kiss his feet and pray to him every day.

I believe that if I use the brains that he gave me and educate myself to a point where I figure out how it all started and how it all happened, that he will be rather pleased that I went and used those brains to come to my own conclusions.

I live, and I use those gifts that I have to educate myself and use what I have been born with, that is enough.


You know, I've got to tell you, when you create these HUMUNGOUSE posts, it's too difficult to go over it all, just make your point and be done with it. Geez.

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quote:

Darkling to Jaguar

You know, I've got to tell you, when you create these HUMUNGOUSE posts, it's too difficult to go over it all, just make your point and be done with it. Geez.

There is an old convention from the usenet days that goes something like this:

quote:

Originally posted by Darkling:

quote:

Originally posted by Jaguar:

quote:

Originally posted by Darkling:

quote:

Originally posted by Jaguar:

snip


snip


snip

quote:

snip long article about probabilities


snip



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quote:

Originally posted by Darkling:

You know, I've got to tell you, when you create these HUMUNGOUSE posts, it's too difficult to go over it all, just make your point and be done with it. Geez.

Well, let's see, why would I do that?

You asked a complicated question, I have been told that I need to give facts in order to back up my statements, because just making a point isn't enough. I need back up, so, in order to back, myself up, I make long posts because if I give you just the link, chances are, you're not gonna read it.

I have done these little debates on the net for quite a while, I know how creationists work.

They take quotes out of context, such as you have been doing, they demand more information, so I give as much information as feasibly possible so I don't get that garbage back, and they always seem to get mad when overwhelmed with so many facts that they cannot respond. Just as you just did.

I can be very frustrating to a creationist, because creationist don't wish to understand what they are talking about, they just want to lay it out there and think they look smart. You don't actually expect to be called on the carpet for your nonsense.

So I overload you with facts, that you might not read, but others will, and when you come back with more nonsense along the same lines, I can just point back to the long post and be done.

You are a creationist, I have to hit you with as much information as possible and hope that it sinks in, so that you will continue to believe what you believe, but will actually quit attacking science, because it will come back and bite you.

Quit attacking science, believe what you want, but science is not going to change it's opinion because you're mad that it doesn't agree with you.

Science is not religion, DEAL WITH IT!!

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quote:


Originally posted by Darkling:

quote:

Originally posted by Andergum:

It's amazing to me that people will have so much problem accepting that which is so plainly obvious, yet, so readily believe in the non-explanation, that everything just appeared from nothing.


OK, isn't that what the Big Bang Theory says? So what's the difference?

I believe that God created the Universe out of nothing.

You believe that the Universe Created itself out of nothing.

Which sounds dumber to you?


They both pretty sound dumb to me.

I never said I believed in either.

No one knows what really happened in either case.

That's exactly why I like Sagan's quote so much.

Searching for the answer makes way more sense than pretending you know and then faulting others for not believing as you do.

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Originally posted by Andergum:

Searching for the answer makes way more sense than pretending you know and then faulting others for not believing as you do.

I've never faulted others for not believing as I do, the problem that I have is when they try to fault me for not believing as they do.

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quote:


Originally posted by Darkling:

quote:

Originally posted by Andergum:

Searching for the answer makes way more sense than pretending you know and then faulting others for not believing as you do.


I've never faulted others for not believing as I do, the problem that I have is when they try to fault me for not believing as they do.


You may not have, but the endless wars around the middle east and other places are testament to the fact that many others do.

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quote:

Originally posted by Andergum:

You may not have, but the endless wars around the middle east and other places are testament to the fact that many others do.

It's human nature to want to be right and some will always resort to violence if you don't agree with them. Be it a husband that beats on his wife for not agreeing with his "Authority" or a Dictator like Saddam who brutalized his own people. It's for reasons like this that we need more of God in our lives, but instead of some simply "shaking the dust off thier feet and moving on" as it says to do in the Bible when someone doesn't agree with your views too many resort to violence.

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quote:

Originally posted by Darkling:

quote:

Originally posted by Andergum:

Searching for the answer makes way more sense than pretending you know and then faulting others for not believing as you do.

I've never faulted others for not believing as I do, the problem that I have is when they try to fault me for not believing as they do.


Excellent, then we can agree to disagree, glad we got that out of the way....

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No new species moths or finches came about, kinda similar to how people have many different genetic traits in their DNA but not all are dominant.

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quote:

Originally posted by Eclipse:

No new species moths or finches came about, kinda similar to how people have many different genetic traits in their DNA but not all are dominant.

Evolution is not just about the emergence of new species but changes in pre-existing ones as well.

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"For Man to study the subject of evolution without also considering God, is akin to Man studying the subject of light, without also considering the sun."

-Anonymous-

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quote:

Originally posted by Shingen:

"For Man to study the subject of evolution without also considering God, is akin to Man studying the subject of light, without also considering the sun."

-Anonymous-

That's nice, but the person that said it was not a scientist. Obviously...

Science cannot use God as a causation, because that is not science, it's religion.

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Guest Shingen

Why?

To study the effect without considering the cause is good science?

I guess my point is this:

Everything in existance has an intelligence.

We can see this by observing how atoms interact with each other, certain atoms bond together, others don't. How do they ( the atoms ) know where they should go and what they should do? They have no brains, no "minds", where do they get the knowledge of how they are supposed to behave?

Atoms lead to molocules which lead to everything else. Even molocules "know" what to do and what other molecules that can or can't bond with. Where do they get this knowledge?

We can see this intelligence in how the Earth works, how the eco-system works, how the very Cosmos is arranged in an orderly fashion.

Evolution is no different.

[ 03-04-2004, 05:00 PM: Message edited by: Shingen ]

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quote:

Originally posted by Shingen:

To study the effect without considering the cause is logical?

Yes, because that's how it starts out. If you look at science now and through history, you will find that the study of the effect (with or without the pre-concieved notion of what the cause is) will eventually lead to the cause.

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quote:

Originally posted by Shingen:

Why?

To study the effect without considering the cause is good science?

I guess my point is this:

Everything in existance has an intelligence.

We can see this by observing how atoms interact with each other, certain atoms bond together, others don't. How do they ( the atoms ) know where they should go and what they should do? They have no brains, no "minds", where do they get the knowledge of how they are supposed to behave?

Atoms lead to molocules which lead to everything else. Even molocules "know" what to do and what other molecules that can or can't bond with. Where do they get this knowledge?

We can see this intelligence in how the Earth works, how the eco-system works, how the very Cosmos is arranged in an orderly fashion.

Evolution is no different.

This is NOT science.

The cause to science is unknown, then science goes and looks for the cause.

The intelligence you speak of is NOT science, that is religion.

And the earth and nature having knowledge and doing what it does because it is intelligent, is a wonderful religious philosophy, but, it is NOT scientific.

Chemicals react and interreact because of their chemical makeup, if you want to see intelligence within that, more power to you, but science does not and cannot work that way.

"God did it" is not science.....

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