Saturday, July 21, 2007

A creationism vs. evolution discussion,. Part 1

I am a chief editor and administrator for FunTrivia; the largest trivia site in the world. I have written many quizzes as well. Among those of which I am proudest are a series called “Evidence for Evolution” which explores and refutes various creationist arguments and claims. Naturally, these quizzes, as well as my first quiz on evolution, “Evolution and the Creationists,” have been the target of creationist criticism.

One recent writer , whose FunTrivia handle is “Marcsana,” took the time to write quite a long critique of that first quiz. I decided to explore some of that critique here. As it’s long, we’ll go question by question.

My question:
Question 5:
A popular argument by creationists is that evolution could never have occurred because it is so unlikely. As one example, they have stated,' There are n! (n-factorial: n x n-1 x n-2 x...x 1) ways of an enzyme or DNA strand of n parts forming prebiotically. Since the smallest proteins have at least 100 amino acids, the chance of forming a particular enzyme prebiotically is at most 1divided by 100!, which is small enough to be disregarded.' What is wrong with this argument?
Possible answers
  • Complex molecules don't form by chance alone
  • Larger proteins have fewer amino acids
  • The math is incorrect
  • Enzymes can only be formed in living things

The correct answer is Complex molecules don't form by chance alone.
While this argument correctly demonstrates that no given protein could have come into existence all at once by pure chance, such a demonstration is irrelevant to current origin-of-life research. As Iris Fry points out, 'origin-of-life theories rely on various organizing principles, including selection mechanisms and catalysis, that are supposed to have limited and constrained the wide scope of possible prebiotic possibilities, thus constructing the scaffolding out of which the living arch eventually emerged'

The critique from Marcsana:
5. You have the following explanatory material: [repeats Fry quote above.] Actually, such a demonstration IS relevant to current origin-of-life research. Complex molecules, proteins, or anything else can't just evolve because it is mathematically impossible. Iris Fry says that origin-of-life theories rely on various organizing principles including selection mechanisms and catalysts...but never mentions one. Why? Because no known mechanisms or catalysts exist. And natural selection can only go so far. This has been observed operating with existing information in a species. Never has it been observed changing a species into another one.

My response:
I’ll deal with the “we have never observed one species changing into another” argument in another post, as it isn’t specifically related to the main question- can complex molecules evolve? It seems Marcsana says no- it’s mathematically impossible, and no known mechanisms or catalysts exist that can facilitate what Fry claims, that such organizing principles allowed the evolution of complex molecules from simpler ones. Unfortunately, Marcsana gave no references, scientific or otherwise, to support his claim. Therefore, it’s difficult to understand what is meant by “no known mechanisms or catalysts exist.”

Let’s look at the potential for evolution of complex molecules. For a moment, let’s suppose “no known mechanisms or catalysts exist” (although they do, and we’ll discuss that later.)

The chief mistake that creationists make is thinking that, just because one event has a tiny probability, that event could never occur. The problem with this line of thinking is that, rather obviously, the probability of an event occurring rises dramatically when you have more opportunities for that event to occur. To put this in plainer English- if I buy one lottery ticket and have to guess 6 random numbers to win a prize, I am very unlikely to ever win. But I cannot therefore state that the probability of winning the lottery is so infinitesimally tiny that no one will ever win. There are millions of people attempting to win and guessing at the numbers, and thus millions of trials. And, as we know, someone usually does win the lottery.

The same is true of forming molecules. Even if the chances of forming a particular molecule are very tiny in one trial, if there are billions upon billions of trials, the chances of that molecule being formed are very great.

There is an elegant explanation of this in “Lies, Damned Lies, Statistics,and Probability of Abiogenesis Calculations

To quote this fine article briefly:
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 efficient 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).


Now let’s get back to the claim that “no known mechanisms or catalysts exist.” Not so. In fact, the scientific literature on this subject is overwhelmingly large and complex. There are two major theories for the mechanism of origin of complex organic molecules, and hundreds of experiments have been done and articles published on each one. One, often known as “genes first,” or “the RNA world,” deals with RNA, which can both store information and act as a catalyst for self-replication. As replicated molecules would have some mutations, selection would operate upon them. The second, known as “metabolism first,” or “the iron-sulfur world,” deals with the creation of organic materials in deep-sea hydrothermal vents. Let’s look at that hypothesis more closely.

In the ocean even today, deep-sea vents are areas of extreme chemical activity. In one type of vent, water warmed beneath the earth bubbles up through tiny chambers of iron sulfide. Each tiny chamber acts as a chemical reactor, as the iron sulfide surface provides a substrate for molecules to grow. One molecule that forms easily in such chambers is acetate, a vital molecule in many organic reactions. Living bacteria have an acetate-production mechanism almost identical to that which produces acetate in these vents. These tiny chambers also functioned much like cell walls, allowing chemical structures to be protected while they formed.

The chemistry of these reactions is quite complex, but here are some sources:

Jump-Starting a Cellular World: Investigating the Origin of Life, from Soup to Networks

The emergence of life from iron monosulphide bubbles at a submarine hydrothermal
redox and pH front


From geochemistry to biochemistry:
Chemiosmotic coupling and transition element clusters in the onset of life and photosynthesis


And this is only a tiny slice of the immense body of research surrounding just one of the mechanisms by which organic molecules evolved.

So, in closing, it is mathematically and scientifically possible for complex molecules to evolve, and several mechanisms have been shown to produce the proper conditions for such evolution to occur.

5 comments:

Marcsana said...

This will be written to counter the first post regarding evolution vs. creation. Before I start, however, I would like to discuss the difference between operational science and origins science. Operational science is a systematic approach to understanding that uses observable, testable, repeatable, and falsifiable experimentation to understand how nature commonly behaves. This form of science is what gives us so much knowledge today. We have radios, cell phones, TVs and a bunch of other inventions that are rooted deeply in this form of science. Further, through it, we know how far away stars are and we can determine various facts about the universe. Origins science is interpreting evidence from the unobservable, unrepeatable past based on a presupposed philosophical point of view. Enter worldview. Evolutionists and creationists alike cannot directly observe, test, repeat, or falsify the past. Both are based on certain assumptions. Evolution says there is no god (according to evolutionary scientists, one can't allow a supernatural foot in the door...this is, in effect, the same thing as saying no god), and creationists say there is. So the evidence is approached using these opposing paradigms. Both sides have the same evidence...but the question is how should this evidence be interpreted? Which paradigm should the evidence be viewed through? As will be shown over the length of these discussions, the evidence is far more in favor of the biblical worldview than a naturalistic one rendering it the correct paradigm with which to view the evidence.
Let's begin with probability since it is the first topic in this discussion. Probability IS a powerful argument for creation.
Regarding probability, I would like to begin with this quote from Hubert P. Yockey:
"Although at the beginning the paradigm was worth consideration, now the entire effort in the primeval soup paradigm is self-deception on the ideology of its champions."
"The history of science shows that a paradigm, once it has achieved the status of acceptance (and is incorporated in textbooks) and regardless of its failures, is declared invalid only when a new paradigm is available to replace it. Nevertheless, in order to make progress in science, it is necessary to clear the decks, so to speak, of failed paradigms. This must be done even if this leaves the decks entirely clear and no paradigms survive. It is a characteristic of the true believer in religion, philosophy and ideology that he must have a set of beliefs, come what may (Hoffer, 1951). Belief in a primeval soup on the grounds that no other paradigm is available is an example of the logical fallacy of the false alternative. In science it is a virtue to acknowledge ignorance. This has been universally the case in the history of science as Kuhn (1970) has discussed in detail. There is no reason that this should be different in the research on the origin of life."
Hubert P. Yockey, 1992 (a non-creationist). Information Theory and Molecular Biology, Cambridge University Press, UK, p. 336.

He also said, "The origin of life by chance in a primeval soup is impossible in probability in the same way that a perpetual machine is in probability. The extremely small probabilities calculated in this chapter are not discouraging to true believers ... [however] A practical person must conclude that life didn't happen by chance."
Evolutionary scientists try to cloak how great the probability argument is through a series of clever and intelligent-sounding arguments. When possible as I write my arguments, I will refer to the experts. The following two articles treat the issue of probability. It's easier to copy and paste the web link into your browser.


www.iscid.org/pcid/2002/1/4/mullan_primitive_cell.php>

www.answersingenesis.org/creation/v17/i2/chance.asp>



This explains the problems with an RNA world (which was lightly touched on in your response.

www.answersingenesis.org/tj/v11/i1/enzymes.asp>


These three sections deal with the problems of the thermal vent idea (among other things). I would like to apologize in advance for one comment you'll read in the second choice. Here it is. "Not to be too harsh about it, but it is akin to some of the fairy tales I read to my daughter before she goes to bed at night-fanciful and entertaining, but long on imagination and short on substance." As we go through this discussion, I won't deliberately say things that are inflammatory. I may reference how evolutionary theories ARE big on imagination, but short on substance...but I won't call your belief system a fairy tale. It took years for you to arrive to these conclusions and I respect your thinking. But as human beings, we are frequently wrong about things that we took years to come up with. Anyway, here is the information.

www.answersingenesis.org/creation/v3/i4/atmosphere.asp>

www.answersingenesis.org/articles/am/v1/n1/origins-of-life-simple-approach>

www.answersingenesis.org/docs/4220.asp>


In conclusion, it is sufficiently demonstrated that evolutionists must rely on over simplified models to explain something as complex as life (much more in later installments). While it's true they say that other factors besides chance and time played a role and, therefore, reduced the probabilities...this isn't compelling enough to detract from the creation argument. The problem lies in the fact that these other factors lack evidence either because it hasn't been observed, or other factors would have rendered it useless (like the atmosphere that would need to be present during an alleged primordial soup phase or the toxic by-products in the Miller experiments). Probability IS a good argument against evolutionists when understood correctly. Further, deep-sea vents do not solve the problem at all. Neither does an RNA world. These are two possibilities that have severe problems.

I would like to end with this installment with this quote:

Professor Richard Lewontin, a geneticist (and self-proclaimed Marxist), is a renowned champion of neo-Darwinism, and certainly one of the world's leaders in evolutionary biology. He wrote this very revealing comment (the italics were in the original). It illustrates the implicit philosophical bias against Genesis creation-regardless of whether or not the facts support it.
'We take the side of science in spite of the patent absurdity of some of its constructs, in spite of its failure to fulfill many of its extravagant promises of health and life, in spite of the tolerance of the scientific community for unsubstantiated just-so stories, because we have a prior commitment, a commitment to materialism. It is not that the methods and institutions of science somehow compel us to accept a material explanation of the phenomenal world, but, on the contrary, that we are forced by our a priori adherence to material causes to create an apparatus of investigation and a set of concepts that produce material explanations, no matter how counter-intuitive, no matter how mystifying to the uninitiated. Moreover, that materialism is an absolute, for we cannot allow a Divine Foot in the door.'

Cris said...

Marcsana- rather than links to creationist websites and a lot of verbiage on topics different from the one in my original post, I would appreciate some direct discussion of the issues that I raised in mine. I don't see that you directly discuss any of the issues that I raised (other than to provide links to creationist websites.) I'd like to hear your explanations of your theories, and your thoughts on my comments, not just the words of others. So, for example, can you personally address the issue of whether acetates can form on an iron-sulfur substrate?
I'll look into the Yockey stuff and get back to you on that issue, as his name is only vaguely familiar to me.

Cris said...

Well, right off the bat, I'm afraid you're being either dishonest or misinformed to state that Hubert P. Yockey is a "non-creationist." He is on the board of Leadership U, a creationist website (http://www.leaderu.com/truth/1truth18c.html) and a "Friend of Access Research Network," an intelligent design website (http://www.arn.org/infopage/yockey.htm)

I found this with about 1 minute of Google searching (as I am at work right now and really should be doing other things!)

Of course, his stance doesn't invalidate whatever research he has published, ad I'll look into that when I get home and have some time. But to posit him as a non-biased source is incorrect at best and deceitful at worst.

Marcsana said...

Before I write about what the thermal vents theory presented, I would like to point out that this theory is far from agreed upon within the evolutionary community. In fact, origins is still a hot topic among evolutionists and there are many different theories out there competing for the prize, so to speak. Furthermore, this particular variant of the thermal vent theory is only one of several. If this theory was so solid, then everyone would agree on it. They do not.
And next, regarding Yockey. Isn't there another possibility? Can there be a chance that I'm not either dishonest or misinformed? What could I possibly be referring to? Oh, right. The fact that he is one of several scientists who hold to the idea of an old Earth AND a Designer. A creationist is someone who holds to a literal 6-day creation. We do differentiate. You also have an amazing ability to twist what I say or disfigure and misrepresent the creationist position. To that, I say that you should read what I write more carefully or be more honest. You have done this several times and I will deal with each one as I write the posts on various topics. Did I say Yockey was a "non-biased source?" NO! There is no such thing when it comes to origins which I treated in great detail. Maybe you didn't read it thoroughly. Origins deals with the unobservable, unrepeatable past. As such, one must have a preexisting bias toward a particular theory. Evolutionists prefer long ages and Christians hold the idea of a Creator. The question is interpreting the evidence we have which is what our discussion is about. Before you accuse me of dishonesty or misinformation, you better make sure that you have correctly understood what I wrote. I will call it out every time. Dr. Yockey is no friend to creation science and yet he still recognized the validity of the probability argument. That is why I chose the quote. He is not alone. I will treat probability again in another post.
Let's take a closer look at thermal vents. First of all, the theory of thermal vents posted here is not enough in and of itself. The following quote is from article at http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0030396&ct=1.
"This metabolism-first model is not an alternative to life based on RNA. “We can't work without an RNA world either,” says Martin. But it does propose that geology at hydrothermal vents provided the structure in which life emerged, and suggests that understanding prebiotic organic chemistry at these vents may provide the key to understanding the emergence of life from nonlife."
You asked me if I think acetates can form on an iron-sulfur substrate. Probably. But this has little to do with adenine, uracil, guanine or cytosine. I will back up for a second. Many evolutionists favor the "warm little pond" origin-of-life theory or the thermal vent theories because they postulate that the oldest known organisms are hyperthermophiles that would have required temperatures between 80 and 110 degrees Celsius. A major problem for any of these theories is that adequate concentrations of certain complex compounds necessary for life are not accounted for. There has to be a requisite level of stability so that synthesis is at higher levels than degradation. What you proposed is an attempt to cover for these lacking components. By saying that those chambers function like cell walls is overly simplistic to say the least. While the vents you speak of may themselves be more stable (the one article mentioned they'd be stable for thousands of years...this is highly argumentative to say the least), we haven't yet touched the biggest problems with this proposed model. They have also been highly criticized because experimental research has shown that the half-lives of many vitally important compounds to be “too short to allow for the adequate accumulation of these compounds” (Levy and Miller, 1998, p. 7933)." Levy and Miller go on to say that, "“unless the origin of life took place extremely rapidly (in less than 100 years), we conclude that a high temperature origin of life... cannot involve adenine, uracil, guanine or cytosine” because these compounds break down far too fast in a warm environment. In a hydrothermal environment, most of these compounds could neither form in the first place, nor exist for a significant amount of time (Levy and Miller, p. 7933)." They continue, "the rapid rates of hydrolysis of the nucleotide bases A,U,G and T at temperatures much above 0° Celsius would present a major problem in the accumulation of these presumed essential components on the early earth” (p. 7933). Below is the website:
http://www.pnas.org/cgi/content/abstract/95/14/7933

As a result of this, they theorized that either a two-letter code or an alternative base pair was used instead. This has the distinction of demanding an absolutely different kind of life was formed. This is not only highly speculative, but likely impossible because only A, U, G and T have the requisite properties for life. So now, life would have had to evolve completely differently than we know it today, and then re-evolve into the known code of life we see today. This change, by the way, appears to be impossible based on current knowledge of molecular biology.
And lastly, the authors found that given the minimum amount of time needed for evolution, cytosine is unstable even at temperatures as cold as 0 degrees Celsius. If Cytosine is lacking, then it is impossible to have DNA. It is also impossible to have RNA.

For a related source, see below:
http://www.creationresearch.org/crsq/articles/36/36_4/abiogenesis.html

In conclusion, the thermal vents theory speculated on is nowhere near as strong as presented and it is clearly seen why not everyone in the evolutionary community is ready to jump on board. We also have the problems of the Second Law of Thermodynamics and probability. These will be treated again in other posts.

‘If there were a basic principle of matter which somehow drove organic systems toward life, its existence should easily be demonstrable in the laboratory. One could, for instance, take a swimming bath to represent the primordial soup. Fill it with any chemicals of a non-biological nature you please. Pump any gases over it, or through it, you please, and shine any kind of radiation on it that takes your fancy. Let the experiment proceed for a year and see how many of those 2,000 enzymes [proteins produced by living cells] have appeared in the bath. I will give the answer, and so save the time and trouble and expense of actually doing the experiment. You would find nothing at all, except possibly for a tarry sludge composed of amino acids and other simple organic chemicals. How can I be so confident of this statement? Well, if it were otherwise, the experiment would long since have been done and would be well-known and famous throughout the world. The cost of it would be trivial compared to the cost of landing a man on the Moon… . In short there is not a shred of objective evidence to support the hypothesis that life began in an organic soup here on the Earth.’

Sir Fred Hoyle, British physicist and astronomer, The Intelligent Universe, Michael Joseph, London, 1983, pp. 20-21, 23.

I should add that Sir Fred Hoyle was a proponent of 'intelligent cosmic control.' This quote is very much in line with the context.

Marcsana said...

Here is a much shorter posting about probability. Statisticians say that for something to be impossible, the probability has to be 10 to the 50th power.

When you wrote about probability, you wrote this:
“The same is true of forming molecules. Even if the chances of forming a particular molecule are very tiny in one trial, if there are billions upon billions of trials, the chances of that molecule being formed are very great.”

To quote the article you cited, here is what creationists allegedly do wrong (this is from http://www.talkorigins.org/faqs/abioprob/abioprob.html):

“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.”

Number 1 is wrong. No we don’t. We calculate an average size protein. What is wrong with number 2, by the way? Number 3 is just plain wrong. Probability doesn’t work that way. Probability says that for each attempt, the odds are for this. You can’t look at all the attempts as an aggregate whole. Each individual attempt has the same odds of assembling itself. The lottery example holds no water. This assumes there is a prize and since evolution is undirected, there is no “prize.” Please consider these words:
“Evolutionists often try to bluff their way out of this problem by using analogies to argue that improbable things happen every day, so why should the naturalistic origin of life be considered impossible. For example, they say the odds of winning the lottery are pretty remote, but someone wins it every week. Or, the chances of getting the particular arrangement of cards obtained by shuffling a deck is remote, but a rare combination happens every time the cards are shuffled. Or the arrangement of the sand grains in a pile of sand obtained by randomly pouring the sand is extremely complex, but this complex and improbable arrangement did occur as a result of random processes. Or the exact combination and arrangement of people walking across a busy city street is highly improbable, but such improbable arrangements happen all the time. So they argue from these analogies to try to dilute the force of this powerful argument for creation.

You probably realize there is something illogical about this line of argument. But what is it?

In all the analogies cited above, there has to be an outcome. Someone has to win the lottery. There will be an arrangement of cards. There will be a pile of sand. There will be people walking across the busy street. By contrast, in the processes by which life is supposed to have formed, there need not necessarily be an outcome. Indeed the probabilities argue against any outcome. That is the whole point of the argument.”
http://www.answersingenesis.org/creation/v17/i2/chance.asp

Number 4 is wrong too. And number 5 is also ridiculous. Please read this article:
http://www.answersingenesis.org/tj/v11/i1/enzymes.asp

As with most things, evolutionists require that things be much simpler than they really are. Even all this aside, the probabilities are so high for the first cell to form, that it just can’t happen. There isn’t enough time in the universe.

This model was shown in http://www.talkorigins.org/faqs/abioprob/abioprob.html#Search

Creationists do this with probability:
Simple chemicals---bacteria

Evolutionists say it’s not that simple:
Simple chemicals—polymers—replicating polymers—hypercycle—protobiont—bacteria

But you still don’t get around information theory arguments. And this still doesn’t explain the first protein very well. Nor does it offer how any of this is possible within the constraints of what we know about biology. And it doesn’t show how each of these made those small leaps since it requires increasingly more information and proteins.

http://www.answersingenesis.org/articles/wow/can-natural-processes-explain#fnMark_1_19_1