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Author Topic:   Self-Replicating Molecules - Life's Building Blocks (Part II)
Posts: 5460
Joined: 05-02-2006
Member Rating: 2.8

Message 18 of 97 (612812)
04-19-2011 1:25 AM
Reply to: Message 13 by Hunter
04-18-2011 5:01 PM

Re: Probability
You say that you think it’s very possible that there was debris left behind from the life cycle of previous stars and planets, but have you ever really looked into or calculated the probability of one protein molecule forming from such debris or mineral like material. The probability of one single protein molecule randomly forming on its own is 2.02 in 10^321. This doesn't even touch the probability of thousands of these protein molecules forming into DNA strands; which turns out to be 1 in 10^40,000.
That one's so old its whiskers have whiskers growing on them. How long have you been feeding on creationist claims? A few years? Most of those claims are three decades or older and were soundly refuted almost immediately (ie, decades ago); on this forum, we use an abbreviation for them, PRATT, "Point Refuted A Thousand Times". And many critics of those claims have been studying them for nearly as long and have been active in discussing them with creationists. OTOH, very few creationists last very long in such discussions. Indeed, many of those who now oppose "creation science" creationism had been "creation science" creationists themselves, until they tried in vain to defend the indefensible and learned that those claims are false.
I know that's a helluva welcome to give you, but you deserve to hear the truth at least once. Stay, participate, learn.
Back to your probability claim. I know that you got it from another source, a book on the philosophy of religion -- which makes me wonder about their approach -- so I won't ask you to show us your work or your model. That's right, your model. You've undoubtedly heard the saying that figures don't lie, but liars sure can figure. The basis for that saying lies in yet another simple fact that is enshired in yet another familiar saying: Garbage in, garbage out. Which means here that the veracity of a probability calculation depends on the veracity of the model that it's based on.
Maybe this will help to explain things (my emphasis added):
Setting aside the improbability of protein molecules and DNA strands forming on their own, the chance that our universe could/would be laid out the way it is, is extremely improbable. It's 1 in 10^133, to be exact.
Now, we know how dice roll. We know how cards get shuffled and dealt. We know how a roulette wheel turns. We know how lottery balls produce the winning numbers. But just what the hell do we know about how the universe came to become the exact way that it did? With our knowledge of dice, cards, roulette wheels, and the lottery, we can calculate exact probabilities for those systems. With our extremely limited knowledge of every single aspect of the universe, just how are we supposed to produce anything close to an "exact" probability for the universe, both the extremely limited portion that we do know and the extremely vast portion that we do not?
An exact probability calculation requires complete knowledge of the system. Are you telling us that the authors of that book have complete knowledge of the universe? C'mon! We both know full well that such knowledge is humanly impossible. In fact, my own fundamentalist training emphasized that fact very explicitly and very heavily.
In order to produce an accurate, or at the very least reliable, probability calculation, you need to have a model that is itself accurate. What was your model for the protein probability? (since you presented it, I'm going to let you take responsibility for it -- ignoring for the moment that the fundamentalist approach to morality is one of shifting responsibility away from oneself) Based on past experience, let me guess:
What is the probability of a specific modern protein consisting of n amino acids coming together in one single attempt and with one single specific amino acid sequence?
Was that it? We've been through this canard far too many times. Creationism is P.T. Barnum's famous quote come to life: There's a sucker born every minute. And I say that with all due respect. (as per Woody Allen)
Are you expecting a modern protein to fall together from out of nothing? Who would expect such a thing? Evolutionary theory? No, evolutionary theory would posit that the modern protein had evolved from a pre-existing protein. Rather, the idea of a modern protein just falling together out of nothing is pure creationism. Word of advice: if you are going to criticize what somebody believes, you really should take a little time and effort to learn what they actually believe.
The next problem with this "model" is the requirement that the amino acids be in only one single specific sequence for this protein to work. That is wrong. Easy refutation: the same protein in different species are have different sequences. Indeed, we find that the differences in the same proteins in different species do indeed match what we would expect if evolution were right -- despite creationism's flagrantly false claims about proteins (oh, the things I could tell you!).
Now here's the less easy refutation. Many years ago, two professors at San Diego State University, Bill Thwaites and Frank Awbrey, had the only true "two-model" course. They gave half the lectures and professional creationists from the then-nearby Institute for Creation Research (ICR), literally the men who wrote the book on "creation science", gave the other half of the lectures. Since the students were able to learn what the actual evidence is, creationism never fared well. Thwaites and Awbrey finally had to discontinue the course because of the extreme pressure the Christian clubs exerted against the university administration. So much for Christians and Truth.
In their class notes, which was published by the university bookstore, they examined this claim. Here is my presentation of it on my website (which is no longer on-line since my webhost abruptly went out of the business):
Rather than brandying about a hypothetical protein, let's look at a specific case. In the class notes of Frank Awbrey & William Thwaites' creation/evolution class at UCSD (the Institute for Creation Research conducted half the lectures and Awbrey & Thwaites the other half), they give the example of a calcium binding site with 29 amino acid positions: only 2 positions (7%) require specific amino acids, 8 positions (28%) can be filled by any of 5 hydrophobic amino acids, 3 positions (10%) can be filled by any one of 4 other amino acids, 2 positions (7%) can be filled with two different amino acids, and 14 of the positions (48%) can be filled by virtually any of the 20 amino acids.
The sequence of the 15 specified positions is:
L* L*L* L*D D* D*G* I*D* EL* L*L* L*
L* = hydrophobic - Leu, Val, Ilu, Phe, or Met
Prob = (5/20)^8
D* = (a) Asp, Glu, Ser, or Asn
Prob = (4/20)^3
OR (b) theoretically also Gls or Thr
Prob = (6/20)^3
D = Asp
Prob = (1/20)
E = Glu
Prob = (1/20)
G* = Gly or Asp
Prob = (2/20)
I* = Ilu or Val
Prob = (2/20)
Remaining positions = any of 20
Prob = (20/20)^14 = 1^14 = 1
Total Prob = Prob(L*) * Prob(D*) * Prob(D) * Prob(E) * Prob(G*) * Prob(I*)
= (a) 3.05 x 10^(-12)
OR (b) 10.2 x 10^(-12)
Your own calculation of the probability of a functional order coming up (ie, the standard
creation science method) would be: (1/20)^29 = 1.86 x 10^(-38).

Comparing the lower probability to yours shows it to be 1.64 x 10^26 times greater.
This invalidates your colored-box-car analogy as it stands (to correct it, you would need to allow for a variety of different combinations) and it invalidates your probability calculations.
So if your model requires specific amino acid sequences, you now see that that is a false assumption.
The other problem is your single-step selection probabilities vs Dawkins' cumulative selection probabilities (as presented in Chapter 3 of The Blind Watchmaker). Your model undoubtedly is single-step, requiring each effort to start completely from scratch. That is not how evolution works -- remember my recommendation that you first learn that which you wish to refute? Evolutionary change is cumulative; each small step is from a point that was reached by a sequence of other small steps.
I have done the math! Have you? We do not have room here for me to present the entire essay, but I did do the math. In Dawkins' book, he described his WEASEL program that would generate a line from Shakespeare, "Methinks it is like a weasel", but he did not print the code. Many of us, including myself (back around 1990), wrote our own WEASEL programs, though I named mine MONKEY after Eddington's "infinite monkeys" (from my monkey.html page):

A. S. Eddington. The Nature of the Physical World: The Gifford Lectures, 1927:

... If I let my fingers wander idly over the keys of a typewriter it might happen that
my screed made an intelligible sentence. If an army of monkeys were strumming on
typewriters they might write all the books in the British Museum. The chance of
their doing so is decidedly more favourable than the chance of the molecules
returning to one half of the vessel.
Douglas Adams. The Hitchhikers' Guide to the Galaxy:

"Ford!" [Arthur] said, "there's an infinite number of monkeys outside who
want to talk to us about this script for Hamlet they've worked out."
Lennon and McCartney:

Everybody's got something to hide, except for me and my monkey!
RFC 2795: The Infinite Monkey Protocol Suite (IMPS)


This memo describes a protocol suite which supports an infinite
number of monkeys that sit at an infinite number of typewriters in
order to determine when they have either produced the entire works of
William Shakespeare or a good television show. The suite includes
communications and control protocols for monkeys and the
organizations that interact with them.

Years ago, Ian Musgrave collected these WEASEL programs and created a page that still exists: http://health.adelaide.edu.au/...m/Musgrave/essays/whale.htm On that page, he also notes that my own MONKEY was critisized in a book by one Walter ReMine, who claimed that it demonstrates Haldane's Dilemma, though that is doubtful.
Here's the bottom line. The standard target of MONKEY, although you could specify your own, was the Roman alphabet in alphabetical order. If we were to use single-step selection to attempt to produce it and it were to take our computer one millisecond for each attempt (remember, this was back when PCs ran at a few Norton Indices -- one NI equaled a true-blue-IBM PC/XT running a 8086 at 4.77 MHz), then it would take the program 20 times the current age of the universe, about 12 billion years, for the program to have one-in-a-million chance of producing the target. But using the cumulative-selection method, it took MONKEY less than a few minutes to produce the target -- nowadays, it would take a few seconds. I did the math. I analyzed the math, using Markovian chains:
This discussion was meant to compare the probabilities involved in the two methods of selection described by Richard Dawkins: single-step selection and cumulative selection. In applying both methods to the problem of randomly generating the alphabet in alphabetical order, we have seen that cumulative selection far surpasses single-step selection in obtaining the desired results. In calculating the probabilities involved in both methods, we have found that cumulative selection enjoys vastly greater chances for success than does single-step selection. In summary:
                   Single-Step      Cumulative:
10 copies 20 copies 100 copies
----------- --------- --------- ----------
Prob of success
in 100 steps: 1.6244 E -37 6.829 E -6 3.45 % 99.99 %
Number of Steps
Needed: 2.0 E 37 (est.) 21,136 383 42
Time needed to
succeed: 1.5 E 26 yr (est.) 22.15 min 41.5 sec 25.6 sec

Again, those times were from a time when we were running no faster than 10 NIs. Nowadays, we are running how many hundreds or even thousands of NIs -- I don't even know whether the Norton Index is even alive anymore. My interpretation of the results was that the real calculation was for cumulative selection to fail. If a generation fails to advance, no loss. If a generation were to back-slide one or two places, then OK it was still viable. The bottom line was that for cumulative selection to fail, then each and every generation had to fail. For each step (and it was different for each step, depending on how far we were from the target), we could calculate the probability of advancing, staying put, and back-sliding. The probability that we would not advance or would even back-slide each and every time became vanishingly small. It quite literally reached a point where the probability of success approached certainty, swamping out any possibility of failure.
But that's not the important part. I read Richard Dawkins' description of his WEASEL and do you know what my reaction was? Disbelief! I had already been an atheist for 25 years. I had already started learning about evolution and been supportive thereof thoroughly convinced thereof for at least 20 years. But I could not believe what he had just told me. So what did I do? I put it to the test! I wrote my own WEASEL, albeit named MONKEY, and I tested it. And, not believing the results I saw, I analyzed it! And in the end I found that it was right and I knew why it was right!
Would you do the same? Would you take a creationist claim and test it? Would you ever even question any creationist claim?
Here's one, from Kent Hovind. He notes that the sun is burning up 5 million tons of matter each second and he claims therefrom that 5 billion years ago the sun would have been so incredibly massive as to "such the earth in". What about that claim? He is almost right about that "5 million tons" -- actually, it's more like 4.7 million tons. So what about the rest of his claim? How would you approach this claim? Would you be skeptical? Or would you accept it at face value because he is also opposing that common evil, Evolution and an old earth? I had been skeptical about Dawkins' claim; could you be skeptical about Hovind's claim?
Do the math. Hovind, self-proclaimed expert at science and math because he had taught both subjects for 15 years (as he would repeatedly boast in his seminar tapes) -- in a Christian school that he had founded -- should have done at least that. But he hadn't. I emailed him with questions about where he had gotten this claim from and whether he had ever done the math. His "response" was to try, twice, to pick a fight with me over my AOL screenname, DWise1 (which has an incredibly mundane origin).
Do the math. Forget that Hovind seems to think that something like combustion is happening (I have evidence that that is what he thought), even though there is no loss of mass in combustion (something that anybody with even the slightest knowledge of chemistry would know). Forget that Hovind thinks that part of the sun's energy output is due to gravitational collapse (this being part-and-parcel of the "shrinking sun" claim), which would entail absolutely no mass loss. Calculate how many tons of matter would have been lost at that rate, 5 million tons per second, over a period of 5 billion years (5x109, since Europe has a different value for "billion"). Then compare that to the current mass of the sun. You will find that the total solar mass lost at the stated rate (calculated by measuring the sun's current energy output and plugging that into Einstein's e = mc2) over all those billions of years will only amount to a few hundredths of one percent of the sun's total mass. How far would the earth get "sucked in" by that additional mass? About 60,000 miles. How critical is that? Every year, the earth gets 1.5 million miles closer and farther away from the sun, which makes 60,000 miles insignificant. Do you know when we are 1.5 million miles closer to the sun? Around 4 January, in the dead of winter.
Chief Inspecteur Jacques Clouseau (yes, of the "Pink Panther" movie series) once said something very wise: I assume nothing! I suspect everything! (in the beginning of A Shot in the Dark as he unknowingly poked his nose into cold cream). Assume nothing! Suspect everything! Test everything!
There is also the research by Sidney Fox in the late 1970's. He showed that amino acids in a dilute solution and subject to high-enough temperatures -- or at lower temperatures with catalysts present -- will readily form into protein-like chains which have been called either thermal proteins or proteinoids (http://en.wikipedia.org/wiki/Proteinoid).
The up-shot here is that amino acids will produce protein-like chains very readily.
{Edit test - Adminnemooseus}
Edited by dwise1, : proteinoids
Edited by Adminnemooseus, : dwise1 had reported an editing quirk.
Edited by Admin, : Fix message width.

This message is a reply to:
 Message 13 by Hunter, posted 04-18-2011 5:01 PM Hunter has not replied

Replies to this message:
 Message 21 by Ed67, posted 04-23-2014 10:04 AM dwise1 has not replied

Posts: 5460
Joined: 05-02-2006
Member Rating: 2.8

Message 89 of 97 (816234)
08-01-2017 10:27 AM
Reply to: Message 87 by CRR
07-31-2017 7:33 PM

Re: Diversification of self-replicating molecules
{the cartoon}
Yes, that's the Catch-22 that creationists keep setting up to trap us in a lose-lose situation: abiogenesis cannot be proven to work until we've created life in the lab -- by creating life in the lab you've proven that it takes intelligence to create life and that it could not happen in nature.
A PhD Chemistry friend told me that it is impossible for us to cause a chemical reaction that cannot happen in nature. All we can do is to create the conditions for that reaction to happen, but if the reaction cannot happen in nature then we cannot force it to happen.
Therefore, if in the laboratory we can get the reactions going for life to start, then that would mean that those reactions would have also happened in nature under the right conditions. Your Catch-22 is bullshit.
So why don't we see new life springing up all the time in nature? Sidney Fox' experience with proteinoid microspheres offers the answer. Previous batches appeared to be unstable, degenerating after a few days. Then he created a new batch under sterile conditions which remained stable for years until they destroyed it because the research was completed. The reason why we do not see new life springing up all the time in nature is because of its name: food! The life that's already here just eats that stuff up!
Edited by dwise1, : Added "to trap us in a lose-lose situation"

This message is a reply to:
 Message 87 by CRR, posted 07-31-2017 7:33 PM CRR has replied

Replies to this message:
 Message 90 by CRR, posted 08-01-2017 8:16 PM dwise1 has not replied

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