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Author Topic:   The Simplest Protein of Life
Blue Jay
Member (Idle past 1483 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


(1)
Message 10 of 281 (674758)
10-02-2012 4:14 PM
Reply to: Message 6 by BoredomSetsIn
10-02-2012 6:33 AM


Hi, BoredomSetsIn.

Welcome to EvC!

Note: you can click the "peek" button to see the codes we use for quoting each other's messages, like I'm using to make these quote boxes:

BoredomSetsIn writes:

Taq writes:

Also, you falsely claim that every single one of those 124 amino acids positions on that protein are specified for one and only one amino acid.

I never said that. Read carefully. The other versions don't matter right now.

But, you calculated the probability of getting that specific sequence. So, while you didn't actually say that, it was implicit in the math you did.

-----

You also quoted this from Wikipedia:

quote:
Ribonucleoprotein (RNP) is a nucleoprotein that contains RNA, i.e. it is an association that combines ribonucleic acid and protein together. A few known examples include the ribosome, the enzyme telomerase, vault ribonucleoproteins, RNase P, hnRNP and small nuclear RNPs (snRNPs), which are implicated in pre-mRNA splicing (spliceosome) and are among the main components of the nucleolus. 'RNP' can also refer to ribonucleoprotein particles, distinct intracellular foci for post-transcriptional regulation.

"Ribonucleoprotein" and "ribonuclease" are not the same thing. Specifically, the "ribonuclease" you referred to was probably RNase A (which has 124 amino acid residues). Note that RNase A is not a ribonucleoprotein: it is just a protein. Ribonucleoproteins contains both amino acids and ribonucleic acids (RNA) in them, while RNase A has only amino acids.

-----

BoredomSetsIn writes:

Actually, even giving the protein the maximum time frame to form, that being about 4 billion years I think it is, as an educated guess, I think that there would have to be an attempt of forming the protein once almost every day. But honestly I have know idea. You do the math. And I'm unsure as to how long one of these trials would take anyway.

I'm not a molecular biologist, a biochemist or even very good at math, so I did a Google Search for "peptide bond rate," and that led me to this paper abstract. Here's a relevant quote:

quote:
The rate of peptide bond formation with unmodified Phe-tRNA(Phe) is estimated to be >300 s(-1).

So, at least some peptide bonds form at a rate of more than 300 per second. I think the rate depends on the amino-acid residue (in this case, phenylalanine), but I don't know that for sure. But, at the rate reported here, you could get about 200,000 attempts every single day, and that's only if you can only do one protein at a time. But, in a simple jar of chemical solution, you can easily have thousands or millions of individual reactions happening, side-by-side.

So, I would be willing to bet that it would take nowhere near 4 billion years for any specific 124-residue sequence to form by random chance. But, this increasingly-hypothetical example is really not very much like how these things happen in the real world, anyway, so it's of questionable relevance.


-Bluejay (a.k.a. Mantis, Thylacosmilus)

Darwin loves you.


This message is a reply to:
 Message 6 by BoredomSetsIn, posted 10-02-2012 6:33 AM BoredomSetsIn has not yet responded

  
Blue Jay
Member (Idle past 1483 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


(1)
Message 30 of 281 (675211)
10-08-2012 12:36 PM
Reply to: Message 28 by zaius137
10-06-2012 1:09 AM


Re: Your case is lost...
Hi, Zaius.

I don't believe I've had the pleasure.

Forgive me, but I'm only going to quote a couple phrases from the exchange between you and dwise1 here:

zaius127 writes:

dwise1 writes:

In the real world, proteins are formed within the tissues of organisms with great regularity through mechanisms that are fairly well understood ....

I think a high school student can draw the conclusion that this participant is talking about the forming of a protein in a pre-biotic environment.

Dwise1's argument is that the specific protein in question (RNasa A) did not form in a prebiotic soup: rather, it is formed in the cells of living organisms. Some other peptide (possibly a much shorter one) was formed in a prebiotic soup or somesuch, and the sequence was gradually edited over long periods of time in a decidedly non-random fashion, until it became the 124-acid sequence that it is today.

I realize that probably neither you nor BoredomSetsIn accepts that this is how the protein formed, but this is how evolutionists think this protein formed. So, math questioning the feasibility of a modern protein forming randomly in prebiotic conditions is not relevant.

If you or BoredomSetsIn were able to provide some math demonstrating the infeasibility of forming a random peptide and selectively editing it over billions of years until it looks like modern RNase A, then your math would be relevant to the evolution/creation debate.

zaius137 writes:

In an uncontrolled environment, who is to say what natural amino-acids are floating around. My point is that you cannot pick out 22 or so and disregard the other possible candidates for forming a polypeptide (a protein). This is like stacking the deck prior to drawing the card.

Actually, I kind of agree with you here, but only kind of. I have no idea why life uses only 20-22 amino acids. Maybe the other 480 were less available, and were thus not incorporated, or maybe they were less suitable, and were weeded out early in the selective process---this is beyond my expertise.

But, I have to imagine that, whether the origin of life was natural or designed, the exclusive use of those amino acids was not entirely random: those 20-22 acids were used because they filled the role better than others would have.

So, perhaps a compromise is best. We'd need to figure out which amino acids might have been available, and which amino acids were likely to be dropped because of unsuitability. But, certainly it is reasonable to count more than just 22 amino acids as candidates for protein production.

I do not think this will significantly alter the probabilities, though, because it's a change of 1 order of magnitude, which would shift the exponent on the probability from 111 to 110. Once the exponents get that high, one more zero isn't that big a deal.


-Bluejay (a.k.a. Mantis, Thylacosmilus)

Darwin loves you.


This message is a reply to:
 Message 28 by zaius137, posted 10-06-2012 1:09 AM zaius137 has not yet responded

Replies to this message:
 Message 31 by onifre, posted 10-08-2012 1:04 PM Blue Jay has not yet responded
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Blue Jay
Member (Idle past 1483 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


(1)
Message 39 of 281 (675635)
10-13-2012 5:38 PM
Reply to: Message 34 by zaius137
10-13-2012 3:21 AM


Hi, Zaius.

zaius137 writes:

Taq writes:

Let's use another card analogy. You deal yourself a five card hand. You then calculate the odds of getting that hand, and it is quite high. You then claim that you must be extremely lucky for getting such a hand. This is the Sharpshooter Fallacy.

Maybe you do not understand probability; it must describe a predicted outcome. The five cards you chose followed a prediction or else you are not testing a probability, you are gathering data. Funny, it is like betting on a horse race after the race is over… I like those odds.

So, since you can point out how Taq's deliberately fallacious analogy of your fallacious argument is fallacious, does this mean you understand that your original argument is fallacious?


-Bluejay (a.k.a. Mantis, Thylacosmilus)

Darwin loves you.


This message is a reply to:
 Message 34 by zaius137, posted 10-13-2012 3:21 AM zaius137 has not yet responded

  
Blue Jay
Member (Idle past 1483 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


(1)
Message 52 of 281 (675729)
10-15-2012 10:17 AM
Reply to: Message 46 by zaius137
10-15-2012 1:42 AM


Borel's limit
Hi, Zaius.

zaius137 writes:

For instance this number is not only higher that the total number of atoms in the universe it also exceeds Borel’s limit (10^50) which basically sets a limit on the total number of chemical reactions that could have taken place since the Big Bang.

I'd never heard of Borel's limit before, so I Googled it. After reading two or three short articles on it, I am obviously still not a world authority on the topic; I am, however, reasonably certain that you are not using it correctly here.

It turns out that there is something that creationists regularly call "Borel's law," and it involves the number 1050, so I assume this is what you were talking about.

However, what it states is both very different from what you proposed and very mundane in comparison: basically, Borel's law states that very improbable events simply do not occur. Émile Borel proposed that the value 1:1050 marks the probability threshold beyond which events are effectively impossible.

Of course, this law only works if the event is due to random chance. Here's an example from the first Google hit (which is an essay by Dr Loren Cobb, a mathematician at the University of Colorado):

quote:
In one small corner of the great San Luis valley of Colorado, near the border of New Mexico, there is a dramatic sight: thirty square miles of arid sand dunes, looking for all the world as though a piece of the Sahara desert had been dropped onto the valley floor. One wouldn't be shocked to see a caravan of camels winding their way through the 700-foot-high dunes.

What is the probability that all of that sand ended up in that tiny area of the valley by chance? If we were to follow the line of thought advocated by creationists, we would calculate the probability that each grain of sand wound up purely by chance in the 30 square mile zone of the valley, which is 8500 square miles in area. By my conservative estimate there are at least 1020 grains of sand in the dunes, and so it turns out that the probability that all these grains of sand drifted into the given zone is 16 orders of magnitude smaller than the threshold for impossibility stated in "Borel's Law." In other words, by creationist logic, the sand dunes could not have originated from a natural process. God must have put them there!


Source

So, if all that sand drifted randomly into that portion of the San Luis valley, it would have violated "Borel's law." However, if we accept "Borel's law" as accurate, it's still pretty easy to see how that sand could still have gotten there without violating "Borel's law," if non-random processes such as the wind and local topography interacted to influence the behavior of the sand.

Does this make sense?

Edited by Blue Jay, : two "all"s


-Bluejay (a.k.a. Mantis, Thylacosmilus)

Darwin loves you.


This message is a reply to:
 Message 46 by zaius137, posted 10-15-2012 1:42 AM zaius137 has not yet responded

  
Blue Jay
Member (Idle past 1483 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


Message 58 of 281 (675738)
10-15-2012 11:48 AM
Reply to: Message 44 by Alfred Maddenstein
10-14-2012 9:26 PM


Re: Your case is lost...
Hi, Alfred.

Alfred Maddenstein writes:

Life is a system of death-avoiding machines, Percy.

I think you're anthropomorphizing the machine a bit here. I wouldn't characterize life as "death-avoiding," because that also sort of entails anthropomorphizing death. Rather, I would characterize it as "self-sustaining." But, that kind of undermines your argument.

Alfred Maddenstein writes:

Your suggestion that the putative ancient proteins were less of an intricate affair implies that death could be more merciful at any place and time than it is known to be presently.

Are you arguing that complex proteins are better survivors than simple proteins?

If you aren't, then you're probably too far off-topic for me to follow you there.
If you are, then you're just wrong.


-Bluejay (a.k.a. Mantis, Thylacosmilus)

Darwin loves you.


This message is a reply to:
 Message 44 by Alfred Maddenstein, posted 10-14-2012 9:26 PM Alfred Maddenstein has responded

Replies to this message:
 Message 62 by Alfred Maddenstein, posted 10-15-2012 12:31 PM Blue Jay has acknowledged this reply

  
Blue Jay
Member (Idle past 1483 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


Message 106 of 281 (675883)
10-16-2012 11:45 PM
Reply to: Message 95 by Percy
10-16-2012 2:26 PM


Re: Your case is lost...
Hi, Percy.

Percy writes:

While there are some conjectures and hypotheses, we don't really know.

But one thing we're fairly sure of is that the molecules of life, including proteins, did not form by way of all the necessary atoms and molecules just happening to come together all at once in the right order by chance.

I think it's fair to say that the scientific explanation includes something forming by random chance. So, presumably, once we have a handle on what that first proto-living thing was, we could theoretically do these sort of calculations on the probabilities involved.


-Bluejay (a.k.a. Mantis, Thylacosmilus)

Darwin loves you.


This message is a reply to:
 Message 95 by Percy, posted 10-16-2012 2:26 PM Percy has acknowledged this reply

  
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