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Author Topic:   The Simplest Protein of Life
BoredomSetsIn
Junior Member (Idle past 1752 days)
Posts: 2
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Message 1 of 281 (674632)
10-01-2012 9:00 AM


The Ribonuclease protein is the simplest protein that we know of, and can be considered the most basic building block of a cell. It is made from 124 amino acids, the first one in the strand being Lysine. There are 17 different amino acids in this protein, so to simplify it, lets say that there is a 1/17 chance of Lysine coming first. The second one in line, is Glutamic acid. The odds of it coming second are 1/289. Then comes Threonine. Chances of it coming 3rd are 1/4913. If we continue down the list, the end result is 1 followed by 552 zeroes. To put that in perspective, It's the same as a poker player drawing 19 royal flushes in a row, with out trading in any cards. If this is a million: 1,000,000. And this is a billion: 1,000,000,000. And this is a trillion: 1,000,000,000,000, We still have 546, 543, and 540 zeroes to go, respectively. To conclude, I think the chances of a living cell forming from chemicals that just happened to bond, is ridiculously unlikely.
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Message 2 of 281 (674634)
10-01-2012 9:55 AM


Thread Copied from Proposed New Topics Forum
Thread copied here from the The Simplest Protein of Life thread in the Proposed New Topics forum.
    
Dr Adequate
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Message 3 of 281 (674636)
10-01-2012 10:27 AM
Reply to: Message 1 by BoredomSetsIn
10-01-2012 9:00 AM


To conclude, I think the chances of a living cell forming from chemicals that just happened to bond, is ridiculously unlikely.

And every biologist in the world agrees with you. That is indeed not how living cells are produced: the chemicals don't "just happen to bond". Well done.

Edited by Dr Adequate, : No reason given.


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Taq
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Message 4 of 281 (674661)
10-01-2012 1:55 PM
Reply to: Message 1 by BoredomSetsIn
10-01-2012 9:00 AM


The Ribonuclease protein is the simplest protein that we know of, and can be considered the most basic building block of a cell. It is made from 124 amino acids, the first one in the strand being Lysine.

Insulin is around 50 amino acids, and there are simple ferredoxins such as the 78 amino acid ferredoxin from Bacillus schlegelii :

http://www.ncbi.nlm.nih.gov/protein/BAA06187.1

There are 17 different amino acids in this protein, so to simplify it, lets say that there is a 1/17 chance of Lysine coming first. The second one in line, is Glutamic acid. The odds of it coming second are 1/289. Then comes Threonine. Chances of it coming 3rd are 1/4913. If we continue down the list, the end result is 1 followed by 552 zeroes. To put that in perspective, It's the same as a poker player drawing 19 royal flushes in a row, with out trading in any cards. If this is a million: 1,000,000. And this is a billion: 1,000,000,000. And this is a trillion: 1,000,000,000,000, We still have 546, 543, and 540 zeroes to go, respectively. To conclude, I think the chances of a living cell forming from chemicals that just happened to bond, is ridiculously unlikely.

You are committing the Sharpshooter fallacy. There is no reason that life must have this protein. There are trillions and trillions of other proteins that life could have developed early on. You are simply painting the bull's eye around this target and ignoring the fact that things could have been different.


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dwise1
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Message 5 of 281 (674682)
10-01-2012 2:55 PM
Reply to: Message 1 by BoredomSetsIn
10-01-2012 9:00 AM


Yet another boring presentation of that silly old creationist probability PRATT*.

What you describe, a protein being created by falling together by chance, is descriptive of creation ex nihilo, which most certainly is extremely improbable. Rather, we would expect a protein to have evolved from a predecessor, which is far more probable, approaching inevitable. You are falsely attributing the probability of a creation ex nihilo event to evolution, which is wrong on so many levels.

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. That is not the rule with proteins, as is evidenced by comparing the same protein in different organisms and which differs by several amino acids between species, even by tens of amino acids being different -- indeed, one form of creationist PRATT is to lie about what those comparison studies show. What do inter-species ribonuclease comparisons show?

To do a proper job of creating your probability analysis for creation ex nihilo (since it has nothing to do with evolution) would be to determine the exact requirements. For example, in the notes for their two-model class, Drs Thwaites and Awbrey give the example of a calcium-binding site on a protein. Consisting of 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. You would erroneously calculate the probability of that calcium-binding site just falling together ex nihilo as being (1/20)29 (there are 20 amino acids, not 17, so your original calculations were flawed in that respect as well), which would be 1.86e-38. However, because of the variety of amino acids that most of the positions would allow, the ex nihilo probability would actually be 3.05e-12, 26 orders of magnitude greater (ie, more probable). But then, neither calculation has anything to do with evolution, do they?

But then another mistake you made was assuming just one player, just one attempt. You just came up with a probability (which was wrong) for a single event, when actually that single event would be played out many times over, so in reality you would need to come up with the probability that, given a very large number of trials (each attempt is called a "trial"), you would never once have a single success. As it turns out, with enough trials the probability of constant failure becomes vanishingly small.

Let's use poker as an example. With 52 cards, there are 311,875,200 possible 5-card hands, so the probability of getting any one specific hand is 1/311,875,200 = 3.20641e-9. That probability is the same for a specific royal flush and for a specific hand full of nothing. Now, there are many more ways to get a hand full of nothing than there are to get a royal flush, so it is more probable to get a hand full of nothing than to get a royal flush.

Specifically, there are four ways to get a royal flush, so the probability of a royal flush (p) is 1.2825643e-8 and the probability against (q) is 0.999999987. Very unlikely that you would deal a royal flush in one single hand. But get 10,000,000 poker players to deal 100 hands each for a total of one billion hands and the probabilities reverse themselves such that p becomes 0.9999973 (very near dead certainty) while q becomes 2.6908776e-6 (very unlikely) -- it's around 50 million hands where the odds become 50/50.

Similarly, in your creation ex nihilo scenario of ribonuclease spontaneously forming, there would not be just one single trial, but rather a very large number of trials going on all around the single event you were dealing with. Assuming that proteins would form as you describe (they would not, though proteinoids, AKA "thermal proteins" as per Sidney Fox's research, would), then with all those other trials going on in parallel the probability that every single one would fail becomes smaller and smaller.

Which brings us to yet another of your many mistakes. I've just been dealt a hand. What is the probability of my having been dealt that particular hand? 3.20641e-9? No, the probability is 1.0, dead certainty. It is a fixed point in time; it has already happened. Nothing can possibly change the fact that that is the hand that I had just been dealt. Now, what is the probability that I will be dealt the exact same hand again? Now that would be 3.20641e-9.

IOW, it is meaningless to build a probability argument based on what has already happened. Because the probability of something that has already happened is and will always be 1.0, dead certainty.

That was all just scratching the surface of what's wrong with your claim.

And just out of curiosity, did you yourself perform those "calculations"? Or did you just simply crib it from another creationist? Would you care to reveal your source?

For further reading, you may read two of my pages: The "Random" Proteins Argument and The Bullfrog Affair. And as an example of calculating probabilities: MONKEY PROBABILITIES (MPROBS), a companion page to my own version of Dawkins' WEASEL, MONKEY.


* FOOTNOTE:
PRATT = "Point Refuted A Thousand Times", though that number is a gross underestimate. Creationist arguments consist primarily and often times entirely of false claims that have been addressed and refuted many times before, many of them decades ago. But creationists are still being fed those same old false claims and they keep presenting them as if they were actually worth something and we keep on repeating the same refutation over and over again. One person has described it as "slaying the dead." It doesn't matter how many times you tell your lies, they still will never be true. Goebbels was wrong.

Edited by dwise1, : Corrected two links


This message is a reply to:
 Message 1 by BoredomSetsIn, posted 10-01-2012 9:00 AM BoredomSetsIn has responded

Replies to this message:
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BoredomSetsIn
Junior Member (Idle past 1752 days)
Posts: 2
Joined: 10-01-2012


Message 6 of 281 (674718)
10-02-2012 6:33 AM
Reply to: Message 5 by dwise1
10-01-2012 2:55 PM


When did I ever say this has to do with evolution??

Let's go back to my question...

The Ribonuclease protein is the simplest protein that we know of, and can be considered the most basic building block of a cell. It is made from 124 amino acids, the first one in the strand being Lysine. There are 17 different amino acids in this protein, so to simplify it, lets say that there is a 1/17 chance of Lysine coming first. The second one in line, is Glutamic acid. The odds of it coming second are 1/289. Then comes Threonine. Chances of it coming 3rd are 1/4913. If we continue down the list, the end result is 1 followed by 552 zeroes. To put that in perspective, It's the same as a poker player drawing 19 royal flushes in a row, with out trading in any cards. If this is a million: 1,000,000. And this is a billion: 1,000,000,000. And this is a trillion: 1,000,000,000,000, We still have 546, 543, and 540 zeroes to go, respectively. To conclude, I think the chances of a living cell forming from chemicals that just happened to bond, is ridiculously unlikely.

First of all, bravo to all of you. The first person failed to respond properly, but I brought something away from the second and third persons posts.

"And every biologist in the world agrees with you. That is indeed not how living cells are produced: the chemicals don't "just happen to bond". Well done."

Maybe you can elaborate on that? I am unaware as to how the bonds form, so enlighten me.

"Insulin is around 50 amino acids, and there are simple ferredoxins such as the 78 amino acid ferredoxin from Bacillus schlegelii"

I have acknowledged that, but half the things in the link didn't make sense to me.

source 1..78
/organism="Bacillus schlegelii"
/db_xref="taxon:1484"
Protein 1..78
/product="ferredoxin"
mat_peptide 2..78
/product="ferredoxin"
Region 4..65
/region_name="COG1146"
/note="Ferredoxin [Energy production and conversion]"
/db_xref="CDD:31341"
Region 33..56
/region_name="Fer4"
/note="4Fe-4S binding domain; pfam00037"
/db_xref="CDD:200947"
CDS 1..78
/coded_by="D29804.1:8..244"
/note="7Fe type ferredoxin"
/transl_table=11

I did notice the 1..78. But I think a little more research is required before I come to conclusions.

"You are committing the Sharpshooter fallacy. There is no reason that life must have this protein. There are trillions and trillions of other proteins that life could have developed early on. You are simply painting the bull's eye around this target and ignoring the fact that things could have been different."

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.

This is taken from wikipedia. I'd think its probably pretty important. And if its not needed for life, why would it evolve.

And speaking of evolving...

"Rather, we would expect a protein to have evolved from a predecessor, which is far more probable, approaching inevitable."

I was unaware proteins could evolve...and of course something the human eye has never witnessed is inevitable.

"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.

"To do a proper job of creating your probability analysis for creation ex nihilo (since it has nothing to do with evolution) would be to determine the exact requirements. For example, in the notes for their two-model class, Drs Thwaites and Awbrey give the example of a calcium-binding site on a protein. Consisting of 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. You would erroneously calculate the probability of that calcium-binding site just falling together ex nihilo as being (1/20)29 (there are 20 amino acids, not 17, so your original calculations were flawed in that respect as well), which would be 1.86e-38. However, because of the variety of amino acids that most of the positions would allow, the ex nihilo probability would actually be 3.05e-12, 26 orders of magnitude greater (ie, more probable). But then, neither calculation has anything to do with evolution, do they?"

Actually, there are 24 amino acids. And I'm sorry, I guess the way I said it is rather vague.

"There are 17 different amino acids in this protein, -------->so to simplify it<-------, lets say that there is a 1/17 chance of Lysine coming first."

"But then another mistake you made was assuming just one player, just one attempt. You just came up with a probability (which was wrong) for a single event, when actually that single event would be played out many times over, so in reality you would need to come up with the probability that, given a very large number of trials (each attempt is called a "trial"), you would never once have a single success. As it turns out, with enough trials the probability of constant failure becomes vanishingly small."

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.

"Which brings us to yet another of your many mistakes. I've just been dealt a hand. What is the probability of my having been dealt that particular hand? 3.20641e-9? No, the probability is 1.0, dead certainty. It is a fixed point in time; it has already happened. Nothing can possibly change the fact that that is the hand that I had just been dealt. Now, what is the probability that I will be dealt the exact same hand again? Now that would be 3.20641e-9.

IOW, it is meaningless to build a probability argument based on what has already happened. Because the probability of something that has already happened is and will always be 1.0, dead certainty."

Yes, but we are talking about the chances of it forming, with out a creator. So, since we are talking about an unconfirmed theory, I believe its fine to talk about the chances of something happening like this.

And to answer you question, I did some of the calculations. The rest I got out of my biology book. But give me a break, I'm in grade 9.


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crashfrog
Inactive Member


Message 7 of 281 (674721)
10-02-2012 7:55 AM
Reply to: Message 6 by BoredomSetsIn
10-02-2012 6:33 AM


Yes, but we are talking about the chances of it forming, with out a creator.

Proteins don't form by being created by a creator; they form by the condensation reaction that creates peptide bonds. (A peptide bond is the C-N bond between two amino acids. It's called a condensation reaction because water comes out, the opposite of hydrolysis.)


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Coragyps
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Posts: 5292
From: Snyder, Texas, USA
Joined: 11-12-2002
Member Rating: 3.3


Message 8 of 281 (674723)
10-02-2012 9:56 AM
Reply to: Message 7 by crashfrog
10-02-2012 7:55 AM


And, in addition to that, the volcanic gas carbonyl sulfide promotes that peptide bond formation even in a "warm pond" of water.
http://www.ncbi.nlm.nih.gov/pubmed/15472077 is one link to one study on that....
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ringo
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(1)
Message 9 of 281 (674747)
10-02-2012 2:54 PM
Reply to: Message 6 by BoredomSetsIn
10-02-2012 6:33 AM


BoredomSetsIn writes:

I am unaware as to how the bonds form, so enlighten me.


Consider a room full of children, each one holding a toy. As they mill about aimlessly, a child sees another toy that he'd like to have, so he reaches for it. But the other child won't let go and he, in turn, reaches for the first child's toy. Soon all of the children are "bonded" together in pairs, held together by the toys that both children want.

The children are like protons and the toys are like electrons and the pairs of children are like hydrogen atoms, bonded together by a pair of electrons that they both want.

And it all happens naturally. The probability that the bonds will form is 100%.


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Blue Jay
Member (Idle past 254 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
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(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.


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shadow71
Member (Idle past 490 days)
Posts: 706
From: Joliet, il, USA
Joined: 08-31-2010


Message 11 of 281 (674767)
10-02-2012 7:28 PM
Reply to: Message 9 by ringo
10-02-2012 2:54 PM


ringo writes:

Consider a room full of children, each one holding a toy. As they mill about aimlessly, a child sees another toy that he'd like to have, so he reaches for it. But the other child won't let go and he, in turn, reaches for the first child's toy. Soon all of the children are "bonded" together in pairs, held together by the toys that both children want.
The children are like protons and the toys are like electrons and the pairs of children are like hydrogen atoms, bonded together by a pair of electrons that they both want.

And it all happens naturally. The probability that the bonds will form is 100%.

Can you tell us how the protons, electrons and hydrogen atoms came into existence?

The fallacy of your argument is that you assume everything happens naturally.
Do you have evidence for this natural origin?

What seems more logical, a planned reason for these events, or "well stuff happens" and we don't want to speculate about how it happened.
Just assume it was a natural event?
--------------------------------------------------------------------------------


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jar
Member
Posts: 29433
From: Texas!!
Joined: 04-20-2004
Member Rating: 2.3


(2)
Message 12 of 281 (674768)
10-02-2012 7:30 PM
Reply to: Message 11 by shadow71
10-02-2012 7:28 PM


Evidence
There is evidence of natural events.

There is no evidence of supernatural or non-natural events.

It really is that simple.


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shadow71
Member (Idle past 490 days)
Posts: 706
From: Joliet, il, USA
Joined: 08-31-2010


Message 13 of 281 (674770)
10-02-2012 7:43 PM
Reply to: Message 12 by jar
10-02-2012 7:30 PM


Re: Evidence
jar writes:

There is evidence of natural events.

What evidence is their of natural events that caused life?


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jar
Member
Posts: 29433
From: Texas!!
Joined: 04-20-2004
Member Rating: 2.3


(2)
Message 14 of 281 (674772)
10-02-2012 7:48 PM
Reply to: Message 13 by shadow71
10-02-2012 7:43 PM


Re: Evidence
More and more everyday.

But the point is that there is NO evidence of the supernatural or non-natural ever causing anything.


Anyone so limited that they can only spell a word one way is severely handicapped!

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Admin
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Posts: 12533
From: EvC Forum
Joined: 06-14-2002
Member Rating: 1.8


Message 15 of 281 (674781)
10-02-2012 9:28 PM
Reply to: Message 13 by shadow71
10-02-2012 7:43 PM


Re: Evidence
Hi Shadow,

If you'd like to discuss the simplest protein of life, which is the topic of this thread, then please continue participating here.

If you'd like to discuss the topics you're attempting to discuss here, which are not the topic of this thread, then please find threads where they would be on-topic, or propose a new thread over at Proposed New Topics.

Or just continue as you are and I will suspend your posting permissions in this forum.


--Percy
EvC Forum Director

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