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Author Topic:   The Simplest Protein of Life
Percy
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Posts: 18806
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.2


(2)
Message 32 of 281 (675221)
10-08-2012 6:00 PM
Reply to: Message 30 by Blue Jay
10-08-2012 12:36 PM


Re: Your case is lost...
Blue Jay writes:

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.

Just to put a finer point on it, we already know that the random formation of any modern protein out of a prebiotic soup is incredibly unlikely. That's why we don't think they formed that way.

If they're interested in some evolutionary conjectures about how the first proteins might have formed then they should just let us know. Suffice to say for now that the first proteins likely bore very little resemblance to any modern protein.

--Percy


This message is a reply to:
 Message 30 by Blue Jay, posted 10-08-2012 12:36 PM Blue Jay has not yet responded

Replies to this message:
 Message 44 by Alfred Maddenstein, posted 10-14-2012 9:26 PM Percy has responded

    
Percy
Member
Posts: 18806
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.2


(2)
Message 35 of 281 (675616)
10-13-2012 8:25 AM
Reply to: Message 34 by zaius137
10-13-2012 3:21 AM


zaius137 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.

Maybe you do not understand the Sharpshooter Fallacy. It means you're calculating the probability of the wrong thing. If you fire a gun at a blank target where the goal is to simply hit the target, but you then draw a bulls eye around the bullet hole and calculate the odds of hitting that precise point on the target then you are guilty of the Sharpshooter Fallacy. The proper probability to calculate is the odds for putting a bullet hole anywhere on the target.

In the cards analogy the proper probability to calculate is the odds of getting any hand that is better than anyone else's in the game. You're committing the Sharpshooter Fallacy if you instead calculate the odds of getting the specific cards in your hand.

When it comes to a protein that successfully carries out a specific biological role, the proper probability to calculate is the odds of producing any protein that successfully fills that role. If you instead calculate the odds of producing the specific sequence of amino acids in that protein then you're committing the Sharpshooter Fallacy.

So if Yockey et al's calculation is correct that there are 2.3 x 1093 possible functional cytochrome C protein sequences, the odds of obtaining one of them improve substantially, especially in a process of repeated cycles of selection of mutated candidates.

--Percy


This message is a reply to:
 Message 34 by zaius137, posted 10-13-2012 3:21 AM zaius137 has responded

Replies to this message:
 Message 37 by zaius137, posted 10-13-2012 1:44 PM Percy has responded

    
Percy
Member
Posts: 18806
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.2


(2)
Message 41 of 281 (675663)
10-14-2012 9:43 AM
Reply to: Message 37 by zaius137
10-13-2012 1:44 PM


zaius137 writes:

In the cards analogy the proper probability to calculate is the odds of getting any hand that is better than anyone else's in the game. You're committing the Sharpshooter Fallacy if you instead calculate the odds of getting the specific cards in your hand.

Both of these “preferred outcomes” can be assigned probability. Predicting the specific probability of drawing certain cards out of a deck is not a fallacy.

You're still misunderstanding the Sharpshooter Fallacy. You can calculate the odds of having the best hand at the table, and that's not a fallacy. And you can calculate the odds of having been dealt the specific cards in your hand, and that's not a fallacy. But if you calculate the odds of having been dealt the specific cards in your hand when what you needed was the odds of having the best hand at the table, then you've just committed the Sharpshooter Fallacy. It means that you calculated the odds of what specifically happened to cause the outcome (winning) instead of calculating the odds of any of the set of things that could have caused the outcome.

So if Yockey et al's calculation is correct that there are 2.3 x 1093 possible functional cytochrome C protein sequences, the odds of obtaining one of them improve substantially, especially in a process of repeated cycles of selection of mutated candidates.

Please give me a direct citation of Yockey’s calculation in this regard, I can not find it.

I don't know why you're having trouble finding it since it's the Yockey citation you provided in your Message 34:

"Importantly, Hubert Yockey has done a careful study in which he calculated that there are a minimum of 2.3 x 1093 possible functional cytochrome c protein sequences, based on these genetic mutational analyses (Hampsey et al. 1986; Hampsey et al. 1988; Yockey 1992, Ch. 6, p. 254). "
http://www.talkorigins.org/...ction4.html#protein_redundancy

So if there are "2.3 x 1093 possible functional cytochrome c protein sequences" then the odds you need to calculate are not for one specific protein sequence (the Sharpshooter Fallacy) but the odds for obtaining any in the set of 2.3 x 1093 sequences.

--Percy

Edited by Percy, : Fix message link.

Edited by Percy, : Fix link to Yockey quote.


This message is a reply to:
 Message 37 by zaius137, posted 10-13-2012 1:44 PM zaius137 has responded

Replies to this message:
 Message 42 by zaius137, posted 10-14-2012 4:28 PM Percy has responded
 Message 45 by NoNukes, posted 10-14-2012 9:52 PM Percy has responded

    
Percy
Member
Posts: 18806
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.2


(2)
Message 43 of 281 (675684)
10-14-2012 4:44 PM
Reply to: Message 42 by zaius137
10-14-2012 4:28 PM


Re: don’t blow a gasket
Hi Zaius,

I take it that your off-topic response means that you don't accept that what you're doing constitutes a fallacy. If it's that you don't understand why it's a fallacy then could you ask some questions so that we can gain some idea of where the problem lies so that we can try to clear this up? Of if you really believe this is an Occam's razor issue then could you explain where the unnecessary complexity lies?

But it's important we don't forget your other error of calculating probabilities for sudden de novo creation of proteins. Biologists believe such occurrences are as unlikely as you do. Evolution is a gradual and incremental process.

--Percy


This message is a reply to:
 Message 42 by zaius137, posted 10-14-2012 4:28 PM zaius137 has responded

Replies to this message:
 Message 46 by zaius137, posted 10-15-2012 1:42 AM Percy has responded

    
Percy
Member
Posts: 18806
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.2


Message 51 of 281 (675725)
10-15-2012 8:58 AM
Reply to: Message 45 by NoNukes
10-14-2012 9:52 PM


NoNukes writes:

I think Taq provided the citation. Message 33 belongs to Taq. Zaius137 did referred to the quote in a later message, but not in a way that ought to make him responsible for the initial citation. I think it is legitimate for zaius137 to ask for a source.

Whoops, thanks! I evidently accidentally hit "3" instead of "4", Zaius's was the next message 34. I fixed my link to Zaius's message. I know Taq provided the original citation, but when Zaius quoted it he included it, and since I copied Zaius's quote I unwittingly included a bad link, which I just fixed, and here it is again:

http://www.talkorigins.org/...ction4.html#protein_redundancy

Hopefully the correct links will help Zaius explain how his misuse of probability constitutes an example of Occam's razor.

--Percy


This message is a reply to:
 Message 45 by NoNukes, posted 10-14-2012 9:52 PM NoNukes has acknowledged this reply

    
Percy
Member
Posts: 18806
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.2


(1)
Message 84 of 281 (675811)
10-16-2012 9:52 AM
Reply to: Message 44 by Alfred Maddenstein
10-14-2012 9:26 PM


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

We understand you don't accept evolution, but understanding evolution doesn't require accepting it. In fact, it makes much more sense to reject a position you understand than one you don't.

What we're trying to explain in this thread is that evolution doesn't believe that the first proteins just popped spontaneously and randomly into existence. We all agree that that would be incredibly unlikely.

As a sort of side issue we're also trying to explain that calculating the odds of a specific protein forming suddenly and randomly is the wrong problem. It's a side issue because evolution doesn't believe that's how the first proteins formed. In this case we're just trying to correct the misunderstanding about probability. Had proteins actually formed suddenly and randomly then you'd want to calculate the odds of obtaining any protein that could be successful, not just the specific protein that was actually created.

--Percy


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 94 by Alfred Maddenstein, posted 10-16-2012 12:39 PM Percy has responded

    
Percy
Member
Posts: 18806
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.2


(1)
Message 85 of 281 (675815)
10-16-2012 10:45 AM
Reply to: Message 46 by zaius137
10-15-2012 1:42 AM


Re: don’t blow a gasket
zaius137 writes:

My point is that there must be a desired outcome prior to testing an outcome. Consider the following relation….

Singular Probability = Desired outcome/possible outcomes

I can use your equation to explain the mistake in thinking that you're making. Let's say you're playing roulette and you bet on red. The ball lands on 34 red, you win. What were the odds of you winning.

If you calculate the odds of landing on 34 red, which is 1/38, then you are guilty of the Sharpshooter fallacy. The odds you should be calculating are 18/38, because the ball had 18 chances out of 38 of landing on a red slot.

Applied to the spontaneous random formation of a protein (which isn't how evolution believes the first proteins came about, we're just explaining this error in using probability as a side issue), this means that instead of calculating the odds of a specific sequence of amino acids coming together, you must instead calculate the odds of any sequence of amino acids coming together that can perform that function.

I cannot deny the context of the used quotation because I do not have the actual material to form an objection to its use.

Here again is the link to webpage where the quote was found:

http://www.talkorigins.org/faqs/comdesc/section4.html

And here's the quote again, which is about 20% down the document:

"Importantly, Hubert Yockey has done a careful study in which he calculated that there are a minimum of 2.3 x 1093 possible functional cytochrome c protein sequences, based on these genetic mutational analyses (Hampsey et al. 1986; Hampsey et al. 1988; Yockey 1992, Ch. 6, p. 254). "

So you're saying that you're not sure you can accept this claim because you can't examine the three citations, one of which is to a book by Yockey titled Information Theory and Molecular Biology. I don't have the book either, but here are links to the abstracts of the papers, and these are the papers that Yockey must have drawn upon for his book, since he's an author on neither paper:

The abstracts describe research investigating how much variation iso-1-cytochrome can tolerate while still performing its function. The probability of forming one these variations is what must be calculated, not the probability of forming the specific version of the protein that actually happened. If you calculate the probability of forming that specific version of the protein then you're committing the Sharpshooter Fallacy.

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. So I am pointing out that since the possible number of chemical reactions in the universe was exceeded by 45 orders of magnitude there could never be 2.3 x 10^93 configurations. I simply need to read the citation.

Independent of whether the 2.3 x 1093 figure attributed to Yockey is correct, what it represents is the number of possibilities, not the number of things that have actually happened. This is basic probability, not sure why you're having a problem with this. I hope you're not falling under Alfred's sway, who seems to reject both math and science.

--Percy

Edited by Percy, : Grammar.


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

Replies to this message:
 Message 89 by Taq, posted 10-16-2012 11:09 AM Percy has acknowledged this reply

    
Percy
Member
Posts: 18806
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.2


(1)
Message 95 of 281 (675851)
10-16-2012 2:26 PM
Reply to: Message 94 by Alfred Maddenstein
10-16-2012 12:39 PM


Re: Your case is lost...
Alfred Maddenstein writes:

So, Percy, could you specify for the cat your beliefs as to how exactly the first proteins came about and what they were?

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.

--Percy


This message is a reply to:
 Message 94 by Alfred Maddenstein, posted 10-16-2012 12:39 PM Alfred Maddenstein has responded

Replies to this message:
 Message 106 by Blue Jay, posted 10-16-2012 11:45 PM Percy has acknowledged this reply
 Message 107 by Alfred Maddenstein, posted 10-17-2012 2:32 AM Percy has responded

    
Percy
Member
Posts: 18806
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.2


(2)
Message 108 of 281 (675890)
10-17-2012 8:01 AM
Reply to: Message 107 by Alfred Maddenstein
10-17-2012 2:32 AM


Re: Your case is lost...
Alfred Maddenstein writes:

Any known system of death escaping machines is way too intricate to have self-assembled by chance all at once. Yet gradualism is not too convincing a proposal either given how deadly is the Mother Nature's well known nature.

I'll ignore the rather poetic but scientifically questionable characterization of lifeforms as death avoiding machines and just make a couple comments about the rest. You're reasoning for why the first protein didn't come about by random chance makes perfect sense and is the same as everyone else's: it's too incredibly unlikely.

But you're rejection of formation through gradual change by a process of successive cycles of modification and selection has no corresponding rationale, plus one of the biggest dangers in Mother Nature is other life, which was absent before life began. A beaker of proteins dumped into a pond today would be quickly consumed and disappear, but not in the ancient past before there was any life.

--Percy


This message is a reply to:
 Message 107 by Alfred Maddenstein, posted 10-17-2012 2:32 AM Alfred Maddenstein has responded

Replies to this message:
 Message 110 by Alfred Maddenstein, posted 10-17-2012 12:40 PM Percy has responded

    
Percy
Member
Posts: 18806
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.2


(1)
Message 114 of 281 (675957)
10-17-2012 7:28 PM
Reply to: Message 110 by Alfred Maddenstein
10-17-2012 12:40 PM


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

You're again drifting off topic. We're not trying to answer the question, "Can we convince Alfred Maddenstein that life developed through a gradual process of successive cycles of modification and selection?" We're trying to answer the question, "How does evolution believe the first proteins came about?" You don't have to believe that the gradual process is the way it really happened, but please do believe that that's what evolution says.

About the rest, I'm not sure why you believe water degrades organic molecules. Life requires water, and if water were antagonistic to life then there would be no life on this wet planet whose surface is 3/4 aqueous.

If you think the opinions of Kelvin and Helmholtz are relevant (to the actual topic) then you'll have to describe those opinions.

That the inert matter must precede life necessarily is just a belief without any firm foundations.

And yet just breathing incorporates oxygen into living matter.

--Percy


This message is a reply to:
 Message 110 by Alfred Maddenstein, posted 10-17-2012 12:40 PM Alfred Maddenstein has responded

Replies to this message:
 Message 119 by Alfred Maddenstein, posted 10-17-2012 11:00 PM Percy has responded

    
Percy
Member
Posts: 18806
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.2


Message 123 of 281 (675994)
10-18-2012 8:54 AM
Reply to: Message 119 by Alfred Maddenstein
10-17-2012 11:00 PM


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

If you think something Shapiro has to say is relevant to the thread's actual topic then go ahead and tell us about it.

The rest of your post pretty clearly has nothing to do with the topic.

--Percy


This message is a reply to:
 Message 119 by Alfred Maddenstein, posted 10-17-2012 11:00 PM Alfred Maddenstein has not yet responded

    
Percy
Member
Posts: 18806
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.2


Message 139 of 281 (676095)
10-19-2012 9:37 AM


Suggestion
I again suggest that we only reply to Al when he happens to touch rationally upon the topic.

--Percy


    
Percy
Member
Posts: 18806
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.2


Message 150 of 281 (676192)
10-20-2012 11:12 AM


Revised Suggestion
Revising my previous suggestion, I now suggest that we only reply to Al or ICANT (or anyone, for that matter) when they happen to touch rationally upon the topic. Something about the simplest protein, I think.

--Percy


Replies to this message:
 Message 152 by ICANT, posted 10-20-2012 11:22 AM Percy has responded

    
Percy
Member
Posts: 18806
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.2


Message 157 of 281 (676230)
10-20-2012 5:19 PM
Reply to: Message 152 by ICANT
10-20-2012 11:22 AM


Re: Revised Suggestion
ICANT writes:

Do you have any evidence of how the simplest protein or life form began to exist?

NoNukes already explained why this isn't the correct question, but let me answer anyway. There's very little 4 billion year-old evidence to be found, but we're very certain that however it happened it followed the same physical laws of the universe that we're familiar with today. It certainly didn't happen anything like the opening post suggests, with all the amino acids coming together in the correct order by chance because that would be incredibly unlikely.

Since proteins are manufactured by orders that are placed by the DNA in a cell, wouldn't the information in the DNA be required before the protein could begin to exist?

The opening post asks about the ribonuclease protein, which is relevant to one of the abiogenesis hypotheses where the first life used RNA instead of DNA. As has been pointed out in this thread many times, the ribonuclease protein of the earliest life may have borne little resemblance to modern versions.

--Percy


This message is a reply to:
 Message 152 by ICANT, posted 10-20-2012 11:22 AM ICANT has responded

Replies to this message:
 Message 174 by ICANT, posted 10-21-2012 1:56 PM Percy has responded

    
Percy
Member
Posts: 18806
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.2


Message 176 of 281 (676298)
10-21-2012 3:04 PM
Reply to: Message 174 by ICANT
10-21-2012 1:56 PM


Re: Revised Suggestion
Hi ICANT,

It is believed that the complex molecules of life and the information they contain developed over time through a process of repeated cycles of modification and selection, because this is the kind of process we observe in life today.

--Percy


This message is a reply to:
 Message 174 by ICANT, posted 10-21-2012 1:56 PM ICANT has responded

Replies to this message:
 Message 178 by ICANT, posted 10-21-2012 4:39 PM Percy has responded

    
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