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Author Topic:   The Simplest Protein of Life
onifre
Member (Idle past 1205 days)
Posts: 4854
From: Dark Side of the Moon
Joined: 02-20-2008


Message 31 of 281 (675212)
10-08-2012 1:04 PM
Reply to: Message 30 by Blue Jay
10-08-2012 12:36 PM


Re: Your case is lost...
but this is how evolutionists think this protein formed.

Don't you mean this is the leading theory in science? This is basic biology of life, right? ...or is there some other theory being taught at universities?

So, math questioning the feasibility of a modern protein forming randomly in prebiotic conditions is not relevant.

This seems to be the only point to continue to make in this thread, as both Zeus and Boredom keep swinging at strawmen.

- Oni


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

    
Percy
Member
Posts: 18842
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.5


(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

    
Taq
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Posts: 7999
Joined: 03-06-2009
Member Rating: 4.1


(2)
Message 33 of 281 (675276)
10-09-2012 3:45 PM
Reply to: Message 22 by zaius137
10-04-2012 2:47 AM


The common way evolutionists minimize the problems of forming a protein ex nihilo (I do not like this term but it seems you do) is to minimize the vastness of the very low probabilities. For example, the probability of drawing 19 royal flushes in a row.

What we do is point out the obvious flaws in your argument. If the ribonuclease was specified AHEAD OF TIME then you may have a point. If the only way for life to originate is by the formation of a specific 125 amino acid protein then you may have a point. However, you have established neither. Instead, you are specifying AFTERWARDS what had to form. You are painting the bull's eye around the bullet hole.

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.

Even worse, the opening post is using a MODERN protein, a protein that has passed through billions of years of evolution. For all we know, the origin of life may not have even needed a single protein.

Secondly, you minimize the replacing of a single amino acid in a protein. Did you know that a protein exhibits four critical organizations… by changing a single amino acid you may not significantly change one organization but will certainly alter one of the other critical organizations.

But does that change significantly alter function?

Human cytochrome C and yeast cytochrome C differ by 40% at the amino acid level. Guess what? You can replace yeast cytC with human cytC and the yeast doesn't even notice. The two proteins are functionally identical even though they differ by 40%.

"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

Let that sink in for a second. There are, at a minimum, 2.3 x 1093 possible functional cytochrome c protein sequences. How many ways are there to make a royal flush again?


This message is a reply to:
 Message 22 by zaius137, posted 10-04-2012 2:47 AM zaius137 has responded

Replies to this message:
 Message 34 by zaius137, posted 10-13-2012 3:21 AM Taq has responded

  
zaius137
Member (Idle past 1663 days)
Posts: 407
Joined: 05-08-2012


Message 34 of 281 (675609)
10-13-2012 3:21 AM
Reply to: Message 33 by Taq
10-09-2012 3:45 PM


Taq,

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.

Concerning proteins…

But does that change significantly alter function?

New findings show that a silent or synonymous mutation can and does change protein function even though it does not change amino acid sequence.

quote:
A mutation in a human gene that does not change the resulting amino acid can nevertheless change a protein's function, according to an online report from Science. The research marks the first time that the phenomenon has been confirmed in mammals. http://www.the-scientist.com/?articles.view/articleNo/24630

About the article in talkorigins…

Human cytochrome C and yeast cytochrome C differ by 40% at the amino acid level. Guess what? You can replace yeast cytC with human cytC and the yeast doesn't even notice. The two proteins are functionally identical even though they differ by 40%.

Read the article. The premise here is cytochrome C and other proteins can suggest common ancestry by applying the molecular clock hypothesis. The author claims a molecular clock in some proteins can imply genealogical relationships.

quote:
(C) Thus, similar ubiquitous genes indicate genealogical relationship: It follows that organisms which have similar sequences for ubiquitous proteins are genealogically related. Roughly, the more similar the sequences, the closer the genealogical relationship. http://www.talkorigins.org/...ction4.html#protein_redundancy

This claim is contrary to facts.

The problem is t hat there is no consistent way of mathematically producing an order between species and in particular dating their divergence by using molecular clocks in these ubiquitous genes. If you could, then producing a common linage of descent and dates between common ancestors would be no problem. To date success in this area is bleak to say the least.

Theoretically, you could compare the cytochrome C in humans and that in yeast and using a uniform mutation rate you could determine how many years there are between divergence of the two organisms (Linus Pauling and Emile Zuckerkandl).

Now if you also use other proteins in those same organisms and compare them there should be some agreement in those dates you derive. I like the idea that the author included hemoglobin and cytochrome C in the same article. Consider the following findings between carp and humans…

quote:
"But there is an additional twist to the clock hypothesis. As we saw above, different proteins exhibit different degrees of interspecies variation. While haemoglobin sequences differ by fifty per cent between man and carp; cytochrome C differs by only thirteen per cent.” http://www.creationinthecrossfire.com/...olecularClock1.html

Further, quote from talkorigins:

quote:
…the phylogenetic tree constructed from the cytochrome c data exactly recapitulates the relationships of major taxa as determined by the completely independent morphological data (McLaughlin and Dayhoff 1973)…

Now throw in hemoglobin and the entire premise falls apart. However that is only consistent with all evolutions assumptions.

As a matter of fact, recent research has found a great disparity in “molecular clocks”, especially when applied to proteins.

I especially like the use of Hubert Yockey, I have used quotes by him many times in calculating the probability of abiogenesis.

"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

Concerning Yockey...I think this guy is on my side…

quote:
“He has studied the application of information theory to problems in biology and published his conclusions in the Journal of Theoretical Biology from 1974 onwards. He is very critical of the primordial soup theory of the origin of life, and believes that "the origin of life is unsolvable as a scientific problem." http://en.wikipedia.org/wiki/Hubert_Yockey

Let that sink in for a second. There are, at a minimum, 2.3 x 1093 possible functional cytochrome c protein sequences. How many ways are there to make a royal flush again?

To bad Yockey’s position here is taken way out of context and that discoveries like silent mutations are not really silent followed the citations.


This message is a reply to:
 Message 33 by Taq, posted 10-09-2012 3:45 PM Taq has responded

Replies to this message:
 Message 35 by Percy, posted 10-13-2012 8:25 AM zaius137 has responded
 Message 36 by NoNukes, posted 10-13-2012 9:49 AM zaius137 has not yet responded
 Message 39 by Blue Jay, posted 10-13-2012 5:38 PM zaius137 has not yet responded
 Message 87 by Taq, posted 10-16-2012 10:47 AM zaius137 has not yet responded

  
Percy
Member
Posts: 18842
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.5


(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

    
NoNukes
Inactive Member


(1)
Message 36 of 281 (675617)
10-13-2012 9:49 AM
Reply to: Message 34 by zaius137
10-13-2012 3:21 AM


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.

Percy has made an attempt to explain your error. I'll make a second attempt.

quote:
"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).

If Yockey had found only one possible functional cytochrome c protein sequence, would that increase or decrease the probability that a functitonal sequence had formed without guidance?

According to your logic, a smaller number than 2.3 x 1093 would mean an increased possibility of forming functional cytochrome C protein sequences in an unguided process. Of course that would simply be wrong.

When you deal out a deck of cards, every combination of cards is equally improbable. It would be a simple matter to look at the cards you receive after the fact and to say that you have received an improbable hand. In fact, once you sat down at the table, the odds of receiving an improbable hand under that definition were essentially 100%.

He is very critical of the primordial soup theory of the origin of life, and believes that "the origin of life is unsolvable as a scientific problem."

Is this an enemy of my enemy is my friend argument? Is this really a supportive opinion? Is Yockey really supportive of the arguments you make here?

Edited by NoNukes, : No reason given.

Edited by NoNukes, : No reason given.


Under a government which imprisons any unjustly, the true place for a just man is also in prison. Thoreau: Civil Disobedience (1846)

The apathy of the people is enough to make every statue leap from its pedestal and hasten the resurrection of the dead. William Lloyd Garrison.

Well, you may still have time to register to vote. Even North Carolinians can still register for early voting. State Registration Deadlines


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

  
zaius137
Member (Idle past 1663 days)
Posts: 407
Joined: 05-08-2012


Message 37 of 281 (675626)
10-13-2012 1:44 PM
Reply to: Message 35 by Percy
10-13-2012 8:25 AM


Percy,

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.

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.

There are problems with your statement here. First, you must have perfect knowledge of all the aspects of the protein fulfilling a specific role (my citation casts doubt on that possibility). If there is a fine-tuning of that protein to a specific role you are speaking of every amino acid in the polypeptide chain not only in order but if it was formed by a silent or synonymous mutation.

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.


This message is a reply to:
 Message 35 by Percy, posted 10-13-2012 8:25 AM Percy has responded

Replies to this message:
 Message 41 by Percy, posted 10-14-2012 9:43 AM zaius137 has responded

  
Coyote
Member (Idle past 360 days)
Posts: 6117
Joined: 01-12-2008


Message 38 of 281 (675627)
10-13-2012 1:56 PM


Time out for some evidence
I think at this point some evidence on genetic networks and how they are derived might be of help.

Here is an excellent on-line lecture: Making Genetic Networks Operate Robustly: Unintelligent Non-design Suffices, by Professor Garrett Odell (University of Washington).

Abstract: Mathematical computer models of two ancient and famous genetic networks act early in embryos of many different species to determine the body plan. Models revealed these networks to be astonishingly robust, despite their 'unintelligent design.' This examines the use of mathematical models to shed light on how biological, pattern-forming gene networks operate and how thoughtless, haphazard, non-design produces networks whose robustness seems inspired, begging the question what else unintelligent non-design might be capable of.


Replies to this message:
 Message 40 by zaius137, posted 10-14-2012 2:33 AM Coyote has not yet responded

  
Blue Jay
Member (Idle past 952 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

  
zaius137
Member (Idle past 1663 days)
Posts: 407
Joined: 05-08-2012


Message 40 of 281 (675646)
10-14-2012 2:33 AM
Reply to: Message 38 by Coyote
10-13-2012 1:56 PM


Re: Time out for some evidence
Coyote,

Watched the video, it was very interesting. Thanks for presenting it…

I have done some electronic engineering so the electronic schematic particularly interested me. How he related it to the lecture made the entire exercise more meaningful.

I would like to know what other participants concluded from this presentation. Are you familiar with Langton’s ant and how complex patterns can come out of a simple set of basic rules?

http://en.wikipedia.org/wiki/Langton's_ant

You can plainly see that some very basic rules are built into the segment polarity network nodes. Maybe what the researchers are observing is the result of the basic rules built into the nodes and not so much reliant on the larger network. Someone might say that a null hypothesis could include the observation that the broader network was less significant than the composition of the nodes.

What do think the professor meant when he said:

“Robustness has to come before natural selection”

Is he saying that evolution could not produce such a network? If so you do notice that the professor structured the nodes of the segment polarity network as those found in logical block diagram nodes. Intelligent design?


This message is a reply to:
 Message 38 by Coyote, posted 10-13-2012 1:56 PM Coyote has not yet responded

  
Percy
Member
Posts: 18842
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.5


(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

    
zaius137
Member (Idle past 1663 days)
Posts: 407
Joined: 05-08-2012


Message 42 of 281 (675681)
10-14-2012 4:28 PM
Reply to: Message 41 by Percy
10-14-2012 9:43 AM


don’t blow a gasket
I once had a professor, who had the privilege of teaching a truly brilliant student. I compliment my professor for recognizing this individual and understanding what the student’s gift was all about. My professor said that this student was able to break any complex problem down to its simplest terms and then tackle a seemingly impossible task in steps. This is not a trivial ability, but we lesser individuals can glean an important message from this insight.

Never apply more complication to an issue than is absolutely necessary.

quote:
“Truth is ever to be found in the simplicity, and not in the multiplicity and confusion of things.”
― Isaac Newton

In other words don’t blow a gasket.


This message is a reply to:
 Message 41 by Percy, posted 10-14-2012 9:43 AM Percy has responded

Replies to this message:
 Message 43 by Percy, posted 10-14-2012 4:44 PM zaius137 has responded

  
Percy
Member
Posts: 18842
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.5


(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

    
Alfred Maddenstein
Member (Idle past 2221 days)
Posts: 565
Joined: 04-01-2011


Message 44 of 281 (675694)
10-14-2012 9:26 PM
Reply to: Message 32 by Percy
10-08-2012 6:00 PM


Re: Your case is lost...
Life is a system of death-avoiding machines, Percy. 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. That is, requiring fewer tricks to cheat. Is that possible though? The cat thinks not. Full intelligence is needed to do the job. So life must be smartly organised of necessity. Always.
This message is a reply to:
 Message 32 by Percy, posted 10-08-2012 6:00 PM Percy has responded

Replies to this message:
 Message 48 by Larni, posted 10-15-2012 6:53 AM Alfred Maddenstein has responded
 Message 58 by Blue Jay, posted 10-15-2012 11:48 AM Alfred Maddenstein has responded
 Message 84 by Percy, posted 10-16-2012 9:52 AM Alfred Maddenstein has responded

  
NoNukes
Inactive Member


Message 45 of 281 (675697)
10-14-2012 9:52 PM
Reply to: Message 41 by Percy
10-14-2012 9:43 AM


don't know why you're having trouble finding it since it's the Yockey citation you provided in your Message 33:

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.

That said, we can follow the footnotes at the link Taq provided. The Yockey footnote is to a textbook I don't have access to.


Under a government which imprisons any unjustly, the true place for a just man is also in prison. Thoreau: Civil Disobedience (1846)

The apathy of the people is enough to make every statue leap from its pedestal and hasten the resurrection of the dead. William Lloyd Garrison.

Well, you may still have time to register to vote. Even North Carolinians can still register for early voting. State Registration Deadlines


This message is a reply to:
 Message 41 by Percy, posted 10-14-2012 9:43 AM Percy has responded

Replies to this message:
 Message 51 by Percy, posted 10-15-2012 8:58 AM NoNukes has acknowledged this reply

  
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