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Author Topic:   The Simplest Protein of Life
Larni
Member
Posts: 3990
From: Liverpool
Joined: 09-16-2005
Member Rating: 5.5


Message 76 of 281 (675773)
10-15-2012 5:12 PM
Reply to: Message 75 by Alfred Maddenstein
10-15-2012 5:05 PM


Re: Your case is lost...
None of which has anything to do with the topic.

The above ontological example models the zero premise to BB theory. It does so by applying the relative uniformity assumption that the alleged zero event eventually ontologically progressed from the compressed alleged sub-microscopic chaos to bloom/expand into all of the present observable order, more than it models the Biblical record evidence for the existence of Jehovah, the maximal Biblical god designer.
-Attributed to Buzsaw Message 53

The explain to them any scientific investigation that explains the existence of things qualifies as science and as an explanation
-Attributed to Dawn Bertot Message 286

Does a query (thats a question Stile) that uses this physical reality, to look for an answer to its existence and properties become theoretical, considering its deductive conclusions are based against objective verifiable realities.
-Attributed to Dawn Bertot Message 134


This message is a reply to:
 Message 75 by Alfred Maddenstein, posted 10-15-2012 5:05 PM Alfred Maddenstein has not yet responded

    
Alfred Maddenstein
Member (Idle past 2200 days)
Posts: 565
Joined: 04-01-2011


Message 77 of 281 (675774)
10-15-2012 5:35 PM
Reply to: Message 73 by Larni
10-15-2012 4:02 PM


Re: Your case is lost...
Abiogenesis? Simple, Larn. Am I wrong in betting on you lot here all believing that life on Earth originated from either the primordial soup of Oparin-Haldane, hot vents spouting RNA world molecules or by riding on crystals, ice and such like. In any case life from non-life which putative process is called abiogenesis? Moreover, my educated guess is that ya'll believe the process to be absolutely necessary since no life can possibly survive in the quark-gluon soup of the big bunk which you also hold for an indisputable fact of nature.
That's how a fancy cosmology puts constraints on biology, by the way.

Edited by Alfred Maddenstein, : No reason given.


This message is a reply to:
 Message 73 by Larni, posted 10-15-2012 4:02 PM Larni has responded

Replies to this message:
 Message 82 by Larni, posted 10-16-2012 3:27 AM Alfred Maddenstein has responded

  
PaulK
Member
Posts: 15334
Joined: 01-10-2003
Member Rating: 2.7


Message 78 of 281 (675775)
10-15-2012 5:52 PM
Reply to: Message 1 by BoredomSetsIn
10-01-2012 9:00 AM


Did anyone else notice that the calculation in the OP was horribly wrong ? 17 ^ 124 isn't anywhere near 10 ^ 552 - and anyone who does even a rough check can easily see that. (100 ^ 124 is "only" 10 ^ 248 !)

The correct figure is of the order of 10 ^ 152, a difference of 400 orders of magnitude.


This message is a reply to:
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Replies to this message:
 Message 80 by Alfred Maddenstein, posted 10-15-2012 8:40 PM PaulK has not yet responded
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Dr Adequate
Member
Posts: 16097
Joined: 07-20-2006


Message 79 of 281 (675776)
10-15-2012 5:52 PM
Reply to: Message 72 by Alfred Maddenstein
10-15-2012 3:56 PM


Re: Your case is lost...
Was that intended to mean anything, and if so was it related in any way to the topic?
This message is a reply to:
 Message 72 by Alfred Maddenstein, posted 10-15-2012 3:56 PM Alfred Maddenstein has not yet responded

  
Alfred Maddenstein
Member (Idle past 2200 days)
Posts: 565
Joined: 04-01-2011


Message 80 of 281 (675785)
10-15-2012 8:40 PM
Reply to: Message 78 by PaulK
10-15-2012 5:52 PM


Probabilities nonsense on both sides
Calculating probabilities is just a fun mathematical game. Both sides cheat: one ups the ante, the other downs it while none has a real clue what the ante was to begin with. The issue is to be decided on conceptual merits only. It's irrelevant what are the probabilities in Hoyle's example of tornado sweeping a junkyard to result in a brand new Boeing. The point to decide is whether tornadoes and junk ever interact in such a way as to produce a plane.
And the issue is, I reiterate, creating death out of nothing and living memory out of the inert oblivion. If that is possible, the conditions of such happening must be specified and the whole thing must be tested. If not or all the tests fail, then the conclusion is that life is not to be created but can only exist in parallel with inert matter. Always.
This message is a reply to:
 Message 78 by PaulK, posted 10-15-2012 5:52 PM PaulK has not yet responded

Replies to this message:
 Message 88 by Taq, posted 10-16-2012 11:06 AM Alfred Maddenstein has responded

  
dwise1
Member
Posts: 3656
Joined: 05-02-2006
Member Rating: 3.8


(1)
Message 81 of 281 (675786)
10-15-2012 9:29 PM
Reply to: Message 78 by PaulK
10-15-2012 5:52 PM


Did anyone else notice that the calculation in the OP was horribly wrong ? 17 ^ 124 isn't anywhere near 10 ^ 552 - and anyone who does even a rough check can easily see that. (100 ^ 124 is "only" 10 ^ 248 !)

The correct figure is of the order of 10 ^ 152, a difference of 400 orders of magnitude.


Yes, in Message 16 in reply to the OP:

DWise1 writes:

And BTW, your calculation is off. The entire probability should be (1/17)124, which comes out to be 2.6566463724254902266033244604965e-153, or 1 to 3.7641441871204352510844975399203e+152, hundreds of orders of magnitude higher than you had come up with. Could you please show some of your work on that? Or if that's not the part you had done, then provide your source.

{ABE}
PS
For that matter, did your probability argument come from your "textbook"? What is the title of your textbook and who are the authors? And what kind of school are you in?

Not only did the OP and his supporters here fail by using false premises and a false model, but at the very least he should have tried to get the calculations right. With Windows' calc in Scientific View or whatever Apple and Linux offer, there's just no excuse for failure to do basic number crunching.

And no answer to those questions either. I suspect that the OP was yet another "post to an evil-ution forum" homework assignment. Hopefully he learned something, doubtful though that may be.


This message is a reply to:
 Message 78 by PaulK, posted 10-15-2012 5:52 PM PaulK has not yet responded

    
Larni
Member
Posts: 3990
From: Liverpool
Joined: 09-16-2005
Member Rating: 5.5


Message 82 of 281 (675803)
10-16-2012 3:27 AM
Reply to: Message 77 by Alfred Maddenstein
10-15-2012 5:35 PM


Re: Your case is lost...
Okay. I'll phrase it as a question.

What does your drivel about time and distance have to do with abiogenesis?

Please try to answer the question.

Edited by Larni, : No reason given.


The above ontological example models the zero premise to BB theory. It does so by applying the relative uniformity assumption that the alleged zero event eventually ontologically progressed from the compressed alleged sub-microscopic chaos to bloom/expand into all of the present observable order, more than it models the Biblical record evidence for the existence of Jehovah, the maximal Biblical god designer.
-Attributed to Buzsaw Message 53

The explain to them any scientific investigation that explains the existence of things qualifies as science and as an explanation
-Attributed to Dawn Bertot Message 286

Does a query (thats a question Stile) that uses this physical reality, to look for an answer to its existence and properties become theoretical, considering its deductive conclusions are based against objective verifiable realities.
-Attributed to Dawn Bertot Message 134


This message is a reply to:
 Message 77 by Alfred Maddenstein, posted 10-15-2012 5:35 PM Alfred Maddenstein has responded

Replies to this message:
 Message 83 by Alfred Maddenstein, posted 10-16-2012 9:12 AM Larni has not yet responded

    
Alfred Maddenstein
Member (Idle past 2200 days)
Posts: 565
Joined: 04-01-2011


Message 83 of 281 (675807)
10-16-2012 9:12 AM
Reply to: Message 82 by Larni
10-16-2012 3:27 AM


Re: Your case is lost...
It's about whether abiogenesis is obligatory or not. If the question when is cosmologically a relative where, then the question of ultimate origin of anything is a wrong one to ask. Impossible to pin down. Aren't you a bit on the simple side? Or just playing dumb, Larn? What I say is elementary geometry. You can verify it easily with everyday analogies, circles, triangles and stuff.
The only chance for my reasoning to be off is for space to become a real and not a paper substance and start to be able to inflate and expand faster than the velocity of light. For real. Can that be? Would you bet your pants on it? In cold British weather?
Or should you start paying attention to what the neglected panspermia theorists are saying?
This message is a reply to:
 Message 82 by Larni, posted 10-16-2012 3:27 AM Larni has not yet responded

  
Percy
Member
Posts: 18813
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: 18813
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:
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Aware Wolf
Member (Idle past 721 days)
Posts: 154
From: New Hampshire, USA
Joined: 02-13-2009


Message 86 of 281 (675816)
10-16-2012 10:46 AM
Reply to: Message 62 by Alfred Maddenstein
10-15-2012 12:31 PM


Re: Your case is lost...
Anything inert is always one step behind something else either alive or equally inert.

So, two inert things will always be a step behind each other. Infinite regress, I guess.


This message is a reply to:
 Message 62 by Alfred Maddenstein, posted 10-15-2012 12:31 PM Alfred Maddenstein has responded

Replies to this message:
 Message 90 by Alfred Maddenstein, posted 10-16-2012 11:45 AM Aware Wolf has acknowledged this reply

  
Taq
Member
Posts: 7997
Joined: 03-06-2009
Member Rating: 3.8


(1)
Message 87 of 281 (675817)
10-16-2012 10:47 AM
Reply to: Message 34 by zaius137
10-13-2012 3:21 AM


Maybe you do not understand probability; it must describe a predicted outcome.

The sequence of ribonuclease was not predicted. The odds of it appearing were calculated after it had already appeared. That is why it suffers from the Sharpshooter Fallacy.

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

But does it always? No.

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.

That is a secondary point. The point is that a protein can differ by 40% at the amino acid sequence and still have the same function to the point that one can be replaced by the other without losing function.

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…

Why is that a problem? It would only indicate that there is more functional constraint in hemoglobin than in cytc.

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).

That would only work for sequences not under selection. Cytochrome C is under selection.

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

So you agree that there are ~1x10^93 possible functional cytc sequences?

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.

Pointing to one case does not show that all silent mutations change function.


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

  
Taq
Member
Posts: 7997
Joined: 03-06-2009
Member Rating: 3.8


(1)
Message 88 of 281 (675819)
10-16-2012 11:06 AM
Reply to: Message 80 by Alfred Maddenstein
10-15-2012 8:40 PM


Re: Probabilities nonsense on both sides
It's irrelevant what are the probabilities in Hoyle's example of tornado sweeping a junkyard to result in a brand new Boeing. The point to decide is whether tornadoes and junk ever interact in such a way as to produce a plane.

The problem is that the analogy does not illustrate how chemistry works. If you put a bolt and nut in a box and shake it around it is very unlikely that the nut will spin around the bolt and make a tight connection. However, if you take two molecules and shake them about you could get a reaction that puts them together.

Even more, can a "tornado" produce a viable enzyme? The answer is yes.

quote:
Science. 1993 Sep 10;261(5127):1411-8.

Isolation of new ribozymes from a large pool of random sequences [see comment].

Bartel DP, Szostak JW.
Collaborators (1)Szostak JW.

Department of Molecular Biology, Massachusetts General Hospital, Boston 02114.

Abstract
An iterative in vitro selection procedure was used to isolate a new class of catalytic RNAs (ribozymes) from a large pool of random-sequence RNA molecules. These ribozymes ligate two RNA molecules that are aligned on a template by catalyzing the attack of a 3'-hydroxyl on an adjacent 5'-triphosphate--a reaction similar to that employed by the familiar protein enzymes that synthesize RNA. The corresponding uncatalyzed reaction also yields a 3',5'-phosphodiester bond. In vitro evolution of the population of new ribozymes led to improvement of the average ligation activity and the emergence of ribozymes with reaction rates 7 million times faster than the uncatalyzed reaction rate.
[emphasis mine]



This message is a reply to:
 Message 80 by Alfred Maddenstein, posted 10-15-2012 8:40 PM Alfred Maddenstein has responded

Replies to this message:
 Message 91 by Alfred Maddenstein, posted 10-16-2012 11:59 AM Taq has responded

  
Taq
Member
Posts: 7997
Joined: 03-06-2009
Member Rating: 3.8


(1)
Message 89 of 281 (675820)
10-16-2012 11:09 AM
Reply to: Message 85 by Percy
10-16-2012 10:45 AM


Re: don’t blow a gasket
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.

More importantly, if we are talking about abiogenesis then you must also calculate the number of chemical combinations that will result in life. As far as I know, no creationist has even attempted to produce this probability. Quite frankly, no one is capable of producing this probability because we do not know which or how many chemical combinations result in life.


This message is a reply to:
 Message 85 by Percy, posted 10-16-2012 10:45 AM Percy has acknowledged this reply

  
Alfred Maddenstein
Member (Idle past 2200 days)
Posts: 565
Joined: 04-01-2011


Message 90 of 281 (675824)
10-16-2012 11:45 AM
Reply to: Message 86 by Aware Wolf
10-16-2012 10:46 AM


Re: Your case is lost...
No, Wolfie, no regress at all. There is no single file you imagine. Things push and pull every which way. Round and round it goes.
This message is a reply to:
 Message 86 by Aware Wolf, posted 10-16-2012 10:46 AM Aware Wolf has acknowledged this reply

  
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