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EvC Forum Science Forums Origin of Life

# The Simplest Protein of Life

Author Topic:   The Simplest Protein of Life
zaius137
Member (Idle past 1638 days)
Posts: 407
Joined: 05-08-2012

 Message 22 of 281 (674901) 10-04-2012 2:47 AM Reply to: Message 16 by dwise110-02-2012 9:40 PM

dwise1,

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.

 The probability of drawing a royal flush is 1.539e-6, so the probability of drawing it 19 times in a row is (1.539e-6)19, which is 3.610e-111.

From the wiki it clearly states:

quote:
The following enumerates the (absolute) frequency of each hand, given all combinations of 5 cards randomly drawn from a full deck of 52 without replacement…. 649,739:1

Raise this to the 19th power you get 2.767195 e^110:1. Applying a little perspective, you get the following scenario.

The universe is estimated to contain ~1080 atoms. To pick an exact single atom say that was labeled ahead of time (marked in some way) a single first choice would be 1080:1. However, the probability of your choice is ~ 10100:1, trillions and trillions of times less. So where is that atom? Is it in the computer screen in front of you or in one of the trillions of co-universes out there somewhere floating around an unnamed nebula?

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.

quote:
Structure in a protein:
http://en.wikipedia.org/wiki/Protein_structure

You further assert….

 No, rather there are about 500 known amino acids, but only 22 are proteinogenic. And of those 22, only twenty (20) are used by humans and other eukaryotes in creating proteins. From Wikipedia's Amino Acid:

But the fact that life does not favor the rest of the amino acids does not say that they will not form peptides and poly peptides even with the 20 present in life. Still they must be considered in a random chance for assembly. That would force the probability to take the form (1/500^n). Any calculation of a random forming poly peptide would start with (1/500)n. Unless you remove all the other naturally forming amino acids from the flask in the lab before you start you experiment. Wait that is an intervention by an intelligent being.

It is late where I am at so I will redo your mistakes in calculations tomorrow.

Good night my friend.

P.S. we have not even discussed the limits established in very small probabilities…

 This message is a reply to: Message 16 by dwise1, posted 10-02-2012 9:40 PM dwise1 has responded

 Replies to this message: Message 23 by Dr Adequate, posted 10-04-2012 3:19 AM zaius137 has not yet responded Message 24 by dwise1, posted 10-04-2012 3:12 PM zaius137 has responded Message 33 by Taq, posted 10-09-2012 3:45 PM zaius137 has responded

zaius137
Member (Idle past 1638 days)
Posts: 407
Joined: 05-08-2012

 Message 28 of 281 (675117) 10-06-2012 1:09 AM Reply to: Message 24 by dwise110-04-2012 3:12 PM

(dwise1)

Poker probability by wiki…http://en.wikipedia.org/wiki/Poker_probability

 Furthermore, it is a purely speculative scenario that does not exist in reality. In the real world, proteins are formed within the tissues of organisms with great regularity through mechanisms that are fairly well understood by scientists and educated normals, but apparently not by creationists who keep coming up with these imaginary probability arguments.

Apparently, you are reading something into the thread that was not in the P.O.s originating statement.

P.O.

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

Do you catch the phrase “living cell forming from chemicals”...

I think a high school student can draw the conclusion that this participant is talking about the forming of a protein in a pre-biotic environment. Albeit poorly stated the alternate conclusion is not apropos a controversy.

 At no point did I ever say that the other amino acids will not form peptides. But then not all peptides are proteins, now are they? Rather, only 22 amino acids are used to form proteins and only twenty, termed "standard proteinogenic", are used by eukaryotes to form proteins.

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

Now if you examined the Urey-Miller results there were as follows…

quote:
…what about the results of Miller’s experiment? He obtained a “soup” that contained around 9 amino acids, 2% of the simplest, glycine and alanine, and traces of 7 others. (A number of other organic compounds were produced in small quantities but they have no significance in the origin of life scenario and could even hinder further progress by reacting with the amino acids). http://www.truthinscience.org.uk/.../content/article/51.html

You do notice how many amino acids were formed. Besides probability, you must also calculate in the equilibrium constant for the appropriate reaction (unless an intelligent agent tips the equilibrium in one direction).

You talk about how ignorant creationist arguments are. My good friend, look in the mirror before sticking your foot directly into your mouth. This argument is so one sided in the Creationists camp that I hardly believe I am wasting my time.

 …We are, after all, talking about forming proteins rather than just any old peptide, and for that matter we are talking specifically about eukaryote proteins…

You may be but the P.O. is not. (A PROTEIN IS A POLYPEPTIDE)….

 This message is a reply to: Message 24 by dwise1, posted 10-04-2012 3:12 PM dwise1 has not yet responded

 Replies to this message: Message 30 by Blue Jay, posted 10-08-2012 12:36 PM zaius137 has not yet responded

zaius137
Member (Idle past 1638 days)
Posts: 407
Joined: 05-08-2012

 Message 34 of 281 (675609) 10-13-2012 3:21 AM Reply to: Message 33 by Taq10-09-2012 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

 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

zaius137
Member (Idle past 1638 days)
Posts: 407
Joined: 05-08-2012

 Message 37 of 281 (675626) 10-13-2012 1:44 PM Reply to: Message 35 by Percy10-13-2012 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

zaius137
Member (Idle past 1638 days)
Posts: 407
Joined: 05-08-2012

 Message 40 of 281 (675646) 10-14-2012 2:33 AM Reply to: Message 38 by Coyote10-13-2012 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

zaius137
Member (Idle past 1638 days)
Posts: 407
Joined: 05-08-2012

 Message 42 of 281 (675681) 10-14-2012 4:28 PM Reply to: Message 41 by Percy10-14-2012 9:43 AM

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

zaius137
Member (Idle past 1638 days)
Posts: 407
Joined: 05-08-2012

 Message 46 of 281 (675701) 10-15-2012 1:42 AM Reply to: Message 43 by Percy10-14-2012 4:44 PM

Percy,

 …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.

Percy, I have honestly tried decipher your logic. If I am correct, you are trying to place the cart before the horse.

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

quote:
“Probability may be defined as a ratio of specific outcomes to total (possible) outcomes.” http://iamechatronics.com/...-of-probability-and-reliability

Plainly, without a desired outcome you violate the basic formulation of a probability. Your desired outcome cannot come after testing the event. As to my comment on “simplicity” (not Occam’s razor). It is important not to confuse ourselves by obscuration.

 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 1093sequences.

I cannot deny the context of the used quotation because I do not have the actual material to form an objection to its use. That doesn’t stop me from having reservations about the enormous number cited for alternate functional cytochrome C. 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.

I am in the same boat as another participant here in that I do not have the book.

Edited by zaius137, : No reason given.

 This message is a reply to: Message 43 by Percy, posted 10-14-2012 4:44 PM Percy has responded

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