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Author Topic:   The Simplest Protein of Life
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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Taq
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Posts: 7997
Joined: 03-06-2009
Member Rating: 3.8


(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:
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Taq
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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.


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Taq
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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
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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.


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


(1)
Message 93 of 281 (675828)
10-16-2012 12:06 PM
Reply to: Message 91 by Alfred Maddenstein
10-16-2012 11:59 AM


Re: Probabilities nonsense on both sides
What is a viable enzyme, Taq?

One that catalyzes a reaction.

From what I understand about the living I conclude that an enzyme by itself is no more alive than a hammer.

However, enzymes are crucial to life and would have been important in the process of abiogenesis which is the topic of the thread.

Just one tiny element in a network of death escaping machines.

From what I can tell, organisms die all of the time.

My point was that life is not known to exist other than in such a network.

I don't disagree. However, tornados in a junkyard is a very poor model/analogy for how chemistry works. That is my point. Showing how random arrangements of nucleotides can produce functioning enzymes is a step towards understand how those networks develop.


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


Message 99 of 281 (675864)
10-16-2012 4:32 PM
Reply to: Message 97 by Alfred Maddenstein
10-16-2012 4:12 PM


Re: brains washed thin
What exactly in the cat's explanation keeps the pair of you so deep in the dark?

What exactly in the cat's explanation is pertinent to the discussion at hand?


This message is a reply to:
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Taq
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Posts: 7997
Joined: 03-06-2009
Member Rating: 3.8


(2)
Message 109 of 281 (675904)
10-17-2012 10:16 AM
Reply to: Message 107 by Alfred Maddenstein
10-17-2012 2:32 AM


Re: Your case is lost...
Any known system of death escaping machines is way too intricate to have self-assembled by chance all at once.

I am not aware of a single organism that is going to or has escaped death, so that is a strange way to describe life. All species that I know of have individuals who die.

Next, we are not saying that organisms we know of NOW were created by abiogenesis. We are saying that much simpler forms of life that left no fossil record came about through abiogenesis. You are attacking a strawman.

All life is hell-bent on avoiding death

Then why do organisms always fail at avoiding death?


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 111 by Alfred Maddenstein, posted 10-17-2012 4:31 PM Taq has responded

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


(2)
Message 112 of 281 (675946)
10-17-2012 4:47 PM
Reply to: Message 111 by Alfred Maddenstein
10-17-2012 4:31 PM


Re: Your case is lost...
Tacky, a much simpler life that left no fossil is no strawman. It is a ghost.

It wouldn't have left fossils. We don't have fossils for most of the unicellular life that existed prior to the Cambrian, but we have massive iron deposits showing that they were busy putting oxygen into the atmosphere. They were there.

You just need it to have been there for purely theoretical reasons.

The problem is that you are mischaracterizing the theory. No one is claiming that modern species came together through random interactions of chemicals. Perhaps you should stop trying to pretend that this is what we are proposing.


This message is a reply to:
 Message 111 by Alfred Maddenstein, posted 10-17-2012 4:31 PM Alfred Maddenstein has responded

Replies to this message:
 Message 113 by Alfred Maddenstein, posted 10-17-2012 5:18 PM Taq has responded

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


(1)
Message 124 of 281 (676009)
10-18-2012 11:11 AM
Reply to: Message 113 by Alfred Maddenstein
10-17-2012 5:18 PM


Re: Your case is lost...
That they were putting out oxygen is no indication of a much greater simplicity you postulate.

The lack of any complex multicellular organisms does indicate greater simplicity. Also, the presence of oxygen and the lack of fossils also demonstrates that life can exist without a direct fossil record.

It is actually only an indication of presence.

You did contest it, mockingly calling them "ghosts".

We are not talking about how modern species came together. The topic is the first ones to appear on earth and the relative complexity of their bits and pieces.

So what was the complexity of the first life? Did it have a ribonuclease protein like that described in the opening post? If we are not talking about how modern species came together then why are people using proteins from modern species to calcuate the odds of abiogenesis? Why are people using the complexity of modern organisms to argue against abiogenesis?


This message is a reply to:
 Message 113 by Alfred Maddenstein, posted 10-17-2012 5:18 PM Alfred Maddenstein has responded

Replies to this message:
 Message 126 by Alfred Maddenstein, posted 10-18-2012 5:47 PM Taq has responded
 Message 142 by ICANT, posted 10-20-2012 12:51 AM Taq has responded

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


(2)
Message 125 of 281 (676011)
10-18-2012 11:18 AM
Reply to: Message 116 by Alfred Maddenstein
10-17-2012 9:19 PM


Re: Your case is lost...
I am not saying that those who believe that life on earth originated through abiogenesis should stop doing their research in that direction. It's just that I see the insistence that this must have been the case by all means to be very foolish and hardly scientific.

I don't really see how abiogenesis research is limited to Earth. If panspermia is true then life originated somewhere through processes that would have been the same as those on Earth, or the same as on meteors/comets in our own solar system. The field of abiogenesis is really only trying to find possible routes of how life could originate, not how life could originate on Earth and Earth only.

I don't think it is that much of a stretch to suppose that life could have originated on an Earth-like planet elsewhere. Water makes an obvious medium in which abiogenesis would occur. Heat would make a very good source of energy to drive thermodynamically unfavorable reactions. Rocks and soils make for very good solid substrates for catalyzing reactions and collecting those products. So studying how life could originate on Earth is also a study on how life could originate on any Earth-like planet.

But most of all, this is not inert matter. Far from it. This is reactive matter. It chemically combines and recombines to create new and interesting molecules. Time and again you use very poor descripters of what you are talking about. You describe organisms who die as death avoiding machines. You describe reactive matter as inert matter. Why is that?

Edited by Taq, : No reason given.


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 Message 116 by Alfred Maddenstein, posted 10-17-2012 9:19 PM Alfred Maddenstein has not yet responded

Replies to this message:
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Taq
Member
Posts: 7997
Joined: 03-06-2009
Member Rating: 3.8


(2)
Message 128 of 281 (676063)
10-18-2012 6:03 PM
Reply to: Message 126 by Alfred Maddenstein
10-18-2012 5:47 PM


Re: Your case is lost...
What is exactly the simplest possible chemical and mechanical configuration that is that limit?

No one knows, which is why every creationist attempt to calculate the probability of abiogenesis is a steaming pile of bullshit.


This message is a reply to:
 Message 126 by Alfred Maddenstein, posted 10-18-2012 5:47 PM Alfred Maddenstein has not yet responded

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


Message 140 of 281 (676115)
10-19-2012 11:06 AM
Reply to: Message 132 by Alfred Maddenstein
10-18-2012 9:45 PM


Re: Your case is lost...
Inadequate, let's face it. Ascribing an age to the existence as a whole is a silly fallacy. Minkowski and Einstein did not dream of committing such a stupid mistake. You, on the other hand, defend in a public forum the category error the bigbangism is founded upon. So who looks stupid, you or I? Why do you do that? You are a university prof or something and since all other profs around you do the same, you just can't do otherwise. Simple. Take the mirror and face it.

None of this touches on the topic at hand. Perhaps you could get back to the topic?


This message is a reply to:
 Message 132 by Alfred Maddenstein, posted 10-18-2012 9:45 PM Alfred Maddenstein has not yet responded

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


(1)
Message 208 of 281 (676369)
10-22-2012 1:10 PM
Reply to: Message 142 by ICANT
10-20-2012 12:51 AM


Re: Your case is lost...
If there are no fossils how do you prove there was life?

By looking for the chemistry of life. One of the biggest pieces of evidence are the banded iron formations:

http://en.wikipedia.org/wiki/Banded_iron_formation

Production of oxygen from water just doesn't happen regularly in abiotic reactions. However, it does happen regularly in photosynthetic reactions within organisms. This causes a massive buildup of oxygen in the atmosphere where it was not found before. This resulted in the oxidation of iron that was found in water. When iron is oxidated it produces iron oxide, also known as rust, and it become insoluble. This produced massive iron deposits. This is a sure sign of life.

These same biochemical reactions also tend to favor one isotope of carbon over another. This can possibly also be used as evidence for the presence of life:

http://www.ncbi.nlm.nih.gov/pubmed/11537367

It does have limitations, but it is shaping up as a promising technology.


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


(1)
Message 209 of 281 (676370)
10-22-2012 1:13 PM
Reply to: Message 144 by ICANT
10-20-2012 1:36 AM


Re: Your case is lost...
Darwin seemed to think life produced the first life forms on earth.

No he didn't. Darwin, in that quote, stated that the higher animals evolved from lower life forms. That is, complex life evolved from simple life. For the actual origin of the first life he has a much more theistic description:

"having been originally breathed into a few forme or into one "

It also has proven that non-life can not produce life.

No it hasn't.


This message is a reply to:
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