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Author Topic:   Origin of Translation
jjburklo
Inactive Member


Message 1 of 51 (160613)
11-17-2004 4:13 PM


I will not go into exact details of translation. But if we look at translation what is specifically needed:
- the ribosome
- the message
- the initiating factors
- the elongating factors
- the energy transfer system
- the tRNA's
- the amino acids
- the chaparonins
- the coding system
All of these had to be dependently and coordinately evolved slowly over millenia with continous selection pressure on the non- functioning intermediate systems in order for a single fully functional, selectively useful protein to be generated. It is possible to "imagine" simplified versions of the system in which protein products were all much simpler and therefore, chaparonins, for example, would be redundant. However, there is no evidence that such simple systems existed or could have existed.

But! perhaps we are looking at the artwork of a masterful designer who saw the whole system and designed all the parts whose specific functions I have not defined rigorously. So we find ourselves staring at these glorious diagrams- simplifications of the actual machines. Hmmm is this a fortuitous series of accidents or the work of a superior Designer?

Faith is critical to either of these two interpretations. So the next question becomes: Where is it more rational to lodge my faith? Looking at the final product, which is more plausible? Or, more determinantly, which of these two interpretations do you want to believe in, for that is where your intellect will go to brouse!


Replies to this message:
 Message 2 by AdminNosy, posted 11-17-2004 4:31 PM jjburklo has responded
 Message 7 by crashfrog, posted 11-17-2004 5:48 PM jjburklo has responded
 Message 8 by Loudmouth, posted 11-17-2004 5:51 PM jjburklo has responded

  
AdminNosy
Administrator
Posts: 4754
From: Vancouver, BC, Canada
Joined: 11-11-2003


Message 2 of 51 (160619)
11-17-2004 4:31 PM
Reply to: Message 1 by jjburklo
11-17-2004 4:13 PM


No!
There, is that clear enough?

I will not (others may if they choose) promote any topics if you are simply going to ignore suggestions made about other topics you have proposed. I'm beginning to become convinced that you don't intend to discuss these in good faith at all.

I will be closing those that you have outstanding in a few more days if you take no action on them.

If you continue to propose new topics and ignore suggestions to get them promoted then you will loose your priviledges to start new topics.


This message is a reply to:
 Message 1 by jjburklo, posted 11-17-2004 4:13 PM jjburklo has responded

Replies to this message:
 Message 3 by jjburklo, posted 11-17-2004 4:34 PM AdminNosy has not yet responded

  
jjburklo
Inactive Member


Message 3 of 51 (160622)
11-17-2004 4:34 PM
Reply to: Message 2 by AdminNosy
11-17-2004 4:31 PM


Re: No!
Sorry about that. I guess maybe I'm in too much of a rush to get a topic out there. Sorry again
This message is a reply to:
 Message 2 by AdminNosy, posted 11-17-2004 4:31 PM AdminNosy has not yet responded

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jjburklo
Inactive Member


Message 4 of 51 (160623)
11-17-2004 4:47 PM
Reply to: Message 3 by jjburklo
11-17-2004 4:34 PM


Re: No!
Also the other 2 topics you I proposed can be closed. I've already gone through the site and found related threads that address the topic and have posted there. I don't see any reason to start another.

But as far as this post goes, what exactly is wrong with it? In my other proposed topics, they'd already been discussed quite thoroughly. You suggested that I read through the threads and take a new angle on it. As for this topic, I've not found a ton of conversation on this topic. Maybe that's my fault. If you could specifically point out problems, I'd be glad to try and edit it. Thanks


This message is a reply to:
 Message 3 by jjburklo, posted 11-17-2004 4:34 PM jjburklo has not yet responded

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AdminNosy
Administrator
Posts: 4754
From: Vancouver, BC, Canada
Joined: 11-11-2003


Message 5 of 51 (160638)
11-17-2004 5:36 PM
Reply to: Message 4 by jjburklo
11-17-2004 4:47 PM


Let me have a look
K, I will close the others and have a more careful look at this one.
This message is a reply to:
 Message 4 by jjburklo, posted 11-17-2004 4:47 PM jjburklo has not yet responded

  
AdminNosy
Administrator
Posts: 4754
From: Vancouver, BC, Canada
Joined: 11-11-2003


Message 6 of 51 (160640)
11-17-2004 5:38 PM


Thread moved here from the Proposed New Topics forum.
  
crashfrog
Inactive Member


Message 7 of 51 (160653)
11-17-2004 5:48 PM
Reply to: Message 1 by jjburklo
11-17-2004 4:13 PM


Hmmm is this a fortuitous series of accidents or the work of a superior Designer?

There's no evidence that such a Designer existed or could have existed.

Where is it more rational to lodge my faith?

Probably in the view supported by the methodology with proven results. That would be the methodological naturalism of the scientific method.

But science isn't a place for faith, and the origin of life is not a question of faith. You shouldn't be so quick to demand a settling of the question when we're hardly looked into it, yet. There's much to discover about the origin of life. Why can't "I don't know yet" be an appropriate answer to that question?

Or, more determinantly, which of these two interpretations do you want to believe in

The one that is correct. I, for one, do not allow what I want to be true to affect my conception of what is true, and I don't understand why a rational person would think otherwise. What does it matter which one of those interpretations we want to be true?

The one we should "believe in" is the one that is right. Which one is that? We don't know yet. Why isn't that answer good enough for you?


This message is a reply to:
 Message 1 by jjburklo, posted 11-17-2004 4:13 PM jjburklo has responded

Replies to this message:
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Loudmouth
Inactive Member


Message 8 of 51 (160657)
11-17-2004 5:51 PM
Reply to: Message 1 by jjburklo
11-17-2004 4:13 PM


quote:
All of these had to be dependently and coordinately evolved slowly over millenia with continous selection pressure on the non- functioning intermediate systems in order for a single fully functional, selectively useful protein to be generated.

Why would they have to be non-functioning in those intermediate steps? It is very possible for a one mutation to result in new protein function. This new function, through further mutation, could become more specific and more active over time, but still be functional from the very outset.

quote:
It is possible to "imagine" simplified versions of the system in which protein products were all much simpler and therefore, chaparonins, for example, would be redundant. However, there is no evidence that such simple systems existed or could have existed.

By chaparonins do you mean chaperone proteins? Post translational modification is also a viable evolutionary mechanism that might have been important in early life.

Next, there is no doubt that simpler systems COULD HAVE existed. Whether or not they did is devoid of evidence due to the fact that proteins and DNA don't fossilize. So we are left with what we observe today. We know that mutations can lead to novel proteins, increases in specificty, and increases in enzyme function. Therefore, we know that simpler proteins COULD HAVE been refined through mutation and natural selection over time resulting in the well oiled machine that is RNA translation.

quote:
But! perhaps we are looking at the artwork of a masterful designer who saw the whole system and designed all the parts whose specific functions I have not defined rigorously. So we find ourselves staring at these glorious diagrams- simplifications of the actual machines. Hmmm is this a fortuitous series of accidents or the work of a superior Designer?

The difference between evolution and supernatural explanations is that the mechanisms of evolution can be tested. As I stated before, we can observe the capabilities of mutation and natural selection, and we can test those mechanisms as well. No one has ever observed a supernatural deity designing anything in biology, nor is it possible to test the mechanisms of supernatural design. Evolution is not taken on faith, but on the evidenciary support of empirical data and the testing of hypotheses. A supernatural deity/designer rests solely on religious faith and is not testable nor observable.

quote:
Faith is critical to either of these two interpretations.

Absolutely false. There is no faith involved in the sciences, except in the metaphysical underpinnings of objective observations. Every theory put forth has to be testable and BASED on observations. This is the opposite of what is found with a supernatural designer theory, where the theory is untestable and the evidence is subjective.

quote:
Or, more determinantly, which of these two interpretations do you want to believe in, for that is where your intellect will go to brouse!

I trust in the view that can be tested by objective data and the view that is based on testable theories.


This message is a reply to:
 Message 1 by jjburklo, posted 11-17-2004 4:13 PM jjburklo has responded

Replies to this message:
 Message 10 by Ben!, posted 11-18-2004 2:53 AM Loudmouth has responded
 Message 19 by jjburklo, posted 11-18-2004 11:25 PM Loudmouth has responded
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Nic Tamzek
Inactive Member


Message 9 of 51 (160841)
11-18-2004 1:41 AM


The opening post would be much more impressive if the poster surveyed and critiqued the origin of life literature, instead of asking us random internet folks to do all of his research for him.

That said, I have read a bit about this. The basic concept missing is the RNA World, which is based in part on the fact that most of the core parts of the translation machinery you are talking about are made from RNA. RNA can both (1) store information and (2) catalyze reactions. So the DNA-->RNA-->protein system actually got started in the middle, with DNA being added as a more stable information storage system, and proteins added as a better set of catalysts.

If you want a pretty detailed model on how the very basics of replication and translation originated, read this:

Cavalier-Smith T. (2001) Obcells as proto-organisms: membrane heredity, lithophosphorylation, and the origins of the genetic code, the first cells, and photosynthesis. J Mol Evol. 53(4-5):555-95.

On a related topic, I just came across this fairly mind-blowing paper, which actually does specifically test some models about early events in the evolution of life:

Chomin Cunchillos and Guillaume Lecointre (2003)
Evolution of Amino Acid Metabolism Inferred through Cladistic Analysis
J. Biol. Chem., Vol. 278, Issue 48, 47960-47970
http://www.jbc.org/cgi/content/full/278/48/47960

This message has been edited by Nic Tamzek, 11-18-2004 01:43 AM


  
Ben!
Member (Idle past 1669 days)
Posts: 1154
From: San Diego, CA
Joined: 10-14-2004


Message 10 of 51 (160860)
11-18-2004 2:53 AM
Reply to: Message 8 by Loudmouth
11-17-2004 5:51 PM


LM,

I don't know, I'm inclined to give some points to the original poster that you're unwilling. Can you explain why you're unwilling?

Talking about ambiogenesis,

ab writes:

But! perhaps we are looking at the artwork of a masterful designer who saw the whole system and designed all the parts whose specific functions I have not defined rigorously. So we find ourselves staring at these glorious diagrams- simplifications of the actual machines. Hmmm is this a fortuitous series of accidents or the work of a superior Designer?

and you write

There is no doubt that simpler systems COULD HAVE existed. Whether or not they did is devoid of evidence due to the fact that proteins and DNA don't fossilize.

I don't see the difference. All we can establish for either case is the POSSIBILITY of it happening.

Intelligent design is governed only by the rules of logic; chemical ambiogenesis is ruled by chemistry. You go on to argue (and I think convincingly) that the rules of chemistry say that ambiogenesis IS POSSIBLE.

Nonetheless, you haven't shown that it DID happen... only that there's no reason AGAINST beleiving the hypothesis. Well, that's EXACTLY the same level that intelligent design (at least, those who believe in a story that is consistent with what we can observe and is logically consistent) is.

I don't think we should just wash this fact away by saying many people who believe in intelligent design believe in inconsistent stories. That is a fault in THEM--not a fault in intelligent design itself. I don't see a difference between the two. As usual, the only argument might be 'parsimony.'

So, I think saying

Faith is critical to either of these two interpretations.

Absolutely false. There is no faith involved in the sciences, except in the metaphysical underpinnings of objective observations. Every theory put forth has to be testable and BASED on observations. This is the opposite of what is found with a supernatural designer theory, where the theory is untestable and the evidence is subjective.

is clearly, at least in this specific case, misleading.

Ben


This message is a reply to:
 Message 8 by Loudmouth, posted 11-17-2004 5:51 PM Loudmouth has responded

Replies to this message:
 Message 11 by Silent H, posted 11-18-2004 10:02 AM Ben! has responded
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Silent H
Member (Idle past 3866 days)
Posts: 7405
From: satellite of love
Joined: 12-11-2002


Message 11 of 51 (160980)
11-18-2004 10:02 AM
Reply to: Message 10 by Ben!
11-18-2004 2:53 AM


I don't see the difference. All we can establish for either case is the POSSIBILITY of it happening.

Possibility is all we need in order to posit it as a route for abiogenesis to occur naturally. Of course we would then continue research into chemical interactions and environments and may one day even discover definite possible pathways, rather than theoretical possible pathways.

The difference lies wholly with the evidence. We have many complex chemicals, we have many complex environments, and we have a definite sign that life exists. Thus chemicals and environments interacted in some way to form life.

Natural routes require only what we have seen so far and so is logically the best explanation for abiogenesis (and then speciation).

ID routes require something else altogether. That requires an intelligence which we have never encountered, nor have evidence of, unless we are to circularly accept life as the sign that an ID existed to make life.

The amazing complexity of life or chemical interactions does not add towards evidence that an ID existed, as the complexity may have more to do with our current lack of knowledge than what is actually there.

Given all of this there is an obvious gap between the credibility or probability of natural abiogenesis, and artifical abiogenesis.


holmes
"...what a fool believes he sees, no wise man has the power to reason away.."(D. Bros)
This message is a reply to:
 Message 10 by Ben!, posted 11-18-2004 2:53 AM Ben! has responded

Replies to this message:
 Message 12 by Ben!, posted 11-18-2004 10:23 AM Silent H has responded
 Message 22 by jjburklo, posted 11-18-2004 11:38 PM Silent H has responded

    
Ben!
Member (Idle past 1669 days)
Posts: 1154
From: San Diego, CA
Joined: 10-14-2004


Message 12 of 51 (160993)
11-18-2004 10:23 AM
Reply to: Message 11 by Silent H
11-18-2004 10:02 AM


Let me try again.

Possibility is all we need in order to posit it as a route for abiogenesis to occur naturally. Of course we would then continue research into chemical interactions and environments and may one day even discover definite possible pathways, rather than theoretical possible pathways.

So we agree on this point.

The difference lies wholly with the evidence. We have many complex chemicals, we have many complex environments, and we have a definite sign that life exists. Thus chemicals and environments interacted in some way to form life.

Ah, but I disagree. How can you call this evidence? This is only circumstantial. You have to have some concrete evidence that links all of this information DIRECTLY to the timeframe that you're talking about. Right now, we don't have a single scrap of evidence of WHAT complex environment was ACTUALLY at the time, only speculation. We don't have any evidence of any of these molecules or mixtures being around at the proper times, because these things don't fossilize. What proper, true, non-speculative evidence do we have about what was actually happening at that time? I haven't seen it so far. I'm just starting at this. But I haven't seen it so far.

Circumstantial evidence just isn't convincing enough. Even creos can get that. All we have is enough motivation to say that it's possible. No evidence to say that it actually happened.

Natural routes require only what we have seen so far and so is logically the best explanation for abiogenesis (and then speciation).

ID routes require something else altogether. That requires an intelligence which we have never encountered, nor have evidence of, unless we are to circularly accept life as the sign that an ID existed to make life.

To me, this is pretty much the principle of parsimony, which I mentioned as the only real reason to choose ambiogenesis over creationist accounts (well that, and the fact that so many creationist accounts are so ... internally inconsistent).

But the thing about the principle of parsimony is that... it's a principle about theory-building, and not about 'truth.' It's better theory to make these moves, but in no way is that evidence for the truth. The evidence for both remains the same--circumstantial only.

The amazing complexity of life or chemical interactions does not add towards evidence that an ID existed, as the complexity may have more to do with our current lack of knowledge than what is actually there.

No doubt about that!

Given all of this there is an obvious gap between the credibility or probability of natural abiogenesis, and artifical abiogenesis.

I don't like the word probability. If you ever hear me use the word probability when NOT doing a calculation or explanation of some mathematics, please yell at me.

Probability in this sentence, to me, seems like... your 'gut feeling.' If there's one thing we can learn from this site, it's this: when there's simply circumstantial evidence going both ways, people's gut feeling of what is credible and probable are simply divergent.

Personally, my gut says AMBIOGENESIS. But gut is not science. The science, for what I've seen so far, is too weak for all the strong claims I feel I see around here.

I hope I've done a good job expressing myself. Thanks for taking the time to read.

Ben


This message is a reply to:
 Message 11 by Silent H, posted 11-18-2004 10:02 AM Silent H has responded

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Loudmouth
Inactive Member


Message 13 of 51 (161083)
11-18-2004 1:19 PM
Reply to: Message 10 by Ben!
11-18-2004 2:53 AM


quote:
I don't see the difference. All we can establish for either case is the POSSIBILITY of it happening.

Intelligent design is governed only by the rules of logic; chemical ambiogenesis is ruled by chemistry. You go on to argue (and I think convincingly) that the rules of chemistry say that ambiogenesis IS POSSIBLE.


I would argue that ID is governed by philosophy, not logical scientific arguments. Hopefully I can make this clear.

Abiogenesis is governed by chemistry. The rules of chemistry can be tested and checked. We can directly test whether certain pathways are possible through natural means. If we are able to produce life through natural mechanisms in the lab, then this is a very possible pathway for life to arise on an early Earth. However, we can't know whether or not this pathway occured on Earth because that evidence has long since been destroyed.

Now, let's move to ID. ID is a philosophical/theological argument. It states that a Designer should be assumed without evidence. This is in stark contrast to abiogenesis, where the active mechanisms can be observed, tested, and need not be assumed. This is the problem with ID, it requires one to assume that a Designer exists without evidence and without testing. This is why abiogenesis is the better scientific theory and ID is incapable of making headway in scientific circles.

There is no faith needed in abiogenesis. The mechanisms are there for everyone to touch, feel, manipulate, and test. ID does require faith in that the Designer has to be assumed to exist on faith alone. The Designer can not be tested, touched, manipulated, etc. Also, theories in abiogenesis are inherently tentative. They are not held as absolute truths but ideas that are continually tested and modified if necessary. This is the opposite of ID "theory" in that the Designer can not be questioned and assumed to be "true" without one ounce of tentativity. Without a Designer, what do we need ID theory for?

quote:
I don't think we should just wash this fact away by saying many people who believe in intelligent design believe in inconsistent stories.

No, they all believe in the same inconsistent storie, that a Designer is self evident and should be assumed to exist without any evidence whatsoever.


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Replies to this message:
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Silent H
Member (Idle past 3866 days)
Posts: 7405
From: satellite of love
Joined: 12-11-2002


Message 14 of 51 (161084)
11-18-2004 1:20 PM
Reply to: Message 12 by Ben!
11-18-2004 10:23 AM


Right now, we don't have a single scrap of evidence of WHAT complex environment was ACTUALLY at the time, only speculation. We don't have any evidence of any of these molecules or mixtures being around at the proper times

Uhhhh... I think you misunderstood what I was saying. I didn't say we know what complex chemicals and environments existed which created life.

What I was saying is that on the earth we know there are complex chemicals (not talking as complex as biological organisms) and environments.

I assume you are not claiming that it is only theoretical that there were diverse complex chemicals and environments deep in earth's past? If so, then we are dealing with some other discussion entirely.

The point then, is something in that mix of chemicals and environments happened, out of which life formed. Either it was a natural route using the existing materials, or according to ID, an intelligent agent (previous to the existence of earth environment or not) played with the elements such that they would form life.

Given that "intelligent agent" is an added "element" for which we have absolutely no evidence besides someone asserting it, and it would require a whole additional set of explanations, this is less credible and less probable.

And yes probable is the correct word. If you follow any ID accounts it is almost always posed as the correct answer after probabilities are calculated for the formation of biochemicals. Yet they never discuss that on top of this, in order to hold their own theory, there must be the same calculations for the IDer.

It would be the height of inconsistency to say that it is somehow immune to evidence and calculation of probability.

Why do you keep saying ambiogenesis, instead of abiogenesis?


holmes
"...what a fool believes he sees, no wise man has the power to reason away.."(D. Bros)
This message is a reply to:
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Silent H
Member (Idle past 3866 days)
Posts: 7405
From: satellite of love
Joined: 12-11-2002


Message 15 of 51 (161090)
11-18-2004 1:42 PM
Reply to: Message 13 by Loudmouth
11-18-2004 1:19 PM


I would argue that ID is governed by philosophy

This would be completely wrong. ID contains logical fallacies incompatible with good philosophy. That is why Dembski has actually come up with a new "fallacy" which is just an assertion that the argument from ignorance is not a fallacy.

As soon as you have someone having to reject "occam's razor" and "the fallacy of the argument from ignorance" as valid and necessary to proper philosophy, they are clearly rejecting philosophy.

ID is theology.


holmes
"...what a fool believes he sees, no wise man has the power to reason away.."(D. Bros)
This message is a reply to:
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Replies to this message:
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