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Author Topic:   The $5,000,000 ID Research Challenge
Taq
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Posts: 7997
Joined: 03-06-2009
Member Rating: 3.8


(1)
Message 31 of 285 (672266)
09-05-2012 10:49 AM
Reply to: Message 29 by Percy
09-05-2012 8:30 AM


Re: My Take
I don't understand the nitpicking about Genomicus's research proposals. If the ID crowd were actually engaged in any of the investigations he proposes I, for one, would be applauding. I'd still think the research was unfounded upon any real world observations, but at least it would be actual research on ID. It would be a welcome break from all the dishonest portrayals of evolution they usually engage in.

Scientists are nitpickers to the nth degree. That we feel it necessary to nitpick to the extent we do is actually a complement.

Also, there is a difference between doing research and doing experiments. A research program should have a sense of progress where each set of experiments leads to a new direction, new questions, and a new set of experiments. Genomicus' proposal lacks that. Instead, it is very rigid and pre-determined. It would seem that the conclusion has already been reached, experimental results be damned.

The one idea that does interest me is the proposed work on the ur-flagellum. A few people have given this a go, but have not really worked towards a functional ancestral sequence. Most of the analyses I have seen are focused on phylogenetic signals instead of functional proteins. This would certainly be new knowledge, so this idea already has a major leg up on the other proposals. However, there are very major hurdles. Given the time since the ur-flagellum and HGT I think it would be extremely difficult to get an accurate ancestral genome, not to mention the epistatic interactions with the rest of the ur-genome. So while it is a very, very interesting proposal I don't think it has much chance of real success.


This message is a reply to:
 Message 29 by Percy, posted 09-05-2012 8:30 AM Percy has acknowledged this reply

  
Genomicus
Member (Idle past 172 days)
Posts: 852
Joined: 02-15-2012


Message 32 of 285 (672277)
09-05-2012 7:01 PM
Reply to: Message 25 by Taq
09-04-2012 1:24 PM


This really doesn't separate ID from other existing, unguided mechanisms for the production of LUCA. However, you could convince me otherwise.

Yes, but a fundamental distinction needs to be made. In one instance (the non-telic model), we are simply able to explain the potential observation that the LUCA had unnecessary genomic information. On the other hand, the front-loading hypothesis predicts that the LUCA had unnecessary information. Confirmation of predictions is a very crucial part of science, and a track-record of successfully confirmed predictions is what catalyzes the elevation of a scientific hypothesis to the level of theory.

It would be relatively simple to falsify front-loading. If it was found that the LUCA possessed only those genes necessary for life, the front-loading hypothesis would have been effectively falsified. Thus, it is possible to test the hypothesis, and it is the testing of ID hypotheses that would make up an ID research program. This is what this challenge is all about, after all, if I am not mistaken.

Sharpshooter fallacy. If evolution took a different turn and favored A-T transitions instead you would be talking about how proteins that evolved though A-T transitions were front loaded. You are simply taking the result and painting a bull's eye around it. This is a major problem for all of your approaches.

Two points:

1. When it comes to cytosine deamination specifically, there is nothing in evolution that would have caused A-T transversions (sorry Taq, but the phrase "A-T transitions" is technically incorrect) to be favored precisely because it is chemistry that causes cytosine deamination. In short, we are met with the following objective fact: cytosine is part of DNA, and cytosine is prone to deamination. If DNA was engineered, then we need to account for why cytosine was chosen instead of a base that was not so prone to deamination (indeed, it has been argued that no engineer would use cytosine as a base in DNA because of this). Curiously, if we look to the genetic code, we see an interesting pattern: the vast majority of non-synonymous mutations that result from C --> T transitions increase hydrophobicity. We therefore have the first basic step in the scientific method: make an observation. Next, we can ask questions, such as "why has this pattern been chosen for the genetic code?" Then you form a hypothesis: from an ID perspective, a plausible explanation for this pattern is that it can be exploited for front-loading, such that an initially designed protein fold can turn into a completely novel fold quite quickly through multiple cytosine deamination events. It would be an effective mechanism for producing key multi-cellular specific proteins, particularly for molecular machines that have system-dependent parts. Next, we'd go out and experimentally test this hypothesis. Then the results would be analyzed and we'd determine if the hypothesis has been falsified or strengthened. I fail to see how following the scientific method ends up as the "Sharpshooter fallacy."

2. You've brought up the Sharpshooter fallacy before, and it's a quick way to dismiss the various hypotheses I have discussed before (e.g., the design hypothesis proposed in the "Nature's Engines and Engineering" thread, and front-loading). However, IMHO you've never really succinctly defined how I'm using the Sharpshooter fallacy. The whole ID position is that some of the actually existing features of life were designed. So if one were to argue that the flagellum was designed based on its discontinuity from the rest of the biological universe, you could easily say "Sharpshooter fallacy." But there really wouldn't be any rational basis for that. A much better approach would be to examine if the flagellum actually does have discontinuity from the rest of the biological world.

So how precisely am I using the Sharpshooter fallacy, and what exact definition of the Sharpshooter fallacy are you using?

Edited by Genomicus, : No reason given.


This message is a reply to:
 Message 25 by Taq, posted 09-04-2012 1:24 PM Taq has responded

Replies to this message:
 Message 33 by jar, posted 09-05-2012 7:22 PM Genomicus has not yet responded
 Message 34 by PaulK, posted 09-06-2012 1:26 AM Genomicus has not yet responded
 Message 35 by Taq, posted 09-06-2012 10:57 AM Genomicus has not yet responded

  
jar
Member
Posts: 31191
From: Texas!!
Joined: 04-20-2004
Member Rating: 2.7


Message 33 of 285 (672278)
09-05-2012 7:22 PM
Reply to: Message 32 by Genomicus
09-05-2012 7:01 PM


Yes, but a fundamental distinction needs to be made. In one instance (the non-telic model), we are simply able to explain the potential observation that the LUCA had unnecessary genomic information. On the other hand, the front-loading hypothesis predicts that the LUCA had unnecessary information.

Utter nonsense.

If changes to the genome are random related to fitness and only those changes that prevent reproduction get filtered out, there MUST be unnecessary information present.


Anyone so limited that they can only spell a word one way is severely handicapped!

This message is a reply to:
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PaulK
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Posts: 15328
Joined: 01-10-2003
Member Rating: 2.7


(1)
Message 34 of 285 (672288)
09-06-2012 1:26 AM
Reply to: Message 32 by Genomicus
09-05-2012 7:01 PM


quote:

Yes, but a fundamental distinction needs to be made. In one instance (the non-telic model), we are simply able to explain the potential observation that the LUCA had unnecessary genomic information. On the other hand, the front-loading hypothesis predicts that the LUCA had unnecessary information.

So far as I can tell this "distinction" relies on a double standard. Under both hypotheses we expect extra genes in the LUCA. In the case of non-telic evolution the fact that we can't guarantee it is used to disqualify it as a prediction, in the case of FLE this criterion is ignored. Without a real distinction there's no case here.

quote:

1. When it comes to cytosine deamination specifically, there is nothing in evolution that would have caused A-T transversions (sorry Taq, but the phrase "A-T transitions" is technically incorrect) to be favored precisely because it is chemistry that causes cytosine deamination. In short, we are met with the following objective fact: cytosine is part of DNA, and cytosine is prone to deamination. If DNA was engineered, then we need to account for why cytosine was chosen instead of a base that was not so prone to deamination (indeed, it has been argued that no engineer would use cytosine as a base in DNA because of this). Curiously, if we look to the genetic code, we see an interesting pattern: the vast majority of non-synonymous mutations that result from C --> T transitions increase hydrophobicity. We therefore have the first basic step in the scientific method: make an observation. Next, we can ask questions, such as "why has this pattern been chosen for the genetic code?" Then you form a hypothesis: from an ID perspective, a plausible explanation for this pattern is that it can be exploited for front-loading, such that an initially designed protein fold can turn into a completely novel fold quite quickly through multiple cytosine deamination events. It would be an effective mechanism for producing key multi-cellular specific proteins, particularly for molecular machines that have system-dependent parts. Next, we'd go out and experimentally test this hypothesis. Then the results would be analyzed and we'd determine if the hypothesis has been falsified or strengthened. I fail to see how following the scientific method ends up as the "Sharpshooter fallacy."

There still doesn't seem to be much of a case here. Or even an attempt to provide an analysis. There is a pretty limited selection of bases that are likely to be available, so analysing the alternatives would seem to be the next step but I don't see any sign of that having even been tried.

The other point is that if this can happen, then it is likely that it has happened at some point in evolutionary history. The only interesting claim is that a "hidden" structure was designed in, but we can't determine that just by finding a case where C->T transitions have produced useful genes.


This message is a reply to:
 Message 32 by Genomicus, posted 09-05-2012 7:01 PM Genomicus has not yet responded

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


(1)
Message 35 of 285 (672307)
09-06-2012 10:57 AM
Reply to: Message 32 by Genomicus
09-05-2012 7:01 PM


Yes, but a fundamental distinction needs to be made. In one instance (the non-telic model), we are simply able to explain the potential observation that the LUCA had unnecessary genomic information.

Right. What you need to find is an observation that could not be explained by non-telic processes but can be explained by telic processes.

Also, I would have every expectation that the LUCA would have unnecessary genes since all modern life has DNA sequence that they don't need. I would stop short of calling it a prediction, but every observation of evolution that we have made points to the strong possibility that the LUCA would have unnecessary DNA.

If DNA was engineered, then we need to account for why cytosine was chosen instead of a base that was not so prone to deamination (indeed, it has been argued that no engineer would use cytosine as a base in DNA because of this).

You need to answer that if statement at the beginning before you can proceed to the other ideas.

Then you form a hypothesis: from an ID perspective, a plausible explanation for this pattern is that it can be exploited for front-loading, such that an initially designed protein fold can turn into a completely novel fold quite quickly through multiple cytosine deamination events. It would be an effective mechanism for producing key multi-cellular specific proteins, particularly for molecular machines that have system-dependent parts. Next, we'd go out and experimentally test this hypothesis.

I still fail to see how you test for intent. For all we know, the designer meant for life to stay unicellular. It could be that the designer did not forsee C-T transitions leading to the evolution of multicellular organisms.

You keep painting the bull's eye around multicellular life, but you have no way of showing that this was ever the target. Likewise with C-T transitions being the target for front loading. That is why I keep referring to the Sharpshooter Fallacy, because that is the fallacy you are committing.


This message is a reply to:
 Message 32 by Genomicus, posted 09-05-2012 7:01 PM Genomicus has not yet responded

  
Zargon
Junior Member (Idle past 2435 days)
Posts: 4
From: The United Kingdom
Joined: 09-21-2012


Message 36 of 285 (673742)
09-21-2012 9:22 PM


Intelligence
Creationists don't seem to know what Intelligence actually is:

They have this idea of an intelligent God which exists out side of space, time and the laws of nature. This understanding of an supernatural being completely contradicts our understanding of intelligence. Our human intelligence (We must remember that intelligence is a value or concept we apply to very complicated chemical systems and maybe soon, quantum mechanical systems) is the only known intelligence and it relies completely on the laws of nature. The choices we make are governed, when you delve deep enough, by quantum mechanics.

So how can a spaceless and time less God, beyond the control of the laws of science, be intelligent?

An intelligent God couldn't have created the Universe (absolutely everything, laws and all) because intelligence requires there to be a Universe (laws) in the first place.

The watch was created by an intelligent source: The Universe.


Replies to this message:
 Message 37 by Percy, posted 09-21-2012 10:32 PM Zargon has responded

  
Percy
Member
Posts: 18807
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.2


Message 37 of 285 (673744)
09-21-2012 10:32 PM
Reply to: Message 36 by Zargon
09-21-2012 9:22 PM


Re: Intelligence
Zargon writes:

So how can a spaceless and time less God, beyond the control of the laws of science, be intelligent?

The fallacy in your logic is to conclude that because the only intelligence we know of works within the confines of the laws of science that all intelligence must share that constraint.

--Percy


This message is a reply to:
 Message 36 by Zargon, posted 09-21-2012 9:22 PM Zargon has responded

Replies to this message:
 Message 38 by Zargon, posted 09-22-2012 6:33 AM Percy has responded
 Message 40 by Dr Adequate, posted 09-22-2012 7:30 AM Percy has acknowledged this reply

    
Zargon
Junior Member (Idle past 2435 days)
Posts: 4
From: The United Kingdom
Joined: 09-21-2012


Message 38 of 285 (673756)
09-22-2012 6:33 AM
Reply to: Message 37 by Percy
09-21-2012 10:32 PM


Re: Intelligence
Well, yes. What can really exist beyond the laws of science?

"...the only intelligence we know of works within the confines of the laws of science..."

I did say that but what I was also trying to portray was the idea that intelligence is actually just apart of these laws. It almost sounds like I'm all for the programmed universe with one set of codes that we and everything around us (laws and all) exist in.


This message is a reply to:
 Message 37 by Percy, posted 09-21-2012 10:32 PM Percy has responded

Replies to this message:
 Message 39 by Percy, posted 09-22-2012 7:27 AM Zargon has responded

  
Percy
Member
Posts: 18807
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.2


Message 39 of 285 (673757)
09-22-2012 7:27 AM
Reply to: Message 38 by Zargon
09-22-2012 6:33 AM


Re: Intelligence
Zargon writes:

Well, yes. What can really exist beyond the laws of science?

I don't know, but it sounds like you are saying that you know and that the answer is "Nothing."

There's an old saying in science: "Absence of evidence is not evidence of absence." Your conclusions outreach your evidence. Or as Wittgenstein said, "Whereof one cannot speak, thereof one must be silent."

Whatever speculations creationists or IDists might have about the nature of the creative intelligence responsible for life in our universe, if they want to claim it exists in a realm outside our universe then there's nothing science can say about it because we have no evidence. Of course, they also have no evidence, but they don't seem to understand that.

--Percy


This message is a reply to:
 Message 38 by Zargon, posted 09-22-2012 6:33 AM Zargon has responded

Replies to this message:
 Message 41 by Zargon, posted 09-22-2012 7:55 AM Percy has responded

    
Dr Adequate
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Posts: 16097
Joined: 07-20-2006


(2)
Message 40 of 285 (673758)
09-22-2012 7:30 AM
Reply to: Message 37 by Percy
09-21-2012 10:32 PM


Re: Intelligence
The fallacy in your logic is to conclude that because the only intelligence we know of works within the confines of the laws of science that all intelligence must share that constraint.

"The fallacy in your logic is to conclude that because the only pigs we know of can't fly that all pigs must share that constraint."

That's not a fallacy in logic, that's a correct application of empiricism.


This message is a reply to:
 Message 37 by Percy, posted 09-21-2012 10:32 PM Percy has acknowledged this reply

  
Zargon
Junior Member (Idle past 2435 days)
Posts: 4
From: The United Kingdom
Joined: 09-21-2012


Message 41 of 285 (673762)
09-22-2012 7:55 AM
Reply to: Message 39 by Percy
09-22-2012 7:27 AM


Re: Intelligence
Yes, I'm familiar with this point and completely agree. I feel that this point can be applied to my argument? Creationists only know of intelligence controlled by laws so creationists must claim that God is controlled by laws or claim that God is not intelligent and purely a natural event that created the Universe (Which follows scientific understanding).

This goes back to one of my original questions: So how can a spaceless and time less God, beyond the control of the laws of science, be intelligent? It (supernatural God) contradicts our understanding of the world.


This message is a reply to:
 Message 39 by Percy, posted 09-22-2012 7:27 AM Percy has responded

Replies to this message:
 Message 42 by Percy, posted 09-22-2012 8:54 AM Zargon has responded

  
Percy
Member
Posts: 18807
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.2


Message 42 of 285 (673765)
09-22-2012 8:54 AM
Reply to: Message 41 by Zargon
09-22-2012 7:55 AM


Re: Intelligence
Sorry, your chain of logic makes no sense to me.

--Percy


This message is a reply to:
 Message 41 by Zargon, posted 09-22-2012 7:55 AM Zargon has responded

Replies to this message:
 Message 43 by Zargon, posted 09-22-2012 11:51 AM Percy has acknowledged this reply

    
Zargon
Junior Member (Idle past 2435 days)
Posts: 4
From: The United Kingdom
Joined: 09-21-2012


Message 43 of 285 (673771)
09-22-2012 11:51 AM
Reply to: Message 42 by Percy
09-22-2012 8:54 AM


Re: Intelligence
It doesn't matter. I don't think my point is valid in this thread anyway.
This message is a reply to:
 Message 42 by Percy, posted 09-22-2012 8:54 AM Percy has acknowledged this reply

  
tesla
Member (Idle past 2288 days)
Posts: 1198
Joined: 12-22-2007


Message 44 of 285 (678590)
11-09-2012 8:49 AM
Reply to: Message 1 by Taq
08-30-2012 12:39 PM


spend it on space exploration/ Brain research.
Perhaps there is a species that is more advanced than the human race on another planet. Maybe that species could shed light on some of our ignorance, or even have higher capabilities of consciousness that human minds cannot even imagine.

Dump the money into designing ships and satellites to head for the earth-like planets we are discovering, dump it into light-speed research. Basically: dump it into space.

The only other way to research possibilities of discovering ID truth is to better understand our own consciousness. So it could also be dumped into brain research, and brain mapping. Maybe we could learn to ‘read’ brain waves via understanding how our brains record and relay information so well, that we could both read or write to a brain from a moderate distance. Maybe being able to do so would open the door to communication with an intelligence that is distant, yet still communicable with the right understanding.

So, there you have it. That’s what I would do if I was advocating or performing research on ID.


keep your mind from this way of enquiry, for never will you show that not-being is
~parmenides

This message is a reply to:
 Message 1 by Taq, posted 08-30-2012 12:39 PM Taq has responded

Replies to this message:
 Message 45 by Taq, posted 11-09-2012 12:49 PM tesla has responded

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


Message 45 of 285 (678624)
11-09-2012 12:49 PM
Reply to: Message 44 by tesla
11-09-2012 8:49 AM


Re: spend it on space exploration/ Brain research.
Perhaps there is a species that is more advanced than the human race on another planet. Maybe that species could shed light on some of our ignorance, or even have higher capabilities of consciousness that human minds cannot even imagine.
Dump the money into designing ships and satellites to head for the earth-like planets we are discovering, dump it into light-speed research. Basically: dump it into space.

The only other way to research possibilities of discovering ID truth is to better understand our own consciousness. So it could also be dumped into brain research, and brain mapping. Maybe we could learn to ‘read’ brain waves via understanding how our brains record and relay information so well, that we could both read or write to a brain from a moderate distance. Maybe being able to do so would open the door to communication with an intelligence that is distant, yet still communicable with the right understanding.

So, there you have it. That’s what I would do if I was advocating or performing research on ID.

Perhaps there is a species that is more advanced than the human race on another planet. Maybe that species could shed light on some of our ignorance, or even have higher capabilities of consciousness that human minds cannot even imagine.
Dump the money into designing ships and satellites to head for the earth-like planets we are discovering, dump it into light-speed research. Basically: dump it into space.

The only other way to research possibilities of discovering ID truth is to better understand our own consciousness. So it could also be dumped into brain research, and brain mapping. Maybe we could learn to ‘read’ brain waves via understanding how our brains record and relay information so well, that we could both read or write to a brain from a moderate distance. Maybe being able to do so would open the door to communication with an intelligence that is distant, yet still communicable with the right understanding.

So, there you have it. That’s what I would do if I was advocating or performing research on ID.

So your research would be more on how we could use ID in the future to design technology, correct?


This message is a reply to:
 Message 44 by tesla, posted 11-09-2012 8:49 AM tesla has responded

Replies to this message:
 Message 46 by tesla, posted 11-09-2012 8:59 PM Taq has responded

  
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