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Author Topic: Specification and Design  (Read 1674 times)
Reasoned Faith
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« Reply #15 on: October 31, 2007, 02:52:38 AM »

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As far as we know there are three modes of expanaition.  Two involve material mechanisms and include necessity driven by one or more of the physical laws and chance contingency based on random events.

I would think that chance and natural law are both part of the same domain. Random events at some level are driven by natural laws. The stray photon that alters DNA has itself a causal history. You can't assess probabilities without adequate background knowlege. You certainly can't work backward from a specific function and determine that its causal history is so improbable as to require some sort of unknown intervention by an unknown agent. Can you account for all the complex chemical interactions on a global scale that can lead to the vast number of possible functional proteins? Process of elimination at this level doesn't work.

Sure you can.  You can identify the number of permutations possible and identify probability distribution, without specific information.


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A second type of contingency is purposeful and we call it design.

"We" need a better definition of purposeful.


 If it is true that necessity, chance and design are the only three modes and since we have a good definition of necessity and a good definition of chance, everything else must be design.
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Reasoned Faith
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« Reply #16 on: October 31, 2007, 02:55:47 AM »

The thing is, if complexity can be measured by some kind of probability, it would help if actual values for one complex and one not complex enough example from molecular biology would be provided.

Yes, and this is why the test for Specified Complexity is set up the way it is so the we have an objective rather than subjective or a relative indicator.

Numbers please.

While I agree that an objective measure of complexity would be a great thing, I think that so far all examples we discussed were the type of:

- not complex enough (say sickle cell anemia)
- to complex to be a result of chance event (flagellum)

Unless probability values are attached, this is a very subjective evaluation of how complex this examples are.

The actual numbers depend on the event and permutations and probability distribution.  Fo numbers we need a specific situation.  Dice games work nicely to illustrate the process.  But, you may pick a specific case.
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Reasoned Faith
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« Reply #17 on: November 01, 2007, 04:00:47 AM »


I was trying to point out the futility of using an eliminative filter such as the one RF proposes to prove that what happened didn't happen particularly since what happened didn't need to happen in the way that it happened (?).

Scripto, using an eliminative filter it is not futile unless you are clairvoyant that something happened a particular way.

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Any event is so improbable at some level as to be almost mathematically impossible. Anyway, since the work goes on as far as finding evolutionary mechanisms,

And yet improbable events do happen all the time.  This is why probability analysis must address replication resources to ensure all the opportunities were considered and specification resources to ensure that the event was unique and distinguishable from all the other unlikely but incoherent results chance events generate.  It is interesting that as this work continues to find evolutionary mechanisms in the last 20 years no new mechanisms have been identified.

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there is insufficient background knowlege to assess the probabilities to apply this filter for specified complexity.


Nonsense.  Probability analysis does not require complete background information.

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I don't see the utility of it (and apparently neither do any working research biologists). At what level can you apply it? Certainly not in the observed fossil transitions from reptile to mammal and the hominid sequence.

History does provide us observed fossil transitions.  There is nothing to observe. It is nothing but presupposition.  There is no way to empirically confirm it. 

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Does it account for novel functions such as the observed evolution of the nylase enzyme?

Yes, it can and does demonstrate that frame shift that breaks usefull function and infrequently exploits new selection pressure with the modified protein is not beyond chance occurrence and existing evolutionary processes.

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It uses artificially constricted parameters to set a boundary which doesn't really appear to exist in the natural world in order to default the results to concepts of intelligence and design based on faulty analogies of human technologies.

In statistics and probability there is nothing artificial about objectively identifying and accounting for probabilistic resources and comparing those to the probability distribution of the events in question.  This is not an arbitrary process.
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« Reply #18 on: November 01, 2007, 04:11:16 AM »

The thing is, if complexity can be measured by some kind of probability, it would help if actual values for one complex and one not complex enough example from molecular biology would be provided.

Yes, and this is why the test for Specified Complexity is set up the way it is so the we have an objective rather than subjective or a relative indicator.

Numbers please.

While I agree that an objective measure of complexity would be a great thing, I think that so far all examples we discussed were the type of:

- not complex enough (say sickle cell anemia)
- to complex to be a result of chance event (flagellum)

Unless probability values are attached, this is a very subjective evaluation of how complex this examples are.

The actual numbers depend on the event and permutations and probability distribution.  Fo numbers we need a specific situation.  Dice games work nicely to illustrate the process.  But, you may pick a specific case.

I did pick specific cases, as seen from quotes. Sickle call anemia and flagellum.
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« Reply #19 on: November 01, 2007, 04:19:10 AM »

The argument is fundamentally silly. Complexity = God is a worthless explanation,

Indeed.  I avoid making this argument. But that doesn't stop you from falsly reframing the premise.

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as it quickly collapses in on itself due to using the trait to explain the trait under investigation while simultaneously having no evidence for the non-explanation in the first place.

The trait is used to explain the cause not the trait itself.  The evidence is that millions and millions of items and events with the same traits are known to be designed while no items with the traits has ever been adequately and specifically explained by materialistic mechanisms and no materialistic mechanism has ever been observed generating the subject traits.

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If God must have done X because it's too complex to have arisen naturally, then the same applies also to God, since is equally complex if not more so.

Non-sequiter I don't make this claim.

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Therefore, he's a shitty rationale for the existence of all complexity in the first place. Of course, you will just use your special pleading to put God outside the scope of the problem, as theists always do.

A designer is outside the scope of the problem.  We are looking at causation.  We are not looking for the cause of the cause.   This is not a special pleading because I do not ask those who argue for chance and necessity to explain how material causes chance and necestity to work and how it causes material to exist in the first place.

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You are also repeating the bogus nonsense about evolution not providing any evidence. Complete lie.

Go ahaed and start a new thread and prove that I lie about what evolution can and can't accomplish and what has and has not been observed with respect to evolutionary processes.  If it is as you say, it should be easy since in science lies are easy to expose.  Be careful though, empirical science requires observation, tests and repeatable results.  Historical artifacts provide clues about what might have been but they are not evidence about how those fossils came to be the way they are.
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Reasoned Faith
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« Reply #20 on: November 01, 2007, 04:29:27 AM »


Numbers please.

While I agree that an objective measure of complexity would be a great thing, I think that so far all examples we discussed were the type of:

- not complex enough (say sickle cell anemia)
- to complex to be a result of chance event (flagellum)

Unless probability values are attached, this is a very subjective evaluation of how complex this examples are.

The actual numbers depend on the event and permutations and probability distribution.  Fo numbers we need a specific situation.  Dice games work nicely to illustrate the process.  But, you may pick a specific case.

I did pick specific cases, as seen from quotes. Sickle call anemia and flagellum.

I'm not sure what you are asking for then.  You seem to be in agreement (without doing the math) that advent of the sickle trait is not very complex does not contain Specified Complexity and therefore chance events can account for it and that flagellum does exibit Specified Complexity.  Do you suggest that advent of the sickle gene by evolutionary process is an event that should be considered specified and complex?  Do you suggest that you know of specific evolutionary processes that could have built out flagellum from a bacteria gene pool that totally lacked flagellum?

Or are you simply asking that we go through the math for these examples?
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« Reply #21 on: November 01, 2007, 07:56:56 AM »

Or are you simply asking that we go through the math for these examples?

That's it. I want values of probability for these two examples. Numbers that will determine if these two events occured by chance or not.

You seem to be in agreement (without doing the math) that advent of the sickle trait is not very complex does not contain Specified Complexity and therefore chance events can account for it and that flagellum does exibit Specified Complexity.

No I am not. I want to see the math for these two.
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« Reply #22 on: November 01, 2007, 05:46:40 PM »

OK, the advent of Sickle Cell trait in hemoglobin first. The Sickle Cell gene is one base pair different from the far more common typical human Hb gene at position 6 of the 146 amino acids.  At position six in sickle trait the gene codes for valine instead of glutamic acid. One chance hypothesis for this event is that Hb at some time in the past underwent a single chance substitution of a base pair in one or more persons.  We know from empirical analysis that this kind of substitution occurs about once for every 100,000,000 base pairs.  This gene contains 146*3 or 438 base pairs (not relevant for this analysis) and at that slot there were three errors possible. By this hypothesis, the combined odds of this mechanism is 1/300,000,000.  Next let's consider the number of replication resources available to derive this event.  For this we take the estimate that there have been about 120,000,000,000 human births (~4,000,000,000 5,000 years ago) and perhaps three times as many miscarriages. Thus without considering the specification resources we already have a 99.998% probability (better since I have approximated) that this event could have occurred by chance over 5,000 years ago. By this we conclude that this event was not complex and did occur by chance.
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scripto
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« Reply #23 on: November 02, 2007, 07:22:25 AM »


I was trying to point out the futility of using an eliminative filter such as the one RF proposes to prove that what happened didn't happen particularly since what happened didn't need to happen in the way that it happened (?).

Scripto, using an eliminative filter it is not futile unless you are clairvoyant that something happened a particular way.

What I was attempting to say was that the probability calculations for the filter are based on the assumption that the target function was the only function that could arise. Not only are there redundant proteins with the same potential function (Cytochrome C) there have been independently evolved observed functions (Lactase tolerance).
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Any event is so improbable at some level as to be almost mathematically impossible. Anyway, since the work goes on as far as finding evolutionary mechanisms,

And yet improbable events do happen all the time.  This is why probability analysis must address replication resources to ensure all the opportunities were considered and specification resources to ensure that the event was unique and distinguishable from all the other unlikely but incoherent results chance events generate.  It is interesting that as this work continues to find evolutionary mechanisms in the last 20 years no new mechanisms have been identified.

As I understand it, small changes in regulatory genes can result in rather large changes in phenotype. I believe that is a relatively new field.
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there is insufficient background knowlege to assess the probabilities to apply this filter for specified complexity.


Nonsense.  Probability analysis does not require complete background information.

I said there is insufficient background knowlege.
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I don't see the utility of it (and apparently neither do any working research biologists). At what level can you apply it? Certainly not in the observed fossil transitions from reptile to mammal and the hominid sequence.

History does provide us observed fossil transitions.  There is nothing to observe. It is nothing but presupposition.  There is no way to empirically confirm it.

Not true. The fossil record fits rather nicely with the molecular and genetic evidence. It is also amenable to prediction, witness the findings of cetacean intermediates as predicted in the Indus river valley and that croc-fishy thing titika rosea, not to mention the hominid record. Fulfilled predictions put it in the realm of empiricism. 
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Does it account for novel functions such as the observed evolution of the nylase enzyme?

Yes, it can and does demonstrate that frame shift that breaks usefull function and infrequently exploits new selection pressure with the modified protein is not beyond chance occurrence and existing evolutionary processes.

Duplication and frame shift. It retained its original function and added a new one. The idea that all mutation results in broken function is wrong. And since there are numerous other evolved bacteria feeding on synthetic products (PCB,trinitrotoluene) these mutations aren't all that infrequent.
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It uses artificially constricted parameters to set a boundary which doesn't really appear to exist in the natural world in order to default the results to concepts of intelligence and design based on faulty analogies of human technologies.

In statistics and probability there is nothing artificial about objectively identifying and accounting for probabilistic resources and comparing those to the probability distribution of the events in question.  This is not an arbitrary process.


Demski's filter does not account for the observed data. Setting the parameters is arbritrary and the definitions are inadequate. Surely, if it had any utility, someone, somewhere would be using it. It's been more than 10 years.
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« Reply #24 on: November 02, 2007, 06:45:24 PM »

Scripto, using an eliminative filter it is not futile unless you are clairvoyant that something happened a particular way.

What I was attempting to say was that the probability calculations for the filter are based on the assumption that the target function was the only function that could arise.

The filter considers a rejection region of similar events and then identifies all other regions in sample space with equal or less probability distribution that are of equal specificity.  In this way all the events in all these regions are considered.  Your claim is false.


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Not only are there redundant proteins with the same potential function (Cytochrome C) there have been independently evolved observed functions (Lactase tolerance).

We observe that there are different and redundant proteins but we have no information about how they came to exist.  You accept presupposition that evolutionary processes generated these proteins but it is not empirically validated and furthermore we have never identified any processes that can accomplish what you assume has happened.


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And yet improbable events do happen all the time.  This is why probability analysis must address replication resources to ensure all the opportunities were considered and specification resources to ensure that the event was unique and distinguishable from all the other unlikely but incoherent results chance events generate.  It is interesting that as this work continues to find evolutionary mechanisms in the last 20 years no new mechanisms have been identified.

As I understand it, small changes in regulatory genes can result in rather large changes in phenotype. I believe that is a relatively new field.

This was discovered in the 1970's, and the processes are the same mutation process that have been known for some time.


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I said there is insufficient background knowlege.

You are splitting hairs.  Probability theory includes theorems that cover unknowns.  If one possible chance hypothesis is identified, all other must honor the number of permutations and degrees of freedom so far identified.


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Not true. The fossil record fits rather nicely with the molecular and genetic evidence.

Actually, it fits very poorly.  Also it would tell us only that some organisms are similar to others.  It cannot and does not informs us at all how that came to be.  We are discussing here the how.


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Duplication and frame shift. It retained its original function and added a new one. The idea that all mutation results in broken function is wrong.

Thus far experiment has failed to confirm duplication and frame shift so even it remains speculation.  Perhaps you have new information on this?


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And since there are numerous other evolved bacteria feeding on synthetic products (PCB,trinitrotoluene) these mutations aren't all that infrequent.

Point mutations (including frame shift) and duplications are quit frequent, you are correct.  At the same time, they don't generate much new information and seem limited to monoprotein function such as enzymes too.  Given the starting point and mode, they are similar to the sickle cell trait complexity example above.
 

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Demski's filter does not account for the observed data.

On the contrary, the fact that it accounts for the data very well is the power of it as a filter.  You turn a blind eye to those who have used the filter.
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« Reply #25 on: November 04, 2007, 09:35:08 PM »

By this we conclude that this event was not complex and did occur by chance.

And now an example that is too complex to happen by chance.
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« Reply #26 on: November 04, 2007, 11:22:05 PM »

The problem is that creationists tend to misrepresent evolution as some giant implausible saltation event. It couldn't be farther from the truth. If it were the case, then yes, it would be unlikely and the complexity would argue against "evolution" of that form, but reality defeats that assumption.

Evolution is unguided, but non-random algorithm. It's a slow build-up from A to F, not a direct jump immediately. Given the times involved and the slow process of build-up wherein you can lock-in changes, it's very unlikely at all and complexity doesn't negate it.

But positing "design" as the necessity because it's complex is a non-answer anyway, since God is far more or at least equally as complex. It doesn't answer the problem to use the very trait your looking to answer to answer itself, especially when the "answer" is effectively an unknown variable.
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scripto
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« Reply #27 on: November 06, 2007, 07:12:17 AM »

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I said there is insufficient background knowledge.

You are splitting hairs.  Probability theory includes theorems that cover unknowns.  If one possible chance hypothesis is identified, all other must honor the number of permutations and degrees of freedom so far identified.

That may be true if you have a defined alternative event to match the probabilities against. In fact, the very definition of design using the filter depends on eliminating all other considerations. This requires more background knowledge than we have. Even if the filter worked, without a firm definition of design, there is no reason to conclude that specified complexity automatically defaults to design when the alternatives can include unknown or as yet to be discovered processes. Intelligent design, whatever that might be, would only be one of many possibilities.

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Demski's filter does not account for the observed data.


On the contrary, the fact that it accounts for the data very well is the power of it as a filter.  You turn a blind eye to those who have used the filter.

I can't see what I can't find. Some independent corroboration, please.
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« Reply #28 on: November 06, 2007, 04:29:58 PM »

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I said there is insufficient background knowledge.

You are splitting hairs.  Probability theory includes theorems that cover unknowns.  If one possible chance hypothesis is identified, all other must honor the number of permutations and degrees of freedom so far identified.

That may be true if you have a defined alternative event to match the probabilities against. In fact, the very definition of design using the filter depends on eliminating all other considerations. This requires more background knowledge than we have.

Probability studies are ideal for situations where background information is sparse.  With background knowledge, we don't need probability to predict cause.

 
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Even if the filter worked, without a firm definition of design, there is no reason to conclude that specified complexity automatically defaults to design when the alternatives can include unknown or as yet to be discovered processes. Intelligent design, whatever that might be, would only be one of many possibilities.

this is why it is important to identify the modes of causation.

1. Necessity -- driven by physical law
2. Unconstrained contingency - Pure Chance
3. Unintentional constrained contingency - for example mutation and natural selection
4. Intentional constrained contingency - design

Perhaps you can improve on this model by adding a fifth mode.  The SC filter eliminates option one through three. If there are no others then it has to be design.

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I can't see what I can't find. Some independent corroboration, please.


Perhaps you should open your eyes first.  SC is an objective but otherwise unaltered application of the Fisherian probability model.  You will find that Fisher's probability mode is widely accepted.
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« Reply #29 on: November 07, 2007, 05:09:56 AM »

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I said there is insufficient background knowledge.

You are splitting hairs.  Probability theory includes theorems that cover unknowns.  If one possible chance hypothesis is identified, all other must honor the number of permutations and degrees of freedom so far identified.

That may be true if you have a defined alternative event to match the probabilities against. In fact, the very definition of design using the filter depends on eliminating all other considerations. This requires more background knowledge than we have.

Probability studies are ideal for situations where background information is sparse.  With background knowledge, we don't need probability to predict cause.

You miss my point. Design events will change as the background information changes. It has no definitive existence on its own. Certainly not one outside of natural processes.
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Even if the filter worked, without a firm definition of design, there is no reason to conclude that specified complexity automatically defaults to design when the alternatives can include unknown or as yet to be discovered processes. Intelligent design, whatever that might be, would only be one of many possibilities.

this is why it is important to identify the modes of causation.

1. Necessity -- driven by physical law
2. Unconstrained contingency - Pure Chance
3. Unintentional constrained contingency - for example mutation and natural selection
4. Intentional constrained contingency - design

Perhaps you can improve on this model by adding a fifth mode.  The SC filter eliminates option one through three. If there are no others then it has to be design.

Not without some empirical evidence for design it isn't.

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I can't see what I can't find. Some independent corroboration, please.


Perhaps you should open your eyes first.  SC is an objective but otherwise unaltered application of the Fisherian probability model.  You will find that Fisher's probability mode is widely accepted.

That's not my question. What is the utility of the eliminative filter, what biologists are using it and at what level can they apply it?
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