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OgreMkV



Posts: 3668
Joined: Oct. 2009

(Permalink) Posted: Jan. 16 2015,08:04   

This is a thread for a creationist that has been visiting my blog. You can review his comments here: http://www.skepticink.com/smilodo....omputer

He seems to have some questions that he can't get answers to. Feel free to chime in.

He has stated that he will come by. We'll see.

--------------
Ignored by those who can't provide evidence for their claims.

http://skepticink.com/smilodo....retreat

   
cryptoguru



Posts: 53
Joined: Jan. 2015

(Permalink) Posted: Jan. 16 2015,09:09   

Hi Kevin,

thanks for the introduction.

I'm going to pose the following definition/algorithm of biological evolution, please feel free to disagree and post what you think it actually is.

Here are some assumptions:
1) DNA is a self-replicating computer code, a list of instructions that is used by a cell to build a specific organism by a very complex and highly non-linear process that involves transcription and translation.
2) DNA is randomly mutated at the level of nucleotides (i.e. the letters of the programming code, not the functional/gene level)
3) Natural selection is not an intelligent entity, therefore it cannot evaluate the performance of an organism. It is the name given to the process whereby more suitable organisms survive and others die ... achieved by a selective pressure being applied to the environment (e.g. availability of food/water, predators etc.)

Evolution is:
1) take an organism and let it replicate
2) random mutations should be introduced to the offspring DNA.
3) a selective pressure is applied to the environment the organisms live in
4) less fit organisms will die before replicating due to the pressure
5) most fit organisms will continue to replicate and mutate
6) eventually new functions and traits will emerge

Biological Evolution is presented as a scientific law, it is simple to define, so should be simple to model

My challenge is this.
Show me a computer model that models this process and shows new functions and information being added to the genome.

caveats:
- Mutation can't simply combine functions in different arrangements. Mutation must occur on the code that defines the functions themselves, and affect the ability of the organism to build itself, to function and to replicate.
- the selective process can't include measuring properties of the organism to remove them from the population, the selective process must rely on organisms dying off due to the environmental factors. (e.g. energy)

It may sound subtle ... but breaking these laws means that you're not modelling biological evolution, you're performing functional optimisation. This is VERY different, as the degrees of freedom of the problem have been limited so that a solution is either stochastically highly likely or definite.

So far I have seen no model that satisfies the conditions to be a true model of biological evolution. I am not doubting that there are numerous models that show the seeming emergence of complexity. However, when you limit the problem to randomly selecting functions to solve a problem, if the problem space is well defined and the functional space is limited then you are simply performing a stochastic search .. this is NOT evolution. You are not inventing functions out of nothing, you are finding the best way to perform a pre-determined function.

I assert that it is impossible for a truly random mutation process to create new functionality if that functionality doesn't exist already in component form.
EXAMPLE
Given all the parts for a clock in sensible quantities it is reasonable to assume that randomly choosing components until you get a functioning clock through an optimisation algorithm is completely achievable.
Blind Watchmaker Evolution
However, if you didn't define the component parts and allowed random shaped parts to be randomly mutated as well as selected and combined through a similar optimisation algorithm, you would never expect to get a working clock. (this is what biological evolution is claimed to do)

I know of AVIDA, but it uses 26 predefined functions to combine to solve optimisation problems ... it doesn't mutate the code that defines these functions or how they're executed. It also doesn't model real-world selection.

I am a computer modeller and Mathematical Biology researcher, so I'm writing my own code which I believe will demonstrate the proposed mechanism more accurately ... I will share (with source) when it's done.

I am interested in an intellectual discussion here, not a creationist-bashing flame-war ... if you don't have any scientific answers that hold up to scrutiny please don't just post insults as though that's going to help. And please don't just make unsubstantiated claims, back them up with logic or research that can be shown to be applicable to this issue.

Cheers

Crypto

  
JonF



Posts: 634
Joined: Feb. 2005

(Permalink) Posted: Jan. 16 2015,09:22   

Define "adding information".

  
midwifetoad



Posts: 4003
Joined: Mar. 2008

(Permalink) Posted: Jan. 16 2015,09:33   

Quote
- Mutation can't simply combine functions in different arrangements. Mutation must occur on the code that defines the functions themselves, and affect the ability of the organism to build itself, to function and to replicate.


Well that's not exactly what happens in biological evolution. It is rare for the infrastructure of translation to change. It would seem that the likelihood of a mutation being tolerated is inversely proportional to its effect on the cell infrastructure.

That's a rather sloppy way of saying that vital functions are highly conserved.

--------------
Any version of ID consistent with all the evidence is indistinguishable from evolution.

  
NoName



Posts: 2729
Joined: Mar. 2013

(Permalink) Posted: Jan. 16 2015,09:33   

Many things are simple to define but appallingly complex, if not impossible, to model.  Fluid flow is one vast field where there are simple descriptions and definitions of phenomena that resist modeling.
The same goes for economics.
The same goes for such iterative functions as produce the Mandelbrot and Julia sets, as well as a host of other similar phenomena.  I add these because while we can 'model' them by virtue of producing the simple equation and iteration process involved, we cannot, in principle, predict what will be the result at any given point.  Models are not perfect predictors, nor is that their purpose.
Finally, let us note that the current absence of a model does not say anything about the possibility of ever modeling any particular phenomenon.  What we can say is that, in principle, it is impossible to assert that any given model can be predictive of real-world results, regardless of how many models are, in fact, predictive of such results.

  
midwifetoad



Posts: 4003
Joined: Mar. 2008

(Permalink) Posted: Jan. 16 2015,09:46   

Quote
However, if you didn't define the component parts and allowed random shaped parts to be randomly mutated as well as selected and combined through a similar optimisation algorithm, you would never expect to get a working clock. (this is what biological evolution is claimed to do)


If you intend to model evolution (possibly with the intention of demonstrating that life cannot arise "spontaneously," Your component parts will be expressed as chemistry.

Before wasting your time, please solve the problem of emergence. Demonstrate that you can predict, for example, the properties of water by deriving them from the properties of hydrogen and oxygen.

--------------
Any version of ID consistent with all the evidence is indistinguishable from evolution.

  
damitall



Posts: 331
Joined: Jan. 2009

(Permalink) Posted: Jan. 16 2015,09:51   

I believe that Dr Elizabeth Liddle ("Febble", and "Pingu") has ideed modelled the addition of new information in an computer simulation of evolutionary process - at least that type of information known to IDists as "CSI" or any one of a number of related acronyms.

I can't be arsed to look it out, but an intelligent search of The Skeptical Zone should reveal it.

It certainly caused an outbreak of the malice and vituperation to be expected from IDists with no answers

  
NoName



Posts: 2729
Joined: Mar. 2013

(Permalink) Posted: Jan. 16 2015,09:55   

Quote (cryptoguru @ Jan. 16 2015,10:09)
...
Here are some assumptions:
1) DNA is a self-replicating computer code, a list of instructions that is used by a cell to build a specific organism by a very complex and highly non-linear process that involves transcription and translation.

Questionable definition -- it is almost certainly question-begging, if not entirely incorrect, to assert that DNA is a 'computer code'.  To do so is to take metaphorical language and reify it to the point where the specific phrase becomes meaningless.
 
Quote
2) DNA is randomly mutated at the level of nucleotides (i.e. the letters of the programming code, not the functional/gene level)

OK, but this obscures the fact that function is tied to specific DNA arrangements.  Note, too, that those arrangements include physical folding and proximity to other DNA fragments.
 
Quote
3) Natural selection is not an intelligent entity, therefore it cannot evaluate the performance of an organism.

Half true, half radically false.  Yes, 'Natural Selection' is not an intelligent entity, but this is because it is not an entity at all.  It is a process.  The distinction matters.  Whether this process can, or need be, called 'intelligent' really depends on what your operational definition of 'intelligence' is.  I know researchers who take a stance towards intelligence that includes processes such as natural selection within the scope of intelligent behavior.  I know others who reject that judgement.  You appear to be taking an anthropomorphic, physicalist (i.e., embodied) approach to intelligence such that 'natural selection', not having a body (or a soul?) cannot be 'intelligent'.  What's your operational definition of 'intelligence' such that you can support your assertions using the term?
 
Quote
It is the name given to the process whereby more suitable organisms survive and others die ... achieved by a selective pressure being applied to the environment (e.g. availability of food/water, predators etc.)

Correct but misleading.  What natural selection does is always negative.  It weeds out failures.  The failures are always with respect to the organism's current environment and is only usefully evaluated at the group level.
 
Quote

Evolution is:
1) take an organism and let it replicate
2) random mutations should be introduced to the offspring DNA.
3) a selective pressure is applied to the environment the organisms live in
4) less fit organisms will die before replicating due to the pressure
5) most fit organisms will continue to replicate and mutate
6) eventually new functions and traits will emerge

Biological Evolution is presented as a scientific law, it is simple to define, so should be simple to model

See my previous reply.
 
Quote
My challenge is this.
Show me a computer model that models this process and shows new functions and information being added to the genome.

Why the insistence on a computer model?  Lenski et al have performed this over tens of thousands of generations in the lab and verified the process.  What more is required?
How is gene duplication not an increase of information in an organism?  Trivially, the information of the number of genes, and therefore DNA base pairs, has changed, in fact, increased.
 
Quote
caveats:
- Mutation can't simply combine functions in different arrangements. Mutation must occur on the code that defines the functions themselves, and affect the ability of the organism to build itself, to function and to replicate.

Why?
 
Quote
- the selective process can't include measuring properties of the organism to remove them from the population, the selective process must rely on organisms dying off due to the environmental factors. (e.g. energy)

Weasel-worded and a distinction without a difference.
If it's done in a computer model, measurement will happen, albeit properly the measurement does indeed need to be of survival(reproduction)/failure(to survive and to reproduce).  How else do you propose to determine the whether selection occurred at all in a computer model?  Randomly?  That is invalid for ecosystems due to the inherently constrained nature of the 'change space'.  See below.
 
Quote
It may sound subtle ... but breaking these laws means that you're not modelling biological evolution, you're performing functional optimisation. This is VERY different, as the degrees of freedom of the problem have been limited so that a solution is either stochastically highly likely or definite.

As I said before, weasel-worded.  A distinction without a difference.  Natural selection is a functional optimization.  And the work has been done in the lab that verifies it.

Quote
So far I have seen no model that satisfies the conditions to be a true model of biological evolution. I am not doubting that there are numerous models that show the seeming emergence of complexity. However, when you limit the problem to randomly selecting functions to solve a problem, if the problem space is well defined and the functional space is limited then you are simply performing a stochastic search .. this is NOT evolution. ...

No, that is simply confused.
The problem, in part, is that the random changes are inherently constrained by the laws of physics, chemistry, and thermodynamics.  The 'change space' is not infinite although it may be unimaginably large.  The ever changing 'problem space' against which the specific changes which occur are evaluated is also inherently constrained by the laws of physics, chemistry, and thermodynamics.  It is not infinite even if it might be unimaginably large.  
Neither the 'change space' nor the 'problem space' is free to vary perfectly randomly.  
There is also the factor of time.  Either space may hold relatively constant while the other space changes at a greater or lesser rate.  Both spaces may change relatively quickly or slowly.  Neither space may vary much.  Over varying spans of time, these temporal factors matter tremendously.

  
cryptoguru



Posts: 53
Joined: Jan. 2015

(Permalink) Posted: Jan. 16 2015,10:06   

My field of research originally was fluid mechanics, lately I've applied that to biological chaotic flows. I've written a LOT of programs that model fluids. We can accurately model the components of fluid flow (as well as chemical reactions with them), sure it's complicated but we can do it ... and we can compare them to real-world observations. (Watch any Disney 3D animated movie). We can model complex environmental interactions too ... it's done everyday and applied to thousands of useful real-world problems.

The definition of evolution is simple and it's implementation is simple too ... a self-building, self-replicating entity is mutated so that the code that runs it is mutated at an atomic (nucleotide) level. That's easy to model, I can write code to do that in a couple of hours ... my point is the other models that are used as "proofs" of the theory evolution do not prove anything, they simply solve optimisation problems, which is not the same thing.

JonF: "adding information" - new and novel functions that didn't exist before that solve a problem that wasn't solved previously.

midwifetoad: I'm not just asking that vital functions be conserved I'm asking that the overall net effect is improvement after mutation occurs on the definition of the code that is being run. DNA is an information system, it defines the process by which something is built ... we are mutating THAT. Not simply selecting between functions.

midwifetoad: the properties of water are observed, we understand the physics and chemistry behind them. We don't need to model things from atoms ... but we do need a model that reflects the theory to test the theory is sound, we don't have that with evolution.

  
NoName



Posts: 2729
Joined: Mar. 2013

(Permalink) Posted: Jan. 16 2015,10:19   

Quote (cryptoguru @ Jan. 16 2015,11:06)
... That's easy to model, I can write code to do that in a couple of hours ... my point is the other models that are used as "proofs" of the theory evolution do not prove anything, they simply solve optimisation problems, which is not the same thing.

Why and how not?

Evolution is the solution of an optimization problem.  Optimize the reproductive success of ever changing, in constrained ways, collections of organisms in an every changing, in constrained ways, environment.

As to 'easy to model, I can write code to do that in a couple of hours', well, no you can't.  Not and model all the factors involved in physically functional (in all senses) genes or chromosomes.  If you could, we'd have a trivial solution to the folding problem, and we don't.  Physical structure is inherently bound to a wide variety of factors impacting the existence and functionality of specific DNA segments in situ.  Slight changes to chemical structure can have anywhere from minor to overwhelming impact on the physical structure, and vice versa.  Your 'couple of hours effort' model is so flawed as to be meaningless for an actual simulation of the reality you are attempting to assess or reject.  It provides essentially zero guidance to what can and does happen in the living environment in the chemical, physical, and thermodynamic realities constantly at play at the level of DNA.  You might as well be solving the 3 body problem by recourse to the behavior of balls swung on the end of strings.

Also, I note you ignored a couple of my key points in your rejoinder:  the success of any number of computer molding strategies says nothing whatsoever about the in principle solvability of all problems with computer modeling strategies.  This has been proven as well as demonstrated, countless times in countless fields.
Nor does the present absence of any particular model or computer simulation speak to the in principle possibility or lack thereof of a future model.

  
midwifetoad



Posts: 4003
Joined: Mar. 2008

(Permalink) Posted: Jan. 16 2015,10:19   

It has already been noted that you are reifying a metaphor. DNA is not a computer program, It is a molecule.

The map is not the territory. Dawkins' Weasel does not prove evolution (although it would be interesting if it didn't work).

Now if you, in your brilliance, can model the HOX gene and can model how variations in form and body plan can be made by varying the timing of developmental events, you might have something useful.

But what will be demonstrated if you fail to model biological evolution? I can write a program that doesn't work.

I'm trying to get a grip on your hypothesis. What are you trying to demonstrate?

--------------
Any version of ID consistent with all the evidence is indistinguishable from evolution.

  
cryptoguru



Posts: 53
Joined: Jan. 2015

(Permalink) Posted: Jan. 16 2015,10:33   

Quote
if not entirely incorrect, to assert that DNA is a 'computer code'


I've been over this ground on the other site.
DNA is a computer code ... a living cell is a computer, not analogous to a computer, but IS a computer.
This is a true statement because it fulfils the definition of a computer as a Turing machine.
This is also proved by the fact that we use the living cell as a computer ourselves now
DNA computing - Wikipedia
There are LOTS of evolutionists who attest to this fact.

The reason you're avoiding this definition is because you want to keep it mysterious and difficult to pin down.

Quote
OK, but this obscures the fact that function is tied to specific DNA arrangements.  Note, too, that those arrangements include physical folding and proximity to other DNA fragments.

I don't see how what I said contradicts that? I'm just speaking in generic terms.



Quote
You appear to be taking an anthropomorphic, physicalist (i.e., embodied) approach to intelligence such that 'natural selection', not having a body (or a soul?) cannot be 'intelligent'.

I think you're jumping the gun here, I'm not claiming Natural Selection is powerless to do anything, I'm just asserting that it is not like a god ... it can't measure and evaluate, it's not magic. It is simply the process of filtering organisms that don't work in their environment. It's not the Grim Reaper going around choosing who to kill. Therefore modelling processes that attempt to model natural selection as though it is intelligent are incorrect.

Quote
Correct but misleading

Again, I complete agree with your definition there ... I am not trying to be sneaky. Nothing I said disagrees with your understanding of natural selection, unless you think it IS magic.


Quote
Lenski et al have performed this over tens of thousands of generations in the lab and verified the process

Lenski has demonstrated E. Coli doing exactly what E Coli is programmed to do, it adapts (this is true of all viruses and bacteria) ... this does not demonstrate new features. They've performed an equivalent of millions of years of evolution ... where's the more complex life-forms? They're still bacteria!

Again ... a computer model should be able to at least prove the theory is possible.


Quote
The problem, in part, is that the random changes are inherently constrained by the laws of physics, chemistry, and thermodynamics

You're grasping at straws ... random mutations are random. Natural selection is purely the ability for the organism to keep on reproducing. It can fail to do that for many reasons e.g. competition for food, disease etc
But the process is simple


Quote
If it's done in a computer model, measurement will happen, albeit properly the measurement does indeed need to be of survival(reproduction)/failure(to survive and to reproduce).  How else do you propose to determine the whether selection occurred at all in a computer model?  Randomly?

I completely agree ... but we should be doing as you suggest measuring survival and not measuring for example how fast something goes. If we want to measure speed competition, we need to let the organisms have speed and see which survive, not calculate speeds and set an arbitrary threshold ... does that make sense to what I'm saying now?

  
Cubist



Posts: 558
Joined: Oct. 2007

(Permalink) Posted: Jan. 16 2015,10:37   

Quote (cryptoguru @ Jan. 16 2015,09:09)
My challenge is this.
Show me a computer model that models this process and shows new functions and information being added to the genome. [emphasis added]

Whether or not you, yourself, are a Creationist, cryptoguru, this challenge of yours is (whether you realize it or not) the hoary old mutations can't create new information argument beloved of Creationists, just dressed up in computer terminology. So please, tell us if you will: What does "new information" look like? Given an arbitrary string of nucleotides, and a mutation which alters that string of nucleotides, how can you tell whether or not the post-mutation version of that string contains any "new" information?

  
cryptoguru



Posts: 53
Joined: Jan. 2015

(Permalink) Posted: Jan. 16 2015,10:43   

midwifetoad:

I explained to you why it is a computer program. You call DNA a double helix, it is a definition of it's shape. A computer program is a definition of its function.
You need to understand the definition of a computer.
Nature article on cell being Turing machine

I'm not trying to model the WHOLE of proposed biological evolution ... what nonsense are you suggesting?

I'm modelling the key components ... a key component is the code that is executed by the cell's operating system is mutated, which gives the possibility of it crashing (death) ... this is what we observe through genetic mutations.

I'm suggesting we model the core tennets of evolution ... existing models do not do this.

  
midwifetoad



Posts: 4003
Joined: Mar. 2008

(Permalink) Posted: Jan. 16 2015,10:51   

When you build such a model that works, I'll be impressed.

Explain why I should be impressed by a model that fails.

--------------
Any version of ID consistent with all the evidence is indistinguishable from evolution.

  
Wesley R. Elsberry



Posts: 4991
Joined: May 2002

(Permalink) Posted: Jan. 16 2015,10:52   

Avida.

--------------
"You can't teach an old dogma new tricks." - Dorothy Parker

    
midwifetoad



Posts: 4003
Joined: Mar. 2008

(Permalink) Posted: Jan. 16 2015,10:55   

Quote
I explained to you why it is a computer program. You call DNA a double helix, it is a definition of it's shape. A computer program is a definition of its function.


The word program is a metaphor. You cannot determine the limitations of DNA from the limitations of a computer program.

Just as you cannot determine the existence or non-existence of a landscape feature from a map.

--------------
Any version of ID consistent with all the evidence is indistinguishable from evolution.

  
Doc Bill



Posts: 1039
Joined: April 2007

(Permalink) Posted: Jan. 16 2015,10:55   

Greetings, NotGuru, we meet again!

Perhaps a full disclosure of your real purpose is in order.  I present to you NotGuru's Agenda:

Quote
I paint evolution (non-science) as faith ... because it is.
It's an absurd unsupported set of stories, based on the premise that there is no possibility of non-material causation. It satisfies a huge amount of self-centred god-haters, who've wanted nothing more than a decent excuse to pretend that there are no eternal consequences for their actions.

You still don't address any of the gaping black holes that I've pointed out.


I'm thinking this one is a Gary Gaulin clone, but super tard charged.  If you don't mind I'll duck out and get some popcorn.

  
rossum



Posts: 289
Joined: Dec. 2008

(Permalink) Posted: Jan. 16 2015,11:03   

Quote (cryptoguru @ Jan. 16 2015,09:09)
My challenge is this.
Show me a computer model that models this process and shows new functions and information being added to the genome.

Certainly.  Dr. Lenski used the Avida program to show the evolution of new functions.

The cover page is The Evolutionary Origin of Complex Features

The detail is line of descent.

For "new informaiton" you will need to tell us how you are calculating the quantity of information present.  Evolution can increase both Shannon and Kolmogorov information.  Are you using a different measure?

rossum

--------------
The ultimate truth is that there is no ultimate truth.

  
OgreMkV



Posts: 3668
Joined: Oct. 2009

(Permalink) Posted: Jan. 16 2015,11:18   

Perhaps, he will listen to you guys. I've said all this already.

crypto, perhaps you should explain, in detail why AVIDA does not do what the writers of the software say it does... and show that it does in the paper I provided you.

This ought to be entertaining.

We desperately need a popcorn smiley.

--------------
Ignored by those who can't provide evidence for their claims.

http://skepticink.com/smilodo....retreat

   
NoName



Posts: 2729
Joined: Mar. 2013

(Permalink) Posted: Jan. 16 2015,11:47   

Quote (cryptoguru @ Jan. 16 2015,11:33)
   
Quote
if not entirely incorrect, to assert that DNA is a 'computer code'


I've been over this ground on the other site.
DNA is a computer code ... a living cell is a computer, not analogous to a computer, but IS a computer.

Prove it.  Don't assert it, prove it.
You can't because there simply are no significant respects in which it is true.
The entire realms of thermodynamic effects and of self-assembly, with constrained errors, and self-repair, with constrained errors, simply have no equivalent in computers.  At all.
This metaphor is wildly less accurate and wildly less appropriate to the cases at hand than 'natural selection'.
So, once again, prove it.  Don't assert it, don't point me to garbage sites where you've also asserted it.
It's a simple proposition, it should be simple to prove, without abstracting away all the differences that make a difference.
   
Quote
This is a true statement because it fulfils the definition of a computer as a Turing machine.

A computer is a Turing machine.  Are all Turing machines computers?  Proof please.
   
Quote
This is also proved by the fact that we use the living cell as a computer ourselves now
DNA computing - Wikipedia
There are LOTS of evolutionists who attest to this fact.

Irrelevant and absurd.  We can use strings and beads as calculating machines, this does not mean that strings and beads are calculators.

   
Quote
The reason you're avoiding this definition is because you want to keep it mysterious and difficult to pin down.

No.  And offensive.
We're 'avoiding' this definition because it is not a definition and because it is incorrect.  It is analogy run amuck.
   
Quote

     
Quote
OK, but this obscures the fact that function is tied to specific DNA arrangements.  Note, too, that those arrangements include physical folding and proximity to other DNA fragments.

I don't see how what I said contradicts that? I'm just speaking in generic terms.

And the genericity is where you go wrong.  The same set of DNA patterns operate, or fail to operate, depending on the physical arrangement of other DNA patterns, which are dynamic over time.
That you don't understand this fundamental fact demonstrates that you are unprepared to make the claims you are in fact making.
Do you even know what the folding problem is?  Or why it matters, and matters particularly in this problem space?

   
Quote
     
Quote
You appear to be taking an anthropomorphic, physicalist (i.e., embodied) approach to intelligence such that 'natural selection', not having a body (or a soul?) cannot be 'intelligent'.

I think you're jumping the gun here, I'm not claiming Natural Selection is powerless to do anything, I'm just asserting that it is not like a god ... it can't measure and evaluate, it's not magic.

Disagreement without basis.  No one is claiming it is, or 'is like' a god (for one thing, it is not fictional or mythical, it does not operate by miracles, and it can be seen in action in controlled and well-defined tests, none of which can be done with any god ever proposed).  It is, in the sense it which you are using it here, a description of a process of evaluation, of measurement.  It measures, it evaluates, reproductive failure.  That's all it has to do.
We have operational definitions.  It appears you do not.
   
Quote
It is simply the process of filtering organisms that don't work in their environment. It's not the Grim Reaper going around choosing who to kill. Therefore modelling processes that attempt to model natural selection as though it is intelligent are incorrect.

     
Quote
Correct but misleading

Again, I complete agree with your definition there ... I am not trying to be sneaky. Nothing I said disagrees with your understanding of natural selection, unless you think it IS magic.


     
Quote
Lenski et al have performed this over tens of thousands of generations in the lab and verified the process

Lenski has demonstrated E. Coli doing exactly what E Coli is programmed to do, it adapts (this is true of all viruses and bacteria)

Can you say 'begging the question'?  You appear to be arguing that cells/organisms are programmed by asserting as one of your premises that cells/organisms are programmed.
You are also making recourse to a particularly problematic undefined metric -- what and how do you determine which organism is 'more advanced' than some other?  What is the metric of advancement?  It is, in fact, a holdover from superstition that saw all life as a glorious unfolding of lower creatures to higher creatures, culminating in mankind.  Which is indefensibly stupid not least because it is entirely unsupported by facts of any sort.
Either all creatures are equally advanced, or bacteria are far more advanced than humans because they've been evolving for more generations.
Either drop this 'more advanced' crap or provide facts, evidence, logic, and operational definitions to make it clear and unequivocal for all to see.
   
Quote
... this does not demonstrate new features. They've performed an equivalent of millions of years of evolution ... where's the more complex life-forms? They're still bacteria!

They are 'more advanced' bacteria in that they demonstrate features strictly absent from the parent population.
How does this not meet your challenge?  You're refusing to accept it because it leaves you without a foundation for your creationism.
 
Quote
Again ... a computer model should be able to at least prove the theory is possible.

See responses from others.

     
Quote
 
Quote
The problem, in part, is that the random changes are inherently constrained by the laws of physics, chemistry, and thermodynamics

You're grasping at straws ... random mutations are random.
No, they are only random with respect to certain factors, such as future needs of the organism.  They are highly constrained.  You are handwaving away the hard problem, essentially by ignoring it.  The results of that act of ignorance are errors which permeate your argument from the point of deciding these critical factors don't matter.  It's as if you were arguing that the SR-71 could not be supersonic because your plastic model would melt at the friction imposed at mach speeds.
 
Quote
Natural selection is purely the ability for the organism to keep on reproducing. It can fail to do that for many reasons e.g. competition for food, disease etc
But the process is simple


     
Quote
If it's done in a computer model, measurement will happen, albeit properly the measurement does indeed need to be of survival(reproduction)/failure(to survive and to reproduce).  How else do you propose to determine the whether selection occurred at all in a computer model?  Randomly?

I completely agree ... but we should be doing as you suggest measuring survival and not measuring for example how fast something goes. If we want to measure speed competition, we need to let the organisms have speed and see which survive, not calculate speeds and set an arbitrary threshold ... does that make sense to what I'm saying now?

And we're back to the critical issue of exactly what do you mean by 'intelligent'.  As you use it here, you appear to  mean that intelligence is inherently purposive, that it operates with 'purpose aforethought'.  That is a peculiarly anthropomorphic, and ultimately too tightly restrictive, a definition of 'intelligence'.
It's clear you throw the word around as a magic wand because you do not, and likely cannot, provide an operational definition that will suit in all cases of your use of the term.
NO ONE is asserting that 'natural selection' is any sort of Grim Reaper going around and thinking about which individuals out of which groups are going to live or die at any given time.  Why would anyone assert that when it is so clearly incorrect?
What 'natural selection' is is simply a description of the failure of certain contained-random changes in the genome to persist in a population across time in a given constrained-random environment.  It requires no purpose, no planning, no intention or intentionality.  It's how the world works.  No one has ever shown otherwise.
Nor has anyone shown that changes to the genome do not occur, randomly with respect to their environment and constrained by the laws of physics, chemistry, and thermodynamics.
Nor has anyone shown that information cannot increase due to simply chemical and physical processes, constrained in various natural ways including thermodynamically and by containment.
You've ignored the examples that demonstrate this.
Why is that?
Is 'information' another magic word that you throw around without being able to provide a consistent coherent operational definition for?

  
qetzal



Posts: 311
Joined: Feb. 2006

(Permalink) Posted: Jan. 16 2015,11:53   

Quote (cryptoguru @ Jan. 16 2015,9:09)
My challenge is this.
Show me a computer model that models this process and shows new functions and information being added to the genome.


Quote (cryptoguru @ Jan. 16 2015,10:33)
[A] living cell is a computer, not analogous to a computer, but IS a computer.


Perfect. Lenski already demonstrated new functions being added to the genome using E. coli, which are living cells, and therefore ARE computers.

You're welcome.

  
NoName



Posts: 2729
Joined: Mar. 2013

(Permalink) Posted: Jan. 16 2015,12:03   

Quote (qetzal @ Jan. 16 2015,12:53)
Quote (cryptoguru @ Jan. 16 2015,9:09)
My challenge is this.
Show me a computer model that models this process and shows new functions and information being added to the genome.


 
Quote (cryptoguru @ Jan. 16 2015,10:33)
[A] living cell is a computer, not analogous to a computer, but IS a computer.


Perfect. Lenski already demonstrated new functions being added to the genome using E. coli, which are living cells, and therefore ARE computers.

You're welcome.

Heh.  ha.  haHaHa!  Bwahahahahahahaha!
ROFL

I think we're done here.

Except, of course, he's not accepting Lenski's work as having done what it has so clearly done.
What's wrong with Lenski's work, crypto?  How are your challenges not already met?

  
OgreMkV



Posts: 3668
Joined: Oct. 2009

(Permalink) Posted: Jan. 16 2015,12:04   

I'd like to add that natural selection is not always a death.

It can be an effective removal of the gene pool. For example, the strongest, fittest, most efficient lion ever born might have a problem reproducing. Which means that he is removed from the gene pool. He can't pass his genes on to the next generation, so he's out of contention.

I'll note that the paper by Lenski (http://myxo.css.msu.edu/papers....lex.pdf specifically mentions that happening in some of their digital organisms.

Quote
However, two mutations reduced fitness by >50%.
One was a point mutation that disrupted replication efficiency. Its
harmful effect was eliminated by the next mutation in the line of
descent, which occurred at a distant site in the genome. The other
very deleterious step was a point mutation, at depth 110, that
knocked out NAND, one of the simplest logic functions. Only two
individuals had this maladapted genotype, yet their descendants
emerged as eventual winners. In fact, in the very next step, this
genotype produced the mutation that gave rise to EQU. Was that
deleterious mutation extremely lucky to hitchhike with such a
beneficial mutation? Or was the deleterious mutation a prerequisite
for producing the EQU function within that genome context? To
distinguish between these hypotheses, we reversed this one-stepprior
mutation in the genotype that first expressed EQU. This
reversal eliminated the EQU function. Therefore, a mutation that
was highly deleterious when it appeared was highly beneficial in
combination with a subsequent mutation. The evolution of a
complex feature, such as EQU, is not always an inexorably upward
climb toward a fitness peak, but instead may involve sideways and
even backward steps, some of which are important.


Note that the "deleterious" mutation, which dropped fitness by greater than 50% was one mutation that resulted in the most fit individuals.

If you program this kind of thing OUT of an evolutionary algorithm, then it is not matching biology (as crypto demands of it).

I will ask a third time, crypto, have you read this paper? It's sort of a massively important paper in the field.

--------------
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midwifetoad



Posts: 4003
Joined: Mar. 2008

(Permalink) Posted: Jan. 16 2015,12:13   

First, I think Crypto needs to model and replicate in silico, Lenski's result. That would be the bare minimum for a competent model.

If that isn't sufficient, we could discuss the insufficiency later. But first things first. Let's see if we can model microevolution.

--------------
Any version of ID consistent with all the evidence is indistinguishable from evolution.

  
OgreMkV



Posts: 3668
Joined: Oct. 2009

(Permalink) Posted: Jan. 16 2015,12:17   

BTW: Here's an interesting interpretation of that duon article you linked to.

http://sandwalk.blogspot.ca/2014....ion.htm

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Ignored by those who can't provide evidence for their claims.

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stevestory



Posts: 13407
Joined: Oct. 2005

(Permalink) Posted: Jan. 16 2015,12:18   

i wonder if he has something not already covered in the Index to Creationist Claims

I doubt it.

   
midwifetoad



Posts: 4003
Joined: Mar. 2008

(Permalink) Posted: Jan. 16 2015,12:22   

The most important thing that needs to be modeled is the robustness of biochemistry, it's ability to tolerate variation.

Living populations contain multitudes of unique mutations. Individuals are seldom exact copies of other individuals.

So the model operating system and cpu need to have this kind of flexibility built in.

That's why I said early on, that if one is trying to model the origin of life or early evolution, one needs to model chemistry.

Current living things rarely (successfully) change their operating system.

--------------
Any version of ID consistent with all the evidence is indistinguishable from evolution.

  
midwifetoad



Posts: 4003
Joined: Mar. 2008

(Permalink) Posted: Jan. 16 2015,12:55   

Quote (OgreMkV @ Jan. 16 2015,12:17)
BTW: Here's an interesting interpretation of that duon article you linked to.

http://sandwalk.blogspot.ca/2014.......ion.htm

That doesn't work for me. I'll try again.

http://sandwalk.blogspot.com/2014....on.html

--------------
Any version of ID consistent with all the evidence is indistinguishable from evolution.

  
midwifetoad



Posts: 4003
Joined: Mar. 2008

(Permalink) Posted: Jan. 16 2015,13:16   

I guess he'll be back in a couple of hours with his model.

--------------
Any version of ID consistent with all the evidence is indistinguishable from evolution.

  
Cubist



Posts: 558
Joined: Oct. 2007

(Permalink) Posted: Jan. 16 2015,18:57   

Quote (Doc Bill @ Jan. 16 2015,10:55)
Greetings, NotGuru, we meet again!

Perhaps a full disclosure of your real purpose is in order.  I present to you NotGuru's Agenda:

 
Quote
I paint evolution (non-science) as faith ... because it is.
It's an absurd unsupported set of stories, based on the premise that there is no possibility of non-material causation. It satisfies a huge amount of self-centred god-haters, who've wanted nothing more than a decent excuse to pretend that there are no eternal consequences for their actions.

You still don't address any of the gaping black holes that I've pointed out.


I'm thinking this one is a Gary Gaulin clone, but super tard charged.  If you don't mind I'll duck out and get some popcorn.

Is that text an actual quote from cryptoguru, or is it a concise summary of cryptoguru's ideas which doesn't actually use their specific phrasing? I ask because I tried googling that quote, and I couldn't find a source.

  
cryptoguru



Posts: 53
Joined: Jan. 2015

(Permalink) Posted: Jan. 16 2015,19:14   

yeah I thought this would happen ... too many people with different points to address, and not enough time.
(and you guys accuse creationists of Gish Gallop)

Let me address some key ones ....
RE: living cell IS a Turing machine, therefore is computer
Quote

Prove it.  Don't assert it, prove it.
You can't because there simply are no significant respects in which it is true.
The entire realms of thermodynamic effects and of self-assembly, with constrained errors, and self-repair, with constrained errors, simply have no equivalent in computers.  At all.


Thermodynamic effects, self-assembly and self-repair are all things that a digital computer can do. We use thermodynamic effects in random noise generators, we can build computers using robots that are run by the same computers. Self-repair of the operating system, programs and data is one of the most common things implemented by computer hardware and software.
What do you mean by constrained errors?
So no ... why is it important to you to contradict this simple definition of how DNA in a cell works?

Here is the definition of a turing machine
Turing machine formal definition
The way DNA is processed in a living cell satisfies this definition as agreed with by the evolutionary biologist in the Nature Journal entry I linked to earlier.

Here is the definition of a computer
"A computer is a general purpose device that can be programmed to carry out a set of arithmetic or logical operations automatically. Since a sequence of operations can be readily changed, the computer can solve more than one kind of problem."

DNA as it is transcribed and translated satisfies this definition. We know for example that DNA is functionally non-linear and controls the expression of other parts of the DNA (eg HOX genes and other regulator genes) ... these are complex flow and boolean logic operations. The expression of multiple reading frames (6 we know of ... and potentially others in 3 dimensional space when DNA is folded) in DNA is an example of complex logical operations, which is controlled by boolean logic.

A computer is a Turing machine and vice versa.
DNA is a functional code ... it is processed as a code in the living cell, the functions in the code are used to efficiently describe how to build highly complex structures and to be able to replicate and differentiate its function as it progresses. This is more complicated, robust and versatile than any computer we've ever built or could probably conceive of building.
So my point is DNA is a code that runs in the computer of the living cell, it is more complex than any computer we know .... so how can corruption (mutation) to the operating system code and the program code result in better function? This contradicts our experience, and I claim has still not been demonstrated to happen.

Quote
I'd like to add that natural selection is not always a death.

It can be an effective removal of the gene pool. For example, the strongest, fittest, most efficient lion ever born might have a problem reproducing. Which means that he is removed from the gene pool. He can't pass his genes on to the next generation, so he's out of contention.


Haha amazing ... how did he get removed from the gene pool? A Gene pool isn't actually like a swimming pool you know, genes don't get thrown out for breaking the rules by the life-guard ... He gets removed from the "Gene pool" (population) by dying ... he dies before reproducing (for whatever reason), so his genes aren't passed on. Natural Selection is not looking at his Genes and saying "hey this guy isn't fit enough ... throw him out" ... Natural Selection is just a name given to the fact we have lions that are still reproducing, and that lion isn't because he was less fit so simply dies.
You're picking a fight over something we agree on here. I'm demystifying the explanation of how Natural Selection works, it is death ... it is not just general competition. Yes it IS competition, but only competition that results in something dying and other things not. Remember "Natural Selection is a Blind, Mindless and Unguided Watchmaker" (Dawkins)


Quote
in detail why AVIDA does not do what the writers of the software say it does

No detail needed ... it's simple. AVIDA defines the entity by prescribing a set of 26 functions that can be randomly selected in random combinations. Then evaluation functions are used to test how fit an organism is. Both these things are inaccurate and create a trivial subset of the proposed evolution theory. As I explained before, selected from existing functions is not the same as mutating the code that defines those functions. Biological function is determined on the protein level, proteins are equivalent to AVIDA's 26 functions, and a complex combination of proteins to create higher level function in an organism is equivalent to the combination of functions that AVIDA is "mutating" between. i.e. AVIDA is shuffling protein orders to get different high level functions, and only using 26 proteins. This is NOT the same as mutating the code that defines how the proteins are built .... the equivalence of this in AVIDA would be mutating the code that defines the 26 functions. This is a VERY different problem ... no-one has done that ... mainly because they know it will result in junk.
The problem of trying 26 functions in different combinations to optimise a specific trait is NOT the same as what you are proposing happens in biological evolution.

Quote
Can you say 'begging the question'?  You appear to be arguing that cells/organisms are programmed by asserting as one of your premises that cells/organisms are programmed.

No, not begging the question, I'm merely pointing out that Lenski's results don't show anything either way ... you can claim it's evolution, but I can claim that what he observes is part of its original programming, as the bacteria is still E. Coli ... it may have adapted and changed to resist death, because we know that is part of the inherent functionality of bacteria, they swap genetic code with other bacteria. Like a computer virus, the code is mostly concerned with reproduction and not any complex functionality. We embed all sorts of randomisation algorithms into computer viruses to make them harder to identify by the host and harder to stop ... this is engineered resistance. I'm claiming that all the research so far does not contradict that explanation. And in fact, if anything the experiment has proved that nothing has changed in millions of years of evolution. If evolution is so easy and happens everywhere to every organism world-wide to some degree, why are they still E. Coli and not Bananas or Dolphins or Pygmy Elephants? (that one's for Kevin)
This is why I ask for a simple model, that models the core features of the proposed theory of evolution. So far no-one has shown me one.
If you have a biological experiment showing one kind of animal naturally changing into another or developing completely new complex features then show me .... but so far all I've seen from experiments is no different to dog breeding and showing that a Poodle looks wildly different to a Great Dane or a Finch has a bigger beak. This is not evolution, this is artificially breeding out features and standard Mendelian genetics, and certainly isn't anything to do with mutations.

I'm a mathematician and programmer, last time I looked at the laws of logic you can't get information without a sender, matter does not contain the properties of information in itself, as information is outside of matter, it is the arrangement of matter that is information ... so if you're contesting that information can come out of matter by itself simply because of the environment it's in I want you to show me algorithmically how this is possible. Hence the request for a model.

  
Doc Bill



Posts: 1039
Joined: April 2007

(Permalink) Posted: Jan. 16 2015,19:19   

Quote (Cubist @ Jan. 16 2015,18:57)
Quote (Doc Bill @ Jan. 16 2015,10:55)
Greetings, NotGuru, we meet again!

Perhaps a full disclosure of your real purpose is in order.  I present to you NotGuru's Agenda:

   
Quote
I paint evolution (non-science) as faith ... because it is.
It's an absurd unsupported set of stories, based on the premise that there is no possibility of non-material causation. It satisfies a huge amount of self-centred god-haters, who've wanted nothing more than a decent excuse to pretend that there are no eternal consequences for their actions.

You still don't address any of the gaping black holes that I've pointed out.


I'm thinking this one is a Gary Gaulin clone, but super tard charged.  If you don't mind I'll duck out and get some popcorn.

Is that text an actual quote from cryptoguru, or is it a concise summary of cryptoguru's ideas which doesn't actually use their specific phrasing? I ask because I tried googling that quote, and I couldn't find a source.

It's over at Smilodon's Retreat under the "DNA is not like a computer" thread.  Near the bottom of about 4 pages of comments.

Yeah, it's a direct quote.  Think Quest/FL/JoeG/a mule/two thick planks/bag of doorknobs - and you'll get the general sense of this guy.

Back to my popcorn!

  
QED



Posts: 41
Joined: July 2008

(Permalink) Posted: Jan. 16 2015,19:30   

In that case, I'm guessing it's not a Gaulin clone at all.

I'm betting on the pidgeon/chess gambit: "wah wah wah - you're being mean to me, so jesus doesn't love you and besides you're wrong - I'm outta here..."

  
Wesley R. Elsberry



Posts: 4991
Joined: May 2002

(Permalink) Posted: Jan. 16 2015,19:34   

Cryptoguru:

   
Quote

Evolution is:
1) take an organism and let it replicate
2) random mutations should be introduced to the offspring DNA.
3) a selective pressure is applied to the environment the organisms live in
4) less fit organisms will die before replicating due to the pressure
5) most fit organisms will continue to replicate and mutate
6) eventually new functions and traits will emerge

Biological Evolution is presented as a scientific law, it is simple to define, so should be simple to model

My challenge is this.
Show me a computer model that models this process and shows new functions and information being added to the genome.

caveats:
- Mutation can't simply combine functions in different arrangements. Mutation must occur on the code that defines the functions themselves, and affect the ability of the organism to build itself, to function and to replicate.
- the selective process can't include measuring properties of the organism to remove them from the population, the selective process must rely on organisms dying off due to the environmental factors. (e.g. energy)



Avida does everything specified there except "model this process", given that Avida's model doesn't include misconceptions.

It is certainly possible to find points of disanalogy between Avida and biological evolution, since Avida's purpose is to establish a "computational chemistry" rather than to be an exact simulation of biological evolution via DNA. However, none of those points of disanalogy appear to have any bearing on the specific "challenge" quoted above. So any dismissals of Avida on grounds other than those stated in the "challenge" above are irrelevant. And, looking back at the discussion on OgreMkV's blog, I'm not seeing any accurate objection made concerning Avida that falls within the parameters of the "challenge".

One such invalid response is the one that equivocates about "functions". In Avida, the functions that can possibly accrue merit are logic operations, none of which are themselves singular codes in an Avidian's genome. Referring to those codes as "functions" in the sense of the quoted "challenge" is a mistake.

It's easy enough to modify "challenges" to be unfulfilled on some point or another. The point isn't to satisfy those with unreasonable doubt; it is to satisfy those who don't have inflexible precommitments.

--------------
"You can't teach an old dogma new tricks." - Dorothy Parker

    
cryptoguru



Posts: 53
Joined: Jan. 2015

(Permalink) Posted: Jan. 16 2015,19:45   

Quote

Greetings, NotGuru, we meet again!

Perhaps a full disclosure of your real purpose is in order.  I present to you NotGuru's Agenda:

Quote

I paint evolution (non-science) as faith ... because it is.
It's an absurd unsupported set of stories, based on the premise that there is no possibility of non-material causation. It satisfies a huge amount of self-centred god-haters, who've wanted nothing more than a decent excuse to pretend that there are no eternal consequences for their actions.

You still don't address any of the gaping black holes that I've pointed out.


I'm thinking this one is a Gary Gaulin clone, but super tard charged.  If you don't mind I'll duck out and get some popcorn.


Oh it's that angry Bilbo baggins character who just swears and says I know nothing ... and here he is quoting me out of context.

it was in response to this post from Bilbo, probably one of his least offensive ones

Quote
Typical useless god bot. Argument from incredulity. Has to paint science as a faith because of a narrow, restricted, dogmatic worldview. Forest full of straw men, drenched in tard and burning with the fire of the willfully ignorant. Sucks to be you, NotGuru. Enjoy howling in the darkness.


I was trying to contest in the context of many faith-related insults that in my opinion evolution is not science, evolution is a belief and based on the religion of atheism ... and the reason it's so popular is that people hate the idea of God, mainly because they hate the idea of eternal consequences. So I don't see it as science vs religion ... I see it as religion vs religion and science vs science.
I didn't want to get into a faith discussion there and I'm not after one now ... I want to discuss the science.
This was me reacting, which I wish I hadn't ... in fact I should never have engaged with Bilbo at all.

  
OgreMkV



Posts: 3668
Joined: Oct. 2009

(Permalink) Posted: Jan. 16 2015,20:08   

Quote (cryptoguru @ Jan. 16 2015,19:14)
Quote
I'd like to add that natural selection is not always a death.

It can be an effective removal of the gene pool. For example, the strongest, fittest, most efficient lion ever born might have a problem reproducing. Which means that he is removed from the gene pool. He can't pass his genes on to the next generation, so he's out of contention.


Haha amazing ... how did he get removed from the gene pool?

[/QUOTE]Wrong. Because he couldn't reproduce.

This is an example of you having a basic misunderstanding and I'm trying to correct it.

An organism that cannot reproduce, no matter how fit it is in every other particular cannot pass his genes on. He could live for decades longer (some research seems to indicate that being a eunuch means a male could add 25% to his lifespan... at the cost of not passing those genes on).

It doesn't have to be dead. It usually is, but it doesn't have to be. [/QUOTE]

A Gene pool isn't actually like a swimming pool you know, genes don't get thrown out for breaking the rules by the life-guard

[/quote]
Yes, you are correct, I should say, "the breeding population". I'm sorry, I will no longer use analogies in conversation with you.

Quote

... He gets removed from the "Gene pool" (population) by dying ...
he dies before reproducing (for whatever reason), so his genes aren't passed on.

And yet, I just gave you an example of a method, by which an individual could NOT ever contribute their genetics into the population and yet, still be alive.

What you are saying here, is that every woman who has a hysterectomy has died. Every male that has his tubes tied has died. Every cat and dog that's been neutered or spayed has died.

This is trivially wrong.

Quote

Natural Selection is not looking at his Genes and saying "hey this guy isn't fit enough ... throw him out" ... Natural Selection is just a name given to the fact we have lions that are still reproducing, and that lion isn't because he was less fit so simply dies.


No, selection is a process by which the organism is tested against the environment (including other organisms). Those are more fit TEND to reproduce more and those that are less fit TEND to reproduce less.

Again, less fit doesn't imply death. Indeed, you apparently have not read the AVIDA paper (or the part I quoted for you) showing that not only do less fit organisms sometimes reproduce. Those less fit organisms sometimes end up being the most fit.

This has been done with actual biological entities as well. Darwinian Evolution on a Chip by G. Joyce. Same thing as AVIDA. Some mutations resulted in lowered fitness, but they still reproduced and resulted in organisms with much greater fitness.

A simplistic view of life that is wrong.

Quote

You're picking a fight over something we agree on here.


No, because I don't agree with you. Scientists don't agree with you. Reality doesn't agree with you. Lab experiments don't agree with you. Observations of population genetics doesn't agree with you.

Quote

I'm demystifying the explanation of how Natural Selection works, it is death ... it is not just general competition.


No it's not. No matter how many times you say it, doesn't make it true.

Quote

Yes it IS competition, but only competition that results in something dying and other things not.


WHAT is competition? Competition for resources can often result in death. Competition for mates rarely does. But there are numerous cases of less fit organisms that discover a few tricks and reproduce anyway.

Quote

Remember "Natural Selection is a Blind, Mindless and Unguided Watchmaker" (Dawkins)

I love when you guys take Dawkins out of context. It's so telling. Tell me crypto, which book is that from? What page?

What does "unguided" mean to you? That's a critical definition.

For example, to most creationists (well, all that I have met so far), unguided means "random". While "guided" means shaped by an intelligence.

That's a false dichotomy. Guided doesn't mean an intelligence was involved. Fractals are guided by their equations. There are limits to them, but no intelligence has decided and enforced those limits.

When Dawkins speaks of unguided, he means that there is no purpose to life. No guiding hand. The only concern of this generation is to live long enough to reproduce. What happens before or after is not important to them.

The surviving offspring are in the same boat. None of them prepares for the future. None of them think, "Well, it's getting colder, we better let all the long furred ones mate." And yes, this have driven species to extinction... and will again.

I know you creationists don't like this because you feel that God is your guiding hand and things happen because they should. This tends to happen a lot with creationist engineers, programmers, and mathematicians.

I would encourage you to stop that thinking. It's not correct.

Why don't we ask Wesley, he was at a talk given by Dawkins about this? here's a link to his report of the talk. http://pandasthumb.org/archive....-2.html

--------------
Ignored by those who can't provide evidence for their claims.

http://skepticink.com/smilodo....retreat

   
OgreMkV



Posts: 3668
Joined: Oct. 2009

(Permalink) Posted: Jan. 16 2015,20:09   

Quote (cryptoguru @ Jan. 16 2015,19:45)
Quote

Greetings, NotGuru, we meet again!

Perhaps a full disclosure of your real purpose is in order.  I present to you NotGuru's Agenda:

Quote

I paint evolution (non-science) as faith ... because it is.
It's an absurd unsupported set of stories, based on the premise that there is no possibility of non-material causation. It satisfies a huge amount of self-centred god-haters, who've wanted nothing more than a decent excuse to pretend that there are no eternal consequences for their actions.

You still don't address any of the gaping black holes that I've pointed out.


I'm thinking this one is a Gary Gaulin clone, but super tard charged.  If you don't mind I'll duck out and get some popcorn.


Oh it's that angry Bilbo baggins character who just swears and says I know nothing ... and here he is quoting me out of context.

it was in response to this post from Bilbo, probably one of his least offensive ones

Quote
Typical useless god bot. Argument from incredulity. Has to paint science as a faith because of a narrow, restricted, dogmatic worldview. Forest full of straw men, drenched in tard and burning with the fire of the willfully ignorant. Sucks to be you, NotGuru. Enjoy howling in the darkness.


I was trying to contest in the context of many faith-related insults that in my opinion evolution is not science, evolution is a belief and based on the religion of atheism ... and the reason it's so popular is that people hate the idea of God, mainly because they hate the idea of eternal consequences. So I don't see it as science vs religion ... I see it as religion vs religion and science vs science.
I didn't want to get into a faith discussion there and I'm not after one now ... I want to discuss the science.
This was me reacting, which I wish I hadn't ... in fact I should never have engaged with Bilbo at all.

The problem is that you can't discuss science because your view of it so biased by your religion.

You're so obsessed with the way it should be, that you can't see the way it actually is.

--------------
Ignored by those who can't provide evidence for their claims.

http://skepticink.com/smilodo....retreat

   
midwifetoad



Posts: 4003
Joined: Mar. 2008

(Permalink) Posted: Jan. 16 2015,21:14   

All the verbiage about information is fascinating,  but why not cut to the chase? What specific physical phenomenon described by Darwin or his successors cannot happen? What specific point in the chain of descent is unreachable via the process described by Lenski, Thornton,  et al?

--------------
Any version of ID consistent with all the evidence is indistinguishable from evolution.

  
Acartia_Bogart



Posts: 2927
Joined: Sep. 2014

(Permalink) Posted: Jan. 16 2015,23:38   

Quote


I was trying to contest in the context of many faith-related insults that in my opinion evolution is not science, evolution is a belief and based on the religion of atheism ... and the reason it's so popular is that people hate the idea of God, mainly because they hate the idea of eternal consequences. So I don't see it as science vs religion ... I see it as religion vs religion and science vs science.
I didn't want to get into a faith discussion there and I'm not after one now ... I want to discuss the science.
This was me reacting, which I wish I hadn't ... in fact I should never have engaged with Bilbo at all.


If by "so popular" you mean a minority opinion in the US, then I guess it is popular.

What you are referring to is its general acceptance by scientists, the people who have actually conducted research on this. As opposed to religious fanatics who approach the subject with their "minds" already made up.

  
Cubist



Posts: 558
Joined: Oct. 2007

(Permalink) Posted: Jan. 17 2015,01:08   

Quote (cryptoguru @ Jan. 16 2015,09:09)
My challenge is this.
Show me a computer model that models this process and shows new functions and information being added to the genome. [emphasis added]

Whether or not you, yourself, are a Creationist, cryptoguru, this challenge of yours is (whether you realize it or not) the hoary old mutations can't create new information argument beloved of Creationists, just dressed up in computer terminology. So please, tell us if you will: What does "new information" look like? Given an arbitrary string of nucleotides, and a mutation which alters that string of nucleotides, how can you tell whether or not the post-mutation version of that string contains any "new" information?

Yes, this is a verbatim re-post. Perhaps cryptoguru will deign to respond to it this time. Perhaps they won't. We shall see.

  
Quack



Posts: 1961
Joined: May 2007

(Permalink) Posted: Jan. 17 2015,05:14   

Maybe I am an oddball; Everywhere I look I observe objects and may extract information from them. The info just sits there ready for detection and observation without any external or supernatural operator having put it there. It sticks to the object like some red dye in a glass of water.

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Rocks have no biology.
              Robert Byers.

  
JonF



Posts: 634
Joined: Feb. 2005

(Permalink) Posted: Jan. 17 2015,07:04   

Quote (cryptoguru @ Jan. 16 2015,11:06)

JonF: "adding information" - new and novel functions that didn't exist before that solve a problem that wasn't solved previously.

Such as evolving EQU in Avida or evolving the ability to digest citrate in Lenski's experiments?  Why are those not new and novel?

  
NoName



Posts: 2729
Joined: Mar. 2013

(Permalink) Posted: Jan. 17 2015,09:50   

Quote (cryptoguru @ Jan. 16 2015,20:45)
...
I was trying to contest in the context of many faith-related insults that in my opinion evolution is not science, evolution is a belief and based on the religion of atheism ... and the reason it's so popular is that people hate the idea of God, mainly because they hate the idea of eternal consequences. So I don't see it as science vs religion ... I see it as religion vs religion and science vs science.
I didn't want to get into a faith discussion there and I'm not after one now ... I want to discuss the science.
This was me reacting, which I wish I hadn't ... in fact I should never have engaged with Bilbo at all.

On the one hand you put it all down to faith versus faith, or faith versus science, and on the other you insist you "didn't want to get into a faith discussion."
You really can't have it both ways.

You are entitled to your opinions, as opinions, even when they are loony [I'm not (yet) saying any particular one(s) of your  beliefs is/are loony].
But if you want to argue from a position that evolution is faith, not science, that it is based on a hatred for the idea of God, you have to establish the truth and accuracy of that premise.  As a presupposition, it is ludicrous and unsupportable, not least because so very many of the founders and developers of evolutionary theory were and are deeply religious.
To say nothing of how totally insane it is to assert that people hate 'the idea of' God.  Generally, ideas as such are neither hated nor adored.  But more importantly, the idea of God is one that may or may not be true.  The nature of said God is asserted to be all sorts of things, all over the map.  We know nothing useful about the nature of any particular deity, and before we can make recourse to the referent of the idea of God, we need to know in some detail and with some considerable precision [can you say 'operational definition'?  Do you know what it means?] what the nature and character of the referent actually is.
Otherwise the term is a magic word, swung about to fulfill any current rhetorical needs, which it can do solely because it is an idea unburdened with content.

Evolution is science because it fits all the criteria of science.  It is based on demonstrable facts, it makes predictions which can be falsified, it's theoretical structure is logically sound and provides a framework within which a broad variety of objective facts can be placed.  It has explanatory and predictive power, it has meaningful operational definitions for its key terms and concepts.  It suggests fruitful lines of inquiry and it has withstood the most concerted, and occasionally devious, attacks a host of small-minded ignoramuses, as well as highly intelligent knowledgable individuals have brought to bear.
It is not faith because it is susceptible to revision based on new insights and new facts, it operates in a consistent fashion such that it makes predictions which as a general rule turn out, and is capable of revision in light of those cases where the prediction fails.

I'll get back to your lengthy, but largely pointless and obfuscatory response to portions of my earlier post later in the day or early tomorrow.  I actually lack the time to do the fishing it so richly deserves.

The core challenge to you has already been raised, repeatedly:  what facts on the table, specifically the known laws of chemistry, physics, and thermodynamics are alleged to be violated by evolution?  Where has it been shown that the laws of chemistry, physics, and thermodynamics do not suffice to explain biological phenomena?  Which phenomena, and how was it proven that they are not susceptible to natural explanations via chemistry, physics, and thermodynamics?

You find evolutionary theory distasteful, for reasons having nothing at all to do with science, so you attempt to shift out of the realm of science into faith.  How is that justified?
Show your work.

  
qetzal



Posts: 311
Joined: Feb. 2006

(Permalink) Posted: Jan. 17 2015,12:32   

Quote (cryptoguru @ Jan. 16 2015,19:14)
No, not begging the question, I'm merely pointing out that Lenski's results don't show anything either way ... you can claim it's evolution, but I can claim that what he observes is part of its original programming, as the bacteria is still E. Coli ... it may have adapted and changed to resist death, because we know that is part of the inherent functionality of bacteria, they swap genetic code with other bacteria. Like a computer virus, the code is mostly concerned with reproduction and not any complex functionality. We embed all sorts of randomisation algorithms into computer viruses to make them harder to identify by the host and harder to stop ... this is engineered resistance. I'm claiming that all the research so far does not contradict that explanation. And in fact, if anything the experiment has proved that nothing has changed in millions of years of evolution. If evolution is so easy and happens everywhere to every organism world-wide to some degree, why are they still E. Coli and not Bananas or Dolphins or Pygmy Elephants? (that one's for Kevin)
This is why I ask for a simple model, that models the core features of the proposed theory of evolution.

Actually, what you asked for was this:
 
Quote
My challenge is this.
Show me a computer model that models this process and shows new functions and information being added to the genome.

You didn't ask for a model that shows E. coli turning into bananas or dolphins. You asked for a model that shows new functions and information being added, and you've been given multiple examples. If what you really want is a model that turns E. coli into bananas, then you're right. We're not currently capable of modeling evolution on that scale. But as others have pointed out, not being able to model something on a computer is not strong evidence that it doesn't happen.

Also, I'm curious. Were you just being mocking, or do you really understand so little about evolution that you think it means bacteria should turn into bananas (or any complex multicellular organism) over a few decades? Because if it's the former, then it suggests you're not interested in honest discussion. And if it's the latter, then your understanding of evolution is so poor that rational discussion is probably impossible. Of course, the two aren't mutually exclusive.

But hey, it's possible that I'm wrong on both counts. I'm a scientist; I believe in empirical evidence. So show me some evidence that you understand what evolution actually claims, and that you're willing to discuss the validity of those claims honestly.

  
cryptoguru



Posts: 53
Joined: Jan. 2015

(Permalink) Posted: Jan. 17 2015,15:11   

Re. faith:

DocBilbo has tried to smuggle in a discussion from another board, which I didn't want to even have there about faith. That is not the point of this subject thread and is an attempt to derail the discussion so it gets into an endless circle of atheists claiming creation-based belief is not science.
Let's leave this subject as it is really a philosophical argument and not something I'm wanting to get sidetracked with here.

Re. experiments:

the point I'm making about experiments (e.g. Lenski's) is that all they have shown is that variation within a kind has occurred ... creationists agree that variation within a kind is happening (e.g. viruses mutate, Finches change beak sizes etc) this is not proof of evolution. This can just as easily be explained as the normal function of the genome to vary. Epigenomic function allows for much variety within an organism on top of variation that already exists in DNA, where entire modules of DNA are regulated and switched on and off by other genes. This is not evolution ... it can happen in one generation, it is not as a result of mutation. So my point here is that these experiments do not demonstrate new features and traits being introduced to the genome, they can be explained as existing information and code being expressed in new ways that is controlled in how the genome responds to input from the environment. This is widely accepted ... hormone responses can switch on silenced genes and vice versa, allowing an organism to adapt to its environment.

Quote
do you really understand so little about evolution that you think it means bacteria should turn into bananas (or any complex multicellular organism) over a few decades?

Lenski's experiment has achieved 60,000 generations in April 2014.
You need to understand, the proposed theory of evolution is not about "time"  ... it is about how many generations. Lenski's E. Coli has run for the equivalent of 1 million years of human generations. So evolution doesn't need time, it just needs lots of generations, which is what the E. Coli experiment has performed. Forgive me for being sceptical, but I'd expect more from 1 million years' worth of evolution than a change in metabolism, which could be attributed to the regulation of existing genes ... Behe explains this here Lenski article

SO ... this is why I'm asking for proof of the algorithm of evolution. Why is everyone being so sketchy about this? The evolutionary algorithm is simple ... randomly mutate the core code at the resolution of letters (not functions). Enforce selection by allowing organisms to compete for resources and allow them to die under natural conditions. AVIDA does NOT mutate on the nucleotide level, it mutates on the functional level, which is the same as choosing randomly from 26 functions and optimising. It also calculates selection on a feature level, measuring properties ... that is NOT natural selection. This is what their paper says it does. Has anyone read AVIDA's paper here?

  
midwifetoad



Posts: 4003
Joined: Mar. 2008

(Permalink) Posted: Jan. 17 2015,15:13   

Quote
the point I'm making about experiments (e.g. Lenski's) is that all they have shown is that variation within a kind has occurred


Surely you are not that stupid.

--------------
Any version of ID consistent with all the evidence is indistinguishable from evolution.

  
rossum



Posts: 289
Joined: Dec. 2008

(Permalink) Posted: Jan. 17 2015,15:26   

Quote (cryptoguru @ Jan. 17 2015,15:11)
the point I'm making about experiments (e.g. Lenski's) is that all they have shown is that variation within a kind has occurred ...

Everyone agrees.  It is just that we disagree about where the boundaries between the different kinds lie.  For biologists, all evolution occurs within the "Life on Earth" kind.

If you think that Dr. Lenski's experiments show only evolution within the "Eubacteria kind", then we are already in reasonably close agreement.  That implies that you also accept evolution within the "Eukaryote kind", since Eubacteria and Eukaryotes are at the same level of classification.

If you want to split things below that level, then you are going to have to list the different kind boundaries, and show how you arrived at those particular boundaries.

rossum

--------------
The ultimate truth is that there is no ultimate truth.

  
midwifetoad



Posts: 4003
Joined: Mar. 2008

(Permalink) Posted: Jan. 17 2015,16:04   

That's not all the Lenski experiment shows.

The Lenski experiment shows that mutations that reduce reproductive success can survive in a population long enough to enable further mutations that leapfrog function for a given environment.

That is precisely what Behe said couldn't happen. And it is precisely what is necessary to move beyond local maxima.

--------------
Any version of ID consistent with all the evidence is indistinguishable from evolution.

  
cryptoguru



Posts: 53
Joined: Jan. 2015

(Permalink) Posted: Jan. 17 2015,18:28   

Quote
Surely you are not that stupid.

Yes, I AM that stupid :-)
I'm making the point that nothing in the Lenski experiment proves evolution, it can just as easily be explained as programmed behaviour. Considering we're discovering more and more deterministic complexity in the genome, it is more than reasonable to assume that all the variation we see is specified complexity that already exists within the genome, and is not the result of random mutation. This has NOT been contradicted by any experiment yet, it is simply being asserted.

Therefore I again ask why there is no workable computer model of the theory of evolution in the form in which it is supposed to occur in the wild?


Quote
If you want to split things below that level, then you are going to have to list the different kind boundaries

Rossum, I'm saying that the variation we see can be explained by deterministic behaviour in the genome and need not be explained by "mutation". A control gene that regulates another gene dependent on an environmental input may make it look like something is evolving, but that function could already exist in the genome.
In fact the more layers of complexity and non-linearity we observe in the genome and how it is processed makes it more difficult to explain how a mutation could ever be understood to be advantageous; with multiple reading frames a mutation to a nucleotide could be imagined to have a positive effect somehow on the expression of a protein, but what about the other types of protein that get expressed from the same code? They're now broken.

This is a multi-layered code, I have previously worked in Cryptography and compression algorithms for many years. The genome implements compression to represent data in an efficient way. Corrupting even one bit of compressed data usually has an effect on multiple parts of the data ... if that data is a program, you can expect the program to crash if enough bits are corrupted.

This makes sense for the genome too (and is observed through genetic diseases) ... that along with the fact that Lenski's experiments fails to show evolution from one kind of an organism (bacteria) to a different, more complex organism despite an equivalent of 1 Million human years of evolution suggests this process doesn't work; except that everyone is the field is saying it works. I'm a sceptic, I want to see actual scientific proof that doesn't just gloss over the facts and pretend that mutation could be the only reason for an increase in cell size or a change in metabolism.

A working and accurate computer model still wouldn't prove evolution is happening in the wild, but it at least would show that it is theoretically viable. Currently I don't see how it is even theoretically possible, from an algorithmic perspective.

Quote
The Lenski experiment shows that mutations that reduce reproductive success can survive in a population long enough to enable further mutations that leapfrog function for a given environment.

Bacteria is also a bad example because it seems to deliberately use fuzzy logic and implement randomness in its genome as part of the programming ... so although a change may look random, it may be deterministic in function.
This is exactly how we program computer viruses. We expect them to evolve in a deliberate way.
So I do think there is some application for evolution as a concept in the modelling of bacteria and viruses, but their function is still deterministic and constrained by the master code, they may reprogram themselves (and transfer/shuffle genes with other bacteria) for versatility, but they can never vary to become a frog. In the case of viruses and bacteria I expect randomness is being used like we use pseudo-random noise generators in computers. We generate random variables and use them in our code ... we are NOT varying the functional part of the code itself randomly.

I think therefore it is misleading to look at what happens in bacteria and extrapolate it to other organisms, when we don't see the same processes happening in them.

  
Cubist



Posts: 558
Joined: Oct. 2007

(Permalink) Posted: Jan. 17 2015,18:28   

Quote (cryptoguru @ Jan. 16 2015,09:09)
My challenge is this.
Show me a computer model that models this process and shows new functions and information being added to the genome. [emphasis added]

Whether or not you, yourself, are a Creationist, cryptoguru, this challenge of yours is (whether you realize it or not) the hoary old mutations can't create new information argument beloved of Creationists, just dressed up in computer terminology. So please, tell us if you will: What does "new information" look like? Given an arbitrary string of nucleotides, and a mutation which alters that string of nucleotides, how can you tell whether or not the post-mutation version of that string contains any "new" information?

cryptoguru did not respond to this the first two times I posted it; perhaps they merely overlooked it in the rush of responses. Maybe they'll notice it (and respond to it) if the text is larger?

  
midwifetoad



Posts: 4003
Joined: Mar. 2008

(Permalink) Posted: Jan. 17 2015,20:13   

Will microbes may not be a good example for creationists to use,  but microbes account for the entirety of life for 6/7 of the time during which life existed. And microbes are still the dominant life form,  by any measure.

Nearly all genes were invented by microbial evolution. So stop posting shit. If you assert that mutation is not random with respect to selection, prove it.

--------------
Any version of ID consistent with all the evidence is indistinguishable from evolution.

  
Wesley R. Elsberry



Posts: 4991
Joined: May 2002

(Permalink) Posted: Jan. 17 2015,20:17   

Cryptoguru:

   
Quote

AVIDA does NOT mutate on the nucleotide level, it mutates on the functional level, which is the same as choosing randomly from 26 functions and optimising.


That's still the erroneous equivocation that was already pointed out to be a mistake on Cryptoguru's part. None of the logic functions that obtain merit in Avida are due to singular codes in an Avidian's genome. The functions that accrue merit are built out of multiple codes in the genome, just as specified in Cryptoguru's "challenge" near the start of the thread.

 
Quote

It also calculates selection on a feature level, measuring properties ... that is NOT natural selection. This is what their paper says it does. Has anyone read AVIDA's paper here?


I'm not sure what the word salad above is supposed to convey other than dismissal. What's a "feature level" and "measuring properties"? If that's supposed to mean that Avida recognizes genomic patterns and rewards those, nothing could be further from the truth. It is the outcome of functional behavior that is the trigger for assigning merit to an Avidian.

But, yes, not only have I read that paper, I've also contributed to the Avida code base.

Lenski et al. 2003:

   
Quote

As in nature, selection in Avida depends on the phenotypic effects of a mutation in its genetic context and in relation to the organism’s environment; the researcher does not specify a distribution of selection coefficients.


This indicates that what Avida is doing is analogous to what occurs in natural selection. I think Cryptoguru needs more than cryptic dismissal to make his case.

--------------
"You can't teach an old dogma new tricks." - Dorothy Parker

    
Wesley R. Elsberry



Posts: 4991
Joined: May 2002

(Permalink) Posted: Jan. 17 2015,20:35   

Not understanding how Avida works is seen in other antievolutionary argumentation, too.

--------------
"You can't teach an old dogma new tricks." - Dorothy Parker

    
The whole truth



Posts: 1554
Joined: Jan. 2012

(Permalink) Posted: Jan. 17 2015,21:34   

Quote (NoName @ Jan. 17 2015,07:50)
Quote (cryptoguru @ Jan. 16 2015,20:45)
...
I was trying to contest in the context of many faith-related insults that in my opinion evolution is not science, evolution is a belief and based on the religion of atheism ... and the reason it's so popular is that people hate the idea of God, mainly because they hate the idea of eternal consequences. So I don't see it as science vs religion ... I see it as religion vs religion and science vs science.
I didn't want to get into a faith discussion there and I'm not after one now ... I want to discuss the science.
This was me reacting, which I wish I hadn't ... in fact I should never have engaged with Bilbo at all.

On the one hand you put it all down to faith versus faith, or faith versus science, and on the other you insist you "didn't want to get into a faith discussion."
You really can't have it both ways.

You are entitled to your opinions, as opinions, even when they are loony [I'm not (yet) saying any particular one(s) of your  beliefs is/are loony].
But if you want to argue from a position that evolution is faith, not science, that it is based on a hatred for the idea of God, you have to establish the truth and accuracy of that premise.  As a presupposition, it is ludicrous and unsupportable, not least because so very many of the founders and developers of evolutionary theory were and are deeply religious.
To say nothing of how totally insane it is to assert that people hate 'the idea of' God.  Generally, ideas as such are neither hated nor adored.  But more importantly, the idea of God is one that may or may not be true.  The nature of said God is asserted to be all sorts of things, all over the map.  We know nothing useful about the nature of any particular deity, and before we can make recourse to the referent of the idea of God, we need to know in some detail and with some considerable precision [can you say 'operational definition'?  Do you know what it means?] what the nature and character of the referent actually is.
Otherwise the term is a magic word, swung about to fulfill any current rhetorical needs, which it can do solely because it is an idea unburdened with content.

Evolution is science because it fits all the criteria of science.  It is based on demonstrable facts, it makes predictions which can be falsified, it's theoretical structure is logically sound and provides a framework within which a broad variety of objective facts can be placed.  It has explanatory and predictive power, it has meaningful operational definitions for its key terms and concepts.  It suggests fruitful lines of inquiry and it has withstood the most concerted, and occasionally devious, attacks a host of small-minded ignoramuses, as well as highly intelligent knowledgable individuals have brought to bear.
It is not faith because it is susceptible to revision based on new insights and new facts, it operates in a consistent fashion such that it makes predictions which as a general rule turn out, and is capable of revision in light of those cases where the prediction fails.

I'll get back to your lengthy, but largely pointless and obfuscatory response to portions of my earlier post later in the day or early tomorrow.  I actually lack the time to do the fishing it so richly deserves.

The core challenge to you has already been raised, repeatedly:  what facts on the table, specifically the known laws of chemistry, physics, and thermodynamics are alleged to be violated by evolution?  Where has it been shown that the laws of chemistry, physics, and thermodynamics do not suffice to explain biological phenomena?  Which phenomena, and how was it proven that they are not susceptible to natural explanations via chemistry, physics, and thermodynamics?

You find evolutionary theory distasteful, for reasons having nothing at all to do with science, so you attempt to shift out of the realm of science into faith.  How is that justified?
Show your work.

"Evolution is science because it fits all the criteria of science.  It is based on demonstrable facts, it makes predictions which can be falsified, it's theoretical structure is logically sound and provides a framework within which a broad variety of objective facts can be placed.  It has explanatory and predictive power, it has meaningful operational definitions for its key terms and concepts.  It suggests fruitful lines of inquiry and it has withstood the most concerted, and occasionally devious, attacks a host of small-minded ignoramuses, as well as highly intelligent knowledgable individuals have brought to bear.
It is not faith because it is susceptible to revision based on new insights and new facts, it operates in a consistent fashion such that it makes predictions which as a general rule turn out, and is capable of revision in light of those cases where the prediction fails."

No, evolution is none of those things. Evolutionary theory is.

--------------
Think not that I am come to send peace on earth: I came not to send peace, but a sword. - Jesus in Matthew 10:34

But those mine enemies, which would not that I should reign over them, bring hither, and slay them before me. -Jesus in Luke 19:27

   
The whole truth



Posts: 1554
Joined: Jan. 2012

(Permalink) Posted: Jan. 17 2015,22:17   

Quote (cryptoguru @ Jan. 17 2015,16:28)
Quote
Surely you are not that stupid.

Yes, I AM that stupid :-)
I'm making the point that nothing in the Lenski experiment proves evolution, it can just as easily be explained as programmed behaviour. Considering we're discovering more and more deterministic complexity in the genome, it is more than reasonable to assume that all the variation we see is specified complexity that already exists within the genome, and is not the result of random mutation. This has NOT been contradicted by any experiment yet, it is simply being asserted.

Therefore I again ask why there is no workable computer model of the theory of evolution in the form in which it is supposed to occur in the wild?


Quote
If you want to split things below that level, then you are going to have to list the different kind boundaries

Rossum, I'm saying that the variation we see can be explained by deterministic behaviour in the genome and need not be explained by "mutation". A control gene that regulates another gene dependent on an environmental input may make it look like something is evolving, but that function could already exist in the genome.
In fact the more layers of complexity and non-linearity we observe in the genome and how it is processed makes it more difficult to explain how a mutation could ever be understood to be advantageous; with multiple reading frames a mutation to a nucleotide could be imagined to have a positive effect somehow on the expression of a protein, but what about the other types of protein that get expressed from the same code? They're now broken.

This is a multi-layered code, I have previously worked in Cryptography and compression algorithms for many years. The genome implements compression to represent data in an efficient way. Corrupting even one bit of compressed data usually has an effect on multiple parts of the data ... if that data is a program, you can expect the program to crash if enough bits are corrupted.

This makes sense for the genome too (and is observed through genetic diseases) ... that along with the fact that Lenski's experiments fails to show evolution from one kind of an organism (bacteria) to a different, more complex organism despite an equivalent of 1 Million human years of evolution suggests this process doesn't work; except that everyone is the field is saying it works. I'm a sceptic, I want to see actual scientific proof that doesn't just gloss over the facts and pretend that mutation could be the only reason for an increase in cell size or a change in metabolism.

A working and accurate computer model still wouldn't prove evolution is happening in the wild, but it at least would show that it is theoretically viable. Currently I don't see how it is even theoretically possible, from an algorithmic perspective.

Quote
The Lenski experiment shows that mutations that reduce reproductive success can survive in a population long enough to enable further mutations that leapfrog function for a given environment.

Bacteria is also a bad example because it seems to deliberately use fuzzy logic and implement randomness in its genome as part of the programming ... so although a change may look random, it may be deterministic in function.
This is exactly how we program computer viruses. We expect them to evolve in a deliberate way.
So I do think there is some application for evolution as a concept in the modelling of bacteria and viruses, but their function is still deterministic and constrained by the master code, they may reprogram themselves (and transfer/shuffle genes with other bacteria) for versatility, but they can never vary to become a frog. In the case of viruses and bacteria I expect randomness is being used like we use pseudo-random noise generators in computers. We generate random variables and use them in our code ... we are NOT varying the functional part of the code itself randomly.

I think therefore it is misleading to look at what happens in bacteria and extrapolate it to other organisms, when we don't see the same processes happening in them.

"I think therefore it is misleading to look at what happens in bacteria and extrapolate it to other organisms, when we don't see the same processes happening in them."

Since that's how you feel, you might want to reconsider making statements like this:

"Lenski's experiment has achieved 60,000 generations in April 2014.
You need to understand, the proposed theory of evolution is not about "time"  ... it is about how many generations. Lenski's E. Coli has run for the equivalent of 1 million years of human generations."

Bacteria are not "equivalent" to humans.

I'm looking forward to your response to Cubist.

--------------
Think not that I am come to send peace on earth: I came not to send peace, but a sword. - Jesus in Matthew 10:34

But those mine enemies, which would not that I should reign over them, bring hither, and slay them before me. -Jesus in Luke 19:27

   
cryptoguru



Posts: 53
Joined: Jan. 2015

(Permalink) Posted: Jan. 18 2015,03:46   

Quote
What does "new information" look like?


New information is new and novel genetic material that codes for new function or traits in the organism i.e. not a point mutation in a control gene that switches other pre-existing functionality off/on or a trade/inheriting of genetic material between bacteria ...NEW genetic material that codes for new function; this has never been observed.



Quote
Nearly all genes were invented by microbial evolution.

begging the question! Demonstrate the process ... don't simply assert it happens.



Quote
Bacteria are not "equivalent" to humans.

Straw-man argument ... I never said they were, I was equivocating the process of evolution in both organisms. Bacteria can "evolve" quicker because their generation time is MUCH shorter (hence why Lenski chose E. Coli). So I can compare 26 years of E. Coli to 1 Million years of human evolution ... they are exactly the same amount of the same process. We would expect to see novel traits emerge in humans over 1 million years and be able to identify new genes that didn't exists previously that code for that new trait. We don't see this in Lenski's experiment.

Quote
None of the logic functions that obtain merit in Avida are due to singular codes in an Avidian's genome

You're misunderstanding the point. The original 26 functions (commands) that AVIDA uses are not subject themselves to mutation. So finding new logical functions that are combinations of these elemental functions is trivial using an optimisation algorithm (which is what AVIDA is). You will only get functionality that is described by compounds of those functions.

This is equivalent to having a chemistry set with 26 elements, you combine them randomly and select combinations of chemicals that produce interesting reactions, you optimise over those. You will NEVER create a new chemical element from this process. The elemental level in AVIDA is the function (command), these should therefore be evolved, not prescribed.
AVIDA is a very interesting modelling algorithm, great for solving some real-world competition problems. It does NOT model biological evolution.
I have clarified this point countless times, I don't see how I can simplify it any more for people to understand here.

Explain precisely where, in my description of AVIDA and the biological evolution algorithm I have got any of the details wrong.
AGAIN (to explain this problem one last time)
1) evolution mutates DNA on a nucleotide level affecting function (gene level) and selects on the organism level.
2) AVIDA mutates "DNA" on the gene level affecting compound function and selects on the compound function level.

These are VERY simple concepts to grasp.
Please explain how AVIDA is possibly modelling biological evolution when the core functions (commands) cannot be corrupted under mutation and the selection process is working on the compound functional level (by rewarding compound functions).

  
rossum



Posts: 289
Joined: Dec. 2008

(Permalink) Posted: Jan. 18 2015,04:10   

Quote (cryptoguru @ Jan. 18 2015,03:46)
New information is new and novel genetic material that codes for new function or traits in the organism i.e. not a point mutation in a control gene that switches other pre-existing functionality off/on or a trade/inheriting of genetic material between bacteria ...NEW genetic material that codes for new function; this has never been observed.

Yes it has.  Lenski's long term experiment showed bacteria developing a new function, the ability to digest citrate.  That function was not there previously, and that new function evolved during the experiment.

I can also point to the example of the  from Japan, "Nylon digesting bacteria" which happened naturally.

--------------
The ultimate truth is that there is no ultimate truth.

  
Soapy Sam



Posts: 659
Joined: Jan. 2012

(Permalink) Posted: Jan. 18 2015,05:09   

Quote (cryptoguru @ Jan. 18 2015,09:46)
These are VERY simple concepts to grasp.
Please explain how AVIDA is possibly modelling biological evolution when the core functions (commands) cannot be corrupted under mutation


A model does not have to include everything. It would be a simple matter (in many GAs, at least) to permit 'core function' to be subject to mutation also. If it happened to be fatal when it occurred, the evolving population would remain unperturbed by these occurrences. Mutational change is not 'not evolution' simply because it is not 'core function' change.

   
Quote
and the selection process is working on the compound functional level (by rewarding compound functions).


The entirety of a genome can be considered a 'compound function'. The survival or otherwise of a genome is assessed at a compound level - whole-genome survival and replication. But there are multiple levels of selection when aggregated over many generations.

Edited by Soapy Sam on Jan. 18 2015,11:12

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SoapySam is a pathetic asswiper. Joe G

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Wesley R. Elsberry



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(Permalink) Posted: Jan. 18 2015,05:49   

Cryptoguru:

   
Quote

You're misunderstanding the point. The original 26 functions (commands) that AVIDA uses are not subject themselves to mutation. So finding new logical functions that are combinations of these elemental functions is trivial using an optimisation algorithm (which is what AVIDA is). You will only get functionality that is described by compounds of those functions.

This is equivalent to having a chemistry set with 26 elements, you combine them randomly and select combinations of chemicals that produce interesting reactions, you optimise over those. You will NEVER create a new chemical element from this process. The elemental level in AVIDA is the function (command), these should therefore be evolved, not prescribed.


No, I understand "the point" quite well. I've shown the error there before, and I can do it again.

Cryptoguru's analogy would require that he somehow believes biological organisms create new chemical elements. Cryptogurru is wrong. Biological organisms do create novel chemical compounds out of the plain, ordinary elements that are hanging around. Mostly, these are novel proteins, constructed out of a toolkit of 20 amino acids. Cryptoguru's "challenge" conditions are handily met by Avida, which mutates the "code that defines the functions themselves". (That's one leve of indirection, not multiple levels.) Avidian instruction sequences define the functions that accrue merit. Those instruction sequences are mutated, changing the functions. In biology, nucleotide sequences are mutated, resulting in changes in function. And it is not a matter of "optimization" alone: the seed Avidian program is composed of a series of NOP instructions and a section that handles self-replication; the only function performed by the initial Avidian is self-replication. (The self-replication code is also subject to mutation, and Avidians routinely die without progeny due to mutations there that do not preserve self-replication capability.) The logical functions that accrue merit all have to be constructed de novo, they are not performed at some low level and increased, as Cryptoguru erroneously asserts with the "optimising" comments. Cryptoguru wants to endlessly modify his "challenge" to avoid admitting that its conditions have been met. That leads to absurdities in his analogizing, like the one about creating new elements, and in his perversely clinging to error that has clearly been called out.

In biology, you only get codons that are three-tuple combinations of four DNA nucleotides, and you only get proteins that are n-tuple combinations of the fixed set of amino acids that organism uses. (There's a canonical set of twenty amino acids.) The situation in Avida is analogous to one level of indirection, though not two. Fortunately, Cryptoguru's "challenge" only requested one level of indirection. The complaint that functions are built out of combinations is a non-starter, since that is exactly how the biology works, too.

Cryptoguru:

   
Quote

Explain precisely where, in my description of AVIDA and the biological evolution algorithm I have got any of the details wrong.


There are too many misconceptions in Cryptoguru's discussion of biology to bother with. The notion that biology produces new chemical elements is just the absurd topping on a cake of error.

   
Quote

AGAIN (to explain this problem one last time)
1) evolution mutates DNA on a nucleotide level affecting function (gene level) and selects on the organism level.
2) AVIDA mutates "DNA" on the gene level affecting compound function and selects on the compound function level.


The first point is pretty sloppy, because most functionality in organisms is at the protein or higher levels.

As for point 2, Cryptoguru apparently has no clue how Avida works, because Avida as in the Lenski et al. 2003 paper doesn''t do anything but select at the Avidian level. There is no process in Avida that permits the propagation of the instruction sequences that define a logic function on its own. This is an own-goal on Cryptoguru's part.

   
Quote

These are VERY simple concepts to grasp.


Certainly. The problem being that Cryptoguru is completely wrong about point 2.

   
Quote

Please explain how AVIDA is possibly modelling biological evolution when the core functions (commands) cannot be corrupted under mutation and the selection process is working on the compound functional level (by rewarding compound functions).


I haven't claimed that Avida models "biological evolution". I have claimed that Avida is sufficient to meet the terms of the "challenge" as it was stated early in the thread.

The functions that are awarded merit in Avida can be lost via mutation (the paper Cryptoguru claims to have read discusses this at length), so that is another plain error on his part. And I have noted already the error in claiming that Avida selects at any level lower than that of the Avidian.

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Wesley R. Elsberry



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(Permalink) Posted: Jan. 18 2015,05:52   

Cryptoguru:

Quote
I never said they were, I was equivocating the process of evolution in both organisms


That word... I do not think it means what you think it means.

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"You can't teach an old dogma new tricks." - Dorothy Parker

    
Cubist



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(Permalink) Posted: Jan. 18 2015,06:18   

Quote (cryptoguru @ Jan. 18 2015,03:46)
     
Quote
What does "new information" look like?

New information is new and novel genetic material that codes for new function or traits in the organism i.e. not a point mutation in a control gene that switches other pre-existing functionality off/on or a trade/inheriting of genetic material between bacteria ...NEW genetic material that codes for new function; this has never been observed.

"Never been observed", you say. Well, I say, show me a person who's never heard of a kinkajou, and I'll show you a person who wouldn't recognize a kinkajou if a rabid one was chewing on their face. And in my experience, it's awfully damned common for Creationists who claim that thus-and-such has never been observed, do not actually know what thus-and-such would look like, and therefore those Creationists don't actually have any valid grounds for asserting that thus-and-such "has never been observed". So I want to drill down on your verbiage here, cryptoguru, and see whether you actually do know what you're talking about.

You have a definition of "new information". Groovy. I note that your definition of "new information" is sufficiently imprecise that it doesn't provide any way to tell whether or not a given string of nucleotides qualifies as "new information" under your definition. So let's see if we can dispel the vagueness, shall we?

Your definition of "new information" includes a clause about "new and novel genetic material".  Why must the "genetic material" of "new information" be both "new" and "novel"? I ask because "new" and "novel" strike me as basically synonymous, hence, using both words is gratiutous redundancy. But perhaps you weren't being redundant; perhaps you actually are using distinct referents for "new" and "novel", such that the two words are not, in fact, gratuitously redundant. Please explain how "genetic material" which is "new" differs from "genetic material" which is "novel".  Is it possible for "genetic material" to be "new" without also being "novel"? Is it possible for "genetic material" to be "novel" without also being "new"?

What does "new and novel genetic material" look like? I'm going to provide some concrete data to work with. Here's an arbitrary nucleotide sequence, with a randomly-picked nucleotide—the thymine in the 4th codon—colored red:
gcc tac agg gat cgt ggg gac ctt acg aat ggc ctt ttt gac tat tct tcg aat cta agc tca gca tca ttc ccg tct acg gga agt ccc ttc cca ata cat atc ctc ggc acc gca ctt gca ggc tca cgc ttc gcg tca ttt agg tca
That sequence of codons yields the following sequence of amino acids, with the 4th amino acid colored red on account of it's the AA that's yielded by the codon with the red-colored nucleotide:
alanine, tyrosine, arginine, aspartic acid, arginine, glycine, aspartic acid, leucine, threonine, asparagine, glycine, leucine, phenylalanine, aspartic acid, tyrosine, serine, serine, asparagine, leucine, serine, serine, alanine, serine, phenylalanine, proline, serine, threonine, glycine, serine, proline, phenylalanine, proline, isoleucine, histidine, isoleucine, leucine, glycine, threonine, alanine, leucine, alanine, glycine, serine, arginine, phenylalanine, alanine, serine, phenylalanine, arginine, serine

One possible mutation of that sequence would be if the thymine in the 4th codon was deleted, like so (and the thereby-altered 4th codon is colored red here):
gcc tac agg gac gtg ggg acc tta cga atg gcc ttt ttg act att ctt cga atc taa gct cag cat cat tcc cgt cta cgg gaa gtc cct tcc caa tac ata tcc tcg gca ccg cac ttg cag gct cac gct tcg cgt cat tta ggt ca
Since a codon is three nucleotides in a row, deleting that one nucleotide from the 4th codon in the original sequence doesn't just change that 4th codon; it also has the effect of changing pretty much every codon after that altered 4th codon. This, in turn, yields a very different sequence of amino acids than the original, unmutated sequence. The red-colored AAs are ones which don't occur at all in the original, unmutated sequence:
alanine, tyrosine, arginine, aspartic acid, valine, glycine, threonine, leucine, arginine, methionine, alanine, phenylalanine, leucine, threonine, isoleucine, leucine, arginine, isoleucine, [end], alanine, glutamine, histidine, histidine, serine, arginine, leucine, arginine, glutamic acid, valine, proline, serine, glutamine, tyrosine, isoleucine, serine, serine, alanine, proline, histidine, leucine, glutamine, alanine, histidine, alanine, serine, arginine, histidine, leucine, glycine, [???]

Does the mutated nucleotide sequence qualify as "new and novel genetic material"? Does the mutated nucleotide sequence contain any "new and novel genetic material"?

  
Wesley R. Elsberry



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(Permalink) Posted: Jan. 18 2015,06:21   

And my post here still stands as an accurate summation of things. Avida meets the requirements of Cryptoguru's "challenge" and Cryptoguru's further dismissals have been distributed between the irrelevant and the erroneous.

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"You can't teach an old dogma new tricks." - Dorothy Parker

    
cryptoguru



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(Permalink) Posted: Jan. 18 2015,06:26   

Okay let me explain this in another way ... you seem to keep missing the point.

Let's see if we can agree on this point:-
The genome is a code comprised of symbols (G, A, C, T) stored in nucleotides (the same as computer code characters can be stored in bytes).
This code defines how to build proteins from amino acids arrange them and fold them. Proteins are an elemental functional component. The genome also defines how to assemble the proteins into complex structures, with complex function. The genome is mutated at the nucleotide (symbol) level.

AGREE?

AVIDA is providing 26 elemental functional components (commands) as the building blocks to optimise compound functionality. This is the same as providing 26 proteins and performing stochastic optimisation to find compound functionality. AVIDA only selects BETWEEN these components, it doesn't allow mutation of them at the symbol level (the code that defines these components). Therefore the integrity of those component commands is never affected by the mutation process in AVIDA, and new components commands cannot emerge, there will always be 26 commands.

THIS IS NOT EQUIVALENT!

Pleas explain how any of my assertions here are wrong.

It could be argued that AVIDA is modelling the selection of combination of entire genes to create new functionality and adaptation of an organism to its environment ... I would not dispute that happens in real organisms ... but the elemental functionality never extends, so limits the functionality of the organism.

e.g. a robot that is built to support commands to go forward, backwards, left and right on the ground cannot learn to fly by combining those commands in an optimal order. You cannot select what isn't there to select. This is the level that AVIDA is working on, not the symbol or code level.

  
Wesley R. Elsberry



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(Permalink) Posted: Jan. 18 2015,06:26   

Cubist:

Quote
Your definition of "new information" includes a clause about "new and novel genetic material".  Why must the "genetic material" of "new information" be both "new" and "novel"?


In my experience, antievolutionists do this because they think that evolution is supposed to replace de novo creation, so they require that it should look just like de novo creation. They don't want to hear about co-opting function, duplication and divergence, and all the other ways that evolutionary processes actually do things that haven't been done before. Because evolution doesn't do "poof!", they think that they have identified a problem. The fact that nobody else sees this as a problem is very frustrating to them.

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"You can't teach an old dogma new tricks." - Dorothy Parker

    
cryptoguru



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(Permalink) Posted: Jan. 18 2015,06:28   

Quote
That word... I do not think it means what you think it means.


you're right ... it was late when I wrote it ;-)

  
Wesley R. Elsberry



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(Permalink) Posted: Jan. 18 2015,07:00   

I am not "missing the point", I am rebutting erroneous claims.

Cryptoguru:

 
Quote
Pleas explain how any of my assertions here are wrong.


Already done for a bunch of stuff. Pardon me if I simply review where we are at.

The assertion that biological organisms created new chemical elements was wrong.

The assertion that Avida selected at something lower than the Avidian level was wrong.

The assertion that Avida composing functions out of instruction sequences is not analogous to biological organisms composing proteins out of amino acids is wrong.

The assertion that nobody besides Cryptoguru had read Lenski et al. 2003 was wrong.

Cryptoguru wanted an analogy between critters and computers. He's just unhappy that this exists. Avida provides an instruction set. The sequences of instructions form programs. A computer's instruction set is fixed; changing code sequences does not change the instruction set. Likewise, Avida's instruction set is fixed. Cryptoguru has invoked Turing machines, and the analogous piece there is the tape, and nothing on the tape changes the reader. Biological organisms aren't, in the common course of things, changing either the set of DNA nucleotides or the set of amino acids they use. If Cryptoguru doesn't like the way Avida gets to the functions it rewards, the problem isn't with Avida; the problem is with Cryptoguru's analogy/equivalence between biology and computation. The elements of Cryptoguru's stated "challenge" have been met. He seems intent to change the "challenge" post hoc to exclude things that meet it.

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"You can't teach an old dogma new tricks." - Dorothy Parker

    
JonF



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(Permalink) Posted: Jan. 18 2015,08:10   

Quote (cryptoguru @ Jan. 17 2015,19:28)
I'm making the point that nothing in the Lenski experiment proves evolution, it can just as easily be explained as programmed behaviour. Considering we're discovering more and more deterministic complexity in the genome, it is more than reasonable to assume that all the variation we see is specified complexity that already exists within the genome, and is not the result of random mutation. This has NOT been contradicted by any experiment yet, it is simply being asserted.

Lenski identified the mutations that led to citrate utilization, a new and novel function.  Are you alleging that there is some currently unknown information storage and processing mechanism in the cell that pre-programmed those mutations?

If so, interesting theory.  Got any evidence for it?

  
NoName



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(Permalink) Posted: Jan. 18 2015,08:14   

Quote (cryptoguru @ Jan. 18 2015,07:26)
Okay let me explain this in another way ... you seem to keep missing the point.

Let's see if we can agree on this point:-
The genome is a code comprised of symbols (G, A, C, T) stored in nucleotides (the same as computer code characters can be stored in bytes).
This code defines how to build proteins from amino acids arrange them and fold them.[/quote]
Strictly false.  The code is comprised of more than just the symbols.  Their specific arrangement and adjacencies matter critically.  This is entirely unlike computer code.
Secondly, the code emphatically does not define how proteins fold.  Physics and chemistry do, and they do so based on the local environment in which the genetic material and its products exist, as well as the local environment excluding the genetic material and its products.
Quote
Proteins are an elemental functional component. The genome also defines how to assemble the proteins into complex structures, with complex function.

Again, strictly false.  There is no one-to-one mapping between genes and the resulting structures of the life-form.
Quote
The genome is mutated at the nucleotide (symbol) level.

AGREE?

With the tiny bit you got correct, yes.  With the gross misunderstandings that are sufficient to warrant dismissal of all your claims, of course not.
Quote
...
Pleas explain how any of my assertions here are wrong.

Done and done.

I'll also note that you are ignoring the fact that your original challenge, as yet lacking any explicit modification or discussion by you, has been met in multiples ways by multiple posters.  That you ignore this suggests strongly that you see a single path of argument that reaches the conclusion you desire, that you are arguing from what amounts to a script that hangs off that particular singular path, and that you are unwilling and/or unable to deviate from that  script when others don't play along.  It also indicates strongly that  you are unwilling and/or unable to acknowledge that your challenge has been met, because that doesn't match the results you get by your singular preferred argument.  The rest of the world understands what it means when one 'preferred' argument out of many appears to succeed, but the facts show it to be incorrect, regardless of how appealing or apparently sound it is.  You appear not to understand this.
Your challenge has been met.
Revise it into a different challenge and admit defeat on this front.  Of course, that means admitting that you have no basis other than faith and a generalized distaste for rejecting evolutionary theory.
I thank 'The whole truth' for pointing out my careless wording that failed to make the distinction between evolution the fact and 'evolutionary theory'.  He's absolutely correct, and my post needs that correction.

I'll also note that it is strictly false to assert that the cell is a Turing machine.  The cell does not operate on a strictly clocked mechanism, does not have infinite storage, does not operate by singular read/write operations on singular 'memory cells', etc.  That the cell can be modeled by a Turing machine does not make the cell a Turing machine.
That the entirety of the living processes, all essential to the existence of a cell, can be modeled by a single Turing machine is a laughable claim.  At the very least, it requires proof, and said proof would be notable and prize-worthy.
Whole-cell modeling is still a very difficult enterprise and does not have a general solution.  I've worked in the field, I know this to be true.

And I'll note that you conspicuously fail to understand the point of thermodynamics as a problematic for cells that does not apply to computers.  The analogous problem for computers is high-energy gamma radiation randomly flipping bits in memory cells.  That phenomenon is rare enough that it did not become problematic 'in the field' until the late 90's, when ECC memory began to be required.  Do you understand why this is so?  Do you understand the analogy, and its limits?

Finally, I see no point in going back and addressing your response to my post from near the top of the previous page.  You give every evidence of being one of those "I've got my mind made up, don't confuse me with facts" people.  That a computer can use the various things noted, or can demonstrate them, is irrelevant to the argument, and it is tragic that you do not see that.

  
Wesley R. Elsberry



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(Permalink) Posted: Jan. 18 2015,08:25   

Cryptoguru:

   
Quote

e.g. a robot that is built to support commands to go forward, backwards, left and right on the ground cannot learn to fly by combining those commands in an optimal order. You cannot select what isn't there to select. This is the level that AVIDA is working on, not the symbol or code level.


Avida's instruction set is Turing-complete. Avidian genomes are sequences of instructions. Any computable function is possible to encode with Avida instructions. The notion that Avida is not capable of doing what computers and Turing machines do is wrong. This is not arguable.

It is possible that Cryptoguru has confused himself. Selection is an effect of the organism interacting with its environment, either in biology or Avida. That there are only certain things that are set up for selection in an Avida experimental environment is analogous to the limits of particular natural environments. Cave-dwelling fish, for instance, aren't in a position to evolve flight in air, either. As it turns out, there are some 60+ logic functions that stock Avida can evaluate in its environmental setup, only nine of which were activated in the Lenski et al. 2003 paper. And as I noted, Avida instruction set programs can encode any computable function. Faulting Avida for not having every computable function set up for reward in every experimental environment is quite ludicrous, and also quite beside the point of the original "challenge", which was that new functions arise from the model genome changes, not that every possible function must arise thereby.

If Cryptoguru means by his objections that Avida cannot be an analogy for biology because of the limits of computation, he has also refuted his own insistence that biology is computation.

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OgreMkV



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(Permalink) Posted: Jan. 18 2015,08:38   

Quote (Wesley R. Elsberry @ Jan. 18 2015,08:25)
Cryptoguru:

     
Quote

e.g. a robot that is built to support commands to go forward, backwards, left and right on the ground cannot learn to fly by combining those commands in an optimal order. You cannot select what isn't there to select. This is the level that AVIDA is working on, not the symbol or code level.

This is also interesting in that cryptoguru has previously rejected my statements that evolution can only build on previously existing DNA.

In fact, cryptoguru appears to be using evolutionary science as evidence that evolution can't work.

Truly a strawman of epic proportions.

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Ignored by those who can't provide evidence for their claims.

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Texas Teach



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(Permalink) Posted: Jan. 18 2015,09:09   

Quote (OgreMkV @ Jan. 18 2015,08:38)
Quote (Wesley R. Elsberry @ Jan. 18 2015,08:25)
Cryptoguru:

     
Quote

e.g. a robot that is built to support commands to go forward, backwards, left and right on the ground cannot learn to fly by combining those commands in an optimal order. You cannot select what isn't there to select. This is the level that AVIDA is working on, not the symbol or code level.

This is also interesting in that cryptoguru has previously rejected my statements that evolution can only build on previously existing DNA.

In fact, cryptoguru appears to be using evolutionary science as evidence that evolution can't work.

Truly a strawman of epic proportions.

He's also trying the old creationist trick of dividing mutation and selection to claim that each is insufficient for evolution.  Here we have the "natural selection can't do anything new since all the DNA sequences are the same" variant.  Others prefer the "mutations can't randomly assemble all the DNA pieces, tornado in a junkyard, blah, blah, blah" variant.

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"Creationists think everything Genesis says is true. I don't even think Phil Collins is a good drummer." --J. Carr

"I suspect that the English grammar books where you live are outdated" --G. Gaulin

  
The whole truth



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(Permalink) Posted: Jan. 18 2015,10:08   

Quote (cryptoguru @ Jan. 18 2015,01:46)
Quote
What does "new information" look like?


New information is new and novel genetic material that codes for new function or traits in the organism i.e. not a point mutation in a control gene that switches other pre-existing functionality off/on or a trade/inheriting of genetic material between bacteria ...NEW genetic material that codes for new function; this has never been observed.



Quote
Nearly all genes were invented by microbial evolution.

begging the question! Demonstrate the process ... don't simply assert it happens.



Quote
Bacteria are not "equivalent" to humans.

Straw-man argument ... I never said they were, I was equivocating the process of evolution in both organisms. Bacteria can "evolve" quicker because their generation time is MUCH shorter (hence why Lenski chose E. Coli). So I can compare 26 years of E. Coli to 1 Million years of human evolution ... they are exactly the same amount of the same process. We would expect to see novel traits emerge in humans over 1 million years and be able to identify new genes that didn't exists previously that code for that new trait. We don't see this in Lenski's experiment.

Quote
None of the logic functions that obtain merit in Avida are due to singular codes in an Avidian's genome

You're misunderstanding the point. The original 26 functions (commands) that AVIDA uses are not subject themselves to mutation. So finding new logical functions that are combinations of these elemental functions is trivial using an optimisation algorithm (which is what AVIDA is). You will only get functionality that is described by compounds of those functions.

This is equivalent to having a chemistry set with 26 elements, you combine them randomly and select combinations of chemicals that produce interesting reactions, you optimise over those. You will NEVER create a new chemical element from this process. The elemental level in AVIDA is the function (command), these should therefore be evolved, not prescribed.
AVIDA is a very interesting modelling algorithm, great for solving some real-world competition problems. It does NOT model biological evolution.
I have clarified this point countless times, I don't see how I can simplify it any more for people to understand here.

Explain precisely where, in my description of AVIDA and the biological evolution algorithm I have got any of the details wrong.
AGAIN (to explain this problem one last time)
1) evolution mutates DNA on a nucleotide level affecting function (gene level) and selects on the organism level.
2) AVIDA mutates "DNA" on the gene level affecting compound function and selects on the compound function level.

These are VERY simple concepts to grasp.
Please explain how AVIDA is possibly modelling biological evolution when the core functions (commands) cannot be corrupted under mutation and the selection process is working on the compound functional level (by rewarding compound functions).

"... I was equivocating the process of evolution in both organisms."

I know.

"Bacteria can "evolve" quicker because their generation time is MUCH shorter (hence why Lenski chose E. Coli). So I can compare 26 years of E. Coli to 1 Million years of human evolution ... they are exactly the same amount of the same process."

Where do you get the idea that every biological entity* evolves by exactly the same amount from one generation to the next?


*I would have said life form instead of biological entity but I'm including viruses, and not everyone thinks that viruses are life forms.

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Think not that I am come to send peace on earth: I came not to send peace, but a sword. - Jesus in Matthew 10:34

But those mine enemies, which would not that I should reign over them, bring hither, and slay them before me. -Jesus in Luke 19:27

   
Jim_Wynne



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(Permalink) Posted: Jan. 18 2015,10:35   

Cryptoguru, condensed:

1.  All of biology and most of science is wrong.
2.  Frontloading.
3.  No evidence, no mechanisms.

I'll put the over/under on this thread at six pages.

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Evolution is not about laws but about randomness on happanchance.--Robert Byers, at PT

  
Texas Teach



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(Permalink) Posted: Jan. 18 2015,10:41   

Quote (Jim_Wynne @ Jan. 18 2015,10:35)
Cryptoguru, condensed:

1.  All of biology and most of science is wrong.
2.  Frontloading.
3.  No evidence, no mechanisms.

I'll put the over/under on this thread at six pages.

Gaulin has no more than that, and his thread is at 429 pages.  Never underestimate the needs of TARD-addicts.

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"Creationists think everything Genesis says is true. I don't even think Phil Collins is a good drummer." --J. Carr

"I suspect that the English grammar books where you live are outdated" --G. Gaulin

  
The whole truth



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(Permalink) Posted: Jan. 18 2015,10:46   

NoName, thanks for taking what I said so graciously. :)

--------------
Think not that I am come to send peace on earth: I came not to send peace, but a sword. - Jesus in Matthew 10:34

But those mine enemies, which would not that I should reign over them, bring hither, and slay them before me. -Jesus in Luke 19:27

   
N.Wells



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(Permalink) Posted: Jan. 18 2015,11:53   

Quote (cryptoguru @ Jan. 16 2015,19:14)
Quote
I'd like to add that natural selection is not always a death.

It can be an effective removal of the gene pool. For example, the strongest, fittest, most efficient lion ever born might have a problem reproducing. Which means that he is removed from the gene pool. He can't pass his genes on to the next generation, so he's out of contention.


Haha amazing ... how did he get removed from the gene pool? A Gene pool isn't actually like a swimming pool you know, genes don't get thrown out for breaking the rules by the life-guard ... He gets removed from the "Gene pool" (population) by dying ... he dies before reproducing (for whatever reason), so his genes aren't passed on. Natural Selection is not looking at his Genes and saying "hey this guy isn't fit enough ... throw him out" ... Natural Selection is just a name given to the fact we have lions that are still reproducing, and that lion isn't because he was less fit so simply dies.
You're picking a fight over something we agree on here. I'm demystifying the explanation of how Natural Selection works, it is death ... it is not just general competition. Yes it IS competition, but only competition that results in something dying and other things not.

My two cents on this earlier comment: Natural selection is not solely and only about death.  It's differential reproductive success, which may or may not be attributable to dying early.  

A long-term study of reproductive successes of 142 female sparrowhawks from 1971 to 1984 showed that 23 had no fledglings, 70 had only 1 to 4 fledglings, and 3 had more than 20 fledgelings (21, 22, & 23).  Obviously, the genes of the last three become much more widely represented in subsequent generations.  Some of the mothers died early, but others simply weren't successful at parenting.  This can involve a whole host of reasons other than dying.

  
Wesley R. Elsberry



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(Permalink) Posted: Jan. 18 2015,12:32   

Cryptoguru:

Quote

Haha amazing ... how did he get removed from the gene pool? A Gene pool isn't actually like a swimming pool you know, genes don't get thrown out for breaking the rules by the life-guard ... He gets removed from the "Gene pool" (population) by dying ... he dies before reproducing (for whatever reason), so his genes aren't passed on. Natural Selection is not looking at his Genes and saying "hey this guy isn't fit enough ... throw him out" ... Natural Selection is just a name given to the fact we have lions that are still reproducing, and that lion isn't because he was less fit so simply dies.
You're picking a fight over something we agree on here. I'm demystifying the explanation of how Natural Selection works, it is death ... it is not just general competition. Yes it IS competition, but only competition that results in something dying and other things not.


Here's another way Avida differs from Cryptoguru selection. Avidians get CPU time according to merit. It is perfectly possible for an Avidian to replicate while other Avidians have greater merit. The other Avidians, though, replicate themselves more often and thus the population comes to have more Avidians like those with more merit, and fewer Avidians like those with less.

This, by the way, is not a way in which Avida is distinguished from natural selection.

--------------
"You can't teach an old dogma new tricks." - Dorothy Parker

    
cryptoguru



Posts: 53
Joined: Jan. 2015

(Permalink) Posted: Jan. 18 2015,14:18   

Wesley R. Elsberry:

Again you've missed the point ... I'm not saying AVIDA should model every possible function, I'm saying that it doesn't model the proposed form of evolution. Real evolution is supposed to mutate the base code ... so you should be mutating the under-the-hood program code that defines the NAND, SWAP, DEC, IO, SUB etc. in AVIDA as this is what happens in a real genome.

I'm not doubting that AVIDA is excellent at solving generic optimisation problems, but it is misleading to pretend it is modelling biological evolution, because the core feature of biological evolution is random mutation of nucleotides (point, insertion, deletion). The variability of that problem is orders of magnitude greater than the simple optimisation problems you're solving with AVIDA.

In DNA, mutations occur at the symbol level of the code that is used to build and assemble proteins, direct their sub-assembly (amino acids ... translational pausing etc) and further controls the protein assembly into complex functional parts. These themselves are part of the whole organism, where cells are differentiated in function and perform many complementary roles with other cells.

AVIDA is basically 26 assembly code instructions, which are mutated randomly under competition until something useful happens. This is not analogous to DNA mutation and selection.

I say it again, THIS is like mutating 26 proteins in DNA to make different complex structures and rewarding certain combinations that give known favourable complex structures. AVIDA is applying mutations on a much higher level than occurs in the Genome, so doesn't allow the possibility of code corruption, base functionality regression and crash, which a real genome does.

This effect is amplified by the fact that the instruction set is Turing-complete ... AVIDA is MOST likely to find useful combinations of the 26 functions ... this is a cumulative SEARCH (similar to WEASEL it has targets), and not like biological evolution. The human genome has billions of base pairs, even mutating 3 neighbouring nucleotides to any codon anywhere in the genome is less likely than winning the lottery twice in a row. Being able to mutate an AVIDA command to another functioning command is 100% likely. DO YOU GET IT YET??? (I doubt it)

Most of the responses I've had so far are so off-the-wall and lacking in fundamental logic that it's impossible to even address their stupidity.

If you guys can't see the difference between a process which mutates nucleotides in a huge code that has MANY layers of complexity, inter-dependency and non-linear function and a process which randomly mutates 26 assembly instructions in different ways, scores combinations that perform a simple function and allows them to compete ... then you're more wilfully ignorant than I had initially assumed.

It's wishful thinking of the highest degree to expect useful behaviour to come out corrupting a computer program. Comparing that to shuffling assembler instructions until you get a useful function is absolutely laughable. I suppose you have to come up with something like this though to keep the funding rolling in and slap the word "evolution" all over the papers so the similarly confused peer reviewers get all excited and happy that evolution is a FACT and we can all sleep soundly.

Also the minion-like responses I've had concerning Lenski's experiment on here are equally hilarious. Trying to deny that after he's performed 60,000 generational steps seeing a small metabolic change is not something to get excited about is utterly self-deceptive.

This is a dying theory indeed when models can't model it ... and experiments don't demonstrate it.
The power behind this theory is you guys ... your zeal at flocking around any assailant and trying to neutralise any attacks on the precious, by employing as much ridicule, incredulity, slander and mock as you can muster whilst still attempting to sound scientific.

I'm going to go and do some actual work that isn't based on fairy tales now ...
... and leave you all to your mutual backslapping and peddling the nonsense postulation that random mutations plus a sprinkling of magic selection (which is the secret ingredient that we should never really define properly lest it became understandably deficient) will eventually mutate a Banana into Barack Obama. I do hope some of you get to use your brains for things that actually benefit people and this is just a hobby thing that you do in your sparetime.

Have fun folks.

Oh ... please DO let me know when Lenski suddenly finds a fish in his E. Coli. That will be a monumental day for all of us.

  
cryptoguru



Posts: 53
Joined: Jan. 2015

(Permalink) Posted: Jan. 18 2015,14:39   

final point to N. Wells


Natural Selection is about death. It doesn't matter what the reasons are for advantage, whether it's because some are stronger, or shorter, or bluer, or have better ovaries, or avoid nightclubs .. whatever. The selective agent is death. If an organism dies before it can reproduce it will be removed from the gene pool. Things that haven't died yet compete for resources, eventually a hereditary line will die off removing it from the competition (death again).

The whole premise of natural selection can be simplified to be death. Differential reproduction is a misleading concept, because the preservation of an advantageous trait can only occur when eventually all other competing hereditary lines are extinct. (death). Otherwise you evolutionists would expect to see millions of intermediate evolutionary stages living now alongside the "favoured" one ... and you don't believe that, so all other lines must become extinct to allow the favoured line to become the parent to the next stage. (I obviously think this is crackers ... I'm just explaining that the evolutionary concept of natural selection is very simple)

My point is that the evolutionary concept of natural selection is easy to model, you just set natural conditions and environments for the organisms to live and compete in and see which survive, you shouldn't be measuring the advantages and rewarding them ... nature does not do that, it just provides conditions for death, those who survive it are considered "selected".

I don't see what all the fuss is about ... just trying to demystify the Natural Selection deity.

Bye for now

  
rossum



Posts: 289
Joined: Dec. 2008

(Permalink) Posted: Jan. 18 2015,15:00   

Quote (cryptoguru @ Jan. 18 2015,14:39)
Natural Selection is about death.

No, natural selection is about reproductive success, not death.  Death may be important, but only because of its impact on reproductive success.  Dying at 20, leaving two children is better than dying at 80, with no children.

The process of natural selection is a bit like compound interest.  As an example, take a stable population of 100 organisms; on average each organism has one descendant in the next generation.  Now let a beneficial mutation appear with a 1% advantage, so the mutated organism will have on average 1.01 descendants in the next generation.  For comparison I include a second mutated organism with a 1% disadvantage.  Start with a population of 1 deleterious, 98 neutral and 1 beneficial mutations.  See what happens if we let the population reproduce for one thousand generations:

Code Sample

Generation  Deleterious   Normal   Beneficial
----------  -----------   ------   ----------
    0         1.00       98.00          1.00
    1         0.99       98.00          1.01
   10         0.90       98.00          1.10
  100         0.37       98.00          2.70
  500         0.01       98.00        144.77
  700         0.00       98.00       1059.16
 1000         0.00       98.00      20959.16

(That should be monospaced, but I can't get it to work well.  Sorry.)

You can see how the small 1% advantage is amplified over the generations as the beneficial variant spreads through the population.  The deleterious mutation disappears.

This is a very simple model, but it is enough to show the advantage a beneficial mutation has and how it can spread through a population.

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The ultimate truth is that there is no ultimate truth.

  
N.Wells



Posts: 1836
Joined: Oct. 2005

(Permalink) Posted: Jan. 18 2015,15:06   

Quote (cryptoguru @ Jan. 18 2015,14:39)
final point to N. Wells


Natural Selection is about death. It doesn't matter what the reasons are for advantage, whether it's because some are stronger, or shorter, or bluer, or have better ovaries, or avoid nightclubs .. whatever. The selective agent is death. If an organism dies before it can reproduce it will be removed from the gene pool. Things that haven't died yet compete for resources, eventually a hereditary line will die off removing it from the competition (death again).

The whole premise of natural selection can be simplified to be death. Differential reproduction is a misleading concept, because the preservation of an advantageous trait can only occur when eventually all other competing hereditary lines are extinct. (death). Otherwise you evolutionists would expect to see millions of intermediate evolutionary stages living now alongside the "favoured" one ... and you don't believe that, so all other lines must become extinct to allow the favoured line to become the parent to the next stage. (I obviously think this is crackers ... I'm just explaining that the evolutionary concept of natural selection is very simple)

My point is that the evolutionary concept of natural selection is easy to model, you just set natural conditions and environments for the organisms to live and compete in and see which survive, you shouldn't be measuring the advantages and rewarding them ... nature does not do that, it just provides conditions for death, those who survive it are considered "selected".

I don't see what all the fuss is about ... just trying to demystify the Natural Selection deity.

Bye for now

You are pervasively wrong here, because you are simplifying natural selection incorrectly.

Death, although important, is just one of many "selective agents", so differential reproductive success can be extremely different from "life versus death", and simplifying natural selection to "life versus death" has led to many misunderstandings about evolution, such as your misunderstandings.  Natural selection is usually much more subtle than just differential mortality rates.

An organism that fails to reproduce as successfully as the neighbors will have a smaller proportion of genes in the next generation.  That (with recombination and many generations) can indeed cause the genes to become very rare and eventually be lost from the population.  Because of recombination and multiple generations, lineages do not have to go extinct for genes to be lost.

   
Quote
Otherwise you evolutionists would expect to see millions of intermediate evolutionary stages living now alongside the "favoured" one ... and you don't believe that....
"Millions" is an overstatement, but polymorphic alleles are indeed very common, as are races, sister species, and overlapping ranges between competitors, all of which indicate that the world does not function as simply as you imply.

From http://www.biologyreference.com/Mo-Nu......on.html
Quote
A persistent misconception is that natural selection occurs mainly through differences between organisms in death rates, or differential mortality. Differential mortality can be selective but only to the degree that it creates differences between individuals in the number of reproductive offspring they produce. Reproductive rate, rather than death rate, drives natural selection. A cautious tomcat that seldom crosses busy streets might live to a ripe old age without leaving behind as many descendent kittens as another less staid tomcat killed on a highway at a much younger age. If the short-lived cat leaves more descendants, its genes will spread faster than those of the long-lived cat, and natural selection will favor a short life span. Unless living longer allows or results in higher reproductive success, long life is not favored by natural selection.

See also http://www.zo.utexas.edu/courses....on.html

Edited to add: Thanks for a more specific response, Rossum - you posted while I was writing offline, or I'd have mentioned it.

  
Cubist



Posts: 558
Joined: Oct. 2007

(Permalink) Posted: Jan. 18 2015,16:25   

Verbatim re-post. I fully realize that cryptoguru's schedule is full up with telling evolutionists how wrong they are, but perhaps they will find the time to explain what they mean when they say "new and novel genetic material", or even determine whether or not one specific concrete example of a mutated nucleotide sequence qualifies as "new or novel genetic material". Or perhaps they will continue to make noise about how wrong evolutionists are. I dunno.

 
Quote (cryptoguru @ Jan. 18 2015,03:46)
         
Quote
What does "new information" look like?

New information is new and novel genetic material that codes for new function or traits in the organism i.e. not a point mutation in a control gene that switches other pre-existing functionality off/on or a trade/inheriting of genetic material between bacteria ...NEW genetic material that codes for new function; this has never been observed.

"Never been observed", you say. Well, I say, show me a person who's never heard of a kinkajou, and I'll show you a person who wouldn't recognize a kinkajou if a rabid one was chewing on their face. And in my experience, it's awfully damned common for Creationists who claim that thus-and-such has never been observed, do not actually know what thus-and-such would look like, and therefore those Creationists don't actually have any valid grounds for asserting that thus-and-such "has never been observed". So I want to drill down on your verbiage here, cryptoguru, and see whether you actually do know what you're talking about.

You have a definition of "new information". Groovy. I note that your definition of "new information" is sufficiently imprecise that it doesn't provide any way to tell whether or not a given string of nucleotides qualifies as "new information" under your definition. So let's see if we can dispel the vagueness, shall we?

Your definition of "new information" includes a clause about "new and novel genetic material".  Why must the "genetic material" of "new information" be both "new" and "novel"? I ask because "new" and "novel" strike me as basically synonymous, hence, using both words is gratiutous redundancy. But perhaps you weren't being redundant; perhaps you actually are using distinct referents for "new" and "novel", such that the two words are not, in fact, gratuitously redundant. Please explain how "genetic material" which is "new" differs from "genetic material" which is "novel".  Is it possible for "genetic material" to be "new" without also being "novel"? Is it possible for "genetic material" to be "novel" without also being "new"?

What does "new and novel genetic material" look like? I'm going to provide some concrete data to work with. Here's an arbitrary nucleotide sequence, with a randomly-picked nucleotide—the thymine in the 4th codon—colored red:
gcc tac agg gat cgt ggg gac ctt acg aat ggc ctt ttt gac tat tct tcg aat cta agc tca gca tca ttc ccg tct acg gga agt ccc ttc cca ata cat atc ctc ggc acc gca ctt gca ggc tca cgc ttc gcg tca ttt agg tca
That sequence of codons yields the following sequence of amino acids, with the 4th amino acid colored red on account of it's the AA that's yielded by the codon with the red-colored nucleotide:
alanine, tyrosine, arginine, aspartic acid, arginine, glycine, aspartic acid, leucine, threonine, asparagine, glycine, leucine, phenylalanine, aspartic acid, tyrosine, serine, serine, asparagine, leucine, serine, serine, alanine, serine, phenylalanine, proline, serine, threonine, glycine, serine, proline, phenylalanine, proline, isoleucine, histidine, isoleucine, leucine, glycine, threonine, alanine, leucine, alanine, glycine, serine, arginine, phenylalanine, alanine, serine, phenylalanine, arginine, serine

One possible mutation of that sequence would be if the thymine in the 4th codon was deleted, like so (and the thereby-altered 4th codon is colored red here):
gcc tac agg gac gtg ggg acc tta cga atg gcc ttt ttg act att ctt cga atc taa gct cag cat cat tcc cgt cta cgg gaa gtc cct tcc caa tac ata tcc tcg gca ccg cac ttg cag gct cac gct tcg cgt cat tta ggt ca
Since a codon is three nucleotides in a row, deleting that one nucleotide from the 4th codon in the original sequence doesn't just change that 4th codon; it also has the effect of changing pretty much every codon after that altered 4th codon. This, in turn, yields a very different sequence of amino acids than the original, unmutated sequence. The red-colored AAs are ones which don't occur at all in the original, unmutated sequence:
alanine, tyrosine, arginine, aspartic acid, valine, glycine, threonine, leucine, arginine, methionine, alanine, phenylalanine, leucine, threonine, isoleucine, leucine, arginine, isoleucine, [end], alanine, glutamine, histidine, histidine, serine, arginine, leucine, arginine, glutamic acid, valine, proline, serine, glutamine, tyrosine, isoleucine, serine, serine, alanine, proline, histidine, leucine, glutamine, alanine, histidine, alanine, serine, arginine, histidine, leucine, glycine, [???]

Does the mutated nucleotide sequence qualify as "new and novel genetic material"? Does the mutated nucleotide sequence contain any "new and novel genetic material"?

  
Doc Bill



Posts: 1039
Joined: April 2007

(Permalink) Posted: Jan. 18 2015,16:49   

That was quick!  I don't think I've ever seen someone go through the Stages of a Creationist as quickly as CreeptoGuru.

1.  Disingenuous Introduction (Hi, everybody!  I've got some questions.  Hope you can help.  Feel free to correct any misconceptions I have!)

2.  Creationist boilerplate.

3.  Patient explanations by Saint Wes and others.  (Doc Bill heavily sedated with DramaTARD to prevent chronic mockery.)

4.  There is no evilution!  Lenski benski!  Whaaaaaa, you're mean to me!  Jesus!

5.  Flounce.

Thank you, Creepto, for providing us with this hilarious brick of TARD, although it probably won't make it into the Hall of Flame:

Quote
Also the minion-like responses I've had concerning Lenski's experiment on here are equally hilarious. Trying to deny that after he's performed 60,000 generational steps seeing a small metabolic change is not something to get excited about is utterly self-deceptive.

This is a dying theory indeed when models can't model it ... and experiments don't demonstrate it.
The power behind this theory is you guys ... your zeal at flocking around any assailant and trying to neutralise any attacks on the precious, by employing as much ridicule, incredulity, slander and mock as you can muster whilst still attempting to sound scientific.


In the future, Creepto, try to work in some flourish like "altar of Darwin" or "high priests of science."  That's a crowd pleaser!

  
Wesley R. Elsberry



Posts: 4991
Joined: May 2002

(Permalink) Posted: Jan. 18 2015,18:06   

Cryptoguru:

 
Quote

The power behind this theory is you guys ... your zeal at flocking around any assailant and trying to neutralise any attacks on the precious, by employing as much ridicule, incredulity, slander and mock as you can muster whilst still attempting to sound scientific.


Anyone whose analogies require living organisms to create new chemical elements is eminently mockable on their own demerits.

And, by the way, what I engaged in was disagreeing with Cryptoguru, not "missing the point". Given the many exceedingly basic errors I pointed out in his commentary, one would think he'd be a bit less full of himself. Anybody reviewing the thread is likely to see what I see, that Cryptoguru made a bunch of erroneous claims, got told they were erroneous and why they were erroneous, and made his exit with exceedingly bad grace.

Unless, of course, he's one of those people who makes endless farewell tours, and he's just given his first farewell concert.

--------------
"You can't teach an old dogma new tricks." - Dorothy Parker

    
OgreMkV



Posts: 3668
Joined: Oct. 2009

(Permalink) Posted: Jan. 18 2015,18:16   

Quote (cryptoguru @ Jan. 18 2015,14:39)
final point to N. Wells


Natural Selection is about death. It doesn't matter what the reasons are for advantage, whether it's because some are stronger, or shorter, or bluer, or have better ovaries, or avoid nightclubs .. whatever. The selective agent is death. If an organism dies before it can reproduce it will be removed from the gene pool. Things that haven't died yet compete for resources, eventually a hereditary line will die off removing it from the competition (death again).

The whole premise of natural selection can be simplified to be death. Differential reproduction is a misleading concept, because the preservation of an advantageous trait can only occur when eventually all other competing hereditary lines are extinct. (death). Otherwise you evolutionists would expect to see millions of intermediate evolutionary stages living now alongside the "favoured" one ... and you don't believe that, so all other lines must become extinct to allow the favoured line to become the parent to the next stage. (I obviously think this is crackers ... I'm just explaining that the evolutionary concept of natural selection is very simple)

My point is that the evolutionary concept of natural selection is easy to model, you just set natural conditions and environments for the organisms to live and compete in and see which survive, you shouldn't be measuring the advantages and rewarding them ... nature does not do that, it just provides conditions for death, those who survive it are considered "selected".

I don't see what all the fuss is about ... just trying to demystify the Natural Selection deity.

Bye for now

The selective agent doesn't have to be death. Again, this is trivially untrue... unless you think that neutering a dog kills it.

The animal is alive, but totally unable to pass it's genes on to the next generation. This is an extreme example, but there are plenty in the real world. Especially among herd animals with a single dominant male. Either you are the dominant male or you don't contribute to the genetic population of the group.

"The whole premise of natural selection can be simplified to be death."

No. The whole premise of natural selection is what Darwin said. You might read what the people who came up with the idea actually said instead of attacking a strawman.

Quote
Otherwise you evolutionists would expect to see millions of intermediate evolutionary stages living now alongside the "favoured" one ... and you don't believe that,


I think that this is especially funny. Because biologists think that every single organism is transitional. You are transitional between your parents and your kids. You are transitional between your uncle's kids and your aunt's kids.

There are millions of intermediate evolutionary stages. We don't see all of them because a vast majority are dead and not everything fossilizes. But still, we see them.

We even see transitionals in the genes. In fact, that is one of the reasons that multi-species whole genome studies can work. I've provided you with a paper that shows the transitional nature of genes among closely related species.

So, again, you are attacking a strawman. You say that we believe one thing... which we don't. And then you attack it (incorrectly).

Natural selection is fairly simple. When will you ever understand what it actually is?

To model it, you have to understand it correctly... and you don't.

--------------
Ignored by those who can't provide evidence for their claims.

http://skepticink.com/smilodo....retreat

   
midwifetoad



Posts: 4003
Joined: Mar. 2008

(Permalink) Posted: Jan. 18 2015,18:22   

He does write better than GG.

--------------
Any version of ID consistent with all the evidence is indistinguishable from evolution.

  
Doc Bill



Posts: 1039
Joined: April 2007

(Permalink) Posted: Jan. 18 2015,18:29   

Quote (Wesley R. Elsberry @ Jan. 18 2015,18:06)
Cryptoguru:

 
Quote

The power behind this theory is you guys ... your zeal at flocking around any assailant and trying to neutralise any attacks on the precious, by employing as much ridicule, incredulity, slander and mock as you can muster whilst still attempting to sound scientific.


Anyone whose analogies require living organisms to create new chemical elements is eminently mockable on their own demerits.

And, by the way, what I engaged in was disagreeing with Cryptoguru, not "missing the point". Given the many exceedingly basic errors I pointed out in his commentary, one would think he'd be a bit less full of himself. Anybody reviewing the thread is likely to see what I see, that Cryptoguru made a bunch of erroneous claims, got told they were erroneous and why they were erroneous, and made his exit with exceedingly bad grace.

Unless, of course, he's one of those people who makes endless farewell tours, and he's just given his first farewell concert.

Saint Wes, an eternal fan of the Ungrateful Dead.

  
Woodbine



Posts: 1218
Joined: June 2007

(Permalink) Posted: Jan. 18 2015,19:07   

Quote (midwifetoad @ Jan. 19 2015,00:22)
He does write better than GG.

The fish drowning in Lenski's e-coli writes better than Gary.

  
Doc Bill



Posts: 1039
Joined: April 2007

(Permalink) Posted: Jan. 18 2015,19:34   

Quote (Woodbine @ Jan. 18 2015,19:07)
Quote (midwifetoad @ Jan. 19 2015,00:22)
He does write better than GG.

The fish drowning in Lenski's e-coli writes better than Gary.

Well, this is the typical creationist's view of evolution, isn't it?

CreeptoGuru demanded "new" and "novel" thingies and what he was demanding was a New Ford Chromosome 2015 with triple exhausts and a 13 cylinder engine, or some such.

Going back to Pandas, the hedge was "fish with fins and birds with feathers" with no ancestors.

That's what CreeptoGuru is demanding.  Ironically, that's the definition of creationism.  The fact that CreeptoGuru claims it's never been observed means that creationism has never been observed and that is totally correct.  It hasn't!

Well done, CreeptoGuru, you just disproved creationism!  Drinks on me.

  
QED



Posts: 41
Joined: July 2008

(Permalink) Posted: Jan. 18 2015,21:25   

Told ya'...fly pigeon, fly!

  
cryptoguru



Posts: 53
Joined: Jan. 2015

(Permalink) Posted: Jan. 19 2015,07:45   

wow ... OK, to avoid being labelled as running from a fight ... I'm going to try once more to see where we can get with a more structured approach
(I'm an amateur MMA fighter so not used to that sort of accusation)

I'm not expecting agreement, but at least it should help clarify where the sticking points are. If discussing a point, instead of posting an essay and saying it covers EVERYTHING, please refer to section and subsection so we all know which point you're contesting. Then we can get to a list of agreed principles, which should allow us to concentrate on the important controversial bits. (What was happening before was a full-scale assault on anything I said or the way I said it irrespective of whether there was agreement on the underlying principles or not.) Please also mark which points you agree on, otherwise I don't know where the common ground is.

Section A: How does the cell work (very very basic version)
1) living cells process a program called DNA
2) DNA is a code (a sequence of 3 symbols codes for amino acid)
3) DNA is processed in a non-linear fashion through regulatory mechanisms with multiple reading frames.
4) The cell eventually produces folded proteins, which are determined by which genes are being read, the reading frame, the regulatory process ... tonnes of stuff ... but it's deterministic (ignoring mutations) and the whole process is defined by the code. (this includes regulation in response to external stimuli ... i.e. input)
5) folded proteins are assembled into complex structures, again this process is controlled by mechanisms which are defined in the code.
6) the cells replicate and differentiate their function in a continuous morphological (yet continually compositionally functional) fashion based on their position in the organism, this process is also controlled by the code.

Section B:
What is Biological Evolution
1) given a population of self-replicating entities (a living cell)
2) random mutation of symbols in the raw code (usually point mutations ... about 50-100 de novo germline mutations per generation in humans)
3) advantages are introduced via the mutations by chance, the advantages are preserved and propagate through the population by "natural selection"
4) Natural selection is the name given to the process whereby environmental conditions apply a pressure for survival on the entities.
5) Entities therefore compete for resources and the ultimately surviving hereditary line is preserved, presumably carrying the genetic advantage that allowed it to overcome its competition.
6) Differential reproduction is a fancy way of saying that the hereditary line of some organisms, due to their inferiority in how they are suited to the environment, eventually (at some level of descent) produce no offspring before dying and therefore leave the competition.
7) Death is the only agent in natural selection, regardless of whether some organisms are only slightly better adapted than others, there will eventually be a point where an entire inferior hereditary line is removed (ultimately by death) from the population (i.e. a discrete process, not a continuous one). It is now as though that line had never existed. This is why death is the only important selector, comparisons between organisms do not come into the selection process ... it is simply a case of whether an organism is sufficiently fit to survive long enough in the environment to reproduce.

(I imagine point 7 will draw the most controversy ... TBH it's not important that you agree on that point for the sake of my argument, so happy to leave Natural Selection as an ambiguous and mysterious force if people would prefer so we can move on to where the actual disagreement should occur)

Section C:
What does AVIDA model
(I'm going to change my analogy here to focus the disagreement away from mutation)
1) 26 logical commands are provided and randomly selected and combined by "mutating" an original arrangement of them.
2) the commands are a list of functional operators (building blocks) that a computer code can be built from. They are Turing complete, so we should expect to be able to build any computer code from them in the correct combination
3) self-replicating digital entities, which have their own virtual processor run and mutate these programs
4) any entities are rewarded when a sequence of commands forms a logical function by increasing their resources

Section D:
comparison of AVIDA to biological evolution
1) an analogy must be drawn between AVIDA commands and the genome
2) it possibly makes most sense (I concede) to assume that AVIDA commands are analogous to codons (and not proteins), so that any mutation will always create a set of valid codons.
3) the level AVIDA is selecting at is therefore analogous to a folded functional protein.

Section E:
problems with model
1) the multi-dimensionality of the genome due to multiple reading frames means that a point mutation in the genome will likely affect the expression of multiple proteins (19K coding genes code for at least 100K different proteins in the human genome). Mutations in AVIDA are mutually exclusive and therefore don't have a regressive effect on the expression of other COMMANDS. This is not a trivial difference, it is analogous to the difference between a bisection method (AVIDA mutation) and a bisection method where the root can change at each iteration (Genome mutation).
2) It is not just multiple reading frames that introduce polymorphism into the genome, but regulatory genes can effect the expression of an entire coding gene. This non-linearity is not modelled in AVIDA, which is a linear sequential code (like assembler). That is, the Genome executes a higher-level language than a sequential instruction set.
3) AVIDA enforces selection by rewarding at the functional level ... it identifies a function as a logical operation and rewards the organism that is presenting it. This is equivalent to natural selection providing feedback scores to the organism on a per-protein level. e.g. protein 1 7/10, protein 2 3/10, protein 3 9/10. This kind of micro-management can't happen in real-life as natural selection is blind and is applied not even to an organism but an entire population. This feature artificially boosts the productivity of hopeful combinations of commands, which otherwise wouldn't be encouraged.
4) The level of variability in AVIDA compared to the genome is like comparing solving a Rubik's cube with cracking 2048-bit RSA encryption. The logical functions which AVIDA selects and guide the optimisation process are trivial ... and also non-distinct. There are infinitely many ways to implement the EQU function using the AVIDA instruction set. Proteins are specific in their form, not just in an abstract functional way. The likelihood of randomly selecting a combination of AVIDA commands that performs a logical function is extremely high, I don't know if it's even possible to work this out considering there are infinitely many combinations that could represent each logical function. (e.g. inc dec inc dec inc dec is equivalent to leaving a register unchanged). In the genome the possibility of just mutating 3 neighbouring nucleotides anywhere in the genome to produce a different codon is less than the chances of winning the national lottery twice in a row, and two proteins with different amino acid chains can likely never be equivalent in function. (unless randomness of function is the required function for the protein)

DISCUSS!

  
JonF



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(Permalink) Posted: Jan. 19 2015,08:16   

You need to supply some serious support for E.4. Particularly, two proteins with different amino acid chains are often equivalent in function. Nobody has any idea how many proteins there are that perform some specified function, but the evidence suggest there's loads of 'em. Plus there are proteins that perform multiple functions.

  
Zachriel



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(Permalink) Posted: Jan. 19 2015,08:21   

cryptoguru: evolution mutates DNA on a nucleotide level affecting function (gene level) and selects on the organism level.

Evolution also involves recombination and the splicing of new structures from subcomponents.  

cryptoguru: The whole premise of natural selection can be simplified to be death.

That is also false. The whole premise of natural selection is reproductive success.



--------------

You never step on the same tard twice—for it's not the same tard and you're not the same person.

   
rossum



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(Permalink) Posted: Jan. 19 2015,08:33   

Quote (JonF @ Jan. 19 2015,08:16)
You need to supply some serious support for E.4. Particularly, two proteins with different amino acid chains are often equivalent in function. Nobody has any idea how many proteins there are that perform some specified function, but the evidence suggest there's loads of 'em. Plus there are proteins that perform multiple functions.

The calculation has been done for Cytochrome C: Yockey (1992) calculated that there are  2.3 x 10^93 different amino acid sequences that could make a working Cytochrome C.

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The ultimate truth is that there is no ultimate truth.

  
cryptoguru



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(Permalink) Posted: Jan. 19 2015,08:39   

Cubism: (this is not directly about my last post but answering an earlier clarification from Cubism)

Quote
Does the mutated nucleotide sequence qualify as "new and novel genetic material"? Does the mutated nucleotide sequence contain any "new and novel genetic material"?


The issue here is one of scale ... changing a single nucleotide and getting new functionality is more adequately describing a side-effect of switching a control gene rather than amazingly arriving at a new functional sequence through mutation and selection.

So evolution claims that all the differences between a chimp's DNA and ours are caused by random mutation on 2 hereditary lines from a common ancestor. Find a sequence of unique DNA in the human genome (yup you can use the "junk DNA" now too, now we know it's not junk). Now that string you're holding has arrived by random mutation ... selection has preserved it, but mutation created it. That's what I mean by new/novel/unique information. You may be able to handwave that the switching of a few control genes could happen randomly .... we can all accept that.
But ALL that new (unique) code you're holding had to be created by random mutation and it all had to be preserved through natural selection. The mathematician in me is screaming IMPOSSIBLE! The sheer amount of new and structured information that works not in a sequential code way but in an interdependent, non-linear, overlapping code manner that has been randomly mutated piecewise and each intermediate stage is functionally advantageous is off-the-scale probabilistically impossible (in my opinion ... because those stats couldn't even be quantified).

So my point is ... it's easy to show in a small amount of variability that something magic can happen once in a blue moon (that's just normal probability) ... but for magic to be preserved and extended to the level that evolutionists assert is an obvious extrapolation (molecules-to-man), we need to be seeing a LOT of magic and all the time, everywhere. Nobody gets that much luck ... never-mind claiming that every currently existing organism has had this kind of luck. The computer models (like AVIDA) oversimplify the proposed process by hugely simplifying the organism and only modelling tiny problems, this does not demonstrate the kind of variability and specified complexity we observe ... you should be able to model it to these levels if evolution works.

So to summarise my answer ... when I'm talking about new information ... I'm talking about a unique DNA sequence in an organism. I can't see how it would ever be possible for random mutation to create that much dumb luck even given billions of years. That's not an argument from incredulity ... that's me saying from my knowledge of statistics I can't see how it could ever be possible, so the extraordinary claim of evolutionists needs to be demonstrated in a model that addresses the difficult-to-believe parts of the claim, not just that we can randomly arrive at something useful sometimes

  
N.Wells



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(Permalink) Posted: Jan. 19 2015,09:14   

Quote
1) living cells process a program called DNA
2) DNA is a code (a sequence of 3 symbols codes for amino acid)

Analogies between DNA and either codes or blueprints are convenient, but they can derail very easily. DNA is a very complex organic molecule that interacts with a very large number of other complex molecules in exceedingly complicated ways.  It is more like a catalyst than a set of instructions.
http://www.huffingtonpost.com/agustin....36.html
http://www.science20.com/chatter....ot_code
http://livinglifewithoutanet.com/2009.......-a-code



   
Quote
5) folded proteins are assembled into complex structures, again this process is controlled by mechanisms which are defined in the code.
The process is affected chemically by both the environment and by other proteins formed from other bits of DNA: No "mechanisms" are "defined" by a "code".


   
Quote

1) given a population of self-replicating entities (a living cell)
2) random mutation of symbols in the raw code (usually point mutations ... about 50-100 de novo germline mutations per generation in humans)
3) advantages are introduced via the mutations by chance, the advantages are preserved and propagate through the population by "natural selection"

1) or multicellular organisms
2) They aren't symbols: if so, what does adenine symbolize?
You are talking about point mutations.  These can be dramatic (cf. myostatin blocker mutations).  However, even more interesting are larger mutations lilke duplications (read up on polyploidy in ornamental and agricultural plants) and translocations.  (You are clear that the advantages are by chance, and not necessarily the mutations, correct?)
3) Also by genetic drift.  Differential advantages are also introduced by recombination, far more than by new mutations (cf. dogs, pet hamsters, pet guppies, the genus Brassica, ornamental pigeons, varieties of chickens, etc., etc.).

   
Quote
4) Natural selection is the name given to the process whereby environmental conditions apply a pressure for survival on the entities.
Genetic drift can also be environmental.  If an ice storm wipes out 100% of the birds of one particular species overwintering in a large area, that will have huge effects via genetic drift and none via selection, at least in the area of 100% mortality.

   
Quote
5) Entities therefore compete for resources and the ultimately surviving hereditary line is preserved, presumably carrying the genetic advantage that allowed it to overcome its competition.
6) Differential reproduction is a fancy way of saying that the hereditary line of some organisms, due to their inferiority in how they are suited to the environment, eventually (at some level of descent) produce no offspring before dying and therefore leave the competition.
7) Death is the only agent in natural selection, regardless of whether some organisms are only slightly better adapted than others, there will eventually be a point where an entire inferior hereditary line is removed (ultimately by death) from the population (i.e. a discrete process, not a continuous one). It is now as though that line had never existed. This is why death is the only important selector, comparisons between organisms do not come into the selection process ... it is simply a case of whether an organism is sufficiently fit to survive long enough in the environment to reproduce.

Because of recombination, two genes in you are not forever linked in your progeny.  Even if they occur close together on the same chromosome, translocations etc. can separate them.  

It is far easier to understand natural selection in terms of differential reproductive success than differential mortality: for example, think of male praying mantises and similar species where reproductive success means getting eaten by their mates, or cecidomyiian gall midges, where reproductive success means the children eating their way out of the mother and killing her.  Yes, sometimes a mutation is very bad, and as a result its owner gets eaten or otherwise dies very quickly, or doesn't even get born in the first place.  However, most variations are not that dramatic, and result in slightly more or slightly fewer offspring, and the genes' fortunes rise and fall on that slight difference.  The less timid mouse may well get eaten sooner by a cat or an owl, but may well have found more food, mated with more females, and fathered more offspring than its neighbor who rarely ventured out of its burrow and died in its bed at a ripe old age (http://www.jstor.org/discover/10.2307/2462815?sid=21105655083353&uid=4&uid=2).

Mortality rates are important, but if you don't do evolutionary accounting in terms of reproductive success, you will severely misunderstand whole areas such as average age of first reproduction, age-specific expectation of future offspring, r & k strategies, kin selection, and so on and so forth
http://www.zo.utexas.edu/courses....ry.html
http://www.zo.utexas.edu/courses....th.html

  
cryptoguru



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(Permalink) Posted: Jan. 19 2015,09:14   

JonF:
you're right ... I can't quantify it. But are you asserting that the variability in the human genome to build a fully functional human, with a functioning brain (and preprogrammed reflexes) and nervous system is equivalent to a sequentially  processed assembler code that just has to make some logic functions?
These are galaxies apart in complexity. And you certainly can't extrapolate the simple case.

Zachriel:
Quote
Evolution also involves recombination and the splicing of new structures from subcomponents.

Sure, but that wouldn't account for significantly long unique sequences that haven't appeared before in the history of that genome. They could only be explained by random mutation coming in somewhere along the way.

Quote
The whole premise of natural selection can be simplified to be death.

People kept saying this ... but it didn't make sense to me to see anything else as the reason for a winner to emerge. Actually you guys may be right about this, now I've thought about it a bit more. If an organism can be removed from the competition through another means other than death (e.g. location) that would work too. So yes, let me retract my statements about Natural Selection only being able to be possibly enforced by death ... ooh I've learned something.

Quote
there are 2.3 x 10^93 different amino acid sequences that could make a working Cytochrome C.

This may be true for a few proteins but certainly isn't the case for all proteins, which require a specific form to be functional. We need to be able to account for the origin of all of them.

  
Zachriel



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(Permalink) Posted: Jan. 19 2015,09:32   

Quote (cryptoguru @ Jan. 19 2015,09:14)
Zachriel:
Quote
Evolution also involves recombination and the splicing of new structures from subcomponents.

Sure, but that wouldn't account for significantly long unique sequences that haven't appeared before in the history of that genome. They could only be explained by random mutation coming in somewhere along the way.

The process of splicing subcomponents can create new functional structures.

Quote (cryptoguru @ Jan. 19 2015,09:14)
Zachriel:  
Quote
The whole premise of natural selection can be simplified to be death.

People kept saying this ... but it didn't make sense to me to see anything else as the reason for a winner to emerge.

An example was provided, of pacific salmon. They all die. Some die before reproducing. Some die immediately after reproducing. Some produce more or healthier eggs. But they all die.

 
Quote (cryptoguru @ Jan. 19 2015,09:14)
Actually you guys may be right about this, now I've thought about it a bit more. If an organism can be removed from the competition through another means other than death (e.g. location) that would work too. So yes, let me retract my statements about Natural Selection only being able to be possibly enforced by death ... ooh I've learned something.

Good. It's an important point.

--------------

You never step on the same tard twice—for it's not the same tard and you're not the same person.

   
QED



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(Permalink) Posted: Jan. 19 2015,09:35   

"plus a sprinkling of magic selection (which is the secret ingredient that we should never really define properly lest it became understandably deficient) will eventually mutate a Banana into Barack Obama."

Yep- it was inevitable - your "fight" isn't about science at all - it's a socio-political one, crypto. But thanks for letting everyone know.

Next up - why ID should be taught in schools, in
3...2...1...

  
cryptoguru



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(Permalink) Posted: Jan. 19 2015,09:37   

Quote
Analogies between DNA and either codes or blueprints are convenient, but they can derail very easily


I've said this before and I'll assert this again ... DNA is not like a code ... it IS a code and the cell is a Turing-complete computer (not an analogy ... a definition).
It is NOT like a blueprint, a blueprint is a diagram that shows how to build something, it doesn't contain the ability to build the object and necessary materials for the object in itself.


Quote
No "mechanisms" are "defined" by a "code".

That isn't true. DNA code is functionally non-linear ... it is processed by the cell, the expression of proteins is a deterministic process, which is explicitly defined by the DNA code. It uses chemical processes to respond to the environment and toggle control genes and expression of genes, but this functionality is prescribed in the DNA ... if it wasn't deterministic, the DNA could accidentally make a coconut instead of a baby ... my wife would be livid, if she went through all that pain just for a coconut. DNA only does something different if it's responding (according to its own programming) to external events or if it is mutated. Chemistry only describes the physical processes, they do not describe the functionality, which is abstract. That is akin to trying to analyse the functionality of Mac OSX by looking at the flow of electricity through your motherboard, that does not explain the functionality in the program that it is running; just the medium it is using to execute it.

Quote
They aren't symbols: if so, what does adenine symbolize?

They ARE symbols in the representation of the functional code. 3 Symbols constitute a codeword (codon) ... this is what AVIDA works with as its commands. Adenine doesn't "symbolize" anything atomically anymore than the letter 'F' symbolizes anything on your keyboard ... but it is a symbol that is used to build words which are understood in the context of the language they are intended for.

Quote
Genetic drift can also be environmental

True ... I don't see how that affects the scope of what we are considering though.

  
cryptoguru



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(Permalink) Posted: Jan. 19 2015,09:54   

QED'oh:
Quote
Yep- it was inevitable - your "fight" isn't about science at all - it's a socio-political one, crypto. But thanks for letting everyone know.

Your fight with me isn't about science either, it's because I dare to disagree with your paradigm ... who's being socio-political? Science is meant to challenge paradigms, that's how it was started (by creationists).
Quote
wah wah wah
(from earlier)
Come along to an MMA sparring session with me and we'll see who cries first! This pigeon eats off-topic evolutionist evangelists for breakfast. (in a differential fitness sort of way)

So you can shut up now until the conversation ends and you can make your closing speech about how you scared me off good 'n' proper.

At least the other guys on here are having a civil conversation and explaining their view of how it all works.
I'm actually learning something new for once.

  
N.Wells



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(Permalink) Posted: Jan. 19 2015,09:59   

You are wrong about DNA and codes, but you are far more wrong about
 
Quote
 
Quote

Genetic drift can also be environmental


True ... I don't see how that affects the scope of what we are considering though.

If you look at a bird book for North America, you will see a very large number of eastern and western pairs of forest-dwelling species or subspecies, consisting of distinctive differences in coloration and calls, which have varying degrees of interfertility.  The reason for all these pairs of species appear to be far less a matter of adaptive evolution and natural selection than isolation and genetic drift* following removal of forests across the great plains: e.g., red- and yellow-shafted flickers, lazuli and indigo buntings, black-headed and rose-breasted grosbeaks, Baltimore and Bullock's orioles, etc.  Or look at genetic-distance maps of various groups of chimpanzees or gorillas, mollusk sister-species across the Panamanian Isthmus, and so forth.  (*Yes, bird coloration and songs are reinforced by sexual selection, which is a form of natural selection, but the initial changes would logically have been drift, and mating preferences are not relevant in organisms like sessile clams.)

  
QED



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(Permalink) Posted: Jan. 19 2015,10:00   

I'm not fighting with you, crypto. I'm just making observations that you're not producing any "new information". But have at it. I can wait.

  
cryptoguru



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(Permalink) Posted: Jan. 19 2015,10:03   

N. Wells:
Quote
You are wrong about DNA and codes, but you are far more wrong about

Oh OK ... sure I'll just take your word for it, you being the expert and all that.

Quote
If you look at a bird book for North America, you will see a very large number of eastern and western ... blah blah blah

This is irrelevant to the point we're discussing, which is about how well AVIDA models biological evolution and how a non-linear functional code that is randomly mutated can expect to gain new function over time.

  
N.Wells



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(Permalink) Posted: Jan. 19 2015,10:07   

Quote (cryptoguru @ Jan. 19 2015,10:03)
N. Wells:
Quote
You are wrong about DNA and codes, but you are far more wrong about

Oh OK ... sure I'll just take your word for it, you being the expert and all that.

Quote
If you look at a bird book for North America, you will see a very large number of eastern and western ... blah blah blah

This is irrelevant to the point we're discussing, which is about how well AVIDA models biological evolution and how a non-linear functional code that is randomly mutated can expect to gain new function over time.

Don't take my word: I gave you three links, and many more can be found to discuss the same issue.

No, at that point you were generalizing about evolution, not discussing Avida.

  
cryptoguru



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(Permalink) Posted: Jan. 19 2015,10:16   

QED:
I explained what "new information" is:-

Quote
when I'm talking about new information ... I'm talking about a unique DNA sequence in an organism.


Not a point-mutated nucleotide or a spliced copy, look at unique continuous sequences of nucleotides in human DNA that are unrepresented in our purported genetic relatives and perform necessary function. You need to explain how those huge amounts of information originated. You guys claim we get those by successive random mutation, I want to see the possibility of that modelled; because to me when you're dealing with that amount of variability, it's completely impossible.
I worked in cryptography for years ... so I am used to evaluating the likelihood of difficult problems being solved by stochastic processes ... I've got a reasonable handle on the statistics and the process (as well as specialising in biological mathematical & computer modelling - PhD) ... to me this is impossible; so show me a working model that represents even some of the complexity of "real" evolution.

  
N.Wells



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(Permalink) Posted: Jan. 19 2015,10:19   

DNA is not symbolic.  It is a chemical, not a code (or if it is a code, so is water.)  Strictly speaking it is not coded, nor is it decoded or interpreted.  It is a chemical that interacts chemically, which is not true of any other known codes.  (Unless you want to make an issue of smoke signallers coughing.......? :) )

From http://www.antievolution.org/cgi-bin....;t=9614
 
Quote
The way a computer code works is that the exact sequence of the code - the precise order of the binary 1s and 0s - spells out exactly what operations the computer must perform. But in genetics, the sequence is only part of the picture. Just as important are genetic regulatory networks - which genes are turned on at what times and in combination with which other genes. Phenotypes are not simply the result of particular gene sequences but the result of specific gene-gene (or gene network-gene network) interactions.

But DNA bears little relation to a "code" in a more fundamental way. Consider exactly what a "code" is. A code is a system of arbitrary symbols used to represent  ideas and objects. In a sense, language itself is a "code"; the symbol "dog" represents that furry tetrapod with a waggly tail, for example. In a code, the symbols themselves have no inherent meaning. The letter "d" is meaningless by itself, as are the letters "o" and "g". It is only in combination that they derive meaning, and their meaning is derived from the idea that they represent. Furthermore, they only have meaning because we give them meaning. "Dog" is merely the label we apply to Fido; in a universe without sentient beings, "dog" would be meaningless. DNA does not fit this description at all. DNA is not arbitrary in any way; each letter of the genetic "code" is an actual biological compound. ACCGTCGA might be the gene for determining how long your toe hair is, but unlike a code, A, C, T and G each have their own non-arbitrary meaning. And this meaning exists independently of human sentience - the sequence of nucleotides does not have meaning only because we give it meaning. It would have meaning even if humans didn't exist at all.

What DNA is, is a polymeric chemical that follows a dynamic chemical process, governed by universal physical rules. It is only a "code" in the same sense that nuclear fusion is a "code" for how stars produce light


From http://www.talkorigins.org/indexcc....80.html
 
Quote
    The genetic code is not a true code; it is more of a cypher. DNA is a sequence of four different bases (denoted A, C, G, and T) along a backbone. When DNA gets translated to protein, triplets of bases (codons) get converted sequentially to the amino acids that make up the protein, with some codons acting as a "stop" marker. The mapping from codon to amino acid is arbitrary (not completely arbitrary, but close enough for purposes of argument). However, that one mapping step -- from 64 possible codons to 20 amino acids and a stop signal -- is the only arbitrariness in the genetic code. The protein itself is a physical object whose function is determined by its physical properties.

   Furthermore, DNA gets used for more than making proteins. Much DNA is transcribed directly to functional RNA. Other DNA acts to regulate genetic processes. The physical properties of the DNA and RNA, not any arbitrary meanings, determine how they act.

   An essential property of language is that any word can refer to any object. That is not true in genetics. The genetic code which maps codons to proteins could be changed, but doing so would change the meaning of all sequences that code for proteins, and it could not create arbitrary new meanings for all DNA sequences. Genetics is not true language.

   The word frequencies of all natural languages follow a power law (Zipf's Law). DNA does not follow this pattern (Tsonis et al. 1997).

   Language, although symbolic, is still material. For a word to have meaning, the link between the word and its meaning has to be recorded somewhere, usually in people's brains, books, and/or computer memories. Without this material manifestation, language cannot work.


DNA is understandable as a specialized alternative to RNA, and RNA is simultaneously the information, the tools to make stuff, and the material out of which both the tools and the structures are made.  DNA simply holds the information and hands the rest of the capabilities off to proteins.

I mentioned "DNA as blueprints" not because you said it but because it is another common and partially useful analogy for DNA that can similarly derail horrendously when one extends the analogy to areas where it does not apply.

Quote
You need to explain how those huge amounts of information originated. You guys claim we get those by successive random mutation, I want to see the possibility of that modelled; because to me when you're dealing with that amount of variability, it's completely impossible.

Duplication and mutation create new "information", and so does recombination (because so many developmental outcomes result from chemical interactions between gene products rather than just the presence or absence of individual genes - yet another reason why DNA is not just a code).  Also, there is no single "target", but rather a selection of what works well enough or better than the alternatives in terms of resultant numbers of offspring, so simplistic probability calculations don't apply, and neither do simplistic life-or-death dichotomies.

  
JonF



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(Permalink) Posted: Jan. 19 2015,10:31   

Quote (cryptoguru @ Jan. 19 2015,09:39)
Cubism: (this is not directly about my last post but answering an earlier clarification from Cubism)

   
Quote
Does the mutated nucleotide sequence qualify as "new and novel genetic material"? Does the mutated nucleotide sequence contain any "new and novel genetic material"?


The issue here is one of scale ... changing a single nucleotide and getting new functionality is more adequately describing a side-effect of switching a control gene rather than amazingly arriving at a new functional sequence through mutation and selection.

Why?

Quote
The mathematician in me is screaming IMPOSSIBLE!

The mathematician in me is screaming SHOW ME THE NUMBERS!  So far all you've shown is personal incredulity.

  
JonF



Posts: 634
Joined: Feb. 2005

(Permalink) Posted: Jan. 19 2015,10:34   

Quote (cryptoguru @ Jan. 19 2015,10:14)
JonF:
you're right ... I can't quantify it. But are you asserting that the variability in the human genome to build a fully functional human, with a functioning brain (and preprogrammed reflexes) and nervous system is equivalent to a sequentially  processed assembler code that just has to make some logic functions?
These are galaxies apart in complexity. And you certainly can't extrapolate the simple case.

You are asserting a qualitative difference between Avida and biological evolution.  Quantifiable or not, yes, the human body is a lot more complex that what Avida can produce.  Partly due to the lack of time and lots of trials.  But I see no reason why the process that produced EQU in Avida can't produce a human being in real life.

  
JonF



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Joined: Feb. 2005

(Permalink) Posted: Jan. 19 2015,10:35   

Quote (cryptoguru @ Jan. 19 2015,10:37)
Quote
Analogies between DNA and either codes or blueprints are convenient, but they can derail very easily


I've said this before and I'll assert this again ... DNA is not like a code ... it IS a code and the cell is a Turing-complete computer (not an analogy ... a definition).

You don't get to just define a cell as a Turing-complete computer.  You need to demonstrate that the cell meets the requirements of a Turing-complete computer. Which you supposedly know.

I could define a pair of scissors as a Turing-complete computer. But I would be objectively wrong.  Calling a tail a leg doesn't make it one.

  
cryptoguru



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(Permalink) Posted: Jan. 19 2015,10:40   

N.Wells:
who wrote that nonsense??
This point isn't even worth arguing ... it's called "Genetic code" and they're called "codons" for a reason.
It fulfils all the criterion for being a code ... in fact, a computer code; as it is processed by the cell in a Turing-complete manner.
I don't think many people on here would agree with your point ... and interestingly AVIDA itself models the cell as a computer with a processed instruction set.

Information is the arrangement of matter, the DNA code is in the arrangement of the chemicals (not in the chemicals themselves). Information is abstract. DNA is not just a chemical zipper! It is addressable and uses boolean logic to regulate parts of the code, so is functional.
The information in a book is not described by the chemical constituents of the ink and the pages, it is the arrangement of these molecules that contains the information.

  
N.Wells



Posts: 1836
Joined: Oct. 2005

(Permalink) Posted: Jan. 19 2015,10:48   

Quote (cryptoguru @ Jan. 19 2015,10:40)
N.Wells:
who wrote that nonsense??
This point isn't even worth arguing ... it's called "Genetic code" and they're called "codons" for a reason.
It fulfils all the criterion for being a code ... in fact, a computer code; as it is processed by the cell in a Turing-complete manner.
I don't think many people on here would agree with your point ... and interestingly AVIDA itself models the cell as a computer with a processed instruction set.

DNA is extremely complicated, so we do not have language to do it justice, so we use analogies and metaphors.  That's fine, until we mistake the analogy or the metaphor for reality and drive the analogy into areas where it does not pertain.  That's what you are doing.  

Quote
Information is the arrangement of matter, the DNA code is in the arrangement of the chemicals (not in the chemicals themselves). Information is abstract. DNA is not just a chemical zipper! It is addressable and uses boolean logic to regulate parts of the code, so is functional.  The information in a book is not described by the chemical constituents of the ink and the pages, it is the arrangement of these molecules that contains the information.

I'm not sure what you are getting at.   The sequence of nucleotides in a gene determine what protein is produced and how it folds, but a) a lot of variation is tolerated and some makes no difference at all, and b) information in DNA is most specifically not in its arrangement in terms of the physical arrangement of the genes, but merely in the timing of production of proteins and the chemistry of how those proteins interacts.  (Proximity on a chromosome affects the likely of two genes getting separated, but does not mean that they will be expressed at the same time: as you said, not a zipper.)

  
JonF



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(Permalink) Posted: Jan. 19 2015,10:49   

Quote (cryptoguru @ Jan. 19 2015,11:16)
QED:
I explained what "new information" is:-

 
Quote
when I'm talking about new information ... I'm talking about a unique DNA sequence in an organism.


Not a point-mutated nucleotide or a spliced copy, look at unique continuous sequences of nucleotides in human DNA that are unrepresented in our purported genetic relatives and perform necessary function.

That explanation is incompatible with the previous definition. A point mutation produces a unique DNA sequence.  You are trying to be as vague as possible. Some mathematician.

Do you know what an operational definition is?  Your first try was one, your second try isn't.

Quote
You need to explain how those huge amounts of information originated. You guys claim we get those by successive random mutation, I want to see the possibility of that modelled; because to me when you're dealing with that amount of variability, it's completely impossible.

Yeah, good ol' personal incredulity.  Much better than evidence.

Quote
I worked in cryptography for years ... so I am used to evaluating the likelihood of difficult problems being solved by stochastic processes ... I've got a reasonable handle on the statistics and the process (as well as specialising in biological mathematical & computer modelling - PhD) ... to me this is impossible; so show me a working model that represents even some of the complexity of "real" evolution.

You need to define exactly want you mean by representing some of the complexity of "real" evolution.  You need to have an operational definition of the product of such a model, and you need to demonstrate that such a model is practical.

Meanwhile we've got lots of examples of real and modeled complex evolution, not as complex as human evolution, but nobody's found any reason why the results we have cannot be extrapolated to "real " evolution. And there have been lots of studies of what rates of various processes are required to produce what we see.  Are you familiar with those studies?  Would you care to guess what their results are?

  
cryptoguru



Posts: 53
Joined: Jan. 2015

(Permalink) Posted: Jan. 19 2015,11:06   

JonF:
Yes I am personally incredulous ... I am not asserting that proves anything ... I'm saying that the burden of proof is on you to show that this (relatively new) proposed mechanism which seems to defy laws of logic could even theoretically do what is suggested

Quote
But I see no reason why the process that produced EQU in Avida can't produce a human being in real life.

That's because you want to believe that ... it hasn't been demonstrated that it's even possible. People are claiming that AVIDA proves biological evolution ... it doesn't! We just showed that ... It proves you can find a logical function using stochastic process on a Turing-complete set of instructions.


Quote
You don't get to just define a cell as a Turing-complete computer.

It's actually probably even Turing-universal
Efficient Turing-universal computation with DNA polymers

  
cryptoguru



Posts: 53
Joined: Jan. 2015

(Permalink) Posted: Jan. 19 2015,11:19   

Quote
That explanation is incompatible with the previous definition. A point mutation produces a unique DNA sequence.  You are trying to be as vague as possible. Some mathematician.

You misunderstood what I said there. I said "point mutation" singular ... not sequence of point mutations.

EXAMPLE

GCATTUCAGUUGATUCCATATGGCTU
GCATTUCAGTUGATUCCATATGGCTU

The U has been point-mutated to a T ... I don't consider the whole sequence new information. I'm not even going to consider it "new information" until there is a reasonably sized sequence of unique information. Let's set it to be bigger than you could create by chance.

For example, a sequence of 200 nucleotides that is unique to that organism requires 1 in 4^200 chance of arriving at randomly in the traditional way of monkeys typing randomly on a base-4 keyboard. So I want to see how the process of evolution could theoretically produce something of that complexity ... i.e. too difficult to get using monkeys, yet functional.

  
midwifetoad



Posts: 4003
Joined: Mar. 2008

(Permalink) Posted: Jan. 19 2015,11:48   

Quote
The U has been point-mutated to a T ... I don't consider the whole sequence new information. I'm not even going to consider it "new information" until there is a reasonably sized sequence of unique information. Let's set it to be bigger than you could create by chance.


What's the minimal size sequence change necessary to make a difference in viability or relative reproductive success?

--------------
Any version of ID consistent with all the evidence is indistinguishable from evolution.

  
JonF



Posts: 634
Joined: Feb. 2005

(Permalink) Posted: Jan. 19 2015,11:51   

Quote (cryptoguru @ Jan. 19 2015,12:06)
JonF:
Yes I am personally incredulous ... I am not asserting that proves anything ... I'm saying that the burden of proof is on you to show that this (relatively new) proposed mechanism which seems to defy laws of logic could even theoretically do what is suggested

I don't see it as defying the laws of logic. Eaxactly what laws nd how do they defy them?

It is nice that you admitted all you have is armchair philosophizing.  

Quote
 
Quote
But I see no reason why the process that produced EQU in Avida can't produce a human being in real life.

That's because you want to believe that ... it hasn't been demonstrated that it's even possible.

Indeed we have not directly observed biological evolution on the scale of hundreds of thousands of years and widely varying environments. There's good reasons for that; it's totally impractical.  I haven't seen any objective reasons why the extrapolation isn't reasonable. From you or anyone.

Quote
People are claiming that AVIDA proves biological evolution ... it doesn't! We just showed that ... It proves you can find a logical function using stochastic process on a Turing-complete set of instructions.

The stochastic process of descent with modification and selection.  I.e. evolution.

Quote
Quote
You don't get to just define a cell as a Turing-complete computer.

It's actually probably even Turing-universal
Efficient Turing-universal computation with DNA polymers

DNA can be used as a computer in a test tube. That's not what it does in the cell. Try again.
xxx

  
Doc Bill



Posts: 1039
Joined: April 2007

(Permalink) Posted: Jan. 19 2015,12:01   

It appears that CreeptoGuru suffered a concussion to have written this creationist boilerplate tripe:

Quote
You misunderstood what I said there. I said "point mutation" singular ... not sequence of point mutations.

EXAMPLE

GCATTUCAGUUGATUCCATATGGCTU
GCATTUCAGTUGATUCCATATGGCTU

The U has been point-mutated to a T ... I don't consider the whole sequence new information. I'm not even going to consider it "new information" until there is a reasonably sized sequence of unique information. Let's set it to be bigger than you could create by chance.


Now Creepto is defining his own terms again in fine creationist style.  You'll have to better than this to impress us, boy-o!

Creepto ate the dog.
Creepto ate the hog.

In Creepto-speak there is no new information.  I guess you'd need something like this:

Creepto ate the dog.
Creepto prepared the mongoose in a rich butter sauce.

Oh, now I get it.  The mongoose recipe is definitely bigger than I could get by chance, although instead of butter I would have fried that puppy in tard.

  
JonF



Posts: 634
Joined: Feb. 2005

(Permalink) Posted: Jan. 19 2015,12:02   

Quote (cryptoguru @ Jan. 19 2015,12:19)
 
Quote
That explanation is incompatible with the previous definition. A point mutation produces a unique DNA sequence.  You are trying to be as vague as possible. Some mathematician.

You misunderstood what I said there. I said "point mutation" singular ... not sequence of point mutations.

EXAMPLE

GCATTUCAGUUGATUCCATATGGCTU
GCATTUCAGTUGATUCCATATGGCTU

The U has been point-mutated to a T ... I don't consider the whole sequence new information. I'm not even going to consider it "new information" until there is a reasonably sized sequence of unique information. Let's set it to be bigger than you could create by chance.

For example, a sequence of 200 nucleotides that is unique to that organism requires 1 in 4^200 chance of arriving at randomly in the traditional way of monkeys typing randomly on a base-4 keyboard. So I want to see how the process of evolution could theoretically produce something of that complexity ... i.e. too difficult to get using monkeys, yet functional.

Then you need a new operational definition of information, since by your original definition a point mutation adds information.

Gene duplication followed by point mutation.  Much longer than 200 nucleotides. and observed over and over again.

{ABE}Gene Genesis: Scientists Observe New Genes Evolving from Mutated Copies
Evolution by gene duplication: an update

  
N.Wells



Posts: 1836
Joined: Oct. 2005

(Permalink) Posted: Jan. 19 2015,12:03   

Point mutations change the information in a sequence and can have major consequences.  The best known are deleterious, because we examine diseases for genetic components, but this doesn't have to be the case.  Duplications of DNA plus a point mutation in one of the pair are indisputably new information.  

Some of the myostatin blocker mutations are quite simple: http://en.wikipedia.org/wiki.......ostatin
and show how you could get more body mass and muscle for the same Shannon information (if you "broke" the myostatin blocker gene without deleting anything) or even from less of the vague information that IDists like to talk about (cases that result from deletion of a gene or portion of a gene).

See regular cows and http://mhpstrong.com/wp-cont....cow.jpg
regular and "bully" whippets
http://articles.elitefts.com/wp-cont....cs1.jpg
regular mice and "supermice"
http://www.havokjournal.com/wp-cont....g11.png
and google to learn about Liam Hoekstra.

  
OgreMkV



Posts: 3668
Joined: Oct. 2009

(Permalink) Posted: Jan. 19 2015,12:06   

Quote (cryptoguru @ Jan. 19 2015,11:19)
Quote
That explanation is incompatible with the previous definition. A point mutation produces a unique DNA sequence.  You are trying to be as vague as possible. Some mathematician.

You misunderstood what I said there. I said "point mutation" singular ... not sequence of point mutations.



So you agree that point mutations can happen. So, what law (biological, chemical, physical, or logical) prevents multiple point mutations from happening over time?

Quote

EXAMPLE

GCATTUCAGUUGATUCCATATGGCTU
GCATTUCAGTUGATUCCATATGGCTU

The U has been point-mutated to a T ... I don't consider the whole sequence new information. I'm not even going to consider it "new information" until there is a reasonably sized sequence of unique information.


What is the "reasonably sized sequence"?

What units?

Why?

Quote


Let's set it to be bigger than you could create by chance.



Why?

Show that something other than chance AND known biochemical processes control mutations.
Quote


For example, a sequence of 200 nucleotides that is unique to that organism requires 1 in 4^200 chance of arriving at randomly in the traditional way of monkeys typing randomly on a base-4 keyboard. So I want to see how the process of evolution could theoretically produce something of that complexity ... i.e. too difficult to get using monkeys, yet functional.

This is an EXTREMELY common misconception among creationists.

Somehow, they all have this notion, that like computer program... DNA springs into existence, fully formed, with the exact sequence that needs to exist for the organism now.

1) This is false. Each gene, allele, ERV, SNP, etc has a long history of existence. This long history shows the many changes each one of these genes (et. al.) has gone through to reach the point it is now.

You are actually saying that biologists must defend the creationist point of view... that is that all genes (et. al.) must have appeared exactly as they are now.

2) Your value of 1 in 4^200 does not include any of the other thousands of values that can directly or indirectly affect the sequence. You need a bit for methylation. You need bits for histone complexes. You need bits that include regulatory sequences. etc. etc. etc.

You can't even accurately calculate the probability for these events.

3) Even if you could, you are not considering the number of attempts. AND the value of successful, but not complete attempts. Genes are not computer programs that must be formed exactly correct or they will not work. There are plenty of genes that work pretty well. The literature is full of examples of this... I've given you papers that show this. It also exists in evolutionary algorithms.

Further, as has been shown to you both in biochemical examples and genetic algorithms examples, mutations that would cause deleterious effects can be propagated through the population and eventually result in a net benefit.

For example, Joyce's Darwinian Evolution on a Chip paper shows that in less than 72 hours, there were four complexes of mutations that resulted in a 92 fold increase in substrate attachment efficiency.

Of course, you have also ignored (apparently) both living examples in humans of mutations that confer large advantages. That of the HIV immunity of a small group of Northern Scandinavians and the heart disease immunity of a small group of Italians.

Finally, I think it important to point out that your sequence specificity requirement doesn't actually match reality. There are several genes in the human population with several thousand alleles. You do know that alleles are variations in a gene, yes? That is, the variation of a DNA sequence.

For example, HBB-A has some 2000+ alleles and HBB-B (IIRC) has over 3000 alleles.

Another point is that THIS is what Dawkin's WEASEL program was trying to show. That, while it would take very, very long time for monkeys to randomly produce the phrase, any form of selection reduces that time significantly.

Talking about mutations and genes is meaningless without including selection, drift, and the multiple other methods of winnowing.

Edited by OgreMkV on Jan. 19 2015,12:06

--------------
Ignored by those who can't provide evidence for their claims.

http://skepticink.com/smilodo....retreat

   
midwifetoad



Posts: 4003
Joined: Mar. 2008

(Permalink) Posted: Jan. 19 2015,14:48   

The allele thing is the creationism killer. Any simulation of evolution has to include the possibility of neutral and nearly neutral variations.

And the ability of neutral and slightly detrimental variations to give rise to beneficial inventions.

--------------
Any version of ID consistent with all the evidence is indistinguishable from evolution.

  
cryptoguru



Posts: 53
Joined: Jan. 2015

(Permalink) Posted: Jan. 19 2015,15:43   

Quote

Creepto ate the dog.
Creepto ate the hog.

In Creepto-speak there is no new information.  I guess you'd need something like this:

Creepto ate the dog.
Creepto prepared the mongoose in a rich butter sauce.


You should definitely be proud of yourself Bilbo, those English lessons are starting to pay off.

Of course I was being arbitrary ... my definition of "new information" is substantial unique sequences in a genome (i.e. not shared with assumed relative species) that wouldn't be expected by a series of random events.

So if you showed me

BILBO PAID OVER THE ODDS FOR SHOES
and
BILBO PAID OVER THE ODDS FOR HOES

Although both those sentences make sense to me, I can quite easily explain that the first one arose by chance rather than any optimisation process requiring natural selection.

So I'm asking for a unique sequence that couldn't just arrive fully formed by accident ... i.e. I want proof of the evolution process producing something hard that Bilbo couldn't just cook up by throwing a die.

Saying ... "well here we are ... tada, the human!" is just begging the question, so I'm after proof of the theory

Quote
So, what law (biological, chemical, physical, or logical) prevents multiple point mutations from happening over time?

None ... never said it couldn't


Quote
Somehow, they all have this notion, that like computer program... DNA springs into existence, fully formed

You're straw-manning again Mr Ogre McCarthy ... I never said that's what I think evolutionists believe ... and I obviously don't believe that. My point was that if you compare a chimp to a human there are unique sequences of DNA in humans, evolution needs to explain how a sequence that big can appear over time (yes kazillions of years if you like) ... but it still has to be functional and there right? So whether it was caused by thousands of point mutations, or a whole bunch of splicing and point mutations and stuff until you got that unique functional sequence that comprises compressed instruction sets for building proteins. You need to demonstrate that.

AVIDA is not demonstrating that level of magic, it just optimises the combination of some functions to create logical functions. We're not talking a few logical operands on the genome that have been created, we're talking MULTI-DIMENSIONAL SUPERCODES ... Supercodes ... supercodes ... super... (echoes into distance)

and Lenski has some E. Coli on his farm E-I-E-I-O
But on that farm there's not a chicken E-I-E-I-O
(join with me Bilbo)

So Lenski hasn't observed anything unbacteria-like going on yet after 60,000 generations, and AVIDA is unable to model anything more complicated than joining a few assembler instructions in sequence and rewarding the organism every time a logical function is found. METHINKS IT IS NOT A WEASEL YET

More proof please

BTW Kevin, please don't write the word Allele again ... you're banned from using it from now on from overuse.

  
midwifetoad



Posts: 4003
Joined: Mar. 2008

(Permalink) Posted: Jan. 19 2015,16:02   

Quote
So Lenski hasn't observed anything unbacteria-like going on yet after 60,000 generations
And this is supposed to be a surprise?

--------------
Any version of ID consistent with all the evidence is indistinguishable from evolution.

  
Texas Teach



Posts: 2084
Joined: April 2007

(Permalink) Posted: Jan. 19 2015,16:15   

Quote (midwifetoad @ Jan. 19 2015,16:02)
Quote
So Lenski hasn't observed anything unbacteria-like going on yet after 60,000 generations
And this is supposed to be a surprise?

Only because creationists think that we should see bacteria giving birth to a crocoduck if evolution were true.

--------------
"Creationists think everything Genesis says is true. I don't even think Phil Collins is a good drummer." --J. Carr

"I suspect that the English grammar books where you live are outdated" --G. Gaulin

  
midwifetoad



Posts: 4003
Joined: Mar. 2008

(Permalink) Posted: Jan. 19 2015,16:18   

Your straw man reeks of oil of ad hominem.

It's fairly ready to disprove evolution if you define evolution as creationism minus a deity.

--------------
Any version of ID consistent with all the evidence is indistinguishable from evolution.

  
Doc Bill



Posts: 1039
Joined: April 2007

(Permalink) Posted: Jan. 19 2015,16:31   

This is why it's impossible to have a discussion with a creationist.  They just don't possess human brains.

Creepto's argument from incredulity expressed thusly:

Quote
So to summarise my answer ... when I'm talking about new information ... I'm talking about a unique DNA sequence in an organism. I can't see how it would ever be possible (argument from incredulity) for random mutation to create that much dumb luck (argument from incredulity)even given billions of years. That's not an argument from incredulity (OH, YES IT IS!!)... that's me saying from my knowledge of statistics (No, you haz not!!) I can't see how it could ever be possible (argument from incredulity), so the extraordinary claim of evolutionists (argument from incredulity) needs to be demonstrated in a model that addresses the difficult-to-believe parts (argument from incredulity) of the claim, not just that we can randomly arrive (argument from incredulity) at something useful sometimes



That argument of Creepto's is quite incredible!  Really, this is better than GG?  Perhaps, but only on the Loony Tunes scale.

  
OgreMkV



Posts: 3668
Joined: Oct. 2009

(Permalink) Posted: Jan. 19 2015,16:37   

Quote (cryptoguru @ Jan. 19 2015,15:43)
Quote

Creepto ate the dog.
Creepto ate the hog.

In Creepto-speak there is no new information.  I guess you'd need something like this:

Creepto ate the dog.
Creepto prepared the mongoose in a rich butter sauce.


You should definitely be proud of yourself Bilbo, those English lessons are starting to pay off.

Of course I was being arbitrary ... my definition of "new information" is substantial unique sequences in a genome (i.e. not shared with assumed relative species) that wouldn't be expected by a series of random events.

So if you showed me

BILBO PAID OVER THE ODDS FOR SHOES
and
BILBO PAID OVER THE ODDS FOR HOES

Although both those sentences make sense to me, I can quite easily explain that the first one arose by chance rather than any optimisation process requiring natural selection.



I'd like to point out that this is ANALOGY and therefore, not really good for talking about evolution or even genetics.

What's interesting though, is that it actually proves the point that evolution works by incremental steps that actually work.

Of course, unlike words, DNA/proteins can have variations that make small changes to efficiency. As, the aforementioned papers I mentioned to you show.
Quote


So I'm asking for a unique sequence that couldn't just arrive fully formed by accident ... i.e. I want proof of the evolution process producing something hard that Bilbo couldn't just cook up by throwing a die.


So, you're asking for proof that evolution doesn't work?

Man, you are all over the place.

You do understand that selection is involved... and multiple other factors. right?

Whatever, it's been shown to happen. Already. You don't accept the evidence, but the models and the experiments and the observations and the whole genome studies and the partial genome studies all show that this happens.
Quote


Saying ... "well here we are ... tada, the human!" is just begging the question, so I'm after proof of the theory


Which shows you know nothing about science.
Quote


 
Quote
So, what law (biological, chemical, physical, or logical) prevents multiple point mutations from happening over time?

None ... never said it couldn't



That's not true. You have stated multiple times that it contradicts that laws of nature and logic.

What laws were you referring to?

Quote


 
Quote
Somehow, they all have this notion, that like computer program... DNA springs into existence, fully formed

You're straw-manning again Mr Ogre McCarthy ... I never said that's what I think evolutionists believe ... and I obviously don't believe that.



It's not obvious at all that don't believe that. You have stated it multiple times.

You want to know what the odds are that a modern gene sequence can appear by random processes. That's what you asked for.

You don't understand that modern genes (and their various alleles) came from the previous generation's genes (and their various alleles) and those came from the previous generation's genes (and their various alleles), etc, etc, etc.
Quote


My point was that if you compare a chimp to a human there are unique sequences of DNA in humans,


Not as many as you seem to think.
Quote

evolution needs to explain how a sequence that big can appear over time (yes kazillions of years if you like) ... but it still has to be functional and there right?


There was an entire issue of Nature devoted to this, several years ago. Surely  you have read all those articles right? Those whole genome studies of Pan and Homo and Gorilla shows this.

Oh, I'm sorry, do you require a step-by-step, mutation-by-mutation change.

I'm sure we can do that, right after you provide a step-by-step ancestral tree for yourself, from present, to the first human. Can't do that? It's unreasonable? Yeah, we know.

Quote


So whether it was caused by thousands of point mutations, or a whole bunch of splicing and point mutations and stuff until you got that unique functional sequence that comprises compressed instruction sets for building proteins. You need to demonstrate that.



Again, it's been done. You don't accept it. Fortunately no one who does the work cares what you think.

Quote


AVIDA is not demonstrating that level of magic, it just optimises the combination of some functions to create logical functions. We're not talking a few logical operands on the genome that have been created, we're talking MULTI-DIMENSIONAL SUPERCODES ... Supercodes ... supercodes ... super... (echoes into distance)



Because we all know that EQU is just an optimization of NAND, right?

Quote


and Lenski has some E. Coli on his farm E-I-E-I-O
But on that farm there's not a chicken E-I-E-I-O
(join with me Bilbo)



I find it funny that whenever creationists are given the information that they desire, they immediately transition to "It's still a bacteria".

You obviously only read one article in my blog.

http://www.skepticink.com/smilodo....l-a-dog

Quote

So Lenski hasn't observed anything unbacteria-like going on yet after 60,000 generations, and AVIDA is unable to model anything more complicated than joining a few assembler instructions in sequence and rewarding the organism every time a logical function is found. METHINKS IT IS NOT A WEASEL YET

More proof please


And no one, except creationists, expect him to. He's discovered, for all intents and purposes, a new species.  It's happened before.

Perhaps you need to learn a little more about biology and why no one expects to find a crocoduck.

As far as AVIDA, I think it's clear to everyone that the organisms created the coding structure for logic functions without any input from humans.

That's pretty impressive, except to someone who must, for whatever reason, deny that such a thing happened.
[/quote]

BTW Kevin, please don't write the word Allele again ... you're banned from using it from now on from overuse.[/quote]
Wow, you've been on this forum for almost 3 whole days and already have the power of banning.

You are either supremely arrogant or an utter ass, with a significant fraction voting for both.

Unlike you, I use terminology as is appropriate.

Finally, I note that while you responded to a minor point I made, you ignored some significant questions. I'm sure that this was a minor oversight on your part, for your reference, I've included those questions below.

What is the "reasonably sized sequence"?

What units?

Why?

edit: because I keep forgetting about the preview bug.

Edited by OgreMkV on Jan. 19 2015,16:37

--------------
Ignored by those who can't provide evidence for their claims.

http://skepticink.com/smilodo....retreat

   
midwifetoad



Posts: 4003
Joined: Mar. 2008

(Permalink) Posted: Jan. 19 2015,16:37   

The writing is better. The ideas are pretty standard straw man boilerplate.

The basic argument is that you can never get from there to here by walking. No calculations presented.

--------------
Any version of ID consistent with all the evidence is indistinguishable from evolution.

  
OgreMkV



Posts: 3668
Joined: Oct. 2009

(Permalink) Posted: Jan. 19 2015,16:47   

Quote (Doc Bill @ Jan. 19 2015,16:31)
This is why it's impossible to have a discussion with a creationist.  They just don't possess human brains.

Creepto's argument from incredulity expressed thusly:

 
Quote
So to summarise my answer ... when I'm talking about new information ... I'm talking about a unique DNA sequence in an organism. I can't see how it would ever be possible (argument from incredulity) for random mutation to create that much dumb luck (argument from incredulity)even given billions of years. That's not an argument from incredulity (OH, YES IT IS!!)... that's me saying from my knowledge of statistics (No, you haz not!!) I can't see how it could ever be possible (argument from incredulity), so the extraordinary claim of evolutionists (argument from incredulity) needs to be demonstrated in a model that addresses the difficult-to-believe parts (argument from incredulity) of the claim, not just that we can randomly arrive (argument from incredulity) at something useful sometimes



That argument of Creepto's is quite incredible!  Really, this is better than GG?  Perhaps, but only on the Loony Tunes scale.

It's funny because this is the exact same line of thinking that tripped of Behe in the Kitzmiller trial.

Behe: The maths say it's a really big number.
Rothschild: But there's 7 orders of magnitude more bacteria in one ton of soil... 16 orders of magnitude more bacteria on Earth... and that's in any one year... of which we have to consider the multi-billion year history of the planet.
Behe: Well, yeah... but...

There is no "but". There's only the really big, scary number and the creationist demand that we produce a modern protein by totally random processes... and crypto has stated multiple times.

--------------
Ignored by those who can't provide evidence for their claims.

http://skepticink.com/smilodo....retreat

   
midwifetoad



Posts: 4003
Joined: Mar. 2008

(Permalink) Posted: Jan. 19 2015,16:56   

That, plus the minor detail that a modern bacterium is adapted to it's current ecosystem and isn't bloody likely to evolve into a squirrel.

--------------
Any version of ID consistent with all the evidence is indistinguishable from evolution.

  
cryptoguru



Posts: 53
Joined: Jan. 2015

(Permalink) Posted: Jan. 19 2015,17:41   

Quote
That, plus the minor detail that a modern bacterium is adapted to it's current ecosystem and isn't bloody likely to evolve into a squirrel.

Not even a squirrel was likely to evolve into a squirrel.

It's just amazing what variety a little bit of random mutation, a fight for survival and an overactive imagination can do. (don't forget 3D graphics and bold statements of fact in narration over the top)

Well this HAS been fun gentlemen ... I think we've done a full circle, which probably means you're right and I'm wrong, just because you say so. And because it makes complete sense, right!

Also remember to say that I don't know anything about biology, or evolution ... or mathematics ... or the mystical natural selection angel after I'm gone.

It's time for QED to give his closing statement ... and for Bilbo to do his Sesame Street ending ... "and today we learned the number 6 and the letter Z and learned all about how evolution is a fact ... and that's a fact children ... see you all next week"

And probably time for Kevin to get the wrong end of a stick again and gnaw on it.

It's been an absolute pleasurable pleasure

  
midwifetoad



Posts: 4003
Joined: Mar. 2008

(Permalink) Posted: Jan. 19 2015,18:06   

Flounce II.

--------------
Any version of ID consistent with all the evidence is indistinguishable from evolution.

  
Doc Bill



Posts: 1039
Joined: April 2007

(Permalink) Posted: Jan. 19 2015,18:09   

Flounce Deux for the amateur MMA "expert."

That's what I call cut-and-run.

Too bad.  I was working on a post showing how a point bit mutation or a frame shift didn't necessarily cause a program to crash.  It would do something different quite likely, but it would do something!

In the early days of using microprocessors we were so tight on RAM that tight code and very clever programming was not only the rage but often necessary.  I recall writing an algorithm that changed a couple of lines of command code depending on what was going on.  It might be "shift left" in one iteration and "shift right" in another.

So, Creepto summary:

Knows jack about the theory of evolution.
Knows jack about statistics.
Knows jack about probability.
Knows jack about chemistry.
Knows jack about the English language.
Knows jack about computers.

The perfect creationist!  

He's probably asking himself, "Who's Jack?"

  
JonF



Posts: 634
Joined: Feb. 2005

(Permalink) Posted: Jan. 19 2015,18:09   

Yeah, standard creationist refusal to learn.

Tell you MMA pals you're too much of a pussy to learn about what you're criticizing. Plus no mathematician would make claims about such a complex process based on intuitionp plus ignorance of the system.

What a poseur.

  
Wesley R. Elsberry



Posts: 4991
Joined: May 2002

(Permalink) Posted: Jan. 19 2015,18:18   

Congrats to Cryptoguru for reading some of the responses and making some changes to his argumentation. This is not commonly observed in these sorts of exchanges. Plus, welcome back to the beginning of the second farewell tour. (I wrote that last sentence before the second flounce.) I'm still not inclined to accept changes in the original challenge, though, so I will be specifically noting those.

                 
Quote (cryptoguru @ Jan. 19 2015,07:45)

[...]

Section D:
comparison of AVIDA to biological evolution
1) an analogy must be drawn between AVIDA commands and the genome
2) it possibly makes most sense (I concede) to assume that AVIDA commands are analogous to codons (and not proteins), so that any mutation will always create a set of valid codons.
3) the level AVIDA is selecting at is therefore analogous to a folded functional protein.


A problem with (3) is that I've already pointed out the level of selection is the Avidian, not any sub-sequence of its genomic instruction sequence.

         
Quote (cryptoguru @ Jan. 19 2015,07:45)

Section E:
problems with model
1) the multi-dimensionality of the genome due to multiple reading frames means that a point mutation in the genome will likely affect the expression of multiple proteins (19K coding genes code for at least 100K different proteins in the human genome). Mutations in AVIDA are mutually exclusive and therefore don't have a regressive effect on the expression of other COMMANDS. This is not a trivial difference, it is analogous to the difference between a bisection method (AVIDA mutation) and a bisection method where the root can change at each iteration (Genome mutation).


This is not in the original challenge, and is thus irrelevant to answering the original challenge. The Avida instruction set includes "mov-head", "jump-head", and "set-flow", which can and do change expression dramatically. Avida itself has been used to perform in silico experimentation on overlapping genes:

                 
Quote

One consequence of overlapping genes is to reduce the tolerance for mutation. Virtual experiments conducted within the past several years using a software system called Avida have indicated that overlapping reduces the probability of accumulating so-called neutral mutations in a gene (mutations that have no effect). Neutral mutations are unlikely with overlapping genes, because the mutation must have no effect on two genes with different reading frames.


But like I said, that's all irrelevant to the original challenge.

                 
Quote (cryptoguru @ Jan. 19 2015,07:45)

2) It is not just multiple reading frames that introduce polymorphism into the genome, but regulatory genes can effect the expression of an entire coding gene. This non-linearity is not modelled in AVIDA, which is a linear sequential code (like assembler). That is, the Genome executes a higher-level language than a sequential instruction set.


Again, this concern is nowhere to be seen in the original challenge, and is thus irrelevant to the original challenge. Plus, the Avida documentation notes:

                 
Quote

One major concept that differentiates this virtual assembly language from its real-world counterparts is in the additional uses of nop instructions (no-operation commands). These have no direct effect on the virtual CPU when executed, but often modify the effect of any instruction that precedes them. In a sense, you can think of them as purely regulatory genes. The default instruction set has three such nop instructions: nop-A, nop-B, and nop-C.


But like I said, that's all irrelevant to the original challenge.

                 
Quote (cryptoguru @ Jan. 19 2015,07:45)


3) AVIDA enforces selection by rewarding at the functional level ... it identifies a function as a logical operation and rewards the organism that is presenting it. This is equivalent to natural selection providing feedback scores to the organism on a per-protein level. e.g. protein 1 7/10, protein 2 3/10, protein 3 9/10. This kind of micro-management can't happen in real-life as natural selection is blind and is applied not even to an organism but an entire population. This feature artificially boosts the productivity of hopeful combinations of commands, which otherwise wouldn't be encouraged.


Bogus in many particulars. Group selection is about as dead a concept as it is possible to get in biology. Not so long ago, Cryptoguru asserted this:

                 
Quote

1) evolution mutates DNA on a nucleotide level affecting function (gene level) and selects on the organism level.


which appears to be that rarity in logical fallacies, a contradiction. It also indicates that Cryptoguru's conceptual movement on this particular is in a bad direction.

Avida does not examine the genomic instruction sequence to recognize something. It examines the output from the IO instruction of the Avidian that indicates that it correctly performed a behavior, in the Lenski et al. 2003 paper the rewarded behaviors comprised a set of nine logic operations. An Avidian can internally compute every logic function around and receive exactly zero extra CPU cycles of merit if it fails to output the results to the environment via the IO instruction. I've already mentioned this before. The assertion that things are otherwise is a persistent misunderstanding on Cryptoguru's part.

Avida's award of merit for Avidian behaviors is analogous to biological organisms getting better/more nutrition, or greater movement efficiency, or better artifact construction (nest, hive, or tools) due to a favorable trait. There is really nothing to object to on this point, and this is no problem for the model.

As far as the final quoted sentence goes, some traits have to have relative benefits in order to simulate natural selection. This has to happen in the model since it happens in biology. This is not a problem for the model.

                 
Quote (cryptoguru @ Jan. 19 2015,07:45)


4) The level of variability in AVIDA compared to the genome is like comparing solving a Rubik's cube with cracking 2048-bit RSA encryption. The logical functions which AVIDA selects and guide the optimisation process are trivial ... and also non-distinct. There are infinitely many ways to implement the EQU function using the AVIDA instruction set. Proteins are specific in their form, not just in an abstract functional way. The likelihood of randomly selecting a combination of AVIDA commands that performs a logical function is extremely high, I don't know if it's even possible to work this out considering there are infinitely many combinations that could represent each logical function. (e.g. inc dec inc dec inc dec is equivalent to leaving a register unchanged). In the genome the possibility of just mutating 3 neighbouring nucleotides anywhere in the genome to produce a different codon is less than the chances of winning the national lottery twice in a row, and two proteins with different amino acid chains can likely never be equivalent in function. (unless randomness of function is the required function for the protein)



Again, this concern is nowhere to be seen in the original challenge, and is thus irrelevant to the original challenge. The original challenge made no restrictions on the size of a novel function.

Proteins are not absolute, on-off switches of function for a given amino acid sequence/fold configuration. Proteins often exhibit partial functionality. Physiologists also know that proteins work better and worse for a given function at different temperatures. Proteins also often tolerate substitutions of amino acids without drastic changes in function. Even Douglas Axe's work shows that he had to go to swapping out large swaths of amino acids in order to almost entirely eradicate barnase function. So perhaps the two proteins are not equivalent; that does not mean that they are significantly different, which is what Cryptoguru's argument requires. See also Dayhoff's Atlas of Protein Sequence and Structure, which shows the differences in the proteins used for the same purpose across a variety of organisms. Those often show multiple amino acid differences in even a relatively short protein like cytochrome-c. That's been around since the 50's, so there's not much excuse for not knowing that before spewing.

About "In the genome the possibility of just mutating 3 neighbouring nucleotides anywhere in the genome to produce a different codon is less than the chances of winning the national lottery twice in a row"...

That is really unclear. Does Cryptoguru mean the odds of getting a different codon given three neighboring nucleotides mutate? Three nucleotides specify a codon, given four nucleotides, that's a total of sixty-four possible codons. Randomly picking new values for each of the three nucleotides will only yield the same codon in 1/4*1/4*1/4 = 1/12 of the time, or about 8%. The complement of that is about 92%.  Does he mean instead, as I suspect, that single nucleotide mutations are rare, and that getting three adjacent ones are even rarer? True, but it doesn't work out as he seems to wish. Changing a single nucleotide would give a different codon by definition, and given a uniform sampling of codons, that yields about an 80% chance of a different codon that yields a different amino acid as a result. Yeah, the SNP event is ~1e-9, but a change in amino acid resulting is pretty common as a result of an SNP. One does not need to change all three nucleotides to get a different codon, nor to get a different amino acid as a result.

Nor do I buy the "probability is extremely high" gambit based on arm-waving. Cryptoguru should either show his work or give it up. Towards that work...Sure, there are infinite ways to get EQU function. And for each one of those, Cryptoguru needs to estimate the number of Avida programs of the same length that do not provide EQU function. For his claim, he needs to show that number is far from L^26-1, where L is the program length. A probability will incorporate that other number, and not just count the "hits". A sample of program lengths from the minimal EQU length to, say, 50, should suffice. My own assessment of probability of EQU, based on actually having used Avida, programmed Avida, and programming and testing Avida-ED changes, is that hitting on EQU randomly is a tiny, tiny probability. That's arm-waving, too, but with some experience to back it. Then there is the result in the Lenski et al. 2003 paper that directly addresses this concern experimentally:

             
Quote

At the other extreme, 50 populations evolved in an environment where only EQU was rewarded, and no simpler function yielded energy. We expected that EQU would evolve much less often because selection would not preserve the simpler functions that provide foundations to build more complex features. Indeed, none of these populations evolved EQU, a highly significant difference from the fraction that did so in the reward-all environment (P ~ 4.3 x 10^-9, Fisher's exact test). However, these populations tested more genotypes, on average, than did those in the reward-all environment (2.15 x 10^7 versus 1.22 x 10^7; P < 0.0001, Mann-Whitney test), because they tended to have smaller genomes, faster generations, and thus turn over more quickly. However, all populations explored only a tiny fraction of the total genotypic space. Given the ancestral genome of length 50 and 26 possible instructions at each site, there are ~5.6 x 10^70 genotypes; and even this number underestimates the genotype space because length evolves.


The only real numbers in this particular aspect of the discussion indicate that for Cryptoguru "extremely high likelihood" can refer to a probability smaller than 1 in 2.15 x 10^7. Your mileage may vary.

But like I said, that's all irrelevant to the original challenge.

                 
Quote (cryptoguru @ Jan. 19 2015,07:45)
DISCUSS!



Cryptoguru's original challenge has been met. If Cryptoguru wants to move on to a different challenge as his objections seem to indicate, he should at least acknowledge that his prior one was met before stating a new challenge.

Much of the discussion that ensued after Cryptoguru's original challenge was due to Cryptoguru's inability to focus on the terms of the challenge he himself wrote. There seems to be a curious vagueness about whether Cryptoguru wants a model of natural selection, a model of genetic inheritance, a model of codon replacement, or a model of abiogenesis itself. Certainly the objections raised afterwards have touched upon all of those. There is a concept called salience that Cryptoguru ought to get familiar with. A model aimed at determining whether new information can arise in computer code via an evolutionary process doesn't need to be freighted with most of the irrelevancies that he has discussed. In the extreme, it appears that Cryptoguru wants the equivalent for biology of the "theory of everything".

The other significant fraction of Cryptoguru's output concerned things that he believed were true, but weren't. For instance, the majority of Cryptoguru's claims concerning the Avida system were and are, charitably speaking, bunk. This didn't prevent Cryptoguru spouting falsehoods with fervor and vehemence, and ironically insisting that others had gotten their facts wrong on that score.

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"You can't teach an old dogma new tricks." - Dorothy Parker

    
The whole truth



Posts: 1554
Joined: Jan. 2012

(Permalink) Posted: Jan. 19 2015,18:29   

Quote (cryptoguru @ Jan. 19 2015,13:43)
Quote

Creepto ate the dog.
Creepto ate the hog.

In Creepto-speak there is no new information.  I guess you'd need something like this:

Creepto ate the dog.
Creepto prepared the mongoose in a rich butter sauce.


You should definitely be proud of yourself Bilbo, those English lessons are starting to pay off.

Of course I was being arbitrary ... my definition of "new information" is substantial unique sequences in a genome (i.e. not shared with assumed relative species) that wouldn't be expected by a series of random events.

So if you showed me

BILBO PAID OVER THE ODDS FOR SHOES
and
BILBO PAID OVER THE ODDS FOR HOES

Although both those sentences make sense to me, I can quite easily explain that the first one arose by chance rather than any optimisation process requiring natural selection.

So I'm asking for a unique sequence that couldn't just arrive fully formed by accident ... i.e. I want proof of the evolution process producing something hard that Bilbo couldn't just cook up by throwing a die.

Saying ... "well here we are ... tada, the human!" is just begging the question, so I'm after proof of the theory

Quote
So, what law (biological, chemical, physical, or logical) prevents multiple point mutations from happening over time?

None ... never said it couldn't


Quote
Somehow, they all have this notion, that like computer program... DNA springs into existence, fully formed

You're straw-manning again Mr Ogre McCarthy ... I never said that's what I think evolutionists believe ... and I obviously don't believe that. My point was that if you compare a chimp to a human there are unique sequences of DNA in humans, evolution needs to explain how a sequence that big can appear over time (yes kazillions of years if you like) ... but it still has to be functional and there right? So whether it was caused by thousands of point mutations, or a whole bunch of splicing and point mutations and stuff until you got that unique functional sequence that comprises compressed instruction sets for building proteins. You need to demonstrate that.

AVIDA is not demonstrating that level of magic, it just optimises the combination of some functions to create logical functions. We're not talking a few logical operands on the genome that have been created, we're talking MULTI-DIMENSIONAL SUPERCODES ... Supercodes ... supercodes ... super... (echoes into distance)

and Lenski has some E. Coli on his farm E-I-E-I-O
But on that farm there's not a chicken E-I-E-I-O
(join with me Bilbo)

So Lenski hasn't observed anything unbacteria-like going on yet after 60,000 generations, and AVIDA is unable to model anything more complicated than joining a few assembler instructions in sequence and rewarding the organism every time a logical function is found. METHINKS IT IS NOT A WEASEL YET

More proof please

BTW Kevin, please don't write the word Allele again ... you're banned from using it from now on from overuse.

cryptoguru, I'm trying to understand your arguments and I have some questions. First, will you please answer this one that I asked earlier:

Where do you get the idea that every biological entity evolves by exactly the same amount from one generation to the next? I would have said life form instead of biological entity but I'm including viruses, and not everyone thinks that viruses are life forms.

In regard to this:

"Of course I was being arbitrary ... my definition of "new information" is substantial unique sequences in a genome (i.e. not shared with assumed relative species) that wouldn't be expected by a series of random events."

I don't understand what you're asking for. Will you explain more fully and provide some examples of what would satisfy your definition of new information?

Also:

What is your stance in regard to CSI, FSCI, dFSCI, FSCO/I, and IC?

From an intelligent design perspective, how would you explain diseases, parasites, deformities/aberrations, and extinctions?

Do you believe that humans are not descended from earlier life forms?

Do you believe that all humans have identical genomes?

Do you believe that all butterflies have identical genomes?

Do you believe that all butterflies that can mate and have viable offspring with each other (the same 'biological species') have identical genomes?

Do you accept that evolution occurs, including evolution in/of humans? If so, do you believe that evolution has a goal? If so, what is the goal, especially in regard to humans? And do you believe that the goal was/is designed/created/directed by a supernatural 'God'?

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Think not that I am come to send peace on earth: I came not to send peace, but a sword. - Jesus in Matthew 10:34

But those mine enemies, which would not that I should reign over them, bring hither, and slay them before me. -Jesus in Luke 19:27

   
OgreMkV



Posts: 3668
Joined: Oct. 2009

(Permalink) Posted: Jan. 19 2015,18:49   

Yep, it's been fun. Cryptoguru has been utterly crushed. Shown to have limited knowledge of biology... and computing for that matter (which is odd because he claims to be an expert).

He does seem to be an expert in using creationist arguments, without understanding the implications. He is definitely an expert in not answer questions asked of him and demanding that we answer all his questions (even though they make no sense) perfectly.

In other words, he will go on and claim that he won.

I will definitely link back to this thread in any further replies to crypto elseswhere. And remind him that he ignored several questions by myself and others and he might want to get on those...

Thanks everyone!

--------------
Ignored by those who can't provide evidence for their claims.

http://skepticink.com/smilodo....retreat

   
Wesley R. Elsberry



Posts: 4991
Joined: May 2002

(Permalink) Posted: Jan. 19 2015,19:30   

Cryptoguru:

 
Quote

So Lenski hasn't observed anything unbacteria-like going on yet after 60,000 generations, and AVIDA is unable to model anything more complicated than joining a few assembler instructions in sequence and rewarding the organism every time a logical function is found. METHINKS IT IS NOT A WEASEL YET


Strike whatever-number-of-clueless-claims-he's-made-about-Avida.

Avida has been used to generate and evaluate UML models and for the generation of firmware for wireless sensors to be deployed in wireless sensor networks, and those are a couple of applications that I knew about before I left MSU back in 2009. MSU got the BEACON grant shortly thereafter, and things have been hot in the lab since then.

Question: how much research did Cryptoguru do about the topic of his claim before vomiting it forth? My guess is zero, zip, zilch, and nada.

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"You can't teach an old dogma new tricks." - Dorothy Parker

    
Doc Bill



Posts: 1039
Joined: April 2007

(Permalink) Posted: Jan. 19 2015,19:51   

Surprisingly, one interesting thing came out of the Creepto exchange over on Smiledon's Retreat and that was an update to the Paley argument.

Paley imagined a pocket watch being found on the heath because the pocket watch was the most sophisticated instrument of his time.  Likewise, Creepto imagines the cell as a computer because it is the most sophisticated instrument of his time (although I might vote for the non-stick pan - I digress.)

So, over on Ogre's site I imagined Paley finding a fully charged iPhone on the heath.  He would pick it up and after a bit of fiddling let's say he turns it on.  Magic, he would think!  Sure, there's no ATT and no WiFi but he could run a few stand-alone apps and the camera.

Imagine his joy and wonder at this incredible thing!

But, by the next day when he gathered his scientific pals at his house, alas, the iPhone is discharged and sits there, mute and a black screen.  Nothing Paley does can revive it.

Subsequently, he and his friends take it apart and what do they see?  Nothing recognizable.  Not a single part.  It's just all black squares and strings of copper and a substance they can't recognize as plastic.  It's a total mystery.

I thought about this given Creepto's fascination with his computer analogy.  Why a computer?  Because that's all he knows.  He doesn't have the imagination to think beyond that analogy.

And, clearly, he doesn't have the faintest inkling about chemistry.

So, my question to my fellow Mornington Crescent travelers is this:  what would you find on the heath?

  
N.Wells



Posts: 1836
Joined: Oct. 2005

(Permalink) Posted: Jan. 19 2015,19:59   

Quote (cryptoguru @ Jan. 19 2015,17:41)
Not even a squirrel was likely to evolve into a squirrel.

http://www.newscientist.com/article....ng.html
Doesn't count because this is change in age of first reproduction and not DEATH.

http://web.mit.edu/~jfc.......dae.pdf
Doesn't count because it's a pain to deal with all that data, and it's only two genes and more than one point mutation.

http://www.washingtonpost.com/wp-dyn....._2.html
Doesn't count because it's just one population replacing another and I don't want to hear about alleles

 
Quote
From http://squirrelmapper.org/faq_evo....olution
What is the genetic difference between black and gray squirrels?

Black and gray squirrels are only different based on one gene. Alleles are variations on DNA sequences at a specific location on a chromosome (usually different forms of the same gene). The allele for squirrel fur color has two different possible sequences – one that codes for gray fur and one that codes for black fur. Each squirrel has two copies of this allele. If a squirrel has two copies of the gray allele, then it will be gray, but if it has either one copy of the gray and one of the black or if it has two copies of the black allele, then it will be black. The gray type is actually genetically recessive, which is somewhat counterintuitive since it is the more common genotype these days!

Most dark pigmentation in mammals is associated with the MC1R gene. The MC1R gene regulates how much brown/black pigment (eumelanin) versus pale red/yellow pigment (phaeomelanin) is added to hairs as they grow. When the alpha melanocyte-stimulating stimulating hormone (αMSH) binds to the MC1R gene, eumelanin (dark pigment) is produced; otherwise phaeomelanin (light pigment) is produced. In black squirrels, the MC1R gene has undergone a small deletion (24 base pairs of DNA) that corresponds to just 8 amino acids. This deletion hastens binding of the αMSH to the MC1R gene increasing production of eumelanin (the mechanism is not yet known). This is known as the EB allele. In the gray squirrel a complete MC1R gene (lacking the deletion) blocks binding of αMSH increasing production of phaeomelanin. This is known as the E+ allele. The EB allele is incompletely dominant to the E+ allele. So E+/E+ is the genotype of the gray squirrel, EB/EB is the genotype of the black squirrel, and EB/E+ (or E+/EB) is the genotype of the brown-black squirrel. In the field it’s hard to distinguish a black EB/EB from a black EB/E+ squirrel but look carefully: the EB/EB is jet black all over but and EB/E+ squirrel have mostly brown-black backs but a distinctly lighter-colored (often orange-colored) belly. It’s quite likely that there are other genes and alleles at work but at present this is our best understanding of the genetic mechanism at work.

Still just a damn squirrel.  What did I tell you?

Kaibab squirrels from Albert squirrels:  http://www.sbs.utexas.edu/levin/bio213/evolution/speciation.html
Doesn't count because I can't imagine a black belly and forelimbs leading to DEATH.  Plus no one saw it happen.

http://link.springer.com/article....6065.f0
Doesn't count because I was talking about TREE squirrels.

http://link.springer.com/article....-9250-7
Once again, not TREE squirrels, plus it talks about global warming, so it's clearly biased.

http://www.scielo.sa.cr/scielo.....0100020
Doesn't count because most of them have "sciurus" in their name, so of course they're all going to be similar.


http://evolution.berkeley.edu/evolibr....br....4
Heck, that's birds and pine cones and they're still birds and pine cones, and besides which not one single squirrel died preferentially.  Also, if you are going to talk about co-evolution, you have to prove evolution first.

http://today.duke.edu/2003.......02.html
They left out one of the 51 genera of squirrels, so get back to me when they do a real study.

https://pure.york.ac.uk/portal.....29.html
Cranial characters support findings from studies of mandibles, which support molecular results ( http://goodnight.corral.tacc.utexas.edu/UAF........ses.pdf ), which confirm biogeographic patterns, which show that a high degree of sociality must have evolved twice.  Well, I've been antisocial my entire life, so I can't believe that would have happened.

http://www.ncbi.nlm.nih.gov/pubmed.....7921359
http://evolution.berkeley.edu/evolibr....ipmunks
Lots of death, and all we get is bottlenecks.  I want evolution!!!


http://link.springer.com/article....ss=true
Oh for god's sake, I asked for squirrels, those are frigging chipmunks.

Well, that was fun.  Get back to me when you have someone who saw it happen.

  
Driver



Posts: 649
Joined: June 2011

(Permalink) Posted: Jan. 19 2015,20:39   

Quote (Doc Bill @ Jan. 20 2015,00:51)
So, my question to my fellow Mornington Crescent travelers is this:  what would you find on the heath?

Which part of the Heath?

Lots of condoms on West Heath.

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Why would I concern myself with evidence, when IMO "evidence" is only the mind arranging thought and matter to support what one already wishes to believe? - William J Murray

[A]t this time a forum like this one is nothing less than a national security risk. - Gary Gaulin

  
Doc Bill



Posts: 1039
Joined: April 2007

(Permalink) Posted: Jan. 19 2015,21:03   

Quote (Driver @ Jan. 19 2015,20:39)
Quote (Doc Bill @ Jan. 20 2015,00:51)
So, my question to my fellow Mornington Crescent travelers is this:  what would you find on the heath?

Which part of the Heath?

Lots of condoms on West Heath.

I was thinking Heath Robinson who shot a condom from the Albert Memorial to Kensington Palace, that bounced into Pan's ... well, best not said where it bounced.

Enough said that Creepto couldn't find his way from South Kensington to Green Park on a Sunday, much less to Mornington Crescent on any day.

You will find me at King's Cross, platform 9 3/4.

  
midwifetoad



Posts: 4003
Joined: Mar. 2008

(Permalink) Posted: Jan. 19 2015,21:16   

On the moor, one might find a hound from hell.

--------------
Any version of ID consistent with all the evidence is indistinguishable from evolution.

  
Doc Bill



Posts: 1039
Joined: April 2007

(Permalink) Posted: Jan. 19 2015,21:19   

Only in Kate's bush.

  
Quack



Posts: 1961
Joined: May 2007

(Permalink) Posted: Jan. 20 2015,00:59   

Quote (Zachriel @ Jan. 19 2015,08:21)
cryptoguru: evolution mutates DNA on a nucleotide level affecting function (gene level) and selects on the organism level.

Evolution also involves recombination and the splicing of new structures from subcomponents.  

cryptoguru: The whole premise of natural selection can be simplified to be death.

That is also false. The whole premise of natural selection is reproductive success.


How true. Ratio of death is fixed at 100%. Ratio of reproduction most likely never reach that figure.

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Rocks have no biology.
              Robert Byers.

  
Cubist



Posts: 558
Joined: Oct. 2007

(Permalink) Posted: Jan. 20 2015,04:40   

Quote (cryptoguru @ Jan. 19 2015,08:39)
Cubism: (this is not directly about my last post but answering an earlier clarification from Cubism)

Bad start. For the record, cryptoguru: The 'handle' I use online does not, in fact, have an "m" in it. Said handle is Cubist, not Cubism. I don't find your (repeated!) Cubism-not-Cubist error to be offensive or anything, but I gotta admit it strikes me as indicative of… hmm… a certain level of attentiveness and/or general intellectual ability, let's say.

 
Quote
 
Quote
Does the mutated nucleotide sequence qualify as "new and novel genetic material"? Does the mutated nucleotide sequence contain any "new and novel genetic material"?

The issue here is one of scale…

…and a bad continuation following on from a bad start, in that it ignores my query re: how come you (cryptoguru) said that the "new information" of "genetic material" has to be both "novel" and "new".

Re-posting the paragraph about how come it's gotta be both "new" and "novel" which you ignored: Why must the "genetic material" of "new information" be both "new" and "novel"? I ask because "new" and "novel" strike me as basically synonymous, hence, using both words is gratuitous redundancy. But perhaps you weren't being redundant; perhaps you actually are using distinct referents for "new" and "novel", such that the two words are not, in fact, gratuitously redundant. Please explain how "genetic material" which is "new" differs from "genetic material" which is "novel".  Is it possible for "genetic material" to be "new" without also being "novel"? Is it possible for "genetic material" to be "novel" without also being "new"?

Perhaps you'll deign to honor the questions in that paragraph with answers, cryptoguru. Or not. [shrug]

Onward.

 
Quote
 
Quote
Does the mutated nucleotide sequence qualify as "new and novel genetic material"? Does the mutated nucleotide sequence contain any "new and novel genetic material"?

The issue here is one of scale ... changing a single nucleotide and getting new functionality is more adequately describing a side-effect of switching a control gene rather than amazingly arriving at a new functional sequence through mutation and selection.

You may be right that "scale" is, indeed, the "issue". But regardless of whether or not "scale" is any kind of "issue" anywhere, I note that you didn't answer either of the questions in the text you quoted. That's okay, I can ask those questions again.

[clears throat]

Let's say that Sequence X is the arbitrary 150-nucleotide sequence "gcc tac agg gat cgt ggg gac ctt acg aat ggc ctt ttt gac tat tct tcg aat cta agc tca gca tca ttc ccg tct acg gga agt ccc ttc cca ata cat atc ctc ggc acc gca ctt gca ggc tca cgc ttc gcg tca ttt agg tca". Let's also say that Sequence X1 is the 149-nucleotide sequence "gcc tac agg gac gtg ggg acc tta cga atg gcc ttt ttg act att ctt cga atc taa gct cag cat cat tcc cgt cta cgg gaa gtc cct tcc caa tac ata tcc tcg gca ccg cac ttg cag gct cac gct tcg cgt cat tta ggt ca" that results when one removes the "t" from the fourth codon in Sequence X.

One: Does Sequence X1 qualify as "new and novel genetic material"? It's a yes-or-no question, cryptoguru; either yes, Sequence X1 does, in fact, qualify as "new and novel genetic material", or no, Sequence X1 does not, in fact, qualify as "new or novel genetic material". It's all well and good to go on about "probability" and "scale" and yada yada, but I really would like to see a yes or a no, and thus far, I ain't seen a yes or a no.

Two: Does Sequence X1 contain any "new and novel genetic material"? Again, it's a yes-or-no question, to which either yes, it does or no, it doesn't would both be relevant responses. Going on about "scale" and "probability" and yada yada, contrariwise, is not a particularly relevant response, as best I can tell.

Quote
So evolution claims that all the differences between a chimp's DNA and ours are caused by random mutation on 2 hereditary lines from a common ancestor. Find a sequence of unique DNA in the human genome (yup you can use the "junk DNA" now too, now we know it's not junk). Now that string you're holding has arrived by random mutation ... selection has preserved it, but mutation created it. That's what I mean by new/novel/unique information.

That's nice. You didn't mention "unique" before. Please explain how "genetic material" which is "unique" differs from "genetic material" which is either "new" or "novel".  Is it possible for "genetic material" to be "unique" without also being either "new" or "novel"? Is it possible for "genetic material" to be "novel" without also being "new" or "novel"?

Does Sequence X1 qualify as "unique"?

 
Quote
You may be able to handwave that the switching of a few control genes could happen randomly…

I'm not handwaving a thing, cryptoguru. I'm attempting to get you to explain the meaning of your statement that "New information is new and novel genetic material…".

 
Quote
So to summarise my answer ... when I'm talking about new information ... I'm talking about a unique DNA sequence in an organism.

Groovy. Is Sequence X1 a "unique" DNA sequence?

  
Wesley R. Elsberry



Posts: 4991
Joined: May 2002

(Permalink) Posted: Jan. 20 2015,07:22   

Quote (OgreMkV @ Jan. 19 2015,18:49)
Yep, it's been fun. Cryptoguru has been utterly crushed. Shown to have limited knowledge of biology... and computing for that matter (which is odd because he claims to be an expert).

He does seem to be an expert in using creationist arguments, without understanding the implications. He is definitely an expert in not answer questions asked of him and demanding that we answer all his questions (even though they make no sense) perfectly.

In other words, he will go on and claim that he won.

I will definitely link back to this thread in any further replies to crypto elseswhere. And remind him that he ignored several questions by myself and others and he might want to get on those...

Thanks everyone!

I've found claims of expertise on the part of antievolutionists to be routinely exaggerated. The examples of old-school "creation scientists" claiming doctoral degrees who either didn't have them or were based on things tantamount to diploma mill paper were legendary. In discussions online, it is a commonplace that an antievolutionist will attempt to bolster a bogus claim with an appeal to personal authority. The late Bob Schadewald had a wonderful phrase about the general social phenomena in creationist circles about claiming that they themselves comprised a group of "top scientists": "the elevation of mediocrities". It does work out to another way to say "a big fish in a small pond", but it was so elegantly stated.

Cryptoguru's various complaints about computer models did seem to indicate that he didn't have much of a grounding in computational theory. There are many ways to get to a paycheck in computer technology that do not require that, so I don't really have an issue with the claim that someone is paying him for computer work, but I have deep suspicions about the relevance of his experience to what he is trying to discuss. (Cryptography itself seems to have a closer-than-usual relation to computational theory, so that aspect is pretty puzzling.) He certainly didn't let his deep specific ignorance of Avida stop him from making baldly ridiculous claims about it.

--------------
"You can't teach an old dogma new tricks." - Dorothy Parker

    
NoName



Posts: 2729
Joined: Mar. 2013

(Permalink) Posted: Jan. 20 2015,08:55   

Just in case he pops back in, didn't want him to miss this.

     
Quote (cryptoguru @ Jan. 18 2015,14:39)
final point to N. Wells

Natural Selection is about death. It doesn't matter what the reasons are for advantage, whether it's because some are stronger, or shorter, or bluer, or have better ovaries, or avoid nightclubs .. whatever. The selective agent is death. If an organism dies before it can reproduce it will be removed from the gene pool. Things that haven't died yet compete for resources, eventually a hereditary line will die off removing it from the competition (death again).

The whole premise of natural selection can be simplified to be death. Differential reproduction is a misleading concept, because the preservation of an advantageous trait can only occur when eventually all other competing hereditary lines are extinct. (death). Otherwise you evolutionists would expect to see millions of intermediate evolutionary stages living now alongside the "favoured" one ... and you don't believe that, so all other lines must become extinct to allow the favoured line to become the parent to the next stage. (I obviously think this is crackers ... I'm just explaining that the evolutionary concept of natural selection is very simple)

My point is that the evolutionary concept of natural selection is easy to model, you just set natural conditions and environments for the organisms to live and compete in and see which survive, you shouldn't be measuring the advantages and rewarding them ... nature does not do that, it just provides conditions for death, those who survive it are considered "selected".

I don't see what all the fuss is about ... just trying to demystify the Natural Selection deity.

Bye for now

Crypto, no one but you treats 'Natural Selection' as a deity, or a putative deity.  Not least because there's nothing magic about it.  You almost get it, but your prejudices prevent you from seeing how badly you beg the question and distort the facts, all to reach a pre-determined answer that fits your biases rather than the facts.  If that means the facts have to be changed, too bad for the facts, right?
I've bolded and italicized one of the significant parts where you goe completely wrong.  
I've underlined the next significant bit where you go completely wrong.  Note in particular the error where you assert that there is, or evolutionists somehow thing there is or must be an a priori 'favored  one'.  Ludicrous and a fantasy of your own imagination and biases.
We do, in fact, see exactly what you assert we do not but should expect.  It's (slightly) obscured in the present because we do not yet have the next stages with respect to which everything now alive is an 'intermediate'. But more to the point, within any species (an artificial distinction, entirely conceptual) we see a wide variety of traits -- cats, cows, rats, rutabagas, dogs, dolphins, none are cookie-cutter identical to all other members of the species.  Your conception is that a 'species' is a set of identical clones, which is ludicrous.  No one but creationists make this claim or try so hard to mask the underlying reality of variation within constraints.
Your argument hasn't a leg to stand on.  It has all the conceptual rigor of a fever dream.  It's content has all the grounding in facts and evidence that the DT's do.

  
Amadan



Posts: 1337
Joined: Jan. 2007

(Permalink) Posted: Jan. 20 2015,15:36   

Quote (Wesley R. Elsberry @ Jan. 20 2015,13:22)
Quote (OgreMkV @ Jan. 19 2015,18:49)
Yep, it's been fun. Cryptoguru has been utterly crushed. Shown to have limited knowledge of biology... and computing for that matter (which is odd because he claims to be an expert).

He does seem to be an expert in using creationist arguments, without understanding the implications. He is definitely an expert in not answer questions asked of him and demanding that we answer all his questions (even though they make no sense) perfectly.

In other words, he will go on and claim that he won.

I will definitely link back to this thread in any further replies to crypto elseswhere. And remind him that he ignored several questions by myself and others and he might want to get on those...

Thanks everyone!

I've found claims of expertise on the part of antievolutionists to be routinely exaggerated. The examples of old-school "creation scientists" claiming doctoral degrees who either didn't have them or were based on things tantamount to diploma mill paper were legendary. In discussions online, it is a commonplace that an antievolutionist will attempt to bolster a bogus claim with an appeal to personal authority. The late Bob Schadewald had a wonderful phrase about the general social phenomena in creationist circles about claiming that they themselves comprised a group of "top scientists": "the elevation of mediocrities". It does work out to another way to say "a big fish in a small pond", but it was so elegantly stated.

Cryptoguru's various complaints about computer models did seem to indicate that he didn't have much of a grounding in computational theory. There are many ways to get to a paycheck in computer technology that do not require that, so I don't really have an issue with the claim that someone is paying him for computer work, but I have deep suspicions about the relevance of his experience to what he is trying to discuss. (Cryptography itself seems to have a closer-than-usual relation to computational theory, so that aspect is pretty puzzling.) He certainly didn't let his deep specific ignorance of Avida stop him from making baldly ridiculous claims about it.

On a related note: approach with Extreme Caution any book whose author perceives a need to place "Ph.D" after their name on the cover.

--------------
"People are always looking for natural selection to generate random mutations" - Densye  4-4-2011
JoeG BTW dumbass- some variations help ensure reproductive fitness so they cannot be random wrt it.

   
KevinB



Posts: 525
Joined: April 2013

(Permalink) Posted: Jan. 20 2015,16:57   

Quote (Doc Bill @ Jan. 19 2015,19:51)
So, my question to my fellow Mornington Crescent travelers is this:  what would you find on the heath?

I'd play Heathrow Terminal 4, and expect to find a Boeing 747, though not necessarily in conjunction with either a tornado or a junkyard.

  
Amadan



Posts: 1337
Joined: Jan. 2007

(Permalink) Posted: Jan. 21 2015,13:25   

Quote (KevinB @ Jan. 20 2015,22:57)
Quote (Doc Bill @ Jan. 19 2015,19:51)
So, my question to my fellow Mornington Crescent travelers is this:  what would you find on the heath?

I'd play Heathrow Terminal 4, and expect to find a Boeing 747, though not necessarily in conjunction with either a tornado or a junkyard.

You've obviously never experienced Terminal 1 on Christmas Eve, which bears an uncanny resemblance to both.

--------------
"People are always looking for natural selection to generate random mutations" - Densye  4-4-2011
JoeG BTW dumbass- some variations help ensure reproductive fitness so they cannot be random wrt it.

   
OgreMkV



Posts: 3668
Joined: Oct. 2009

(Permalink) Posted: Jan. 21 2015,16:27   

I find it especially amusing when an article comes out the same week (or day) we're discussing something.

http://www.nature.com/ng....96.html

Quote
We describe a new computational method for estimating the probability that a point mutation at each position in a genome will influence fitness. These 'fitness consequence' (fitCons) scores serve as evolution-based measures of potential genomic function. Our approach is to cluster genomic positions into groups exhibiting distinct 'fingerprints' on the basis of high-throughput functional genomic data, then to estimate a probability of fitness consequences for each group from associated patterns of genetic polymorphism and divergence. We have generated fitCons scores for three human cell types on the basis of public data from ENCODE. In comparison with conventional conservation scores, fitCons scores show considerably improved prediction power for cis regulatory elements. In addition, fitCons scores indicate that 4.2–7.5% of nucleotides in the human genome have influenced fitness since the human-chimpanzee divergence, and they suggest that recent evolutionary turnover has had limited impact on the functional content of the genome.


--------------
Ignored by those who can't provide evidence for their claims.

http://skepticink.com/smilodo....retreat

   
Quack



Posts: 1961
Joined: May 2007

(Permalink) Posted: Jan. 22 2015,00:21   

Quote (Amadan @ Jan. 20 2015,15:36)

 
Quote (Wesley R. Elsberry @ Jan. 20 2015,13:22)
    
Quote (OgreMkV @ Jan. 19 2015,18:49)
Yep, it's been fun. Cryptoguru has been utterly crushed. Shown to have limited knowledge of biology... and computing for that matter (which is odd because he claims to be an expert).

He does seem to be an expert in using creationist arguments, without understanding the implications. He is definitely an expert in not answer questions asked of him and demanding that we answer all his questions (even though they make no sense) perfectly.

In other words, he will go on and claim that he won.

I will definitely link back to this thread in any further replies to crypto elseswhere. And remind him that he ignored several questions by myself and others and he might want to get on those...

Thanks everyone!

I've found claims of expertise on the part of antievolutionists to be routinely exaggerated. The examples of old-school "creation scientists" claiming doctoral degrees who either didn't have them or were based on things tantamount to diploma mill paper were legendary. In discussions online, it is a commonplace that an antievolutionist will attempt to bolster a bogus claim with an appeal to personal authority. The late Bob Schadewald had a wonderful phrase about the general social phenomena in creationist circles about claiming that they themselves comprised a group of "top scientists": "the elevation of mediocrities". It does work out to another way to say "a big fish in a small pond", but it was so elegantly stated.

Cryptoguru's various complaints about computer models did seem to indicate that he didn't have much of a grounding in computational theory. There are many ways to get to a paycheck in computer technology that do not require that, so I don't really have an issue with the claim that someone is paying him for computer work, but I have deep suspicions about the relevance of his experience to what he is trying to discuss. (Cryptography itself seems to have a closer-than-usual relation to computational theory, so that aspect is pretty puzzling.) He certainly didn't let his deep specific ignorance of Avida stop him from making baldly ridiculous claims about it.

On a related note: approach with Extreme Caution any book whose author perceives a need to place "Ph.D" after their name on the cover.

From Norway, “The Mystery of Life – Intelligent Causation in Nature”

https://d3oh18gu5j3rjh.cloudfront.net/9788271....71....0

ETA Sure looks designed, but intelligent?

Edited by Quack on Jan. 22 2015,14:17

--------------
Rocks have no biology.
              Robert Byers.

  
Quack



Posts: 1961
Joined: May 2007

(Permalink) Posted: Jan. 22 2015,00:26   

Deleted.

Edited by Quack on Jan. 22 2015,00:34

--------------
Rocks have no biology.
              Robert Byers.

  
NoName



Posts: 2729
Joined: Mar. 2013

(Permalink) Posted: Jan. 22 2015,07:54   

The 'crypt-keeper' may be beyond the reach of reason, lost deep in his confusions and errors, but this would repay his attention:
Winning vs. Not Losing

Evolution never requires 'the best', it only ever "requires" the adequate, the 'good enough'.  It is pitiless and remorseless in that there is no point at which it can be guaranteed that there will be 'good enough'.  The universe, far from being 'fine tuned' for life, is incredibly hostile to it.

  
midwifetoad



Posts: 4003
Joined: Mar. 2008

(Permalink) Posted: Jan. 22 2015,09:24   

There's a thread at UD where they are arguing that unexpected permissiveness or robustness in the genome -- allowing mutations that have little or no effect on viability -- is a certain sign of Jebus.

They are citing the book, "Arrival of the Fittest" as evidence against evolution.

--------------
Any version of ID consistent with all the evidence is indistinguishable from evolution.

  
stevestory



Posts: 13407
Joined: Oct. 2005

(Permalink) Posted: Jan. 22 2015,13:08   

the islands of functions are incredibly isolated. That proves Baby Jesus Intelligent Designer! You know what's even more proof? The exact opposite!

Socrates's grandkids these are not...

   
midwifetoad



Posts: 4003
Joined: Mar. 2008

(Permalink) Posted: Jan. 22 2015,15:29   

Quote (stevestory @ Jan. 22 2015,13:08)
the islands of functions are incredibly isolated. That proves Baby Jesus Intelligent Designer! You know what's even more proof? The exact opposite!

Socrates's grandkids these are not...

Makes sense. The best evidence for design would be evidence that evolution works.

If evolution works, it is designed. Therefore Jebus.

--------------
Any version of ID consistent with all the evidence is indistinguishable from evolution.

  
Wesley R. Elsberry



Posts: 4991
Joined: May 2002

(Permalink) Posted: Jan. 22 2015,17:25   

Quote (midwifetoad @ Jan. 22 2015,15:29)
Quote (stevestory @ Jan. 22 2015,13:08)
the islands of functions are incredibly isolated. That proves Baby Jesus Intelligent Designer! You know what's even more proof? The exact opposite!

Socrates's grandkids these are not...

Makes sense. The best evidence for design would be evidence that evolution works.

If evolution works, it is designed. Therefore Jebus.

Dembski didn't like it when I pointed out that his triad of properties for a designer were shared by natural selection.

--------------
"You can't teach an old dogma new tricks." - Dorothy Parker

    
OgreMkV



Posts: 3668
Joined: Oct. 2009

(Permalink) Posted: Jan. 22 2015,20:00   

Quote (Wesley R. Elsberry @ Jan. 22 2015,17:25)
Quote (midwifetoad @ Jan. 22 2015,15:29)
Quote (stevestory @ Jan. 22 2015,13:08)
the islands of functions are incredibly isolated. That proves Baby Jesus Intelligent Designer! You know what's even more proof? The exact opposite!

Socrates's grandkids these are not...

Makes sense. The best evidence for design would be evidence that evolution works.

If evolution works, it is designed. Therefore Jebus.

Dembski didn't like it when I pointed out that his triad of properties for a designer were shared by natural selection.

So far, in the years since Darwin's Black Box... no ID proponent has even tried to talk about the "I".  They just talk about the "D"...

O.o

--------------
Ignored by those who can't provide evidence for their claims.

http://skepticink.com/smilodo....retreat

   
Cubist



Posts: 558
Joined: Oct. 2007

(Permalink) Posted: Jan. 22 2015,21:51   

Quote (OgreMkV @ Jan. 22 2015,20:00)
 
Quote (Wesley R. Elsberry @ Jan. 22 2015,17:25)
 
Quote (midwifetoad @ Jan. 22 2015,15:29)
   
Quote (stevestory @ Jan. 22 2015,13:08)
the islands of functions are incredibly isolated. That proves Baby Jesus Intelligent Designer! You know what's even more proof? The exact opposite!

Socrates's grandkids these are not...

Makes sense. The best evidence for design would be evidence that evolution works.

If evolution works, it is designed. Therefore Jebus.

Dembski didn't like it when I pointed out that his triad of properties for a designer were shared by natural selection.

So far, in the years since Darwin's Black Box... no ID proponent has even tried to talk about the "I".  They just talk about the "D"...

O.o

ID-pushers also don't talk about the Manufacturer. Which is rather a curious omission, if ID really is the dispassionate search for truth that ID-pushers like to claim ID is. After all, people have come up with any number of Designs for thingies that don't actually exist, on account of nobody manufactured any physical instances of those Designs. And leave us not forget that real scientists actually do have a protocol for detecting Design, a protocol which is based on forming a testable hypothesis of Manufacture. Because, like, if whatever-it-is wasn't Manufactured, there wouldn't be any whatever-it-is to declare Designed or otherwise, you know?

  
The whole truth



Posts: 1554
Joined: Jan. 2012

(Permalink) Posted: Jan. 23 2015,00:08   

Quote (Cubist @ Jan. 22 2015,19:51)
Quote (OgreMkV @ Jan. 22 2015,20:00)
 
Quote (Wesley R. Elsberry @ Jan. 22 2015,17:25)
   
Quote (midwifetoad @ Jan. 22 2015,15:29)
   
Quote (stevestory @ Jan. 22 2015,13:08)
the islands of functions are incredibly isolated. That proves Baby Jesus Intelligent Designer! You know what's even more proof? The exact opposite!

Socrates's grandkids these are not...

Makes sense. The best evidence for design would be evidence that evolution works.

If evolution works, it is designed. Therefore Jebus.

Dembski didn't like it when I pointed out that his triad of properties for a designer were shared by natural selection.

So far, in the years since Darwin's Black Box... no ID proponent has even tried to talk about the "I".  They just talk about the "D"...

O.o

ID-pushers also don't talk about the Manufacturer. Which is rather a curious omission, if ID really is the dispassionate search for truth that ID-pushers like to claim ID is. After all, people have come up with any number of Designs for thingies that don't actually exist, on account of nobody manufactured any physical instances of those Designs. And leave us not forget that real scientists actually do have a protocol for detecting Design, a protocol which is based on forming a testable hypothesis of Manufacture. Because, like, if whatever-it-is wasn't Manufactured, there wouldn't be any whatever-it-is to declare Designed or otherwise, you know?

Good points.

IMO the IDiots (cdesignproponentists) omit the manufacture part because it's the 'creation' part and using the 'c' word is a no-no in their agenda to dishonestly shove their religious dogma into schools, etc., and call it science.

--------------
Think not that I am come to send peace on earth: I came not to send peace, but a sword. - Jesus in Matthew 10:34

But those mine enemies, which would not that I should reign over them, bring hither, and slay them before me. -Jesus in Luke 19:27

   
Quack



Posts: 1961
Joined: May 2007

(Permalink) Posted: Jan. 23 2015,01:50   

Quote (Cubist @ Jan. 22 2015,21:51)
 
Quote (OgreMkV @ Jan. 22 2015,20:00)
   
Quote (Wesley R. Elsberry @ Jan. 22 2015,17:25)
     
Quote (midwifetoad @ Jan. 22 2015,15:29)
     
Quote (stevestory @ Jan. 22 2015,13:08)
the islands of functions are incredibly isolated. That proves Baby Jesus Intelligent Designer! You know what's even more proof? The exact opposite!

Socrates's grandkids these are not...

Makes sense. The best evidence for design would be evidence that evolution works.

If evolution works, it is designed. Therefore Jebus.

Dembski didn't like it when I pointed out that his triad of properties for a designer were shared by natural selection.

So far, in the years since Darwin's Black Box... no ID proponent has even tried to talk about the "I".  They just talk about the "D"...

O.o

ID-pushers also don't talk about the Manufacturer. Which is rather a curious omission, if ID really is the dispassionate search for truth that ID-pushers like to claim ID is. After all, people have come up with any number of Designs for thingies that don't actually exist, on account of nobody manufactured any physical instances of those Designs. And leave us not forget that real scientists actually do have a protocol for detecting Design, a protocol which is based on forming a testable hypothesis of Manufacture. Because, like, if whatever-it-is wasn't Manufactured, there wouldn't be any whatever-it-is to declare Designed or otherwise, you know?

ID is best explained as the concept of magic in action. And that kind of magic is best explained by the existence of an Intelligent Magician. But what is the best explanation of His fondness of beetles?

--------------
Rocks have no biology.
              Robert Byers.

  
KevinB



Posts: 525
Joined: April 2013

(Permalink) Posted: Jan. 23 2015,14:14   

Quote (Quack @ Jan. 23 2015,01:50)
But what is the best explanation of His fondness of beetles?

Perhaps He just got caught out by the order multiple in the Creation Supplies catalogue. (Like ordering 1000 boxes of paperclips, instead of 1 box of 1000 paperclips.)

  
JohnW



Posts: 3217
Joined: Aug. 2006

(Permalink) Posted: Jan. 23 2015,14:54   

Quote (KevinB @ Jan. 23 2015,12:14)
Quote (Quack @ Jan. 23 2015,01:50)
But what is the best explanation of His fondness of beetles?

Perhaps He just got caught out by the order multiple in the Creation Supplies catalogue. (Like ordering 1000 boxes of paperclips, instead of 1 box of 1000 paperclips.)

"Customers who ordered tiger beetles also ordered:
Rove beetles
Stag beetles
Scarab beetles
Weevils
..."

--------------
Math is just a language of reality. Its a waste of time to know it. - Robert Byers

There isn't any probability that the letter d is in the word "mathematics"...  The correct answer would be "not even 0" - JoeG

  
midwifetoad



Posts: 4003
Joined: Mar. 2008

(Permalink) Posted: Jan. 23 2015,15:01   

He couldn't resist free shipping.

ETA:

No doubt she subscribed to Mover Prime.

Edited by midwifetoad on Jan. 23 2015,15:02

--------------
Any version of ID consistent with all the evidence is indistinguishable from evolution.

  
Henry J



Posts: 5786
Joined: Mar. 2005

(Permalink) Posted: Jan. 23 2015,15:22   

Quote (JohnW @ Jan. 23 2015,13:54)
Quote (KevinB @ Jan. 23 2015,12:14)
Quote (Quack @ Jan. 23 2015,01:50)
But what is the best explanation of His fondness of beetles?

Perhaps He just got caught out by the order multiple in the Creation Supplies catalogue. (Like ordering 1000 boxes of paperclips, instead of 1 box of 1000 paperclips.)

"Customers who ordered tiger beetles also ordered:
Rove beetles
Stag beetles
Scarab beetles
Weevils
..."

VW Beetle...
Beetle Bailey...

  
KevinB



Posts: 525
Joined: April 2013

(Permalink) Posted: Jan. 23 2015,16:24   

Quote (Henry J @ Jan. 23 2015,15:22)
Quote (JohnW @ Jan. 23 2015,13:54)
 
Quote (KevinB @ Jan. 23 2015,12:14)
 
Quote (Quack @ Jan. 23 2015,01:50)
But what is the best explanation of His fondness of beetles?

Perhaps He just got caught out by the order multiple in the Creation Supplies catalogue. (Like ordering 1000 boxes of paperclips, instead of 1 box of 1000 paperclips.)

"Customers who ordered tiger beetles also ordered:
Rove beetles
Stag beetles
Scarab beetles
Weevils
..."

VW Beetle...
Beetle Bailey...

Yeah, yeah, yeah.

ie.  => Rock Ferry (Birkenhead), which forces the next move to be Pier Head, due to the Gerry Marsden codacil.

  
Jim_Wynne



Posts: 1208
Joined: June 2006

(Permalink) Posted: Feb. 07 2015,11:01   

Quote (Jim_Wynne @ Jan. 18 2015,10:35)
Cryptoguru, condensed:

1.  All of biology and most of science is wrong.
2.  Frontloading.
3.  No evidence, no mechanisms.

I'll put the over/under on this thread at six pages.

The house wins.

--------------
Evolution is not about laws but about randomness on happanchance.--Robert Byers, at PT

  
OgreMkV



Posts: 3668
Joined: Oct. 2009

(Permalink) Posted: Feb. 12 2015,19:31   

AND he's back... on Smilodon's Retreat. He refuses to come here.

Although, he hasn't said word one about information or DNA is a computer.

Now, he's on about how radiometric dating is flawed and can't work. I think he's using that dino bone "paper" with the black "tissue" as evidence. We won't say though.

He's also got this thing about birds... though I think I shut him up about that one too.

Cthulhu he's dumb.

--------------
Ignored by those who can't provide evidence for their claims.

http://skepticink.com/smilodo....retreat

   
rossum



Posts: 289
Joined: Dec. 2008

(Permalink) Posted: Feb. 13 2015,03:50   

Quote (KevinB @ Jan. 23 2015,16:24)
ie.  => Rock Ferry (Birkenhead), which forces the next move to be Pier Head, due to the Gerry Marsden codacil.

"Why did Jesus not appear in Liverpool?"

"Because his miracle of walking on the water is nothing special in Liverpool."

"How come?"

"The quality of Mersey is unstrained."

Ba-dum, tish.

--------------
The ultimate truth is that there is no ultimate truth.

  
KevinB



Posts: 525
Joined: April 2013

(Permalink) Posted: Feb. 13 2015,05:17   

Quote (rossum @ Feb. 13 2015,03:50)
 
Quote (KevinB @ Jan. 23 2015,16:24)
ie.  => Rock Ferry (Birkenhead), which forces the next move to be Pier Head, due to the Gerry Marsden codacil.

"Why did Jesus not appear in Liverpool?"

"Because his miracle of walking on the water is nothing special in Liverpool."

"How come?"

"The quality of Mersey is unstrained."

Ba-dum, tish.

Given the atrociously Bard pun, are you playing Stratford Upon Avon, Stratford International or Fenny Stratford?

  
cryptoguru



Posts: 53
Joined: Jan. 2015

(Permalink) Posted: Feb. 17 2015,09:39   

I'm back through popular demand ... can't be bothered to read through all the replies since I last visited. But happy to debate on one topic at a time.
Yeah I never answered all the questions, because some I didn't read as there were so many, and some I didn't have time to answer as the conversation kept changing direction or different angles were being approached by different people at the same time, plus the entropy of contributors who think discussion is simply calling your opponent stupid and rejecting everything they say without basis. So let's take this at a more reasonable pace ... because I do have a life.

So McOgre (Kevin),
When you say I lost the debate about dinos->birds ... is that the one where you said that dinos evolved into birds and I showed that hundreds of birds in their modern form appear in the fossil record alongside dinos in the Cretaceous layer without transitional form? And you got upset because I said that therefore Velociraptor and T-Rex couldn't have been bird ancestors as they have been widely depicted in the media and literature and museums. And you just wanted to talk about Archaeopteryx? (which looks remarkably like a Hoatzin) And they've found another "earlier" Jurassic feathered bird fossil in China (Xiaotingia). Anyway the birds from dinos thing is quite funny, but even assuming evolution is true there's no proof for dino-bird evo at all, it's simply assumed. Arguing from similar morphology is stupid, as we could simply assert that sharks (fish) and dolphins (mammals) are closely related.

Anyway back to the original problem. (we can discuss the other issues once the allegations that I'm avoiding answering questions stops)

Let me rephrase my original question again, because it seemed to keep getting lost in piles of straw men.
Show me a mechanism that can generate the equivalent information of an ORFan gene (i.e. significant amount of new genetic material, not just a couple of point mutations in regulatory genes that switch other code off/on) using only random mutations and an environmentally driven competition model (i.e. doesn't cheat by rewarding micro-feature improvements that wouldn't be selectable in a natural environment.)
Avida cheats on 2 accounts, it rewards micro-feature improvements by testing if a logic function (target) has been achieved on mutation and not simply on the performance of the resultant organism ... and it only requires a small amount of new information to generate new features (e.g. 9 commands can perform EQU). ORFan genes represent thousands of unique sequences of base-pairs that must be demonstrated can arrive through simple mutation and natural selection.

For those who may be tempted to argue that you don't need to prove anything algorithmically, I've previously shown that the physical evidence is open to interpretation .... but even if it wasn't, you should be able to demonstrate that the general theory of evolution applied to biology can work in principle. (random mutation plus competition can create significantly quantifiable, more complex and apparently designed solutions to problems). We can't use known targets for this, or it is simply a stochastic search and not evolution. Mutation should also allow degeneration of functionality, in the genome, all the organism's functionality can be affected by mutation; even it's most basic operations are defined and built by the code itself. Therefore mutations should be able to break replication and all other basic survival processes of the organism, not only shuffle some existing functionality.

BTW: I'm not an ID person ... I'm a pure-pedigree young earth, bible-thumping creationist. (like Newton & Keppler & Boyle and loads of other religious wingnut scientists before me) But hold back on the abuse .. and the radio-dating arguments (which we can have a bit later if you like) ... let's stay on topic

  
midwifetoad



Posts: 4003
Joined: Mar. 2008

(Permalink) Posted: Feb. 17 2015,10:06   

Pick up a copy of Wagner's "Arrival of the Fittest" and get back. Your  point mutations can accumulate indefinitely (as per the title of Wallace's original paper).

In lieu of that, please present an argument based on actual research, why mutations can't accumulate indefinitely.

--------------
Any version of ID consistent with all the evidence is indistinguishable from evolution.

  
cryptoguru



Posts: 53
Joined: Jan. 2015

(Permalink) Posted: Feb. 17 2015,10:18   

Quote
please present an argument based on actual research, why mutations can't accumulate indefinitely


Of course mutations can accumulate indefinitely ... they do.
I'm asking you to prove that random accumulative mutations can create new functional code and not break the original code.
What we observe in biology is mutations accumulating in the genome and causing more degenerative disease every generation. Show me how THAT is not the case and that there is new information arising somewhere, somehow. Show me algorithmically how information could possibly arise randomly (without sneaking it in using target-based search algorithms) and without calling a point mutation on a regulatory gene "new information".
I want to see from an informatics perspective how useful, functional and non-linear information that solves a problem can arise automatically.

  
N.Wells



Posts: 1836
Joined: Oct. 2005

(Permalink) Posted: Feb. 17 2015,10:32   

Quote (cryptoguru @ Feb. 17 2015,09:39)
I'm back through popular demand ... can't be bothered to read through all the replies since I last visited. But happy to debate on one topic at a time.
Yeah I never answered all the questions, because some I didn't read as there were so many, and some I didn't have time to answer as the conversation kept changing direction or different angles were being approached by different people at the same time, plus the entropy of contributors who think discussion is simply calling your opponent stupid and rejecting everything they say without basis. So let's take this at a more reasonable pace ... because I do have a life.

So McOgre (Kevin),
When you say I lost the debate about dinos->birds ... is that the one where you said that dinos evolved into birds and I showed that hundreds of birds in their modern form appear in the fossil record alongside dinos in the Cretaceous layer without transitional form? And you got upset because I said that therefore Velociraptor and T-Rex couldn't have been bird ancestors as they have been widely depicted in the media and literature and museums. And you just wanted to talk about Archaeopteryx? (which looks remarkably like a Hoatzin) And they've found another "earlier" Jurassic feathered bird fossil in China (Xiaotingia). Anyway the birds from dinos thing is quite funny, but even assuming evolution is true there's no proof for dino-bird evo at all, it's simply assumed. Arguing from similar morphology is stupid, as we could simply assert that sharks (fish) and dolphins (mammals) are closely related.


Cretaceous birds are often "modern" (used very loosely) in some aspects while not in others.  Xiaotingia is one of a growing number of fossils somewhere in the base of archaeopterygids, dromaeosaurs, and troodontids, and how it gets classified depends on how the groups are defined.  However, it isn't a bird in most senses of the word.  The most detailed analysis (Senter et al., 2012) found Archaeopteryx to be a avialian, Anchiornis to be a troodontid, and Xiaotingia to be a basal deinonychosaurian, but this is likely to change as new fossils are found of other critters and as definitions shift to accomodate the new information.  This complexity happens because all these guys are extremely similar in a great many details.  Modern classification of fossils without DNA depends on statistical analysis of similarity using many dozens of characters, because similarity overall matches relatedness in living forms.  Classification no longer rests on single characters picked by an expert (the "it has feathers, so it's a bird" school of classification), and absolutely never relied on gross similarities unsupported by similarities in fine details (your "Archaeopteryx looks like a hoatzin" idea). Archaeopteryx does not look very like a hoatzin at all when one looks at its fine details.  However, it does match Velociraptor in quite a lot of details.

Descent of birds from theropods is not an "assumption", but a comclusion, based on cladistic analysis of data from comparative anatomy.  No dinosaur experts claim that  Tyrannosaurus and Velociraptor were direct ancestors of birds: they are close relatives (Tyrannosaurus a bit less so), but T & V are Cretaceous, whereas birds apparently date back to the Jurassic.  

Bear in mind that the Cretaceous lasted about 80 million years (longer than the time since the non-avian dinosaurs went extinct), so the presence of primitive members of comparatively modern Neornithine bird groups by the end of the Cretaceous should not be confused with the abundance of Enantiornithine birds without any neornithines earlier in the Cretaceous.

  
OgreMkV



Posts: 3668
Joined: Oct. 2009

(Permalink) Posted: Feb. 17 2015,10:40   

Quote (cryptoguru @ Feb. 17 2015,10:18)
Of course mutations can accumulate indefinitely ... they do.
I'm asking you to prove that random accumulative mutations can create new functional code and not break the original code.

Sure. Here.

Zhao, L., Saelao, P., Jones, C. D. & Begun, D. J. Origin and Spread of de Novo Genes in Drosophila melanogaster Populations. Science (2014). doi:10.1126/science.1248286

and

Wu, D.-D. D., Irwin, D. M. & Zhang, Y.-P. P. De novo origin of human protein-coding genes. PLoS Genet. 7, e1002379 (2011).

Done.
Next.

We don't have to show it mathematically (although, that's trivial). Because it happens in the real world.

--------------
Ignored by those who can't provide evidence for their claims.

http://skepticink.com/smilodo....retreat

   
Wesley R. Elsberry



Posts: 4991
Joined: May 2002

(Permalink) Posted: Feb. 17 2015,10:41   

Cryptoguru at the plate:

 
Quote

Avida cheats on 2 accounts, it rewards micro-feature improvements by testing if a logic function (target) has been achieved on mutation and not simply on the performance of the resultant organism ... and it only requires a small amount of new information to generate new features (e.g. 9 commands can perform EQU). ORFan genes represent thousands of unique sequences of base-pairs that must be demonstrated can arrive through simple mutation and natural selection.


Three swings, three misses.

First, I have on at least two prior occasions corrected Cryptoguru's bizarre hallucinations regarding Avida and awarding merit. There is no merit to Cryptoguru's first claim.

Second, it is an interesting claim there, that a 9-instruction Avida program exists to instantiate EQU. The shortest known such program mentioned in the 2003 paper was 17 instructions long.

So let's see it, please. Let's have the listing so that we can confirm this discovery. Otherwise, it looks like just one more made-up dismissal, and since that is *all* that Cryptoguru has proven capable of before when it comes to Avida, I'm not going to waste time extending the benefit of doubt on this point.

The only "cheating" going on concerns Cryptoguru trying to be able to dismiss something he plainly has not a single clue about.

Third, the assertion that ORFans must be thousands of bases in length shows Cryptoguru apparently knows bugger-all about ORFans, too.

 
Quote

Das et al. noted that the sequence length distribution for the orphan genes, in the initial annotations of the yeast genome, peaks at 100–110 codons, which is closer to the arbitrary minimum length cut-off of 100 codons used in the original ORF definition


Fukuchi S and Nishikawa K. 2004. "Estimation of the number of authentic orphan genes in bacterial genomes." DNA Res. 2004 Aug 31;11(4):219-31, 311-313.)

That indicates that a bunch of ORFans exist with lengths shorter than where the distribution peaks.

(Alternatively, Cryptoguru might say that he meant that in sum, a genome's ORFans represent thousands of bases of sequence, but then that would be utterly irrelevant to an argument about the coding of any particular ORFan and thus stupid for him to bring up, so I'll go with the interpretation that leads to an inference of mere ignorance.)

--------------
"You can't teach an old dogma new tricks." - Dorothy Parker

    
NoName



Posts: 2729
Joined: Mar. 2013

(Permalink) Posted: Feb. 17 2015,10:44   

Quote (cryptoguru @ Feb. 17 2015,10:39)
...
Let me rephrase my original question again, because it seemed to keep getting lost in piles of straw men.
Show me a mechanism that can generate the equivalent information of an ORFan gene (i.e. significant amount of new genetic material, not just a couple of point mutations in regulatory genes that switch other code off/on) using only random mutations and an environmentally driven competition model (i.e. doesn't cheat by rewarding micro-feature improvements that wouldn't be selectable in a natural environment.)
...

I've bolded and italicized the  2 entirely unwarranted and unjustified assumptions that prejudice the result, oddly enough, in your favor.
Duplication and modification of the duplicate suffices.

  
cryptoguru



Posts: 53
Joined: Jan. 2015

(Permalink) Posted: Feb. 17 2015,10:45   

Quote
Cretaceous birds are often "modern" in some aspects while not in others

Incorrect, birds have been found in modern form ... and this parrot!
http://www.berkeley.edu/news....il.html
Where are the transitional forms? We just have Archaeopteryx, which could be argued is a Mendelian variant on a modern day Hoatzin ... or equally argued a distinct avian variety that is extinct.

Quote
Descent of birds from theropods is not an "assumption", but a comclusion, based on cladistic analysis of data from comparative anatomy

Cladistic analysis is extremely subjective, you can make it say what you want. That's synonymous with an assumption. Lot's of evolutionists don't accept the dinos->bird story anyway ... so we creationists are not the only ones banging this drum.

But let's leave the bird chat to later ... I don't want to go off-topic yet.

  
N.Wells



Posts: 1836
Joined: Oct. 2005

(Permalink) Posted: Feb. 17 2015,10:48   

Quote
Let me rephrase my original question again, because it seemed to keep getting lost in piles of straw men.
Show me a mechanism that can generate the equivalent information of an ORFan gene (i.e. significant amount of new genetic material, not just a couple of point mutations in regulatory genes that switch other code off/on) using only random mutations and an environmentally driven competition model (i.e. doesn't cheat by rewarding micro-feature improvements that wouldn't be selectable in a natural environment.)
Avida cheats on 2 accounts, it rewards micro-feature improvements by testing if a logic function (target) has been achieved on mutation and not simply on the performance of the resultant organism ... and it only requires a small amount of new information to generate new features (e.g. 9 commands can perform EQU). ORFan genes represent thousands of unique sequences of base-pairs that must be demonstrated can arrive through simple mutation and natural selection.

For those who may be tempted to argue that you don't need to prove anything algorithmically, I've previously shown that the physical evidence is open to interpretation .... but even if it wasn't, you should be able to demonstrate that the general theory of evolution applied to biology can work in principle. (random mutation plus competition can create significantly quantifiable, more complex and apparently designed solutions to problems). We can't use known targets for this, or it is simply a stochastic search and not evolution. Mutation should also allow degeneration of functionality, in the genome, all the organism's functionality can be affected by mutation; even it's most basic operations are defined and built by the code itself. Therefore mutations should be able to break replication and all other basic survival processes of the organism, not only shuffle some existing functionality.


Although the public is mostly aware of mutations that have bad effects, the majority of mutations have no effect whatsoever, but some are indeed beneficial.  "Disadvantageous" and "beneficial" can also depend on context.  One form of mutation that happens quite commonly (in geological terms in some types of organisms is whole-genome duplication: this is how many plants have become garden-plant ornamentals and crop plants for food.  Duplication of smaller numbers of genes can be helpful by providing back-ups for key genes that might fail, or workable genetic material that can get modified later (the immune system and the vision system have benefitted from multiple versions of genes that have been slightly modified by minor mutations.  Myostatin-blocker mutations offer some obvious benefits for their possessors, along with some potential disadvantages, depending on which blocker mutation we are considering, so there it is a matter of whether the advantages outweigh the disadvantages in any given situation or not.  Lenski's E.coli becoming able to live on a new food resource was a significant novelty arrived at by mutation.

  
N.Wells



Posts: 1836
Joined: Oct. 2005

(Permalink) Posted: Feb. 17 2015,10:55   

Quote (cryptoguru @ Feb. 17 2015,10:45)
Quote
Cretaceous birds are often "modern" in some aspects while not in others

Incorrect, birds have been found in modern form ... and this parrot!
http://www.berkeley.edu/news.......il.html
Where are the transitional forms? We just have Archaeopteryx, which could be argued is a Mendelian variant on a modern day Hoatzin ... or equally argued a distinct avian variety that is extinct.

Quote
Descent of birds from theropods is not an "assumption", but a comclusion, based on cladistic analysis of data from comparative anatomy

Cladistic analysis is extremely subjective, you can make it say what you want. That's synonymous with an assumption. Lot's of evolutionists don't accept the dinos->bird story anyway ... so we creationists are not the only ones banging this drum.

But let's leave the bird chat to later ... I don't want to go off-topic yet.

That agrees with what I said.  That fossil is a Neornithine from the very end of the Cretaceous (65-70 m.y. ago, Maastrichtian: http://www.nature.com/nature....a0.html ), after Neornithines began to replace enantiornithines, which began about 80 million years ago.  Most Cretaceous birds, through most of the Cretaceous, were markedly more primitive and not like modern birds in their details.

  
OgreMkV



Posts: 3668
Joined: Oct. 2009

(Permalink) Posted: Feb. 17 2015,11:02   

Crypto, Archaeopteryx is a bird? Are you sure?

Table of archaeopteryx features

1 = present; * = present in some; ? = possibly present; x = absent
    Dinosaurs           Archae            Birds
1        *                  1                1
2        x                  1                1
3        *                  1                1
4        *                  1                1
5        x                  x                1
6        x                  x                1
7        *                  x                1
8        *                  1                x
9        1                  1                x
10       1                  1                x
11       1                  1                x
12       1                  1                x
13       1                  1                x
14       1                  1                x
15       1                  1                x
16       6                  6            11-23
17       1                  1                x
18       1                  1                *
19       1                  1                x
20       1                  1                x
21       1                  1                x
22       1                  1                x
23       1                  1                x

From Talk origins and references are here: http://www.talkorigins.org/faqs....fo.html

--------------
Ignored by those who can't provide evidence for their claims.

http://skepticink.com/smilodo....retreat

   
Wesley R. Elsberry



Posts: 4991
Joined: May 2002

(Permalink) Posted: Feb. 17 2015,11:14   

Speaking of going off-topic, Cryptoguru missed an important step:

Admitting that his original "challenge" has been met.

After that, he can set up another challenge. But until that time, it would be off-topic to treat Cryptoguru's digression as anything other than exactly that.

--------------
"You can't teach an old dogma new tricks." - Dorothy Parker

    
cryptoguru



Posts: 53
Joined: Jan. 2015

(Permalink) Posted: Feb. 17 2015,11:15   

Wesley R. Elsberry: sorry, you are correct ... it was 17 .. which is still trivial from a cumulative search point of view.
In fact it's always a trivial problem if you set targets at that level.

I do understand how it works

Avida selects by using complete logic gates plus IO as symbols, this could be compared to bacterial "evolution", which is accomplished by swapping entire operons (multiple genes) on one plasmid symbol. I agree that swapping out an entire chromosome is large enough to select on. But, a nucleotide is waaay too small a symbol to select for universally in multi-cellular organisms, except of course for a few edge cases where a point mutation happens to have the effect of switching on/off a whole gene ... but this cannot explain the arrival of new information.

A single improvement needs to have an increase in fitness of greater than 10% (probably more like 50%) to be selected over environmental noise.

Also, you would need less than 1 average symbol mutation per organism  per generation to keep any advantages you have accrued. There are thousands more "neutral" or bad mutations compared to advantages, so there's no way to hold any good ground you may have covered in your previous mutations.

Also, only bacteria have hundreds or thousands of offspring. These evolutionary algorithms only work in large populations with small mutation rates. Mammals particularly don't have hundreds of children.

So as I was saying, you may be able to demonstrate a simple shuffling on the order of bacterial operons, with large populations and very short generation lengths. But anything more complex cannot be modelled by Avida or anything else, and to a mathematician like me ... seems utterly dumb!

Maybe others are fooled when you use really long time scales ... but the complexity ramps up exponentially from these simple toy problems you're solving with programs like Avida. You don't have anywhere near enough time .. and even if you did, you wouldn't be able to keep hold of any benefits anyway. This is what we observe.

  
N.Wells



Posts: 1836
Joined: Oct. 2005

(Permalink) Posted: Feb. 17 2015,11:36   

Quote (cryptoguru @ Feb. 17 2015,10:45)
               
Quote
Cretaceous birds are often "modern" in some aspects while not in others

Incorrect, birds have been found in modern form ... and this parrot!
http://www.berkeley.edu/news.......il.html
Where are the transitional forms? We just have Archaeopteryx, which could be argued is a Mendelian variant on a modern day Hoatzin ... or equally argued a distinct avian variety that is extinct.

               
Quote
Descent of birds from theropods is not an "assumption", but a comclusion, based on cladistic analysis of data from comparative anatomy

Cladistic analysis is extremely subjective, you can make it say what you want. That's synonymous with an assumption. Lot's of evolutionists don't accept the dinos->bird story anyway ... so we creationists are not the only ones banging this drum.

But let's leave the bird chat to later ... I don't want to go off-topic yet.


Sorry, a little more on birds, since you brought it up and unloaded a pile of manure.

You are just tossing words in the air.  Cladistic analyses are closer to objective than subjective.

From Jaime Headden at https://qilong.wordpress.com/2013.......ding-me                
Quote
Cladistic analysis is a robust, ever improving process of using mathematical algorithms to find “best-fit” arrangements of fixed morphological sequences to unfixed species arrangements, and under various assumptions (all spelled out and clear) how robust this data is and how “well” these species are arranged in comparison to variation in the resultant trees.


One could throw an analysis by ignoring a bunch of data (the Birds Are Not Dinosaurs people have done this repeatedly by removing characters that link birds to dinosaurs), but it is obvious when that happens, and any competent re-analysis shows when this happened.  It's blazingly obvious.  See http://dml.cmnh.org/2001Feb....05.html

With regard to where the transitional forms are, bear in mind that the nature of a transitional form (particularly structural intermediates and stem forms, rather than a guaranteed blood-line ancestor; a great-uncle rather than a grandfather if you will) between A & B is that you can't tell whether it belongs to the A or B lineage.  In this regard, Archaeopteryx, Anchiornis, Xiaotingia, Eosinopteryx, Aurornis, Jinfengopteryx, and scansoriopterygians are excellent examples of of creatures that are extremely hard to identify as basal troodontids, basal dromaeosaurs, basal "birds", or other small side-branches near the bottom of the same bush.  They show quite well what the ancestor to birds must have looked like, because it is highly unlikely that all their many shared characteristics were all separately but identically evolved from an entirely different common ancestor. (One or two features can be evolved convergently, but that is unlikely for all of them, including nonfunctional features and features with very different functions.)

Hoatzins differ from Archaeopteryx in having fused carpals and metacarpals, fusion of the astragalus and the calcaneum, fusion of that into a fused tarsometatarsus, lighter (more hollow) bones, a stronger supracoracoideus muscle that goes over a bony process lacking in Archaeopteryx, lots of heterocoelous cervical vertebrae, many more vertebrae fused into the sacrum, a retroverted hallux (apparently lacking in Archaeopteryx on the basis of the most recent restudy), a short pygostyle-type tail, a strut-like coracoid, a sternum that is both bony and fused, reduced manual unguals, flattened manual phalanx II-1, no pubic symphysis or foot, a highly retroverted pubis, trochanteric crest, hypotarsus, no teeth, no third-finger claws, no long ascending astragalar process, no interdental plates, no obturator process of the ischium, no long chevrons in the tail, and no abdominal ribs.  Other than that, dang near identical (snark, if that wasn't clear).  If all that is available to "Mendelian variations" (a few different alleles), then you ascribe much greater evolutionary powers to minor mutational differences than I do.

Edited to add: I see OgreMkV got there first with much the same information, while I was busy typing things like "no pubic symphysis".

Note the irony in your dissing cladistics by asserting (wrongly) that "Cladistic analysis is extremely subjective, you can make it say what you want", while in the exact same post you made the completely subjective but objectively totally wrong statement, "Archaeopteryx, which could be argued is a Mendelian variant on a modern day Hoatzin".  Sorry, based on that performance, I'll take science over you any day.

  
cryptoguru



Posts: 53
Joined: Jan. 2015

(Permalink) Posted: Feb. 17 2015,17:58   

N.Wells: last thing on the bird topic for now ...

Quote
while in the exact same post you made the completely subjective but objectively totally wrong statement


That is my point, if I wanted to I could use cladistics to assert that Archaeopteryx is directly related to Hoatzin. I can do what I like with cladistics ... it'll only be an "accepted answer" if it supports the pre-existing evolutionary assumption of common descent.

Cladistics is just terminology that means "hey this looks like this and does the same sort of thing, therefore one of them morphed into the other over time" ... but tries to make it sound like proper science. Actually Phylogenetic Systematics sounds even more sciency doesn't it, you should probably use that next time to convince the ignorant creationist that you're doing some really heavily objective analytical stuff.
Ancestry is assumed, therefore it is circular reasoning whether you use a Consistency Index or a Retention Index.
It's just fancy language designed to make it sound like you're doing something way more advanced than pointing at animals and saying "cow goes moo" ... "sheep goes baaa".

Let's get back to the genome discussion, which is much less slippery. In my last post I put forth a coherent argument for why I think evolution of multi-cellular organisms is impossible ... explain how I am wrong without either just saying "you are wrong" or "you don't understand evolution" ... or doing what McOgre does and linking to articles without explaining how they apply to the argument. e.g. "here's 5 articles I'm linking to, if you read them all you will see I'm completely correct and you are completely wrong"

You keep assuming Common Descent in your argument, which is circular reasoning ... I don't accept CD for the origin of different kinds of living things. I believe in variation within a kind, which is what we observe. We see dogs become hugely variant different types of dogs (in that case artificially bred by humans), not by evolution but by standard Mendelian genetics. We don't see them becoming something other than a dog ... the genome restricts the limit of variation. You may want to call them new species of dog because they look different, but they are still dogs and my toddler could identify that.

Your assumption of evolution has led you down the path that you have to be able to explain the morphology of one kind of animal to the next ... we don't see that in the fossil record, or happening now. Sure you can pick an animal out that looks similar to another and claim it's an ancestor, but you have absolutely no evidence for this assertion except for the fact you believe the rock layers denote different ages of history and you believe that all living organisms on earth came from one blob of soup.
So my point stands, claiming one thing evolved from another because they look similar is begging the question ... you have to assume Common Descent, and even with that assumption you can't prove that fossil you're holding ever had any offspring.

  
Cubist



Posts: 558
Joined: Oct. 2007

(Permalink) Posted: Feb. 17 2015,18:05   

Quote (cryptoguru @ Feb. 17 2015,09:39)
I'm back through popular demand ... can't be bothered to read through all the replies since I last visited.

Okey-dokey. I'll just cut-and-paste from one of those earlier replies that you "can't be bothered to read", in the hope that this time you'll actually define your terms and clarify WTF you mean and all that good stuff.

Or if you choose to continue with the bafflegab, that's good, too.

Re-posting the paragraph about how come it's gotta be both "new" and "novel" which you ignored: Why must the "genetic material" of "new information" be both "new" and "novel"? I ask because "new" and "novel" strike me as basically synonymous, hence, using both words is gratuitous redundancy. But perhaps you weren't being redundant; perhaps you actually are using distinct referents for "new" and "novel", such that the two words are not, in fact, gratuitously redundant. Please explain how "genetic material" which is "new" differs from "genetic material" which is "novel".  Is it possible for "genetic material" to be "new" without also being "novel"? Is it possible for "genetic material" to be "novel" without also being "new"?

Perhaps you'll deign to honor the questions in that paragraph with answers, cryptoguru. Or not. [shrug]

Onward.

     
Quote
     
Quote
Does the mutated nucleotide sequence qualify as "new and novel genetic material"? Does the mutated nucleotide sequence contain any "new and novel genetic material"?

The issue here is one of scale ... changing a single nucleotide and getting new functionality is more adequately describing a side-effect of switching a control gene rather than amazingly arriving at a new functional sequence through mutation and selection.

You may be right that "scale" is, indeed, the "issue". But regardless of whether or not "scale" is any kind of "issue" anywhere, I note that you didn't answer either of the questions in the text you quoted. That's okay, I can ask those questions again.

[clears throat]

Let's say that Sequence X is the arbitrary 150-nucleotide sequence "gcc tac agg gat cgt ggg gac ctt acg aat ggc ctt ttt gac tat tct tcg aat cta agc tca gca tca ttc ccg tct acg gga agt ccc ttc cca ata cat atc ctc ggc acc gca ctt gca ggc tca cgc ttc gcg tca ttt agg tca". Let's also say that Sequence X1 is the 149-nucleotide sequence "gcc tac agg gac gtg ggg acc tta cga atg gcc ttt ttg act att ctt cga atc taa gct cag cat cat tcc cgt cta cgg gaa gtc cct tcc caa tac ata tcc tcg gca ccg cac ttg cag gct cac gct tcg cgt cat tta ggt ca" that results when one removes the "t" from the fourth codon in Sequence X.

One: Does Sequence X1 qualify as "new and novel genetic material"? It's a yes-or-no question, cryptoguru; either yes, Sequence X1 does, in fact, qualify as "new and novel genetic material", or no, Sequence X1 does not, in fact, qualify as "new or novel genetic material". It's all well and good to go on about "probability" and "scale" and yada yada, but I really would like to see a yes or a no, and thus far, I ain't seen a yes or a no.

Two: Does Sequence X1 contain any "new and novel genetic material"? Again, it's a yes-or-no question, to which either yes, it does or no, it doesn't would both be relevant responses. Going on about "scale" and "probability" and yada yada, contrariwise, is not a particularly relevant response, as best I can tell.

 
Quote
So evolution claims that all the differences between a chimp's DNA and ours are caused by random mutation on 2 hereditary lines from a common ancestor. Find a sequence of unique DNA in the human genome (yup you can use the "junk DNA" now too, now we know it's not junk). Now that string you're holding has arrived by random mutation ... selection has preserved it, but mutation created it. That's what I mean by new/novel/unique information.

That's nice. You didn't mention "unique" before. Please explain how "genetic material" which is "unique" differs from "genetic material" which is either "new" or "novel".  Is it possible for "genetic material" to be "unique" without also being either "new" or "novel"? Is it possible for "genetic material" to be "novel" without also being "new" or "novel"?

Does Sequence X1 qualify as "unique"?

     
Quote
You may be able to handwave that the switching of a few control genes could happen randomly…

I'm not handwaving a thing, cryptoguru. I'm attempting to get you to explain the meaning of your statement that "New information is new and novel genetic material…".

     
Quote
So to summarise my answer ... when I'm talking about new information ... I'm talking about a unique DNA sequence in an organism.

Groovy. Is Sequence X1 a "unique" DNA sequence?

  
Doc Bill



Posts: 1039
Joined: April 2007

(Permalink) Posted: Feb. 17 2015,19:28   

Quote (cryptoguru @ Feb. 17 2015,17:58)
N.Wells: last thing on the bird topic for now ...

Quote
while in the exact same post you made the completely subjective but objectively totally wrong statement


That is my point, if I wanted to I could use cladistics to assert that Archaeopteryx is directly related to Hoatzin. I can do what I like with cladistics ... it'll only be an "accepted answer" if it supports the pre-existing evolutionary assumption of common descent.

Cladistics is just terminology that means "hey this looks like this and does the same sort of thing, therefore one of them morphed into the other over time" ... but tries to make it sound like proper science. Actually Phylogenetic Systematics sounds even more sciency doesn't it, you should probably use that next time to convince the ignorant creationist that you're doing some really heavily objective analytical stuff.
Ancestry is assumed, therefore it is circular reasoning whether you use a Consistency Index or a Retention Index.
It's just fancy language designed to make it sound like you're doing something way more advanced than pointing at animals and saying "cow goes moo" ... "sheep goes baaa".

Let's get back to the genome discussion, which is much less slippery. In my last post I put forth a coherent argument for why I think evolution of multi-cellular organisms is impossible ... explain how I am wrong without either just saying "you are wrong" or "you don't understand evolution" ... or doing what McOgre does and linking to articles without explaining how they apply to the argument. e.g. "here's 5 articles I'm linking to, if you read them all you will see I'm completely correct and you are completely wrong"

You keep assuming Common Descent in your argument, which is circular reasoning ... I don't accept CD for the origin of different kinds of living things. I believe in variation within a kind, which is what we observe. We see dogs become hugely variant different types of dogs (in that case artificially bred by humans), not by evolution but by standard Mendelian genetics. We don't see them becoming something other than a dog ... the genome restricts the limit of variation. You may want to call them new species of dog because they look different, but they are still dogs and my toddler could identify that.

Your assumption of evolution has led you down the path that you have to be able to explain the morphology of one kind of animal to the next ... we don't see that in the fossil record, or happening now. Sure you can pick an animal out that looks similar to another and claim it's an ancestor, but you have absolutely no evidence for this assertion except for the fact you believe the rock layers denote different ages of history and you believe that all living organisms on earth came from one blob of soup.
So my point stands, claiming one thing evolved from another because they look similar is begging the question ... you have to assume Common Descent, and even with that assumption you can't prove that fossil you're holding ever had any offspring.

Creepto, common descent is a conclusion based on observation of the evidence, not an assumption.

How fucking stupid are you having been told that countless times not to get it?

Please, Creepto fuck head, provide evidence that common descent is an assumption.

Right, I didn't think so.

  
N.Wells



Posts: 1836
Joined: Oct. 2005

(Permalink) Posted: Feb. 17 2015,19:28   

Quote (cryptoguru @ Feb. 17 2015,17:58)
N.Wells: last thing on the bird topic for now ...

     
Quote
while in the exact same post you made the completely subjective but objectively totally wrong statement


That is my point, if I wanted to I could use cladistics to assert that Archaeopteryx is directly related to Hoatzin. I can do what I like with cladistics ... it'll only be an "accepted answer" if it supports the pre-existing evolutionary assumption of common descent.

Cladistics is just terminology that means "hey this looks like this and does the same sort of thing, therefore one of them morphed into the other over time" ... but tries to make it sound like proper science. Actually Phylogenetic Systematics sounds even more sciency doesn't it, you should probably use that next time to convince the ignorant creationist that you're doing some really heavily objective analytical stuff.
Ancestry is assumed, therefore it is circular reasoning whether you use a Consistency Index or a Retention Index.
It's just fancy language designed to make it sound like you're doing something way more advanced than pointing at animals and saying "cow goes moo" ... "sheep goes baaa".

Let's get back to the genome discussion, which is much less slippery. In my last post I put forth a coherent argument for why I think evolution of multi-cellular organisms is impossible ... explain how I am wrong without either just saying "you are wrong" or "you don't understand evolution" ... or doing what McOgre does and linking to articles without explaining how they apply to the argument. e.g. "here's 5 articles I'm linking to, if you read them all you will see I'm completely correct and you are completely wrong"

You keep assuming Common Descent in your argument, which is circular reasoning ... I don't accept CD for the origin of different kinds of living things. I believe in variation within a kind, which is what we observe. We see dogs become hugely variant different types of dogs (in that case artificially bred by humans), not by evolution but by standard Mendelian genetics. We don't see them becoming something other than a dog ... the genome restricts the limit of variation. You may want to call them new species of dog because they look different, but they are still dogs and my toddler could identify that.

Your assumption of evolution has led you down the path that you have to be able to explain the morphology of one kind of animal to the next ... we don't see that in the fossil record, or happening now. Sure you can pick an animal out that looks similar to another and claim it's an ancestor, but you have absolutely no evidence for this assertion except for the fact you believe the rock layers denote different ages of history and you believe that all living organisms on earth came from one blob of soup.
So my point stands, claiming one thing evolved from another because they look similar is begging the question ... you have to assume Common Descent, and even with that assumption you can't prove that fossil you're holding ever had any offspring.


"That is my point, if I wanted to I could use cladistics to assert that Archaeopteryx is directly related to Hoatzin."  Then you made your point unbelievably badly and you do not understand cladistics.  You made a noncladistic assertion that was wrong, without any evidence.  Cladistics does not work the way you say: it is a statistical analysis of similarity akin to cluster analysis and in its fundamental form without shortcuts no assumptions of ancestry are needed to perform the analysis.  Cladistics would (entirely legitimately, if pointlessly) pair hoatzins and the Archaeopteryx as sister groups if and only if you had no other birds (even an enantiornithine) and no other maniraptorans in the analysis (for example in an analysis of a beetle, a newt, an elephant, Archaeopteryx, and the hoatzin).  Otherwise, you would need to lie and make up or delete data in order to create a desired outcome, but that would be obvious the moment anyone checked your data or redid your analysis.

If you pay attention to my words, I never claim "direct ancestry" when dealing with fossils, precisely because that cannot be known.  I claim degrees of similarity from which I infer degrees of relatedness, and I use words like "structural intermediate" and "stem members" and "basal forms", and I will say that one animal is the closest candidate that we currently know of to the ancestry of a group.  If you are going to argue over something, get your facts right and don't argue about strawmen.

In the same vein, you are apparently under a delusion that change through recombination does not constitute evolutionary change (even below the level of speciation).  Again, you might try arguing with argue with real issues, rather than your misunderstandings of them.

Your claim that the Archaeopteryx is a "Mendelian variant" of the hoatzin is a more extreme assertion of ancestry than anything I care to make.  However, if you could show that you could get from the one to the other by genetic recombination you would in fact have lost your war: you would have just demonstrated an easy transition across a very large morphological/anatomical distance (did you not understand the lists that OgreMvK and I provided?) and you would have demonstrated that evolution is much easier than I think it is, let alone than you think it is.


Edited to add: I want to add to something Doc Bill said.  You keep saying that biologists assume evolution, and people keep replying that it's a conclusion, not an assumption.  Just as in day-to-day physics people do not go about re-proving Newtonian mechanics and the electron theory of electricity, biologists find the evidence in favor of evolution to be so overwhelming that they spend very little time directly testing the overall idea and instead spend most of their time trying to expand on the theory of evolution and to test its predictions and implications and find some new wrinkles.  In that sense one could say that there is a sort of an assumption of evolution.  However, evolutionary theory has passed so many tests that biologists see it as proven.  Also, if it were false, standard ongoing research would be generating endless quantities of enigmas and contradictions each year, and that is just not happening.  The fact that there are people who must reject the evidence because of their religious beliefs and because they clearly don't understand it does not enter into the calculation.  Geographers do not put off making maps while awaiting yet another test of the spherical earth theory just because there are still a few vocal flat-earthers out there.  Until you show that your criticisms are founded in knowledge rather than ignorance and blindness (or, somewhat more likely, until fundamentalist republicans get their act together to the extent of defunding the sciences they don't like), your objections are not going to be relevant.

  
The whole truth



Posts: 1554
Joined: Jan. 2012

(Permalink) Posted: Feb. 17 2015,19:42   

Quote (cryptoguru @ Feb. 17 2015,15:58)
N.Wells: last thing on the bird topic for now ...

Quote
while in the exact same post you made the completely subjective but objectively totally wrong statement


That is my point, if I wanted to I could use cladistics to assert that Archaeopteryx is directly related to Hoatzin. I can do what I like with cladistics ... it'll only be an "accepted answer" if it supports the pre-existing evolutionary assumption of common descent.

Cladistics is just terminology that means "hey this looks like this and does the same sort of thing, therefore one of them morphed into the other over time" ... but tries to make it sound like proper science. Actually Phylogenetic Systematics sounds even more sciency doesn't it, you should probably use that next time to convince the ignorant creationist that you're doing some really heavily objective analytical stuff.
Ancestry is assumed, therefore it is circular reasoning whether you use a Consistency Index or a Retention Index.
It's just fancy language designed to make it sound like you're doing something way more advanced than pointing at animals and saying "cow goes moo" ... "sheep goes baaa".

Let's get back to the genome discussion, which is much less slippery. In my last post I put forth a coherent argument for why I think evolution of multi-cellular organisms is impossible ... explain how I am wrong without either just saying "you are wrong" or "you don't understand evolution" ... or doing what McOgre does and linking to articles without explaining how they apply to the argument. e.g. "here's 5 articles I'm linking to, if you read them all you will see I'm completely correct and you are completely wrong"

You keep assuming Common Descent in your argument, which is circular reasoning ... I don't accept CD for the origin of different kinds of living things. I believe in variation within a kind, which is what we observe. We see dogs become hugely variant different types of dogs (in that case artificially bred by humans), not by evolution but by standard Mendelian genetics. We don't see them becoming something other than a dog ... the genome restricts the limit of variation. You may want to call them new species of dog because they look different, but they are still dogs and my toddler could identify that.

Your assumption of evolution has led you down the path that you have to be able to explain the morphology of one kind of animal to the next ... we don't see that in the fossil record, or happening now. Sure you can pick an animal out that looks similar to another and claim it's an ancestor, but you have absolutely no evidence for this assertion except for the fact you believe the rock layers denote different ages of history and you believe that all living organisms on earth came from one blob of soup.
So my point stands, claiming one thing evolved from another because they look similar is begging the question ... you have to assume Common Descent, and even with that assumption you can't prove that fossil you're holding ever had any offspring.

Wow, there are so many things wrong with what you preach.

With this in mind:

"You keep assuming Common Descent in your argument, which is circular reasoning ... I don't accept CD for the origin of different kinds of living things. I believe in variation within a kind, which is what we observe. We see dogs become hugely variant different types of dogs (in that case artificially bred by humans), not by evolution but by standard Mendelian genetics. We don't see them becoming something other than a dog ... the genome restricts the limit of variation. You may want to call them new species of dog because they look different, but they are still dogs and my toddler could identify that."

Tell me about the insects that were taken on the so-called ark during the alleged year long, world wide flud 4,000 years ago. There were just two insects (one pair of one 'kind'), right? A male and a female, right? Which species were they? How did that pair of insects become all of the insect species that have existed since the flud?

In regard to some non-insect critters, what about the microscopic arachnids that live in/on peoples' skin (including yours) and the skin of other mammals? There was just one pair of one species (one pair of one 'kind') of them on the ark, right? Which person's or animal's skin did that pair live in/on during the flud and how did noah know that he was taking just one pair of one species on the ark? If he had taken more than one pair he would have been defying a command from 'God', right? And did that pair of microscopic arachnids become, without evolving, all of the species of arachnids that have existed since the flud? If that pair wasn't the source of all post-flud arachnids, which other pair of one arachnid species was?

--------------
Think not that I am come to send peace on earth: I came not to send peace, but a sword. - Jesus in Matthew 10:34

But those mine enemies, which would not that I should reign over them, bring hither, and slay them before me. -Jesus in Luke 19:27

   
N.Wells



Posts: 1836
Joined: Oct. 2005

(Permalink) Posted: Feb. 17 2015,20:07   

Quote
Which person's or animal's skin did that pair live in/on during the flud and how did noah know that he was taking just one pair of one species on the ark? If he had taken more than one pair he would have been defying a command from 'God', right?

And which of Noah's family carried syphilis, which one had gonorrhea, who had AIDS, who had chlamydia, who carried smallpox, who had measles, who had chickenpox, who carried rubella, who had tapeworms, who had guinea worm, who had HPV, who had genital herpes, who had trichomoniasis, who had all the pubic lice and head lice, etc., etc., etc. and how did they manage to care for the animals while suffering from all those diseases and parasites, let alone walk off the ark and repopulate the planet?

  
fnxtr



Posts: 3504
Joined: June 2006

(Permalink) Posted: Feb. 17 2015,22:19   

Holy crap.

Did he really just use the Crockoduck Argument?

Game, set, and match.

--------------
"[A] book said there were 5 trillion witnesses. Who am I supposed to believe, 5 trillion witnesses or you? That shit's, like, ironclad. " -- stevestory

"Wow, you must be retarded. I said that CO2 does not trap heat. If it did then it would not cool down at night."  Joe G

  
The whole truth



Posts: 1554
Joined: Jan. 2012

(Permalink) Posted: Feb. 17 2015,22:40   

cryptoguru, I don't recall anyone here claiming that different dog breeds are different species.

If someone were to claim that, why would it bother you? The only reason would seem to be that you don't accept the fact (or even the idea) that there are different species of biological entities, whether they be different species of dogs (canids) or anything else, and it appears that you lump all biological entities into 'kinds'.

How many 'kinds' are there right now, and what 'kinds' are they? How many 'kinds' were originally created on Earth by your chosen, so-called 'God', and what 'kinds' were they? How many 'kinds' were there on Earth the day before the flud started, and what 'kinds' were they? How many 'kinds' were  taken on the ark, and what 'kinds' were they? How many 'kinds' got off the ark after the flud, and what 'kinds' were they? How many 'kinds' were there on Earth 1000 years, 2000 years, and 3000 years after the flud, and what 'kinds' were they? And on what basis do (or could) you know any of that?

And one more question for now: If you had a great, great, great, great, great, great, great, great, great aunt, would it be accurate to label her as one of your ancestors?

Edited by The whole truth on Feb. 17 2015,20:46

--------------
Think not that I am come to send peace on earth: I came not to send peace, but a sword. - Jesus in Matthew 10:34

But those mine enemies, which would not that I should reign over them, bring hither, and slay them before me. -Jesus in Luke 19:27

   
Wesley R. Elsberry



Posts: 4991
Joined: May 2002

(Permalink) Posted: Feb. 18 2015,05:23   

Quote (cryptoguru @ Feb. 17 2015,11:15)
Wesley R. Elsberry: sorry, you are correct ... it was 17 .. which is still trivial from a cumulative search point of view.
In fact it's always a trivial problem if you set targets at that level.


26^17 ~= 10^24, which looks like a pretty non-trivial problem space. Even Cryptoguru's fake number of 9 instructions for EQU leads to 26^9 ~= 10^12, which would be an excessively large for a lottery. Powerball uses a base space of a bit more than 10^8.

Nor is "cumulative search" appropriate as a dismissal for what is happening in Avida. I've already noted multiple times that Avida is awarding merit on behavior, not on any examination of Avidian genome content.

   
Quote (cryptoguru @ Feb. 17 2015,11:15)

I do understand how it works


Then why is it that pretty much everything Cryptoguru has said about Avida other than that it is a computer program is wrong?

   
Quote (cryptoguru @ Feb. 17 2015,11:15)

Avida selects by using complete logic gates plus IO as symbols,


Wrong. Avidian instructions in the 2003 paper do not correspond to digital circuit logic gates. The functions being awarded merit in the 2003 paper correspond to typical logic functions (AND, OR, NOT, etc.). Cryptoguru is making this into a persistently repeated error.

   
Quote (cryptoguru @ Feb. 17 2015,11:15)

this could be compared to bacterial "evolution", which is accomplished by swapping entire operons (multiple genes) on one plasmid symbol.


What a confused statement. Between the utter ignorance of anything to do with Avida and the confusions about the biology, saying the above declaration is worthless insults rubbish. "Plasmid symbol" is apparently jargon from the "Bioshock" game. Nor is Avida limited to broad-brush analysis as Cryptoguru claims, which he should now by now because I told him before:

   
Quote

This is not in the original challenge, and is thus irrelevant to answering the original challenge. The Avida instruction set includes "mov-head", "jump-head", and "set-flow", which can and do change expression dramatically. Avida itself has been used to perform in silico experimentation on overlapping genes:
               
   
Quote

One consequence of overlapping genes is to reduce the tolerance for mutation. Virtual experiments conducted within the past several years using a software system called Avida have indicated that overlapping reduces the probability of accumulating so-called neutral mutations in a gene (mutations that have no effect). Neutral mutations are unlikely with overlapping genes, because the mutation must have no effect on two genes with different reading frames.



You can't do experimentation about overlapping genes if your model doesn't permit changes within its gene model. QED.

But wait, there's more... some time back, Cryptoguru made a different claim about level of Avidian genome:

   
Quote

Section D:
comparison of AVIDA to biological evolution
1) an analogy must be drawn between AVIDA commands and the genome
2) it possibly makes most sense (I concede) to assume that AVIDA commands are analogous to codons (and not proteins), so that any mutation will always create a set of valid codons.
3) the level AVIDA is selecting at is therefore analogous to a folded functional protein.


That this is entirely incompatible with the new claim that Avida only acts on multi-genic blocks is evident.

   
Quote (cryptoguru @ Feb. 17 2015,11:15)

I agree that swapping out an entire chromosome is large enough to select on. But, a nucleotide is waaay too small a symbol to select for universally in multi-cellular organisms, except of course for a few edge cases where a point mutation happens to have the effect of switching on/off a whole gene ... but this cannot explain the arrival of new information.


The premise was false, thus whatever conclusion was drawn has no validity.

   
Quote (cryptoguru @ Feb. 17 2015,11:15)

A single improvement needs to have an increase in fitness of greater than 10% (probably more like 50%) to be selected over environmental noise.


Um, BS. Effectiveness of selection over drift is a function of a variety of factors conveniently omitted from the above. Nor do I see any authority stating any such thing, nor do I recall any such large change in fitness being mentioned as necessary in my classes or further reading.

   
Quote (cryptoguru @ Feb. 17 2015,11:15)

Also, you would need less than 1 average symbol mutation per organism  per generation to keep any advantages you have accrued. There are thousands more "neutral" or bad mutations compared to advantages, so there's no way to hold any good ground you may have covered in your previous mutations.


Cryptoguru also is confused about the potential of where mutations happen and the actual extent to which they happen. Yes, there are lots more ways things can go wrong than ways they can go right. But selection can both eliminate the bad and preserve the good (assuming those turn up in separate organisms). So, what about Cryptoguru's claim of 1 average base mutation per organism?

From here:

   
Quote

In particular, examination of sequence conservation between humans and primates implies that ~ 38% of coding sites are maintained by selection, and that the net mutation rate is high: U ~ 4.2 per generation. (46)


That's an average of 4.2 SNP mutations per human individual. The notion that 1 is a limit is false. If it were true, the human race would be in a world of hurt from mutational load already. One has to look at the likelihood that a mutation will effect the gene that has accrued an advantage, not just the general mutational load. I discuss the general form of that calculation with respect to the "weasel" program here.

The quoted article covers a variety of limiting factors for selection. Unlike Cryptoguru, it sets things out in a reasonable way and takes notice of actual evidence.

   
Quote (cryptoguru @ Feb. 17 2015,11:15)

Also, only bacteria have hundreds or thousands of offspring. These evolutionary algorithms only work in large populations with small mutation rates. Mammals particularly don't have hundreds of children.


Bacteria don't have hundreds or thousands of offspring, at least not at one time.

Since we were talking about Avida in particular, we once again come up with the simple observation that Cryptoguru is completely clueless on the topic. The Avida environment of the 2003 paper had a limit of 3,600 Avidians. While that is a sizable number, it isn't a large effective population relative to the sorts of biological populations whose members do have hundreds or more offspring at a whack. Nor is the Avida mutation rate "small" by comparison to biological exemplars.

Finally, Cryptoguru knows bugger-all about mammalian biology. It took seconds to find this discussing naked mole rats, a mammal:

   
Quote

Many breeding females in captivity have reared offspring for more than 15 years, and our most fecund female reared >900 pups over her 11-year reign (10).


   
Quote (cryptoguru @ Feb. 17 2015,11:15)

So as I was saying, you may be able to demonstrate a simple shuffling on the order of bacterial operons, with large populations and very short generation lengths. But anything more complex cannot be modelled by Avida or anything else, and to a mathematician like me ... seems utterly dumb!


What seems to me to be utterly dumb is to continue to spout fabricated nonsense about topics one doesn't have a clue about, but Cryptoguru seems eminently comfortable doing just that. Avida is not doing shuffling on the order of bacterial operons. The notion that Avida cannot model anything more complex than what we have been discussing is wrong, too. I've mentioned that before, so one wonders exactly how slow Cryptoguru is on the uptake:

 
Quote

Avida has been used to generate and evaluate UML models and for the generation of firmware for wireless sensors to be deployed in wireless sensor networks, and those are a couple of applications that I knew about before I left MSU back in 2009. MSU got the BEACON grant shortly thereafter, and things have been hot in the lab since then.


   
Quote (cryptoguru @ Feb. 17 2015,11:15)

Maybe others are fooled when you use really long time scales ... but the complexity ramps up exponentially from these simple toy problems you're solving with programs like Avida. You don't have anywhere near enough time .. and even if you did, you wouldn't be able to keep hold of any benefits anyway. This is what we observe.


Wrong again. Cryptoguru hasn't been right often enough to be able to substantiate a claim to have observed anything. I've noted Cryptoguru's complete lack of addressing the math of retaining genetic benefits. Nor would I characterize what Avida has been applied to as being all toy problems. (And that's a list from just one of my former colleagues.)

--------------
"You can't teach an old dogma new tricks." - Dorothy Parker

    
cryptoguru



Posts: 53
Joined: Jan. 2015

(Permalink) Posted: Feb. 18 2015,05:58   

Quote
And which of Noah's family carried syphilis, which one had gonorrhea, who had AIDS, who had chlamydia, who carried smallpox, who had measles, who had chickenpox, who carried rubella, who had tapeworms, who had guinea worm, who had HPV, who had genital herpes, who had trichomoniasis, who had all the pubic lice and head lice, etc., etc., etc. and how did they manage to care for the animals while suffering from all those diseases and parasites, let alone walk off the ark and repopulate the planet?

Hehe that's the stupidest logic I've heard so far on this thread .. maybe next to the guy who talks about the "flud".

The HIV virus that causes AIDS in humans came from a different species, where it wasn't harmful. I don't believe that viruses that are harmful to an organism originated in that organism, observation backs that up. This is similar to bacteria ... which are very useful (good) in certain applications (e.g. digestion, plant decomposition etc), but can be very bad if the wrong bacteria is carried by the wrong organism, or if the balance of a specific bacteria is violated. So no, I don't think all these negative-effect viruses, parasites were carried by Noah & family etc (some may have been) ... but much more likely, they were carried by animals that had a symbiotic relationship with them. (as is the case now)

Quote
Which person's or animal's skin did that pair live in/on during the flud and how did noah know that he was taking just one pair of one species on the ark?

Man ... this is so off-topic it hurts, so very quick answer. Noah was never commanded to take one of every species on the ark, he was told what kinds of animals to take. He wasn't instructed to take fish or microscopic organisms or sea-dwelling mammals or molluscs etc. etc.


Quote
If you pay attention to my words, I never claim "direct ancestry" when dealing with fossils, precisely because that cannot be known.  I claim degrees of similarity from which I infer degrees of relatedness, and I use words like "structural intermediate" and "stem members" and "basal forms", and I will say that one animal is the closest candidate that we currently know of to the ancestry of a group.  If you are going to argue over something, get your facts right and don't argue about strawmen.

OK, so you don't know then ... it isn't hard fact that birds came from dinos? You simply know that there are "degrees of similarity" upon which you are inferring descent.

Quote
You keep saying that biologists assume evolution, and people keep replying that it's a conclusion, not an assumption.  Just as in day-to-day physics people do not go about re-proving Newtonian mechanics and the electron theory of electricity, biologists find the evidence in favor of evolution to be so overwhelming that they spend very little time directly testing the overall idea and instead spend most of their time trying to expand on the theory of evolution and to test its predictions and implications and find some new wrinkles.  In that sense one could say that there is a sort of an assumption of evolution.

A conclusion based on a faulty premise is the wrong conclusion, and holding to it as fact in the face of challenges to the faulty premise is an assumption. Common Descent was assumed to be true by Darwin, this has been accepted as an atheistic axiom. i.e. if you don't believe there's a God, then there was no creation. Therefore, everything must have happened spontaneously and the unlikely spontaneous arrival of life must have started off as a simple cell that natural processes worked on to create the diversity of life that we now see. This is an assumption ... based on the belief in no creator. When you start with that assumption you look at similarities as proof of your assumption, but THAT is circular reasoning. There is no hard evidence to show ancestry from one kind of animal to another, except that you believe it did and you interpret any data in that light. Even when the data disagrees (ORFan genes, no junk DNA, no clear transitional forms in fossils, no observed DNA mutation to produce a fundamentally different organism) you will simply state that perceived contradictions don't actually contradict Common Descent and you will adapt your argument to accommodate the new data somehow without challenging the core assumption.

I am simply pointing out that none of the science you've mentioned proves anything; it only supports your view when you hold to the assumption of Common Descent and a purely natural explanation of all variation must be adhered to. This does not make what you are believing science ... just because you say it is objective, does not make it so.

Quote
Also, if it were false, standard ongoing research would be generating endless quantities of enigmas and contradictions each year, and that is just not happening.

Well yes it does, but unsurprisingly they don't get published as contradictions ... these are the things that creationists comment on that annoy evolutionists. Evolutionists will defend their view of the world irrespective of the data, you seem to have a romantic view of scientists as objective, impartial and purely truth-seeking ... when in fact scientists are human with the need to be recognised, the desire for fame and wealth, the fear of being ridiculed and mocked, the need to fit in and be accepted. Funding is not available to people who have evidence that contradicts the primary axiom that all life can be explained through random mutation and natural selection. Academics who already have influential position and change their mind and reject evolution on the basis of their research are shunned, mocked, sacked from their positions and denied the ability to publish or share their results in the scientific community. This level of censorship and ethnic cleansing has driven most professional scientists who are creationists to keep their mouths shut and toe the party line in fear of not having a job. Some areas of academia will humour anti-evolutionists (e.g. mathematics, engineering), but it is not tolerated in any area of science that has an influence in origins.

Quote
One: Does Sequence X1 qualify as "new and novel genetic material"? It's a yes-or-no question, cryptoguru; either yes, Sequence X1 does, in fact, qualify as "new and novel genetic material", or no, Sequence X1 does not, in fact, qualify as "new or novel genetic material". It's all well and good to go on about "probability" and "scale" and yada yada, but I really would like to see a yes or a no, and thus far, I ain't seen a yes or a no.

Two: Does Sequence X1 contain any "new and novel genetic material"? Again, it's a yes-or-no question, to which either yes, it does or no, it doesn't would both be relevant responses. Going on about "scale" and "probability" and yada yada, contrariwise, is not a particularly relevant response, as best I can tell.

This is the fallacy of many questions (e.g. Do you still beat your wife?) ... it is the rhetorical trick of asking a question that cannot be answered without admitting a presupposition that may be false.
I defined what I meant by "new and novel" ... I am qualifying new material as that which is quantifiably non-trivial. A small change can occur by chance, so can a few small changes. A lot of change in a short period of time that is quantifiably useful for new purpose and not pre-existant is what we observe in ORFan genes. Scale is important and is affected exponentially. So when you use a single symbol mutation to try and demonstrate how an entire program could arise, you have missed the mark by a catastrophic proportion.
Let me expose your argument with a similar analogy:-
I present to you a piece of sheet metal ... I show you that if I drop it on the floor it bends a corner of it. I show you that the angle that the corner is bent at matches a bend on an Aston Martin Vantage, you agree. I claim that if I drop that piece of metal enough times, I will eventually get an Aston Martin Vantage body. Now you would agree that is stupid reasoning .. that is what you are doing here. You want me to agree that X1 is different to X, yes it is ... but you're wanting to claim that just applying a single mutation multiple times will produce the complexity ... well it maybe would if you had a big enough population size and low enough mutation rate and an intelligent scoring mechanism so that the problem becomes a stochastic search algorithm with an in-built target. This is not the problem we are trying to solve, it is a different problem to what you claim is happening in Biology
You are conflating the idea of any change ...  with specific, substantial and complex change that solves a complex problem.

It seems that the assumption of purely natural processes being able to create new information is making it difficult for you guys to be able to argue rationally.

  
N.Wells



Posts: 1836
Joined: Oct. 2005

(Permalink) Posted: Feb. 18 2015,07:36   

Sorry, my mistake on AIDS.  However, if you are looking for bad logic on this thread, I'd go with your false claims about AVIDA that Wesley has documented, or your claim that there's no great difference between having and lacking fused carpals and metacarpals, fusion of the astragalus and the calcaneum, fusion of that into a fused tarsometatarsus, lighter (more hollow) bones, a stronger supracoracoideus muscle that goes over a bony process, heterocoelous cervical vertebrae, large numbers of vertebrae fused into the sacrum, a retroverted hallux, a short pygostyle-type tail, a strut-like coracoid, a sternum that is both bony and fused, reduced manual unguals, flattened manual phalanx II-1, no pubic symphysis or foot, a highly retroverted pubis, trochanteric crest, hypotarsus, no teeth, no third-finger claws, no long ascending astragalar process, no interdental plates, no obturator process of the ischium, no long chevrons in the tail, and no abdominal ribs.

 
Quote
Noah was never commanded to take one of every species on the ark, he was told what kinds of animals to take. He wasn't instructed to take fish or microscopic organisms or sea-dwelling mammals or molluscs etc. etc.
That does point to some flaws in the story.  Setting aside the problem that the water would have been well beyond boiling due to either the potential energy released in its fall from the heavens or due to release of heat on turning from vapour to liquid (http://www.holysmoke.org/cretins/fludmath.htm ; http://infidels.org/library....od.html ), you could maybe get saltwater fish to survive in a salty flood or freshwater fish to survive in a fresh flood, but not both.  Worse, in the creation-science interpretation, the Noachian flood laid down all or most of the world's Phanerozoic strata, which requires a flood that is muddy enough to lay down an average of 8000 m of sedimentary strata over the continents (but much less in the ocean basins, and how did that happen?).  Let's suppose a flood that is 10000 m deep over the continents: that suggests a flood that is on the order of 8 buckets of mud to every 10 buckets of water over the continents: good luck getting any fish or aquatic mammals to survive in that!  2000 to 20000 NTU over merely 24 hours is lethal for 50% of individuals in a variety of riverine fish species, which generally have very high tolerances for mud.  How this translates to ppm depends on the nature of the sediment, but it's on the order of 7000 to 70000 ppm, which is .7 to 7% suspended sediment.  
https://www.niwa.co.nz/freshwa....ish-dss
https://www.niwa.co.nz/our-sci........eak
http://www.transportation.alberta.ca/Content....its.pdf
Worse, all the Phanerozoic evaporites would have had to be dissolved in the flood waters, which would have rendered it hypersaline, which none of the fish could have survived.

Quote
ethnic cleansing
.   Really?

  
OgreMkV



Posts: 3668
Joined: Oct. 2009

(Permalink) Posted: Feb. 18 2015,08:06   

Having been schooled, Crypto now takes that most common of creationist tactics... change the subject by seizing on some minor point that someone else brought up.

I suspect that we will hear about AVIDA again in a few weeks once he thinks we've forgotten about the comments.

This never works. But they always try.

Crypto: Define "kind".

Keeping in mind that if your definition is at any taxonomic level above genus, then you have to explain evolution at rates 10 times higher than any biologists thinks is even possible, much less safe.

Of course, if you choose kind to be at a taxonomic level of genus or lower, then you have to explain how Noah got a bajillion organisms on his boat and cared for them for a year.

And you might want to talk to Ken Ham. He needs some help. Apparently, he just discovered that you can go OUT of the same door you came IN. His mind is just astounding.

--------------
Ignored by those who can't provide evidence for their claims.

http://skepticink.com/smilodo....retreat

   
NoName



Posts: 2729
Joined: Mar. 2013

(Permalink) Posted: Feb. 18 2015,09:24   

I'd be very interested to hear his definition of 'information'.
Clearly, pretty much unarguably, natural processes can produce vast amounts of information.
Stellar spectra are information.  They are produced by natural phenomena.
Tides are information.  They are produced by natural phenomena.
Fingerprints are information.  They are produced by natural phenomena.

I would be very interested in hearing about any sort of information at all that isn't produced by 'natural phenomena'.  Humans are as natural as protozoa, and by most measures, less complex than stars.
To assume, or rather assert that humans aren't natural phenomena and so must be explained by recourse to other non-natural phenomena is a huge case of question begging.
We have precisely zero reason for assuming humans are not natural phenomena.
We are, in fact, still waiting for clarification on what the heck a 'non-natural phenomenon' is.

But please, 'information' first.  What is information?  How is it determined that it is never produced by natural phenomena, particularly given the examples of stellar spectra, absorption spectra, the orientation of slightly magnetized iron needles in a magnetic field, and a host of other purely natural phenomena.
The only recourse is to use double-talk for 'information' or to abandon the notion of 'natural phenomena', which goes not further than does taking all phenomena as natural, except it violates Ockham's razor in a big way.

  
OgreMkV



Posts: 3668
Joined: Oct. 2009

(Permalink) Posted: Feb. 18 2015,10:05   

Quote (NoName @ Feb. 18 2015,09:24)
I'd be very interested to hear his definition of 'information'.

Dollars to donuts it'll involve "meaning", "new functions", and/or "complexity".

--------------
Ignored by those who can't provide evidence for their claims.

http://skepticink.com/smilodo....retreat

   
Doc Bill



Posts: 1039
Joined: April 2007

(Permalink) Posted: Feb. 18 2015,10:24   

Creepto wrote:
Quote
I am simply pointing out that none of the science you've mentioned proves anything;


Another fine graduate of Kurt Wise U.

I about blew my coffee when Creepto wrote that he was a "mathematician."

Right!  And I once pulled lobsters from Jane Mansfield's arse!

  
cryptoguru



Posts: 53
Joined: Jan. 2015

(Permalink) Posted: Feb. 18 2015,10:53   

Quote
I'd be very interested to hear his definition of 'information'.
Clearly, pretty much unarguably, natural processes can produce vast amounts of information.
Stellar spectra are information.  They are produced by natural phenomena.
Tides are information.  They are produced by natural phenomena.
Fingerprints are information.  They are produced by natural phenomena.


Natural laws can produce ordered output, e.g. fractals, orbits, crystals etc.
This is not information ... information is "What is conveyed or represented by a particular arrangement or sequence of things" i.e. has meaning
http://www.oxforddictionaries.com/definit....rmation

Waves can produce patterns on the beach, this is not information ... it is a pattern enforced by a natural system.

DNA holds information about how to build an organism ... it is an instruction set that is meaningful to the processing logic of a biological cell. This is not like a fractal or a wave, this is a deterministic sequence of instructions that is understood by the cell and is used to perform specific tasks.
The data sent to a radio controlled car is information, which has intended purpose in the control of the car ... the wind blowing the car off course is not information, even if it makes a pattern, the car is not deriving meaning from the interaction.

this is stuff a 3 year old would understand ... if you put a sandwich in a DVD player it won't play a movie. In fact, you can't put a CD in a DVD player and expect to watch a movie ... the information isn't there.

Information can't be created randomly. That's utter nonsense.


Quote
Wrong. Avidian instructions in the 2003 paper do not correspond to digital circuit logic gates. The functions being awarded merit in the 2003 paper correspond to typical logic functions (AND, OR, NOT, etc.). Cryptoguru is making this into a persistently repeated error.

You obviously don't know what a logic gate is ... AND, OR & NOT are all logic gates. I did not mean in a digital circuit, we are both talking about the same thing ... wow talk about completely misrepresenting what I'm saying.
Avida tests the instruction set to see if it is performing a logical operation (AND, OR, NOT) and rewards the organism if it is. This IS CHEATING!!! I can only assume you don't really understand programming or even basic logic if you don't get this point ... rewarding the organism for performing an anatomical operation is biasing the organism to win based on the fact it has achieved a known target. Explain how this is not so.

Quote
which he should now by now because I told him before

Yeah you keep saying you "told me before" and that should be proof of your argument. I've made a clear description of the issue at stake here and you keep side-stepping it and then simply claiming you've already told me that I got it wrong.

AVIDA REWARDS THE ORGANISM BASED ON KNOWN LOGICAL TARGETS (AND, OR, NOT ...) THIS IS NOT NATURAL SELECTION

This is not new information magically appearing, this is testing a random sequence of commands that we know can result in logical operations against the known logical operations ... blatantly cheating!

Quote


Quote

Section D:
comparison of AVIDA to biological evolution
1) an analogy must be drawn between AVIDA commands and the genome
2) it possibly makes most sense (I concede) to assume that AVIDA commands are analogous to codons (and not proteins), so that any mutation will always create a set of valid codons.
3) the level AVIDA is selecting at is therefore analogous to a folded functional protein.


That this is entirely incompatible with the new claim that Avida only acts on multi-genic blocks is evident.


It's the same issue written a different way. Avida is rewarding fitness at a level high enough to identify functionality (like a protein or a multi-genic block) but low enough to not be concerned with the overall fitness (like an organism or a whole genome). Again, the scale of the Avida complexity is orders of magnitude lower than a real genome

[/QUOTE]26^17 ~= 10^24, which looks like a pretty non-trivial problem space[QUOTE]
That's a completely arbitrary statement ... 10^24 is non-trivial if you're randomly searching ... but that's not what Avida is doing, it rewards combinations that we know get us closer to the final solution. This is more like a decision tree bisection method, where we have a good confidence level for making the right decision at each branch based on the bias that the reward system has enforced. The problem space is now possibly of order log(N), maybe even linear. Can you not see that? Can you not see that it is pushing the solution to a convergence by falsely rewarding the correct organisms based on a criterion that REAL natural selection could not work on?

  
socle



Posts: 322
Joined: July 2009

(Permalink) Posted: Feb. 18 2015,10:54   

Quote (cryptoguru @ Feb. 17 2015,11:15)
So as I was saying, you may be able to demonstrate a simple shuffling on the order of bacterial operons, with large populations and very short generation lengths. But anything more complex cannot be modelled by Avida or anything else, and to a mathematician like me ... seems utterly dumb!

Just out of curiosity, what's your field, if you don't mind me asking?

  
NoName



Posts: 2729
Joined: Mar. 2013

(Permalink) Posted: Feb. 18 2015,11:22   

Quote (cryptoguru @ Feb. 18 2015,11:53)
     
Quote
I'd be very interested to hear his definition of 'information'.
Clearly, pretty much unarguably, natural processes can produce vast amounts of information.
Stellar spectra are information.  They are produced by natural phenomena.
Tides are information.  They are produced by natural phenomena.
Fingerprints are information.  They are produced by natural phenomena.


Natural laws can produce ordered output, e.g. fractals, orbits, crystals etc.
This is not information ... information is "What is conveyed or represented by a particular arrangement or sequence of things" i.e. has meaning
http://www.oxforddictionaries.com/definit....rmation

Waves can produce patterns on the beach, this is not information ... it is a pattern enforced by a natural system.

And you're saying that these patterns are meaningless???
That's absurd.  The patterns enforced by the natural system of physics and chemistry provides meaningful information about the stellar composition and processes of stars.  This isn't 'just some random pattern', it is incredibly meaningful, and the meaning is tightly coupled to very specific and very precise natural laws.

     
Quote
DNA holds information about how to build an organism ... it is an instruction set that is meaningful to the processing logic of a biological cell. This is not like a fractal or a wave, this is a deterministic sequence of instructions that is understood by the cell and is used to perform specific tasks.
The data sent to a radio controlled car is information, which has intended purpose in the control of the car ... the wind blowing the car off course is not information, even if it makes a pattern, the car is not deriving meaning from the interaction.

this is stuff a 3 year old would understand ... if you put a sandwich in a DVD player it won't play a movie. In fact, you can't put a CD in a DVD player and expect to watch a movie ... the information isn't there.

The information contained in a sandwich is not the same as the information contained in a DVD or a CD.  But that it is useless for one purpose does not mean it is meaningless, or that it is without purpose.
You're cheating, badly and transparently, by applying entirely artificial constraints on to what meaning you find, and  where, solely due to your preselected purposes.
That's not how it's done.

     
Quote
Information can't be created randomly. That's utter nonsense.

Blatant assertion, without support.  Information is precisely distinct from randomness, viz. Shannon.
Constrained randomness produces information literally all the time.
[your argument with Wesley snipped]
New information does not appear by magic.  
Yet your claim amounts to the assertion that it does.
We have two alternatives -- natural law and magic.
If you reject the one, and look, you did so right at the top of your post, then you're stuck with magic.
It is YOUR position that information appears by magic.
It is OUR position that information appears naturally, by the operations of nature, which, btw, include randomness.

  
NoName



Posts: 2729
Joined: Mar. 2013

(Permalink) Posted: Feb. 18 2015,11:33   

To append to my previous post -- it is only because the operations of natural law provide information, in your sense not just Shannon's, that science is possible.

One wonders why you are pleased to use the products and insights of science in all parts of your life, in all aspects applying to the world, except when it comes to biology.  And generally, not biology as such, but human biology.

You are the very picture of prejudiced thinking, of seeking support for conclusions you've already adopted, without evidence or reason.

So once again, science, what we do, or magic, what you and your ilk do.
I'll take science and a world filled with information.

As a coda, I think we need to ask you just what you mean by 'random'.  It's a slipperier term than you might suppose, but it's clear you're leveraging every bit of slipperiness you can in service of your prejudiced agenda.
So, what do you mean by 'random'?

  
Freddie



Posts: 371
Joined: Oct. 2009

(Permalink) Posted: Feb. 18 2015,11:42   

Quote
this is stuff a 3 year old would understand ... if you put a sandwich in a DVD player it won't play a movie. In fact, you can't put a CD in a DVD player and expect to watch a movie ... the information isn't there.

Ahem ... Video CD Format.  Still supported on many DVD/BD players today, actually!

--------------
Joe: Most criticisims of ID stem from ignorance and jealousy.
Joe: As for the authors of the books in the Bible, well the OT was authored by Moses and the NT was authored by various people.
Byers: The eskimo would not need hairy hair growth as hair, I say, is for keeping people dry. Not warm.

  
NoName



Posts: 2729
Joined: Mar. 2013

(Permalink) Posted: Feb. 18 2015,11:52   

Quote (Freddie @ Feb. 18 2015,12:42)
Quote
this is stuff a 3 year old would understand ... if you put a sandwich in a DVD player it won't play a movie. In fact, you can't put a CD in a DVD player and expect to watch a movie ... the information isn't there.

Ahem ... Video CD Format.  Still supported on many DVD/BD players today, actually!

And you can put a CD in and listen to music.
That the information he wants/needs/expects is not there is no warrant for assuming that therefore there is no information there.  My DVD players happily recognize CDs, SACDs, DVD-As, etc., and do the right thing based on the information read from the disk.

The level of dishonesty it takes to put forth the sorts of arguments he does is far beyond what a 3 year old would be able to muster up.  Or recognize.

  
OgreMkV



Posts: 3668
Joined: Oct. 2009

(Permalink) Posted: Feb. 18 2015,12:03   

So, I guess the question is

If a DVD contains data, but you don't have a device to read it, then does it contain information?

What if the DVD contains data, but it's in Swahili, then does it contain information (you can't read it)?

If the DVD contains data, but you must use a decryption program, with the proper passcode, does it contain information?

If the answer to any of those is "yes", then the you must accept that information is not equal to meaning. None of those DVDs will have any meaning for you, but they all contain information.

As usual, we have someone who rejects evolution because they don't understand how information works and how it's different than meaning.

Let's try again.

Let's say you have a gene. A person is born with a mutant allele for that gene. It results in a 1% decrease in efficiency of that protein. Has information in the gene changed? Has the information content OF THE POPULATION changed?

What if that mutant allele, decades later has another effect that increases the chance of survival of the organism? Has the information increased, decreased, or stayed the same? Why?

I know you won't answer these questions. No ID/creationist has yet.

--------------
Ignored by those who can't provide evidence for their claims.

http://skepticink.com/smilodo....retreat

   
JohnW



Posts: 3217
Joined: Aug. 2006

(Permalink) Posted: Feb. 18 2015,12:12   

Quote (NoName @ Feb. 18 2015,09:22)
Quote (cryptoguru @ Feb. 18 2015,11:53)
     
Quote
I'd be very interested to hear his definition of 'information'.
Clearly, pretty much unarguably, natural processes can produce vast amounts of information.
Stellar spectra are information.  They are produced by natural phenomena.
Tides are information.  They are produced by natural phenomena.
Fingerprints are information.  They are produced by natural phenomena.


Natural laws can produce ordered output, e.g. fractals, orbits, crystals etc.
This is not information ... information is "What is conveyed or represented by a particular arrangement or sequence of things" i.e. has meaning
http://www.oxforddictionaries.com/definit....rmation

Waves can produce patterns on the beach, this is not information ... it is a pattern enforced by a natural system.

And you're saying that these patterns are meaningless???
That's absurd.  The patterns enforced by the natural system of physics and chemistry provides meaningful information about the stellar composition and processes of stars.  This isn't 'just some random pattern', it is incredibly meaningful, and the meaning is tightly coupled to very specific and very precise natural laws.

     
Quote
DNA holds information about how to build an organism ... it is an instruction set that is meaningful to the processing logic of a biological cell. This is not like a fractal or a wave, this is a deterministic sequence of instructions that is understood by the cell and is used to perform specific tasks.
The data sent to a radio controlled car is information, which has intended purpose in the control of the car ... the wind blowing the car off course is not information, even if it makes a pattern, the car is not deriving meaning from the interaction.

this is stuff a 3 year old would understand ... if you put a sandwich in a DVD player it won't play a movie. In fact, you can't put a CD in a DVD player and expect to watch a movie ... the information isn't there.

The information contained in a sandwich is not the same as the information contained in a DVD or a CD.  But that it is useless for one purpose does not mean it is meaningless, or that it is without purpose.
You're cheating, badly and transparently, by applying entirely artificial constraints on to what meaning you find, and  where, solely due to your preselected purposes.
That's not how it's done.

     
Quote
Information can't be created randomly. That's utter nonsense.

Blatant assertion, without support.  Information is precisely distinct from randomness, viz. Shannon.
Constrained randomness produces information literally all the time.
[your argument with Wesley snipped]
New information does not appear by magic.  
Yet your claim amounts to the assertion that it does.
We have two alternatives -- natural law and magic.
If you reject the one, and look, you did so right at the top of your post, then you're stuck with magic.
It is YOUR position that information appears by magic.
It is OUR position that information appears naturally, by the operations of nature, which, btw, include randomness.

Looks like "information" is being defined in the same way as CSI, FIASCO and all the other ID sciency terms: "The property of things which look designed to me which makes them look designed to me."

--------------
Math is just a language of reality. Its a waste of time to know it. - Robert Byers

There isn't any probability that the letter d is in the word "mathematics"...  The correct answer would be "not even 0" - JoeG

  
NoName



Posts: 2729
Joined: Mar. 2013

(Permalink) Posted: Feb. 18 2015,12:16   

Quote (JohnW @ Feb. 18 2015,13:12)
Quote (NoName @ Feb. 18 2015,09:22)
Quote (cryptoguru @ Feb. 18 2015,11:53)
       
Quote
I'd be very interested to hear his definition of 'information'.
Clearly, pretty much unarguably, natural processes can produce vast amounts of information.
Stellar spectra are information.  They are produced by natural phenomena.
Tides are information.  They are produced by natural phenomena.
Fingerprints are information.  They are produced by natural phenomena.


Natural laws can produce ordered output, e.g. fractals, orbits, crystals etc.
This is not information ... information is "What is conveyed or represented by a particular arrangement or sequence of things" i.e. has meaning
http://www.oxforddictionaries.com/definit....rmation

Waves can produce patterns on the beach, this is not information ... it is a pattern enforced by a natural system.

And you're saying that these patterns are meaningless???
That's absurd.  The patterns enforced by the natural system of physics and chemistry provides meaningful information about the stellar composition and processes of stars.  This isn't 'just some random pattern', it is incredibly meaningful, and the meaning is tightly coupled to very specific and very precise natural laws.

       
Quote
DNA holds information about how to build an organism ... it is an instruction set that is meaningful to the processing logic of a biological cell. This is not like a fractal or a wave, this is a deterministic sequence of instructions that is understood by the cell and is used to perform specific tasks.
The data sent to a radio controlled car is information, which has intended purpose in the control of the car ... the wind blowing the car off course is not information, even if it makes a pattern, the car is not deriving meaning from the interaction.

this is stuff a 3 year old would understand ... if you put a sandwich in a DVD player it won't play a movie. In fact, you can't put a CD in a DVD player and expect to watch a movie ... the information isn't there.

The information contained in a sandwich is not the same as the information contained in a DVD or a CD.  But that it is useless for one purpose does not mean it is meaningless, or that it is without purpose.
You're cheating, badly and transparently, by applying entirely artificial constraints on to what meaning you find, and  where, solely due to your preselected purposes.
That's not how it's done.

       
Quote
Information can't be created randomly. That's utter nonsense.

Blatant assertion, without support.  Information is precisely distinct from randomness, viz. Shannon.
Constrained randomness produces information literally all the time.
[your argument with Wesley snipped]
New information does not appear by magic.  
Yet your claim amounts to the assertion that it does.
We have two alternatives -- natural law and magic.
If you reject the one, and look, you did so right at the top of your post, then you're stuck with magic.
It is YOUR position that information appears by magic.
It is OUR position that information appears naturally, by the operations of nature, which, btw, include randomness.

Looks like "information" is being defined in the same way as CSI, FIASCO and all the other ID sciency terms: "The property of things which look designed to me which makes them look designed to me."

Which, amusingly enough, is both meaningless and unspecifiable.

And, of course, renders all science impossible, renders 'information' something that can only be produced by magic, and ultimately renders all output by the claimants inherently information-less.

  
stevestory



Posts: 13407
Joined: Oct. 2005

(Permalink) Posted: Feb. 18 2015,13:46   

Crypto, do you have an objection to evolution which hasn't already been answered?

   
cryptoguru



Posts: 53
Joined: Jan. 2015

(Permalink) Posted: Feb. 18 2015,14:35   

Quote
Crypto, do you have an objection to evolution which hasn't already been answered?


I didn't get any answers to my questions, just assertions that I'm wrong.

Quite entertaining though ... so I suppose, yeah if you're allowed to redefine what information is to prove that information can magically emerge from randomness, and say that observing any change means that you've proved evolution, and that if we assume Common Descent is the reason for diversity that we can explain the similarities between different organisms as them having a common ancestor.

Yeah I suppose you've all answered all the questions to the satisfaction of someone who would be satisfied with an answer that they themselves gave.

I showed quite clearly how Avida is biasing the results and "proving" that information emerges by rewarding organisms using known targets. But someone said it isn't ... so yeah I reckon they probably proved it beyond all reasonable doubt ... and that's me looking like a TOTAL idiot now.

(now cue everyone quoting my last sentence as though it wasn't sarcastic)

  
NoName



Posts: 2729
Joined: Mar. 2013

(Permalink) Posted: Feb. 18 2015,14:52   

Quote (cryptoguru @ Feb. 18 2015,15:35)
 
Quote
Crypto, do you have an objection to evolution which hasn't already been answered?


I didn't get any answers to my questions, just assertions that I'm wrong.


That, sir, is a flat-out lie.
And even if it were true, you'd be a fine one to talk.  You're not exactly forthcoming with honest straightforward answers to questions yourself.

 
Quote
Quite entertaining though ... so I suppose, yeah if you're allowed to redefine what information is to prove that information can magically emerge from randomness,

You'll note that that is not what I, nor others here, have done.
You'll also note that we have noted that you have not addressed the examples of information emerging from the operation of natural law.
Finally, stop using the word 'randomness' until you provide a precise operational definition.  It's not a magic wand that  can get you out of trouble.

 
Quote
and say that observing any change means that you've proved evolution, and that if we assume Common Descent is the reason for diversity that we can explain the similarities between different organisms as them having a common ancestor.

Again with the confusion over assumptions and well-supported conclusions.
I thought lying made baby jesus cry?

Quote
Yeah I suppose you've all answered all the questions to the satisfaction of someone who would be satisfied with an answer that they themselves gave.

I showed quite clearly how Avida is biasing the results and "proving" that information emerges by rewarding organisms using known targets. But someone said it isn't ... so yeah I reckon they probably proved it beyond all reasonable doubt ... and that's me looking like a TOTAL idiot now.

(now cue everyone quoting my last sentence as though it wasn't sarcastic)

You've done no such thing.

Most notable is how you continue to shift goal-posts, fail to address substantive points  that  call your entire schtick into question, and lie continuously about what others say and have said.  That last is particularly odd given that the words are all right here.

Stellar spectra are information.  They emerge from natural processes.  Deal with it.
Provide any case of information arising from non-natural processes.  Just be very careful to demonstrate that the alleged 'non-natural causes' are in fact non-natural and yet causal.
Kindly explain how your dismissal of information arising from natural law being impossible is anything other than a bow towards magic, and a flight from science.  How else does science function except through examination of the information provided by natural processes?
If you don't know the answers to these questions, if you don't understand the dilemma your own expression of your own position have placed you in, you ought not to be making the "arguments" you make.

  
Cubist



Posts: 558
Joined: Oct. 2007

(Permalink) Posted: Feb. 18 2015,19:06   

Quote (cryptoguru @ Feb. 18 2015,05:58)
   
Quote
One: Does Sequence X1 qualify as "new and novel genetic material"? It's a yes-or-no question, cryptoguru; either yes, Sequence X1 does, in fact, qualify as "new and novel genetic material", or no, Sequence X1 does not, in fact, qualify as "new or novel genetic material". It's all well and good to go on about "probability" and "scale" and yada yada, but I really would like to see a yes or a no, and thus far, I ain't seen a yes or a no.

Two: Does Sequence X1 contain any "new and novel genetic material"? Again, it's a yes-or-no question, to which either yes, it does or no, it doesn't would both be relevant responses. Going on about "scale" and "probability" and yada yada, contrariwise, is not a particularly relevant response, as best I can tell.

This is the fallacy of many questions (e.g. Do you still beat your wife?)...

Bullshit it’s “the fallacy of many questions”. It is, rather, an attempt to get you to apply your definition of “new and novel genetic material” to a specific nucleotide sequence, and indicate whether that specific nucleotide sequence either is (entirely) "new and novel genetic material", or else contains (some amount of) "new and novel genetic material".

Transparent rationalization/excuse for not even attempting to answer the question is noted.

Way back on page 1 of this thread, I asked, "What does 'new information' look like? Given an arbitrary string of nucleotides, and a mutation which alters that string of nucleotides, how can you tell whether or not the post-mutation version of that string contains any "new" information?"

Your reply to this question, which appeared on page 2 of this thread, is "New information is new and novel genetic material that codes for new function or traits in the organism i.e. not a point mutation in a control gene that switches other pre-existing functionality off/on or a trade/inheriting of genetic material between bacteria ...NEW genetic material that codes for new function; this has never been observed." So according to cryptoguru, the specific case of "a point mutation in a control gene that switches other pre-existing functionality off/on or a trade/inheriting of genetic material between bacteria" does not either "new information", or "new and novel genetic material". Fine—but this definition does nothing to help us determine whether a point mutation in a control gene that does something other than switch pre-existing functionality on/off constitutes "new information" or "new and novel genetic material". This definition also does nothing to help us determine whether any mutation other than a point mutation in a control gene constitutes "new information" or "new and novel genetic material". This definition also does nothing to help us determine whether any mutation that affects DNA other than the DNA in a control gene constitutes "new information" or "new and novel genetic material".

There is, of course, nothing wrong with a statement whose applicability is highly restricted. But if one does make a statement whose applicability is highly restricted, one ought not go on to declare that said statement has any effect on anything outside the highly restricted domain of said statement's applicability.

 
Quote
[the fallacy of many questions] is the rhetorical trick of asking a question that cannot be answered without admitting a presupposition that may be false.

The only "presupposition" I am aware of in the question does Sequence X1 qualify as “new and novel genetic material? is the "presupposition" that there actually is a meaningful, usable definition of “new and novel” in the phrase "new and novel genetic material". This presupposition may well be false, and the more bafflegab you disgorge instead of, you know, answering the question, the more likely it becomes that this presupposition is, in fact, false.

   
Quote
I defined what I meant by "new and novel" ...

Bullshit you did. Feel free to provide a link to the post in which you defined this term… or, more likely, provide another unfounded I did define my terms I did I did I did so define my terms! assertion.

 
Quote
I am qualifying new material as that which is quantifiably non-trivial.

Okay… so in addition to "new and novel", and "unique", the "new material" you speak of has to be "quantifiably non-trivial". Please explain, as you have conspicuously neglected to do thus far, how to distinguish "genetic material" which is "new", from "genetic material" which is "novel", and from "genetic material" which is "unique". Oh, and now that you've thrown "quantifiably non-trivial" into the pot, please explain how to distinguish "genetic material" which is "new", from "genetic material" which is "quantifiably non-trivial". Or, if you cannot explain how to distinguish "genetic material" which is "new" from "genetic material" which is "novel" and/or "unique" and/or "quantifiably non-trivial", please explain how your use of "new" as a separate term is supposed to help anyone understand what the heck is going on.

Please explain how to distinguish "genetic material" which is "novel", from "genetic material" which is "unique", and from "genetic material" which is "quantifiably non-trivial". Or, if you cannot explain how to distinguish "genetic material" which is "novel" from "genetic material" which is "unique" and/or "quantifiably non-trivial", please explain how your use of "novel" as a separate term is supposed to help anyone understand what the heck is going on.

Please explain how to distinguish "genetic material" which is "unique", from "genetic material" which is "quantifiably non-trivial". Or, if you cannot explain how to distinguish "genetic material" which is "unique" from "genetic material" which is "quantifiably non-trivial", please explain how your use of "unique" as a separate term is supposed to help anyone understand what the heck is going on.

 
Quote
A small change can occur by chance, so can a few small changes. A lot of change in a short period of time that is quantifiably useful for new purpose and not pre-existant is what we observe in ORFan genes. Scale is important

That's nice, cryptoguru. It doesn't appear to have anything to do with determining whether or not a given nucleotide sequence does or doesn't constitute/contain "genetic material" which is "new" and/or "novel" and/or "unique" and/or "quantifiably non-trivial", but it's nice. I'll just cut-and-paste the original iteration of my is this 'new' 'genetic information'? question from the post in which it appeared…

Here's an arbitrary nucleotide sequence, with a randomly-picked nucleotide—the thymine in the 4th codon—colored red:
gcc tac agg gat cgt ggg gac ctt acg aat ggc ctt ttt gac tat tct tcg aat cta agc tca gca tca ttc ccg tct acg gga agt ccc ttc cca ata cat atc ctc ggc acc gca ctt gca ggc tca cgc ttc gcg tca ttt agg tca
That sequence of codons yields the following sequence of amino acids, with the 4th amino acid colored red on account of it's the AA that's yielded by the codon with the red-colored nucleotide:
alanine, tyrosine, arginine, aspartic acid, arginine, glycine, aspartic acid, leucine, threonine, asparagine, glycine, leucine, phenylalanine, aspartic acid, tyrosine, serine, serine, asparagine, leucine, serine, serine, alanine, serine, phenylalanine, proline, serine, threonine, glycine, serine, proline, phenylalanine, proline, isoleucine, histidine, isoleucine, leucine, glycine, threonine, alanine, leucine, alanine, glycine, serine, arginine, phenylalanine, alanine, serine, phenylalanine, arginine, serine

One possible mutation of that sequence would be if the thymine in the 4th codon was deleted, like so (and the thereby-altered 4th codon is colored red here):
gcc tac agg gac gtg ggg acc tta cga atg gcc ttt ttg act att ctt cga atc taa gct cag cat cat tcc cgt cta cgg gaa gtc cct tcc caa tac ata tcc tcg gca ccg cac ttg cag gct cac gct tcg cgt cat tta ggt ca
Since a codon is three nucleotides in a row, deleting that one nucleotide from the 4th codon in the original sequence doesn't just change that 4th codon; it also has the effect of changing pretty much every codon after that altered 4th codon. This, in turn, yields a very different sequence of amino acids than the original, unmutated sequence. The red-colored AAs are ones which don't occur at all in the original, unmutated sequence:
alanine, tyrosine, arginine, aspartic acid, valine, glycine, threonine, leucine, arginine, methionine, alanine, phenylalanine, leucine, threonine, isoleucine, leucine, arginine, isoleucine, [end], alanine, glutamine, histidine, histidine, serine, arginine, leucine, arginine, glutamic acid, valine, proline, serine, glutamine, tyrosine, isoleucine, serine, serine, alanine, proline, histidine, leucine, glutamine, alanine, histidine, alanine, serine, arginine, histidine, leucine, glycine, [???]

Does the mutated nucleotide sequence qualify as "new and novel genetic material"? Does the mutated nucleotide sequence contain any "new and novel genetic material"?

 
Quote
So when you use a single symbol mutation to try and demonstrate how an entire program could arise, you have missed the mark by a catastrophic proportion.

That may be so, cryptoguru. However, I, at least, have not "use[d] a single symbol mutation to try and demonstrate how an entire program could arise"; rather, I have been asking questions with the intent of getting you to explain what the heck you mean.

 
Quote
Let me expose your argument with a similar analogy…

BZZT! Wrong. I'm not making an argument at all, cryptoguru. I am, instead, asking you to explain what the heck you mean. It's unclear whether you intend to do so any time in the foreseeable future, but that's okay; for my purposes, a Creationist who replies to cogent questions with diversionary bafflegab is as good as a Creationist who actually answers cogent questions.

  
N.Wells



Posts: 1836
Joined: Oct. 2005

(Permalink) Posted: Feb. 18 2015,20:24   

A cool new paper on one major way in that the early birds (stemward of Confuciusornis) were significantly more primitive than later Cretaceous and Cenozoic birds:
http://rspb.royalsocietypublishing.org/content....0142864

  
Wesley R. Elsberry



Posts: 4991
Joined: May 2002

(Permalink) Posted: Feb. 19 2015,09:18   

Cryptoguru:

 
Quote

Avida selects by using complete logic gates plus IO as symbols,


Me:

     
Quote

Wrong. Avidian instructions in the 2003 paper do not correspond to digital circuit logic gates. The functions being awarded merit in the 2003 paper correspond to typical logic functions (AND, OR, NOT, etc.). Cryptoguru is making this into a persistently repeated error.


Cryptoguru:

     
Quote

You obviously don't know what a logic gate is ... AND, OR & NOT are all logic gates. I did not mean in a digital circuit, we are both talking about the same thing ... wow talk about completely misrepresenting what I'm saying.


"Logic gate" is a technical term whose source context is digital circuit design. See Google 'define "logic gate"'. AND, OR, and NOT are examples of logical functions which can be realized in electronic circuitry, and such idealized or realized circuits are called "logic gates". If Cryptoguru "did not mean in a digital circuit", he shouldn't have used jargon from digital circuit design.

Going back to the original statement, Cryptoguru says that Avida "symbols" are "complete logic gates" and "IO". "Symbol" there is only interpretable as "instruction", the units that comprise Avidian genomes/programs. I will need to walk back my statement above by 1/9th: there is an Avidian instruction called "nand" and there is a rewarded function called NAND. None of the other eight rewarded functions has an instruction named the same thing, nor that even arguably are conceptually similar. And it must be noted that the instruction "nand" does not itself accrue any merit by its presence in an Avidian program. In order to get the reward for the NAND function, there has to be an executed program sequence in the Avidian genome that implements the NAND function, and the shortest known hand-written NAND function program is five Avida instructions long, thus: io io nop-c nand io. This is the crucial distinction Cryptoguru is having trouble with: the instructions that make up the Avida genomes/programs are not what gets awarded merit. This distinction makes a difference. Avidians are rewarded for what they *do*, not what their programs *are*. When I say "rewarded function", I am referring to the behavior that gets rewarded, and when I say "instruction", I am referring to an element of the Avidian program sequence. So, no, Cryptoguru and I are not talking about the same thing, because there is the analogous distinction between the Avidian program instruction sequence and the Avidian behavior that results from its execution as exists between a biological organism's genotype and its phenotype. Cryptoguru is confused on this point, since "Avida selects ... symbols" clearly shows that Cryptoguru is referring to an Avida genotype as the thing being selected, and, as I have stated over and over, that is false. Cryptoguru has a problem with me saying that he is wrong, and there is certainly a way for Cryptoguru to establish his claim: produce the Avida source code showing any reward of merit for Avida genomic contents. It's his claim, will he abandon it?

--------------
"You can't teach an old dogma new tricks." - Dorothy Parker

    
OgreMkV



Posts: 3668
Joined: Oct. 2009

(Permalink) Posted: Feb. 19 2015,09:29   

It's HIGHLY amusing to watch crytpoguru argue about Avida to someone who worked on Avida.

Thank you Wes!

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Ignored by those who can't provide evidence for their claims.

http://skepticink.com/smilodo....retreat

   
NoName



Posts: 2729
Joined: Mar. 2013

(Permalink) Posted: Feb. 19 2015,09:53   

Indeed.

It's also amusing to see how desperate he is to argue about AVIDA rather than Lenski's work.  Apparently, if it "can't" be modeled, it can't be real, it can't exist.
How convenient for him, and others.  It lets them ignore messy reality in favor of neat, small-minded, limited conceptualizations which are inevitably, as we have seen, prejudicially selected, set up, described, and used.

  
midwifetoad



Posts: 4003
Joined: Mar. 2008

(Permalink) Posted: Feb. 19 2015,09:57   

Question for Wes:

Have you read Wagner's book, in which he discusses systems of AND, OR and NOT operators and asserts that when you reach a certain "genome" length, you can almost always find a mutation that does not change the output?

Furthermore, having mutated an element, you can almost certainly find another element that can be mutated without affecting the output. And that you can stepwise change 80 percent or more of the elements without affecting output.

He calls this inovability. I think an equivalent term would be evolvability. His assertion is that it is a characteristic of any complex system, and that the level of complexity doesn't have to be high. His digital genomes have 16 elements.

What he is arguing against is the ID claim that functional sequences are isolated and cannot be bridged by point mutations. Or Dembski's claim that some special or designed search process is required.

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Any version of ID consistent with all the evidence is indistinguishable from evolution.

  
cryptoguru



Posts: 53
Joined: Jan. 2015

(Permalink) Posted: Feb. 19 2015,11:14   

Quote
Cryptoguru is having trouble with: the instructions that make up the Avida genomes/programs are not what gets awarded merit. This distinction makes a difference. Avidians are rewarded for what they *do*, not what their programs *are*. When I say "rewarded function", I am referring to the behavior that gets rewarded, and when I say "instruction", I am referring to an element of the Avidian program sequence. So, no, Cryptoguru and I are not talking about the same thing, because there is the analogous distinction between the Avidian program instruction sequence and the Avidian behavior that results from its execution as exists between a biological organism's genotype and its phenotype


Nope that is what I thought was happening ... my point isn't that they're being rewarded on the symbol level, rather that the "function" they're being rewarded for is a known target that the algorithm is testing against, and it is only one level of complexity above the symbols. this is synonymous with mutating at the codon level, but assuming that the codon has a linear affect on output (which it doesn't, because you could have mutated a regulatory gene or mutated a codon in a multiple reading frame which would affect multiple outputs) then Avida is rewarding at the protein level (the level up from the codons) ... not on an organism level. Tell me, how is this analogous to what is purported to happen in nature? How is this modelling Natural Selection?
YES I know the selection in Avida is occurring on the population level because of competition, but the competition is fixed, the organisms are being rewarded according to sub-organism level functionality and they are being rewarded proportional to them matching a known target i.e. a logical function.
(I'm trying to use your terminology to avoid ambiguity)

So you can try to use equivocation to pretend I'm saying something other than I am if you like ... but I think it's pretty clear what I'm saying now. Address the issue at hand, not the straw man you keep claiming I'm making.

let's say it again
Avida mutates symbols and rewards linear combinations of them according to known targets (logical functions). Biology combines symbols in a non-linear fashion (multiple reading frames and control sequences) and the organism is rewarded based on its suitability in the environment compared to its competitors, not at the level up from symbols (which would be proteins in biology). These are 2 vast simplifications to the algorithm of biological evolution and Avida therefore models a much more trivial problem than evolution proposes ... in essence it's not much different to the Weasel algorithm that uses a known target to fix the odds of the stochastic search.

I can show you another system which appears to create ordered functional complexity out of randomness, it's called fractal image compression (Barnsley et al). A map is applied to a 2D image which creates contractive transforms across the problem space so that only transforms and relationships are saved. Random noise is now placed into the 2D image and the relationships are iterated, the image magically appears. Did information come from nowhere? NO! It looked like it did, but the information was stored efficiently in the algorithm, not in the image data. (where we would expect). Avida is imposing intelligence on the system by rewarding at a level that effects the competition, the intelligence is put in by the algorithm that determines whether or not the organism has achieved a logical function, THAT is not a natural process.

So in summary ... Avida cheats in 2 ways, it has reduced the non-linear genome to linear. It artificially rewards by imposing a known target at the level directly above symbols, that requires intelligence and is not a natural process.

  
Wesley R. Elsberry



Posts: 4991
Joined: May 2002

(Permalink) Posted: Feb. 19 2015,11:38   

Quote (midwifetoad @ Feb. 19 2015,09:57)
Question for Wes:

Have you read Wagner's book, in which he discusses systems of AND, OR and NOT operators and asserts that when you reach a certain "genome" length, you can almost always find a mutation that does not change the output?

Furthermore, having mutated an element, you can almost certainly find another element that can be mutated without affecting the output. And that you can stepwise change 80 percent or more of the elements without affecting output.

He calls this inovability. I think an equivalent term would be evolvability. His assertion is that it is a characteristic of any complex system, and that the level of complexity doesn't have to be high. His digital genomes have 16 elements.

What he is arguing against is the ID claim that functional sequences are isolated and cannot be bridged by point mutations. Or Dembski's claim that some special or designed search process is required.

I haven't read Wagner's book, so I can't speak to that.

However, the phenomenon described might not be as weighty as it looks from the short description here. It's pretty easy to get "don't care" conditions in digital circuits, and anything upstream of a "don't care" input could be changed without effect. In biology, you'd be looking at the distinction between epistasis and evolvability. The extent to which you report Wagner is able to change things in stepwise fashion does make it sound like it probably isn't all some sort of digital circuit "epistasis", though.

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"You can't teach an old dogma new tricks." - Dorothy Parker

    
Wesley R. Elsberry



Posts: 4991
Joined: May 2002

(Permalink) Posted: Feb. 19 2015,11:45   

Cryptoguru:

Quote

Nope that is what I thought was happening ...


Too bad, then, that what you said was happening was the opposite.

--------------
"You can't teach an old dogma new tricks." - Dorothy Parker

    
Wesley R. Elsberry



Posts: 4991
Joined: May 2002

(Permalink) Posted: Feb. 19 2015,12:13   

The "linear" vs. "non-linear" issue... It's been raised before, and stomped flat before, though Cryptoguru seems to have missed it, like most indications that he is talking nonsense.

Quote


[Cryptoguru:]
Quote

2) It is not just multiple reading frames that introduce polymorphism into the genome, but regulatory genes can effect the expression of an entire coding gene. This non-linearity is not modelled in AVIDA, which is a linear sequential code (like assembler). That is, the Genome executes a higher-level language than a sequential instruction set.


Again, this concern is nowhere to be seen in the original challenge, and is thus irrelevant to the original challenge. Plus, the Avida documentation notes:

               
Quote


One major concept that differentiates this virtual assembly language from its real-world counterparts is in the additional uses of nop instructions (no-operation commands). These have no direct effect on the virtual CPU when executed, but often modify the effect of any instruction that precedes them. In a sense, you can think of them as purely regulatory genes. The default instruction set has three such nop instructions: nop-A, nop-B, and nop-C.


But like I said, that's all irrelevant to the original challenge.


The regulatory effects are non-linear, which qualitatively puts paid to Cryptoguru's ignorant prattle. But wait, there's more... Avida genomes are programs in a Turing-complete instruction set, including the full panoply of branching instructions needed to make that happen. The Avida instruction set includes mov-head, jmp-head, and set-flow. Turing-completeness implies that if the Avida instruction set is inadequate to model what Cryptoguru wants modeled, then no other computer language is capable of the job, either.

Cryptoguru has a choice of dropping his particular objection to Avida, or his claim that biology equals computation. There is no third option.

--------------
"You can't teach an old dogma new tricks." - Dorothy Parker

    
NoName



Posts: 2729
Joined: Mar. 2013

(Permalink) Posted: Feb. 19 2015,12:25   

He's already gone for 'biology equals magic'*, so I'm not sure that 'computation equals magic' is beyond his reach.

*Not directly and in so many words, of course, he would never be so boorish as to be that transparent.
But it's hard to see how else to take his assertions that
Quote
Natural laws can produce ordered output
This is not information
DNA holds information about how to build an organism

other than as 'information cannot come from natural law, therefore biology has nothing to do with natural law therefore magic'.

  
midwifetoad



Posts: 4003
Joined: Mar. 2008

(Permalink) Posted: Feb. 19 2015,13:01   

I'm not sure Wagner presents any new science, but he does present a compelling metaphor.

Stasis is the beginning rather than the end of his argument. He has a long section on equivalent metabolisms, arguing that there are are an indefinitely large number of equivalent metabolisms, and that microbes -- for example -- can walk from one set of metabolisms to another without having to bridge any large gaps. So even mutations that change enzymes can result in a functionally equivalent or viable organism. And once such a change occurs, it opens up a new dimension or direction of non-lethal change.

It's all about the permissiveness of biochemistry, the ability of change to occur without being fatal. More specifically, change accomplished via small steps.

I think it's worth discussing, because it really crushes the arguments of Behe and Dembski. Assuming Wagner is correct.

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Any version of ID consistent with all the evidence is indistinguishable from evolution.

  
OgreMkV



Posts: 3668
Joined: Oct. 2009

(Permalink) Posted: Feb. 19 2015,13:09   

Quote (midwifetoad @ Feb. 19 2015,13:01)
I'm not sure Wagner presents any new science, but he does present a compelling metaphor.

Stasis is the beginning rather than the end of his argument. He has a long section on equivalent metabolisms, arguing that there are are an indefinitely large number of equivalent metabolisms, and that microbes -- for example -- can walk from one set of metabolisms to another without having to bridge any large gaps. So even mutations that change enzymes can result in a functionally equivalent or viable organism. And once such a change occurs, it opens up a new dimension or direction of non-lethal change.

It's all about the permissiveness of biochemistry, the ability of change to occur without being fatal. More specifically, change accomplished via small steps.

I think it's worth discussing, because it really crushes the arguments of Behe and Dembski. Assuming Wagner is correct.

Seems like Lenski's work would support those ideas.

IIRC, the citrate metabolizing bacteria appeared at 40k generations (or thereabouts), but the mutations to support those bacteria appeared at about 23k generations.

So, there were certainly mutations that had no direct effect (or an almost unmeasurable one) on the bacteria, but the final mutation happened and an entirely new food source became available (in oxygen).

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midwifetoad



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(Permalink) Posted: Feb. 19 2015,13:53   

Well, Wagner has some interesting things to say about the minimum viable set of metabolic products, and what is necessary to live on limited food supplies, and his analysis may or may not be original.

But he does credit others for doing the actual research supporting his "Library of Babel" metaphor.

His primary claim is that the number of viable genomic configurations is hyper-astronomical, and that viable configurations are connectable by mutation sized steps.

That answers Behe's Edge claim, and it answers Dembski's Search for a Search Claim.

For dessert, he brings up the Avida-sounding digital logic experiment, which he claims supports the idea that connectedness and evolvability are expected attributes of any complex system. In other words, not fine tuned.

--------------
Any version of ID consistent with all the evidence is indistinguishable from evolution.

  
cryptoguru



Posts: 53
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(Permalink) Posted: Feb. 19 2015,17:47   

Quote
The Avida instruction set includes mov-head, jmp-head, and set-flow. Turing-completeness implies that if the Avida instruction set is inadequate to model what Cryptoguru wants modeled


actually yes you are correct, I forgot that non-linearity is modelled as part of the instruction set through the ability to move the head. I was being stupid about that ... Scratch that part of my argument.

The rest of my argument still holds ... Avida is rewarding by comparing to a known target on the level of complexity directly above the instruction set, not on the level of the organism. Even if it was on the level of the organism it is still cheating by having knowledge of an advantageous target.
Comparing to a known target (in Avida's case, known logical functions) is a confessed cheat of the Weasel algorithm by Dawkins, the same logic holds for Avida.

  
Wesley R. Elsberry



Posts: 4991
Joined: May 2002

(Permalink) Posted: Feb. 19 2015,18:27   

Quote (cryptoguru @ Feb. 19 2015,17:47)
 
Quote
The Avida instruction set includes mov-head, jmp-head, and set-flow. Turing-completeness implies that if the Avida instruction set is inadequate to model what Cryptoguru wants modeled


actually yes you are correct, I forgot that non-linearity is modelled as part of the instruction set through the ability to move the head. I was being stupid about that ... Scratch that part of my argument.

The rest of my argument still holds ... Avida is rewarding by comparing to a known target on the level of complexity directly above the instruction set, not on the level of the organism. Even if it was on the level of the organism it is still cheating by having knowledge of an advantageous target.
Comparing to a known target (in Avida's case, known logical functions) is a confessed cheat of the Weasel algorithm by Dawkins, the same logic holds for Avida.

Well, of course we'll scratch the "linear vs. non-linear" part of Cryptoguru's argument, since we long ago recognized it as rubbish, provided the explanation of why it was rubbish, and had it resurrected as a pathetic zombie argument.

All Cryptoguru's premises have been wrong, but the argument is still just fine.

Riiiiiiii-ghghghghght.

I've already addressed the "level of complexity" issue, and that was irrelevant to the original challenge. If Cryptoguru wants to move on from the original challenge, that is easy: he can just admit that his original challenge was met and *then* propose another challenge.

I've also addressed the level of selection issue, and Cryptoguru remains mistaken on that point. Looking back...

Me:

 
Quote

Avida does not examine the genomic instruction sequence to recognize something. It examines the output from the IO instruction of the Avidian that indicates that it correctly performed a behavior, in the Lenski et al. 2003 paper the rewarded behaviors comprised a set of nine logic operations. An Avidian can internally compute every logic function around and receive exactly zero extra CPU cycles of merit if it fails to output the results to the environment via the IO instruction. I've already mentioned this before. The assertion that things are otherwise is a persistent misunderstanding on Cryptoguru's part.

Avida's award of merit for Avidian behaviors is analogous to biological organisms getting better/more nutrition, or greater movement efficiency, or better artifact construction (nest, hive, or tools) due to a favorable trait. There is really nothing to object to on this point, and this is no problem for the model.

As far as the final quoted sentence goes, some traits have to have relative benefits in order to simulate natural selection. This has to happen in the model since it happens in biology. This is not a problem for the model.


And, no, "the same logic" does not hold for Avida as for "weasel". It's pretty breathtakingly inane to think it would.

Cryptoguru seems to think that repetition somehow makes discredited claims better.

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"You can't teach an old dogma new tricks." - Dorothy Parker

    
Soapy Sam



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(Permalink) Posted: Feb. 19 2015,19:08   

Quote (midwifetoad @ Feb. 19 2015,19:53)
Well, Wagner has some interesting things to say about the minimum viable set of metabolic products, and what is necessary to live on limited food supplies, and his analysis may or may not be original.

But he does credit others for doing the actual research supporting his "Library of Babel" metaphor.

His primary claim is that the number of viable genomic configurations is hyper-astronomical, and that viable configurations are connectable by mutation sized steps.

That answers Behe's Edge claim, and it answers Dembski's Search for a Search Claim.

For dessert, he brings up the Avida-sounding digital logic experiment, which he claims supports the idea that connectedness and evolvability are expected attributes of any complex system. In other words, not fine tuned.

It should be noted that multi-base mechanisms blast through even those barriers which might restrict point-mutational space. Eukaryotic recombination moves far more quickly, and to places otherwise unreachable stepwise. The same goes for LGT. It is clear that motifs, having proven their capacity in one protein, find themselves shuffled into others by various means. It is probable, or certainly possible,  that all proteins have their basis in one ur-protein, segmentally duplicated and changed, rather than a repertoire that-many-bases long to start with gradually amending, base by base.

Edited by Soapy Sam on Feb. 20 2015,14:24

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SoapySam is a pathetic asswiper. Joe G

BTW, when you make little jabs like “I thought basic logic was one thing UDers could handle,” you come off looking especially silly when you turn out to be wrong. - Barry Arrington

  
midwifetoad



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(Permalink) Posted: Feb. 19 2015,19:20   

Well gpuccio at UD is fond of arguing that protein domains appear not to share any code. Wagner doesn't address this, but he does argue that sequences can be replaced one loci at a time until little or nothing is left of the original. Either by conserving function or by finding viable replacement functions.

He also points out that microbes are constantly sharing their inventions. So one lineage does not have to evolve everything.

I don't have the knowledge to evaluate this, but it's on my list of ideas to watch.

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Any version of ID consistent with all the evidence is indistinguishable from evolution.

  
The whole truth



Posts: 1554
Joined: Jan. 2012

(Permalink) Posted: Feb. 19 2015,22:14   

cryptoguru, do you believe that your chosen, so-called 'God' designed, created, and guides the entire universe, including all 'natural laws' and 'natural systems'?

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Think not that I am come to send peace on earth: I came not to send peace, but a sword. - Jesus in Matthew 10:34

But those mine enemies, which would not that I should reign over them, bring hither, and slay them before me. -Jesus in Luke 19:27

   
cryptoguru



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(Permalink) Posted: Feb. 20 2015,04:01   

Wes, it seems either you're not able to see the issue here or you really don't want to. It's a simple issue to understand.
Pretending that rewarding the organism for achieving a target is a natural thing, is cheating when you have an algorithm that is testing the organism to see if it passes a specific test. In doing this you are biasing the organisms that you know are approaching a known solution.

AVIDA has made it so that the test for reward is a known building block of the final solution. This would be like having an exhaustive list of component parts that we know could build an airplane if we had the correct amount in the correct order. We would never expect to randomly be able to vary the list and order of components as well as assembly instructions to get the final result, so we work on assembling simple modules; small modules containing a few components. We optimise the search for components that build modules that we know are needed for the airplane. If the algorithm manages to create a component by chance, we reward the algorithm that produced it so that it out-survives the other algorithms that have not found a component. Before long we should expect to have a few modules that may work together to perform another task that we were expecting.
This algorithm could work (if a module can be made with a small amount of components) and a functional collection of modules would also need to only require a small number of modules.
This is how AVIDA is working ... it knows the modules that are needed, and it knows the final possible collective-module functions ... so it enforces targets. AVIDA also has known logical functions that don't require many commands in the correct order. Remember most of the commands in AVIDA are commutative, so a lot of the time (for boolean logic) the order of commands is not important (e.g. 1 & 0 & 1 & 1 can be re-written in any order). Therefore AVIDA has it easier than the airplane, because there is not an infinite number of ways of building a known physical module for an airplane that is functional. Also we known that finding logical functions that are a combination of commands is of a low order of complexity (tens of commands, not thousands) ... this matters, as the difficulty in finding a combination to reward will exponentiate as the problem space increases. Nevertheless, the enforced target both at the logical function level and the final solution level is artificial and enforced by the intelligence of the algorithm ... you can pretend it's modelling feeding, movement or some other natural advantage, but this is no more a natural advantage than sending a random sequence of words to a speech engine and when you get a few words together that make sense by comparing with known sentences play that through speakers and claim that the computer is artificially intelligent.

I understand that for your world-view to be correct this is a CORE issue, you need to be able to show that information can arise automatically. It's pretty obvious that's not what's happening here. I don't expect you to agree with me ... that would be equivalent to you saying that natural processes can't or haven't been observed to bring specified complexity out of random noise without intelligent interaction. That ain't gonna happen, unless you find Jesus and have a conversion experience and change your mind to believe in a creator  ... then you may find your mind is open to more rational argument.

As I've said before, my world-view permits things that both arise through natural mechanisms and those that can arise through supernatural (outside of our physical universe) causation. You cannot permit supernatural causation in your world-view, so you must explain everything through natural causation, even if it doesn't naturally fit. Who has the closed mind? The evidence and the logic points in the direction of intelligent causation of information ... you're trying to argue that problem-solving designs can emerge from noise. I sure hope you don't work in engineering or software dev :-)

Ironically, I bet you are willing to accept the "supernatural" causation of other universes or dimensions outside of our own measurable and observable universe to answer difficult cosmological questions about origins ... but just not an intelligence ... presumably because you may have to account to them for your actions.

I think we're done here, and yes you've answered some questions, but not with satisfactory answers; you've ducked and dived the key points. I have admitted the part I had presumed and got wrong (about AVIDA being linear), can you admit your incorrect presumptions?

  
Cubist



Posts: 558
Joined: Oct. 2007

(Permalink) Posted: Feb. 20 2015,04:13   

Quote (cryptoguru @ Feb. 20 2015,04:01)
Wes, it seems either you're not able to see the issue here or…

Hi, cryptoguru! I see that you haven't yet clarified what you mean when you talk about "genetic material" that's "new" and/or "novel" and/or "unique" and/or "quantifiably non-trivial". I sure hope you can explain your terms… but if you don't, that's okay, because I can re-post my questions as many times as it takes before you actually do answer them. Seeya later!

  
cryptoguru



Posts: 53
Joined: Jan. 2015

(Permalink) Posted: Feb. 20 2015,04:59   

Cubist: I did answer your question, you just didn't understand the answer.

I explained what I mean by "new" and "novel" for the purposes of this discussion, is that which is too difficult to arise from a purely random event. i.e. one which would probabilistically require natural selection through competition and could not just arise through just a sequence of mutation events.
I would not expect to randomly arrive at a meaningful sentence by randomly selecting letters, however I may expect to get a short 3 or 4-letter word randomly.

You believe that natural selection is the agent that turns random events into information.

So we need to be able to differentiate between noise and information; a sequence of symbols that has specified meaning ... i.e. it solves a problem

Example:
this point deletion creates a new string ... but it is not information, we can't differentiate it from noise, even if it was advantageous we can't call it information yet.
gacgtacga
gcgtacga

this sequence of new symbols (not pre-existant) could be new information
gacgtacga
gacgtacgattcaatgact

we don't known that until we show that the new string does something (has meaning) and is advantageous. Also a new string that small could potentially arise through mutation without any selective guidance.

So I'm back to using ORFan genes, we know that they are functional and advantageous and they have no known ancestor, they are new information and they are significantly large enough to be impossible to achieve purely randomly.
Sure there are things smaller than this that could be information, but how do we know they are? In the case of ORFan genes we have a clear example of new genetic material that is useful to the organism and not pre-existing that would require something other than pure dumb-luck to occur.

So I'm asking for a demonstration of new information on this level (ORFan gene size) to arise out of purely random mutation and natural selection, without using intelligently applied known targets to artificially guide the selective process.

DO YOU UNDERSTAND MY QUESTION YET???
(or do you not want to understand it?)

  
The whole truth



Posts: 1554
Joined: Jan. 2012

(Permalink) Posted: Feb. 20 2015,05:18   

"...unless you find Jesus and have a conversion experience and change your mind to believe in a creator  ... then you may find your mind is open to more rational argument."

Who or what is the "Jesus" thing?

Hey cryptoguru, supernatural green clad leprechauns, rainbow trout, and pink unicorns designed, created, and guide everything in the entire universe and everything outside the universe. See, I'm open minded! More open minded than you!

Edited by The whole truth on Feb. 20 2015,03:18

--------------
Think not that I am come to send peace on earth: I came not to send peace, but a sword. - Jesus in Matthew 10:34

But those mine enemies, which would not that I should reign over them, bring hither, and slay them before me. -Jesus in Luke 19:27

   
cryptoguru



Posts: 53
Joined: Jan. 2015

(Permalink) Posted: Feb. 20 2015,05:29   

Quote
Who or what is the "Jesus" thing?

I'm sure there's a church running an Alpha course near you where you could get the answer to that question.

Quote
supernatural green clad leprechauns, rainbow trout, and pink unicorns designed, created, and guide everything in the entire universe and everything outside the universe. See, I'm open minded! More open minded than you!

Yeah maybe, but you wouldn't be rational if you believed those things ... I'm having a rational discussion about my beliefs on origins. I'm not arguing for ANY supernatural causation, just one that is rational. The designer would have to be infinite in temporal existence, knowledge, presence and power to be able to fulfil the requirement of the infinite regression argument (i.e. who created God?). That rules out trout, unicorns, leprechauns or any other finite beings or creatures.

  
Wesley R. Elsberry



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(Permalink) Posted: Feb. 20 2015,05:36   

A little re-orientation on the relation between merit and Avidians may be in order. I'll refer to work I did during my post-doc for illustration.

I extended Avida to permit Avidians to move about the Avida grid. Instead of 26 instructions, there were 29 used in the experiments related in the paper. The new instructions were sense-diff-facing (put a value of the difference between a resource at the current grid cell and the grid cell the Avidian was facing into a register), move (caused the Avidian to move into the grid cell it was facing), and tumble (randomly changed the facing of the Avidian to another adjacent grid cell). I used a rectangular bounded grid with dimensions of 111 by 101 cells. I also used a resource distribution with high levels in one region of the grid and a gradient of that resource distributed over the rest of the grid:



Note that all information regarding the resource distribution that is available to an Avidian is strictly local, referring only to resources in two adjacent cells.

As in biology, movement has a cost. It cost my Avidians 2% of their merit for each step they took in an executed move instruction. Merit was only awarded as a result of an executed move instruction, and the amount of merit received was a function of the concentration of the resource in the new grid cell the Avidian moved into. This, again, matches what we see in biology: organisms are rewarded for behavior that brings them into contact with greater resources. (It also illustrates handily the fallacy in claiming that there is anything untoward about an Avidian receiving merit for something it does as a behavior.)

The initial organism in the experimental runs was the classic seed Avidian (it has the ability to self-replicate and does nothing else). I collected aggregate "visit" data for the cell grid over intervals of 5,000 updates. Here is a snapshot of a run that had a hand-coded random-walk organism injected at the start and mutation turned off:



Visits in that "check" run were, of course, uncorrelated with the resource distribution.

Here's a series of snapshots made of visits in an experimental run:



In that run, one can see that a variety of movement strategies evolve and become common in the population.

The terms I used for the three most commonly-seen movement strategies were the basis for the paper title: Cockroaches, Drunkards, and Climbers.







The Climber strategy corresponds to programs in the class of optimal responses to the given resource distribution, implementing gradient ascent. A few examples of test runs featuring three different single Avidians and their responses to the resource gradient of the experimental runs:







Of course, one would also like to see that the programs resulting are not, somehow, exploiting some other regularity in the experimental setup besides the resource distribution. So taking the Climber Avidian from that last graph and injecting it into a test run with randomly-placed resource peaks gives these sets of visits:







Something important to note here is that there is no explicit fitness function. Avidians moving around in regions of greater resources get greater merit, just like biological organisms do better when they are in areas with better resources. And there is no "target" at all. There is nothing in this experiment that checks for any particular type of response; the entirety of merit reward is strictly limited to the environmental distribution of the resource. There is no reliance on any hierarchy of rewards. Some movement strategies are relatively more efficient at exploiting the given resource than others, and that is sufficient to drive the evolution of a variety of movement strategies, including those in the optimal class of programs for this context.

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"You can't teach an old dogma new tricks." - Dorothy Parker

    
cryptoguru



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(Permalink) Posted: Feb. 20 2015,05:41   

Wes, very cool optimisation problem, thanks for including your research here ... I'll have a read through before I get back to you on how your variant of the problem is cheating with respect to real biology. :-)

  
Wesley R. Elsberry



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(Permalink) Posted: Feb. 20 2015,05:41   

Cryptoguru:

Quote

I understand that for your world-view to be correct this is a CORE issue


Cryptoguru understands something about my world-view?

I somehow doubt it. That would require actually knowing what my world-view was, and it seems unlikely that is the case. Although like much else about me, that is a matter of public record, and thus something else that Cryptoguru is willing to prattle on about in complete ignorance of reality.

Go ahead, Cryptoguru, tell me what my world-view is and why what you note is supposed to be a core issue for its correctness.

ETA: I hadn't read that message all the way through, so I was gobsmacked to find Cryptoguru finished it up with this stunning bit of projection:

Quote

can you admit your incorrect presumptions?


Edited by Wesley R. Elsberry on Feb. 20 2015,06:01

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"You can't teach an old dogma new tricks." - Dorothy Parker

    
The whole truth



Posts: 1554
Joined: Jan. 2012

(Permalink) Posted: Feb. 20 2015,05:46   

Quote (cryptoguru @ Feb. 20 2015,03:29)
Quote
Who or what is the "Jesus" thing?

I'm sure there's a church running an Alpha course near you where you could get the answer to that question.

Quote
supernatural green clad leprechauns, rainbow trout, and pink unicorns designed, created, and guide everything in the entire universe and everything outside the universe. See, I'm open minded! More open minded than you!

Yeah maybe, but you wouldn't be rational if you believed those things ... I'm having a rational discussion about my beliefs on origins. I'm not arguing for ANY supernatural causation, just one that is rational. The designer would have to be infinite in temporal existence, knowledge, presence and power to be able to fulfil the requirement of the infinite regression argument (i.e. who created God?). That rules out trout, unicorns, leprechauns or any other finite beings or creatures.

But the green clad leprechauns, rainbow trout, and pink unicorns are all
supernatural as I said, and they're triple infinitely infinite in temporal existence, knowledge, presence and power too! They also fart clouds of rose petals and lollipops as they design, create, and guide everything in and outside of the universe, and I'll bet that the "Jesus" thing can't do that!

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Think not that I am come to send peace on earth: I came not to send peace, but a sword. - Jesus in Matthew 10:34

But those mine enemies, which would not that I should reign over them, bring hither, and slay them before me. -Jesus in Luke 19:27

   
cryptoguru



Posts: 53
Joined: Jan. 2015

(Permalink) Posted: Feb. 20 2015,05:53   

Wes, your world-view pre-supposes purely natural causation and excludes supernatural, intelligent causation ... as that is the purpose of the theory of evolution; to explain origins without the need for an intelligent agent.
Evolutionary theory is the science of atheists and fake atheists (agnostics), who need to find a way to explain the origin and diversity of life without a God.

Thus the need to explain that information can arise automatically from noise by purely natural processes.

  
Wesley R. Elsberry



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(Permalink) Posted: Feb. 20 2015,06:02   

Quote (cryptoguru @ Feb. 20 2015,05:53)
Wes, your world-view pre-supposes purely natural causation and excludes supernatural, intelligent causation ... as that is the purpose of the theory of evolution; to explain origins without the need for an intelligent agent.
Evolutionary theory is the science of atheists and fake atheists (agnostics), who need to find a way to explain the origin and diversity of life without a God.

Thus the need to explain that information can arise automatically from noise by purely natural processes.

Wrong.

Why can't Cryptoguru check things out before he makes checkable, false claims about them?

Hint: Wikipedia.

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"You can't teach an old dogma new tricks." - Dorothy Parker

    
The whole truth



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(Permalink) Posted: Feb. 20 2015,06:05   

Quote (cryptoguru @ Feb. 20 2015,03:53)
Wes, your world-view pre-supposes purely natural causation and excludes supernatural, intelligent causation ... as that is the purpose of the theory of evolution; to explain origins without the need for an intelligent agent.
Evolutionary theory is the science of atheists and fake atheists (agnostics), who need to find a way to explain the origin and diversity of life without a God.

Thus the need to explain that information can arise automatically from noise by purely natural processes.

Oh, so you didn't say this:

"I'm not arguing for ANY supernatural causation..."?

You're just another dishonest, arrogant YEC loon who doesn't know squat about science, rationality, and reality.

--------------
Think not that I am come to send peace on earth: I came not to send peace, but a sword. - Jesus in Matthew 10:34

But those mine enemies, which would not that I should reign over them, bring hither, and slay them before me. -Jesus in Luke 19:27

   
Wesley R. Elsberry



Posts: 4991
Joined: May 2002

(Permalink) Posted: Feb. 20 2015,06:10   

Quote (cryptoguru @ Feb. 20 2015,05:41)
Wes, very cool optimisation problem, thanks for including your research here ... I'll have a read through before I get back to you on how your variant of the problem is cheating with respect to real biology. :-)

Given that Cryptoguru preemptively excluded studies of movement, I have no doubt that his boundless capacity for unjustified dismissal will allow him to do just that.

However, I have demonstrated that Avida is not dependent on having anything that corresponds to a Dawkinsian "distant ideal target", nor a hierarchical set of rewarded functions, in order to evolve behavior useful to Avidians.

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"You can't teach an old dogma new tricks." - Dorothy Parker

    
cryptoguru



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(Permalink) Posted: Feb. 20 2015,06:12   

Wes, wow! I'm wrong?!?
So you believe in supernatural causation?
What kind of supernatural causation?

The theory of evolution was proposed by a trained clergyman (Darwin) who rejected God because his favourite daughter died. He is very clear in his writings what his motivation was for his theory, he therefore embraced the old-age naturalistic world-view proposed by Charles Lyell's work and rejected the Bible as a source of truth .. I know that doesn't prove evolution is wrong, but the world-view that birthed the theory (atheism) is the same world-view that propagates and enforces it now.
There's a lot of people who believe in God, who also believe in evolution ... but generally only because they don't understand how it contradicts their faith and is therefore irrational to believe both.

  
midwifetoad



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Joined: Mar. 2008

(Permalink) Posted: Feb. 20 2015,06:24   

Even Godwin's Law mutates and evolves.

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Any version of ID consistent with all the evidence is indistinguishable from evolution.

  
N.Wells



Posts: 1836
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(Permalink) Posted: Feb. 20 2015,06:28   

Quote (Wesley R. Elsberry @ Feb. 20 2015,06:10)
Quote (cryptoguru @ Feb. 20 2015,05:41)
Wes, very cool optimisation problem, thanks for including your research here ... I'll have a read through before I get back to you on how your variant of the problem is cheating with respect to real biology. :-)

Given that Cryptoguru preemptively excluded studies of movement, I have no doubt that his boundless capacity for unjustified dismissal will allow him to do just that.

However, I have demonstrated that Avida is not dependent on having anything that corresponds to a Dawkinsian "distant ideal target", nor a hierarchical set of rewarded functions, in order to evolve behavior useful to Avidians.

But it doesn't even have a single globe rating at Planet Source Code*, so how can it possibly be any good?

*I'll get round to checking whether that's actually true later, but it sounds plausible to me for now, so I'm going with it.

/snark

  
Wesley R. Elsberry



Posts: 4991
Joined: May 2002

(Permalink) Posted: Feb. 20 2015,06:44   

Quote (cryptoguru @ Feb. 20 2015,06:12)
Wes, wow! I'm wrong?!?
So you believe in supernatural causation?
What kind of supernatural causation?

The theory of evolution was proposed by a trained clergyman (Darwin) who rejected God because his favourite daughter died. He is very clear in his writings what his motivation was for his theory, he therefore embraced the old-age naturalistic world-view proposed by Charles Lyell's work and rejected the Bible as a source of truth .. I know that doesn't prove evolution is wrong, but the world-view that birthed the theory (atheism) is the same world-view that propagates and enforces it now.
There's a lot of people who believe in God, who also believe in evolution ... but generally only because they don't understand how it contradicts their faith and is therefore irrational to believe both.

I get that from both ends of the argument. I certainly am familiar with a wide variety of arguments from both directions on why treating evolutionary biology as broadly true is inimical to faith, though I haven't found any yet that I fully agree with. (And this is one of the things I find most annoying about discussing things with Cryptoguru, which is the "you disagree, therefore you don't understand" approach he so often takes.) It doesn't change the facts, though. Facts that are in the public domain and should have been consulted before making blithe, false pronouncements. I think there was something relevant said about "false witness" once or twice somewhere.

Speaking of which, it is by no means clear that Darwin's beliefs are so easily pigeon-holed. He certainly did come to a forceful rejection of the Calvinist doctrine of "utter depravity", but rejecting Calvin is not the same thing as rejecting God.

Darwin:

   
Quote

Authors of the highest eminence seem to be fully satisfied with the view that each species has been independently created. To my mind it accords better with what we know of the laws impressed on matter by the Creator, that the production and extinction of the past and present inhabitants of the world should have been due to secondary causes, like those determining the birth and death of the individual.


It's pretty clear from his own writings that he had drifted far from any formal denominational Christianity, but the tossed-off assignment of causes and internal motivations strikes me as deeply unscholarly. Whether or not one agrees or disagrees with claims about Darwin's theological stance, one can assess for oneself the utility and reasonableness of his claim above. I find it reasonable, and Cryptoguru apparently does not.

And I think that part of being rational is having one's facts straight, and thus one's premises in argument correct, so I don't think Cryptoguru is in any good position to launch an attack on the rationality of anybody else.

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"You can't teach an old dogma new tricks." - Dorothy Parker

    
cryptoguru



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(Permalink) Posted: Feb. 20 2015,07:29   

Quote
Cryptoguru is in any good position to launch an attack on the rationality of anybody else.


that is just your opinion.

I think the others on this board would be quite interested in the paradox that you've raised whereby you believe in God, yet are fundamental in the research and development of what is currently considered a foundational proof of evolution.

Most of the arguments against me on the discussion board here (from others) have been about the stupidity and irrationality of believing in God, presumably given the "truth" of evolution.

So Wes, it's your turn to be bashed for believing in God. :-)


Quote
Speaking of which, it is by no means clear that Darwin's beliefs are so easily pigeon-holed.

In a lot of his public writing and discussion he paid lip-service to God (as did Hitler) because he was aware of the majority view-point at the time. His private writings and letters give more info about his motivations and his actual beliefs.

So where do you think information originates Wes? Do you think information and designs to solve problems can emerge automatically through purely random mutation and a competition? Or do you believe that a creator is needed?

What do you believe about the origin of life itself? Do you believe it came about through supernatural causation ... or do you think life emerged spontaneously from chemical soup?

BTW: I find that making bold statements and black and white claims gets more information from a discussion as it helps polarise people's viewpoint and you get quicker to the real core of the debate. I'm happy to address and change my assumptions if they're proved wrong (as you will have seen me do already on a couple of occasions).

  
NoName



Posts: 2729
Joined: Mar. 2013

(Permalink) Posted: Feb. 20 2015,07:48   

Quote (cryptoguru @ Feb. 20 2015,05:59)
Cubist: I did answer your question, you just didn't understand the answer.

I explained what I mean by "new" and "novel" for the purposes of this discussion, is that which is too difficult to arise from a purely random event. i.e. one which would probabilistically require natural selection through competition and could not just arise through just a sequence of mutation events.
I would not expect to randomly arrive at a meaningful sentence by randomly selecting letters, however I may expect to get a short 3 or 4-letter word randomly.

And yet it can be shown that production of words produced from random selection of characters, combined with a varying set of grammar and syntax rules can generate meaningful sentences.
Similarly, it can be shown that random variations in genetic material can occur and be judged against an existing, and slowly changing, fitness landscape.  The information that results is that "this change fails to fail, that change fails."
This is meaningful information in the only sense that matters.
 
Quote
You believe that natural selection is the agent that turns random events into information.

Yes.  Because it can be shown that it does.  Given a set of randomly generated letters being combined, plus a selection rule that permits collections of letters to be preserved if a given collection occurs in a dictionary, meaningful words will arise, quite rapidly.  The dictionary can be change out and the process continued, and a meaningful collection of words will arise, quite rapidly, and as variations from the original set, which will be initially drastically reduced and will then once again proliferate.
For amusement, and potential enlightenment, see Markov Chain Text Generation Results
 
Quote
So we need to be able to differentiate between noise and information; a sequence of symbols that has specified meaning ... i.e. it solves a problem

That's what  filters do.  Information is what passes through, noise is what's rejected.
You are confusing Shannon information theory with semantics.  They are often confused, but starkly distinct.
Worse, as is clear in  your examples that follow, you demand omniscience in the determination.  How do you know that any given random string is meaningless across all possible languages, or even across all existent languages?  Answer: you don't.  That's why information and meaning are distinct.
 
Quote
Example:
this point deletion creates a new string ... but it is not information, we can't differentiate it from noise, even if it was advantageous we can't call it information yet.
gacgtacga
gcgtacga

this sequence of new symbols (not pre-existant) could be new information
gacgtacga
gacgtacgattcaatgact

we don't known that until we show that the new string does something (has meaning) and is advantageous. Also a new string that small could potentially arise through mutation without any selective guidance.

Mutations arise without any guidance other than physics and chemistry and the constraints they impose.  Genetic mutations are random selection out of a very small pool of possible choices (4 codons, with each codon highly restricted in terms of its own chemical makeup due to physics and chemistry).  No guidance is needed, or possible, for mutations.  Guidance comes in at the stage of replication into a next generation.  Winners of the first lottery get to participate in the second lottery.  Lottery numbers are random with respect to winners/losers at each round.  Selection is from round to round.
You really seem not to get this.
Quote
So I'm back to using ORFan genes, we know that they are functional and advantageous and they have no known ancestor, they are new information and they are significantly large enough to be impossible to achieve purely randomly.

No, we do not know the latter 'fact'.  You assert it, but proof is lacking.  Assuming your conclusion, aren't you?
Quote
Sure there are things smaller than this that could be information, but how do we know they are? In the case of ORFan genes we have a clear example of new genetic material that is useful to the organism and not pre-existing that would require something other than pure dumb-luck to occur.

So I'm asking for a demonstration of new information on this level (ORFan gene size) to arise out of purely random mutation and natural selection, without using intelligently applied known targets to artificially guide the selective process.

DO YOU UNDERSTAND MY QUESTION YET???
(or do you not want to understand it?)

I've bolded and italicized the fatal contradictions and confusions that rig the game against any possibility of a satisfactory answer.
You do realize that demanding evidence or proof that something can arise that is "too difficult to arise from a random event" requires proof that there are things that cannot arise from random events.  No such proof exists.
Worse, such a proof requires an operational definition of 'random' that is accurate, precise, consistent, and used consistently throughout said proof.  You are assuming your conclusions in the manner in which you set up your "challenge."
Then there is the issue that you confuse random mutation and natural selection.  Natural selection does not generate new information, random mutation  does.  Natural selection eliminates the 'unmeaningful'.  Meaning is the fitness of the organism for the environment in which it occurs.  Random mutation perturbs the content of the ever-changing set of entities on which natural selection filters out the less fit, that is, the less meaningful for the current environment, which is also changing, albeit generally at a vastly slower rate.

Your question, your "challenge" is precisely equivalent to "have you stopped beating your wife."
For reasons already adequately presented by others.
It also betrays incredible ignorance, or dishonesty, about how evolution works.
Worse, it ignores the real-world examples that prove that what you insist is impossible does, in fact, happen all the time.  Which is  doubtlessly why you focus on AVIDA and on your own misconceptions of what 'must' be the case, rather than what is clearly, demonstrably, the case.
Of course, if you were to confront Lenski's work head-on, you would have to propose an alternate explanation for the  new and novel information's inception and persistence in the population.  You would have to show when, and how, some intelligence intervened to do what natural processes allegedly cannot.
Until you do, we have no warrant for dismissing the answer 'it was all done by natural processes'.  No other process has been proposed.  The process we propose is a conclusion based on the evidence and known facts.  Not an assumption, not a presupposition.
Whereas you insist that natural processes cannot produce information despite the countless counter-examples that prove this to be incorrect.  Science would not be possible if this were correct.

  
NoName



Posts: 2729
Joined: Mar. 2013

(Permalink) Posted: Feb. 20 2015,07:56   

Quote (cryptoguru @ Feb. 20 2015,06:53)
Wes, your world-view pre-supposes purely natural causation and excludes supernatural, intelligent causation ... as that is the purpose of the theory of evolution; to explain origins without the need for an intelligent agent.
Evolutionary theory is the science of atheists and fake atheists (agnostics), who need to find a way to explain the origin and diversity of life without a God.

Thus the need to explain that information can arise automatically from noise by purely natural processes.

Yet we have evidence of nothing but natural processes.
We have evidence that natural processes result in everything we encounter.
You have assertions, based largely on superstition and misunderstanding of what we conclude based on evidence.

We have no warrant for including 'supernatural intelligent causation' in any explanatory statement, for we have no evidence, and damn close to no meaningful definition of, the terms involved.
Note in particular that supernatural and causal are contradictory terms.  The natural world can be, and often is, defined as the network of possible causal relationships between things, processes, and events.
All causal occurrences are natural.  It is easy to show this to be wrong; all you have to do is show a non-natural cause.  Or demonstrate the existence of any non-natural "thing".  We have no warrant for even considering the existence of such a "thing" other than works of fiction or collections of assertions based on what appear to be fictions.  [NB.  'thing' is used in scare quotes because 'thing' as generally taken means precisely 'natural thing'.  The supernatural is other than 'thing'-like.  It is the opposite of 'thing'-ness, else it is not supernatural.  Ontology 101]

Thus the need to explain that there is information that cannot arise through purely natural processes by first showing that there is a non-natural process.
Go for it.

  
OgreMkV



Posts: 3668
Joined: Oct. 2009

(Permalink) Posted: Feb. 20 2015,07:59   

Quote (cryptoguru @ Feb. 20 2015,04:59)
Cubist: I did answer your question, you just didn't understand the answer.

I explained what I mean by "new" and "novel" for the purposes of this discussion, is that which is too difficult to arise from a purely random event. i.e. one which would probabilistically require natural selection through competition and could not just arise through just a sequence of mutation events.
I would not expect to randomly arrive at a meaningful sentence by randomly selecting letters, however I may expect to get a short 3 or 4-letter word randomly.

You believe that natural selection is the agent that turns random events into information.

So we need to be able to differentiate between noise and information; a sequence of symbols that has specified meaning ... i.e. it solves a problem

Example:
this point deletion creates a new string ... but it is not information, we can't differentiate it from noise, even if it was advantageous we can't call it information yet.
gacgtacga
gcgtacga

this sequence of new symbols (not pre-existant) could be new information
gacgtacga
gacgtacgattcaatgact

we don't known that until we show that the new string does something (has meaning) and is advantageous. Also a new string that small could potentially arise through mutation without any selective guidance.

So I'm back to using ORFan genes, we know that they are functional and advantageous and they have no known ancestor, they are new information and they are significantly large enough to be impossible to achieve purely randomly.
Sure there are things smaller than this that could be information, but how do we know they are? In the case of ORFan genes we have a clear example of new genetic material that is useful to the organism and not pre-existing that would require something other than pure dumb-luck to occur.

So I'm asking for a demonstration of new information on this level (ORFan gene size) to arise out of purely random mutation and natural selection, without using intelligently applied known targets to artificially guide the selective process.

DO YOU UNDERSTAND MY QUESTION YET???
(or do you not want to understand it?)

You reject contingency, which is required for evolution.

In other words, your definitions make it strictly impossible for evolution to meet your requirements.

Good thing no one cares about your definitions.

--------------
Ignored by those who can't provide evidence for their claims.

http://skepticink.com/smilodo....retreat

   
cryptoguru



Posts: 53
Joined: Jan. 2015

(Permalink) Posted: Feb. 20 2015,07:59   

NoName: you seem to keep conflating the 2 distinct concepts

1) purely random mutation - nobody believes this is capable of producing information
2) random mutation plus natural selection - you believe this can create information, I don't

Monkeys typing on typewriters will not produce the works of Shakespeare as Dawkins has attested to, he contests that cumulative natural selection is able to guide the purely random process and create information. I want to see that demonstrated ... you keep jumping around your definitions. This is a simple issue ... find "new information" that couldn't arise purely randomly  by using random mutation and natural selection.

Find a solution that defies simple probability e.g. rolling a die 36 times will likely get you 2 sixes in a row at some point ... this is not what we're talking about, you need to demonstrate complex information that could not occur probabilistically arising because natural selection is doing something that pure dumb-luck can't.

  
OgreMkV



Posts: 3668
Joined: Oct. 2009

(Permalink) Posted: Feb. 20 2015,08:09   

Quote (NoName @ Feb. 20 2015,07:56)
Quote (cryptoguru @ Feb. 20 2015,06:53)
Wes, your world-view pre-supposes purely natural causation and excludes supernatural, intelligent causation ... as that is the purpose of the theory of evolution; to explain origins without the need for an intelligent agent.
Evolutionary theory is the science of atheists and fake atheists (agnostics), who need to find a way to explain the origin and diversity of life without a God.

Thus the need to explain that information can arise automatically from noise by purely natural processes.

Yet we have evidence of nothing but natural processes.
We have evidence that natural processes result in everything we encounter.
You have assertions, based largely on superstition and misunderstanding of what we conclude based on evidence.

We have no warrant for including 'supernatural intelligent causation' in any explanatory statement, for we have no evidence, and damn close to no meaningful definition of, the terms involved.
Note in particular that supernatural and causal are contradictory terms.  The natural world can be, and often is, defined as the network of possible causal relationships between things, processes, and events.
All causal occurrences are natural.  It is easy to show this to be wrong; all you have to do is show a non-natural cause.  Or demonstrate the existence of any non-natural "thing".  We have no warrant for even considering the existence of such a "thing" other than works of fiction or collections of assertions based on what appear to be fictions.  [NB.  'thing' is used in scare quotes because 'thing' as generally taken means precisely 'natural thing'.  The supernatural is other than 'thing'-like.  It is the opposite of 'thing'-ness, else it is not supernatural.  Ontology 101]

Thus the need to explain that there is information that cannot arise through purely natural processes by first showing that there is a non-natural process.
Go for it.

This is an excellent point. Crypto (and other creationists) accept that which has no supporting evidence, because it agrees with their worldview and explicitly reject that which does have evidence solely because it offends their worldview.

I would, however, suggest that Crypto read up on Ken Miller and Robert Bakker.

Finally, we should note that anything that can affect the material world will leave traces of those effects. Much like we can't see wind or electrons, but we can see the leaves blowing and control electricity.

Any supernatural event that affects the material world will leave evidence of that event. Whether or not we can study the cause of that event (the supernatural thing) is immaterial (get it?), we can see the event itself.

And we don't. Despite thousands of years of desperately looking, no event has happened that must be attributable to a supernatural cause.

Crypto has adopted definitions for things that explicitly reject the known causes behind things like evolution. By relying on his own knowledge and rejecting the knowledge of others, he has pigeon holed himself. It's a  shame, he seems like a smart guy, too bad he refuses to learn.

I mean look at his statement, "I haven't read it, but I will and I will find where you are cheating".  One, it's pretty arrogant. Two, it sounds just like Behe at Kitzmiller. "No, I haven't read those 30 books and 75 papers, but I know that they don't answer my question." The reason, of course, is because his question and logic was framed in such a way as that it could, by definition, never be answered. Same with crypto.

--------------
Ignored by those who can't provide evidence for their claims.

http://skepticink.com/smilodo....retreat

   
midwifetoad



Posts: 4003
Joined: Mar. 2008

(Permalink) Posted: Feb. 20 2015,08:12   

Regarding ORFan genes:

What percentage of genomes have been sequenced and cataloged?
Does having no cousins logically prove that one has no parents?

--------------
Any version of ID consistent with all the evidence is indistinguishable from evolution.

  
Wesley R. Elsberry



Posts: 4991
Joined: May 2002

(Permalink) Posted: Feb. 20 2015,08:20   

Cryptoguru:

 
Quote

that is just your opinion.


Sure, though presented with supporting evidence. So perhaps the "just" is out of place there.

As for the others on this board, there's only a small probability that any of them are surprised about what Cryptoguru was completely ignorant of until this morning (but perfectly willing to confidently state falsehoods about). I highly doubt that I will get the kind of excoriation Cryptoguru has received, and there are reasons why that should be the case. One is that I try to get stuff right.

The PI for my post-doc was Prof. Rob Pennock, a Quaker. The post-doc itself was funded under a Templeton Foundation grant. You can Google "John Templeton Foundation".

As for me, I follow the evidence wherever it leads. I take the rampant falsehoods told in furtherance of antievolution as one more indication of where it does not lead.

And that quote from Charles Darwin? It answered several of Cryptoguru's further inquiries.

--------------
"You can't teach an old dogma new tricks." - Dorothy Parker

    
N.Wells



Posts: 1836
Joined: Oct. 2005

(Permalink) Posted: Feb. 20 2015,08:37   

Quote
1) purely random mutation - nobody believes this is capable of producing information
Hold on a moment.  That is true only if we define "nobody" as "only you".  Random mutations produce new Shannon information. Whether that has any usefulness or is neutral or disadvantageous gets determined later.  This is another instance of you smuggling in your conclusions.

As another example of misuse of "information" or "meaning": you remember those "markings on beaches" that you mentioned earlier?  Sedimentologists can use ancient versions of "markings" like that to figure out which way to move the drill rig to find oil: in the right context, that can be several million dollars worth of information and meaning right there.

  
midwifetoad



Posts: 4003
Joined: Mar. 2008

(Permalink) Posted: Feb. 20 2015,08:40   

Whatever Darwin may have believed, he was not likely a young earth creationist. I think it is pretty certain he stopped believing that god steps in to save falling sparrows.

--------------
Any version of ID consistent with all the evidence is indistinguishable from evolution.

  
cryptoguru



Posts: 53
Joined: Jan. 2015

(Permalink) Posted: Feb. 20 2015,08:50   

Quote
Regarding ORFan genes:
What percentage of genomes have been sequenced and cataloged?
Does having no cousins logically prove that one has no parents?


midwifetoad: excellent question ... they assumed this was the case when they first started finding them. The theory went, that the ratio of ORFan genes to those which are represented in other organisms would start to level off as we sequence more genomes. Fact is they are linear and continue to grow linearly the more we sequence.

We obviously know an organism has parents, but this evidence pushes against the assumption of cousins in other species. You can't claim we're 96% chimp and at the same time say that 20-40% of our DNA is not found anywhere else. If you are assuming common ancestry between 2 species you need to be able to explain the divergence of their DNA. Previously we categorised the non-coding DNA as junk, now we know it isn't junk ... so we have to account for the information in the non-coding DNA now too which contains many ORFan genes (i.e. we're not 96% chimp). If we have to account for a minimum of 20% of our DNA being de novo in the last 13 Million years, we have to believe in minimum 500 advantageous mutations preserved every single generation. That is provably false.

http://mic.sgmjournals.org/content....99.full
quote from this article
Quote
Fig. 1(a)⇓ shows that the number of these orphan bacterial genes is continuing to rise in a roughly linear fashion despite the large number of genomes sequenced, and this trend shows no signs of levelling off. In fact, the last 30 species included in this study provided 30 % of the total orphans in our study (mean=441±643 for dataset D1; despite the large standard deviation all species contributed orphans).


and from this New Scientist article
http://ccsb.dfci.harvard.edu/web....013.pdf
Quote
Some other researchers, however, are
starting to think it may be surprisingly
common. A study of 270primate orphan
genes, led by M. Mar Albà and Macarena
Toll-Riera of the Municipal Foundation
Institute for Medical Research in Barcelona,
Spain, found that only a quarter could be
explained by rapid evolution after duplication
(Molecular Biology and Evolution, vol 26, p
603). Instead, around 60 per cent appeared
to be new.

  
Soapy Sam



Posts: 659
Joined: Jan. 2012

(Permalink) Posted: Feb. 20 2015,08:53   

Quote (midwifetoad @ Feb. 20 2015,14:12)
Regarding ORFan genes:

What percentage of genomes have been sequenced and cataloged?
Does having no cousins logically prove that one has no parents?

Most amino acids are substitutable by at least one other. Ultimately, unless there is constraint of some kind, gradual attrition will erase all sequence identity. For example alpha helix turns can be made from any mix of polar/non-polar residues (bar a few) in the appropriate pattern. One can change one's analysis, to score the residues simply on the binary hydrophobic/hydrophilic character - but this would not so readily support the conclusion that all alpha helixes share a common ancestor, because this binary pattern may find a huge set of common matches from convergence and 'chance'. Two consecutive turns would give the same score, but this does not mean they actually arose by original duplication (although well they might).

But the existence of ORFans in itself is fundamentally consistent with incomplete coverage and gradual erosion of signals of descent. If these genes really did come into existence de novo, the possibility on the data that remain that they arose by copying and scrambling would still have to be considered as a hypothesis. It's a classic case of absence of evidence is not evidence of absence, with respect to common ancestors. Which I know bugs the hell out of IDists, who don't see why absence of evidence does not mean evidence FOR something else. The 'null hypothesis' would be descent.

Edited by Soapy Sam on Feb. 20 2015,15:55

--------------
SoapySam is a pathetic asswiper. Joe G

BTW, when you make little jabs like “I thought basic logic was one thing UDers could handle,” you come off looking especially silly when you turn out to be wrong. - Barry Arrington

  
NoName



Posts: 2729
Joined: Mar. 2013

(Permalink) Posted: Feb. 20 2015,08:55   

Quote (cryptoguru @ Feb. 20 2015,07:12)
...
The theory of evolution was proposed by a trained clergyman (Darwin) who rejected God because his favourite daughter died. He is very clear in his writings what his motivation was for his theory, he therefore embraced the old-age naturalistic world-view proposed by Charles Lyell's work and rejected the Bible as a source of truth .. I know that doesn't prove evolution is wrong, but the world-view that birthed the theory (atheism) is the same world-view that propagates and enforces it now.
There's a lot of people who believe in God, who also believe in evolution ... but generally only because they don't understand how it contradicts their faith and is therefore irrational to believe both.

That's appalling and vile.
It amounts to nothing more than a particularly offensive ad hominem argument.

Darwin's motivations for writing Origin of Species are entirely irrelevant to its truth/falsity.  Entirely.
Darwin could have been a mother-murdering puppy torturer who routinely desecrated communion wafers and spit on the pope.  Irrelevant to the truth/falsity of his work.
He may have been a virtual saint, kindly to the poor and downtrodden, a man who routinely exceeded the tithing recommendations of the church, gave all his property to the poor, worked tirelessly to abolish slavery and institute women's suffrage.  Entirely irrelevant to the truth/falsity of his work.

Neither your opinion of  Darwin the man nor mine matters to the truth or falsity of his ideas.

Good men can do bad work.  Bad men can do good work.  It is the work that matters, not the man.  Not when it is the work under consideration.

That his work has stood up so well, has survived falsification, has made, and generated, predictions that have by and large been satisfied, has enabled vast increases in our understanding of the natural world, those are the facts that matter.

That Darwin might have been wrong in the details hardly matters -- his 'big picture' theory of the inter-relatedness of all things, his theory of natural selection, broadly taken, are breathtaking insights that have stood the test of time.  They have stood that test by generating ever-better insights into the information nature serves up by the process of the operation of natural laws, the foundation and cornerstone of science.

You're just desperate to focus on anything other than the information served up by natural processes.  If you don't like the message, attack the messenger.  That's what you're doing, and it is contemptible.

  
midwifetoad



Posts: 4003
Joined: Mar. 2008

(Permalink) Posted: Feb. 20 2015,09:06   

So when there are no fingerprints, and the door is locked from the inside, goddidit. I think I write a detective novel. I don't think anyone has used that plot.

--------------
Any version of ID consistent with all the evidence is indistinguishable from evolution.

  
NoName



Posts: 2729
Joined: Mar. 2013

(Permalink) Posted: Feb. 20 2015,09:16   

Quote (cryptoguru @ Feb. 20 2015,08:59)
NoName: you seem to keep conflating the 2 distinct concepts
No, that would be you.  Random mutation introduces changes.  Natural selection is the descriptive term for the success/failure of those changes to be preserved in the population, generation by generation.

   
Quote
purely random mutation - nobody believes this is capable of producing information

That, sir, is a lie.  Random mutation is capable of producing information in any relevant sense of the term.  That is, in all cases except those where a relevant  term has been prejudicially excluded a priori.  Or where information is conflated with meaning; they are distinct concepts.  It is known that there are 'meaningless' genetic changes.  There are two codons which are interchangeable in some/most/all cases, and thus changing from one to the other is effectively a no-op.  And thus meaningless from an evolutionary perspective.
     
Quote
2) random mutation plus natural selection - you believe this can create information, I don't

And you are demonstrably wrong.  Random noise plus a finely tuned filter can pick out single tones.  Random noise plus a bank of finely tuned filters, which is precisely analogous to  a single step in the  series that constitutes evolution over time, can pick out harmonics.
Or consider the Oklo reactors -- random assortment and arrangement of minerals and liquids resulting in natural nuclear reactors that turn on and off until eventually, over long periods of time, they extinguished for a last time.  The information of the residue allows us to know this, and all of it produced by random processes operating under natural law.
     
Quote
Monkeys typing on typewriters will not produce the works of Shakespeare as Dawkins has attested to, he contests that cumulative natural selection is able to guide the purely random process and create information.

There's that 'guide' notion again.  What guides mutations are the laws of physics and chemistry and the circumstances, the entirely specific context, in which they operate.  Nothing guides random mutation in the sense you keep using.  Natural selection gives the appearance of guiding because it preserves some of the random changes and not others.  Over successive generations, this results in a changed population.  The random changes are still random changes.  The result is selected from the set of all random changes, over time.  And that's where the appearance of 'guided' comes in.  It is guided in a purely naturalistic, historical sense.  And the guide is the slowly changing environment.
     
Quote
I want to see that demonstrated ... you keep jumping around your definitions. This is a simple issue ... find "new information" that couldn't arise purely randomly  by using random mutation and natural selection.

Stop assuming your conclusion.
Prove that random mutations and natural selection cannot generate new information.  You can't.  We have the proof that it can.  Look at life.  Look at Lenski's experiment.  Look at astrophysics.

     
Quote
Find a solution that defies simple probability e.g. rolling a die 36 times will likely get you 2 sixes in a row at some point ... this is not what we're talking about,

Yes it is.  If you have a system that continues to preserve the sixes that come up, you wind up with as many sixes in a row a you have dice.  Or to better simulate nature, you preserve whichever number shows up twice in the set of dice.  You will soon wind up with nothing but that number in the set, no matter how large the set is.
Do you not know the game Yahtzee?  This is precisely what it accomplishes, the task you claim is impossible.
     
Quote
you need to demonstrate complex information that could not occur probabilistically arising because natural selection is doing something that pure dumb-luck can't.

No, you have to demonstrate that 'complex information' cannot arise probabilistically.
You keep asserting it as if it were known, and proven to be the case.
It isn't and it hasn't.

  
Quack



Posts: 1961
Joined: May 2007

(Permalink) Posted: Feb. 20 2015,09:58   

Quote
Monkeys typing on typewriters will not produce the works of Shakespeare as Dawkins has attested to, he contests that cumulative natural selection is able to guide the purely random process and create information.

Anyone ever computed the probability that any number of monkeys with typewriters could produce even one of the works of Shakespeare? I don't think even the Isaac Newton of Information Theory would care to try.

IMHO, not even the entire population of the world typing randomly on their keyboards would do much better.

When people resort to that kind of arguments it is a strong indicator they are somewhat clueless.

--------------
Rocks have no biology.
              Robert Byers.

  
Soapy Sam



Posts: 659
Joined: Jan. 2012

(Permalink) Posted: Feb. 20 2015,10:05   

Quote (midwifetoad @ Feb. 20 2015,15:06)
So when there are no fingerprints, and the door is locked from the inside, goddidit. I think I write a detective novel. I don't think anyone has used that plot.

There is a problem of sorts, when one looks at an ORFan that is restricted to a single species. How do they change so completely in such a short time frame? But ORFans most likely arise in regions that lack substantial constraint anyway. If the parent sequence was constrained, the ORFan would not get off the ground as a variation on it.

They often seem to arise because transcription/translation signals get wrapped around a random stretch of previously untranslated DNA. Since the original sequence, and probably the new one as well, lack selective constraint, they will just keep diverging at twice the neutral rate. If the new sequence proves beneficial, it's unlikely to be perfect, so directional selection will push it yet more rapidly away from the original sequence. Hey Presto! Genes from nowhere!

Edited by Soapy Sam on Feb. 20 2015,18:19

--------------
SoapySam is a pathetic asswiper. Joe G

BTW, when you make little jabs like “I thought basic logic was one thing UDers could handle,” you come off looking especially silly when you turn out to be wrong. - Barry Arrington

  
Wesley R. Elsberry



Posts: 4991
Joined: May 2002

(Permalink) Posted: Feb. 20 2015,10:07   

The "typing monkeys" analogy.

--------------
"You can't teach an old dogma new tricks." - Dorothy Parker

    
NoName



Posts: 2729
Joined: Mar. 2013

(Permalink) Posted: Feb. 20 2015,10:11   

Quote (cryptoguru @ Feb. 20 2015,08:59)
...you need to demonstrate complex information that could not occur probabilistically arising because natural selection is doing something that pure dumb-luck can't.

Narrowing in on what seems to be the key point.
And moving away from biology, which seems to be the sore point, as similar issues in other fields don't result in the same visceral and irrational rejection of natural law plus chance/randomness.

Consider stellar spectra.  They are complex.  They are information, they convey very precise details about the composition of the star and useful information about the intervening matter, if any, plus useful distance information (via red shift).  Much information.  The information is complex, the meaning is not trivially 'read off' the surface data, but the information is there and it is meaningful.
Stellar composition and stellar position are both effectively random.  Natural law working on the random distribution of matter results in stellar genesis, and the life-cycle of the star results, often enough, in nucleogenesis.  The materials and processes involved leave their signature, so to speak, in the stellar spectra.

So how is this not a demonstration that complex information can occur probabilistically, by dumb-luck, which you assert is not possible?
Where is there anything other than dumb-luck and natural law involved?  Why is the information of the stellar spectra not complex and meaningful information?  Why is the red-shift of the spectrum not meaningful and complex information about the distance of the star?
Where does this example fail to meet the honest portions of your criteria for complex meaningful information arising from purely natural law with probabilistic 'dumb-luck'?
Is it, could it be, that it is not about biology, and that it is entirely driven by natural law, which you reject out of hand for biology, for reasons yet to be satisfactorily supported?

  
stevestory



Posts: 13407
Joined: Oct. 2005

(Permalink) Posted: Feb. 20 2015,10:40   

Quote (cryptoguru @ Feb. 20 2015,06:53)
Wes, your world-view pre-supposes purely natural causation and excludes supernatural, intelligent causation ... as that is the purpose of the theory of evolution; to explain origins without the need for an intelligent agent.
Evolutionary theory is the science of atheists and fake atheists (agnostics), who need to find a way to explain the origin and diversity of life without a God.

Thus the need to explain that information can arise automatically from noise by purely natural processes.

hahahahahhahaha. Crypto, you're the best of the 3 creationists here, but you're still not any good.

   
cryptoguru



Posts: 53
Joined: Jan. 2015

(Permalink) Posted: Feb. 20 2015,10:47   

NoName: This statement is fact:
pure randomness by itself cannot account for the arrival of complex information ... evolutionists (educated ones) agree with this point

You are confusing what information is ... information is not simply something that is patterned or useful. A hammer is useful, it is not information. The instructions on how to build a hammer or how to use a hammer to make an object with nails and wood IS information.

Natural occurring patterns and stellar "signatures" are NOT information they have no intended meaning.
The pattern of stripes on a bee's body is not information, the way it moves its body to communicate to other bees where the honey is located IS information.
DNA is information because it means something to the living cell that is interpreting the data. The cell is running an instruction set (DNA) that it understands. The cell can't run ANY instruction set, the instruction set has to mean something to the interpreter, which goes about using that information to build proteins and assemble them into complex structures.

Randomness cannot create information.

Evolutionists assert that natural selection on randomness creates information by filtering out noise and leaving information through competition. I would like to see THAT happen without imposing intelligence on the system by telling it what it should be producing.

EXAMPLE (from InterStellar the movie):
pour dust on the floor, it makes a pile ... does that pile contain information? No. It's just a pile of dust.
interact with the dust to make it form piles that represent morse code and convey a message. It's information now!
What made it information? Has anything changed in the dust itself? No! Did the dust contain the natural properties to create the information itself? No! The information was enforced by an outside intelligence and had meaning to an intended recipient.

I assert that information cannot originate naturalistically, that it must be caused by an intelligence. That's exactly what SETI does ... the search for ET INTELLIGENCE is to find transmitted information or signs of intelligence.
What are they looking for? Messages or structure that you wouldn't expect to originate randomly.
They expect to be able to differentiate between the radio waves sent from stars and those sent from an intelligence. How? Because intelligence is identifiable by us. We understand that a letter that came through our front door with our name on it was sent by an intelligent sender and intended for us, it didn't happen randomly.

Evolutionists believe that natural selection is able to somehow steer the randomness to create information-rich systems that are functional and diverse. I don't believe that and I'm challenging you to show me that happening on a mathematical, information theory level.
Nothing you've mentioned is even in a similar problem space to what I'm talking about.

  
midwifetoad



Posts: 4003
Joined: Mar. 2008

(Permalink) Posted: Feb. 20 2015,10:50   

Quote
pure randomness by itself cannot account for the arrival of complex information


Sure it can, and it does all the time. What you might say is that random process cannot accumulate long strings of "functional" information.

That takes differential reproductive success. And iteration, and time.

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Any version of ID consistent with all the evidence is indistinguishable from evolution.

  
OgreMkV



Posts: 3668
Joined: Oct. 2009

(Permalink) Posted: Feb. 20 2015,10:56   

I was going to right a big explanation, but I realize that I have before and crypto isn't interested in actually learning anything, he's just looking for something else to latch on to in order to try to discredit ideas he doesn't like (or understand).

I'll wait until the radioactive material comes back in vogue.

--------------
Ignored by those who can't provide evidence for their claims.

http://skepticink.com/smilodo....retreat

   
stevestory



Posts: 13407
Joined: Oct. 2005

(Permalink) Posted: Feb. 20 2015,10:58   

Quote (cryptoguru @ Feb. 20 2015,11:47)
Natural occurring patterns and stellar "signatures" are NOT information they have no intended meaning.

wow that's clueless. Please keep going. We can laugh at you with much less guilt than we can laugh at Gary Gaulin.

   
cryptoguru



Posts: 53
Joined: Jan. 2015

(Permalink) Posted: Feb. 20 2015,10:59   

midwifetoad: oh my word, some of you guys are really dense on this issue!

I am differentiating between PURE randomness, that which can arrive through pure probability WITHOUT "differential reproduction success" (i.e. without natural selection e.g. monkeys on typewriters)

and randomness which you're saying CAN produce information by being acted on by natural selection. (which I don't believe)

How hard is it???
this is just a definition ... I'm just clearly delineating between the 2 different kinds of random event that we are talking about. There should be no disagreement here.

1) PURE UNDIRECTED randomness, which simply creates random output and not information
2) randomness with selection, which you're saying can make information

STOP TALKING ABOUT 1) CREATING INFORMATION ... NO-ONE BELIEVES THAT!!!!
WE SHOULD BE ARGUING ABOUT 2) NOT 1)

Can someone with half a brain chip in here to help your evolutionary friend understand what I'm saying?

  
stevestory



Posts: 13407
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(Permalink) Posted: Feb. 20 2015,11:05   

why don't you get a dictionary and look up the word information? You don't seem to know anything about anything.

   
Wesley R. Elsberry



Posts: 4991
Joined: May 2002

(Permalink) Posted: Feb. 20 2015,11:07   

Quote (cryptoguru @ Feb. 20 2015,10:59)
midwifetoad: oh my word, some of you guys are really dense on this issue!

I am differentiating between PURE randomness, that which can arrive through pure probability WITHOUT "differential reproduction success" (i.e. without natural selection e.g. monkeys on typewriters)

and randomness which you're saying CAN produce information by being acted on by natural selection. (which I don't believe)

How hard is it???
this is just a definition ... I'm just clearly delineating between the 2 different kinds of random event that we are talking about. There should be no disagreement here.

1) PURE UNDIRECTED randomness, which simply creates random output and not information
2) randomness with selection, which you're saying can make information

STOP TALKING ABOUT 1) CREATING INFORMATION ... NO-ONE BELIEVES THAT!!!!
WE SHOULD BE ARGUING ABOUT 2) NOT 1)

Can someone with half a brain chip in here to help your evolutionary friend understand what I'm saying?

How long is the program and input needed to output a random string?




I don't think Cryptoguru knows as much about information theory as he is claiming.

--------------
"You can't teach an old dogma new tricks." - Dorothy Parker

    
cryptoguru



Posts: 53
Joined: Jan. 2015

(Permalink) Posted: Feb. 20 2015,11:11   

Quote
why don't you get a dictionary and look up the word information? You don't seem to know anything about anything.


I did that earlier ...
"what is conveyed or represented by a particular arrangement or sequence of things."
it necessitates that it has meaning.

What you're doing is the fallacy of equivocation.

we are not talking about
"facts provided or learned about something or someone."

We are talking about DNA ... DNA is information that represents the instructions on how to build an organism, it necessitates meaning for an intended recipient. The cell is the intended recipient and understands the meaning of the arrangement of nucleotides.

Guys, this is stuff we shouldn't be arguing about ...
sure let's argue about how Natural Selection is able to filter noise and create information out of randomness, but this attempt to say that everything is information is utter stupidity of the highest order and something a 5 year old would rightly laugh at.

  
stevestory



Posts: 13407
Joined: Oct. 2005

(Permalink) Posted: Feb. 20 2015,11:16   

we shouldn't be arguing about this stuff. But you're clueless, so we are. Learn something, and be more interesting in the future.

   
cryptoguru



Posts: 53
Joined: Jan. 2015

(Permalink) Posted: Feb. 20 2015,11:19   

Quote
I don't think Cryptoguru knows as much about information theory as he is claiming.

Wes: There are things written on this discussion topic by those on "your side" which you shouldn't agree with; but you seem happy to kiss your brains goodbye and go along with insane theories like "randomness is information", instead of sticking to the sensible discussion topic which is "can information arise out of randomness via natural selection". Dawkins would laugh at the stupidity of some of the claims made in the last few posts by evolutionists.

This discussion has taken a surreal and utterly ridiculous turn for the irrational

  
midwifetoad



Posts: 4003
Joined: Mar. 2008

(Permalink) Posted: Feb. 20 2015,11:23   

Quote
We are talking about DNA ... DNA is information that represents the instructions on how to build an organism,


And random changes to DNA test the neighborhood. Are there any sequences made by modifying one character that are equivalent or superior?

If you are blind, and want to know about your vicinity, you probe with your hands. You can only test the immediate vicinity. Evolution is a bit like that. It continually tests the immediate vicinity.

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Any version of ID consistent with all the evidence is indistinguishable from evolution.

  
stevestory



Posts: 13407
Joined: Oct. 2005

(Permalink) Posted: Feb. 20 2015,11:29   

i'm hoping cryptoamateur is just a bible-soaked teen who will one day learn some stuff and join the discussion of interesting stuff.

   
N.Wells



Posts: 1836
Joined: Oct. 2005

(Permalink) Posted: Feb. 20 2015,11:29   

Quote (cryptoguru @ Feb. 20 2015,10:59)
midwifetoad: oh my word, some of you guys are really dense on this issue!

I am differentiating between PURE randomness, that which can arrive through pure probability WITHOUT "differential reproduction success" (i.e. without natural selection e.g. monkeys on typewriters)

and randomness which you're saying CAN produce information by being acted on by natural selection. (which I don't believe)

How hard is it???
this is just a definition ... I'm just clearly delineating between the 2 different kinds of random event that we are talking about. There should be no disagreement here.

1) PURE UNDIRECTED randomness, which simply creates random output and not information
2) randomness with selection, which you're saying can make information

STOP TALKING ABOUT 1) CREATING INFORMATION ... NO-ONE BELIEVES THAT!!!!
WE SHOULD BE ARGUING ABOUT 2) NOT 1)

Can someone with half a brain chip in here to help your evolutionary friend understand what I'm saying?

You can't possibly want a mathematical discussion on the level of information theory if you reject basic definitions of information.  #1 creates a perfectly good form of information (Shannon information), but you don't like that definition.  You want information to have "intended meaning".  Well, at that point you've tried to rig the game, because how could can anything have intention if it isn't intelligent, so of course it seems to you that information has to be generated by intelligence.

However, on what basis do you determine that the existence of an organism carries intended meaning?

Seismic stratigraphy involves exploding some dynamite (or creating shock waves some other way), having the shockwaves propagate down into the subsurface, all the while bouncing off fractures, rock layers, and so forth.  This is a very noisy process.  A small fraction of the shockwaves make it back up to the surface, bouncing all over the place on the way back up.  The resulting signal has a huge amount of "noise", very little "signal", and absolutely no intended meaning.  However, it is all information.  Filtering it and processing it, using techniques created via information theory, allows geologists to reconstruct the thickness and orientations of the beds underground, which is extremely valuable and useful information, worth hundreds of millions of dollars, all with absolutely no intended meaning whatsoever.

The pattern of stripes on a bee's body is information: it communicates species membership to other bees.  (And the waggle dance communicates the location of nectar, not honey.  In fact, the bee's stripes, among other things, communicates to other bees whether it legitimately belongs in the honey location where it is doing its waggle dance.)

 
Quote
natural selection is able to somehow steer the randomness
You had it right with "filter": "steer" is very wrong.

Lenski's citrate-eating bacteria didn't have to happen.  They weren't bred for it.  Citrate was not present in the growth medium with the intention of providing a challenge to the bacteria.  The key mutation was unable to happen without a prior mutation that didn't appear to contribute anything. Both mutations occurred about as randomly as can be in mutations. That is new information.

Of course, the first mutation was new information too, even if it had no meaning, no function, and no benefit at the time.  Up until the second mutation, the first mutation was to all intents and purposes (phrase used advisedly) just noise.

Take a functioning gene.  Duplicate it (that happens all the time).  That is new Shannon information, because your compressed version has now been increased by the need to say "x2".  It probably doesn't do anything useful, although an extra copy of a gene can have its uses.  Now if one of the two copies suffers a mutation that disables its function, that's no longer a problem, and the duplicated can go on to suffer additional changes, some of which might develop other uses.  Actually, the first mutation probably didn't disable the primary function, but shifted it, thereby contributing to a different suite or range of capabilities.

Check out the story of the genetic accidents that created domesticated wheat.

  
Wesley R. Elsberry



Posts: 4991
Joined: May 2002

(Permalink) Posted: Feb. 20 2015,11:36   

Quote (cryptoguru @ Feb. 20 2015,11:19)
 
Quote
I don't think Cryptoguru knows as much about information theory as he is claiming.

Wes: There are things written on this discussion topic by those on "your side" which you shouldn't agree with; but you seem happy to kiss your brains goodbye and go along with insane theories like "randomness is information", instead of sticking to the sensible discussion topic which is "can information arise out of randomness via natural selection". Dawkins would laugh at the stupidity of some of the claims made in the last few posts by evolutionists.

This discussion has taken a surreal and utterly ridiculous turn for the irrational

Do the names Kolmogorov, Solomonoff, or Chaitin ring a bell?

If Cryptoguru wants to discuss this stuff and not look ignorant, he ought to.

Again, this is a matter of disgreeing with Cryptoguru, not "kissing my brains goodbye". And, as it happens, I know that there is good reason to disagree, precisely on those mathematical grounds Cryptoguru likes to invoke in his cargo-cult fashion.

Again: How long is the program and input needed to output a random string?

--------------
"You can't teach an old dogma new tricks." - Dorothy Parker

    
NoName



Posts: 2729
Joined: Mar. 2013

(Permalink) Posted: Feb. 20 2015,12:01   

Quote (cryptoguru @ Feb. 20 2015,11:47)
NoName: This statement is fact:
pure randomness by itself cannot account for the arrival of complex information ... evolutionists (educated ones) agree with this point

Citation needed.  
And just what do you mean by 'pure' randomness?
And just what do you mean by 'complex information'?
I gave a set of very clear questions which you did not answer.  Why?  They would clear up a great deal, but instead you fall back and make another run at, let's face it, vague and prejudicial verbiage.

   
Quote
You are confusing what information is ... information is not simply something that is patterned or useful. A hammer is useful, it is not information. The instructions on how to build a hammer or how to use a hammer to make an object with nails and wood IS information.

Natural occurring patterns and stellar "signatures" are NOT information they have no intended meaning.

That's a highly prejudicial, and short-sighted, and ultimately wrong, definition of information.
A hammer is information -- it tells you a great deal about the kind of creator who created it, the kinds of technologies involved, the intended uses, other possible uses, etc.  There is a host of information in everything we encounter.
But now you want 'information' to apply only where there is intent.  And worse, only when the intent is known beforehand.
That's bullshit, because it requires prior knowledge of intent in order to determine anything whatsoever.  We did not know the intent behind the construction of the Antikythera mechanism, but we knew a great deal about it regardless.
Similarly, we knew a great deal about stellar spectra before we knew what they meant.  They have meaning, and you have not addressed that salient fact.
You want to fall back to the ridiculous notion that information requires prior intent.  In a world filled with information, that amounts to assuming your conclusion.
I am rejecting your notion of 'information' as not only not helpful or useful, but wrong.  Flat-out wrong.

 
Quote
The pattern of stripes on a bee's body is not information, the way it moves its body to communicate to other bees where the honey is located IS information.

How do you know?
A very few years ago you could have made a similar argument about the stripes on a zebra.  But it turns out the stripes fulfill a purpose with respect to pest attacks.
You want to restrict 'information' to 'informative'.  That requires knowledge that may or may not exist, which means the same item may be information to one person and not to another.
The exact same case as your foolishness with DVD players.
Worse, the information content of the dance of the bees did not change when we learned it was meaningful to the bees.  That information content was always there, but we only learned it recently.  This fact blows your pseudo-definnition out of the water.  Our knowledge of a thing does not change the nature of the thing, it only changes what we know.  
You're simply wrong here, wrong because you are using non-standard, prejudicial, and ultimately useless definitions that are derived not from the facts of the matters at hand but from your prejudices.  
   
Quote
DNA is information because it means something to the living cell that is interpreting the data.

So meaning is use?  That's rather odd, because that amounts to saying that oxygen is meaningful to hydrogen because it means something to the water molecule they form when they bind.  Gary Gaulin is at the end of that path, and it's wrong.  Worse, it is absurd; absurd because it can only be applied selectively and with intent aforethought.  
   
Quote
The cell is running an instruction set (DNA) that it understands. The cell can't run ANY instruction set, the instruction set has to mean something to the interpreter, which goes about using that information to build proteins and assemble them into complex structures.

That is so wildly oversimplified that it is false for the uses you require of it.
The DNA and the cell are not independent artificial constructs that are 'brought together' to fill a function.  They are part of one whole, and there is zero reason to suppose that any external intent was required for that to happen.  Worse, for you, there is absolutely zero evidence not only for the need for an external intent, but absolutely no evidence of any possible external intent that could accomplish this, nor any traces of such intent.
The actions and behavior of the separable parts of the whole that is a cell are as explicable, and as natural, as the binding of hydrogen and oxygen to form water or the binding of sodium and chlorine to form salt or the atomic decay of certain isotopes of uranium that generated the natural nuclear reactors at Oklo.
One might think, not knowing any better, that something as complex as a nuclear reactor, in a system that is self-damped and that cycles on and off, requires external intent and assembly by external forces.  One would be wrong, as Oklo conclusively demonstrates.
You're wrong here and we've explained why.

   
Quote
Randomness cannot create information.

Why not?  Pi is information.  The digits of the expansion of pi include the first n digits of the expansion of pi as a subset.
There is a table of random numbers that contains a series of integers in numeric order; randomness has no difficulty accomplishing that other than sufficient runs, sufficiently long outputs.
You keep asserting that 'randomness cannot do x' without ever proving it or referencing a proof.  I've rejected it and I've offered reasons to reject it.
Worse, you toss around 'randomness' without ever relating it to natural law, and you toss around 'natural law' without ever relating it to randomness.
You objected to my phrase 'constrained randomness' when I used it during your first visit here.  Let me elaborate.  You seem to be taking an extreme view of what 'random' means, a view that amounts to 'anything at all is possible as the next result in a random  series'. That is nonsense.  'Constrained random' is always and only what we get.  A series of random numbers does not run '1, 2, e*, eggplant**, supernova**, 57, '57 Chevy'**, the law of non-contradiction**, wind from the NW at 5 knots**, etc.'
**where each of these terms is the thing named, not the name of the thing named
Random does not mean "anything at all without limits and  selected from all possible existent items".  The DNA codons are random, but you only ever encounter A,G,C, or T in the natural case.  Constrained randomness.
And what of natural law and randomness?  Clarify what you mean by the two, what their relationship is, how they operate together or in opposition.
You appear to have lost on this point.
   
Quote
Evolutionists assert that natural selection on randomness creates information by filtering out noise and leaving information through competition. I would like to see THAT happen without imposing intelligence on the system by telling it what it should be producing.

If your sense of 'intelligence' is sufficiently broad as to include nature, you can't.  If it's not, you're not talking abut the real world.
We've seen it, we have no reason to doubt it, and you have no alternative mechanism that is supported by evidence of ever having occurred.
You lose on this point.

   
Quote
EXAMPLE (from InterStellar the movie):
pour dust on the floor, it makes a pile ... does that pile contain information? No. It's just a pile of dust.

Shortsighted and incredibly wrong.  Dust is made up of stuff.  The kinds of stuff that make up the pile of dust is information about who has been in the room, what else has  been in the room, how long the room has been left uncleaned to some degree of precision, etc.  The size and shape of the pile contain information about how the pile was formed, as does the position of the pile with respect to the larger context (doors, windows, walls, floor, ceiling, etc.)  You're picking and choosing what you choose to call 'information' by eliminating all the things that you aren't focused on.  Not focusing on it, not being able to see it, doesn't mean it's not information.  Consult a forensics team and tell them a pile of dust has no information.  Once they get done picking their jaws up off the floor, they'll be laughing hysterically.

   
Quote
interact with the dust to make it form piles that represent morse code and convey a message. It's information now!
There's different, possibly more, information now, but that's because you're playing fast and loose with what you're prepared to count as information at any given point.  And what you choose to consider as information is entirely constrained by what you know now.  That's a precarious, at best, meaning of the term 'information'.  It again hearkens back to 'informative' rather than 'information'.
What if you don't know Morse code?  What if Samuel Morse had chosen different patterns for the code?
It's the Simpson's episode with Kang and Kodos looking at a skull shaped island and  saying "shaped just like our number 4.  Really makes you think, doesn't it?"

   
Quote
What made it information? Has anything changed in the dust itself? No! Did the dust contain the natural properties to create the information itself? No! The information was enforced by an outside intelligence and had meaning to an intended recipient.

Wrong, across the board.  There is nothing that prevents the wind, or the pattern of broom strokes, to create patterns in the dust that can be taken to be  Morse Code.  Or some analog to Morse code that we don't know.
Just as the stellar spectra were information even before we knew what they meant.
If natural laws do not lead to information, science is not possible.
   
Quote
I assert that information cannot originate naturalistically, that it must be caused by an intelligence.

And that's where you define science as impossible.  Your assertion is a blatant unsupported and unsupportable assertion.  It is not supported by evidence, it is only supported by the rejection of evidence and the acceptance of culturally driven fictions.
   
Quote
That's exactly what SETI does ... the search for ET INTELLIGENCE is to find transmitted information or signs of intelligence.

Misinterpretation.  SETI is looking for patterns such as we know could be produced by intelligence.  This does not restrict the field of information to what can be produced by intelligence, yet with that caveat accepted, your argument falls.  Stellar spectra are information and they are not assumed to be the product of intent.  There is no need to make such an assumption because natural law suffices.  We have learned that over time; the information content of starlight has not changed, our ability to extract the informative from it has.

   
Quote
What are they looking for? Messages or structure that you wouldn't expect to originate randomly.

Not quite.  Structure that are highly unlikely to originate randomly, but not  structure that is impossible to randomly occur.  The processes we understand, by the information we have extracted from natural laws, place limits on the probabilities.  If we knew less, the probabilities we used would be other than they are.  When we know more, they will be different.
It is an absurdity to tie information to the receiver of it.  To think otherwise is to reject the possibility of science and of knowledge.
   
Quote
They expect to be able to differentiate between the radio waves sent from stars and those sent from an intelligence. How? Because intelligence is identifiable by us. We understand that a letter that came through our front door with our name on it was sent by an intelligent sender and intended for us, it didn't happen randomly.

There's that abuse of 'random' again.
As well as the prejudicial ad hoc selection of what counts as information.

   
Quote
Evolutionists believe that natural selection is able to somehow steer the randomness to create information-rich systems that are functional and diverse. I don't believe that and I'm challenging you to show me that happening on a mathematical, information theory level.

With a precise operational definition of 'information', 'meaning', and 'random', the answer is 'stellar spectra', 'belousov zhabotinsky reactions', 'DNA patterns between parent/child and between individuals with more distant relationships', ecosystems, the Oklo reactors, etc.

   
Quote
Nothing you've mentioned is even in a similar problem space to what I'm talking about.

That's largely because you choose your problem space ad hoc, as you go, redefining terms, excluding data, and setting up contradictory conditions, or conditions that have far more extreme results than you would be willing to accept as you go.
Your problem  space is imaginary.  It is the child insisting that *this* wolf is friendly and will look out for people because of a disney movie he has seen, while that wolf is bad and will hurt people.  It is the refusal to accept data, to accept and acknowledge evidence, and the continuous generation of new pseudo-problems in a futile attempt to find a thought experiment that will invalidate 150 years of biology.  Lenski alone suffices, and he is not alone.
You're simply wrong.
You can't accept that, so you keep making up pseudo-problems and rejecting the answers you get because they're not the answers you want.
You can't counter the evidence we've provided, so you keep trying to recast the shape of the problem.
Stellar spectra are complex information, produced by natural law, without intent.
If information relies on the knowledge of the person who encounters it, you are accepting an extreme subjectivism of the worst sort, and rending science and human knowledge impossible.
Deal with it.

  
midwifetoad



Posts: 4003
Joined: Mar. 2008

(Permalink) Posted: Feb. 20 2015,12:30   

Zebra stripes are so 15 minutes ago. Maybe yes, maybe no.

Larry Moran says the verdict is not in.

--------------
Any version of ID consistent with all the evidence is indistinguishable from evolution.

  
stevestory



Posts: 13407
Joined: Oct. 2005

(Permalink) Posted: Feb. 20 2015,12:42   

I think NoName and N.Wells deserve some sort of lifetime achievement award for doing the tedious explanatory work the rest of us shrug off. And Wesley of course, but we're working with his primary care physician to take his ultra-comprehensive OCD down to healthy levels.  :p

   
N.Wells



Posts: 1836
Joined: Oct. 2005

(Permalink) Posted: Feb. 20 2015,12:49   

Quote
It is an absurdity to tie information to the receiver of it.  To think otherwise is to reject the possibility of science and of knowledge.

That does explain how he is able to dismiss all the responses to his stuff: he isn't receiving the information, therefore there isn't any.

  
OgreMkV



Posts: 3668
Joined: Oct. 2009

(Permalink) Posted: Feb. 20 2015,12:59   

Quote (N.Wells @ Feb. 20 2015,12:49)
Quote
It is an absurdity to tie information to the receiver of it.  To think otherwise is to reject the possibility of science and of knowledge.

That does explain how he is able to dismiss all the responses to his stuff: he isn't receiving the information, therefore there isn't any.

Apparently, the only information (meaning) that he accepts is that generated by himself.

I do think that he's the only person I've seen who has said (in effect), "yes, all your points are correct, but you're still wrong".

It's pretty impressive actually .

--------------
Ignored by those who can't provide evidence for their claims.

http://skepticink.com/smilodo....retreat

   
NoName



Posts: 2729
Joined: Mar. 2013

(Permalink) Posted: Feb. 20 2015,13:00   

Quote (N.Wells @ Feb. 20 2015,13:49)
Quote
It is an absurdity to tie information to the receiver of it.  To think otherwise is to reject the possibility of science and of knowledge.

That does explain how he is able to dismiss all the responses to his stuff: he isn't receiving the information, therefore there isn't any.

I think you're right.
I'm about done here, at least at the level of detail I've been providing up to now.  If he's not willing to directly address the direct questions aimed at him, it's pretty clear he's not arguing in good faith, he's not really carrying on a discussion.

  
Wesley R. Elsberry



Posts: 4991
Joined: May 2002

(Permalink) Posted: Feb. 20 2015,13:00   

Cryptoguru:

 
Quote

I assert that information cannot originate naturalistically, that it must be caused by an intelligence. That's exactly what SETI does ... the search for ET INTELLIGENCE is to find transmitted information or signs of intelligence.
What are they looking for? Messages or structure that you wouldn't expect to originate randomly.
They expect to be able to differentiate between the radio waves sent from stars and those sent from an intelligence. How? Because intelligence is identifiable by us. We understand that a letter that came through our front door with our name on it was sent by an intelligent sender and intended for us, it didn't happen randomly.


Answers to IDC questions

 
Quote

2. RELEVANCE OF SETI. The search for extraterrestrial intelligence (SETI) is a scientific research program that searches for signs of non-human intelligence from distant space. Should biologists likewise search for signs of non-human intelligence in biological systems? Why or why not?

A. SETI is a good example of scientific approaches to "detecting design". SETI works precisely by taking information from human experience and using that to help decide what would constitute a signal that would indicate the existence of a non-human extra-terrestrial intelligence. SETI does not use procedures such as those talked about by "intelligent design" advocates. Instead, SETI looks for narrowband radio sources, the sort of radio sources that humans would build if we decided to send a radio message to other intelligent beings in space. This has nothing to do with the content that may be broadcast in such a signal, but rather this distinguishes a manufactured radio source from natural radio sources, which typically are spread over many frequencies. Most biological systems do not produce appreciable radio waves, and certainly not narrowband signals of the sort that the SETI project looks for.

Additional reading: SETI Project FAQ that notes the search for narrowband carriers, and that their current equipment is not even capable of recording signal content.


See also The advantages of theft over toil for more about the distinction between ordinary design hypotheses and rarefied design conjectures.

--------------
"You can't teach an old dogma new tricks." - Dorothy Parker

    
NoName



Posts: 2729
Joined: Mar. 2013

(Permalink) Posted: Feb. 20 2015,13:04   

Quote (stevestory @ Feb. 20 2015,13:42)
I think NoName and N.Wells deserve some sort of lifetime achievement award for doing the tedious explanatory work the rest of us shrug off. And Wesley of course, but we're working with his primary care physician to take his ultra-comprehensive OCD down to healthy levels.  :p

Why thank you!
I actually kind of enjoy it, there are so many things  an interested amateur, and that's all I am, can bring to the table.  
Cutting through the bafflegab and getting to the core issues and the direct implications of statements made is a useful skill to hone.

  
JohnW



Posts: 3217
Joined: Aug. 2006

(Permalink) Posted: Feb. 20 2015,13:05   

Quote (stevestory @ Feb. 20 2015,08:40)
Quote (cryptoguru @ Feb. 20 2015,06:53)
Wes, your world-view pre-supposes purely natural causation and excludes supernatural, intelligent causation ... as that is the purpose of the theory of evolution; to explain origins without the need for an intelligent agent.
Evolutionary theory is the science of atheists and fake atheists (agnostics), who need to find a way to explain the origin and diversity of life without a God.

Thus the need to explain that information can arise automatically from noise by purely natural processes.

hahahahahhahaha. Crypto, you're the best of the 3 creationists here, but you're still not any good.

Better than Joe and Gary.  

When are the trials for the US Olympic Damning With Faint Praise Team?

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Math is just a language of reality. Its a waste of time to know it. - Robert Byers

There isn't any probability that the letter d is in the word "mathematics"...  The correct answer would be "not even 0" - JoeG

  
Wesley R. Elsberry



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(Permalink) Posted: Feb. 20 2015,13:11   

Quote (stevestory @ Feb. 20 2015,12:42)
I think NoName and N.Wells deserve some sort of lifetime achievement award for doing the tedious explanatory work the rest of us shrug off. And Wesley of course, but we're working with his primary care physician to take his ultra-comprehensive OCD down to healthy levels.  :p

What was it this time? The "typing monkeys" essay?

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"You can't teach an old dogma new tricks." - Dorothy Parker

    
cryptoguru



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(Permalink) Posted: Feb. 20 2015,15:16   

Wes, you really are confused mate! (re: Kolmogorov et al)
Fractal algorithms and stochastic algorithms are very cool and all ... I've written plenty of them over the years. In fact my PhD is in Chaos Theory amongst other things. What those fields show is that the information is in the algorithms. This is what we see in AVIDA, what we see in Weasel etc.
I'm not impressed with you name-dropping as though they support your theory. Sure, machine learning and inductive reasoning are great optimisation techniques, but you're still optimising using intelligent algorithms and decision making written by the designer. Look at Quantum computing, we use a probabilistic method to produce a deterministic result. The system is probabilistic, but our algorithms are written to harness the predictability even though the qu-bits are in a superposition and we can't know deterministically which superposition will be observed, we write algorithms to force the outcome deterministically. Information does not simply appear from nowhere .... information does not emerge from noise (unless it was deliberately put there) and random processes cannot generate meaningful information without being acted upon by an intelligent process. You claim that Natural Selection is that intelligent process, I'd like to see it work without the known targets, rewarding for functions that you know will get you to the solution. But don't try claiming that a random distribution contains information ... that is absurdity of the highest degree ... randomness (disorder) is the exact opposite of information (enforced order)


N Wells: Shannon would laugh in your face, the whole point of Shannon's theory is that a purely random distribution has maximal entropy (i.e. no information) ... he's saying the exact opposite of what you are trying to get him to say.

  
midwifetoad



Posts: 4003
Joined: Mar. 2008

(Permalink) Posted: Feb. 20 2015,15:31   

Quote
But don't try claiming that a random distribution contains information .


I don't think anyone is claiming a random distribution contains information that would make a useful target.

But that isn't relevant to evolution.

For any working genomic sequence there are almost certainly going to be equivalent sequences within one point mutation. That's why drift is possible and why we have alleles.

There is no target. There is chemistry and the properties of amino acid sequences. If you wish, you could say that a library of alleles contains information about sequences that work. And dead organism contain information about what doesn't work.

That's a pretty primitive metaphor, but some simplification seems necessary to communicate.

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Any version of ID consistent with all the evidence is indistinguishable from evolution.

  
NoName



Posts: 2729
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(Permalink) Posted: Feb. 20 2015,15:36   

Quote (cryptoguru @ Feb. 20 2015,16:16)
Wes, you really are confused mate! (re: Kolmogorov et al)
Fractal algorithms and stochastic algorithms are very cool and all ... I've written plenty of them over the years. In fact my PhD is in Chaos Theory amongst other things. What those fields show is that the information is in the algorithms. This is what we see in AVIDA, what we see in Weasel etc.
I'm not impressed with you name-dropping as though they support your theory. Sure, machine learning and inductive reasoning are great optimisation techniques, but you're still optimising using intelligent algorithms and decision making written by the designer. Look at Quantum computing, we use a probabilistic method to produce a deterministic result. The system is probabilistic, but our algorithms are written to harness the predictability even though the qu-bits are in a superposition and we can't know deterministically which superposition will be observed, we write algorithms to force the outcome deterministically. Information does not simply appear from nowhere .... information does not emerge from noise (unless it was deliberately put there) and random processes cannot generate meaningful information without being acted upon by an intelligent process. You claim that Natural Selection is that intelligent process, I'd like to see it work without the known targets, rewarding for functions that you know will get you to the solution. But don't try claiming that a random distribution contains information ... that is absurdity of the highest degree ... randomness (disorder) is the exact opposite of information (enforced order)


N Wells: Shannon would laugh in your face, the whole point of Shannon's theory is that a purely random distribution has maximal entropy (i.e. no information) ... he's saying the exact opposite of what you are trying to get him to say.

You, sir, are an idiot.
You have gotten Shannon entirely incorrect, leading to serious doubts about your degree claims.
A random distribution has maximum entropy.  It thus has maximum uncertainty about the next piece of data, and thus has maximum information.  It is incompressible.
A random distribution has maximum entropy and thus has maximum Shannon information.  Quoting Wikipedia, sans link, "In information theory, entropy is the average amount of information contained in each message received."
Which means, to speakers of standard English and those whose IQ is greater than room temperature, that maximum entropy is maximum information.  That is is also likely to be 'minimum meaning' obliterates your entire sad schtick that information equals meaning.
You continue to confuse information with meaning, with 'informativeness'.   Address the facts on the ground, which you seem anxious to avoid for some reason.

  
midwifetoad



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(Permalink) Posted: Feb. 20 2015,15:44   

Hey, you are interfering with a perfectly good instance of equivocation.

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Any version of ID consistent with all the evidence is indistinguishable from evolution.

  
Wesley R. Elsberry



Posts: 4991
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(Permalink) Posted: Feb. 20 2015,16:02   

Sorry, Cryptoguru, but your Ph.D. apparently gave you little insight into algorithmic information theory (AIT). (Maybe it's from the one of the fine institutions that "Drs." Barnes, Baugh, Bliss, Burdick, and Hovind got their paper from? BTW, my Ph.D. is from TAMU, and that can be confirmed easily.)

The appendix to this essay could be helpful, if Cryptoguru were looking to learn something. In particular, what is defined as a random string in AIT is mentioned in there.

The notion that information production by algorithms is bounded is mistaken. Algorithms with random inputs can generate "arbitrarily more Kolmogorov complexity than the total information contained in the algorithm and input combined". We present such an algorithm as an example there.

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"You can't teach an old dogma new tricks." - Dorothy Parker

    
cryptoguru



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(Permalink) Posted: Feb. 20 2015,16:25   

Quote
I don't think anyone is claiming a random distribution contains information that would make a useful target.

Yup that's exactly what the other contributors are claiming

Quote
A random distribution has maximum entropy.  It thus has maximum uncertainty about the next piece of data, and thus has maximum information.  It is incompressible.

Entropy, is a measure for how compressible an information stream is, random noise is not compressible, just like high frequency information. But that doesn't mean the signal contains meaningful information. We're not talking about wanting to losslessly transmit random noise here, we're talking about if noise contains meaningful information. Shannon's theorem isn't interested in the content of the signal ... it treats all signals as information. We're talking about the content of the signal, is it noise or is it information.
You are using entropy theorem which is concerned with lossless compression of data to fallaciously determine whether a noisy signal contains meaningful information or not. Do you not see the difference?

Maybe we should use a different word if you're finding it hard to understand what we're talking about (or deliberately trying to muddy the waters with equivocal terms). Let's call it a MESSAGE instead of information. So I can encrypt a message and make it highly entropic so that the message is hidden, this is not random noise ... it can appear random, but the message is hidden in the signal. Does a random signal contain a message? NO! Random noise does not contain ordered and meaningful messages. DNA is a message ... a message to the cell about how to build an organism. So let's stop pretending that we can get MESSAGES automatically from random data.

  
OgreMkV



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(Permalink) Posted: Feb. 20 2015,16:34   

So is a signal of a message encrypted on a purely random one-time pad random noise or a meaningful message?


eta: I guess the real question... can you determine whether information is meaningful or not, just by looking at it? If you can, then you have done more than every ID proponent ever. But I don't think that it is even possible mathematically.

Edited by OgreMkV on Feb. 20 2015,16:42

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midwifetoad



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(Permalink) Posted: Feb. 20 2015,17:44   

Quote
Yup that's exactly what the other contributors are claiming


You keep aiming for the floor and missing. It's quite a talent.

Random noise (white noise) contains all frequencies. So you can apply filters and get pure frequencies. At least in theory.

So the random noise is how the new alleles arrive. Random mutation creates the new sequence.

Now apply selection (purifying or adaptive, or both). You get a "meaningful signal". Out of all the random mutations, a few survive and reproduce. (Bear in mind that, meanwhile, zillions of unmutated individuals also survive and reproduce.)

The selector is the properties of chemistry. Some sequences create folds or regulators that either don't change viability or improve it. This is not a designer. It's chemistry.

And it's not a target. It's just that some sequences are functional equivalent to other sequences. That's why genomes can change while the phenotype remains static. That's why we have alleles and variants.

If a genome reaches one of Doug Axe's dreaded local maxima, it is not stuck, because every time a neutral mutation occurs, it opens new pathways, new dimensions in the search space. A new mutation might produce a breakthrough in functionality. See Lensky.

But viable alleles are not targets. They are not searched for.

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Any version of ID consistent with all the evidence is indistinguishable from evolution.

  
N.Wells



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(Permalink) Posted: Feb. 20 2015,17:45   

Quote (cryptoguru @ Feb. 20 2015,15:16)
N Wells: Shannon would laugh in your face, the whole point of Shannon's theory is that a purely random distribution has maximal entropy (i.e. no information) ... he's saying the exact opposite of what you are trying to get him to say.

From Peter Grunwald and Paul Vitanyi, 2008, Shannon Information and Kolmogorov Complexity
http://homepages.cwi.nl/~paulv.....nfo.pdf

     
Quote
[with my emphasis] Both [Shannon information theory and Komogorov complexity theory] aim at providing a means for measuring ‘information’. They use the same unit to do this: the bit. In both cases, the amount of information in an object may be interpreted as the length of a description of the object. ***In the Shannon approach, however, the method of encoding objects is based on the presupposition that the objects to be encoded are outcomes of a known random source—it is only the characteristics of that random source that determine the encoding, not the characteristics of the objects that are its outcomes.*** In the Kolmogorov complexity approach we consider the individual objects themselves, in isolation so-to-speak, and the encoding of an object is a short computer program (compressed version of the object) that generates it and then halts.  In the Shannon approach we are interested in the minimum expected number of bits to transmit a message from a random source of known characteristics through an error-free channel.
..............
In Kolmogorov complexity we are interested in the minimum number of bits from which a particular message or file can effectively be reconstructed: the minimum number of bits that suffice to store the file in reproducible format. This is the basic question of the ultimate compression of given individual files. A little reflection reveals that this is a great difference: for every source emitting but two messages the Shannon information (entropy) is at most 1 bit, but we can choose both messages concerned of arbitrarily high Kolmogorov complexity. Shannon stresses in his founding article that his notion is only concerned with communication, while Kolmogorov stresses in his founding article that his notion aims at supplementing the gap left by Shannon theory concerning the information in individual objects.



The ellipsis is a quote from C.E. Shannon, 1948, The mathematical theory of communication,  Bell System Tech. J., 27:379–423, 623–656: “The fundamental problem of communication is that of reproducing at one point either exactly or approximately a message selected at another point. Frequently the messages have meaning; that is they refer to or are correlated according to some system with certain physical or conceptual entities. These semantic aspects of communication are irrelevant to the engineering problem.  The significant aspect is that the actual message is one selected from a set of possible messages. The system must be designed to operate for each possible selection, not just the one which will actually be chosen since this is unknown at the time of design.”


Let's recap:
Cryptoguru:
     
Quote
1) PURE UNDIRECTED randomness, which simply creates random output and not information


Me:
     
Quote
#1 creates a perfectly good form of information (Shannon information), but you don't like that definition.  You want information to have "intended meaning".


From the source above: "outcomes of a known random source", i.e. random output constitutes Shannon information.  Shannon wouldn't have said that messages frequently have meaning if he hadn't recognized that sometimes they don't.  Yes, random strings equate with maximum entropy and little "meaning", but they still comprise "Shannon information". Shannon information is not concerned with contained meaning, but with the number of bits required for transmitting it. Kolmogorov was concerned about how much the meaning in the information could be compressed.  Different things.  

You have it correct that "random noise is not compressible, just like high frequency information. But that doesn't mean the signal contains meaningful information.  .....  Shannon's theorem isn't interested in the content of the signal ... it treats all signals as information."  However, you also denied that random noise is information, which is untrue: for Shannon it is maximally entropic information (and it is incompressible), but it is still information by his definition, contrary to your statement #1.

 
Quote
Take a functioning gene.  Duplicate it (that happens all the time).  That is new Shannon information, because your compressed version has now been increased by the need to say "x2".  It probably doesn't do anything useful, although an extra copy of a gene can have its uses.  Now if one of the two copies suffers a mutation that disables its function, that's no longer a problem, and the duplicated can go on to suffer additional changes, some of which might develop other uses.  Actually, the first mutation probably didn't disable the primary function, but shifted it, thereby contributing to a different suite or range of capabilities.
I wrote my third sentence very poorly (ironically, I overcompressed what I meant to say :) ): The duplication comprises new information, both new Shannon information and new Kolmogorov information: in the case of the former the message has doubled in length, while in the case of the latter, you at least have to expand your previous message by saying "times 2".  New meaning comes in with the events in second half of the paragraph: that this sort of thing happened is the most parsimonious interpretation of all the genes that aren't ORFans. You have yet to address this.

  
cryptoguru



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(Permalink) Posted: Feb. 20 2015,18:01   

Quote
Sorry, Cryptoguru, but your Ph.D. apparently gave you little insight into algorithmic information theory (AIT). (Maybe it's from the one of the fine institutions that "Drs." Barnes, Baugh, Bliss, Burdick, and Hovind got their paper from? BTW, my Ph.D. is from TAMU, and that can be confirmed easily.)


I am still writing up my PhD part-time at the request of the department after leaving years ago part-way through writing-up; (due to being offered commercial opportunities that I would have been an imbecile to decline) ... it is for a reputable University in the UK.

Hehe ... you're the one who studied in the Bible-Belt  :D

  
midwifetoad



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(Permalink) Posted: Feb. 20 2015,18:03   

You are trying to reify a metaphor. In biology, information is a metaphor. It's an abstraction. Abstraction are maps, not territories.

You can't get away with arguing that because a feature isn't on the map, it doesn't exist.

If you encounter a glitch in your understanding based on information theory, yoy are mistaking the map for the territory, You are stretching a metaphor beyond applicability.

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Any version of ID consistent with all the evidence is indistinguishable from evolution.

  
Wesley R. Elsberry



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(Permalink) Posted: Feb. 20 2015,18:22   

ABD is not Ph.D.

And it isn't even certain that ABD is the status.

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"You can't teach an old dogma new tricks." - Dorothy Parker

    
cryptoguru



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(Permalink) Posted: Feb. 20 2015,19:01   

N Wells: Amazing ... actually unbelievable, you've just equivocated over the word MESSAGES now instead of INFORMATION.

The "message" or "information" that Shannon is describing is something to be transmitted across a noisy channel. He is not interested in the content of the "message" or "information". He merely wants to recover the "message" or "information".

We are not talking about THAT kind of "message" or "information" ... we are talking about information (or a message ... call it what you like) that is the content of the transmission. Sure you can send random noise to a recipient, but that's NOT what we're talking about ... we're talking about something that is ordered with intent for the purpose of being understood by the recipient i.e. it has meaning.

A biological cell when it reads DNA understands the format of the information and deterministically processes that information as instructions that it understands to build an organism. This is why I call DNA computer code (but everyone gets upset with that too) as it is processed as a turing machine ... so you can't just say it's ANY kind of message or information ... it's meaningful sets of non-linear instructions. (similar to AVIDA)
THIS kind of information (e.g. computer code) is only known to originate from an intelligence.
AVIDA attempts to refute this by trying to build a computer code through random mutation and natural selection. But it enforces a known target by measuring if sequences of commands produce a known logical function. The randomness isn't generating a useful set of instructions (meaningful code) by itself. The randomness is being filtered using the known target to eliminate functionally useless output and just leave the stuff we wanted.
YES you can say that all the unwanted random variations are information too if you like, but they're not the kind of information we're talking about, we're talking about information that solves a problem, not just randomly distributed instructions that have no use.

If I randomly throw a pile of sticks on the floor, it's a pile of sticks ... you could say that the arrangement of them is information, but it has no meaning if their orientations are randomly distributed. Then I arrange the sticks to spell out the word "DANGER". You understand the message, it is written in a language that you understand and you presume that an intelligent agent left the sticks in that arrangement to communicate that there is danger (this may not be the originator's intention, but you would not be stupid to assume the message could be intended for you). You would say this is a message or information. You would not claim the original pile of sticks is information (in the normal use of the word).

My argument (and it pains me to have had to explain to adults what the normal use of the word information or message means) is that the meaningful information isn't expected to arise randomly. Evolutionists also claim that it can't arrive purely randomly; except that natural selection can work on random material and preserve good stuff and filter out bad and eventually we're left with meaningful information that solves a problem.

I put it to you that the only kind of process that would allow successive random arrangements of the sticks problem to result in the message, are those that can test against correct stick positions and attempt to preserve them somehow. This is similar to what AVIDA is doing by testing against known logical functions except that there are an infinite number of ways that Avidian commands can produce each logical function, so it becomes relatively easy for it to find combinations that work and similarly to get to a final solution (e.g EQU) and carry on optimising until it has the smallest and most efficient set of commands possible to perform the task.

Anyway I've got a life and I think the current topic has run its course .... so I'm going to leave you all to argue amongst yourselves about whether a stick is information and leave you with this last almost off-topic thought.

... what came first? the genetic instruction set or the cell to run it in? If it was the genetic instructions, how would it even arise without the mechanism to run it? (i.e. it would die without replicating) ...  If it was the cell that came first, how did it get built? and how then did it generate the instruction set to run on it? And how did it not die before it was able to generate the instruction set to allow it to replicate etc.?
Remember a minimal genome would need enough complexity to build, fold and assemble proteins, respire and replicate.
Is that not a good example of irreducible complexity?

  
OgreMkV



Posts: 3668
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(Permalink) Posted: Feb. 20 2015,19:01   

Quote (midwifetoad @ Feb. 20 2015,17:44)
Quote
Yup that's exactly what the other contributors are claiming


You keep aiming for the floor and missing. It's quite a talent.

Random noise (white noise) contains all frequencies. So you can apply filters and get pure frequencies. At least in theory.

So the random noise is how the new alleles arrive. Random mutation creates the new sequence.

Now apply selection (purifying or adaptive, or both). You get a "meaningful signal". Out of all the random mutations, a few survive and reproduce. (Bear in mind that, meanwhile, zillions of unmutated individuals also survive and reproduce.)

The selector is the properties of chemistry. Some sequences create folds or regulators that either don't change viability or improve it. This is not a designer. It's chemistry.

And it's not a target. It's just that some sequences are functional equivalent to other sequences. That's why genomes can change while the phenotype remains static. That's why we have alleles and variants.

If a genome reaches one of Doug Axe's dreaded local maxima, it is not stuck, because every time a neutral mutation occurs, it opens new pathways, new dimensions in the search space. A new mutation might produce a breakthrough in functionality. See Lensky.

But viable alleles are not targets. They are not searched for.

I think it important to add that local maxima in biology/DNA is only the case as long as the environment is totally static. Any minor change (even a few months of drought) can result in what was the maxima one month being useless the next.

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OgreMkV



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(Permalink) Posted: Feb. 20 2015,19:04   

Quote (cryptoguru @ Feb. 20 2015,19:01)
N Wells: Amazing ... actually unbelievable, you've just equivocated over the word MESSAGES now instead of INFORMATION.

The "message" or "information" that Shannon is describing is something to be transmitted across a noisy channel. He is not interested in the content of the "message" or "information". He merely wants to recover the "message" or "information".

We are not talking about THAT kind of "message" or "information" ... we are talking about information (or a message ... call it what you like) that is the content of the transmission. Sure you can send random noise to a recipient, but that's NOT what we're talking about ... we're talking about something that is ordered with intent for the purpose of being understood by the recipient i.e. it has meaning.

A biological cell when it reads DNA understands the format of the information and deterministically processes that information as instructions that it understands to build an organism. This is why I call DNA computer code (but everyone gets upset with that too) as it is processed as a turing machine ... so you can't just say it's ANY kind of message or information ... it's meaningful sets of non-linear instructions. (similar to AVIDA)
THIS kind of information (e.g. computer code) is only known to originate from an intelligence.
AVIDA attempts to refute this by trying to build a computer code through random mutation and natural selection. But it enforces a known target by measuring if sequences of commands produce a known logical function. The randomness isn't generating a useful set of instructions (meaningful code) by itself. The randomness is being filtered using the known target to eliminate functionally useless output and just leave the stuff we wanted.
YES you can say that all the unwanted random variations are information too if you like, but they're not the kind of information we're talking about, we're talking about information that solves a problem, not just randomly distributed instructions that have no use.

If I randomly throw a pile of sticks on the floor, it's a pile of sticks ... you could say that the arrangement of them is information, but it has no meaning if their orientations are randomly distributed. Then I arrange the sticks to spell out the word "DANGER". You understand the message, it is written in a language that you understand and you presume that an intelligent agent left the sticks in that arrangement to communicate that there is danger (this may not be the originator's intention, but you would not be stupid to assume the message could be intended for you). You would say this is a message or information. You would not claim the original pile of sticks is information (in the normal use of the word).

My argument (and it pains me to have had to explain to adults what the normal use of the word information or message means) is that the meaningful information isn't expected to arise randomly. Evolutionists also claim that it can't arrive purely randomly; except that natural selection can work on random material and preserve good stuff and filter out bad and eventually we're left with meaningful information that solves a problem.

I put it to you that the only kind of process that would allow successive random arrangements of the sticks problem to result in the message, are those that can test against correct stick positions and attempt to preserve them somehow. This is similar to what AVIDA is doing by testing against known logical functions except that there are an infinite number of ways that Avidian commands can produce each logical function, so it becomes relatively easy for it to find combinations that work and similarly to get to a final solution (e.g EQU) and carry on optimising until it has the smallest and most efficient set of commands possible to perform the task.

Anyway I've got a life and I think the current topic has run its course .... so I'm going to leave you all to argue amongst yourselves about whether a stick is information and leave you with this last almost off-topic thought.

... what came first? the genetic instruction set or the cell to run it in? If it was the genetic instructions, how would it even arise without the mechanism to run it? (i.e. it would die without replicating) ...  If it was the cell that came first, how did it get built? and how then did it generate the instruction set to run on it? And how did it not die before it was able to generate the instruction set to allow it to replicate etc.?
Remember a minimal genome would need enough complexity to build, fold and assemble proteins, respire and replicate.
Is that not a good example of irreducible complexity?

Let me ask this again, since it's critically important

Quote

So is a signal of a message encrypted on a purely random one-time pad random noise or a meaningful message?

eta: I guess the real question... can you determine whether information is meaningful or not, just by looking at it? If you can, then you have done more than every ID proponent ever. But I don't think that it is even possible mathematically.


But since you have been soundly trounced, it's time to run away.

I give it a week before you're back on my blog, whining about something totally unrelated to all of this.

I really did want to talk about radiometric dating, but we already know you lost that battle... Mr. Never-Provide-the-Source-of-My-Claims.

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OgreMkV



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(Permalink) Posted: Feb. 20 2015,19:06   

Quote
My argument (and it pains me to have had to explain to adults what the normal use of the word information or message means) is that the meaningful information isn't expected to arise randomly.


That must be a record, three conflations of terms in the same sentence. Even Joe couldn't accomplish that.

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cryptoguru



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(Permalink) Posted: Feb. 20 2015,19:13   

Don't worry Kevin I'll stay away from your very sad excuse for a blog from now on.

An encrypted message that looks like random noise is a meaningful message even if you can't see it is ... it's about the intended recipient. If the intended recipient can recover and understand the message and it has meaning to them, then it is a meaningful message, you can't ascertain this by analysing the encrypted message.
This is my point ... we are not concerned with transmitted data, we are purely talking about meaningful messages to a biological cell. If the DNA instruction set when processed by the cell doesn't result in a meaningful result (i.e. functionally advantageous trait) then it is not information I am interested in seeing you create with your magical natural selection formula.

Will happily come back here another time to discuss radio-dating.

Peace!

  
The whole truth



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(Permalink) Posted: Feb. 20 2015,19:21   

cryptoguru said:

"Dawkins would laugh at the stupidity of some of the claims made in the last few posts by evolutionists."

And your point is ? Here, let me clue you in on something: I really don't think that anyone here sees Dawkins as some sort of 'God' or as THE SPOKESMAN for all evolutionists or atheists. You obviously believe that what Dawkins may or may not laugh at is of HUGE importance to what all evolutionists and/or atheists think or don't think, and say or don't say. Some or all of us evolutionists and/or atheists may or may not agree with some or all of what Dawkins thinks, says, or may or may not laugh at. He's a man, not a 'God', and we all know that.  

"This discussion has taken a surreal and utterly ridiculous turn for the irrational"

Dang, you IDiot-creationists sure are hard on irony meters.


P.S. If you're really want to know what or who Dawkins would laugh at, ask him to look at this thread and see what he says.

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Think not that I am come to send peace on earth: I came not to send peace, but a sword. - Jesus in Matthew 10:34

But those mine enemies, which would not that I should reign over them, bring hither, and slay them before me. -Jesus in Luke 19:27

   
Wesley R. Elsberry



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(Permalink) Posted: Feb. 20 2015,19:42   

Cryptoguru:

 
Quote

AVIDA attempts to refute this by trying to build a computer code through random mutation and natural selection. But it enforces a known target by measuring if sequences of commands produce a known logical function.


Wrong.

I don't recall exactly how many times Cryptoguru has been corrected on this very point, but it's a lot.

Avida does not examine sequences of genomes for rewarding merit. Avida rewards Avidian *behavior*. As I said, Avidians are rewarded for what they do, not what their genomes are.

As I related about my own research, the merit reward has nothing to do with the sequence of instructions in the genome. If that were true, it would be difficult to be able to deliver multiple examples of different Avidian sequences accomplishing the same task, as I have related.

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Wesley R. Elsberry



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(Permalink) Posted: Feb. 20 2015,19:51   

And I'll note that in the research I related about my work in Avida, there was no target, no fitness function, no hierarchy of rewards, and yet there was evolution of multiple lineages to a diversity of programs in the optimal class of gradient ascent programs.

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N.Wells



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Joined: Oct. 2005

(Permalink) Posted: Feb. 20 2015,20:03   

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we are talking about information (or a message ... call it what you like) that is the content of the transmission.

YOU are talking about the content of the message, not "us".  YOU said that "1) PURE UNDIRECTED randomness, which simply creates random output and not information".  I'm saying that that claim is wrong, according to Shannon's definition of information.  If the message being transmitted is a randomly generated string (i.e. random output), then that random string is information, according to Shannon's definition of information as the number of bits required to transmit a message, without regard to whether the message has "meaning" or not.  A message that consists of a random string is maximally entropic and is not compressible, but it is nonetheless information that can be quantified in bits.  Noise is something else, basically whatever is added or subtracted that degrades the original message (not its meaning, but just the "recapturability" of the original string, again regardless of whether it carried "meaning" or not).



   
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Maybe we should use a different word if you're finding it hard to understand what we're talking about (or deliberately trying to muddy the waters with equivocal terms). Let's call it a MESSAGE instead of information. So I can encrypt a message and make it highly entropic so that the message is hidden, this is not random noise ... it can appear random, but the message is hidden in the signal. Does a random signal contain a message? NO! Random noise does not contain ordered and meaningful messages. DNA is a message ... a message to the cell about how to build an organism. So let's stop pretending that we can get MESSAGES automatically from random data.

"Message" (in your sense, not Shannon's) and "meaning" are elusive.  White light is a mixture of all wavelengths in the visible range.  While not exactly random, this is not very promising as a meaningful signal or a message.  However, you can process it to carry messages: morse code, light in optical fibres, "one if by land, two if by sea", etc.  Animals that have eyes find all kinds of meanings and significance amidst the noise of all its many reflections from all the various surfaces around them.  Filtering or scattering can separate out any particular narrow range of wavelengths (giving us a blue sky and a sun that looks yellow), or white light can be refracted by raindrops into a rainbow, which fervent christians used to take as a direct message from their god reminding them of his promise never to create another Noachian flood.  So, how much meaning exists in the rainbow, or just in the ray of light, and when did it get there?  Shannon shortcircuited all that by ignoring meaning and shortcutting to "how many bits are needed to transmit a quantity of information?"  

   
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I really did want to talk about radiometric dating
Fire away - that's a topic I really love.  Do you want to start with concordia curves, or would you prefer to work up to them?

  
Texas Teach



Posts: 2084
Joined: April 2007

(Permalink) Posted: Feb. 20 2015,20:23   

Quote (N.Wells @ Feb. 20 2015,20:03)
 
Quote
I really did want to talk about radiometric dating
Fire away - that's a topic I really love.  Do you want to start with concordia curves, or would you prefer to work up to them?

I think he'd like to start with "were you there?" and then work through the (ir)relevant parts of this list

--------------
"Creationists think everything Genesis says is true. I don't even think Phil Collins is a good drummer." --J. Carr

"I suspect that the English grammar books where you live are outdated" --G. Gaulin

  
OgreMkV



Posts: 3668
Joined: Oct. 2009

(Permalink) Posted: Feb. 20 2015,20:58   

Here's where he started: http://www.skepticink.com/smilodo....-dating

I think he hit most of the major ones, including refusing to supply sources for his claims.

Anyway, the point I was making about information and encryption is the same point that crypto isn't getting about ID. To him, things only have meaning if he knows that they have some meaning to him. An encrypted message won't have meaning to him... and therefore, by his definitions, contains no information.

So a gene that he can't identify a protein for or one that's a known regulatory sequence contains no information. But when it is found to have a function or a protein, then it will have information.

Which makes absolutely no sense, because to measure the information content in DNA, he has to know, in advance, what every single part does.

--------------
Ignored by those who can't provide evidence for their claims.

http://skepticink.com/smilodo....retreat

   
N.Wells



Posts: 1836
Joined: Oct. 2005

(Permalink) Posted: Feb. 21 2015,01:03   

Sorry for overkill, but as I said, I like radiometric dating, and over at Smilodon's Retreat, Cryptoguru is wrong out of the gate and rapidly gets worse:    
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There are 3 faulty assumptions with radiometric dating ... all 3 have been proven to factor into dating inaccuracies

1) we know the initial conditions
2) there has never been any contamination
3) the decay rate is constant


Three out of three statements that are misleading or wrong right up front!  #2 is not an assumption; #3 is a conclusion that is known to work in crustal conditions but is not claimed for other situations; and #1 is a testable inference that is re-investigated with each study.

First, decay rates, like any other process, can of course be sped up or slowed down.  This is not news.  Some types of acceleration of decay rates are well known: we call them nuclear bombs and nuclear power plants.  The trouble is that to accelerate decays appreciably require the sorts of temperatures and pressures found inside stars, or massive bombardment by decay products nearby concentrations of other radioactive isotopes, as at the Oklo natural nuclear reactor site.  On the basis of experiments and calculations, the comparatively mild conditions of metamorphism (2,000 degrees K and 100 kbar should melt pretty much anything in the crust) aren't sufficient to influence the process.  Intense gamma ray bombardment can trigger decays in some isotopes (as with neutrons in other isotopes).  Embedding in metal and cooling to a few degrees above 0K can do in alpha emitters.  You get the idea: there are ways to speed these up, as with any physical or chemical process, but there aren't any that will operate in crustal conditions without leaving evidence of an Oklo type reaction or a nuclear bomb going off.  In short, in crustal environments, they're constant, so a) decay rates are known to vary but b) this doesn't happen under crustal conditions absent an Oklo reactor.

Second, there's always contamination.  It's inevitable.  This is not news either but again it is not a fatal flaw for all of radiometric dating.  The questions are how much, can we evaluate it, and can we adjust for it?  If you handle a dinosaur bone with bare hands, oil and sweat and dandruff can contaminate it and give the bone a very old radiocarbon age (30,000 years or older for trace contamination by modern organic carbon).  If the bone was prepared with shellac or glue or cleaned with detergent or carried in a burlap bag or picked up with leather or cotton gloves, or got mold growing in it in the museum basement, or (most commonly) was invaded by plant root hairs while lying in the soil prior to discovery, that's potentially significant contamination.  But those are known issues and are easily avoided: don't do those things, and extract the sample for analysis by drilling a sample out of a pristine part of the interior, treat it with peroxide, and inspect it for any root hairs, fungal hyphae, etc.  If the sample is in bad shape, then you can't date it.   However, there are even more subtle and pernicious sources of contamination: the lubricant that you use in your instrument's vacuum pump;  the grease that you use to seal your access port; does your instrument have any plastic piping?; modern carbon in the acids you used to dissolve the sample, and so on.  These can all be mitigated to a degree, but ultimately there will always be enough contamination to give some kind of a very old date to something like diamond dust or ancient coal.  The nature of exponential decay is that a little contamination will not throw off a date for a sample that only a few half-lives off, but as you get to 40kyr to 60 kyrs, there is so little original C14 left that contamination will be a problem.  Several decades ago, people hoped to get improved C14 dates on materials 100 to even 200 kyr by individually counting C14 atoms with a cyclotron (accelerator mass spectroscopy) dating, which did extend dating ranges a little, but contamination issues dashed those hopes.  40-60 kyr is about the limit, depending on the quality of the sample and other issues.

A reverse example of contamination is if you have a modern lacustrine clam or snail living in a lake on limestone bedrock, it may well be getting some or most of its carbon not from atmospheric CO2 that becomes dissolved in the lake water but from "dead" carbon i.e. carbonate via dissolution by the lake water of the calcium carbonate in the bedrock.  That way, living organisms can easily date as 10-20 thousand years old.  Moral, you usually can't reliably date things living on limestone.

Other decay systems have other contamination issues and other solutions.  K-Ar for igneous rocks is very nice for this: not only is argon a natural gas, which won’t link up in crystals, but argon in the magma will bubble out before it has a chance to get trapped in a crystal.  However, once in a while argon will flood up a hotspring pipe or a fracture or an apatite vein and will soak into adjacent crystals, but those issues are expected in those situations and can be tested for by testing samples progressively farther from the fracture (and then throwing out the contaminated samples, or simply not sampling near veins and the like in the first place).  For U-Pb and Th-Pb, we rarely any longer try to do whole-rock analyses because there’s there’s too high a possibility of some old lead from previous decays that got into the magma from melted host rock.  Magmas do in part melt their way up to the surface, so a lava that erupted 10 million years ago can have picked up chunks of 2 b.y. old rock that it passed through (the chunks may be visible xenoliths) or a few crystals that melted out of the host rock but floated around in the magma (more on those in a moment), or simply melt products that included some old radiogenic lead from long-ago decay events.  The last is resolved by no longer doing whole-rock dates.  Instead, we pick out crystals of minerals that for various reasons will incorporate the parent isotope but won’t naturally incorporate the daughter element, such as zircon and monazite.  Zircon has the added advantage of forming after most of the lead has gone into other minerals, of having a very high melting point, of being chemically and physically very resistant to weathering and breakage.  This means that it won’t leak daughter radon during the decay process, and is comparatively hard to mess up during mild metamorphism.  As I mentioned, it is possible for old zircons to melt out of host rock, not dissolve in the magma, and get included in the new igneous rock, or to be recycled though an even older rock cycle.  However, when this happens, you get a corrosion rim around the old crystal and then a new growth band around the old core with nice new crystal faces: these are easily recognized, and we date several sample spots across the crystal and can see date the old core and the new rim separately
http://cjes.geoscienceworld.org/content....rge.jpg
http://specialpapers.gsapubs.org/content....rge.jpg
http://www.google.com/imgres?....rl=http
It’s an extremely cool technique.


Third, ‘it is wrong to assume that you know the initial conditions’  Well, that’s rather vague.  We can melt granites and gabbros and so forth in the lab, so we know conditions of crystallization.  Crystal chemistry and mineralogy give us constraints on whether daughter isotope could be incorporated in a growing crystal or not.  Sure, if you let a zircon grow in a puddle of lead, some lead would get incorporated even though incorporation is thermodynamically strongly disfavored.  On the other hand, your sample would be in a lead ore body, and you’d know that.  You can count atoms of uranium-235 and atoms of lead-207, but also atoms of other isotopes of lead as well.  If we don’t have any nonradiogenic lead (isotope 204) then we wouldn’t have had any original 207 either.  If by chance we did have some PB 204, we could use the amount and typical ratios between the isotopes to correct the radiogenic lead contents by an appropriate ratio and then attribute the excess to decay of uranium (I’m oversimplifying a bit here).  There are some other techniques like Pb-Pb dating that can be used.

Still on #3: It is always possible that something else went wrong that we haven’t yet anticipated or corrected for.  Most typically for Precambrian rocks, we had a little later metamorphism that caused partial to total recrystallization, kicking out some to all of the daughter isotope formed since the original crystallization.  We have multiple lines of defense here including one truly awesome technique that gives us two useful bits of information for the price of one.  First, we don’t just date one sample, and we don’t just date by one technique.  All radiometric decay chains decay at their own unique decay rates.  This means that it is impossible to mess up a crystal in such a way as to force a wrong date*, while having two different decay chains agree on the same wrong result.  (*If you completely melt the crystal, you will force out all the accumulated daughters for all decay chains, resetting the clocks to 0, but the new crystal is brand new, so 0 is now the correct age.)  So if different isotopes in the same crystal give you the same dates, you’re golden.  We typically date multiple different decay chains in multiple different crystals in a rock, which always give different dates because different minerals crystallize at different temperatures, and a granite can easily take tens of millions of years to cool from crystallizing a temperature with a high melting point to another with a low melting point.  That’s a colling history for the granite, and we expect it to show a logical progression, so if that is present, good.  Most important, we can calculate how the U-235/Pb-207 ratio should be changing over time and how the U-238/Pb-206 should also be changing over time, if everything worked.  This gives you a concordia curve, and if your sample has exactly the right pair of ratios then everything is peachy keen
http://www.tulane.edu/~sanels....ull.jpg

When rocks experience a little metamorphism, the crystals can be partially reset, by losing a fraction of their daughter isotope.  The exact fraction is going to vary: more from little crystals than big ones (it’s harder for lead to diffuse out of the center of a large crystal); more from broken crystals or crystals with cracks than from pristine ones; and so forth.  This results in discordant dates.  However, the result of different percents of losses is typically a line (or long narrow field) of dates on the concave side of the concordia curve.
http://www.uwgb.edu/dutchs.....dia.gif
The math for this is inexorable: where the line through the discordant points hits the older part of the concordia curve, that would be the age for crystals that have lost 0% of the daughter, i.e. the original age of crstallization.  Where the line hits the younger end of the concordia curve, that would be the age of crystals that lost 100% of the daughter atoms, i.e. the age of metamorphism.

 
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We can't possibly assert that we can prove 1 or 2 because neither is observable, except we can maybe enforce 2 in the case of diamonds. We have cases where we have later proved that our initial assumptions for 1) and 2) were wrong ... so how do we know when we've got it right?
For 3 we do know that decay rates can be effected by external factors
http://www.earth.sinica.edu.tw.../....u.t....u.tw...

Well, that’s you making bogus arguments because they sound good to you, rather than because you understand what’s going on.

 
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So answer me the following
A) how is there C14 in diamonds?
B) how is there C14 in dino bones?
C) why do professionally processed rock datings on the same sample give WILDLY varying results?
D) why do professionally processed rock datings on known age samples (100 years) give billions of years?

I’ve answered most of these already, but there’s a little more to say on all of them, especially diamonds.

C & D) Stratigraphically young lavas that passed through much older rocks on the way up can get contaminated in terms of chunks of old rock (recognizable in outcrop and thin section, so don’t take dates of xenoliths as dates of the rock), & old crystals that get melted out of the host rock and end up in the new rock (SEM  / EDAX examination, & date the cores and the rims separately).  Different minerals in a single rock can and should give different ages when they have different crystallization temperatures, meaning that they formed at different times, and one with the lower melting temperature can get reset by low-grade metamorphism that will not affect the more refractory crystal.

There are some excellent and famous examples in Hawaii, where comparatively young lavas have yielded ancient dates.  Hawaiian volcanoes are “hot spot” volcanoes, with magmas coming up from mantle depths, and they have a habit of picking up chunks of mantle and lower crust as they come up.  These are easily identified, and can be avoided or dated as you wish.
http://academic.emporia.edu/abersus....ith.JPG (not from Hawaii)
http://peridot1.blogspot.com/....pot....pot.com
Creationists implied that these are legitimately confusing dates: they cited a study of the xenoliths as if it were a study of the lava, and they failed to point out that these sorts of studies are done routinely to see if a rock can be dated, and the authors concluded that their data showed that dating could not be done and that their results had no geological meaning.

Most of your “data” here is likely to come from the creationist literature, which involves a truly mind-blowing quantity of lies, misrepresentations, misunderstandings, and mistakes regarding legitimate work done by legitimate sciencists.  These are dealt with in a wonderfully readable essay by Brent Dalrymple, available at
http://www.talkorigins.org/faqs.......ng.html
Note in particular how creationists use data such as tests of a potential dating system where the scientists decided it was too vulnerable to getting screwed up so they concluded that it should not be used, but the creationists used it as evidence of geologists being unable to justify radiometric dating:
 
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The two ages from gulf coast localities (Table 2) are from a report by Evernden and others (43). These are K-Ar data obtained on glauconite, a potassium-bearing clay mineral that forms in some marine sediment. Woodmorappe (134) fails to mention, however, that these data were obtained as part of a controlled experiment to test, on samples of known age, the applicability of the K-Ar method to glauconite and to illite, another clay mineral. He also neglects to mention that most of the 89 K-Ar ages reported in their study agree very well with the expected ages. Evernden and others (43) found that these clay minerals are extremely susceptible to argon loss when heated even slightly, such as occurs when sedimentary rocks are deeply buried. As a result, glauconite is used for dating only with extreme caution. Woodmorappe’s gulf coast examples are, in fact, examples from a carefully designed experiment to test the validity of a new technique on an untried material.


Another classic example of abuse of this sort involves the Plateau and Cardenas Basalts in the Grand Canyon: see http://www.talkorigins.org/faqs.......ce.html for details.

B) How is there C-14 in dinosaur bones?  First, see the answers for diamonds below.  Second, contamination: a very little modern Carbon can give a very old age to a rock with no carbon of its own.  Contamination is hard to avoid in the best of times.  There is also an issue of trust: people who want young ages and fib about other aspects of science perhaps shouldn’t be trusted to have handled the samples carefully enough to avoid contamination, when just a little contamination could appear to validate their beliefs. Third, misuse of data.  I attended a creationist talk in the late sixties where the creationist presented a C14 date on a geologically ancient fossilized wood and showed a lab report that he claimed said the fossil was only 36000 years old.  Unfortunately, the photo of the lab report showed the lab report saying “>36000 yrs" (or something close to that), which I presume was radiocarbon infinity for that lab at that time, and in any case just says “>”.  However, I haven’t seen any creationists do that since, and this guy was a jaw-droppingly sorry example (he also complained about paleontologists not being able to produce any transitional fossils between a fish and a starfish).  

A) How about C14 ages on diamonds?  Scientists use industrial diamonds to test their C14 instruments and methods precisely because diamond should have very little C14 in it.  (They have also used coal and oil.)  This is how they learn how much contamination is entering their samples and whether it’s a problem.  They publish their results to show the resolution achievable in their labs (and bear in mind that if you have so little contamination that you only get a date of 50,000 years, you have done a very good job of avoiding contamination, and dates only a little less than that will be trustworthy).  Typically, chemical preparation of samples adds about 1 microgram of modern carbon, so a standard sample of 1 milligram will inevitably have 0.1% modern carbon in it, which will give a date younger than radiocarbon infinity (57136 yrs, to be precise).  It is therefore dishonest of creationists to say that this proves that all C14 dating is problematic, because the work shows that dates are reliable nearly up to those ages, but not beyond.  Because decay is exponential, “backing up to the recent” a little means that any samples of a slightly younger age will have a LOT more of their own original C14, so the trace amount of C14 that your procedures or machine introduced will be insignificant.  There is a great treatment of these issues by Karl Bertsche:
http://www.talkorigins.org/faqs.......ue.html
Bertsche has an interesting discussion of “instrument background” (the values reported by an instrument with no sample in it).  This includes    
Quote

   ion source “memory” of previous samples, due to radiocarbon sticking to the walls of the ion source, thermally desorbing, and then sticking to another sample
   mass spectrometer background, non-radiocarbon ions that are misidentified as radiocarbon, sometimes through unexpected mechanisms
   detector background, including cosmic rays and electronics noise


I would also add that coal and diamonds contain nitrogen as a trace component (up to 1% of a diamond is nitrogen).  If that gets bombarded by beta particles (neutrons, from nearby radioactive atoms), then some nitrogen could get converted to C14.  I don’t know if the amounts are significant, however.

These topics are complicated, way more than I presented here, so there is always endless scope for trying to throw doubt by bringing up more complications.  Geochronologists are always testing their systems, investigating situations where something didn't work, and trying out new techniques and new dating methods, where some of them work while others turn out to get discarded as unworkable or problematic.  Regardless, creationists have made a dishonorable but standard practice of taking those complex results where scientists determined that a potential technique was unworkable or where they determined why an enigmatic result happened and then representing them as evidence that dating overall does not work.

  
Soapy Sam



Posts: 659
Joined: Jan. 2012

(Permalink) Posted: Feb. 21 2015,04:44   

Quote (midwifetoad @ Feb. 20 2015,14:12)
Regarding ORFan genes:

What percentage of genomes have been sequenced and cataloged?
Does having no cousins logically prove that one has no parents?

One of the reasons I follow Creo-debate is that I learn stuff, via unexpected avenues. You also may find this interesting.

http://bioinfo2.ugr.es/PDFsCla....011.pdf

--------------
SoapySam is a pathetic asswiper. Joe G

BTW, when you make little jabs like “I thought basic logic was one thing UDers could handle,” you come off looking especially silly when you turn out to be wrong. - Barry Arrington

  
NoName



Posts: 2729
Joined: Mar. 2013

(Permalink) Posted: Feb. 21 2015,06:59   

Quote (cryptoguru @ Feb. 20 2015,20:13)
...
An encrypted message that looks like random noise is a meaningful message even if you can't see it is ... it's about the intended recipient. ...

You've given the whole game away with that statement.

You can never know that you have a 'meaningful message' unless you are omniscient.  There is always, always, the possibility that there is a recipient for whom the item under consideration is meaningful.
There is no a priori mechanism to determine that any given item is meaningless.
This is why we talk about information.  Meaning is found, everything has meaning.  If we don't know the meaning yet, well, we keep looking.
You, on the other hand, stop dead in your tracks as soon as there is no meaning to you in your current context and under your current focus.  You then commit the astounding hubris of insisting that because there is no meaning there for you, why, then there is no meaning there for anybody.  Meaning magically springs into existence when your focus changes, when your context changes, when you learn something from someone else.  As, for example, stellar spectra.  Or learning Morse Code and suddenly seeing that those 'random' piles of dust were, all along, a secret message by a person held prisoner in the room at some point.  As we have seen you do throughout this thread.
You have no way to determine intent or the existence of a recipient in all cases.  You must inject a massive subjectivist load of presuppositions into everything you encounter, and thus you are incapable of doing science or even understanding the scientific enterprise.  The world and everything in it is meaningful, abundantly, fully, maximally densely packed with information.  With no intent or intended recipient necessary a priori.  It is the nature of existence that it is self-revealing, and what is revealed, exposed, the simple 'standing forth' of being what it is is meaningful.
You prefer to take on board culture superstitions and insert an intender into this to somehow 'insure' that information is  meaning is message, that the world becomes the meaning of the one who intended it as a message.
That attempt must fail because the presumed intender is itself an existing thing.  it is either meaningful in and of itself, or its meaning comes from its nature as an intended message from some 'intender-intender'.  It becomes meaning-assigners all the way down, it is a vicious regress.
And you're stuck with it because you have denied that things are meaningful, that things exhibit/provide/contain/are information in and of themselves.  If everything gets its meaning from something else, then nothing ever has meaning.  QED
You have to cheat and assert, along with the assertion of some 'prime intender' that it and only it is information in its own right.  Piling unjustified nonsense on top of unjustified nonsense.
Our approach is much more straight-forward, much more honest, doesn't violate Ockham's razor, and, btw, works.  We have evidence, you don't.

  
stevestory



Posts: 13407
Joined: Oct. 2005

(Permalink) Posted: Feb. 21 2015,07:49   

Quote (OgreMkV @ Feb. 20 2015,20:06)
Quote
My argument (and it pains me to have had to explain to adults what the normal use of the word information or message means) is that the meaningful information isn't expected to arise randomly.


That must be a record, three conflations of terms in the same sentence. Even Joe couldn't accomplish that.

Well, Joe's just an idiot with a rage disorder. Cryptoamateur's thing is incredulity as argument. It's not any more scientific, but it's a little less boring. There's hope for crypto, not so much for Joe or Gary.

   
NoName



Posts: 2729
Joined: Mar. 2013

(Permalink) Posted: Feb. 21 2015,08:02   

Quote (cryptoguru @ Feb. 20 2015,20:01)
...
A biological cell when it reads DNA understands the format of the information and deterministically processes that information as instructions that it understands to build an organism. ...

Rank anthropomorphism.
Cells no more understand DNA than organic acids understand equilibria equations or conditions.
Nor than hydrogen understands how to bond with oxygen to form water.
Nor than water knows how to dissociate into H+ and OH- ions until they are in balance at pH 7.
It is entirely improper to speak of cells 'understanding' DNA except in metaphorical language.  Easily seen once you accept that there is nothing going on but chemistry and physics, just as in water or organic acids in solution.
What's that you say?  There is *too* something else going on, there just has to be?  Well, what is it?  Point to a real phenomenon that cannot be explained by chemistry and physics, prove that it cannot, or that there is demonstrably another cause other than chemistry or physics operating there.  But remember, incredulity is neither a proof nor an argument.
The reality is that chemical reactions are chemical reactions.  There is no 'understanding' going on.
Understand?

  
JonF



Posts: 634
Joined: Feb. 2005

(Permalink) Posted: Feb. 21 2015,08:07   

[quote=OgreMkV,Feb. 20 2015,20:04]
Quote (cryptoguru @ Feb. 20 2015,19:01)

I really did want to talk about radiometric dating, but we already know you lost that battle... Mr. Never-Provide-the-Source-of-My-Claims.

Ooh!  Oooh!  Oooh1oneelevetyone!

Please please please do talk about radiometric dating. I haven't seen a good radiometric dating chew-toy in quite some time.

Let me guess... you'll start with the ol' "three assumptions that underlie radiometric dating" canard?

{ABE} I see I was right.

Cryppie ol' pal, the one thing that is absolutely sure about anyone who brings up those old tired errors is that the person knows nothing of radiometric dating.

More to come...

  
JonF



Posts: 634
Joined: Feb. 2005

(Permalink) Posted: Feb. 21 2015,08:57   

Quote (cryptoguru @ Feb. 20 2015,19:01)

I really did want to talk about radiometric dating, but we already know you lost that battle... Mr. Never-Provide-the-Source-of-My-Claims.


1) In the most widely used (by far) modern methods the initial conditions are known by basic physics or are produced as a part of the application of the method.  In U-Pb dating we know that zircons strongly reject lead when forming and the only way that significant amounts of lead can get into a zircon is by radioactive decay.  The RATE group, made up apparently of the only creationists who have somewhat of a clue, acknowledged this in Helium Diffusion Rates Support Accelerated Nuclear Decay:

 
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Samples 1 through 3 had helium retentions of 58, 27, and 17 percent. The fact that these percentages are high confirms that a large amount of nuclear decay did indeed occur in the zircons. Other evidence strongly supports much nuclear decay having occurred in the past (Humphreys, 2000, pp. 335–337). We emphasize that “old” radioisotopic ages are merely an artifact of analysis, not really indicating the occurrence of large amounts of nuclear decay. But according to the measured amount of lead physically present in the zircons, approximately 1.5 billion years worth—at today’s rates—of nuclear decay occurred. Supporting that, sample 1 still retains 58% of all the alpha particles (the helium) that would have been emitted during this decay of uranium and thorium to lead.

It is the uniformitarian assumption of invariant decay rates, of course, that leads to the usual conclusion that this much decay required 1.5 billion years....


In the second most widely used method, Ar-Ar, "excess argon" at solidification is shown by a high  value for the lower-temperature samples.  Even with excess argon Ar-Ar often produces a valid date, as in the Berkeley Geochronological Lab's  tour-de-force of dating the eruption of Vesuvius in 79AD.  See 40Ar/39Ar Dating into the Historical Realm: Calibration Against Pliny the Younger (free registration required for full text):

 
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Laser incremental heating of sanidine from the pumice deposited by the Plinian eruption of Vesuvius in 79 A.D. yielded a40Ar/39Ar isochron age of 1925 ± 94 years ago. Close agreement with the Gregorian calendar–based age of 1918 years ago demonstrates that the 40Ar/39Ar method can be reliably extended into the temporal range of recorded history. Excess 40Ar is present in the sanidine in concentrations that would cause significant errors if ignored in dating Holocene samples.

{emphasis added}

And from Radiogenic Isotope Geochronology, the textbook on radiometric dating, section 10.2.3:

 
Quote
Because the potassium signature of a sample is converted in situ to an argon signature by the 40)39 technique, it is possible to liberate argon in stages from different domains of the sample and still recover full age information from each step. Merrihue and Turner (1966) demonstrated the effectiveness of this ‘step heating’ technique in their original Ar)Ar dating study of meteorites, adapting the method from its previous application to I)Xe analysis of meteorites (section 15.3.1).

The great advantage of the step heating technique over the conventional ‘total fusion’ technique is that progressive outgassing allows the possibility that anomalous sub-systems within a sample may be identified, and, ideally, excluded from an analysis of the ‘properly behaved’ parts of the sample. This can apply to both separated minerals and whole-rock samples. Most commonly the technique is used to understand samples which have suffered argon loss, but it may also be a help in interpreting samples with inherited argon.

{emphasis added}

2) The same most widely used dating methods detect whether there has been gain or loss of relevant material over time, and they often produce a valid age even when there has been such gain or loss. See the two references above.  Also from Radiogenic Isotope Geology section 10.2.3:

 
Quote
To construct a spectrum plot, the size of each gas release at successively higher temperature is measured in terms of the magnitude of the 39Ar ion beam produced. Each gas release can then be plotted as a bar, whose length represents its volume as a fraction of the total 39Ar released from the sample, and whose value on the y axis is the corrected 40Ar/39Ar ratio from equation [10.12]. The latter is proportional to age, which is sometimes plotted on a log scale, and sometimes linear. Determination of a reliable crystallisation age from the spectrum plot depends on the identification of an age ‘plateau’. A rigorous criterion for a plateau age is the identification of a series of adjacent steps which together comprise more than 50% of the total argon release, each of which yields an age within 2 standard deviations of the mean (Dalrymple and Lanphere, 1974; Lee et al. 1991). However, plateaus have been ‘identified’ in many instances on the basis of weaker evidence.


Here's an example of a step heating plot showing loss of argon from the portions of the sample in which it was less strongly contained, from Fluid inclusion study on mesothermal gold deposits of the Pataz province (La Libertad, Peru):


Note the strong plateau indicating that argon was not lost from those portions of the sample and a solid age could be obtained.

In U-Pb dating of zircons (and some other materials) we know that the initial lead is essentially zero from basic physics.  The technique is to do a simple-accumulation date based on 235U decaying to 206Pb and another simple-accumulation date based on 235U decaying to 207Pb. if the dates are the same that's strong evidence that the date is good and if the date is plotted on a standard plot it will fall on the "concordia curve". Geochronologists have gotten very good at sample preparation and obtaining concordant dates. But sometimes you get discordant dates that don't fall on the curve, usually due to loss of lead which is comparatively volatile. In that case you do multiple measurements on the same sample or co-genetic samples and plot them. Many times for various reasons that are too technical to go into right now the points will form a line and the upper intersection of that line with the concordia curve is the date. For example, the Jack Hills zircons analysed in Evidence from detrital zircons for the existence of continental crust and oceans on the Earth 4.4 Gyr ago (the oldest known minerals formed on Earth):



3) Finally, the constancy of radioactive decay rates (under conditions that could apply on earth)  is an extremely fundamental property of our universe, and any changes at any time would have left unmistakable traces. Many have looked for those traces and they aren't there.  Also theoretical physicists understand radioactive decay pretty well, and know theoretically why they are constant.  At The Constancy of Constants, Part 2 physicist Steve Carlip lists some effects that variable decay rates would have:

  • searches for changes in the radius of Mercury, the Moon, and Mars (these would change because of changes in the strength of interactions within the materials that they are formed from);
  • searches for long term ("secular") changes in the orbits of the Moon and the Earth --- measured by looking at such diverse phenomena as ancient solar eclipses and coral growth patterns;
  • ranging data for the distance from Earth to Mars, using the Viking spacecraft;
  • data on the orbital motion of a binary pulsar PSR 1913+16;
  • observations of long-lived isotopes that decay by beta decay (Re 187, K 40, Rb 87) and comparisons to isotopes that decay by different mechanisms;
  • the Oklo natural nuclear reactor (mentioned in another posting);
  • experimental searches for differences in gravitational attraction between different elements (Eotvos-type experiments);
  • absorption lines of quasars (fine structure and hyperfine splittings);
  • laboratory searches for changes in the mass difference between the K0 meson and its antiparticle;
  • searches for geological evidence of "exotic" decays, such as double beta decay of Uranium 238 or the decay of Osmium to Rhenium by electron emission, which are impossible with the present values of basic physical constants but would become possible if these changed;
  • laboratory comparisons of atomic clocks that rely on different atomic processes (e.g., fine structure vs. hyperfine transitions);
  • analysis of the effect of varying "constants" on primordial nucleosynthesis in the very early Universe.

The constancy of decay rates is not an assumption; it is a conclusion based on decades of experiments and theoretical development.

  
JonF



Posts: 634
Joined: Feb. 2005

(Permalink) Posted: Feb. 21 2015,09:35   

This is fun!  I want to address Cryppie's questions:

 
Quote
C) why do professionally processed rock datings on the same sample give WILDLY varying results?
D) why do professionally processed rock datings on known age samples (100 years) give billions of years?

Short answer; either fraud on the part of the creationist performing the research or misunderstanding/misrepresentation on the part of the creationist presenting the data.

Nick's given you an example of the latter.  My personal favorite creationist fraud is an example of the former.  It's my favorite because Snelling made the fraud so obvious in the "technical" version of his paper.

From the "feed the sheeple" version at Radioactive “Dating” Failure: Recent New Zealand Lava Flows Yield “Ages” of Millions of Years:

 
Quote
The radioactive potassium-argon dating method has been demonstrated to fail on 1949, 1954, and 1975 lava flows at Mt Ngauruhoe, New Zealand, in spite of the quality of the laboratory’s K–Ar analytical work. Argon gas, brought up from deep inside the earth within the molten rock, was already present in the lavas when they cooled. We know the true ages of the rocks because they were observed to form less than 50 years ago. Yet they yield “ages” up to 3.5 million years which are thus false. How can we trust the use of this same “dating” on rocks whose ages we don’t know? If the method fails on rocks when we have an independent eye-witness account, then why should we trust it on other rocks where there are no independent historical cross-checks?


Of course the cognoscenti immediately realize that using K-Ar dating at the end of the 90's was a pretty stupid thing to do; he could have used Ar-Ar.  But that wouldn't yield the results he wanted.

When we look at the "technical" paper we need to know two technical terms:

  • "Whole rock": pretty much says it all. Grind up the entire sample into a fine powder and test the powder, which is a mixture of everything that was in the rock.
  • "Xenolith": literally "foreign rock". Chunks of foreign material embedded in the rock matrix, unmelted or partially melted, which formed long before the parent rock solidified.


Ready?  From The Cause of Anomalous Potassium-Argon "Ages" for Recent Andesite Flows at Mt. Ngauruhoe, New Zealand, and the Implications for Potassium-Argon "Dating":

 
Quote
All samples were sent first for sectioning one thin section from each sample for petrographic analysis. A set of representative pieces from each sample (approximately 100 g) was then despatched to the AMDEL Laboratory in Adelaide, South Australia, for whole-rock major, minor and trace element analyses. A second representative set (50–100 g from each sample) was sent progressively to Geochron Laboratories in Cambridge (Boston), Massachusetts, for whole-rock potassium-argon (K-Ar) dating first a split from one sample from each flow, then a split from the second sample from each flow after the first set of results was received, and finally, the split from the third sample from the June 30, 1954 flow.

...

Steiner (1958) stressed that xenoliths are a common constituent of the 1954 Ngauruhoe lava, but also noted that Battey (1949) reported the 1949 Ngauruhoe lava was rich in xenoliths. All samples in this study contained xenoliths, including those from the 1975 avalanche material. However, many of these aggregates are more accurately described as glomerocrysts and mafic (gabbro, websterite) nodules (Graham et al., 1995). They are 3–5 mm across, generally have hypidiomorphic-granular textures, and consist of plagioclase, orthopyroxene, and clinopyroxene in varying proportions, and very occasionally olivine. The true xenoliths are often rounded and invariably consist of fine quartzose material. Steiner also described much larger xenoliths of quartzo-feldspathic composition and relic gneissic structure.

...

Xenoliths are present in the Ngauruhoe andesite flows (Table 3), but they are minor and less significant as the location of the excess 40Ar* residing in these flows than the plagioclase and pyroxene phenocrysts, and the much larger glomerocrysts of plagioclase, pyroxene, or plagioclase and pyroxene that predominate. The latter are probably the earlyformed phenocrysts that accumulated together in the magma within its chamber prior to eruption of the lava flows. Nevertheless, any excess 40Ar* they might contain had to have been supplied to the magma from its source. The xenoliths that are in the andesite flows have been described by Steiner (1958) as gneissic, and are therefore of crustal origin, presumably from the basement rocks through which the magma passed on its way to eruption.

{emphasis added}

Note the handwaving dismissal of the importance of the xenoliths without presenting any data supporting his claim.

He dated a mixture of old and new material with an inappropriate method and expressed surprise when the result was not the date of the young material.  What a breakthrough!

I also note that the "technical" paper contains an excellent example of the latter type of misrepresentation, possibly fraud, in his discussion of  Dalrymple's results as presented in Snelling's table on the page numbered 8.  Dalrymple studied 26 recent lava flows using Ar-Ar which detects excess Ar.  21 of those flows had no excess Ar.  Four of them had a little excess Ar but not enough to effect an age if it were but a few million years old rather than very young. One had enough excess argon to confuse the dating of a rock that is only a few but not several million years old.  Dalrymple concluded, quite correctly, that these results imply the excess argon is rare in concentrations high enough to confuse the dating of rocks several million years old and older:

 
Quote
With the exception of the Hualalai flow, the amounts of excess 40Ar and 36Ar found in the flows with anomalous 40Ar/36Ar ratios were too small to cause serious errors in potassium-argon dating of rocks a few million years old or older. However, these anomalous 40Ar/36Ar ratios could be a problem in dating very young rocks. If the present data are representative, argon of slightly anomalous composition can be expected in approximately one out of three volcanic rocks.


But Snelling says:

 
Quote
However, these dogmatic statements by Dalrymple are inconsistent with even his own work on historic lava flows (Dalrymple, 1969), some of which he found had non-zero concentrations of 40Ar* in violation of this key assumption of the K-Ar dating method. He does go on to admit that “Some cases of initial 40Ar remaining in rocks have been documented but they are uncommon” (Dalrymple, 1991), but then refers to his study of 26 historic, subaerial lava flows (Dalrymple, 1969). Five (almost 20%) of those flows contained “excess argon,” but Dalrymple still then says “that ‘excess’ argon is rare in these rocks!”


I think the misrepresentation is clear.

(I have the Dalrymple paper 40Ar/36Ar analyses of historic lava flows in an OCR'd PDF if anyone is interested and doesn't have appropriate access.)

  
NoName



Posts: 2729
Joined: Mar. 2013

(Permalink) Posted: Feb. 21 2015,09:53   

Is anyone else getting flashbacks to afdave?  This is just so reminiscent of his stuff here and at other sites he moved to after giving up here.
Sadly, the marvelous 'Formal Debate:  Dendrochronology  and C-14' has vanished from the web.  Or at least from my limited google-fu.

  
JonF



Posts: 634
Joined: Feb. 2005

(Permalink) Posted: Feb. 21 2015,10:11   

Nyah Nyah Nyah!  Gone from the Web but not gone.  I and a few others have pretty much the whole shootin' match but only as HTML files.  Once you are into the thread the links work.  Drool away:


  
JonF



Posts: 634
Joined: Feb. 2005

(Permalink) Posted: Feb. 21 2015,10:14   

Nick, one comment.  If lead was lost in a single brief heating event the lower intersection of discordia and concordia is the date of the event.  But there are many scenarios in which that intersection does not have age-significance, and it's often difficult to determine if it does have age-significance, so you don't see a lot of interpretations of that intersection.

  
N.Wells



Posts: 1836
Joined: Oct. 2005

(Permalink) Posted: Feb. 21 2015,10:16   

JonF, Yes, I need to back off that point, thanks.

The Hualalai Flow should get a Purple Heart or something for suffering so much at the hands of creationists.  From a summary by Brent Dalrymple, who has written a lot of great stuff about creationist abuse of data from his field, at http://www.talkorigins.org/faqs.......ng.html at

   
Quote
Two extensive K-Ar studies on historical lava flows from around the world (31, 79) showed that excess argon is not a serious problem for dating lava flows. The authors of these reports “dated” numerous lava flows whose age was known from historical records. In nearly every case, the measured K-Ar age was zero, as expected if excess argon is uncommon. An exception is the lava from the 1801 Hualalai flow, which is so badly contaminated by the xenoliths that it is impossible to obtain a completely inclusion-free sample.


Dalrymple provides further details:    
Quote
The 1801 Flow from Hualalai Volcano

   
Quote
 [from creationist literature]  Volcanic rocks produced by lava flows which occurred in Hawaii in the years 1800-1801 were dated by the potassium-argon method. Excess argon produced apparent ages ranging from 160 million to 2.96 billion years. (77, p. 200)

   Similar modern rocks formed in 1801 near Hualalai, Hawaii, were found to give potassium-argon ages ranging from 160 million years to 3 billion years. (92, p. 147)


Kofahl and Segraves (77) and Morris (92) cite a study by Funkhouser and Naughton (51) on xenolithic inclusions in the 1801 flow from Hualalai Volcano on the Island of Hawaii.  The 1801 flow is unusual because it carries very abundant inclusions of rocks foreign to the lava. These inclusions, called xenoliths (meaning foreign rocks), consist primarily of olivine, a pale-green iron-magnesium silicate mineral. They come from deep within the mantle and were carried upward to the surface by the lava. In the field, they look like large raisins in a pudding and even occur in beds piled one on top of the other, glued together by the lava. The study by Funkhouser and Naughton (51) was on the xenoliths, not on the lava. The xenoliths, which vary in composition and range in size from single mineral grains to rocks as big as basketballs, do, indeed, carry excess argon in large amounts. Funkhouser and Naughton were quite careful to point out that the apparent “ages” they measured were not geologically meaningful. Quite simply, xenoliths are one of the types of rocks that cannot be dated by the K-Ar technique. Funkhouser and Naughton were able to determine that the excess gas resides primarily in fluid bubbles in the minerals of the xenoliths, where it cannot escape upon reaching the surface. Studies such as the one by Funkhouser and Naughton are routinely done to ascertain which materials are suitable for dating and which are not, and to determine the cause of sometimes strange results. They are part of a continuing effort to learn.


Note that the title of the Funkhouser and Naughton paper was "Radiogenic helium and argon in ultramafic inclusions from Hawaii."  That's "In inclusions" and 'of a different rock type'  - it's kind of hard to miss those details, so we are down to incompetency and/or dishonesty as a explanation for presenting the results as dates of the lava flows.

I liked two other cases as well:
   
Quote
The Liberian example (Table 2) is from a report by Dalrymple and others (34). These authors studied dikes of basalt that intruded Precambrian crystalline basement rocks and Mesozoic sedimentary rocks in western Liberia. The dikes cutting the Precambrian basement gave K-Ar ages ranging from 186 to 1213 million years (Woodmorappe erroneously lists this higher age as 1230 million years), whereas those cutting the Mesozoic sedimentary rocks gave K-Ar ages of from 173 to 192 million years. 40Ar/39Ar experiments4 on samples of the dikes showed that the dikes cutting the Precambrian basement contained excess 40Ar and that the calculated ages of the dikes do not represent crystallization ages. The 40Ar/39Ar experiments on the dikes that intrude the Mesozoic sedimentary rocks, however, showed that the ages on these dikes were reliable. Woodmorappe (134) does not mention that the experiments in this study were designed such that the anomalous results were evident, the cause of the anomalous results was discovered, and the crystallization ages of the Liberian dikes were unambiguously determined. The Liberian study is, in fact, an excellent example of how geochronologists design experiments so that the results can be checked and verified.
 That seems to be a massive misrepresentation due to "I don't care because none of faithful are ever going to catch me on this".


Also from Dalrymple, an example of a creationist using an argument that is so stupid that he must have misunderstood the science:  
Quote
The Hawaiian Basalts

 
Quote
  [from creationist literature]   Still another study on Hawaiian basalts obtained seven “ages” of these basalts ranging all the way from zero years to 3.34 million years. The authors, by an obviously unorthodox application of statistical reasoning, felt justified in recording the “age” of these basalts as 250,000 years. (92, p. 147)


The data Morris (92) refers to were published by Evernden and others (44), but include samples from different islands that formed at different times! The age of 3.34 million years is from the Napali Formation on the Island of Kauai and is consistent with other ages on this formation (86, 87). The approximate age of 250,000 years was the mean of the results from four samples from the Island of Hawaii, which is much younger than Kauai. Contrary to Morris’ concerns, nothing is amiss with these data, and the statistical reasoning used by Evernden and his colleagues is perfectly rational and orthodox.

  
JonF



Posts: 634
Joined: Feb. 2005

(Permalink) Posted: Feb. 21 2015,10:39   

Yes, that's a great resource.  I am proud that I'm the one who scanned and proofread it, then Harlequin did the HTML.

  
N.Wells



Posts: 1836
Joined: Oct. 2005

(Permalink) Posted: Feb. 21 2015,10:53   

Well, thank you.

  
Jim_Wynne



Posts: 1208
Joined: June 2006

(Permalink) Posted: Feb. 21 2015,13:37   

Quote (stevestory @ Feb. 21 2015,07:49)
Quote (OgreMkV @ Feb. 20 2015,20:06)
Quote
My argument (and it pains me to have had to explain to adults what the normal use of the word information or message means) is that the meaningful information isn't expected to arise randomly.


That must be a record, three conflations of terms in the same sentence. Even Joe couldn't accomplish that.

Well, Joe's just an idiot with a rage disorder. Cryptoamateur's thing is incredulity as argument. It's not any more scientific, but it's a little less boring. There's hope for crypto, not so much for Joe or Gary.

Crypto is just a garden variety reasonably smart creationist who is too deluded to understand that his entire thesis is based on an argument that assumes its own conclusion.  In that particular variety of "science," that's a feature, not a defect.  I think GG is far more entertaining.

--------------
Evolution is not about laws but about randomness on happanchance.--Robert Byers, at PT

  
OgreMkV



Posts: 3668
Joined: Oct. 2009

(Permalink) Posted: Feb. 22 2015,15:42   

I think this pretty much destroys crypto's claims... http://molbio.mgh.harvard.edu/szostak...._01.pdf

--------------
Ignored by those who can't provide evidence for their claims.

http://skepticink.com/smilodo....retreat

   
NoName



Posts: 2729
Joined: Mar. 2013

(Permalink) Posted: Feb. 22 2015,17:18   

Quote (OgreMkV @ Feb. 22 2015,16:42)
I think this pretty much destroys crypto's claims... http://molbio.mgh.harvard.edu/szostak...._01.pdf

Well, it would, but crypto seems not to trust the real world.  If it can't be demonstrated with a simple set of formulas, a couple of tautologies, and a suppressed premise or three, within the scope of a self-contradictory set of prejudicial conditions, well, it just can't happen.  No matter what actually happens.

Lovely reference, though.  Thanks for posting the link!

  
OgreMkV



Posts: 3668
Joined: Oct. 2009

(Permalink) Posted: Feb. 22 2015,17:19   

Quote (NoName @ Feb. 22 2015,17:18)
Quote (OgreMkV @ Feb. 22 2015,16:42)
I think this pretty much destroys crypto's claims... http://molbio.mgh.harvard.edu/szostak...._01.pdf

Well, it would, but crypto seems not to trust the real world.  If it can't be demonstrated with a simple set of formulas, a couple of tautologies, and a suppressed premise or three, within the scope of a self-contradictory set of prejudicial conditions, well, it just can't happen.  No matter what actually happens.

Lovely reference, though.  Thanks for posting the link!

Soon as I get some questions answered, I will be writing this up for my blog.

--------------
Ignored by those who can't provide evidence for their claims.

http://skepticink.com/smilodo....retreat

   
Doc Bill



Posts: 1039
Joined: April 2007

(Permalink) Posted: Feb. 24 2015,19:14   

I don't think Guru is going to return.  All of his "arguments" have been met, documented and dismissed with examples and documentation.

However, I remember over at UD, the swamp, the denizens including the great Luskin "demonstrating" that Dawkins' weasel program "latched" output.  The fact that it could not be shown in the code led Luskin to claim that the program "virtually latched."  OMG, that was fun to watch!  Such desperation.

  
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