@Rumraket

Every three dimensional object in our universe consists of the atoms. Each atom has an x,y and z coordinate. Using this coordinates we can map every three dimensional object into one dimensional linear space, like organism is mapped in DNA.
Let's suppose we do this mapping process for 1886 Swift Safety Bicycle, which results in a long linear information in binary form(bicycle DNA).

According to evolutionary thinking, if bicycle's DNA undergoes a series of copying events and between each copying event is influenced by a random variation and selected in "ability to drive" environment, eventually, new functional bicycle parts will start popping into existence, and modern bicycle will appear. Rinse and repeat.... and..... Bmw r75 motorcycle come on the scene. Rinse and repeat.... and..... Ferrari spider emerges.

This type of ridiculous beliefs are at the core of evolutionary thoughts. That is why you are repeatedly, by quoting completely irrelevant things, attempting to shift attention away from scientific discussion on functionality emergence by processes of random variation and natural selection.

MarioNovak wrote:@Rumraket

Every three dimensional object in our universe consists of the atoms. Each atom has an x,y and z coordinate. Using this coordinates we can map every three dimensional object into one dimensional linear space, like organism is mapped in DNA.
Let's suppose we do this mapping process for 1886 Swift Safety Bicycle, which results in a long linear information in binary form(bicycle DNA).

According to evolutionary thinking, if bicycle's DNA undergoes a series of copying events and between each copying event is influenced by a random variation and selected in "ability to drive" environment, eventually, new functional bicycle parts will start popping into existence, and modern bicycle will appear. Rinse and repeat.... and..... Bmw r75 motorcycle come on the scene. Rinse and repeat.... and..... Ferrari spider emerges.

This type of ridiculous beliefs are at the core of evolutionary thoughts. That is why you are repeatedly, by quoting completely irrelevant things, attempting to shift attention away from scientific discussion on functionality emergence by processes of random variation and natural selection.

Again, scientists actually bothered to make a simulation of evolution, it's called Avida. You don't like it because you don't like the results you get when you run it. You have no sensible argument against it so all you can do is a knee-jerk reaction to dismiss it because it works.

Rumraket wrote:
Again, scientists actually bothered to make a simulation of evolution, it's called Avida. You don't like it because you don't like the results you get when you run it. You have no sensible argument against it so all you can do is a knee-jerk reaction to dismiss it because it works.

Here you have peer reviewed scientific paper that refutes AVIDA. Enjoy.

http://marksmannet.com/RobertMarks/REPR ... thesis.pdf

MarioNovak wrote:

Rumraket wrote:
Again, scientists actually bothered to make a simulation of evolution, it's called Avida. You don't like it because you don't like the results you get when you run it. You have no sensible argument against it so all you can do is a knee-jerk reaction to dismiss it because it works.

Here you have peer reviewed scientific paper that refutes AVIDA. Enjoy.

http://marksmannet.com/RobertMarks/REPR ... thesis.pdf

Explain what that paper says.

Also, that paper doesn't seem to have been through any standard peer review, it was "published" at a conference.

MarioNovak wrote:

Rumraket wrote:
Again, scientists actually bothered to make a simulation of evolution, it's called Avida. You don't like it because you don't like the results you get when you run it. You have no sensible argument against it so all you can do is a knee-jerk reaction to dismiss it because it works.

Here you have peer reviewed scientific paper that refutes AVIDA. Enjoy.

http://marksmannet.com/RobertMarks/REPR ... thesis.pdf

William Dembski?

MarioNovak wrote:

Rumraket wrote:
Again, scientists actually bothered to make a simulation of evolution, it's called Avida. You don't like it because you don't like the results you get when you run it. You have no sensible argument against it so all you can do is a knee-jerk reaction to dismiss it because it works.

Here you have peer reviewed scientific paper that refutes AVIDA. Enjoy.

http://marksmannet.com/RobertMarks/REPR ... thesis.pdf

Domain expertise and prior knowledge
about search space structure or target location is therefore
essential in crafting the search algorithm.

Now if this paper wasn't a response to a blind but recursive algorithm that did in fact preform better then chance and in some cases better then design it may have a leg to stand on.

Further what is being described as prior knowledge being input into the system isn't a stacked deck but the actual code to wright run the programs. To use an analogy to real life it's not that an organism knows that cold is coming so must adapt it's that cold is coming and animals that don't adapt die.

Why isn't this thread in the cretinism forum?

I do have to note, that that pseudopublication makes multiple references to Dembski's own "theorem" which has been totally rejected by professional mathematicians and information theorists. Now I'm no mathematician, so I have no choice but to rely on the concensus views of the experts in this matter.

Nylonase MN. Whenever you're ready.

Funny coincidence is that a guy with an argument a bit like Mario's turned up over on the Panda's Thumb forums a few days ago:
http://www.antievolution.org/cgi-bin/ikonboard/ikonboard.cgi?s=54c0a69016e60b28;act=ST;f=14;t=9614;st=0

The discussion quickly came down to the same points: No rigorous definition of "new" is given, some blather about simulations, and then Avida.

It didn't go so well for that dude either.

I really liked this post:

Doc Bill wrote: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?

I'm not a mathematician, but I've been trying to figure out what Mario's paper is saying, since he's neglected to help us there. A couple of things occur to me:

Have a look at p3051, numbered paragraph 2 in the right hand column:

Dembski wrote:If the fitness of the organism does not decrease, we keep the mutation and repeat the iteration. If the fitness does increase, the mutation is discarded and the process repeated.

This sounds like a natural selection simulation to me, except that there appears to be a very glaring typo, that I've emphasised. It seems to me that it should say "does decrease", not "does increase". The sentence makes no sense to me otherwise, either in terms of how we understand natural selection, or in the semantics.

If I've read this right, then it seems to be a blatant review failure. If even I can find that on a quick read-through, what else is in there?

Secondly, the more I read the discussion, the more it seems to boil down to one main point:

If the EQU (the most advanced feature) is the only one rewarded by the natural selection process, it isn't observed to evolve, and requires the rewarding of lower level features that have to act as stepping stones on the way.

This seems unsurprising to me, and completely consistent with how we understand evolution to have taken place. More complex organisms arise from simpler ones; no one suggests that a complex multicellular organism arose suddenly from nothing, even after a very long time.

So I'm suspecting that the paper a) has had inadequate review, and b) is really an elaborate straw man.

I'd be glad if anyone can either confirm or correct my reading of the paper.

I want to dissect this argument because it seems to be hinting at what is lurking at the bottom of Mario's many difficulties with evolution. Unstated assumptions about functionality and appeals to personal convictions and intuitions.

MarioNovak wrote:@Rumraket

Every three dimensional object in our universe consists of the atoms.

Not really. Not that this point is important for the discussion but that isn't technically true. For example the atom itself is a 3-dimensional structure, and it's not made of atoms. But whatever, I do take your point.

MarioNovak wrote: Each atom has an x,y and z coordinate. Using this coordinates we can map every three dimensional object into one dimensional linear space, like organism is mapped in DNA.

But that's really, really not how DNA works.

There is no nucleotide sequence for the spatial locations of atoms, or even proteins, in the chromosomes. The higher order structures that we see in cells and even in multicellular organisms made of large clusters of cells, do not have specific sequences of code for, for example, the specific location of your elbow join on your arm. These higher order structures are emergent properties of the interactions between the compounds produced from gene expression, cell-cell signaling and so on.

You can't just look at a piece of DNA and say "this particular thing says that the elbow joint goes over here". There is always a context in which the clusters of genes expressed have to be looked at. This can become quite a digression if you wish to go further, but I just wanted to point out that your analogy is very inexact. It fails to capture how DNA actually works.

MarioNovak wrote:Let's suppose we do this mapping process for 1886 Swift Safety Bicycle, which results in a long linear information in binary form(bicycle DNA).

Ignoring the thing about how DNA works, I do see what you are trying to say. We just make an extremely long list of XYZ coordinates of all the atoms that make up a bicycle, and then we call this list the "genome". Ignoring for a moment that no computer on earth can simulate such a large macroscopic structure at the atomic level, let's just go with it.

MarioNovak wrote:According to evolutionary thinking, if bicycle's DNA undergoes a series of copying events and between each copying event is influenced by a random variation and selected in "ability to drive" environment

So let me get this straight. You say we actually computationally simulate the full physics of a functional driving bike(as in, it actually drives in the simulation, the pedals turn, which pull on the chain which makes the wheels turn and so on), at the atomic scale.
And then, we start making copies of this "bike" in the simulation, but we allow "mutations" in the spatial locations(XYZ coordinates) of atoms. And then we evaluate these copies under a selection criterion: Can they drive?

That's what you mean, right?

MarioNovak wrote:eventually, new functional bicycle parts will start popping into existence, and modern bicycle will appear.

Why a modern bicycle? Why not just a bicycle that also works, does it really have to be some specific "modern model"? Bicycles look the way they do in part because of functionality, but also in part because human beings find them aesthetically appealing when they look like that. If you merely select for function, why would the resulting bicycle come to look like things humans designed to look "sporty", or "fast" or "pretty"?

Why would this simulation not be able to mutate the bicycle into another type of still functional bicycle? You seem to be acting extremely dismissive of this possibility. Why? If you really get down to it, what is this dismissal based on? Why can't the bicycle change while remaining functional, when you copy and mutate it while keeping the selection criterion active? Why? Explain what this dismissal is based on, other than "I just don't believe it because it sounds ridiculous".

MarioNovak wrote:Rinse and repeat.... and..... Bmw r75 motorcycle come on the scene. Rinse and repeat.... and..... Ferrari spider emerges.

Why would these specific vehicle models appear? What is the analogy to real biology here?

MarioNovak wrote:This type of ridiculous beliefs are at the core of evolutionary thoughts.

What is this but an appeal to your personal denial and incredulity?

I have never seen anyone produce an argument for, or an account of evolution, that could be said to be analogous to this imagined scenario of yours.

What does the 1886 Swift Safety Bicycle, BMW r75, or Ferrari Spider represent in real life? Why must the one change into the other, who says this must or should happen in real biological evolution?

MarioNovak wrote:That is why you are repeatedly, by quoting completely irrelevant things, attempting to shift attention away from scientific discussion on functionality emergence by processes of random variation and natural selection.

I have quoted nothing of irrelevance. And unlike you, I don't copy-paste things without correctly attributing them to their original authors and pretend I wrote them myself, or ever referenced something I didn't understand.

TopCat wrote:I'm not a mathematician, but I've been trying to figure out what Mario's paper is saying, since he's neglected to help us there. A couple of things occur to me:

Have a look at p3051, numbered paragraph 2 in the right hand column:

Dembski wrote:If the fitness of the organism does not decrease, we keep the mutation and repeat the iteration. If the fitness does increase, the mutation is discarded and the process repeated.

This sounds like a natural selection simulation to me, except that there appears to be a very glaring typo, that I've emphasised. It seems to me that it should say "does decrease", not "does increase". The sentence makes no sense to me otherwise, either in terms of how we understand natural selection, or in the semantics.

If I've read this right, then it seems to be a blatant review failure. If even I can find that on a quick read-through, what else is in there?

Secondly, the more I read the discussion, the more it seems to boil down to one main point:

If the EQU (the most advanced feature) is the only one rewarded by the natural selection process, it isn't observed to evolve, and requires the rewarding of lower level features that have to act as stepping stones on the way.

This seems unsurprising to me, and completely consistent with how we understand evolution to have taken place. More complex organisms arise from simpler ones; no one suggests that a complex multicellular organism arose suddenly from nothing, even after a very long time.

So I'm suspecting that the paper a) has had inadequate review, and b) is really an elaborate straw man.

I'd be glad if anyone can either confirm or correct my reading of the paper.

I agree with your analysis, and it really does seem to boil down to that specific statement.

In effect, it is another version of the list of quotes given by ID proponents I gave in the previous posts. It's an assertion that mutating and copying things that already exist will never produce new functions, it will only destroy and degrade these things, because there is too far in phenotypical space between "stuff that works". So it requires a supernaturamagical designer to handpick them with his divine foresight.

Or in the case of human constructions, a human designer with foresight.

Again, the fundamental lie being propagated is that "mutations always destroy", because things that work are isolated and cannot be changed into each other through accumulations of small changes, because there are vast seas of lethal nonfunctionality "surrounding" it.

All ID arguments, when they aren't just plain appeals to willful denial, reduce to that statement.

TopCat wrote:I'm not a mathematician, but I've been trying to figure out what Mario's paper is saying, since he's neglected to help us there.

Dembski is an abysmal writer, and that's being generous. I sometimes suspect that his articles are actually complete gibberish, because he knows anyone who understands bioinformatics is not going to bother reading an article by such an incompetent non-entity, and those who do read it are people like Mario Novak, who figure that if it's printed on paper and has a lot of big words, diagrams and equations, then that makes it science. No need to actually understand what is written there.

But maybe Mario Novak can prove me wrong and give his plain English summary of the Dembski paper.

Rumraket wrote:Funny coincidence is that a guy with an argument a bit like Mario's turned up over on the Panda's Thumb forums a few days ago:
http://www.antievolution.org/cgi-bin/ikonboard/ikonboard.cgi?s=54c0a69016e60b28;act=ST;f=14;t=9614;st=0

The discussion quickly came down to the same points: No rigorous definition of "new" is given, some blather about simulations, and then Avida.

It didn't go so well for that dude either.

I really liked this post:

Doc Bill wrote: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?

I know I've said this before, but what strikes me about Paley's watchmaker analogy is that he fails to realize how it is self-refuting. He instantly recognizes that the watch is of a different origin than the heath that surrounds it. But it is the origin of the heath itself that he is trying to explain.

MarioNovak wrote:

Rumraket wrote:
Again, scientists actually bothered to make a simulation of evolution, it's called Avida. You don't like it because you don't like the results you get when you run it. You have no sensible argument against it so all you can do is a knee-jerk reaction to dismiss it because it works.

Here you have peer reviewed scientific paper that refutes AVIDA. Enjoy.

http://marksmannet.com/RobertMarks/REPR ... thesis.pdf

Hint: Anything with Dembski as an author is neither a scientific paper, nor is it likely to have passed scientific peer-review.

Rumraket wrote:...
In effect, it is another version of the list of quotes given by ID proponents I gave in the previous posts. It's an assertion that mutating and copying things that already exist will never produce new functions, it will only destroy and degrade these things, because there is too far in phenotypical space between "stuff that works". So it requires a supernaturamagical designer to handpick them with his divine foresight.

Or in the case of human constructions, a human designer with foresight.

Again, the fundamental lie being propagated is that "mutations always destroy", because things that work are isolated and cannot be changed into each other through accumulations of small changes, because there are vast seas of lethal nonfunctionality "surrounding" it.

All ID arguments, when they aren't just plain appeals to willful denial, reduce to that statement.

From your objection to ID, that mutating and copying things that already exist will not alway destroy and degrade these things, it does not follow evolution can create new complex things. Also, suggestion that function is not isolated and can be changed into other function through accumulations of small changes is another non sequitur and i will explain why.

I already said your explanations are based on hidden implicit assumptions that evolution has intelligence and foresight in creating new complex things or finding solutions for some harmful/lethal state in a cellular life, like intron insertions. To this intron-exon problem, you responded that introns coevolved gradually with the mechanism of splicing. I will now, by using an analogy, demonstrate how nonsensical this type of reasoning is when we put ourselves in evolution shoes. But we must first examine, on a general level, what is life, in order to prevent strawman attacks to my argument/analogy.

From the most general perspective, life is the ability to do something that inanimate natural processes can't do, e.g. to maintain or to replicate some complex dynamical arrangement of molecules. Now, what is this ability to maintain or to replicate? Where this ability comes from? Well, it comes from the right combination of molecules. The myriad of biochemical reactions in organism, all forms of movement, all types of functions... are nothing but right combination of molecules in the right place at the right time. In the same way, the ability of a cell to respond to a harmful or lethal state of intron insertion comes from the right combination of molecules called mRNA splicing process. So, processes of evolution have to do something that is easy to accomplish, right? All they have to do is to find the right combination of molecules and put those molecules to the right place at the right time. Well let's check out if that is the case, with the help of analogy.

We know that if cells get introns inserted into a genes, cells will eventually die out. To prevent this from happening evolution have to find a solution. And according to proponents of the evolution theory evolution did find a solution, because in present day eukaryotic life introns are successfully removed from the mRNA molecule. We can say that this intronic insertions are threat for cellular life and that right combination of molecules(mRNA splicing process) is the solution to this threat.

Now consider the following analogy: someone holds a gun up to you and threatens to kill you if you don't know the answer to a random question he asks. So, your life will be spared if you provide the right combination of letters and words, just like cell's life will be "spared" if evolution provides the right combination of molecules. Now we are at a crucial point, and we will put ourselves in evolution shoes.

We know that evolution have no intelligence, no purpose, no vision, no mind, no foresight... and therefore no knowledge that cells will eventually die out if solution or right combination of molecules is not found. So, what can evolution do? Well, it can find a solution by chance, from random copying mistakes that occur in the copying of existing information(DNA). Ok. Now, let's go back to the man that holds a gun up and threatens to kill you. You have to provide the answer to a random question he asked. But...you are in evolution shoes. So you don't know what the question is. You cannot grasp the problem. How then can you solve the problem in front of you and save your life? Well, the same as evolution. You can combine existing letters, words and sentences that exist in books, newspapers, magazines, ...or in your mind. You can use pre-adaptation, exaptation, co-option, you can create new information that is not present in existing literature. You can do whatever you want in creating new combinations of linguistic elements. The only constraint is your inability to use engineering and design principles in solving a problem(answering a question). You are unable to notice or become aware of the question, or in other words, to create a mental representation of perceived question and then co-opt right solution - the combination of letters, words and sentences according to this mental representation. In short, no intelligence allowed.

So, you don't know what words or letters to use, how to combine them, you don't know what amount of words constitute the correct answer. You just pick letters and words randomly, put them together randomly and hope correct solution will pop up.
Now, does your ability to co-opt or to produce new information is helping you to find solution to the problem? No. The problem is not in producing new combinations of molecules(letters, words, sentences), the problem is in producing right combination of molecules in the space of nearly infinite number of possible combinations.

So even if we assume (contrary to experimental evidence) that evolution can produce new information, new genes, new enzymes or new functions in some random tempotal point, what does that have to do with the solution to harmful or lethal state in a cellular life, like intron insertions. Nothing. Just like your ability to produce meaningful words and sentences has nothing to do with providing the potential killer with the right answer to the question you cannot perceive. That is why your claim that function can be changed into other function through accumulations of small changes is noting but non sequitur. Problem is not in creating some new random function, problem is in creating function that solves a particular problem.

Every observable level of biological organization exhibit "question-answer" or "problem-solution" relationship. Enzyme(answer) and the substrate(question) possess specific complementary geometric shapes that fit exactly into one another and this is referred to as "the lock and key" model. Enzymes that catalyze reactions in metabolic pathways often require variety of cofactors(not random, but specific) in order to function properly. Sperm-egg interaction that allows the two gametes to fuse and create the zygote is impossible without specific complementary of these two complex structures. Molecules that constitute a sperm cell can be arranged in a myriad of ways. So how can a process with no intelligence, no vision, no mind, no foresight... produce the right combination of molecules for egg cell to interact functionally? Well, it can, exactly the same way you can complete the questionnaire you never saw - you just pick letters and words randomly, put them together randomly and hope coherent answers will pop up. This is a central and foundational assumption of evolution theory - solution will pop up through accumulations of small changes if we wait long enough.

"Accumulations of small changes" is like asking a question one letter at a time or answering question one letter at a time or finding a target one step at a time, but it does nothing to help in finding a correct answer. Inserting one random functional molecule at a time into a cell won't cause splicing pathway to emerge. Without intelligent guidance(knowledge of correct molecules) you can accumulate small changes from now till the heat death of the universe but you will not find a solution.

STFU

That about covers it.

What a load of ignorant fucking drivel. Anybody who thinks we operate on the assumption that evolution has foresight has failed dismally to understand evolutionary theory, which is quite a special achievement, since it's simple enough to be understood by anybody with two or more functioning neurons. That anybody could hold that position and still be able to turn on a computer to expose such a failure to the world at large seems somewhat paradoxical.