Cell Reports special Darwin Day issue

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Cell Reports, an open access journal of cell biology, has a special Darwin Day issue:

In celebration of Darwin Day 2013, we offer this collection of papers published in Cell Reports on various aspects of evolutionary biology. Topics range from experimental evolution in real time to explorations of the origins of signaling pathways in existence for nearly a billion years. Like all papers in Cell Reports, these articles are open access, free to read and distribute. We hope you enjoy the collection, which is perhaps best prefaced by Mr. Darwin himself:

It is interesting to contemplate an entangled bank, clothed with many plants of many kinds, with birds singing on the bushes, with various insects flitting about, and with worms crawling through the damp earth, and to reflect that these elaborately constructed forms, so different from each other, and dependent on each other in so complex a manner, have all been produced by laws acting around us. These laws, taken in the largest sense, being Growth with Reproduction; Inheritance which is almost implied by reproduction; Variability from the indirect and direct action of the external conditions of life, and from use and disuse; a Ratio of Increase so high as to lead to a Struggle for Life, and as a consequence to Natural Selection, entailing Divergence of Character and the Extinction of less-improved forms. Thus, from the war of nature, from famine and death, the most exalted object which we are capable of conceiving, namely, the production of the higher animals, directly follows. There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.

- On the Origin of Species, first edition, closing paragraph

Enjoy!

88 Comments

And the American Museum of Natural History just unveiled the Darwin Manuscripts Project

And still Darwin does it better. Who, upon reading that clear, concise, economic description of the variety in life, would dare put up a weak, castrated god, in opposition?

“dependent on each other in so complex a manner,…” The origins of modern Environmental Science?

It is impossible to distinguish what came first the chicken or the egg, and all evolution stands by is adaptation. Every organism fight for survival every day. That why the the term survival of the fittest comes into play. Look at Sociologist Herbert Spencer he believed that one shouldn’t help the poor. It was Social Darwinism. I cant sit here and say that I agree with it but it happens in life. Not every creature is suppose to live for ever.

Wrong thread, I think. I’ll leave it, but responses are discouraged.

jhender8 said:

It is impossible to distinguish what came first the chicken or the egg, and all evolution stands by is adaptation. Every organism fight for survival every day. That why the the term survival of the fittest comes into play. Look at Sociologist Herbert Spencer he believed that one shouldn’t help the poor. It was Social Darwinism. I cant sit here and say that I agree with it but it happens in life. Not every creature is suppose to live for ever.

robert van bakel said:

And still Darwin does it better. Who, upon reading that clear, concise, economic description of the variety in life, would dare put up a weak, castrated god, in opposition?

“dependent on each other in so complex a manner,…” The origins of modern Environmental Science?

God is not needed to oppose Neo-Darwinism. Darwin did not know of the complexity contained within cells. This is why he postulated an idea that cannot explain the realities of biological systems. DNA is an example of specified complexity that Darwin cannot explain. Neither can it explain the irreducible complexity of such systems as the bacterial flagella.

It has been shown that genetic variations and natural selection cannot directly account for systems such as the flagella. Indirect means such as coevolution are extremely improbable and near the range of impossible.

So why are we celebrating Darwin Day? Darwin published a book about an idea that for over 150 years has unsuccessfully been able to explain the origin of life on earth. It seems like it is time to start exploring other explanations. Intelligence is the only known cause of specific complexity and irreducible complexity. Perhaps research in biology should be redirected towards understanding the origin of life in this manner.

Maybe we will celebrate Panspermia Day in the near future. It would be more fun…the costumes would be better anyway.

Prometheist said:

It has been shown that genetic variations and natural selection cannot directly account for systems such as the flagella.

Ah yes. Now I remember. You must be referring to the Dover Trial where Michael Behe showed conclusively in court that genetic variations and natural selection cannot directly account for the flagella. Or maybe it was Ken Miller who showed that? All this “irreducible complexity” stuff is so confusing, it’s hard to keep track sometimes. [/sarcasm]

Or perhaps you were thinking of something or someone else that has “shown” this. Perhaps you would be willing to share this evidence with others, so that we may all learn. I’m betting that you know of know such evidence.

Unlike others here, I won’t even ask for “scientific” evidence. “Legal” evidence is fine. Even “wiki” evidence is fine. Got any?

Thought not.

Prometheist said:

God is not needed to oppose Neo-Darwinism. Darwin did not know of the complexity contained within cells. This is why he postulated an idea that cannot explain the realities of biological systems. DNA is an example of specified complexity that Darwin cannot explain. Neither can it explain the irreducible complexity of such systems as the bacterial flagella.

It has been shown that genetic variations and natural selection cannot directly account for systems such as the flagella. Indirect means such as coevolution are extremely improbable and near the range of impossible.

So why are we celebrating Darwin Day? Darwin published a book about an idea that for over 150 years has unsuccessfully been able to explain the origin of life on earth. It seems like it is time to start exploring other explanations. Intelligence is the only known cause of specific complexity and irreducible complexity. Perhaps research in biology should be redirected towards understanding the origin of life in this manner.

Maybe we will celebrate Panspermia Day in the near future. It would be more fun…the costumes would be better anyway.

Please define “specified complexity” and show me how to compute how much of it something has – or even to tell whether something has it or not.

Do you think it’s fair to expect Darwin to explain the “specified complexity” of DNA, which wasn’t discovered until about a CENTURY after Darwin?

“It has been shown that genetic variations and natural selection cannot directly account for systems such as the flagella. Indirect means such as coevolution are extremely improbable and near the range of impossible.” Gee, why don’t biologists know these “facts”? You must be smarter than they are!

“Darwin published a book about an idea that for over 150 years has unsuccessfully been able to explain the origin of life on earth.” Umm… I’ve read it. He never tried to explain the origin of life in Origin. That’s like saying the Bible has “unsuccessfully been able to explain the origin of” the iPod in over 2,000 years. And your sentence is very odd. If it couldn’t explain something when it was written, how could it be expected to in the subsequent 150 years?

“Perhaps research in biology should be redirected towards understanding the origin of life [by an intelligent being].” Excellent idea. Please outline a research program that could establish the “intelligent design” of the origin of life. Just claiming it’s too complex or improbable to have arisen naturally is not a scientific result. The mathematics behind such claims are bogus, and have failed to impress biologists or biochemists. That’s just the argument from incredulity: It’s too hard for me to understand, so God must have done it.

Just Bob said:

Do you think it’s fair to expect Darwin to explain the “specified complexity” of DNA, which wasn’t discovered until about a CENTURY after Darwin?

Clarification for Creationists:

Just Bob meant that DNA “wasn’t discovered until about a CENTURY {later}”.

“specified complexity” has NEVER been discovered because it cannot be DEFINED.

I don’t want FL to quote-mine Just Bob and say that Pandas admit that “specified complexity” has been DISCOVERED.

Prometheist is Joe. The thesis is his, (it’s too complex to have evolved, and I know this because) and the tone and vocabulary is unmistakeable. His “it has been shown” means “I have written an error-strewn review paper that hasn’t been published about it”, or possibly just “I think”.

Scott yes, I was referring to what I read in Behe’s book, Darwin’s Black Box. He explained that biochemical systems are composed of numerous parts that all needed to evolve at once in order for the entire system to work. So for example, the flagella is composed of: a filament, hook, L ring, P ring, MS ring, C ring, rod, stator, etc.

For natural selection to explain this system, it would need to show that each part evolved in a step-wise fashion and that each step in the process provided the entire system with an advantage. Natural selection does not have the completed flagella in mind, but only variations that provide an advantage. I haven’t searched for it, but I wonder if research has been done to determine the evolutionary advantage that an L ring or a P ring, or whatever is postulated to have arrived first, bestow onto early bacteria.

Or the system can be explained to have evolved indirectly. In this way it is explained that the parts were already in place, but performing other functions, and then through another variation they converged to create the new system. This presupposes that all of the parts just so happened to be just right for each other when they converged although they were performing different functions.

So the argument, as I understand it, basically goes:

1. Natural selection only selects variations that give a system an advantage.

2. The bacterial flagella is composed of parts that only perform functions which are specific to the flagella (i.e. the individual parts would not provide an advantage for the system by themselves).

3. It is extremely close to impossible that all of the parts for the bacterial flagella evolved in one step.

Therefore, the bacterial flagella did not evolve directly.

That argument alone seems to explain the process in a logical manner. I did not actually look at an article in a journal that empirically proved it. I am serious when I ask: are there any articles that show how flagella evolved?

I have read that the type III secretory system is possibly something from which the flagella evolved. However, the fact that they share about ten proteins and are structurally similar does not seem to me to be convincing. I would like to see all of the functional and advantageous systems that fill the gap between the two before I am compelled.

Scott F said:

Prometheist said:

It has been shown that genetic variations and natural selection cannot directly account for systems such as the flagella.

Ah yes. Now I remember. You must be referring to the Dover Trial where Michael Behe showed conclusively in court that genetic variations and natural selection cannot directly account for the flagella. Or maybe it was Ken Miller who showed that? All this “irreducible complexity” stuff is so confusing, it’s hard to keep track sometimes. [/sarcasm]

Or perhaps you were thinking of something or someone else that has “shown” this. Perhaps you would be willing to share this evidence with others, so that we may all learn. I’m betting that you know of know such evidence.

Unlike others here, I won’t even ask for “scientific” evidence. “Legal” evidence is fine. Even “wiki” evidence is fine. Got any?

Thought not.

Prometheist said: I have read that the type III secretory system is possibly something from which the flagella evolved. However, the fact that they share about ten proteins and are structurally similar does not seem to me to be convincing.

Thank for demonstrating “Argument from incredulity.”

Prometheist said: DNA is an example of specified complexity that Darwin cannot explain.

Let’s assume that you’re right about this.

Let’s assume that it is a flaw, not being able to explain that.

Now, tell us how your alternative is not subject to the same flaw.

Better yet, give us an example of something, anything, which your alternative can explain.

For example, tell us, given your alternative, how (or why or when or where) it turns out that humans have the generic vertebrate eye, rather than eyes like insects, or like octopuses, or like potatoes. (Can’t “intelligent designer(s)” give us eyesight with potato eyes?) Or that humans are most similar (among all of today’s kinds of life) to chimps and other apes. Or, indeed, that DNA has “specified complexity”, rather than specified simplicity, generic complexity, or middling ordinariness.

Just Bob said: Do you think it’s fair to expect Darwin to explain the “specified complexity” of DNA, which wasn’t discovered until about a CENTURY after Darwin?

CLarifying nitpick… DNA was discovered in 1869 (per Wikipdia, originally called “nuclein”). The double-helix *structure* of DNA was confirmed in 1953. though DNAs role in inheritance was discovered earlier: 1928.

Prometheist said:

Scott yes, I was referring to what I read in Behe’s book, Darwin’s Black Box. He explained that biochemical systems are composed of numerous parts that all needed to evolve at once in order for the entire system to work. So for example, the flagella is composed of: a filament, hook, L ring, P ring, MS ring, C ring, rod, stator, etc.

For natural selection to explain this system, it would need to show that each part evolved in a step-wise fashion and that each step in the process provided the entire system with an advantage. Natural selection does not have the completed flagella in mind, but only variations that provide an advantage. I haven’t searched for it, but I wonder if research has been done to determine the evolutionary advantage that an L ring or a P ring, or whatever is postulated to have arrived first, bestow onto early bacteria.

Or the system can be explained to have evolved indirectly. In this way it is explained that the parts were already in place, but performing other functions, and then through another variation they converged to create the new system. This presupposes that all of the parts just so happened to be just right for each other when they converged although they were performing different functions.

So the argument, as I understand it, basically goes:

1. Natural selection only selects variations that give a system an advantage.

2. The bacterial flagella is composed of parts that only perform functions which are specific to the flagella (i.e. the individual parts would not provide an advantage for the system by themselves).

3. It is extremely close to impossible that all of the parts for the bacterial flagella evolved in one step.

Therefore, the bacterial flagella did not evolve directly.

That argument alone seems to explain the process in a logical manner. I did not actually look at an article in a journal that empirically proved it. I am serious when I ask: are there any articles that show how flagella evolved?

I have read that the type III secretory system is possibly something from which the flagella evolved. However, the fact that they share about ten proteins and are structurally similar does not seem to me to be convincing. I would like to see all of the functional and advantageous systems that fill the gap between the two before I am compelled.

Well, if you google “flagella evolution” the fourth hit is this paper by Nick Matzke:

http://www.talkdesign.org/faqs/flagellum.html

Why don’t you read the paper and let us know what you think? And don’t bother coming back and saying something like “I don’t believe it so it can’t be true.” I can already tell you that my response will be: “ I don’t believe that you really think that, so you don’t.”

And you might want to check out the “Update” section of the paper, describes lists several more recent publications that dramatically confirm some of the predictions Nick made based on his model.

We would love to hear your alternative explanation for the origin of flagella, and what predictions it makes that have been confirmed.

Yo, Promo, someone so knowledgeable about the motile appendages of bacteria – and who has read a WHOLE BOOK about them! – should know that the singular is flagellum.

Once again we see evidence of what I call the Paradox of Creationism: the creationist brain is such a malfunctioning organ that it should have been filtered out of the gene pool eons ago, yet it persists. This cannot be the result of natural processes.

It is self-evident that an unnatural agency must be responsible. Therefore, I have proposed the Theory of Abominable Befuddlement (AB), which holds that certain features of the creationist brain are best explained as the product of an Abominable Befuddler, and not by evolution. A befuddlement theorist studies the output of creationists for evidence of specified befuddlement, and is thus able to determine whether it is the rational product of an evolved brain, or an example of AB.

You know I always wondered why this supposed designer likes flagella so much. It’s not even best designed mode of motility around. Couldn’t the designer put impellers in the bacteria instead. How awesomely fast would bacteria be if they had a micro-motor that used principles similar to jet-ski’s and submarines. And for motility on dry-surfaces they could have wheels powered by a chemically powered rotary micro-engine. Flagella in comparison can’t produce high velocities and controlling the direction of the motion is a crap-shoot at best. Seems like the designer prefers sub-optimal design Prometheus. Could you give us your reasoning as to why the designer(s) seems to co-opt pieces previously used for other purposes to create novel but sub-optimal design, much like how evolution is envisioned to work? That is, why does the designer do this instead of designing optimal systems with precision parts designed for a specific purpose?

How awesomely fast would bacteria be if they had a micro-motor that used principles similar to jet-ski’s and submarines.

But then we’d need better immune systems to fight them off!

It seems like it is time to start exploring other explanations. Intelligence is the only known cause of specific complexity and irreducible complexity.

Great idea! Just come up with some positive evidence for design (attacks on evolution don’t count, as that would be a logical fallacy.)

Henry J said:

How awesomely fast would bacteria be if they had a micro-motor that used principles similar to jet-ski’s and submarines.

But then we’d need better immune systems to fight them off!

No problem, the designer can just come up with some killer T lymphocytes with chemically powered computer guided torpedoes. If we are talking design then there shouldn’t be any limitations to what the designer can do. Or perhaps I’m getting it wrong. What do you think about that Prometheus? Is the designer limited as to what designs it can implement?

Hi Just Bob,

I am seriously interested in discussing arguments for and against Darwinism and intelligent design. I am going to reply to you point for point, but know that I am not just trying to prove that I am right or claim than I am smarter than you or anyone else either here or in academia.

1. Specified complexity is a “statistical criterion for identifying the effects of intelligence.” In order to determine if something possesses specified complexity, there are a few things to consider: probabilistic complexity, descriptive complexity, and probabilistic resources.

First you determine the probabilistic complexity. This is how probable the event or sequence that you are observing is. So take a functional protein that is 50 amino acids in length for instance. Lets be conservative and say our amino acid alphabet will consist of only five amino acids (as opposed to the present alphabet of twenty amino acids) that are available to place in any of the 50 positions on the chain. I have read that there are a few thousand folds discrete folds that can produce all functional proteins. So the probability of any given sequence comes out to ~3,000 in 5 to the 50th power.

Then consider descriptive complexity or Kolmogorov complexity. This refers to how easy it is to describe any given pattern or sequence. When testing for specified complexity, the sequence must have a low descriptive complexity. An oft-quoted example is a series of coin tosses: HHHHHHHHH and HHTHTTTHTH. The first series has lower descriptive complexity because it can be described as “ten heads in a row.” The second series would be described as “two heads, then one tail, then one head, etc…” In the case of the protein the search is for a functional protein. So the description of any given sequence will be either “functional protein” or something longer such as “85% of a functional protein,” etc…

Next probabilistic resources are taken into consideration. Probabilistic resources are basically how many tries are allowed to reach a certain random event (probabilistic complexity is the probability of getting a jackpot on a slot machine and its probabilistic resource is how many times the lever is pulled). In the case of the protein, this refers to how many times a random sequence will be produced in the search for one certain sequence. If the probabilistic resources of a random search are very high, for instance 10 to the 50,000th power number of searches, then a certain sequence probability of ~3,000 in 5 to the 50th power turns out to not be so improbable. If only, say 10 searches are allowed, then ~3,000 in 5 to the 50th is almost impossible, but still probable nonetheless.

There are not certain amounts of specified complexity, something is either inferred to be specifically complex or not. So in the above case of a functional protein, 50 amino acids in length with an alphabet of five amino acids, functional proteins seem to be specifically complex because they meet the criteria. Given a random search, ~3,000 in 5 to the 50th power is a low probability and therefore an example of high probabilistic complexity. Next since it is easier to explain functional versus non-functional sequences, they meet the low descriptive complexity requirement. Lastly is the question of the probabilistic resources. I have read that the conditions on early earth were extremely hostile for the development of life. The atmosphere was not reducing; organic compounds had little chance of being preserved if formed; etc… If what I read is correct then it seems that the probabilistic resources for this search are small and this would lead to an overall conclusion that these functional proteins possess specific complexity.

2. It would not be fair to say that Darwin could not explain the origin of life. But this is not what I was doing. I was saying that his idea (having been researched and improved upon since) has not been able to solve the origin of life in the 150 years since it originated. This is why I suggested that possible alternatives should be explored.

3. I’m sure that biologists are aware of Michael Behe’s arguments, however I do not think that they all disagree with him as you suggest.

4. As stated above, I was not requiring the book to solve the problems I am discussing. So my sentence should have been interpreted to mean that his idea has not been able to solve the problem of the origin of life in over 150 years. So I am saying that Neo-Darwinism cannot explain it.

5. I like your reply on this one. So if everyone* somehow agreed that we cannot ignore the design in biological systems, what now? I feel like throwing up your arms and saying, “Well now that I admit design, scientific inquiry is over and we are all intellectually fulfilled creationists.” Remember that intelligent design does not answer any metaphysical questions such as “who or what created life on earth?” The explanation for that could be: aliens, biomolecules from space, Yahweh, Allah, Mormon Gods, Platonic heaven, etc. It just says that there is intelligence behind the design observed in nature and that natural processes are not the cause.

So to perform scientific research with intelligent design as the guiding principle, several things can be done. One I have heard is the idea that, due to the law of conservation of information, perhaps the first cell was a sort of “supercell” that contained all of the information needed for the diversity of life on earth. This first cell, however it arrived on earth, would have formed life leading to LUCA. Efforts could be made to research this supposed supercell.

Another idea is that if all life was designed, perhaps there are “user-manuals” encoded within DNA. Steganographical information within organisms, that which would not be useful to the organism but useful for designers, could provide profound incite into biological systems. Research into this idea would be very interesting and fruitful if successful.

Also, if intelligent design were used as a guiding principle, or at least alongside Darwinism, future research will avoid “junk DNA” scenarios. If scientists at least entertain the possibility of design, they will find things that they may have overlooked with a Darwinian mindset. It does not make sense to me that admitting design should mean that all scientific research and learning about biological systems should come to a halt. Of course we would still try to learn as much about our world as possible. Refuting Darwinism aside, using intelligent design as a supplementary science would be nice and is guaranteed to help in the long run.

*”Biology is study of complicated things that give the appearance of having been designed for a purpose.” –Richard Dawkins

“Biologists must constantly keep in mind that what they see was not designed, but rather evolved.” –Francis Crick

(I’m sure these have been seen before but I thought “why not”)

Just Bob said:

1. Please define “specified complexity” and show me how to compute how much of it something has – or even to tell whether something has it or not.

2. Do you think it’s fair to expect Darwin to explain the “specified complexity” of DNA, which wasn’t discovered until about a CENTURY after Darwin?

3. “It has been shown that genetic variations and natural selection cannot directly account for systems such as the flagella. Indirect means such as coevolution are extremely improbable and near the range of impossible.” Gee, why don’t biologists know these “facts”? You must be smarter than they are!

4. Umm… I’ve read it. He never tried to explain the origin of life in Origin. That’s like saying the Bible has “unsuccessfully been able to explain the origin of” the iPod in over 2,000 years. And your sentence is very odd. If it couldn’t explain something when it was written, how could it be expected to in the subsequent 150 years?

5. “Perhaps research in biology should be redirected towards understanding the origin of life [by an intelligent being].” Excellent idea. Please outline a research program that could establish the “intelligent design” of the origin of life. Just claiming it’s too complex or improbable to have arisen naturally is not a scientific result. The mathematics behind such claims are bogus, and have failed to impress biologists or biochemists. That’s just the argument from incredulity: It’s too hard for me to understand, so God must have done it.

As far as I can see, you’re just parroting ID propaganda.

Answer me this: is a snowflake designed? Is a tornado designed?

Please show how to calculate your purported measures for Paley’s watch.

Prometheist said:

First you determine the probabilistic complexity. This is how probable the event or sequence that you are observing is. So take a functional protein that is 50 amino acids in length for instance. Lets be conservative and say our amino acid alphabet will consist of only five amino acids (as opposed to the present alphabet of twenty amino acids) that are available to place in any of the 50 positions on the chain. I have read that there are a few thousand folds discrete folds that can produce all functional proteins. So the probability of any given sequence comes out to ~3,000 in 5 to the 50th power.

I have a high school level physics/chemistry calculation for you to do.

Scale up the charge-to-mass rations of protons and electrons to macroscopic masses on the order of kilograms. Then use that calculation to calculate the energies of interaction of kilogram-sized masses separated by distances on the order of meters. You should be able to estimate that electron volt energies for protons separated by distances on the order of nanometers scale up to energies on the order of 1010 megatons of TNT.

I have given you an answer that you can verify and use to estimate similar energies of interactions among molecules and scale them up to macroscopic sized objects.

So here is a question for you: How do you justify those probabilities you calculated in the light of the fact that the interactions among atoms and molecules are not trivial?

One I have heard is the idea that, due to the law of conservation of information, perhaps the first cell was a sort of “supercell” that contained all of the information needed for the diversity of life on earth. This

There is no such thing as “the law of conservation of information.” This is a made up idea by William Dembski; and he has never demonstrated that such a law exists. He simply asserted it. In fact, it has been easily shown to be false.

Prometheist said:

Hi Just Bob,

I am seriously interested in discussing arguments for and against Darwinism and intelligent design.

No, you’re not. You’re just here to assert that “since Darwinism is so deficient, we really should give unevidenced and useless ‘intelligent design’ a try !!”

I am going to reply to you point for point, but know that I am not just trying to prove that I am right or claim than I am smarter than you or anyone else either here or in academia.

You’ll just IMPLY that you are, then get upset when no one falls for your bluffing.

1. Specified complexity is a “statistical criterion for identifying the effects of intelligence.” In order to determine if something possesses specified complexity, there are a few things to consider: probabilistic complexity, descriptive complexity, and probabilistic resources.

First you determine the probabilistic complexity. This is how probable the event or sequence that you are observing is. So take a functional protein that is 50 amino acids in length for instance. Lets be conservative and say our amino acid alphabet will consist of only five amino acids (as opposed to the present alphabet of twenty amino acids) that are available to place in any of the 50 positions on the chain. I have read that there are a few thousand folds discrete folds that can produce all functional proteins. So the probability of any given sequence comes out to ~3,000 in 5 to the 50th power.

A nonsensical calculation of gibbering numerology if there was one.

By your ‘math’, you are essentially stating there are 3000 ways to get ONE SPECIFIC SEQUENCE.

If there are only, say, 2000 discrete folds that can produce all functional proteins, then the odds of a functional protein is then 1/2000.

You have fallen for the One True Sequence fallacy common amongst IDiots - the ridiculous notion that one (and ONLY one) sequence can work, and that it MUST be formed by having amino acids fall together all at once.

Real world experiments have shown that the odds of a peptide 70 random amino acids long having a selectable function is 1 in 10^9 to 1 in 10^12 - about 40 orders of magnitude MORE likely than your ‘math’ suggests !

Then consider descriptive complexity or Kolmogorov complexity. This refers to how easy it is to describe any given pattern or sequence. When testing for specified complexity, the sequence must have a low descriptive complexity. An oft-quoted example is a series of coin tosses: HHHHHHHHH and HHTHTTTHTH. The first series has lower descriptive complexity because it can be described as “ten heads in a row.” The second series would be described as “two heads, then one tail, then one head, etc…” In the case of the protein the search is for a functional protein. So the description of any given sequence will be either “functional protein” or something longer such as “85% of a functional protein,” etc…

Does anyone actually DO that calculation, or did you just hear about it, thought it was impressive, and so decided to throw it in to try to fool people into thinking you were worth listening to ?

Next probabilistic resources are taken into consideration. Probabilistic resources are basically how many tries are allowed to reach a certain random event (probabilistic complexity is the probability of getting a jackpot on a slot machine and its probabilistic resource is how many times the lever is pulled). In the case of the protein, this refers to how many times a random sequence will be produced in the search for one certain sequence. If the probabilistic resources of a random search are very high, for instance 10 to the 50,000th power number of searches, then a certain sequence probability of ~3,000 in 5 to the 50th power turns out to not be so improbable. If only, say 10 searches are allowed, then ~3,000 in 5 to the 50th is almost impossible, but still probable nonetheless.

There are not certain amounts of specified complexity, something is either inferred to be specifically complex or not. So in the above case of a functional protein, 50 amino acids in length with an alphabet of five amino acids, functional proteins seem to be specifically complex because they meet the criteria. Given a random search, ~3,000 in 5 to the 50th power is a low probability and therefore an example of high probabilistic complexity. Next since it is easier to explain functional versus non-functional sequences, they meet the low descriptive complexity requirement.

Your numerology is off by about 40 orders of magnitude, given the FACT that the odds of a peptide 70 random amino acids long having a selectable function is in 1 10^9 to 1 in 10^15.

Lastly is the question of the probabilistic resources. I have read that the conditions on early earth were extremely hostile for the development of life. The atmosphere was not reducing; organic compounds had little chance of being preserved if formed; etc… If what I read is correct then it seems that the probabilistic resources for this search are small and this would lead to an overall conclusion that these functional proteins possess specific complexity.

Actually, real world experiments show that organic compounds have good changes of being preserved if formed - all it takes to get ribose from ‘nearly impossible to get enough to work with’ to ‘mundane production’ via abiotic means is the presence of common minerals.

2. It would not be fair to say that Darwin could not explain the origin of life. But this is not what I was doing. I was saying that his idea (having been researched and improved upon since) has not been able to solve the origin of life in the 150 years since it originated. This is why I suggested that possible alternatives should be explored.

You are being underhanded here, since evolution was never INTENDED to explain the origin of life; what you are essentially claiming is that since evolution cannot explain something IT WAS NEVER INTENDED TO EXPLAIN, other, evidence-free, utterly useless IDiocies should be entertained as ‘explanations’.

3. I’m sure that biologists are aware of Michael Behe’s arguments, however I do not think that they all disagree with him as you suggest.

They are aware of his arguments - and how silly and ridiculous they are.

4. As stated above, I was not requiring the book to solve the problems I am discussing. So my sentence should have been interpreted to mean that his idea has not been able to solve the problem of the origin of life in over 150 years. So I am saying that Neo-Darwinism cannot explain it.

Who, exactly, says that a theory that explains the relatedness of life MUST explain the origin of that life ?

HOW life arose is a different question than ‘what happened to it as generations go by’.

Whether life arose via natural means, ‘POOFED !!1!!!!’ into existence by the words of a Magical Sky Pixie, or farted out the back end of a 4.625 dimensional mouse, ONCE life was here, it evolved.

And how, EXACTLY, is blubbering ‘IT WUZ DEEZINED !!!!1!!!’ actually explain anything at all ?

Valid and useful explanations define the unknown in terms of the known (and thus knowledge progresses); IDiots, creationuts and theoloons strive to explain the unknown in terms of the unknowable, then pretend they have answered the question.

“How did this arise ?”

“An unknowable being with unknowable motives somehow did something sometime in the past !!”

5. I like your reply on this one. So if everyone* somehow agreed that we cannot ignore the design in biological systems, what now? I feel like throwing up your arms and saying, “Well now that I admit design, scientific inquiry is over and we are all intellectually fulfilled creationists.” Remember that intelligent design does not answer any metaphysical questions such as “who or what created life on earth?” The explanation for that could be: aliens, biomolecules from space, Yahweh, Allah, Mormon Gods, Platonic heaven, etc. It just says that there is intelligence behind the design observed in nature and that natural processes are not the cause.

In other words, simply gives up and PRETENDS to have found an answer.

It SAYS there is intelligence behind every tree and under every rock, but is UNABLE to actually BACK UP THE ASSERTION, and instead relies purely on negative argumentation (ie, ‘since reality-based science cannot explain X, DESIGNERDIDIT !!!!!1!’), misrepresentations, numerology, misinformation theory, and personal incredulity.

So to perform scientific research with intelligent design as the guiding principle, several things can be done. One I have heard is the idea that, due to the law of conservation of information, perhaps the first cell was a sort of “supercell” that contained all of the information needed for the diversity of life on earth. This first cell, however it arrived on earth, would have formed life leading to LUCA. Efforts could be made to research this supposed supercell.

There is no such thing as a “Law of Conservation of Information”.

A ‘supercell’ with all information needed for all life on earth could not exist, given what we know of REAL WORLD BIOLOGY - you’d have to have sequences lying dormant for billions of years WITHOUT BEING MUTATED INTO USELESSNESS.

Examination of reality shows that novel genes can be produced by known, reality-based mechanisms, so there is no point in giving much thought to your imbecilic notion of ‘da first cell had all the information that would ever exist in the biosphere !!1!!!’.

Another idea is that if all life was designed, perhaps there are “user-manuals” encoded within DNA. Steganographical information within organisms, that which would not be useful to the organism but useful for designers, could provide profound incite into biological systems. Research into this idea would be very interesting and fruitful if successful.

Examination of the genomes of actual organisms reveals NO SUCH THING.

DNA not useful to an organism TENDS TO BECOME MUTATED, since there is no selective pressure to maintain it. Any such ‘users-manual’ would be scrambled into gibberish even LESS coherent than ID rationalizations rather quickly.

Also, if intelligent design were used as a guiding principle, or at least alongside Darwinism, future research will avoid “junk DNA” scenarios.

RiiIIiiiIIight ! Everyone will just jump to the conclusion that a block of DNA that can be REMOVED with no ill effects is SOMEHOW doing something !!

Evolution PERMITS the existence of ‘junk DNA’, but does not require all non-coding DNA to be functionless; whereas IDiocy requires every single base to have a function of some sort (because they ‘know’ their unstated, unknowable designer would not install functionless sequences).

What, exactly, do you ‘think’ the “junk DNA” scenarios were ? Reality not conforming to what the IDiots claim evolution ‘requires’ ?

If scientists at least entertain the possibility of design, they will find things that they may have overlooked with a Darwinian mindset. It does not make sense to me that admitting design should mean that all scientific research and learning about biological systems should come to a halt. Of course we would still try to learn as much about our world as possible. Refuting Darwinism aside, using intelligent design as a supplementary science would be nice and is guaranteed to help in the long run.

RiiIiiiIIight ! No one has even DEMONSTRATED that ID is of any use whatsoever, and you ‘guarantee it can help in the long run’ ?!

Scientists will entertain the possibility of design - AS SOON AS SOMEONE CAN DEMONSTRATE IT EXISTS. Or can even define what to look for that isn’t gibbering arguments from personal incredulity, misinformation theory, etc.

Or a way to TEST ideas about design - how, EXACTLY, would one determine that something was designed by an unknowable being with unknowable motives and unknown abilities ?

Mike Elzinga said:

There is no such thing as “the law of conservation of information.” This is a made up idea by William Dembski; and he has never demonstrated that such a law exists. He simply asserted it. In fact, it has been easily shown to be false.

Dembski did have a Law of Conservation of Complex Specified Information (LCCSI). This was needed to show that CSI could not be put into genomes by natural selection, (Otherwise Dembski’s Design Inference would merely be a Design-or-Natural-Selection Inference). Prometheist’s exposition of Demsbki’s argument left that part out. And in fact, the LCCSI is both (a) unproven, and (b) stated in a way that makes it unable to do the job of showing that CSI cannot get into living organisms by natural selection. For details see my paper on this.

So what Prometheist should be asked is, even if CSI were to be a sensible and useful concept, do you have some argument showing that it cannot come to be in a genome by natural selection?

Then consider descriptive complexity or Kolmogorov complexity. This refers to how easy it is to describe any given pattern or sequence. When testing for specified complexity, the sequence must have a low descriptive complexity. An oft-quoted example is a series of coin tosses: HHHHHHHHH and HHTHTTTHTH. The first series has lower descriptive complexity because it can be described as “ten heads in a row.” The second series would be described as “two heads, then one tail, then one head, etc…” In the case of the protein the search is for a functional protein. So the description of any given sequence will be either “functional protein” or something longer such as “85% of a functional protein,” etc…

This is such a mishmash of misapprehension, befuddlement, and outright wrongness that despite my relative naivete wrt Kolmogorov complexity, I feel compelled to comment.

First, Kolmogorov complexity has no connection whatsoever to coin tosses. That’s an utterly irrelevant red herring, present, presumably, for its undeniable contribution to the overall confusion of the reader. Similarly, Kolmogorov complexity has no connection with search, in the computing sense.

Kolmogorov complexity applies to a sequence of characters in an alphabet, or a string, for short. For example, this sequence of nine characters is a string: HHHHHHHHH

The mechanism of string description is NOT a natural language such as English. Such a description of string s must be a formal computer program (in an executable computer programming language) which produces string s.

I’ll use pidgin C here for my examples, so a program which produces the string HHHHHHHHH is

printf(“HHHHHHHHH”);

Note that in pidgin C, the string HHHHHHHHH contains nine characters from the ASCII alphabet.

For this program, a measure of the Kolmogorov complexity of s is nineteen, or the number of characters necessary to write the C program. If a program d (for description) which prints s (we say (d(s)) is of minimal length (i.e. it requires the fewest characters of all programs which print s), it is called a minimal description of s. Thus, the length of d(s) (i.e. the number of characters in the description) is the Kolmogorov complexity of s.

Note that there are other, different C programs which produce string s. For example, the program

for(i=0; i<9; i++) printf(‘H’);

also produces string s. And it has a character count different from the first example.

I have no idea at all what Prometheist means when he says “description of any given sequence will be either “functional protein” or something longer such as “85% of a functional protein”. As far as I can tell, neither does he.

But won’t Prometheist just write his own computer program which, given some string s, just computes its minimum Kolmogorov complexity?

Nope. He won’t. That’s impossible.

phhht said:

printf(“HHHHHHHHH”);

For this program, … nineteen [is] the number of characters necessary to write the C program…

That should be twenty (right?). Sorry.

Prometheist -

I’m willing to listen.

I don’t agree with your arguments against evolution, so far, but maybe at least you can provide some positive evidence for ID.

1) Could any evidence convince you of the theory of evolution, and if so, what type of evidence is now lacking, that would convince you, if present?

2) The Supreme Court ruled against the direct teaching of Biblical Young Earth Creationism as science in public schools; however, if that ruling were overturned, which would you support more, teaching of ID, or direct teaching of Bible-based YEC?

3) Do you think it is important for opponents of the theory of evolution to fully understand the theory of evolution? If so, can you explain it, and if not, can you explain why not?

4) Who is the designer? How can we test your answer?

5) What did that designer do? How can we test your answer?

6) How did the designer do it? How can we test your answer?

7) When did the designer do it? How can we test your answer?

8) What is an example of something that was not designed by the designer?

JimNorth said:

Also, why did you switch from specified complexity to a word salad of probabilistic pseudoscience?

Since when was it possible to explain or defend Intelligent Design Theory through science, logic or coherent thought?

Prometheist said:

Prometheist said:

It has been shown that genetic variations and natural selection cannot directly account for systems such as the flagella.

Scott F said: Ah yes. Now I remember. You must be referring to the Dover Trial where Michael Behe showed conclusively in court that genetic variations and natural selection cannot directly account for the flagella. Or maybe it was Ken Miller who showed that? All this “irreducible complexity” stuff is so confusing, it’s hard to keep track sometimes. [/sarcasm]

Scott yes, I was referring to what I read in Behe’s book, Darwin’s Black Box. He explained that biochemical systems are composed of numerous parts that all needed to evolve at once in order for the entire system to work. So for example, the flagella is composed of: a filament, hook, L ring, P ring, MS ring, C ring, rod, stator, etc.

For natural selection to explain this system, it would need to show that each part evolved in a step-wise fashion and that each step in the process provided the entire system with an advantage. Natural selection does not have the completed flagella in mind, but only variations that provide an advantage. I haven’t searched for it, but I wonder if research has been done to determine the evolutionary advantage that an L ring or a P ring, or whatever is postulated to have arrived first, bestow onto early bacteria.

Or the system can be explained to have evolved indirectly. In this way it is explained that the parts were already in place, but performing other functions, and then through another variation they converged to create the new system. This presupposes that all of the parts just so happened to be just right for each other when they converged although they were performing different functions.

So the argument, as I understand it, basically goes:

1. Natural selection only selects variations that give a system an advantage.

2. The bacterial flagella is composed of parts that only perform functions which are specific to the flagella (i.e. the individual parts would not provide an advantage for the system by themselves).

3. It is extremely close to impossible that all of the parts for the bacterial flagella evolved in one step.

Therefore, the bacterial flagella did not evolve directly.

That argument alone seems to explain the process in a logical manner. I did not actually look at an article in a journal that empirically proved it. I am serious when I ask: are there any articles that show how flagella evolved?

I have read that the type III secretory system is possibly something from which the flagella evolved. However, the fact that they share about ten proteins and are structurally similar does not seem to me to be convincing. I would like to see all of the functional and advantageous systems that fill the gap between the two before I am compelled.

Prometheist, thank you for your responses. I have a few return comments.

You do realize, I hope, that through 6 weeks of trial, Behe was unable to convince anyone, especially the judge, of his ideas. (See the reference trial transcripts.) In that context, the most open and unbiased context possible, when offered the best opportunity of his life to make his case, he was completely and utterly unable to “show” “that genetic variations and natural selection cannot directly account for systems such as the flagella [sp]”. In fact, he made himself a laughing stock.

To your numbered points.

1. You said, “Natural selection only selects variations that give a system an advantage.” [emphasis added] I am not a biologist, but AFAIK “Natural Selection” can “select” any expressed variation, be it a) advantageous, or b) deleterious. When a deleterious trait is “selected”, it tends to be selected against and such selection is, shall we say, self limiting. It’s being “selected” for removal from the gene pool. It’s a picky point (and my understanding could be wrong), so I won’t hold it against you.

2. Again, I’m not a biologist, but my understanding is that your statement is not correct. There are parts of the flagellum (different protein sub-units) that perform other functions for the cell, quite apart from the flagellum. Further, there is not one, but many different kinds of flagella, belonging to different kinds of creatures. (Even humans have a flagella.) Each different kind has a different number of similar parts. If a flagellum was truly “irreducibly complex”, then other flagella with fewer parts should not function. Yet they obviously do.

3. No one, except creationists, ever claimed that the flagellum “evolved in one step”. You “claim” it needs to be “one step” because of your disproved “claim” of “irreducible complexity”. But that is not the case. That’s not how evolution works. Evolution works by gradual, though sometimes step-wise changes to existing systems. Since we know that the component proteins of the flagellum are used by the cell for other functions, since we know that different kinds of flagella have different numbers of parts, and because we can identify a potential sequence of plausible changes from one kind to another, we conclude that it is possible for a flagellum to have “evolved” from earlier cellular structures.

Does that prove that the flagellum evolved? No. It shows that the flagellum could have evolved; that there is a possible path from a simpler system to a more complex one. What the possible sequence does “prove” however, is that the system is not irreducibly complex. If it were irreducibly complex, then it would be impossible to identify any possible sequence of mutations that could have led to the flagellum. It is not necessary to identify the exact sequence that actually was used. Any possible sequence of changes is sufficient to disprove “irreducible complexity”.

Is that sufficient to, in turn, disprove “design”? No, but it knocks one of the crucial legs out from under your argument.

Others have mentioned the Natural Bridges. These are obviously “irreducibly complex”. Take away any part, and the whole will collapse. Yet, they are completely “natural”. No “intelligent designer” was needed. And no, each bridge did not just poof into existence “all at once”. But using your argument for #3, one must conclude that every Natural Bridge must have been the work of an Intelligent Designer. Such an argument is obviously silly.

You also have to realize that the mutations required for evolution don’t have to happen sequentially. Life is not a single-core computer program. Life happens in a vastly parallel system. I did some back-of-the-envelope calculations one time. Even assuming the enormously unlikely probabilities that Behe attributes to the appearance of “beneficial” mutations in bacteria, there are so many, many bacteria in the entire biosphere of the Earth (about 5x10^30), and they reproduce so rapidly, that a “beneficial” mutation occurs (on average) about once every 20 minutes, even using Behe’s numbers. Every 20 minutes for several billion years. That’s about 8x10^13 advantageous mutations. And once those mutations happen, they spread quickly to the other bacteria. That’s more than enough to account for your “irreducibly complex” system.

So, no, your scary big probability numbers tend to look not so big compared to the vastness of life on Earth.

For natural selection to explain this system, it would need to show that each part evolved in a step-wise fashion and that each step in the process provided the entire system with an advantage.

That statement is incorrect. It is not necessary to show that each mutation along the sequence of changes is advantageous. Neutral mutations are sufficient. By definition, neutral mutations that neither improve nor detract from function may survive to breed. In fact, if the environment were to change in some way, it is entirely possible that even deleterious mutations could survive through enough generations to provide a “bridge” from one advantageous function to another.

I would like to see all of the functional and advantageous systems that fill the gap between the two before I am compelled.

First, you are lying. You would not be so compelled. If the entire sequence was laid bare for you, you would still conclude “Design”, because you have a structural, pre-conceived belief system that compels you to see “Design” in everything.

Second, evolution doesn’t work that way. Science doesn’t work that way. Science can demonstrate a possible evolutionary pathway, which it plausibly has. You so far refuse to see any of that. If you were presented with a complete sequence of changes, you would ask to see proof that this was thee sequence that was actually used.

Finally, please use your 3 point system, and your “irreducible complexity” to explain Ring Species.

harold Wrote:

Not really.

A certain Anglo-Persian individual, whose infamous and universally banned username I won’t mention, once stated that the designer was “the Elohim”.

Someone else, while evading all the other questions, claimed that “a rock” isn’t designed.

To be fair, Prometheist has stated that snowflakes and tornadoes aren’t designed. So he’s answered one indirectly.

That’s been it.

I have an even better example. FL once admitted that human conception is a design implementation event. That alone destroys any DI games to pretend that such events are “remote” and “don’t ask, don’t tell where, when or how.”

Note that these examples are all about the designer’s identity or “what’s designed, what’s not.” The most important part of your answer is “while evading all the other questions.” That shows that these people, whether in on the scam or hoplelessly paranoid, are hell-bent on keeping the “debate” away from the crucial “what happened when” issues. Which is especially egregious given their demand for such details from us - ansd moving the goalposts with each answer! I call that a “double standard,” but if anything that’s too kind a word for that scam.

What does all that mean? You say:

However, of course, it has a further weakness. It’s obvious that ID isn’t the product of sincere, spontaneous thought, and is rather, an effort to present creation science in a disguised, coded form.

I say that that’s only half of the answer. The other half is that they know that the “what happened when” of creation “science,” the testable claims that don’t require “Creator” or “designer” language and would be fully legal to teach in publicly funded science class, have zero evidence to back them up, and fatal contradictions (among several YE and OE variants) to boot! And that they are hell-bent on censoring that from students. Whenever we omit or downplay that crucial part of the story we are giving the scam artists just what they want.

prongs said:

Just Bob said:

Do you think it’s fair to expect Darwin to explain the “specified complexity” of DNA, which wasn’t discovered until about a CENTURY after Darwin?

Clarification for Creationists:

Just Bob meant that DNA “wasn’t discovered until about a CENTURY {later}”.

“specified complexity” has NEVER been discovered because it cannot be DEFINED.

I don’t want FL to quote-mine Just Bob and say that Pandas admit that “specified complexity” has been DISCOVERED.

Actually DNA was discovered in 1869. Its structure wasn’t understood until 100 years after Origins..

Mike Elzinga said:

Joe Felsenstein said:

Dembski did have a Law of Conservation of Complex Specified Information (LCCSI).

Yeah; I don’t know where the “law of conservation of information” comes from other than the fact that some of the people over at UD use it as do some of the ID/creationists who show up here. I may also be remembering something from over at The Skeptical Zone.

What I remember is something that was a computation that was comparable to the computation for entropy; which, of course, is not conserved.

These ID/creationists can’t even keep their pseudoscience consistent. It’s all just free-for-all blather that is apparently meant to look erudite.

And it is really funny to watch the huffery-puffery proliferation of “laws” and “principles” and acronyms by the denizens of UD. I don’t even try to keep track any longer.

I thought information was continually being destroyed since the fall.

Dembski is a heretic.

Scott F. -

Excellent points but you gave ID a tiny bit too much credit (it’s almost impossible not to).

1. You said, “Natural selection only selects variations that give a system an advantage.” [emphasis added] I am not a biologist, but AFAIK “Natural Selection” can “select” any expressed variation, be it a) advantageous, or b) deleterious. When a deleterious trait is “selected”, it tends to be selected against and such selection is, shall we say, self limiting. It’s being “selected” for removal from the gene pool. It’s a picky point (and my understanding could be wrong), so I won’t hold it against you.

Neutral or even moderately deleterious alleles can increase in frequency in a population due to genetic drift, or due to linkage to a favorable allele which is being selected for.

In diploid or polyploid organisms, a recessive allele will behave essentially as if it were neutral, even if homozygosity is deleterious. Some alleles may be beneficial when heterozygous and deleterious when homozygous, e.g. sickle hemoglobin.

Naturally, some alleles may be deleterious in one environment and beneficial in another, or vice versa, and environments change.

An allele won’t increase in frequency if it is so deleterious that it prevents successful reproduction in all carriers (even in heterozygotes), but there are plenty of ways for alleles that don’t directly “give a system an advantage” to increase in frequency.

The person you are discoursing with could not pass the biology portion of a GED exam.

If it were irreducibly complex, then it would be impossible to identify any possible sequence of mutations that could have led to the flagellum. It is not necessary to identify the exact sequence that actually was used. Any possible sequence of changes is sufficient to disprove “irreducible complexity”.

You’re giving Behe too much credit. His definition of “irreducibly complex” is merely, in my fair paraphrase, that if you remove one part the system won’t work any more.

His famous example was a spring-loaded bar mouse trap, which has been shown not to be irreducibly complex.

However, it’s also true that things that are irreducibly complex can easily evolve through intermediate states; all that needs to happen is for one step to become redundant and later be removed. This is intuitively obvious.

bigdakine Wrote:

I thought information was continually being destroyed since the fall.

Dembski is a heretic.

Sure, but he knows that his target audience is very forgiving. The Biblical literalist subset is astonishingly good at “tuning out” anything inconvenient as long as it comes from those who feed them the anti-evolution sound bites that they crave. The nonliteralist subset (panspermists, other “new agey” types) plays along because they know that it’s good politics to keep literalists in the big tent.

robert van bakel said:

And still Darwin does it better. Who, upon reading that clear, concise, economic description of the variety in life, would dare put up a weak, castrated god, in opposition?

“dependent on each other in so complex a manner,…” The origins of modern Environmental Science?

creationists.

bigdakine said:

I thought information was continually being destroyed since the fall.

Dembski is a heretic.

Yup; Henry Morris formalized it when he started the Institute for Creation “Research;” and it has been a regular part of ID/creationist arguments ever since; from Thomas Kindell’s snarky video, to John Sanford’s “genetic entropy,” to Granville Sewell’s eleven year crusade to prove the physics community wrong by not checking units when he plugs things into his equations.

Lifetimes in the Christian bible are purported to be getting shorter.

The argument is basically that, if evolution is true, entropy is decreasing (“information” is increasing), and everything is getting better and better. But the second law of thermodynamics says that entropy is increasing (“information” decreasing) and the universe is coming all apart.

Of course, these are creationist evolution, creationist thermodynamics, and creationist “information” that they are passing off as science. It’s a manufactured contradiction.

Why even Dembski can prove evolution wrong by not initialize variables in his computer programs.

So it is very easy for ID/creationists to “prove” evolution wrong. They just have to make sure that their followers are not only ignorant of science, they must also be sure they have firmly ingrained misconceptions that they believe are real science.

So far we have not been able to get any of the ID/creationist trolls who show up here to demonstrate that they understand even middle school and high school science. The ID/creationist leaders know their audience pretty well.

Scott F said:

So, no, your scary big probability numbers tend to look not so big compared to the vastness of life on Earth.

For natural selection to explain this system, it would need to show that each part evolved in a step-wise fashion and that each step in the process provided the entire system with an advantage.

That statement is incorrect. It is not necessary to show that each mutation along the sequence of changes is advantageous. Neutral mutations are sufficient. By definition, neutral mutations that neither improve nor detract from function may survive to breed. In fact, if the environment were to change in some way, it is entirely possible that even deleterious mutations could survive through enough generations to provide a “bridge” from one advantageous function to another.

I would like to see all of the functional and advantageous systems that fill the gap between the two before I am compelled.

First, you are lying. You would not be so compelled. If the entire sequence was laid bare for you, you would still conclude “Design”, because you have a structural, pre-conceived belief system that compels you to see “Design” in everything.

Second, evolution doesn’t work that way. Science doesn’t work that way. Science can demonstrate a possible evolutionary pathway, which it plausibly has. You so far refuse to see any of that. If you were presented with a complete sequence of changes, you would ask to see proof that this was thee sequence that was actually used.

What about Lenski’s Escherichia coli experiment, and how he went back to document the step-by-step of mutations that lead to his bacteria developing genes for enzymatically digesting citrate by looking at the various samples of 50,000+ bacteria generations?

Hello Harold,

I would like to understand.

When answering me, citations would be appreciated, but please also give the answers in your own words. Note: I am familiar with the works of Behe, Dembski, etc, what I am asking for here is YOUR explanation. Among other things, I would like to confirm that you understand even the works of ID that you borrow words from.

I assure you I have not been copying and pasting words from intelligent design literature. I did in fact explain the concepts of specified complexity, irreducible complexity, and the intelligent design explanatory filter in my own words. If you understand the works of Behe, Dembski, etc. (I’m not charging that you don’t), then it would be clear that I did this in my last few posts.

A) You haven’t explained how to determine these things. I have a particular problem with the use of the term “complex” here. Your use implies a binary condition.

In my post you quoted, I was describing the explanatory filter. I described the filter because in my earlier post I only described specified complexity, which only involves the last two steps in the filter. phhht rightly emphasized that what I had described, did not take into account the “Is it contingent?” portion of the filter. So in order to be clearer, I should have explained how the filter aligns with what I have already discussed.

You are saying that my answer to the filter’s question of “Is it complex?” is either yes or no. As I said before, specified complexity takes into account: probabilistic complexity, descriptive complexity, and probabilistic resources. The “Is it complex?” question of the explanatory filter is the node at which you determine probabilistic complexity. I explained my understanding of probabilistic complexity in an earlier post.

So your question actually involves the “Is it specific?” step of the filter. This is the node at which you consider descriptive complexity. I said in the earlier post describing my understanding of descriptive complexity that a low descriptive complexity is needed if design is going to be inferred.

So there is no boundary between complex or not complex as your understanding of my explanation of the filter demands. If the probabilistic complexity is found to be high, in relation to the probabilistic resources, at the “Is it complex?” step, the answer to this question in the filter is “yes.” Afterwards, if the descriptive complexity is found to be low, then the answer to “Is it specified?” is “yes.”

Since you are familiar with Dembski’s work, you should know that when he describes these components of specified complexity, he does not give the answer to the question you are asking me. He does not give an objective boundary at which it can be determined that probabilistic complexity or descriptive (Kolmogorov) complexity pass from being low to high. I will not pretend that these methods do not seem to be subjective. However, there is plenty of literature on this subject at www.mdl-research.org. I find this paper on the Mininum Description Length Principle interesting.

B) You also haven’t explained why on earth these things should be taken as proof of “design”, but first things first - please show me precisely how to at least replicate your claims that certain things have these traits.

Yes I have not explained why this shows proof of design. The explanatory filter leads to a “design inference,” not proof of design, if the answer to all of its questions is “yes.” Design is inferred because specified complexity has only been observed to be the product of intelligence.

I attempted to show how this process works in my reply to Just Bob. Due to PA Poland’s reply to my example using functional protein amino acid sequences, I did an extremely poor job from a Panda’s perspective. I will admit to being an armchair philosopher of science and not a biologist or statician. To this end, I would need someone more versed in biology to plug in the correct numbers into my explanation and then we could re-evaluate the answers to the “yes” or “no” questions the explanatory filter poses.

PA Poland said: By your ‘math’, you are essentially stating there are 3000 ways to get ONE SPECIFIC SEQUENCE.

If there are only, say, 2000 discrete folds that can produce all functional proteins, then the odds of a functional protein is then 1/2000.

You have fallen for the One True Sequence fallacy common amongst IDiots - the ridiculous notion that one (and ONLY one) sequence can work, and that it MUST be formed by having amino acids fall together all at once.

Real world experiments have shown that the odds of a peptide 70 random amino acids long having a selectable function is 1 in 10^9 to 1 in 10^12 - about 40 orders of magnitude MORE likely than your ‘math’ suggests !

I know there are only twenty amino acids that code for proteins, but research suggests that as low as four or five were needed to form functional proteins. I took my numbers from here. I used the numbers between their highest and lowest. Are these outdated?

So to my understanding, the probability of any given sequence of a protein as described by my source will be 1 in 5 to the 50th power. However, the paper suggested that about three thousand of those sequences were functional. So this means to me that the random probability for any given functional sequence would be 3000 in 5 to the 50th power.

I am saying that there are 3,000 “true” or functional sequences out of the 5 to the 50th power sequences that are possible. I do not see how the probability of a functional protein sequence would be one in 3,000 given a five amino acid alphabet and 50 positions on the sequence chain.

Knowing that the source I used is from 2008 and could very well be outdated, perhaps PA Poland’s new number of 1 in 10 to the 9-15th power is correct. However, probabilistic resources still need to be taken into account. If the number of chances to randomly combine the amino acids are low, then this new number would seem high.

Why does this mean that they “lack contingency”?

The explanatory filter asks, “Is it contingent?” Contingent meaning that something is not a necessary consequence of the laws of nature. The freezing of droplets in clouds can easily be explained using the laws of nature. If it is cold and there is a cloud in the sky, snowflakes will form. This formation of snowflakes can be observed anywhere in the world on any given day if it is cold enough. This is why snowflakes and tornadoes, to my understanding, should not make it through the first node of the explanatory filter.

Although I agree that colloquially, snowflakes can be perceived as “complex”, please explain how you define and measure complexity.

Also, what do you mean by “specified”? How do I measure whether or not something is “specified”?

I would not like to spend too much time providing clarification on this point because, as I said, snowflakes do not make it through the first node. When I said “complex” I was referring to probabilistic complexity along with probabilistic resources and when I said “specified” I was referring to descriptive complexity.

I do not understand. Watches are constructed by animals, namely, human beings. The construction of watches does require the firing of neurons in human brains. The construction of watches does not require any miracles. The fact that humans can construct watches now does not tell us anything about whether or not miracles are required for the origin of cellular life, let alone the subsequent evolution of life. I would have thought that anyone, regardless of religious sect, would agree with these obvious points.

I should have worded this explanation differently and emphasized the necessary aspect. I can see why you might have thought I was invoking miracles or supernatural causes. Something is contingent if it is not a necessary consequence of natural laws. Science can explain it, but it is not necessary. Again to clarify, intelligent design and reaching a design inference do not require a miracle. If aliens arrived from another planet and seeded the earth with life, the entire scenario could be explained with the laws of nature. However, the presence of life on earth would not be necessary according to the laws of nature, but simply the consequence of a decision made by aliens.

This is merely an assertion that a watch subjectively seems “complex” to you. I don’t disagree that a watch can subjectively seem “complex”. On the other hand, it might subjectively seem “simple” to someone else.

Do you have an objective, reproducible method that others can use to determine if something meets your definition of “complex”? If not, your use of the term is irrelevant.

This was another example of a misunderstanding after I failed to explain my terms in my response. So again in this case I was referring to probabilistic complexity and probabilistic resources. This would probably be a case in which the watch gets extradited through the filter. When looking at proteins, we used the number of amino acids needed to make a functional sequence. In this case, we would use the minimum amount of mechanical parts that are needed to make a functional watch. However, the parts that comprise this watch are not found anywhere in nature.

So perhaps you would need to look even closer and run the different parts of the watch through the filter. Then you would need to find the number of molecules that comprise the part and determine the minimal amount of molecules needed to form a functioning watch part. The possibility of nature necessarily forming a watch part will be very high and produce a “yes” answer to the question “Is it complex?” This makes me think of the fact that a statue is contained within a block of marble, but that it takes intelligence to chip away the unnecessary pieces.

Again, I see no rigorous definition of your key terms. You say it is “specific” and offer some word salad. Do you have a methodology that I can use to determine whether or not something is “specified”, by your own standards, yes or no?

As I feel like I have clarified the terms I was using, I don’t feel like this needs an explanation. I explained how descriptive complexity, whether high or low, is used to infer design or not to infer design. The watch as a whole would not be considered at this node until watch parts were found to be necessary due to the laws of nature.

While that is a very specific contradiction of the beliefs of many Christians, it is totally irrelevant to biomedical science.

Yes to say that the universe, and everything in it, is not designed would be a contradiction of the Christian worldview. However, Christianity is not taken into consideration when determining if something warrants a design inference. This is why the explanatory filter was created.

1) Could any evidence convince you of the theory of evolution, and if so, what type of evidence is now lacking, that would convince you, if present?

2) The Supreme Court ruled against the direct teaching of Biblical Young Earth Creationism as science in public schools; however, if that ruling were overturned, which would you support more, teaching of ID, or direct teaching of Bible-based YEC?

3) Do you think it is important for opponents of the theory of evolution to fully understand the theory of evolution? If so, can you explain it, and if not, can you explain why not?

4) Who is the designer? How can we test your answer?

5) What did that designer do? How can we test your answer?

6) How did the designer do it? How can we test your answer?

7) When did the designer do it? How can we test your answer?

8) What is an example of something that was not designed by the designer?

1. Yes. Michael Behe’s argument from irreducible complexity and also the existence of information in DNA are two of the main reasons why I am skeptical. I think these show that events such as the random formation of functional proteins on early earth and indirect Darwinian pathways producing something such as a bacterial flagellum are contingent. So in this regard I need to be convinced that scientists have determined the exact pathways and have proof that they are explained naturally.

Lining up a few skeletons that look similar in structure, but are divided by vast step-wise gaps, would not be good enough to destroy my skepticism of universal ancestry. Accordingly, emphasizing that a bacterial flagellum shares a handful of proteins with a type III secretory system would be compelling, but I am being honest when I say that I would still doubt.

DC showed me a link to Nicholas Matzke’s 2003 paper on the flagellum. I was discouraged with language like: “Obviously “detailed” cannot mean that every mutation and substitution event be recorded – for events that occurred billions of years ago this is impossible. A detailed evolutionary model should reduce a puzzling event like the origin of the flagellum into a series of events that occur by well-understood processes.” Am I asking too much of Evolutionary Biology? I was further discouraged when I read a 2011 article by Jonathan M. from the Design Institute. Among other things he said, “Why exactly is flagellum biosynthesis so tightly regulated and orchestrated? Not only do the energy demands render the flagellum an extremely expensive system to run, but untimely expression of flagellum proteins may induce a strong immune response in the host system, something no bacterium wants to do.”

But it wouldn’t stop at the flagellum. I’m hoping for the same explanation for all supposedly irreducibly complex systems such as blood clotting and eyes.

Also, the information content in DNA is huge. I know that Darwinistic materialism can explain all of the letters on a page in a book. But I do not believe it can claim that the configuration and meaning of the letters are not contingent. So I would need a Darwinistic explanation for the presence of information in biological systems. Or an extremely compelling argument that says there is no information in biological systems.

The above mentioned included, I would need to see the positive claims of intelligent design refuted, as well as its negative claims against evolution refuted.

2. My skepticism does not call for abolishing the teaching of evolution in schools. I’ll be happy with the teach the controversy stance until I am 100% convinced one way or the other. I would be against including YEC in any science curriculum because it makes metaphysical claims that I do not believe are to be decided by science. If parents want YEC for their children there is home schooling or private schools.

3. Yes! Honestly if intelligent design theorists were all uneducated I would not have listened to their arguments in the first place. However, I can only assume that the number of design theorists holding PhDs in biology fully understand evolution. For instance, if I assumed Michael Behe did not understand evolution because I don’t like his conclusions, I would need to start doubting the comprehension of all biology professors that hold to conclusions I do not like.

I know that design proponents and Darwinists hold to varying worldviews so I am not interested in whether someone is a Christian, atheist, Buddhist, etc. I am only interested in their arguments.

4. If Darwinism is false, then the origin of life is contingent and due to intelligence. As you might have guessed from my name I am a theist, but that does not mean that I think God is the direct cause of the origin of life. Panspermia would still need to be proven false. As it stands, I think the signs of intelligence in biological systems is the best explanation.

5-7. As you know intelligent design has not gained widespread acceptance and is still in its infancy. Since you are familiar with Dembski’s writings you should know that he says at this stage, intelligent design is mainly concerned with emphasizing the existence of the effects of intelligence. If intelligent design theorists don’t know then I don’t see how I can be required to answer these questions due to my armchair status. Darwinism hasn’t answered the when and how questions for the origin of life. Correct?

8. Snowflakes

harold said:

Prometheist said -

Great examples! Remember that intelligent design does not claim that everything in nature is designed.

I would like to understand.

When answering me, citations would be appreciated, but please also give the answers in your own words. Note: I am familiar with the works of Behe, Dembski, etc, what I am asking for here is YOUR explanation. Among other things, I would like to confirm that you understand even the works of ID that you borrow words from.

Please be very precise and specific and don’t waste both of our time with dissembling.

It is the study of signs of intelligence. Specified complexity is only a part of the process when inferring design. An explanatory filter is used for this purpose. It asks three questions about what is being observed: Is it contingent? Is it complex? Is it specified? If the answer to all three questions is “yes,” then design is inferred.

A) You haven’t explained how to determine these things. I have a particular problem with the use of the term “complex” here. Your use implies a binary condition. Something is either “complex” or it isn’t, to you, it would seem. By most treatments, certainly including Kolmogorov, complexity is not an either/or binary state, unless an arbitrary cutoff is deliberately employed for some reason, rather, all entities to which the analysis can be applied have some degree of complexity, but it can be low or high. Please explain very carefully to me how you determine the precise boundary between “complex” and “not complex”.

B) You also haven’t explained why on earth these things should be taken as proof of “design”, but first things first - please show me precisely how to at least replicate your claims that certain things have these traits.

Leslie Orgel, the late Oxford trained chemist, first used the term specified complexity in 1973 in his book, The Origins of Life. His quote is helpful when thinking about specified complexity and its application to things in nature: “Living organisms are distinguished by their specified complexity. Crystals such as granite fail to qualify as living because they lack complexity; mixtures of random polymers fail to qualify because they lack specificity.”

This represents a serious misrepresentation of the views of Leslie Orgel, since he had a particular interest in the natural origin of life.

It is uncivil to misrepresent the views of others, even if this is done by mistake. To have a civil discourse, one must sometimes apologize for uncivil behavior. Do you apologize for this misrepresentation of Leslie Orgel, who, I might note, died in 2007 and cannot correct such misrepresentations himself?

Snowflakes and tornadoes seem to lack contingency because the laws of nature can easily explain them. Snowflakes are formed when droplets of moisture from clouds freeze. Tornadoes form when several weather conditions converge to produce a violent column of air. If you know the rules for how they form, you can go outside and travel to where you think the conditions are right and observe these phenomena happen directly

Why does this mean that they “lack contingency”?

Also, snowflakes seem to form in random and unique patterns. There is no question as to whether snowflakes are complex with the vast probabilities for any given snowflake pattern. But are they specific? Do any of the patterns mean anything? Pretending that snowflakes are contingent, each pattern that you find would have the same high descriptive complexity and thus snowflakes would not warrant inferring design.

Although I agree that colloquially, snowflakes can be perceived as “complex”, please explain how you define and measure complexity.

Also, what do you mean by “specified”? How do I measure whether or not something is “specified”?

Paley’s watch will warrant a design inference. Let’s run it through the explanatory filter.

Is Paley’s watch contingent? It would seem so. There are no laws of nature that explain the necessary formations of watches (unless of course materialism is true; then “a theory of everything” might possibly be discovered one day that will explain the chance origin of life on earth and then the subsequent firing of neurons in the man’s brain who made the watch).

I do not understand. Watches are constructed by animals, namely, human beings. The construction of watches does require the firing of neurons in human brains. The construction of watches does not require any miracles. The fact that humans can construct watches now does not tell us anything about whether or not miracles are required for the origin of cellular life, let alone the subsequent evolution of life. I would have thought that anyone, regardless of religious sect, would agree with these obvious points.

Is Paley’s watch complex? Yes it is! There are several parts that compose a watch. Take one of the parts from the watch and you will notice that it does not work anymore. This means that a watch needs a certain configuration of mechanical components in order for it to function as such. So I would say the vast amount of configurations of mechanical components would make for a very large number; and the number of configurations that form a functioning watch would be relatively small.

This is merely an assertion that a watch subjectively seems “complex” to you. I don’t disagree that a watch can subjectively seem “complex”. On the other hand, it might subjectively seem “simple” to someone else.

Do you have an objective, reproducible method that others can use to determine if something meets your definition of “complex”? If not, your use of the term is irrelevant.

Is Paley’s watch specific? Just like proteins there are right ways and wrong ways to make Paley’s watch. Considering explanatory complexity, a functioning watch configuration will be easily explained while it will take much more to explain the configurations that do not make a functioning watch. So this is how design would be inferred on Paley’s watch if common sense fails or if we are skeptical of everyday experience.

Again, I see no rigorous definition of your key terms. You say it is “specific” and offer some word salad. Do you have a methodology that I can use to determine whether or not something is “specified”, by your own standards, yes or no?

Right now, all you seem to be doing is claiming that watches are designed and snowflakes and tornadoes aren’t designed. While that is a very specific contradiction of the beliefs of many Christians, it is totally irrelevant to biomedical science. And worse, you won’t even explain your methodology such that others can even try to reproduce your own measurements, whatever those measurements may mean.

1) Could any evidence convince you of the theory of evolution, and if so, what type of evidence is now lacking, that would convince you, if present?

2) The Supreme Court ruled against the direct teaching of Biblical Young Earth Creationism as science in public schools; however, if that ruling were overturned, which would you support more, teaching of ID, or direct teaching of Bible-based YEC?

3) Do you think it is important for opponents of the theory of evolution to fully understand the theory of evolution? If so, can you explain it, and if not, can you explain why not?

4) Who is the designer? How can we test your answer?

5) What did that designer do? How can we test your answer?

6) How did the designer do it? How can we test your answer?

7) When did the designer do it? How can we test your answer?

8) What is an example of something that was not designed by the designer?

I didn’t emphasize anything, but I will this time.

YOUR INVOCATIONS OF KOLMOGOROV COMPLEXITY ARE NONSENSE.

You don’t know what you’re talking about.

If Paley’s watch displays Kolmogorov complexity, then show the string of characters at issue, and show the descriptive computer program which produces them.

Otherwise, YOU ARE FULL OF SHIT.

Is that emphatic enough for you, poseur?

It appears to be standing in the middle of a crowded room with its eyes closed and believing it is invisible.

Weird.

1. Yes. Michael Behe’s argument from irreducible complexity and also the existence of information in DNA are two of the main reasons why I am skeptical. I think these show that events such as the random formation of functional proteins on early earth and indirect Darwinian pathways producing something such as a bacterial flagellum are contingent. So in this regard I need to be convinced that scientists have determined the exact pathways and have proof that they are explained naturally.

Lining up a few skeletons that look similar in structure, but are divided by vast step-wise gaps, would not be good enough to destroy my skepticism of universal ancestry. Accordingly, emphasizing that a bacterial flagellum shares a handful of proteins with a type III secretory system would be compelling, but I am being honest when I say that I would still doubt.

DC showed me a link to Nicholas Matzke’s 2003 paper on the flagellum. I was discouraged with language like: “Obviously “detailed” cannot mean that every mutation and substitution event be recorded – for events that occurred billions of years ago this is impossible. A detailed evolutionary model should reduce a puzzling event like the origin of the flagellum into a series of events that occur by well-understood processes.” Am I asking too much of Evolutionary Biology? I was further discouraged when I read a 2011 article by Jonathan M. from the Design Institute. Among other things he said, “Why exactly is flagellum biosynthesis so tightly regulated and orchestrated? Not only do the energy demands render the flagellum an extremely expensive system to run, but untimely expression of flagellum proteins may induce a strong immune response in the host system, something no bacterium wants to do.”

But it wouldn’t stop at the flagellum. I’m hoping for the same explanation for all supposedly irreducibly complex systems such as blood clotting and eyes.

Also, the information content in DNA is huge. I know that Darwinistic materialism can explain all of the letters on a page in a book. But I do not believe it can claim that the configuration and meaning of the letters are not contingent. So I would need a Darwinistic explanation for the presence of information in biological systems. Or an extremely compelling argument that says there is no information in biological systems.

The above mentioned included, I would need to see the positive claims of intelligent design refuted, as well as its negative claims against evolution refuted.

You could have just honestly said “no, no evidence could convince me”. Instead you resorted to the silly Scarborough Fair strategy - trying clumsily to set up an impossible barrier, and then saying you “could be convinced” if it were met.

Incidentally, most of what you do above is babbling nonsense.

2. My skepticism does not call for abolishing the teaching of evolution in schools. I’ll be happy with the teach the controversy stance until I am 100% convinced one way or the other. I would be against including YEC in any science curriculum because it makes metaphysical claims that I do not believe are to be decided by science. If parents want YEC for their children there is home schooling or private schools.

Fortunately, whether you are “100% convinced” is 100% irrelevant to what is taught in public high schools. There is no scientific controversy.

It is stupid to censor, distort, or deny science for any reason, and illegal to do that, in public school science class, in the service of one particular religious dogma.

3. Yes! Honestly if intelligent design theorists were all uneducated I would not have listened to their arguments in the first place. However, I can only assume that the number of design theorists holding PhDs in biology fully understand evolution. For instance, if I assumed Michael Behe did not understand evolution because I don’t like his conclusions, I would need to start doubting the comprehension of all biology professors that hold to conclusions I do not like.

The level of projection here is quite astounding. You do “doubt the comprehenion” of all other faculty in the biology department at Lehigh University. None of the rest of them agree with Behe. They all have the same qualifications as he does. So do all the biology faculty at all other universities. Virtually none of them agree with Behe. It’s utterly absurd to tout the PhD degrees of a handful of creationists, while scorning the value of the same PhD degrees if held by anyone else.

You evaded the part of the question about whether or not YOU can understand the theory of evolution. I’ll answer it for you. YOU DON’T. Based on your comments here, I can predict that you would not know the correct answer to a single biology question on a GED exam.

I know that design proponents and Darwinists hold to varying worldviews so I am not interested in whether someone is a Christian, atheist, Buddhist, etc. I am only interested in their arguments.

I suppose this is “true” in the sense that you value evolution denial from any source.

4. If Darwinism is false, then the origin of life is contingent and due to intelligence. As you might have guessed from my name I am a theist, but that does not mean that I think God is the direct cause of the origin of life. Panspermia would still need to be proven false. As it stands, I think the signs of intelligence in biological systems is the best explanation.

The ignorance, the illogic…where to begin?

“Darwinism” would refer to the study of the life of Charles Darwin, an active field, not to mainstream biomedical science. The theory of evolution doe not deal with the origin of cellular life. Your argument is a false dichotomy - if the theory of evolution were false, it would not mean that life had to originate magically. Panspermia is a rational and somewhat supported hypothesis (just not the only one) about how elements of early life may have gotten to the early Earth; it is a scientific hypothesis and does not in the slightest propose including miracles or magic.

5-7. As you know intelligent design has not gained widespread acceptance and is still in its infancy.

As I know, Intelligent Design was always a scheme to thinly disguise creationism, has never been accepted except by creationists, was found to be illegal favoritism for a narrow religious sect, when taught as science in public high school, in 2005, and is now largely defunct, even to the extent that some recent creationist science denial bills specifically deny any association with “intelligent design”.

Is your real name “Rip Van Winkle”? You seem to have been asleep for at least seven or eight years.

Since you are familiar with Dembski’s writings you should know that he says at this stage, intelligent design is mainly concerned with emphasizing the existence of the effects of intelligence. If intelligent design theorists don’t know then I don’t see how I can be required to answer these questions due to my armchair status. Darwinism hasn’t answered the when and how questions for the origin of life. Correct?

If you admit that they “don’t know” the answers to these key questions, why do you give them any credit whatsoever?

8. Snowflakes

So if I manufactured a natural looking snowflake, something that could easily be done, and presented it to you among a group of natural snowflakes, you could always tell the difference under any circumstances? Remember, if you say “no”, or even “not necessarily”, everything else you have said is falsified.

This will be my last comment, and I recommend to the moderators that repetitive comments in an effort to appear to have “gotten the last word” be pushed to the BW.

Prometheist answered harold:

{A long discourse about ID, a very long discourse}

Well, I suppose examples and long descriptions and much verbiage are helpful in describing a new notion that is difficult to communicate. But at some point mere words fail - they can so easily be misinterpreted.

Thus it is with Prometheist’s response. Unless he can speak the language of science and describe what he’s talking about with equations, which can be evaluated by any third party who will arrive at the same numerical result, then his words are just so much herbage, as harold has suggested.

He has admitted he is an armchair IDist, so I don’t expect to see any mathematics (much use of the word ‘probabilistic’ but in such a way as the common definition of ‘probably’). And this is exactly why armchair opinions are not accorded scientific validity. Science is a meritocracy.

Until ID can speak in the language of science, and prove its worth, terms like ‘specified complexity’ and ‘irreducible complexity’ remain Trojan Horses to bypass the Court of Merit and Court of Justice to introduce narrow religious concepts into the public schools.

prongs said:

Prometheist answered harold:

{A long discourse about ID, a very long discourse}

Well, I suppose examples and long descriptions and much verbiage are helpful in describing a new notion that is difficult to communicate. But at some point mere words fail - they can so easily be misinterpreted.

Thus it is with Prometheist’s response. Unless he can speak the language of science and describe what he’s talking about with equations, which can be evaluated by any third party who will arrive at the same numerical result, then his words are just so much herbage, as harold has suggested.

He has admitted he is an armchair IDist, so I don’t expect to see any mathematics (much use of the word ‘probabilistic’ but in such a way as the common definition of ‘probably’). And this is exactly why armchair opinions are not accorded scientific validity. Science is a meritocracy.

Until ID can speak in the language of science, and prove its worth, terms like ‘specified complexity’ and ‘irreducible complexity’ remain Trojan Horses to bypass the Court of Merit and Court of Justice to introduce narrow religious concepts into the public schools.

1) He has not provided any positive evidence for ID whatsoever.

2) He uses outdated “evolution can’t explain it, therefore ID” arguments, mainly from Behe’s work in the 1990’s. This would be a false dichotomy even if there was some legitimate barrier to an evolutionary explanation. However, he doesn’t show any understanding of actual biology. Therefore he is not equipped to determine whether evolution can explain something or not.

3) He makes extensive use of biased, unfair double standards and special pleading. Just the “ID must be true if evolution is false” structure to begin with. He puts value on the scientific credentials of a tiny number of creationists, but scorns the equal or better credentials of all other scientists. He wants his own armchair “doubts” to literally be taught to students as “science”, yet it is highly unlikely that he would tolerate teaching the different “doubts” of other unqualified individuals.

4) To some degree this is a finished battle. The claims that Rip Van Prometheist is still repeating were dealt with at Dover, and even the more up to date creationists have moved away with them. But it’s always worthwhile to rebut them.

prongs said:

Prometheist answered harold:

{A long discourse about ID, a very long discourse}

Well, I suppose examples and long descriptions and much verbiage are helpful in describing a new notion that is difficult to communicate. But at some point mere words fail - they can so easily be misinterpreted.

Thus it is with Prometheist’s response. Unless he can speak the language of science and describe what he’s talking about with equations, which can be evaluated by any third party who will arrive at the same numerical result, then his words are just so much herbage, as harold has suggested.

He has admitted he is an armchair IDist, so I don’t expect to see any mathematics (much use of the word ‘probabilistic’ but in such a way as the common definition of ‘probably’). And this is exactly why armchair opinions are not accorded scientific validity. Science is a meritocracy.

Until ID can speak in the language of science, and prove its worth, terms like ‘specified complexity’ and ‘irreducible complexity’ remain Trojan Horses to bypass the Court of Merit and Court of Justice to introduce narrow religious concepts into the public schools.

Actually, it is until Intelligent Design can explain anything, not when it can speak the language of science, will anyone other than the pithed Toadies of Jesus ever bother to consider it to be a science.

But, the sad joke is is that Intelligent Design was never intended to be a science, only a shoddily constructed Trojan Horse for Young Earth Creationism and Evolution-Denialism.

The only thing Intelligent Design can do is make repeated reiteration of “Evolution is wrong because GODDIDIT”

And the closest thing Intelligent Design proponents can produce to give a justification are, as our latest troll easily demonstrates, is an unreadable word-salad smokescreen.

I presented Prometheist with a detailed model of how the flagellum could have evolved, exactly what he demanded. His response - essentially, not good enough. TFB. He has no real objection to the model, except he doesn’t want to believe it. And this after claiming that no such model existed and demanding references. Likewise with the other examples he cites. Each has been shown NOT to be irreducibly complex and good models exist for all, he just needs to be shown every mutation in every organism or else he refuses to believe it. Just like a real Behe acolyte, hE is willing to ignore all of the evidence and provides no explanation and no alternative. It’s worthless trying to discuss science with him. As if the fake “probability” calculations weren’t enough to convince everyone of that long ago.

Hi Prometheist. In your most recent comment, you said that you had explained what you meant by “descriptive complexity”.

Prometheist more recently said:

So your question actually involves the “Is it specific?” step of the filter. This is the node at which you consider descriptive complexity. I said in the earlier post describing my understanding of descriptive complexity that a low descriptive complexity is needed if design is going to be inferred.

So I went back and looked it up. Here it is.

Prometheist earlier said:

Then consider descriptive complexity or Kolmogorov complexity. This refers to how easy it is to describe any given pattern or sequence. When testing for specified complexity, the sequence must have a low descriptive complexity. An oft-quoted example is a series of coin tosses: HHHHHHHHH and HHTHTTTHTH. The first series has lower descriptive complexity because it can be described as “ten heads in a row.” The second series would be described as “two heads, then one tail, then one head, etc…” In the case of the protein the search is for a functional protein. So the description of any given sequence will be either “functional protein” or something longer such as “85% of a functional protein,” etc…

You have me confused. You say that “functional protein” is a shorter description than “85% of a functional protein”, and therefore has a lower “descriptive complexity”. Therefore, given “functional protein”, you would infer “design”, whereas given “85% of a functional protein” you would be less likely to infer “design”.

So it appears that you are describing a continuum of “descriptive complexity”. There are things with small “descriptive complexity”, and things with large “descriptive complexity”. By the example you gave, it appears that one can tell which object has greater “descriptive complexity” by a simple test of the number of characters used in the description of the object. Over this continuum of “descriptive complexity”, at one end a person can infer “design”. At the other end, a person cannot infer “design”. Presumably, at some point (perhaps in a broad gray area), there is a dividing line between those things that are “designed”, and those things that are not.

First, your definition of “descriptive complexity” depends on the language and the terms that one chooses to use. Which has more “descriptive complexity”: the object “car”, or the object “automobile”?

Second, your example makes no intuitive sense. You say that “functional protein” is a shorter description than “85% of a functional protein”, and therefore has a lower “descriptive complexity”. Therefore, “functional protein” infers design more than “85% of a functional protein”. But the former is describing 100% percent of a functional protein. The latter is describing 85% of a functional protein. Would not a description of 100% of an object by necessity be longer than 85% of the same object? By your definition, the description of any part of an object has more “descriptive complexity” than the object as a whole.

Using your definition, which has more “descriptive complexity”: the object “Pi” or the object “God”? The description “Pi” appears to be shorter, therefore (by your definition) we must infer design. Yet, the description “God” appears (by your definition) to have shorter “descriptive complexity” than “Prometheist”. Since I assume that you assume that the person “Prometheist” was designed (since you appear to be arguing that all life is “designed”), and that “God” has a lower “descriptive complexity”, then you must also conclude that “God” was designed. So if “Pi” is “designed”, and “Prometheist” is “designed”, and the “descriptive complexity” of “God” is between “Pi” and “Prometheist”, therefore we are forced to conclude “God” is “designed”.

Conversely, you have declared that “snow flake” is *not* designed. Yet by your definition “snow flake” has less “descriptive complexity” than “Prometheist”, which we know that you assume to be “designed”.

Correct?

apokryltaros said:

Scott F said:

Second, evolution doesn’t work that way. Science doesn’t work that way. Science can demonstrate a possible evolutionary pathway, which it plausibly has. You so far refuse to see any of that. If you were presented with a complete sequence of changes, you would ask to see proof that this was thee sequence that was actually used.

What about Lenski’s Escherichia coli experiment, and how he went back to document the step-by-step of mutations that lead to his bacteria developing genes for enzymatically digesting citrate by looking at the various samples of 50,000+ bacteria generations?

I was referring to “historical” evolutionary events for which specific sequences of events were not observed but must be inferred, rather than lab experiments where the events are more rigorously known.

But of course we always circle back to the creationist “gotcha” that any lab experiment is “designed”, therefore any results observed in a lab experiment are also “designed”. Creationists propose a dichotomy within a dichotomy. If you weren’t there to observe the event, you must conclude “design” because you cannot provenot design”. Yet, if you set up a situation so that you were there to observe the event, you must also conclude “design” because the very act of setting up for the observation imparts “design”. Heads I win, tails you lose.

Scott F said:

Conversely, you have declared that “snow flake” is *not* designed. Yet by your definition “snow flake” has less “descriptive complexity” than “Prometheist”, which we know that you assume to be “designed”.

Correct?

My apologies. I tend to get too verbose at times.

In case I wasn’t clear enough, your description (I hesitate to use the term “definition”) of “descriptive complexity” appears on the face of it to be nonsense. Since it is nonsense, and it is a necessary part of your triad for inferring design, then your whole “design inference” method appears to be nonsense.

harold said:

4) To some degree this is a finished battle. The claims that Rip Van Prometheist is still repeating were dealt with at Dover, and even the more up to date creationists have moved away with them. But it’s always worthwhile to rebut them.

I agree completely.

Like some modern day Southerners who pretend that really the Confederacy won the war, because they are still Southerners and still here, Dover is dismissed by creationists with a hand-waive as if it counted for nothing and actually went the other way.

JimNorth said:

Promotheist quoted Orgel’s work:

Living organisms are distinguished by their specified complexity. Crystals such as granite fail to qualify as living because they lack complexity; mixtures of random polymers fail to qualify because they lack specificity

Orgel was using this term in a qualitative manner, Dembski attempts to use it in a quantitative way. Specified as in sequential or non-random and complex as in not simple or made of many parts. He then uses two non-living examples to hammer home his point (crystals of granite clearly contain some sort of order, but are made of very few parts, whereas polymers can be composed of many interconnected parts that lack an orderly structure). Living organisms, on the other hand, display a method to their madness. This is a great example of cdesign proponentsist repurposing words. The great Inigo Montoya phrase comes to mind…

Also, why did you switch from specified complexity to a word salad of probabilistic pseudoscience?

I suppose Orgel must be forgiven for not knowing that there is no such thing as a “crystal of granite.” Granite is a rock comprised of a multitude of anhedral crystals of many different kinds. The most common crystals are of quartz, feldspars (of more than one kind), and mica, but the trace minerals must surely run more than a hundred.

A granite batholith must have billions, if not trillions, of individual crystals. How anyone can say it is ‘made of very few parts’ I cannot fathom. It seems awfully complex to me.

Consider my humble quartz crystal. Is it complex? Complexity, like beauty, is in the eye of the beholder. Surely it is symmetrical, and I would argue it is indeed complex, by virtue of that symmetry. A random collection of silica atoms is just that, a random collection. But well organized collection of silica atoms, better than any standing army? Now that’s complex.

It is ‘irreducibly complex’ because if you take away its silicon atoms you don’t have my quartz crystal. If you take away its oxygen atoms you don’t have my quartz crystal. The perfect example of ‘irreducibly complex.’

Furthermore it is ‘specific.’ It is silica, but specifically alpha quartz (also known as low quartz), as opposed to beta quartz (high quartz), coesite, stishovite, keatite, cristobalite, low tridymite, middle tidymite, high tridymite, opal, or lechatelierite, all specifically different forms of silica. It is ‘specific’ amongst at least eleven atomic arrangements of silica.

It has ‘specified complexity’ because it can be specified simply by reciting the specific arrangement of silicon and oxygen, in very simple terms, which must be repeated ad infinitum to make a macroscopic crystal. It has low ‘descriptive complexity’ therefore the answer to the question, “Is it specified?” must be “Yes.”

Is it contingent? Yes, it is contingent upon that fact that I live on a planet at about 298 degrees Kelvin, with an atmosphere, water, and a silicate crust. If my planet were at much higher temperature, or pressure, my quartz crystal (and I) would not exist. It is indeed contingent.

I declare it has passed the explanatory filter. My quartz crystal warrants the design inference.

Whence cometh this design? Intelligence, like a quartz crystal made in a laboratory by Man? Or by the Laws of Nature, in the earth? (I have both these kinds of crystals in my collection, by the way.)

I declare my crystal a Design of Nature, designed by the Laws of Nature fully and truly expressed.

I am an NDist (a Natural Design proponent, no smirks please).

I will allow Prometheist to ponder his snowflake, which he contends is not designed, while my quartz crystal is designed.

Prometheist said:

PA Poland said: By your ‘math’, you are essentially stating there are 3000 ways to get ONE SPECIFIC SEQUENCE.

If there are only, say, 2000 discrete folds that can produce all functional proteins, then the odds of a functional protein is then 1/2000.

You have fallen for the One True Sequence fallacy common amongst IDiots - the ridiculous notion that one (and ONLY one) sequence can work, and that it MUST be formed by having amino acids fall together all at once.

Real world experiments have shown that the odds of a peptide 70 random amino acids long having a selectable function is 1 in 10^9 to 1 in 10^12 - about 40 orders of magnitude MORE likely than your ‘math’ suggests !

I know there are only twenty amino acids that code for proteins, but research suggests that as low as four or five were needed to form functional proteins. I took my numbers from here. I used the numbers between their highest and lowest. Are these outdated?

Not as far as I know - but you are using them wrong !

The odds of a SPECIFIC sequence is 1 in 5^100 - but that’s the odds of every single amino acid of the reduced set conforming to a PREDETERMINED sequence all at once purely by chance.

NOWHERE in the Dryden paper did he say anything about multiplying that number by anything !

There are only a few thousand known stable folds - any given sequence belongs to one of those groups of folds. WHICH fold is a difficult question to answer - modern computers still have trouble calculating the secondary structure (how a given string of amino acids folds) from just the sequence; determining WHAT (if any) reactions it does, or how well it does it has not been done yet. Most of time, that sort of determination would be done by comparing the sequence to a database of known proteins to see how well it matches - at most, they could say ‘it has good resemblance to this protein which catalyzes reaction X’, but that would be about the most they could say.

And a novel fold NOT in the database would confound the computers.

So to my understanding, the probability of any given sequence of a protein as described by my source will be 1 in 5 to the 50th power. However, the paper suggested that about three thousand of those sequences were functional. So this means to me that the random probability for any given functional sequence would be 3000 in 5 to the 50th power.

Nope - the paper said there are only a few thousand known stable folds FUNCTIONAL OR NOT !

Whether a given sequence is functional or not cannot be determined directly from its amino acid sequence - the computations are at present too difficult (even figuring out HOW a protein folds given just the amino acid sequence is still rather sketchy sometimes !)

For example, for one protein, the sequence starts MKKR LLVLLILVLVLLIILLAVLALVL *************.

If all that is required is a few basic amino acids (the KKR), there are 2^3 (or 8) combinations that qualify : KKK, RRR, KKR, KRK, RKK, RRK, RKR, RRK.

The next stretch is a membrane anchor, so all that is needed is a string of hydrophobic amino acids. There are 5 choices : A, I, L, F, V. Gives 5^23 combinations.

If the rest of the protein is unchanged, there would (2^3)*(5^23) DIFFERENT amino acid strings with identical function !

I’m reasonably sure 9.5367 x 10^16 is a bit more than 3000 … !

I am saying that there are 3,000 “true” or functional sequences out of the 5 to the 50th power sequences that are possible. I do not see how the probability of a functional protein sequence would be one in 3,000 given a five amino acid alphabet and 50 positions on the sequence chain.

Knowing that the source I used is from 2008 and could very well be outdated, perhaps PA Poland’s new number of 1 in 10 to the 9-15th power is correct. However, probabilistic resources still need to be taken into account. If the number of chances to randomly combine the amino acids are low, then this new number would seem high.

From the paper you linked to :

“These two limits are shown in figure 1. Although the oft-quoted 20^100 (approx. 10^130) size of sequence space is far above these limits, the other more plausible estimates for the size of sequence space, particularly with limited amino acid diversity or reduced length, are near to or within these two limits. Considering the upper limit, all sequences containing 20, 8 and 3 types of amino acids have been explored if the chains are 33, 50 and 100 amino acids in length, respectively. Considering the lower limit, then virtually all chains of length 33 and 50 amino acids containing five or three types of amino acid, respectively, could have been explored. (The exploration of longer chains of 100 amino acids with only two types of residue is obviously much less complete but it is not a negligible fraction of the total.) Therefore it is entirely feasible that for all practical (i.e. functional and structural) purposes, protein sequence space has been fully explored during the course of evolution of life on Earth (perhaps even before the appearance of eukaryotes).

3. Discussion

Protein sequence space is often viewed as a limitless desert of maladjusted sequences with only a few oases of working sequences linked by narrow pathways (Axe 2000, 2004). The navigation over this space by natural selection is difficult and could take many different routes thus resulting in organisms with largely different protein compositions. This idea of contingency, if taken at the level of species, led Gould to suggest that if one was to rerun the ‘tape of life’ then evolution would take a totally different path and we, as a species, would only appear as a highly improbable accident (Gould 1991; Luisi 2003; de Duve 2007a,b). However, if there is any merit to our simple calculation then protein sequence analysis provides no support for the idea of contingency at a molecular level and it provides strong support for the ideas of convergence (Conway Morris 2000, 2004; Dawkins 2005; Vermeij 2006; de Duve 2007a,b). If one was to rerun the tape, then the protein composition of organisms would be similar. Our calculation removes the almost impossibly unrealistic pressure on natural selection to navigate through protein sequence space avoiding the vast number of functionless sequences by simply indicating that most sequences have been tried are useful in some way, and that there are many possible routes to obtain proteins with desirable functions (Nagano et al. 2002; Anantharaman et al. 2003; Holliday et al. 2007).

Finally, we conclude that the number 20^100 and similar large numbers (e.g. Salisbury 1969; Maynard Smith 1970; Mandecki 1998; Luisi 2003; Carrier 2004; de Duve 2005) are simply ‘straw men’ advanced to initiate discussion in the same spirit as the ‘Levinthal paradox’ of protein folding rates (Levinthal 1969; Zwanzig et al. 1992). 20^100 is now no more useful than the approximate 2×101 834 097 books present in Borges’ (1999) fantastical ‘Library of Babel’ and has no connection with the real world of amino acids and proteins. Hence, we hope that our calculation will also rule out any possible use of this big numbers ‘game’ to provide justification for postulating divine intervention (Bradley 2004; Dembski 2004).

Did you actually READ that article ? Or understand it ?

Or were you just looking for scientific things to toss out to bluff people with ?

One has to wonder at the paucity of intellectual stimulation these ID/creationists received as children.

If they had even experienced things like Zen Magnets or magnetic marbles, or simply played with magnets, or picked up bits of paper with static electricity, they might realize that there is something wrong with ID/creationist calculations of molecular assemblies.

And some high school chemistry and physics wouldn’t hurt either.

But instead, we get arm chair philosophers, who have never interacted with a real world, pontificating about what is or is not possible; and then they demand proof from people who are in touch with reality while claiming that they will believe it only if one can track the motion of every atom and molecule from a stochastic soup to a specified assembly.

It’s just not possible to communicate with someone like that.

Ken Ham has built an entire home-school curriculum for children and adolescents that is guaranteed to keep them in a complete state of intellectual deprivation so that they will be impervious to learning when they get to be (physical) adults.

That’s funny. Prometheist never answered my question: how does Prometheist show that CSI cannot arise by natural selection? (Because if we can’t show that, we can’t use CSI as evidence for Design).

Anybody but a silly troll would have some answer to that.

Scott F said: But of course we always circle back to the creationist “gotcha” that any lab experiment is “designed”, therefore any results observed in a lab experiment are also “designed”. Creationists propose a dichotomy within a dichotomy. If you weren’t there to observe the event, you must conclude “design” because you cannot provenot design”. Yet, if you set up a situation so that you were there to observe the event, you must also conclude “design” because the very act of setting up for the observation imparts “design”. Heads I win, tails you lose.

Interestingly, just last week the Sensuous Curmudgeon called our attention to exactly that kind of argument from the Disco ‘Tute. The matter at issue was the “directed evolution” of an enzyme via the random generation of variants and selection for an enzymatic function. (Paper here.)

The Disco ‘Tute writer says

This is not “natural selection and evolution.” It is artificial selection – a form of intelligent design. Artificial selection implies intelligent minds selecting roses, cattle, dogs or any other living organisms for a “desired function.” It doesn’t matter if the intelligent agent works by creating a random pool to select from, or outlines a carefully planned sequence of rational steps: selection by a mind for a purpose is intelligent design.

On that account, every lab experiment ever performed is evidence of intelligent design. No wonder the Disco ‘Tute author is anonymous.

Should it really be necessary to point out that there isn’t any reason to assume that currently used biochemistry is the only biochemistry that would work?

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This page contains a single entry by Richard B. Hoppe published on February 12, 2013 1:29 PM.

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