Darwin Day Festivities

Thanks Carl. For any other Austonians that happen to be reading, UT is showing the movie on campus at Welch Hall 2.224 at 7pm on the 12th. Make an appearance.

Carl wrote:

"My talk is entitled, "The Descent of Man, From Darwin to DNA."

How you can continue to advocate darwinism in the 21st century simply boggles the mind. It's like a 30 year old man still believing in the tooth fairy! Surely someone with your education and intelligence can see the bankruptcy of Darwin's proposed mechanism of evolution.
The only thing of value that Darwin contributed was to debunk the notion of special creation. But what he offered in it's place is a woefully inadequate mechanism that has been and still is, nothing more than a gigantic leap of faith. It doesn't even qualify as science because it is not subject to the well established and accepted scientific method. It is ideology, plain and simple.
There is not a shred of empirical evidence, either experimental or observational, that supports the notion that there is a nexus between the trivial effects of mutation and selection and the emergence of highly organized structures, processes and systems.

What part of that do you not understand?

The Militant Agnostic - "I don't know and neither do you!"

The Militant Agnostic --- Oh, I understand it alright. It's wrong, as in false.

For example, genetic algorithms, based just on mutation and sexual selection, are routinely used to evolve X-band antennas, patenable analogue circuits, and to program FPGAs.

Then, of course, there is all the biological evidence...

There is not a shred of empirical evidence, either experimental or observational, that supports the notion that there is a nexus between the trivial effects of mutation and selection and the emergence of highly organized structures, processes and systems.

You can construct very nice molecular phylogenetic trees out of Hox and other developmental genes, within and between species, essentially charting the time course of their mutational history. These are the genes that control the devlopment of complex biological structures. That would seem to be a trivial refutation of your assertion.

I'd really like to talk about this some more but I'm kind of busy at the moment. Why don't you give me a call? My phone number is ***-***-****. It shouldn't take you too long to get me. Just start dialing randomly and sooner or later my phone will ring. Or, if you don't want to wait that long, just dial any ten digits and discuss the matter with whomever answers the phone!

"Genetic" algorithms have nothing at all to do with genetics or evolution. It sounds like they might, but they don't. They aren't used to model evolution and cannot be used to support any kind of evolutionary scenario. There is nothing random about using these algorithms. They only work because of the thoughtful and rigorous input provided by the investigator, and there is nothing haphazard or accidental about them.

The algorithms do not control the output, the investigators do. They tweak and coax until they get something useful (as determined by them, because one algorithm cannot be used to ascertain the validity of another algorithm. That requires *insight* which is a product of a higher intelligence, in this case the investigator)

There is no evidence that what you see happening on the computer screen resembles in any way what is happening in real life. This is the first thing a competent investigator will tell you. Ask Adrien Thompson what his opinion is.

I'd really like to talk about this some more but I'm kind of busy at the moment. Why don't you give me a call? My phone number is ***-***-****. It shouldn't take you too long to get me. Just start dialing randomly and sooner or later my phone will ring. Or, if you don't want to wait that long, just dial any ten digits and discuss the matter with whomever answers the phone!

Troll, troll, troll your boat...

If you live in the Bay Area, UC Berkeley is also having festivities. Tours of the Entomology museum from 1- 4pm, a Darwin lookalike contest, and birthday cake starting at 5:30 in Wellman Hall (2nd floor) on the UCB campus.

I'll tell you why the 31 are big science venues - the small science venues can't afford Dodos. My fiancee has been DESPERATELY trying to bring Dodos to the science museum (Montshire Museum of Science, next to Dartmouth) in Vermont, but the price tag is KILLER.

Here's what Randy said:
Date: January 24, 2007 1:30:07 PM EST
Subject: Re: no dodos in northern new england!

Well, having been a professor at UNH, I feel pretty certain that when I
tell you about the $2500 screening fee we ask for you will say, "Whaaaat?
We don't have that kind of money." But do you think you have any funds
for a screening? Most of the museums are either paying $10K for me to
attend the screening, or $2500 without me. And its not to get rich off
the film -- it was financed with no grants or foundation involvement which
means we have huge debt to pay off, which is where the bucks go.

Any thoughts on this?

- Randy Olson

Gerard wrote:

"You can construct very nice molecular phylogenetic trees out of Hox and other developmental genes, within and between species, essentially charting the time course of their mutational history."

Indeed you can. But how can you tell if these changes are random and accidental or intelligently guided? My assertion is not that evolution has not occurred, it is that it was intelligently guided, not random or accidental.

Definition of troll: 1. anyone who comes to a blog or newsgroup and expresses an opinion different from the prevailing wisdom. 2. anyone who is open-minded enough to challenge the conventional wisdom.

Militant Agnostic- "I don't know and neither do you!"

The militant seems to militantly hold on to ignorance.....

I feel better know. I know it was ad hominum, but the militant argument simply starts wrong and keeps circling wrongness in an endless spiral of stupidity. The Gish Gallop all over again...not worth dismissing it point by point, someone please refer the gentleman to T.O.

Militant Agnostic said:

"Gerard wrote:

"'You can construct very nice molecular phylogenetic trees out of Hox and other developmental genes, within and between species, essentially charting the time course of their mutational history.'

"Indeed you can. But how can you tell if these changes are random and accidental or intelligently guided? My assertion is not that evolution has not occurred, it is that it was intelligently guided, not random or accidental."

If you agree that evolution occurred, down to the molecular genetic level showing what certainly appears to be radiation from common ancestry; and dispute only whether the mutations occurred through unguided means or through the intervention of intelligence; then short of Sal Cordova's hoped-for DNA steganography (which I take to be the molecular equivalent of the little plate next to the door of GM cars that said "Body by Fisher"), what sort of proof would you consider adequate to resolve that dispute?

Jud wrote:

"what sort of proof would you consider adequate to resolve that dispute?"

Well, you can't prove that mutation and selection is the mechanism of evolution because it's not. Randomly generated systems do not adapt means to ends, they do not adapt structure and process to function and they do not self-organize. On the other hand, I allege that you can prove that organized systems require intelligent input to emerge. Organized systems require intelligent guidance. They need to be put together with intent and their assembly requires insight. They need to be the product of intelligence because it is necessary to determine if they are functioning properly and that can only be achieved by insight. Since living systems display organization, they display means adapted to ends and structures and processes assembled to perform specific functions, it becomes self-evident that they are the product of a higher intelligence.
Living systems are made up of structures and processes integrated in such a way that they not only support each other, but they contribute to the overall function of the living system. This type of organization, in which means are adapted to ends and multiple structures and processes perform multiple functions, all of which contribute to the overall functioning of the organism are unattainable by any kind of random process or chance occurrence. It requires insight and insight means intelligence. There's simply no way to get around that basic point.

see:
http://www.charliewagner.com/casefor.htm

The Militant Agnostic- "I don't know and neither do you!"

If your in the NYC area The New York Hall of Science is screening the movie all weekend with discussion afterward lead by one of staff scientists Dr. Martin Weiss.

nyscience.org

Wagner is a well known idiot. In both the IDiot sense, and the intelligence sense. He's been making a fool of himself for many, many years, and shows no sign of stopping. There's really no point in arguing with him - just let him talk to himself.

"Militant Agnostic" links to the website of Charlie Wagner, well-known to readers of The Panda's Thumb, Pharyngula, and talk.origins.

The posts above are pretty indicative of his style.

jackd wrote:

"The posts above are pretty indicative of his style."

Which includes not reponding to personal attacks, insults and name-calling, which it seems is the only response to legitimate criticism that some people can muster. Pathetic.

The Militant Atheist - "I don't know and neither do you!"

Carl, you're going to be so close... just a couple hours from our godforsaken little hamlet of Grand Junction. Am trying to talk Husband into finding us a babysitter so we can make the trip (to the coldest spot in Colorado, incidentally... bundle up).

Militant Agnostic:

Since I asked for what proof you would consider adequate that evolution was guided by intelligence, and you responded with a description of the reasoning by which you reached that conclusion (if I may summarize, that no unguided mechanism could produce the features we see in living things), I take it you feel the proposition of design is proved as self-evident, and no additional "proof" (in the sense of data) is needed?

What the?!? Darwin Day - again? I'm getting too old for this.

If you feel like you're getting too old for Darwin Day, think how creaky and cranky Charles D. must be feeling at almost 198! But, like his theory, he seems to hang in there...

Charlie W., if you stuck to rock'n'roll criticism, you might actually command some respect, or at least a polite hearing. Evolutionary biology, however, is a field that requires judgments to be formed based on something more than personal preferences and "taste."

Steviepinhead wrote:

"if you stuck to rock'n'roll criticism, you might actually command some respect,"

Good. I could use a full measure of respect ;-)

I just got the new album by Rickie Lee Jones "The Sermon on Exposition Boulevard"

Blew me right the **** out of my chair. Run, don't walk!
Also, Patty Griffin scores with "Children Running Through".

Jud wrote:

"I take it you feel the proposition of design is proved as self-evident, and no additional "proof" (in the sense of data) is needed?"

Like any good scientist, I understand that nothing is ever proven. The best we can hope for is "most likely". So more data should be collected, more observations done and perhaps some experimentation designed to falsify the premise that the emergence of highly organized processes, structures and systems can be achieved by random, accidental variation (the darwinian claim) or that these systems cannot emerge without intelligent input (my claim).

The Militant Agnostic - "I don't know and neither do you!"

Militant Agnostic:

The field of mathematics has demonstrated repeatedly that "highly-organized processes, structures, and systems" are emergent properties of systems exhibiting random variation.

For that matter, so does your salt shaker--sodium and chlorine ions are randomly distributed in aqueous solution, and precipitate out into highly-ordered crystals.

In addition, focusing on the emergence of order out of random variation appears to rather miss the point altogether, since the key insight is that evolution is driven by selection (via differential survival), i.e., has a strong non-random component.

I'm scratching my head here wondering about this troll. Is this "Militant Agnostic" really arguing for ID? If so, is he really agnostic?

Militant Agnostic wrote:

I allege that you can prove that organized systems require intelligent input to emerge. Organized systems require intelligent guidance. They need to be put together with intent and their assembly requires insight. They need to be the product of intelligence because it is necessary to determine if they are functioning properly and that can only be achieved by insight.

I say: This chain of allegations, all apparently depending on the last claim, is refuted by the fact that death, survival and differential reproductive success occur with no insight required. If an organized system is "functioning properly" it persists or causes copies of itself to appear; any other definition of "proper function" merely imports the intelligent designer as an assumption, which is your logical fallacy.

I like the fact that Chuck has "here begins Homo ignoramus". It provides foreshadowing of what one will find when reading the site.

The sad part is, that he has a post on gun control. Being one of those in"duh"viduals who personally loves the Second Amendment, it does scares me that someone who could support ID would also be one who would also support the Second Amendment. That smacks of cognitive dissonance of the first degree.

The Militant Agnostic said: "[M]ore data should be collected, more observations done and perhaps some experimentation designed to falsify the premise that the emergence of highly organized processes, structures and systems can be achieved by random, accidental variation (the darwinian claim) or that these systems cannot emerge without intelligent input (my claim)."

Experiments and data collection on the means by which apparently "irreducibly complex" effects can proceed from much simpler beginnings is happening in labs all over the world - see, e.g., http://www.physorg.com/pdf64046019.pdf or http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1… . I don't know if such efforts meet your criteria for proof, but they interest me greatly.

My birthday is the 15th, and my wife got me From So Simple a Beginning. I plan on cracking that baby open on Monday to celebrate Darwin Day. Of course, it helps that she'll be out of the country for the week, leaving me with oodles of free time to fill.

Jud wrote:

"Experiments and data collection on the means by which apparently "irreducibly complex" effects can proceed from much simpler beginnings is happening in labs all over the world -"

That's fine, but I am not a proponent of irreducible complexity. I've discussed this matter with Mike Behe and hopefully have convinced him that there are serious flaws in his thinking.

"In his book "Darwin's Black Box", Michael Behe discusses what he refers to as "irreducible complexity". He defines IC as "a single system, composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning". He goes on to say that "an irreducibly complex system cannot be produced directly by slight, successive modifications of a precursor system, because any precursor to an irreducibly complex system that is missing a part is by definition non-functional". He should have seen it coming. The critics had a field day with this because he handed them on a silver platter the means to defeat his claim. All the detractors had to do was to show that even if a part is removed some function, perhaps a different function, still remains and that there can be a workable but simpler form of the system. One can readily see by the most cursory of examinations that one could easily remove the platform and nail the other parts to the floor. Clearly Behe's mousetrap is not irreducibly complex when measured against the definition that he provided. Behe missed the boat by measuring irreducibly complexity against simpler, non-functional systems. He approached the problem backwards by saying that if any part was removed the system would become non-functional. He should have known better. But Behe was right about one thing. The mousetrap is unevolvable by random, non-directed, accidental processes but not for the reason he provided. The reason for this is that a mousetrap has a quality called organization, which is much different from complexity or order. Each part of the mousetrap, the platform, the holding bar, the spring, the hammer and the catch each have specific functions. And each of these functions are organized in such a way that they support the overall function of the mousetrap, which is to catch mice. The function of the platform is to hold the parts, but it's there ultimately to facilitate the process of mouse catching. The function of the spring is to exert a force on the hammer, but it's ultimate goal is to enable the process of mouse catching. All of the parts have functions that not only support the other functions, but ultimately support the overall function of the device. This type of organization is not obtainable without insight, and insight always requires intelligence. There is no way that these parts could be assembled in such a manner without insight. A mousetrap is a simple machine, made up of several structures and processes and exists for a purpose. The construction of the mousetrap was initiated with intent, and fashioned for a purpose. Living organisms are similarly machines, with structures and processes that work together to create a function. In fact, all complex, highly organized machines in which means are adapted to ends are the product of intelligent design. The important point is that the adaptation of means to ends, the adaptation of structure and process to function requires insight. Behe's mousetrap is unevolvable, not because you can't take it apart without it losing it's function, it's unevolvable because you can't put it together in the first place using only random, non-directed, accidental occurrences. The selection of the parts, the configuration in which they're aligned, the assembly into one unit all require intelligent decisions at every step of the way. Similarly, living organisms show the same characteristics. It's not that you can't remove parts and lose total function, it's that you can't explain why these particular parts were selected, why they're integrated together in just such a way and how they were assembled from raw materials without invoking an intelligent agent."

John Scanlon wrote:

"I say: This chain of allegations, all apparently depending on the last claim, is refuted by the fact that death, survival and differential reproductive success occur with no insight required. If an organized system is "functioning properly" it persists or causes copies of itself to appear; any other definition of "proper function" merely imports the intelligent designer as an assumption, which is your logical fallacy."

Death, survival and reproductive success do not require insight. But they can only work on what is already present. The issue is not natural selection, which is a real phenomenon and will select variation based on fitness. The issue is about the step before natural selection acts, the step in which the structures, processes and systems emerge.
I might have mice in my house and I can go to the hardware store and find dozens of different variations of the mousetrap. I select from those numerous variations to find the best mousetrap for my situation. But this process of selecting between competing mousetraps cannot create a functional moustrap where there was none. All of the mousetraps available are the product of intelligent input. Not one of them bootstrapped itself into existence by random, accidental or fortuitous events.
The assertion that random, accidental, fortuitous mutations can somehow accumulate in such a way as to result in the appearance of complex structures, processes and systems is totally unsupported by observational or experimental data. It represents a huge leap of faith by evolutionary theorists. With respect to the eye, evolutionary biologists have proposed an arrangement of the various morphological forms of the eye into what appears to be a convincing series of steps leading from the simple eye cup of patella to the lens eye of nucella. While this is aesthetically pleasing and suggestive of gradual evolution of the eye, the fact is that there is no evidence at all that these examples represent phyletic evolution accomplishing a major morphological transition from eye cup to lens eye. Similar errors in assuming gradual transitions have been made many times in the past and have proven to be apocryphal.
You are being fooled into believing that the impossible becomes possible if it is only broken down into a sufficient number of smaller steps, each of which, on it's own merits appears to be attainable. This is no different from a gambler who goes to Las Vegas knowing full well that he can never beat the odds, yet holding out hope that by some magical "system" he can build a fortune. The basic point is that we know from experience that random processes cannot result in organization, no matter how much we want to believe it. Any evolutionary mechanism that relies only on random processes and rejects intelligent input is doomed to failure no matter what clever debating tricks are used to make it seem possible.
Evolutionary theory would attribute to natural selection, the same kind of intelligent insight that an engineer employs when he designs and builds a complex, highly organized functional machine. But this model fails because the creation of the improvement must occur before natural selection acts. Natural selection can only act on existing variation, it has no power within itself to create new variation. The new variation, the improvements, so to speak, must occur as a result of purely random processes, which is known to be impossible.

The Militant Agnostic - "I don't know and neither do you!"

"it does scares me that someone who could support ID would also be one who would also support the Second Amendment. That smacks of cognitive dissonance of the first degree."

I don't get your point. I'm also against abortion, pro-choice, against the death penalty and an agnostic who doesn't believe that humans are responsible for global warming. I also do not believe in the Big Bang and I believe that our ancestors came to earth from elsewhere. How's that for cognitive dissonance? Sorry that I don't fall into some neat little niche so you can label me and put me in a little box.

...I don't fall into some neat little niche so you can label me and put me in a little box.

You do. We can. We do.

(I beg our host's pardon for participating in this thread. It won't happen again, thanks to this little Greasemonkey script I'm about to use.)

The Militant Agnostic said:

"...I am not a proponent of irreducible complexity....

"But Behe was right about one thing. The mousetrap is unevolvable by random, non-directed, accidental processes but not for the reason he provided. The reason for this is that a mousetrap has a quality called organization, which is much different from complexity or order. Each part of the mousetrap, the platform, the holding bar, the spring, the hammer and the catch each have specific functions. And each of these functions are organized in such a way that they support the overall function of the mousetrap, which is to catch mice."

That's one reason I put "irreducible complexity" in quotes. I could have said "Experiments and data collection on the means by which apparently 'organized' effects can proceed from less 'organized' beginnings is happening in labs all over the world...."

I do realize that even bacteria have wonderfully 'organized' biochemical systems. Thus, even when scientists can show (as they are now doing) that evolutionary changes can and do occur under natural environmental conditions without the necessity of intelligent intervention, we're still back to an 'organized' entity. (Perhaps if it would become apparent at some point that viruses once utilized non-living matter rather than living cells to help them reproduce, they, rather than bacteria, might come to be considered evolution's beginning. But viruses must be said to show quite a degree of biochemical organization.)

Yet the history of organic chemistry, from urea through Urey and beyond, convinces me it is possible life began on Earth without intelligent intervention. My guess is that you would disagree, and that in fact on this point we shall have to agree to disagree.

You think the dodos are scary? I think the font is scary. How is it that the same artistic geniuses that brought us the Flash-Flatulence video are now making stills that look like they were made by a sixth grade A/V club? Blech!

Jud wrote:

"Experiments and data collection on the means by which apparently 'organized' effects can proceed from less 'organized' beginnings is happening in labs all over the world...."

I would like to see some of those experiments. I have never seen a case of organization emerging from random events.
Organization is not the same as order. One must be careful not to confuse organization with order. There's a lot of talk about ordered systems in the non-living world, snowflakes, tornadoes, etc. but this is not the issue. Order is simply a condition of logical or comprehensible arrangement among the separate elements of a group. Like putting files in alphabetical order or using a sieve to separate items by size. Organization is a much different structure in which something is made up of elements with varied functions that contribute to the whole and to collective functions of the system. Ordered systems can result from non-intelligent processes, as has been seen many times and cited by numerous examples.
Also, don't confuse organization with complexity. Highly complex systems can be generated by random events. For example, the Mandelbrot set.
Organization is much different from complexity or order.
All of the parts of an organized system have functions that not only support the other functions, but ultimately support the overall function of the system. This type of organization is not obtainable without insight, and insight always requires intelligence. There is no way that these parts could be assembled in such a manner without insight.
Living organisms are machines, with structures and processes that work together to create a function. In fact, all complex, highly organized machines in which means are adapted to ends are the product of intelligent design. The important point is that the adaptation of means to ends, the adaptation of structure and process to function requires insight.

Militant "Agnostic" again:

"...The new variation, the improvements, so to speak, must occur as a result of purely random processes, which is known to be impossible."

Who said "I don't know and neither do you!"? Now you claim to know something definite. And it's wrong.

If you insist on a gambling analogy, here's a non-misleading one: replicators make multiple copies [you can't do that at Las Vegas AFAIK] each of which bets its whole stake, the bad bets lose and the winners play on with another round of replication. 'Random processes' cause variation during copying, and some variants do better than others (more or less non-randomly, and perhaps with perfect determinism) in competing for some replication-limiting resource. Variants which outcompete more accurate copies of their own ancestors are obviously not impossible, and a posteriori they can be described as having 'improvements' or 'adaptations'. There's absolutely no reason why these shouldn't include increase in complexity, and it's the ONLY non-circular explanation for adaptive complexity anyone has come up with.

Really, it's not that difficult to get, is it?

The Militant Agnostic said:

"Living organisms are machines, with structures and processes that work together to create a function."

Two final points:

1 - When you say function, do you mean purpose? Many inanimate objects are brilliantly constructed to achieve various functions. A streambed, for example, serves the function of posing the lowest resistance to water flow at any point throughout its length, for the streambed materials existing at that point. If you do mean purpose, what is the purpose of a bacterium? Is it the bacterium's own purpose, or some other entity's? To what end?

2 - If you feel that life on Earth was the product of intent and intelligence, you have not solved the basic problem of how life arose, but only changed its venue. Life must have emerged from non-life somewhere, sometime, and evolved to a state of intelligence, unless one posits an eternal, incredibly sophisticated intelligence. So which do you feel is a more likely beginning, by your own reasoning - primitive biochemistry from available chemical building blocks, or an undying entity of staggering intellect from no precursors at all?

Jud wrote:

"When you say function, do you mean purpose?"

I don't think you can separate function from purpose. Function is what a structure, process or system does but you also must consider whether it exists to perform that action or just happens to perform that action incidentally.
For example, I have a brick holding my door open. It only has this function because I have used it for that purpose. It doesn't exist to hold the door open.
Likewise, a stream bed has no function because it does not exist to allow the water to flow, it just happens to do that. On the other hand, a chloroplast has the function of producing glucose in a plant and it exists for that reason.
A bacterium has a function, which is to remain alive and produce more bacteria. All of the structures, processes and systems in a bacterium have their own separate functions but they all support each other and they support the function of the bacterium, the reason it exists: to grow and reproduce. What ultimate function the bacterium might have in the scheme of things is not clear. The question "why are there bacteria?" is no different from the question "why is there life" or for that matter "why is there anything instead of nothing" which is more in the realm of philosopy than science.

Jud wrote:

"So which do you feel is a more likely beginning, by your own reasoning - primitive biochemistry from available chemical building blocks, or an undying entity of staggering intellect from no precursors at all?"

Well, I feel that life emerging de novo from primitive chemicals is highly unlikely because these chemicals would have to become organized into amino acids, proteins, cells, and living systems and we know that this kind of organization cannot occur by random, acciedental or fortuitous occurrences. No highly organized systems have ever bootstrapped themselves into existence from nothing without intelligent input.
As to the question of where life came from, the short answer is "elsewhere". I believe that life is endemic in the universe and most likely came to earth at some time in the past and found conditions that were supportive.
As to the ultimate question you pose, where did this life begin and how did it begin, I certainly don't know and neither does anyone else. But I have no reason to declare that life had a beginning because, like matter itself, it may have always existed.

The Militant Agnostic - "I don't know and neither do you!"

The Militant Agnostic wrote
"Natural selection can only act on existing variation, it has no power within itself to create new variation. The new variation, the improvements, so to speak, must occur as a result of purely random processes, which is known to be impossible."

New variation is known to occur as a result of purely random processes[1]: Simple mutation of one base pair in a DNA sequence can specify different functions[2]. One base-pair mutations can happy trivially - the problem is actually to avoid them happening when doing reproduction. A simple Google search[3] will give you ample data about this kind of mutation, as well as other ones, induced by various agents and occuring spontaneously. If you investigate the agents, you will also find that we know how many of them work - why they cause the mutations.

So, do we agree that that this is enough to show that mutations introduce variation, and that we can explain mutations, or is there any *specific* question you want to ask? Nothing about purpose or parts that need to operate toegher, please - I'll deal with that misunderstanding in the next post once you've OKed that you've understood the mutation aspect. Do you understand the mutation aspect and how that can introduce variation?

[1] I am assuming the existance of physics, and the existance of DNA in a reproducing entity. Both are in different domains than the discussion of the existence of evolution: The origin of physics is unknown (and possibly unknowable), the origin of self-reproducing entities is a discussion of abiogenesis, which is different from evolution, and which is an area we have little evidence.

[2] http://mcb.asm.org/cgi/content/abstract/26/17/6535

[3] http://www.google.com/search?q=single+base+transcription+error+frequency

Elvind wrote:
"once you've OKed that you've understood the mutation aspect. Do you understand the mutation aspect and how that can introduce variation?"

I think you are laboring under the illusion that the impossible becomes possible if only it is broken down into a series of small enough steps, each of which is theoretically plausible.
Yes, I understand mutations. But I also understand that there is a sophisticated set of processes by which the cell corrects damage to the DNA. Clearly the cell "understands" that lesions in the DNA are bad, and if they accumulate, they will result in senescense, apoptosis or unregulated cell division. On a cellular level, the term "beneficial mutation" is an oxymoron. The DNA repair mechanism is vital to the integrity of its genome and the normal functioning of the cell and the organism. All random mutations degrade the genome, and therefore must be considered detrimental to the integrity of the cell and the organism.

The Militant Agnostic- "I don't know and neither do you!"

Militant Agnostic said: "All random mutations degrade the genome...."

And you would then account for, e.g., Yao Ming's height in what way?

Eivind,
Sorry for getting your name wrong. My eyesight isn't very good despite this 20" monitor ;-)
If you will just abide me while I make one more point.
There may actually be two different kinds of mutations, random or accidental and directed mutations. Random mutations occur because of environmental factors such as mutagens, UV light, etc and are always deleterious to the integrity of the genome. On the other hand, some changes in the genome, which are mutations in one sense of the word may in fact be dynamic responses by the genome to environmental stresses or changes. I would agree that these kinds of directed mutations probably are beneficial to the genome.
In most cases however, the evolution we see is actually nothing more than changes in the frequency of already existing genes. This variation is already present in the gene pool and not the result of the accumulation of point mutations. There is no doubt that genes can change, the question is "where did the original genes come from?"

Jud wrote:

"And you would then account for, e.g., Yao Ming's height in what way?"

There is probably a genetic basis for this but I would suspect that the genetic potential was already present in his family gene pool. I would not conclude that it was the result of a random, accidental mutation. Besides, this is a quantitative change in height, not the emergence of any new structures, processes or systems.

here's the fundamental problem with ID.

to postulate a designer explains nothing. one must then also ask what designed the designer. and what designed the designer of the designer. an infinite regress results.

ID is defiantly incurious.

djlactin wrote:

"here's the fundamental problem with ID.

to postulate a designer explains nothing. one must then also ask what designed the designer. and what designed the designer of the designer. an infinite regress results."

Why, for pity's sake?

One of the oldest problems facing humankind is the problem of "First Cause". Why is there anything, instead of nothing? When and how did it all start? Is it "turtles all the way down"? Evolution has the same problem of infinite regress. All evolved forms were modified from pre-existing forms. But is it just an infinite regression of pre-existing forms? When and how did it all start?

The question of First Cause has been addressed by Philosophers and Scientists since the beginning of time. No solution has been forthcoming, although I will offer one for your contemplation. The First Cause problem stems from the belief that everything in the world has a cause. Because of this, you eventually must come to a primary cause, which religions call God. But this begs the question: "who made god?".
If everything must have a cause, then God too must have a cause. Religion says: "not so, God has always existed." and leave it at that.
But I contend that if there is anything in the universe without a cause, it might as well be the universe itself, rather than God. Since I don't believe in God, there's only one option as far as I can see: the universe and the life in it have always existed. There's simply no
reason for thinking that the universe had a beginning. Cosmologists seem to have an even different view. They claim that the universe came into existence without a cause. It's really only poverty of our limited human imagination that everything must have a beginning. For evolutionists, the question "where did life come from" may be no different from the question "where did matter come from?"

The big problem with Charlie's thinking (and I see this a lot with IDists and creationists) is that they declare certain things to be true based on intuition alone. The problem is that they don't really understand what's going on, and they use their intellect to preserve their original ideas while making excuses as to why our counterexamples don't prove anything. There's a whole bunch of erroneous statements Charlie (The Militant Agnostic) makes on genetic algorithms, the existence of beneficial mutations, etc etc. He won't accept these things, and if he were right, he would be correct in pointing out that evolutionary theory doesn't work. But, he doesn't understand these things, and he gets them wrong, despite his outspokeness.

BC wrote:

"The big problem with Charlie's thinking (and I see this a lot with IDists and creationists) is that they declare certain things to be true based on intuition alone."

An approach undoubtedly learned from darwinists and evolutionists ;-)

After all, that's all we have at this point is intuition. There isn't a shred of empirical evidence to support the notion that mutation and natural selection is the mechanism by which highly organized systems emerged. All Darwin offered was intuition and that's all evolutionists offer today.
So, we're all in the same boat: "I don't know and neither do you!"

The Militant Agnostic

"After all, that's all we have at this point is intuition."

That's funny. Regarding beneficial mutations, not only can I prove they can exist from a theoretical and mathematical perspective, but we have empirical evidence for beneficial mutations - nylonase gene in bacteria, antibiotic resistance in bacteria, antiviral resistance in HIV, the antifreeze gene in cod versus notothenioids, the existence of lactose digestion in adult humans. All you have is intuition, and that intuition is often wrong. "All" we evolutionists have is evidence, mathematical support, and intuition. I could point you to studies showing the recent appearance of many of these beneficial mutations, though I've seen you around quite a bit trolling on the evolution message boards, so I have very little confidence that you'd actually open your mind to the possibility. And the standard, "those alleles already existed in the population (since the beginning of time)" is just a way for creationists and IDists to dodge the fact that they are *new* mutations. If you weren't so committed to the "All random mutations degrade the genome" meme, you would be able to see that.

The Militant Agnostic said:

"Since I don't believe in God, there's only one option as far as I can see: the universe and the life in it have always existed. There's simply no reason for thinking that the universe had a beginning. Cosmologists seem to have an even different view. They claim that the universe came into existence without a cause. It's really only poverty of our limited human imagination that everything must have a beginning."

To be fair to Hoyle, I don't know that his picture of a steady state universe necessarily includes life throughout its duration (life sufficiently intelligent to design other life, at that). And to be fair to cosmologists, I don't read much of what's been written about the Big Bang, inflation, etc., as precluding a cause.

But, more to the original point of the post and comments, when we get to discussions of a steady state universe, the perpetual existence of life in that universe, the existence or non-existence of first causes, etc., we're well into the realm of speculation and thus quite far from any sort of conclusive demonstration of "the bankruptcy of Darwin's proposed mechanism of evolution."

The crying shame in Militant Agnostic's view is that (1) there are self-organizing systems and (2) that says something deeply profound about the universe. Creative slippery slopes abound, where evolving organisms (or curious minds, or genetic algorithms) converge to elegant solutions, often from very different starting points.

Whether or not you believe that "God" endowed the universe with this hidden creativity, it's amazing. But instead of just standing with our mouths agape in awe, we can study the origins of complexity, as Seth Lloyd and others are doing. We may never know exactly how it works, but trying to figure out will be exciting science.

Thanks, Militant Agnostic, for reminding me exactly why I don't like the term. Agnosticisim implies a downright cowardly pride in not knowing.

Militant Agnostic said: "Why, for pity's sake? ...." and nothing more in many words.

This is the most verbose dodge I've seen yet.

The idea that the universe and life have always existed is Hoyle's steady-state hypothesis (yes, Jud, he supposes that life is just a characteristic of the universe, like matter and energy), and it has been refuted by the evidence that points overwhelmingly to a sudden origin of the universe some 15 billion years ago.

The how and why are in the realm of cosmology. They are difficult questions and the subject of intense speculation, but no cosmologist is ready to say: "it's turtle all the way down".

I second Jud: this has nothing to do with either the fact of evolution or the theory (Darwin et al.) of how this process occurs.

djlactin wrote:

"I second Jud: this has nothing to do with either the fact of evolution or the theory (Darwin et al.) of how this process occurs."

Agreed.
So let's get back to the main issue:
What empirical evidence exists (not intuition, speculation or just-so stories) that establishes a link between the observed effects of random mutation and natural selection and the emergence of highly organized structures, processes and systems that exist in living things?
This is why darwinism fails. It is nothing more than an audacious leap of faith unsupported by hard evidence. Can you demonstrate that random mutation and natural selection has the power vested in it by Darwin? I don't think so.
In fact, I know so.

The Militant Agnostic - "I don't know and neither do you!"

Gee, Charlie/Militant Agnostic, you're not even going to respond to my critique of your erroneous statement that "All random mutations degrade the genome"? Not even going to ask how beneficial mutations can occur from a mathematical/statistical viewpoint? Uh, huh. But, I'll bet you'll be back repeating yourself ad nauseum.

The Militant Agnostic wrote:

"djlactin wrote:

"'I second Jud: this has nothing to do with either the fact of evolution or the theory (Darwin et al.) of how this process occurs.'

"Agreed."

Sorry I was unclear, as it seems you've both mistaken my meaning.

In fact this has everything to do with evolution. Either primitive life originated from non-life at some time somewhere in the universe and evolved to an intelligent state; or entities sufficiently intelligent to design life have always existed. If you believe the latter, then barring supernatural intervention, the only possible choice regarding cosmology is Hoyle's steady state. Hoyle's steady state is at best speculative, and at worst virtually impossible based on the most recent scientific data. (For details - or just pure fascination at the incredible level of knowledge we've now got about some very exciting subjects, and what smart people can do with that knowledge - see last year's second most cited high energy physics paper on arxiv.org: http://arxiv.org/pdf/astro-ph/0603449 )

Thus, since evolution must have occurred in our universe unless Hoyle's steady state is fact, it is plainly impossible to give *scientific* assurance based on current knowledge that evolution does not occur.

Jud wrote:

"see last year's second most cited high energy physics paper"

I see Ned Wright's name on that paper. I've been meaning to call him and ask him about this:

http://www.astro.ucla.edu/~wright/tiredlit.htm

and this:

http://tinyurl.com/2hvxqs

"Harvard physicists have shown that they can not only bring a pulse of light, the fleetest of nature's particles, to a complete halt, but also resuscitate the light at a different location and let it continue on its way."

Anyway, I think you're being too restrictive in your thinking. You have no basis to limit your thinking to only two choices: "Either primitive life originated from non-life at some time somewhere in the universe and evolved to an intelligent state; or entities sufficiently intelligent to design life have always existed." There certainly may be some totally natural, yet unknown "first principle" at work that we simple do not comprehend.
I take more exception to your claim that: "If you believe the latter, then barring supernatural intervention, the only possible choice regarding cosmology is Hoyle's steady state." There are reasons to question Hoyle's model that do not impact on the possibility of an eternal universe.
With all due respect, I don't have a lot of confidence in the Standard Model as it relates to cosmology or to the Big Bang in general.
http://www.charliewagner.net/big.htm

The Militant Agnostic - "I don't know and neither do you!"

Jud wrote:

"see last year's second most cited high energy physics paper"

(I'm forced to repost this to defeat the spam blocker.)

I see Ned Wright's name on that paper. I've been meaning to call him and ask him about this:

www dot astro.ucla.edu/~wright/tiredlit.htm

and this:

tinyurl.com/2hvxqs

"Harvard physicists have shown that they can not only bring a pulse of light, the fleetest of nature's particles, to a complete halt, but also resuscitate the light at a different location and let it continue on its way."

Anyway, I think you're being too restrictive in your thinking. You have no basis to limit your thinking to only two choices: "Either primitive life originated from non-life at some time somewhere in the universe and evolved to an intelligent state; or entities sufficiently intelligent to design life have always existed." There certainly may be some totally natural, yet unknown "first principle" at work that we simple do not comprehend.
I take more exception to your claim that: "If you believe the latter, then barring supernatural intervention, the only possible choice regarding cosmology is Hoyle's steady state." There are reasons to question Hoyle's model that do not impact on the possibility of an eternal universe.
With all due respect, I don't have a lot of confidence in the Standard Model as it relates to cosmology or to the Big Bang in general.
http://www.charliewagner.net/big.htm

The Militant Agnostic - "I don't know and neither do you!"

BC wrote:

"nylonase gene in bacteria, antibiotic resistance in bacteria, antiviral resistance in HIV, the antifreeze gene in cod versus notothenioids, the existence of lactose digestion in adult humans."

Would it surprise you if I told you that not only am I aware of these examples, I have discussed them elsewhere at length?
First of all, you can't say if those mutations are random or directed. They may simply be responses by a dynamic genome to environmental stresses and challenges.
Even if there are such things as "beneficial mutations" there is still no empirical evidence that they can accumulate in a way that leads to the emergence of new structures, processes and systems where they did not exist before.
The nylonase example particularly nauseates me. I've been over this a number of times with Ian Musgrave and others. I've never eaten rattlesnake meat before, but I'm certain my body would have no trouble digesting it. The fact that there was no nylon before whenever is irrelevant. The basic process is the hydrolyzation of polymers. Bacteria already had genes to do this. This is not a new process, but simply a modification of an already existing process.

The Militant Agnostic said:

"You have no basis to limit your thinking to only two choices...."

Re the two choices, perhaps you'll accept the limitation if I state the choices more simply: either (1) life began at some time somewhere in the universe; or (2) it didn't. If #2 is the case, since life exists today and did not have a beginning, then it has always existed. Fair enough?

The Militant Agnostic also said: "I take more exception to your claim that: 'If you believe the latter, then barring supernatural intervention, the only possible choice regarding cosmology is Hoyle's steady state.' There are reasons to question Hoyle's model that do not impact on the possibility of an eternal universe."

You're right, I should have said if one believes life has always existed (choice #2 above), then the only possible option regarding cosmology is a universe that has always existed.

But the great weight of detailed scientific data and careful observations strongly contraindicate a universe that has always existed, and thus equally strongly contraindicates life that has always existed, or any other eternal entity of any kind, e.g., any entity with sufficient intelligence to design or create life.

If we are to believe the great weight of scientific evidence, then, we are left with the conclusion that life arose at some time somewhere in the universe. We are then left with two further options: Either this life was invested with intelligence instanter, or it was not, and thus the intelligence that exists today arose in the descendants of the first life forms. This starts to sound suspiciously like evolution, doesn't it? ;-)

Now, circling back once more to the post and your initial comment on it: Since the opinion that evolution could not occur depends on a cosmological view unsupported by the great weight of current scientific evidence, don't you think castigating Carl Zimmer for "believing in the tooth fairy" was overreaching? In other words, while you are certainly free to believe that science will prove you correct one day after all, is it really fair to call other folks dunderheads for not sharing that opinion?

Jud wrote:

"perhaps you'll accept the limitation..."

Barring some completely bizarre quantum thingy, I will agree that life either had a beginning or it always existed.

Jud wrote:

"the great weight of detailed scientific data and careful observations strongly contraindicate a universe that has always existed,"

I'm sorry, I just don't see that. Perhaps you would like to explain your reasoning. What evidence is there that the universe had a beginning? Even if there was a "creation" event like the Big Bang, you cannot rule out an oscillating universe that has multiple "beginnings"
You might want to read Sir Fred's book "The Intelligent Universe" if you have not already. The first chapter is on my website to get you started. It's out of print and might be difficult to find but it's well worth the effort.

Jud wrote:

"don't you think castigating Carl Zimmer for "believing in the tooth fairy" was overreaching? "

I respect Carl Zimmer and I enjoy reading this blog. Certainly it is light years ahead of Pharyngula in the science realm. Zimmer is not an intolerant bigot like PZ Myers and he usually sticks to the science. I think it's a shame that Pharyngula won the award for Best Science Blog and this blog was not even mentioned or considered.
Nevertheless, Carl is an apologist for darwinism, which I consider to be a debunked theory, lacking any empirical support. I know that Carl is intelligent and well educated so it boggles my mind how he can not see this.
Besides, I moderated my comments before printing them here. I was tempted to say that a person would have to be brain-dead to believe in darwinism. That seemed like a genuine hyperbole ;-)

The Militant Agnostic - "I don't know and neither do you!"

Would it surprise you if I told you that not only am I aware of these examples, I have discussed them elsewhere at length?

But, you obviously haven't absorbed their implications.

First of all, you can't say if those mutations are random or directed. They may simply be responses by a dynamic genome to environmental stresses and challenges.

And this forward-thinking mechanism capable of rewriting the genome to help organisms survive is what? Naturalistic evolution can produce these effects (and based on the sequence similarity between the old, non-functional version and the new, functional version says it doesn't take an improbable series of events to explain this as random mutation) Your argument is essentially that beneficial mutations *cannot* happen because - uh, we could get these effects by other mechanisms. That's not even a reasonable response. If you want to claim that beneficial mutations can't happen, you don't support your argument by saying that beneficial mutations can occur by other mechanisms that you can dream up.

Even if there are such things as "beneficial mutations" there is still no empirical evidence that they can accumulate in a way that leads to the emergence of new structures, processes and systems where they did not exist before.

Yeah, I've encountered this response from IDists in the past. It's essentially, a "let's change the subject" response. Are you going to defend your claim that you made purely on the basis of your erroneous intuition that beneficial mutations can't happen, or not?

The nylonase example particularly nauseates me. I've been over this a number of times with Ian Musgrave and others. I've never eaten rattlesnake meat before, but I'm certain my body would have no trouble digesting it. The fact that there was no nylon before whenever is irrelevant. The basic process is the hydrolyzation of polymers. Bacteria already had genes to do this. This is not a new process, but simply a modification of an already existing process.

The nylonase example is not what you make it out to be. It's not simply that bacteria can metabolize nylon using it's normal digestive pathway, it's that a specific gene appeared recently in bacteria which allows it to metabolize nylon. Where did that gene come from? Further, lab tests have been able to reproduce the appearance of this beneficial mutation.

Anyway, I know it's pointless to argue with you. Based on your history, I think you have no intention in changing your views or ideas. So, it's a waste of my time to put any more effort into this discussion. I only write my rebuttals as a public service to show the problems in your ideas to other readers.

BC wrote:

"And this forward-thinking mechanism capable of rewriting the genome to help organisms survive is what?"

Adaptive mutation, I would suspect. Meaning that the potential to adapt, rather than the actual adaptation, was already present in the genome of the bacteria. If you've never heard of adaptive mutation, a quick Google search will be useful.

BC wrote:

"Yeah, I've encountered this response from IDists in the past. It's essentially, a "let's change the subject" response. "

No, actually it is the crux of the whole matter. We know that mutations can occur, both random and adaptive. We know that natural selection can change the frequency of alleles in populations. The missing piece is the nexus between mutation and selection and the emergence of highly organized structures, processes and systems. This is why darwinism fails. No link has been established with empirical evidence. It's still just a story.

BC wrote:

"It's not simply that bacteria can metabolize nylon using it's normal digestive pathway, it's that a specific gene appeared recently in bacteria which allows it to metabolize nylon. Where did that gene come from?"

Adaptive (directed) mutations. Experiments suggest that bacteria can program mutations according to the selective pressures that they are placed under. In other words, it seems that the environment can sometimes affect the genotype. This re-programming is carried out by machinery already present in the bacterial cell. Unfortunately, while adaptive mutation has been well documented over the last 10-15 years, most evolutionists (darwinians in particular) find the very notion abhorrent because it smacks of LaMarckism.

BC wrote:

"Anyway, I know it's pointless to argue with you. Based on your history, I think you have no intention in changing your views or ideas."

Most likely you are correct. However, it is fun. And maybe I can change your views and ideas. Anyway, thanks for taking the time to reply.

Said CharlieAgnostic the question is "where did the original genes come from?"

Enlighten us o wise one: What is your proposal?

Again, since we are 'discussing' evolution, this is off-topic, since evolutionary theory deals only with the diversification of life, not its origin. That subject is Origin of life 'theory' (I put theory in quotes because it is little more than speculation at this point, although there are some very interesting ideas. The point is that many people are putting effort into understanding, rather than just quitting.)

Further: Adaptive (directed) mutations. Experiments suggest that bacteria can program mutations according to the selective pressures that they are placed under. In other words, it seems that the environment can sometimes affect the genotype . Cite the paper!

Actually, as I recall, 'programming' is not the word. In some cases, stress causes a greater mutation rate in some bacteria. (Mechanism unclear, AIR, but possibly a result of faulty DNA repair systems.) Of the many mutants produced, some afford better survival chances and their descendants come to dominate the population. There is no intellect necessary.

He also emotes: My assertion is not that evolution has not occurred, it is that it was intelligently guided, not random or accidental.

Here arises a fundamental difficulty: you say that it is "intelligently guided" yet you deny belief in a 'designer' (deity). It also seems that you believe that design originates at the level of the genome. Explain: how can a chemical [DNA] identify what changes are needed and decide which of its bases to alter in order to accomplish this change?
WHERE'S THE MECHANISM?!

Sez he also: Even if there was a "creation" event like the Big Bang, you cannot rule out an oscillating universe that has multiple "beginnings"

Of course not. Many cosmologists are puzzling over this. Linde's Multiverse Hypothesis is an example. But you seem to imply that because of the repeated iterations of the universe, life might have existed since the 'first' one. You still have to explain how the organization of living systems survived the singularities (big bangs at 10^holy shit!! kelvins) between incarnations.

However, it is fun. here is self-identification as a troll: "I enjoy posting vapid, pointless messages to stir people up and get them to pay attention to me". You really need to get out more.

djlactin wrote:

"here is self-identification as a troll: "I enjoy posting vapid, pointless messages to stir people up and get them to pay attention to me"."

I strongly disagree with your characterization of me as a "troll". A troll is defined as "a person who intentionally tries to cause disruption, often in the form of posting messages that are inflammatory, insulting, incorrect, inaccurate, or off-topic, with the intent of provoking a reaction from others."

I have done none of those things. I do raise issues and ask pointed questions with the hope of stimulating discussion and getting people to think about these matters and I do have a controversial point of view on many subjects. The fact that some people are troubled by this is not my problem, it is theirs.

djlactin wrote:

"Adaptive (directed) mutations...Cite the paper!

A simple search of PubMed or Google will turn up hundreds of papers from John Cairns to Barry Hall. Do the research!

djlactin wrote:

"He also emotes:"

Too much negativity! You give the impression that your mind is closed on this matter. Scientists should never close their minds on any matter or reject any possibility of change. A lot of people look at darwinism from an ideological perspective and not a scientific perspective. For many people, it is their religion and they are reluctant to give it up. Well, I had a religion once too, but when I started to see the facts, I did not hesitate to reject it. Unfortunately many people simply substitute one religion for another.
If you can open your mind and separate ideology from science you will understand what I'm saying. I know it's hard to give up a belief that has been so long held and dear to your heart, but science demands it.
Take a piece of paper and begin to write down all the empirical evidence linking mutation and selection with the emergence of highly organized structures, processes and systems. Then bring the list here (or e-mail it to me) at:
charlie@charliewagner.com
I guarantee that if you can produce anything more than a just-so story I will consider it.

I've got a quick question (only slightly off-topic) for the Militant Agnostic. I am a molecular neurobiologist, sitting here eating a late dinner in lab while puzzling over how the brain works. I'm going to assume that you think the brain falls into the same category as a flagellum: designed and irreducibly complex. So here is my question - what good does your ID theory do me? As I see it, it has no predictive power, and so its scientific utility is zero. Let say that you are right (ID rules!) and I am wrong (evolution stinks!). I and every other biologist I know thinks about evolution in crafting arguments and - more importantly - in designing experiments to mechanistically explain the world around us. Our use of evolution as a intellectual framework to hang our experiments upon has been clearly and undeniably successful REGARDLESS OF WHETHER OR NOT EVOLUTION IS "TRUE". In contrast, I don't know anyone who has ever explained anything by asking "Hmmm...I wonder how the Intelligent Designer might have built this system...he did so well with the flagellum!" So, what do you want me to do? I could incorrectly believe in my "evolution delusion" which leads me to correct answers to interesting questions, or I can believe in your "truth" which...well, I don't know. Leads me to a life as an ID blogger?

BTW Carl, missed you at the Knicks-Nets. Was a great game - maybe next time.

dodge: "do the research" this is not how science writing is done. If i (you) say X then it is my (your) duty to cite the references which support it; it is not up to the reader to find it.

dodge: "so much negativity!" (1)

you object to 'darwinism' by opining that there is no evidence that RM x NS can assemble complex structures.
first, you have to define "complex structure".
* a brain? i have no problem with the idea that it originated as a small anterior assemblage of neurons that was elaborated over millions of generations by selection acting on variants with larger assemblages.
* an eye? been done to death
* a flagellum? this is apparently a more difficult problem, possibly because they're so hard to study up close (can't hold one in your hand). but there is progress being made: current idea is that it arose by cooption of a sectretory apparatus.
http://www.health.adelaide.edu.au/Pharm/Musgrave/essays/flagella_1.htm
Nick Matzke speculated on this quite eloquently http://www.talkdesign.org/faqs/flagellum.html
see also commentary at
http://chem.tufts.edu/AnswersInScience/PallenMatzke2006.html
and if you have a subscription, download
Palen and Matzke's recent article in Nature Reviews Microbiology:
http://www.nature.com/nrmicro/journal/vaop/ncurrent/pdf/nrmicro1493.pdf
Before you dismiss this as a 'just so story' i would like to point out that it is a detailed, *falsifiable* hypothesis. research is ongoing and may lead to surprising conclusions.

second, i have philosophy: i believe that before i criticise an idea, i should have an alternative that i think is superior. i have seen no evidence that you can do this. your opinion that 'therefore it must be designed' (comment: at some level that does not involve any designer) is vague hand-waving.

evolutionary theory has led to some astonishing insights into biology and has immense value in, among other things, medicine. there are still unanswered problems but this is not cause to toss out the idea.

dodge: "so much negativity!" (2)
(what, me negative?) have a look at your own statements.

Finished my rattlesnake. Off to eat some nylon.

The Handsome Hindu wrote:

"I've got a quick question (only slightly off-topic) for the Militant Agnostic."

You're apparently unfamiliar with my work so there are a few points I should clear up first. I am not claiming that the brain (or other living systems) were "designed". I am claiming that they could not have arisen without intelligent input. I know the difference is subtle and I'm not trying to parse my words. There is a difference. Also, I am not a proponent of irreducible complexity as described by Mike Behe and other religious creationists.
My contention, as I have stated on numerous occasions, is that highly organized structures, processes and systems, in which means are adapted to ends and structure and function are integrated in such a way that they work together to produce an action or a product, cannot emerge from random, accidental or non-directed fortuitous occurrences.
In addition, I have never questioned evolution as a process, only darwinism as a mechanism. Science is based upon empirical evidence, observational and experimental. Darwinism or any kind of random process fails because the empirical evidence linking the mechanism and the process is missing.
The purpose of science is to figure out how things work. So studying neurobiology, genetics, molecular biology etc. falls squarely within the realm of science. Even the study of mutation and natural selection (population genetics) falls in our realm.
But the ultimate questions, why it is the way it is and how it got that way belong more comfortably in the realm of philosophy. Knowing that life emerged through intelligent input or through a random, accidental processes is really irrelevant to the day to day workings of science. It's really nothing more than an interesting question. On the other hand, the study of mutation and selection as well as molecular genetics and molecular biology has great usefulness in our day to day pursuit of scientific knowledge.
Believing in mutation and natural selection and believing that they led to the emergence of the brain and other highly organized systems are two different matters. You can accept the scientific reality of mutation and selection and use those concepts in your research without taking the audacious leap of faith that they have the power to create the structures, processes and systems that science studies.

http://www.charliewagner.net/casefor.htm

The Militant Agnostic - "I don't know and neither do you!"

The Handsome Hindu wrote:

"I am a molecular neurobiologist,"

Do you have an opinion about the Penrose-Hameroff Orch OR model?

http://www.quantumconsciousness.org/publications.html#penrose

The Militant Agnostic wrote:

"But the ultimate questions, why it is the way it is and how it got that way belong more comfortably in the realm of philosophy....
Knowing that life emerged through intelligent input or through a random, accidental processes is really irrelevant to the day to day workings of science...
You can accept the scientific reality of mutation and selection and use those concepts in your research without taking the audacious leap of faith that they have the power to create the structures, processes and systems that science studies."

Sorry, Charlie. You obviously do not understand (or are interested in understanding) how real biologists work, which is your loss given your interests. Ultimately developmental biology - the underpinning of all of our current understanding of biology as a whole - is about the creation of new structures, and so the neat divorce you propose between mutation and "Darwinism" doesn't really work out here in reality-land. I am glad, however, that you acknowledge that you are really dabbling in philosophy (nice sophistry, by the way!), but why then post here? One last point. You are really embracing a kind of pseudointellectual null hypothesis (as ID has no predictive value), which from a scientific perspective makes you a bore. I know you were going for iconoclastic, but there it is. You won't be getting any Christmas Dinner invitations from me.

About the Penrose-tubulin thing (now really off topic): the general consensus is that only in the Addams family are weird things necessarily related.

I just noticed that my overzealous junk filter snagged a couple legitimate comments over the past few days. I've put them into the comment thread, but they may make the flow a bit confusing now.

Carl. Thanks for providing a venue at which intelligent persons (no matter how they were designed or accidentally arrived) may state their points of view on such important issues. I spent an hour pondering 69 posts and some of the links. It was not a waste of time.

John X wrote:

"Thanks for providing a venue at which intelligent persons (no matter how they were designed or accidentally arrived) may state their points of view on such important issues."

I second that.

In my book, this is the "Science Blog of the Year".

Wow... I saw the title on this post and wondered "hmm, I think this is the time to ask the readers of The Loom, about their opinion on the whole debate between the creationists and the sane (sorry, how ignorant of me)," I was totally unaware that you guys still are having problems with the degree of science-teaching in schools in some states, I really thought it all had cleared up in the 90's - yup, I live in a dreamworld... Its fun to observe the differences between continents regarding the number of creationists here in Denmark and in the states. I guess that?s why I was shocked to read all these comments - Im not used to this at all.
But creationism has its highlights - for example the FAQ on www.creationism.org ... The very first question that is brought up is the question that I?ve dealt with since I ever came to realize what creationists do believe. ?Are you insane?? I haven?t laughed harder for ages, but I admire the creationists for believing that Noah build a refuge for every single species on earth, and that humans outlived the T-rex - even I don?t have that much faith in the Homo Sapiens.

I would be delighted to hear you talk Mr. Zimmer, but unfortunately, I live too far away... But hey, I enjoy your books, so I can?t complain. I wish Darwin was celebrated here in the same degree as in America, - how ironic, we lack both the creationists AND the celebration of the father of genesis.

A good morning to all of you!

Have y'all seen this?:

http://www.ajc.com/blogs/content/shared-blogs/ajc/georgia/entries/2007/…

Apparently, evolutionary theory is a consipiracy predicted by...Kabbalah!! Awesome - I've always wanted to meet Madonna!