Comments on Dembski-Marks's "active information."

Posted 7 October 2007 by

This is a guest appearance of Erik Tellgren. I (Mark Perakh) have not contributed anything to this essay and am posting it as a courtesy to Erik. Here starts Erik’s text: William Dembski has been one of the most influential contributors to the Intelligent Design (ID) movement. Among other things, his work has added the terms specified information, specified complexity, and complex specified information to the basic vocabulary of the ID movement. These terms are all directly related to the logarithms of special types of probabilities, e.g. the probability of a pattern of interest given that it was produced in some way that excludes the foresight and guidance of an intelligent agent. In a recent draft manuscript, Dembski and his coauthor Marks extend the vocabulary with three new terms [1]: endogenous information, exogenous information, and active information. They consider as given a search space and a fixed subset, called a target, that makes up some fraction ps of the search space. An issue of interest to them is how to measure how well a search algorithm [2] exploits the structure of the search problem. Two possible candidates are the probability p that a search algorithm is successful and the ratio p/ps. Readers of Dembski's previous writings will not be surprised to discover that Marks and Dembski prefer to log-transform their probabilities and rename them 'information'. In equations, their definitions are endogenous information = -log2(ps), exogenous information = -log2(p), active information = -log2(ps/p). Continue reading Comments on Active Information at Talk Reason

87 Comments

PvM · 7 October 2007

Thanks Mark, excellent and timely postings on the work by Dembski and Marks.

Nigel D · 7 October 2007

Once again, Dembski seems to have forgotten that the NFL theorem applies only to all possible search spaces, never to only one.

Also, no doubt, Dembski will once again claim that his work has something to do with evolution (the alleged impossibility thereof), ignoring the fact that no targeted search can ever be analogous to the biological process of evolution.

Lurker · 7 October 2007

On reading Marks' paper, a simple question arose for me. Take a simple search algorithm, such as Newton's root-finding method. Now I apply it to a problem with one zero. And then I apply it to a problem with many zeros. By random search, the second problem is easier. Yet according to Marks' 'active information' it would seem that Newton's root-finding method had different amounts of external information input to the first problem than the second. Where did this extra information come from? The programmer?

Corkscrew · 7 October 2007

A couple of weeks back I stumbled across a blog that was discussing application of information theory to evolution in terms of the "surprisal" of a survival or death. It started off with a post by MarkCC and had about three or four more going.

Unfortunately I was using a library computer when I read this, and now can't remember the URL. Google has nothing. Can anyone help?

SteveF · 7 October 2007

Funnily enough, since they both appear on the same day, the Haggstrom paper criticises Tellegren (see footnote on page 5). I don't think this is possible by random chance!

Mark Perakh · 7 October 2007

Re: Comment 130886 by Steve F.

Olle's critical remark is about another post by Tellgren ( see here. It relates to a specific point in Tellgren's referenced essay and is not generally refuting Tellgren's thesis. As to this new essay by Tellgren, Olle's remark is not about it at all. While there may normally be certain divergences of opinions between Erik Tellgren and Olle Haggstrom, both are in general agreement that Dembski/Marks's arguments are baseless.

Art · 7 October 2007

The problem for Dembski et al. is that the quantity of "endogenous information" in biological systems is pretty small.

Do ID proponents explore scenarios whereby "ps" is much greater than "p"? This would seem to be the closest that their ideas can come to biological reality.

Bond, James Bond · 7 October 2007

Funny that the empirical work of Behe in "Edge of Evolution" for the high populations of malaria and HIV both back up Dembski's postulation that the CSI needed to be found for protein/protein binding sights is correct in its assertion!!! Where is Olle's and Haggstrom's empirical validation for their assertion that CSI is easy to find???

secondclass · 7 October 2007

Bond, James Bond,

"Olle's and Haggstrom's" ???

Have you read the papers in question? It's Dembski who says that certain evolutionary outcomes are easy to find. (See Dembski's paper, last paragraph in section 4, where he says that the environment and the laws of physics and chemistry make certain endpoints likely, per Simon Conway Morris.)

Doc Bill · 7 October 2007

Funny that Behe hasn't done any empirical work.

PvM · 7 October 2007

Bond, James Bond: Funny that the empirical work of Behe in "Edge of Evolution" for the high populations of malaria and HIV both back up Dembski's postulation that the CSI needed to be found for protein/protein binding sights is correct in its assertion!!! Where is Olle's and Haggstrom's empirical validation for their assertion that CSI is easy to find???
There is no empirical work, all there is, is a poorly founded estimate based on a sidenote in a paper to suggest a poorly founded thesis. Funny how poorly these ID activists respond to their world falling to pieces when science gets involved. So many expectations from Marks and Dembski and yet, so many problems right from the start.

PvM · 7 October 2007

Of course, CSI as defined by Dembski is incredibly hard to find, since any time science can provide a detailed explanation, CSI disappears. Poof... In other words, CSI, is a meaningless concept.

Remember: CSI stands for Complex Specified Information

Specified is trivial, all we need is biological function
Complex Information is when the -log2P(A) is sufficiently large or the probability that A can be explained by a known regularity/chance path is sufficiently low.

Note that Dembski has failed to show that CSI exists for instance for the bacterial flagella.

In fact, it may be all but impossible to calculate the probabilities involved, making CSI a totally impractical concept.

Don't be fooled by ID's terminology. It's all smoke and mirrors.

Mark Perakh · 7 October 2007

Correction: The URL for Tellgren's post referred to by Olle was misspelt in my earlier comment. Here is the correct URL.

Bond, James Bond · 7 October 2007

Maybe you guys can get your highly touted mathematical illusionists to save the, now thoroughly, trashed population genetics of Haldane, Fisher and Wright. For the main weakness of your hypothesis of evolution at this point in time, is not so much the threat from Dembski's CSI, but it is the fact that the Genome is now absolutely proven to have severe epistasis (to be a complex interwoven network) by the ENCODE project!!!!

http://www.boston.com/news/globe/health_science/articles/2007/09/24/dna_unraveled/?page=1

For you see guys, it is commonly taught in evolutionary biology classes that evolution is absolutely required to have little or no epistasis (no complex interwoven network) for it to have the plasticity it needs, on the genetic level, to accomplish evolutionary novelty seen in life.

http://en.wikipedia.org/wiki/Epistasis

In fact, in order for evolution to avoid being overturned last century by Mendelian genetics,Haldane, Fisher and Wright developed population genetics in which the unit of selection was transfered to the gene instead of the whole organism like it originally was for evolution!!! (pg. 52-53, Sanford: Genetic Entropy) Thus, with this ENCODE revelation, natural selection is now rendered mute and powerless in its ability to select mutations!!!

http://en.wikipedia.org/wiki/Population_genetics

… You see guys Mendelian genetics, contrary to evolution, is empirically verified and thus the genome was required to be considered a multiple independent collection of genes by evolution in which genes could be selected or discarded as natural selection saw fit…
This is absolutely the only way that evolution could have been considered scientifically plausible with the established fact of Mendelian Genetics…

Put simply…IF genes cannot be selected on an individual basis then no new novelty can arise by RM/NS for natural selection cannot select for a completely novel trait..Thus evolution is clearly demonstrated to be scientifically denied the plasticity it needs for novelty!!!

With the shattering revelation of ENCODE,, Evolutionary biology classes have absolutely no basic mechanism left to teach their students for evolution….All Haldane’s, Wright’s and Fisher’s work in population Genetics is pure and utter Garbage…

It really is going to take some mathematical contortion by evolutionists to get out of this jam!!!!

Stanton · 7 October 2007

So, then, James Bond, Plagiarist for Jesus, how does this alleged explanation account for the fact that no one, not even Dembski, himself, has ever used Dembski's explanatory filter to do science?
How does this explanation of yours explain the diversity of birds of paradise seen in Papau New Guinea?

Elf Eye · 7 October 2007

Bond, James Bond

These are your sources!?

http://www.boston.com/news/globe/health_science/ar…
http://en.wikipedia.org/wiki/Epistasis
http://en.wikipedia.org/wiki/Population_genetics

You are lucky that you are not in my freshman research class because you have just failed it. First rule of thumb: If you wish to claim expertise in a subject, read--and cite--primary sources.

PvM · 7 October 2007

Maybe you guys can get your highly touted mathematical illusionists to save the, now thoroughly, trashed population genetics of Haldane, Fisher and Wright. For the main weakness of your hypothesis of evolution at this point in time, is not so much the threat from Dembski’s CSI, but it is the fact that the Genome is now absolutely proven to have severe epistasis (to be a complex interwoven network) by the ENCODE project!!!!

Now that Dembski's CSI has been shown to be without merrit, ID quickly moves to the ENCODE project, which shows an interwoven network. Perhaps Bond has missed the postings in which I addressed how such networks, contrary to 'common sense', are actually quite open to evolution. How many times will Bond repeat his ignorant claims before he admits, like in this instance with CSI, that ID is full of it?

For you see guys, it is commonly taught in evolutionary biology classes that evolution is absolutely required to have little or no epistasis (no complex interwoven network) for it to have the plasticity it needs, on the genetic level, to accomplish evolutionary novelty seen in life.

Could I get some references for this 'common claim'? As far as epistasis is concerned, you may have missed the scientific work on scale free networks. For instance

In a study of simple and complex digital organisms (organisms that could only replicate vs. organisms with computational abilites) Lenski et al. [11] showed that simple organisms in general are more fragile compared to the complex ones.

Remember how in the Avida experiments it was shown that there exists a strong epistasis in these evolved systems.

The results from our experiments with Avida show that for both low and high mutation rates the genetic architecture of Avida creatures tends to a scale-free structure. Although the genome does not form a network in a strict sense, the overlap of genes can be interpreted as interactions between different genes, which in turn can be seen as an interaction network. It is known that scale-free networks can be generated using a simple growth algorithm that relies on growth of the network and preferential attachment. The emergence of a scale-free architecture in the genetic architecture therefore suggests that it is the preferential attachment or gene clustering that is the dominating force behind gene development.

Science is so far ahead of your understanding of these issues. Yet it's good to see you move away from Dembski... Another gap of ignorance has been closed

Stanton · 7 October 2007

How many times will Bond repeat his ignorant claims before he admits, like in this instance with CSI, that ID is full of it?
To paraphrase the lyrics of an old song the singer Dennis Day used to sing, the mountains will crumble to dust, and the seas will dry up before Bond will swallow his pride to admit this. Considering Bond's monstrous ego and conceit, it would be far easier for the mountains to crumble to dust and let the seas dry up than to wait for him to do so.

PvM · 8 October 2007

Well said. Shows you how denial is the first stage towards recovery.

Coin · 8 October 2007

The problem I have with "James Bond", as opposed to other local trolls, is that most of the time I cannot even understand what it is he is trying to express. Parsing his grammar is like trying to pick apart some elaborate code.

With this in mind, I can't help but wonder-- weren't Haldane, Fischer, and Wright working in the 1920s? If the goal is to refute mainstream population genetics, is this really the most appropriate source to be attacking?

Stuart Weinstein · 8 October 2007

"The problem I have with “James Bond”, as opposed to other local trolls, is that most of the time I cannot even understand what it is he is trying to express."

Neither does he. That is the problem.

Nigel D · 8 October 2007

Bond, James Bond [snip] You are lucky that you are not in my freshman research class because you have just failed it.

— Elf Eye
Nicely said, Elf Eye. I suspect that BJB would fail even the most elementary biology class, since (s)he seems to revel in ignorance, and also seems incapable of expressing a coherent idea. Whether this latter represents the absence of coherent ideas or dyslexia is something for which we curently have no empirical data.

The problem I have with “James Bond”, as opposed to other local trolls, is that most of the time I cannot even understand what it is he is trying to express.

— Coin

Neither does he. That is the problem.

— Stuart Weinstein
With respect, I think it is only a part of the problem. BJB appears to enjoy being ignorant. (S)he also apears incapable of rational thought and/or expression thereof. BJB certainly apears to be incapable of understanding biological science to any useful level of detail. The question we should ask ourselves is: does BJB have a genuine learning difficulty, or is (s)he making a deliberate effort to remain ignorant? Meanwhile, back on-topic (more or less), I find it astonishing that Dembski can claim so many special properties of information with a straight face, when his definition of information is simply the inverse log of a probability. A probability that neither he nor anyone else has sufficient data to calculate. Remember also that Dembski's definition of a "design process" would actually encompass both modern evolutionary theory and something as simple as a seive.

Bond, James Bond · 8 October 2007

The results from our experiments with Avida show that for both low and high mutation rates the genetic architecture of Avida creatures tends to a scale-free structure.

Empirical Evidence,We Don't Need NO Stinking Empirical Evidence!!!
Watch closely,,, nothing up the sleeves, behold the magic of evolution right before your eyes on my handy dandy computer program called Avida...

And presto, I hit a few buttons and then whazam evolution made to order all day long... Bet I impressed you simpletons!!!!!

If you guys think this is empirical proof for evolution,,, You guys really need a urinalysis!!!!

WHENEVER you guys get thrown out of science, as is proper in the greater scheme of things, maybe you can get jobs as magicians!!!!

JGB · 8 October 2007

Here's some real biochemistry showing how real evolution happens Bond. I could attempt to reason out why your arguments are horribly wrong or I could just present all the evidence that Behe ever asked for
http://www.cbs.umn.edu/labs/deanlab/PDF%20files/55LunzerMillerFelsheimDean05.pdf

Alternatively if you want to see how fast natural selection acts read some of the following
http://www.msu.edu/~lenski/

E. Tellgren · 8 October 2007

SteveF wrote: Funnily enough, since they both appear on the same day, the Haggstrom paper criticises Tellegren (see footnote on page 5). I don\x{2019}t think this is possible by random chance!

As others pointed out above, Häggström is criticizing an earlier text by me. However, I repeat the cricitized comments in my new text.

In brief, Häggström describes me as "confused" because I claim that optimization is easy in the NFL scenario. As a counter-example, he offers the possibility of concocting a scale for fitness that is absurdly more fine-grained for inviable genomes than viable genomes. E.g. there might be 10^1000 grades in the inviable range for every grade in viable range. To this I reply, firstly, that fitness cannot be measured to such an absurdly high precision so this is a purely hypothetical scale. Secondly, we must remember the context at hand, which includes Dembski's default assumption of uniform probability. If Dembski were to say "uniform probability is only the default assumption when we choose a fitness scale with 10^1000 inviable grades for every viable grade", then I think the debate is lost for him. Thirdly, later in the new article, Häggström himself commits the same sin of confusion that he accuses me of. E.g. in his discussion of black-and-white pictures, he assumes without comment that 'black' and 'white' are equally probable and does not take into account the possibility of, say, having 10^1000 shades of 'black'. If I must take into completely absurd fitness scales, why shouldn't Häggström have to take into account completely absurd colour scales?

The fact that optimization is generally easy in the NFL scenario remains, because the performance is independent of the size of the search space. The only way to make it difficult is to impose some artifical and absurd fitness scale, but then it is misleading to point to the vastness of the search space as the source of the difficulty because it is really isn't the source.

Bond, James Bond · 8 October 2007

JGB: Refer to Edge of Evolution" for solid refutation of long term e coli experiment!!!

The first paragraph of your other reference states the following:

Although all natural IMDHs use
nicotinamide adenine dinucleotide (NAD) as a coenzyme, they can be
engineered to use nicotinamide adenine dinucleotide phosphate (NADP) instead.
Intermediates between these two phenotypic extremes show that each
amino acid contributes additively to enzyme function, with epistatic contributions
confined to fitness. The genotype-phenotype-fitness map shows that
NAD use is a global optimum.

Ok JGB: it states that NAD is the normal enzymne and NAD is the global optimum,,, thus NADP substitution demonstrated Genetic Entropy.

I will gladly cite your paper as proof of Genetic Entropy for organism from optimal condition with the amino acid substitutions!!!

David Stanton · 8 October 2007

BJ Bond wrote:

"Empirical Evidence,We Don’t Need NO Stinking Empirical Evidence!!!"

And there you have it folks, as succinct a summary of ID as you will ever find.

Bond, check out the thread on mammalian molar evolution. It shows how minor genetic changes can cause morphological evolution on a micro or macroevolutionary scale. ID may have no need for empirical evidence, but real science does.

Bond, James Bond · 8 October 2007

Behold PZ myers, the great illusionists, watch as he mystifies audiences with his ability to turn fox teeth into other mammalian teeth !!!! Watch closely, nothing up his sleeves...He points to the fox teeth...the audience goes UUHHH AAAAHHH at his de^ath defying manuever... he points to similarities of fox teeth to other similar mammalian teeth, a women faints in the audience from the suspense, and presto fox teeth can, with a lot of help from the audience's imagination, turn into monkey teeth!!!!
To PZ's dismay a boy in the audience says "Hey!!!,,, wait a minute!,, He didn't actually change anything into anything else, he just said that the fox teeth could change into mammalian teeth and then did the ole switcheroo!!!"
But the audience (a bunch of PT bloggers actually) shouts the boy down, and calls him all sorts of vulgar names, I believe if allowed they would actually beat the boy senseless, for ruining their belief in the magic of the magic show...

Cedric Katesby · 8 October 2007

Bond, James Bond.

Are you taking any medications?

Artfulskeptic · 8 October 2007

Bond, James Bond: Behold PZ myers, the great illusionists, watch as he mystifies audiences with his ability to turn fox teeth into other mammalian teeth !!!! Watch closely, nothing up his sleeves...He points to the fox teeth...the audience goes UUHHH AAAAHHH at his de^ath defying manuever... he points to similarities of fox teeth to other similar mammalian teeth, a women faints in the audience from the suspense, and presto fox teeth can, with a lot of help from the audience's imagination, turn into monkey teeth!!!! To PZ's dismay a boy in the audience says "Hey!!!,,, wait a minute!,, He didn't actually change anything into anything else, he just said that the fox teeth could change into mammalian teeth and then did the ole switcheroo!!!" But the audience (a bunch of PT bloggers actually) shouts the boy down, and calls him all sorts of vulgar names, I believe if allowed they would actually beat the boy senseless, for ruining their belief in the magic of the magic show...
BJ Bond: This my be slightly off topic, but please take a course in English composition. Using proper grammar should be non-controversial, even to you. After all, grammar is an arbitrary standard created by humans. Unlike science, which works whether anyone wants it to or not, English only works if everyone uses the same basic set of rules. Any English teacher will tell you that the overuse of exclamation points is an indication of weak writing, and the use of multiple exclamation points after a simple declarative sentence is just plain incorrect grammar. You also have problems with your use of commas, ellipsis, capitalization, paragraphs, and argumentative structure. In particular, it is hard to understand what reason you have to deny something you personally haven't witnessed and don't understand (evolution), only to replace it with something no one can ever possibly witness or understand (creation). Doesn't that amount to replacing one sort of magic with another?

wamba · 8 October 2007

This troll is so incompetent, he's not even on the right thread.

demallien · 8 October 2007

Cedric Katesby: Bond, James Bond. Are you taking any medications?
Evidently not. Probably should be though....

Bond, James Bond · 8 October 2007

Artful Skeptic!!!!!!!!!

I follow the evidence period.........

For Example!!!!!!!!!!!!

Naturalists always try to establish scientific validity for evolution by pointing to suggestive similarities while ignoring the foundational principle of science (genetic entropy) that contradicts their preconceived philosophical bias. For example, naturalists say that evolution is proven true when we look at the 98.8% similarity between certain segments of the DNA in a Chimpanzee and compare them with the same segments of DNA of a Human. Yet that similarity is not nearly good enough to be considered “conclusive” scientific proof. For starters, preliminary comparisons of the complete genome of chimps and the complete genome of man yield a similarity of only 96%. Dr. Hugh Ross states the similarity may actually be closer to 85% to 90%. Secondarily, at the protein level only 29% of genes code for the exact same amino acid sequences in chimps and humans (Nature, 2005). As well, our DNA is 92% similar to mice as well as 92% similar to zebrafish (Simmons PhD., Billions of Missing Links). So are we 92% mouse or are we 92% zebrafish? Our DNA is 70% similar to a fruit fly; So are we therefore 70% fruit fly? Our DNA is 75% similar to a worm; So are we 75% worm? No, of course not!! This type of reasoning is simple minded in its approach and clearly flawed in establishing a solid scientific foundation on which to draw valid inferences from! Clearly, we must find if the DNA is flexible enough to accommodate any type of mutations happening to it in the first place. This one point of evidence, (The actual flexibility of DNA to any random mutations), must be firmly established, first and foremost, before we can draw any meaningful inferences from the genetic data we gather from organisms!! Fortunately we, through the miracle of science, can now establish this crucial point of DNA flexibility. The primary thing that is crushing to the evolutionary theory is this fact. Of the random mutations that do occur, and have manifested traits in organisms that can be measured, at least 999,999 out of 1,000,000 (99.9999%) of these mutations to the DNA have been found to produce traits in organisms that are harmful and/or to the life-form having the mutation (Gerrish and Lenski, 1998)! Professional evolutionary biologists are hard-pressed to cite even one clear-cut example of evolution through a beneficial mutation to DNA that would violate the principle of genetic entropy. Although evolutionists try to claim the lactase persistence mutation as a lonely example of a beneficial mutation in humans, lactase persistence is actually a loss of a instruction in the genome to turn the lactase enzyme off, so the mutation clearly does not violate genetic entropy. Yet at the same time, the evidence for the detrimental nature of mutations in humans is clearly overwhelming, for doctors have already cited over 3500 mutational disorders (Dr. Gary Parker).

“It is entirely in line with the al nature of naturally occurring mutations that extensive tests have agreed in showing the vast majority of them to be detrimental to the organisms in its job of surviving and reproducing, just as changes ally introduced into any artificial mechanism are predominantly harmful to its useful operation” H.J. Muller (Received a Nobel Prize for his work on mutations to DNA)
“But there is no evidence that DNA mutations can provide the sorts of variation needed for evolution… There is no evidence for beneficial mutations at the level of macroevolution, but there is also no evidence at the level of what is commonly regarded as microevolution.” Jonathan Wells (PhD. Molecular Biology)

Man has over 3 billion base pairs of DNA code. Even if there were just a 1% difference of DNA between monkeys and humans, that would still be 30 million base pairs of DNA difference. It is easily shown, mathematically, for it to be fantastically impossible for evolution to ever occur between monkeys and man, or monkeys and anything else for that matter. Since, it is an established fact that at least 999,999 in 1,000,000 of any mutations to DNA will be harmful and/or , then it is also an established fact that there is at least a 999,99930,000,000 to one chance that the monkey will fail to reach man by evolutionary processes. The monkey will hit a end of harmful/fatal mutations that will kill him or severely mutilate him before him. The poor monkey barely even gets out of the evolutionary starting gate before he is crushed by blind chance. This would still be true even if the entire universe were populated with nothing but monkeys to begin with! This number (999,99930,000,000), is fantastically impossible for any hypothetical beneficial mutation to ever overcome! Worse yet for the naturalists, mathematician William Dembski PhD. has worked out the foundational math that shows the mutation/natural selection scenario to be impossible EVEN IF the harmful/fatal rate for mutation to the DNA were only 50%. The naturalist stamps his feet again and says that symbiotic gene transfer, cross-breeding (yes they, desperately, suggested cross-breeding as a solution), gene duplication and multiplication of chromosomes, alternative splicing etc .. etc .. are the reasons for the changes in DNA between humans and apes. They say these things with utmost confidence without even batting an eye. Incredibly, this is done in spite of solid evidences testifying to the contrary. Indeed, even if a hypothetical beneficial mutation to the DNA ever did occur, it would be of absolutely no use for it would be swallowed in a vast ocean of slightly detrimental mutations that would be far below the culling power of natural selection to remove from a genome!
“The theory of gene duplication in its present form is unable to account for the origin of new genetic information” Ray Bohlin, (PhD. in molecular and cell biology)

“Evolution through random duplications”... While it sounds quite sophisticated and respectable, it does not withstand honest and critical assessment” John C. Sanford (PhD Genetics; inventor of the biolistic “gene gun” process! Holds over 25 patents!)

The human genome, according to Bill Gates the founder of Microsoft, far, far surpasses in complexity any computer program ever written by man. The data compression (multiple meanings) of some stretches of human DNA is estimated to be up to 12 codes thick (Trifonov, 1989)! No line of computer code ever written by man approaches that level of data compression (poly-functional complexity). Further evidence for the inherent complexity of the DNA is found in a another study. In June 2007, a international team of scientists, named ENCODE, published a study that indicates the genome contains very little unused sequences and, in fact, is a complex, interwoven network. This “complex interwoven network” throughout the entire DNA code makes the human genome severely poly-constrained to random mutations (Sanford; Genetic Entropy, 2005; page 141). This means the DNA code is now much more severely limited in its chance of ever having a hypothetical beneficial mutation since almost the entire DNA code is now proven to be intimately connected to many other parts of the DNA code. Thus even though a random mutation to DNA may be able to change one part of an organism for the better, it is now proven much more likely to harm many other parts of the organism that depend on that one particular part being as it originally was. Since evolution was forced, by the established proof of Mendelian genetics, to no longer view the whole organism as to what natural selection works upon, but to view the whole organism as a multiple independent collection of genes that can be selected or discarded as natural selection sees fit, this “complex interwoven network” finding is extremely bad news, if not absolutely crushing, for the population genetics scenario of evolution developed by Haldane, Fisher and Wright (page 52 and 53: Genetic Entropy: Sanford 2005)!

http://www.boston.com/news/globe/health_science/articles/2007/09/24/dna_unraveled/?page=1

Naturalists truly believe you can get such staggering complexity of information in the DNA from some process based on blind chance. They cannot seem to fathom that any variation to a basic component in a species is going to require precise modifications to the entire range of interconnected components related to that basic component. NO natural law based on blind chance, would have the wisdom to implement the multitude of precise modifications on the molecular level in order to effect a positive change from one species to another. Only a “vastly superior intelligence” would have the wisdom to know exactly which amino acids in which proteins, which letters in the DNA code and exactly which repositioning of the 25 million nucleosomes (DNA spools) etc .. etc .. would need to be precisely modified to effect a positive change in a species. For men to imagine blind chance has the inherently vast wisdom to create such stunning interrelated complexity is even more foolish than some pagan culture worshipping a stone statue as their god and creator. Even if evolution of man were true, then only God could have made man through evolution. For only He would have the vast wisdom to master the complexity that would be required to accomplish such a thing. Anyone who fails to see this fails to appreciate the truly astonishing interwoven complexity of life at the molecular level. Even though God could have created us through “directed evolution”, the fossil record (Lucy fossil proven not ancestral in 2007) and other recent “hard” evidence (Neanderthal mtDNA sequenced and proven “out of human range”) indicates God chose to create man as a completely unique and distinct species. But, alas, our naturalistic friend is as blind and deaf as the blind chance he relies on to produce such changes and cannot bring himself to face this truth. Most naturalists I’ve met, by and large, are undaunted when faced with such overwhelming evidence for Divine Intelligence and are convinced they have conclusive proof for naturalistic evolution somewhere. They will tell us exactly what it is when they find it. The trouble with this line of thinking for naturalists is they will always take small pieces of suggestive evidence and focus on them, to the exclusion of the overriding vast body of conclusive evidence that has already been established. They fail to realize that they are viewing the evidence from the wrong overall perspective to begin with. After listening to their point of view describing (with really big words) some imagined evolutionary pathway on the molecular level, sometimes I think they might just be right. Then when I examine their evidence in detail and find it wanting, I realize they are just good story tellers with small pieces of “suggestive” evidence ignoring the overwhelming weight of “hard” evidence that doesn’t fit their naturalistic worldview. Instead of them thinking,” WOW look how God accomplishes life on the molecular level,” they think” WOW look what , dumb and blind chance accomplished on the molecular level.” Naturalists have an all too human tendency to over-emphasize and sometimes even distort the small pieces of suggestive evidence that are taken out of context from the overwhelming body of “conclusive” evidence. This is done just to support their own preconceived philosophical bias of naturalism. This is clearly the practice of very bad science, since they have already decided what the evidence must say prior to their investigation.
I could help them find the conclusive proof for evolution they are so desperately looking for if they would just listen to me. For I know exactly where this conclusive proof for evolution is; it is right there in their own imagination. What really amazes me is that most naturalists are people trained in exacting standards of science. Yet, they are accepting such piddling and weak suggestive evidence in the face of such overwhelming conclusive evidence to begin with. This blatant deception; , dumb, blind chance has the inherent wisdom to produce staggering complexity, is surprisingly powerful in its ability to deceive! That it should ensnare so many supposedly rational men and women is remarkable. Then, again, I have also been easily misled by blatant deception many times in my life, so, maybe it is not that astonishing after all. Maybe it is just a painful and all too human weakness we all share that allows us to be so easily deceived.

PvM · 8 October 2007

Children, look at Bond, this is a mind on ID. You have been warned, it's not worth it.

ben · 8 October 2007

The odds against a given creationist being able to form a coherent paragraph are apparently 999,99930,000,000 to one.

raven · 8 October 2007

Bond babbling away: Naturalists always try to establish scientific validity for evolution by pointing to suggestive similarities while ignoring the foundational principle of science (genetic entropy)
Genetic entropy doesn't exist. That is as far as I got, first sentence. My life span is limited to another 40-50 years and too valuable to waste time on this nonsense. I want those 10 seconds back!!! Bond is either mentally ill or 10 years old and bored with his home school course.

David vun Kannon · 8 October 2007

BJB must be an alias for bornagain77 at UCD, because I have never seen a person more in love with throwing Sanford's Genetic Entropy at any subject, coupled with !!! to end a sentence. Genetic Entropy seems to have achieved the status of a sacred text with this person.

Shirley Knott · 8 October 2007

PvM, I was with you right up to the point where you accused Bond of having a mind.
So far, there is no evidence of this whatsoever.
Otherwise, spot on.

Who is Bond really? Denyse? WAD? ScaveDot?
Nah, almost incoherent enough to be Charlie Wagner, Javison, or VMartin.
Could it be? Inquiring minds want to know, while Bond and its ilk rest in their nescience.

no hugs for thugs,
Shirley Knott

Bond, James Bond · 8 October 2007

You guy's are amazing!!!

You are astounded by PZ's magical illusions with fox teeth, and show no skepticism towards it, Then when ENCODE comes along with hard scientific proof of astounding complexity in the Genome...you yawn!!! as if its no big deal. For crying out loud...WAKE UP PEOPLE!!!!

SteveF · 8 October 2007

Eric

As others pointed out above, Häggström is criticizing an earlier text by me. However, I repeat the cricitized comments in my new text.

I was aware that he was critiquing an earlier effort, I just thought it was a funny coincidence. Probably just me! Anyway, thanks for your response.

PvM · 8 October 2007

Bond, James Bond: You guy's are amazing!!! You are astounded by PZ's magical illusions with fox teeth, and show no skepticism towards it, Then when ENCODE comes along with hard scientific proof of astounding complexity in the Genome...you yawn!!! as if its no big deal. For crying out loud...WAKE UP PEOPLE!!!!
Encode comes along which shows how the genetic code contains fascinating sources of information, and somehow this should be a problem for evolutionary theory? Seems that Bond is confusing complexity with 'design' and 'design' with 'intelligent design' and 'intelligent design' with 'intelligent designer'. Yes, the data from the ENCODE project are fascinating and the result of real scientists doing hard word. One of the interesting side effects is the concept of a gene which used to be relatively simple and straightforward and is now more complex due to the many levels of interactions. However, ID activists have taken the data to suggest that because of the many levels of codes and interactions, evolution becomes impossible. In fact, some have gone as far as misrepresenting evolution as requiring independent genes. Nothing of course is farther from the truth. And as I have shown, theoretical and empirical research has shown that such intricate networks which share a scale free structure, can evolve quite easily from simple processes of for instance gene duplication (observed) and preferential attachment. So while ID activists are 'arguing' that science cannot explain the 'complexity' found in the ENCODE pilot, real scientists are slowly unraveling the how. That's the differences my friends between science and ID, the latter remains totally empty handed and the few 'papers' it produces are quickly disassembled on websites.

PvM · 8 October 2007

Bond shows the level of ignorance amongst ID proponents when he argues

Man has over 3 billion base pairs of DNA code. Even if there were just a 1% difference of DNA between monkeys and humans, that would still be 30 million base pairs of DNA difference. It is easily shown, mathematically, for it to be fantastically impossible for evolution to ever occur between monkeys and man, or monkeys and anything else for that matter. Since, it is an established fact that at least 999,999 in 1,000,000 of any mutations to DNA will be harmful and/or , then it is also an established fact that there is at least a 999,99930,000,000 to one chance that the monkey will fail to reach man by evolutionary processes.

Most mutations in DNA are in fact neutral... Not surprisingly these simplistic arguments have since long been rejected by science. However, ID, unable to accept science, has to make up statistics which place evolution in its worst perspective. IF ID could take the best case for evolution and showed that it was still unlikely then perhaps it had a case against evolutionary pathways as we know them, being able to explain the system. But instead ID takes some small numbers, multiplies them and then 'argues' see how unlikely pure chance evolution is... What a farce. And this is what ID leads to, a total abandonment of reason and logic. A mind on ID is a terrible ignorance.

PvM · 8 October 2007

Notice how ID is reduced to misrepresenting science and misleading calculations.

Why would a bornagain do such things?

Bond, James Bond: bornagain77 · 8 October 2007

PvM,
AVIDA does not overcome many obstacles for evolution without "manipulating" many parameters in favor of evolution!!! For instance one obstacle that had to be "manipulated" through in the early going of AVIDA, was the fact that the most fit life forms in the program were "mutational powerhouses" with small genomes that did not allow larger genomes with slower mutational rates to evolve!!!, This was a major problem, until, of course, the programmers "doctored" the parameters to allow larger genomes to form!!! And of course the whole computer program is removed from real life,,programed by men,,and thus ripe for distortion from reality!!!

You are quite wrong in your assertion that most all mutations are neutral,, as vividly illustrated by Dr. Sanford in his book Genetic Entropy,,,most mutations are in fact slightly detrimental and thus BELOW THE CULLING POWER OF NATURAL SELECTION TO REMOVE THEM FROM THE GENOME BEFORE THE SPREAD THROUGHOUT THE POPULATION!!!

It is an absolutely necessary trick of semantics to reclassify the vast majority of mutations as neutral, so as to avoid the obvious pitfall for Darwinism!!

Tricks on words cannot overcome this established and crushing fact of science for evolution!!!

You accuse IDers of ignoring facts of science but it is obvious that Evolutionists are the ones who ignore and twist facts that are inconvenient for them.

PvM · 8 October 2007

Note how Born Again James Bond quotes from Lenski and Gerrish, 1998 to support his mutation probabilities for humans.

Of the random mutations that do occur, and have manifested traits in organisms that can be measured, at least 999,999 out of 1,000,000 (99.9999%) of these mutations to the DNA have been found to produce traits in organisms that are harmful and/or to the life-form having the mutation (Gerrish and Lenski, 1998)!

— Born Again
Gerrish PJ, Lenski RE. "The fate of competing beneficial mutations in an asexual population"Genetica. 1998;102-103(1-6):127-44.

In sexual populations, beneficial mutations that occur in different lineages may be recombined into a single lineage. In asexual populations, however, clones that carry such alternative beneficial mutations compete with one another and, thereby, interfere with the expected progression of a given mutation to fixation. From theoretical exploration of such 'clonal interference', we have derived (1) a fixation probability for beneficial mutations, (2) an expected substitution rate, (3) an expected coefficient of selection for realized substitutions, (4) an expected rate of fitness increase, (5) the probability that a beneficial mutation transiently achieves polymorphic frequency (> or = 1%), and (6) the probability that a beneficial mutation transiently achieves majority status. Based on (2) and (3), we were able to estimate the beneficial mutation rate and the distribution of mutational effects from changes in mean fitness in an evolving E. coli population.

I hope that Bornagain understands the differences between sexual and asexual organisms. And while Born Again is at it, could he show what Gerrish and Lenski really did? This my friends is what ID does to your mind...

PvM · 8 October 2007

But it's good to hear that BornAgain is abandoning CSI and other Dembski nonsense, and is now returning to the age old probability abuses so typical of creationists. Old habits are hard to break it seems.

Quote mining, misleading calculations and that's the 'best' ID has to offer my friends.

Stanton · 8 October 2007

Anyone else notice how James Bond still not explained how his incoherent copying and pasting why Dembski has not done any scientific research to begin with?

PvM · 8 October 2007

Good observation Stanton. Bond is attempting to distract with cut and paste and other common ID techniques when confronted with data that does not match their faith.
It's almost like an evolved trait...

Glen Davidson · 8 October 2007

Of course this is it again, "Bond" is amazed that we'd follow "suggestive similarities" instead of some faked "principle", genetic entropy. When, of course, this is exactly what science does, it makes inferences from suggestive similarities, patterns, and repetitions, and only comes up with "principles" if those principles agree with the "suggestive similarities".

Unsurprisingly, "Bond" and the rest of them turn science upside down, coming up with "authoritative reasons" to totally ignore the evidence. "Bond" has had this all explained to him repeatedly, but he's very stupid and very prejudiced, so he never learns a scintilla about science and thus he continually tries to void all scientific practice via his a priori stupidity.

The crux of the matter is that idiot "Bond" cannot explain anything in biology using "genetic entropy," or with his belief in magic. He doesn't want to explain anything better, as a real alternative scientific theory would, or even to explain anything at all. He just hates the explanation that actual science has produced.

Beyond that I can't think of much to say. "Bond" is only driven by a pathological hatred of science's results, and will do whatever it takes to discredit science. Fortunately, he's not very good at that, either.

Glen D
http://tinyurl.com/2kxyc7

raven · 8 October 2007

Beneficial mutations are neither rare nor trivial. A recent paper in Science found a rate of 1/100,000 beneficial mutations per genome per generation in an E. coli model system. Mutations beneficial to pests and pathogens are a continuous, well known, and major problem in medicine and agriculture.
Science. 2007 Aug 10;317(5839):813-5. Links Adaptive mutations in bacteria: high rate and small effects.Perfeito L, Fernandes L, Mota C, Gordo I. Instituto Gulbenkian de Cincia, Rua da Quinta Grande, number 6, 2780-156 Oeiras, Portugal. Evolution by natural selection is driven by the continuous generation of adaptive mutations. We measured the genomic mutation rate that generates beneficial mutations and their effects on fitness in Escherichia coli under conditions in which the effect of competition between lineages carrying different beneficial mutations is minimized. We found a rate on the order of 10(-5) per genome per generation, which is 1000 times as high as previous estimates, and a mean selective advantage of 1%. Such a high rate of adaptive evolution has implications for the evolution of antibiotic resistance and pathogenicity.

Tom Ames · 8 October 2007

Bond, James Bond: For you see guys, it is commonly taught in evolutionary biology classes that evolution is absolutely required to have little or no epistasis (no complex interwoven network) for it to have the plasticity it needs, on the genetic level, to accomplish evolutionary novelty seen in life.
Oh really? How many evolutionary biology classes have you taken?

Stanton · 8 October 2007

Tom, my guess is that Bond hasn't even set foot into an elementary school science class.

Bond, James Bond: bornagain77 · 8 October 2007

Raven:
Well let's take a close look at Bacteria,,, Do changes in Bacteria prove evolution?,,The short answer is,,, NO!!!!!

I would like to point out that scientists have never changed any one type of bacteria into any another type of bacteria, despite years of exhaustive experimentation trying to change any bacteria type into any other bacteria type. In fact, it is commonly known that the further scientists deviate any particular bacteria type from its original state, the more unfit for survival the manipulated population will quickly become. As esteemed French scientist Pierre P. Grasse has stated “What is the use of their unceasing mutations, if they do not change? In sum, the mutations of bacteria and viruses are merely hereditary fluctuations around a median position; a swing to the right, a swing to the left, but no final evolutionary effect.” Needless to say, this limit to the variability of bacteria is extremely bad news for the naturalists.

As well what is the treatment for "super-evolved-bacteria" that are resistant to multiple antibiotics??

"When I was finally discharged from hospital, I still had a strain of supergerm colonizing my body. Nothing had been able to get rid of it, after months in hospital. However, I was told that all I had to do on going home was to ‘get outdoors a lot, occasionally even roll in the dirt, and wait.’ In less than two weeks of this advice, the supergerms were gone. Why? The reason is that supergerms are actually defective in other ways, as explained. Therefore, when they are forced to compete with the ordinary bacteria which normally thrive on our skin, they do not have a chance. They thrive in hospital because all the antibiotics and antiseptics being used there keep wiping out the ordinary bacteria which would normally outcompete, wipe out and otherwise keep in check these ‘superwimps’."

Or how about the first bacteria on earth?? Can we find purpose for them? The short answer ...YES!!!

From 3.8 to .6 billion years ago photosynthetic bacteria, and to a lesser degree sulfate-reducing bacteria, ted the geologic and fossil record (that’s over 80% of the entire time life has existed on earth). The geologic and fossil record also reveals that during this time a large portion of these very first bacterial life-forms lived in complex symbiotic (mutually beneficial) colonies called Stromatolites. Stromatolites are rock like structures that the photo-synthetic bacteria built up over many years (much like coral reefs are slowly built up over many years by the tiny creatures called corals). Although Stromatolites are not nearly as widespread as they once were, they are still around today in a few sparse places like Shark’s Bay Australia. Contrary to what naturalistic thought would expect, these very first photosynthetic bacteria scientists find in the geologic and fossil record are shown to have been preparing the earth for more advanced life to appear from the very start of their existence by reducing the greenhouse gases of earth’s early atmosphere and producing the necessary oxygen for higher life-forms to exist. Photosynthetic bacteria slowly built the oxygen up in the earth’s atmosphere by removing the carbon-dioxide (and other greenhouse gases) from the atmosphere; separated the carbon from the oxygen; then released the oxygen back into the atmosphere (and into the earth’s ocean & crust) while they retained the carbon. Interestingly, the gradual removal of greenhouse gases corresponds exactly to the gradual 15% increase of light and heat coming from the sun during that time (Ross; PhD. Astrophysics; Creation as Science 2006). This “lucky” correspondence of the slow increase of heat from the sun with the same perfectly timed slow removal of greenhouse gases from the earth’s atmosphere was absolutely necessary for the bacteria to continue to live to do their work of preparing the earth for more advanced life to appear. Bacteria obviously depended on the temperature of the earth to remain relatively stable during the billions of years they prepared the earth for higher life forms to appear. More interesting still, the byproducts of greenhouse gas removal by these early bacteria are limestone, marble, gypsum, phosphates, sand, and to a lesser extent, coal, oil and natural gas (note; though some coal, oil and natural gas are from this early era of bacterial life, most coal, oil and natural gas deposits originated on earth after the Cambrian explosion of higher life forms some 540 million years ago). These natural resources produced by these early photosynthetic bacteria are very useful to modern civilizations. Interestingly, while the photo-synthetic bacteria were reducing greenhouse gases and producing natural resources that would be of benefit to modern man, the sulfate-reducing bacteria were also producing their own natural resources that would be very useful to modern man. Sulfate-reducing bacteria helped prepare the earth for advanced life by “detoxifying” the primeval earth and oceans of “poisonous” levels of heavy metals while depositing them as relatively inert metal ore deposits (iron, zinc, magnesium, lead etc.. etc..). To this day, sulfate-reducing bacteria maintain an essential minimal level of these metals in the ecosystem that are high enough so as to be available to the biological systems of the higher life forms that need them, yet low enough so as not to be poisonous to those very same higher life forms. Needless to say, the metal ores deposited by these sulfate-reducing bacteria in the early history of the earth’s geologic record are indispensable to man’s rise above the stone age to modern civilization. Yet even more evidence has been found tying other early types of bacterial life to the anthropic hypothesis. Many different types of bacteria in earths early history lived in complex symbiotic (mutually beneficial) relationships in what are called cryptogamic colonies on the earths primeval continents. These colonies “dramatically” transformed the “primeval land” into “nutrient filled soils” that were receptive for future advanced vegetation to appear. Naturalism has no answers for why all these different bacterial types and colonies found in the geologic and fossil record would start working in precise concert with each other preparing the earth for future life to appear. -// Since oxygen readily reacts and bonds with almost all of the solid elements making up the earth itself, it took photosynthetic bacteria over 3 billion years before the earth’s crust and mantle was saturated with enough oxygen to allow an excess of oxygen to be built up in the atmosphere. Once this was accomplished, higher life forms could finally be introduced on earth. Moreover, scientists find the rise in oxygen percentages in the geologic record to correspond exactly to the sudden appearance of large animals in the fossil record that depended on those particular percentages of oxygen. The geologic record shows a 10% oxygen level at the time of the Cambrian explosion of higher life-forms in the fossil record some 540 million years ago. The geologic record also shows a strange and very quick rise from the 17% oxygen level, of 50 million years ago, to a 23% oxygen level 40 million years ago (Falkowski 2005)). This strange rise in oxygen levels corresponds exactly to the appearance of large mammals in the fossil record who depend on high oxygen levels. Interestingly, for the last 10 million years the oxygen percentage has been holding steady around 21%. 21% happens to be the exact percentage that is of maximum biological utility for humans to exist. If the oxygen level were only a few percentage lower, large mammals would become severely hampered in their ability to metabolize energy; if only three to four percentage higher, there would be uncontrollable outbreaks of fire across the land. Because of this basic chemical requirement of photosynthetic bacterial life establishing and helping maintain the proper oxygen levels for higher life forms on any earth-like planet, this gives us further reason to believe the earth is extremely unique in its ability to support intelligent life in this universe. All these preliminary studies of early life on earth fall right in line with the anthropic hypothesis and have no explanation from any naturalistic theory based on blind chance as to why the very first bacterial life found in the fossil record would suddenly, from the very start of their appearance on earth, start working in precise harmony with each other to prepare the earth for future life to appear. Nor can naturalism explain why, once the bacteria had helped prepare the earth for higher life forms, they continue to work in precise harmony with each other to help maintain the proper balanced conditions that are of primary benefit for the complex life that is above them.

Glen Davidson · 8 October 2007

Are paragraphs just an atheist conspiracy, too, "Bond"?

Glen D
http://tinyurl.com/2kxyc7

Venus Mousetrap · 8 October 2007

Bornagain: and the puddle outside my house exactly fits the water in it. What are the chances!!!!!!?1

Seriously, you are colossally, weapons grade stupid. As has been pointed out, you can make your stupidity a little more presentable by applying line breaks. They're not atheistic, even Dembski uses them. (In fact, I'm pretty sure the Bible has them too.)

Aren't you even remotely curious why, if God made these bacteria to make the world habitable for 'higher' life, it took them three billion years?

Gerard Harbison · 8 October 2007

For you see guys, it is commonly taught in evolutionary biology classes that evolution is absolutely required to have little or no epistasis (no complex interwoven network) for it to have the plasticity it needs, on the genetic level, to accomplish evolutionary novelty seen in life.
Whenever a creationist quotes me some fundamental premise of evolution, it turns out I always missed class that day. Someone remind me again why fitness cannot be a complex, non-linear function of the genetic sequence?

PvM · 8 October 2007

Bornagain continues his ignorance by quote mining and making more foolish statements, undermining not just science but also Christian faith.

Poor St Augustine

Bond, James Bond · 8 October 2007

Venus Mousetrap said:
Aren’t you even remotely curious why, if God made these bacteria to make the world habitable for ‘higher’ life, it took them three billion years?

Yes, of course I am!! and I find comfort in Einstein's special theory of relativity, which shows time, as we understand it, coming to a complete stop at the speed of light...which coincidentally conforms to the ancient Theistic assertion that Almighty God exist in a timeless eternity!!!, So now I have to ask you a question "Are you not remotely curious as to why naturalism/evolution has no answers for why the first life on earth would work in concert to produce a habitable earth that is of primary benefit for the complex life that is above them?"

Just Bob · 8 October 2007

Bond: This is a high school English teacher speaking. Pay attention.

Never, ever, use more than ONE ending punctuation mark. No multiple !!!!!!!!!, ???????, or abominations before the Lord, such as !!??.

They don't make anyone pay any more attention; they don't show that you're any more excited or angry or curious. They're just irritating.

If you want anyone to take your message seriously, try not to write like a 12-year-old in her diary.

PvM · 8 October 2007

Since science does not deal in proof, Bond's suggestion that bacteria do not prove evolution is just plain silly.

However, evolution does explain the diversity in bacteria by using observed mechanisms (horizontal and lateral gene transfer) as well as processes such as selection or random drift. Not surprisingly, bacteria form nicely nested hierarchies, just as evolution would predict.

Of course, bacteria still remain bacteria when they evolve, and thus by Bond's logic, they do not evolve.

Since Bond is unable to discuss these details he resorts to text bombing the threads.

A classical instance of denial, the first step towards recovery.

PvM · 8 October 2007

Of course, Bond's ignorance also requires him to ignore the contradicting evidence

5.9.2 Morphological Changes in Bacteria Shikano, et al. (1990) reported that an unidentified bacterium underwent a major morphological change when grown in the presence of a ciliate predator. This bacterium's normal morphology is a short (1.5 um) rod. After 8 - 10 weeks of growing with the predator it assumed the form of long (20 um) cells. These cells have no cross walls. Filaments of this type have also been produced under circumstances similar to Boraas' induction of multicellularity in Chlorella. Microscopic examination of these filaments is described in Gillott et al. (1993). Multicellularity has also been produced in unicellular bacterial by predation (Nakajima and Kurihara 1994). In this study, growth in the presence of protozoal grazers resulted in the production of chains of bacterial cells.

Source: Observed Instances of Speciation by Boxhorn Shikano, S., L. S. Luckinbill and Y. Kurihara. 1990. Changes of traits in a bacterial population associated with protozoal predation. Microbial Ecology. 20:75-84.

In an attempt to understand the significance of predation in the evolution of prey species, the ecological and morphological characteristics of bacterial species under predation by a ciliated protozoa,Cyclidium sp., were investigated. Serial transfer at 7 day intervals was applied to the bacterial populations in the presence or absence of Cyclidium. Although cells of the parental bacterial strain are typically short rods up to 1.5 μm long, cells of much greater length, up to 20 μm long (type L) were found in populations exposed to predation from Cyclidium. However, the wildtype, shorter length bacteria persisted even after the appearance of type L. Type L was not observed in the singlr bacterial culture throughout the serial transfers. Type L appeared to improve the ability to escape predation by elongating cell size, but growth rate and saturation density were decreased.

PvM · 8 October 2007

Btw the various cut and pastes were plagiarized from

Superbugs at AIG others are from UcD where Bornagain77 presents his 'arguments'

Ignorance begets ignorance it seems

PvM · 8 October 2007

Yes, of course I am!! and I find comfort in Einstein’s special theory of relativity, which shows time, as we understand it, coming to a complete stop at the speed of light…which coincidentally conforms to the ancient Theistic assertion that Almighty God exist in a timeless eternity!!!,

Still ignorant about science I notice?

Stanton · 8 October 2007

Anyone else notice that Jesus' self-proclaimed plagiarist cleverly failed to broach the topic of the appearance of the enzyme in two strains of Flavobacterium, and one strain of Pseudomonas aerugenosa in his copy and pasted rant about the non-existance of evolution in bacteria?

PvM · 8 October 2007

Stanton: Anyone else notice that Jesus' self-proclaimed plagiarist cleverly failed to broach the topic of the appearance of the enzyme in two strains of Flavobacterium, and one strain of Pseudomonas aerugenosa in his copy and pasted rant about the non-existance of evolution in bacteria?
ID creationists seldomly can deal with facts, especially when the usual creationists websites don't spoon feed the 'answer'.

Stanton · 8 October 2007

ID creationists seldomly can deal with facts, especially when the usual creationists websites don’t spoon feed the ‘answer’.
I keep forgetting that facts are to Creationists what vancomycin is to penicillin-resistant Staphylococcus

Dale Husband · 8 October 2007

People like Bond, James Bond are good reasons I don't let such idiots into my Evolution Education group.
http://www.care2.com/c2c/group/evolution_education

Bond, James Bond · 8 October 2007

Stanton asserts evolution is proven by:

The repeated independent evolution of nylonase in two different strains of Flavobacterium and one strain of Pseudomonas.

Yet this is not as clear cut proof as he would like:

http://www.answersingenesis.org/tj/v17/i3/bacteria.asp

of special note:
It seems clear that plasmids are designed features of bacteria that enable adaptation to new food sources or the degradation of toxins. The details of just how they do this remains to be elucidated. The results so far clearly suggest that these adaptations did not come about by chance mutations, but by some designed mechanism. This mechanism might be analogous to the way that vertebrates rapidly generate novel effective antibodies with hypermutation in B-cell maturation, which does not lend credibility to the grand scheme of neo-Darwinian evolution.

Thus the Genome itself remains the same...the enzyme is generated in a sort time defying tremendous mathematical odds, thus indicates a "front loaded" instruction to manufacture the enzyme.

Naturalists claim stunning proof for evolution because bacteria can quickly adapt to detoxify new man-made materials, such as nylon and polystyrene. Yet once again, when carefully looked at on the molecular level, the bacteria still have not demonstrated a gain in genetic (genome) information. And of course in an environment without nylon the "adapted" bacteria are quickly "out competed", thus are not as fit for survival on earth as the parent bacteria!!!!! Indeed, it is not nearly as novel as they think it is, for the bacteria are still, only, complacently detoxifying the earth of toxins as they have always been doing for billions of years. Even though naturalists claim this is something brand new, that should be considered stunning proof for evolution, I’m not nearly as impressed, with their stunning proof, as they think I should be!

David Stanton · 8 October 2007

BJ Bond,

Please define the term epistasis. Please state exactly why you think this is a problem for modern evolutionary theory. Please cite a reference where any real scientist has made this claim (creationists want-to-bes do not count).

By the way, please also explain the results of all of the models that account for epistasis in population genetics. You have read all of these references haven't you? No? Well then why are you trying to convince professional biologists that you know better than they do? If ignorance really is bliss, you should be very happy.

I see that you have not read the thread on mammalian molar evolution yet. The reference in that thread shows that very simple genetic changes can affect more than one phenotypic trait. Far from being a problem, this explains the correlations we see between various phenotypes for various traits. Contrary to your claims, epistasis is not only no impediment to evolution, but complex interactions in development can provide very powerful mechanisms for making coordinated morphological changes. Oh well, better luck with your next cut and paste argument.

Just Bob · 8 October 2007

BJB: You're getting better. I'd give the last one a D-. You refrained for the most part, but just couldn't help dropping in a !!!!!. But if you keep it up, I'm sure you can overcome that bad habit.

Next lesson: Eliminate ALL exclamation points. You overuse them egregiously, which devalues them, so you end up quadrupling them, when a simple period would have been better all along.

Now let's work on ellipses (...). The only time you should use them is when you're acknowledging a deletion from a quote (which, by the way, should never be done if it changes the meaning or sense of the quote). Don't use them for "dramatic pauses," like [Thus the Genome itself remains the same…the enzyme...].

Bond, James Bond · 8 October 2007

Stanton,, Your nylon bacteria bit the dust??? Shame!!!!

My reference for epistasis is page 52 and 53 of the book "Genetic Entropy" by Dr. J.C. Sanford, (PhD Genetics; inventor of the biolistic “gene gun” process! He holds over 25 patents for inventions relating to genetics! If you ate today you have probably eaten some food touched by his work in genetics!!!!)

He just may know a thing or two about genetics!

So are you trying to say that evolution has absolutely no problem with the fact that the genome is now proven to be a "complex interwoven network"????

Are you obfuscating the fact that Haldane's, Fisher's, and Wright's work in population genetics is now utterly meaningless?

If you can contort your way out of this, It just goes to show that evolution can explain anything! And can be falsified by absolutely nothing!
Sir, A theory that can explain anything and be falsified by nothing, is not a theory of science but an article of faith that belongs with the easter bunny and the flying spaghetti monster!

Just Bob · 8 October 2007

Now if we could just get you to learn some actual biology, instead of just parroting sciency-sounding stuff that you don't really understand. But it backs up your prejudices, so you use it to try to impress someone. No one here is impressed.

Perhaps it's yourself you're impressing.

Just Bob · 8 October 2007

I give up. He's back to !!!! and ????.

He can't learn simple punctuation rules, and he sure as hell doesn't know diddly about biology. How about if everyone just ignores him?

Maybe, for innocent lurkers, someone could write up a boiler-plate statement to post after every one of his blathers. Something like "We ignore this guy because he just copies and pastes crap that he doesn't understand, he doesn't respond to questions, and he refuses to learn."

fnxtr · 8 October 2007

bondagain:
Are you obfuscating the fact that Haldane’s, Fisher’s, and Wright’s work in population genetics is now utterly meaningless?
Even if this were true, isn't it kind of like disparaging the ether theory? They were early investigators, doing real science, with the real information, and the real tools available at the time. They weren't engaged in wishful thinking based on their bronze-age superstition.

Bill Gascoyne · 8 October 2007

I follow the evidence period... ... ...

— BJB
BJB uses evidence as a drunk uses a lamppost, for support rather than illumination.

Cedric Katesby · 8 October 2007

BJB.

Do you mind if I just call you 'BJ'?

Are you home-schooled?
Are you taking medication?

Oh, and please stop cutting and pasting.

RBH · 8 October 2007

I wish derailments of PT threads could be as easily moderated as they are on Infidels. I'm interested in the topic of the OP, but it has unfortunately disappeared, sunk in a welter of bullshit from a pure troll.

RBH

Stanton · 8 October 2007

Bond, that bullcrap you copy and pasted from Answers In Genesis does not explain why, if there was a precursor to all the genes ever found in bacteria, including nylonase, the nylonase gene enzymes in all three strains, as well as the nylonase genes that have appeared in newer strains ever since, are all different.
Furthermore, if you actually had an elementary school level grasp of evolutionary biology, you would realize that beneficial genes are only beneficial when their host is in an environment conductive to those new genes' end products. This is in fact the reason why sickle cell anemia persists in Subsaharan Africa, why thalassemia persists in the Mediterranean, and why the ice fish were able to colonize the coastal waters of Antarctica when it froze over during the Miocene. It is also the reason why microbiologists and pharmacologists recommend ceasing the use of a popular antibiotic when a new resistant strain of pathogen appears, in the hopes that, without the popular antibiotic to kill off competing, susceptible strains, the resistant train will hopefully be out-competed by other strains that are not metabolically burdened with metabolically expensive anti-antibiotic countermeasures.
But, given as how you used Answers In Genesis, a site that insists that Steve Irwin is burning in Hell as we type because he made the unforgivable sin of not believing in God in the exact same way as Ken Ham, I'm not at all surprised that no one here at this blog was swayed by your reply.

Furthermore, the only reason why I did not immediately respond to your moronic post was because, at the time, I was in class. Unlike you, I happen to be trying to enrich my education.
Let me tell you something: no one here dislikes and or hates you because of your relationship with God. Most of us don't care, in fact. The reason why we all dislike and or hate you is because you are a moronic imbecile so appallingly arrogant, that you actually masturbate to your own stupidity, and then you have the unmitigated gall to claim that it's divine inspiration.
What would Jesus say to someone who spouts lies like "Hitler was inspired by Darwinism," or "Evolution is false because beneficial mutations hinder their hosts when in unfavorable environment," and thinks he defeats his opponents with incoherent nonsense? Let me answer my own question: Our Lord, Jesus, would knock your table down, and castigate you so furiously that the first, second and third layers of skin on your nose would peel off, just like he knocked down the tables of the moneychangers and castigated the Pharisees for deciding who among the Jews could enter Heaven or not. Please show us who among the regular posters at the Panda's Thumb, or Pharyngula that you have convinced to give up Evolutionary Biology?
I mean, honestly, you type like a 30 year-old high school dropout who was barred from ever setting foot in a 4th rate community college campus because you have the grammatical skill of a C- caliber 2nd grader. And yet, you have the gall to honestly think you're eloquent.

JGB · 8 October 2007

Of all the entertaining nonsense Bonds "definition" that just because a bacteria has evolved a new function in response to a new environment (nylon) is not evolution because the environment didn't exist on Earth before. Well technically by that reasoning Bond since all environments on present day Earth are unique from a quantum mechanical perspective you've really managed to twist yourself into a most laughable pose.

PvM · 8 October 2007

My reference for epistasis is page 52 and 53 of the book “Genetic Entropy” by Dr. J.C. Sanford, (PhD Genetics; inventor of the biolistic “gene gun” process! He holds over 25 patents for inventions relating to genetics! If you ate today you have probably eaten some food touched by his work in genetics!!!!)

Nice appeal to authority. Another endearing Christian abuse of science

So are you trying to say that evolution has absolutely no problem with the fact that the genome is now proven to be a “complex interwoven network”???? Are you obfuscating the fact that Haldane’s, Fisher’s, and Wright’s work in population genetics is now utterly meaningless?

Fine, Haldane's dilemma is no more. Will you break the news to your creationist friends? In the mean time, you do realize that these population dynamics were but a zero'th order approximation to reality? Are you sure you are not familiar with the progress made by science in these areas, allowing one to take into consideration these new findings? Sigh... The ignorance is abundant once again

PvM · 8 October 2007

If you can contort your way out of this, It just goes to show that evolution can explain anything! And can be falsified by absolutely nothing! Sir, A theory that can explain anything and be falsified by nothing, is not a theory of science but an article of faith that belongs with the easter bunny and the flying spaghetti monster!

Don't forget ID :-) Of course, evolution is not a theory that can explain anything and like with for instance oceanography, when fine scale details emerged showing turbulence being a major factor, oceanography was not disproven, rather new mechanisms were added to explain previously unknown data and help understand the details of air-sea interactions. You have a very simplistic view of science it seems.

Stanton · 8 October 2007

You have a very simplistic view of science it seems.
What view? The prize in a box of Crackerjacks has more science in it that James Bond has ever had in that empty head of his.

PvM · 8 October 2007

Feel free to send all to the unpublished bin until we have the bathroom wall back in place.

David Stanton · 8 October 2007

BJ,

Well I see you ignored all of my questions once again. So I guess I can safely ignore you from now on. Just one last thing before I get back to ignoring you, do you really think that Fisher was the last population geneticist to work in the field?

Zeratul · 11 October 2007

Bond, James Bond, How come that you directly refer to "Almighty God" when you can also say "Almighty Zeus" or "Almighty Allah" or "Almighty Dog"?
PvM:

Yes, of course I am!! and I find comfort in Einstein’s special theory of relativity, which shows time, as we understand it, coming to a complete stop at the speed of light…which coincidentally conforms to the ancient Theistic assertion that Almighty God exist in a timeless eternity!!!,

Still ignorant about science I notice?

Zeratul · 11 October 2007

Bond, James Bond, How come that you directly refer to "Almighty God" when you can also say "Almighty Zeus" or "Almighty Allah" or "Almighty Dog"?
PvM:

Yes, of course I am!! and I find comfort in Einstein’s special theory of relativity, which shows time, as we understand it, coming to a complete stop at the speed of light…which coincidentally conforms to the ancient Theistic assertion that Almighty God exist in a timeless eternity!!!,

Still ignorant about science I notice?

DP · 11 October 2007

Yes but back to information.

I hereby pronounce that:

Endogenous Self Deception = -log2(ps),

Exogenous Self Deception = -log2(p),

Active Self Deception = -log2(ps/p).

With units in "bits of moral failure".

Standardization of terms? To hell with that, I want to take somone elses equations and make up completely new names for them. Out of thin air? I don't really have to answer to anyone so sure why not?

And nevermind that it somehow validates my position and nevermind that it looks self aggrandizing and above all, nevermind that alot of people will be mislead.