Tool Time: In My Best Tim Taylor I say “Huh?” to RabbitDawg

I’d really like a clear metric for information content as used by IDists, or a reference to one. If someone could provide that, it would be cool.

What's wrong with Shannon Information as a metric? Yockey's not an ID'ist, but ... Information Theory, Evolution, and The Origin of Life Mung

Snakes are cool Snakes are cold-blooded. And anti-darwinian.

Mung

DrREC and Eric Anderson, Since it is now shown that not only does 'classical information' reside in life encoded on DNA and proteins, but also 'quantum information' is now found in life which is found to be, among other things, 'holding the DNA together', and since the 10^12 bit number is derived directly from entropic considerations, then I feel very safe in saying that their entropic measure for 'total expressed information' is valid in so far as accuracy was achieved for their initial assumptions. note: Maxwell’s demon demonstration turns information into energy – November 2010 Excerpt: Until now, demonstrating the conversion of information to energy has been elusive, but University of Tokyo physicist Masaki Sano and colleagues have succeeded in demonstrating it in a nano-scale experiment. In a paper published in Nature Physics they describe how they coaxed a Brownian particle to travel upwards on a “spiral-staircase-like” potential energy created by an electric field solely on the basis of information on its location. As the particle traveled up the staircase it gained energy from moving to an area of higher potential, and the team was able to measure precisely how much energy had been converted from information. http://www.physorg.com/news/2010-11-maxwell-demon-energy.html bornagain77

Elizabeth Liddle:

That doesn’t mean that the simplest critters couldn’t, in principle, have stayed simple. It’s just that any branching could only be in the more complex direction.

Once there was something even the teensiest little bit more complex, branching could have gone back in the direction of simpler. So it is not the case that branching could only be in the more complex direction. DrRec:

I guess this highlights the dangers of estimating complexity, instead of empirically determining it (by genome sequencing).

So once we've sequenced the genome, how do we tell how complex the organism is? Mung

EL:

P(T|H) for an open-ended target like “a way of surviving in this environment” which is the target achieved by each living thing, as opposed to the closed target of a particular hand of cards out of a finite maximum.

Not every pattern is identifiable. Not every target is identifiable. There are other targets that are identifiable: such as particular proteins. The same applies to your second issue. CSI/"specified complexity" doesn't claim to be able to identify "every" designed object, and every conceivable "target" the imagination can come up with. PaV

Eric Anderson @24 "I think you’ve put up a strawman. I’ve read extensively from ID literature and I have never found a single major proponent of ID to ever suggest anything like the atomistic definition of information you so easily dismissed. I’m not sure where you heard such usage." No, this is bornagain77's references way of getting to large numbers for a bacteria: "“The problem then is to choose the right atoms and put them in the right places. The instructions for doing so, in binary form, are the information content….We next need to know the number of atoms" A process oriented estimate came up with 10^4 bits. DrREC

Barry, Thank you for your response, and my thanks to all of the subsequent commentators. Gee, I was fishing for a cogent rebuttal, and I netted a boatload! RabbitDawg

PS, I am aware of this:

(iv) In the current formulation, as at 2005, [Dembski's] metric for CSI, ? (chi), is: ? = – log2[10^120 ·?S(T)·P(T|H)] P(T|H) is the probability of being in a given target zone in a search space, on a relevant chance hypothesis, (E.g. Probability of a hand of 13 spades form a shuffled standard deck of cards) ?S(T) is a multiplier based on the number of similarly simply and independently specifiable targets (e.g. having hands that are all Hearts, all Diamonds, all Clubs or all Spades) 10^120 is the Seth Lloyd estimate for the maximum number of elementary bit-based operations possible in our observed universe, serving as a reasonable upper limit on the number of search operations. – log2 [ . . . ] converts the modified probability into a measure of information in binary digits, i.e. specified bits. When this value is at least + 1, then we may reasonably infer to the presence of design from the evidence of CSI alone. (For the example being discussed, ? = -361, i.e. The odds of 1 in 635 billions are insufficient to confidently infer to design, on the gamut of the universe as a whole. But, on the gamut of a card game here on Earth, that would be a very different story.)

from the UK glossary. But I don't see how to calculate: P(T|H) for an open-ended target like "a way of surviving in this environment" which is the target achieved by each living thing, as opposed to the closed target of a particular hand of cards out of a finite maximum. Nor: ?S(T) for the same reason (apart from the fact of how to then calculate the quantity, which presumably is given in one of Dembski's papers). Help would be appreciated :) Elizabeth Liddle

I'd really like a clear metric for information content as used by IDists, or a reference to one. If someone could provide that, it would be cool. Thanks! Elizabeth Elizabeth Liddle

DrRec: "You aren’t suggesting the information content of the dictionary is defined by the atom type, bonding, and position of every atom in it, are you?" Uh, no. Not sure where that idea would come from. I wouldn't view the deterministic bonding of atoms as having much (if any) information content. What does contain information content is the contingent arrangement of parts in the cell. The base pairing of DNA is but one aspect of the information content in a bacterium. This is particularly obvious in areas where there is overlapping genetic coding. In addition, there is a lot of epigenetic information in every cell. All of the coordinated, functioning parts are based on complex specified information, not just the brute physics of atomic bonding. DNA cannot replicate itself, but requires a whole suite of machines to do so, and that is just one subset of what goes on in the cell. The entire operation is a carefully controlled orchestration, all of which depends on information. Chemistry and physics alone do not explain the functional parts of the cell. Those depend on information that has been brought to bear. I think you've put up a strawman. I've read extensively from ID literature and I have never found a single major proponent of ID to ever suggest anything like the atomistic definition of information you so easily dismissed. I'm not sure where you heard such usage. This is not mysterious. Information in the real-world, usual sense that we use it -- engineering, computing, design principles -- is ubiquitious throughout the cell. What do we make of the fact that there is information in life, and lots of it? That is the real crux of the matter. Eric Anderson

DrREC, it matters not one iota to me that you refuse to accept the evidence we now have in hand!!! You testify to your own dogmatic atheistic beliefs when you do as such, and further the case against neo-Darwinists when you do as such, so as far as I'm concerned RANT AWAY!!! bornagain77

"information, which is transcendent and dominate of matter and energy' Dominant of matter and energy! If I burn my hard drive, does the information on it transcend the gases and ash left and energy expended? If I kill an organism, does the information it contained continue to keep the biology of the organism away from equilibrium? I'd be careful in the more 'magical' interpretations of quantum entanglement, etc. DrREC

@18 Eric Anderson "DrRec: You aren’t really suggesting that the “information content” of a cell is determined by counting basepairs are you?" You aren't suggesting the information content of the dictionary is defined by the atom type, bonding, and position of every atom in it, are you? My point is that 'information' gets thrown around a lot, and some (atomistic) definitions would say the information content of my hard drive exceeds the computer resources of the whole world. If we have to record the X,Y,Z positon, bonding, and atom type for 1/10 a mole of silicon atoms, we're orders of magnitude past that. It is a silly way to define information. How would you define the information content of a bacterium? DrREC

DrREC, information, which is transcendent and dominate of matter and energy, is now shown to be what is constraining the cell to be so far out of thermodynamic equilibrium. Information and entropy – top-down or bottom-up development in living systems? A.C. McINTOSH Excerpt: It is proposed in conclusion that it is the non-material information (transcendent to the matter and energy) that is actually itself constraining the local thermodynamics to be in ordered disequilibrium and with specified raised free energy levels necessary for the molecular and cellular machinery to operate. http://journals.witpress.com/journals.asp?iid=47 Quantum Action confirmed in DNA by direct empirical research; DNA Can Discern Between Two Quantum States, Research Shows - June 2011 Excerpt: -- DNA -- can discern between quantum states known as spin. - The researchers fabricated self-assembling, single layers of DNA attached to a gold substrate. They then exposed the DNA to mixed groups of electrons with both directions of spin. Indeed, the team's results surpassed expectations: The biological molecules reacted strongly with the electrons carrying one of those spins, and hardly at all with the others. The longer the molecule, the more efficient it was at choosing electrons with the desired spin, while single strands and damaged bits of DNA did not exhibit this property. http://www.sciencedaily.com/releases/2011/03/110331104014.htm Quantum entanglement holds together life’s blueprint - 2010 Excerpt: When the researchers analysed the DNA without its helical structure, they found that the electron clouds were not entangled. But when they incorporated DNA’s helical structure into the model, they saw that the electron clouds of each base pair became entangled with those of its neighbours. “If you didn’t have entanglement, then DNA would have a simple flat structure, and you would never get the twist that seems to be important to the functioning of DNA,” says team member Vlatko Vedral of the University of Oxford. http://neshealthblog.wordpress.com/2010/09/15/quantum-entanglement-holds-together-lifes-blueprint/ Does DNA Have Telepathic Properties?-A Galaxy Insight Excerpt: DNA has been found to have a bizarre ability to put itself together, even at a distance, when according to known science it shouldn't be able to. Explanation: None, at least not yet.,,, The recognition of similar sequences in DNA’s chemical subunits, occurs in a way unrecognized by science. There is no known reason why the DNA is able to combine the way it does, and from a current theoretical standpoint this feat should be chemically impossible. http://www.dailygalaxy.com/my_weblog/2009/04/does-dna-have-t.html Quantum Information/Entanglement In DNA & Protein Folding - short video http://www.metacafe.com/watch/5936605/ further notes: Maxwell's demon demonstration turns information into energy - November 2010 Excerpt: Until now, demonstrating the conversion of information to energy has been elusive, but University of Tokyo physicist Masaki Sano and colleagues have succeeded in demonstrating it in a nano-scale experiment. In a paper published in Nature Physics they describe how they coaxed a Brownian particle to travel upwards on a "spiral-staircase-like" potential energy created by an electric field solely on the basis of information on its location. As the particle traveled up the staircase it gained energy from moving to an area of higher potential, and the team was able to measure precisely how much energy had been converted from information. http://www.physorg.com/news/2010-11-maxwell-demon-energy.html etc.. etc.. etc.. bornagain77

Oh Dear, that is quite the reference. If I build some IKEA furniture using IKEA instructions, it might be five pages of information. If I record the positions of all atoms in the object, and build it ala star-trek transporter, I end up with volumes of data. And your source seems to have tried the latter! "The problem then is to choose the right atoms and put them in the right places. The instructions for doing so, in binary form, are the information content....We next need to know the number of atoms. If the average atomic weight is taken as six, the ....this means there are 6x10^10 atoms to locate" Wow! "It is clear that the process chosen for assembly is most important.... if walls are built by a process of pouring concrete into molds instead of the brick-by-brick method, the amount of information needed decreases. In the cell there is the possibility that certain growth patterns are required to develop from others. .... For a bacterium, an estimate based on reasoning due to Dancoff and Quastler gives 10^4 bits" This really highlights the flaw in 'information' calculations to me. If we consider the placement of all atoms in a bacterium, there is a huge sum of information. If we consider just the instructions-the genome, we have a small sum. If we consider a modern protein spontaneously arising, the odds are low. If we look at pathways going from small folding units, we drop from resources the size of the universe to resources the size of billions of bacteria. If I take 60 carbons, and consider the number of ways 60 carbon atoms and associated hydrogens can arrange themselves, I'd arrive at a very large number. If I recorded the 'information' which according to this reference is the precise position of each atom of each possibility, I'd have a very large file. Yet every time you blow out a candle, you create some C60 fullerene-icosahedral, functional in trapping other atoms, and by certain calculations-much like those favored by ID-highly improbable. DrREC

DrRec: You aren't really suggesting that the "information content" of a cell is determined by counting basepairs are you? Eric Anderson

as to this caveat: 'If the entropy calculated from the caloric values of the nutrient process is actually very wasteful, then the amount of entropy used to estimate information is lower.' yet we find: Life Leads the Way to Invention - Feb. 2010 Excerpt: a cell is 10,000 times more energy-efficient than a transistor. “ In one second, a cell performs about 10 million energy-consuming chemical reactions, which altogether require about one picowatt (one millionth millionth of a watt) of power.” This and other amazing facts lead to an obvious conclusion: inventors ought to look to life for ideas.,,, Essentially, cells may be viewed as circuits that use molecules, ions, proteins and DNA instead of electrons and transistors. That analogy suggests that it should be possible to build electronic chips – what Sarpeshkar calls “cellular chemical computers” – that mimic chemical reactions very efficiently and on a very fast timescale. http://creationsafaris.com/crev201002.htm#20100226a Also of interest is that a cell apparently seems to be successfully designed along the very stringent guidelines laid out by Landauer's principle of 'reversible computation' in order to achieve such amazing energy efficiency, something man has yet to accomplish in any meaningful way for computers: Notes on Landauer’s principle, reversible computation, and Maxwell’s Demon - Charles H. Bennett Excerpt: Of course, in practice, almost all data processing is done on macroscopic apparatus, dissipating macroscopic amounts of energy far in excess of what would be required by Landauer’s principle. Nevertheless, some stages of biomolecular information processing, such as transcription of DNA to RNA, appear to be accomplished by chemical reactions that are reversible not only in principle but in practice.,,,, http://www.hep.princeton.edu/~mcdonald/examples/QM/bennett_shpmp_34_501_03.pdf thus the 10^12 bit calculation holds and may be a bit low due to the fact they probably over-estimated 'wastefulness' in their original calculation! bornagain77

DrREC, as to source; Moleular Biophysics - Setlow-Pollard Ed. Addison Wesley - pp 66-74 3-8 Information theory. Relation between information and entropy. Excerpt: The number of cells in our mental honeycomb is then 8x10^-24/8x10^-30 or 10^6, an uncertainty which takes 20 binary choices. The total per atom is then 21.5, and since the total number of atoms is 6x1010 the total information content is then 1.3x10^12 or, in round numbers, 10^12 bits. Linschitz gave the figure 9.3x10^-12 cal/deg or 9.3x10^-12x4.2 joules/deg for the entropy of a bacterial cell. Using the relation H = S/(k In 2), we find that the information content is 4 x 10^12 bits http://www.astroscu.unam.mx/~angel/tsb/ec07.GIF Morowitz' deduction from the work of Bayne-Jones and Rhees gives the lower value of 5.6x10^11 bits, which is still in the neighborhood of 10^12 bits. Thus two quite different approaches give rather concordant figures. It must be pointed out that both methods tend to give high values. If the entropy calculated from the caloric values of the nutrient process is actually very wasteful, then the amount of entropy used to estimate information is lower. In the second approach, it is quite possible that many of the actual locations of atoms are not critical to life. Indeed, Holter has shown that a centrifuged amoeba that has actually developed stratification of its components can still live. Even with these reservations, the value of 10^12 bits is very high. Morowitz has pointed out that the random concatenation of a bacterium from its component atoms is very unlikely indeed. Those who wish to speculate on the origin of life can speculate about these values and see what impact they have on their prejudices. http://www.astroscu.unam.mx/~angel/tsb/molecular.htm Sources are very important indeed DrREC!!! That's why I'm very happy 'The Source' of the entire universe and all life in it, and indeed the possessor of all wisdom, has accepted me, as insignificant and inconsequential as I am, into His everlasting family through the work of His Son Jesus Christ!!! Hillsong United - Lord of Lords - With Subtitles/Lyrics http://www.youtube.com/watch?v=GFkY5-Xp710 Revelation 3:20 'Behold, I stand at the door and knock; if anyone hears My voice and opens the door, I will come in to him and will dine with him, and he with Me.' bornagain77

"‘The information content of a simple cell has been estimated as around 10^12 bits, comparable to about a hundred million pages of the Encyclopedia Britannica.” Carl Sagan, “Life” in Encyclopedia Britannica: Macropaedia (1974 ed.), pp. 893-894" I guess this highlights the dangers of estimating complexity, instead of empirically determining it (by genome sequencing). E. coli has about 4.6 million basepairs. Unless it takes 25 pages to write down a single pair, I think we're a bit off. The human genome has about 3 billion basepairs. at 3000 letters a page, this could be recorded on a million pages (or a single DVD). Huge still-but you've got to watch your sources. DrREC

Elizabeth provides this 'scientific fact'; 'That doesn’t mean that the simplest critters couldn’t, in principle, have stayed simple. It’s just that any branching could only be in the more complex direction.' And so the story goes Elizabeth: Yet 'simple' life is no where near as simple as we thought it would be; Three Subsets of Sequence Complexity and Their Relevance to Biopolymeric Information - David L. Abel and Jack T. Trevors - Theoretical Biology & Medical Modelling, Vol. 2, 11 August 2005, page 8 "No man-made program comes close to the technical brilliance of even Mycoplasmal genetic algorithms. Mycoplasmas are the simplest known organism with the smallest known genome, to date. How was its genome and other living organisms' genomes programmed?" http://www.biomedcentral.com/content/pdf/1742-4682-2-29.pdf Simplest Microbes More Complex than Thought - Dec. 2009 Excerpt: PhysOrg reported that a species of Mycoplasma,, “The bacteria appeared to be assembled in a far more complex way than had been thought.” Many molecules were found to have multiple functions: for instance, some enzymes could catalyze unrelated reactions, and some proteins were involved in multiple protein complexes." http://www.creationsafaris.com/crev200912.htm#20091229a Ben Stein - EXPELLED - The Staggering Complexity Of The Cell - video http://www.metacafe.com/watch/4227700 “Although the tiniest living things known to science, bacterial cells, are incredibly small (10^-12 grams), each is a veritable micro-miniaturized factory containing thousands of elegantly designed pieces of intricate molecular machinery, made up altogether of one hundred thousand million atoms, far more complicated than any machine built by man and absolutely without parallel in the non-living world”. Michael Denton, "Evolution: A Theory in Crisis," 1986, p. 250. “The difference between a mixture of simple chemicals and a bacterium, is much more profound than the gulf between a bacterium and an elephant.” (Dr. Robert Shapiro, Professor Emeritus of Chemistry, NYU) 'The information content of a simple cell has been estimated as around 10^12 bits, comparable to about a hundred million pages of the Encyclopedia Britannica." Carl Sagan, "Life" in Encyclopedia Britannica: Macropaedia (1974 ed.), pp. 893-894 Moreover, despite the fact that 'simple' life is overflowing with information, that vastly exceeds in complexity anything man has ever done, neo-Darwinists have NEVER demonstrated even the most trivial of gains in functional information above and beyond what was already present in a parent species bacterium!! Is Antibiotic Resistance evidence for evolution? - 'The Fitness Test' - video http://www.metacafe.com/watch/3995248 Testing Evolution in the Lab With Biologic Institute's Ann Gauger - podcast with link to peer-reviewed paper Excerpt: Dr. Gauger experimentally tested two-step adaptive paths that should have been within easy reach for bacterial populations. Listen in and learn what Dr. Gauger was surprised to find as she discusses the implications of these experiments for Darwinian evolution. Dr. Gauger's paper, "Reductive Evolution Can Prevent Populations from Taking Simple Adaptive Paths to High Fitness,". http://intelligentdesign.podomatic.com/entry/2010-05-10T15_24_13-07_00 The GS (genetic selection) Principle – David L. Abel – 2009 Excerpt: Stunningly, information has been shown not to increase in the coding regions of DNA with evolution. Mutations do not produce increased information. Mira et al (65) showed that the amount of coding in DNA actually decreases with evolution of bacterial genomes, not increases. This paper parallels Petrov’s papers starting with (66) showing a net DNA loss with Drosophila evolution (67). Konopka (68) found strong evidence against the contention of Subba Rao et al (69, 70) that information increases with mutations. The information content of the coding regions in DNA does not tend to increase with evolution as hypothesized. Konopka also found Shannon complexity not to be a suitable indicator of evolutionary progress over a wide range of evolving genes. Konopka’s work applies Shannon theory to known functional text. Kok et al. (71) also found that information does not increase in DNA with evolution. As with Konopka, this finding is in the context of the change in mere Shannon uncertainty. The latter is a far more forgiving definition of information than that required for prescriptive information (PI) (21, 22, 33, 72). It is all the more significant that mutations do not program increased PI. Prescriptive information either instructs or directly produces formal function. No increase in Shannon or Prescriptive information occurs in duplication. What the above papers show is that not even variation of the duplication produces new information, not even Shannon “information.” http://www.bioscience.org/2009/v14/af/3426/3426.pdf The Law of Physicodynamic Insufficiency - Dr David L. Abel - November 2010 Excerpt: “If decision-node programming selections are made randomly or by law rather than with purposeful intent, no non-trivial (sophisticated) function will spontaneously arise.”,,, After ten years of continual republication of the null hypothesis with appeals for falsification, no falsification has been provided. The time has come to extend this null hypothesis into a formal scientific prediction: “No non trivial algorithmic/computational utility will ever arise from chance and/or necessity alone.” http://www.scitopics.com/The_Law_of_Physicodynamic_Insufficiency.html Elizabeth, not only do you not have observational evidence for any 'vertical' evolution WHATSOEVER, you don't even have any evidence that it ever did occur!!! Static evolution: is pond scum the same now as billions of years ago? Excerpt: But what intrigues (paleo-biologist) J. William Schopf most is lack of change. Schopf was struck 30 years ago by the apparent similarities between some 1-billion-year-old fossils of blue-green bacteria and their modern microbial microbial. "They surprisingly looked exactly like modern species," Schopf recalls. Now, after comparing data from throughout the world, Schopf and others have concluded that modern pond scum differs little from the ancient blue-greens. "This similarity in morphology is widespread among fossils of [varying] times," says Schopf. As evidence, he cites the 3,000 such fossils found; http://www.thefreelibrary.com/Static+evolution%3A+is+pond+scum+the+same+now+as+billions+of+years+ago%3F-a014909330 The Paradox of the "Ancient" Bacterium Which Contains "Modern" Protein-Coding Genes: “Almost without exception, bacteria isolated from ancient material have proven to closely resemble modern bacteria at both morphological and molecular levels.” Heather Maughan*, C. William Birky Jr., Wayne L. Nicholson, William D. Rosenzweig§ and Russell H. Vreeland ; http://mbe.oxfordjournals.org/cgi/content/full/19/9/1637 etc.. etc.. etc.. bornagain77

PS, although having branched off in a more complex direction, simpler directions become possible again. So we have snakes, which though in the tetrapod lineage, don't actually have tetra pods. Snakes are cool :) Elizabeth Liddle

A quick point: If life started simple (which most scientists populate) and increased in diversity, clearly mean complexity would rise, because you can't get more simple than simplest. That doesn't mean that the simplest critters couldn't, in principle, have stayed simple. It's just that any branching could only be in the more complex direction. Elizabeth Liddle

I see, So the original post should have perhaps said "the authors are focused on a kind of evolution that does not concern intelligent design advocates" instead of: "Nevertheless, I am amazed that they would suggest that a particular event (this gene swap) explains increasing complexity " ...which is not something the they suggested. DrREC

There has been a increase in the maximum complexity of life, but there is nothing intrinsic to evolution directing life towards greater complexity.

Biology's First Law: The Tendency for Diversity and Complexity to Increase in Evolutionary Systems But there has sure been a lot of ink spilled on the topic. Mung

DrREC, what Chris Doyle said. :-) Barry Arrington

The only terms of evolution worth talking about are those which refer to increasing complexity, REC. This is because, only by providing a scientific basis for that kind of macro-evolutionary power can we understand how it is that human beings evolved from a single-celled eukaryotic ancestor in the first place. In the stark absence of evidence for "greater complexity" through evolution, evolutionists point toward frankly trivial "adaptation to local conditions" involving "decreases, or no change of complexity" as if that'll do. Well, it won't do. It won't do at all. If there is a mountain of evidence for evolution, then that is only because of examples such as these which make massive mountains out of tiny molehills. Chris Doyle

"I know the Darwinsts who suggest this gene swap is a slam dunk for evolution in action are not deeply stupid. Nevertheless, I am amazed that they would suggest that a particular event (this gene swap) explains increasing complexity." I think you're faulting the authors for not adhering to your definition of evolution (not theirs). Your mistake in this is couching evolution strictly in terms of increasing complexity-which is not a definition they or I would likely agree with. There has been a increase in the maximum complexity of life, but there is nothing intrinsic to evolution directing life towards greater complexity. Adaptation to local conditions could require increases, decreases, or no change of complexity. DrREC

Another victory for neo-Paleyism! paragwinn

http://microbewiki.kenyon.edu/index.php/E._coli_O157_in_North_America

Although Shigella and Escherichia represent different genera of bacteria, they are considered to be very close, both genetically and biochemically. The isoforms of Shiga toxins produced by these different pathogens are also very closely related in structure and function. the exact origin of O157:H7 is not known http://www.bioscience.org/1997/v2/d/obrig/2.htm

The disease causing strains of E. coli can evolve naturally from safe ones by processes of gene-swapping. One form of gene swapping that they us is called conjugation (mating), and some E.coli can conjugate with almost anything. That’s what they do naturally. http://www.biofortified.org/2011/05/natural-gmos-part-83-natural-biology-comes-with-no-guarantee-of-safety/

Mung

Well, it is an interesting example of development, adaptability, whatever we want to call it; although it may not be a good example of RM+NS. What I want to know is how bacterium A grabs a gene from bacterium B and successfully incorporates it into itself. How does this actually work? Does bacterium A recognize that the particular sequence in question, from codon 1 . . . n constitutes a complete gene? How does it "borrow it" once recognized, by literally cutting the gene from the genome of bacterium B, thereby disabling bacterium B, or by going in and copying that specific sequence? Or is bacterium A just regularly grabbing large swaths of genetic material, which very occasionally contain a functional sequence it can use? Once borrowed, how does bacterium A successfully incorporate the gene into its own system, after all, it is one thing to have the code for a gene lying around, quite another to express it at the right time, in the right amount, etc. It might be true that the process is a random trial-and-error process demanded by traditional evolutionary theory, but until we know a lot more about what is going on, I'm not comfortable just assuming the absence of some underlying control process/mechanism. Eric Anderson

As always, affirming the consequent. toc

"Unlike previously known E. coli, O157 borrowed a gene from a completely different bacterium ..." As I understand it, it has been known for years -- as in decades -- that bacteria can, and do, swap genes with other organisms of other species (I intentionally phrased it that way); and, for that matter, can incorporate "found" genes into their genomes. What? Didn't Darwinists get the memo? Ilion

Here's a little background info as to 'swapping genes';,,, there is actually found to be a fairly large pool of 'character' genes that are known to be shared amongst different species of bacteria for different particular environmental niches; Please note the 7:50 minute mark of following video; ORFan Genes Challenge Common Descent - Paul Nelson - video - short version http://www.vimeo.com/17135166 referenced paper: Estimating the size of the bacterial pan-genome - Pascal Lapierre and J. Peter Gogarten - 2008 Excerpt: We have found >139 000 rare (ORFan) gene families scattered throughout the bacterial genomes included in this study. The finding that the fitted exponential function approaches a plateau indicates an open pan-genome (i.e. the bacterial protein universe is of infinite size) (i.e. each new bacteria genome sequenced is expected to have a fairly large percentage of genes that are completely unique to that individual bacteria); a finding supported through extrapolation using a Kezdy-Swinbourne plot (Figure S3). This does not exclude the possibility that, with many more sampled genomes, the number of novel genes per additional genome might ultimately decline; however, our analyses and those presented in Ref. [11] do not provide any indication for such a decline and confirm earlier observations that many new protein families with few members remain to be discovered. http://www.paulyu.org/wp-content/uploads/2010/02/Estimating-the-size-of-the-bacterial-pan-genome.pdf of particular note from preceding paper underneath figure 2 on page 3 of the article: Figure 2. The bacterial pan-genome. Each gene found in the bacterial genome represents one of three pools: genes found in all but a few bacterial genomes comprise the extended core of essential genes (250 gene families that encode proteins involved in translation, replication and energy homeostasis); the character genes (7900 gene families) represent genes essential for colonization and survival in particular environmental niches (e.g. symbiosis and photosynthesis) ; and finally, the accessory genes, a pool of apparently infinite size, contains genes that can be used to distinguish strains and serotypes; the function of most genes in this category is unknown. At the genomic level, a typical bacterial genome is composed of 8% of core genes, 64% of character genes and 28% of accessory genes. Although the character genes contain only 7900 gene families, they are the most abundant at the genomic level. Expanding the gene centered approach to 573 bacterial genomes or sampling of 508 genomes, excluding highly reduced genomes, yields similar results (Table S2), except that the total number of families in the accessory pool is increased as expected for an open pan-genome. further notes as to 'gene swapping' amongst bacteria species: bacterial species have acquired several mechanisms by which to exchange genetic materials. Transformation - the uptake of naked DNA is a common mode of horizontal gene transfer that can mediate the exchange of any part of a chromosome; this process is most common in bacteria that are naturally transformable; typically only short DNA fragments are exchanged. Conjugation - the transfer of DNA mediated by conjugal plasmids or conjugal transposons; requires cell to cell contact but can occur between distantly related bacteria or even bacteria and eukaryotic cells; can transfer long fragments of DNA. Transduction - the transfer of DNA by phage requires that the donor and recipient share cell surface receptors for phage binding and thus is usually limited to closely related bacteria; the length of DNA transferred is limited by the size of the phage head. ,,, It is also of interest to note that bacteria are now shown to communicate 'wirelessly', something that was completely unexpected from the neo-Darwinian framework; New study shows that bacteria can communicate through the air Excerpt: Professor Alan Parsons and Dr Richard Heal of QinetiQ ltd, have shown that physically separated colonies of bacteria can transmit signals conferring resistance to commonly used antibiotics. http://www.biology-online.org/kb/article.php?p=study-shows-bacteria-communicate-air Cellular Communication through Light Excerpt: As there were significant differences when separating the populations with glass or quartz, it is suggested that the cell populations use two (or more) frequencies for cellular information transfer, which influences at least energy uptake, cell division rate and growth correlation. Altogether the study strongly supports a cellular communication system, which is different from a molecule-receptor-based system and hints that photon-triggering is a fine tuning principle in cell chemistry. http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0005086 Paramecium caudatum can communicate with neighbors using a non-molecular method, probably photons. The cell populations were separated either with glass allowing photon transmission from 340 nm to longer waves, or quartz being transmittable from 150 nm, i.e. from UVlight to longer waves. Energy uptake, cell division rate and growth correlation were influenced. http://en.wikipedia.org/wiki/Paramecium_caudatum i.e. this, as well as many other evidences give the firm conclusion that bacteria are far more advanced in their inherent complexity than neo-Darwinian expectations would lead us to believe!!! bornagain77