Ken Miller in Birmingham
| November 7, 2009 | Posted by Flannery under Evolution, Intelligent Design, theistic evolution |
Noted Brown University biologist and slayer of windmills, Kenneth Miller, came to Birmingham, Alabama, on Thursday November 5. The room was packed with what seemed to be about 200 (mostly students and some faculty). Overall, Miller displayed the affable but subliminally arrogant attitude I’ve come to expect in some academics. Miller began by giving a long list of his publications interspersed along with some obligatory self-deprecating humor, the apparent take-home message being “look at what a smart and prolific boy I am.” He then launched into Kitzmiller v. Dover and said (whether out of genuine misinformation or outright disingenuousness I cannot say) that the Discovery Institute “put them [the school board] up to it.” After giving a wholly inaccurate definition of ID as the idea that “design in the form of outside intelligent intervention is required to account for the origin of living things,” he launched into the bulk of his lecture most of which simply gave examples of common descent as “proof” of Darwinian evolution. I must say that I was surprised by the degree to which Miller absolutely savaged ID. It’s not that he simply disagrees with ID, the substance of his message was that ID is a creationist group (no one was mentioned by name) with the Discovery Institute as its front organization working (in his words) “against scientific rationality.” The thrust of his ID comments were wholly denigrating and dismissive. Miller later admitted that evolution was the product of “design in nature” in search of “adaptive spaces.” His discussion of design was frankly bizarre; at times he almost sounded like a Gaia proponent—I couldn’t figure out if by design he meant just some sort of unfolding or self-direction or if “design” was somehow synonymous with natural selection. The entire presentation in this regard was quite fuzzy. There was a lot of conflation of concepts—my personal favorite being his conflation of evolution, genetics, and Gregor Mendel. Anyone listening to Miller on this would have thought that Mendel was simply carrying Darwin’s ideas forward; he did not, of course, point out that Darwin’s adherence to pangenesis and the notion of inheritance of acquired characteristics was quite different from that of Mendel. The rest was pretty predictable.
I finally did get to ask Miller a question. It was the second to last one, and Miller was pretty euphoric having hit a series of Q & A home runs from softballs pitched at T-ball speeds mostly by students. The good thing was that by the time I got to pose my question a lot of questioners had prefaced their questions with comments (mostly “thank you, thank you, for supporting theism and science,” “oh what an important struggle we have before us promoting good science, your presentation was marvelous,” etc., etc.). I started by saying that I sincerely wished that this country could get away from this overly simplistic “evolution versus creation” discourse as unhistorical and unhelpful. We talk about evolution as though Wallace and Mivart never existed. Then I said, “Dr. Miller, as you well know, Alfred Russel Wallace, the co-discoverer of natural selection, broke with Darwin over the role of natural selection in creating the human mind. Wallace didn’t think it could account for it; Mivart agreed. Now these objections are still with us today. They haven’t gone away. Surely you’re familiar with the April issue of Nature in which Bolhuis and Wynne asked, ‘Can evolution explain how minds work?’. Don’t we have an educational obligation to give the WHOLE story of evolution? I mean we talk about evolution as if it was simply the story of Darwin and science on the march when, if fact, many of the original objections raised to his theory remain today. This is Whiggish history of the worst kind! How can we get past this and tell the more complete and accurate story of evolution? ” Miller replied by nodding in apparent approval, which seemed inappropriate given his presentation, but then simply didn’t answer the question. The upshot of his reply was to utter some vague generalizations about the Templeton Foundation and that he was working with them on this very thing. Huh??
Well that’s my report. I must say Miller is an engaging and powerful speaker. His points are persuasive to the uninformed and although I have no objection to his having his say in a free markeplace of ideas, I suspect that he does considerable intellectual damage where ever he goes.
262 Responses to Ken Miller in Birmingham
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bornagain77 at 240,
Mustela, I am still waiting for YOU to verify your grand claim that evolution HAS happened
Evolution is defined as a change in allele frequencies in populations over time. It has been observed. It has been documented. It has happened.
The mechanisms identified as generating heritable variability by modern evolutionary theory have been observed and documented. They occur and they generate novel features. Two of those have been pointed out to you very recently: Lenski’s citrate eating e. coli and nylonase synthesizing bacteria. Again, evolution has been observed.
Mustela, both of those examples came at a overall loss of functional complexity that was inherent in the parent bacteria….As amply witnessed by the fact that the nylonase will be less fit for survival once the nylon is removed from the environment, and that the citrate bacteria will not pass the fitness test in the parent bateria’s native environment… What you need is to generate functional complexity greater than was already present,,, You clearly have not done so!!! Why is it so important for you to believe this tripe you are trying so desperately to sell me? Did God hurt you somehow? What offense has He committed to you to make you so dogmatic in your atheism? Do you think God owes you something?
BA77,
if oxygen levels returned to those of the precambrian, human beings will be less fit for survival. does that mean that we are less functionally complex than cyanobacteria?
Mustela Nivalis:
No you don’t see.
It appears that you are incapable of seeing anything but your personal biases.
I am not defining anything.
I am using the standard and accepted definition of nested hierarchy.
And you don’t seem to know anything about nested hierarchies.
And you think your ignorance refutes the facts I have presented.
Evolutionary biologists do not get to change the meaning of nested hierarchies to suit their needs.
Summary of the pronciples of hierarchy theory
That is from the ISSS-International Society for the System Sciences.
The fact is nested hierarchies are constructed based on defined characteristics.
Again you appear ignorant of nested hierarchies and you think your ignorance is meaningful discourse.
Mustela Nivalis:
Evolution is not being debated.
The debate is about the mechanism(s)- are they undirected and without a goal, or are they directed and target oriented?
So thank you for once again displaying your ignorance.
Even YECs accept that allele frequencies change over time.
Lenski’s experiment falls in line with the YEC variation within a Kind.
Nylonase falls within the same parameters.
IOW if all you have is evidence for the YEC model of biological evcolution- ie baraminology- you don’t have anything that supports your position.
Khan, asks:
Well let’s take a look at evidence for terra-forming of the primeval earth Kahn:
Contrary to what materialism would expect, these very first photosynthetic bacteria found 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 producing the necessary oxygen for higher life-forms to exist, and by reducing the greenhouse gases of earth’s early atmosphere.
The Oxygen and Carbon Dioxide Cycle – video
http://videos.howstuffworks.co.....-video.htm
Photosynthetic bacteria slowly removed the carbon dioxide, and built the oxygen up, in the earth’s atmosphere primarily by this following photosynthetic chemical reaction:
6H2O + 6CO2 ———-> C6H12O6+ 6O2
The above chemical equation translates as:
Six molecules of water plus six molecules of carbon dioxide produce one molecule of sugar plus six molecules of oxygen
Interestingly, the gradual removal of greenhouse gases corresponded to the gradual 15% increase of light and heat coming from the sun during that time (Ross; Creation as Science). 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 necessary for the bacteria to continue to live to do their work of preparing the earth for more advanced life to appear. More interesting still, the by products of the complex biogeochemical processes involved in the oxygen production and greenhouse gas removal by these early bacteria are (red banded) iron formations, limestone, marble, gypsum, phosphates, sand, and to a lesser extent, coal, oil and natural gas (note; though some coal, oil and natural gas deposits 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). The resources produced by these early photosynthetic bacteria are very useful, one could even say necessary, for the technologically advanced civilizations of today to exist.
The following video is good for seeing just how far back the red banded iron formations really go (3.8 billion years ago). But be warned, Dr. Newman operates from a materialistic worldview and makes many unwarranted allusions of the “magical” power of evolution to produce photosynthetic bacteria. Although to be fair, she does readily acknowledge the staggering level of complexity being dealt with in photosynthesis, as well as admitting that no one really knows how photosynthesis “evolved”.
Exploring the deep connection between bacteria and rocks – Dianne Newman – MIT lecture video
http://mitworld.mit.edu/video/496
This following article explores some of the other complex geochemical processes that are also involved in the forming of the red banded iron formations.
Banded Rocks Reveal Early Earth Conditions, Changes
Excerpt: Called banded iron formations or BIFs, these ancient rocks formed between 3.8 and 1.7 billion years ago at what was then the bottom of the ocean. The stripes represent alternating layers of silica-rich chert and iron-rich minerals like hematite and magnetite. First mined as a major iron source for modern industrialization, BIFs are also a rich source of information about the geochemical conditions that existed on Earth when the rocks were made. http://www.sciencedaily.com/re.....184428.htm
Interestingly, while the photo-synthetic bacteria were reducing greenhouse gases and producing oxygen, and metal, and minerals, which would all be of benefit to modern man, “sulfate-reducing” bacteria were also producing their own natural resources which 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 ores. Metal ores which are very useful for modern man, as well as fairly easy for man to extract today (mercury, cadmium, zinc, cobalt, arsenic, chromate, tellurium and copper to name a few). To this day, sulfate-reducing bacteria maintain an essential minimal level of these heavy metals in the ecosystem which 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.
Bacterial Heavy Metal Detoxification and Resistance Systems:
excerpt: Bacterial plasmids contain genetic determinants for resistance systems for Hg2+ (and organomercurials), Cd2+, AsO2, AsO43-, CrO4 2-, TeO3 2-, Cu2+, Ag+, Co2+, Pb2+, and other metals of environmental concern.
http://www.springerlink.com/co.....04577v8t3/
http://www.int-res.com/article.....26p203.pdf
The role of bacteria in hydrogeochemistry, metal cycling and ore deposit formation:
Textures of sulfide minerals formed by SRB (sulfate-reducing bacteria) during bioremediation (most notably pyrite and sphalerite) have textures reminiscent of those in certain sediment-hosted ores, supporting the concept that SRB may have been directly involved in forming ore minerals. http://www.goldschmidt2009.org...../A1161.pdf
Transitional Metals And Cytochrome C oxidase – Michael Denton – Nature’s Destiny
http://books.google.com/books?.....3&lpg
As well, geological processes helped detoxify the earth of dangerous levels of metal:
The Concentration of Metals for Humanity’s Benefit:
Excerpt: They demonstrated that hydrothermal fluid flow could enrich the concentration of metals like zinc, lead, and copper by at least a factor of a thousand. They also showed that ore deposits formed by hydrothermal fluid flows at or above these concentration levels exist throughout Earth’s crust. The necessary just-right precipitation conditions needed to yield such high concentrations demand extraordinary fine-tuning. That such ore deposits are common in Earth’s crust strongly suggests supernatural design.
Kahn: further notes on Terra-Forming:
And on top of the fact that poisonous heavy metals on the primordial earth were brought into “life-enabling” balance by complex biogeochemical processes, there was also an explosion of minerals on earth which were a result of that first life, as well as being a result of each subsequent “Big Bang” of life there afterwards.
The Creation of Minerals:
Excerpt: Thanks to the way life was introduced on Earth, the early 250 mineral species have exploded to the present 4,300 known mineral species. And because of this abundance, humans possessed all the necessary mineral resources to easily launch and sustain global, high-technology civilization. http://www.reasons.org/The-Creation-of-Minerals
To put it mildly, this minimization of poisonous elements, and “explosion” of useful minerals, is strong evidence for Intelligently Designed terra-forming of the earth that “just so happens” to be of great benefit to modern man.
Man has only recently caught on to harnessing the ancient detoxification ability of bacteria to cleanup his accidental toxic spills, as well as his toxic waste, from industry:
What is Bioremediation? – video
http://www.youtube.com/watch?v=pSpjRPWYJPg
Clearly many, if not all, of these metal ores and minerals laid down by these sulfate-reducing bacteria, as well as laid down by the biogeochemistry of more complex life, as well as laid down by finely-tuned geological conditions throughout the early history of the earth, have many unique properties which are crucial for technologically advanced life, and are thus indispensable to man’s rise above the stone age to the advanced “space-age” technology of modern civilization.
Metallurgy
http://en.wikipedia.org/wiki/Metallurgy
Inventions: Elements and Compounds – video
http://videos.howstuffworks.co.....-video.htm
Bombardment Makes Civilization Possible
What is the common thread among the following items: pacemakers, spark plugs, fountain pens and compass bearings? Give up? All of them currently use (or used in early versions) the two densest elements, osmium and iridium. These two elements play important roles in technological advancements. However, if certain special events hadn’t occurred early in Earth’s history, no osmium or iridium would exist near the planet’s surface. http://www.reasons.org/Bombard.....onPossible
As well, many types of bacteria in earth’s early history lived in what are called cryptogamic colonies on the earth’s primeval continents. These colonies dramatically transformed the primeval land into stable nutrient filled soils which were receptive for future advanced vegetation to appear.
CRYPTOBIOTIC SOIL -
Excerpt: When moistened, cyanobacteria become active, moving through the soil and leaving a trail of sticky material behind. The sheath material sticks to surfaces such as rock or soil particles, forming an intricate web of fibers throughout the soil. In this way, loose soil particles are joined together, and an otherwise unstable surface becomes very resistant to both wind and water erosion.
Materialism has no answers for why these different bacterial types, colonies, and processes, would start working in precise concert with each other preparing the earth for future life to appear from the very start of their appearance on earth.
As well, several different types of bacteria are found to be integral, “key”, for the nitrogen fixation cycle required for plants:
nitrogen fixation – illustration
http://www.bio.miami.edu/dana/.....ncycle.gif
Kahn further notes on terra-forming:
Planet’s Nitrogen Cycle Overturned – Oct. 2009
Excerpt: “Ammonia is a waste product that can be toxic to animals.,,, archaea can scavenge nitrogen-containing ammonia in the most barren environments of the deep sea, solving a long-running mystery of how the microorganisms can survive in that environment. Archaea therefore not only play a role, but are central to the planetary nitrogen cycles on which all life depends.,,,the organism can survive on a mere whiff of ammonia – 10 nanomolar concentration, equivalent to a teaspoon of ammonia salt in 10 million gallons of water.”
http://www.sciencedaily.com/re.....132656.htm
Novel Nitrogen Uptake Design – Oct. 2009
Excerpt: The exceptionality of the snow roots and their nitrogen-capturing machinery, their extraordinarily complex designs, and their optimal efficiency qualifies them as evidence, not for evolution, but rather for supernatural design.
http://www.reasons.org/NovelNitrogenUptakeDesign
Moreover, the overall principle of long term balanced symbiosis, which is what we have with the overall chemical cycles of the earth, is a very anti-random chance fact which pervades the entire ecology of our planet:
God’s Creation – Symbiotic (Cooperative) Relationships – video
http://www.youtube.com/watch?v=bgVkeXRkZec
Since oxygen readily reacts and bonds with many of the solid elements making up the earth itself, and since the slow process of tectonic activity controls the turnover of the earth’s crust, it took photosynthetic bacteria a few billion years before the earth’s crust was saturated with enough oxygen to allow a “sufficient level” of oxygen to be built up in the atmosphere, as evidenced by the red banded iron formations and other geological evidence.
New Wrinkle In Ancient Ocean Chemistry – Oct. 2009
Excerpt: “Our data point to oxygen-producing photosynthesis long before concentrations of oxygen in the atmosphere were even a tiny fraction of what they are today, suggesting that oxygen-consuming chemical reactions were offsetting much of the production,”
http://www.sciencedaily.com/re.....141217.htm
Once oxygenation of the earth’s mantle and atmosphere 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 abrupt appearance of large mammals in the fossil record who depend on those high oxygen levels. Interestingly, for the last 10 million years the oxygen percentage has been holding steady around 21%. 21% happens to be a “very comfortable” percentage for humans to exist. If the oxygen level was only a few percentage lower, large mammals would become severely hampered in their ability to metabolize energy; if only a few percentage higher, there would be uncontrollable outbreaks of fire across the land (Denton; Nature’s Destiny).
This following article and video clearly indicate that the life sustaining balanced symbiosis of the atmosphere is far more robust that Global Warming alarmist would have us believe:
Earth’s Capacity To Absorb CO2 Much Greater Than Expected: Nov. 2009
Excerpt: New data show that the balance between the airborne and the absorbed fraction of carbon dioxide has stayed approximately constant since 1850, despite emissions of carbon dioxide having risen from about 2 billion tons a year in 1850 to 35 billion tons a year now. This suggests that terrestrial ecosystems and the oceans have a much greater capacity to absorb CO2 than had been previously expected.
http://www.sciencedaily.com/re.....141842.htm
Global Warming Apocalypse? No! – video
http://video.google.com/videop.....165214524#
Because of this basic chemical requirement of complex photosynthetic bacterial life establishing and helping maintain the proper oxygen levels necessary for higher life forms on any earth-like planet, this gives us further reason to strongly believe the earth is extremely unique in its ability to support intelligent life in this universe. Remember, this balance for the atmosphere is maintained through complex symbiotic relationships with other bacteria, all of which are intertwined in a very complex biogeochemical process. All these preliminary studies of early life, and processes, on early earth fall in line with the anthropic hypothesis and have no rational explanation, from any materialistic theory based on blind chance, as to why all the first types of 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 materialism 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.
Microbial life can easily live without us; we, however, cannot survive without the global catalysis and environmental transformations it provides. – Paul G. Falkowski – Professor Geological Sciences – Rutgers
bornagain77 at 242,
Mustela, both of those examples came at a overall loss of functional complexity that was inherent in the parent bacteria
Please define “functional complexity” in a mathematically rigorous manner and then demonstrate your calculations for each variant of e. coli under discussion.
Joseph at 244,
“The meaning of “nested hierarchy” as used by evolutionary biologists does not include immutable and additive defining characteristics, however much you may wish it to be otherwise.”
Evolutionary biologists do not get to change the meaning of nested hierarchies to suit their needs.
You do not get to change the definition being used by evolutionary biologists.
Summary of the pronciples of hierarchy theory
That is from the ISSS-International Society for the System Sciences.
“The facts are that all living species fall into a nested hierarchy based on their genetic heritage.”
The fact is nested hierarchies are constructed based on defined characteristics.
Again, you are playing word games instead of addressing the underlying empirical evidence.
It is a fact that, regardless of the traits under consideration, the same phylogeny is derived for all living things. This is truly remarkable support for modern evolutionary theory.
Regardless of your disagreement with the way that evolutionary biologists define the term, arguing against their definition is by no means equivalent to arguing against modern evolutionary theory. The evidence is there, for anyone who wants to educate themselves on the topic.
Joseph at 245,
Evolution is not being debated.
Actually, bornagain77 appears to be asserting that evolution does not, in fact, occur. If I am misinterpreting his or her position, I look forward to being corrected.
Mustela, actually since the fitness test is not passed, I do not have to hunt down the genes and proteins that confer increased functional complexity of 140 functional bits (FITS) since there are in fact no new genes and proteins that have given the bacteria increased functional complexity. But if you want to challenge my assertion here is the fitness test and math:
It has now been demonstrated Irreducible Complexity can be mathematically quantified as functional information bits(Fits).
Functional information and the emergence of bio-complexity:
Robert M. Hazen, Patrick L. Griffin, James M. Carothers, and Jack W. Szostak:
Abstract: Complex emergent systems of many interacting components, including complex biological systems, have the potential to perform quantifiable functions. Accordingly, we define ‘functional information,’ I(Ex), as a measure of system complexity. For a given system and function, x (e.g., a folded RNA sequence that binds to GTP), and degree of function, Ex (e.g., the RNA-GTP binding energy), I(Ex)= -log2 [F(Ex)], where F(Ex) is the fraction of all possible configurations of the system that possess a degree of function > Ex. Functional information, which we illustrate with letter sequences, artificial life, and biopolymers, thus represents the probability that an arbitrary configuration of a system will achieve a specific function to a specified degree. In each case we observe evidence for several distinct solutions with different maximum degrees of function, features that lead to steps in plots of information versus degree of functions.
http://genetics.mgh.harvard.ed.....S_2007.pdf
Mathematically Defining Functional Information In Molecular Biology – Kirk Durston – short video
http://www.youtube.com/watch?v=vUeCgTN7pOo
Entire video:
http://www.seraphmedia.org.uk/ID.xml
Is Antibiotic Resistance evidence for evolution? – “The Fitness Test” – video
http://www.youtube.com/watch?v=_BwWpRSYgOE
Testing the Biological Fitness of Antibiotic Resistant Bacteria – 2008
http://www.answersingenesis.or.....-drugstore
List Of Degraded Molecular Abilities Of Antibiotic Resistant Bacteria:
http://www.trueorigin.org/bacteria01.asp
bornagain77 at 252,
Mustela, actually since the fitness test is not passed, I do not have to hunt down the genes and proteins that confer increased functional complexity of 140 functional bits (FITS) since there are in fact no new genes and proteins that have given the bacteria increased functional complexity.
What fitness test isn’t passed? The strains of bacteria under discussion evolved the ability to digest citrate and nylon, respectively. These are new characteristics. You claimed that the evolution of new characteristics is impossible. You have been proven wrong.
Mustela, When the nylon is consumed from the environment the parent strain is “more fit” than the nylonase sub-strain:
As well Mustela,
excerpt:
Some materialists also believe they have conclusive proof for evolution because bacteria can quickly adapt to detoxify new man-made materials, such as nylon, even though it is, once again, just a minor variation within kind, i.e. though the bacteria adapt they still do not demonstrate a gain in fitness over the parent strain once the nylon is consumed (Genetic Entropy). I’m not nearly as impressed with their “stunning” proof as they think I should be. In fact recent research has shown the correct explanation for the nylon-eating enzyme, produced on the plasmids, seems to be a special mechanism which recombines parts of the genes in the plasmids in a way that is non-random. This is shown by the absence of stop codons, which would be generated if the variation were truly random. The non-randomness and “clockwork” repeatability of the adaptation clearly indicates a designed mechanism that fits perfectly within the limited “variation within kind” model of Theism, and stays well within the principle of Genetic Entropy since the parent strain is still more fit for survival once the nylon is consumed from the environment. (Answers In Genesis)
Why Scientists Should NOT Dismiss Intelligent Design – William Dembski
Excerpt: “the nylonase enzyme seems “pre-designed” in the sense that the original DNA sequence was preadapted for frame-shift mutations to occur without destroying the protein-coding potential of the original gene. Indeed, this protein sequence seems designed to be specifically adaptable to novel functions.” http://www.uncommondescent.com.....nt-design/
In fact almost all “changes” in the genome, which are deemed to be “beneficial”, are now found to be “designed” changes that still stay within the overriding principle of Genetic Entropy:
Revisiting The Central Dogma (Of Evolution) In The 21st Century – James Shapiro – 2008
Excerpt: Genetic change is almost always the result of cellular action on the genome (not replication errors). (of interest – 12 methods of information transfer in the cell are noted in the paper) http://www.uncommondescent.com.....revisited/
“There is no known law of nature, no known process and no known sequence of events which can cause information to originate by itself in matter.” Werner Gitt, “In the Beginning was Information”, 1997, p. 106. (Dr. Gitt was the Director at the German Federal Institute of Physics and Technology) His challenge to scientifically falsify this statement has remained unanswered since first published.
i.e. Abel Null Hypothesis
The Capabilities of Chaos and Complexity: David L. Abel – Null Hypothesis For Information Generation – 2009
To focus the scientific community’s attention on its own tendencies toward overzealous metaphysical imagination bordering on “wish-fulfillment,” we propose the following readily falsifiable null hypothesis, and invite rigorous experimental attempts to falsify it: “Physicodynamics cannot spontaneously traverse The Cybernetic Cut: physicodynamics alone cannot organize itself into formally functional systems requiring algorithmic optimization, computational halting, and circuit integration.” A single exception of non trivial, unaided spontaneous optimization of formal function by truly natural process would falsify this null hypothesis.
http://www.mdpi.com/1422-0067/10/1/247/pdf
http://mdpi.com/1422-0067/10/1/247/ag
Further note Mustela:
Nylon Degradation
Nylon 6 is a synthetic polymer consisting of more than 100 units of 6-aminohexanoic acid. Other forms of cyclic and non-cyclic nylon oligomers are formed as part of nylon 6 synthesis. Because nylon is not a natural occurring molecule, bacteria would not have been exposed to this polymer until the 20th century. The recent appearance of nylon degrading bacteria presents an interesting demonstration of bacterial ability to adapt to an ever changing environment and substrate. It has also lead to a few highly exaggerated claims regarding bacterial evolution.69
At the phenotypic level, the appearance of nylon degrading bacteria would seem to involve “evolution” of new enzymes and transport systems. However, further molecular analysis of the bacterial transformation reveals mutations resulting in degeneration of pre-existing systems. The most studied of the nylon degrading bacteria is Arthrobacter sp. K172 (formerly Flavobacterium sp.70). This bacterium employs three enzymes for nylon degradation, EI (NylA), EII (NylB), and EIII (NylC), which are found on the plasmid, pOAD2.71, 72
EI and EIII (also NylC in Agromyces sp.) have been initially characterized.73, 72 They apparently hydrolyze the cyclic forms of some nylons, which provides a linear substrate for EII. However, no detailed analysis of the mutational changes of EI or EIII has yet been performed.
Confirmational Change of the Carboxyesterase
Figure 4. Confirmational change of the carboxyesterase. The esterase (left) can hydrolyze carboxy esters, but the confirmation specificity of the enzyme’s catalytic site does not allow hydrolysis of other polymers, such as nylon. Point mutations in the enzymes’ gene can cause a conformational alteration of the enzyme’s catalytic site so that specificity is reduced (right). This reduced specificity now allows the enzyme to hydrolyze a wider variety of oligomers, including the linear polymer, nylon-6.
The mutational changes of EII (6-aminohexanoatedimer hydrolase) have been characterized in detail. This analysis suggests that point mutations in a carboxyesterase gene lead to amino acid substitutions in the enzyme’s catalytic cleft. This altered the enzyme’s substrate specificity sufficiently that it could also hydrolyze linear nylon oligomers.74, 75 Yet, the EII enzyme still possesses the esterase function of the parent esterase. Thus, the mutational alteration results in a reduction of the parent enzyme’s specificity (Figure 4). This enables it to hydrolyze a wider range of oligomers that include nylon oligomers.76
Nonetheless, reduced specificity of a pre-existing enzyme is biochemically degenerative to the enzyme,77, 78 even if it provides a presumed phenotypic benefit. The “beneficial” phenotype of nylon degradation requires the a priori existence of the enzyme and its specificity. Its degeneration is not a mechanism that accounts for the origin of either the enzyme or its specificity.
Also on pOAD2 is a DNA region with a high homology to opp genes.79 These genes are involved in oligopeptide transport. Nylon oligomers have many chemical similarities to oligopeptides, thus genes on this region of the plasmid may be involved in nylon transport into the cell. No analysis of how these genes may have been altered by mutations has yet been preformed. However, it is reasonable to speculate that a pre-existing opp gene or set of genes has been altered sufficiently by mutations so that the transport proteins now have an affinity for nylon in addition to naturally occurring oligopeptides. As with enzymes, reduction of transport protein specificity is biochemically degenerative.
The enzyme and putative transport genes on pOAD2 appear to form a nylon degrading operon.79 As a plasmid based operon, it can be transferred to various bacterial species. Thus, this gives it the potential for widespread distribution in the bacterial world. What is more, the increasing amount of microbial degradation of synthetic material11 may likely involve a similar mutational strategy as found with nylon degradation. This is a testament to the versatility of bacterial adaptation. However, these mutations do not account for the origin of the enzyme or transport protein specificity, merely their degeneration. Thus, this adaptive versatility has imposed limits as well, and this fits well within the types of mutational changes predicted by a creation model.
http://www.answersingenesis.or.....n-bacteria
bornagain77 at 254,
When the nylon is consumed from the environment the parent strain is “more fit” than the nylonase sub-strain:
Assuming, ad arguendo, that this is correct, so what? This exchange started with your 218:
Mustela states:
“It’s perfectly possible for characteristics to be added, modified, or deleted within a nested inheritance hierarchy.”
Well Mustela just how possible is it for characteristics to be added ?
I have explained exactly how this is possible and given two very well documented examples of evolutionary mechanisms adding new characteristics. In the case of nylonase, the new characteristic appears to be the result of a single point or frameshift mutation. In Lenski’s experiment, it appears to require two or possibly three separate mutations. Regardless, both demonstrate the creation of new characteristics via evolutionary mechanisms.
The only appropriate response from you at this point is “Thank you, I stand corrected.”
Mustela, I’m sorry but you are clearly wrong in this matter. The adaptations are clearly designed adaptations that degrade from what was already present in the parent stocks genome. You have only deluded yourself if you think otherwise, I suggest you honestly and rigorously account for the evolution, as I have outlined previously with the proper test and math, to do otherwise is to fudge the evidence due to your philosophical bias::
This following articles refute Lenski’s supposed “evolution” of the citrate ability for the E-Coli bacteria after 20,000 generations of the E-Coli:
Multiple Mutations Needed for E. Coli – Michael Behe
Excerpt: As Lenski put it, “The only known barrier to aerobic growth on citrate is its inability to transport citrate under oxic conditions.” (1) Other workers (cited by Lenski) in the past several decades have also identified mutant E. coli that could use citrate as a food source. In one instance the mutation wasn’t tracked down. (2) In another instance a protein coded by a gene called citT, which normally transports citrate in the absence of oxygen, was overexpressed. (3) The overexpressed protein allowed E. coli to grow on citrate in the presence of oxygen. It seems likely that Lenski’s mutant will turn out to be either this gene or another of the bacterium’s citrate-using genes, tweaked a bit to allow it to transport citrate in the presence of oxygen. (He hasn’t yet tracked down the mutation.),,, If Lenski’s results are about the best we’ve seen evolution do, then there’s no reason to believe evolution could produce many of the complex biological features we see in the cell.
http://www.amazon.com/gp/blog/.....96N278Z93O
Lenski’s e-coli – Detailed Analysis of Genetic Entropy
Excerpt: Mutants of E. coli obtained after 20,000 generations at 37°C were less “fit” than the wild-type strain when cultivated at either 20°C or 42°C. Other E. coli mutants obtained after 20,000 generations in medium where glucose was their sole catabolite tended to lose the ability to catabolize other carbohydrates. Such a reduction can be beneficially selected only as long as the organism remains in that constant environment. Ultimately, the genetic effect of these mutations is a loss of a function useful for one type of environment as a trade-off for adaptation to a different environment.
http://www.answersingenesis.or.....n-bacteria
Upon closer inspection, it seems Lenski’s “cuddled” E. coli are actually headed for “genetic meltdown” instead of evolving into something better.
New Work by Richard Lenski:
Excerpt: Interestingly, in this paper they report that the E. coli strain became a “mutator.” That means it lost at least some of its ability to repair its DNA, so mutations are accumulating now at a rate about seventy times faster than normal.
http://www.evolutionnews.org/2.....enski.html
Excerpt of summary of Nylon adaptation:
Why Scientists Should NOT Dismiss Intelligent Design – William Dembski
Excerpt: “the nylonase enzyme seems “pre-designed” in the sense that the original DNA sequence was preadapted for frame-shift mutations to occur without destroying the protein-coding potential of the original gene. Indeed, this protein sequence seems designed to be specifically adaptable to novel functions.” http://www.uncommondescent.com.....nt-design/
Nylon Degradation – Analysis of Genetic Entropy
Excerpt: At the phenotypic level, the appearance of nylon degrading bacteria would seem to involve “evolution” of new enzymes and transport systems. However, further molecular analysis of the bacterial transformation reveals mutations resulting in degeneration of pre-existing systems.
http://www.answersingenesis.or.....n-bacteria
to use your own words against you:
The only appropriate response from you at this point is “Thank you, I stand corrected.”
bornagain77 at 258,
The adaptations are clearly designed adaptations
Really? Then you should have no problem identifying the designer and explaining when and, most importantly, how these acts of designs were accomplished.
If you cannot, one would be justified in believing that you are simply making another baseless assertion and that you are incapable of admitting error even when it is clearly pointed out to you.
Actually Mustela, the proper response was to admit you have no examples to substantiate your claims for evolution, than to go off half-cocked. The designer???? For me the answer that is consistent with reality as revealed to us by quantum mechanics is John 1:1 !!!!
I see that further discussion is unlikely to prove fruitful. The last word is yours.
Mustela it would only be unfruitful for the person committed to a false premise of materialism.