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Thursday, December 11, 2008

The Philosopher's Stone


The following statements are similar:

Abraham Lincoln was born in the United States of America.


My birthday is August 15th.

These are factual statements that can be backed up with evidences so strong that they can be construed as proof.


The following statements are similar:

Some people believe in evolution. Natural selection and mutation can account for all living beings.



I believe in creation. A Creator God designed and produced all living things.

They are similar because both are statements of faith that have not been proven to be true.

You can believe in the Easter Bunny.
You can believe in astrology.



Believe what you like, unless you can prove it you cannot pretend that it has become fact. Unfortunately, the scientific community pretends that evolution is proven fact (sometimes resorting to euphemisms) rather than an unproven hypothesis lacking in hard evidences.

Make no mistake about this, macroevolution has not only not been proven, it has never been demonstrated to have happened and years of study of microorganisms and species such as fruit flies have only tended to produce evidence that supports creationist and/or intelligent design viewpoints. But no proof. Not on either side. I cannot prove that God exists nor can I prove that He created everything. I can, however review the evidence and see that the preponderance of evidence indicates a designed and created world, a world that underwent a massive global flood event with catastrophic effects upon the global climate and topology for many years afterwards.

The Philosopher's Stone or, actually, the search for it was the primary driving force behind alchemy...for one thousand years!

"The philosopher's stone is a legendary substance, allegedly capable of turning inexpensive metals into gold. It was sometimes believed to be an elixir of life, useful for rejuvenation and possibly for achieving immortality. For a long time, it was the most sought-after goal in Western alchemy. In the view of spiritual alchemy, making the philosopher's stone would bring enlightenment upon the maker and conclude the Great Work. It is also known by several other names, such as 'materia prima.' "

Real science was born during the futile search for a magic substance or formula that could transmute, for instance, lead into gold. Eventually all but the fringiest of "scientists" gave up on the idea in its original form.

"The concept of a substance that could turn inexpensive metals into valuable gold naturally attracted the attention of many entrepreneurs of all sorts - learned and amateurish, skeptical and gullible, honest and dishonest. An example that illustrates the spirit of the times is that of Rudolf II (1552-1612). This king of Bohemia, having found himself in financial difficulties, decided to invest heavily in the search for the philosopher's stone. He thus attracted to Prague a large number of alchemists, who were given ample material and financial support, and promised rewards if they could solve the problem. This "virtual gold rush" may have involved even the Danish astronomer Tycho Brahe, then at Rudolf's court, who had an alchemical lab built on the grounds of his observatory.

Rudolf never saw his dream realized, and he eventually became insane and had to be deposed by his relatives. It is not known whether his insanity was due to natural causes, or to misuse of alchemical "remedies" which often included toxic materials like sulphur, lead, mercury, arsenic, and antimony. "

Oddly enough, in the spiritual realm the seach for the Stone leads many a man, including myself, to Jesus Christ...the Cornerstone of the Christian faith. My personal and sometimes bizarre quest to understand what Truth is eventually led me to a God Who had never been more than a heartbeat away from me. I would have been destined to meet Him on bad terms had I died before discerning His saving grace.

The search for the Stone in the physical realm greatly advanced the cause of the science of chemistry, despite the hopelessness of the quest itself.

Research scientists in various disciplines of biology and chemistry in particular have sought clues within organisms to demonstrate how evolution must have happened. The desire to find hard evidences for macroevolution and its mechanisms has fueled millions of hours of study and had billions of dollars spent in the process. While the basic quest has and will continue to fail, advances in our knowledge of biology and chemistry have resulted.

There is a material now widely known as Gore-Tex. It was developed for the space industry in the 1970's. However, it was also the material that doctors used to save the life of my one-day-old daughter in 1985 as an artificial aorta in a critical surgical procedure that saved her life. The developers of Gore-Tex were not thinking of finding a substance that could take the place of an infant's aorta while working on developing it, they were looking for a substance that could be useful in the extreme environments encountered by astronauts. Turns out that it has become a major fabric in the rainwear industry as well as in medical implants, gaskets and other uses. It has had many unintended uses.

Neo-Darwinist researchers have advanced the cause of science in learning more about the makeup of organisms and the systems they use. We know a great deal more about the effects of mutation on populations as well as more efficient ways of producing plants and animals that more efficiently provide our food supply.

However, claims that scientists have generated proof of evolution are simply not true. Allow me to present an example:


Is Bacterial Resistance
To Antibiotics An Appropriate Example Of Evolutionary Change?


"
Kevin Anderson, Ph.D.© 2005 by Creation Research Society. All rights reserved. Used by permission. This article first appeared in Vol. 41, No. 4 of the Creation Research Society Quarterly, a peer-reviewed journal published by the Creation Research Society.

Abstract

Evolutionists frequently point to the development of antibiotic resistance by bacteria as a demonstration of evolutionary change. However, molecular analysis of the genetic events that lead to antibiotic resistance do not support this common assumption. Many bacteria become resistant by acquiring genes from plasmids or transposons via horizontal gene transfer.
Horizontal transfer, though, does not account for the origin of resistance genes, only their spread among bacteria. Mutations, on the other hand, can potentially account for the origin of antibiotic resistance within the bacterial world, but involve mutational processes that are contrary to the predictions of evolution. Instead, such mutations consistently reduce or eliminate the function of transport proteins or porins, protein binding affinities, enzyme activities, the proton motive force, or regulatory control systems. While such mutations can be regarded as “beneficial,” in that they increase the survival rate of bacteria in the presence of the antibiotic, they involve mutational processes that do not provide a genetic mechanism for common “descent with modification.” Also, some “relative fitness” cost is often associated with such mutations, although reversion mutations may eventually recover most, if not all, of this cost for some bacteria. A true biological cost does occur, however, in the loss of pre-existing cellular systems or functions. Such loss of cellular activity cannot legitimately be offered as a genetic means of demonstrating evolution.

Introduction

Because of their rapid rate of replication, ease of laboratory analysis, and the wide diversity of laboratory-generated mutants that can be obtained, bacteria have been described as an excellent model for studying the processes of evolution (Mortlock, 1984). Acquiring resistance to a specific antibiotic provides a clear benefit to the bacterium when exposed to that antibiotic. Thus, the acquisition of antibiotic resistance is commonly cited as an example of “evolutionary change,” and has become a popular example of so-called “evolution in a Petri dish.” Miller (1999) refers to the development of antibiotic resistance as an example of evolution’s “creative force.” Barlow and Hall (2002) refer to it as “the unique opportunity to observe evolutionary processes over the course of a few decades instead of the several millennia that are generally required for these processes to occur.” (p. 314)

Evolution is often described simply as ‘change’ or ‘change in gene frequency over time’ (Dillon, 1978; Johnson, 2000; Patterson, 1978), and evolutionists have almost universally maintained that any change in genotype (or even phenotype) is an “evolutionary change.” As such, any biological change of an organism, including antibiotic resistance, would fit within this definition. However, mere biological change also fits within a creation model, and thus this “vanilla” definition does not readily distinguish itself from creation. This definition also does not specify the type of change (such as deleterious versus beneficial), thus it fails to offer any predictive value to the theory.

What is more, any change that appears to provide a so-called “beneficial” adaptation is commonly seen as a driving force of evolution. Indeed, some mutations, such as antibiotic resistance, can be beneficial since they may provide the organism an increased ability to survive under very specific environmental conditions. Thus, evolutionists typically conclude that genetic examples of “evolutionary change” are abundant and that creationists are forced to deny this readily observed evidence.

However, the theory of evolution proposes that all life on Earth had a common origin. Hence, all life shares a common evolutionary ancestry from which it has descended, i.e., the “common descent” of life. In a summarizing statement, Darwin (1936) states that “the theory of descent with modification embraces all the members of the same great class or kingdom ... all animals and plants are descended from some one prototype.” (p. 370). Therefore, through this overall common “descent with modification,” the theory of evolution claims to account for the origin and diversity of all biological development on Earth. Thus, common “descent with modification” provides a more appropriate and functional definition of the theory of evolution, and this article will refer to evolution in this context. This definition also entails several “predictions” regarding the types of genetic change necessary for common evolutionary descent (predictions that are in sharp contrast to the “predictions” of a creation model). Such changes must provide more than mere changes in phenotype; they must provide a genetic mechanism that accounts for the origin of cellular functions and activities (i.e., regulatory systems, transport systems, enzyme specificity, protein binding affinity, etc.).

Genetic changes that reduce or eliminate any of these cellular systems provide no genetic mechanism for common “descent with modification.” Rather, such changes are actually the antithesis of this descent, reducing or eliminating a pre-existing system of biological complexity (a reversal of “descent with modification”). Therefore, these genetic changes offer no example of a genetic mechanism for the “evolutionary” acquisition of flight by non-flying organisms, cognition by non-cognitive organisms, photosynthesis by non-photosynthesizing organisms, etc. Yet the theory of evolution requires such events to have occurred, and requires mutations capable of such genetic changes. Hence, the predictions of evolution require specific types of changes, not just so-called “beneficial” mutations. Therefore, despite the great claims that have been made, it is imperative to question whether acquisition of antibiotic resistance is a valid example of evolutionary change that supports the predictions of the evolutionary theory (i.e., the theory of common “descent with modification”).

The author continues to give specific examples. I will copy the rest here and then intersperse some comments (in black) with his article, which continues in blue.


Horizontal Gene Transfer

One means by which bacteria can acquire antibiotic resistance is via the horizontal transfer of antibiotic resistant genes. Such transfer of resistance genes is common (Gómez, 1998; Top et al., 2000), accounting for many examples of resistant bacteria. But, horizontal transfer merely involves the transfer of resistance genes already present in the bacterial world.

While horizontal acquisition of resistant genes is “beneficial” to those bacteria exposed to a given antibiotic, such gene transfer does not account for the origin or the diverse variety of these genes. As such, it fails to provide a genetic mechanism for the origin of any antibiotic resistance genes in the biological world. Evolution, through the process of common “descent with modification,” predicts it can account for the origin and diversity of life on earth; however, the mere shuffling of pre-existing genes between organisms via gene transfer does not provide the necessary genetic mechanism to satisfy this prediction. Nor can it readily account for the simultaneous development of both the antibiotic biosynthesis and resistance genes—an evolutionary enigma (Penrose, 1998). Thus, horizontal transfer of resistant genes cannot be offered as an appropriate example of “evolution in a Petri dish.”

Transfer of genetic material from one organism to another does not constitute evidence for macroevolution because no new systems are being introduced. Easy to understand this.

Mutations

Mutations, defined as any changes in the DNA sequence (Snyder and Champness, 2003), provide the only known genetic mechanism for producing new genetic activity and function in the biological world. In light of this, only mutations have the potential to provide evolution a mechanism that accounts for the origin of antibiotic resistance. Thus, only that resistance resulting from a mutation is a potential example of “evolution in action” (i.e., common “descent with modification”).

In the presence of a particular antibiotic (or other antimicrobial), any mutation that protects the bacterium from the lethality of that compound clearly has a “beneficial” phenotype. Natural selection will strongly and somewhat precisely select for those resistant mutants, which fits within the framework of an adaptive response. But, molecular analysis of such mutations reveals a large inconsistency between the true nature of the mutation and the requirements for the theory of evolution (Table I).

Table I. Mutation Phenotypes Leading to Resistances of Specific Antibiotics.


Antibiotic - Phenotype Providing Resistance
Actinonin - Loss of enzyme activity
Ampicillin - SOS response halting cell division
Azithromycin - Loss of a regulatory protein
Chloramphenicol -Reduced formation of a porin or a regulatory protein
Ciprofloxacin - Loss of a porin or loss of a regulatory protein
Erythromycin - Reduced affinity to 23S rRNA or loss of a regulatory protein
Fluoroquinolones - Loss of affinity to gyrase
Imioenem - Reduced formation of a porin
Kanamycin - Reduced formation of a transport protein
Nalidixic Acid - Loss or inactivation of a regulatory protein
Rifampin - Loss of affinity to RNA polymerase
Streptomycin - Reduced affinity to 16S rRNA or reduction of transport activity
Tetracycline - Reduced formation of a porin or a regulatory protein
Zittermicin A - Loss of proton motive force

Bacterial resistance to the antibiotic, rifampin, can result from a commonly occurring spontaneous mutation. Rifampin inhibits bacterial transcription by interfering with normal RNA polymerase activity (Gale et al., 1981; Levin and Hatfull, 1993). Bacteria can acquire resistance by a point mutation of the ß-subunit of RNA polymerase, which is encoded by the rpoB gene (Enright et al., 1998; Taniguchi et al., 1996; Wang et al., 2001; Williams et al., 1998). This mutation sufficiently alters the structure of the ß-subunit so that it loses specificity for the rifampin molecule. As a result, the RNA polymerase no longer has an affinity for rifampin, and is no longer affected by the inhibitory effect of the antibiotic.

In fact, the level of rifampin resistance that a bacterium can spontaneously acquire can be extremely high. In my laboratory, we routinely obtain mutant strains with a resistance level that is orders of magnitude greater than that of the wild-type strain. When rifampin is present, this mutation provides a decided advantage for survival compared with those cells lacking these specific mutations. But, each of these mutations eliminates binding affinity of RNA polymerase for the rifampin. As such, these mutations do not provide a mechanism accounting for the origin of that binding affinity, only its loss.

Spontaneous resistance to fluoroquinolones (such as ciprofloxacin or norfloxacin) is also a frequent mutation in some bacteria. The primary target of the antibiotic is the enzyme, DNA gyrase, which is comprised of two proteins encoded by the genes, gyrA and gyrB (Hooper and Wolfson, 1993). Genetic analysis has found that resistance to this class of antibiotics can result from a point mutation in either of these genes (Barnard and Maxwell, 2001; Griggs et al., 1996; Heddle and Maxwell, 2002; Heisig et al., 1993, Willmott and Maxwell, 1993). These mutations of the gyrase subunits apparently cause a sufficient conformational change to the gyrase so that its affinity for the fluoroquinolones is reduced or lost (Figure 1). Again, despite their “beneficial” nature, these mutations provide no useful model that explains the origin of the gyrase’s affinity for the fluoroquinolones.

Figure 1. Mechanism of ciprofloxacin resistance.(A) Ciprofloxacin interacts with gyrase, inhibiting its enzymatic activity. (B) A mutation in either of the genes, gyrA or gyrB, can change the conformational structure of gyrase, and reduce the binding affinity of the enzyme for ciprofloxacin. This results in an inability of the antibiotic to inhibit the gyrase, and the cell becomes resistant to the antibiotic.






Resistance to streptomycin can also result from spontaneous bacterial mutations. In this case, streptomycin blocks bacterial protein synthesis apparently by binding to the 16S rRNA segment of the ribosome and interfering with ribosome activity (Carter et al., 2000; Leclerc et al., 1991). Resistance to the antibiotic can occur by mutations in the 16S rRNA gene, which reduces the affinity of streptomycin for the 16S molecule (Springer et al., 2001). Reduction of specific oligopeptide transport activities also leads to spontaneous resistance of several antibiotics, including streptomycin (Kashiwagi et al., 1998). In these examples, resistance occurred as a result of the loss of a functional component/activity.

Loss of enzymatic activity can result in metronidazole resistance. Interacellular metronidazole must be enzymatically activated before it can serve as an antimicrobial agent. This activation is achieved by the enzyme, NADPH nitroreductase (Figure 2). If the metronidazole is not activated it has no inhibitory effect on the bacterium. Thus, if NADPH nitroreductase activity is absent in the cell metronidazole remains inactive. Loss of the reductase activity can occur by nonsense or deletion mutations in rdxA (Debets-Ossenkopp et al., 1999; Goodwin et al., 1998; Tankovic et al., 2000). In addition, NADPH nitroreductase activity can be severely reduced by a single missense mutation (a single amino acid change), which reduces its ability to activate metronidazole (Paul et al., 2001). All these mutations result in loss of the enzyme activity necessary for the drug to be effective in the cell, hence the cell becomes resistant to metronidazole. But, loss of enzymatic activity does not provide a genetic example of how that enzyme originally “evolved.” Hence, mutations that provide resistance to metronidazole cannot be offered as true examples of “evolution in a Petri dish.”

Several bacteria, including Escherichia coli, construct a mulitiple-antibiotic-resistance (MAR) efflux pump that provides the bacterium with resistance to multiple types of antibiotics, including erythromycin, tetracycline, ampicillin, and nalidixic acid. This pump expels the antibiotic from the cell’s cytoplasm, helping to maintain the intracellular levels below a lethal concentration (Grkovic et al., 2002; Okusu et al., 1996) (Figure 3). The MAR pump is composed of the proteins MarA and MarB, whose synthesis is inhibited by the regulatory protein, MarR (Alekshun and Levy, 1999; Poole, 2000) (Figure 3). Mutations that reduce or eliminate the repression control of MarR result in over-production of the MarAB efflux pump, which enables the cell to expel higher concentrations of antibiotics or other antibacterial agents (Oethinger et al., 1998; Poole, 2000; Zarantonelli et al., 1999).

Figure 2. Activation of the antimicrobial agent, metronidazole.After being transported into the cell, metronidazole requires structural modification to obtain its active, antimicrobial form. This activation is achieved by the enzyme, NADPH nitroreductase, which is a product of the rdxA gene. Mutations in rdxA can prevent synthesis of a functional NADPH nitroreductase activity, which prevents metronidazole from becoming activated.



The protein MarA also acts as a positive regulator by stimulating increased production of both MarA and MarB proteins (Alekshun and Levy, 1999) (Figure 3). In addition, the MarA protein indirectly inhibits the production of the porin, OmpF, a channel in the membrane that allows entry of some antibiotics into the cell (Cohen et al., 1988). Therefore, increased expression of MarA increases the efflux of antibiotics out of the cell, and reduces the transport of some antibiotics into the cell (Figure 3). Mutations of marR that reduce expression or activity of the MarR protein will thus enable over-expression of the MarAB efflux pump (Linde et al., 2000; Okusu et al., 1996), and provide an increased resistance of the bacterium to various antibiotics (Eaves et al., 2004; Hans-Jorg et al., 2000; Notka et al., 2002) (Figure 3). MarR defective mutants also possess increased bacterial tolerance to some organic chemical agents, such as cyclohexane (Aono et al., 1998).

Mutations that increase production of this efflux pump enable these bacteria to survive exposure to various antibiotics. As such, this is a beneficial mutation when the antibiotic is present in the environment. However, a mutation that causes loss of regulatory control (in this case the repressor protein, MarR) does not offer a genetic mechanism that can account for the origin of this regulatory control.

Figure 3. Multidrug resistance efflux pump.(A) Antibiotic sensitive bacterium. The antibiotics enter the cell through various portals, including the OmpF porin. Expression of the marR gene produces the regulatory protein, MarR. This protein binds to the promoter (labeled as P) of the multidrug resistant operon, inhibiting expression of genes marA and marB. (B) Antibiotic resistant bacterium. A mutation of marR that reduces the activity of MarR enables the promoter to function constitutively. Both marA and marB are now expressed. These two proteins form an efflux pump, which transports antibiotic molecules out of the cell’s cytoplasm. MarA also binds to the promoter (labeled as P) and increases the transcription rate of the operon, which increases production of both MarA and MarB. In addition, production of MarA indirectly reduces the synthesis of the OmpF porin, thereby reducing the number of these porins in the membrane. The combination of fewer porins for transport of an antibiotic into the cell, and the increased number of MarAB efflux pumps removing the antibiotic out of the cell, provides the bacterium an increased tolerance to several antibiotics.

In other examples, resistance to erythromycin can also result from the loss of an 11 base pair segment of the 23S rRNA gene (Douthwaite et al., 1985), or a mutation that alters the confirmation of the 23S rRNA-reducing the affinity of the ribosome for the antibiotic (Gregory and Dahlberg, 1999; Vannuffel et al., 1992). Chloramphenicol resistance was obtained by deletion of a 12 base pair region in domain II of the peptidyltransferase gene (Douthwaite, 1992). Resistance to cephalosporins has been linked to a dramatic alteration of membrane transport kinetics that is similar to porin-deficient strains (Chevalier et al., 1999). Actinonin resistance in Staphylococcus aureusresults from mutations that eliminate expression of the fmt gene (Margolis et al., 2000). Zwittermicin A resistance in E. coli is associated with loss of proton motive force (Stabb and Handelsoman, 1998). For Streptococcus gordonii, penicillin tolerance may involve loss of regulatory control of the arc operon (Caldelari et al., 2000). And, E. coli can survive the presence of ß-lactams, such as ampicillin, by halting cell division, making the cell less sensitive to the lethal affect of the antibiotic (Miller et al., 2004).

These resistance mutations described above cause the loss of a pre-existing biological system, including cell division and proton motive force. Even though antibiotic survival is a “beneficial” phenotype, these mutations fail to provide a genetic example of how each of these systems originated. As such, they fail to provide a genetic means to fulfill the predictions of “descent with modification.”

Resistance to other antibiotics, such as kanamycin, can result from loss or reduction of synthesis of a transport protein (OppA) (Kashiwagi et al., 1998). Ciprofloxacin and imipenem resistance can result, at least in part, from the decreased formation of the outer membrane porin, OmpF (Armand-Lefèvre et al., 2003; Hooper et al., 1987; Yigit et al., 2002). An increase in meropenem and cefepime resistance is also associated with loss of OmpF, and another porin, OmpC (Yigit et al., 2002). And, Enterobacter aerogenes can become resistant to various antibiotics when a mutation dramatically reduces the conductance of a membrane porin (Dé et al., 2001).

Each of these resistances described in the previous paragraph result from the reduction or loss of a transport system. However, genetic mechanisms necessary for evolution would need to account for the origin of these various transport systems. Thus, these antibiotic resistance mutations do not provide the necessary genetic changes for “common descent.” Rather, they are genetically inconsistent with the requirements of evolution, each involving the loss of a pre-existing transport activity.

As a group, the mutations associated with antibiotic resistance involve the loss or reduction of a pre-existing cellular function/activity, i.e., the target molecule lost an affinity for the antibiotic, the antibiotic transport system was reduced or eliminated, a regulatory system or enzyme activity was reduced or eliminated, etc. (Table I). These are not mutations that can account for the origin of those cellular systems and activities. While these mutations would certainly be “beneficial” for bacterial survival when an antibiotic is present in the environment, this benefit is at the expense of a previously existing function. This is analogous to removing an interior wall of a house to make a larger dining room. While this larger dining room may be desirable (i.e., beneficial), the mechanism of removing this wall cannot legitimately be offered as an example of how this interior wall was originally built. Hence, the survival benefit of a mutation is only a portion of the genetic characteristics necessary for mutations to achieve “evolution in a Petri dish.” Such mutations must also provide the genetic basis for common “descent with modification.” While this directly contradicts the claims made by many proponents of evolution, the molecular data for antibiotic resistance are very clear.

These mutations also cannot provide a mechanism that continues to “evolve” the level of protein specificity or protein activity that is necessary for normal cellular function. While such mutations are excellent examples of bacterial adaptation, they are actually the antithesis of the mutational change necessary for evolution. Yet, these are the very examples evolutionists offer as verifiable demonstrations of “evolutionary change.” Ironically, these mutations are, in fact, verifiable examples of a creation model—initial complexity being mutated to a level of greater simplicity.

The spontaneous acquisition of antibiotic resistance is often referred to as “gaining” resistance, but it is more appropriately identified as a loss of sensitivity. Thus, antibiotic resistance results from the loss of pre-existing systems in the bacterial cell. Such changes clearly provide no genetic mechanism for the origin of such cellular features as enzyme specificity, transport activity, regulatory activity, or protein binding affinity. Yet, evolutionists consistently claim that mutations do provide a genetic mechanism for the origin of biological activity and common “descent with modification,” and consistently offer the types of mutations described above as examples.

Suppose that the world was full of trap-door man-eating worms that build their nests in grassy fields. A man walking innocently across his lawn, not perceiving that such a worm had built it's trap on his property, might well walk out towards the mailbox but be snatched and eaten before he could get there by one of these worms. However, a man born without legs would be more likely to stay indoors and let others go outside for him. He would be therefore safe from the TDME worms. He would also have less mobility and be less attractive as a mate. His lack of legs would save him from the worms but make him a less viable organism in other ways. Such are many of the mutations that occur within microorganisms.

Dr. Anderson's example of a house in which an interior wall is removed is a simple illustration of what scientists find when they study changes within gene pools. Information loss and not gain is the way of the biological world. That interior wall may have had some weight-bearing responsibilities and so the house could well be less sturdy. Even if the wall had no other purpose, the removal of the wall is completely unlike the building of a new wall or adding a porch. It is a subtraction rather than addition. One cannot find evidences of new walls being built in nature but rather one finds examples of subtraction of walls. Even if such subtractions have a use in some way for the organism it is an evidence of design more so than evolution. A wise designer allows for redundancies and plans for all sorts of possibilities. A gene pool that allows for great variation within kinds of organisms in order to survive within a wide range of possible environments makes for an organism that will not be as likely to become extinct.

Whether or not survival is threatened by such mutations is beside the point, as is addressed below.

Fitness Cost of Antibiotic Resistance

While mutations that provide resistance to an antibiotic can be considered “beneficial,” they often come with a physiological cost (Andersson and Levin, 1999; Maisnier-Patin et al., 2002). In fact, Björkman et al. (2000) conclude that most types of antibiotic resistance will impart some biological cost to the organism. For example, rifampin resistance in Mycobacterium tuberculosis (Billington et al., 1999), E. coli (Reynolds, 2000), and Staphylococcus aureus (Wichelhaus et al., 2002) resulted from mutations to the RNA polymerase that also reduced the relative fitness of most of the mutant strains. Although the biological cost reported by these researchers was generally not severe, it was measurable.

Mutations resulting in clarithromycin resistance in Helicobacter pylori reduce the relative fitness of the organism (Björkholm et al., 2001). Resistance to high levels of fluroquinolone by Salmonella entericainvolves mutations that impart a high fitness cost to the organism (Giraud et al., 2003). And, fusA mutations that provide fusidic acid resistance to Staphylococcus sp. impose a significant loss of “relative fitness” (Gustafsson et al., 2003; MacVanin et al., 2000). Resistance to actinonin by S. aureus also accompanies a dramatic loss of “fitness” resulting in significant growth impairment (Margolis et al., 2000). E. coli resistance to streptomycin may dramatically reduce the rate of protein biosynthesis (Zengel et al., 1977). And, some bacteria suspend cell division to minimize their sensitivity to ampicillin (Miller et al., 2004), which clearly reduces the overall fitness of the organism.

This cost of “relative fitness” appears to vary considerably depending on both the organism and the antibiotic. Many of the resistant mutants that have been studied, however, including some of those mentioned above, can subsequently eliminate some or much of the fitness cost by reversion or suppression mutations, which also stabilizes the mutation (Andersson and Levin, 1999; Lenski, 1998; Massey et al., 2001). The degree that a reversion mutation restores fitness probably depends on the location of the mutation and whether a single mutation is able to restore some or all of the wild-type “fitness.”

Clearly the fitness of some mutant strains is permanently reduced (sometimes dramatically), and evolutionists have typically ignored such affects in their rush to promote antibiotic resistance as “evolution in the Petri dish.” In fact, they often test relative fitness of these mutants under very narrow cultivation parameters, which minimizes the detectable loss of fitness for a given mutation. On the other hand, the fitness loss of some mutants is negligible (esp. following reversion mutations). So, the effect of spontaneous resistance on bacterial fitness appears to vary from mutant to mutant. Thus, creationists have probably tended to over-stress the significance of reduced “fitness” in antibiotic resistant bacteria by applying the concept to all such mutants.

Resistant mutations do impose a biological cost, though, in the loss of pre-existing biological systems and activities. Such biological cost is not compensated by reversion or suppression mutations. Even though such mutations may not always result in detectable levels of reduced “fitness,” they stand as the antithesis of common “descent with modification.”

Now Dr. Anderson summarizes succinctly. I have included the references after the summary, and you won't find them interesting unless you are a research microbiologist and want to read all of them for yourself. I will just say that I find the summary to be clearly scientific and in no way a statement of belief. That is how science ought to work. Any bolding you see in these article excerpts are mine.


Summary

Resistance to antibiotics and other antimicrobials is often claimed to be a clear demonstration of “evolution in a Petri dish.” However, analysis of the genetic events causing this resistance reveals that they are not consistent with the genetic events necessary for evolution (defined as common “descent with modification”). Rather, resistance resulting from horizontal gene transfer merely provides a mechanism for transferring pre-existing resistance genes. Horizontal transfer does not provide a mechanism for the origin of those genes.

Spontaneous mutation does provide a potential genetic mechanism for the origin of these genes, but such an origin has never been demonstrated. Instead, all known examples of antibiotic resistance via mutation are inconsistent with the genetic requirements of evolution. These mutations result in the loss of pre-existing cellular systems/activities, such as porins and other transport systems, regulatory systems, enzyme activity, and protein binding. Antibiotic resistance may also impart some decrease of “relative fitness” (severe in a few cases), although for many mutants this is compensated by reversion. The real biological cost, though, is loss of pre-existing systems and activities. Such losses are never compensated, unless resistance is lost, and cannot validly be offered as examples of true evolutionary change.



References


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Alekshun, M.N., and S.B. Levy. 1999. The mar regulon: multiple resistance to antibiotics and other toxic chemicals. Trends in Microbiology 7:410-412.
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2 comments:

Anonymous said...

Radar,

From what I can tell, there are roughly three distinct sections in this blog post, your initial bit on some sort of "logic", then the part about the motivations of scientists (which IIRC we've also previously addressed at some point) and then the big cut and paste. I don't have time to tackle them all at once, but here's my response to the first part for now:

"The following statements are similar:

Abraham Lincoln was born in the United States of America.

My birthday is August 15th.

These are factual statements that can be backed up with evidences so strong that they can be construed as proof."


So far, so good... though, interestingly enough, I note that in both cases you chose "factual statements" that you yourself did not personally and consciously witness. (Yes, you were there for your birth of course, but you didn't look at the calendar right then and commit that to memory, so it's entirely possible, for example, that you were born, say, on August 16th, or in a different year, and someone made a mistake in the paperwork. In theory.)

My point here is that in both cases, instead of your own perception you're relying on sources that tell you something about the past and you consider those sources reliable to the point of accepting them as "evidences so strong that they can be construed as proof". How do you judge what is reliable and what isn't?

"The following statements are similar:

Some people believe in evolution. Natural selection and mutation can account for all living beings.

I believe in creation. A Creator God designed and produced all living things.

They are similar because both are statements of faith that have not been proven to be true."


You're getting a little muddled and sloppy already. Let's take these two statements:

Some people believe in evolution.

I believe in creationism.


When a person says he or she "believes" in something and does not act in any way to the contrary, then we can take it that they do believe in that thing. So in a way we can't "prove" these, but to an extent we can take it as a fact, for example, that you believe in God.

But these are still pretty sloppy comparisons. "Evolution" is a very general term describing gradual change, while "creationism" is a belief in itself (in other words, you're saying you believe in a belief.)

Also, you're sticking to "believe" and completely sidestepping the realm of scientific investigation. For example, YEC positions can be scientifically investigated. Testable predictions can be made re. YEC. Unfortunately, they fail, which is why you have to obfuscate and present strawman arguments and purposely misrepresent arguments.

And third, "creationism" and "evolution" are not incompatible.

Now for the second halves of those sentences:

"Natural selection and mutation can account for all living beings.

A Creator God designed and produced all living things."


Again, even though the first statement is poorly worded (the usual conflation of evolution and biogenesis: the claim of the modern evolutionary synthesis is that natural selection and mutation account for the variety of living things, not their origin) these are not incompatible statements.

The gaping hole at the heart of creationism (both YEC and OEC) is that it does not provide any alternative mechanisms for how the variety of living things and their variation over time (as reflected in the fossil record) came to be. Claiming that "God did it" only reflects the ultimate (and foregone) conclusion. It offers no explanation as to how God supposedly did it.

Meanwhile, scientists are investigating those mechanisms, and all evidence they uncover does point to the mechanisms commonly referred to as the modern evolutionary synthesis.

Faith and science are different approaches, but they are not necessarily incompatible. It's simply apples and oranges, or rather coming at the problem from two different ends. Where it gets problematic is when people try to make the conclusions indicated by scientific research fit in with their religious beliefs.

Wasn't it one of the Popes who referred to this as a "class error" or something like that? The existence or non-existence of God (or gods) can not be proven scientifically, and there is indeed no scientific evidence of a god existing; believing in God is a matter of faith.

Science, on the other hand, can only proceed from the observable outward, and since God can not be observed, science can never reach God. Nor does it have to. Faith and science are in different "classes" of human perception, and trying to conflate them makes no sense.

"Believe what you like, unless you can prove it you cannot pretend that it has become fact."

I take it you recall the scientific method, which has been chewed over in previous discussions here ad nauseam.

"Unfortunately, the scientific community pretends that evolution is proven fact (sometimes resorting to euphemisms) rather than an unproven hypothesis lacking in hard evidences."

You recently made a similar claim (something about every major part of evolution having been disproven or something to that effect), and I asked you to back that up. Same here.

That evolution has taken place is considered a fact at this point, since the evidence for it is vast and irrefutable. In the fossil record we see living beings and how they evolved over time.

We have a pretty clear idea of what kind of creatures lived in which periods. When scientists now investigate a certain layer that they've dated to a certain period, they can say with reasonable certainty what kind of creatures they will find, if any. Sometimes new finds flesh out the overall picture, but they never fundamentally contradict the big picture that indicates evolution over time.

It's important to realize that what is found in the fossil record is completely incompatible with a belief in YEC and a global flood that jumbled them all together. The theory of evolution and YEC can both make testable predictions in this regard, and the theory of evolution wins this hand down. (Tiktaalik being a particularly clear example of the predictive power of the theory of evolution - according to YEC, it should not have been possible. And yet it happened.)

No doubt you'll mutter something about how you disagree with dating methods (even though you run away from those debates), but that is only part of the point. What's just as important is the predictability of what is found in which layers. Even if you want to argue against all sense that 800,000 layers of ice core data represent 6,000 years and so on, you'd then still have to explain how those creatures fall so neatly into those layers that supposedly were all laid down over the last 6,000 years.

"Make no mistake about this, macroevolution has not only not been proven, it has never been demonstrated to have happened"

That macroevolution has happened is considered as close to scientific fact as you can get on account of the fossil record, which is where it is demonstrated to have happened.

It is the mechanism by which it has happened that is under investigation. Unfortunately, this is where Creationists draw a complete blank, since in large part they seem to merely want to take potshots at the theory of evolution - even in the absence of an alternative mechanism they can propose... The notion that the existence of God and the validity of the theory of evolution are not mutually incompatible doesn't enter their minds for some reason.

I don't think it's the first time we've discussed this...

" and years of study of microorganisms and species such as fruit flies have only tended to produce evidence that supports creationist and/or intelligent design viewpoints."

1. How do they support creationist viewpoints?

2. Is there any way in which they contradict the theory of evolution? Any way at all?

" But no proof. Not on either side."

For the umpteenth time: proof is something that happens in mathematics. What we're talking about in this case would be the scientific method, which we've also gone over who knows how many times. Hypotheses are tested to become theories and all that.

And it is completely false to say that both sides have nothing to show here. The theory of evolution has been tested for 150 years, and yes, it has advanced and been finetuned since Darwin's day (DNA, for example). Its predictions are routinely confirmed by scientific findings. Sometimes something new is discovered, but never in a way that fundamentally contradicts the bigger picture.

"I cannot prove that God exists nor can I prove that He created everything."

Nor do you need to. It is by definition a matter of faith.

"I can, however review the evidence and see that the preponderance of evidence indicates a designed and created world, a world that underwent a massive global flood event with catastrophic effects upon the global climate and topology for many years afterwards."

Well, no. The evidence contradicts a young Earth and a global flood event 4,000 years ago. If you proceeded from the evidence instead of a foregone conclusion, you would not arrive at the conclusion that there was a global flood 4,000 years ago and that the Earth was created 6,000 years ago. On the contrary, you have to bend everything into place to make it fit that conclusion.

-- creeper

Ben Abba said...

Radar,

I have not yet found a physical "Philosopher's Stone", but I have figuratively found one.

If your interested in my research on this subject, please check out my main blog at: Ben-Abba.com; or check out my podcasts at: Achieving-Immortality.com.