Kolbe Report 1/28/23

Dear Friends of the Kolbe Center,

Glory to Jesus Christ!

The Kolbe Center is incredibly blessed to have such a dedicated team of speakers, researchers, and friends who support us with their prayers and donations.  Our chief biologist, Pamela Acker, has made a tremendous contribution to our defense of the traditional Catholic doctrine of creation.  In this newsletter I would like to share her analysis of an article by Dr. Sean Pittman that I quoted in a newsletter a few weeks ago.  In that article I cited an example from Dr. Pittman of “the most” that mutation-plus-natural-selection could do because I did not want to misrepresent the little that it can accomplish, even as we continue to demonstrate how little mutation-plus-natural-selection can achieve compared to what every system of microbe-to-man evolution requires.  Pamela Acker obtained the original paper referenced by Dr. Pittman and was able to demonstrate that the mutation that allegedly produced a “new enzyme” did not actually produce any new function at all.  I am very grateful for her analysis and I want to share it with you at once, so that you can see that even the very limited claim that he made for new functionality arising through mutation was not valid. (Dr. Pittman’s original article can be read here).

On "Limited Evolutionary Potential" by Dr. Sean Pittman:

There are a few fundamental problems with Dr. Pittman’s attempt to “allow for” Dr. Miller’s claims of the evolution of new functions without contradicting the Biblical account of Creation.  It makes sense to briefly canvas these before we directly address Hall’s experiment.

-- The article supports the bankrupt idea that there are "functionally neutral mutations" and also seems to be favorable to junk DNA (strongly suggested by his "beneficial stepping stones" argument, though in Dr. Pittman’s defense he was writing before the publication of Dr. John Sanford’s Genetic Entropy and Dr. Jonathan Wells’ The Myth of Junk DNA.  But his uncritical assent to both of these now discredited ideas highlights a problem with certain Protestant strains of Creation apologetics:  there is often too quick a movement to accept unquestioningly the newest “revelations” of anyone doing lab work, without looking behind the curtain to ascertain exactly what merit their interpretations of their data may (or may not) have.

-- Dr. Pittman ignores the importance of genetic drift as a counterbalance to natural selection in observable systems, stating simply: "If [mutations] are deemed to be beneficial, they are kept for the next generation to use, but if detrimental, they are eliminated from the gene pool over the course of time."  He later adds, "However brutal this game of survival is, it is a real game and it works very well as a preserving force that keeps the strong and gets rid of the weak."  It is important not to concede this ground from the outset, because even if evolutionists could show development of a single truly novel function, they would also have to explain how such things wouldn't get lost by genetic drift – which, briefly stated, is the tendency of gene frequency to change in populations due to random chance.  If a novel function were to arise the way evolutionists say they do (in this case, though a single point mutation), they would in many cases be more likely to be randomly eliminated from the population (especially if it were small) than fixed in the gene pool.  This is the case even if such a gene were significantly beneficial to the organism.

-- Finally, and perhaps most importantly to our discussion, Pittman is comparing apples to oranges when he discusses the evolution of antibiotic resistance in conjunction with Miller’s claim of the evolution of new functions.  Rather than involving the development of a truly novel function, “evolution” of antibiotic resistance usually involves one of the following:

a. gene transfer from another bacterium that already possesses a fully functional antibiotic resistance gene (thereby providing no help for an explanation of an evolutionary origin of antibiotic resistance)

b. mutations that involve a change in shape of the antibiotic target; these invariably also produce a reduction in the efficacy of the target (the cell walls in MRSA are an example I commonly refer to in my presentations)

c. mutations that cause a protein that normally transports a specific molecule under specific conditions outside of the cell to either (i) transport other molecules (loss of structural specificity) or (ii) transport molecules all the time (loss of temporal/environmental specificity); (i) and (ii) can also coincide

d. mutations that cause a protein to break down an antibiotic; these are invariably in proteins that would normally break down a related protein and also involve loss of structural specificity in the mutated enzyme

e. mutations that cause a protein that has very low catalytic (breaking-down) activity of the antibiotic to be produced constitutively (all the time); this is another loss of temporal/environmental specificity.  The enzyme has not gained an ability, but lost regulation; in its normally regulated state, it could not overcome the antibiotic, but in its unregulated state there is enough of it around (even though each individual protein is so inefficient) to metabolize the antibiotic fast enough to save the bacterium.  This is sort of like not being able to make a living on a product that only profits three cents to the dollar unless you're selling millions of them.

Constitutive expression is particularly detrimental to cells because every protein that is produced in normal cells is tightly regulated to only be produced when and where it is needed; if proteins are produced "out of order" it uses up a considerable amount of energy and raw materials that the cell needs to do other things.  Constitutive production of enzymes is sort of like harnessing up to 20% of the US food production industry to make Twinkies - sure, some people eat them some of the time (and you can sort of live on them) but you'd end up with a lot of wasted energy and materials, and a lot of piled up Twinkies.

As you can see from the above, (a) does not require the development of any novel gene or any mutation at all, and (b-e) all involve the degradation of a protein product (and sometimes other negative consequences).  Since negative mutations are very common, we would expect such results to be fairly common in nature.  This would explain why antibiotic resistance can arise with some frequency in microbial populations.  And - despite the benefit to the bacterium in an antibiotic-laden environment - the varieties that arise via mutation carry with them a fitness cost (i.e. the make the organism less "fit" overall than the wild type, except in the instance where the selective pressure, in this case the antibiotic, is present).

Scanning electron micrograph of Escherichia coli
Credit: Rocky Mountain Laboratories, NIAID, NIH

The Hall E. coli experiment:

The last point above coincides with the first point of the article composed by Dr. Hall.  He begins his discussion of the "evolved beta-galactosidase" (EBG) system (the enzyme that is supposed to have evolved a completely new function, according to Dr. Miller and defended by Dr. Pittman) by briefly canvassing 22 other instances where bacteria supposedly evolved the ability to metabolize a new sugar.  Of these:

a. 9 mutants constitutively (continually) expressed an enzyme that they already possessed that had a slight affinity for the new sugar.  "Unevolved" (wild type) bacteria in these instances were unable to survive on that sugar alone because the enzyme did such a poor job of metabolizing it; "evolved" bacteria only survived because there was an extraordinary excess of the enzyme (up to 20% of the total protein in the bacterial cells).

b. 2 were mutants that had gene duplications of enzymes similar to those described in (a).  The enzymes already possessed the necessary metabolizing functions (though poorly) and were just produced superabundantly.

c. 2 were mutants where an already existing enzyme was not produced constitutively as in (a), but still produced more abundantly than in the wild type.

d. 1 was a mutant that reverted to the ability to metabolize a sugar after the enzyme had been knocked out because it already possessed a second subunit of a protein that could do the same job as the knocked out protein; this second protein was made available to do its new job by the loss of specificity in a different protein which would normally bind to it.

e. 4 mutants "gained" the ability to bind to the new sugar by "losing" specificity for the original sugar they metabolized.  The enzymes in question here were already present, already under appropriate regulatory control, already able to bind to sugar, and already able to break sugar down.  The mutations only caused the enzymes to be less specific for their native sugar, and so made them able to metabolize "new" sugars.

f. 2 mutants had enzymes present that could already metabolize the sugar in question, but were now activated by the presence of a novel sugar; again, the function itself was not new at all.  These mutations probably involved similar structural changes to the biomolecules  such as those described in (e).

g. 1 mutant was able to transport the sugar into the cell when it previously could not; there were no details on this process described, so I suspect it would have been similar to (c) in the section on antibiotic resistance above.

h. 1 mutant was able to metabolize the new sugar "better" (two other mutations of type (a) and (e) had already occurred in this strain) because of a mutation unrelated to the enzyme (it caused the cells to grow clumped together, and this apparently helped them use the sugar more efficiently and so grow more robustly).

A number of the mutations described above occurred in series in the same strains of bacteria.  None of them involve the development of a brand new function.  Neither does the EBG system that Hall describes in his own research.

Briefly, Hall "knocked out" the ability of E. coli  to metabolize lactose by deleting the lacZ gene.  This gene codes for a protein called beta-galactosidase, which breaks lactose down into the simple sugars glucose and galactose.  (The term beta-galactosidase is also used generally to refer to any enzyme that can break down a disaccharide that includes the sugar galactose.)  When Hall plated these knockout bacteria on lactose medium, within a few days a colony of bacteria arose that was able to metabolize lactose - despite still not having a functional lacZ gene.  So they regained a function that they had lost, but in this case it was not from the restoration of the lacZ gene, but from a different gene altogether, named ebg.  This gene produced a protein in the mutated bacteria which has the designation ebgA, and was able to catalyze enough lactose to keep the bacteria alive on the growth medium.

This function, however, is by no means new for the gene and protein in question.  The original unmutated ebg protein, designated ebgO, was found to have catalytic activity on lactose when it was purified from the bacterial cells - in other words, the enzyme possessed a pre-existing ability to metabolize lactose (and also several other related sugars) and was ALREADY a beta-galactosidase.  Its ability to break down lactose was just insufficient in the un-mutated gene to keep the bacteria alive; the point mutation that resulted in the "new function" only allowed the enzyme to bind more efficiently to that particular sugar.  Even that efficiency was compromised, however, as the mutants grew 6-21 times slower than the wild type bacteria that produced normal beta-galactosidase.

The enzyme glucosidase converts the sugar maltose into two glucose sugars. Active site residues in red, maltose substrate in black, and NAD cofactor in yellow. (Wikimedia Commons).

(As a side note, though I went looking for the original function of the ebgO protein to see if the mutation to ebgA compromised this function, I couldn't find any studies on its original function; Hall apparently did not look for one, and just said that its original function was "unknown.")

Hall himself, at the close of the 1982 article, makes the following revealing statement:  "A variety of new functions can arise from single point mutations within a gene.  All of the new functions evolved for the ebg enzyme, however, represent variations upon the general function 'beta-galactosidase,' a function already possessed by the ancestral function.  [...]  The ancestral enzyme ebgO does not hydrolyze lactose, lactulose, galactosylarabinose, or beta-methylgalactoside at biologically significant rates; however, hydrolysis of all of those sugars can be detected and measured in vitro using purified ebgO enzyme.  Thus, in a real sense, the point mutations that generate the evolved enzymes of classes I and II do not result in truly new activities; they simply improve old functions."

He then goes on to describe how the hydrolysis of lactobionic acid by the ebgA enzyme is a "new" function, when in reality this is just another version of the same class of sugars that ebgO already possessed the ability to break down.  In other words, even enzymes - just like organisms - can only change with limited variation to do the same kinds of functions that they are already coded to do.

As a final note, this data comes from the mid-1970s.  So it is almost pitiful that Dr. Kenneth Miller, writing in 2000, would still hold this up as a shining example of the evolution of "novel" functions—seemingly indicating that nothing better had come down the pike in that regard in a quarter of a century.

To have an expert like Pamela Acker on the Kolbe staff is a huge blessing.  But the kind of writing and research that she has done on this and other relevant topics is very demanding and time-consuming.  If you appreciate Pamela’s work and the work of the Kolbe Center, and if you have not made us a regular object of your prayers or made a donation to support our mission, please consider doing so.  You can make a secure one-time or monthly donation at this link.

Yours in Christ through the Immaculata in union with St. Joseph,

Hugh Owen

P.S.  Day One of our new series “How the World Was Made in Six Days” is finally available for online streaming.  The physical DVDs will now be printed and shipped. With the help of your prayers, they will arrive at U.S. addresses in the next couple of weeks.

P.P.S. We would like to thank all of our readers who wrote respectfully to Eric Sammons, the editor in chief of Crisis magazine, to ask that he host a debate between theistic evolution Dr. Darnowski and our own Dr. Kevin Mark.  Thanks to your appeals, Mr. Sammons has contacted Dr. Mark and invited him to participate in a debate with Dr. Darnowski on one of his 90-minute podcasts in the near future.  We will let you know as soon as the exact time and date have been decided.  Please keep Dr. Kevin Mark and the debate in your prayers.

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