No, here is my reply in full, in case you missed it:
I suspect you haven’t actually read either, and you almost definitely haven’t read the second one as it debunks the first.
HERE IS MY ANSWER - PLEASE READ IT THOROUGHLY, THANK YOU IN ADVANCE (spoiler alert: the E. coli long term evolution experiment’s postulated discovery of Cit+ bacteria is a sham and l had already encountered it as referenced here):
Prefatory Notes:
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In the following writeup, citrate = citric acid.
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Cit+ = E. coli bacterial colony which can metabolise citrate
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LTEE refers to a Long Term Evolution Experiment, in this case the decades-old breeding of an E. coli colony and its subsequent cultures, currently approaching their 50,000th generation.
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The LTEE began with E. coli, and there is still nothing but E. coli, and it will end with nothing but E. coli.
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E. coli can natively metabolise citric acid. Just not under oxic conditions (aerobically, oxygen-present). In fact, the CITRIC ACID CYCLE is a key part of E. coli’s biochemistry.
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Phase-Variable Genes vs. Cryptic Genes: Phase-variable and cryptic genes represent different aspects of bacterial gene expression and adaptation. They are NOT random mutations, they are an inbuilt property that allows bacteria to meet environmental demands and thus serve higher lifeforms.
Phase-variable genes are those whose expression can switch between an ON and OFF state across a few generations, allowing bacteria to adapt to changing environments by altering surface structures, for example. The changes are mutations which are usually reversible. They are an inbuilt part of the gene’s functioning.
Cryptic genes, on the other hand, are DNA sequences that are normally not expressed but can be activated under specific conditions, providing a hidden reservoir of genetic variation that can be used for adaptation. Cryptic genetic variation is unexpressed, bottled-up genetic potential (i.e. it was always there). It is not normally seen, but is expressed under abnormal conditions. The changes can be reversible. -
Pinning evolution on something as ambiguous as new molecules, is like linking money to fraud - yes it’s possible, but not by the fact of money existing itself. There must be entire structures built around that money e.g. gangs, networks, buildings, cars. But l’ll still go along with the importing and metabolism of citrate as being a good thing, for argument’s sake.
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As an asides, the experiment actually began way before my degree, but l gather the citrate metabolism was noted long after my degree.
TO CONINUE:
The NIMH article: Lenski, et alia - Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli (Proc Natl Acad Sci U S A
. 2008 Jun 4;105(23):7899–790) opens by predicating the entire experiment on the study of the unique unfolding of gene mutations in history, thus giving rise to evolutionary pathways, each of which will have been unique, like a kaleidoscope i.e. unreplayable. The authors tried to trace what occurred, from frozen samples (thus making history actually replayable) gathered during a decades-old and ongoing Long Term Evolution Experiment (LTEE), this one involving E. coli bred across tens of thousands of generations.
MY VIEW: Of course there will always be arms, legs, red blood, reproductive organs, a tail etc. and exceptions will prove the rule. The arms and legs confer stability owing to earth’s gravity, the haemoglobin is fine tuned to bind oxygen and its iron content makes it red, a tail makes a guy universally handsome and gives a woman much needed stability etc. Therefore it’s not necessarily that they emerged from a single ancestor. Especially considering the 5 or more mass extinctions that happened.
ANALYSIS OF THE FIRST ARTICLE:
Lenski (2008): "*Stephen Jay Gould maintained … Thus, Gould argued … Simon Conway Morris countered that natural selection … He and others point to numerous examples of convergent evolution … Evolution may thus be broadly repeatable …
We started the first replay experiment on the 3rd anniversary of Stephen Jay Gould’s death; we ended it on the 66th anniversary of his birth. *"
MY VIEW: The authors’ motives are clearly to prove Evolution and its protagonist Gould. And lo! They do indeed prove it. Or so they claim.
Lenski (2008): “Twelve initially identical populations of Escherichia coli were founded in 1988 to investigate this issue. They have since evolved in a glucose-limited medium that also contains citrate, which E. coli cannot use as a carbon source under oxic conditions.”
MY VIEW: The conditions are limited to a citrate rich environment, not how it is in the wild. The researches tacitly admit E. coli has the innate ability to metabolise citrate - just not aerobically i.e. in the presence of oxygen. They later explain that the medium was highly concentratd in citrate.
Lenski (2008): “No population evolved the capacity to exploit citrate for >30,000 generations, although each population tested billions of mutations. A citrate-using (Cit+) variant finally evolved in one population by 31,500 generations, causing an increase in population size and diversity. The long-delayed and unique evolution of this function might indicate the involvement of some extremely rare mutation. Alternately, it may involve an ordinary mutation, but one whose physical occurrence or phenotypic expression is contingent on prior mutations in that population. We tested these hypotheses in experiments that “replayed” evolution from different points in that population’s history.”
MY VIEW: It is indicated that billions of neutral (no change in what is expressed) or negative (nasty) mutations occurred. There is some vagueness over the term “prior mutations”, because in biosciences, any variant form of a gene is aribtrarily labelled a “mutant” or “mutation”, even thought it was found like that, not observed to mutate, just found already to be like that. So, are the researches saying the Cit+ ability emerged as a phenotype (real-life expression) of a mutation that may have occurred earlier in the LTEE? Or that it may have proceeded from the sudden expression of a native cryptic gene?
Lenski (2008): “*We observed no Cit+ mutants among 8.4 × 1012 ancestral cells, nor among 9 × 1012 cells from 60 clones sampled in the first 15,000 generations. However, we observed a significantly greater tendency for later clones to evolve Cit+, indicating that some potentiating mutation arose by 20,000 generations. This potentiating change increased the mutation rate to Cit+ but did not cause generalized hypermutability. Thus, the evolution of this phenotype was contingent on the particular history of that population. *”
MY VIEW: Perhaps then, it wasn’t part of a storm of mutations in a prone DNA region (a hypermutable region). Instead, it may have been an unfurling of expression of a hidden gene, a cryptic gene, one that causes citrate metabolism, which E. coli already has.
Lenski (2008): "*Ten populations evolved increased DNA supercoiling … Four have evolved defects in DNA repair, causing mutator phenotypes
MY VIEW: These aren’t good mutations. These are loss of function, like losing the ability to sleep might be a good thing. For a while.
Lenski (2008): "*DM25 medium contains not only glucose, but also citrate at a high concentration.
MY VIEW: The authors used a highly concentrated citric acid medium.
Lenski (2008): “The inability to use citrate as an energy source under oxic conditions has long been a defining characteristic of E. coli as a species (35, 36). Nevertheless, E. coli is not wholly indifferent to citrate. It uses a ferric dicitrate transport system for iron acquisition, although citrate does not enter the cell in this process (37, 38). It also has a complete tricarboxylic acid cycle, and can thus metabolize citrate internally during aerobic growth on other substrates (39). E. coli is able to ferment citrate under anoxic conditions if a cosubstrate is available for reducing power (40). The only known barrier to aerobic growth on citrate is its inability to transport citrate under oxic conditions (41–43). Indeed, atypical E. coli that grow aerobically on citrate (Cit+) have been isolated from agricultural and clinical settings, and were found to harbor plasmids, presumably acquired from other species, that encode citrate transporters (44, 45).”""
MY VIEW: The authors admit that E. coli can natively metabolise citrate. The authors also admit that E. coli has a complete tricarboxylic acid cycle.
Do you know why that is hilarious?
Arguably THE MOST COMMONLY KNOWN TRICARBOXYLIC ACID IS CITRATE and the most common name for the cycle is the Krebs or CITRIC ACID CYCLE!!! - the authors were a bit sly, directing the wording at the layperson, by substituting “citric acid” with “tricarboxylic acid”.
As you can see from Wikipedia, CITRATE IS THE CENTREPIECE OF THIS CYCLE AND CITRATE METABOLISM IS THUS AT THE CORE OF THE CYCLE (by the way, how’s that for oh-so-random evolution, and that’s nowhere near how complex biochemistry gets - you can maybe hold a biochemistry textbook in your hand, but holding two is likely impossible, they are heavy. Biochemistry is not something that random processes give rise to.).
Lenski (2008): “Other findings suggest that E. coli has the potential to evolve a Cit+ phenotype. Hall (41) reported the only documented case of a spontaneous Cit+ mutant in E. coli. He hypothesized that some complex mutation, or multiple mutations, activated cryptic genes that jointly expressed a citrate transporter, although the genes were not identified. Pos et al. (43) identified an operon in E. coli K-12 that apparently allows anaerobic citrate fermentation, and which includes a gene, citT, encoding a citrate–succinate antiporter. High-level constitutive expression of this gene on a multicopy plasmid allows aerobic growth on citrate, but the native operon has a single copy that is presumably induced only under anoxic conditions.”
AND THEN LATER ON IN THE ARTICLE:
“Indeed, the Cit+ clones isolated from generations 32,500 and earlier grow much more slowly on citrate than those from 33,000 generations and later.”
MY VIEW: The authors clearly admit that according to past research, the cause of Cit+ mutation may be a the unfurling expression of a cryptic gene which gets more and more honed to its task of switching to citrate metabolism. The cryptic gene mutates in response to environmental demands - and this is actually an inbuilt property. It is not arbitary gene mutation.
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ANALYSIS OF THE SECOND ARTICLE:
@Flannel_Jesus also posted a twin article, supposedly to support the hypothesis of LTEE Cit+ emergence as being down to random evolutionary beneficial gene mutation. I shall now deal with the article:
https://journals.asm.org/doi/10.1128/jb.00831-15
Hofwegen, Hovde & Minnich - Rapid Evolution of Citrate Utilization by Escherichia coli by Direct Selection Requires citT and dctA (Journal of Bacteriology Vol. 198, No. 7, 2016)
FROM THE ABSTRACT:
Hofwegen (2016): “E. coli cannot use citrate aerobically. Long-term evolution experiments (LTEE) performed by Blount et al. (Z. D. Blount, J. E. Barrick, C. J. Davidson, and R. E. Lenski, Nature 489:513–518, 2012, Genomic analysis of a key innovation in an experimental Escherichia coli population | Nature ) found a single aerobic, citrate-utilizing E. coli strain after 33,000 generations (15 years). This was interpreted as a speciation event. Here we show why it probably was not a speciation event. Using similar media, 46 independent citrate-utilizing mutants were isolated in as few as 12 to 100 generations. Genomic DNA sequencing revealed an amplification of the citT and dctA loci and DNA rearrangements to capture a promoter to express CitT, aerobically. These are members of the same class of mutations identified by the LTEE. We conclude that the rarity of the LTEE mutant was an artifact of the experimental conditions and not a unique evolutionary event. No new genetic information (novel gene function) evolved.”
MY VIEW: As you can see, this FUNDAMENTALLY UNDERMINES Lenski (2008). In fact, it destroys it, because:
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Cit+ emerges not after 15 years of the bacteria slowly evolving, rather, it is seen to have emerged in as few as 12 to 100 generations (Lenski’s LTEE was breeding E, coli at 6.64 generations per day, so we’re talking between 2 days and 2 weeks, not 15 years. In other words, the ability appears to have been latent, native to E. coli.
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The mutation offered in Lenski (2008, here given a slightly different reference as being in Nature magazine, 2012) is in Hofwegen (2016) proposed to be a gene amplification mutation, which gives extra copies of a promoter region, which tells a transcriber enzyme where to attach, for a gene which when fully transcribed, gives a transporter protein that ferries citrate into the cell (actually antiporter, it also pushes succinate out of the cell1) - but that still bolsters my view that E. coli still knew what to do with citrate, and that a citrate crpyto gene was activated at some point, and as its expression unfurled, it may have then required citrate to be actively ferried into the cell via CitT protein.
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Note that gene amplification can occur during development, adaptation to environmental changes (l propose this is the more likely process being invoked here, by a prior crypto gene expression), and in cancer (bacteria don’t get cancer but the point is, it may after all be a genuine new mutation that causes citrate to be brought into the cell, and not triggered by earlier native crypto gene expression … but that isn’t a beneficial gene mutation, it’s the type of thing cancers do and in any case, it’s inescapable that the bacteria already knew what to do with the citrate once it had been ferried into the cell - they already had the citric acid cycle native to their functioning.)
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Note the ultimate assertion here: “No new genetic information (novel gene function) evolved.”
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DISCUSSION
- Notice how these variable gene expression experiments pivot on bacteria (e.g. the phase-variable gene expression in Wolbachia, in the “Microevolution of Wolbachia” article listed in the OP of this thread, and the present E. coli LTEE study. Bacteria are like the quantum world of living organisms, they exhibit a high degree of agility, of changeability - triggered by environmental stress, because they need to be semper fi in order to serve the higher living world - from nitrogen fixing bacteria (atmospheric nitrogen → ammonia) in the soil acting independently of other living organisms, to gut bacteria in the human (breaking food down, synthing vitamins, directly & indirectly fighting harmful microorganisms).
Also, it appears the Answers In Genesis website also noticed the things l noted in my first impressions - the following is based on Richard Lenski, E. coli, and the Long-Term Evolution Experiment (LTEE) | Answers in Genesis
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These lab-dependent E. coli could not survive outside their specialised environment, they are less fit than wild E. coli. Similarly (and l don’t mean this in jest, this is a distressing thing to talk about): Take someone with a lobster claw deformity. Put them in a situation where it suddenly gets very cold. Make sure they cannot obtain gloves. They will probably get frostbite less easily than people with five separated digits on each hand, as the five-digit subjects have far, far greater surface area to lose heat from. Notice you never see an Eskimo with five-fingered gloves, only mittens. Do you consider the lobster claw mutation an evolutionary step? I consider it neither a step forward nor backward, l don’t consider it Evolution at all. I consider it a disability, likely caused by man-made chemicals in the environment, and which can only be a positive if you cynically put a person in a weird situation under strict rules.
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A loss of information occurring in a regulatory region may improve gene product function by increasing its expression, but this would not represent a GONI [gain of novel information]. Neither would a mutation that brings back a function that was previously lost, a decrease in specificity of a protein’s function, a rearrangement of already existing information, the duplication of existing information, or the general increase in diversity over time. A GONI must involve a mutational event or series of events that enable the production of novel protein(s) that can perform a specific and previously unknown activity. This type of mutation has not been observed in the E. coli LTEE.
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… most bacteria are not pathogenic and are still beneficial to plants, animals, and humans, and it is perfectly logical that God designed them to be flexible enough to adapt to differing environments as well as to become resistant to bacteriophages. Imagine if all gut microbiomes were destroyed every time there was a viral infection in an animal or a person. This would be catastrophic to animals and humans alike. In God’s providence, he provided bacteria (and our bodies) with adaptive mechanisms to ensure their survival and often aid our wellness.
As Dr. Georgia Purdom has stated,
“Adaptive mechanisms in bacteria work by altering currently existing genetic information or functional systems [THESE ARE THE PHASE-VARIABLE GENES (Wolbachia article debuked in the OP of this thread) & CRYPTIC GENES (the present E. coli study)] to make the bacteria more suitable for a particular environment. Further understanding of Lenski’s research is valuable for development of a creation model for adaptation of bacterial populations in response to the adverse environmental conditions in a post-Fall, post-Flood world.”
By the way, dear viewers: In a commentary elsewehere on Lenski, Hendrickson and Rainey accept that no new gene was created, but they say the point is, that this is a “mote in the eye” for those who say that phenotypic innovations cannot arise from microevolution (Natural Selection). Phenotypic innovations = the real world appearances of genes. However, the metabolism of citrate isn’t an innovation. Sure, in aerobic conditions it is, but that can be explained by the extreme duress of the experiment. These changes are usually reversible and all built in to E. coli, so, really, there is nothing new under the sun. All Lenski really did was do some extreme act under the sun. A bit like squeezing someone till their eyeballs pop out. That’s possibly a reversible change and eyeballs don’t usually do that, do they? All we did was put the person in an extreme headlock. Well, yes, no, that’s not evolution.
For fullness l’d like to bundle explanations of other postulated “beneficial” genetic mutations arising from the E. coli LTEE, taken from the Answers in Genesis website - apologies for pasting (numbered footnotes are referenced in the excerpt but l’ve left them out), but there’s already been too much to get through and l’m very tired from covering just the supposed “mutation” behind Cit+ E. coli:
The publications allege that several genes underwent a genetic mutation that conferred a benefit to the bacteria. In no particular order, I will review each of these examples and discuss the known or hypothesized biochemical basis of how this benefit was achieved. The scientific jargon may be confusing, but take special note of any trends regarding the mechanism of these changes.
1. First is the pykF gene. This gene encodes one of two pyruvate kinase enzymes that catalyzes the transfer of a phosphate group from phosphoenolpyruvate (PEP) to adenosine diphosphate (ADP) yielding a molecule of adenosine triphosphate (ATP). PEP is also used to help drive the uptake of glucose, a limited energy source in the experiment. The researches noted an insertion in this genetic region that they hypothesized to have inactivated this gene leading to a greater amount of PEP available to drive glucose uptake.9,16
2. Second was an insertion mutation in the regulatory region of the pbpA-rodA operon. This operon (which is a cluster of genes under the control of a similar regulatory unit) encodes two important proteins involved with cell wall synthesis. As all 12 E. coli populations evolved larger cell volumes, the authors hypothesized that altered cell wall synthesis or timing of synthesis may have been beneficial.9,16 The exact mechanism of this mutation regarding a gain or loss of novel information is unknown.
3. A single nucleotide polymorphism (SNP) mutation was found in the mutS gene. This SNP produced a premature stop codon and truncated the MutS protein leading to a defect in DNA repair. This particular mutation was of importance because it greatly increases the number of mutations a bacterial population will accumulate over time.21,27
4. The hokB-sokB gene locus in E. coli is a toxin-antitoxin system. When found in bacterial chromosomes, these systems are commonly involved in responding to stresses and bringing about programmed cell death. The authors hypothesized that the observed insertion mutation would have knocked out this gene, and a disruption of hokB/sokB would likely be beneficial in the experimental environment.9,16
6. The researchers observed that all 12 populations of E. coli lost the ability to catabolize D-ribose, an energy source that was not available in this experimental environment. Furthermore, this loss of function was remarkably quick—within 2,000 generations all populations had lost the ability. It was noted that this loss was caused by deletion mutations in the rbs operon.11,15 Interestingly, ribose is one of the energy sources that commensal E. coli use in the intestine.
7. DNA coiling is an important factor in gene regulation. and a mutation was found in the topA gene that encodes an enzyme that relaxes DNA coils. Along with this, a mutation was found in the genetic region upstream of the fis gene. The product of fis reduces activity of DNA gyrase which itself increases DNA supercoiling. A loss or decrease of function in the protein products of both the topA and fis genes would contribute to the observed increase in DNA supercoiling.14,15
8. The researchers found a small insertion mutation upstream of glmUS, an operon involved in cell wall biosynthesis. It was hypothesized that this mutation inhibited normal binding of a transcriptional activator to this region thereby reducing glmUS expression.23
9. The nadR gene encodes a bi-functional protein involved in aspects of nicotinamide adenine dinucleotide (NAD) metabolism. Specifically, this protein represses several genes involved in NAD synthesis so a disruption of this gene and its corresponding protein, especially the repressor function of the protein, would result in more NAD. Dr. Lenski and colleagues observed an insertion mutation into the nadR gene and hypothesized that an increased intracellular concentration of NAD may be beneficial in this environment.9,16 This increase in NAD would be due to a loss of function in the repressor component of the protein.
10. Dr. Lenski and colleagues noted a mutation in spoT, the product of which is involved in the stringent response through a cell signaling molecule (ppGpp). The precise physiological basis for this advantage is unknown; however no two mutations were identical among bacterial populations that evolved a mutation in this gene.12,15 This finding suggests that any fitness benefits from these mutations were due to a disruption of function.
11. Interestingly, many bacterial populations evolved resistance to a certain virus even though they were not exposed to that virus throughout the experiment. The protein that the bacteria use to transport and metabolize maltose, an energy source that was not present in their experimental environment, is the same protein that the virus targets to infect the bacteria. Since there is no maltose in the growth media, downregulating this unused metabolic pathway would be beneficial for the bacteria and just so happens to confer viral resistance as well. Genetically this change resulted from a mutation in the malT gene, the regulator of maltose metabolism through positive regulation of the LamB surface protein. Mutation in malT likely rendered its protein product nonfunctional thereby eliminating expression of LamB.24
12. Perhaps the most famous of all observations in Dr. Lenski’s long-term evolution experiment was when an E. coli population began to utilize a new energy source (citrate) that they normally could not use under aerobic conditions. It is important to note that E. coli already have the ability to transport and metabolize citrate, but the bacteria typically cannot do so in oxic conditions as it does not produce an appropriate transporter in this type of environment (among other required factors). The genetic changes that underlie this particular adaptation are complex, but a key event involved the replication of a genomic region that regulates a citrate transporter. This amplification captured a previously existing and aerobically expressed promoter (the promoter for rnk) which could then direct transcription of the citrate transporter (citT). Repeated tandem amplifications refined this function.27
Thank you all, and Peace 