E.coli!

For over 10 years, i have seen this study linked to as 'Proof of Common Ancestry!'  'Proof of Speciation!', and/or 'Proof of Gene Creation!'  But is it?  I will provide a brief peer review, for your consideration.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2430337/

Here is a later one, that uses the same data as Lenski's original.   Both have been presented to me, multiple times, as, 'Proof of Common Ancestry!'

https://ec.asm.org/content/4/6/1102.full

If all that is being said is that organisms vary within their genetic parameters, then there is no debate. E coli is unique, in that it has a wide range of adaptability, but there is NO EVIDENCE that it came from (or is going to), some simpler (or complex) genetic structure.

*..genomic evolution was nearly constant for 20,000 generations. Such clock-like regularity is usually viewed as the signature of neutral evolution, but several lines of evidence indicate that almost all of these mutations were beneficial. This same population later evolved an elevated mutation rate and accumulated hundreds of additional mutations dominated by a neutral signature.*

Pathetically, i understand this.. being a science geek, & having followed with great interest this subject for decades. I take issue with the use of the terminology, 'evolution', as it seems to use circular reasoning.. using the premise (and terminology) to prove itself. If by 'genomic evolution' you merely mean minor changes in generations, or micro evolution, that is plainly obvious. But to correlate it with macro is still a false equivalence.

Now, the study is claiming 'beneficial' mutations, among 'several lines of evidence'. I am a bit confused about the statement above, which seems to conflict with the findings of the study:

*Of the 12 populations, six have so far been reported to have developed defects in their ability to repair DNA, greatly increasing the rate of mutation in those strains.[5][19][20] Although the bacteria in each population are thought to have generated hundreds of millions of mutations over the first 20,000 generations, Lenski has estimated that within this time frame,only 10 to 20 beneficial mutations achieved fixation in each population, with fewer than 100 total point mutations (including neutral mutations) reaching fixation in each population.*

So there is a question about the results.. were 'almost all mutations beneficial'? Or were there 'only 10-20 beneficial mutations, out of millions?

That is a fine point, & may be due more to the writer, than the experiment itself.

Ok lets go to the findings, & see what conclusions they compel.

**Change in fitness** 
*All populations showed a pattern of rapid increase in relative fitness during early generations, with this increase decelerating over time* 
**Defects in genome repair** 
*Of the 12 populations, six have so far been reported to have developed defects in their ability to repair DNA, greatly increasing the rate of mutation in those strains*
**Increase in cell size, & morphological change**
*All twelve of the experimental populations show an increase in cell size concurrent with a decline in maximum population density, and in many of the populations, a more rounded cell shape* 
**Polymorphism & phylogenetic comparison** 
*Two distinct variants, S and L, were identified in the population designated Ara-2 at 18,000 generations based on their formation of small and large colonies, respectively.[25] Clones of the S and L types could co-exist stably in co-culture with each other, indicating they occupied distinct niches in the population*
**Citrate usage** 
*The inability to grow aerobically on citrate, referred to as a Cit− phenotype, is considered a defining characteristic of E. coli as a species, and one that has been a valuable means of differentiating E. coli from pathogenic Salmonella. While Cit+ strains of E. coli have been isolated from environmental and agricultural samples, in every such case, the trait was found to be due to the presence of a plasmid containing a foreign citrate transporter.[32] A single, spontaneous Cit+ mutant of E. coli was reported by Hall in 1982.[33] This mutant had been isolated during prolonged selection for growth on another novel substance in a growth broth that also contained citrate. Hall's genetic analysis indicated the underlying mutation was complex, but he was ultimately unable to identify the precise changes or genes involved, leading him to hypothesize activation of a cryptic transporter gene*

There is a bit more in this study, & lots of commentary about the findings. But the primary evidence being presented is the ability of e.coli 'to grow aerobically on citrate', that is, when oxygen is present.

Now, let us examine the claims that this is evidence for macro evolution, which predicts structural changes in the genome.

Has there been a 'structural change' in the genome? No. This is still a strain of e.coli. It is not another, more advanced bacteria, but one of the simplest, most basic ones there is, & even over thousands of generations, it is still e.coli, with a few mutations & variations, perhaps, but genetically, morphologically, & phylogenetically, **unchanged**. It is just slightly different, and almost an exact phenotype.

Here are some other facts about this study.

• E.coli is an asexual organism, able to reproduce by itself. 
• The study began in 1988, & by 2016 has increased to 66,000 generations. 
• E.coli has been found to be extremely adaptive, with ability to survive & adapt to many different conditions. 
• There are many criticisms of this study's conclusions, among peer reviewed scientists. Extrapolations not warranted by the data are made, and it has been sensationalized for marketing or hype. 
• This study provides no evidence for any structural changes in the genome. 

I like this study. I am intrigued by the findings about e.coli, & its amazing adaptability to its environment. It is similar to the shark, in its longevity & ability to live in whatever environmental variables come its way. 

But, for those who think this study provide evidence for common ancestry, you are greatly mistaken. It does not. It merely illustrates the adaptability of e.coli. 

The claim of 'new speciation!', is only an arbitrary definition, not anything compelled by any changes in the morphology or genetic structure of the organism. To claim this is 'real evolution!' is absurd. It is obviously just adaptation, & only demonstrates the viability & adaptability of this particular organism. Some organisms do NOT have this capability, but die under unfriendly conditions. So this phenomenon does not apply universally, as would be expected if this were a mechanism for macro evolution, but is unique to e.coli. 

*Lenski criticizes Van Hofwegen et al.'s description of the initial evolution of Cit+ as a "speciation event" by pointing out that the LTEE was not designed to isolate citrate-using mutants or to deal with speciation since in their 2008 paper they said "that becoming Cit+ was only a first step on the road to possible speciation", and thus did not propose that the Cit+ mutants were a different species, but that speciation might be an eventual consequence of the trait's evolution* 

So the claim of 'new speciation!' is not even claimed by Lenski, the one doing the study, even though hordes of eager Believers cling to it as 'scientific proof!' of common descent.