Constant Evolution

Bacteria growing in an unchanging environment continue to adapt indefinitely.

By | December 16, 2015

WIKIMEDIA, BRIAN BAER AND NEERJA HAJELAIn a 2013 Science paper, researchers running the Long-Term Evolution Experiment (LTEE)—a project that has been monitoring 12 flasks of Escherichia coli for almost three decades—predicted that the bacteria would continue to adapt to their never-changing environment forever. Now, two years and 10,000 bacterial generations on, it’s clear that their prediction is holding true. The team’s latest report, published in Proceedings of the Royal Society B today (December 16), shows that the fitness of the bacterial populations is indeed continuing to improve.

“We would certainly expect, in the real world, where environments are more heterogeneous, where populations are coevolving with other populations, that evolution is going to continue,” said ecologist and evolutionary biologist John Thompson of the University of California, Santa Cruz, who did not take part in the study. “But what this [paper] says is that, even in the absence of any external forces . . . evolution is going to be relentless nonetheless.”

In 1988, evolutionary biologist Richard Lenski of Michigan State University initiated the LTEE. His team divided one starter culture of E. coli into 12 separate flasks and, for the last 27 years, those 12 cultures have been kept in identical conditions, being diluted by a factor of 100—to allow for growth—with the same culture medium each and every day.

The aim was to investigate “the predictability and repeatability of the evolutionary process,” said study coauthor Michael Wiser, also of Michigan State University. Put simply, “the idea was to look and see whether the different populations were achieving the same results as each other and whether they were doing so at the same time,” he said.

As the years passed, the team collected and froze sample after sample, performing various analyses on each. Once the bacteria reached 50,000 generations, the researchers compared the fitness of the then-current cultures with that of the microbes’ predecessors and their common ancestor. The researchers found that fitness was improving.

Initially, rapid adaption would be expected, explained Thompson, but in such a simple system, it was quite possible that the improvements in fitness would eventually plateau (a hyperbolic curve, in mathematical terms). ”After just 20,000 generations, every one of those 12 populations will have had several hundred million point mutations,” Thompson explained, so “you’d think that . . . most gene combinations are going to have been tested by natural selection [and] the odds of getting a new beneficial mutation is going to be vanishingly small.”

From the data, however, Wiser and his colleagues found that a power-law curve—in which there is a constant deceleration in improvement but no upper limit—“was both better at explaining the data and at predicting future data,” Wiser said.

These latest results add yet greater weight to this power-law hypothesis. Wiser and his colleagues compared the fitness of nine of the 12 bacterial populations sampled at 40,000; 50,000; and 60,000 generations, finding that, over the course of those 20,000 generations, the fitness of each population had improved. That is, the 60,000th-generation bacteria could compete with reference bacterial strains better than the 40,000th-generation bacteria were able to. In fact, the observed increases in fitness were greater than even the power-law model predicted.

The new study also showed that although all these E. coli populations are becoming more fit, they are doing so at different rates. This finding reflects the populations’ divergence from each other, Wiser explained.

The LTEE is “quite an abstract concept because, in the real world, environments are changing all the time,” said evolutionary biologist Louise Johnson of the University of Reading, U.K. However, results like these “mean it’s worth keeping going,” she said. “If it had been the case that [adaptation] was grinding to a halt, then you could say, ‘OK, in 15 years time it’s not going to be worth doing anymore.’ But this [paper] seems to suggest that however long you keep going, you’re going to have new surprises and new ways of exploiting the exact same environment.”

R.E. Lenski et al., “Sustained fitness gains and variability in fitness trajectories in the long-term evolution experiment with Escherichia coli,” Proceedings of the Royal Society B, doi:10.1098/rspb.2015.2292, 2015.

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Avatar of: James V. Kohl

James V. Kohl

Posts: 349

December 16, 2015

Re:

...even in the absence of any external forces . . . evolution is going to be relentless nonetheless.

Like other researchers, he is confused about the difference between evolution and how ecological variation is linked to RNA-mediated ecological adapations like the nutrient-dependent pheromone-controlled "re-evolution" of the bacterial flagellum, which occurred over the weekend.

See: Evolutionary Rewiring

Serious scientists have since linked the conserved molecular mechanisms of cell type differentiaiton in microbes across species to humans via RNA-mediated amino acid substitutions in the context of cancer prevention and/or treatment.

See also: Distinct E-cadherin-based complexes regulate cell behaviour through miRNA processing or Src and p120 catenin activity

Note that Louise Johnson of the University of Reading, U.K. reported that two mutations led to the re-evolution of the bacterial flagellum, when it was clearly two RNA-mediated amino acid substitutions that enabled the species to survive via ecological adaptation.

See the video.

If you would like to join other serious scientists who are Combating Evolution to Fight Disease, see also:  All About that Base (Meghan Trainor Parody)

Avatar of: Roy Niles

Roy Niles

Posts: 88

Replied to a comment from James V. Kohl made on December 16, 2015

December 16, 2015

"Like other researchers, he is confused about the difference between evolution and how ecological variation is linked to RNA-mediated ecological adapations like the nutrient-dependent pheromone-controlled "re-evolution" of the bacterial flagellum, which occurred over the weekend."

No, like other researchers, he knows that there is no such thing as pheromone controlled anything.  That's lke arguing that the pencil lead controls what it writes.  Or the smell of a rotten egg constructively comtrols its egg shell.  Pheromones are used to transfer signals, they don't produce them, understand them, or know what they mean.

They were evolved to serve a communicative purpose, and they have no fucntional capacity to carry out a purpose of their own.  The researcher understands that purposes are served by evolution, and may understand that it's the trial and error natures of bacterial intelligence that cause them to continuously evolve.  Pheromones have no inteligence and no mechanisms at all that would be needed for controlling anything.

 

Avatar of: James V. Kohl

James V. Kohl

Posts: 349

Replied to a comment from Roy Niles made on December 16, 2015

December 16, 2015

Feedback loops link odor and pheromone signaling with reproduction

Indications that GnRH peptide plays an important role in the control of sexual behaviors suggest that pheromone effects on these behaviors might also involve GnRH neurons. (p 683)

Nutrient-dependent/pheromone-controlled adaptive evolution: a model

The honeybee already serves as a model organism for studying human immunity, disease resistance, allergic reaction, circadian rhythms, antibiotic resistance, the development of the brain and behavior, mental health, longevity, diseases of the X chromosome, learning and memory, as well as conditioned responses to sensory stimuli (Kohl, 2012).

DNA methylation changes in plasticity genes accompany the formation and maintenance of memory

DNA methylation is RNA-directed .When Roy Niles or anyone else has a model for comparison to mine, which links the conserved molecular mechansims of nutrient-dependent RNA-mediated amino acid substitutions from atoms to ecosystems in all living genera, we can discuss other models in the context of intelligence and the ability to communicate effectively.

But first, serious scientists need an explaination of how weekend evolution of the bacterial flagellum occured via trial and error. Is there a model for that?

Avatar of: Suresh1963

Suresh1963

Posts: 1

December 17, 2015

Theoretically, an organism sees two types of environments, that of nonsocial environment and social environment. Even if you keep nonsocial environment constant, the social environment is going to change drastically. This is because of diversity with in the gene pool.
Avatar of: James V. Kohl

James V. Kohl

Posts: 349

Replied to a comment from Suresh1963 made on December 17, 2015

December 17, 2015

That theoretically nonsense has never been supported by any experimental evidence of biologically-based cause and effect.

Attempts to introduce serious scientists to the ridiculous philosophies that are based on the emergence of diversity in the gene pool are laughable now that all serious scientists know how to link atoms to ecosystems via biophysically constrained nutrient-dependent RNA-mediated protein folding chemistry that links the epigenetic landscape to the physical landscape of supercoiled DNA via microRNAs and cell adhesion proteins.

See: Beyond DNA Epigenetic mechanisms of inheritance

 

Avatar of: Roy Niles

Roy Niles

Posts: 88

Replied to a comment from James V. Kohl made on December 16, 2015

December 17, 2015

Explain first how evolution of the bacterial flagellum evolved without a trial, and how trials work at all, if not in anticipation of an intelligently correctible error.

And explain how your pheromones can, intelligently or otherwise, do anything mechanistically at all.  

Avatar of: James V. Kohl

James V. Kohl

Posts: 349

December 17, 2015

I've already done that, and you know it, Roy Niles.

Others can see:Nutrient-dependent/pheromone-controlled adaptive evolution: a model.

Roy Niles doesn't like the facts about how nutrient-dependent RNA-mediated events are linked to cell type differentiation in species from microbes to humans via the conserved molecular mechanisms we detailed in the section on molecular epigenetics from our 1996 Hormones and Behavior review.

Note that like others who prefer to remain biolgoically uninformed, Roy Niles never addresses the information that can be found by serious scientists in any of the links I provide.

Avatar of: Shivy

Shivy

Posts: 1

December 17, 2015

...even in the absence of any external forces . . .

Uhh...aren't the neighbouring bacteria an external force? If the universe only consisted of two particles, A and B. Then the environment of particle A is the universe and particle B, and vice versa.

Avatar of: James V. Kohl

James V. Kohl

Posts: 349

Replied to a comment from Shivy made on December 17, 2015

December 18, 2015

Thanks. All intelligent scientists know that neighboring bacteria may compete or cooperate. Cooperation in species-specific colony type protects the species from virus-driven genomic entropy. Simply put, viruses cannot steal the nutrient-dependent energy from all the cell types of the colony, and each cell is different at the molecular level.

Only biologically uninformed science idiots, like Roy Niles, want someone to prove that random mutations do not link the anti-entropic force of natural selection to quantum neo-Darwinism.

See also:  In Reality

Excerpt:

Wiser also counterpointed these incredible assumptions with a reminder that evolution on Earth occurs under very different circumstances than in their experiment, which assumes a fixed environment. In the real world, evolution is constantly updating us to an ever-changing environment, meaning that what may qualify as ideal today could be harmful tomorrow.

In reality, atoms are linked to nutrient-dependent ecosystem via nutrient energy-dependent base pair changes and RNA-mediated events that link the epigenetic landscape to the physical landscape of supercoiled DNA via amino acid substitutions in the context of the physiology of reproduction, which is controlled by pheromones in species from microbes to humans.

Avatar of: Roy Niles

Roy Niles

Posts: 88

Replied to a comment from James V. Kohl made on December 17, 2015

December 21, 2015

What I know is that you haven't "explained" anything either accurately or truthfully.

You haven't presented any scientific information that would in any way show that your pheromones can do anything, mechanistically, functionally, intelligently, etc., etc.  They are just excreted smells that act as signals from one animal to another.

They have nothing to do with cell type differentation.  In other words, they don't turn genes off and on, and you have never offered any scientific evidence that there's even the remotest possibility they could.  They have nothing at all to do with molecular epigenetics either, and you've offered no evidence to show otherwise, as of course there is none.  I doubt that you even know what cell type differention or molecular epigentics is all about in any case, as your claims that you're in any respect a scientist or have had any type of legitimte scientific training are bogus.

You're perpetrating a fraud  every time you post these pseudoscientific comments.

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