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UC Irvine evolutionary biologists use Darwinian theory to get bacteria to produce more bacteria

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From Evolution News & Views:

In short, it was hard to find anything beyond a “suggestion” or a “scenario” that these bacteria improved their fitness in any way by genetic mutations, other than the gross observation that some of the clones managed to survive at 45 ̊C. But even the ancestor could do that sometimes through the “Lazarus effect.” The authors also ignored the possibility that E. coli have ways to generate their own mutations under stress. That would be supportive of intelligent design, as would the notion that bacteria contain “a degree of preadaptation” to temperatures beyond their immediate experience.

Some experiment. What we learn from this paper is that under ideal conditions, with the best methods, scientists have a devil of a time trying to establish neo-Darwinian theory in a scientifically rigorous way. A look at their references shows a debt to Lenski’s methods that similarly produced paltry results on one of the longest-running experiments in history trying to demonstrate evolution in a lab.

Is this a theory that deserves to rule the world?

Is this a theory that deserves to rule? Yes, enforced by courts on public school systems, which is good enough for the taxing authority.

It is easy to teach because evidence is not required. And the taxpayers who have enough sense to care are slowly moving their kids out of the public systems anyway.

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11 Replies to “UC Irvine evolutionary biologists use Darwinian theory to get bacteria to produce more bacteria

  1. 1
    bornagain77 says:

    What was interesting in this year long study of bacteria, trying to force bacteria to evolve, was the unsolved problem for neo-Darwinian evolution that they admitted to going into the experiment:

    Researchers Ran a Massive Yearlong Experiment to Get Bacteria to Evolve. Guess What Happened? – August 22, 2014
    Excerpt: Despite the centrality of adaptation to evolution, surprisingly little is known about the diversity of mutations that contribute to adaptation or about their phenotypic and fitness effects (1). There are, in fact, only a few well-known examples linking genotype, phenotype, and adaptation in nature

    Their results, as News pointed out, in addressing this unsolved problem for neo-Darwinian evolution were less than impressive:

    “In short, it was hard to find anything beyond a “suggestion” or a “scenario” that these bacteria improved their fitness in any way by genetic mutations, other than the gross observation that some of the clones managed to survive at 45 °C. But even the ancestor could do that sometimes through the “Lazarus effect.””

    This following papers admit to the same ‘genotype/phenotype’ problem for neo-Darwinian theory

    With a Startling Candor, Oxford Scientist Admits a Gaping Hole in Evolutionary Theory – November 2011
    Excerpt: As of now, we have no good theory of how to read [genetic] networks, how to model them mathematically or how one network meshes with another; worse, we have no obvious experimental lines of investigation for studying these areas. There is a great deal for systems biology to do in order to produce a full explanation of how genotypes generate phenotypes,,,

    The next evolutionary synthesis: Jonathan BL Bard (2011)
    Excerpt: We now know that there are at least 50 possible functions that DNA sequences can fulfill [8], that the networks for traits require many proteins and that they allow for considerable redundancy [9]. The reality is that the evolutionary synthesis says nothing about any of this; for all its claim of being grounded in DNA and mutation, it is actually a theory based on phenotypic traits. This is not to say that the evolutionary synthesis is wrong, but that it is inadequate – it is really only half a theory!

    The following paper holds that phenotype CANNOT be reduced to genotype,,,

    Not Junk After All—Conclusion – August 29, 2013
    Excerpt: Many scientists have pointed out that the relationship between the genome and the organism — the genotype-phenotype mapping — cannot be reduced to a genetic program encoded in DNA sequences. Atlan and Koppel wrote in 1990 that advances in artificial intelligence showed that cellular operations are not controlled by a linear sequence of instructions in DNA but by a “distributed multilayer network” [150]. According to Denton and his co-workers, protein folding appears to involve formal causes that transcend material mechanisms [151], and according to Sternberg this is even more evident at higher levels of the genotype-phenotype mapping [152].

    And please note that varying the temperature at which bacteria can survive, which is what the current study tried to do, is practically the ‘bottom rung of the ladder’ as far as explaining the phenotypic characteristics of an organism,,,

    A phenotype (from Greek phainein, meaning “to show”, and typos, meaning “type”) is the composite of an organism’s observable characteristics or traits, such as its morphology, development, biochemical or physiological properties, phenology, behavior, and products of behavior (such as a bird’s nest).

    Yet, the presupposition of neo-Darwinism is that phenotype is reducible to genotype,,,

    “A phenotype results from the expression of an organism’s genes,,,”
    per wiki

    And even though minor phenotypic characteristics, such as the current study with temperature, may be found to vary within a certain range, the overriding phenotypic characteristic of morphology refuses to be reduced genotype. ,,, i.e. No one has ever witnessed the origination of new body plans by mutations to DNA

    Response to John Wise – October 2010
    Excerpt: A technique called “saturation mutagenesis”1,2 has been used to produce every possible developmental mutation in fruit flies (Drosophila melanogaster),3,4,5 roundworms (Caenorhabditis elegans),6,7 and zebrafish (Danio rerio),8,9,10 and the same technique is now being applied to mice (Mus musculus).11,12 None of the evidence from these and numerous other studies of developmental mutations supports the neo-Darwinian dogma that DNA mutations can lead to new organs or body plans–because none of the observed developmental mutations benefit the organism.

    In fact, as far as we can go back in the fossil record, bacteria demonstrate an extreme conservation of morphology,,,

    Excerpt: These (fossilized bacteria) cells are actually very similar to present day cyanobacteria. This is not only true for an isolated case but many living genera of cyanobacteria can be linked to fossil cyanobacteria. The detail noted in the fossils of this group gives indication of extreme conservation of morphology, more extreme than in other organisms.

    Static evolution: is pond scum the same now as billions of years ago?
    Excerpt: But what intrigues (paleo-biologist) J. William Schopf most is lack of change. Schopf was struck 30 years ago by the apparent similarities between some 1-billion-year-old fossils of blue-green bacteria and their modern microbial counterparts. “They surprisingly looked exactly like modern species,” Schopf recalls. Now, after comparing data from throughout the world, Schopf and others have concluded that modern pond scum differs little from the ancient blue-greens. “This similarity in morphology is widespread among fossils of [varying] times,” says Schopf. As evidence, he cites the 3,000 such fossils found;

    Moreover, not only do bacteria demontrate an extreme conservation of morphology, but, for as far back as can be measured, the molecular sequences demonstrate conservation as well,,

    The Paradox of the “Ancient” (250 Million Year Old) Bacterium Which Contains “Modern” Protein-Coding Genes:
    Excerpt: “Almost without exception, bacteria isolated from ancient material have proven to closely resemble modern bacteria at both morphological and molecular levels.”
    Heather Maughan*, C. William Birky Jr., Wayne L. Nicholson, William D. Rosenzweig§ and Russell H. Vreeland ;

  2. 2
    bornagain77 says:

    According to prevailing evolutionary dogma, i.e. neo-Darwinism, there ‘HAS’ to be substantial ‘genetic drift’ to the DNA of modern bacteria from 250 million years ago, even though the morphology (shape) of the bacteria can, (I guess), be expected to remain exactly the same.

    In spite of their preconceived materialistic bias, scientists find there is no significant genetic drift from the ancient DNA. In fact recent research, with bacteria which are alive right now, tells us that the ‘just so story’ of genetic drift should, due to selection, promote genetic reduction:

    The consequences of genetic drift for bacterial genome complexity – Howard Ochman – 2009
    Excerpt: The increased availability of sequenced bacterial genomes allows application of an alternative estimator of drift, the genome-wide ratio of replacement to silent substitutions in protein-coding sequences. This ratio, which reflects the action of purifying selection across the entire genome, shows a strong inverse relationship with genome size, indicating that drift promotes genome reduction in bacteria.

    Yet, in spite of this complete failure for neo-Darwinism to be empirically validated, (in the fossil record and in the lab), neo-Darwinism is the primary theory of origins being taught in public schools (on pain of lawsuit).
    It is beyond ludicrous that such unsubstantiated tripe that is inherent in neo-Darwinism be forced upon our children in public schools!
    Supplemental notes: The failure of neo-Darwinism, i.e. genotype, to explain ‘form’, i.e. morphological phenotype, is evident right out of the starting gate. Evident with both DNA sequences and protein sequences:

    Getting Over the Code Delusion (Epigenetics) – Talbot – November 2010
    Excerpt: The standard doctrine has it that functionally important sequences, precisely because they are important to the organism, will generally be conserved across considerable evolutionary distances. But the emerging point of view holds that architecture can matter as much as sequence. As bioinformatics researcher Elliott Margulies and his team at the National Human Genome Research Institute put it, “the molecular shape of DNA is under selection” — a shape that can be maintained in its decisive aspects despite changes in the underlying sequence. It’s not enough, they write, to analyze “the order of A’s, C’s, G’s, and T’s,” because “DNA is a molecule with a three-dimensional structure.”[14] Elementary as the point may seem, it’s leading to a considerable reallocation of investigative resources.

    The Gene Myth, Part II – August 2010
    Excerpt: “It was long believed that a protein molecule’s three-dimensional shape, on which its function depends, is uniquely determined by its amino acid sequence. But we now know that this is not always true – the rate at which a protein is synthesized, which depends on factors internal and external to the cell, affects the order in which its different portions fold. So even with the same sequence a given protein can have different shapes and functions. Furthermore, many proteins have no intrinsic shape, taking on different roles in different molecular contexts. So even though genes specify protein sequences they have only a tenuous (very weak or slight) influence over their functions.
    ,,,,So, to reiterate, the genes do not uniquely determine what is in the cell, but what is in the cell determines how the genes get used. Only if the pie were to rise up, take hold of the recipe book and rewrite the instructions for its own production, would this popular analogy for the role of genes be pertinent.
    Stuart A. Newman, Ph.D. – Professor of Cell Biology and Anatomy

    Talbott has another neat way of illustrating how ‘form’ takes precedence over material particulars ,,,

    What Do Organisms Mean? Stephen L. Talbott – Winter 2011
    Excerpt: Harvard biologist Richard Lewontin once described how you can excise the developing limb bud from an amphibian embryo, shake the cells loose from each other, allow them to reaggregate into a random lump, and then replace the lump in the embryo. A normal leg develops. Somehow the form of the limb as a whole is the ruling factor, redefining the parts according to the larger pattern. Lewontin went on to remark: “Unlike a machine whose totality is created by the juxtaposition of bits and pieces with different functions and properties, the bits and pieces of a developing organism seem to come into existence as a consequence of their spatial position at critical moments in the embryo’s development. Such an object is less like a machine than it is like a language whose elements… take unique meaning from their context.[3]”,,,

    further notes:

    Stephen Meyer – Functional Proteins And Information For Body Plans – video

    Dr. Stephen Meyer comments at the end of the preceding video,,,
    ‘Now one more problem as far as the generation of information. It turns out that you don’t only need information to build genes and proteins, it turns out to build Body-Plans you need higher levels of information; Higher order assembly instructions. DNA codes for the building of proteins, but proteins must be arranged into distinctive circuitry to form distinctive cell types. Cell types have to be arranged into tissues. Tissues have to be arranged into organs. Organs and tissues must be specifically arranged to generate whole new Body-Plans, distinctive arrangements of those body parts. We now know that DNA alone is not responsible for those higher orders of organization. DNA codes for proteins, but by itself it does not insure that proteins, cell types, tissues, organs, will all be arranged in the body. And what that means is that the Body-Plan morphogenesis, as it is called, depends upon information that is not encoded on DNA. Which means you can mutate DNA indefinitely. 80 million years, 100 million years, til the cows come home. It doesn’t matter, because in the best case you are just going to find a new protein some place out there in that vast combinatorial sequence space. You are not, by mutating DNA alone, going to generate higher order structures that are necessary to building a body plan. So what we can conclude from that is that the neo-Darwinian mechanism is grossly inadequate to explain the origin of information necessary to build new genes and proteins, and it is also grossly inadequate to explain the origination of novel biological form.’
    Stephen Meyer – (excerpt taken from Meyer/Sternberg vs. Shermer/Prothero debate – 2009)

    Darwin’s Doubt narrated by Paul Giem – The Origin of Body Plans – video

    Body Plans Are Not Mapped-Out by the DNA – Jonathan Wells – video

  3. 3
    bornagain77 says:

    OT: Dr. Paul Giem has a video lecture up on ‘Quantum Weirdness’:

    Quantum Weirdness and God 8-9-2014 by Paul Giem – video

    Of note, I have not watched the entire lecture yet, but I did note that he uses a video from Inspiring Philosophy(IP) on quantum mechanics in his lecture (IP really does his homework!).,,, Should be an interesting lecture for me to watch this afternoon. I hope others enjoy it too.

  4. 4
    DavidD says:

    The News back on August 25th I believe had revealed some prized religious icons left by Darwin himself which were forgotten until recently. They are held as almost something holy from the Guru himself. Can you imagine the euphoria if one of those 77 vials of collected samples from Darwin actually contained a sample of Darwin’s poop ? Think of a Lenski experiment on Steroids. It would be the mother of all holy of holies in experiments in trying to get E-Coli to evolve. Maybe they were search for Darwin DNA and attempt a human cloning experiment in honor of their holy man.

    Yes I know it’s silly, but so is much of what the secular world involves themselves in which mirrors religion and at the same time deny their faith is anything but faith. Clearly, one needs an incredible eye of faith to view exactly what they are looking at.

  5. 5
    Mung says:

    God only knows how bacteria got by before the advent of UC Irvine evolutionary biologists and Darwinian theory.

  6. 6
    DavidD says:

    This experiment and the hallowed Lenski E-coli experiments are attempts at proving evolution, but under artificial circumstances. Aside from the begging question of what the research themselves illustrate with the experiment: Blind unguided forces or an Intelligent Designer, could epigenetics also play a role here ? If genes in a genetic strand are so mechanical in their make up of multiple switches, could it be these switches are turning on and off depending on under what circumstances the bacteria are manipulated by the researcher ? Could there be hidden programs already in existence which are being activated as opposed to some blind mutation getting lucky here ? Watching one documentary which showed switches being turned off in embryos when they are simply placed in a Petri Dish should sound alarms for taking a fresher look at how epigenetics play more of a role in such unnatural conditions experiments. Let’s watch now at how epigenetics starts taking hits from the faithful.

  7. 7
    wallstreeter43 says:

    Really hilarious video on how pro evolutionist atheists think (or don’t think), this is a refutation of the friendly atheist hemant mehta and his arguments against design. I can only hope that we have more atheists like this everywhere as this kind of thinking will convert many atheists to theists.
    enjoy 🙂

  8. 8
    REC says:

    The author of this ENV article should be embarrassed–perhaps they truly are, explaining the lack of a byline.

    Howler one:
    “Researchers Ran a Massive Yearlong Experiment to Get Bacteria to Evolve. Guess What Happened? … they were not even looking for a glamorous innovation, like a wing or an eye.”

    Y’all like calculations, so:

    This experiment:
    10^10 bacteria per generation X 2000 generations X 1 year

    10^30 bacteria per generation X 365* generations X ~10^9 years**
    *(estimate 1 generation/day, generously)
    **for for emergence of eyes or wings from unicellular life (ignoring E. coli is likely a poor stand-in for complex life’s evolutionary ancestor)

    Howler two:
    “The operative word there is “assumed.” For example, all these mutations may have been neutral, with no phenotypic consequences. Or, mutations for better survival in heat might have had negative consequences for surviving cold (an evolutionary trade-off), with no overall gain in fitness. “Whatever the cause, tradeoffs have rarely been linked to specific genetic variants” — another embarrassing revelation”

    ENV’s anonymous author takes a selection of quotes from the part of the paper where the authors are establishing the need to demonstrate the phenotype-genotype link, and that tradeoffs ARE due to genetic variations–which the authors then GO ON TO DO. ENV’s author seems to fault the PNAS authors for not doing the very thing the study does. Whether this is a comprehension fail, or dishonesty, I really can’t tell, but It is right there in the abstract:
    “We associated these niche dynamics with genotypes and confirmed associations by engineering single mutations in the rpoB gene, which encodes the beta subunit of RNA polymerase, and the rho gene, which encodes a termination factor. Single mutations in the rpoB gene exhibit antagonistic pleiotropy, with fitness tradeoffs at 18 °C and fitness benefits at 42.2 °C. In contrast, a mutation within the rho transcriptional terminator, which defines an alternative adaptive pathway from that of rpoB, had no demonstrable effect on fitness at 18 °C.”

    I could go on, but these contentless polemics against empirical research that “news” and ENV write probably do ID more harm than good. They are silly bitter little diatribes.

    ***(my interpretation of some poor writing, apologies if I misconstrue the intent here)

  9. 9
  10. 10
    Mung says:

    my lol @ 9 was upon viewing the vid linked @ 7.

    Go sand dunes!

    I want to know why the UC Irvine researchers did not just play music to the bacteria. Surely that would have resulted in the production of more bacteria (and perhaps even more different bacteria, given the differences in musical tastes) than playing ‘Darwinian theory’ for the bacteria to listen to.

  11. 11
    Querius says:

    Using a bacteria whose genome is sequenced seems like a perfect opportunity to test Darwinian evolution.

    Depending on the bacteria, you could get about 30,000 generations per year (at 15-20 minutes per generation). Then, considering that the bacteria when compared to humans have about a 100x as great radioresistance when you consider LD 50/30 statistics, one could bump up the background radiation to maybe 30 rem/year, giving it a proportionally equivalent effect as on humans. At, let’s say 20 years per reproductive generation, the equivalent would be 600,000 years of human evolution.

    Bumping up the artificial background radiation another factor of 10 and running the experiment for 10 years under a variety of environmental stresses—I’d include several kinds of bacteria to test for later gene transfer—would result in about 60 million years of evolution.

    Regular genome sequencing along the way could provide data on where most of the changes are taking place and to what effect.

    Could be interesting.


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