Darwinism Evolution Intelligent Design Natural selection

Misleading claims about a long running evolution experiment

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Richard Lenski’s experiment is in the news again:

The LTEE required 33,000 generations and many years for the bacteria to acquire the supposedly new trait. In the video Lenski says that one of his lab’s researchers wanted to explore “why did it take so long to evolve this and why has only one population evolved that ability?” The implication is that this is a complex trait that required many slow mutations to arise. Lenski says it was a “difficult” trait to evolve because it required both a “rare mutation” and also a “series of events” where multiple mutations were needed before any advantage was conferred. Van Hofwegen realized there was something fishy about these claims. As he explained to IDTF:

“The only difference is that in the conditions of the [LTEE] experiment, they didn’t have a transporter. They [E. coli bacteria] didn’t have the ability to bring that citrate outside of their cells into the cells and actually use it for energy. And so when I looked at that experiment as a microbiologist I thought, all they have to do is turn that thing on. That’s really easy for bacteria to do. Why did it take them 33,000 generations to do that?”

Van Hofwegen draws a comparison to a light switch. Normal E. coli have the metabolic pathways to live off citrate, and they have the ability to transport it into their cells. But under the conditions of the experiment that “light switch” was turned off. The bacteria didn’t need to evolve a new metabolic pathway or a new transport feature to eat citrate. All they needed to do was turn on their transporter under the oxic conditions of the LTEE experiment. The organisms used the “light switch” to express their citrate transporter. So how did they do it?

A 2016 peer-reviewed study in the Journal of Bacteriology, “Rapid Evolution of Citrate Utilization by Escherichia coli by Direct Selection Requires citT and dctA,” co-authored by Van Hofwegen and biologists Scott Minnich and Carolyn Hovde, has the answer. In their research they witnessed the same trait, the ability to use this “lemony dessert,” arise in under 100 generations and 14 days. This result was repeatable 46 times. They found that the trait is not very genetically complicated — again, akin to flipping a switch — and that there is more to the story than is being been told. Indeed, their paper shows that no new genetic information arose during the evolution of this trait.

Casey Luskin, “Viral Video Overstates the Evidence About Bacterial Evolution” at Evolution News and Science Today

Hey. The Darwinians are marketing magic and it is really difficult to refute magic.

Here’s the vid making the claim:

39 Replies to “Misleading claims about a long running evolution experiment

  1. 1
    ET says:

    The experiment demonstrates the severe limits of evolutionary processes.

  2. 2
    aarceng says:

    In Lenski’s experiment citrate metabolism was only weakly selected for. Van Hofwegen et al modified the experiment so the trait was strongly selected; and so it appeared more rapidly.

  3. 3
    Querius says:

    Yikes!

    Dr. Lenski sure had me fooled. Congratulations . . . I guess.

    -Q

  4. 4
    martin_r says:

    lenski’s experiment is not an evolution but an adaptation. The bacteria (the same species as before) just ADAPTED to digest citrate. That is it. After 33,000 generation, it is still the same E.coli bacteria.

    again, this is an A D A P T A T I O N …. why do Darwinists call it an EVOLUTION ???? Can somebody explain to me? Seversky? JVL ? Anybody ?

    PS: i looked at wikipedia, actually, “The populations reached 73,500 generations in early 2020”
    So, let me repeat, after 73,500 generations, IT IS STILL THE SAME E.COLI BACTERIA…. SO WHERE IS THE EVOLUTION ???? 73,500 generations!!!! WHERE IS THE EVOLUTION ???? WHY IS THIS E-WORD EVEN USED ???? Perhaps one day i will be able to digest petrol… did i evolved into some other species???? I just adapted to eat something else than i used to…

  5. 5
    Sandy says:

    Martin_r
    lenski’s experiment is not an evolution but an adaptation.

    Nope, you don’t understand evolution . If you jump 2m today you will be able to jump to the Moon …one day. :)))

  6. 6
    martin_r says:

    Sandy …right…. my bad….

  7. 7
    bornagain77 says:

    Hmmm,

    Lenski makes it sound like this is an entirely new capability: “E. coli going back to its original definition of a species is incapable of that.” He gives the impression that bacteria suddenly evolved the ability to eat an entirely new food source — a “remarkable” evolutionary adaptation that they were “incapable” of performing previously. But this is simply false. Normal E. coli can eat and metabolize citrate. The pro-evolution website Evo-Ed, at Lenski’s own university, explains:
    “Like many organisms, E. coli has a citric acid cycle, and so metabolizes citrate while growing on various substances. It can also grow anaerobically by fermenting citrate.”

    And that, (being intellectually dishonest towards the evidence), is exactly how Darwinists always fool the general public into believing they have any scientific evidence whatsoever for Darwinian evolution.

    I thought that Minnich’s work might have slowed Lenski down in his over the top claims for having experimental proof for Darwinian evolution.

    Rapid Evolution of Citrate Utilization by Escherichia coli by Direct Selection Requires citT and dctA. – Minnich – Feb. 2016
    The isolation of aerobic citrate-utilizing Escherichia coli (Cit(+)) in long-term evolution experiments (LTEE) has been termed a rare, innovative, presumptive speciation event. We hypothesized that direct selection would rapidly yield the same class of E. coli Cit(+) mutants and follow the same genetic trajectory: potentiation, actualization, and refinement. This hypothesis was tested,,,
    Potentiation/actualization mutations occurred within as few as 12 generations, and refinement mutations occurred within 100 generations.,,,
    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, http://dx.doi.org/10.1038/nature11514 ) 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.
    http://www.ncbi.nlm.nih.gov/pubmed/26833416

    Apparently I was mistaken in my belief that Lenski would be intellectually honest towards the empirical evidence that was presented by Minnich and company.

    As the work by Minnich and company demonstrated, not only is the citrate adaptation not evidence for Darwinian evolution, (since the mutations are obviously not random as Lenski had presupposed), the citrate adaptation is actually evidence AGAINST Darwinian evolution since some unknown epigenetic mechanism is directing the mutations in a non-random, repeatable, fashion.

    Moreover, not only was Lenski’s Citrate adaptation never proof for ‘speciation’, (as Lenski has tentatively tried to claim), but, as Dr Behe points out in the following article, the Citrate adaptation turns out to be proof that evolutionary processes, in the long run, actually send species on a ‘death spiral’, i.e. into “spectacular devolution.”
    Which is exactly the opposite kind of real-time empirical evidence that Darwinists need in order to, (finally), empirically substantiate their theory as to being somewhat feasible.

    Michael Behe, “Citrate Death Spiral” at Evolution News and Science Today – June 17, 2020
    Excerpt: “The new paper now reports on 2,500 generations of further evolution of the citrate mutant, in nutrient media that contains either citrate alone or citrate plus glucose (as for earlier generations). As always with the Lenski lab, the research is well and thoroughly done. But the resulting E. coli is one sick puppy. Inside the paper they report that “The spectrum of mutations identified in evolved clones was dominated by structural variation, including insertions, deletions, and mobile element transpositions.” All of those are exceedingly likely to break or degrade genes. Dozens more genes were lost. The citrate mutant tossed genetic information with mindless abandon for short term advantage.
    In a particularly telling result, the authors “serendipitously discovered evidence of substantial cell death in cultures of a Cit+ clone sampled from … the LTEE at 50,000 generations.” In other words, those initial random “beneficial” citrate mutations that had been seized on by natural selection tens of thousands of generations earlier had led to a death spiral. The death rate of the ancestor of the LTEE was ~10 percent; after 33,000 generations it was ~30 percent; after 50,000, ~40 percent. For the newer set of experiments, the death rate varied for different strains of cells in different media, but exceeded 50 percent for some cell lines in a citrate-only environment. Indeed, the authors identified a number of mutations — again, almost certainly degradative ones — in genes for fatty acid metabolism that, they write with admirable detachment, “suggest adaptation to scavenging on dead and dying cells.”
    The degraded E. coli was eating its dead.
    Lessons to Draw
    Let me emphasize: the only result from the decades-long, 50,000-plus generation E. coli evolution experiment that even seemed at first blush like it had a bit of potential to yield a novel pathway in the bacterium has resulted instead in spectacular devolution.”
    https://evolutionnews.org/2020/06/citrate-death-spiral/

    Besides Lenski constantly overstating what is actually happening in his LTEE, just so as to provide fraudulent evidence for Darwinian evolution, one of Lenski’s students has also pulled this ‘intellectually dishonest’ stunt:

    More Darwinian Degradation – M. Behe – January 2012
    Excerpt: Recently a paper appeared by Ratcliff et al. (2012) entitled “Experimental evolution of mulitcellularity” and received a fair amount of press attention, including a story in the New York Times.,,, It seems to me that Richard Lenski, who knows how to get the most publicity out of exceedingly modest laboratory results, has taught his student well. In fact, the results can be regarded as the loss of two pre-existing abilities: 1) the loss of the ability to separate from the mother cell during cell division; and 2) the loss of control of apoptosis.?http://behe.uncommondescent.co.....gradation/

    Because of such intellectually dishonest antics by Lenski and, at least, one of his students, I would have a very hard time talking face to face with Lenski without getting very angry with him for being so intellectually dishonest towards the general public with what the evidence actually say.

    Lenski’s current fraudulent video now has, as of this writing, over 3,100,000 views. That is a lot of misinformation to the general public that Lenski is responsible for!

    Again, I would have a very hard time talking face to face with Lenski without getting very angry with him for being so intellectually dishonest towards the general public.

    “But this long history of learning how to not fool ourselves—of having utter scientific integrity—is, I’m sorry to say, something that we haven’t specifically included in any particular course that I know of. We just hope you’ve caught on by osmosis.
    The first principle is that you must not fool yourself—and you are the easiest person to fool. So you have to be very careful about that. After you’ve not fooled yourself, it’s easy not to fool other scientists. You just have to be honest in a conventional way after that.
    I would like to add something that’s not essential to the science, but something I kind of believe, which is that you should not fool the layman when you’re talking as a scientist. I’m not trying to tell you what to do about cheating on your wife, or fooling your girlfriend, or something like that, when you’re not trying to be a scientist, but just trying to be an ordinary human being. We’ll leave those problems up to you and your rabbi. I’m talking about a specific, extra type of integrity that is not lying, but bending over backwards to show how you’re maybe wrong, that you ought to do when acting as a scientist. And this is our responsibility as scientists, certainly to other scientists, and I think to laymen.”
    Richard Feynman – Cargo Cult Science

    Verse:

    1 Thessalonians 5: 21
    Test all things; hold fast what is good.

  8. 8
    ET says:

    Martin_r,

    E coli already had the ability to digest citrate. In the presence of oxygen the gene that codes for the citrate transport protein is not expressed. In an anaerobic environment E coli digests citrate just fine. without that protein citrate cannot get through the membrane.

    What happened was that gene was duplicated. The duplicate was put under the control of a binding site that was active in the presence of oxygen. This allows for the protein to be made in the presence of oxygen.

    It involved a change in allele frequency over time and descent with modification. And that means it is a case of evolution..

  9. 9
    doubter says:

    ET@8

    Yes, it was a simple case of evolution, but no new complicated mechanism was created. Very little new information. So Darwinists have absolutely no basis in touting this as proof that Darwinist RM + NS can create complex new structures (like the vertebrate body plans originating in an eyeblink of evolution time at the Cambrian Explosion).

  10. 10
    ET says:

    Doubter, see the first comment.

  11. 11
    Bob O'H says:

    Martin_r @ 4 –

    again, this is an A D A P T A T I O N …. why do Darwinists call it an EVOLUTION ????

    Err, because it is? Evolution isn’t just speciation.

  12. 12
    Sandy says:

    Bob O’H

    Martin_r @ 4 –

    again, this is an A D A P T A T I O N …. why do Darwinists call it an EVOLUTION ????

    Err, because it is? Evolution isn’t just speciation

    Yep evolution isn’t just speciation is also the biggest hoax of 20th century. :)))

  13. 13
    Seversky says:

    Martin_r/4

    lenski’s experiment is not an evolution but an adaptation. The bacteria (the same species as before) just ADAPTED to digest citrate. That is it. After 33,000 generation, it is still the same E.coli bacteria.

    again, this is an A D A P T A T I O N …. why do Darwinists call it an EVOLUTION ???? Can somebody explain to me? Seversky? JVL ? Anybody ?

    I know this is probably difficult for an engineer to grasp but, as Bob O’H pointed out, adaptation is one of the processes of evolution, the way organisms change over time. It’s not just about speciation.

  14. 14
    Querius says:

    According to other sources . . .

    E. coli already have the ability to transport and metabolize citrate where there is no oxygen, but a replication occurred in the DNA so it could now be expressed (or restored?) in the presence of oxygen.

    So nothing here remotely close to the hyped up and deceptive claims that E. coli “evolved” a new ability to metabolize citrate, much less evolve into a kangaroo.

    And Darwinian evolution does indeed require speciation unless you want to go back to “punctuated equilibrium.” Adaptation is all about epigenetics such as was observed in the beaks of a single generation of Darwin’s finches.

    -Q

  15. 15
    Seversky says:

    Bornagain77/7

    Because of such intellectually dishonest antics by Lenski and, at least, one of his students, I would have a very hard time talking face to face with Lenski without getting very angry with him for being so intellectually dishonest towards the general public with what the evidence actually say.

    Lenski’s current fraudulent video now has, as of this writing, over 3,100,000 views. That is a lot of misinformation to the general public that Lenski is responsible for!

    Again, I would have a very hard time talking face to face with Lenski without getting very angry with him for being so intellectually dishonest towards the general public.

    I think I would also have a hard time keeping my temper if I were to discuss such an outrageously defamatory claim with you face-to-face.

    You accuse Lenski of dishonesty based on creationist Scott Minnich’s paper when your own reporting of the science in various fields is dishonest in that it amounts to a collection of cherry-picked quotes culled from the literature because they support your own religious presuppositions rather than any honest attempt to represent fairly other perspectives or interpretations.

    Specifically, in this case, you make no mention of the response written by Lenski and his student Zachary Blount so let me help you by quoting from Larry Moran’s coverage of their response:

    MONDAY, FEBRUARY 22, 2016
    An Intelligent Design Creationist disputes the evolution of citrate utilization in the LTEE … Lenski responds

    Most of you are familiar with the long-term evolution experiment (LTEE) run by Richard Lenski. One of the cultures in that experiment evolved the ability to use citrate as a carbon source. Normally, E. coli cannot use this carbon source under aerobic conditions but the new strain not only utilizes citrate but can grow in cultures where citrate is the only source of organic carbon.

    The pathway to this event is complex and requires multiple mutations [see On the unpredictability of evolution and potentiation in Lenski’s long-term evolution experiment and Lenski’s long-term evolution experiment: the evolution of bacteria that can use citrate as a carbon source].

    Intelligent Design Creationists are not happy about this experiment because it not only shows evolution in action but it also illustrates features of the process that ID proponents don’t understand; features like drift, neutral alleles, and contingency that expose the ignorance of the average creationist. However, there are a few ID proponents who actually understand evolution so they are forced to come up with other kinds of criticism to soften the impact of the results coming out of the Lenksi lab.

    One of those creationists is Scott Minnich1, a professor and researcher at the University of Idaho in Moscow, Idaho (USA). Minnich wants you to believe that the LTEE isn’t significant because no new genetic information was created. This is part of a strategy to accept microevolution but deny that macroevolution can be explained by naturalistic processes.

    Minnich’s lab did some experiments in order to replay the evolution of citrate utilization in E. coli cultures. They found that they could evolve strains that utilized citrate under aerobic conditions but in their hands it took much less time than it took in the LTEE and it was much more likely to occur. (Recall that the Cit+ phenotype only evolved in one of the twelve cultures in the LTEE and it took 30,000 generations.) Here’s the Minnich paper and the abstact.

    Van Hofwegen, D.J., Hovde, C.J., and Minnich, S.A. (2016) Rapid evolution of citrate utilization by Escherichia coli by direct selection requires citT and dctA. Journal of bacteriology, published online Feb. 1, 2016 [doi: 10.1128/JB.00831-15]

    ABSTRACY The isolation of aerobic citrate-utilizing Escherichia coli (Cit+) in long term evolution experiments (LTEE) has been termed a rare, innovative, presumptive speciation event. We hypothesized that direct selection would rapidly yield the same class of E. coli Cit+ mutants and follow the same genetic trajectory: potentiation, actualization, and refinement. This hypothesis was tested with wild-type E. coli B, K12, and three K12 derivatives: E. coli ?rpoS::kan (impaired for stationary phase survival), E. coli ?citT::kan (deleted for the anaerobic citrate/succinate antiporter) and E. coli ?dctA::kan (deleted for the aerobic succinate transporter). E. coli underwent adaptation to aerobic citrate metabolism that was readily and repeatedly achieved using minimal medium supplemented with citrate (M9C), M9C with 0.005% glycerol, or M9C with 0.0025% glucose. Forty-six independent E. coli Cit+ mutants were isolated from all E. coli derivatives except E. coli ?citT::kan. Potentiation/actualization mutations occurred within as few as 12 generations and refinement mutations occurred within 100 generations. Citrate utilization was confirmed using Simmons-, Christensen-, and LeMaster Richards citrate media and quantified by mass spectrometry. E. coli Cit+ mutants grew in clumps and long incompletely divided chains, a phenotype that was reversible in rich media. Genomic DNA sequencing of four E. coli Cit+ mutants revealed the required sequence of mutational events leading to a refined Cit+ mutant. These events showed amplified citT and dctA loci followed by DNA rearrangements consistent with promotor capture events for citT. These mutations were equivalent to the amplification and promoter capture CitT-activating mutations identified in the LTEE.

    IMPORTANCE E. coli cannot use citrate aerobically. Long term evolution experiments (LTEE) by Lenski found a single aerobic, citrate-utilizing E. coli after 33,000 generations (15 years). This is interpreted as a speciation event. Here we show why it probably is not. 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 the same class of mutations identified by the LTEE. We conclude the rarity of the LTEE mutant was an artifact of the experimental conditions, not a unique evolutionary event. No new genetic information (novel gene function) evolved.

    A lot of the work in deciphering the Cit+ phenotype in the LTEE was done by Zachary Blount when he was a graduate student in the Lenksi lab. He is now a post-doc and he and Lenski have teamed up to write a critique of the Van Hofwegan et al. paper. The essay is posted on Lenski’s blog at: On the Evolution of Citrate Use.

    Blount and Lenski discuss two technical points: the rapidity of the events in the Van Hofwegan et al. paper and the criticism of historical contingency in that paper and in an accompanying commentary by Roth and Maisnier-Patin (2016). Neither criticism is valid.

    (Blount has published a nice paper on historical contingency in the LTEE (Blount, 2016). It’s relevant to our discussions about replaying the tape of life.)

    Blount and Lenski also address the creation of new genetic information. They say,

    The claim that “no new genetic information evolved” is based on the fact that the bacteria gained this new ability by rearranging existing structural and regulatory genetic elements. But that’s like saying a new book—say, Darwin’s Origin of Species when it first appeared in 1859—contains no new information, because the text has the same old letters and words that are found in other books.

    In an evolutionary context, a genome encodes not just proteins and patterns of expression, but information about the environments where an organism’s ancestors have lived and how to survive and reproduce in those environments by having useful proteins, expressing them under appropriate conditions (but not others), and so on. So when natural selection—that is, differential survival and reproduction—favors bacteria whose genomes have mutations that enable them to grow on citrate, those mutations most certainly provide new and useful information to the bacteria.

    That’s how evolution works—it’s not as though new genes and functions somehow appear out of thin air. As the bacterial geneticist and Nobel laureate François Jacob wrote (Science, 1977): “[N]atural selection does not work as an engineer works. It works like a tinkerer—a tinkerer who does not know exactly what he is going to produce but uses whatever he finds around him, whether it be pieces of string, fragments of wood, or old cardboards; in short, it works like a tinkerer who uses everything at his disposal to produce some kind of workable object.”

    To say there’s no new genetic information when a new function has evolved (or even when an existing function has improved) is a red herring that is promulgated by the opponents of evolutionary science.

    This is an important point.

    Evolution works by modifying pre-existing DNA to create new genes or new regulatory elements from sequences that were already present in the genome.2 Creationists seem to think that new genetic information has to be “poofed” into existence from nothing or it doesn’t count as new information. They would like very much to demonstrate that there are real examples of such magic because that would lend support to their claim that goddidit. So far they haven’t come up with a single, credible, example of such a gene so they have to be content with denying that evolution can create new genetic information.

    It’s sad, really.

  16. 16
    bornagain77 says:

    Seversky states,

    I think I would also have a hard time keeping my temper if I were to discuss such an outrageously defamatory claim with you face-to-face.

    It is only defamatory because it is true.

    Moran, (and you) think that passage is a refutation of Minnich’s work?

    For crying out loud,. Lenski had dishonestly suggested that it was a ‘unique’ speciation event. Minnich showed the adaptation was a repeatable, i.e. non-random, adaptation that was as easy as falling off a log to achieve.

    Moreover, as Behe showed, the adaptation came at a cost in overall molecular functionality.

    Thus, I stand by every word I wrote about Lenski’s dishonest antics in claiming that the adaptation supports the grandiose claims of Darwinists.

  17. 17
    Bob O'H says:

    For crying out loud,. Lenski had dishonestly suggested that it was a ‘unique’ speciation event.

    Can you point to where he said it was a speciation event?

  18. 18
    AndyClue says:

    @Bob O’H

    Can you point to where he said it was a speciation event?

    “Rapid Evolution of Citrate Utilization by Escherichia coli by Direct Selection Requires citT and dctA”
    https://journals.asm.org/doi/full/10.1128/JB.00831-15

    “Some authors assert that this evolved E. coli Cit+ strain represents an exceedingly rare, innovative gain-of-function mutation and argue for recognition of this E. coli variant as a newly evolved species (3, 13).”

    If you look at citation 13 you’ll see that the article was written by Lenski: “Lenski RE. 2011. Evolution in action: a 50,000-generation salute to Charles Darwin. Microbe 6:30–33.”

    Now let’s have a look at that article:

    “The citrate-eaters still eat glucose, but they aren’t quite as successful at competing for that sugar as they were before. As a consequence of that tradeoff, their cousins persist as glucose specialists. So the bacteria in this simple flaskworld have split into two lineages that coexist by exploiting their common environment in different ways. And one of the lineages makes its living by doing something brand-new, something that its ancestor could not do. That sounds a lot like the origin of species to me.”

  19. 19
    bornagain77 says:

    “Can you point to where he said it was a speciation event?”

    The Man Who Bottled Evolution – 2013
    Excerpt: These citrate users are enabling Blount, now a postdoc in the lab, and Lenski to look at another aspect of evolution: the formation of new species. The usual test of separate species is that they are unable to interbreed successfully, a criterion that can’t be applied to bacteria because they don’t mate. But because one of E. coli’s defining characteristics is the inability to use citrate for energy in the presence of oxygen, the citrate-consuming bacteria could be seen as a new species. And they may even meet the traditional definition. Researchers can’t interbreed bacteria, but they can mix the genomes of separate strains. Bacteria that thrive on citrate do poorly on glucose, and melding the citrate users with the parent strain produces a less fit hybrid, Lenski reported at the June evolution meeting.
    https://science.sciencemag.org/content/342/6160/790.full

    And per Minnich

    Rapid Evolution of Citrate Utilization by Escherichia coli by Direct Selection Requires citT and dctA. – Minnich – Feb. 2016
    The isolation of aerobic citrate-utilizing Escherichia coli (Cit(+)) in long-term evolution experiments (LTEE) has been termed a rare, innovative, presumptive speciation event. We hypothesized that direct selection would rapidly yield the same class of E. coli Cit(+) mutants and follow the same genetic trajectory: potentiation, actualization, and refinement. This hypothesis was tested,,,
    Potentiation/actualization mutations occurred within as few as 12 generations, and refinement mutations occurred within 100 generations.,,,
    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, http://dx.doi.org/10.1038/nature11514 ) 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.
    http://www.ncbi.nlm.nih.gov/pubmed/26833416

  20. 20
    Sandy says:

    Any system that add information REQUIRE much more initial informaton. Problem of information is insurmontable for atheists. Cannot be resolved by materialism.

  21. 21
    Bob O'H says:

    AndyClue – ah, thank you. (although the “unique” is clearly wrong – they replicated it!)

  22. 22
    bornagain77 says:

    Since Seversky appealed to Moran, (of all people), to defend Lenski, It is also worth pointing out that Moran, 8 years past the ENCODE results which found widespread functionality across the entire genome., is still trying to claim, (in the face of constant empirical evidence to the contrary that supports ENCODE and contradicts Moran), that the vast majority of the genome is non-functional junk (in fact, Moran unbelievably claims that upwards to 90% of the genome must be junk). I believe Moran is presently even writing a book on the subject.

    Seversky accused me of being blinded by my own religious bias. Yet I am not the one holding onto to my position in the face of constant empirical evidence that contradicts my position. Moran and Seversky are the ones doing that.

    Might it be too obvious to point out that since Moran, (and apparently Seversky), are the ones who are ignoring the constant onslaught of empirical evidence that contradicts their position, that they are, in fact, the ones who are blinded by their own own religious commitment to atheism?

    Junk No More: ENCODE Project Nature Paper Finds “Biochemical Functions for 80% of the Genome” – Casey Luskin – September 5, 2012
    Excerpt: The Discover Magazine article further explains that the rest of the 20% of the genome is likely to have function as well:
    “And what’s in the remaining 20 percent? Possibly not junk either, according to Ewan Birney, the project’s Lead Analysis Coordinator and self-described “cat-herder-in-chief”. He explains that ENCODE only (!) looked at 147 types of cells, and the human body has a few thousand. A given part of the genome might control a gene in one cell type, but not others. If every cell is included, functions may emerge for the phantom proportion. “It’s likely that 80 percent will go to 100 percent,” says Birney. “We don’t really have any large chunks of redundant DNA. This metaphor of junk isn’t that useful.””
    We will have more to say about this blockbuster paper from ENCODE researchers in coming days, but for now, let’s simply observe that it provides a stunning vindication of the prediction of intelligent design that the genome will turn out to have mass functionality for so-called “junk” DNA. ENCODE researchers use words like “surprising” or “unprecedented.” They talk about of how “human DNA is a lot more active than we expected.” But under an intelligent design paradigm, none of this is surprising. In fact, it is exactly what ID predicted.
    http://www.evolutionnews.org/2.....64001.html

    Discovery Of Useful “Junk DNA” “Has Outstripped The Discovery Of Protein-Coding Genes By A Factor Of Five… – March 30, 2021
    Excerpt: With the HGP draft in hand, the discovery of non-protein-coding elements exploded. So far, that growth has outstripped the discovery of protein-coding genes by a factor of five, and shows no signs of slowing. Likewise, the number of publications about such elements also grew in the period covered by our data set. For example, there are thousands of papers on non-coding RNAs, which regulate gene expression.
    https://uncommondescent.com/intelligent-design/discovery-of-useful-junk-dna-has-outstripped-the-discovery-of-protein-coding-genes-by-a-factor-of-five/

    May 2021 – Refutation of Larry Moran’s 5 reasons for junk DNA
    https://uncommondescent.com/intelligent-design/larry-morans-new-book-sounds-like-a-scorcher/#comment-730443
    https://uncommondescent.com/intelligent-design/larry-morans-new-book-sounds-like-a-scorcher/#comment-730461
    https://uncommondescent.com/intelligent-design/larry-morans-new-book-sounds-like-a-scorcher/#comment-730474

  23. 23
    bornagain77 says:

    Since Bob O’H implies that he has some knowledge as to what would it take to clearly define when a new species has appeared via Darwinian processes, perhaps Bob can disentangle the entire ‘species problem’ mess for us?

    i.e. Darwinists, with their reductive materialistic framework, can’t even define what a species truly is.

    At New Scientist: Questioning The Idea Of Species – Nov. 2020
    Excerpt: Take the apparently simple organising principle of a species. You might have learned at school that a species is a group of individuals that can breed to produce fertile offspring. But this is just one of at least 34 competing definitions concocted over the past century by researchers working in different fields.,,,,
    https://uncommondescent.com/darwinism/at-new-scientist-questioning-the-idea-of-species/

    As the headline of the following article stated, “What is a species? The most important concept in all of biology is a complete mystery”

    What is a species? The most important concept in all of biology is a complete mystery – July 16, 2019
    Excerpt: Enough of species?
    This is only the tip of a deep and confusing iceberg. There is absolutely no agreement among biologists about how we should understand the species. One 2006 article on the subject listed 26 separate definitions of species, all with their advocates and detractors. Even this list is incomplete.
    The mystery surrounding species is well-known in biology, and commonly referred to as “the species problem”. Frustration with the idea of a species goes back at least as far as Darwin.,,,
    some contemporary biologists and philosophers of biology have,,, suggested that biology would be much better off if it didn’t think about life in terms of species at all.,,,
    https://theconversation.com/what-is-a-species-the-most-important-concept-in-all-of-biology-is-a-complete-mystery-119200

    In fact, Charles Darwin himself admitted that he did not have a rigid definition for what the term ‘species’ actually meant when he stated that, “I look at the term species as one arbitrarily given, for the sake of convenience.,,,”

    “I look at the term species as one arbitrarily given, for the sake of convenience, to a set of individuals closely resembling each other, and that it does not essentially differ from the term variety, which is given to less distinct and more fluctuating forms. The term variety, again, in comparison with mere individual differences, is also applied arbitrarily, for convenience’s sake.”
    – Charles Darwin

    As should be needless to say, the inability of a supposedly scientific theory, a supposedly scientific theory that seeks to explain the “Origin of Species”, to clearly define what a species actually is is a clear indication that that supposedly scientific theory cannot possibly be the proper ‘scientific’ explanation for the “Origin of Species”!

    As the old joke goes, “you can’t get there from here.”

    The reason that Darwinists can never give a proper ‘scientific’ definition for what a species actually is because the concept of species turns out to be an abstract, i.e. immaterial, conceptualization of the immaterial mind.

    As the following article states, ”a crucial feature of human reason is its ability to abstract the universal nature from our sense experience of particular organisms.”,,, ” this denial (of true species) is a grave error, because the essence of the individual (the species in the Aristotelian sense) is the true object of our knowledge.”

    Darwin, Design & Thomas Aquinas
    The Mythical Conflict Between Thomism & Intelligent Design by Logan Paul Gage
    Excerpt:,,, In Aristotelian and Thomistic thought, each particular organism belongs to a certain universal class of things. Each individual shares a particular nature—or essence—and acts according to its nature. Squirrels act squirrelly and cats catty. We know with certainty that a squirrel is a squirrel because a crucial feature of human reason is its ability to abstract the universal nature from our sense experience of particular organisms.
    Denial of True Species
    Enter Darwinism. Recall that Darwin sought to explain the origin of “species.” Yet as he pondered his theory, he realized that it destroyed species as a reality altogether. For Darwinism suggests that any matter can potentially morph into any other arrangement of matter without the aid of an organizing principle. He thought cells were like simple blobs of Jell-O, easily re-arrangeable. For Darwin, there is no immaterial, immutable form. In The Origin of Species he writes:
    “I look at the term species as one arbitrarily given, for the sake of convenience, to a set of individuals closely resembling each other, and that it does not essentially differ from the term variety, which is given to less distinct and more fluctuating forms. The term variety, again, in comparison with mere individual differences, is also applied arbitrarily, for convenience’s sake.”
    Statements like this should make card-carrying Thomists shudder.,,,
    The first conflict between Darwinism and Thomism, then, is the denial of true species or essences. For the Thomist, this denial is a grave error, because the essence of the individual (the species in the Aristotelian sense) is the true object of our knowledge. As philosopher Benjamin Wiker observes in Moral Darwinism, Darwin reduced species to “mere epiphenomena of matter in motion.” What we call a “dog,” in other words, is really just an arbitrary snapshot of the way things look at present. If we take the Darwinian view, Wiker suggests, there is no species “dog” but only a collection of individuals, connected in a long chain of changing shapes, which happen to resemble each other today but will not tomorrow.
    What About Man?
    Now we see Chesterton’s point. Man, the universal, does not really exist. According to the late Stanley Jaki, Chesterton detested Darwinism because “it abolishes forms and all that goes with them, including that deepest kind of ontological form which is the immortal human soul.” And if one does not believe in universals, there can be, by extension, no human nature—only a collection of somewhat similar individuals.,,,
    https://www.touchstonemag.com/archives/article.php?id=23-06-037-f

    Within their reductive materialistic framework, Darwinists simply have no foundation on which they can ground the abstract, i.e. immaterial, concept of ‘species’.

    In the Darwinists materialistic worldview, if something is not composed of particles it simply does not exist and is considered an illusion. It is ‘abstract’. Thus, since species is clearly a abstract conceptualization of the immaterial mind, a conceptualization that cannot possibly be reduced to any possible grouping of material particles that Darwinists may wish to invoke, then it should not be surprising to find Darwinists denying the existence of species, i.e. denying the ‘true object of our knowledge’, altogether.

    There simply is no physical measurement that Darwinists can perform and say, ‘and this is exactly what we mean when we say the term ‘species”’. The concept of species does not weigh anything, nor does it have a speed, nor does the concept of species have any particular width or height that we can measure. Again, the entire concept of species is abstract and immaterial.

    And to repeat, the (sheer) inability for a supposedly scientific theory, (a supposedly scientific theory that seeks to explain the “Origin of Species”), to clearly define what a species actually is is a crystal clear indication that that supposedly scientific theory cannot possibly be the proper ‘scientific’ explanation for the “Origin of Species”!

  24. 24
    Bob O'H says:

    ba77 – if I gave that impression, them my apologies for not writing clearly enough to imply that I wasn’t aware that the species problem is always going to be messy, because of the nature of the subject.

  25. 25
    Seversky says:

    Bornagain77/22

    Since Seversky appealed to Moran, (of all people), to defend Lenski, It is also worth pointing out that Moran, 8 years past the ENCODE results which found widespread functionality across the entire genome., is still trying to claim, (in the face of constant empirical evidence to the contrary that supports ENCODE and contradicts Moran), that the vast majority of the genome is non-functional junk (in fact, Moran unbelievably claims that upwards to 90% of the genome must be junk).

    If you read Sandwalk you will find an extensive discussion concerning the so-called “‘function’ wars” which broke out after ENCODE and were fought over the way the researchers played fast and loose with the meaning of the word.

    Might it be too obvious to point out that since Moran, (and apparently Seversky), are the ones who are ignoring the constant onslaught of empirical evidence that contradicts their position, that they are, in fact, the ones who are blinded by their own own religious commitment to atheism?

    What onslaught did you have in mind, other than your dumps of cherry-picked quotes?

  26. 26
    Seversky says:

    Bornagain77/23

    Since Bob O’H implies that he has some knowledge as to what would it take to clearly define when a new species has appeared via Darwinian processes, perhaps Bob can disentangle the entire ‘species problem’ mess for us?

    If you’re actually interested in the complexities of the species concept then you should look to someone like Australian philosopher of science John S Wilkins who has written textbooks on the subject and knows way more about it than either of us. Here is a sample from his blog Evolving Thoughts

    Do we need, and can we get, a single authoritative list of species?

    In a recent paper, Garnett et al. [2020] have set up what they refer to as the principles for creating a single authoritative list of all known species. This is required because there are no such singular lists (one was attempted in the 1990s, and another in the naughties) to which people can refer, and this causes, among other things, miscommunications. The reason it does that, is because species are continuously renamed, reassigned to new genera, or reclassified as synonymous with other, older species names

    First of all is the delimitation problem. Species are identified as separate from other such groups in various ways. Some use genomic clustering algorithms; some use mitochondrial or other organelle DNA sequences at a particular locus (“Barcoding”), and the traditional methods of eyeballing or analysing anatomy are also still in use. However, for there to be a “universal” list, there need to be universally adopted criteria, which are, if possible, objective (or nearly so). And such criteria are not in evidence. There are conventions, of course, but their application depends upon such factors as the sub discipline or group being classified, the collegial practices of that institution or region, and the experience of the taxonomist.

    A recent paper on fungal species concepts illustrates the issues. Fungi have some kind of sexual cycle, but not all of them, and neither DNA sequences nor morphology give universal and unambiguous results. Lücking, et al. [2020] say:

    Hawksworth (1996: 32) pragmatically defined fungal species as “… groups of individuals separated by inheritable character discontinuities and which it is useful to give a species name to …”. Since inheritable character discontinuities can only be assessed by simultaneous analysis of phylogenetic relationships and clade-based phenotype variation, this definition is largely congruent with ‘phylogenetic taxon species’ [Italics in original].

    Fungi are no exception to the notion that species have individual evolutionary histories, and so aspects of their genealogical coherence, reproductive isolation and phenotypic distinctiveness may differ. This implies that there is no single, universal approach to species delimitation and consequently for species identification.

    […]

    Species are used, and have a role in how we employ, enjoy and explore the natural world. They are terms of art on which many items of knowledge are hung. But, as Lücking et al. note, there remains no single useful, coherent, exclusive and universal notion of what a species is, and in my view, there never will be. So a singular list of species would be, at best, useful fiction in some domains of the evolutionary tree, and a complete waste of time in others. Moreover, any description of a species must be held hostage to the empirical data, and so species are redescribed, divided, lumped, and moved around the tree on a regular basis. Given that we would be talking about millions of species, the administrative effort involved in maintaining that list, and moreover revising citations of that list, would be enormous. As taxonomy gets almost no direct funding in biology as it is, this would take many researchers and their grants away from other aspects of their work.

    Why do we even need to have species when talking about biology? There are a few reasons, in my opinion. The first and primary is administrative and tradition: we have used the idea of species as the basal kinds of life for around 500 years. All the literature is cast in that way. Communication is based upon the names and records of species. Education of specialists uses species names and records. This, of course, has no force as knowledge, except in the generic sense of knowing the details of a practice. These species names are not evidence in scientific research, any more than a library record is evidence in the topics covered by books. It is utility, not knowledge.

    Another reason is that we think we must have an ontology in each scientific discipline. That is to say, each field must have basic units. This is a view that I consider unfounded. If one adopts a different approach (say a process rather than an objectual or substantial ontology), the notion of base units becomes otiose. I’m not suggesting this is the case in all science, of course. Physics I think still has basic units. But it is the case in biology, and in all the other special sciences.

    The danger of unit-ontologies in the special sciences is that we become so wedded to the units that we treat them as evidence in inference, and this leads to taking conclusions from constructed categories (“hypotheses” or “impressions”) as probative in our research. And this is how essentialism becomes malign. Class concepts like “race”, “rank” and so on are formed by the acceptance of what are constructed ideas, usually from “common sense” culture, as facts about the universe. In short, this is a subtle form of anthropomorphism, of thinking that we (our categories) are the measure of the universe.

    Science begins in and returns to data. Even allowing that data and ideas in science are somehow irredeemably social (which I do think) and that we are subject to confirmation biases and various kinds, the goal in science must be to construct these categories based upon as much data as we can afford to get. In short, I am an empiricist. I think science should be too.

    Now explain how Lenski was being dishonest in his claim that he could be observing the emergence of a new species in his experiment.

  27. 27
    ET says:

    The only gene that could help transport citrate through the cell membrane was duplicated and put under the control of a binding site that was “on” in the presence of oxygen. This is evidence for a built-in response to an environmental cue, as Dr. Spetner wrote about in 1997.

  28. 28
    Querius says:

    Dismissing someone’s scientific work merely by labeling them as a “creationist,” or dismissing illustrative quotes in support of a position merely by labeling them as “cherry picking quotes” is completely disingenuous.

    Darwinism is as dead as the “Norwegian blue” parrot in Monty Python’s dead parrot skit. It’s a fundamentally racist vestige of the days of wooden ships and European colonialism as Darwin himself demonstrated in his infamous book, The Descent of Man.

    Now that I’ve dug into some of the scientific back-pedaling in response to Lenski’s grossly inflated claims (thanks to some links provided here as well as others), I find myself really resenting being mislead.

    Naturally, Darwin fundamentalists will hold onto their unscientific beliefs and ideological prejudices much like flat earthers and anti-vaxxers, who ignore or rationalize falsifying evidence that turns up with boring regularity, but instead cling to Haeckel’s embryos, fraudulent fossils, and so-called missing links long after they’re exposed.

    The fact remains that E.coli already can metabolize citrate in an anaerobic environment and was able to restore it in aerobic conditions–this is not some novel feature that was grossly inflated to supposedly demonstrate evolution. E.Coli is still E.coli and has not evolved into a chimpanzee any more than someone who is lactose intolerant is a new hominid species.

    -Q

  29. 29
    bornagain77 says:

    In post 23 I pointed out that the reason that the ‘species problem’ persists as a ‘problem’ for Darwinian materialists in the first place is because the entire “concept of species turns out to be an abstract, i.e. immaterial, conceptualization of the immaterial mind”, that cannot be reduced to rigid materialistic definition.

    As I further pointed out in post 23, “There simply is no physical measurement that Darwinists can perform and say, ‘and this is exactly what we mean when we say the term ‘species”’. The concept of species does not weigh anything, nor does it have a speed, nor does the concept of species have any particular width or height that we can measure. Again, the entire concept of species is abstract and immaterial.”

    In post 26 Seversky objected to my fairly straightforward observation of the primary problem confronting Darwinian materialists is the fact that the entire concept of species is abstract and immaterial in its foundational essence.

    Yet the very authority, i.e. John S Wilkins, that Seversky himself quotes from, to supposedly refute my fairly straightforward observation, (far from refuting my observation), agrees with my basic point that the abstract and immaterial concept of species is irreducible to any rigid physical/materialistic measurements, such as weight, speed, length and height.

    In the passage that Seversky himself cited, Wilkins himself honestly admits that, while physics has ‘base units’, (evolutionary) biology does not have ‘base units’ in which to rigidly delimit species into specific categories.

    Specifically Wilkins stated,

    “Another reason is that we think we must have an ontology in each scientific discipline. That is to say, each field must have basic units. This is a view that I consider unfounded. If one adopts a different approach (say a process rather than an objectual or substantial ontology), the notion of base units becomes otiose. I’m not suggesting this is the case in all science, of course. Physics I think still has basic units. But it is the case in biology, and in all the other special sciences.”

    As an aside, and as to Wilkins trying to claim that “all the other special sciences’ have no base units, (whatever Wilkins meant by ‘special sciences’), the fact of the matter is that all the other ‘hard sciences’ are rigidly defined in a clear enough manner so that that they can be realistically modeled. Only Darwinian evolution, out of all the ‘hard sciences’, lacks a clearly defined foundation that can be realistically modeled.

    Top Ten Questions and Objections to ‘Introduction to Evolutionary Informatics’ – Robert J. Marks II – June 12, 2017
    Excerpt: “There exists no model successfully describing undirected Darwinian evolution. Hard sciences are built on foundations of mathematics or definitive simulations. Examples include electromagnetics, Newtonian mechanics, geophysics, relativity, thermodynamics, quantum mechanics, optics, and many areas in biology. Those hoping to establish Darwinian evolution as a hard science with a model have either failed or inadvertently cheated. These models contain guidance mechanisms to land the airplane squarely on the target runway despite stochastic wind gusts. Not only can the guiding assistance be specifically identified in each proposed evolution model, its contribution to the success can be measured, in bits, as active information.,,,”,,, “there exists no model successfully describing undirected Darwinian evolution. According to our current understanding, there never will be.,,,”
    https://evolutionnews.org/2017/06/top-ten-questions-and-objections-to-introduction-to-evolutionary-informatics/

    To continue on with my critique of Seversky’s citation,,,

    Moreover, as if the irreducibility of the abstract, i.e. immaterial, concept of species to physical measurements was not problematic enough, (for those who toe the reductive materialistic party line of Darwinian evolution), the very examples that Wilkins himself cites for delimiting species into specific groups turn out to falsify Darwinian claims.

    Specifically, Wilkins stated that,,,

    “Species are identified as separate from other such groups in various ways. Some use genomic clustering algorithms; some use mitochondrial or other organelle DNA sequences at a particular locus (“Barcoding”), and the traditional methods of eyeballing or analysing anatomy are also still in use.”

    Yet all the examples that Wilkins himself cited, (i.e. genomic clustering algorithms; mitochondrial or other organelle DNA sequences at a particular locus (“Barcoding”), and the traditional methods of eyeballing or analysing anatomy), for delimiting species into specific groups falsify Darwin’s claim that all species should be related via “numerous, successive, slight modifications”.

    Specifically, Darwin himself held that evolution proceeds via “numerous, successive, slight modifications”, and even held that if this were shown to not be the case, then “my theory would absolutely break down.”

    “If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down.”
    –Charles Darwin, Origin of Species – 1860 – pg 189

    Yet, all three of Wilkins’ methods for delimiting species into specific groups falsify Darwin’s claim.

    As to genomic clustering algorithms that Wilkins mentioned,,, although problems with the hypothetical genetic ‘tree of life’ were known about before,,,

    Why Darwin was wrong about the (genetic) tree of life: – 21 January 2009
    Excerpt: Syvanen recently compared 2000 genes that are common to humans, frogs, sea squirts, sea urchins, fruit flies and nematodes. In theory, he should have been able to use the gene sequences to construct an evolutionary tree showing the relationships between the six animals. He failed. The problem was that different genes told contradictory evolutionary stories. This was especially true of sea-squirt genes. Conventionally, sea squirts – also known as tunicates – are lumped together with frogs, humans and other vertebrates in the phylum Chordata, but the genes were sending mixed signals. Some genes did indeed cluster within the chordates, but others indicated that tunicates should be placed with sea urchins, which aren’t chordates. “Roughly 50 per cent of its genes have one evolutionary history and 50 per cent another,” Syvanen says. .”We’ve just annihilated the tree of life. It’s not a tree any more, it’s a different topology entirely,” says Syvanen. “What would Darwin have made of that?”
    http://www.newscientist.com/ar.....-life.html

    ,,, although problems with the hypothetical genetic ‘tree of life’ were known about before, in a (massive) study of genomic data from 2018, Winston Ewert completely blew the hypothesis of a genetic ‘tree of life’, that conformed to the Darwinian expectations, (i.e. of numerous, successive, slight modifications,), completely out of the water.

    As the following article stated about Dr. Ewert’s study, “We are not talking about a few decimal points difference. For one of the data sets (HomoloGene), the dependency graph, (i.e. the Intelligent Design), model was superior to common descent by a factor of 10,064. The comparison of the two models yielded a preference for the dependency graph model of greater than ten thousand.
    Ten thousand is a big number. But it gets worse, much worse.”,,,

    New Paper by Winston Ewert Demonstrates Superiority of Design Model – Cornelius Hunter – July 20, 2018
    Excerpt: Where It Counts
    Let me repeat that in case the point did not sink in. Where it counted, common descent failed compared to the dependency graph model. The other data types served as useful checks, but for the data that mattered — the actual, real, biological species data — the results were unambiguous.
    Ewert amassed a total of nine massive genetic databases. In every single one, without exception, the dependency graph model surpassed common descent.
    Darwin could never have even dreamt of a test on such a massive scale. Darwin also could never have dreamt of the sheer magnitude of the failure of his theory. Because you see, Ewert’s results do not reveal two competitive models with one model edging out the other.
    We are not talking about a few decimal points difference. For one of the data sets (HomoloGene), the dependency graph, (i.e. the Intelligent Design), model was superior to common descent by a factor of 10,064. The comparison of the two models yielded a preference for the dependency graph model of greater than ten thousand.
    Ten thousand is a big number. But it gets worse, much worse.
    https://evolutionnews.org/2018/07/new-paper-by-winston-ewert-demonstrates-superiority-of-design-model/

    In Seversky’s citation, Wilkins also mentioned using mitochondrial DNA, and other organelle DNA, in order to delimit species into specific groups.

    Yet, when trying to define species via mitochondrial DNA (barcoding), the mitochondrial data also falsifies Darwinian expectations.

    The following study found, when comparing the mitochondrial DNA of different species, that “”If individuals are stars, then species are galaxies,” said Thaler. “They are compact clusters in the vastness of empty sequence space.”

    Sweeping gene survey reveals new facets of evolution – May 28, 2018
    Excerpt: Darwin perplexed,,,
    And yet—another unexpected finding from the study—species have very clear genetic boundaries, and there’s nothing much in between.
    “If individuals are stars, then species are galaxies,” said Thaler. “They are compact clusters in the vastness of empty sequence space.”
    The absence of “in-between” species is something that also perplexed Darwin, he said.
    https://phys.org/news/2018-05-gene-survey-reveals-facets-evolution.html

    Why should mitochondria define species? – 2018
    Excerpt: The particular mitochondrial sequence that has become the most widely used, the 648 base pair (bp) segment of the gene encoding mitochondrial cytochrome c oxidase subunit I (COI),,,,
    The pattern of life seen in barcodes is a commensurable whole made from thousands of individual
    studies that together yield a generalization. The clustering of barcodes has two equally important features: 1) the variance within clusters is low, and 2) the sequence gap among clusters is empty, i.e., intermediates are not found.,,,
    https://phe.rockefeller.edu/news/wp-content/uploads/2018/05/Stoeckle-Thaler-Final-reduced.pdf

    Moreover, this “intermediates are not found” in mitochondrial DNA sequences has been known about for at least 35 years.

    Specifically, the preceding study, in over the top fashion, confirms exactly what Michael Denton had found 35 years ago in his book “Evolution: A Theory in Crisis” (1986).

    Specifically Michael Denton found that, “However, the most striking feature of the matrix is that every identifiable subclass is isolated and distinct. Every sequence can be unambiguously assigned to a particular subclass. No sequence or group of sequences can be designated as intermediate with respect to other groups. All the sequences of each subclass are equally isolated from the members of another group. Transitional or intermediate classes are completely absent from the matrix. 4”

    Cytochrome C
    Excerpt: If the existence of cytochrome C in “higher forms” of animals is the result of evolution from a common ancestor, then one would expect to see a logical progression. That is, the cytochrome C of an invertebrate (like a worm) would be slightly different from a bacteria. A “primitive” vertebrate (like a fish) would have those same differences, plus a few more. As you progress along the presumed evolutionary path to amphibians, reptiles, mammals, primates, ending with humans, you should see the changes in cytochrome C accumulate.
    On the other hand, if cytochrome C is a commonly used component employed by a designer, you will not see that logical progression. You will just see minor differences which optimize cytochrome C for that kind of creature.,,,
    Dr. Denton’s Figure 12.1, “The Cytochromes Percent Sequence Difference Matrix” 3, is an abridged version of the 1972 Dayhoff Atlas of Protein Structure and Function Matrix of nearly 1089 entries showing the percent difference between 33 species. Denton’s abridged matrix shows that molecular biologists can easily recognize which cytochrome C sample came from a fish and which came from a mammal.
    “However, the most striking feature of the matrix is that every identifiable subclass is isolated and distinct. Every sequence can be unambiguously assigned to a particular subclass. No sequence or group of sequences can be designated as intermediate with respect to other groups. All the sequences of each subclass are equally isolated from the members of another group. Transitional or intermediate classes are completely absent from the matrix. 4”
    If evolution were true, and creatures gradually evolved from one to another, there should be intermediate forms. Intermediate forms should be found in living creatures, in the fossil record, and in proteins. It should, in at least some cases, be hard to classify things because the boundaries are blurred. (But the boundaries are distinct as would be expected under the Design presupposition)
    http://scienceagainstevolution.info/v7i10f.htm

    So basically, Darwinists have been ignoring, and/or denying, this falsifying empirical evidence against their theory for 35 years.

  30. 30
    bornagain77 says:

    As to the third ‘usual’ method that Wilkins mentioned for delimiting species into specific groups, i.e. the “traditional methods of eyeballing or analysing anatomy”, well that ‘traditional method’ also, unsurprisingly, falsifies Darwinian claims.

    Specifically, when new body plans appear in the fossil record, they appear suddenly and are not led up to by ‘numerous, successive, slight modifications.,,,” as Darwin himself had envisioned in the only (very crude) illustration that he drew in his book “Origin of Species”.

    “In his 1859 masterpiece On the Origin of Species, Charles Darwin included just one illustration — a “tree” depicting branching and extinction through time. … He referred to the genealogical relationships among all living things as “the great Tree of Life.”
    https://peabody.yale.edu/exhibits/tree-of-life/what-tree-life

    That ‘branching pattern’ is simply not what is seen in the fossil record. The ‘lack of transitions’ is particularly acute for the Cambrian explosion.

    As Stephen Meyer noted in his book “Darwin’s Doubt”, “the differences in form between any member of one phylum and any member of another phylum are vast, and paleontologists have utterly failed to find forms that would fill these yawning chasms in what biotechnologists call “morphological space.”

    “Over the past 150 years or so, paleontologists have found many representatives of the phyla that were well-known in Darwin’s time (by analogy, the equivalent of the three primary colors) and a few completely new forms altogether (by analogy, some other distinct colors such as green and orange, perhaps). And, of course, within these phyla, there is a great deal of variety. Nevertheless, the analogy holds at least insofar as the differences in form between any member of one phylum and any member of another phylum are vast, and paleontologists have utterly failed to find forms that would fill these yawning chasms in what biotechnologists call “morphological space.” In other words, they have failed to find the paleolontogical equivalent of the numerous finely graded intermediate colors (Oedleton blue, dusty rose, gun barrel gray, magenta, etc.) that interior designers covet. Instead, extensive sampling of the fossil record has confirmed a strikingly discontinuous pattern in which representatives of the major phyla stand in stark isolation from members of other phyla, without intermediate forms filling the intervening morphological space.”?
    – Stephen Meyer – Darwin’s Doubt (p. 70)

    Moreover, this is not just a problem for Darwinists in the Cambrian explosion, but the ‘problem’ of body plans appearing suddenly in the fossil record is found throughout the fossil record as well, subsequent to the Cambrian explosion.

    Scientific study turns understanding about evolution on its head – July 30, 2013
    Excerpt: evolutionary biologists,,, looked at nearly one hundred fossil groups to test the notion that it takes groups of animals many millions of years to reach their maximum diversity of form.
    Contrary to popular belief, not all animal groups continued to evolve fundamentally new morphologies through time. The majority actually achieved their greatest diversity of form (disparity) relatively early in their histories.
    ,,,Dr Matthew Wills said: “This pattern, known as ‘early high disparity’, turns the traditional V-shaped cone model of evolution on its head. What is equally surprising in our findings is that groups of animals are likely to show early-high disparity regardless of when they originated over the last half a billion years. This isn’t a phenomenon particularly associated with the first radiation of animals (in the Cambrian Explosion), or periods in the immediate wake of mass extinctions.”,,,
    Author Martin Hughes, continued: “Our work implies that there must be constraints on the range of forms within animal groups, and that these limits are often hit relatively early on.
    Co-author Dr Sylvain Gerber, added: “A key question now is what prevents groups from generating fundamentally new forms later on in their evolution.,,,
    http://phys.org/news/2013-07-s.....ution.html

    Günter Bechly video: Fossil Discontinuities: A Refutation of Darwinism and Confirmation of Intelligent Design – 2018
    https://www.youtube.com/watch?v=M7w5QGqcnNs
    The fossil record is dominated by abrupt appearances of new body plans and new groups of organisms. This conflicts with the gradualistic prediction of Darwinian Evolution. Here 18 explosive origins in the history of life are described, demonstrating that the famous Cambrian Explosion is far from being the exception to the rule. Also the fossil record establishes only very brief windows of time for the origin of complex new features, which creates an ubiquitous waiting time problem for the origin and fixation of the required coordinated mutations. This refutes the viability of the Neo-Darwinian evolutionary process as the single conceivable naturalistic or mechanistic explanation for biological origins, and thus confirms Intelligent Design as the only reasonable alternative.

    Thus the three ‘lead-off’ criteria that Wilkins himself listed for delimiting species into specific groups all end up falsifying Darwinian claims for ‘numerous, successive, slight modifications.,,,”

    None of this falsifying evidence against Darwinian evolution should be that surprising.

    The ‘problem’ of delimiting species in a rigidly defined manner is very much a ‘damned if you do, damned if you don’t’ proposition for Darwinists.

    On the one hand, Darwinists hold, because of their materialistic presuppositions, that a dog is not really ever, strictly speaking, a specific species named dog per se, but instead, “If we take the Darwinian view,,, there is no species “dog” but only a collection of individuals, connected in a long chain of changing shapes, which happen to resemble each other today but will not tomorrow.”

    Darwin, Design & Thomas Aquinas
    The Mythical Conflict Between Thomism & Intelligent Design by Logan Paul Gage
    Excerpt:,,, The first conflict between Darwinism and Thomism, then, is the denial of true species or essences. For the Thomist, this denial is a grave error, because the essence of the individual (the species in the Aristotelian sense) is the true object of our knowledge. As philosopher Benjamin Wiker observes in Moral Darwinism, Darwin reduced species to “mere epiphenomena of matter in motion.” What we call a “dog,” in other words, is really just an arbitrary snapshot of the way things look at present. If we take the Darwinian view,,, there is no species “dog” but only a collection of individuals, connected in a long chain of changing shapes, which happen to resemble each other today but will not tomorrow.
    https://www.touchstonemag.com/archives/article.php?id=23-06-037-f

    But on the other hand, when Darwinists try to delimit species into specific groups, and honestly admit what everybody knows to be true, (i.e. a dog really is a dog that is distinct from all other species), well then that attempt at delimiting species into specific groups ends up falsifying their claim that all species are related via ‘numerous, successive, slight modifications.,,,”

    Again, it is very much a ‘damned if you do, damned if you don’t’ proposition for Darwinists.

    So in conclusion, Seversky’s own citation from Wilkins, which he himself provided in order to supposedly refute me, if fact supports my position and refutes his position.

    I would thank Seversky for providing the citation, but I don’t think he would appreciate my gratitude. 🙂

    In short, the ‘usual’ methods that Wilkins himself listed for delimiting species into specific groups, (i.e. genomic clustering algorithms; mitochondrial or other organelle DNA sequences at a particular locus (“Barcoding”), and the traditional methods of eyeballing or analysing anatomy), those very methods themselves of delimiting species actually falsify Darwinian claims that species are related via ‘numerous, successive, slight modifications.,,,”

    Of supplemental note, since Darwinists presuppose that the ‘transmutation of species’ is the defining feature of the history of all life on earth, it should not be surprising to learn that it was not a Darwinian atheist who first developed the basic classification system for life that we have, but instead it was a devout Christian, Carl Linnaeus, who first developed our basic classification system for life.

    Carl Linnaeus, a devout Christian who is is considered the ‘Father of Taxonomy’, and in developing his classification system for life, was motivated to develop his classification system for life so that it would “reveal the Divine Order of God’s creation”.

    “The Earth’s creation is the glory of God, as seen from the works of Nature by Man alone. The study of nature would reveal the Divine Order of God’s creation, and it was the naturalist’s task to construct a ‘natural classification’ that would reveal this Order in the universe.”
    – Carl Linnaeus
    https://www.crosswalk.com/family/homeschool/christians-in-science-carolus-linnaeus-1368814.html

    Also of supplemental note:

    While I vehemently disagree with Louis Agassiz’s scientific racism, I, never-the-less, whole-heartedly agree with Agassiz’s assessment that genera and species must have been ideas in the mind of God prior to their physical creation

    Louis Agassiz
    Excerpt: Agassiz emigrated to the U.S. in 1847 and became a professor of zoology and geology at Harvard University, headed its Lawrence Scientific School and founded its Museum of Comparative Zoology. Agassiz made extensive contributions to the classification of fish (including of extinct species),,,,
    According to Agassiz, genera and species were ideas in the mind of God; their existence in God’s mind prior to their physical creation meant that God could create humans as one species,,,
    https://www.bookofdaystales.com/louis-agassiz/

    As I have pointed out in this thread, there simply is no physical, and/or material, basis that Darwinian materialists can appeal to in order to rigidly ground the ‘abstract’ and immaterial concept of species, which is the ‘true object of our knowledge’.

    Yet, since species clearly and distinctly exist as the ‘true object of out knowledge’, (i.e. a dog really is a dog and is not on its way to becoming a cat, or becoming anything other than a dog), then it necessarily follows that distinct classifications of species must have been ideas in the mind of God prior to their physical creation.

    Genesis 1:26-27
    Then God said, “Let Us make mankind in Our image, according to Our likeness; and let them rule over the fish of the sea and over the birds of the sky and over the livestock and over all the earth, and over every crawling thing that crawls on the earth.” So God created man in His own image, in the image of God He created him; male and female He created them.

    Also see the argument from truth

    Twenty Arguments God’s Existence – Peter Kreeft
    Excerpt: This argument is closely related to the argument from consciousness. It comes mainly from Augustine.
    Our limited minds can discover eternal truths about being.
    Truth properly resides in a mind.
    But the human mind is not eternal.
    Therefore there must exist an eternal mind in which these truths reside.
    https://www.peterkreeft.com/topics-more/20_arguments-gods-existence.htm#11

  31. 31
    Querius says:

    So, let’s “follow the science” regarding the evolutionary tracks left in actual DNA to see what we can learn about The Tree of Life! Ready?

    “For a long time the holy grail was to build a tree of life,” says Eric Bapteste, an evolutionary biologist at the Pierre and Marie Curie University in Paris, France. A few years ago it looked as though the grail was within reach. But today the project lies in tatters, torn to pieces by an onslaught of negative evidence. Many biologists now argue that the tree concept is obsolete and needs to be discarded. “We have no evidence at all that the tree of life is a reality,” says Bapteste. That bombshell has even persuaded some that our fundamental view of biology needs to change.
    Graham Lawton, “Why Darwin was wrong about the tree of life,” New Scientist (January 21, 2009).

    So, here’s how the Darwinists here handle this scientific information:

    Drumroll . . .

    (crickets)

    -Q

  32. 32
    Seversky says:

    Bornagain77/16

    It is only defamatory because it is true.

    No, it is defamatory if it is untrue. There is no defamation of it is true.

    I say your claims of dishonest and even fraudulent behavior by Lenski are defamatory because they are untrue.

    Moran, (and you) think that passage is a refutation of Minnich’s work?

    It is a refutation of the claim that their work somehow undermines Lenski’s work.

    For crying out loud,. Lenski had dishonestly suggested that it was a ‘unique’ speciation event.

    Where did Lenski claim that it was a “unique speciation event”? As far as I can tell he’s been suggesting it might qualify as a speciation event. And that might be the case. There’s no dishonesty and certainly no fraud in that.

    Minnich showed the adaptation was a repeatable, i.e. non-random, adaptation that was as easy as falling off a log to achieve.

    All Minnich showed was that it was an adaptation that could happen more frequently if you set up a more favorable environment. Big deal. The point is that the capacity to adapt to aerobic metabolism of citrates is there, regardless of how frequently it can occur. That means that there is at least the possibility of the formation of a new species, depending on how you define “species” for E Coli.

    Moreover, as Behe showed, the adaptation came at a cost in overall molecular functionality.

    So what? If the cost of evolving a new function which enables you to survive better is the loss of an old function which is no longer necessary then that’s a good deal. That’s what evolution is about, survival. How is that not new information? I could say that all the words I just used were taken from a Richard Dawkins book or the Bible. The same could be true of what you wrote. Does this mean it’s not new information?

  33. 33
    bornagain77 says:

    All your hand-waving in post 32 aside, I think I’ll let my response stand as stated Seversky.

  34. 34
    Seversky says:

    Bornagain77/29

    In post 23 I pointed out that the reason that the ‘species problem’ persists as a ‘problem’ for Darwinian materialists in the first place is because the entire “concept of species turns out to be an abstract, i.e. immaterial, conceptualization of the immaterial mind”, that cannot be reduced to rigid materialistic definition.

    The problem of defining species is what Wilkins is writing about. It is a well-known issue. The whole point of the post I quoted was to question whether there is – or should be – a one-size-fits-all concept of species. This is from a man who has written books about the subject so I think he has a better understanding of the problems than either of us.

    As I further pointed out in post 23, “There simply is no physical measurement that Darwinists can perform and say, ‘and this is exactly what we mean when we say the term ‘species”’. The concept of species does not weigh anything, nor does it have a speed, nor does the concept of species have any particular width or height that we can measure. Again, the entire concept of species is abstract and immaterial.”

    This is just silly and irrelevant. No one has suggested that the concept of species has physical dimensions or properties any more than anyone has suggested that the numeral 2 has weight or width or height.

    In post 26 Seversky objected to my fairly straightforward observation of the primary problem confronting Darwinian materialists is the fact that the entire concept of species is abstract and immaterial in its foundational essence.

    Again, not a problem.

    Yet the very authority, i.e. John S Wilkins, that Seversky himself quotes from, to supposedly refute my fairly straightforward observation, (far from refuting my observation), agrees with my basic point that the abstract and immaterial concept of species is irreducible to any rigid physical/materialistic measurements, such as weight, speed, length and height.

    Complete strawman. Yet again, no one has suggested that the species concept is a physical entity.

    As an aside, and as to Wilkins trying to claim that “all the other special sciences’ have no base units, (whatever Wilkins meant by ‘special sciences’), the fact of the matter is that all the other ‘hard sciences’ are rigidly defined in a clear enough manner so that that they can be realistically modeled.

    Yet the concepts of ‘meter’ or ‘kilogram’ are immaterial abstractions without weight or width or any other physical properties. How is that not a problem for physics?

    Regardless, further down you raise the issue of using mitochondrial DNA as a means of defining species

    The following study found, when comparing the mitochondrial DNA of different species, that “”If individuals are stars, then species are galaxies,” said Thaler. “They are compact clusters in the vastness of empty sequence space.

    Sweeping gene survey reveals new facets of evolution – May 28, 2018
    Excerpt: Darwin perplexed,,,
    And yet—another unexpected finding from the study—species have very clear genetic boundaries, and there’s nothing much in between.
    “If individuals are stars, then species are galaxies,” said Thaler. “They are compact clusters in the vastness of empty sequence space.”
    The absence of “in-between” species is something that also perplexed Darwin, he said.
    https://phys.org/news/2018-05-gene-survey-reveals-facets-evolution.html

    Why should mitochondria define species? – 2018
    Excerpt: The particular mitochondrial sequence that has become the most widely used, the 648 base pair (bp) segment of the gene encoding mitochondrial cytochrome c oxidase subunit I (COI),,,,
    The pattern of life seen in barcodes is a commensurable whole made from thousands of individual
    studies that together yield a generalization. The clustering of barcodes has two equally important features: 1) the variance within clusters is low, and 2) the sequence gap among clusters is empty, i.e., intermediates are not found.,,,
    https://phe.rockefeller.edu/news/wp-content/uploads/2018/05/Stoeckle-Thaler-Final-reduced.pdf

    What is interesting about the second paper you cite is that it includes the following passage

    Differing definitions of species

    There are approximately 30 different definitions of species in the biological, philosophical, and taxonomical literatures [24]. Almost all of them share the idea that species are distinct entities in biology and the corollary idea that there are discontinuities among species. In their clarifying and valuable analyses Mayr and de Queiroz point out that all definitions of species involve separate monophyletic evolutionary lineages (with important exceptions where symbiosis or horizontal gene transfer are
    key [26]). Different distinguishing factors such as mating incompatibility, ecological specialization, and morphological distinctiveness evolve, in various cases, in a different temporal sequence. During the process, as species diverge and emerge some of these characteristics will be fulfilled while others are not. Disagreement is inevitable when different properties are considered necessary and sufficient to fit one or another definition of “species”.

    There are two important observations regarding how COI barcodes fit into the differing definitions of species. First, the cluster structure of the animal world found in
    COI barcode analysis is independent of any definition(s) of species. Second, domain experts’ judgments of species tend to agree with barcode clusters and many apparent deviations turn out to be “exceptions that prove the rule”. Controversy around the edges,e.g. disagreements about whether or not borderline cases constitute species or subspecies [27, 28] should not obscure visualizing the overall structure of animal biodiversity. It is unavoidable that some cases will be considered as species by one definition and not another. Controversial cases can illuminate in the context of William Bateson’s adage to “treasure your exceptions” [29] but they should not obscure the agreement for most cases and an appreciation of the overall structure within the animal kingdom. This pattern of life, close clustering within individual species with spaces around clusters, can be visualized and demonstrated in different ways and with different statistics (e.g., Figs. 1-4). It qualifies as an empirically-determined evolutionary law [30]. Barcode distribution is arrived at independently but consistent with a view of biology as composed of discrete entities that on different levels include organisms and species.

    In other words, far from supporting your position, the authors take much the same view as Wilkins, that there are many differing species concepts in biology. They even refer to an “empirically-determined evolutionary law” which you have previously denied exists. Whether you agree with their views or not a fair and honest reporting of them would require you to at least quote them, so the fact you didn’t means you were either careless or dishonest.

    Now this may have been just a one-off but I would certainly recommend that any readers check out the whole of the papers or articles cited to see if the views of the authors are being accurately and fairly reported.

  35. 35
    ET says:

    Wow. OK, we privileged white people can produce vitamin D, better than the darker skin humans, just by getting a sun tan. We must be a different species. 🙄

    And if the species concept isn’t a physical entity, then it is completely useless in a physical science such as biology.

  36. 36
    bornagain77 says:

    Perhaps Seversky should take his own advice and read my entire posts instead of just parts of it?

    I granted that the mitochondrial sequences clearly differentiated species, yet I also pointed out that “The ‘problem’ of delimiting species in a rigidly defined manner is very much a ‘damned if you do, damned if you don’t’ proposition for Darwinists.”

    On the one hand, Darwinists hold that all species are related via ‘numerous, slight, successive’ modifications, yet Mitochondrial sequences show that no “intermediates are not found”. and also, In their words, “If individuals are stars, then species are galaxies,” “They are compact clusters in the vastness of empty sequence space.”

    That is NOT what Darwinism predicts!

    In other words, to delimit a species in a rigid manner is to falsify the entire notion of gradualistic Darwinian evolution.

  37. 37
    Querius says:

    Bornagain77 @36,

    That is NOT what Darwinism predicts!

    Haha! Their predictions never work out. Reminds me of . . .
    https://www.youtube.com/watch?v=yIBdVkJ9L-k

    -Q

  38. 38
    bornagain77 says:

    In 34, Seversky said a few other, self-defeating, things that are interesting to look at.

    He stated,

    “no one has suggested that the species concept is a physical entity.,,,, the concepts of ‘meter’ or ‘kilogram’ are immaterial abstractions without weight or width or any other physical properties. How is that not a problem for physics?”

    Well, duh, it is not a problem for physics, but it is a huge problem for reductive materialists, (i.e. Darwinists), who insist that everything must be reducible to matter and energy.

    What Does It Mean to Say That Science & Religion Conflict? – M. Anthony Mills – April 16, 2018
    Excerpt: Barr rightly observes that scientific atheists often unwittingly assume not just metaphysical naturalism but an even more controversial philosophical position: reductive materialism, which says all that exists is or is reducible to the material constituents postulated by our most fundamental physical theories.
    As Barr points out, this implies not only that God does not exist — because God is not material — but that you do not exist. For you are not a material constituent postulated by any of our most fundamental physical theories; at best, you are an aggregate of those constituents, arranged in a particular way. Not just you, but tables, chairs, countries, countrymen, symphonies, jokes, legal contracts, moral judgments, and acts of courage or cowardice — all of these must be fully explicable in terms of those more fundamental, material constituents.
    In fact, more problematic for the materialist than the non-existence of persons is the existence of mathematics. Why? Although a committed materialist might be perfectly willing to accept that you do not really exist, (and claim that you are only a ‘neuronal illusion’ generated by your material brain), he will have a harder time accepting that numbers do not exist. The trouble is that numbers — along with other mathematical entities such as classes, sets, and functions — are indispensable for modern science. And yet — here’s the rub — these “abstract objects” are not material. Thus, one cannot take science as the only sure guide to reality and at the same time discount disbelief in all immaterial realities.
    https://www.realclearreligion.org/articles/2018/04/16/what_does_it_mean_to_say_that_science_and_religion_conflict.html

    Naturalism and Self-Refutation – Michael Egnor – January 31, 2018
    Excerpt: Mathematics is certainly something we do. Is mathematics “included in the space-time continuum [with] basic elements … described by physics”?,,, What is the physics behind the Pythagorean theorem? After all, no actual triangle is perfect, and thus no actual triangle in nature has sides such that the Pythagorean theorem holds. There is no real triangle in which the sum of the squares of the sides exactly equals the square of the hypotenuse. That holds true for all of geometry. Geometry is about concepts, not about anything in the natural world or about anything that can be described by physics. What is the “physics” of the fact that the area of a circle is pi multiplied by the square of the radius? And of course what is natural and physical about imaginary numbers, infinite series, irrational numbers, and the mathematics of more than three spatial dimensions? Mathematics is entirely about concepts, which have no precise instantiation in nature,,,
    Furthermore, the very framework of Clark’s argument — logic — is neither material nor natural. Logic, after all, doesn’t exist “in the space-time continuum” and isn’t described by physics. What is the location of modus ponens? How much does Gödel’s incompleteness theorem weigh? What is the physics of non-contradiction? How many millimeters long is Clark’s argument for naturalism? Ironically the very logic that Clark employs to argue for naturalism is outside of any naturalistic frame.
    The strength of Clark’s defense of naturalism is that it is an attempt to present naturalism’s tenets clearly and logically. That is its weakness as well, because it exposes naturalism to scrutiny, and naturalism cannot withstand even minimal scrutiny. Even to define naturalism is to refute it.
    https://evolutionnews.org/2018/01/naturalism-and-self-refutation/

    Here is a straight up contradiction in Seversky’s reductive materialistic, i.e. Darwinian, worldview. Seversky, via his Darwinian worldview, holds that everything, (the universe, life, all our thoughts about the universe, etc..) must be reducible to materialistic explanations, yet mathematics is profoundly immaterial in its foundational essence and refuses to be reduced to any possible materialistic explanations.

    Furthermore, Seversky needs this profoundly immaterial world of mathematics in order for his Darwinian worldview to ever be considered ‘scientific’.

    The predicament that Darwinists find themselves in in regards to denying the reality of this immaterial world of mathematics, and yet needing validation from this immaterial world of mathematics in order for their reductive materialistic theory to even be considered scientific in the first place, should be the very definition of a scientifically self-refuting worldview.

    Moreover, the fact that man himself can think about this transcendent, (i.e. beyond space and time), immaterial world of mathematics, offers compelling evidence that man cannot possibly be a purely material being, as Darwinists hold, but that man, instead, must possess a transcendent, beyond space and time, immaterial mind and/or soul.

    As Charles Darwin’s contemporary, Alfred Russel Wallace, (co-discoverer of Natural Selection), himself stated, “Nothing in evolution can account for the soul of man. The difference between man and the other animals is unbridgeable. Mathematics is alone sufficient to prove in man the possession of a faculty unexistent in other creatures. Then you have music and the artistic faculty. No, the soul was a separate creation.”

    “Nothing in evolution can account for the soul of man. The difference between man and the other animals is unbridgeable. Mathematics is alone sufficient to prove in man the possession of a faculty unexistent in other creatures. Then you have music and the artistic faculty. No, the soul was a separate creation.”
    Alfred Russel Wallace – 1910
    https://evolutionnews.org/2010/08/alfred_russel_wallace_co-disco/

    I have a question for you Seversky

    Mark 8:37
    Is anything worth more than your soul?

    To continue on, with the fact that Darwinian materialism is incompatible with the existence of mathematics now on the table, it should not be surprising to learn, (as was previously mentioned in this thread), that Darwinian evolution has no foundation in mathematics that can be realistically simulated.

    Top Ten Questions and Objections to ‘Introduction to Evolutionary Informatics’ – Robert J. Marks II – June 12, 2017
    Excerpt: “There exists no model successfully describing undirected Darwinian evolution. Hard sciences are built on foundations of mathematics or definitive simulations. Examples include electromagnetics, Newtonian mechanics, geophysics, relativity, thermodynamics, quantum mechanics, optics, and many areas in biology. Those hoping to establish Darwinian evolution as a hard science with a model have either failed or inadvertently cheated. These models contain guidance mechanisms to land the airplane squarely on the target runway despite stochastic wind gusts. Not only can the guiding assistance be specifically identified in each proposed evolution model, its contribution to the success can be measured, in bits, as active information.,,,”,,, “there exists no model successfully describing undirected Darwinian evolution. According to our current understanding, there never will be.,,,”
    https://evolutionnews.org/2017/06/top-ten-questions-and-objections-to-introduction-to-evolutionary-informatics/

    And indeed, mathematics has not been kind to Darwinian claims in the least,

    The waiting time problem in a model hominin population – 2015 Sep 17
    John Sanford, Wesley Brewer, Franzine Smith, and John Baumgardner
    Excerpt: the waiting time for the fixation of a “string-of-one” is by itself problematic (Table 2). Waiting a minimum of 1.5 million years (realistically, much longer), for a single point mutation is not timely adaptation in the face of any type of pressing evolutionary challenge. This is especially problematic when we consider that it is estimated that it only took six million years for the chimp and human genomes to diverge by over 5 % [1]. ,,,
    While fixing one point mutation is problematic, our simulations show that the fixation of two co-dependent mutations is extremely problematic – requiring at least 84 million years (Table 2). This is ten-fold longer than the estimated time required for ape-to-man evolution.,,, Certainly the creation and fixation of a string of three (requiring at least 380 million years) would be extremely untimely (and trivial in effect), in terms of the evolution of modern man.
    ,,, When we increase the hominin population from 10,000 to 1 million (our current upper limit for these types of experiments), the waiting time for creating a string of five is only reduced from two billion to 482 million years.
    http://www.ncbi.nlm.nih.gov/pm.....MC4573302/

    Needless to say, having mathematics falsify your mechanism of natural selection is not a good place for Darwinists to be scientifically speaking.

    Further down Seversky claimed that

    They even refer to an “empirically-determined evolutionary law” which you have previously denied exists.

    And here is the claim:

    This pattern of life, close clustering within individual species with spaces around clusters, can be visualized and demonstrated in different ways and with different statistics (e.g., Figs. 1-4). It qualifies as an empirically-determined evolutionary law [30]. Barcode distribution is arrived at independently but consistent with a view of biology as composed of discrete entities that on different levels include organisms [31] and species [32].
    http://www.educatetruth.com/wp.....educed.pdf

    Funny kind of ‘law’ you have there Seversky. The supposed ‘law’ apparently predicts, directly contrary to what Charles Darwin himself predicted, that “intermediates are not found”. and also, In their words, “If individuals are stars, then species are galaxies,” “They are compact clusters in the vastness of empty sequence space.”

    So Darwinism can apparently predict the existence of intermediates, and the non-existence of intermediates, with equal ease. Others not so enamored with the belief that all life is the result of a nearly endless series of unintended accidents might find the fact that a Theory can predict completely opposite predictions with equal ease to be a sure sign that we are not dealing with a real scientific theory in any meaningful sense of the term ‘scientific theory’;

    “Being an evolutionist means there is no bad news. If new species appear abruptly in the fossil record, that just means evolution operates in spurts. If species then persist for eons with little modification, that just means evolution takes long breaks. If clever mechanisms are discovered in biology, that just means evolution is smarter than we imagined. If strikingly similar designs are found in distant species, that just means evolution repeats itself. If significant differences are found in allied species, that just means evolution sometimes introduces new designs rapidly. If no likely mechanism can be found for the large-scale change evolution requires, that just means evolution is mysterious. If adaptation responds to environmental signals, that just means evolution has more foresight than was thought. If major predictions of evolution are found to be false, that just means evolution is more complex than we thought.”
    ~ Cornelius Hunter

    Moreover, the supposed ‘law’ that Seversky is appealling to try to refute my claim that evolution is not based on any known physical law, is certainly not a universal, physical, law of nature.

    His supposed ‘evolutionary law’ is certainly not on the list of known universal laws.

    Laws of science
    1 Conservation laws
    1.1 Conservation and symmetry
    1.2 Continuity and transfer
    2 Laws of classical mechanics
    2.1 Principle of least action
    3 Laws of gravitation and relativity
    3.1 Modern laws
    3.2 Classical laws
    4 Thermodynamics
    5 Electromagnetism
    6 Photonics
    7 Laws of quantum mechanics
    8 Radiation laws
    9 Laws of chemistry
    10 Geophysical laws
    https://en.wikipedia.org/wiki/Laws_of_science

  39. 39
    bornagain77 says:

    Contrary to what Seversky tried to claim, there simply is no known law of evolution within the physical universe.

    As Ernst Mayr himself conceded, “In biology, as several other people have shown, and I totally agree with them, there are no natural laws in biology corresponding to the natural laws of the physical sciences.”

    The Evolution of Ernst: Interview with Ernst Mayr – 2004 (page 2 of 14)
    Excerpt: biology (Darwinian Evolution) differs from the physical sciences in that in the physical sciences, all theories, I don’t know exceptions so I think it’s probably a safe statement, all theories are based somehow or other on natural laws. In biology, as several other people have shown, and I totally agree with them, there are no natural laws in biology corresponding to the natural laws of the physical sciences.
    ,,, And so that’s what I do in this book. I show that the theoretical basis, you might call it, or I prefer to call it the philosophy of biology, has a totally different basis than the theories of physics.
    https://www.scientificamerican.com/media/pdf/0004D8E1-178C-10EB-978C83414B7F012C.pdf

    In the following article, Roger Highfield makes much the same observation as Ernst Mayr and states, ,,, Whatever the case, those universal truths—’laws’—that physicists and chemists all rely upon appear relatively absent from biology.

    WHAT SCIENTIFIC IDEA IS READY FOR RETIREMENT? Evolution is True – Roger Highfield – January 2014
    Excerpt: If evolutionary biologists are really Seekers of the Truth, they need to focus more on finding the mathematical regularities of biology, following in the giant footsteps of Sewall Wright, JBS Haldane, Ronald Fisher and so on.
    ,,, Whatever the case, those universal truths—’laws’—that physicists and chemists all rely upon appear relatively absent from biology.
    Little seems to have changed from a decade ago when the late and great John Maynard Smith wrote a chapter on evolutionary game theory for a book on the most powerful equations of science: his contribution did not include a single equation.
    http://www.edge.org/response-detail/25468

    Professor Murray Eden of MIT, in a paper entitled “Inadequacies of Neo-Darwinian Evolution as a Scientific Theory” stated that “the randomness postulate is highly implausible and that an adequate scientific theory of evolution must await the discovery and elucidation of new natural laws—physical, physico-chemical, and biological.”

    “It is our contention that if ‘random’ is given a serious and crucial interpretation from a probabilistic point of view, the randomness postulate is highly implausible and that an adequate scientific theory of evolution must await the discovery and elucidation of new natural laws—physical, physico-chemical, and biological.”
    Murray Eden, “Inadequacies of Neo-Darwinian Evolution as a Scientific Theory,” Mathematical Challenges to the Neo-Darwinian Interpretation of Evolution, editors Paul S. Moorhead and Martin M. Kaplan, June 1967, p. 109.
    https://people.eecs.berkeley.edu/~christos/evol/compevol_files/Wistar-Eden-1.pdf

    In fact, not only is there no ‘law of evolution’ within the known physical universe for Darwinists to build a realistic mathematical model upon, the second law of thermodynamics, entropy, a law with great mathematical explanatory power in science, almost directly, if not directly, contradicts the primary Darwinian claim that greater and greater levels of functional complexity can easily be had and/or ‘naturally selected’ for over long periods of time. Indeed, entropy’s main claim is that, over long periods of time, everything in the universe will decay into simpler and simpler states until what is termed thermodynamic equilibrium is finally reached.

    Diffusion – image
    https://upload.wikimedia.org/wikipedia/commons/thumb/1/12/Diffusion.svg/220px-Diffusion.svg.png

    Besides having no universal physical law to build a realistic mathematical model upon, another reason Darwinists will never be able to build a realistic mathematical model for their theory is that Biological form is not even reducible to mutations in DNA in the first place as is presupposed in Darwinian thought.

    On the problem of biological form – Marta Linde-Medina (2020)
    Excerpt: Embryonic development, which inspired the first theories of biological form, was eventually excluded from the conceptual framework of the Modern Synthesis as irrelevant.,,,
    At present, the problem of biological form remains unsolved.
    https://link.springer.com/article/10.1007/s12064-020-00317-3

    Or to put the insurmountable ‘problem of biological form’ in strict mathematical terms, “even a perfect and complete description of the microscopic properties of a material is not enough to predict its macroscopic behaviour.,,,” and “the insurmountable difficulty lies precisely in the derivation of macroscopic properties from a microscopic description.”,

    Quantum physics problem proved unsolvable: Gödel and Turing enter quantum physics – December 9, 2015
    Excerpt: A mathematical problem underlying fundamental questions in particle and quantum physics is provably unsolvable,,,
    It is the first major problem in physics for which such a fundamental limitation could be proven. The findings are important because they show that even a perfect and complete description of the microscopic properties of a material is not enough to predict its macroscopic behaviour.,,,
    “We knew about the possibility of problems that are undecidable in principle since the works of Turing and Gödel in the 1930s,” added Co-author Professor Michael Wolf from Technical University of Munich. “So far, however, this only concerned the very abstract corners of theoretical computer science and mathematical logic. No one had seriously contemplated this as a possibility right in the heart of theoretical physics before. But our results change this picture. From a more philosophical perspective, they also challenge the reductionists’ point of view, as the insurmountable difficulty lies precisely in the derivation of macroscopic properties from a microscopic description.”
    http://phys.org/news/2015-12-q.....godel.html

    As should be needless to say, if your supposedly ‘scientific’ theory cannot even explain ”biological form” in the first place, then any claim that you may make as to having a scientific theory that can explain the transmutation of biological forms into other biological forms is a ‘Alice in Wonderland’ pipe dream that has no basis in scientific reality.

    Psalm 139:13-14
    For You formed my inmost being; You knit me together in my mother’s womb. I praise You, for I am fearfully and wonderfully made. Marvelous are Your works, and I know this very well.

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