Tuesday, November 22, 2016

Here is Why Steven Novella is Wrong About That Harvard Experiment

Going Nowhere Fast

Steven Novella, neurologist at Yale University School of Medicine, has commented on a recent Harvard University experiment for visualizing bacterial adaptation to antibiotics. The Harvard researchers constructed a giant petri dish with spatially-varying antibiotics to watch how bacteria adapt over time and space (the researchers came up with a great name for the experiment: The microbial evolution and growth arena [MEGA]–plate). And adapt they did. Those adaptations, however, were instantly claimed as an example of evolution in action. The researchers wrote that the “MEGA-plate provides a versatile platform for studying microbial adaption and directly visualizing evolutionary dynamics.” And the press release informed the public that the experiment provided “A powerful, unvarnished visualization of bacterial movement, death, and survival; evolution at work, visible to the naked eye.” Likewise, Novella called it “a nice demonstration of evolution at work in a limited context.” There’s only one problem: The experiment did not demonstrate evolution, it falsified evolution.

First off, Novella deserves some credit for acknowledging at least some limitations in the experiment’s results:

Of course, this one piece of evidence does not “prove” something as complex and far ranging as the evolution of life on Earth.

Novella also deserves credit for acknowledging that evolutionary change that requires a few mutations, rather than merely one, is a big problem. Novella has solutions which he believes resolve this problem (as we shall see below), but at least he acknowledges what too often is conveniently ignored.

What Novella does not acknowledge, however, is that bacteria adaptation research, over several decades now, has clearly shown non evolutionary change. For instance, bacterial adaptation has often been found to be rapid, and sensitive to the environmental challenge. In other words, when we look at the details, we do not find the evolutionary model of random variation slowly bringing about change, but rather environmentally directed or influenced variation.

That is not evolution.

And indeed, the Harvard experiment demonstrated, again, very rapid adaptation. In just 10 days the bacteria adapted to high doses of lethal antibiotic. As one of the researchers commented, “This is a stunning demonstration of how quickly microbes evolve.”

True, it is “stunning,” but “evolve” is not the correct term.

The microbes adapted.

The ability of organisms to adapt rapidly falls under the category of epigenetics, a term that encompasses a range of sophisticated mechanisms which promote adaptation which is sensitive to the environment. Given our knowledge of bacterial epigenetics, and how fast the bacteria responded in the Harvard experiment, it certainly is reasonable to think that epigenetics, of some sort, may have been at work.

Such epigenetic change is not a new facet of evolution, it contradicts evolution. Not only would such complex adaptation mechanisms be difficult to evolve via random mutations, they wouldn’t provide fitness improvement, and so would not be selected for, even if they did somehow arise from mutations.

Epigenetic mechanisms respond to future, unforeseen conditions. Their very existence contradicts evolution. So the Harvard experiment, rather than demonstrating evolution in action, is probably yet another example of epigenetic-based adaptation. If so, it would contradict evolution.

Another problem, that Michael Behe has pointed out, is that it appears that most of the mutations that occurred in the experiment served to shutdown genes. In other words, the mutations broke things, they did not build things. This is another way to see that this does not fit the evolutionary model. It’s devolution, not evolution. Novella begs to differ, and says Behe has made a big mistake:

Behe is wrong because there is no such thing as “devolution.” Evolution is simply heritable change, any change, and that change can create more complexity or more simplicity. Further, altering a protein does not “degrade” it – that notion is based on the false premise that there is a “correct” sequence of amino acids in any particular protein. Evolution just makes proteins different. Proteins perform “better” or “worse” only in so much that they contribute to the survival and reproduction of the individual. If it is better for the survival of the organism for an enzyme to be slower, then the slower enzyme is better for that organism.

First, Novella ignores the fact that many of the mutations introduced stop codons, and so did not merely slow an enzyme but rather shut it down altogether.

Secondly, it is not Behe here who is making the mistake, it is Novella. He says “Evolution is simply heritable change …”

But this is an equivocation.

On the one hand, evolutionists want to say that shutting down or slowing a gene is “evolution,” but on the other hand, evolutionists say that a fish turning into a giraffe is “evolution.”

Unfortunately evolutionists routinely make this equivocation. This is because they don’t think of it as an equivocation. In their adherence and promotion of the theory, the distinction is lost on them. All change just smears together in one big long process called evolution. You can see other examples of this here and here.

So the comments, press releases, and articles send a misleading message. Readers are told that the researchers have seen “evolution in action.” The message is clear: This is evolution, the evolution. But it isn’t. There is nothing in these findings that show us how a fish turns into a giraffe.

Multiple mutations

As mentioned above, Novella also believes that evolution coming up with designs requiring multiple mutations is not a problem. Novella’s reasoning is that while this would be a problem if most mutations are harmful, they aren’t. Most mutations are neutral, so evolutionary drift can introduce the many needed mutations, and once the set of required mutations are in place, then you have the new design.

This is a profound misunderstanding of the problem evolution faces. You can’t evolve a protein, for example, with drift. That most mutations are neutral does not suddenly resolve the curse of dimensionality and resolve this astronomical search problem. There just is no free lunch.

Similarly, Novella makes yet another profound mistake involving what he calls “the lottery fallacy.”

The first is basically the lottery fallacy – considering the odds of John Smith winning the lottery by chance alone and concluding it could not have happened by chance. Rather, you should consider the odds that anyone would win the lottery. This is actually pretty good. Behe looks at life on Earth and asks – what are the odds that this specific pathway or protein or whatever evolved by chance alone. He is failing to consider that there may have been billions of possible solutions or pathways down which that creature’s ancestors could have evolved. Species that failed to adapt either migrated to an environment in which they could survive, or they went extinct. In other words, Behe should not be asking what the odds are that this bit of complexity evolved, but rather what are the odds that any complexity evolved. It is difficult to know the number of potential complexities that never evolved – that number may dwarf the odds of any one bit evolving. Right there Behe’s entire premise is demolished …

This is a terribly flawed argument for several reasons. First, life needs proteins. All life that we know of needs proteins.

Thousands of proteins.

Yet proteins are far beyond evolution’s reach. It is true, per Novella’s point, that there are a whole lot of ways to make a given protein. There are many, many different amino acid sequences that give you a globin. But “many, many” is like a grain of sand compared to the astronomical amino acid sequence search space.

There just is no free lunch.

But Novella goes further than this, and this brings us to the second flaw. Novella is not merely arguing there are many different ways to construct life as we know it. He is pointing out that there are, or at least there could be, a whole bunch of different ways to make life, in the first place.

If you take them all together, you could have a pretty big set of possibilities. Perhaps it is astronomical. So what we got in this world—the life forms we observe, are not point designs in an otherwise lifeless design space. Rather, the design space could be chocked full of life forms. And hence, the evolution of life becomes likely, and “Right there Behe’s entire premise is demolished.”

What Novella is arguing for here is unobservable. He is going far beyond science, into an imaginary philosophical world of maybe’s.

Not only is Novella clearly appealing to the unobservable, but even that doesn’t work. At least for any common sense approach. There is no question that the design space is full of useless blobs of chemicals that do nothing. A speculative claim? No, that is what this thing called science has made abundantly clear to us. Even the simple case of a single protein reveals this. Only a relatively few mutations to most proteins rob them of their function. Protein function is known to dramatically reduce as different amino acids are swapped in.

Of course this is all obvious to anyone who understands how things work. Sure, Novella may be right that there are other, unknown, solutions to life. But that isn’t suddenly going to resolve evolution’s astronomical search problem. That problem was never contingent on the life we observe being the only possible life forms possible

Novella calls himself a skeptic. In fact, he is exactly the opposite.

10 comments:

  1. Might many of these experiments simply prove the that "latent DNA" is the cause for change?
    Sleeper cells
    Our strongest antibiotics are being thwarted by bacteria
    that lie dormant, only to bounce back unharmed once the
    pressure is off. Ed Yong investigates
    ”About half of infectious diseases that are
    difficult to treat with antibiotics are not due
    to resistance but persisters”
    http://phenomena.nationalgeographic.com/files/2013/01/Persisters_NewScientist.pdf
    Also:
    Here we show that Arabidopsis plants homozygous for recessive mutant alleles of the organ fusion gene HOTHEAD5 (HTH) can inherit allele-specific DNA sequence information hat was not present in the chromosomal genome of their parents but was present in previous generations. This previously undescribed process is shown to occur at all DNA sequence polymorphisms examined and therefore seems to be a general mechanism for extra-genomic inheritance of DNA sequence information. We postulate that these genetic restoration events are the result of a template-directed process that makes use of an ancestral RNA-sequence cache.”
    http://www.nature.com/nature/journal/v434/n7032/abs/nature03380.html

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  2. Do you really teach your Biola students evolution is false because an experiment with antibiotics didn't show a fish turning into a giraffe? :0

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  3. "The ability of organisms to adapt rapidly falls under the category of epigenetics,..."

    Ugh, no. Rapid adaptation might be epigenetic, but it may be due to single or sequential mutations. The DNA of the resistant cells had gene sequences that had changed from the parental sequences. Epigenetics do not change gene sequences.

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  4. Hi Dr. Hunter -

    Hope you are doing well by God's grace today.

    As your summary of the experiment demonstrates, the research team observed several mutations that explained the changed behavior of the bacteria. For the moment we don't need to determine whether the changes were devolution or evolution; we just recognize that there is strong evidence in favor of inferring DNA mutation as causation for the observed change.

    This being the case, why is there any need to speculate about epigenetics? You seem to be inventing a post facto hypothesis which has no support in this experiment's observations.

    Best regards,

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    1. "You seem to be inventing a post facto hypothesis which has no support in this experiment's observations."

      You have won first place in the "pointing out the blatantly obvious" awards.

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  5. Never ceasing to amaze me how creationists how thoroughly they misunderstand or misrepresent evolutionary theory
    And you give no indication that they understand – OR if they do understand it then they are deliberately misrepresenting it, or they really just don’t understand it
    You just cast doubt on any story claiming to have proof or evidence for evolution – but you don’t have any real coherent theory or position that you are defending. You are literally throwing shit at a wall, just trying to make as much confusion at possible, and see what sticks.
    What we are witnessing with these bacteria is definitely adaptation, but the BIG point that you are missing, or choosing to ignore, is that adaptation IS evolution. WOW! Is that a lightbulb moment for you?
    Guess what buddy… “Evolve” IS THE CORRECT TERM.
    Evolution is adaption. They are genetic changes that are adapting the organism to its local environment. These changes are not occurring SPECIFICALLY because of said environment – I think that’s the misconception you have, they are mutations that are occurring in the billions of bacteria that are multiplying like cells – and the ones that have the most advantageous genes for said environment survive. That’s really ALL evolution is. That’s the CORE of evolution – adaptation through survival of the fittest!
    Basically you are agreeing with the theory, but denying it through a misunderstanding of scientific concepts and terms, or lack of critical reasoning. This is what happens with ideologies get in the way of reality… it’s kind of sad that it blinds people. Especially when you think that Novella is the opposite of a skeptic. He “calls himself a skeptic” DUDE. He IS a skeptic. I think possibly, you don’t understand the definition of a skeptic, - in philosophy, a skeptic holds the position that what cannot be proved by reason, should not be believed.
    Half of this blog post is you making assertions based on god knows what. It’s not critical reasoning, or a sceptical approach at all. I don’t know where you learnt your science, but I think you might need to take a few more bio 101 courses…. Your technobabble is confusing to people who actually understand the science. And your use of epigenetics is completely and utterly wrong – is this just some faux hypothesis you came up with yourself? All I’m reading is a jumble of science-related ideas, from the serious to the ridiculous, which have nothing in common other than they are merely your own delusional reasoning about what science is and should be.
    You can’t use terms loosely that already have definitions – you don’t have wriggle room to re-define things to suit yourself, or to create confusions and twist words and ideas to suit your ideology.

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  6. “because the change was so rapid, it couldn’t be due to random mutations” – That is false. Are you just pulling that out of your arse, or do you have actual proof that random adaptations of genes have to take longer? You know the life cycle of bacteria is pitiful, and they breed asexually… so they basically clone themselves into billion more bacteria - think of ALL those genes that could be slightly mutated at random… and then think of the ones that are advantageous to the environment - all the guys without that die off, in this case due to the antibiotics. The ones with it, multiply, and there we have a colony of anti-biotic resistant bacteria
    Literally that is all evolution is. Millions of bacteria with random mutations breeding like tiny microscopic rabbits through asexual reproduction – which also heightens the chances of there being mutations. Although environmental factors can change genes, most of evolution is due to the mutations themselves and the ones surviving had the best mutations for said environment. That is the adaptation – the evolution taking place – and it’s the species, not the individual that adapts. It’s not like the bacteria are putting on little sweaters to adapt. Antibiotics kills off all the weak little bacteria, and the few with mutations against the antibiotics start to multiple again. That is EXACTLY what genetics is.
    I find it so hard to believe that you can’t see the simple logic in this. It astounds me how delusional people can be. I am very grateful to have rese4arched delusions and logical fallacies enough to understand that you do not think the same way as I do. It still amazes me though, that something so simple, straightforward, and logical…. Is twisted to suit your own ideologies through the use of made up crap.

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    1. Never ceasing to amaze me how creationists how thoroughly they misunderstand or misrepresent evolutionary theory

      Except that I’m not a creationist. Right off the bat evolutionists are not credible.


      You just cast doubt on any story claiming to have proof or evidence for evolution

      No, I cast doubt on false, religious claims.


      You are literally throwing shit at a wall, just trying to make as much confusion at possible, and see what sticks.

      So says those who insist the world arising from random mutations is an undeniable fact. Epicureanism never died.


      What we are witnessing with these bacteria is definitely adaptation, but the BIG point that you are missing, or choosing to ignore, is that adaptation IS evolution. WOW! Is that a lightbulb moment for you? Guess what buddy… “Evolve” IS THE CORRECT TERM.

      OK, “adaptation IS evolution.” Let’s write that down. What next …


      Evolution is adaption. They are genetic changes that are adapting the organism to its local environment. These changes are not occurring SPECIFICALLY because of said environment … Your technobabble is confusing to people who actually understand the science. And your use of epigenetics is completely and utterly wrong – is this just some faux hypothesis you came up with yourself? All I’m reading is a jumble of science-related ideas, from the serious to the ridiculous, which have nothing in common other than they are merely your own delusional reasoning about what science is and should be.

      No, actually, epigenetics (unlike evolution) really is a fact. Evolutionists such as yourself have been fighting for centuries, and the denial, as abundantly revealed in your comment, has reached a fever pitch. And by your own admission, it is not evolution. This is the best own goal we’ve seen from evolutionists all day.


      I find it so hard to believe that you can’t see the simple logic in this. It astounds me how delusional people can be. I am very grateful to have rese4arched delusions and logical fallacies enough to understand that you do not think the same way as I do. It still amazes me though, that something so simple, straightforward, and logical…. Is twisted to suit your own ideologies through the use of made up crap.

      Priceless.

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  7. Dr Hunter,

    Great rebuttal. You actually make total sense. Forget fish to giraffs how is stopping codons and shutting down proteins supposed to make organelles....what I didn't know is that adaptation mechanisms don't give a fitness improvement or do you mean in this case where you are sacrificing the functioning of the protein which just so happens that it cannot bind to the antibiotic active ingredient so it becomes resistant? so it's lost one of biochemical processes? Can you just explain why?

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    1. Gabriel:

      Well adaptation mechanisms don't give a fitness improvement because they are useless until some future time when that particular environmental challenge may arise. So the fitness improvement may come at some future time, but unless and until that time comes, you're left with an incredibly complicated adaptation mechanism that just luckily arose, but gives no fitness improvement.

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