A confused mess, part 2


xkcd Wrong on the Internet

Comic by Randall Munroe, xkcd (of course).

Maybe by the time I have part 2 written up, someone will tell me in the comments why we evolutionary biologists shouldn’t just hang up our hats in light of pre-antibiotic antibiotic resistance.

I really didn’t mean to leave that hanging for three weeks. That was the end of part 1 of my look at Phillip Cunningham’s video, “Darwin vs. Microbes,” in which Cunningham argues that antibiotic resistance is not an example of evolution because (among other reasons),

…contrary to Darwinian thought, it is now found that antibiotic resistance, instead of being an ability that is new for bacteria, is an ability that is ancient.

Boom, game over, creationists win, right? I mean, how can antibiotic resistance have evolved millions of years ago if Alexander Fleming didn’t invent penicillin until 1928? Thankfully, reader jazzlet staved off the collapse of Big Darwin by commenting:

Do they really not know that antibiotics were initially found in other organisms? Organisms the bacteria will have encountered before? Urgh the bare-faced cheek of trying to talk about this stuff when you don’t even know the basics. We did that in school biology, maybe even before O level work started (so before fourteen).

Oh, yeah, that…Fleming didn’t invent penicillin, he discovered it. Penicillin, like a lot of antibiotics, is produced by a living organism, in this case the mold Penicillium. Why has antibiotic resistance been around for millions of years? Because antibiotics have been around for millions of years (probably billions in both cases).

It took me a whole post to get through some of the misconceptions, confusions, and false premises of the first four minutes of the half hour video. It goes steeply downhill from there.

Nearly the entire remainder of the video is a huge Gish gallop of quotes, mostly from other creationists but occasionally from peer-reviewed papers. Honestly, he throws so many quotes at you with so little context or original argument that it’s often difficult to keep track of what, exactly, is the point he’s trying to make.

There’s no way I’m going to take the time to refute every one of his points, but that’s the whole idea of a Gish gallop, right? I will hit a few of the highlights and see if two parts will be enough.

As antibiotic resistance itself indicates, supposed beneficial adaptations that are often touted by Darwinists as proof of evolution are actually the result of degraded molecular abilities. Lee Spetner, in his book ‘Not By Chance’ remarked that, ‘Whoever thinks macroevolution can be made by mutations that lose information is like the merchant who lost a little money on every sale but thought he could make it up on volume.’

So I guess we’re talking about macroevolution now. I thought we were talking about antibiotic resistance, which pretty much everyone agrees is microevolution, but so be it.

In 2016, Lee Spetner went on to remark, ‘there is no example of a random mutation that adds heritable information to the genome, and that statement still stands.’

Gloves Off — Responding to David Levin on the Nonrandom Evolutionary Hypothesis – Lee M. Spetner – Sept. 2016
Excerpt: I wrote in this book (as well in an earlier book) that there is no example of a random mutation that adds heritable information to the genome, and that statement still stands. The statement is important because evolution is about building up information (Spetner 1964, 1968, 1970). Some have offered what they think are counterexamples of my statement, but they are often not of random mutations at all, or they otherwise fail to be valid counterexamples.

Hah, quote within a quote; I never knew how to do that before. First, ‘there is no example of a random mutation that adds heritable information to the genome’ is just wrong. By any reasonable definition, insertions and gene duplications, both of which have been observed in microbial evolution experiments, add information to the genome. I’m sure there’s some way of gerrymandering the definition of ‘information’ to exclude these, but that’s about the purest No true Scotsman I can think of.

As for ‘evolution is about building up information’, no, it isn’t. Did you notice that all of Spetner’s citations are to his own work? Evolution is what I define it to be, as proven by the fact that I’ve said it three times before. No. Evolution is about heritable change over time. Come to think of it, if Cunningham could get that through his head, most of this video would evaporate.

In the following paper, Michael Behe surveyed 4 decades of laboratory evolution experiments with microbes and found that ‘we had already known that the great majority of mutations that have a visible effect on an organism are deleterious,,, [sic] (but now we know) even the great majority of helpful mutations degrade the genome to a greater or lesser extent’

This really deserves a post of its own; maybe I’ll get to it someday. This quote really gets to the heart of Dr. Behe’s (and others’) doublespeak about function.

…we had already known that the great majority of mutations that have a visible effect on an organism are deleterious…

Yeah, that’s true; so far so good.

(but now we know) even the great majority of helpful mutations degrade the genome to a greater or lesser extent.

In other words, there are more loss-of-function mutations than gain-of-function mutations. Also true, by the way. But natural selection doesn’t care. Natural selection increases the frequency of mutations that give the organism a fitness advantage. Sometimes those are gain-of-function; sometimes they are loss-of-function. It does not matter. Behe and others at the Discovery Institute like to pretend that only gain-of-function mutations are candidates for evolution and that fixation of loss-of-function mutations is something else entirely: ‘devolution’. This is complete nonsense, as I’ve explained before (“Devolution isn’t a thing“).

Natural selection does not care about molecular function; it cares (to anthropomorphize) about organismal function. If a loss-of-function mutation gives the organism a fitness advantage, for example by conferring antibiotic resistance, natural selection will cause that mutation to increase in frequency. There is no rational reason not to call that evolution. No true Scotsman again.

Even all the supposedly beneficial mutations in Lenski’s infamous Long Term Evolution Experiment with e-coli can be classified as modification-of-function or loss-of-Function mutations.

The logical contortions creationists have gone through to avoid admitting that Lenski’s citrate-eating E. coli don’t represent a gain of function (NTS #3) also deserve a full post, but I did briefly address it once before:

Despite creationist objections to the contrary, this is a clear example of the evolution of a novel trait. Were the bacteria previously able to consume citrate in the presence of oxygen? No. Everyone agrees on this; it is so universally true of E. coli  that it is considered diagnostic. Can they do so now? Yes, this too is undisputed. If being able to do something that you couldn’t previously do doesn’t qualify as an innovation, I would love to hear your definition of innovation.

Back to the video:

Truly beneficial mutations are simply exceedingly difficult, if not impossible, to find. In the following paper, John Sanford and company state, ‘It is almost universally acknowledged that beneficial mutations are rare compared to deleterious mutations.,,[sic] It appears that beneficial mutations may be too rare to actually allow the accurate measurement of how rare they are’

Aside from contradicting the earlier Behe quote (“even the great majority of helpful mutations degrade the genome”), this is demonstrably false. Gavin Sherlock’s work, which I reported on at AbSciCon 2015, directly measures beneficial mutation rates in yeast, and they’re not all that rare:

Around 20,000 of the 500,000 starting clones gained a beneficial mutation within 200 generations of evolution…

There’s a lot of stuff about overlapping genetic codes, alternative splicing, and epistasis, which are all somehow supposed to make beneficial mutations impossible:

…epistasis is much more pervasive than previously assumed, and that this strongly limits the ability of beneficial mutations to confer fitness on organisms.

Well, since Dr. Sherlock’s work shows pretty conclusively that beneficial mutations do happen, and quite frequently (one lineage in 25 in 200 generations), none of this matters. You can see that the Gish Gallop is tiring me out; I spent a whole post on the first three minutes of the video and dismissed minutes 8-11 in one sentence.

Then there’s a bunch of stuff about the probabilities of two (or more) simultaneous mutations. If you follow intelligent design thinking at all, you’ve heard these arguments before: if one mutation is very improbable, two mutations are (very improbable)2! Thankfully, Larry Moran has done a better job than I ever could of deconstructing these arguments, for example here, here, and here. The tl;dr is that the mutations don’t have to be simultaneous, so squaring the probabilities, while it generates some impressively big numbers, is biologically meaningless.

As should be clear by now, Darwinists simply have no evidence for the unlimited plasticity and/or flexibility in bacteria that they assume must be true in their presuppositions.

I know no one how presupposes that bacteria have ‘unlimited plasticity and/or flexibility’. Next.

Ann Gauger and Doug Axe have found that Darwinian processes would need a trillion trillion years or more—to accomplish the seemingly subtle change in enzyme function that requires just a few mutations.

This is just the argument from big numbers recycled.

Moreover, the supposed beneficial mutations that occur in humans that help humans fight against malaria are also found to be detrimental on the molecular level:

Again, natural selection doesn’t care about ‘detrimental at the molecular level’. Bearers of the sickle cell allele, on average, survive better than non-bearers where malaria is common. That’s all that matters to natural selection.

Thus, contrary to Darwinian thought, and as the preceding evidence indicates, we should expect extreme stasis for bacteria over long periods of time. And indeed that is what we find:

Ancient bacteria spores recovered from amber crystals and salt crystals, which are tens to hundreds of millions of years old, have been ‘revived’,,,

,,, and have now been compared to their living descendants of today. ,,,
To the disbelieving shock of Darwinists, “Almost without exception, bacteria isolated from ancient material have proven to closely resemble modern bacteria at both morphological and molecular levels.”

The Paradox of the “Ancient” (250 Million Year Old) Bacterium Which Contains “Modern” Protein-Coding Genes: Heather Maughan*, C. William Birky Jr., Wayne L. Nicholson, William D. Rosenzweig§ and Russell H. Vreeland ; – 2002
“Almost without exception, bacteria isolated from ancient material have proven to closely resemble modern bacteria at both morphological and molecular levels.”
http://mbe.oxfordjournals.org/cgi/content/full/19/9/1637

Evolutionists were so disbelieving at this stunning lack of change, (far less change than was expected from the neo-Darwinian view), that they insisted the stunning similarity was due to modern contamination in Vreeland’s experiment.

Quote within a quote again; check me out! But hold up, I know Heather Maughan. Bill Birky, too. Dr. (now) Maughan was a couple years ahead of me in grad school at the University of Arizona, and Dr. Birky was on the faculty (he’s since retired). Both are careful, thoughtful scientists. Did they really ‘insist’ that the bacterial spores were contaminants? Well, no:

We have a large set of rigorous geological and microbiological data which can be interpreted in favor of the antiquity of these organisms, and an equally large set of rigorously obtained molecular data which can be interpreted in favor of their modernity. As it stands, our present molecular work can neither confirm nor disprove the age of isolate 2-9-3.

Alright. Gah! I’m only about halfway through, and I’ve had enough. The Gish gallop has worn me down. One terrible argument after another, after another, after another…

I started this in part because the video begins with some nice footage of Volvox and Gonium (uncredited, by the way…anyone know where they came from?), but it never gets back to them or even mentions them. As with the Exxon commercials, they’re there just to be pretty and, presumably, to inspire awe at just how incredibly complex they are! Maybe, unlike the guy in the comic, I can let it go this time. There are better things to write about. Please forgive me if I never get around to part 3.

Comments

  1. jazzlet says

    Seems to me that one fundamental (sorry, couldn’t resist) problem creationists have is the assumption that evolution is directed, that it has a purpose rather than simply being a mechanism that provides variation that enables some organisms are likely to survive to reproduce, it is a problem a lot of otherwise intelligent people have.

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