My last post on Perry Marshall

Once more unto the breach in Perry Marshall’s cranium, dear friends. He is once again trying to claim that he alone has the one true understanding of Barbara McClintock’s work, and he keeps getting it wrong. It’s just embarrassing to watch.

He makes obvious statements like this:

Damage is random. Repair is not.

Well, duh. If the cell were to just go charging in and practice excision repair (a process that snips out a short piece of one strand of DNA and brings in polymerase to re-synthesize it) on random stretches of DNA, it would increase the frequency of errors. Polymerase proofreads as it goes; it checks to see if the nucleotide it just copied into a new strand properly complements the nucleotide on the other strand, and if it doesn’t, it steps back, cuts out the error, and tries again. It doesn’t repeat if they match.

This is familiar stuff. Students in our classes here at UMM get all this kind of material, in far greater detail, by their second year here. The problem is that Marshall carries it too far: he assumes that the cell “knows” the nature of the specific error made, and intelligently acts to directly repair it. It doesn’t. The cell can invoke general mechanisms to attempt repair, but it doesn’t in any way “know” what to do.

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Perry Marshall 2.0

This is weird. Perry Marshall has posted a complete transcript of our discussion on Unbelievable on his website. That’s actually useful, since most of us can read faster than someone else can talk. What’s weird is that he’s annotated it with his rebuttals, after the fact.

It’s like — and this has happened to me — you give a student an exam, and they do poorly on it, and they come in to your office to argue for more points not by pointing out errors in the grading (that happens, too), but by explaining to you how their understanding of the material was vastly superior to yours, and that you’d recognize that their answers were correct if only the professor had their deep understanding of cellular and genetic processes. In these situations, the student is always digging themselves into a deeper hole, and revealing that they don’t understand what they’re talking about at all.

For instance, he seems quite taken with Barbara McClintock’s work, and talked about it a fair bit. He got it all wrong. He claims that she was denying the existence of chance events in genetics — that everything was about patterned, engineered information, which is the damnedest interpretation of McClintock. He urges everyone to read her Nobel speech, which is good, but I’ve read her original papers and lecture on this subject in my genetics class. So it’s amusing to see him take a dig at me about it.

PZ doesn’t appear knowledgeable about McClintock’s work. Her findings perplex Darwinists because Darwinism has no grid for cells re-engineering themselves… but that’s exactly what they do in experiments.

McClintock was studying a phenomenon called chromosomal instability, in which the results of inheritance were not easily predictable. The opening sentences of her Nobel speech set the stage.

An experiment conducted in the mid-nineteen forties prepared me to expect unusual responses of a genome to challenges for which the genome is unprepared to meet in an orderly, programmed manner. In most known instances of this kind, the types of response were not predictable in advance of initial observations of them.

Note: unusual responses, a genome unprepared to meet in an orderly, programmed manner, responses that are not predictable. Most of us would read that and understand that it was going to be about chance events — events without predictable, programmatic, mechanistic responses. Not Perry Marshall! McClintock talks about stress-induced reorganization of the genome, and he leaps to the conclusion that she’s describing a teleological phenomenon in which the genome reshapes itself directly to address the circumstances, when every process she actually describes is about increasing variation.

For instance, he’s obsessed with transposition. He thinks this is engineering.

Transposition is when the cell moves a defined cassette of coding sequences and plugs it into a new location. [The “cassette” link shows transposition cassettes in experiments with zebrafish]

Transposition is not just inserting unspecified DNA sequences. Transpositions are by their very structure non-random, and would be even if there were no pattern to where insertions occur.

Aaargh. Yes. Transposition involves taking a chunk of DNA sequence and moving it to a different place in the genome. We can take advantage of that by making a gene of interest the ‘chunk’ and getting it to insert somewhere. Somewhere random. That’s the whole point. These are called jumping genes for a reason.

McClintock also described the bridge-breakage-fusion cycle. Marshall doesn’t understand it. He read the words in her speech and lacked the background to see what she’s talking about. Here’s the way it works.

You’ve got a chromosome with a duplication of a set of genes, as illustrated below. This allows for a misalignment of the homologous chromosomes, and for a crossover event to produce a peculiar chimera, a dicentric chromosome.


Notice that these chromosomes have two centromeres each. The centromere is a kind of handle that motor fibers grab onto and use to tow the chromosome to one side of the cell or the other during cell division. This chromosome has two, so what can happen is that one centromere gets pulled to the left, the other gets pulled to the right, and you see something called an anaphase bridge form between the two sides. It’s a tug-of-war, with the chromosome the rope stretched between two forming cells, and these opposite poles are pulling on it.

What do you think happens? The rope breaks. It breaks at some random point between the two centromeres.


The breakage point is also typically a dangling bit of single-stranded DNA, with no telomeres. DNA repair mechanisms kick into gear and fuse the two dangling ragged strands of two homologous chromosomes back together, reforming the bridge so that when the cell divides again, it will break at a random point once more. And so the cycle begins again.

That’s why it’s called the bridge-breakage-fusion cycle. The chromosomes reform into a configuration that minimizes exposed, broken ends, but can’t last through cell division, so they’re constantly broken, reassembled, and broken again, producing a changing distribution of genes in each generation.


McClintock describes this in her Nobel speech. Marshall missed the relevant bits. She was trying to explain how a certain strain of corn developed variegations — that is, irregular, unpredictable patterns of streaks or patches in the tissue. It’s basically a random phenomenon, like the pattern of colors in kernels of Indian corn, and she predicted that it was caused by random breakages during cell division of a ring chromosome (a chromosome where the two ends are damaged, and are repaired to form a loop of DNA).

It was the behavior of this ring that proved to be significant. It revealed several basic phenomena. The following was noted: (I) In the majority of mitoses replication of the ring chromosome produced two chromatids that were completely free from each other and thus could separate without difficulty in the following anaphase. (2) Sister strand exchanges do occur between replicated or replicating chromatids, and the frequency of such events increases with increase in the size of the ring. These exchanges produce a double-size ring with two centromeres. (3) Mechanical rupture occurs in each of the two chromatid bridges formed at anaphase by passage of the two centromeres on the double-size ring to opposite poles of the mitotic spindle. (4) The location of a break can be at any one position along any one bridge. (5) The broken ends entering a telophase nucleus then fuse. (6) The size and content of each newly constructed ring depend on the position of the rupture that had occurred in each bridge.

What she’s saying is that crossing over between ring chromosomes can produce dicentric chromosomes, as in my diagram above, and that during cell division the bridge can mechanically rupture, and most importantly for this conversation, in point 4, “The location of a break can be at any one position along any one bridge”. That is, it can break randomly anywhere along the bridge, and then point 6, the gene “content of each newly constructed ring depend on the position of the rupture”. Each daughter cell gets a random selection of the genes along that bridge.

That’s the whole point. You’re trying to explain a random phenotype by looking for a randomization mechanism in the genome. McClintock’s triumph was being able to explain random variation within an organism that by convention ought to be genetically uniform by mechanistic processes like transposition and bridge-breakage-fusion.

As expected, Marshall has just dug himself a deeper hole with his rebuttal. I repeat: he doesn’t understand what McClintock was saying.

The sure-fire, simple way to tell if an article about epigenetics is full of crap

It’s easy. If it uses the word “Lamarckian” without boldly prefixing it with “not“, you can just stop reading. Likewise if the word is prefixed with “pseudo-“, “semi-“, or “quasi-“. Just skip it. It’s too confused to bother with.

Epigenetics is in the news again, and in fact, it’s newsworthiness seems to be rising at a fantastic rate. Eight years ago, would you believe, I wrote a short summary of what epigenetics is, driven largely by the fact that a lot of people were writing about epigenetics without acknowledging that it was a grab-bag of mundane regulatory processes. It’s gotten worse. I had to explain the obvious: epigenetics ain’t magic. I tried to explain it last year again, that people have a lot of misconceptions about epigenetics. It’s frustrating because epigenetics encompasses a lot of cool and important stuff — genetic switches and gene regulation and plasticity and environmental responsiveness — but all the popular press wants to talk about is this weird idea that it’s a way break the tyranny of genetics and evolution and modify your genes for future generations, which is just plain wrong.

What it tells me is that there is still a lot of uneasiness about the implications of evolutionary theory. Not among most evolutionary biologists, of course, but in the general population. They wish for a way to believe that their progeny (and themselves) can be enhanced by an act of will, and they think that a poorly understood phenomenon like epigenetics provides a loophole. The whole idea that evolution is a statistical property of populations rather than something they can game to their advantage as individuals leaves them queasy. So they noodle around with the idea that somehow, by practice, they can change their whole genetic legacy using the buzzword “epigenetics”, not even realizing that epigenetic phenomena are a consequence of the properties of proteins, coded by genes, and regulatory sequences imbedded in their DNA, and that even short term cytoplasmic responses in the cell are ultimately derived from information in their genome.

People who use epigenetics as something that is anti-evolutionary remind me of Perry Marshall, the creationist who thinks Barbara McClintock’s work rebuts Darwinism, because he wrongly thinks somehow that it refutes the role of chance in evolution. They hate the whole idea of chance-driven processes, and want a way to shape genetics by an act of will, instead. It’s painful to see the contortions they put themselves through to run away from the implications of evolution and genetics.

Everything existing in the universe is the fruit of chance and necessity


I’ve been informed that I’ve been at war for a while. I was surprised. Apparently, Perry Marshall thinks he’s been firing salvo after salvo at me…I just hadn’t noticed.

Oh, OK. I would just ignore him, but he’s presenting some fascinatingly common misconceptions. One of his boogeymen is chance, and I’ve noticed that a lot of people hate the idea of chance. Uncle Fred got hit by lightning? He must have done something very bad. It can’t just have been an accident. There are no accidents!

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With a final pretentious squeak, the attack mouse sinks into the sunset


Aww, what sad news. Casey Luskin is leaving the Discovery Institute. Hilariously, he declares victory as he fades away, and cites two instances that he claims have finally validated intelligent design creationism.

The first is that the ENCODE proved that the genome is nearly entirely functional, exactly as ID predicted and against the expectations of those Darwinists. Unfortunately for him, that is not the case, and the ENCODE propagandists relied entirely on a peculiar and narrow definition of function that did not match any kind of function the creationists might have imagined.

The second is — hang on to your hats — epigenetics. Didn’t I just post something about epigenetics? Why, yes I did. I also posted something somewhat lengthy about it. It seems to be a common misconception among creationists.

Interestingly, these were also two of the obsessions of another creationist, Perry Marshall. He didn’t understand those concepts, either.

I think it’s quite appropriate that Luskin should vanish in a puff of misconceptions and ignorance. It’s been his stock in trade all along, after all.

Another day, another creationist

My conversation with Perry Marshall about “evolution 2.0” is now online on the radio show Unbelievable.

Marshall is sales and marketing guy who has written a book titled Evolution 2.0: Breaking the Deadlock Between Darwin and Design, in which he claims to have worked out a reconciliation between science and religion based on arguments he had with his missionary/theologian brother, that hints at the quality of the science you’ll find in it. He has a superficial view of a few biological processes, like DNA error repair and transposition, and has shoehorned them into his religious belief that these are the tools used by some kind of engineering force that makes them purposeful.

He has a challenge with a $100,000 prize. All you have to do is show an example of Information that doesn’t come from a mind. Basically he’s making the clueless argument that there are no processes in genetics that produce novel information. I think Jeffrey Shallit ought to step up and claim it. Actually, he might have to fight through a mob of information theorists to get his money (if it exists, and if the judging wasn’t rigged).

Something else on my plate

Tomorrow, I’m recording a discussion for British Christian radio (how do I get myself into these things?), on the show Unbelievable with Justin Brierley. I’m talking with Perry Marshall, who some of you may remember yapping around these parts a while back, and who has a book out called Evolution 2.0, which I had to read.


I read it.

Dear gob.

Just to help you picture this: he’s an electrical engineer and SEO guy with only the most superficial, and often wrong, knowledge of biology, and he has written a book in which he explains how all those biologists have got everything wrong. I was most entertained by the parts where he explains how there is all this amazing stuff in biology that we never tell anybody about, and one of his examples was something I lectured my cell biology class about last week, and a couple of the examples were things I talked about in my freshman biology course this morning.

In other words, his stunning revelations that will revolutionize evolutionary biology were all known mechanisms that are so well established that we teach them in basic college courses, and often simply take for granted. And he gets them wrong. Wrong wrong wrongity wrong.

But he’s frenetically glib about it all, which is apparently a useful attribute if you’re trying to sell car stereo speakers. It’s not at all impressive when you’re pushing pseudoscience.

Everything you need to know about ID

It’s a wonder that these people know how to tie their own shoes. I was sent a link to Perry Marshall’s Intelligent Evolution Quick Guide, and it is certainly a fine example of the kind of reasoning that allows creationism to thrive. It’s a short guide, but it goes on for over a page, when the essential syllogism that defines ID is actually presented in three all-encompassing lines.

  1. DNA is not just a molecule – it is a coding system with a language & alphabet, and contains a message

  2. All languages, codes and messages come from a mind

  3. Therefore DNA was designed by a Mind

As I’m sure all of you sensible readers can immediately detect, his first premise is a deeply flawed analogy and his second is simply undemonstrated and entirely false, so his “therefore” is unwarranted. Three lines, three errors: a perfect representation of creationist thought.

I give to you the cockroach. It contains DNA, and it copies it and propagates it to the next generation of cockroaches, yet is it even aware of its DNA? Does it use its tiny little cockroach mind to construct a complex molecule? No. Mindless chemistry does it. There is no thought behind the synthesis and modification of the DNA molecule at all, yet it is true that it carries out complex activities with the aid of other molecules in the cytoplasm…but without the assistance of any intelligent beings at all.

Similarly, I give you the creationist. They contain DNA, and a large brain as well, but they don’t use that brain at all in producing progeny. After a little embarrassed tickle and grunt, mindless chemistry takes over in fertilization and development, and 9 months later, another mind emerges from one of their unencephalized wombs. We can trace the origins of that DNA back and back and back, and at no point in its history does it seem to be produced by conscious design, and the farther back we look, the less available potential there was for intelligent intervention. Bacteria are even less clever than cockroaches, you know.

If you want to understand our history and our evolution, the first concept you have to be able to grasp is that natural processes produce all the complexity and diversity of extant life without the guiding hand of any external agents. Once you’ve realized that, it becomes apparent that we can work backwards through our ancestry without invoking magic or cosmic helpers — that Intelligent Design creationism is a superfluous hypothesis that can be dismissed in the absence of any corroborating evidence.

Creationist email: I have a new friend!

I posted a little sample of my creationist junkmail yesterday, and I’ve finally figured something out. The first mailing said, “Original Theory By Perry Marshall, Edited in part by D. Donohew”—what that meant was that D. Donohew had found this crap by Perry Marshall on the web, and was simply doing a copy&paste and sending it to me. How did I figure this out? Because Mr Donohew is now regularly sending me crap that he has written himself. You may be surprised to learn, given that that first email was a pile of spluttering nonsense, that Mr Marshall is a paragon of lucidity and insight compared to his plagiarist.

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Creationist email to the fraternity

One more piece of creationist email for you: this one was addressed to me and all of my fraternity of Godless Atheists, which I think means you readers here. Never mind protesting that some of you are Christian—get used to it, to these guys you will never be truly Christian.

Anyway, it’s not a very entertaining letter. It was, as usual, amusingly formatted (Outlook Express is evil software), but I’ve stripped all that gunky Microsoft html out of it to simplify posting it. It’s your usual argument from poorly understood physics: the Big Bang is evidence of Jesus, really tiny numbers prove Jesus, mangled information theory proves Jesus. It does have one novel argument I haven’t seen before, that a kitchen spray bottle proves Jesus, but I don’t think it’s going to get much traction in the scientific community. I haven’t bothered to reply to it, but if anyone wants to shred the nonsense in the comments, maybe the authors will find it online.

Oh, and welcome to the Atheist Fraternity! Remember, we’re getting together with the Atheist Sorority on Friday night for a Toga Party!

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