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

barn

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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Friday Cephalopod: Baby done growed up

Don’t you just love those photo series of the young’uns at different ages?

Developmental staging of Octopus bimaculoides. a Whole egg photomicrograph illustrates the egg stalk and the animal pole (asterisk) where the embryonic body forms. Extent of epiboly in this stage (st) 8 embryo is marked with arrowheads. b End on view of a stage 8 embryo with the egg capsule and yolk removed. In dark field illumination, the organ primordia are visible as ectodermal and mesodermal thickenings. The mantle anlage (m) is central, the prospective mouth (mo) at the top of the panel is anterior, and the arm bud pairs (1–4) are arrayed peripherally. The folds of the collar (co) and the prospective funnel (fo, ff) fall at intermediate positions. c–f The growth of the organ systems by stage 10 is illustrated in end on (c), anterior (d), posterior (e) and left side (f) views. g–m The shape of the adult octopus emerges at middle (g–l) and late (m) embryonic stages. Illustrated are anterior (g and j), posterior (h and k) and left side (i and l) views of stage 13 (g–i) and stage 18 (j–l) embryos, and an anterior view of a stage 19 embryo (m). n and o Anterior views of O. bimaculoides (n) and its brain (o) at hatching (stage 20). A, anterior view; ey, eye; fun, funnel; gil, gill; L, lateral view; olf, olfactory organ; opt, optic lobe; P, posterior view; pf, funnel pouch; st, statocyst; supes, supraesophageal mass. Scale bars: 1mm (a), 500 μm (b–o)

Developmental staging of Octopus bimaculoides. a Whole egg photomicrograph illustrates the egg stalk and the animal pole (asterisk) where the embryonic body forms. Extent of epiboly in this stage (st) 8 embryo is marked with arrowheads. b End on view of a stage 8 embryo with the egg capsule and yolk removed. In dark field illumination, the organ primordia are visible as ectodermal and mesodermal thickenings. The mantle anlage (m) is central, the prospective mouth (mo) at the top of the panel is anterior, and the arm bud pairs (1–4) are arrayed peripherally. The folds of the collar (co) and the prospective funnel (fo, ff) fall at intermediate positions. c–f The growth of the organ systems by stage 10 is illustrated in end on (c), anterior (d), posterior (e) and left side (f) views. g–m The shape of the adult octopus emerges at middle (g–l) and late (m) embryonic stages. Illustrated are anterior (g and j), posterior (h and k) and left side (i and l) views of stage 13 (g–i) and stage 18 (j–l) embryos, and an anterior view of a stage 19 embryo (m). n and o Anterior views of O. bimaculoides (n) and its brain (o) at hatching (stage 20). A, anterior view; ey, eye; fun, funnel; gil, gill; L, lateral view; olf, olfactory organ; opt, optic lobe; P, posterior view; pf, funnel pouch; st, statocyst; supes, supraesophageal mass. Scale bars: 1mm (a), 500 μm (b–o)

Shigeno et al. Zoological Letters (2015) 1:26

A tale of three arms

octopusarm

Once upon a time, deep in the Precambrian, this was the planet of worms. Well, actually, this was, is, and always will be the planet of bacteria, but if you filter your perspective to just organisms above a particular size, and if you’re an animal writing about it in the modern day with a chauvinistic attitude that allows you to ignore that it was also a planet of algae, that would become a planet of plants, on a world that also is built of soil formed by lichens and saturated with fungus…if you ignore all that, OK, it was a planet of worms.

Late in the Precambrian, the oceans were full of accumulated muck and it was a good time to be a worm — a slender, plastic body, able to burrow and plunder the detritus of it’s nutrients, digging shelters or writhing in the freshest debris up top. Worms were everywhere, and the family was diverse. There were hairy ones, thick ones, slender ones, spiky ones. There were worms beginning to assemble bits of armor, either extracting calcium from their environment or crosslinking stable sugars to create chitin, because there were also worms that were developing the habit of eating other worms, rather than farming the muck.

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Are these people for real?

Carl Court/AFP/Getty Images

Carl Court/AFP/Getty Images

I’m afraid they are. Google sponsored a conference on “Effective Altruism”, which seems to be a code phrase designed to attract technoloons who think science fiction is reality, so the big worries we ought to have aren’t poverty or climate change or pandemics now, but rather, the danger of killer robots in the 25th century. They are very concerned about something they’ve labeled “existential risk”, which means we should be more concerned about they hypothetical existence of gigantic numbers of potential humans than about mere billions of people now. You have to believe them! They use math!

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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.

dicentric

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.

breakage

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.

indian-corn

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.

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

missionmouse

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).