Now you too can pretend you were at Skepticon this year

Here’s my talk on the Cambrian from Skepticon 6.

Oh, hey, I just realized I could post the content of that text-heavy slide I flashed, showing the sources I used. So here you go:

Web reviews from Donald Prothero, Nick Matzke, Larry Moran.

Briggs, D.E.G.; Fortey, R.A. (1989). The early radiation and relationships of the major arthropod groups. Science, 246(4927), 241-243.
Budd, G. E., and S. Jensen. 2000. “A critical reappraisal of the fossil record of the bilaterian phyla.” Biological Reviews 75:253-295.
Erwin D and Valentine J (2013). The Cambrian explosion : the construction of animal biodiversity. Greenwood Village, CO, Roberts and Company Publishers.
Marshall, Charles R. (2006). “Explaining the Cambrian ‘explosion’ of animals.” Annual Review of Earth and Planetary Sciences. 34: 355-384.
Smith MP, Harper DAT (2013) Causes of the Cambrian Explosion. Science 341:1355.
Long M, Betran E, Thornton K, Wang W (2003) The origin of new genes: glimpses from the young and old. Nature Rev Genet 4:865.
Knoll AH, Carroll SB (199) Early Animal Evolution: Emerging Views from Comparative Biology and Geology. Science 284:2129.
Erwin DH, Laflamme M, Tweedt SM, Sperling EA, Pisani D, Peterson KJ (2011) The Cambrian conundrum: early divergence and later ecological success in the early history of animals. Science. 334(6059):1091.
Peterson KJ, Dietrich MR, McPeek MA (2009) MicroRNAs and metazoan macroevolution: insights into canalization, complexity, and the Cambrian explosion. Bioessays. 31(7):736.

The curiously limited argument from convergent evolution raises an ugly tentacle/fin again

I am not a fan of the convergent evolution argument for humanoid aliens. I can well believe that it’s likely that intelligent aliens exist out there in the universe, but I’m not even going to try to predict what they look like: there are too many alternative paths that are possible. But for some reason, many people like to insist that it’s reasonably likely that they’d resemble us in general, if not in detail, and they’ll then go on to extrapolate that behaviorally and culturally they’ll share many properties with us. Usually, as with Simon Conway Morris and now George Dvorsky, this argument relies entirely on the premise of convergent evolution.

It annoys the hell out of me, because it requires waving away or consciously ignoring basic principles of evolution. Here’s how Dvorsky illustrates the concept:

Convergent evolution between ichthyosaurs and dolphins

I’ve seen versions of this illustration a thousand times. Gosh, look, dolphins and ichthyosaurs all have paddle-shaped fins and streamlined bodies! Therefore, this is evidence that aquatic forms all converge on similar morphologies. And therefore, intelligent, terrestrial organisms will also converge on an ideal form for their niche, which is ours also, therefore we represent a morphological ideal.

I hate the argument because it isn’t applicable to alien species. In both cases shown above, the organisms involved belong to the same subphylum, the Vertebrata, and the same superclass, the Tetrapoda. They share a common ancestor, and the same starting point. When you start with a terrestrial creature that looks like this, with four limbs and a suite of similar traits…

Eryops, a kind of amphibian from which other tetrapods evolved

…and then let it re-adapt to a marine life as a free-swimming, active predator after long detours into mammalian and reptilian forms, is it any surprise that they converge on similar structures? They are both constrained by their ancestry! The four-finned torpedo does not necessarily represent an ideal form that will be recreated on every planet we ever someday visit, but is instead a compromise, a form that can be generated from a four-limbed vertebrate with a minimum of fuss.

But what if we look at organisms with more remote ancestry? A whole different phylum, perhaps? If we start down the evolutionary road with a conchiferan sort of creature, a mollusc…

Limpet

…which later evolves into a free-swimming, active predator, you get this:

Lovely torpedo-shaped squid

That’s something that looks completely different from a fish-like ichthysaur or dolphin; it’s got a completely different shape, a completely different set of feeding behaviors, a completely different internal organization.

We could ask the same question of other phyla. Where are the sleek torpedo shaped crustaceans sporting a nice dorsal fin and quartet of paddles? Show me a marine annelid that has followed this same path.

Now keep in mind that life on another planet will share no ancestry with anything on Earth. If our history is any example, they will be the product of a few billion years of single-celled tinkering, with a riotous adaptive radiation of multicellular forms that will explore a small fraction of morphospace…and every step will be contingent on prior states.

You can only make this ludicrous convergence argument if you think 1) contingency is relatively unimportant, that 2) adaptation is extremely powerful and will always drive a species towards an optimum, and that 3) the shape of a relatively tiny subset of species on this planet represent that optimum. There is a fourth requirement as well: you must be oblivious to the fact that (2) and (3) contradict each other.

Methinks it is like a fox terrier

I’ve had, off and on, a minor obsession with a particular number. That number is 210. Look for it in any review of evolutionary complexity; some number in the 200+ range will get trotted out as the estimated number of cell types in a chordate/vertebrate/mammal/human, and it will typically be touted as the peak number of cell types in any organism. We have the most cellular diversity! Yay for us! We are sooo complicated!

It’s an aspect of the Deflated Ego problem, in which scientists exercise a little confirmation bias to find some metric that puts humans at the top of the complexity heap. Larry Moran is talking about the various techniques people use to inflate the complexity of the genome, making special case arguments for novel molecular gimmicks that we mammals use to get far more ooomph out of our genes than those other, lesser organisms do.

As I was reading it, I had this sense of deja vu, and using my psychic powers, I predicted that someone was going to make the argument that because we mammals have so many more cell types than other organisms, there must be some genetic trick we’re playing to increase the number of outcomes from our developmental processes, and that therefore there must be something to it. Because we are measurably more complex than other animals, there must be a mechanism to get more complexity out of our 20,000 genes than nematodes get out of theirs.

And did I call it? I did. Very first comment:

I dont think its a sign of an inflated ego to think mammals are more complex than flies. There are objective measures one could use such as cell type number, number of neurons or neural connectivity.

There’s a problem with this claim, though. Many people, including quite a few prestigious scientists, believe that cell type number in various organisms has actually been measured, and you’ll even find respected people like Valentine putting together charts like this:

cellnumberchart

That chart is total bullshit. You know how I expressed my visceral repugnance for an MRA who made up a “sexual market value” chart? I feel the same rage when I see this chart. There is no data supporting it. There we see humans listed as having 210 cell types, and everything else is lesser: birds have only 187 cell types. Do you believe that? I sure as hell don’t.

I periodically get a bit pissed off about this. I wrote about it in a thread on Talk.Origins in 2000, and I’ve put a copy of that below. I complained about it in a blog post from 2007. It hasn’t sunk in. I still run into this nonsense fairly regularly.

The short answer: this number and imaginary trend in cell type complexity are derived entirely from an otherwise obscure and rarely cited 60 year old review paper that contained no original data on the problem; the values are all guesswork, estimates from the number of cell types listed in histology textbooks. That’s it.

The long answer, my digging from 13 years ago:

This is a topic in which I’ve long had an interest, of a peculiar and morbid sort. It’s been a case of occasionally running into these arguments about cell types, and wondering whether I’m stupidly missing something obvious, or whether the authors of these claims are the cockeyed ones. I can’t see a middle ground, it’s one or the other. Maybe somebody here can point out how idiotic I must be.

The issue is whether we can identify a good measure of organismal complexity. One way, you might think, would be to look at the number of different cell types present. I first ran across this metric in the late ’70s, in JT Bonner’s book _On Development: the biology of form_. He has a number of provocative graphs in that book, that try to relate various parameters of form to life history and evolution. Some of the parameters are easy to assess: maximum length, or approximate number of cells (which is just roughly proportional to volume). Others were messy: number of different cell types. Bonner didn’t push that one too much, just pointing out that a plot of number of types vs. total number of cells was sorta linear on a logarithmic plot, and he kept the comparison crude, looking at a whale vs. a sequoia vs. a sponge, that sort of thing. He also said of counting cell types that it was “in itself an approximate and arbitrary task”, but doesn’t say or cite where the numbers he used came from, or how they were obtained.

It came up again in Stuart Kauffman’s work. He tried to justify his claim that the number of cell states (or types) in an organism was a function of the number of genes, and he put together a chart of genome size vs. number of cell types. It was glaringly bogus. He (or someone) clearly selected the data, leaving out organisms with what I guess he would consider anomalous genome sizes — and Raff and Kaufman thoroughly trashed that entire line of argument in their chapter on the C-value paradox in _Embryos, Genes, and Evolution_, showing that one axis of Kauffman’s graph has to be invalid. Nobody has touched on that other axis, the number of cell types, and I’m still wondering how anybody determined that humans have precisely 210 different kinds of cells, while flies have 50 (those numbers seem to have become canonized, by the way — I’ve found several sources that cite them, +/- a bit, but very few say where they came from).

And then Morton mentions this interesting little paper that I hadn’t seen before:

Valentine, JW, AG Collins, CP Meyer (1994) Morphological complexity increase in metazoans. Paleobiology 20(2):131-142.

[note to Glenn: the citation on your page is incorrect. It's in Paleobiology, not Paleontology]

Abstract.-The number of cell types required fo rthe constructon of a metazoan body plan can serve as an index of morphological (or anatomical) complexity; living metazoans range from four (placozoans) to over 200 (hominids) somatic cell types. A plot of the times of origin of body plans against their cell type numbers suggests that the upper bound of complexity has increased more or less steadily from the earliest metazoans until today, at an average rate of about one cell typer per 3 my (when nerve cells are lumped). Computer models in which increase or decrease in cell type number was random were used to investigate the behavior of the upper bound of cell type number in evolving clades. The models are Markovian; variance in cell type number increases linearly through time. Scaled to the fossil record of the upper bound of cell type numbers, the models suggest that early rates of increase in maximum complexity were relatively high. the models and the data are mutually consistent and suggest that the Metazoa originated near 600 Ma, the the metazoan “explosion” near the Precambrian/Cambrian transition was not associated with any important increase in complexity of body plans, and that important decreases in the upper bound of complexity are unlikely to have occurred.

At least, the paper *sounds* interesting. After reading it, though, I’m left feeling that it is an awful, lousy bit of work.

The first major flaw: there is no data in the paper. The first figure is a plot of cell type number against age, in millions of years before the present — the numbers and groups described are listed on Glenn Morton’s page. These are the observations against which several computer models will be compared. These data were not measured by the authors, but were gleaned from the literature. The sources for these critical numbers are listed in an appendix, about which more in a little bit.

The bulk of the paper is about the computer models they developed. The final figure is the same as the first, showing the data points from the literature with the plot generated by their best-fit simulation superimposed. It’s a very good fit. From this, they make several conclusions: 1) that their model is in good agreement with the historical data, 2) that the rate of increase in complexity was greatest near the origin of metazoans, 3) that that origin was relatively late, and 4) there was no particular change in rate during the Cambrian explosion. It is a fine example of GIGO.

The work is completely reliant on the validity of the data about cell type number, which is not generated by the authors, and worse, which is not even critically evaluated by the authors. It is just accepted. That data left me cold, though, with lots of questions.

What is a cell type? There was no attempt to define it. Histologically, it’s a fuzzy mess — you can go through any histology text and find long lists of cells types that have been recognized by morphology, location, staining properties, and so forth. I just skimmed through the index of an old text I have on hand (Leeson and Leeson), and without trying too hard, counted a bit more than a hundred distinct, named, vertebrate cell types in the first 5 pages…and there were 25 more pages to go. What criteria are the authors using? How well do these superficial criteria for identification mesh with the molecular reality of the processes that shape these cells?

Why did they throw out huge categories of cells? The nervous system is simply not considered — it’s ‘lumped’. This seems to me to be grossly inappropriate. Here is this HUGE heap of cellular diversity, in which half the genome is involved, and it is discarded in what are supposedly quantitative models. I can guess that it was thrown out because it is impossible to quantify…but that doesn’t sound like a good excuse if you are trying to model numbers. Furthermore, they only count cells in adults, so cell types found only in larvae or juveniles are rejected. Whoops. Isn’t that an admission that complexity in arthropods is going to be seriously underestimated? I don’t know, since they don’t say how they define a cell type.

How did they get these tidy single numbers for a whole group? ‘Arthropods’ have only 50 cell types. They admit that “within some groups there is a significant range of cell type numbers”. The range of variation, however, is not reflected in any of their graphs, nor which groups exhibit this range. Instead, they say, they picked a representative “primitive number” of cell types from “the more primitive living forms within each group”. I guess the more primitive living forms haven’t done any evolving.

A really bothersome and related point: the high end of their plot is anchored by the hominids, with 210 cell types and a time of origin within the last few million years. Remember, they are going to fit all these computer-generated curves to these data, and they explicitly scale everything to this endpoint and an earlier one. This point is invalid, though. We humans don’t have any novel cell types that were generated a few million years ago — that number of 210 cells ought to be applied to all of Mammalia, and the time of origin shoved back a hundred million years. Or more. Is there any reason to think 200 million year old therapsids were lacking any significant number of histological cell types found in mammals today?

For that matter, why should we think that these cell type numbers are anything but arbitrary indicators of the relative amount of time histologists have spent picking over the tissues of these various organisms? Do fish really have fewer cell types than mammals, or just different ones? Fish may lack all the cell types associated with hairs, but we don’t have all the ones that form scales. The authors show amphibians as being more complex than fish, on the basis of cell type counts in living forms…and that is completely the reverse of what I would expect, if I thought there was any difference at all.

What was really the killer for me, and what I was really looking for, was the primary sources for these numbers. These are listed at the very end, in a separate appendix. A few are easy: it’s not hard to imagine being able to count all the different cell types in a sponge or a jellyfish. One is admitted speculation by Valentine — he estimates the number of cells a primitive hemocoelic bilaterian must have had. Another, the number of cells in arthropods, is cited as an unpublished ms by Valentine. However, almost all of the counts boil down to one source, a critical source I haven’t yet been able to find. This very important paper, that purports to give cell type numbers for echinoderms, cephalopods, fish, amphibians, lizards, and birds, is:

Sneath, PHA (1964) Comparative biochemical genetics in bacterial taxonomy. pp 565-583 in CA Leone, ed. _Taxonomic biochemistry and serology_. Ronald, New York.

It’s a paper about bacterial taxonomy? And biochemistry? The only discussion in the text of the Valentine paper about this source mentions that it compares DNA content to cell type number, a measure that Raff and Kaufman have shown most emphatically to be invalid. And it’s from 1964, although the author seems to still be around and active in bacterial taxonomy and molecular biology right up until at least a few years ago. He doesn’t look like a histologist or comparative zoologist though, that’s for sure.

It’s from 1964. Oh, boy. I did manage to track down a copy of this volume in a library a few miles away, but I haven’t yet been able to get out and read it. I’m not too inclined to even try right now, because this appendix also has a little subscript in fine print at the bottom…virtually every source in this list, including Sneath, is marked with an asterisk, and the fine print tells us that that means “estimates NOT [my emphasis] documented by lists of cell types or by references to published histological descriptions”. In other words, there ain’t no data there, either.

I’m afraid to look up Sneath, for fear that it will turn out to be an estimate of cell number derived from measures of DNA content, with a bit of subjective eyeballing tossed in. At least that would explain why Kauffmann could find a correlation between DNA content and complexity, though.

From my perspective right now, this whole issue of cell type number is looking like a snipe hunt, a biological myth that is receding away as I pursue it. Does anybody know any different?

I didn’t have quick access to the all-important Sneath paper, but Mel Turner did, and he summarized it for everyone.

…there’s no original data. Here’s the relevant text:

“Although there are many possible correlations, for example, that between cell size and DNA content (135), it seems plausible to suggest that the amount of DNA is largely determined by the amount of genetic information that is required and that this will be greater in the more complex organisms. Fig. 38-2 shows the distribution of DNA contents of haploid nuclei taken from the literature, mostly from several compendia (4,10,87,128,134,135). The haploid nucleus was chosen for uniformity, and because the genetic information in diploids is presumably mostly reduplicated. The values are plotted against the number of histologically distinguishable cell types in the life cycle of the organism (suggested by a figure of Zimmerman (141)). This number is some measure of complexity, and was estimated from standard textbooks (5,13,85,126). In Fig. 38-2 organisms incapable of independent multiplication (e.g., viruses) have been assigned to the 0.1 cell level. The values for some well-known organisms are shown in Fig. 38-3.”

Fig. 38-2 is a graph of number of cell types (Y-axis) vs. log content of DNA/gamete, with a extra superimposed x-axis of “number of bits” (“one nucleotide pair = two bits”).No species names are indicated, but there are clusters of multiple separate points plotted for “mammals”, “birds”, “fish”, “angiosperms”, “bacteria” “algae & fungi”, “viruses”, etc. [oddly, he scores "RNA viruses" as having DNA content].

Fig. 38-3 purports to show “the histological complexity of some well-known organisms” with a log graph placing examples like “Man, Mammals” at the top with ca. 200 cell types, and “birds”, “reptiles”, “amphibia”, “fish” [again, no species names] just below that, then various cited generic names of plants animals, protists and bacteria [e.g., Pteromyzon (sic), Sepia, Helix, Ranunculus, Polypodium, Escherichia, etc.; about 50 taxa altogether]. Strictly unicellular organisms with different cell types during the life cycle [cysts, spores, gametes, etc. are properly scored as having histological complexity; e.g., Plasmodium scored with ca. 6 cell types]

There’s also discussion of the significance of the reported rough correlation of complexity and DNA content, a suggestion that histologically complex organisms should require disprortionately many times the DNA amounts of simple ones [cell specialization and regulation], a mention of some plants and amphibia with ‘unexplained’ very large DNA contents, and a page of stuff on base-pair changes, informational “bits”, & Kimura.

Table 38-3 “estimated amount of genetic and phenetic change in vertebrate evolution” looks pretty odd indeed [especially in a paper on bacterial biochemistry!]; it apparently tries to say something about times of origin and amounts of DNA change [% and in "bits"] for classes, orders, families, genera, species…. a bit dubious, to put it mildly.

Looking at the References list for the anatomical data sources cited for Figs 38-2 and 38-3, the “standard textbooks” were indeed just that:

5. Andrew, W. 1959. Textbook of Comparative histology. Oxford Univ. Press, London

13. Borradaile, L.A., L.E.S. Eastham, F.A. Potts, & J. T. Saunders. 1941. The Invertebrata: A manual for the use of students. 2nd ed. Cambridge Univ. Press, Cambridge.

85. Maximow, A.A. & W. Bloom. 1940. A textbook of histology. W. B. Saunders Co., Philadelphia.

126. Strasburger, E., L. Jost, H. Schenck, & G. Karsten. 1912. A textbook of botany. 4th English ed. Maximillian & Co. Ltd. London.

The Zimmerman citation from above is: Zimmerman, W. 1953. Evolution: Die Geschichte ihrer Probleme und Erkenntnisse. Alber, Freiburg & Munchen 623 pp.

Stephen Jay Gould wrote about a similar issue in Bully for Brontosaurus, in his essay on “The Case of the Creeping Fox Terrier Clone”, which describes how certain conventions, like describing the size of a horse ancestor as being as large as a fox terrier, get canonized in the literature and then get reiterated over and over again in multiple editions of textbooks.

This one isn’t as much a textbook problem as it is a deeply imbedded myth in the scientific literature. We haven’t even defined what a cell type is, yet somehow, again and again, we find papers and books claiming that it has been accurately quantified, and further, that it supports a claim of increasing complexity that puts humans at the pinnacle.

STOP IT.

I seem to have written about this problem every 6 or 7 years, to no avail. I’ll probably complain again in 2020, so look for a version of this post again, then.

My turn

Today is the last day of the Paradigm Symposium, which is good — I don’t know how much more my poor brain could take. But this afternoon, after lunch, it’s my turn to speak. And I’ve been doing my homework, looking into what kinds of things paranormalists often believe about biology and evolution, and it’s been a long exercise in face-palming. They’re all over the map, but there are some common threads: the idea that evolution is inadequate (even while they rather blandly accept it for everything other than humans) and that aliens had to somehow assist us to reach the state we’re in now. Again, there isn’t one simple, coherent formula to describe their ideas — they’re not like the creationists who neatly fall into a few categories — and their hypotheses wobble all over the place. Some believe humans are the aliens, that we immigrated here to Planet Earth hundreds of thousands of years ago. Others believe that we’re hybrids, the product of mating between alien star-lords that we called gods and the common stock. Others think that no, it was planned modification of the ape genetic line by high-tech aliens, who intentionally inserted special genes into our cells to give us higher powers. And some are willing to say we evolved naturally here, but the aliens showed up to give us a technological boost, planting only ideas in human culture. So I’ve got a great big moving target to deal with, and I suspect that if I shoot down one hypothesis people will just glibly shift to one of the other excuses.

Here’s an example of the kind of nonsense I have to deal with.

Why is it that ancient native, cultures all around the world, from the Americas to Africa and Australia speak of advanced ETs ‘seeding’ humanity on earth? How is it that such apparently primitive peoples had in-depth accurate knowledge of constellations such as Sirius – which cannot be seen with the naked eye – several thousand years ago?

It is in my knowing that originally, a group of spiritually and technologically advanced ETs seeded humanity with the apparently ‘benevolent intent’ of mankind becoming ‘custodians’ of Mother Earth and working to live in balance with her. That’s why so many of the original tribal cultures such as the North American Indians, The Mayans, The African Dogon, The Tibetans and the Australian Aborigines all lived largely in harmony with the earth and at balance with nature.

I love that phrase, “It is in my knowing.” So meaningless, so pompous, so vacuous. You also get a taste of that benign assumption that any alien intervention was friendly in intent, and that “tribal cultures” are one with the Earth Mother. No, these cultures had relatively small population sizes and so did not impose any stresses on their environment that the environment could not handle, but give ‘em a chance, and they could overwhelm a place just about as well as Europeans — look at Easter Island, for instance. We are all of us just people.

But that optimism also hides some profound ignorance and some nasty racism. On the ignorance side, this passage is about as annoyingly stupid as anything I’ve heard from creationists:

When Official Science delved deeper [into the question of why humans have 46 chromosomes while other apes have 48], it realised that the reason we have two less, is because the second and third chromosomes have been fused into one. It tries to explain this by saying such a mutation could happen naturally and points to other evidence in nature such as butterflies. Indeed such spontaneous mutation can happen, but what they’re not saying (and quietly brushing under the carpet), is that although this ‘mutation’ offers no natural evolutionary advantage whatsoever, it appears in EVERY SINGLE HUMAN!

How could that be? This fusing of the chromosomes is not what makes us human, and it does not offer any ‘natural’ evolutionary advantage (I’ll return to this in a moment). Yet we all have the mutation? If we supposedly evolved from Hominoids (like Neanderthal) and this mutation offers no advantage, then you’d expect to see some humans with 48 chromosomes and some with 46, but not ALL with 46!

But when you delve deeper into the chromosome story it gets even more curious. Each chromosome has three parts to it: both ends and a middle. Now in eight of the other human chromosomes, there has been an inversion of the middle part – it’s been ‘spun around’. Again, these inversions offer no natural evolutionary advantage – they don’t change the genetic material – yet ALL eight supposed ‘mutations’ appear in ALL humans.

Now you don’t need to be a mathematician to know, that the odds for all nine mutations to happen spontaneously, where no natural evolutionary advantage was gained, and for that to happen to both the original human male and female, at exactly the same time, and in exactly the same place, and for them to breed and produce the entire human offspring is so unlikely, the odds are literally zillions to one!

“Literally zillions to one!” Heh.

Just look at that raging typological thinking, though. This person apparently can’t grasp the idea of long, slow periods of gradual change in relatively neutral properties: it all had to happen all at once. Zing! All at once, all of the differences between humans and chimpanzees had to occur.

And here’s the underlying nastiness. This same post includes the video below with no qualification. It’s a smug little conversation between two racist assholes of the genus Newageius concluding that human races are soooo different that they must have been independently transplanted to earth from different alien worlds.

If you don’t want to listen to the whole awful thing (and I don’t blame you), here’s a representative comment from youtube that nicely illustrates what we’re dealing with.

My studies have actually yielded the idea that there are four basic structures that the Multi-racial structures evolve from: Africans, Asians, Europeans and Native Americans. These will coencide with the colors of the Medicine Wheel being Black, White, Yellow and Red. As with paint in art, you can derive many colors from four basic colors. Cells Are solar systems. We’re making all of this harder than it has to be. Chakra Systems. LOOK for crying out loud.

I can’t possibly address all of this bullshit in one hour; I also don’t assume that most of the audience agrees with this particular brand of lunacy. So I’m going to be giving a very simplified introduction to the human genome and properties of the human population that show that we are entirely children of Earth. Baby steps. Basics first. We’ll see how it goes.

Darwinian bookery

We’re doomed. Evolution is an ineluctable process; once it gets started, it’s not just an optional alternative, it becomes unstoppable, short of nuking the planet from orbit (and even then, all it takes is one surviving bacterium for it to begin again). Charlie Stross has noticed that books have crossed the threshold and are now poised for an adaptive radiation.

An epub ebook file is essentially an HTML5 file, encapsulated with descriptive metadata and an optional DRM layer. The latest draft standard includes support for all aspects of HTML5 including JavaScript. Code implodes into text, and it is only a matter of time before we see books that incorporate software for collaborative reading. Not only will your ebook save your bookmarks and annotations; it’ll let you share bookmarks and annotations with other readers. It’s only logical, no? And the next step is to let readers start discussions with one another, with some sort of tagging mechanism to link the discussions to books, or chapters, or individual scenes, or a named character or footnote.

We already share highlighting — I get a little annoyed when I’m reading on my kindle and suddenly there’s a block of text with a dotted underline — other people thought that section worthy of notice and have shared their emphasis with the world.

I’ve also noticed that the books I’ve bought through Amazon suddenly pop up with a ranking and suggestions page when I reach the end. It used to be you’d finish a book and close it satisfyingly and put it back on the shelf…but no, now it yells at you “Did you like me? Buy more of me!”

As Stross points out, the next dreadful steps, since a book has become code, will be the incorporation of malware and agents to sabotage competing books in your library and insert new ads around the place, or even replicate more of the authors’ works. I’ve downloaded some of those cheap or even free books into my epub library, and some of them are so bad that I suspect they are already intrinsically malware.

Our future:

Books are going to be like cockroaches, hiding and breeding in dark corners and keeping you awake at night with their chittering. There’s no need for you to go in search of them: rather, the problem will be how to keep them from overwhelming you.

Doomed, I tells you. I am squinting at my iPad right now. I think it’s plotting to get me.

A hopeless muddle

James May, one of the presenters on Top Gear, is trying his hand at providing a little science education. I want to say…please stop. Here he is trying to answer the question, “Are humans still evolving?” In the end he says the right answer — yes they are! — but the path he takes to get there is terrible.

It’s little things that make me wonder if anyone is actually editing his copy. For instance, he helpfully explains that you, the viewer, were produced by your parents having sex. Then he says:

That’s how evolution is driven: by reproduction. But is that still true?

Uh, yes? We haven’t stopped reproducing, so we should be able to stop right there then.

But no, he continues on. He tries to explain evolution, and does manage to verbally describe natural selection correctly as differential survival and reproduction, but it’s illustrated with a pair of goats with telescoping necks. That doesn’t help. He’s describing Darwinian selection and showing it as Lamarckian — it’s a very mixed signal. And as we’ll see, he still seems to be thinking like will and experience drive evolutionary changes.

And do I need to mention that he doesn’t seem aware of processes other than selection in evolution? You need to realize the importance of drift to answer the question of whether evolution is continuing in humans, especially when you’re prone to say glib nonsense like “humans have turned the process of natural selection on its head,” whatever that means.

He also claims along the way that Darwin “tracing this evolutionary process backwards proved that all life came from a common source.” No, he didn’t. A hypothesis is not proof. He found morphological evidence for the relatedness of some groups, but the evidence for common ancestry of all forms wouldn’t really become overwhelming until the molecular evidence linked animals and plants and mushrooms and bacteria together.

By the time he gets around to talking the details of human evolution, we’re mired in a hopeless mess. Apparently, one reason we’re still evolving is that “certain characteristics will improve your chances of breeding” but then he helpfully explains that “its not as if ugly and stupid people don’t get to have children”. So which is it? Is natural selection selecting away for chiseled abs, or whatever he regards as a significant advantage, or isn’t it? And if people he judges as unattractive are having children, that driving force of evolution, then isn’t that undermining his understanding of the process?

And please, if you can’t even get selection straight in your head, please don’t try to explain population structure. He has a weird discursion in which he explains that “the genetic mutations that drive evolution can be most commonly found in a small gene pool” and then somehow tries to argue that we’re “too cosmopolitan,” that the fact that people from all over the world can now intermarry somehow “cuts down on those mutations.” I have no idea what he’s talking about. I suspect he doesn’t either.

Then, as evidence that we have been evolving, he points to big screen TVs as proof that we’re smarter than Stone Age people. Great — we now have a new IQ test. Just measure the dimensions of the individual’s TV. It’ll probably work about as well as regular IQ tests.

He tries to get to specific traits: lack of wisdom teeth is evidence of human evolution, apparently. Never mind that the changes are recent and mixed, and that it’s more likely a plastic response to changes in our diet than a trait that’s been selected for specifically. It’s a very bad example, unless he’s going to argue for selection for people with fewer teeth in their jaws. Do you typically count your date’s molars?

His ultimate proof that humans are evolving is the appearance of lactose tolerance in adults. That is pretty good evidence, I’ll agree…but he messes it up completely.

10,000 years ago, before anybody had had the bright idea of milking a cow, no human could digest the lactose in milk beyond childhood. But now, after a hundred years of drinking cream and milk and squeezy cheese in a can, 99% of people can.

He doesn’t even get the numbers right. North Europeans have a frequency of lactose tolerance of about 90%; in South Europeans it is about 30%, and less than 10% in people of Southeast Asian descent. This is not a largely lactose tolerant world.

And of course, his explanation is screaming nonsense. We are not lactose tolerant because we’ve been drinking milk; we’ve been drinking milk because we’re lactose tolerant. It is not a trait that appeared in the last century.

Why is this guy babbling badly about evolution? Did he have any informed, educated scientists to consult who could tell him not to make such a ghastly botch of it all?

This cat is going to be insufferable

You may have heard we’ve got this satanic feline padding about the house now, getting into mischief — she has discovered my collection of cephalopodiana, and her favorite toy is one of my stuffed octopuses that she wrestles and bats around the floor. It’s like she’s rubbing it in.

Anyway, a new paper in Nature Communications describes a comparative analysis of the genomes of tigers, lions, snow leopards, and…housecats. I’m not letting her read it, lest she acquire delusions of grandeur (oh, wait, she’s a cat — she already has that.)

There’s nothing too surprising in the data; as usual, we discover that mammals (well, animals, actually) have a solid core of shared genes and the divergence between species is accounted for by changes in a small number of genes. They also exhibit a high degree of synteny — the arrangement of genes on chromosomes are similar.

(a) Orthologous gene clusters in mammalian species. The Venn diagram shows the number of unique and shared gene families among seven mammalian genomes. (b) Gene expansion or contraction in the tiger genome. Numbers designate the number of gene families that have expanded (green, +) and contracted (red, −) after the split from the common ancestor. The most recent common ancestor (MRCA) has 17,841 gene families. The time lines indicate divergence times among the species.

(a) Orthologous gene clusters in mammalian species. The Venn diagram shows the number of unique and shared gene families among seven mammalian genomes. (b) Gene expansion or contraction in the tiger genome. Numbers designate the number of gene families that have expanded (green, +) and contracted (red, −) after the split from the common ancestor. The most recent common ancestor (MRCA) has 17,841 gene families. The time lines indicate divergence times among the species.

But note the cladogram on the right, and this bit of information we must keep from the cats.

The tiger genome sequence shows 95.6% similarity to the domestic cat from which it diverged approximately 10.8 million years ago (MYA); human and gorilla have 94.8% similarity and diverged around 8.8 MYA.

The difference between a housecat and a tiger is a mere ten million years. If only they knew…

I plan to allow this cat to continue to play with my cephalopods. Distraction, you know.


Cho YS, Hu L, Hou H, Lee H, Xu J, Kwon S, Oh S, Kim H-M, Jho S, Kim S, Shin Y-A,Kim BC, Kim H, Kim C-u, Luo SJ, Johnson WE,Koepfli K-P, Schmidt-Küntzel A, Turner JA, Marker L et al. (2013) The tiger genome and comparative analysis with lion and snow leopard genomes. Nature Communications 4, Article number: 2433 doi:10.1038/ncomms3433

Cool free stuff

I’ve mentioned the Earthviewer app from HHMI before: think of it as a bit like Google Earth, only you can dial it back to any period in the planet’s history. There have been a couple of developments: it’s also available for Android, and it’s added some new features, including tracking for major fossils. So now you can see the long strange journey of Tiktaalik’s bones on the screen.

They’re also making available a lovely big poster of earth’s history. This year, we here at UMM are putting together a teacher training program to be implemented in the summer of 2015, and it’s going to be a lot of work for us — but I’m realizing that HHMI has already done a lot of material preparation that will help a great deal.

I’ve been known to moan in chagrin over all the multimedia garbage that Answers in Genesis provides to corrupt education in this country — you can just pop into AiG’s website and download lesson plans and powerpoint slides to teach creationism. But now HHMI makes them look feeble as well as wrong.