Category Archives: Vertebrate evolution

What’s in a name? The Pensive Primate, or Primate’s Progress? Tell me what you think

Orangutans are capable of having mental maps and calendars of the forest

Orangutans are capable of having mental maps of the forest

Update: Primate’s Progress it is.

And now for something a great deal less serious.

I originally planned to concentrate on scientific topics, especially the quirks of evolution, so I called this blog “Eat Your Brains Out”. I was referring in particular to the sea squirt. A sea squirt is a tunicate, a member of the group most closely related to vertebrates (that’s you and me and frogs and fishes), but you wouldn’t think so to look at it. As I wrote the story, it starts out as a free-swimming larva, clearly related to our tadpole ancestors, but when it grows up it just sticks its head on a rock and turns into a couple of slimy tubes and reabsorbs its juvenile nervous system because it doesn’t need it any more. Nice story but, as a well-informed reader pointed out, it’s more a matter of rearranging than reabsorbing. Besides, I suspect that more people know about Zombie Apocalypse than about the metamorphosis of sea squirts. And in any case, I’ve found myself writing about all kinds of things, such as politics, education, and freedom of speech, not just about science. Time for a new title.

So, after watching the final episode of BBC’s Monkey Planet (“how primates are individuals with a sense of self and why brainpower is essential to primate survival”), I decided to assert my sense of self and advertise my brainpower by renaming my blog The Pensive Primate. But then I discovered a company selling what it calls Pensive Primate gifts, such as mugs and T-shirts with pictures of orangutans on them, so I settled for Primate’s Progress instead. However, I have mixed feelings about the word “progress”. It makes me sound little bit like (perhaps I am a little bit like) a naive optimist left over from an earlier century. More seriously, it suggests a common misconception about evolution, which is that it is somehow always Onwards and Upwards.

Further searching showed that the label “Pensive Primate” has actually been used many times by photographers and artists, and as far as I can see it is not a trademark. It follows that I can use it too if I want to. After all, there’s no real risk that this blog will be mistaken for a multi-million marketing enterprise.

So now I have to decide. Which is it going to be, The Pensive Primate or Primate’s Progress?

Comments welcome

Image: BBC web site

Why the Sea Squirt Eats its Brains Out (Sort of)

Good to eat, in traditional Mediterranean and oriental cuisines. Good food for farmed fish, not that they (the fish, I mean) really have much choice in the matter. Good as a source of possible biofuels. And now good for almost £1,000,000 of research funding. Your sister, the sea squirt, actual species Ciona intestinalis, coming shortly to a fjord near you.

The sea squirt is the ultimate in middle-aged complacency. It starts off looking a little bit like a tadpole, with a brain (of sorts, “cerebral vesicle” in diagram), a tail with a nerve cord and a stiffening rod (the notochord), an eye (ocellus), and a balance organ (statocyst). The reason it looks like a tadpole at this stage is because it is like a tadpole. The notochord is related to the backbone in vertebrates, a spinal cord runs parallel to it along the flexible tail, and at the head end of the spinal cord there primitive brain coordinates sensory inputs.

Anatomy of larval tunicate (John Houseman via Wikimedia)

But when it matures, it sticks its head on a rock, and changes into its adult form, which is not much more than a mouth (branchial siphon), a stomach, and an exit tube (atrial siphon). It is a hermaphrodite, with one testis and one ovary. Both of these ejaculate into the exit tube, and there are rather complicated mechanisms to prevent self-fertilisation. It protects itself by growing an outer coat, or tunic, made of cellulose-like material, hence the scientific name name tunicate. The sea squirt eats, or to more exact reabsorbs, notochord, tail, sense organs and nervous system, since these are no longer needed, while it feeds by wafting water into its mouth cavity, and filtering out suspended particles. Hence the meme (whose evolution deserves a blog post to itself) that speaks of the sea squirt eating its brains out, comparing the process to a Professor gaining tenure (disclosure: I am myself a former tenured Professor).

Actually, it’s a bit more complicated (see Supplementary Reading, especially the 2005  article), which gives me a good excuse to drop the “Eat Your Brains Out” from the title of this blog, and replace it with the more readily understood “Primate’s Progress”.

Generalised anatomy of adult tunicate (loc. cit.) Note what isn’t there any more; original brain, nerve, moveable tail, and sense organs

Tunicates are the sister group to vertebrates, meaning that tunicates and vertebrates are more closely related to each other than to any other group. They may not look like it, and for many years it was thought that the closest group to the vertebrates were lancelets, animals with simple fish-like bodies that burrow into sand. However, one clue to the contrary was the fact that most vertebrates, and tunicates during their adventurous youth, have a sense of smell while lancelets don’t. (Whales don’t have a sense of smell either, not having any use for it. However, their DNA still contains a degraded version of the genes that in other mammals code for sense organs, inherited as we would expect if their terrestrial ancestors.)

The matter was not settled until 2006, when molecular phylogeny (basically the same kind of DNA testing used every day in the courts to establish paternity) showed that vertebrates like you and I, and tunicates like sea squirts, are more closely related, and are what biologists call sister groups, while the lancelets are merely cousins (for a detailed technical discussion, see here). The partings of the ways took place some 550 million years ago, and a lot has happened since to obscure matters. Tunicates now have the simplest genome, but this is the result of gene loss. That of vertebrates shows the effect of doubling and redoubling, one of the many ways in which evolution can give rise to new information.  However, evolution is not necessarily progress, nor are we more highly evolved than tunicates. We just happen to have evolved in what are, for us, more interesting directions.

So appearances can be deceptive. In fact, tunicates have quite a bewildering variety of life histories and reproductive strategies, including (for salps, which are close relatives of sea squirts) cloning, group sex, and a midlife sex change. Molecular comparisons between those tunicates that never settle down, and those that do, suggest that the sedentary habit has been discovered more than once, and that tunicates can evolve new body forms with unusual rapidity.

Seasquirt3

Tunicates raised at a research facility in Øygarden, Norway. (Photo: Bård Amundsen, from Norwegian Government press release)

The Norwegian government has just spent 8.7 million Norwegian krone on these creatures. Why, and what exactly do they hope to gain from it? The idea is to anchor huge sheets of plastic in selected Norwegian fjords, with buoys attached to the top to keep them vertical, and allow the chosen species of sea squirt to colonise them. The fjords are ideal in shape for this, being steep-sided drowned valleys, carved out by ice age glaciers. The sea squirts will require no feeding, because they get enough nutrition from suspended fragments of debris. They will not exhaust this food supply, as the water is replenished twice daily by the tides. Thanks to their cellulose-like tunics, they attract no predators, so harvesting them will not deprive any other species of its normal food, and as an overall accumulator of protein the project is predicted to be 100 times as efficient per unit area as grazing land animals. So you can harvest the sea squirts, grind them up, and use them as fish feed. This is potentially very big business, because Norway is the world’s leading producer of farmed salmon, which until now have needed to be fed, themselves, on fish. The sea squirts are even efficient accumulators of omega-3 fatty acids, produced by microorganisms, which end up in the salmon.

There is more. At the moment, biofuels are of two kinds; those derived from starch, and those from vegetable oils. Both of these compete directly with food. There is very serious doubt as to whether corn alcohol, so beloved of farmers in the American Midwest, actually contributes anything to reduction of global warming, after taking into account the energy spent growing and fertilizing the grain, and the fact that more food will need to be grown elsewhere. My own view is that biofuels will never make a real contribution to the world’s energy supply until we develop a good technology for making alcohol from cellulose. This is more difficult than making it from starch. Both starch and cellulose are polymers derived from glucose, the only difference being the way in which glucose units are joined up, and how to unravel cellulose and convert it into biofuel is a hot research topic. But, as the group funded by the Norwegian Research Council points out, cellulose from wood is blended with a tough polymer called lignin, which is even more indigestible. I would add that other plant sources of cellulose are also complex mixtures, and that in any case, land used to grow biofuel crops becomes unavailable for agriculture, or for natural carbon-fixing processes such as peat formation. So if cellulose biofuels do turn out to have a future, a marine source has many advantages.

Current developments are, I suspect, under wraps for commercial reasons, but the research group involved have already taken out patents on the production of biofuels from tunicates, and the use of tunicate material as feed for (non-human) animals.

Two questions remain unanswered. Can a good way be found, on a bulk scale, to remove the water which makes up 95% of the body mass of the sea squirts? And a further question of my own; what will the farmed salmon taste like?

An earlier version of this post appeared on 3 Quarks Daily. I thank Zen Faulks of UT Pan-American for critical discussion of the “Eat your brains out” concept.

Further reading:

The larval ascidian nervous system: the chordate brain from its small beginnings, A. Meinertzhagen and Y. Okamura, Trends in Neurosciences 24(7). 401-410(2001).

The nervous system in adult tunicates: current research directions, O. Mackie and P. Burighel, Canadian Journal of Zoology 83(1): 151-183, 2005

Deuterostome phylogeny, Sarah J. Bourlat et al., Nature, 444, 2006, 85 (2006).

A chordate with a difference, Linda Z. Holland, Nature, 447, 2007, 153 (2007).

The amphioxus genome, Nicholas H. Putnam and 35 other authors from 18 different institutes, Nature, 453,1064 (2008) (free download); Amphioxus unleashed, Henry Gee, Nature, 453, 999 (2008) [amphioxus, meaning “sharp at both ends”, is a term for lancelet]

A review of the life cycles and life-history adaptations of pelagic tunicates to environmental conditions, Don Diebel and Ben Lowen, ICES Journal of Marine Science, 2012, 358; free download.

 

Reviewed: The Incredible Unlikeliness of Being; Grandmother Fish

In an earlier post, I said that the right way to undermine creationism is to promote appreciation of the science of evolution, by presenting it in ways that are engaging, enjoyable, and above all personal. In this post, I review two more books that succeed in doing this; Alice Roberts The Incredible Unlikeliness of Being and Jonathan Tweet‘s Grandmother Fish.

UnnamedGrandmother Fish is a book like no other I have seen. It is an introduction to evolution, for adults to read to their pre-school children. It is also much more than that, and comes with well-earned commendations from Stephen Pinker, David Sloan Wilson, and Daniel Dennett.

We start with a delightfully drawn Grandmother Fish, who lived a long, long, long, long, long time ago and could wiggle and swim fast and had jaws to chomp with. At once, this is made personally relevant: “Can you wiggle? … Can you chomp?” We proceed by way of Grandmother Reptile, Grandmother Mammal and Grandmother Ape, to Grandmother Human, who lived a long time ago, could walk on two feet and talk and tell stories, and whose many different grandchildren

could wiggle and chomp and crawl and breathe and squeak and cuddle and grab and hoot and walk and talk, and I see one of them … right here!

Each stage has its own little phylogenetic tree, with the various descendants of each successive “grandmother” shown as each other’s cousins, and there is an overall tree, covering all living things, that anyone (of any age) will find interesting to browse on. Finally, after some 20 pages of simple text and lavish illustration, there are around 4 pages of more detailed information, directed at the adult reading the book, but to which I expect children to return, as they mature, remembering the book with affection, as they surely will, years or even decades later.

So here we have nested families, family resemblance, and the development of more and more specific and complex features. And any adult, or indeed any alert child, will readily extend the discussion. Was there a grandmother cat, whose grandchildren include lions and tigers and pussy-cats, and how was she related to grandmother carnivore? Where do fossils fit in? (The tree shown includes pterodactyls, dinosaurs, and early birds.) And the most common arguments against evolution, from “only a theory” to “where are the intermediate forms?” to “if evolution is true, why are there still monkeys?” will stand immediately revealed as the nonsense they are. Indeed, one of the few statements in the endnotes that I disagree with is that “Evolution by natural selection is very difficult to understand because it doesn’t make intuitive sense.” It will, in my opinion, make perfect sense to a child who has met so clear an exposition early on, and who will therefore find it much easier to understand intuitively than, say, Noah’s Ark.

Back story: this project was crowdfunded on FaceBook, on the basis of some initial sketches and text. The author professes a long-standing interest in evolution, but his career hitherto has been elsewhere, in computer games (he was lead designer on the 3rd edition of Dungeons and Dragons). However, he has had expert advice from many people, including Eric Meikle, Education Director at the [US] National Center for Science Education.

Publication: pending. Initial partial draft available on request here (technical note: the mammalian tree shown there has since been updated). Diagram from book draft website.

Disclosure: I have corresponded with the author who tells me I will be thanked on the book’s website. Review based on initial draft + correspondence with author. I will be buying this book for my grandchildren as soon as it becomes available.

Alice Roberts The Incredible Unlikeliness of Being, despite (because of?) coming from an established author and presenter, is as personal as could be. It starts with Alice Roberts’ emotional response to becoming a mother, and the incredibly unlikely being is the reader. The subject matter is (mainly) the development of the human embryo, and that developing embryo is not some third party abstraction, but you. And so evolution is also about you, as example after example throughout the book makes clear:

It’s about your evolutionary heritage, and it is about your own embryological development, when you grew in changed, part of you folding like origami, until you are shaped like a human.… This is the best creation story, because it is true.… This scientific story, pierced together from many different sources of evidence, is more extraordinary, more bizarre, more beautiful, than any creation myth we could have dreamt up.

Alice Roberts is Professor of Public Engagement in Science at the University of Birmingham, and one of the new generation of writers and TV presenters who in the UK fill much the same role as Bill Nye and Neil deGrassie Tyson in the US. She is by training a doctor and anatomist, and much of her own research has involved forensic examination of pre-human hominin skeletons, the coldest of “cold cases”. This background shows up clearly in her detailed descriptions of your developing structures, and she shares with us her emotions about coming face-to-face (in one case literally) with her own anatomy, as when, after x-ray tomography, she was given a replica of her own skull.

My Day on a Plate

Prof Alice Roberts holding a replica of a skull (not, in this case, her own)

The unlikeliness is not just the obvious unlikeliness of your two particular parents meeting, of that one egg becoming fertilised, and of that one sperm out of the enormous number available on being successful. Nor even of the improbability of your parents in turn having come into existence, and so on. Behind all this, and multiplying all those improbabilities, is the meandering history of our evolution:

The more I delve into the structure and workings of the human body, the more I realise what a cobbled-together hodge-podge of bits and pieces this thing we inhabit really is. It is brilliant, but it is also flawed. Our evolutionary history is woven into our embryological development and even adult anatomy in surprising ways; many of our body’s flaws can only understood in an evolutionary context.

We start with a history of ideas, and here it struck me as remarkable how long it took for it to be generally recognised that both parents contribute to the form of their offspring, despite the obvious evidence from physical resemblances. Leeuwenhoek with his microscope first observing sperm, the much later discovery of the mammalian ovum, a comical (in hindsight) controversy between “spermists” and “ovists”, the puzzle, insoluble even in principle until the advent of genetics, of how both parents could contribute to what we now call the information content of their offspring, and the further conundrum, unsolved until DNA was identified as the genetic material, of the material means by which they did so.

Most of the book is concerned with the complex process that leads from first release of the ovum, through fertilisation, implantation, and the many subsequent stages of development, through to birth. This story is inextricably intertwined with the story of your evolution, and I can only pick out a few of the most salient points from a wealth of fascinating detail.

From cell division to implantation, with the cells beginning to form separate layers

There are, of course, vestigial or discarded organs. In your second week of development, when you were not much more than a couple of layers of cells, you generated a yolk sac, homologous with the yolk sac of fish, amphibians, reptiles, and even those mammals (the platypus and the spiny anteater) that lay eggs. The difference is that in these the yolk sac is filled with the nourishment that will sustain the growing animal until its birth, whereas in placental mammals like us, it has been without function for the past 90 million years or so. Nonetheless, the recipe for making it has never been deleted from your assembly instructions.

At an early stage, it is very difficult to distinguish the embryo of a mammal (that includes you, of course) from that of a fish; a little later it is still difficult to distinguish it from a reptile or a bird, and different mammalian embryos continue to resemble each other for even longer. For a while, it was suggested that this is because you were retracing your evolutionary history, but we now know that this idea is based on a mistaken model of evolution. You are not more highly evolved, than, say, a chicken; you have just evolved in a different direction. The earliest stages of development are shared with fish, later stages with reptiles and birds, and later stages yet only with mammals and eventually only with our fellow apes. Thus we do not, strictly speaking, recapitulate our evolution from a fish, nor should we, since the present-day fish is as remote as you are from your last common ancestor with a halibut, but we do recapitulate shared development until the parting of the ways. The new science of “evo-devo” is now beginning to take this story down to the most fundamental level, identifying the molecular basis for the parts of the construction plan that you share with a fish, and the parts, activated later, that you do not.

The cartilage base of human skull resembles that of other mammals.  It is only later, when this is being transformed to bone, that it acquires its specifically human form, with the enlarged dome required to house the brain towering above the rest of the head.

Working down from the head takes us to the larynx, and the unanswered question of the origin of human speech. Here the problem is that the really important working parts – the larynx itself, its associated muscles, and, above all, the tongue – are soft tissues and leave no trace in the fossil record. The position of the larynx lower in the throat, compared with other mammals, may be no more than an accidental consequence of the way our oversized brainboxes sit on top of our spinal column.

The origin of the larynx leads us to the most striking embryological evidence for evolution, namely the direct resemblance between the branchial (gill) bars of fish, and the related structures found, early in development, in terrestrial vertebrates. Then comparative embryology allows us to map our own organs against their fishy counterparts, and to explain some of the more absurd features of our own anatomy.

Our fishy origins are clearest early in development. By week four, the bundle of cells on its way to becoming you has separated into three separate layers, a tube within a tube within a tube. On the outside, ectoderm, which will give rise to your skin; on the inside, endoderm, which will give rise to your digestive tract, from one end to the other, and in between mesoderm, giving rise to a variety of structures. By week five, we can see what will become the backbone, the eye, and the branchial bars in the neck. Each branchial bar has ectoderm on the outside, endoderm inside, and in between a mixture of cells, some from mesoderm and some from neural crest. This in-between layer will develop into a cartilage bar and muscles, and each bar will develop an artery and a nerve.

Land animals and fish have shared much the same developmental instruction manual until this point, but now they begin to diverge. In fish, the branchial arteries accept blood directly from the heart, and the cartilage forms the gill arches. In land animals, development is far more complex. One set of gill muscles becomes larynx muscles, and a nerve that leads to it runs down into the chest, before making its way back up to the top of the throat. Why so? Because the blood vessels that, in fish, run directly between the heart and the gills have become, in land animals, the aorta and main arteries leading from it. And as a consequence, the recurrent laryngeal nerve, as it is called, is trapped beneath the aortic arch when the heart moves downwards, as it does in land animals but not in fishes, and forced to take this convoluted path. Bad design, but an unavoidable consequence of evolutionary history. A creationist with whom I once discussed this suggested that this really was a good design, because it protects the nerve from damage. Tell that to a giraffe.

The first branchial arch gives rise to bones that are part of the jaw joint in reptiles, but in mammals have shifted and shrunk and become two of the bones of the inner ear. And yes, there is an intermediate form, an early mammal with two jaw joints, the outer one thus being made free to move closer to the ear to improve resonance, and, ultimately, to detach itself. Gill flap muscles in the fish end up as face muscles in primates including us, and so on. The cleft between the first and second branchial arch gives rise, in us, to our ears, and to the tubes that connect the middle ear to the throat, thus enabling pressure to equalise.

Descending to the molecular level, these developments are orchestrated by a set of control genes, prominent among them the so-called “homeobox” or Hoxgenes, first discovered in fruit flies, where they regulate the formation of the segments of head, thorax, and abdomen. Similar genes are found in every segmented animal, including us (if you don’t think you’re segmented, think of your backbone and ribs). This arrangement must be very ancient, since your last common ancestor with a fruit fly was some 800,000,000 years ago, but has undergone elaboration. The fruitfly has 8 Hox genes, lined up in a row, that come into play one after the other. In the lancelet, this has been expanded to 14. At some stage between the lancelet and jawed fishes, the entire genome seems to have doubled and redoubled, so that you have four sets of Hox genes, each on a different chromosome.

Some aspects of this regulatory system are much more flexible than others. All land vertebrates have a spine with the same basic sections: neck, chest, lower back, sacrum, and tail. All mammals have just seven neck vertebrae, whereas the number of tail vertebrae is highly variable, being up to 49 in one species of porpoise, which flexes its tail to swim, while our tail, or coccyx, has only 3 to 5 fused together. This tail can be considered as a vestigial organ, since it is a mere relic of that sported by our monkey-like ancestors, but like many so-called vestigial organs it continues to earn its keep, in this case by acting as an anchor for muscles. Our lower backs have one more vertebra then our chimp cousins, and are less securely held in place, developments thought to be related to our habitual walking on two feet

Relevant to Professor Roberts’ own anatomical interests, although less directly so to the question of embryological development, is the detailed history of our limbs. This indicates us to have been truly bipedal as long ago as 3.2 million years ago (Lucy), while long legs at 1.5 million years ago (Narikotome boy) suggest adaptation for running. In popular imagination, we learned to stand upright as we evolved away from knuckle-walking ancestors, but the reverse may be the case. Monkeys, like us, have feet far harder and less flexible than those of modern non-human apes, and Prof Roberts speculates that our ancestors were tree walkers. If so, it is the apes, with their prehensile toes, rather than us, who have diverged from the form of our common ancestor.

But once we started walking on the ground, that change in behaviour, which could occur within a group in a single generation, would have suddenly generated a new set of selection pressures in favour of long distance walking and running. This is an activity for which we are superbly adapted, even though only a few groups, such as the Tarahumara in Mexico, still regularly practice it.

The final Chapter reviews our present understanding, and considers our place in nature.  Development is controlled, more or less, by DNA, including control genes as well as directly expressed genes. It is not, as Haeckel thought, a true recapitulation, but shows clear echoes of earlier stages – segments, gills, fish hearts, the lancelet brain. Our developmental biology is, to use one of Prof Roberts’ many memorable metaphors, a palimpsest.

Similar environmental pressures can give rise to similar adaptations, so that the mammalian ear with its three tiny bones has evolved at least four times in different lineages, while, as hinted above, different ways of moving around including bipedalism may have arisen more than once among our ancestors and their close cousins. But nonetheless, evolution remains unpredictable, if only because changes in the environment are unpredictable. One such change was that triggered by the asteroid that did for the (non-avian) dinosaurs. Selection acts without foresight, and without that asteroid, we would not have had humans (for what it’s worth, my own view is that we would have had the intelligent descendants of the velociraptors instead).

Evolution takes place in context, and that context, for a species capable of learning from each other, includes a technology. An innovation in toolmaking could have spread through a group of our ancestors in a single generation, triggering a new set of selection pressures that moulded their hands and bodies to a new set of tasks. We speak of the survival of the fittest, but fitness here refers to the cultural, as well as the natural, environment. And we are more influenced in our lives, and our evolution, by our own culture and its artefacts than any other species.

The book concludes with reflections on our similarities (profound) and differences (striking, yet perhaps more quantitative than qualitative) from other species, our contingent and transitory nature, and our uniqueness both as species and, returning to the starting point, individuals.

There are numerous drawings (Prof Roberts is an award-winning artist), and an extensive bibliography.

A few detailed comments. Prof Roberts shows, early on, a series of drawings copied from Haeckel. Connoisseurs of creationism will recognise this as a deliberate provocation, since creationist writers repeatedly point to alleged shortcomings in these, as reason to ignore the whole of developmental science. Lancelets are shown as sister group to vertebrates; in fact, we are closer to tunicates (the subphylum that includes sea squirts) than we are to lancelets, although tunicates only acquired their sessile habit after we and they had gone our separate ways (Prof Roberts tells me that this will be corrected in later editions. I occasionally found the layout of diagrams and their explanations rather awkward. This may be an inherent limitation of the e-book format that I was using.

Figures from Prof Roberts’ personal website, and Amazon website.

Disclosure: this review is of the first Kindle edition, personal purchase.

These reviews first appeared here, on 3 Quarks Daily

The Problem with Pandas

Keywords: sex, violence, baby swapping, mistaken identity, DNA testing, international relations, Richard Nixon, Viagra, Sixth Mass Extinction

 449px-RedPandaDescent

Rotation of back paw allows red panda to descend head first down tree. Taken at the Cincinnati Zoo. Photo by Greg Humethrough Wikipedia

Same thumb, different family

Names can be deceptive. The red panda and the giant panda are not two different varieties of the same species; they are completely different species, and only distantly related.  They do not even look very similar. The red panda is much smaller than the giant panda, coloured brown and cream, and has a long striped tail. The giant panda is, of course, black and white, with a very short tail, and black patches over its eyes. These patches help give it the cuddly appearance that makes it so popular in zoos.

Both animals are found in China, although the red panda spills over into Nepal and northern India; both are anatomically carnivores, but live on bamboo; and both have the same kind of false “thumb”. This “thumb” is, really, nothing of the sort, but simply a modified wrist bone, while all five true digits are used in walking. The “thumb” is opposable, meaning that it can be moved to grip against the other digits, but has no joints or claw.

Grosser_Panda

Giant panda in Ocean Park Zoo, Hong Kong. Photo by J. Patrick Fischer through Wikipedia

As early as 1825, Frédéric Cuvier (brother of the more famous Georges) described the red panda and proposed that was related to the racoon. The giant panda, however, did not become known in the West until considerably later. A French missionary in China described a skin in 1869; Teddy Roosevelt Jr and his brother Kermit, sons of President Teddy Roosevelt, saw a giant panda in China in the 1920s (true to family tradition, they promptly shot it); and it was not until 1936 that the first giant panda arrived in a Western zoo. Most zoologists considered it to be a kind of bear, on the basis of its anatomy, although a few thought that the two kinds of “panda” really were closely related. The matter was finally and conclusively resolved by comparing the DNA of both animals with that of other species. As expected, the giant panda belongs to the bear family, while it turns out that the red panda is in a genus all of its own, with skunks, raccoons and badgers as its closest relatives. But you do not find the false thumb in raccoons and skunks, and you do not find it in polar bears and grizzlies. So it is not a shared feature of this branch of the carnivore family tree, but a separate similar development in the two “pandas”. A similar false thumb is also found in some species of mole. These are examples of what is called parallel evolution, in which the same modification arises independently in different species. To use technical language, the thumbs are analogous (similar, and performing the same function), but not homologous (not a feature inherited from a common ancestor).

 Courtroom pandamonium

Update: the film Judgement Day, regarding the Dover trial,is now available to UK viewers here

The giant panda occupies a special place in US legal history. It was given a starring role in the 1989 “alternative textbook”, Of Pandas and People, an Booksattack on the science of evolution in general, and on common descent in particular. The book carries an attractive photo of a giant panda on its cover, and argues at great length that since the analogies between the “thumbs” of the red and giant panda are not due to common descent, therefore all anatomical arguments in favour of common descent should be regarded as suspect. One particular School Board, in Dover, Pennsylvania, voted to introduce this book into its high school, with a statement to be read to students. This statement described the book as a way of exploring “Intelligent Design”, and declared that “Darwin’s Theory … is not a fact. Gaps in the Theory exist for which there is no evidence… Intelligent Design is an explanation of the origin of life that differs from Darwin’s view.”

I should explain that “Intelligent Design” in this context means the view that biological complexity is due to the activity of an intelligent designer. It offers no suggestions as to how or why the designer operates, or how the design comes to be embodied, so I find it difficult to see how it is an explanation of anything. The reference to the origin of life is bizarre, given that Darwinexplicitly refused to discuss this topic. As for the expression “Darwin’s Theory”, and the creationist obsession with Darwin, I have already discussed these here and here.

The biology teachers, very courageously, refused to read out any such statement, because they said they could not tell their students what was simply not true, so the School Board told the Principal to read it to the class instead. A group of outraged parents promptly took the School Board to court, on the grounds that Intelligent Design is not a scientific theory but a religiously inspired doctrine. This would mean that propounding it in a publicly funded school is contrary to the establishment Clause of the First Amendment to the US Constitution. During the trial, the plaintiffs were able to demand drafts of the book as evidence, and discovered that it had its own evolutionary history. It was originally written in terms of “creation science” and “creationism”, terms that for legal reasons were transformed by horizontal meme transfer into “intelligent design”. One of the subpoenaed drafts even contained the expression “cIntelligent Designism”. The Missing Link!

For this and many other reasons, the judge had no difficulty in concluding that “intelligent design” was nothing more than religiously motivated creationism. He set out his reasons in a detailed and powerful judgement, and while his decision is strictly applicable only to the States covered by that particular court, it seems most unlikely to be challenged unless the US Supreme Court falls into the hands of extreme religious conservatives.

For a work arguing in favour of Intelligent Design, the panda was a singularly unfortunate choice. The so-called puzzle of the two kinds of “panda” was solved over a century ago, and the results confirmed much more recently by modern molecular techniques. All the more reason to trust evolution science. The inflexible “thumb” is not what a designer would have chosen, but what the evolving animal was stuck with. All five of the panda’s claws are used for walking or climbing, so it was not possible to coopt one of these to hold on to bamboo, even though the extra joints present inside a real thumb would have made it much better at this job. Finally, the panda’s digestive system is very poorly adapted to its way of life, because it is descended from carnivores. An intelligent designer would have given the panda a digestive system rather like that of a cow. The panda is a wonderfully clear example of how an animal’s form is constrained by its evolutionary history. In fact, the great essayist Stephen Jay Gould named one of his books in its honour way back in 1980, and http://www.pandasthumb.org, one of the world’s top science blogs, follows his lead.

So what were the authors of Of Pandas and People thinking? They were neither stupid nor unqualified, and were well aware of, and indeed they themselves quote, the scientific literature that showed how the “problem” of panda species had long since been resolved. So how could they have imagined that they were putting forward a credible argument? There is a serious philosophical or psychological point here. It seems to me that for them and their supporters, the problem of the pandas really did illustrate an argument against evolution science. Some comparative anatomists had thought that the two kinds of panda were closely related. They were wrong. Therefore, the argument runs, comparative anatomy in the service of evolution is untrustworthy. Creationists think in absolutes. So they regard the awareness of fallibility, which lies at the very heart of the scientific method, as an admission of weakness. This could explain why creationism is so appealing to lawyers, who rely on cases being finally settled, and to conservative theologians, who regard their dogmas as established and revision as heresy.

Pandas have eating problems

It was the giant panda that graced the front cover of Pandas, that appears in the logo of the World Wildlife Fund, and that pulls in visitors to zoos Edinburgh zoo even has a pandacam for remote viewing). Panda diplomacy also played a role in the restoration of normal relations between China and the West, one of the major achievements of the much-maligned Nixon administration. The chubby-faced cuddly looking creature, with the big black patches round its eyes, has great emotional appeal. Unfortunately, its very survival in the wild is threatened, and attempts to maintain numbers in captivity have run into great difficulties.

Pandas (from here on in,I just mean giant pandas) have painted themselves into a corner, adapting to a very narrow niche, for which their ancestry had not really equipped them. They live almost entirely on bamboo. Unfortunately, bamboo is of very low nutritional value to them. Pandas are, after all, members of the carnivore family, and have carnivore type digestive systems and enzymes, leaving them dependent on bacteria in their gut to break down their food. This is such an inefficient system that they need to eat around 20 kg a day, and in the wild just doing this can take them up to 14 hours. They need very powerful jaw muscles because of the chewing involved, and these, together with wide cheeks to accommodate large grinding molars, are what give the pandas their appealing round faces. We have fossil skulls and teeth showing that pandas had already adapted in this way 2 million years ago. But fossilised bones cannot tell us the history of those appealing black eye patches, which are probably favoured by evolution in the pandas’ snowy habitat, because they reduce glare, like footballers’ facepaint.

Pandas can only survive in areas where more than one species of bamboo is flourishing, so that when one species flowers and dies back, they do not lose their only food source. They extract so little nutrition from their food that they have little energy to spare, and find it a problem to make their way up steep slopes. This may not have mattered too much in their original habitat in the Chinese lowlands, but now that people have taken up all the land suitable for agriculture, they find themselves forced into shrinking and fragmented habitats in the mountains. Climate change is expected to make things even worse. There are probably fewer than 3000 surviving n the wild. So the number in captivity, which now exceeds 300, is a considerable fraction of the total population.

Sex problems too

Update, 9 July 2014: Tian Tian, the Edinburgh zoo panda who was artificially inseminated in April after she and her partner, Yang Guang, failed to mate naturally, has conceived, but it is not yet known if she is pregnant, as the embryo is not implanted into the womb immediately in pandas.

In the wild, pandas are solitary animals, each one marking its own range by clawing and spraying urine, but they do gather together during the annual breeding season, when their endeavours are evidently successful, otherwise they would not be here. However, it has turned out to be enormously difficult to breed pandas in captivity, a feat not accomplished at all until 1963. What’s the problem? Why not just put a male and a female panda together and let them get on with it?

Firstly, the female panda only comes into heat once a year, for about three days, during which she is only fertile for 12 to 24 hours (this fertile period can be detected by testing her urine). Then, most attempted romantic encounters proved very disappointing. The male (according to the BBC, no less) has a very short penis, so that accurate positioning is necessary, and they are not very good at doing this. Moreover, preliminaries in the wild involve fighting among males for the privilege of mating, and this spectacle seems to be an important part of what it takes to get the female interested. So despite measures ranging from sex education videos, to stimulating the males with sticks of bamboo carrying the female scent, to the use of Viagra, managed encounters in the zoo often end in disappointment or even violence. “Close, but no cigar” is how Edinburgh Zoo described the situation of their own two pandas, when in April 2012 Yang Guang (Sunshine) mounted female panda Tian Tian (Sweetie) several times, without full mating taking place. 

The present successful breeding program in China has resorted to artificial insemination (don’t ask!) However, that does not put an end to the problems. Pandas very often display pseudo-pregnancies, quite difficult to distinguish from the real thing, even by hormonal testing. Ultrasound can be helpful here, but requires considerable skill because of the smallness of the foetus, as well as the cooperation of the animal. (The mother weighs around 100 kg or more; the new-born offspring, a mere 100g.) In human and most animal pregnancy, we know when to start the countdown to birth, but not with pandas. These, like other bears, show delayed implantation of the foetus. So the time between fertilisation and birth can range from 11 weeks to 11 months. Pregnancy can end in miscarriage, as recently happened at Edinburgh Zoo. Finally, because of the small size of the foetus, and the common occurrence of pseudo-pregnancies, true pregnancy does not become obvious until shortly before birth.

Pandas usually give birth to two clubs at a time, but only make enough milk for one. So the expert panda breeders at the world’s leading centre in Chengdu have resorted to trickery, caring for the abandoned cub in an incubator, swapping the two clubs around when their mother is not paying attention, and supplementing the mother’s milk with imitation bear milk. Both cubs do, however, need their share of mother’s attention. They have weak immune systems, so they rely on antibodies in their mother’s milk. They also need help in defecating, which the mother supplies by stroking their lower abdomens with her tongue. However, this particular problem clearly resolves itself by adulthood, since a full-grown panda makes 40 panda-pats a day.

The panda breeding programme is big business, with the Chinese retaining ownership of the beasts, and renting them out to Western zoos for $1 million a year. This is over and above the cost of looking after them. Even so, major zoos consider this a worthwhile investment, because of added visitors and publicity. Centre-bred pandas are now also being reintroduced into the wild. Suitable habitat has been bought, and will no doubt in due course be a major attraction for eco-tourists. Keepers involved in the reintroduction have been dressing up as pandas, in the hope that their charges will feel more at home when released. However, critics of reintroduction point out that the entire exercise is meaningless unless these pandas are given enough protected habitat, and the first released panda died after only a few months in the wild.

And finally, the hard question

Biologists warn that we are on the threshold of a sixth great extinction, comparable to the demise of the dinosaurs. Unless we change our ways, or brute circumstance changes them for us, we could lose 75% of living mammals within the next 300 years. To say nothing of other life-forms, and with consequences for ourselves that we can only guess at. Amidst this mayhem, is the panda worth saving? If so, why? If not, why not? 

This piece originally appeared at http://www.3quarksdaily.com/3quarksdaily/2013/11/the-problem-with-pandas.html#sthash.ONwwiWM7.dpuf

Rethinking the earliest mammals

In a recent Earth-Pages post, Steve Drury, of the Open University, reports on latest developments in the ever-expanding tail of the giant Miocene Sciuridae of the Western Ghats  of Karnataka. I cannot attempt to do justice to the surprising and revolutionary implications of these discoveries, not only for the squirrels themselves but for the primitive hamsters that appear to have been their pray. More, much more, can be expected from the laterite

Artist's impression of the Sringeri carnivorous squirrel (credit: network54.com)

Artist’s impression of T. sringeriensis (credit:network54.com). From Drury, op.cit.

deposits now being unearthed, with major scatological and eschatological implications.  My only concern is that these deposits may be insufficiently collateralised, and therefore liable to subsidence and enforced repossession before exploitation is complete. As for the hamsters themselves, the present author (me; not Stephen Drury who has not authorised and is not likely to authorise this account) suspects that although they may be distantly related to Felis domesticus cheshirensis, they do indeed belong to an early intelligently designed form of Cricetinae. If so,  they would have been particularly nutritious because of their cheek-pouch contents, thus providing a balanced diet of carbohydrate and protein, in accord with current dietary guidelines, in a single meal.

Embargoed until 00:00:o5, 01/04/2014 BST

No evidence for evolution, says the Reverend

The Rev David Blunt is Minister at North Uist and Grimsay Free Church of Scotland (Continuing), Bayhead, North Uist, not to be confused (Heaven forbid!) with the benighted folks at North Uist, Grimsay, and Berneray Free Church of Scotland, Carinish.

He subscribes to a catechism that states that unless God arbitrarily decides otherwise, I (he, too, come to think of it) am “foreordained to dishonour and wrath, … to the praise of the glory of his (God’s,not the Reverend’s) justice” because of the guilt of Adam’s first sin, rendering us liable to “everlasting separation from the comfortable presence of God, and most grievous torments in soul and body, without intermission, in hell-fire for ever.”

If he really believes that  that is what he believes and preaches, that is no one’s business but his own and his congregations (although I would have grave misgivings should he be preaching such sadistic doctrine to children.)

The Reverend also believes that the devil seeks to confuse us through the teaching of evolution, and  that everything was created over a period of six days, and in order to justify this belief he takes from time to time to the pages of the Hebridean News, where he tells us that

The notion that evolution is responsible for a process of development in living things, beginning with microbes and leading ultimately to men, must be rejected as there is not a single proven fact to support it.

I initially responded,

The Rev David Blunt says that “there is not a single proven fact” to support evolution. If he goes to the website http://www.talkorigins.org/faqs/comdesc/ he will find, spelt out in detail, 29 separate arguments and hundreds of supporting facts that show that evolution is true. If he goes to the Biologs website, and looks up Dennis Venema, he will find a brilliant explanation of all this by a  devout evangelical.

If the Rev does not choose to inform himself about the facts,that is his business. But he denies their existence, he is bearing false witness.

The Reverend is clearly a fast reader, since within two days he had digested the 60 or so sections in talkorigins, and Dennis Venema’s excellent 28-part series. And so he was able to reply:

The sort of ‘facts’ which are essential for the theory of evolution to be true include the following: the existence of mutations representing the increase in genetic information necessary to arrive at more advanced life forms; the existence of life forms (extant or extinct) which are obviously transitional in character; the existence of billions of years of time.

Mutations … overwhelmingly detrimental… We still look in vain for specimens which are intermediate between one life form and another. The fossil record, which Darwin expected to provide examples of missing links, has yet to yield them.

Aeons of time are crucial to the theory of evolution yet it cannot be proved that the earth is billions of years old: indeed many scientific facts point to a much younger earth… [Evolution] must be able to account not simply for microbes to men but molecules to men – or even more precisely – particles to people. In other words it must be able to explain how life can arise from non-life. That is a real leap of faith!

There is no observable evidence for the theory of evolution. It is not testable over time and cannot be verified.

My response:

To pretend that biological evolution has to include an explanation of the origins of life is at best mistaken, at worst dishonest. Consider that before the 1950s, we did not know the origin of atoms. Nonetheless, atomic theory had been the central concept of chemistry since before the 1820s. Similarly, we do not know the origins of life, but evolution has been the central concept of biology since before the 1870s.

No one doubts that most mutations are harmful. A few of them do increase fitness. Harmful mutations are bred out, while fitness-enhancing mutations spread. It’s really that simple. Indeed, the whole of plant and animal breeding is one vast demonstration of evolution, albeit evolution directed by us rather than by the pressures of the natural environment. The Rev Blunt admits the occurrence of evolution under the pressure of artificial selection. How then can he claim that it is in principle impossible under natural selection, or that evolution has never been verified?

Australopithecus afarensis skull, through www.sculpturegallery.com
Museums are full of intermediate forms, if not the great-great-grandparents of living species, then at any rate their great-uncles. If the Rev cares to visit http://link.springer.com/article/10.1007%2Fs12052-009-0135-2  (free article) he will find a whole series of intermediates between land mammals and present-day whales. If he visits the Smithsonian museum‘s site at http://humanorigins.si.edu/evidence/human-fossils/species, he will find out about over a dozen extinct species intermediate between apes and modern humans. If evolution is not true, why were these intermediates ever created?The age of the Earth is dated at over 4 billion years using some half-dozen different radiometric techniques. These the Rev Blunt will find explained, by an evangelical Christian, at “Radiometric Dating – A Christian Perspective“. We have known since 1928 that radioactive decay rates depend on the general laws of physics. If these had been different 4 billion years ago, the rocks wouldn’t have formed in the first place. If they had been almost 1000 fold faster in the past, as Young Earth creationists must claim, the rocks would have been melted by the heat produced.

doi.org/10.1016/j.ympev.2012.10.012

I conclude by pointing out that the fossil record clearly shows that whales are descended from land mammals. Yet Genesis states that whales were created on Day 5, and land mammals on Day 6. One of two things follows. Either Genesis is not, and was never meant to be, a science textbook. Or God has deliberately deceived us by creating a highly detailed but totally misleading fossil record.
This is a choice that each of us has to make in our own way. There are no alternatives.
I predict that the Reverend will reply, challenging me to turn a bacterium into a biochemist within the timescale of a research grant.
Update: Actually, rereading his material, I see that he did better than that, accusing me of clutching at whiskers (that’s a good line, I think I’ll use it) in my discussion of whale phylogeny, repeating the claim, long since refuted,  that data from Mt St Helen’s shows radiometric dating to be unreliable, and finally asserting that the only valid evidence is eye-witness evidence.
There is no eye-witness evidence of the Ice Ages, which helped shape the mountains of North Uist. Does the reverend therefore think they never happened?
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