Werner Arber: Molecular Darwinism

This talk has me a little concerned: it’s proposing something rather radical, for which Arber is going to have to show me some unambiguous evidence to convince me, and I’m coming into it with a very skeptical mindset. Here’s the relevant portion of his abstract:

The theory of molecular evolution that we also call “Molecular Darwinism” is based on the acquired knowledge on genetic variation. In genetic variation, products of evolution genes are involved as variation generators and/or as modulators of the rates of genetic variation. These evolution gene products act together with several non-genetic elements that can be assigned to intrinsic properties of matter, to environmental mutagens and to random encounter. We conclude that natural reality takes actively care of biological evolution. The evolution genes must have been fine-tuned for their functions by second-order selection, so that spontaneous genetic variation with different evolutionary qualities occurs at quite low rates. This ensures a relatively high genetic stability to individuals, as well as an evolutionary progress at the level of populations.

The presence of evolution genes points to a duality of the genome: while many genes act to the benefit of the individuals for the fulfillment of their lives, the evolution genes act to the benefit of an evolutionary development, for a slow, but steady expansion of life and biodiversity.

You see the problem, I hope. These hypothetical genes that do not necessarily directly affect the fitness of the individual are assumed to be promoted in lineages by a higher level of selection. This is not easily supported by evolutionary theory: there isn’t a mechanism given for individuals to maintain a gene that will only help its many-times-great-grandchildren. It is inferring a kind of foresight to evolution that is doesn’t have a mechanism…unless, perhaps, Arber is going to give use one. We’ll see. This talk will start in about 15 minutes, and I’ll update this post as he fills us in.

A simple history lesson: modern evolutionary biology is the convergence of work that began with Miescher (1874: nucleic acids) which led to molecular biology, Mendel (1876) which led to genetics, and Darwin (1859) that approached the problem at the level of organisms and species. The neo-Darwinian synthesis fused the genetic and Darwinian line, molecular genetics brought together genetics and biochemistry/molecular biology, and molecular evolution brings all three together—he seems to claim some kind of intellectual ownership of the last concept, which is what he calls molecular darwinism.

How do bacteria generate new variants? By transformation, conjugation, or transduction. All are mechanisms that transfer genes from an external source to the bacterium. Work in the 1940s demonstrated that DNA was the carrier of genetic information.

Arber gave a little summary of E. coli gene structure, which I suppose would be helpful to all the chemists here. He defines mutation as an alteration of the nucleotide sequence; in classical genetics, it’s defined differently, as an altered phenotype that is transmitted to progeny.

Mutations are rarely favorable; often unfavorable, and very often silent or neutral. There is no good evidence for directedness of spontaneous mutations. Mutations do not appear in response to a need.

He argues that there are three elements to evolution: evolution is driven by genetic variation (mutation), directed by natural selection, and modulated by isolation as a mechanism for speciation. There are multiple mechanisms generating genetic variation: spontaneous DNA sequence alteration, DNA rearrangement or recombination, and DNA acquisition (horizontal gene transfer).

So far, this is all very unchallenging and basic, at least for someone with any background in genetics and cell biology. After sitting through one talk that completely lost me with a failure to explain the basic terms of the work, I can’t complain, but I confess, I’m having trouble staying alert through all this.

Some genes can affect the rate of occurence of mutations — these are modulators of the frequency of genetic variation. He calls these evolution genes. He says neatral reality actively takes care of biological evolution, and that this is an expansion of the biological theory of evolution. This leads to an expansion of biological diversity, and, he argues, higher complexity.

I’m not very impressed. This is a combination of the commonplace and some odd interpretations. Of course there is variation in fidelity of replication that is influenced by genetic variation. Some of it is simply thermodynamically necessary: perfect fidelity is impossible to achieve, and greater fidelity has a metabolic cost, so some of that variation is utterly unsurprising. Some is; when we have organisms that have specializations to directly generate greater genetic variation — and sex is the first to come to my mind — we have a problem to explain. I don’t see that Arber has proposed anything to explain the real problems.

At the same time, what Arber said here does not make him a friend to intelligent design creationism, or creationism of any kind, despite the claims of some unreliable creationist sources, a claim that Arber has directly rejected.

I’d have to say it was a nice enough overview, but didn’t really propose anything novel, and definitely didn’t demonstrate anything that can’t be explained in the context of modern evolutionary theory.

Visiting village dogs

I am horribly envious. I am speaking of the Village Dog Project, some current research going on that looks very cool.

Understanding the evolution and domestication in dogs requires genetic analysis of a global and diverse panel of non-breed-affiliated village dogs. With a network of worldwide and Cornell-affiliated collaborators, we plan to gather dog samples from remote villages, establish a genetic archive containing DNA and phenotypic information from these dogs, carry out genetic analyses on these samples, and develop computational methods for analyzing this dataset. In particular, we are interested in understanding the location, timing, and demographic conditions underlying domestication; the genetic changes involved in the transition of wolf to dog; the relationship between these village dogs and the breed dogs; and the effect that historical forces have shaped village dog diversity.

That looks informative and useful, and I’ll be looking forward to the publication of the research. That’s not what’s got me envious, though: for that, you have to look at their field work. The researchers are spending the summer traveling to exotic, remote locations (admittedly, to the kinds of places rife with scavenging village dogs, but still…) to collect blood samples. They have a travel blog that will be recounting their adventures, and also explains the science a little more.

After initial domestication, dogs probably lived “breed-less” lives as human commensals (hanging around humans, not really helping or harming them but living off their trash) for many thousands of years. During this time, dog populations quickly expanded and spread across the globe. In the last few hundreds of years, several hundred dog breeds were formed from local dogs in many parts of the world; these breed dogs have entirely replaced the non-breed “indigenous” dogs in some parts of the world, notably in Western Europe and the USA. However, most dogs throughout the world still live their lives as non-breed, indigenous, commensal dogs. We refer to these dogs as “pariah” or “village” dogs. They tend to be smallish (25-40 pounds), often tan, short-haired dogs, though the type varies a bit according to the region you’re in. The important point is that these dogs have not undergone the intense genetic bottleneck associated with breed formation. Thus, while breed dogs have only a small subset of the total genetic diversity of all dogs, it is likely that village dogs have a much greater range of the total diversity. Thus, they are very useful for looking at the original domestication event. They are informative of the original genetic bottleneck that led to the formation of domestic dogs many thousands of years ago.

Hmmm. We don’t seem to have many dogs running loose around exotic, remote Morris, Minnesota, but there are a few feral cats living off the dumpsters near the grocery store.

I probably wouldn’t try to read about visiting small midwestern towns to collect cats, though.

Big love among the ostracods

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How can anyone resist an article titled “Sexual Intercourse Involving Giant Sperm in Cretaceous Ostracode”? You can’t, I tell you. It’s like a giant brain magnet, you open the journal to the index, and there’s that title, and you must read it before you can even consider continuing on to anything else.

Some organisms have evolved immensely long sperm tails — Drosophila bifurca, for instance, has sperm cells that are about 60mm long, or 20 times longer than the length of the entire adult body. The excessively long sperm tail is obviously not a structure that has evolved for better swimming; instead, it is thought to act as a tangled barrier in the female reproductive tract to prevent other males from fertilizing the female, and there is also some very interesting evidence that sperm coevolves with the female reproductive tract, so some sexual selection at the level of the gametes is going on.

At the same time, sperm morphology is extremely diverse, and seems to evolve very rapidly. Perhaps these mega-sperm are a transient fad? Not all species of Drosophila exhibit the phenomenon, and those that do vary considerably from species to species. What we’d like to know is if there are any lineages that maintain these patterns of giant sperm over long periods of evolutionary time…so what do we need to do? We need to go spelunking for sperm in fossils!

That’s what this short letter in Science is about: the authors looked at ostracodes, a class of tiny crustacea that invests heavily in reproduction. About a third of their volume is their reproductive system, with males building giant (relative to their size) sperm pumps, and females having large seminal receptacles for sperm storage. The individual sperm are also large, often longer than the body length of the adult, and are also aflagellate — no flagellar tail at all, just a long, threadlike cell body. You can tell if a female ostracod is a virgin just by looking at those seminal receptacles, since they inflate hugely with all the giant sperm tucked inside.

So, if you look at the large orange blobs, the seminal receptacles, in this 3-D scan of a fossil female ostracod (bottom right of this image), you can tell that she was inseminated before she died, and that her mate had very large sperm. Her condition was also very similar to that of modern ostracodes (bottom left).

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Partial reconstruction of E. virens (extant) and H. micropapillosa (fossil). Anterior is to the left. Orange structures indicate central tubes of Zenker organs in males or seminal receptacles in females; brown, esophagus; turquoise, mandible; purple, upper lip; pink, lower lip; green, valves; and gray scales, whole-body reconstruction. All scale bars indicate 100 µm. (A) Lateral view of male E. virens with several organs included for comparison. (B) Male H. micropapillosa in lateral view with several organs in context of whole-body reconstruction. (C and D) Ventral views of several organs including tubes of Zenker organs of male H. micropapillosa. (E) Lateral view of female E. virens with several organs included for comparison. (F) Female H. micropapillosa in lateral view with several organs in context of whole-body reconstruction, including seminal receptacles.

So, the conclusion is that boinking with giant sperm is an enduring property of at least some lineages: they’ve been going at it for a hundred million years. The authors also suggest that this kind of technique could be useful for measuring sexual selection by assessing pre-mating parental investment in fossil invertebrates.

Matzke-Karasz R, Smith RJ, Symonova R, Miller CG, Tafforeau P (2009) Sexual Intercourse Involving Giant Sperm in Cretaceous Ostracode. Science 324(5934):1535.

Miller GT, Pitnick S (2002) Sperm-Female Coevolution in Drosophila. Science 298(5596):1230-1233.

Limusaurus inextricabilis

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My previous repost was made to give the background on a recent discovery of Jurassic ceratosaur, Limusaurus inextricabilis, and what it tells us about digit evolution. Here’s Limusaurus—beautiful little beastie, isn’t it?

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Photograph (a) and line drawing (b) of IVPP V 15923. Arrows in a point to a nearly complete and fully articulated basal crocodyliform skeleton preserved next to IVPP V 15923 (scale bar, 5 cm). c, Histological section from the fibular shaft of Limusaurus inextricabilis (IVPP V 15924) under polarized light. Arrows denote growth lines used to age the specimen; HC refers to round haversian canals and EB to layers of endosteal bone. The specimen is inferred to represent a five-year-old individual and to be at a young adult ontogenetic stage, based on a combination of histological features including narrower outermost zones, dense haversian bone, extensive and multiple endosteal bone depositional events and absence of an external fundamental system. d, Close up of the gastroliths (scale bar, 2 cm). Abbreviations: cav, caudal vertebrae; cv, cervical vertebrae; dr, dorsal ribs; ga, gastroliths; lf, left femur; lfl, left forelimb; li, left ilium; lis, left ischium; lp, left pes; lpu, left pubis; lsc, left scapulocoracoid; lt, left tibiotarsus; md, mandible; rfl, right forelimb; ri, right ilium; rp, right pes; sk, skull.

What’s especially interesting about it is that it catches an evolutionary hypothesis in the act, and is another genuine transitional fossil. The hypothesis is about how fingers were modified over time to produce the patterns we see in dinosaurs and birds.

Birds have greatly reduced digits, but when we examine them embryologically, we can see precisely what has happened: they’ve lost the outermost digits, the thumb (I) and pinky (V), and retain the forefinger, middle finger, and ring finger (II-IV), which have been reduced and fused together. This is called Bilateral Digit Reduction, BDR, because they’ve lost digits from the medial and lateral sides, leaving the middle set intact.

Dinosaurs, when examined anatomically, seem to have a different pattern: they have a thumb (I), forefinger (II) and middle finger (III), and have lost the lateral two digits, the ring and pinky finger (IV-V). This arrangement has been advanced as evidence that birds did not evolve from dinosaurs, since they have different bones in their hands, and getting from one pattern to the other is complicated and difficult and very unlikely.

The alternative hypothesis is that there is no conflict, and that dinosaurs actually underwent BDR and their digits are II-III-IV…but that what has also happened is a frame shift in digit identities. So dinosaurs actually have three digits, which are the index, middle, and ring finger, but they’ve undergone a subtle shift in morphology so that their forefinger develops as a thumb, and so forth.

Now we could resolve all this easily if only the physicists would get to work and build that time machine so we could go back to the Mesozoic and study dinosaur embryology, but they’re too busy playing with strings and quanta and dark matter to do the important experiments, so we’ve got to settle for another plan: find intermediate forms in the fossil record. That’s where Limusaurus steps in.

Limusaurus has a thumb, a tiny vestigial nubbin, and has lost its pinky completely. This is a (I)-II-III-IV pattern, and is evidence of bilateral digit reduction in a basal ceratosaur. In addition, the forefinger has become very robust, and while still distinctly a digit II, has been caught in the early stages of a transformation into a saurian first digit. It’s evidence in support of the dinosaurian II-III-IV hypothesis and the frameshift in digit identity! It’s almost as good as having a time machine.

Want to learn more? Carl Zimmer has a summary of the digit changes, while one of the authors of the paper, David Hone, also discusses the digits (the story is a little more complicated than I’ve laid out), and also has more on the rest of the animal—it’s a herbivorous ceratosaur, which is interesting in itself.

Xu X, Clark JM, Mo J, Choiniere J, Forster CA, Erickson GM, Hone DWE, Sullivan C, Eberth DA, Nesbitt S, Zhao Q, Hernandez R, Jia C-k, Han F-l, Guo Y (2009) A Jurassic ceratosaur from China helps clarify avian digit homologies. Nature 459(18):940-944.

Digit numbering and limb development

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Answers in Genesis has evolutionary biology on the run now. In an article from 2002, Ostrich eggs break dino-to-bird theory, they explain that development shows that evolution is all wrong, since developmental pathways in different animals are completely different, and can’t possibly be the result of gradual transformations.

The first piece of evidence against evolution is the old avian digit problem. Birds couldn’t have evolved from dinosaurs, because they have the wrong finger order!

The research conclusively showed that only digits two, three and four (corresponding to our index, middle and ring fingers) develop in birds. This contrasts with dinosaur hands that developed from digits one, two and three. Feduccia pointed out:

‘This creates a new problem for those who insist that dinosaurs were ancestors of modern birds. How can a bird hand, for example, with digits two, three and four evolve from a dinosaur hand that has only digits one, two and three? That would be almost impossible.’

The second problem is that frogs and people develop hands in completely different ways, ways that are even more different than the order of the digits.

This is not the only example where superficially homologous structures actually develop in totally different ways. One of the most commonly argued proofs of evolution is the pentadactyl limb pattern, i.e. the five-digit limbs found in amphibians, reptiles, birds and mammals. However, they develop in a completely different manner in amphibians and the other groups. To illustrate, the human embryo develops a thickening on the limb tip called the AER (apical ectodermal ridge), then programmed cell death (apoptosis) divides the AER into five regions that then develop into digits (fingers and toes). By contrast, in frogs, the digits grow outwards from buds as cells divide (see diagram, right).

Dang. I might as well hang it up right now. There is no possible way around these intractable differences. Take me, Jesus, I have seen the ligh…oh, wait a minute. That isn’t right. It looks to me like Jonathan Sarfati is just hopelessly confused on the first problem (I can’t really blame him, though—it is a complicated issue that has been the subject of scientific arguments for two centuries), and is simply completely wrong on the second (and that one I do blame him for. Tsk, tsk.)

So first, let’s tackle the tricky problem, digit identity in evolution. Extend your right hand out in front of you, palm down. Your thumb should be sticking out towards the left, and by convention, that’s Digit I. Counting from left to right, your index finger is Digit II, middle finger is Digit III, ring finger is digit IV, and your pinky is Digit V. We have the primitive pentadactyl (five-fingered) hand, so figuring out who is who is fairly easy. The difficulties arise in species that have reduced the number of their digits—when they extend their three-fingered hand, we have to figure out which digits are missing before we assign numbers to the remaining fingers.

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One way is by looking at the adult anatomy. Looking at your hand, you probably notice that your thumb is quantitatively different from the other fingers: it only has two joints, instead of three. This is common, that Digit I has fewer phalanges, or segments, than the others, and this is the kind of property that allows anatomists to figure out whether Digit I is present or not. To the right, for instance, is the hand of the raptor Deinonychus (the left hand, sorry to confuse you) with its digit numbering, from DI to DII to DIII, an assignment that was made on the basis of the anatomy. You can see that the ‘thumb’, DI, has fewer phalanges than the others.

You can try to do the same thing with the digits of birds, but it’s harder. Avian digits are reduced and fused into that pointy thing you find at the end of a chicken wing, and it takes an expert to sort out what bones are blended together in there. Anatomists tried, though, and initially and long ago (Meckel came to this conclusion in 1825), decided the bones were numbered DI, DII, and DIII, just like the ones we see in three-fingered dinosaurs…so no dilemma, right?

Wrong. There’s another way of looking at the identity of these bones, and that is by watching them develop. What some birds do is start to make five fingers—they form four or five little nubbins of cartilage, called condensations, and then shut down the development of some of them. What another old time anatomist noticed (Owen, in 1836) was that one of the condensations that got thrown away was the first one—which means that the bird digits are actually derived from Condensation II, Condensation III, and Condensation IV. The data is even stronger in this day of molecular markers: bird digits arise embryonically from the second, third, and fourth cartilaginous condensations.

Now this is a complication for evolution. We have three-fingered dinosaurs, and three-fingered birds, but it looks like they aren’t the same fingers. Bird ancestors would have had to resurrect their discarded Digit IV, then eliminate Digit I, all before fusing the whole assemblage into a bony gemisch anyway. It’s not parsimonious at all. (Of course, it’s even less parsimonious to throw away more than a century of data supporting evolution, as Jonathan Sarfati would like us to do.)

There is another, better explanation that Wagner and Gauthier have made that clarifies everything to me, at least.

Note that anatomists initially assigned digit numbers I, II, and III to bird limbs on the basis of their form, but later had to revise that to II, III, and IV on the basis of embryology. Dinosaur digits are assigned numbers I, II, and III on the basis of their adult form (which is admittedly much less ambiguous than adult bird digits!)…but what about their embryology? If we had access to information about expression of molecular markers and early condensations in the dinosaur limb, would we have to revise their digit numbers?

We don’t have fetal dinosaur hands to experiment on, but our growing knowledge about how limbs develop suggests that that might just be the case. This diagram illustrates the sequence of development in the hand of an alligator (a) and an ostrich (b).

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What you’re seeing is the pattern of early condensations in the limb. We tetrapods have a standard pattern: the very first digit to develop as an extension of the limb is Condensation IV, your ring finger, forming what is called the metapterygial axis. Next, the pinky (CV) forms as a little afterthought along one side of the metapterygial axis, and a new axis of condensation hooks over the palm, with the middle finger (CIII) forming next, then the index finger (CII), and lastly the thumb (CI). From a developmental standpoint, the easiest digits to lose are that odd little CV, and the thumb, CI. CI is the very last to form, so you can stop its formation by changing the timing of development in a process called heterochrony, and just halting the development of that axis hooking across the palm early. You can see that in the ostrich, which just stops making fingers after CII, so CI doesn’t form. The hardest digit to lose is CIV, because it’s kind of the lynchpin of the process—all the other digits follow after IV, so it would be difficult to suppress IV without losing all of the other digits. (Who would have thought that the ring finger was so central and important to hand development?)

The numbering of the dinosaur limb is a problem then…it suggests that they don’t have a Digit IV, which looks like a complicated and unlikely thing to do. But they do have a ‘thumb’, or Digit I. How do we resolve this seeming contradiction?

The answer is that there are two developmental processes going on. The first is the formation of the condensations, CI through CV. This process partitions the terminal region into an appropriate number of chunks, but doesn’t actually specify the identity of the digits. The second process takes each of those chunks and assigns a digit identity to them, and this process is to some degree independent of the first and uses a different set of signals. Wolpert et al. have noticed this in modern embryos:

For example, digit identity is specified at a surprisingly late stage in limb development, and identity remains labile even when the digit primordia have formed. It now appears that digit identity is specified by the interdigital mesenchyme and requires BMP signaling. There is also evidence that mechanisms other than a diffusible morphogen operate to lay down the initial pattern of cartilage, which is then modified by a signal from the polarizing region…

What Wagner and Gauthier propose is that three-fingered dinosaurs accomplished that reduction by shedding the two easiest digits to lose, CI and CV, so that if we enumerated them by the same criteria we use in modern birds, they possess Condensations II, III, and IV. What also happened, though, was that there was a frame shift in the mechanism that assigns digit identity, so CII develops as DI, CIII as DII, and CIV as DIII.

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The timing of this shift can be mapped onto saurian phylogeny, and it all makes sense and is consistent. And it doesn’t involve taking seriously the silly sequence of the biblical account, which has birds appearing before all of the land animals.

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What about Sarfati’s second line of evidence against evolution, that frogs and humans use completely different mechanisms to build their limbs?

Simple answer: it’s all bullshit. It’s a blatant denial of basic information you’ll find in any developmental biology textbook.

We’ve got a pretty good handle on the outline of limb development in multiple tetrapod lineages now, and they all use the same tools. Contrary to Sarfati’s implication, they all have apical ectodermal ridges (with some rare exceptions in a few highly derived, direct-developing frogs) and zones of polarizing activity, they all use the same set of molecules, including FGF-4 and FGF-8 and the same Hox genes and retinoic acid and BMPs. If there’s one thing we know, it’s that limb development is dazzlingly well conserved.

It is true that frogs have less apoptosis between their digits than we do, but that’s because they have webbed feet. Suppress apoptosis in other vertebrates, and you get the same phenomenon, retention of membranous webs between the digits. There is a simple functional reason why they differ in this regard, and it takes advantage of a common property of limb development in all tetrapods.

I can sympathize with Sarfati having difficulty sorting out digit numbering—it’s subtle and sneaky and has puzzled smarter people than either of us. But the uninformed rejection of some of the most straightforward, clearest examples of common mechanisms in development, something that you can find described in the most introductory biology textbook…that’s hard to forgive.

Wagner GP, Gauthier JA (1999) 1,2,3=2,3,4: A solution to the problem of the homology of the digits in the avian hand. Proc. Natl. Acad. Sci. 96:5111-5116.

Wolpert L, Beddington R, Jessel T, Lawrence P, Meyerowitz E, Smith J (2002) Principles of Development. Oxford University Press.

Stephen Jay Gould and the Politics of Evolution

When I was growing up, I had no introduction to evolutionary theory. Sure, I assumed it was true, and I went through the usual long phase of dinosaur fandom, but I was never taught anything at all about evolution throughout my grade school education, and what little I did know was largely stamp-collecting. That all changed, though, when I went off to college.

I can’t credit the schools I went to, unfortunately: most of my undergraduate education (with a few wonderful exceptions) was the usual mega-survey course, where the instructor stuck a funnel in our heads and poured in facts for a term — so more stamp-collecting. What happened to me, though, was that I was struck by two thunderbolts at almost the same time. The hot science book that was published during my freshman year was E.O. Wilson’s Sociobiology, and I bought it and devoured it and thoroughly enjoyed it. It was more buckets of facts, but in this case, these facts were deployed to illuminate an overarching idea about how the world works…and I found it wonderful.

The second thunderbolt was Stephen Jay Gould. He was doing the same thing, promoting ideas powerfully with evidence and rhetoric, and he was far easier to read than Wilson, and communicated even more clearly. It was also wonderful.

Of course, if you know anything about the intellectual landscape of the 1970s, you know that I had acquired as two scientific god-parents two warring camps who were hellbent against one another in a period of angry evolutionary ferment. I am the product of a broken home! It was especially tragic, because in my naiveté, I thought most of the conflict was a waste, that each side had an important perspective, and that the right answer was an appreciation of the power of selection and an understanding of the other modes of change operating over history.

I’ve long been interested in the battle royale that went on in that period — it’s like a child’s morbid dwelling on the scab of an ugly parental divorce — and in particular with that central figure, Steve Gould. Last week I was sent a copy of a book by David F. Prindle, Stephen Jay Gould and the Politics of Evolution(amzn/b&n/abe/pwll), so of course I had to read it.

[Read more…]

Life Ascending

I admit, I was initially put off by the mere title of Nick Lane’s new book, Life Ascending: The Ten Great Inventions of Evolution(amzn/b&n/abe/pwll). I’m one of those many biologists who is adamant about the absence of direction in evolutionary history, and ascending just sounds too much like life climbing the rungs of the ladder of life, so I picked it up in a somewhat prejudicial mood.

Have no fear, though, I was won over. Right at the beginning, he admits that it is a subjective list; his criteria for including the ten chosen evolutionary innovations are that it had to revolutionize the living world, that it was important to a significant subset of life today, that it was a product of biological (not cultural) evolution, and that it had to be iconic — it had to symbolic and arrestingly interesting to human beings. That’s fair enough; one could write a book on just the evolved properties of prokaryotes, but yeah, operons and chemical sensing and secretion and motility are of vast importance, but they’re only going to be iconic to a rather restricted set of readers. And since my own personal interests run more to metazoan innovations, I’m not going to complain about a book that gives my hobby horses a more substantial run.

Even better, though, what enlivens the book is the biochemist’s perspective: Lane isn’t so much interested in the superficial matters of morphology, but in the emergence of new properties in the molecular machinery of the cell, and how it affects the world around us. Somehow, it always thrills me when we drill down right to the interactions of molecules to explain how biology works.

So here are the ten evolutionary inventions Lane describes.

  1. Origins of life: Where and how did life arise? A review of some of the models for abiogenesis.

  2. DNA: What conditions would allow for the synthesis of nucleotides? Where did the genetic code come from?

  3. Photosynthesis: The photosynthetic pathway is a combination of two very different functional pathways — what does this tell us about their evolution?

  4. Complex cells: How did cells become more complex? A chapter on horizontal transfer and endosymbiosis — borrowing and stealing and kidnaping by ancient cells.

  5. Sex: Why do we have sexual reproduction? A question that focuses on the cytological and genetic machinery.

  6. Movement: How do organisms get around? Cytoskeletons and motor proteins, and where they came from.

  7. Sight: How did vision evolve? A fairly wide-ranging discussion of opsins and crystallins and Hox genes and the weird glow of black smokers.

  8. Hot blood: Another chapter with a little taste of everything: respiration, metabolism, insulation, and how a key feature of our physiology affects everything.

  9. Consciousness: Where did our awareness come from? You won’t be surprised to learn that Lane is a materialist — the answer lies in the wiring of the brain.

  10. Death: Why do all organisms die, and why do we even have genes that contribute to senescence and death?

So the topics aren’t that biased: only three exclusive to multicellular animals, and six that are about eukaryotes almost exclusively — and even in those our prokaryotic heritage is discussed. And really, when you’re talking about genes and biochemistry, you can’t get away from the fact that you are dealing with genuinely universal processes.

The book is also a fun read, deep enough to give you some substance, yet clearly written with the general public in mind. If you aren’t a biologist or biochemist, don’t shy away — you will be able to read this book, and you will learn a lot from it. When I was reading it, I was thinking this would be a really enjoyable text to build a freshman seminar course around. The chapters are readable and each one addresses an interesting topic in biology, bringing up both current research and pending questions, and it’s meaty enough to spark some good discussions.

The Darwinius hype is beginning to burn

Oh, man. I’m willing to keep saying that Darwinius masillae was an important discovery, but the PR machine is making it hard to do so without cringing. Carl Zimmer has the History Channel ad for their program on it.

Oh. My. Dog. “The most important find in 47 million years”? “A global event: this changes everything”? This is not helping. It is inflating a good discovery beyond all reason, and when the public hears the creationists declare that it’s one fossil of a monkey-like creature, and they’re right, it’s going to damage the credibility of science.

Seed Media has a bit of a scoop: they’ve got an interview with a PLoS One editor, a History Channel executive, and Jørn Hurum, the scientist behind all the promotion. It’s appalling. They’re bragging about how a “production company got in on the ground floor”. Shall we anticipate the brave new world when paleontologists have to beg for McDonald’s happy meal tie-ins to get funding?

And I’m sorry, but Hurum comes off as a complete ass.

But in order for the story and the film to pack the most punch–and to reach the public–Hurum and the production company knew they had to keep it secret. Hurum seemed particularly preoccupied with the way the blogosphere is able to dissipate a story, mentioning an Arctic excavation he worked on several years ago that was picked-up by a blog in Japan within three hours of posting his pictures on the internet. “I’ve seen Chinese specimens of dinosaurs and so on destroyed like this with lots of bad early descriptions [from] blogging,” he says. Hurum wanted to subvert the system and take his story straight to the masses in a way that would appeal to the average person, especially kids: “If we really want kids to get involved with exciting scientific findings, no matter what kind of field, we really need to start [thinking] about reaching people other than [our] fellow scientists. This paper could have been drowned in other papers and would have been read by 15 people around the world.”

That’s revealing. The fossils would not be destroyed by someone blogging about it prematurely; what would be destroyed would be Hurum’s chance to play P.T. Barnum and make himself the center of the show. Apparently, those are the same thing to him. And he thinks it a problem that his paper would be “drowned” in a large volume of papers on the fossil? Jebus. This is what we want in science, lots of open discussion.

And if he thinks a few bloggers chatting prematurely about a find would ruin it for him, he should take a look at the damage this commercial hype and bogus hysteria about the specimen is doing. Misperception is rife, and the exaggeration is diminishing the importance of other finds.

It gets worse. Here’s the trailer for the show.

Darwinius masillae

This is an important new fossil, a 47 million year old primate nicknamed Ida. She’s a female juvenile who was probably caught in a toxic gas cloud from a volcanic lake, and her body settled into the soft sediments of the lake, where she was buried undisturbed.

i-7c1a746bdef84283eca6d89008d65a2c-darwinius.jpeg

What’s so cool about it?

Age. It’s 47 million years old. That’s interestingly old…it puts us deep into the primate family tree.

Preservation. This is an awesome fossil: it’s almost perfectly complete, with all the bones in place, preserved in its death posture. There is a halo of darkly stained material around it; this is a remnant of the flesh and fur that rotted in place, and allows us to see a rough outline of the body and make estimates of muscle size. Furthermore, the guts and stomach contents are preserved. Ida’s last meal was fruit and leaves, in case you wanted to know.

Life stage. Ida is a young juvenile, estimate to be right on the transition from requiring parental care to independent living. That means she has a mix of baby teeth and adult teeth — she’s a two-fer, giving us information about both.

Phylogeny. A cladistic analysis of the fossil revealed another interesting point. There are two broad groups of primates: the strepsirrhines, which includes the lemurs and lorises, and the haplorhines, which includes monkeys and apes…and us, of course. Ida’s anatomy places her in the haplorhines with us, but at the same time she’s primitive. This is an animal caught shortly after a major branch point in primate evolutionary history.

She’s beautiful and interesting and important, but I do have to take exception to the surprisingly frantic news coverage I’m seeing. She’s being called the “missing link in human evolution”, which is annoying. The whole “missing link” category is a bit of journalistic trumpery: almost every fossil could be called a link, and it feeds the simplistic notion that there could be a single definitive bridge between ancient and modern species. There isn’t: there is the slow shift of whole populations which can branch and diverge. It’s also inappropriate to tag this discovery to human evolution. She’s 47 million years old; she’s also a missing link in chimp evolution, or rhesus monkey evolution. She’s got wider significance than just her relationship to our narrow line.

People have been using remarkable hyperbole when discussing Darwinius. She’s going to affect paleontology “like an asteroid falling down to earth”; she’s the “Mona Lisa” of fossils; she answers all of Darwin’s questions about transitional fossils; she’s “something that the world has never seen before”; “a revolutionary scientific find that will change everything”. Well, OK. I was impressed enough that I immediately made Ida my desktop wallpaper, so I’m not trying to diminish the importance of the find. But let’s not forget that there are lots of transitional forms found all the time. She’s unique as a representative of a new species, but she isn’t at all unique as a representative of the complex history of life on earth.

When Laelaps says, “I have the feeling that this fossil, while spectacular, is being oversold,” I think he’s being spectacularly understated. Wilkins also knocks down the whole “missing link” label. The hype is bad news, not because Ida is unimportant, but because it detracts from the larger body of the fossil record — I doubt that the media will be able to muster as much excitement from whatever new fossil gets published in Nature or Science next week, no matter how significant it may be.

Go ahead and be excited by this find, I know I am. Just remember to be excited tomorrow and the day after and the day after that, because this is perfectly normal science, and it will go on.

Laelaps has some serious reservations about the analysis — the authors may not have done as solid a cladistic analysis as they should, and its position in the family tree may not be as clear as it has been made out to be.

Franzen JL, Gingerich PD, Habersetzer J, Hurum JH, von Koenigswald W, Smith BH (2009) Complete Primate Skeleton from the Middle Eocene of Messel in Germany: Morphology and Paleobiology. PLoS ONE 4(5): e5723. doi:10.1371/journal.pone.0005723.