Category Archives: Evolution

Odd Ancient South African Human “Ancestor” Is Young

You’ve heard of Homo naledi, the strange “human ancestor” (really, a cousin) found a while back in South Africa. There were many skeletal remains in a cave, in the kind of shape you’d expect if they had crawled into the cave and died there, not much disturbed. They look enough like other members of our genus, Homo, to be called Homo, but if we assume that increase in brain size is the hallmark of our species, they seem to be an early grade.

Over the last ten years, we have come to appreciate the fact that our genus may have differentiated into multiple species that did not have a large brain after all, and Homo naledi is one of the reasons we think that. And, just as the “Hobbit” of Indonesia (flores) has recently been re-dated to be a bit older than people thought, Homo naledi is now dated to be a bit later than people may have thought.

Schematic of the Rising Star cave system. Picture: Marina Elliott/Wits University
Schematic of the Rising Star cave system. Picture: Marina Elliott/Wits University

For me, this is an “I told you so” moment. First, I understand, as do most of my colleagues (but not all), that a regular change over time in a trait in one lineage does not magically cause a parallel change in another lineage (though the co-evolution of a single trait in a similar direction along parallel lineages is certainly possible.) So, there was no reason to require that all later period hominins be like all other later period hominins in those later-emerging traits. Also, since no one has ever adequately explained what the heck our big brains are for, I don’t subscribe to the presumption that all evolution will always evolve the big brain just because our own big brains insist that they are really cool. So, a late small brained hominin in our genus but existing long after the split with us is actually somewhat expected.

Then, there is my sense of age based on the things I’ve seen in the area’s caves.

Geologist Dr Hannah Hilbert-Wolf studying difficult to reach flowstones in a small side passage in the Dinaledi Chamber. Picture: Wits University
Geologist Dr Hannah Hilbert-Wolf studying difficult to reach flowstones in a small side passage in the Dinaledi Chamber. Picture: Wits University
Some time ago, Lee Berger took me around some of the cave he had poking around in (long before this hominin was discovered) and showed me several animals that had crawled into the caves, probably looking for water during an arid period (this is already a fairly dry area). They had died in place and become mummified. In other caves, I’ve seen similar things, like a troop of baboons that somehow got into a cave with no known entrance and died, as well as bats that died in situ and mummified against the rock they died on.

On another occasion, Ron Clarke, another anthropologist working in the area, showed me the famous “Little Foot” which is a fossil that represents that mummy-to-stone transition, while mostly sitting on the surface of the floor(ish) of a very deep and inaccessible cave. Meanwhile, I’d been working with my friend and colleague Francis Thackeray, and he demonstrated to me how many of the diverse bits and pieces we find of australopithecines are actually probably part of individual skeletons, but discovered and excavated at very different times. These are creatures that got in the cave somehow, and were only somewhat disarticulated after death.

The whole “crawled into the cave” mode of entering the fossil record, and its presumed variant, “fell to one’s death in the cave” is different from the previously presumed process of “leopard kills you, drags you onto a tree branch hanging over a cave entrance and your bones fall into the cave” means of becoming a fossil. It is of course possible, even likely, that both of these processes occurred at various times and places.

Homo naledi, according to Lee Berger, may represent a third way of getting into one of these famous caves. He suggests that the hominins themselves dragged the dead bodies of each other into the caves, as a form of treatment of the dead. That is a spectacularly controversial claim, of course, since with a small brain how can you have a god, and without a god, how can you have ritual or burial? Of course, elephants treat their dead specially sometimes, and their brain is right where it is supposed to be on the famous mouse-to-elephant curve of brain size. And, I’d bet a dozen donuts that even though Homo naledi has a small brain compared to, say, yours or mine, it is probably a good measure above that comparative curve. It was a primate, after all.

left to right: Marina Elliott, Maropeng Ramalepa and Mpume Hlophe. Picture: Wits University/Wayne Crichton
left to right: Marina Elliott, Maropeng Ramalepa and Mpume Hlophe. Picture: Wits University/Wayne Crichton
But I digress in several directions, lets get to the point. The site of Rising Star Cave, South Africa, where Homo naledi was discovered, is now dated. These things are always subject to revision and updating, but for now, it seems like we have a pretty good estimate of the age of this incredible site.

The site dates to some time between about 414,000 years ago and 236,000 years ago. That means that the site overlaps with the approximate age of the earliest, probably, modern humans. Here are the details from the abstract of the paper, published this morning:

New ages for flowstone, sediments and fossil bones from the Dinaledi Chamber are presented. We combined optically stimulated luminescence dating of sediments with U-Th and palaeomagnetic analyses of flowstones to establish that all sediments containing Homo naledi fossils can be allocated to a single stratigraphic entity (sub-unit 3b), interpreted to be deposited between 236 ka and 414 ka. This result has been confirmed independently by dating three H. naledi teeth with combined U-series and electron spin resonance (US-ESR) dating. Two dating scenarios for the fossils were tested by varying the assumed levels of 222Rn loss in the encasing sediments: a maximum age scenario provides an average age for the two least altered fossil teeth of 253 +82/–70 ka, whilst a minimum age scenario yields an average age of 200 +70/–61 ka. We consider the maximum age scenario to more closely reflect conditions in the cave, and therefore, the true age of the fossils. By combining the US-ESR maximum age estimate obtained from the teeth, with the U-Th age for the oldest flowstone overlying Homo naledi fossils, we have constrained the depositional age of Homo naledi to a period between 236 ka and 335 ka. These age results demonstrate that a morphologically primitive hominin, Homo naledi, survived into the later parts of the Pleistocene in Africa, and indicate a much younger age for the Homo naledi fossils than have previously been hypothesized based on their morphology.

"Neo" skull of Homo naledi from the Lesedi Chamber. Photo credit: Wits University/John Hawks
“Neo” skull of Homo naledi from the Lesedi Chamber. Photo credit: Wits University/John Hawks
In addition to this date, it is reported that there are more fossil remains, from another cave called Lesedi Chamber. Here is the paper for that, which reports “… Further exploration led to the discovery of hominin material, now comprising 131 hominin specimens, within a second chamber, the Lesedi Chamber. The Lesedi Chamber is far separated from the Dinaledi Chamber within the Rising Star cave system, and represents a second depositional context for hominin remains. In each of three collection areas within the Lesedi Chamber, diagnostic skeletal material allows a clear attribution to H. naledi. Both adult and immature material is present. The hominin remains represent at least three individuals based upon duplication of elements, but more individuals are likely present based upon the spatial context. The most significant specimen is the near-complete cranium of a large individual, designated LES1, with an endocranial volume of approximately 610 ml and associated postcranial remains. The Lesedi Chamber skeletal sample extends our knowledge of the morphology and variation of H. naledi, and evidence of H. naledi from both recovery localities shows a consistent pattern of differentiation from other hominin species.”

Since both articles are OpenAccess, you can see them for yourself. Kudos to the authors for publishing in an OpenAccess journal.

And now, back to my original digression. One gets a sense of how landscapes and land forms develop, and while this can be misleading, it is not entirely absurd to postulate rough comparative ages for things you can see based on other things you’ve seen. I had assumed from the way they were described originally that the Rising Star hominins would not be millions of years old. Even though Bigfoot (found by Clarke) was millions of years old and essentially on the surface (of a deeply buried unfilled chamber) I guessed that over a million-year time scale, the Rising Star material would either become diagenetically inviable as fossils or buried in sediment, or both. But over hundreds of thousands of years? That was plausible to me. In fact, I figured the remains to possibly have been even younger, and if a date half the age as suggested was calculated, I would not have been surprised.

The evolution of our thinking about human evolution went through a period when we threw out all of our old conceptions about a gradual ape to human process, replacing that with a linear evolutionary pattern with things happening in what was then a surprising order, with many human traits emerging one at a time long before brains got big. There was some diversity observed then, but the next phase of our thinking involved understanding a dramatic diverstiy of pre Homo (the genus) life forms followed by the essential erasure of variation with the rise of Homo erectus and the like. Over the last decade and a half, we are now realizing that while the later members of our genus probably did cause, or at least, were associated with, a general decrease in that early diversity, later diversity arose anyway, and there were more different kinds of hominids, very different in some cases, late into our history. Word on the street is that we can expect to learn about even more diversity in coming years.


Paul HGM Dirks, Eric M Roberts, Hannah Hilbert-Wolf, Jan D Kramers, John Hawks, Anthony Dosseto, Mathieu Duval, Marina Elliott, Mary Evans, Rainer Grün, John Hellstrom, Andy IR Herries, Renaud Joannes-Boyau, Tebogo V Makhubela, Christa J Placzek, Jessie Robbins, Carl Spandler, Jelle Wiersma, Jon Woodhead, Lee R Berger. 2017. The age of Homo naledi and associated sediments in the Rising Star Cave, South Africa. May 2017. eLife.

Related books:

Almost Human: The Astonishing Tale of Homo naledi and the Discovery That Changed Our Human Story

Field Guide to the Cradle of Humankind: Sterkfontein, Swartkrans, Kromdraai & Environs World Heritage Site

From Apes to Angels: Essays in Anthropology in Honor of Phillip V. Tobias

Earliest, or nearly earliest, fossils found in Quebec?

The earliest life must have been something like a small single celled organism, like a bacterium. Or at least, the earliest life that we can usefully conceive of, and potentially connect with living life. It has been suggested that life could have initially evolved at the site of submarine hydrothermal vents, which is a place these days teeming with life. So, it make sense to look for fossils of these early life forms in rocks formed at hydrothermal vents, but a long time ago.

The Nuvvuagittuq belt in Quebec is a geological formation that includes such rock.

There are two basic ways to identify a tiny bacteria like life form. Well, sort of three. Method 1 is to find a physical structure that looks like the life form. So, little bacteria shaped do-dads might be bacteria fossils. Method 1a would be to find that, method 1b would be to find something slightly less direct, such as stramotlites, which is a kind of rock formed from the accumulation of bacteria byproducts. Method 2 is to look at the isotopes of key elements, usually carbon. There are a lot of ways for carbon to get mixed up in a rock. But, the non-life connected sequence of events that put carbon in a rock would sample the ambient carbon in a characteristic way. Since carbon comes in more than one stable isotope, the stable isotope ratio of the carbon in the abiogenic rock would reflect this pattern. But living systems tend to use carbon in a different way. The carbon atoms that get used by the tiny molecular processes involved in assembling molecules are biased in which carbon isotope they end up using. This results in a carbon isotope profile different than the expected ambient one, and suggests life.

Today in Nature, a paper by Matthew S. Dodd, Dominic Papineau, Tor Grenne, John F. Slack, Martin Rittner, Franco Pirajno, Jonathan O’Neil, and Crispin T. S. Little entitled “Evidence for early life in Earth’s oldest hydrothermal vent precipitates” (Nature 543, 60-64) reports, from the abstract:

… we describe putative fossilized microorganisms that are at least 3,770 million and possibly 4,280 million years old in ferruginous sedimentary rocks, interpreted as seafloor-hydrothermal vent-related precipitates, from the Nuvvuagittuq belt in Quebec, Canada. These structures occur as micrometre-scale haematite tubes and filaments with morphologies and mineral assemblages similar to those of filamentous microorganisms from modern hydrothermal vent precipitates and analogous microfossils in younger rocks. The Nuvvuagittuq rocks contain isotopically light carbon in carbonate and carbonaceous material, which occurs as graphitic inclusions in diagenetic carbonate rosettes, apatite blades intergrown among carbonate rosettes and magnetite–haematite granules, and is associated with carbonate in direct contact with the putative microfossils. Collectively, these observations are consistent with an oxidized biomass and provide evidence for biological activity in submarine-hydrothermal environments more than 3,770 million years ago.

I used to work down the hall from a guy who was involved in the search for early life. I won’t mention names, but at the time, I remember the fighting among scientists about whether or not this or that piece of evidence was legit was pretty intense. I think things have calmed down a bit. Back then, the battle was between Australia and Greenland. These days, apparently, Canada is in the act.

At present, the oldest evidence of life that is widely accepted is probably close to about 3.0 mya, with several older sites in contention. The newest find, as noted, dates to between 3.77 and 4.28 billion, and I understand the dates are somewhat controversial. If this site ends up as representing early life, it may well be the earliest, assuming the date is anywhere in this range. There are other cases that are close to 3.8 billion but the current study’s argument may be stronger. Over the last few years, the very nature of the study of early life on earth has gained a significant amount of perspective and methodological philosophy which I think will allow future work to be considered more sensibly. By this, I mean, that rather than asserting that this or that evidence is certainly indicative of early life vs. not conclusive (or not evidence of life) we will start seeing a more unified characterization of early environments and conditions, along side a better set of models for how life could originate. In that context we may never have an “earliest life” fossil, but we may have a much better story to tell about how early life could start.

I’ll add this: Consider the number of scientists working on a problem like aging in muscles, or how to attack a certain kind of cancer. Tens of thousands. Now, consider the number of scientists dedicated to working on the origin of life. Not many. Given the magnitude and difficulty of the problem — in the field, in the lab, and in the theories — there is no wonder it is taking science many decades to nail this problem down.

And, no, the origin of life is NOT different from evolution, no matter what the creationists tell you.

See: The Story Of Life in 25 Fossils by Don Prothero: Review

Discovering the Mammoth: A Tale of Giants, Unicorns, Ivory … by John McKay

Large hairy elephants got me into paleoanthropology, eventually.

Cohoes Mastodon Exhibit in old New York State Museum, Albany, NY.
Cohoes Mastodon Exhibit in old New York State Museum, Albany, NY.
I had a strong interest in science, and it was nurtured and expanded by my frequent visits to the New York State Museum, and there was never a doubt in anyone’s mind, anywhere, that the coolest exhibit at that museum was the Cohoes Mastodon exhibit. Barbarians eventually came along and tore that exhibit down, along with all the other fantastic and traditional museum displays, when they made the new, slick, produced for consumption and not intense engagement with materials knowledge building museum.

My friend John McKay also got into paleo studies as a young child because of a hairy elephant, but in his case, it was diminutive and green, unlike the large hairy Cohoes elephant. But John persevered in the large elephant area, while I went in somewhat different directions (though I did get to help dig up an extinct four tusker in Africa once). Eventually, John became the Go To Guy in all matters Mammoth and related things. John is an historian, so his focus has been the emerging understanding of the past (and present) as western (and other) civilization(s) repeatedly encountered and grappled with the remains of ancient and unbelievable beasts.

The reason I mention any of this at all is because John wrote a book, Discovering the Mammoth: A Tale of Giants, Unicorns, Ivory, and the Birth of a New Science, that is now available for pre-order, and that you must read.

I’ve not seen the book yet, but I’ve read some of the stuff that is going into it. Think Stephen Jay Gould meets Don Prothero. Rich, engagingly written, context-rich, carefully done description and analyses of the afore mentioned process.

This book promises to be an interesting and important, and very readable, exploration of the development of natural history and modern science. I know John, this is what I expect of him, and this is what I’m confident he is going to give us.

The book will be available in hardcover or kindle. Of course, I’ll write a review as soon as I can. The book is slated for publication in June 2017.

Prehistoric Mammals by Don Prothero: Review of excellent new book

The Princeton Field Guide to Prehistoric Mammals ,by Donald R. Prothero, is the first extinct animal book that you, dear reader, are going to give to someone for the holidays.

screen-shot-2016-11-15-at-11-31-25-amThis book is an interesting idea. Never mind the field guide part for a moment. This isn’t really set up like a field guide, though it is produced by the excellent producers of excellent field guides at Princeton. But think about the core idea here. Take every group of mammal, typically at the level of Order (Mammal is class, there are more than two dozen living orders with about 5,000 species) and ask for each one, “what does the fossil record look like.” In some cases, a very few living species are related to a huge diversity of extinct ones. In some cases, a highly diverse living fauna is related to a much smaller number of extinct ones. And each of these different relationships between the present and the past is a different and interesting evolutionary story.

If you looked only at the living mammals, you would miss a lot because there has been so much change in the past.

The giant sloths may be extinct, but Don Prothero himself is a giant of our age among fossil experts. His primary area of expertise includes the fossil mammals (especially but not at all limited to rhinos). I believe it is true that he has personally handled more fossil mammalian material, in terms of taxonomic breath and time depth, across more institutional collections, than anyone.

Don has written several different monographs on fossil mammal groups, and recently, a general fossil book for the masses, that have, I think added to his expertise on how to produce a book like this. Illustrations by Mary Persis Williams are excellent as well.

screen-shot-2016-11-15-at-11-31-36-amA typical entry focuses on an order, and the orders are arranged in a taxonomically logical manner. A living or classic fossil representative is depicted, along with some boney material, in the form of drawings. Artist’s reconstructions, photographs, maps, and other material, with phylogenetic charting where appropriate, fills out the overview of that order.

The text is expert and informative, and very interesting. the quality of the presentation is to notch. The format of the book is large enough to let the artistry of the production emerge, but it is not a big too heavy floppy monster like some coffee table books are. This is a very comforatable book to sit and read, or browse.

It turns out that if you combine living and fossil forms for a given group, you get a much bigger picture of the facts underlying any one of a number of interesting evolutionary stories.

In addition to the order by order entries, front matter provides background to the science of paleontology, including phylogenetic method, taphonomy, etc. There is a bit of functional anatomy, and extra detailed material on teeth because, after all, the evolutionary history of man mammal groups is known primarily by analysis of (and discovery almost exclusively of) teeth.

The end matter includes a discussion of mammalian diversification, extinction, and an excellent index.

screen-shot-2016-11-15-at-11-31-46-amIf you wold like some background on how a scientist like Don Prothero writes a book like this, you can listen to this interview, in which we discuss this process in some detail.

One of the most important things about this book is that it is fully up to date, and thus, the only current mammalian evolutionary overview that is available, to my knowledge. In some areas of fossil mammal research (including in our own Order, Primates) there has been a lot of work over recent years, so this is important.

I highly recommend this excellent book.

The book as 240 pages, and 303 illustrations.

For your reference, I’ve pasted the TOC below.

TABLE OF CONTENTS:

  • Preface 6
  • 1 The Age of Mammals 7
  • Dating Rocks 8
  • Clocks in Rocks 10
  • What’s in a Name? 11
  • How Do We Classify Animals? 12
  • Bones vs Molecules 15
  • Bones and Teeth 15
  • 2 The Origin and Early Evolution of Mammals 20
  • Synapsids (Protomammals or Stem Mammals) 20
  • Mammals in the Age of Dinosaurs 23
  • Morganucodonts 23
  • Docodonts 25
  • Monotremes (Platypus and Echidna) and Their Relatives 27
  • Multituberculates 30
  • Triconodonts 31
  • Theria 34
  • 3 Marsupials: Pouched Mammals 37
  • Marsupial vs Placental 37
  • Marsupial Evolution 38
  • Ameridelphia 39
  • Australiadelphia 41
  • 4 Placental Mammals (Eutheria) 47
  • The Interrelationships of Placentals 50
  • 5 Xenarthra: Sloths, Anteaters, and Armadillos 51
  • Edentate vs Xenarthran 51
  • Order Cingulata (Armadillos) 53
  • Order Pilosa (Anteaters and Sloths) 55
  • 6 Afrotheria: Elephants, Hyraxes, Sea Cows, Aardvarks, and Their Relatives 58
  • Tethytheres and Afrotheres 58
  • Order Proboscidea (Elephants, Mammoths, Mastodonts, and Their Relatives) 60
  • Order Sirenia (Manatees and Dugongs, or Sea Cows) 67
  • Order Embrithopoda (Arsinoitheres) 72
  • Order Desmostylia (Desmostylians) 73
  • Order Hyracoidea (Hyraxes) 75
  • Order Tubulidentata (Aardvarks) 77
  • Order Macroscelidia (Elephant Shrews) 78
  • Order Afrosoricida 79
  • 7 Euarchontoglires: Euarchonta Primates, Tree Shrews, and Colugos 80
  • Archontans 80
  • Order Scandentia (Tree Shrews) 82
  • Order Dermoptera (Colugos, or Flying Lemurs) 82
  • Order Plesiadapiformes (Plesiadapids) 84
  • Order Primates (Euprimates) 86
  • 8 Euarchontoglires: Glires Rodents and Lagomorphs 94
  • Chisel Teeth 94
  • Order Rodentia (Rodents) 95
  • Order Lagomorpha (Rabbits, Hares, and Pikas) 101
  • 9 Laurasiatheria: Insectivores Order Eulipotyphla and Other Insectivorous Mammals 103
  • Order Eulipotyphla 103
  • Extinct Insectivorous Groups 107
  • 10 Laurasiatheria: Chiroptera Bats 112
  • Bat Origins 114
  • 11 Laurasiatheria: Pholidota Pangolins, or Scaly Anteaters 117
  • Order Pholidota (Pangolins) 118
  • Palaeanodonts 120
  • 12 Laurasiatheria: Carnivora and Creodonta Predatory Mammals 122
  • Carnivores, Carnivorans, and Creodonts 122
  • Order Creodonta 124
  • Order Carnivora 127
  • 13 Laurasiatheria: Ungulata Hoofed Mammals and Their Relatives 146
  • Condylarths 147
  • 14 Laurasiatheria: Artiodactyla Even-Toed Hoofed Mammals: Pigs, Hippos, Whales, Camels, Ruminants, and Their Extinct Relatives 151
  • Artiodactyl Origins 153
  • Suoid Artiodactyls 154
  • Whippomorpha 160
  • Tylopods 169
  • Ruminantia 175
  • 15 Laurasiatheria: Perissodactyla Odd-Toed Hoofed Mammals: Horses, Rhinos, Tapirs, and Their Extinct Relatives 186
  • Equoids 187
  • Tapiroids 191
  • Rhinocerotoids 196
  • Brontotheres, or Titanotheres 199
  • 16 Laurasiatheria: Meridiungulata South American Hoofed Mammals 203
  • Order Notoungulata (Southern Ungulates) 205
  • Order Pyrotheria (Fire Beasts) 206
  • Order Astrapotheria (Lightning Beasts) 207
  • Order Litopterna (Litopterns, or Smooth Heels) 207
  • 17 Uintatheres, Pantodonts, Taeniodonts, and Tillodonts 209
  • Order Dinocerata (Uintatheres) 209
  • Order Pantodonta (Pantodonts) 212
  • Order Taeniodonta (Taeniodonts) 214
  • Order Tillodontia (Tillodonts) 216
  • 18 Mammalian Evolution and Extinction 218
  • Why Were Prehistoric Mammals So Big? 218
  • Where Have All the Megamammals Gone? 219
  • How Did Mammals Diversify after the Dinosaurs Vanished? 222
  • What about Mass Extinctions? 228
  • The Future of Mammals 229
  • Illustration Credits 231
  • Further Reading 232
  • Index (with Pronunciation Guide for Taxonomic Names) 234
  • Venomous: How the Earth’s Deadliest Creatures Mastered Biochemistry

    You can read this book review, or you can just go HERE and listen to our interview with author Christie Wilcox. I promise you in advance that you will want to read her book!

    But, if you want to read the book review, here it is…

    Did you ever do anything that hurt, then you had to do it again and you knew it would still hurt, and you didn’t like that? Like getting your teeth cleaned, or licking a nine volt battery. OK, maybe you didn’t have to lick the nine volt battery, but you get my point.

    When I was working in the Ituri Forest, in the Congo, taking a walk in the forest was one of those things. All sorts of things hurt. Your feet hurt because of jungle rot combined with sandy gritty stuff permanently indurated in your shoes. The leaves and branches you would have to move through hurt because it was early in the morning and they were cold and wet. And so on.

    But one of the things that was not inevitable, but nearly daily, was being stung by a venomous beast of some kind. The most serious threat, of course, was snakes but that never happened to me. Much more common, but more common a night, was to be bitten or stung by a venomous ant. But that only happened, maybe, once a week or so. But nearly every day, if I would walk far enough in the forest (hundreds of meters) especially early in the morning, would be the venomous caterpillars.

    Cute little caterpillars with some extra long furry thingies sticking out of them. When you brush against them, there is instant local pain, a bit like a bee sting (but different) followed quickly by shooting pains from the site of contact to the nearest major lymph node (usually the arm pit), followed by pain in the lymph node. The pain would eventually go away, after minutes, sometimes a bit longer. Most gentile urbane suburban or urban dwelling Americans and Europeans can go for years between envenomations. But if you are a human, or some other creature, living in certain environments, the risk of envenomation is not only constant, but the actual smaller scale, not deadly, envenomation events are a regular occurrence, and the threat of The Big One (such as a Black Mamba bite or a Cobra strike) is always there.

    In Venomous: How Earth’s Deadliest Creatures Mastered Biochemistry, Chritie Wilcox explains why this is important. We tend to think of the interaction between animals, within or between species — those interactions that have to do with sexual competition, feeding, or predator avoidance — as involving tooth, nail, squiggly appendages, and all that. But these interactions also involve, very often, some sort of envenomation. Also, using venom isn’t always about stinging, paralyzing, or killing. Mosquitos use venom to make blood sucking possible, as the chemicals used to stop their host from feeling the bite, and to make it easier to suck the blood, etc., are venoms. Indeed, the parasites we know to be so commonly associated with mosquitos get into the host by hanging out with the venom, free riding with the injected biochemicals.

    So, the evolution and diversification of venom and strategies of attack or defense, and other things, associated with venom co-evolved with anti-strategies to avoid the pain, paralysis, to avoid the bite or sting or brush of the venomous hair of the caterpillar. Indeed, understanding the evolutionary history and patterns of adaptation associated with the use of venom is just as good as any syndrome of interaction or behavior for the study of how evolution itself works.

    Christie Wilcox’s book is one of the better science books I’ve read in some time. This is an area I should know something about, as a biological scientist, and as a person who has lived for years in the venom-rich rain forest. But I still found myself learning something new with every page turn. Wilcox has studied venom for years — this is her area of specialty — and her text is enriched with well placed and well told stories of her own sometimes harrowing experiences.

    The book is very well written and very well documented with copious notes.

    A fascinating subtext has to do with human evolution and experience. There is a theory that primates generally are tuned to venomous creatures, especially snakes, and some of the key primate evolutionary adaptations are shaped by the experience of living in trees where large venomous snakes hunt. In the present day, there is what looks to me almost like a cult of self envenomation, found among people who keep venomous snakes (mainly), who inject themselves with venom regularly in order to stay, maybe, immune in case of an accidental bite. But they seem to be doing something more than this, almost using the venom as a sort of drug or, fascinatingly, as an elixir to extend life. On top of this, there is even an expanding practice of using snake bites, or ingesting the powdered form of snake venom, as a recreational drug. This set of not too unrelated human stories sits intriguingly amid myriad stories of venom use among a wide range of animals, including several mammals, fish, cone snails, snakes and lizards, etc.

    I get the impression that bad scientific knowledge (generally older), folk stories, and meemish yammering about venom is among the most widespread form of falsehood in our parascientific discourse. As I read this book, I remembered may instances of hearing or reading this or that thing about this or that venomous animal, or category of animal, that turned out wrong as more recent science exposed what was really happening. For many years, scientists were not sure if the platypus was venomous (it is) or why (it is all about sex for them). How does the Komodo Dragon kill large prey such as the Water Buffalo? If you look it up, you may find out that the Komodo Dragon maintains a bacterial flora in its mouth that causes necrosis in a bite victim. That is not true. Read Christie Wilcox’s book to find out the real story! And so on.

    Venomous: How Earth’s Deadliest Creatures Mastered Biochemistry is out in August, but available for pre order.

    Mike Haubrich and I interviewed Christie on the Ikonokast podcast, and it turns out to have been a fantastic interview. Listen to it here!

    Christie Wilcox blogs at Science Sushi.

    An Interview with Don Prothero

    Ikonokast interviews Don Prothero.

    Don Prothero is the author of just over 30 books and a gazillion scientific papers covering a wide range of topics in paleontology and skepticism. Mike Haubrich and I spoke with Don about most of these topics, including the recent history of the skeptics movement, the conflict and potentials between DNA and fossil research, extinctions and impacts, evolution in general, and the interesting projects Don is working on now.

    The interview is here. Please click through and give this fascinating conversation a listen!

    How the Venus Flytrap Evolved

    The trick to understanding evolution is less about finding good answer to questions, but rather, finding good questions to answer.

    Read that sentence twice, because it is very important.

    Years ago, Niko Tinbergen developed a method of formulating questions about biology. I’m pretty sure the Tinbergenian method has not been integrated into most science standards and teaching curriculum. It should be.

    There are four types of questions one could formulate about a biological system, trait, or observation.

    1) Mechanistic. How does this thing work? What cellular processes are involved in a metabolic process, or how do the lever forces work in a joint, or how does a heterotroph get some food into its gut.

    2) Ontogenetic. Given the various parts of an organism, how did they arise initially during development? Thinking only of multi-celled animals for a moment, all animals can be divided into large categories that have a common body plan, and that body plan is easily seen in the embryonic state. Looking at a fully formed adult, at any particular organ or part of an organ, we can ask, how did this thing form during the process of differentiating this particular taxonomic category? For example, mammalian pituitary glands are a combination of a bit of what would otherwise be brain, and a bit of what otherwise would be the roof of the mouth. This helps make sense of the pituitary gland.

    3) Phylogenetic. How is a particular feature of an organism potentiated or constrained, in its development or function, by ancestry? Birds have either two or four wings (the four winged birds are all extinct). Birds with two wings have two legs. Why not have two legs, two arms, and two wings? Because birds evolve within a taxonomic group that have four limbs, so wings are modified versions of those limbs.

    4) Functional. Sometimes called “ultimate” this category of question is largely (but not entirely) about natural selection. What is it about this trait, or this particular form of this train in this species (or sex of a given species) that enhances fitness. This is about the aspect of the trait that presumably caused the trait to spread and become typical, or that caused a particular population (the population with this specific trait) to become more representative over time, due to selection.

    A simpler version of this divides all features into two categories, “proximate” and “ultimate.” The proximate stuff is the immediate description, what it looks like, how it works, etc. The “ultimate” bit is the functional question (number 4 above). I prefer to keep the four categories in mind.

    By the way, there is a thing I call Greg’s Rule of Tinbergenian Inquisition (GROTI). This is not a hard and fast rule of nature or logic, but just a common occurrence. If you consider all four Tinbergenian questions in relation to a given trait, one of the four questions will produce a boring answer or a tautology. There are probably deep underlying philosophically interesting reasons for this, but the rule is more important as a guide to teachers. If you want to teach the Tinbergenian method of asking questions about evolution, by example, you will probably need to come up with two or more examples in order to not have one of the four approaches look silly. But I digress.

    You want to know how the Venus Flytrap evolved, and some recent research sheds some light on this by looking at the ontogenetic and phyogenetic aspects of known traits.

    Venus flytraps are plants that capture and then digest insects (or other small critters). The ultimate reason they do this may have to do with nutrients. Capturing and absorbing the tissues of insects provides nitrogen and some other often rare nutrients. So, the adaptation is to nutrient poor environments. One might guess that this is a trait that was selected for in nutrient poor environments, or one might guess that it is a trait that emerged largely by accident and then allows plants that do this to do better in nutrient poor environments. Or, one might not be too concerned by this distinction and guess that both features of the emergence of a trait are likely to be involved in the evolutionary history of a particular species and its adaptations. But, again, I digress.

    So, the Venus flytrap has sensors on it that tell the plant that there is prey present. Then it snaps shut (that is the coolest ting about the plant, but we’re not actually going to go into that here). Then a liquid engulfs the prey and digestion happens, then a different liquid is exuded and this facilitates the transport of nutrients into the plant.

    Now, think about plants, generally. Plants have all sorts of chemicals in them, or on them, that do all sorts of things. Is there anything about plants in general, about what they normally do, that could provide the genetic (and therefore metabolic or processual) basis for any of these things?

    Yes.

    Plants have hairs on the that detect the presence of possible herbivores.

    Herbivores may use certain chemicals to break down plant tissue, for ingestion and digestion.

    Plants have evolved chemicals that break down those chemicals.

    The chemicals that counteract the breakdown of plant tissues probably scare off herbivores, or limit their success, but the can also break down some of the molecules that herbivores are made of.

    Meanwhile, plants have genes that are expressed in roots that produce chemicals that facilitate the transport of nutrients from the roots into the rest of the plant.

    So, from a recent write-up in Science:

    To catch an invertebrate that has blundered into its snare, the flytrap relies on an ancient alarm system. It starts ringing when the victim jostles trigger hairs. The hairs in turn generate electrical impulses that somehow stimulate glands in the trap to produce jasmonic acid—the same signal that noncarnivorous plants use to initiate defensive action against herbivores. Patterns of gene expression in the two kinds of plants confirm the similarity…

    …In noncarnivorous plants, jasmonic acid triggers the synthesis of self-defense toxins and molecules that inhibit hydrolases, enzymes that herbivores secrete to break down the plant’s proteins. As part of their counterattack, plants also produce their own hydrolases, which can destroy chitin and other components of insects or microbes. In the flytrap, … [t]ens of thousands of tiny glands make and secrete hydrolases. The trapped invertebrate is drenched in the same digestive enzymes that another plant might use in smaller quantities to ward off an enemy….

    Then, plant genes code for chemicals that help absorb the nutrients from the insect.

    Experiments showed that many of these genes are the same ones expressed in the roots of other plants. “We looked at each other and said, ‘Yes, it’s a root,’” Hedrich says. “It made immediate sense,” because the flytrap draws its nutrition not from soil, but from its prey.

    We now have a phylogenetic look at a large part of the Venus flytrap’s unique insectivores adaptation. As is generally the case, these novel adaptations are reworkings of pre-existing adaptations.

    And, ontogenetic questions arise (but are not directly addressed by this research). How did the genes and their products normally found in roots get into the “stomach” thingie of the flytrap? Did the site of differentiation of root structures move to elsewhere in the plant, or is it just the genes being expressed in different cells? This question came to my mind reading this story, but I’m more of an animal guy than a plant guy. Animals have homeobox genes that control the overall differentiation of tissues, and stem cells that determine and limit, at various levels, what the possible cell types are in a give part of the developing animal. Plants are different. This is one of the reasons that plants can propagate vegetatively and few animals do anything similar.

    So I asked Dr. Rainer Hedrich, the flytrap guy who produced, with his team, this research, if this was a case of the movement of root tissue into the business end of the flytrap, or, alternatively, the expression of genes in tissue that are not normally expressed there in a plant.

    He told me, “The flytrap develops from tips of Dionaea leaves. So, the trap is a leaf on one side. The inner surface of the trap is covered by a turf of glands, and these glands express genes one otherwise finds in roots. So, the trap is a leaf with root function. Most likely, to serve carnivory, Dionea modified a transcription foactor or promoter of root genes and so directed them into the glands.”

    So, the story remains one of phylogeny, not ontogeny. The ontogeny part of the story is uninteresting, but the funcitonal, phyogenetic, and mechanistic parts of the story are fascinating.


    The paper:

    Venus flytrap carnivorous lifestyle builds on herbivore defense strategies. Felix Bemm, Dirk Becker, Christina Larisch, Ines Kreuzer, Maria Escalante-Perez, Waltraud X. Schulze, Markus Ankenbrand, Anna-Lena Van de Weyer, Elzbieta Krol, Khaled A. Al-Rasheid, Axel Mithöfer, Andreas P. Weber, Jörg Schultz, and Rainer Hedrich. Genome Res. Published in Advance May 4, 2016, doi:10.1101/gr.202200.115

    Graphic at the top of the post from here. Caption: Venus flytrap with its turf of glands and some gland complexes under the microscope – color enhanced transmission electron micrograph (TEM). B) Cross section of a gland complex showing the three characteristic cell types (Picture: Dirk Becker, Sönke Scherzer, Christina Larisch)

    The Serengeti Rules: The Quest to Discover How Life Works and Why It Matters (Book Review)

    Sean B. Carroll is coming out with a new book called The Serengeti Rules: The Quest to Discover How Life Works and Why It Matters.

    This is the molecular biologist Sean Carroll, as distinct from the physicist (who wrote this).

    Homeostasis is one of the basic principles of biology. The term can be applied broadly to mean that certain numbers are maintained within a certain range. This could refer to energy flowing through a system, numbers of specific cellular products like enzymes, numbers of individual organisms in an ecological system, etc. It is not so much that numbers don’t change. Change in numbers is often central to a physiological process. But the change is either demanded by a system of regulating numbers, or is a perturbation in a system that is responded to by regulation. Regulation is one of those key concepts that can be applied across pretty much all systems, and provides a powerful point of view from which to understand what is happening in any living system.

    Carroll is a molecular biologist, so much of his training and work is about regulation: identifying it, characterizing it, figuring it out. What Carroll has done in this book is to apply this point of view broadly to biological systems, looking at things inside cells and things inside major ecosystems. The title of the book comes from his own experience visiting the Serengeti as a safari-going tourist, in combination with the fact that this particular ecosystem is one of the best studied in the world. Many different scientists studying everything from grass to microbes to lions to antelopes have spent countless hours observing, characterizing, and trying to explain the dynamics of the Serengeti. As Carroll points out, this is true of a number of different ecosystems, and he could well have named his book, “The Lake Erie Rules,” but that would not have been as cool of a name.

    So Carroll has done, then, something that is very dangerous and often does not go well. He’s taken insight derived from his expertise in small scale, mostly sub-cellular, biological systems, and using the touchstone of regulation, applied this insight to help observe, describe, and understand biological systems generally, with a strong focus on ecology. When a scientist steps out of their normal realm to do such a thing, we often get something better ignored, because, in fact, it is not easy or, in some cases, appropriate to make this leap. In this case, however, it worked beautifully. Carroll’s book is fantastic, a success story in going form the specific to the general.

    It helps that Carroll is a gifted writer, captivating and thoughtful, and highly respectful of the reader.

    Carroll brings in the history of thought and research in the relevant areas of physiology, ecology etc. His messages are framed in the larger context of the Earth’s overall health and important environmental issues. He links the subject matter to key central themes in biological theory (such as natural selection and evolution). And this is all done very well.

    You’ve seen the synthetic overviews of life and evolution framed in chaos theory, complexity theory, even quantum physics. This is better.

    This is a book to give to your favorite biology teacher (high school or college), and that teacher will take from it examples, connections, lessons, ways of telling, that will enrich their teaching immeasurably.

    I don’t think the book is available yet, but you can pre-order it.

    The Story Of Life in 25 Fossils by Don Prothero: Review

    This is a review of The Story of Life in 25 Fossils: Tales of Intrepid Fossil Hunters and the Wonders of Evolution.

    Don Prothero
    Don Prothero
    Fossils are cool. Why? Two very big and complex reasons. First, fossils allow us to reconstruct species that don’t exist any more. This is usually done by studying species that do exist, and using the information we glean from living things to interpret the details of the fossil species, giving it life. Second, fossils tell us about evolutionary change, both by showing us what evolutionary events happened that we would not be able to see in living species, and by showing us change. In order to understand the evolutionary history of life on our planet, we need to look at a lot of different fossil species, to develop histories of change and adaptation.

    (OK, there may be more than two reasons fossils are cool. Feel free to add your fossil are cool ideas in the comments section below. Please to not say “to grind them up to make aphrodisiacs.”)

    So, what if you had to describe the history of life by focusing on a small number of fossils? And, why would you do that? Last year, Paul Taylor and Aaron O’Dea did this with 100 fossils in A History of Life in 100 Fossils. I’ve looked through that book, and it is nice. But here I’m going to review a somewhat more recent book, just out, by Don Prothero, which has at least as much information in it but by focusing on a smaller number of cases: The Story of Life in 25 Fossils: Tales of Intrepid Fossil Hunters and the Wonders of Evolution.

    Several of the fossils Prothero chose to illustrate the story of life represent major events or changes in the planet’s evolutionary history and diversification. For example, the nature of the earliest life forms is represented by the stramotlite, which is really fossil scum. Others illustrate key transitions within major groups such as the origin of hard body parts, or the major divisions of animals, such as the origin of the amphibians. Others are exemplars chosen because they are spectacular and/or because they are touchstones to understanding very different times in the past, or important categories of living and extinct forms. These examples include the extremes, as well as good exemplars of the “diversity in adaptations to size, ecological niche, and habitat.” Generally, the chosen representatives are fossils with good preservation, detailed study, and in general, piles of information.

    Prothero also provides rich detail about discovery, early interpretations, and the role of specific fossils (or extinct species) in the history of thought about evolution. In some ways this may be the most interesting parts of the discussion of several of the fossils. And, the book is chock full of excellent and interesting illustrations.

    Lester Park Stromatolite. (Photograph by G. Laden.)
    Lester Park Stromatolite. (Photograph by G. Laden.)
    As a result, the chosen 25 are somewhat biased towards the more spectacular, and intentionally, towards those extinct forms that people tend to gravitate towards because they are either very interesting or very spectacular (generally, both). It would probably be difficult to develop a panoply of species that ignore the dinosaurs, but the history of life on Earth could probably have been written without humans, as long as “providing a viable existential threat to all known life forms” was not on your list of key attributes to do cover, but Prothero takes on human ancestors, and covers more than one, because most of the book’s readers are likely to be humans.

    There are far more than 25 life forms in The Story of Life in 25 Fossils: Tales of Intrepid Fossil Hunters and the Wonders of Evolution, because the author makes use of a much richer body of information than just the key chapter-titling form.

    Also, Prothero is a world renowned expert on certain fossil groups, found among the mammals. Well, actually, a lot of fossil groups. And, his expertise is applied richly here, with the selection of a disproportionate share of mammals.

    The author writes excellent, readable prose, and vigorously makes connections between evolutionary questions and evolutionary data. It is hard to say if this book supplants or enhances his earlier major monograph for the public on evolution, Evolution: What the Fossils Say and Why It Matters. Either way, you can safely assume the more recent volume is more up to date in areas where research has been active.

    I’m thinking of getting a copy of this book for the local school’s library, as a gift.


    A selection of other books by Donald Prothero:

    Books On Fossils and Evolution

    Over the last several months, a lot of great books on fossils and evolution (as in paleontology) have come out. I’ve selected the best for your consideration. These are great gifts for your favorite science-loving nephew, life science teaching cousin, or local school library. Actually, you might like some of these yourself.

    grandmother_fishLet’s start off with a kid’s book: Grandmother Fish: a child’s first book of Evolution by Jonathan Tweet.

    From the blurb:

    Grandmother Fish is the first book to teach evolution to preschoolers. While listening to the story, the child mimics the motions and sounds of our ancestors, such as wiggling like a fish or hooting like an ape. Like magic, evolution becomes fun, accessible, and personal. Grandmother Fish will be a full-size (10 x 8), full-color, 32-page, hardback book full of appealing animal illustrations, perfect for your bookshelf. US publishers consider evolution to be too “hot” a topic for children, but with your help we can make this book happen ourselves.

    I reviewed the book here before it first came out. This was a kickstarter project, and it may be currently unavailable commercially, but if you click through to the kickstarter project you can probably get a copy of it.

    Donald+Prothero+Story+of+Life+in+25+FossilsThe most recent book to come across my desk is Don Prothero’s The Story of Life in 25 Fossils: Tales of Intrepid Fossil Hunters and the Wonders of Evolution. I’ve got a review of Prothero’s book in my draft file, so look for that post coming out over the next few days.

    One might ask, “how do you choose 25 fossils, among so many choices, to represent evolution?” Well, Don cheated a little by mentioning more than 25 fossils. Also, you really can’t do this. Don selected fossils using several criteria, but one basis for his choice was the availability of rich historical information about a fossil’s discovery, interpretation, and effect on our thinking about evolution. And, he covers all of that.

    Don is one of those rare authors who is both an expert scientist and a great writer, with a proven ability to explain things in a way that is not watered down yet totally accessible.

    Here’s a selection of the many other books written by Prothero:

    EvolutionTheWholeStoryParker41N2zRnkbuL._SX348_BO1,204,203,200_ (1)Evolution: The Whole Story is an astonishing book that needs to be on the bookshelf of anyone interested in evolution. The work is edied by Steve Parker, but authored by nearly a dozen experts in various subfields of fossils and evolution, so it is authoritative and scholarly. At the same time, it is very accessible and enjoyable. This is not a book you read from cover to cover, though you could. Feel free to skip around, and you;ll find yourself looking stuff up all the time.

    The book is divided into major sections, and each section has a series of short pieces on this or that fossil, group of fossils, type of life system, method for studying fossils, etc. There is a running sidebar on the bottom of many pages giving “key events” in evolutionary history of the group of life forms under consideration The book is VERY richly illustrated, with detailed keys to the illustrations. Many of the illustrations are broken down into “focal points” that expand significantly on the illustrations’ details. There are countless additional inserts with more information. The book itself is beautiful, intriguingly organized, and it is full of … well, everything. The book is very well indexed and sourced, and has helpful, up to date, phylogenies and chronological graphics.

    TheBiologyBookGeraldThe Biology Book: From the Origin of Life to Epigenetics, 250 Milestones in the History of Biology (Sterling Milestones) by Michael Gerald and Gloria Gerald is a compendium of biological topics and key moments in the history of biological science, organized in a sort of chronological framework. Major groups (the insects, the amphibians), major ideas (Pliny’s Natural History, Ongogeny and Phylogeny), key physiological and developmental concepts (meiosis, mitosis, many topics in endocrinology), key fossils (like the Coelocanth) and so on are discussed, very nicely illustrated. This is almost like having a gazillian short articles from Natural History Magazine (or similar) all in one book. There are 250 biological “milestones” in all. The charming part of the book is that a milestone can be an evolutionary event, an extinction episode, the emergence of a great idea, or a particular discover. And, as noted, these are ordered across time, as well as one can, from the beginning of life to a selection of the most recent discovery. The book effectively combines history of biology (and related sciences) and the biological history itself.

    lifes_gretest_secret_dna_cobb511J4iZIbrL._SX327_BO1,204,203,200_Life’s Greatest Secret: The Race to Crack the Genetic Code by the well respected scientist and historian Matthew Cobb is a carefully and clearly written history of the discovery of the nature of DNA, covering a lot more than, and since, Watson and Crick. It is extremely well sourced, indexed, and supported, and very readable.

    This is the detailed and authoritative work on all the elements that came together to understand the genetic code. Don’t talk about the discovery and understanding of DNA any more until you’ve read this book. From the publisher:

    Life’s Greatest Secret mixes remarkable insights, theoretical dead-ends, and ingenious experiments with the swift pace of a thriller. From New York to Paris, Cambridge, Massachusetts, to Cambridge, England, and London to Moscow, the greatest discovery of twentieth-century biology was truly a global feat. Biologist and historian of science Matthew Cobb gives the full and rich account of the cooperation and competition between the eccentric characters—mathematicians, physicists, information theorists, and biologists—who contributed to this revolutionary new science. And, while every new discovery was a leap forward for science, Cobb shows how every new answer inevitably led to new questions that were at least as difficult to answer: just ask anyone who had hoped that the successful completion of the Human Genome Project was going to truly yield the book of life, or that a better understanding of epigenetics or “junk DNA” was going to be the final piece of the puzzle. But the setbacks and unexpected discoveries are what make the science exciting, and it is Matthew Cobb’s telling that makes them worth reading. This is a riveting story of humans exploring what it is that makes us human and how the world works, and it is essential reading for anyone who’d like to explore those questions for themselves.

    EldridgeEvolutionExtinctionExtinction and Evolution: What Fossils Reveal About the History of Life is a an updated version of a classic book about evolution and extinction written by one of the scientists who developed our modern way of thinking about evolution and extinction (especially the extinction part).

    Eldredge’s groundbreaking work is now accepted as the definitive statement of how life as we know it evolved on Earth. This book chronicles how Eldredge made his discoveries and traces the history of life through the lenses of paleontology, geology, ecology, anthropology, biology, genetics, zoology, mammalogy, herpetology, entomology and botany. While rigorously accurate, the text is accessible, engaging and free of jargon.

    Honorable Mentions: Older books that are great and may now be avaialable for much reduced prices.

    I really liked The Great Transition: Shifting from Fossil Fuels to Solar and Wind Energy as an expose of a particular time period and major event in geological history. Greenhouse of the Dinosaurs: Evolution, Extinction, and the Future of Our Planet by Prothero is a classic, again, looking at a fairly narrowly defined moment in prehistory. You can get it used for about five bucks.

    The Fossil Chronicles: How Two Controversial Discoveries Changed Our View of Human Evolution by Dean Falk is a great book focusing on one key human fossil. This is a personal story as well as a scientific one. Again, available used for a song.

    Have you read Your Inner Fish: A Journey into the 3.5-Billion-Year History of the Human Body yet? I’m sure you’ve heard about it. It is still a great read, and you can get it used cheap.

    The only book I would recommend that uses the “paleolithic” to advise you on diet and exercise is The Paleolithic Prescription: A Program of Diet and Exercise and a Design for Living.