Jonathan Wells debunks something nobody believes

Black bear

Black bear, Glacier National Park, September 2014.

Charles Darwin speculated that whales might have evolved from bears. He was wrong, but then he didn’t have the benefit of molecular sequence data, detailed morphological comparisons, and sophisticated methods of phylogenetic inference. We’ve known for at least 50 years that cetaceans (whales, dolphins, and porpoises) are most closely related to ungulates, specifically even-toed ungulates (artiodactyls). The current consensus is that the closest living relatives of cetaceans are hippopotamuses. Not everyone agrees with this specific relationship, but no one really doubts that whales are closely related to ungulates.

You wouldn’t learn that from reading Discovery Institute Senior Fellow Jonathan Wells’ recent post, “From Bears to Whales: A Difficult Transition.”

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Uncommon Descent on Elizabeth Pennisi’s Science article

Two-headed quarter

Image from

Yesterday, I ran a bit long about Elizabeth Pennisi’s new article in Science, “The momentous transition to multicellular life may not have been so hard after all.” I’m not the only one who noticed it, though; Uncommon Descent also commented (“At Science: Maybe the transition from single cells to multicellular life wasn’t that hard?“). There’s not much to it, just a longish quote from the article followed by this:

So at the basic level, there is a program that adapts single cells to multicellularity? Yes, that certainly makes multicellularity easier and even swifter but it also make traditional Darwinian explanations sound ever more stretched.

So if the evolution of multicellularity is easy, that’s evidence against “traditional Darwinian explanations.” Remember “Heads I win, tails you lose“?

…if multicellularity is really complicated, that’s evidence for intelligent design. But if multicellularity is really simple, that’s evidence for intelligent design.

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Multicellularity in Science

I spent the last week of June backpacking in Baxter State Park, Maine. When I finally emerged from the woods, my first stop was Shin Pond Village for a pay shower, a non-rehydrated breakfast, and free internet access. Among the week’s worth of unread emails were a nice surprise and a not-so-nice surprise. The not-so-nice surprise was a manuscript rejected without review; the nice surprise was a new article by Elizabeth Pennisi in Science, which came out when I was somewhere between Upper South Branch Pond and Webster Outlet.

Upper South Branch Pond

Upper South Branch Pond, Baxter State Park, Maine. I spent two nights here.

The article, for which I was interviewed before Baxter, synthesizes recent work across a wide range of organisms that suggests that the evolution of multicellularity may not be as difficult a step as we often assume:

The evolutionary histories of some groups of organisms record repeated transitions from single-celled to multicellular forms, suggesting the hurdles could not have been so high. Genetic comparisons between simple multicellular organisms and their single-celled relatives have revealed that much of the molecular equipment needed for cells to band together and coordinate their activities may have been in place well before multicellularity evolved. And clever experiments have shown that in the test tube, single-celled life can evolve the beginnings of multicellularity in just a few hundred generations—an evolutionary instant.

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The Essential Tension

The Essential Tension

When I ran across The Essential Tension by Sonya Bahar, my first thought was that it sounded very much like something my PhD advisor could have written:

‘The Essential Tension’ explores how agents that naturally compete come to act together as a group. The author argues that the controversial concept of multilevel selection is essential to biological evolution, a proposition set to stimulate new debate.

The subtitle is Competition, Cooperation and Multilevel Selection in Evolution, which is more than vaguely reminiscent of the ‘cooperation and conflict’ framework Rick Michod has built over the last twenty years.

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Evolution of outcrossing and selfing

Sex is costly. You could die trying to find a mate. Your mate could kill you, or give you a disease. You could be unable to find a mate in the first place, in which case you’d be better off if you could reproduce asexually. Even without those risks, though, even in a simple genetic simulation, sexual reproduction means you only pass on half of your genes to your offspring.

So why do it? We know that it’s possible to reproduce without sex; lots of things do. It’s not just bacteria and protists, either: asexual reproduction occurs in some plants, insects, snails, amphibians, and reptiles, among many others. The logic of natural selection suggests that sex must confer some benefit that outweighs all the costs, at least in some situations. Essentially all of the proposed benefits of sex have to do with outcrossing, or mixing your genes with those of another, genetically distinct, individual.

Nevertheless, a lot of things that reproduce sexually do so without outcrossing. This is especially common in plants, where it’s called “self-pollination” or just “selfing.” Selfing is thought to provide short-term advantages relative to outcrossing–basically by avoiding the costs I’ve listed above. However, selfing also doesn’t provide most of the benefits associated with sex, so it’s thought to be a bad strategy in the long term. This leads to selfing being thought of as a “dead-end” strategy: the short-term advantages make it unlikely that a selfing species will return to outcrossing, and the reduced genetic variation produced by selfing make diversification less likely.

Erik Hanschen and colleagues have tested these predictions in the volvocine algae (I’m among the “colleagues,” as are John Wiens, Hisayoshi Nozaki, and Rick Michod): do selfing species ever return to outcrossing, and do they have a lower rate of diversification than outcrossing species? Both mating systems exist within the volvocine algae, and so they make a good test case. Roughly speaking, the term heterothallic refers to outcrossing species and homothallic to selfing species:

Hanschen et al. Fig. 1

Figure 1 from Hanschen et al. 2017. Diversity of mating systems in the volvocine green algae and their respective life cycles. (A) In outcrossing (heterothallic) species, distinct genotypes (male on left and female on right) sexually differentiate producing either eggs or sperm. A diploid zygospore (red) is produced after fertilization. Sexual offspring hatch and enter the haploid, asexual phase of the life cycle. (B) In selfing (homothallic) monoecious species, a single genotype is capable of producing both gamete types. Upon sexual differentiation, each sexual colony produces both sperm and eggs. (C) In selfing (homothallic) dioecious species, a single genotype sexually differentiates, producing either eggs or sperm, but not both within the same colony. Cartoons in panels (A–C) are shown with anisogamous, Volvox-like morphology for illustrative purposes only.

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Nice Aeon article on biological individuality

Siphonophores by Ernst Haeckel

By Ernst Haeckel – Kunstformen der Natur (1904), plate 17: Siphonophorae (see here, here and here), Public Domain, Link

Derek Skillings from University of Bordeaux/CNRS has a new article at Aeon about biological individuality:

For millennia, naturalists and philosophers have struggled to define the most fundamental units of living systems and to delimit the precise boundaries of the organisms that inhabit our planet. This difficulty is partly a product of the search for a singular theory that can be used to carve up all of the living world at its joints.

Skillings reviews the deep historical roots of the question, touching on the views of Charles Darwin and his grandfather, both Huxleys (T. H. and Julian), Herbert Spencer, and other 19th and early 20th century thinkers, as well as some more recent authors, including Daniel Janzen and Peter Godfrey Smith.

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Life cycles in major transitions, and some clueless critique

Jordi van Gestel and Corina Tarnita have published a ‘Perspective’ in PNAS, “On the origin of biological construction, with a focus on multicellularity“:

…we propose an integrative bottom-up approach for studying the dynamics underlying hierarchical evolutionary transitions, which builds on and synthesizes existing knowledge. This approach highlights the crucial role of the ecology and development of the solitary ancestor in the emergence and subsequent evolution of groups, and it stresses the paramount importance of the life cycle: only by evaluating groups in the context of their life cycle can we unravel the evolutionary trajectory of hierarchical transitions.

van Gestel 2017 Fig. 2

Figure 2 from van Gestel and Tarnita, 2017. Relationship between life stages in hypothesized life cycles of solitary ancestors and group formation in derived group life cycles. (Upper) Simplified depiction of hypothesized ancestral solitary life cycles of the green alga Volvox carteri, the cellular slime mold Dictyostelium discoideum, and the wasp Polistes metricus. Life cycles here consist of a life stage expressed under good conditions (black) and a life stage expressed under adverse conditions (green). For the latter life stage, we show an environmental signal that might trigger it and some phenotypic consequences. (Lower) Simplified depiction of group life cycles of: V. carteri, D. discoideum, and P. metricus. Developmental program underlying life stages in solitary ancestor is co-opted for group formation (shown in green): differentiation of somatic cells (V. carteri), fruiting body formation (D. discoideum), and appearance of foundress phenotype (P. metricus).

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MicroRNAs in Chlamydomonas

One of the biggest changes in evolutionary theory in the late 20th century was the growing appreciation for the central role of changes in gene expression in macroevolution. Developmental genes, especially Hox genes, turned out to be remarkably conserved across lineages that diverged over half a billion years ago. The subsequent huge changes in morphology were more often due to changes in when and where those genes were expressed than to changes in the coding sequences of the genes themselves.

Even more recently, an entire new class of regulatory mechanisms was discovered and found to be important in developmental processes. MicroRNAs (miRNAs) are short (21-24 nucleotides) sequences of RNA that reduce gene expression by promoting the breakdown of messenger RNAs (mRNAs) and by repressing translation of mRNAs into proteins. We have only known that microRNAs even existed since the early 1990’s, and their importance in gene regulation and development wasn’t appreciated until the 2000’s.

Although they are structurally similar, plant and animal microRNAs repress gene expression through very different mechanisms. A new paper by Betty Y-W. Chung and colleagues in Nature Plants shows that the regulatory mechanisms of Chlamydomonas microRNAs have both striking similarities and important differences with animal miRNAs:

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Another step toward understanding sex determination in Volvox

Volvox and its relatives are a great model system for understanding the evolution of multicellularity. Their simplicity (relative to most other multicellular groups) and the variety of ‘intermediate’ species (‘intermediate’ in terms of size and complexity) make them especially suitable for comparative studies of their morphology, development, genetics, genomics, and so on. David Kirk’s book on the topic thoroughly reviews the work done up through the late ’90s, and advances since then have only increased the pace of discovery.

But in the last ten years or so, I would argue that the volvocine algae have emerged as a leading model system for an entirely different set of questions related to the evolution of the sexes. Males and females are defined by the gametes they produce, and the sexes came into existence when their gametes diverged into two different types. The existence of different male and female gametes (sperm and eggs, in most cases) is called anisogamy, and the ancestral condition of similar gametes is isogamy.

In 2006, Hisayoshi Nozaki and colleagues reported that volvocine males evolved from the minus (isogamous) mating type. To the best of my knowledge, this is the only group for which we know this. Since then, more clues have been forthcoming, and these were competently reviewed last year by Takashi Hamaji and colleagues. A new paper in PLoS ONE, by Kayoko Yamamoto and colleagues, adds another piece to the puzzle.

Figure S2 from Yamamoto et al. 2017. Light microscopic images of Volvox africanus (homothallic, monoecious with males type) and V. reticuliferus (heterothallic, dioecious type). Scale bars = 50 μm. sp: sperm packet, e: egg. A-C. V. africanus strain 2013-0703-VO4. A. Asexual spheroid. B. Monoecious spheroid. C. Male spheroid. D, E. V. reticuliferus. D. Male spheroid in male strain VO123-F1-7. E. Female spheroid in female strain VO123-F1-6.

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