Photo: Insect Camouflage

 I nearly missed this insect as I was sipping my evening coffee.

The rust, black, and white pattern of the insect blends into the pink feldspar, biotite, and quartz of the granite table top. When the restaurant introduced these tables in the 1980’s, insects with a passing resemblance to the table colors survived the gaze of bird predators better than individuals of the same species not having that coloration. Granite colored insects reproduced more, and the match between the insect patterning and the table top became more fine tuned over time.

I made this up. It is what is known as a “Just So Story”, named after writer Rudyard Kipling’s Just So Stories for children. Kipling wrote imaginative fantastical explanations for how animals looked the way they do. The term made its way into biology and was especially used, rather derisively, by evolutionary biologist Stephen Jay Gould as a critique of evolutionary psychology. Gould complained that the field tends to come up with imaginative yet unsupported adaptationist explanations for every aspect of human behavior. They are Just So Stories. The criticism has extended to other areas of biology too. Such as one can make about my story of the insect.

How did this particular insect species get this coloration that matches the granite? Likely its historical origins lies in a very different environment. Perhaps adaptation through natural selection in an ecologic setting of leaves and colored pebbles did play a role in the evolution of this pattern. Or perhaps it is a side effect of some other developmental changes in the insect body plan. Whatever the explanation, it is only chance that its coloration matches the table top stone.

Plastic In Sediment, Antarctica Ice Core, Alfred Wallace

A few interesting readings:

1) Sedimentation Shifted - How rivers move sediment along their course to the sea is an important aspect of sedimentology research. Grain size, shape, and density, all affect how currents move sediment, and where and in what proportions sand, silt, and mud particles come to be deposited. Now there is a new kid on the block: plastic. Catherine Russell has written a fascinating article diving deep into experimental work on how plastic impacts sediment transport. The work she describes has important implications for our understanding of plastic pollution in rivers, and the role plastic particles plays in enhancing erosion rates and sediment redistribution in riverbeds. 

2) Antarctica: 1.2-Million-Year-Old Ice- Scientists use gases trapped in old ice to measure ancient atmospheric composition and estimate past climatic conditions. A long running drilling program in Antarctica had so far recovered 800,000 year old ice. That record has been recently broken. Scientists have reached the very bedrock of the Antarctica continent. The oldest ice at the very bottom is 1.2 million years old. This is the longest continuous record of our climate that we have so far.  It hold much valuable information on climate fluctuations through the Pleistocene and Holocene. This article is a press release of the University of Bern. 

3) Beyond Evolution: Alfred Russel Wallace’s critique of the 19th century world- Alfred Russel Wallace is the co-discover of evolution through natural selection along with Charles Darwin. He was a brilliant naturalist and made foundational contributions to natural history. But he also was very sympathetic to the plight of local people suffering under colonialism and the environmental degradation the race to strip the land of resources was causing. Marshall A. summarizes nicely Wallace's observations on the impact of environmental damage, both in his native Wales and also during his travels in the far away Malay archipelago. 

Let me take this opportunity to share again this lovingly crafted documentary on the life and work of Alfred Wallace. It is made as a paper-puppet animation, produced by Flora Litchman and Sharon Shattuck and narrated by George Beccaloni of the  Natural History Museum London and Andrew Berry of Harvard University.

 

What a fine example of science outreach. 

Lamarckism Continues To Cast A Shadow Over The Archaeological Survey Of India

A friend mentioned that she was planning to visit the famous rock shelters at Bhimbetka in Madhya Pradesh. These sandstone caves are famous for rock art and stone tools ranging in age from Paleolithic to more recent times. The site is looked after by the Archaeological Survey of India (ASI).

I remembered my own trip there over three years ago. Diving into my picture collection I  came up with this gem. This plaque was in front of a cave where Paleolithic stone tools had been found. It describes the grand story of human evolution.

Underlined in yellow is the explanation for the evolution of our dexterous hands. I am not highlighting the language but the very Lamarckian-sounding mechanism. If the claim is that hands capable of making sophisticated tools evolved just by continuous handling of stone, then this is evolution occurring through inheritance of acquired characteristics. Just like a blacksmith passing on his musculature to his children. This is not a viable mechanism of evolution. Physiological changes acquired due to a life experience are not passed on to progeny. Our gametes are sequestered from our somatic cells. I strongly suspect that a lot of people still conflate inheritance of acquired characters with natural selection.

The very first sentence "Millions of  years after Ramapithecus the species Australopethecus and its subspecies came into existence" is confusing too.  As is another plaque which shows the classic linear march of hominin evolution from a more primitive looking ape to modern humans. In it, Ramapithecus appears to be an early ancestor of humans.

Australopithecus (genus, not species), did appear millions of years after Ramapithecus, but there is no ancestor-descendant relationship between the two. Ramapithecus was initially identified as a Miocene ape and a possible ancestor of humans. Its range was the Himalaya foothills, leading to some excitement that the human family roots can be traced to the Indian subcontinent. More fossil finds have changed this early interpretation. Ramapithecus is not even considered a valid taxon anymore. The fossils named Ramapithecus are now subsumed under the genus Sivapithecus. This latter genus includes a great variety of Asian ape species. The lineage is more closely related to the ancestors of the Orangutan and not to living African apes and the hominin family.

This is just a poor show by the ASI. They need to urgently upgrade the information they are providing the public.

Interview- Rosemary And Peter Grant On Watching Evolution In Action

Source: Quanta Magazine; Courtesy Peter and Rosemary Grant

Daphne Major in the Galapagos chain.

Yes, 40 years of field research on that half a square km size island, tracking, generation after generation, changes in body and beak size of different species of ground finches.  Lately, they have supplemented their morphologic and bird song data with genomic analysis to get an understanding of the genetic underpinnings of morphologic change.

Rosemary and Peter Grant interviewed about their epic evolution watch:

"The diminutive island wasn’t a particularly hospitable place for the Grants to spend their winters. At less than one-hundredth the size of Manhattan, Daphne resembles the tip of a volcano rising from the sea. Visitors must leap off the boat onto the edge of a steep ring of land that surrounds a central crater. The island’s vegetation is sparse. Herbs, cactus bushes and low trees provide food for finches — small, medium and large ground finches, as well as cactus finches — and other birds. The Grants brought with them all the food and water they would need and cooked meals in a shallow cave sheltered by a tarp from the baking sun. They camped on Daphne’s one tiny flat spot, barely larger than a picnic table.

...They visited Daphne for several months each year from 1973 to 2012, sometimes bringing their daughters. Over the course of their four-decade tenure, the couple tagged roughly 20,000 birds spanning at least eight generations. (The longest-lived bird on the Grants’ watch survived a whopping 17 years.) They tracked almost every mating and its offspring, creating large, multigenerational pedigrees for different finch species. They took blood samples and recorded the finches’ songs, which allowed them to track genetics and other factors long after the birds themselves died. They have confirmed some of Darwin’s most basic predictions and have earned a variety of prestigious science awards, including the Kyoto Prize in 2009".

indefatigable to the end..

"Do you plan to go back to Daphne?

RG: We stopped intensive work after 40 years, but we do plan to go back.

PG: The oldest person died at 122 years old. That means we have 40 more years".

Ground finches are off course the birds that Charles Darwin famously observed when on tour to the Galapagos, but infamously didn't mention in his book since he never labelled his samples according to their island location. He did borrow correctly labelled samples from other sailors and then had the ornithologist John Gould classify them. Gould's finding was that the islands finches were a group of sibling species despite their widely varying body and beak size and shape.

Habitats varied on different islands. Darwin realized that sometime in the distant past one ancestral population of finches must have immigrated from the South American mainland and then diverged into several morphologically distinct species, each a fit to its habitat. That was one of the threads of reasoning he weaved into a more comprehensive theory of common descent and evolution through natural selection.

The book, Beak of the Finch by Jonathan Weiner, is a bit dated but is still a riveting account of Rosemary and Peter Grant's research.

Update: @avinashtn alerted me to the Grant's book "40 Years of Evolution".

What Is Speciation?

 Here is some evolutionary theory. Its a bit of a hard slog, but worth the effort.

Review article by Jessie Shapiro, Jean-Baptiste Leducq and James Mallet on "why speciation happens (or not) and the nature of the speciation process" -

Concepts and definitions of species have been debated by generations of biologists and remain controversial. Microbes pose a particular challenge because of their genetic diversity, asexual reproduction, and often promiscuous horizontal gene transfer (HGT). However, microbes also present an opportunity to study and understand speciation because of their rapid evolution, both in nature and in the lab, and small, easily sequenced genomes. Here, we review how microbial population genomics has enabled us to catch speciation “in the act” and how the results have challenged and enriched our concepts of species, with implications for all domains of life. We describe how recombination (including HGT and introgression) has shaped the genomes of nascent microbial, animal, and plant species and argue for a prominent role of natural selection in initiating and maintaining speciation. We ask how universal is the process of speciation across the tree of life, and what lessons can be drawn from microbes? Comparative genomics showing the extent of HGT in natural populations certainly jeopardizes the relevance of vertical descent (i.e., the species tree) in speciation. Nevertheless, we conclude that species do indeed exist as clusters of genetic and ecological similarity and that speciation is driven primarily by natural selection, regardless of the balance between horizontal and vertical descent.

The included glossary does help.

Do Marine Animal Lineages Evolve Toward Larger Body Size Over Time

aka Cope's Rule-

I like these big questions about the history of life and I am fascinated and very impressed when palaeontologists take up such questions. It is incredibly laborious and time consuming work, to go through archival data on fossils and often generate new data from museum specimens and older compilations describing fossil taxa.

A recent study in Science Magazine:

Cope’s rule in the evolution of marine animals - Noel A. Heim, Matthew L. Knope1, Ellen K. Schaal, Steve C. Wang, Jonathan L. Payne

Cope’s rule proposes that animal lineages evolve toward larger body size over time. To test this hypothesis across all marine animals, we compiled a data set of body sizes for 17,208 genera of marine animals spanning the past 542 million years. Mean biovolume across genera has increased by a factor of 150 since the Cambrian, whereas minimum biovolume has decreased by less than a factor of 10, and maximum biovolume has increased by more than a factor of 100,000. Neutral drift from a small initial value cannot explain this pattern. Instead, most of the size increase reflects differential diversification across classes, indicating that the pattern does not reflect a simple scaling-up of widespread and persistent selection for larger size within populations.

What that means is that the size increase is not due to a uniform increase across all animal groups. Rather, groups that were larger very early in animal evolution have diversified disproportionally more than smaller sized groups. Why should that happen? The authors suggest that there may be advantages to being larger, such as, ability to move faster, to capture larger prey and to burrow deeper for protection and exploiting additional food resources.

That would seem to make larger animals more resilient to background extinction and make larger sized lineages longer lived. But why would that make larger animals more speciose? i.e. why would larger sized animals species split into more new species than smaller sized animal species? ..because that is what is the claim, that throughout the history of animal evolution larger sized species gave rise to more new species than smaller sized ones (differential diversification). In fact, one could make arguments favoring higher rates of speciation in smaller sized organisms, such as, their ability to disperse over greater geographic area resulting in greater chances of populations getting reproductively isolated resulting in new species, their ability to survive better during environmental crises (survivor fauna after mass extinctions tend to be smaller bodied, mass extinctions seems to kill of larger bodied species disproportionately). If mass extinctions differentially kill off larger bodied species, then is the observed trend really a series of trends, each reset at the aftermath of the crises, resulting in small pioneer /survivor fauna evolving towards larger size. There could be a physical limit to how small one could become and the only direction for size to vary (either through drift or natural selection) would be towards a larger size. I am just speculating without even reading the paper, the authors do mention that drift from a small initial size does not explain their findings, but it would interesting to know what role mass extinctions might be playing in disruption or amplifying trends.

So although a trend is apparent, the answers are not all clear cut. It would also be interesting to group the trends according to life habits, i.e. planktonic versus benthic, sessile versus mobile  and see if any of these life styles particularly favors evolution towards larger size.

Eurekalert has a summary of the study. 

In Darwin's Footsteps: A Book On The Galapagos Daphne Major Finches

Years ago I read Jonathan Weiner's excellent book The Beak Of The Finch. He describes the work of Peter and Rosemary Grant on the finches of Galapagos Islands with its fertile volcanic landscapes and biodiversity having inspired another aspiring naturalist in the 1830's to great discoveries. The Grants studied for decades evolution of finch populations, observing in them natural selection in action.

Now they have written their own book- 40 Years of Evolution: Darwin's Finches on Daphne Major Island.

Jonathan Weiner writes about it in the New York Times:

They kept up their watch during years of downpours and years of drought — seasons of feast and famine for the finches. And Darwin’s process unfolded before their eyes in intense episodes that illustrated better than anything in the Origin the struggle for existence, and the ways that life adapts and emerges fitter from the struggle.

.. and on the possible beginnings of a distinct lineage -

Big Bird’s lineage has now lasted for 30 years and seven generations. The Grants are cautious about its prospects — “It is highly unlikely that we have witnessed the origin of a long-lasting species, but not impossible,” they write — but other scientists are buzzing.

This is exciting work, the stuff that inspires young students of the subject to push ahead with their own dreams and aspirations. The Grants are both 77 years young now... and still studying their beloved finches.

Sherlock Holmes And Long Term Evolutionary Patterns In Dinosaur Body Size

This week's (in Pune, India) Sherlock Holmes Elementary featured a murder mystery involving a smuggled dinosaur fossil. The fossil is believed by some palaeontologists to be entombed in rocks of the earliest Paleocene, making that dinosaur a survivor of the end Cretaceous mass extinction. Other palaeontologists strongly disagree with this survivor fauna scenario, which the drama turns into a motive for murder. There was a fair amount of geology and palaeontology in the episode and a reference to a term "dead clade walking".  This term is real life was coined by David Jablonski a palaeontologist from University of Chicago.  The term means that a clade or a lineage has survived a mass extinction but its fate has been sealed. Over a period of time say a few million years after the mass extinction that group does eventually go extinct.

Some dinosaur species may have survived the mass extinction but by early Palaeocene they were certainly all gone... except one lineage.. the Availea or birds. They prospered in the Cenozoic, radiating into a hundreds of species. Their success may have had deep roots and one important factor may have been the small size of their ancestors.

A paper in PLOS Biology explores the long term evolutionary patterns of dinosaurs and finds a positive relationship between high rates of evolution and small size-

Rates of Dinosaur Body Mass Evolution Indicate 170 Million Years of Sustained Ecological Innovation on the Avian Stem Lineage:

Author Summary

Animals display huge morphological and ecological diversity. One possible explanation of how this diversity evolved is the "niche filling" model of adaptive radiation—under which evolutionary rates are highest early in the evolution of a group, as lineages diversify to fill disparate ecological niches. We studied patterns of body size evolution in dinosaurs and birds to test this model, and to explore the links between modern day diversity and major extinct radiations. We found rapid evolutionary rates in early dinosaur evolution, beginning more than 200 million years ago, as dinosaur body sizes diversified rapidly to fill new ecological niches, including herbivory. High rates were maintained only on the evolutionary line leading to birds, which continued to produce new ecological diversity not seen in other dinosaurs. Small body size might have been key to maintaining evolutionary potential (evolvability) in birds, which broke the lower body size limit of about 1 kg seen in other dinosaurs. Our results suggest that the maintenance of evolvability in only some lineages explains the unbalanced distribution of morphological and ecological diversity seen among groups of animals, both extinct and extant. Important living groups such as birds might therefore result from sustained, rapid evolutionary rates over timescales of hundreds of millions of years.

In general the rapid-evolvers would be the smallest-bodied species -- the ones that reach reproductive age quickly and while they are still small. Rates of evolution depend on generational time. Which predicts that large-bodied/long-generation-time species would have more difficulty adapting to rapidly-changing extinction conditions.

The authors also mention that body size evolution in many non-avian dinosaur lineages seem to follow Cope's Rule, an increase in body size of descendant species over time. The earliest species in that lineage would be small and over time there would be a trend towards evolution of larger bodied species.

What could cause such a trend? Is larger body size advantageous and hence being favored by natural selection? Again the relationship to mass extinctions is intriguing. The authors mention that during the late Triassic mass extinction many branches of dinosaurs became extinct. If larger bodied dinosaur species were disproportionately killed off the survivor species of dinosaurs in early Jurassic would have been small bodied. This could explain Cope's Rule in a rather novel way (as explained by my adviser Anthony Arnold - who has worked on size evolution in foraminfera - in an email to me) - "since it means that rather than evolution favoring size increase, mass extinction selectively removes larger-bodied species, leaving behind the smaller guys as survivors. Since they don't have much room to get smaller the survivors could even speciate at random and the only direction in which the variance has room to expand is toward larger size.

Maybe!.. arm waving.."

So ecological crises may lead to species sorting based on size with smaller size being favored and then evolution of a trend towards larger size that reflects simply an inability to become any smaller!..
 

Book- John Tyler Bonner- Randomness In Evolution

This book is surely worth reading. Randomness in Evolution by John Tyler Bonner. I have loved Bonner's  previous books The Evolution of Complexity and Life Cycles. This promises to be interesting too.

In Current Science Raghavendra Gadagkar gives a positive review. The main premise of the book is that morphologies of unicellular eukaryotes like radiolarians and diatoms to give two examples are neutral phenotypes. That means that the variation of size, shape, ornamentation on skeletal material did not become common because it contributed to reproductive fitness. Rather for example different shapes were selectively neutral i.e. that is they neither gave the organism any advantage over another shape nor a disadvantage. One of the shapes became common just by chance, through random genetic drift.

Size according to Bonner is an important constraint on whether natural selection or drift becomes important in shaping morphology. Randomness is more important in small organisms with relatively simple genetic controls on morphology, while natural selection is more important in larger organisms with elaborate interlocking developmental steps.

I'll reserve comments until I have read the book but just would like to point out that even small unicellular eukaryotes have very sophisticated cellular machinery for processes like photosynthesis and regulating cellular functions. These would have evolved via natural selection.

Natural Selection And Punctuated Equilibrium

A reader asks-

I am still curious as to the mechanism and speed with which evolution by natural selection itself happened, like was it "punctuated equilibrium" or was it a slow and steady (continuous) mode of evolution, or was it a combination of the two, or some altogether third process. Not many programs discuss this unfortunately..

I left a short answer in a comment. Some additional thoughts:

Well.. Natural Selection and Punctuated Equilibrium are not directly connected with each other. Natural selection along with random genetic drift are mechanisms of evolution. Populations change in their genetic character and morphology due to natural selection or random genetic drift or a combination of the two. Punctuated equilibrium on the other hand refers to the tempo and pattern of morphological change seen in the fossil record and its significance. As was originally proposed by Eldridge and Gould it said that morphological change is concentrated in short bursts during cladogenesis i.e. when a new species buds off from an ancestral species. This change in morphology can be driven via natural selection or drift. So Punctuated Equilibrium says nothing about the primacy of any particular mechanism of evolution. Rather the emphasis is on the observed long periods of statis or little directional change in morphology in a lineage interrupted by geologically rapid bursts of change interpreted to be coupled to cladogenesis.

Gould later retracted somewhat from this position. He accepted the explanation for the pattern of Punctuated Equilibrium put forth by evolutionary biologist Douglas Futuyama which was that change could occur at any time during the life of a species but it is only when a small population gets reproductively isolated from its parent population i.e when the two populations stop exchanging genes that any directional change may get fixed or become permanent enough to show up in the fossil record.

Then there are examples of lineages changing in a slow and steady fashion too.. so can't generalize.. Nature has examples of both.

Regarding why programs don't cover this-its true that television programs have to my knowledge not covered this topic. My sense is programs on evolution and fossils stick to popular topics like the discovery of fossils of recognizable creatures like dinosaurs, the first tetrapods, proto-whales or on dramatic events in the history of life such as mass extinctions. A debate that uses detailed morphometric analysis of creatures like trilobites and foraminifers to reveal the pace of evolution (two organisms used extensively to test for patterns of punctuated equilibrium due to their abundance) may be thought of as too arcane to make for great television.

Having said that punctuated equilibrium got its fair share of attention in the print media and mostly for the wrong reasons for it was widely misinterpreted by the media as some kind of alternative to conventional evolution. The biggest mistakes made were in thinking that punctuated equilibrium means that new species form due to large morphological changes that occur suddenly. The primary authors Eldridge and Gould never advocated this, but the garbled version promoted in popular press made it seem so and large changes meant that some unknown genetic mechanism (macromutations?) may be at work. In reality, some of the demonstrated cases of punctuated equilibrium from trilobites showed that the new species differed only slightly from the ancestral species, nothing that could not be explained by well understood processes in an evolving population. So, an interesting theory that sought to explain patterns of appearances of new species in the fossil record as an example of allopatric speciation and migration became sensationalized as an alternative to "Darwin's theory" of evolution.

Creationists loved it,  palaeontologists banged their heads in frustration and much of the reading public have been confused ever since.

 

Neil deGrasse Tyson's Cosmos On Evolution

This past Sunday in India the second episode of Neil deGrasse Tyson's Cosmos was broadcast on National Geographic. The title was "What Molecules Can Do" and it was all about the evolution of life on earth. I quite enjoyed it. .. Just a couple of quibbles.

Dog evolution was showcased as an example of artificial selection which then Dr. Tyson used to argue for the efficacy of natural selection. It was depicted in cartoon form and the dog cartoons though showed quite a modern looking dog barking and scaring a wolf away from a campsite. This was meant to show the very early relationship  between dogs and humans. Early dogs wouldn't have looked as depicted in that frame. Its hard to point to modern dog breeds and find an analogue for the earliest dogs because they have changed so much and so late in their history. Still, a more smaller version of a wolf with a stubbier face would have been a best representative of early dogs, and not the hairier house pet looking one.

Later in the show Dr. Tyson wanting to emphasize that evolution is true says that the the "theory of evolution is a fact". That is a little confusing.  Evolution is a fact. Life has changed over the past 4 billion years and the theory of evolution is a theory that attempts to explain how it happened. There are many theories of evolution. Some like Lamarck's theory rely on organisms responding to environmental stimuli and the inheritance of acquired characters to explain change. Creationists in their garb of Intelligent Design have faith in an unknown intelligence guiding natural processes. Modern evolutionary theory that adds on to Darwin's and Wallace's insights is the most successful one.

Not Just a Puppet! The Animated Life Of Alfred Russel Wallace

Have you seen this documentary?

The Animated Life Of A.R. Wallace.

Produced by Flora Litchman and Sharon Shattuck and narrated by George Beccaloni of the  Natural History Museum London and Andrew Berry of Harvard University, it celebrates the life and work of Alfred Russell Wallace who along with Charles Darwin discovered the principles of evolution through natural selection in the mid 1800's. Wallace also made pioneering contributions to the field of Biogeography.

A fine example of creative science outreach using paper puppet animation. Beautifully produced and narrated.

An Account Of Natural Selection By A Victorian Gentleman

Who wrote this...Darwin or Wallace?

There is a law universal in nature, tending to render every reproductive being the best possible suited to its condition that its kind, or organized matter, is susceptible of, which appears intended to model the physical and mental or instinctive powers to their highest perfection and to continue them so. This law sustains the lion in his strength, the hare in her swiftness, and the fox in his wiles. As nature, in all her modifications of life, has a power of increase far beyond what is needed to supply the place of what falls by Time's decay, those individuals who possess not the requisite strength, swiftness, hardihood, or cunning, fall prematurely without reproducing—either a prey to their natural devourers, or sinking under disease, generally induced by want of nourishment, their place being occupied by the more perfect of their own kind, who are pressing on the means of subsistence . . .

There is more beauty and unity of design in this continual balancing of life to circumstance, and greater conformity to those dispositions of nature which are manifest to us, than in total destruction and new creation . . . [The] progeny of the same parents, under great differences of circumstance, might, in several generations, even become distinct species, incapable of co-reproduction.

The answer is neither.

Field Photo: Adaptation

Location: Slope of Panchgani Tableland- Western Ghats

Do let me know if you can identify this plant.

Multicellularity, Evolution, Life

On NPR's Cosmos and Culture blog biologist Ursula Goodenough has been writing some terrific posts on evolution. Two that recently caught my eye:

Unicellularity Vs. Multicellularity: Why We Bother With More Than One Cell

Time and Life

Both are worth spending some time on.

Coming back to the topic of the evolution of multicellularity the latest issue of Geology has a paper that does some analysis on continental reconfiguration during the early Cambrian and proposes that there was a major movement and rotation of Gondwana resulting in establishment of a new ecological landscape, new conditions that may have provided the impetus for the rapid radiation of metazoans otherwise known as the Cambrian "explosion".

Explanations for the Cambrian explosion have occupied two extremes. One view proposes that the fuse was a biological one. Some crucial biological innovation in terms of gene regulation and molecular cascades remained to be discovered until complex metazoans could evolve. According to this view these changes likely occurred beginning around 600 mya. The other view proposes that practically all the complex genetic machinery necessary for metazoans to function already existed in unicellular eukaryotes. The reason for the delay in the advent of metazoans (complex unicellular eukaryotes date back to more than a billion years) were ecological constraints such as a lack of enough oxygen in the atmosphere.

Lately I sense that the ecological argument is winning out not least because earlier experiments in multicellularity are coming to light. Life getting organized into agglomerates of cells is a  theme that has been independently invented several times and as far back as a couple of billion years ago if recent findings in Gabon and in India's Vindhyan basin hold true.

The thought of genetic potential waiting to be unshackled into new and varied forms is fascinating and one doesn't have to venture into the unfamiliar Cambrian terrain for an example. The transformation of the wolf into the myriad morphs of dogs is a strong example. A recent study (via Panda's Thumb) showed that the morphological variation in skull shape across the entire order of Carnivora is less that the variation seen within dogs. The ecological landscape experienced by ancestral wolves did shift dramatically in recent times not by continental movements as proposed for the Cambrian radiation but by the imposition of new selection pressures by humans. Wolves apparently always had the genetic potential to diversify into what could be described as downright weird forms. The changing human ecology provided the trigger and helped maintain these forms, many who may not have survived in the wild.

The evolution of complexity seems to be open ended. There must have been occasions when there was a significant change in genetic architecture. John Maynard Smith and Eors Szathmary document these steps in their book The Major Transitions in Evolution. Other times it was an exogenous influence that triggered a change, a  matter of filling a new ecological niche.

Species Sorting Through Preferential Survival Of Aragonite Biota

Geological Processes and Evolution - 6

alright... enough about those Deccan Basalts.

A juicy paper on skeletal mineralogy, sea water chemistry and evolution in the December issue of Geology:

Controls on carbonate skeletal mineralogy: Global CO2 evolution and mass extinctions -  Andrey Yu. Zhuravlev and Rachel A. Wood

There has been cyclical shifts in sea-water composition through the Phanerozoic known as Aragonite seas and Calcite seas wherein inorganic aragonite and low-Mg calcite (cements, ooids) respectively preferentially precipitated. That is mimicked by skeletal mineralogy but with a catch. And that is that sea-water chemistry strongly influences the choice of skeletal mineralogy only for those groups that are newly acquiring the ability to build skeletons.  Once skeletonization is acquired most organic groups do not change their skeletal mineralogy through subsequent sea-water compositional changes.

Doing a survey of changes in skeletal mineralogy over time  Zhuravlev and Wood found out that the cyclical shifts in carbonate mineralogy is superposed on a longer shift towards aragonite, both in inorganic phases as well as a skeletal mineral. This they attribute to a gradual decrease in the pCO2 of sea-water (ultimately due to an atmospheric decrease) over the Phanerozoic. As pCO2 decreases the amount of dissolved carbonate ions (CO3) increases. An increased saturation of CO3 increases the supply of this ion to crystal nucleation sites. Such a rapid precipitation environment favors the growth of aragonite over calcite for reasons to do with the atomic structure of aragonite which is constructed more rapidly especially along the C crystallographic axis.

Besides CO3 saturation, ions like SO4 and Mg inhibit the rapid growth of trigonal calcite by poisoning lattice sites for CO3 and Ca. If SO4 and Mg are present in low quantities then in low CO3 saturation states, calcite is favored.  If SO4 and Mg are present in large quantities in sea-water they interfere with the growth of the calcite structure and amplify the kinetic advantage aragonite has over calcite in CO3 saturated waters.

That's not the only story though. The increase in aragonite skeletal groups was not gradual but step-wise, coinciding with mass extinctions. The end -Devonian, end-Permian and the end-Cretaceous mass extinctions ( low pCO2 , high SO4..?) were especially severe on low-Mg calcite skeletal groups wiping them out preferentially.

Figure below shows the step-wise proportional increase in aragonite groups as well as inorganic aragonite (histograms) over the Phanerozoic. Dotted lines are mass extinctions.

This favored the proliferation of aragonite biota which occupied and radiated in the ecological niches emptied by the extinction of calcite biota.

...at this point my posts usually begin to drift towards evolution... and so...

Evolution occurs through a variety of mechanisms. Lord Tennyson's evocative "nature red in tooth and claw" is the one that occupies popular imagination. But that mechanism of evolution - natural selection - as Darwin later explained, works through competition between individuals within a species. Besides natural selection, random genetic drift also is a common mechanism of change acting at the level of the individual or the gene.

But evolution can occur through processes acting at one hierarchical level above the individual i.e at the level of the group or species through mechanisms such as species sorting. In this case the change is driven through the differential extinction and/or reproduction of species that share certain traits. A process of sorting is taking place at the level of species. Certain types of species are surviving while others are going extinct.

Species that precipitate low-Mg calcite or aragonite skeletons are a good example. Evolution is occurring not through a direct competition for resources between calcite skeleton individuals and aragonite skeleton individuals but by conditions preferentially favoring the precipitation of aragonite over calcite.

This is because the ability to precipitate either aragonite or calcite is a property shared by every individual in either of these groups. The variation for evolution to work on comes from differences not between individuals within a group but by differences at a level higher than the individual i.e. the group. Differences between groups such as aragonite mineralogy versus calcite mineralogy determine the differential survival of entire groups.

Adaptive complexity is best explained by natural selection acting at the level of the individual. But not all patterns of life are explainable this way. The history of life has seen large-scale biotic turnovers wherein one group of organisms fade away and another become more common. Many such turnovers coincide with mass extinctions.

It is not always clear and easy to explain why certain groups became extinct while others survived and later prospered. Species sorting can occur for a variety of reasons....like...small size...wider geographic range...higher fecundity...all group properties that may help one type of group do better and survive tough ecological conditions compared to another group...

...or maybe in the case of marine groups that precipitate carbonate skeletons....mineral kinetics.

See: Geological processes and evolution

Tasmanian Devils And One Selfish Gene

Genes don't have real motives. Selfish in the term "selfish gene"  really reflects the metaphorical motives of genes and not the real motives of individuals carrying those genes.

Ordinarily, different genes in the multicellular bodies of organisms co-operate. Such a system has evolved because in sexually reproducing multicellular organisms the reproductive fate of any gene depends on the successful reproduction of the individual. Genes in the somatic cells of the body, cells which form the body mass, can extend their lives only if a copy of themselves in the sex cells gets passed on. Co-operating to build successful bodies is the only way out.

But what if a gene is able bypass this system? What if a gene is able to unlink its reproduction from the reproduction of the individual?

Just such a situation has occurred in the spread of cancerous facial tumor in populations of the Tasmanian Devil - a carnivorous marsupial. Scientists working on these animals have identified a nerve cell type known as Schwann cells as the progenitor of this cancer which must have originated through mutations in one Schwann cell of one individual Tasmanian Devil.

Devils are aggressive creatures and they often bite each other especially during mating. The cancer cells graft themselves on facial tissue of the other individual and grow and spread. As cells divide, the bodies defense may kill some of these cells, but mutants among them which are better able to resist  thus become more common. This is natural selection acting on this cell lineage. Within the lifetime of an individual devil, cancer cells divide hundreds of times. Cells in the nth generation would be different somewhat from their ancestral state. This is evolution, though not in the form we are familiar with or think of commonly.  Ordinarily, this cancer cell lineage would die with the death of the individual. In this case, their evolution continues when they get grafted on another individual. The tumor gene thus spreads through the population by bypassing the normal channels of reproduction. The cancer cells have been able to successfully invade another body in this way because there is very little genetic variation in the immune system of the Tasmanian Devils. That may be because there are a small inbred population. Immune cells don't recognize grafted cancer cells as foreign and don't reject them.

The mutant gene (s) responsible for this cancer can be thought of as a special type of a selfish gene. In a broader sense all genes are selfish since they "try" to maximize copies of themselves by competing against variations of themselves.  Generally, the reproductive fate of the gene is tied to the reproductive fate of the individual and so genes cooperate to make bodies successful. However, in the more specific usage of the term, selfish genes may enhance their own reproduction by subverting the reproductive machinery of the cell and in the process causing harm to the population in the long run.  During sexual reproduction any gene on average has a fifty percent chance of being passed on to the next generation. A selfish gene subverts these odds and ensures a more than even chance for copies of itself to be passed on.

In the case of the Tasmanian Devils, the "selfish gene" is not in the sex cells but is a somatic cell mutant.

We don't think of somatic cells as a separate life form. The cells that make up our bodies are us. But occasionally as in the case of the facial cancer in the Tasmanian Devils the us can morph into the other. Most cancerous cell types which rebel against the body don't have an extended evolutionary future. The cell lineage dies with the death of the individual.  This particular cancer cell however, which was once part of the Tasmanian Devil is evolving into a parasite. It has developed a life of its own.

This situation illustrates several broader principles of evolution.

Firstly that evolution has no foresight. There is no long term benefit of the Tasmanian Devils that evolution is striving towards. Natural selection doesn't work for the benefit of the species. Evolution through natural selection is all about immediate advantage. Mutant cells have found a way to propagate independent of the body and because their life cycles operate quicker than that of an individual, selection will favor the spread of these cells regardless of whether that is harming Devil individuals and populations.

Second, it demonstrates that natural selection doesn't only act at the level of the individual.  It can act on any entities which shows certain properties. If entities vary in certain traits, if these traits are heritable and if these traits affect "fitness" i.e. they enable one variant to reproduce more than the other then natural selection is off and running. In the natural world these conditions are most familiarly met by whole organisms but in principal they can be met by cells or genes within cells.

In this case, selection is operating at two levels. At a lower level cells which contain the mutant gene are fitter than cells that don't contain this gene. But at a higher level individuals that don't contain this mutant gene are fitter than individuals that do. In most cases the "interests" of the gene and the individual coincide. Here, because their reproductive fates have been decoupled the relationship has turned antagonistic.

Finally, the study shows that the reconstruction of a complete evolutionary narrative requires thinking across the entire (or as much as possible) hierarchy of life.  The so called division between reductionists and practitioners of "holistic" biology is and always has been a false dichotomy.  Genes, cells, individuals, social behavior and population history all go to make the unfortunate story of the Tasmanian Devils more complete.

** Wishing readers coming to this post via Desipundit a very Happy New Year. If you missed my earlier announcement do note that my blog Reporting on a Revolution has been renamed Rapid Uplift. ...more in tune with the broad earth sciences / geology theme I write about.  Thanks for your support.

Relaxing Natural Selection In The Wild

Trends in Ecology and Evolution has a paper on the evolutionary fate of traits that are subjected to relaxed selection. More than the paper I enjoyed the journal cover:

Very Gary Larson..ish I thought.

Science Daily has a good summary of the research.

Darwin's 200th: Red Queen And The Lives Of Species

Do species behave like individuals? Do they show the effects of aging reflected in an increased probability of extinction with age?

Darwin argued that natural selection acted at the level of the individual and consequently one type of individual was favored over another. According to him it was competition between individuals within a species that was the engine of evolutionary change.

“But the struggle almost invariably will be most severe between the individuals of the same species, for they frequent the same districts, require the same food, and are exposed to the same dangers.”

But he also recognized the possibility of competition between species leading potentially to species selection.

"The affinities of all the beings of the same class have sometimes been represented by a great tree. I believe this simile largely speaks the truth. The green and budding twigs may represent existing species; and those produced during each former year may represent the long succession of extinct species. At each period of growth all the growing twigs have tried to branch out on all sides, and to overtop and kill the surrounding twigs and branches, in the same manner as species and groups of species have tried to overmaster other species in the great battle for life."

Species selection is analogous to natural selection acting between individuals. With species selection an evolutionary pattern develops as one type of species is favored or another. For example long lived species may give rise to more descendant species than short lived species. Longevity is a species level property, controlled by say a large versus small geographic range. Over time long lived species may become more numerous than short lived species. So, certain types of species proliferate if they have higher rates of speciation or lower rates of extinction. Darwin didn't really develop this concept. The fossil record in his days was poor and there was no way to test any theory of species selection.

I love palaeontology. I am not much of a fossil collector but I like to understand evolution through fossils. I had two paleontologists on my Ph.D committee. My major adviser who also knew a lot about carbonates and another guy who worked almost exclusively on evolution. This post is based on their work on evolutionary patterns in Mesozoic and Cenozoic planktonic foraminifera.

In the early 1970's University of Chicago paleontologist Leigh Van Valen applied survivorship analyses to fossil taxa. This type of analysis is usually done to understand mortality patterns in a population. So in a sample what fraction of individuals died at childbirth, how many as small children, how many as teenagers, and so on at successive intervals. The results are survivorship curves like the one below.


So depending upon socio-economic conditions, parasite loads and other controls a population may be categorized as type I, II or III. Type I is in which mortality rates of the elderly are high. Type III is one where juvenile mortality is high. And Type II is one where the probability of dying is not age depended. The odds of dying at any age are about the same.

Now you would intuitively expect species to show a type III sort of a curve. A newly formed species may not have developed adaptations to a changing environment. But as time goes by the fit between the individuals and the environment increases and so the probability of a longer lived species going extinct decreases. Instead Van Valen found that extinction patterns in fossil taxa follow curve II. The probability of extinction of species is age independent. This became know as Van Valen's law of constant extinction.

Remember to avoid this misunderstanding. The rate of extinction is not constant.

Obviously!

During major environmental perturbations, for example after a meteorite strike, the rate of extinction will increase precipitously. What Van Valen found was that the probability of extinction does not depend of how young or well established (old) the species is. Species of any age have the same chance of going extinct.

Enter the Red Queen. In Lewis Carroll's fantasia novel Through the Looking Glass the Red Queen says to Alice:

`Now, HERE, you see, it takes all the running YOU can do, to keep in the same place. If you want to get somewhere else, you must run at least twice as fast as that!’

Using this wonderfully quirky analogy Van Valen argued that species too are running faster and faster but stay in the same place relative to other species. This happens because species interact with other species in its environment. If a gazelle evolves a slightly faster speed of running so will its predator the cheetah. If a parasite evolved a new dodge to its host immune system, the host will evolve a new way of stopping the parasite. Species may change in an absolute sense but they remain the same relative to their competitors.

And so the extinction probability is stochastically constant with respect to species age.

My advisers along with their students have been testing the Red Queen prediction in a long drawn out study using Mesozoic and Cenozoic planktonic foraminifera. Their recent results have been published in the journal Palaios. Plantonic foraminifera are particularly well suited for survivorship analysis since they have a really good fossil record and their ranges are well known.

After crunching the numbers the results showed that extinction is usually random with respect to age except during major extinction events. There is a significant deviation from Red Queen behavior at and after the Cenomanian-Turonian extinction event and after the late Cretaceous-Tertiary extinction event (the one that did in the dinosaurs). This pattern is seen in figure below ( beta coeff. of zero is ideal Red Queen behavior) where the upward spikes around 96 mya ( C-T event) and 65 mya (K-T event) represent deviation from the Red Queen prediction of constant extinction probability.

Now the pattern of deviation was peculiar in that it showed that the extinction probability increased with species age . It resembled the Type 1 survivorship curve I put up above. Just like individuals, species seem to be going through senescence.

That doesn't make sense. Species don't senescence. An individual exists between the time of birth and the time of death. A species too exists between times of its origin and extinction. But at any one time of its historical range a species is made up of populations of individuals who age and die and are replaced by the next generation of individuals, an unbroken ancestor descendant series.

Yet planktonic foraminifera species after mass extinctions were behaving like individuals, going extinct as they grew older.

The most likely explanation is that during mass extinctions certain types of species were more likely to adapt and survive and the subsequent evolutionary pattern of these survivors was showing up as age dependence of extinction. Postmassextinction species tend to be made up of small sized individuals. Small size is an indicator of early sexual maturity. So these species are characterized by adults who reach sexual maturity early in life and stop growing.

These types of species are rapid evolving taxa. This is because individuals have short generation time. The rate of evolution depends on generation time and not absolute time (bacteria evolve quicker than elephants). During times of environmental disturbances it is these rapid evolvers that can keep adapting to the changing environment and make it through. Using the Red Queen metaphor, if species keep running to stay atop a moving adaptive peak, during times of crises only the sprinters among them keep pace with the rapidly changing conditions.

If you want to get somewhere else, you must run at least twice as fast as that!

As conditions improve after the mass extinction the survivor species retain their rapid response characteristic and keep evolving quickly and eventually get transformed into new morphospecies. It appears that they have gone extinct. So the pattern of increase probability of extinction with species age results from populations of post extinction species evolving rapidly into new species, a process known as pseudoextinction.

How do we understand this in terms of selection acting at different levels of biological organization?

Here again selection is acting on two levels. During environmental crises there is selection for early sexual maturity at the level of the individual. So individuals who reach sexual maturity early are favored over individuals who reach sexual maturity late in life. Early maturer's due to their shorter generation time will become more numerous in the population over time. At the same time species with early maturing individuals are also fitter than species without such characteristics. Because the former are made up of individuals with short generation times, they tend to evolve rapidly and bud off new species. This type of species then becomes more numerous with time. Selection processes acting at the two levels, are complimentary. Unlike the earlier example I gave of the selfish gene where selection was favoring the cell containing the mutant gene but opposing the individual containing that gene.

After mass extinctions the nature and patterns of biotic recovery may depend on the characteristics of the survivor species. Selection can take place above the level of the individual. This species selection or species sorting as many people like to call it may lead to the establishment of long term macro-evolutionary patterns of the sort I described.

Darwin's 200th: Evolution Within Individuals

Do individuals evolve during their lifetime or at least do parts of them evolve? The picture below left of the Tasmanian devil with a facial tumor is an example of evolution within individuals.

Well, I had to write something about evolution on Darwin's 200th birth anniversary coming up February 12. I am going to be writing two posts on evolution and evolutionary patterns that may occur at a biological level of organization below and above that of an individual. Darwin didn't address evolution at these levels of biological organization. I am not taking pot shots at any perceived inadequacies in Darwin's thinking but rather trying to highlight how successful his theory really is.

Darwin's contribution is huge because his theory of natural selection is a general explanation that is scalable to all levels of life. It provides us with the intellectual tools to expand the theory beyond what he used it for and explain life's patterns at the level of cells, individuals and species. You have to say that is a pretty powerful idea. As Richard Dawkins put it, his theory has an extraordinarily high explanatory bang for the buck!



Alright so part 1 is about evolution below the level of the individual.

Darwin didn't know anything about genes or even what causes variation. So his theory of evolution didn't address evolution at the level of molecules or cells. His great obsession was to explain how diversity arises and how organisms acquire adaptations or rather evolve a state of adaptedness to their environment over time. To this effect he argued that natural selection acts at the level of the individual. Birds may evolve smaller or larger beaks over time depending of the food available, butterflies may evolve patterns mimicking a poisonous relative, peppered moths may evolve a dark color that acts as a camouflage. Individuals vary and natural selection filters this variation, retaining traits that help individuals survive and reproduce and eliminating traits that are harmful.

But natural selection doesn't only act at the level of the organism. It can act on any entities which shows certain properties. If entities vary in certain traits, if these traits are heritable and if these traits affect "fitness" i.e. they enable one variant to reproduce more than the other then natural selection is off and running. In the natural world these conditions are most familiarly met by whole organisms but in principal they can be met by cells or genes within cells.

Our cells contains two copies of each gene. During cell reproduction a fair system would ensure that each gene has a 50% chance of being passed down to the next generation. But there is scope of this system being subverted. If a mutant gene acquires the ability to increase its chance of being passed down to more than 50% by copying itself and proliferating inside the cell or by killing its sister gene, natural selection will favor it. Genes might then engage in a war among themselves to increase their own reproduction at the expense of the body. In fact complex bodies will not evolve if such genomic conflict is the norm. Mark Ridley has written an engrossing book on how evolution has come up with ingenious solutions to minimize this conflict enabling complex life to emerge.

Still evolution has not done a perfect job of prevention. Whole organisms - and I am talking about multicellular entities- are made up of populations of cells. During development these cells divide and establish cell lineages that perform different functions in the body. Each cell division comes with a probability of a copying error as 4 billion bases get read and a copy of the genome is assembled. Over time as somatic cells divide differences might arise between cells and natural selection might then act on those differences.

The most well know example of this is cancer, where a mutant somatic cell arises and increases in frequency relative to the "normal" cell type. This happens even though the change is harmful to the body. The birth and death rate of cells is a faster process than the birth and death rates of individuals and so natural selection will favor any mutant cell that concentrates on its own reproduction even if it is to the detriment of the body.

Evolution of cells within an organism that confer benefits to the individual also occurs and a recent paper- Evolution of Highly Polymorphic T Cell Populations in Siblings with the Wiskott-Aldrich Syndrome - in PLoS One describes this. The paper reports on a case of two brothers who have both inherited a disease causing allele. But the researchers found that over time in this cell population there have been multiple corrective somatic mutations. These corrective mutations confer an advantage to the host cell and consequently it occurs at higher frequency in that cell population than the diseased cell type. The researchers found that corrective mutants have been positively selected for and the diseased cells selected against.

The development, function and life cycle of somatic cells is part of a great co-operative venture that make bodies work. But population level evolutionary processes can occur in these cell lines within an individual. This is evolution, though not in a form we are familiar with.

By familiar evolution I mean a form where one type of individual is favored over another. That is what Darwin tried to explain. Darwin didn't know about the genes part. He understood something was passed from parent to child and his theory of natural selection worked just as well with this notion and explained the origin of adaptations. We know now that those adaptations develop and change over time through the flow of genes from the passage of germ line cells.

Somatic cell genes don't flow across generational times of whole organisms. The evolutionary histories of somatic cell lineages are short lived and are terminated as these cell lines go extinct with the death of the organism.

But just when you start getting comfortable with the idea of a well established evolutionary pattern, nature or rather evolution itself finds a way to get around it. A facial tumor that has spread and nearly decimated the Tasmanian devil - a marsupial carnivore - shows that somatic cells can sometimes develop an evolutionary history that can extend beyond the lifetime of an individual. Olivia Judson wrote a nice essay about this tumor and its effect on the Tasmanian Devils. The cancerous cell initially arose through a mutation. Devils are aggressive creatures and they often bite each other especially during mating. The cancer cells graft themselves on facial tissue of the other individual and grow and spread.The tumor gene thus spread from animal to animal by bypassing the normal channels of reproduction.

The mutant gene that produced this cancer is a good example of a selfish gene. This is a concept made famous by Richard Dawkins and represents a way of thinking about natural selection. A selfish gene is a mutant gene that enhances its own reproduction relative to the other copy of the gene or other genes in the cell often to the detriment of the body. So it is not just any old mutation. Most copying accidents or mutations harm the gene as well as the body. But "selfish genes" are mutations that natural selection favors at the level of the gene or the cell and opposes at the level of the individual.

So, selection is operating at two levels here. At a lower level cells which contain the mutant gene are fitter than cells that don't contain this gene. But at a higher level individuals that don't contain this mutant gene are fitter than individuals that do. The gene spreads even though it is harmful to the body since cellular reproduction is faster than the generation times of individuals.

The cancer is spreading rapidly in the Tasmanian Devils. Their populations have crashed in some areas by nearly 90% since the inception of this infectious cancer. It is possible that the devils may become extinct.

Natural selection operates on the immediate advantage. It has no long terms plans.

Our bodies are collections of tightly integrated cells. This fantastic example of co-operation has evolved through natural selection over hundreds of millions of years. We don't think of somatic cells as a separate life form. The cells that make up our bodies are us. But occasionally as in the case of the facial cancer in the Tasmanian devils the us can morph into the other. A cell which was part of the Tasmanian devil is evolving into a parasite.

Natural selection is an unsentimental process. It doesn't care for a billion years of co-operative evolution. If the opportunity arises, cells will just as easily rebel against our elaborate body politic and develop lives of their own.

**************

Tomorrow's post will be on the effect of species selection or species sorting on biotic recovery during and after mass extinctions.