Monday, March 31, 2014

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.


Tuesday, March 25, 2014

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.

Tuesday, March 18, 2014

Dating The Indian Proterozoic Sediments Using Diagenetic Glauconite

Geological radioactive clocks which rely on the known rate of decay of radioactive elements start ticking when these radioactive elements gets trapped in growing minerals and the mineral stops exchanging elements with its surroundings. This commonly occurs in minerals crystallizing out of magma or lava  or when a mineral recrystallizes during metamorphism. A radioactive clock from a mineral in an igneous rock tells us the date of the solidification of the magma or lava while a radioactive clock from a metamorphic rock may time the thermal event during which the host igneous or metamorphic rock recrystallized.

What about directly dating sedimentary rocks using radioactive clocks? Rocks like sandstones for example are made up of pieces of eroded igneous or metamorphic or sedimentary rocks. They may contain minerals like zircon that contain uranium or feldspars that contain radiogenic potassium, but dating these sedimentary particles  means finding out  the age of the source rocks and not neccessarily the timing of deposition of sediment.

One can indirectly date sedimentary rocks using radioactive clocks based on their geological relationship with associated igneous rocks. For example; 1) a sandstone sequence may unconformably overlie a granite. The age of the granite tells us that the sandstone sequence is younger than a particular date. 2) a sedimentary sequence may be intruded by an igneous body. The age of that igneous body if established tells us that the sequence is older than a particular date and 3) a sedimentary sequence may be bounded by igneous bodies, example volcanic eruptions many deposit lava or ash at various intervals synchronous with sediment deposition. In this case, the dates if established tell us that sedimentation occurred between two particular dates.

Often though a fortuitous association with igneous rocks is absent or saying "younger than", or "older than" or "between" leaves tens of millions or even hundreds of millions of years unaccounted for. In a study published a few years ago in GSA Bulletin, James E. Conrad and colleagues use another approach to directly date when sedimentation occurred. Although sedimentary rocks like sandstones are mostly made up of eroded particles they also occasionally contain minerals that grow on the sea floor or a few cms below  the sediment water interface. Such new minerals that form during or just after sedimentation are called diagenetic or authigenic minerals. Glauconite is one such diagenetic mineral which grows on the sea floor. It is a iron potassium (K) silicate and the radiogenic K40 decays into Argon40. Using the ratio of Ar40 to non radiogenic Ar39, the age of glauconite formation and thus sediment deposition was established.

Indian Proterozoic basins are just beginning to get their chronology established more robustly and diagenetic glauconite which is present in many different Indian basins offers another tool besides associated igneous rocks to more firmly establish the timing of basin formation, sedimentation, sequence evolution and changes in ocean geochemical conditions (glauconite forms under reducing conditions on the sea floor) during Proterozoic times.


Ages of some key stratigraphic sequences in central Indian Proterozoic basins are based predominantly on lithostratigraphic relationships that have been constrained by only a few radioisotopic dates. To help improve age constraints, single grains of glauconitic minerals taken from sandstone and limestone in two Proterozoic sequences in the Pranhita-Godavari Valley and the Chattisgarh basin were analyzed by the 40Ar/39Ar incremental heating method. Analysis of the age spectra distinguishes between ages that are interpreted to reflect the time of glauconite formation, and anomalous ages that result from inherited argon or postcrystallization heating. The analyses indicate an age of 1686 ± 6 Ma for the Pandikunta Limestone and 1566 ± 6 Ma for the Ramgundam Sandstone, two units in the western belt of Proterozoic sequences in Pranhita-Godavari Valley. Glauconite from the Chanda Limestone, in the upper part of this sequence, contains inherited 40Ar but is interpreted to reflect an age of ca. 1200 Ma. Glauconite from the Somanpalli Group in the eastern belt of the Pranhita-Godavari Valley gives an age of 1620 ± 6 Ma. In the Chattisgarh basin, glauconite from two units gives disturbed ages that suggest a period of regional heating in the Chattisgarh basin at ca. 960–1000 Ma. These new ages indicate that these sequences are 200–400 m.y. older than previously recognized, which has important implications for geochemical studies of Mesoproterozoic ocean redox conditions in addition to providing important constraints on regional tectonics and lithostratigraphy.

Sunday, March 16, 2014

Creationist Version Of Neanderthal Human Interbreeding

via The Panda's Thumb..

Had to put this up. Apparently creationists have their own take on the recent findings that Neanderthals interbreed with modern humans.

Svante Paabo who has led the effort to sequence the Neanderthal genome and has a popular book about it writes:

There were many others who were interested in the Neanderthal genome – perhaps most surprisingly, some fundamentalist Christians in the United States. A few months after our paper appeared, I met Nicholas J. Matzke, a doctoral candidate at the Center for Theoretical Evolutionary Genomics at UC Berkeley. Unbeknownst to me and the other authors, our paper had apparently caused quite a flurry of discussion in the creationist community. Nick explained to me that creationists come in two varieties. First, there are “young-earth creationists,” who believe that the earth, the heavens, and all life were created by direct acts of God sometime between 5,700 and 10,000 years ago. They tend to consider Neanderthals as “fully human,” sometimes saying they were another, now extinct “race” that was scattered after the fall of the Tower of Babel. As a consequence, young-earth creationists had no problem with our finding that Neanderthals and modern humans had mixed. Then there are “old-earth creationists,” who accept that the earth is old but reject evolution by natural, nondivine means. One major old-earth ministry is “Reasons to Believe,” headed by a Hugh Ross. He believes that modern humans were specially created around 50,000 years ago and that Neanderthals weren’t humans, but animals. Ross and other old-earth creationists didn’t like the finding that Neanderthals and modern humans had mixed. Nick sent me a transcript from a radio show in which he [meaning Hugh Ross] commented on our work, saying interbreeding was predictable “because the story of Genesis is early humanity getting into exceptionally wicked behavior practices,” and that God may have had to “forcibly scatter humanity over the face of the Earth” to stop this kind of interbreeding, which he compared to “animal bestiality.”

Clearly our paper was reaching a broader audience than we had ever imagined.

Aha.. so that's why humans colonized the entire planet. It was punishment for engaging in bestiality.

There is also a transcript of a bizarre conversation between creationists trying to answer the deep question that while there are references in scripture of God destroying angel-human hybrids, Neanderthal -human hybrids eventually died out too, leaving humans to be with humans only.

Friday, March 14, 2014

A New Direction For Indian Higher Education And Research Institutes

Seema Singh on her blog writes about the upcoming change in leadership at the Indian Institute of Science Bangalore and suggests different avenues that could invigorate science education and research in India-

Somebody, and who better than the new director, has to take a long shot at how IISc can compete with itself — it has no competition from any other institution in the country and it can continue to do what it is doing –, contribute to the halted economic progress of the country, and break free from the culture of publishing papers to also creating products and processes that the country can use. In the past when I raised the issue of quality research resulting in products, Balaram told me I was “soft” on the industry (and hard on the academics) in not asking them to invest more in R&D. He is right to the extent that journalists cannot question industry’s poor investment in R&D, it’s their money and if they don’t see merit in R&D, their short-sightedness will come to haunt them. But institutions like IISc do research with public funds. Frankly, it’s not about value for public money, it’s about regard for public need. India needs scientists and engineers working on Indian soil to solve its problems, particularly in game-changing fields like energy, healthcare, water and so on.

IISc also has to figure out how to get the smartest people into science. Better still, if it rustles up resources to find a way to educate future discoverers of the country to live up to their potential, we’d all be the beneficiaries.

In the current election frenzy as we hear politicians take credit for good economic growth in the past, it’s sad to see scientists and engineers being left behind as unsung heroes. This perception has to change; IISc has to lead from the front, articulate its vision now that it also has a second 150-acre campus coming up in Chitradurga which offers it a mind-boggling opportunity to create a global institution.

And more suggestions:

1) Break free from the paper-publishing cycle
2) Big ideas, bigger risks
3) Bring engineering on par with science
4) Strike big collaborations with industry
5) Create role models
6) Do all this without losing its basic character

She tells me that she 'll make enemies writing this.. but a little plain speaking is what is needed most.

Read the rest here..

Tuesday, March 4, 2014

Conversation With An Ex Geological Survey Of India Geologist

This is the first of what is hopefully a series of posts with my Pune based geology friends. Indian scientists don't talk enough with the public. We see them only on "Science Day" at various institutions or at major events like satellite launches, nuclear protests and earthquakes. But a more frequent conversation with the public conveying the joys and challenges of a science career is missing. Most scientists don't make momentous discoveries. They spend their careers framing smaller manageable questions and attempt to find answers for them. This process of science and small victories is revealing and inspiring too. So these "conversations over coffee" posts are an attempt to highlight the work of my geology colleagues and friends presented in a more informal casual form and made more accessible via social media.

In this conversation I talk with Dr. Sudha Vaddadi (above left having a coffee with me "The Fractured Geologist") who after a two decade distinguished career with the Geological Survey of India (GSI) is now visiting faculty at Fergusson College, Pune. We talk about her PhD research, mapping the complex Deccan lava flows, lack of direct recruitment in the GSI and resulting career stagnation, teaching stratigraphy and the need for more quantitative methods in Master's degree programs, working as the only woman in the GSI office, and waiting long hours in the field  for bullocks to pull a broken down jeep to the nearest garage.

Our conversation and email question and answers took place from late January through the month of February. The only changes I have made to the email interview document is to add a few hyperlinks.

[modified on March 5th- changed the order of the questions, brought the question about GSI recruitment to the top]