Wednesday, April 25, 2012

The Need For An Indian National Natural History Museum

G.V.R. Prasad calls it a prehistory museum in a correspondence (open access) to Current Science and points to the many outstanding natural history museums in western cities as examples to be emulated by India.  We don't have such a museum which fills a double role of a public repository of the geological and biological history of India as well as a research center.

Something Dr. Prasad wrote caught my attention:

The importance of these fossils has been fully understood by the Western geoscientists. As a consequence, a large number of geoscientists, palaeontologists and evolutionary biologists from Europe,USA, Canada, Australia and New Zealand visit various high-altitude areas in the Himalaya such as Zanskar, Spiti, Ladakh and Kargil to study the life forms that existed prior to and after the origin of the Himalayan mountain chain.

On the other hand, even after 65 years of independence, we have not realized the potential of the above-cited areas for the recovery of diversified fossil groups and their importance in understanding evolution and the geological, chemical and physical processes that led to the formation of the Himalayan mountain chain.

I am going to go on a tangent here because I want to share an observation with you. Paleontology in India has by and large not been applied to understanding evolution. Most geology programs in India don't cover evolution in any detail. Geologists here are not well versed in the theory of evolution. Interdisciplinary projects with biology departments are rare. As a result, we don't have paleontologists in India with the kind of career profiles like John Sepkoski Jr., Elizabeth Vrba, Stephen Jay Gould, Leigh Van Valen, Simon Conway Morris, to name just a few luminaries among the many evolutionary paleontologists working in western Universities and research museums. 

These palaeontologists collect and analyze fossil assemblages with the specific intent of understanding patterns of evolution and have made important and original contributions to evolutionary theory. Over here, paleontological studies focus on biostratigraphy i.e. organizing geological strata and correlating geographically disparate geological sections based on their fossils and on interpreting ancient ecologic conditions.

Its funny that Dr. Prasad mentions that large number of western geologists visit the Himalayan region to collect fossils. That western attraction towards the Himalayas goes well beyond fossils. A graduate student I was talking to some time back pointed out that virtually all "synthesis" papers in big journals published on  Himalayan tectonics, metamorphism and structure i.e. papers that deal with reconstructing histories of large litho-tectonic Himalayan belts have an all western authorship with maybe one Indian collaborator.

Is it money problems that is hindering Indian geologists from attempting such studies?

Anyways, coming back to the museum issue, I support Dr. Prasad's view of the need for a national natural history museum. Why stop at one? We should have many of them.

We have a very utilitarian perception of geology here in India. Geologists are looked upon as people who find stuff.. water, minerals, oil and fossils. People don't look at us as historians. And if we don't study history, then why do we need a museum?  But ultimately that is what we are. Geologists reconstruct the most important history there is.. that of our planet. Fragments of that history are hidden away in rocks, minerals, structures, fossils and in elemental ratios. We study these alphabets and piece together the grandest story of all, how our planet originated and evolved and changed over time.

That rich, inspiring and outlook changing story deserves to be told in our very own national natural history museum.

Tuesday, April 24, 2012

Increasing Interest In Teaching At Community Colleges

Rob Jenkins writes in The Chronicle of Higher Education on the recent interest expressed by more graduate students in a career teaching at 2 year community colleges:

In any hiring cycle, about 40 percent of the available teaching positions are at two-year campuses. Moreover, a surprisingly large number of Ph.D. students are actually, and actively, interested in community-college careers, perhaps because they've discovered (as I did) that what they really enjoy most is teaching....

....However, the fact is, community colleges have been hiring more and more Ph.D.'s—mostly because they can, given the glut of Ph.D.'s on the market, but also because many two-year colleges these days aspire to become four-year institutions. I know of a few that are now hiring Ph.D.'s exclusively. I think it's a really bad idea for a teaching institution to effectively eliminate so many outstanding, qualified teachers from consideration just because they don't have research degrees. I also think that, in its own way, that sort of intellectual posturing on the part of some two-year colleges may actually contribute to the glut of Ph.D.'s. But alas, nobody asked me.

His advice for aspiring applicants for a community college job: Teach, teach, teach.. put as much teaching experience on your resume as possible.

Thursday, April 19, 2012

A Buried Devonian Manhattan Made Of Calcium Carbonate

I'm continuing with the theme of carbonate reservoir rocks - and for good reason. I found this gem of a story about coral reef oil reservoirs from the Devonian carbonate depositional basins of Alberta, Canada in the comments thread of a post on the Oil Drum -

RockyMtnGuy writes:

Well, yes, carbonate reservoirs do test your wits. The ones in Alberta are particularly difficult to deal with. They are just like the girl with the curl right, in the middle of her forehead: when they are good, they are very good, but when they are bad, they are horrid.

A classic was the Rumsey Reef, which they found not too far from where I grew up.

In 1982, Gulf Canada Resources discovered a small pinnacle, called the Rumsey Reef, just to leeward of the Stettler-Fenn-Big Valley reefs. It produced over 3.7 million barrels of high gravity oil from one well; 90% was recovered during the first three years. During that period it flowed 3,000-4,000 bbls/day. A decade later, Gulf explorers, Lemon and Taylor (1993) presented a paper with the wistful title, “The Rumsey Leduc Pinnacle Reef: Where are the Rest?”

The Rumsey Reef is an oil field about the size and shape of a New York skyscraper, just full of oil waiting to be sucked out. Based on the geological history of the area, there must be thousands of similar reefs out there, but they just don't show up on seismic.

Probably most of the remaining Leduc pinnacle reefs in central Alberta, and we have measured many of them, are physically too small to be adequately resolved by reconnaissance seismic exploration, whether 2D or 3D. Our measurements suggest pinnacle reefs, similar to Rumsey in size, are pillars of coral growing between 550' to 700' high from the Cooking Lake carbonate platform. They appear to range from 70' to 225' in diameter.

Wow! .. where does one start?

The Rumsey Reef is an oil field about the size and shape of a New York skyscraper, just full of oil waiting to be sucked out. 

Today most of the Devonian strata of Alberta is in the subsurface, buried underneath younger sediment.

But imagine a sea floor 400 million years ago, where thousands of self assembled towers were being built by organisms scavenging calcium and carbonate ions from sea water to form skeletons made up of the mineral aragonite or calcite. A  living breathing city of underwater skyscrapers hundreds of feet tall, extending in narrow zones tens of kilometers in length, along the edges of depositional basins, where the shallow sea bed suddenly slope into an abyss. The Devonian Alberta basin was a flat shallow water area that gave way along steeper slopes possibly due to faulting activity to deeper waters. These are classic settings for a pinnacle reef to form.

The schematic figure below shows the different settings where reefs form. The patch reefs shaped like towers are the pinnacle reefs. They are called patch reefs because they occur as isolated communities.


A Pinnacle reef is a type of reef wherein the structure is a shape of a pinnacle or tower.  Reefs are biologically constructed structures that rise from the sea floor to form mounds. They are made up of the skeletons of organisms that prefer sunlight depths. Ordinarily, in shallow seas, the upward growth of reefs stop when the reef organisms start getting exposed to the atmosphere at low tides. The reef then grows laterally forming a broad structure.

In certain settings though, a rapidly subsiding sea floor creates space, maintaining a certain water depth, and the reef grows upwards maintaining its colonies in the optimal sunlight zone. Such conditions are present around volcanic islands. As volcanoes become dormant and erode and subside, reefs nucleate along their flanks and grow upwards as pinnacles. This situation is observed today along many tropical volcanic chains in the Pacific ocean.

Another environment for the formation of pinnacle reefs occurs when rapid sea level rise creates sufficient water depth. Pioneer colonies of reef building organisms tolerant of greater water depths may initiate the building of a bio-structure. As the reef grows into shallower water, a different species assemblage may become more common. The communities that build pinnacle reefs may change as the towers grow through different water depths.

The image below is of the coast of Belize. You can see a long north south trending white barrier reef in the center of the image. To the right is the open Caribbean sea. To the left are relatively deeper and quieter lagoons, environments where pinnacle reefs would likely grow. Some of the white isolated patches you see may be pinnacle reefs. This is just to give you an idea of the setting for pinnacle reefs, but I can't say for sure whether those patches are pinnacle reefs from this particular image.

Many of these Holocene reefs in Belize and the West Indies islands have grown on a Pleistocene limestone substrate (figure to the left, SEPM, which during the last sea level fall was weathered into an undulating topography known as karst. In early Holocene, sea level rose and flooded this limestone substrate. Reefs that took root in the depressions i.e. greater water depths, grew upwards to form pinnacles. In Alberta, the situation was different. The basin was an extensive shallow sea and the sea bed was broken into deeper and shallower areas by faults. My guess is that the Alberta basin experienced many episodes of sea level rise in the Devonian, and reef communities growing along the edges and flanks of fault blocks repeatedly grew upwards to form pinnacles.

Today, the dominant reef building organism are species of scleractinian corals, a group of coral organisms which have a symbiotic live in relationship with algae. In the Devonian, the community structure of reefs was different. There were corals present, but they predominantly belonged to two now extinct groups known as tabulate corals and rugose corals. Along with corals were stromatoporoids, an important coral like colonial organism, also now extinct. And there was a supporting cast of algae and molluscs.

The reef building activity in the Alberta basin lasted hundreds of thousands of years. It was not a continuous process. Sea level falls would have interrupted reef formation. A subsequent sea level rise would have allowed reef builders like stromatoporoids to colonize older reef substrates and resume the construction of these enormous towers. Each reef building episode may have lasted a few tens of thousands of years.

Eventually, water depths become considerably deeper, stopping reef growth. Sedimentary conditions changed and buried the reef under layers of mud or fine grained sediment. The reef itself, because it is built by organisms having branching structures is quite porous. Besides this primary porosity, the Alberta basin reefs underwent extensive alteration during burial. The minerals aragonite and calcite were replaced in patches by dolomite. This created more porosity as the replacement dissolved the original minerals and a denser dolomite occupied the space. Oil then migrated into the open pores and got trapped because the reef is capped by fine impervious material. Many of these living towers got transformed over time into a reservoir rock,  a buried skyscraper full of oil.

Regarding the Alberta basin, all these reefs are in the subsurface, and although they are invisible to seismic surveys, new exploration methods using  telluric currents have successfully identified more pinnacle reefs. Many of them will turn out to be prolific oil reservoirs.

But I can't get that 400 million year old underwater Manhattan of calcium carbonate out of my mind!

Thursday, April 12, 2012

Reservoir Rock In World's Biggest Oil Field Is Made Of Shit

From Ken Deffeyes book “Hubbert’s Peak”, via the Oil Drum:

Most massive and nonporous limestones contain textures made by invertebrate animals that ingest sediment and turn out fecal pellets. Usually, the pellets get squished into the mud. Rarely do the fecal pellets themselves form a porous sedimentary rock. In the 1970s, the first native-born Saudi to earn a doctorate in petroleum geology arrived for a year of work at Princeton. I used the occasion to twist Aramco’s collective arm for samples from the super-giant Ghawar field. As soon as the samples were ready, I made an appointment with our Saudi visitor to examine together the samples using petrographic microscopes. That morning, I was really excited. Examining the reservoir rock of the world’s biggest oil field was for me a thrill bigger than climbing Mount Everest. A small part of the reservoir was dolomite, but most of it turned out to be a fecal-pellet limestone. I had to go home that evening and explain to my family that the reservoir rock in the world’s biggest oil field was made of shit.

A bewildering variety of particle types get bound together to form limestones. Post Cambrian times, the calcium carbonate shells of marine organisms have been the most common particle type, the primary building blocks of limestones. But other particle types like fecal pellets are also common.

For carbonate sedimentologists involved in oil exploration, the most important task , is understanding the origin and distribution of porosity and permeability i.e. the open spaces in which oil migrates and is naturally stored. Sedimentologists recognize two broad categories of porosity. Primary porosity and secondary porosity.  Primary porosity is the open space between the grains and forms as grains settle down during deposition into different packing configurations depending on their shape and size.  Sediments that are deposited in environments where wave and tidal movements are vigorous will have high primary porosity because in such settings finer mud that can clog up interstices between coarser grains is winnowed away, leaving behind a lag of clean sand.

The image below is a photomicrograph of a fecal pellet sand from the Jurassic of England. The shining white material between the dark pellets is calcium carbonate cement which has filled up the primary porosity. Occasionally, there may be no precipitation of cement as the sand gets buried. In such situations the primary porosity is preserved and the deposit may become a reservoir rock.

Source:  SEPM Strata

And here is a picture of the Bahama Banks of the coast of Florida.

Arrows and labels show environments facing open ocean where currents and waves are vigorous and where primary porosity in sediment will be high. In the interior of the Bahamas, wave energy is much lower, resulting in sediment with less primary porosity. Fecal pellets may originate in the interior of platforms, in low energy settings. They often harden in these settings due to precipitation of cement in micro-pores within the grains. Often due to storms, these hardened pellets are then transported to high energy settings. Due to this early hardening, pellets resist getting squished against each other as the sediment is buried. Open spaces are thus preserved in such early hardened fecal pellet deposits.

Although the paleo-geographic setting would have been different than the Bahamas, the sediments of the Jurassic Ghawar reservoir limestone would have been deposited in high energy settings resulting in substantial primary porosity.

 Another category of porosity is secondary porosity that forms due to the reaction of the sediment with water during burial. It results in open spaces being created by the dissolution and leaching away of mud and grains and also due to volume changes as calcite gets replaced by the denser dolomite. This type of porosity is also present in the Ghawar limestone.

Since 1950's the Ghawar field has produced over 65 billion barrels of oil. Daily production is about 5 million barrels, about 6% of global production.

And.. what do  you know?  Glenn Morton has found another use for those famous fecal pellets..refuting young earth creationism:

One of the interesting things about Ghawar is the nature of its reservoir which provides an argument against an ideology I fight all the time, Young-earth Creationism. Ghawar is largely made of dung, which would be hard pressed to be concentrated during a global flood and thus contradicts the young-earth creationist claims.

A chaotic flood would have dispersed and broken up fecal pellets in to mud. Only long periods of  wave action and winnowing and early cementation on a sea floor would have produce the well sorted fecal pellet sands of the Ghawar reservoir deposit.

Tuesday, April 10, 2012

Spreading Altruism By Jumping On A Live Grenade

On the comments thread of Why Evolution Is True, Prof. Jerry Coyne uses a fun example to explain the concept of inclusive fitness to a reader:

josh ozersky-
Can someone please explain what inclusive fitness is?

Basically, it’s calculated for a gene that does something like affect behavior, and it’s the relative fitness of that form of a gene compared to other forms that don’t have that behavior, counting the copies of that gene in related individuals. For example, a gene that codes for this behavior: “commit suicide (e.g. by falling on a grenade) if you can save more than two brothers or sisters by doing so” has a higher inclusive fitness than a gene that says “don’t fall on the grenade”, because if you die you lose one copy of that gene but save 1.5 others (you’re 50% related to those three siblings), while if you don’t fall on the grenade (and run away), you save your own copy but lose 1.5 others. The gene for the “altruisitc” behavior will spread because genes for it have a higher INCLUSIVE FITNESS than the other form of the gene.

Is that clear?

The discussion is with reference to Prof. Coyne's post on E.O. Wilson's book Sociobiology and his recent profile by Jenny Schuessler in the New York Times. 

Head In The Sand On Global Warming

 A most telling observation on social attitudes to global warming from @TheTweetOfGod, retweeted by @callanbentley

"U.S. Records Warmest March in History". Na na na na not listening na na na Mad Men na na na baseball na na na lifestyle just fine na na na.

One talking point that comes up in debates is the connection between extreme weather events like a heat wave and long term climate change.  Questioning this connection is not just a tactic of warming deniers or skeptics but is of genuine interest to people who are curious and want to know more about how global warming may be impacting weather patterns today.

Real Climate clarifies the impact  long term changes in climate has on extreme weather events accompanied by a terrific graphic:

Source: IPCC (2001)

Monday, April 2, 2012

A Plea To Change The American Research University

An Inside Higher Ed essay by Hunter R Rawlings:

The combination of drastic state disinvestment in public universities, student careerism, and pedagogical failings of our own has serious consequences for the country. To take one significant example, we now know that more than 50 percent of the students starting college with a stated desire to major in science or engineering drop out of those majors before graduating.

We can no longer blame this problem entirely on the nation’s high schools. A substantial body of research demonstrates conclusively that the problem is frequently caused by poor undergraduate teaching in physics, chemistry, biology, math, and engineering, particularly in the freshman and sophomore years. Students are consigned to large lecture courses that offer almost no engagement, no monitoring, and little support and personal attention.  The combination of poor high school preparation and uninspiring freshman and sophomore pedagogy has produced a stunning dearth of science and engineering majors in the U.S.  Our country now falls well behind countries like China and India in turning out graduates with strong quantitative skills.

Among other things one complaint I have heard is the excessive importance given to research.  All roads on campus are seen to lead to the research lab, an intellectual mecca where all the "important" work takes place. Undergraduate teaching is often seen to suffer as research oriented faculty are not that interested in teaching freshman and introductory level courses.

In India, the exact opposite has been diagnosed as the problem, which is that our Universities have too little research! One view here is that the biggest mistake India made is to create elite research institutes as an entity separate from the University, which remained mostly a degree giving teaching institution with less than desirable amount of in-house research capability. University students especially undergraduates, since most Universities conduct undergraduate degree courses in separate colleges,  have little exposure and interaction with top level researchers. The quality of undergraduate teaching has suffered not because researchers punt teaching responsibilities to graduate students but because of the complete absence of researchers from undergraduate campuses.