Tuesday, September 29, 2009

Not Left Out! My Interview At The Reef Tank Is Online

There is a geology bonanza going on over at The Reef Tank which is a blog and forum dedicated to marine science topics including climate change, marine energy, ocean acidification and marine conservation. There have started a marine geology section in their community blog. Brian@ Clastic Detritus was the first to be interviewed. Dr. Erik W. Klemetti of Eruptions was second. The Lost Geologist was interviewed a few days ago.

Now its my turn. My interview is online (thanks to Brian who recommended my name) on their community blog page. I thought the questions were quite challenging and interesting dealing with how carbonate sedimentology relates to marine sciences and ecosystems and what my background in carbonates tells me about the current crises marine ecosystems may be facing due to global warming. There were a couple of questions on my posts on groundwater.

My favorite question though and I thank Ava the blog moderator for asking that-

You also blog on evolution. How important was/is marine life and marine ecosystems to the theory of evolution and why? 

I got a chance to write about how carbonate sediments help us understand evolution and also the question gave me a chance to highlight the work of two of my advisers who inspired me into studying carbonates and evolution.

Go over to The Reef Tank and take a look.

Friday, September 25, 2009

Genetic Ancestry of Indians. A New Paper Is Creating a Ruckus

A new paper about the genetic history of Indian populations in Nature is making waves in press releases. A reader asked me if I could explain the finding in plain english. Since I am not an expert in population genetics I will instead point to two posts that have dissected the paper. John Hawks writes about the topic here. Gene Expression details it here.

The salient points as I understand:

1) This is not some pioneering work as some of the Indian press reports suggest it is. The broad finding of this study have antecedents and are not that surprising or shocking.This study though does expand on earlier work by using a larger number of genetic data points and so is significant in its scope.

2) Modern Indian populations are derived from two ancient populations referred to as the Ancestral North Indians (ANI) and the Ancestral South Indians (ASI). Ancestral North Indians were Caucasoids, genetically closer to Eurasians, Europeans and central Asians while the Ancestral South Indians  were distinct from Caucasoids and Mongoloids. The Onge of the Andamans are a good model for the original Ancestral South Indians. The modern Indians are admixtures of these two populations (the Onge are not ancestral but an early branch of the ASI)

3) The findings indicate that there is a larger amount of genetic variation between Indian groups than there is between say European groups. This the authors suggest is a result of a small number of individuals founding different ethnic groups that then remained endogamous and therefore genetically divergent. This has important medical value as recessive diseases may correlate with ethnic groups.

4) Despite these inter group differences on average Indians from various groups and across castes are more closely related to each other than they are to outgroups like Europeans or East Asians. This points to the deep residence time of people in the subcontinent and continued gene flow across groups. This has led to reporting in the press that there is no north south divide and the Aryan-Dravidian divide is a myth. Again this finding is not new. There is earlier work that suggest similar genetic relationships among Indians.

5) The study also clearly shows that for some genetic lineages there is a gradient in relationship to ANI (west Eurasian) that is a function of geography and caste. For some genes north Indians (Indo European speakers) and upper castes are more closely related to ANI than are south Indians and lower castes. Here is a table that summarizes this result. The first few samples in the table are from south India (Dravidian and Tribal) and the lower portion of the table represents north Indians (Indo-European speaking people).

6) The paper says little about when this admixture with west Eurasian genes occurred but hints it may coincide with the arrival of Indo-European speakers which has generally been timed post collapse of the Harrappan city states around 1800 - 1600 B.C. This is off course is a controversial topic. The amounts of admixture with ANI is high in some samples. This may be taken by some as a validation of the Aryan Invasion scenario in which there was a massive migration and population replacement of indigenous people in northern India by Indo-European tribes. I don't see it that way. The northwestern region has always been a conduit into India. There would have been people movements from the Central and West Asia into this region related to the spread of agriculture (6000 - 8000 B.C ?). City states like the Harrapan complex had extensive trading ties (2600 - 2000 B.C) with the Bactria Margiana Complex in the Turkmenistan - northern Afghanistan - Tajikistan - Uzbekistan area and with the Elamite civilizations in western Iran. The people involved in trading  with these city states included those from the Pontic -Caspian Eurasian steppes.

So it is unlikely that any one historical event shaped these genetic relationships. Migration and population movements of Caucasoid people into India have been taking place longer than the advent of the Aryans although it does seem that the arrival of Indo-European speakers did leave a recognizable genetic imprint on older Indian populations. 

7) The Indian Press has made a hash of the finding. For example they have only reported those parts of the study that deal with the kinship among Indians and have stressed that castes and tribes cannot be differentiated or that there is no divide between the Aryans (roughly north Indians) and Dravidians (south Indians). That is all true for average relatedness. But the study also clearly points out that there are genetic differences between north and south Indians and between upper and lower caste in terms of the degree of relatedness to Eurasians. North Indians and upper castes are more closely related to  Eurasians. North Indian upper castes have even more Eurasian ancestry. This part was ignored by the press.

But I can't blame the press entirely. The scientists who gave interviews to the press didn't mention this. They wimped out on reporting this potential inflammatory and politically incorrect finding. This is just poor and irresponsible science outreach on part of the scientists. How can you ignore a finding that is staring out at you from the very paper you are talking about? The press may be guilty of not digging in but it was just reporting what the scientists told them.

Thursday, September 24, 2009

Phew! We Finally Know When the Quaternary Period Began

Its official. The Quaternary now begins 2.58 Million years ago. Everyone knew the Quaternary corresponded with the ice ages but there was doubt on which geological horizon to use as a base.

In June 2009, the Executive Committee of the International Union of Geological Sciences (IUGS) formally ratified a proposal by the International Commission on Stratigraphy to lower the base of the Quaternary System/Period to the Global Stratotype Section and Point (GSSP) of the Gelasian Stage/Age at Monte San Nicola, Sicily, Italy. The Gelasian until then had been the uppermost stage of the Pliocene Series/Epoch. The base of the Gelasian corresponds to Marine Isotope Stage 103, and has an astronomically tuned age of 2.58 Ma. A proposal that the base of the Pleistocene Series/Epoch be lowered to coincide with that of the Quaternary (the Gelasian GSSP) was also accepted by the IUGS Executive Committee. The GSSP at Vrica, Calabria, Italy, which had hitherto defined the basal boundary of both the Quaternary and the Pleistocene, remains available as the base of the Calabrian Stage/Age (now the second stage of the revised Pleistocene). In ratifying these proposals, the IUGS has acknowledged the distinctive qualities of the Quaternary by reaffirming it as a full system/period, correctly complied with the hierarchical requirements of the geological timescale by lowering the base of the Pleistocene to that of the Quaternary, and fully respected the historical and widespread current usage of both the terms 'Quaternary' and 'Pleistocene'.

Confused? Me too!

What that means is that earth history can be subdivided into geological time units like the Quaternary based on some natural break in earth conditions. That break should be one of geological significance and one which is easily recognizable all over the world. In this case that break is the beginnings of the global ice ages at around 2.58 Million years ago and it is best represented by the geological section in San Nicola Italy which is being used as the standard or type section. A type section contains a continuous sequence of rock / sediment spanning the break. The base of the new geological time unit can thus be clearly highlighted in the rock record at the type section.  Sections marking the beginnings of the ice age are found elsewhere too but it may be exceptionally well preserved at the type section.

Science Daily has the press release.

Tuesday, September 22, 2009

How Do We Know Fossils Were Once Living Organisms?

In the September issue of Geology there is a good give and take (open access) on the origin of early Neoproterozoic carbonate rock textures. The debate revolves around an interpretation made by Neuweiler et al. (2009) that certain cement filled cavity and mud textures in Neoproterozoic carbonate bioherms (carbonate mounds formed by aggregating and colonial organisms) look very similar to younger sponge replacement fabrics found in Palaeozoic and modern bioherms.

Even though there is no recognizable fossil sponge body parts in the studied Neoproterozoic carbonate (little Dal reefs, Canada)  the authors interpret the diagenetic fabric as indicative of a metazoan origin (they say they cannot conclusively link it to any specific sponge taxon) pushing in their view the geological evidence for multicellular animals to around 875 million years ago. This is about 200 million years older than what most scientists acknowledge. Noah Planavsky in the comment section disagrees about the metazoan origins of the texture and suggests that microbiota can also form similar fabrics.

I found the study interesting in itself. I have worked with some pretty complex diagenetic fabrics and it is always a challenge to tease out components that are purely inorganic from those that have a biogenic origin.

I feel though that a study like this fulfills another important role in science - it is of epistemological value. I used to help my PhD adviser with the paleontology exhibit on Science Day at the local mall in Tallahassee and we had people coming up to us and asking " ...but how do you know that this fossil was once a living creature...?"

A study like this tells us about the methodology and chains of reasoning scientists use to gather a body of knowledge about how fossils form. In this case the authors compared sponge remains from modern bioherms with older and older deposits. In the modern bioherms the sponge organism had died relatively recently and the organic tissue and other skeletal parts were still joined together as a coherent organism. Some organic material had degraded and in its place were tiny carbonate crystals. In some internal body cavities carbonate mud had accumulated forming a sort of a cast of the body part. This is a clear indication that as organic material degrades its place is taken up by inorganic material which retains the same shape as the organic matrix.

The researchers then went further back in time and looked at Cretaceous and Paleozoic rocks. In these samples there was no organic matter, that had decayed away long back,  but other typical sponge skeletal hard parts like spicules were still preserved and recognizable as sponge remains. The shape and form of the interior of the sponge the characteristic canal system was now completely filled by cement and mud. So although there was no coherent organism with linked body parts the association of spicules with a cement and mud filled connected cavity system which had a shape just like the canal system of the sponge gives us confidence that we are looking at sponge fossil fabrics.

One can then go one step further as the authors have done and interpret fabrics with characteristic shapes but no sponge remains (no spicules or anything) as having formed by the alteration of a large multicellular creature. That specific interpretation may be right or wrong in this case but that's the way scientists "know" that fossils were once living creatures. It's a good example to use to explain - How do we know what we know?

5 Things You Should Know About Evolution

Over at one of my favorite science /tech sites - Arstechnica - John Timmer has a good write up about 5 essential aspects of evolution that you should know:

  1. A really inefficient solution can be a lot better than the alternative
  2. Evolution solves problems in parallel
  3. Evolution doesn't happen overnight
  4. A million years is a lot longer than we think it is
  5. We wouldn't recognize a key transition while it was happening
Useful to keep these in mind when explaining and /or arguing about how evolution works.

Friday, September 18, 2009

Evolution Is A Tinkerer: Using Homology To Understand How

Here is an evolution link to bookmark. Homology is one of the most fundamental concepts in biology used for comparative analysis and for ferreting out evolutionary relationships. It refers to structures, traits that were present in the common ancestor of related species and which were inherited and since then differently modified in the descendants. The forelimbs of different mammal species although adapted for different functions are homologous since the basic structure was inherited from their last common ancestor.

If we include a wider group of organisms for comparison say the vertebrates and the invertebrates then the limbs of these two groups are not homologous since the last common ancestor of these two groups was limbless. Limbs evolved independently in these two groups. They are analogous structures.

But analogous structures can still be built by genes which are homologous!

Evolution is a tinkerer and uses the same gene networks to build new structures with similar functions in different groups of distantly related organisms.

PZ Myers explains this concept of deep homology and the consequences for understanding how evolution works in an article for Seed Magazine:

Evolution is a tinkerer that cobbles together new functions from old ones, and the genome is a kind of parts bin of recyclable elements. When new features evolve, the parts in the bin are co-opted to operate in new roles. As a result, the same parts appear in anatomically and evolutionarily distinct structures because it is faster and easier to reuse an old gene network that almost does what is needed, than it is to spend another few million years evolving a distinct gene for the function.

This makes these master genes precisely analogous to the stock of goods found in a hobbyist’s electronics store. Standard subunits—oscillators, op-amps, field effect transistors, switches, rheostats, and so forth—will get incorporated into many different kinds of projects; whether she is building a radio or a synthesizer or a burglar alarm, the hobbyist will find it easier to just grab an oscillator integrated circuit off the shelf than to design her own. We could sample devices built by different hobbyists with different purposes, and when we rummaged about in their insides, we would find the same subunits incorporated into novel, larger assemblies.

An important concept - homology- explained elegantly using ...an analogy ...he.. he...

Read the rest here....

Tip: 3QuarksDaily

Tuesday, September 15, 2009

Imagining An Underground Venice In The American Southwest

From BldgBlog post Hexagonal Hydropolis I went to the source Matsys where Andrew Kudless has created a futuristic and imaginative vision of a subterranean urban landscape in a dessicated American southwest.

The concept and architecture is stunning. Vast underground water reservoirs are connected to the cityscape via canals which also are the means of transport.

Image; Sietch Nevada / renderings by Nenad Katic

This is a grand and impressive outlook and I keep thinking on another track when I come across the many futuristic adaptive scenarios that are being proposed as responses to changing climate and resulting changes to our living space. The problems are varied, deep underground water storage, deep underground CO2 storage, coastal erosion, understanding changing river dynamics in the north Indian plains as glaciers shrink, exploring for uranium to boost nuclear energy....geology and geologists will play an increasingly important role as we explore and implement solutions to meet this challenge.

Monday, September 14, 2009

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.

Wednesday, September 9, 2009

Undergraduate Degree By Salary: Geologists Not Doing Too Badly

PayScale College Salary Report has published a list of best undergraduate college degree by salary for the United States. Undergraduates who go on to earn a Master's or a PhD are not included in this survey.

Annual pay for Bachelors graduates without higher degrees. Typical starting graduates have 2 years of experience; mid-career have 15 years. See full methodology for more.

Among the pure sciences, physics, statistics, math and biochemistry are ranked higher but geology comes next with a starting median salary of $ 45,100 and a mid career median salary of $ 84,200.

See the full list here and the methodology here. Tip: Greg Mankiw

Olivia Judson Reviews A New Film On Charles Darwin

Olivia Judson in the New York Times has a nice essay on a new film on the life of Charles Darwin:

Unlike most biographies of Darwin, its central event is not the publication of the “Origin,” but the death of Darwin’s adored eldest daughter, Annie, at the age of 10......

.....“Creation” thus takes on two main themes. The first is the difference in religious outlook between Darwin and his wife — and, more broadly, between Darwin and much of Victorian society. This is inevitable in any account of Darwin’s life. The second, and more unusual, theme is the mental hell of guilt and anguish that the death of a loved one can bring, and how that can fracture a family.

It's always refreshing to come across works that get past being hagiographies of a venerable historical figure and which bring out the human instead.

Monday, September 7, 2009

Richard Dawkins New Book Is Out

A long time back a fan from the U.S gave Richard Dawkins a printed T-shirt titled

Evolution: The Greatest Show on Earth The Only Game in Town. I don't know if that inspired the title of his latest book - The Greatest Show on Earth: The Evidence For Evolution... but...

The U.K edition is out and the U.S edition will be released September 22. Not sure about the India release date.

I doubt anyone from the creationist community will be swayed into accepting evolution but if you are genuinely curious about evolution then this might be as good a book as any to start learning.

Early reviews are positive although a bit uneasy about Dawkins propensity to insult creationists. That's his style. It won't win him new readers of the fundamentalist mindset but then I think he's long given up winning those over.

For the rest as always it promises to be a treat. I really enjoyed his previous book on evolution The Ancestor's Tale and I am looking forward to reading this one.

Maybe not creationists but I am curious to know if Dawkins has made any attempt to win over another disgruntled lot; biologists who complain that Dawkins puts too much emphasis on natural selection and gives too little attention to random genetic drift and chance events as important drivers of evolution. Although he has never denied the role of drift and chance many of his previous books focused on adaptive evolution and so an emphasis on natural selection as an explanation was inevitable.

This book though is titled the Evidence For Evolution and not Evidence For Evolution through Natural Selection and I wonder if he has been more generous in explaining the role of drift as another important mechanism of evolution and how drift can generate recognizable patterns that can be powerful evidence for evolution. One example that comes to mind is mutations that affect non-coding sections of DNA. This portion of DNA since it has no functionality will be invisible to natural selection and mutations will accumulate and become fixed through random drift.

If two species have such identical patterns in the same region of their non coding DNA that is strong evidence of a shared ancestry and a shared evolutionary history. You might argue that a creator would put identical functions in two species but why would He place identical non functional bits in different species. Its a bit like recognizing plagiarism. If you copy the dud parts and mistakes from someone's essay then...

From the early reviews though natural selection still seems to be the only game in town for  Richard Dawkins.

Thursday, September 3, 2009

Geological Refurbishings For Your House

A friend sent me this image:

I haven't made much use of geological motifs in my house. This is the farthest I have gone:

A Precambrian  chert cemented conglomerate from the west coast Konkan region and a giant Nautilus from the Cretaceous of South India stop the balcony door from being slammed shut by the monsoon winds.

Evocative Images Of The Eurasian Steppes

I liked these passages about the Eurasian steppes from David Anthony's The Horse The Wheel and Language:

Walking on the steppes...

It is possible, if one is inclined, to walk, 5,000 km from the Danube delta across the center of the Eurasian continent to Mongolia without ever leaving the steppes. But a person on foot in the Eurasian steppes feels very small. Every footfall raises the scent of crushed sage, and a puff of tiny white grasshoppers skips ahead of your boot. Although the flowers that grow among the fescue and feathergrass (Festuca and Stipa) make a wonderful boiled tea, the grass is inedible, and outside the forested river valleys there is not much else to eat.

On the impact of the wagon....

The sight of wagons creaking and swaying across the grasslands amid herds of woolly sheep changed from a weirdly fascinating vision to a normal part of steppe life between 3300 and 3100 BCE. At about the same time the climate in the steppes became significantly drier and generally cooler than it had been during the Eneolithic..... As the steppes dried and expanded, people tried to keep their animals fed by moving them more frequently. They discovered that with a wagon you could keep moving indefinitely.

On the difference in warfare between pre-Iron Age pastoral societies and Iron Age States:

But organizing an army of mounted archers was not a simple matter. The technical advances in bows, arrows, and castings were meaningless without a change in mentality, in the identity of the fighter, from a heroic single warrior to a nameless solider. An ideological model of fighting appropriate for a state had to be grafted onto the mentality of tribal horseback riders. Pre-Iron Age warfare in the Eurasian steppes, from what we can glean from sources like the Iliad and the Rig-Veda, probably emphasized personal glory and heroism.

See: My Book Shelf

Tuesday, September 1, 2009

Indian Petroleum Geoscientists Are Being Unshackled

Geology and livelihoods - 6

The September issue of Journal of Sedimentary Research has a paper on the sedimentology and stratigraphy of continental slope reservoir facies of the Krishna- Godavari Basin south east India.

Sandy Debrites and Tidalites of Pliocene Reservoir Sands in Upper-Slope Canyon Environments, Offshore Krishna–Godavari Basin (India): Implications

I am not that interested in the contents of the paper. Instead I am going to point to the authorship-

G. Shanmugam1, S.K. Shrivastava2 and Bhagaban Das3

1 Department of Earth and Environmental Sciences, The University of Texas at Arlington, P.O. Box 19049, Arlington, Texas 76019-0049, U.S.A.; shanshanmugam@aol.com
2 Reliance Industries Limited, E&P Business, Reliance Corporate Park, Thane Belapur Road, Ghansoli, Navi Mumbai-400701, India
3 Reliance Industries Limited, E&P Business, Reliance Corporate Park, Thane Belapur Road, Ghansoli, Navi Mumbai-400701, India

This is just about the first paper I have come across in a top sed geology journal authored by researchers working for a private Indian petroleum /energy company and it is just one sign that the Indian hydrocarbon industry intellectual landscape is undergoing a rapid change the last decade or so. Previously all Indian oil fields were managed and operated by nationalized petroleum companies. But in the last few years the government has thrown open exploration blocks to private players and Reliance Industries Limited is one of the most active of the lot.

Private participation has caused quite a ruffle in government operations since lots of talented middle and senior level geologists has left government companies to work for the private sector. Financial gain allied with inducements of greater intellectual freedom especially for the Ph.D types are the main reasons for the move. Reliance for example has set up a well funded sedimentology research lab and the results are showing.

Companies like the Oil and Natural Gas Corporation (ONGC) - a nationalized behemoth- are feeling the pain of this fleeing human capital. One complaint I have heard is that specialization is not always respected and handled with care at these government oil companies. A Ph.D with an expertise in micropalaeontology and biostratigraphy may spend long years doing some other work. That essentially is a waste of talent. No wonder lots of specialists are jumping ship and heading for private organizations who are putting their specialization to a challenging test.

A better use of specialization is good news for geoscientists and for the industry. ONGC will have to follow suit if it wants to retain talent. That in fact will be critical for exploration and exploitation of emerging oil fields. Out of the 160 blocks auctioned for licensing since the year 2000 ONGC has leases for about half of them. A lack of specialists in the government sector could limit India's future oil and gas production capacity.

See: Geology and livelihoods