Rapid Uplift

Its In The Syllabus

noreply@blogger.com (Suvrat Kher) — Mon, 20 May 2013 15:28:00 +0000

The tables can very easily be turned on you, the faculty, when a student goes over the syllabus with a tooth comb and then holds you to every dot and comma in it.

My friend who is an igneous petrologist and faculty at a local university here in Pune saw the nasty side of the syllabus centered education. As a researcher, my friend is highly enthusiastic about his work and often launches into long excursions about it during lecture time. He didn't think the students minded until he posed a question about his research in an exam. There, some students objected... it was not in the syllabus you see! They took their complaint to the Vice Chancellor of the University and had the exam annulled.

This happened at a post-graduate level i.e. these were students studying for their Masters degree, a level at which students should be learning not just the fundamentals of a subject but also exploring the boundaries of knowledge about a topic by diving into the research literature and hungrily biting at anything extra that comes their way. It makes you wonder about the motivation and mindset of these students that they so quickly and vehemently protested against a faculty who actually wanted to go out of his way and teach more than is required of him.

I hate to think that the narrow minded focus on rigid syllabus and passing exams has reached such a level that it is destroying any curiosity to learn more.

Again! Charles Darwin Was Wrong.. About The Tree Of Life

noreply@blogger.com (Suvrat Kher) — Thu, 16 May 2013 10:17:00 +0000

Well.. I guess the headline "Darwin Was Wrong" always sells!

But The Guardian should have thought a little before publishing this. It is an article which appeared sometime back but is the most viewed in the science section and is about how the recognition of lateral gene transfer i.e. the transfer of genes aross taxonomic groups is proving Darwin's idea of a tree of life wrong.

Read this passage:

Evolutionary biologists say crossbreeding between species is far more common than previously thought, making a nonsense of the idea of discrete evolutionary branches.

I don't think their science correspondence Ian Sample thought enough to see the contradiction in this passage.

Cross breeding between species implies that species exist in the first place which in turn means that there has been in existence discrete evolutionary branches i.e. long periods of independent evolution of different populations so as to have accumulated unique features recognizably different from other populations. Its only when there are discrete unique branches is it possible to recognize lateral gene transfer between the two!

For example, coyotes and wolves are closely related animals that occasionally interbreed in the wild. But the fact that we can recognize coyotes from wolves means that these are two discrete lineages having diverged from a common ancestor at some point in the past and have since followed separate evolutionary trajectories accumulating unique traits along the way. Occasional interbreeding between the two does not wipe away all these differences. They remain two distinct branches on the canid family tree.

Gene trees are not the same as species trees. Gene trees reflect the evolutionary history of a gene which may be transferred across taxonomic groups by a variety of processes. Early in the divergent history of populations genes may be exchanged through interbreeding. Or, for example a not so insignificant portion of the genome of mammals is made up of fragments of genes from other species transferred into us long ago by viral infections. However, that does not change the historical fact that the coyote and the wolf, or for that matter humans and chimps diverged from a common ancestor. Species trees or the tree of life reflects this history of speciation. So, Darwin's tree of life idea is about diverging populations from a common ancestor. These populations despite occasional transfer of genes maintain reproductive integrity and become different enough over time. Life has become diverse over time by such branching. Darwin was not wrong about that.

And what does one make of this confused para- Last year, scientists at the University of Texas at Arlington found a strange chunk of DNA in the genetic make-up of eight animals, including the mouse, rat and the African clawed frog. The same chunk is missing from chickens, elephants and humans, suggesting it must have become wedged into the genomes of some animals by crossbreeding.

Does that mean there was interbreeding between mouse, rats and the African clawed frog? Ridiculous!

Update May 16 2013: There is another potentially misleading passage in the article:

But modern genetics has revealed that representing evolutionary history as a tree is misleading, with scientists saying a more realistic way to represent the origins and inter-relatedness of species would be an impenetrable thicket. Darwin himself also wrote about evolution and ecosystems as a "tangled bank".

Now, the "tangled bank" has nothing to do with lateral gene transfer and interbreeding at all. It should not be conflated with evolutionary relationships being described as a web or a thicket. Darwin was describing the complex inter-dependencies in an ecosystem as organisms compete and co-operate with each other for resources.

Genghis Khan And Interdisciplinary Research

noreply@blogger.com (Suvrat Kher) — Tue, 14 May 2013 14:22:00 +0000

State of the Planet has quite a readable account of how a period of warm climate in the early 1200's may have produced an abundance of grass and livestock in Mongolia, fueling the expansionist ambitions of Genghis Khan.

Here is an interesting passage from the article:

In 2013, Avery Shinneman, a biologist at the University of Washington, will analyze sediments at selected lakes in order to estimate abundances of livestock over time, using varying levels of fungal spores that live in the dung of grazing animals, and algae fertilized by that dung. The data will be fed into a model developed by Hanqin Tian, an ecologist at Auburn University in Alabama, who studies the weather of modern Mongolia and its relation to grassland productivity. The Mongols left few written records, but Nicola di Cosmo, a historian at the Institute for Advanced Study in Princeton, N.J., will look into contemporary accounts from China, Persia and Europe for clues to climate and military events. From all this, the researchers hope to develop a picture of how sun, water, soil and animals might have created an energy system that the Mongols could have tapped into.

Biologists, theoretical ecologists, historians... increasingly big projects like this one become interdisciplinary by necessity.

If you have been following my posts on the controversy over a paper by Giosan et al on the geomorphology of rivers feeding the Harappan civilization..now that was a big project involving geomorphologists, climate experts, paleobotanists, sedimentologists and geochemists. The paper had 15 authors. You could have confused the author citations for the abstract! :)

OF Flies Mice And Men- Francois Jacob 1920 -2013

noreply@blogger.com (Suvrat Kher) — Fri, 10 May 2013 15:31:00 +0000

The great French biologist Francois Jacob died on April 19th 2013. I started this post and left it lingering in draft. I want to post it now.

Carl Zimmer at The Loom has an essay which outlines one of the key moments of Jacob's career- when he realized how cells turn genes on and off. That formed the basis of understanding gene regulation and laid the foundation of the field of developmental biology. For that work he shared the Nobel Prize in 1965 with Andre Lwoff and Jacques Monod.

Francois Jacob also wrote beautifully about evolution. His description of evolution as a tinkerer has become a popular way to think about how evolution builds novelties and puts together complex structures and traits. From his elegant essay on evolution and tinkering published in Science in 1977 :

Natural selection has no analogy with any aspect of human behavior, However, if one wanted to play with a comparision, one would have to say natural selection does not work as an engineer works. It works like a tinkerer - a tinkerer who does not know exactly what he is going to produce but uses whatever he finds around him whether it be pieces of string, fragments or wood, or old cardboards; in short it works like a tinkerer who uses everything at his disposal to produce some kind of workable object. For the engineer, the realization of his task depends on his having the raw materials and the tools that exactly fit his project. The tinkerer, in contrast, always manages with odds and ends. What he ultimately produces is generally related to no special project, and it results from a series of contingent events, of all the opportunities he had to enrich his stock with leftovers. As was discussed by Levi Strauss (5) none of these materials at the tinkerer's disposal has a precise and definite function. Each can be used in a number of different ways. In contrast with the engineers's tools, those of the tinkerer cannot be defined by a project. What these objects have in common is "it might well be of some use". For what? That depends on the opportunities.

I enjoyed reading his books; The Statue Within and Of Flies Mice and Men.

Here is a passage from his book Of Flies Mice and Men where he describes the fear and excitement of changing course midway through his career:

The word "courage" is not too strong. The daily interaction over years with a living organism, however humble, entails a certain familiarity. You could almost say that you acquire a certain tenderness for it. After 15 years of working with a particular colon bacillus, I had accumulated hundreds of mutants. In each of these mutants, one or another of the cellular functions, many of them indispensable to the life and reproduction of the bacteria, had been altered. To abandon this work and all that it offered; to renounce the kind of intimacy that comes with the knowledge of little unwritten quirks, the folklore that surrounds the work of any one organism; to start again from zero with another, unknown organism whose idiosyncrasies I would have to discover - all this was a considerable sacrifice. It was a little like leaving a loved one . But, at the same time, the new project was an exciting one. It would mean entering an unknown world, beginning a new life, becoming young again....

Summer In My Neighborhood

noreply@blogger.com (Suvrat Kher) — Thu, 09 May 2013 16:00:00 +0000

Its been a blazing week with temperatures over 100 deg F. Pune this past few days has been as hot as I can ever recall. Time for ice tea and cool stewed mango drinks. Evenings are very warm too. We are giving our rugby kids water breaks every 10 minutes.

But walking through the small lanes near my house are sights like this one:

Summer can be glorious too. And the alphonso mangoes and cold beer is helping!

V.K Gaur On Earthquake Research, Jaitapur Seismic Risk And Role Of Scientists

noreply@blogger.com (Suvrat Kher) — Wed, 01 May 2013 10:37:00 +0000

The Hindu carried an interview with Vinod Kumar Gaur, seismologist with the Centre for Mathematical Modelling and Computer Simulation. His work on the seisimic risk at Jaitapur southern Maharashtra where a nuclear power plant has been proposed was criticized by the Indian government and his colleague Roger Bilham denied entry into India on the grounds that he violated the terms of his tourist visa. I share the suspicion of many that the Indian government is too sensitive and insecure about anyone raising questions about nuclear safety and reacted pettily by banning Dr. Bilham.

Some excerpts:

You have been vocal in your scepticism of Jaitapur as the location for a proposed 10,000 MW nuclear power plant...

Not for the construction of the plant, which can be designed with safety features. But India’s western coast, a well-recognised zone of potential seismic vulnerabilities, is likely laced with ancient faultlines buried under sediments and waiting to spring back like a piano accordion under continental compression. It is intriguing that Jaitapur [on the Maharashtra coast], the chosen site for the world’s biggest nuclear power plant, should have been declared seismically safe without refuting these possibilities.

My concern is that the various geological proxies of faultlines around Jaitapur and their possible implications on the plant and public safety have been neither adequately studied nor communicated. A clear picture of Jaitapur’s vulnerabilities and their quantification, needed in order to calculate the level of safety measures to be incorporated, is missing from the earthquake hazard assessment of the site.

What, in your opinion, prevents a more thorough safety analysis of Jaitapur?

We have every technological possibility to exhaustively investigate the subsurface geology of Jaitapur including high resolution seismic imaging that can be carried out at a fraction of the project cost.

Scientists tend to downplay earthquake risks. It is convenient to do so. You keep everybody happy when you maintain status quo. But science only grows by addressing challenges, by considering alternative views and designing incisive experiments to prove or refute conjectures.

and he has some harsh words about the lack of outreach role played by Indian scientists.

....Sadly, our scientific culture lacks responsibility and rigour towards public safety, and so denies society the advantage of information, and consequently resilience, against the natural disaster.

Read the full interview here.

My previous posts on this topic:

1) Politics And Pettiness In Indian Seismology
2) Note To Indian Govt: It Is Pointless Banning Seismologist Roger Bilham

My Criticism Of K.S Valdiya's Paper Published In Current Science

noreply@blogger.com (Suvrat Kher) — Thu, 25 Apr 2013 14:55:00 +0000

and Valdiya's reply was not satisfactory at all..

To those unfamiliar with the sequence of events:

1) Giosan et al publish a paper in the May 2012 issue of PNAS on fluvial geomorphology of rivers around the Harappan civilization and conclude amongst other things that the Sutlej and Yamuna rivers got diverted from the channels now occupied by the river Ghaggar (Haryana Punjab plains) to their present day course by Late Pleistocene. This meant that the Harappan civilization along the river named Ghaggar -also identified as the Vedic Saraswati by many- was watered by a monsoonal river and not a glacially connected river.,

2) I write a blog post of this paper on June 15 2012. I comment that some Indian geologists working on this problem accepted the scenario of a glacial Ghaggar /Saraswati during Harappan times without critically assessing the evidence.

3) My blog post appears on the Indo-Archaeology forum. In the confusion due to many cross links my comments about the role of Indian geologists are misattributed to Giosan et al. Giosan tries to set the record straight. K.S. Valdiya based on his correspondence with S. Kalyanaraman also confuses the source of those comments and misattributes them to Giosan et al in his article in Current Science. Valdiya accuses Giosan et al of diminishing the research of Indian geologists partly because he misidentifies Giosan et al as the authors of those comments and partly because of Giosan's comment on the Indo Archaeology forum that they have only referred to 'papers and authors presenting reliable data and facts’. S. Kalyanaraman forwarded this comment to Valdiya who then regarded it as a slight on the work of Indian geologists.

These below are my words that got misattributed to Giosan et al:

A geological narrative constructed without rigorous evidence has been promoted to support a theory of cultural evolution in northwest India.

and

.. now be revised or at the very least these geologists need to admit that their theory has been seriously challenged.

4) I write a blog post on the geological problems in Valdiya's Current Science article.

5) Giosan et al protest the misattribution in the Correspondence section of February 10 issue of Current Science.

6) My comments and Valdiya's reply to Giosan et al and my comment published in the April 25 issue of Current Science.

phew... I didn't know writing a nerdy geology blog will land me in such a controversy! :)

Moving on to Valdiya's reply to my comment I want to elaborate on Valdiya's denial that he misrepresented the work of other authors.

1) Valdiya commenting upon Saini et al writes:

Kher accuses me of misinterpreting the deduction of Saini et al. [..], who clearly state that the sedimentary succession of the area between Tohana and Sirsa which is ‘considered as a part of the area’ through which the ‘lost’ Saraswati flowed (p. 1634), contains grey sandyfacies with ‘grey sediments similar to the modern day sediments of the mountainfed rivers’, ‘like Ganga and Yamuna’ (p. 1637) and ‘The mineralogical characters, extent and style of the grey micaceous sand suggests that it was a Himalayan mountain-fed multi-channel fluvial system.’ Taking in conjunction with the findings of Courty [..], I concluded that this fluvial system belonged to the Saraswati. Logical deduction cannot be construed as misrepresentation’.

The devil is in the details. Saini et al discover two phases of fluvial activity in the Haryana plains. They find that fluvial activity weakened from the Pleistocene to the mid late Holocene. The sentences that Valdiya refers to are descriptions of a large fluvial system - termed F-1- active in the Pleistocene, before the Last Glacial Maximum about 25,000 to 30,000 years ago. Saini et al discover another much younger phase of fluvial activity (F-2) active between 6000 B.P and 2900 B.P (Before Present) covering a much smaller extent than the buried older Pleistocene system. This younger activity corresponds in age to the Harappan civilization and its sediments are mostly mud and silt, with less of the grey sand present. Of relevance to the problem of the glacial Saraswati is not the older fluvial phase but whether the younger fluvial system overlapping the Harappan civilization was glacially fed or not. Valdiya is his reply doesn't make this distinction.

On the question of the provenance of the younger system Saini et al draw no conclusions.

They say:

The F-2 phase, part of a relict landform, considered as a part of the ‘lost’ Saraswati drainage by previous workers [..] in this part of Haryana matches with the time span of the ‘Vedic’ Saraswati. However, the upstream and downstream connectivity of this segment to the postulated Saraswati course remains elusive and needs further exploration.

Validya on the other hand referring to this younger fluvial activity comments in his paper

Which river deposited these younger sediments in the Hakra reach of the Ghagghar–Hakra river? We believe that it was the Saraswati River originating in the Himalaya.

I have several problems with the way Valdiya has represented Saini et al. In his reply he has cherry picked sentences from Saini et al about the existence of a large multi-channel Himalayan fed -which could be interpreted as a glacial fed- river network without explaining that this described system was active in the Pleistocene and not during the Harappan civilization. Moreover, he never clarifies in his original paper that Saini et al don't draw any conclusions about the provenance of the younger fluvial system. He wrongly says in his reply that Saini et al allude to the river coming from the Siwaliks. That remark is not from Saini et al but from Saini and Mujtaba who suggest that river active during Harappan times was fed only from the Siwaliks. To that, Valdiya's reply is that the Siwaliks are the Outer Himalayas (the southernmost range) and he has always stated that the Himalaya-born Saraswati flowed through the Siwalik terrain! He misses the point that Saini and Mujtaba's work indicates that the river could not have been glacially fed during Harappan times

Finally, he is not a co-author on Saini et al. Despite that he uses the word "We" which might confuse readers into thinking that Saini et al are going along with Valdiya's conclusions. Presumably the "We" doesn't include Saini et al but stands for the collection of geologists who support the theory of a glacial Saraswati as Saini et al decidedly do not come to the same conclusions as Valdiya regarding this younger fluvial phase.

2) On the issue of misquotation of Giosan et al, Valdiya writes in his reply:

I have correctly interpreted what Giosan et al.1 have written in their article. The only error I committed was the wrong placement of quotation mark. I am sorry for this inadvertent mistake. But
the meaning conveyed is the same as what Giosan et al.1 intended.

Let me place next to each other the original passage from Giosan et al and Valdiya's reproduction:

This is from Giosan et al:

‘Provenance detection (...) suggests that the Yamuna may have contributed sediment to this region during the last glacial period, but switched to the Ganges basin before Harappan times. The present Ghaggar– Hakra valley and its tributary rivers are currently dry or have seasonal flows. Yet rivers were undoubtedly active in this region during the Urban Harappan Phase. We recovered sandy fluvial deposits approximately 5,400 years-old at Fort Abbas in Pakistan (SI Text)…’.

And Valdiya's reproduction:

‘Interestingly, Giosan et al. (...) concede that... “the Yamuna may have contributed sediment to this region…” (Hakra– Ghagghar) “before the Mature Harappan Phase. For we recovered 5400-year-old
sandy flood deposit at Fort Abbas (in Cholistan) Pakistan”…’.

Valdiya is now saying in his reply that his only mistake is wrong placement of quotation marks. Which means the phrase "before the Mature Harappan Phase" and the word "For" should have been outside quotation marks and they really are Valdiya's words and not Giosan et al. But does he not realize that adding this text along with his phrase "Interestingly, Giosan et al. (...) concede that" changes the meaning of the original passage? Giosan et al conclude based on Clift et al's provenance work that the Yamuna was diverted from this area and was captured by the Ganges basin in the Pleistocene perhaps as early as 50,000 years ago.

Phrases like Giosan et al concede- before Mature Harappan Phase- For make it appear that Giosan et al's work indicate that the Yamuna was flowing in this region around 5400 years ago i.e. during early Harappan times. That is certainly not the meaning Giosan et al intend. And in their respective papers these two passages end with very different conclusions. According to Giosan et al, a monsoonal river was flowing through this region all through Holocene. In contrast, Valdiya has been arguing all along that glacial rivers were flowing in this region until late Harappan times i.e. around 4000 B.P or so.

Giosan et al will be writing about the scientific issues Valdiya has raised in an upcoming issue of PNAS. I do hope Valdiya sends in his critique too.

Review Article: Recurrence Of Great Subduction Zone Earthquakes

noreply@blogger.com (Suvrat Kher) — Mon, 22 Apr 2013 09:38:00 +0000

Open Access in Current Science:

Kusala Rajendran

The last decade has witnessed two unusually large tsunamigenic earthquakes. The devastation from the 2004 Sumatra–Andaman and the 2011 Tohoku-Oki earthquakes (both of moment magnitude ≥ 9.0) and their ensuing tsunamis comes as a harsh reminder on the need to assess and mitigate coastal hazards due to earthquakes and tsunamis worldwide. Along any given subduction zone, megathrust tsunamigenic earthquakes occur over intervals considerably longer than their documented histories and thus, 2004-type events may appear totally ‘out of the blue’. In order to understand and assess the risk from tsunamis, we need to know their long-term frequency and magnitude, going beyond documented history, to recent geological records. The ability to do this depends on our knowledge of the processes that govern subduction zones, their responses to interseismic and coseismic deformation, and on our expertise to identify and relate tsunami deposits to earthquake sources. In this article, we review the current state of understanding on the recurrence of great thrust earthquakes along global subduction zones.

The figure above shows the Cascadia subduction zone, Pacific coast of N. America (source Rajendran 2013) . I looked through the Reference section and saw a number of recent papers addressing both the evidence for past earthquakes as well as the impact of the 2004 Sumatra earthquake on the Indian coastline. The acknowledgements indicate funding for this paper from the Ministry of Earth Sciences, Govt. of India. Its good to see basic geological research into subduction zone earthquakes being supported this way.

On The Use Of The Word Archaic In Writing About Evolution

noreply@blogger.com (Suvrat Kher) — Wed, 17 Apr 2013 16:45:00 +0000

In an interesting article on hybridization in human evolution in Earth Pages by Steve Drury I came across the following sentence:

Multi-regional evolution posits archaic populations originally living in and outside Africa being gradually assimilated by migration and interbreeding that transferred modern traits everywhere yet retained some regionally distinct features of the archaic groups. The first model clearly has to be modified as evidence accumulates for some degree of hybridisation with archaic groups outside Africa. The second of the two pre-genome ideas seemed to be rendered obsolete by the DNA evidence for significant interbreeding between early immigrants from Africa and Eurasian and Asian populations of earlier archaic migrants – Neanderthals and Denisovans respectively – whereas modern Africans show no sign of recent contact with these archaic groups. However, not all regions of the genome have been examined for signs of more universal hybridisation.

What meaning should one read into the term "archaic". A common misconception is that archaic means "less evolved". But when migrants from Africa came in contact with Neanderthals or Denisovans or some other unnamed human population, it was a meeting between two human populations who had been evolving for the same amount of time since their divergence from a common ancestor. So there is no sense in saying that one group was less evolved than the other.

So then, archaic could mean that at the time of contact one population was resident in the area for a long period. They were early migrants into that area, making them an old population. Or, archaic could mean that one population had been isolated from the common gene pool for a longer period of time than the other, meaning, one population branched off much earlier from the ancestral population. The branching event could have been a migration resulting in genetic isolation. Or, archaic could mean that one population resembled the common ancestor more than the other population i.e. it had retained many ancestral traits and had undergone less morphological changes, while the other population had accumulated more new morphological traits since diverging from an ancestral population. In all the above three, the term archaic could well be used to describe a living population. Lastly, archaic could be used to describe features that are now extinct.

When "modern" humans migrating from Africa met Neanderthals in Europe, they were not meeting people who were less evolved , but people who had been evolving along a different trajectory for as long as any other then living branch of humans. We think of the jutting brow ridges and barrel chest of Neanderthals as archaic because that trait is no longer visible or very rare in humans living today. We see it only in fossils. They are features of antiquity.

But at the time "modern humans" met Neanderthals there was no archaic or modern in the sense of less or more evolved. Neanderthals were archaic in the sense that they were the earlier residents of Europe and had been genetically isolated from African populations for a long time. Both populations had some archaic traits in the sense of traits retained from their ancestors. Both also had changed morphologically, having evolved some new traits since their divergence from a common ancestor. There was no way of knowing then which collection of traits would survive till today to be categorized as modern and which would be consigned to archaic in the sense of being extinct. At that time they were just two sibling populations with their own unique evolutionary histories.

Science Proceeds By Funerals

noreply@blogger.com (Suvrat Kher) — Tue, 16 Apr 2013 09:57:00 +0000

Above all, science is a human institution. And as a machine for thinking, it's greater and more powerful than any of its single participants. You said that science proceeds by tiny steps. It also proceeds by funerals.

University departments are just waiting for the professor to get out of the way so the younger guys can get in.

That was author Ian McEwan on a very listenable hour of Science Friday on the importance of science writing in science books as well as science in fiction. The other guests were cosmologists Brian Greene and Lawrence Krauss.

I thought Ian McEwan gave a really good account of why he includes science in his books:

FLATOW: Ian, why do you put science in your books? What - why do we have to know about quantum mechanics? Are you purposely doing that to teach us something or just to...

MCEWAN: No, absolutely not. No.

FLATOW: No.

MCEWAN: It just came along with the character. It's a reflection of my own pleasure in it, but it seems just a human enterprise. I mean, this is - I mean, the standard measure of how alive you are is the measure of your curiosity, and I think of science as organized curiosity.

We once relied on priests to tell us the shape and nature and purpose of the cosmos and life itself. It's been a long, slow story of that undoing. We now have a far more interesting story, and it's also penetrated our lives. I mean, there's climate change, and we all have these intricate, beautiful machines in our hands, and it's impacting on our decisions about bioethics and many other things.

So if we think of the novel as an investigation of the human condition, technology and science is now so woven into that condition. You cannot escape it. So it's inevitable, I think, that...

Download / Transcript

Paranoia Over Google Mapping Tools Persists In Indian Officialdom

noreply@blogger.com (Suvrat Kher) — Mon, 08 Apr 2013 15:50:00 +0000

sigh... I keep writing about this only partly as comedy.. but mostly in frustration...

From an article in the Hindu about the recently held "mapathon"contest organized by Google.

As Delhi Police investigates whether Google violated rules in holding a competition that asked users to add information about their local areas for its online map, the U.S. Internet giant on Saturday said it had responded to queries raised by Survey of India more than 10 days back and hasn’t heard from it yet. (emphasis mine)

Apparently, the Survey of India and the Defence establishment is worried that such initiatives will have grave security repercussions. The problem is that Google has been asking users to add information about their local areas for its online map for several years now. I just don't comprehend how a mapping contest wherein lots of enthusiasts add places of interest on a map within a short span of time becomes a greater security threat than an individual using Google Maps on any other day of the year.

more from this article in the Economic Times... But on behalf of the Surveyor General of India Swarna Subba Rao, his deputy major general R C Padhi told the three ministries that Mapathon was "not in accordance with the national Mapping Policy 2005 and map restriction policies issued by the defence ministry from time to time", sources said.

Added a senior defence officer, "Such activities can have serious security repercussions in case mapping of restricted areas is undertaken by members of the general public."

The words "general public" come out of the mouths of our officials with such contempt and suspicion. These archaic mapping policies which restrict the "general public" from mapping certain areas have long been rendered meaningless by the many roving eyes that hover above the earth. I am sure the government understands this.. but relinquishing control over anything has always been hard for Indian officialdom.

The exceedingly vast majority of people using Google applications to map India don't want to harm India.

Those who do... might I remind the Indian Government that the terrorists who attacked Mumbai on November 26 2008 did not wait for a mapping contest to survey the city.

Biogeography And Teaching Evolution

noreply@blogger.com (Suvrat Kher) — Fri, 05 Apr 2013 15:49:00 +0000

Joshua Rosenau of the National Center for Science Education, Oakland, CA, USA has a wonderful essay in Evolution: Education and Outreach on how observations of the bio-geographic distribution of species helped Darwin and Wallace to work out independently their theories of evolution through natural selection.

He suggests that many of today' students who are often reluctant to accept evolution because they see differences between species as unbridgeable gaps can overcome this obstacle by observing the actual patterns of differences between closely related species living amongst them.

From the article:

The greatest challenge many students face in understanding evolution is what Wallace faced in 1846: they haven’t seen the sort of diversity that calls for explanation in terms of evolution. The world most students encounter seems to contain organisms in discrete categories: squirrels and rabbits, robins and sparrows, grass and daisies, oaks and pines. They are unlikely to notice that two ladybird beetles actually represent different species or that there are several species of grass in their lawn, let alone to recognize that there are two local species of chipmunk which can only be distinguished by dissection or DNA analysis. What diversity they notice represents groups that are quite distinct, with differences so large that it is impossible to imagine how their members could share a common ancestry.

As a result, students today, much like Darwin in 1835, tend to see species as distinct entities. Presenting students with a similar experience of the often subtle differences between species can similarly shake this misconception. When they realize how low the barriers can be between different species, they can place lessons on speciation in a more accurate context. Rather than imagining that speciation means turning lions into tigers, or bears into cows, or fish into humans, they will see that speciation involves a subtle divergence in the evolutionary trajectories taken by populations. Because the Galápagos mockingbirds were still early in their divergence, Darwin was able to recognize the process. Students today can learn similar lessons by examining the subtle differences between species on neighboring islands. The Evolution and Nature of Science Institute has a lesson plan in which students compare lizards in the Canary Islands (http://www.indiana.edu/~ensiweb/lessons/island.html), while Understanding Evolution offers a lesson plan looking at Anolis lizard biogeography in the Caribbean (http://www.ucmp.berkeley.edu/education/lessons/anolis/teacher_directions.html).

Very relevant advice but applicable only to those students who are willing to examine the evidence with an open mind. People indoctrinated with a fundamentalist ideology are unlikely to be impressed by two very similar species of beetles in their backyard. .

By the way this journal, Evolution: Education and Outreach is now open access.

So dip into it.

Lessons In Carbon Storage From Geological Analogues - Open Access Geology

noreply@blogger.com (Suvrat Kher) — Thu, 04 Apr 2013 16:06:00 +0000

Mike Bickle and Niko Kampman in an open access article in the April issue of Geology summarize the findings of two papers (1 , 2) published in the same issue on naturally occurring CO2 accumulations in sedimentary reservoirs and inferences drawn on their long term fate.

One potential strategy to manage growing atmospheric CO2 is to inject and store it in deep sedimentary aquifers with a retention time of at least ten thousand years.

The article identifies the key questions:

(1) how quickly will the buoyant CO2 dissolve in formation brines (good), (2) how quickly will the CO2 brines react with silicate minerals and precipitate solid carbonate phases (good), (3) will CO2 or CO2-charged brines corrode cap-rocks and escape upward (bad), and (4) will CO2 penetrate up fault zones (bad)?

It is dense but rewarding reading for those into mineralogy, phase equilibria and fluid-rock interaction.

This is something that should be of enormous interest to Indian sedimentary basin specialists and climate change mitigation planners. In a recent post I mentioned about India's plans to build 400 odd more coal power plants in the next few decades. Many will be located near sources of coal in the continental rift basins of eastern India. Is carbon dioxide sequestration in natural reservoirs economically viable? Do these basins have favorable conditions deep underground for long term storage of CO2? It is research well worth funding given that our dependance on coal will last several more decades.

Huh? Thousands Of Rivers Wiped Off Map Of China

noreply@blogger.com (Suvrat Kher) — Tue, 02 Apr 2013 07:06:00 +0000

The first national water census pointed out that thousands of rivers (28 thousand was the figure given) shown on previous maps are now missing from China' s state water maps. See this article.

Explanations:

Official- Climate change is to blame for the drying of some waterways. Plus some earlier mistakes by cartographers

Environmentalists: Ill conceived development and over use of underground water resources.

That last one is an important point. Much of the base flow of rivers, especially those which are not sourced from glaciers comes from groundwater discharging as springs. That means the water you see flowing in the river channel months after the rains are over is actually groundwater seeping out along river banks. Even rivers connected to glaciers may have a significant component of their flow provided for by groundwater discharge. A survey in the Nepal Himalayas revealed that groundwater contributes more than melting glaciers to the annual discharge of the rivers.

Rivers may gain water from groundwater over long stretches. Such streams are called effluent (fig on left: source: USGS) . Rivers that lose water to groundwater are called influent. Here is an excellent USGS primer on the impacts of groundwater exploitation on surface water.

All the important monsoonal rivers in Peninsular India as well, Narmada, Mahanadi, Cauvery, Krishna and Godavari depend on groundwater discharge to remain perennial. If the local water table plummets well below the river bed due to over extraction of groundwater then discharge into the river will cease.

River management must include management of groundwater resources as well. The USGS article I linked to points out: " From a sustainability perspective, the key point is that pumping decisions today will affect surface-water availability; however, these effects may not be fully realized for many years".

A lesson not taken seriously in China and in India as well.

Health Impact Study Of India Coal Power Plants

noreply@blogger.com (Suvrat Kher) — Tue, 26 Mar 2013 16:08:00 +0000

Do check out this New York Times interview with Dr. Sarath Guttikunda on the impact of India's coal power plants on health and environment. Dr. Guttikunda founded Urban Emissions, an air pollution research firm based in New Delhi and is also affiliate associate research professor at the Desert Research Institute, the environmental research arm of the Nevada System of Higher Education. He blogs at Urban Emissions.

Why are such studies important?

From the interview:

From epidemiological studies and the recent Global Burden of Disease assessments, it is evident that outdoor air pollution is one of the key sources of disease and death in India.

In order for the public to demand action on controlling the air pollution, we feel that the information is the key element. We need to know the status of air pollution and contributions from various sources like transport, power plants, industries, household fuels, and others.

We feel that this study is important on two fronts. First, it presents data on emissions, concentrations and health impacts of the coal power sector. While this may seem basic, it is unfortunate that this sort of information has not been published previously and we hope that it presents policy makers with evidence as to air pollution and health impacts of the sector. Second, it shows that despite the air pollution it causes, there are minimal regulations in place to address the air pollution impacts.

If the study convinces policy makers of the need to put in place stringent standards and enforce them – then it may be a start to a broader conversation on our energy needs and the environmental and health costs of supplying them.

111 coal plants currently meeting about 60% of our electricity needs, but around 455 new ones planned according to the World Resources Institute. Dr. Guttikunda says that with so many new plants a mere tightening of emission standards may not be sufficient to negate the health impacts of these plants. An alternate cleaner energy source needs to be available in really large amounts to avoid building so many new coal plants.

Nuclear power.... natural gas... solar... wind..? There will be no silver bullet solution to India's energy needs. We'll have to end up using an energy mix. That will include coal for several decades at least.

India Energy Report- Some Rambling Thoughts

noreply@blogger.com (Suvrat Kher) — Mon, 25 Mar 2013 14:31:00 +0000

The latest from the U.S. Energy Information Administration. For those who follow the energy sector, nothing terribly new here, but it is a useful document to keep bookmarked for quick reference.

Meanwhile, Swaminathan Aiyar takes an optimistic look at the future of methane hydrate deposits which he thinks can provide significantly to India's energy needs. These deposits are formed when methane is trapped within a crystalline cage of water molecules. They occur in cold deep sea sediments and also onshore in permafrost settings.There are estimates that resources in sediments in India offshore basins on both the west and east coast may be around 1800-1900 trillion cubic meters.

My take is that whatever the estimates, we may be decades away from successfully exploiting them. Of more relevance over the short to medium term is onshore shale gas. Estimates for those vary wildly from an earlier EIA estimate of about 63 trillion cubic feet to a revised USGS estimate of only 6-7 trillion cubic feet to a figure often quoted in the India media of about 500 trillion cubic feet to 300-1200 trillion cubic meters! These disparate estimates only underscores the need for a more detailed exploration of Indian sedimentary basins.

Targeted exploration though is an expensive venture to get into. To enable that, India is promising to put in place a shale gas exploration and exploitation policy by March 2013 and to auction of blocks for exploration by the end of 2013.

Oil Minister M Veerappa Moily is quite gung-ho about India's energy prospects. I came across this passage in an article : India currently imports as much as 79% of its oil needs and the Ministry wants this to be cut to 50% by 2020 through intensive exploration and exploitation of untapped reserves. "I see import dependence coming down by 50% by 2020 and by 75% in 2025. By 2030, we should be self-reliant,"

That was Minister Moily quoted. It's worth parsing through this projection. India currently imports 79% of its oil needs. A large influx of natural gas from Indian basins will not necessarily lead to a reduction in our oil imports. The reason is that oil and natural gas serve different sectors in our economy. Oil is primarily used for transportation and natural gas primarily for power generation (45%) and as feed stock of producing fertilizer (28%) . These two priority allocations for natural gas will impose limits on how much can be allocated for transportation that could potentially displace our oil imports.

Would we be ever self sufficient in natural gas due to some shale gas bonanza? Currently, India consumes about 2.23 trillion cubic feet per year of natural gas and produces about 1.65 trillion cubic feet per year. We import about 25% of our needs. Demand for natural gas is set to double over the next couple of decades. Production from conventional natural gas fields may level off as older fields decline. In fact some Reliance Industry gas fields in the Krishna Godavari offshore have seen marked decline in production over the last couple of years. They have in fact cut their reserve estimates from 10 trillion cubic feet to 3.4 trillion cubic feet. Can shale gas make up the large shortfall in supply expected in the future?

I see some limitations ahead. .

The first relates to the whether a new shale gas policy will be attractive enough to invite foreign capital and expertise. Previous attempts to auction offshore blocks for exploring conventional oil and gas deposits did not invite too much interest from major energy companies.

The second is the actual amount of shale gas in Indian basins. Are the figures for potential resources as high 1200 trillion cubic meters or as low as few tens of trillion cubic feet? Only more detailed exploration will give that answer and that in turn depends upon a business friendly shale gas policy.

The third limitation is related to the second but depends on the actual recoverable amount of shale gas. A basin may contain a very large amount of shale gas, but is it technically and economically recoverable? One reason why the USGS may have revised figures for India from 63 trillion cubic feet of resource to just 6 trillion cubic feet of recoverable resource is the experience of well performance from the U.S. Marcellus and Barnett shales. After a couple of years or so of prolific yield, gas production has declined dramatically. This probably has to do with the petro-physical properties of shale rock.

Gas over millenia has migrated and localized around cracks and fractures. When the shale is hydro-fractured this localized gas gushes out. However, the migration of gas trapped in the matrix of the rock towards these cracks is quite slow. So, once the low hanging fruit have been extracted, further production at that spot slows down. A different well at a different spot may have to be drilled. Even conventional sandstone reservoirs face the problem of decline in production, but the decline is slow, several years to even decades. Production decline seems to be more rapid in the finer grained shale formations. As wells decline, we may need to drill more new wells just to maintain a particular level of production.

That brings us to the fourth limitation. Land acquisition and availability of water. Land will have to be acquired for setting up drilling rigs and supporting infrastructure. India's record of compensation and rehabilitation of displaced people is poor, so expect conflicts. And further, several millions of liters of water per well is required to hydraulically fracture a shale formation at one spot. A gas field may have tens to hundreds of wells. In many sites, this water will be taken up from the same groundwater system farmers use to irrigate their fields. Such a large demand of water by energy companies will strain the already precarious situation of diminishing groundwater resources. Thus water allocation agreements (if necessary arbitrated by Courts) between farmers and energy companies might put the brakes on gas production.

ISRO Plans New High Resolution Remote Sensing Satellite

noreply@blogger.com (Suvrat Kher) — Mon, 18 Mar 2013 16:13:00 +0000

...but will the public have easy access to the data?

Something this article does not address. India's remote sensing program is no doubt a great science and technology success and the imagery and digital data is being used by scientists for research and natural resource management.

Where India and ISRO are falling short is the continued denial of the best quality images to the public at large. Bhuvan - ISRO's answer to Google Maps - launched a few years ago is still serving images of India which are frustratingly inadequate for users who have by now become accustomed to razor sharp quality images of their cities and countryside from Google Maps and Google Earth.

The remote sensing satellite Cartosat-2 series has been imaging India using a panchromatic sensor at a 0.8 meter resolution since 2007. In July 2011 India announced a new Remote Sensing data policy which allowed distribution of 1 meter resolution imagery without additional security checks. The previous policy did not allow unrestricted access to imagery finer than 5.8 meters. The policy change should ideally have resulted in image streaming applications like Bhuvan to present much sharper images of India. Almost two years since we are still getting a grainy view of India from Bhuvan. Is the new policy not extendable to open access image streaming applications? If so, why not? Pointing to reasons of national security does not make sense since fine resolution imagery is already available through applications like Google Maps to users in India.

The image below of a portion of Pune city is the best resolution available via Bhuvan and it means that tens of millions of potential users will stay away and use Google instead.

Florida Sinkholes Also Pose A More Subtle Danger

noreply@blogger.com (Suvrat Kher) — Thu, 07 Mar 2013 11:30:00 +0000

Last week, a fatality, as the ground gave way under a Tampa Bay area home. However, the more common concern regarding sinkholes is their connection to groundwater quality. Despite its reputation as a great tourist destination, Florida is also a major agricultural state. The soil is reenforced with fertilizers, and crops are sprayed extensively with pesticides. Environmental managers worry that these chemicals might find their way into groundwater.

This concern is not unique to Florida but is amplified due to the presence of karst topography. Extensive limestone formations underlie Florida. Limestone reacts with the weakly acidic groundwater and over the last few million years these limestone beds have dissolved away in varying degree to create an underground network of caves and pipes. The overlying strata may bear its own weight for long periods depending on how thick it is and how porous the underground limestone has become, but occasionally the cover collapses into the underlying cavity forming surface craters or sinkholes.

Fatalities are rare, but sinkhole formation is quite common over geological time. The map below shows an area just east of Gainsville.

Notice the circular and irregular shaped lakes. Most of them are sinkholes now filled with water. This surface water makes its way through fractures and pipes into the underlying limestone which make up the Floridan aquifer system. Sinkholes thus provide a direct and quick connection for potential pollutants to contaminate groundwater which is the main source of drinking water in Florida.

The question is then: what combination of geological conditions will make aquifers at one location more vulnerable to contamination than at some other location? The Florida Department of Environmental Protection (FDEP) has been wrestling with this question for quite some time. The 1996 amendment of the Safe Drinking Water Act required each state to have a Source Water Assessment and Protection program to proactively protect the State's water resources from potential contamination.

As one approach to better understand aquifer vulnerability, the FDEP came up with a Geographic Information Systems methodology known as the Florida Aquifer Vulnerability Assessment model. I contributed to this work during my time as a researcher with FDEP some years ago. This model uses the Weights of Evidence method which is a Bayesian statistical method based on probability. The basic idea was to create GIS layers representing different geological conditions or predictors of vulnerability such as a) density of/proximity to sinkholes b) soil permeability c) thickness of formations d) depth to water table/confined aquifer. Known occurrences of contamination (example: levels of nitrate above a certain baseline measured from monitoring wells) were used to develop a spatial correlation between contamination and a geological condition. Each unit area in each layer was weighted based on the strength of the correlation. Then the layers were added in a GIS (representation on left above: Source- FDEP) As the same geographic location containing different geological indicators was superposed, individual weights from the different layers got added to give a cumulative weight for that location.

The spatial distribution of cumulative weights was represented by a probability map of relative vulnerability.

The poster below summarizes some results from a selection of Florida counties.

Source: FDEP

The tool is now being used by environmental managers and regulatory and planning professionals to better protect Florida's groundwater quality.

Coming back to sinkholes the results of this long drawn out GIS project were what common sense would expect. Proximity to sinkholes was a positive predictor of aquifer vulnerability, meaning, the closer fertilizer and pesticide use is to a sinkhole, the greater the chances that the groundwater would get contaminated. That does offer environmental managers a firm statistical footing to put in place best land use practices such as having conservation buffers i.e. strips of vegetation around the sinkhole that will stop agricultural runoff, prohibiting dumping of any sort in the vicinity of sinkholes and even fencing the sinkhole to prevent animal waste from making its way into the groundwater.

"Submerged Continent" Story Trending For The Wrong Reasons

noreply@blogger.com (Suvrat Kher) — Tue, 05 Mar 2013 11:26:00 +0000

It does seem so judging by the comment stream of this article by Akshat Rathi which appeared in The Hindu last week. The article is currently in the most popular list of the Sci-Tech section of The Hindu.

"This could be another malefic design to make tamils believe they belong to different continent. As the validity of 75 yrs old dravidian myth is busted by science dna researches and rationale thinking. This could be yet another attempt to confuse south people".

from: Periyar

"It is interesting how scientist sometime make outlandish claims with no certainty of counter proofs. In fact it all depends which group you belong to, dominant or struggling, majority view which is stupid or minority non-peer view but sensible. So here we go again. The only certainty is that the world map did not look like today millions of years ago. There are unexplained artifacts many millions of years from different parts of the world which are neither explained or frankly admitted to be un-explainable. The reason being the Scientists calling the shots cannot eat humble pie. There are hundreds if not thousands of such artifacts. Some have conveniently disappeared to stop embarrassment for scientists. And then there are myths and legends, Ramayana and MahaBharat and 'in peoples memories'".

from: Politenotpc

"There was an article several days before that Australian aborgines share the same DNA as the rest of South India. So hypothetically speaking their ancestors would have traveled centuries before to Australia by land. impressive findings these.."

from: Manoj

"I was fascinated to read about the discovery of this new continent and its location so close to India.I was then wondering whether it could be the JAMBUDWIPA of yore which we repeatedly recite in Vedic chants."

from: kumar

People are relating the submerged continent to events that may have taken place in human history with some nationalist pride and suspicions of scientists thrown in as well :)

The finding off course belongs to deep geological history.

Geophysical data indicated that the lithosphere in this region is thicker than what would be expected in an oceanic basin made up of basaltic crust alone. And zircons collected from xenocrysts (fragment of a foreign crystal) within lavas on the island of Mauritius gave a Proterozoic age. The lavas of Mauritius which contained these zircons were about 9-10 million years old. That suggested that these zircons belonged to very ancient continental fragment beneath Mauritius from which they were broken of and brought to the surface by younger lavas.

The continent is a smaller piece of Gondwanaland that separated from Madagascar about 60-80 million years ago as rifting between larger pieces of Gondwanaland (Madagascar and India) stretched and thinned the crust opening up an oceanic basin. Prolific basaltic volcanism later covered this continental fragment . So, there never was a land connection across the Indian Ocean between India and other continents in recent geological history. Some of these continental fragments may have submerged below sea level much earlier and some would have appeared as small islands in the area between Mauritius and Seychelles - well to the south of India - before being covered by lava several millions of years before the presence of any humans on the Indian subcontinent.

But the allure of the "lost continent" endures.

Kaolinite And Chinese-Mexican Pottery In 1600's Mexico

noreply@blogger.com (Suvrat Kher) — Fri, 01 Mar 2013 16:14:00 +0000

My Book Shelf # 25

As with a previous post which pointed to the role of silver as a catalyst for the movement of people across the oceans and a meeting of Asia with the America's in 1600's Mexico, geology in the form of clay deposits played a role in bringing full circle the story of Chinese (Ming) influence on Mexican ceramic art from the mid 1600's onwards.

The district of Puebla in Mexico has kaolin deposits of exceptional quality formed mostly by the hydrothermal alteration of a rhyolitic host rock from the Late Cenozoic Trans Mexican Volcanic Belt considered to part of the Circum-Pacific volcanic chain. This type of clay is used extensively in pottery.

By the late 1600's Puebla city had a tight knit Asian community:

One of the city's most important industries was ceramics - Puebla clay is of exceptional quality. Working with eye-straining attention to detail, skilled potters created pieces that imitated blue-and-white Ming dynasty porcelain. Guild regulations specified that "the coloring should be in imitation of Chinese ware, very blue, finished in the same style". Edward Slack, the Eastern Washington historian, points out that the manufacturers would hardly have ignored the skilled Asian craftspeople in their midst. More than likely, Puebla's fake Chinese pottery was created in part by real Chinese potters. If so, they did a splendid job: talavera ware, as it is known today, is now so highly prized that when I visited Puebla shopkeepers complained that the country was fighting an invasion of counterfeits from China - a Chinese imitation of a Chinese-made Mexican imitation of a Chinese original.

From 1493: Uncovering The New World Columbus Created by Charles Mann.

An Account Of Natural Selection By A Victorian Gentleman

noreply@blogger.com (Suvrat Kher) — Tue, 19 Feb 2013 16:42:00 +0000

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.

Patrick Matthew was the author of this passage written in 1831, many years before either Charles Darwin or Alfred Wallace thought about evolution through natural selection. Matthew wrote this in a book titled Naval Timber and Arboriculture. The link was that he managed orchards and became familiar with the principles of husbandry (and artificial selection) used in forestry and food production. His book elaborated on how to improve the timber used to build the Royal Navy's warships and in the appendix of that book he wrote about artificial selection and natural selection. Those passages and his great insight into evolution though was not appreciated at that time.

And a great passage it is! Apart from its explanation of natural selection in the first paragraph, notice the last few lines:

[The] progeny of the same parents, under great differences of circumstance, might, in several generations, even become distinct species, incapable of co-reproduction.

From the same parents under different circumstances may arise distinct species, incapable of co-reproduction.. i.e. the origin of separate lineages or branches. Several daughter species may thus branch out from a common ancestor. Darwin has been credited of having thought of this idea first. In his Notebook B in 1837 he sketched out his idea of the formation of new varieties from a common parent in a diagram which showed evolution as a branching process.. a tree of life (the only diagram in his book Origin of Species). But reading Matthew's passage I'd say he has come pretty close to stating the theory of common descent (and speciation) about 6 years before Darwin. Matthew though unlike Darwin did not extrapolate from this to draw a grander picture of the unity of all life.

In 1860, upon reading a review of Darwin book On The Origin Of Species in the Gardener's Chronicle, he sent a letter to the publication pointing attention to his earlier published work. Darwin acknowledged Matthew's priority in a subsequent edition of his book.

On his part Matthew freely admitted that Darwin's achievment had greater merit:

"To me the conception of this law of Nature came intuitively as a self-evident fact, almost without an effort of concentrated thought. Mr. Darwin here seems to have more merit in the discovery than I have had; to me it did not appear a discovery. He seems to have worked it out by inductive reason, slowly and with due caution to have made his way synthetically from fact to fact onwards; while with me it was by a general glance at the scheme of Nature that I estimated this select production of species as an à priori recognisable fact—an axiom requiring only to be pointed out to be admitted by unprejudiced minds of sufficient grasp."

It was Darwin Day on February 12, so I thought I would post this interesting bit of science history.

And by the way, don't forget Alfred Wallace. This year is the centenary of his death and a repository of his work is now online. Called Wallace Online and containing twenty nine thousand searchable pages of Wallace's writings, it is managed by John van Whye of the University of Singapore and showcases the many important contributions of Alfred Wallace to the field of biology. Van Whye also manages the website Darwin Online.

Mexican Silver And Japanese Samurai

noreply@blogger.com (Suvrat Kher) — Fri, 15 Feb 2013 06:51:00 +0000

My Book Shelf # 24

A post by Metageologist on tracking the source of silver in English coins from Medieval to early modern times caught my eye.

Silver formed by different geological processes may have distinct isotopic signatures. Metageologist points to a study which recognized English silver coins being sourced initially from silver taken from European mines and then later from the mid 1500's from Mexico via the Atlantic trade route. The silver from rich deposits in Peru primarily took the Pacific route and went to satisfy Chinese demand.

People too moved across continents along with silver. I came across this fascinating passage from 1493- Uncovering The New World Columbus Created by Charles Mann on the outsourcing of security for silver shipments-

Known collectively as chinos, Asian migrants spread slowly along the silver highway from Acapulco to Mexico City, Puebla, and Veracruz. Indeed, the road was patrolled by them- Japanese samurai perhaps in particular. Katana-swinging Japanese helped supress Chinese rebellions in Manila in 1603 and 1609. When Japan closed its borders to foreigners in the 1630's Japanese expatriates were stranded wherever they were. Scores, perhaps hundreds migrated to Mexico. Initially the viceroy had forbidden mestizos, mullatos, negros, zambaigos, and chinos to carry weapons. The Spaniards made an exception for samurai, allowing them to wield their katanas and tantos to protect the silver shipments against the escaped-slaves-turned-highwaymen in the hills.

Charles Mann is right when he calls the Mexico of this period a "crazy soup".

Gorgeous Paper On Carbonate Diagenesis In Journal Sedimentary Research

noreply@blogger.com (Suvrat Kher) — Tue, 12 Feb 2013 15:46:00 +0000

The January 2013 issue of the Journal of Sedimentary Research is open access. There is a long and beautifully illustrated study on the diagenesis of Permian carbonates from the Guadalupe mountains of New Mexico U.S.A. by David A.Budd and colleagues.

These carbonates were fractured very early during their depositional history, in fact the fractures are syndepositional i.e. they formed as the sediments were accumulating. Sometimes calcium carbonate sediments undergo cementation and hardening by sea water just a few centimeters to meters below the sediment water interface and they then are rigid enough to fracture. Budd and co-workers painstakingly analysed the materials filling these fractures using a variety of sedimentary petrology and geochemical techniques and found out that these fractures acted as conduits for the movements of fluids not just early on but through the entire geologic history of these rocks. So the geometry of fluid flow networks may be established very early in the rock history with implications for the distribution of porosity and localization of economic deposits.

I love such detailed petrologic studies. I was consumed by this kind of research during my PhD days, thinking about marine and meteoric cements and porosity formation and the movement of fluids and its interaction with rock from its deposition to deep burial. It was a real pleasure to read this long and exhaustive work.

I said beautifully illustrated so let me post below an example from the paper. The image shows the cementation and interpreted geologic history of a fracture using plain light and cathodoluminescent microscopy.

Explanation from the paper:

A) Paired plane light and B) cathodoluminescent photomosaics through fracture fill B. The wall of the large fracture is lined with bladed dolomite cement (black arrows). Overlying the dolomite is a first generation of luminescently zoned (non to dull to bright orange) calcite cement (CC1). With subsequent refracturing, those first generation cements were mechanically rotated, brecciated, and lightly etched (white box), and then the combined fracture opening was encased in a bright orange luminescent calcite (CC2).

Just to show off, let me put up a similar kind of image from my PhD work in the Upper Ordovician strata of the southern Appalachians U.S.A. Again a pore space illuminated by cathodoluminescence shows different cement generations.

Long live Sedimentary Geology!

Geologist Robert Young On Rebuilding After Superstorm Sandy

noreply@blogger.com (Suvrat Kher) — Sun, 10 Feb 2013 09:32:00 +0000

The complicated decision on whether to and how much to rebuilt coastlines after destruction from a major storm lies at the intersection of geology, climate change, sea level rise, preserving communities and livelihoods, and the economics of insurance risk and the real estate market.

Geologist Robert Young, director of the Program for the Study of Developed Shorelines and professor of coastal geology at Western Carolina University speaks passionately and authoritatively about these issues in a talk hosted by Tom Ashbrook on OnPointRadio.

As he says; The map of the coastal U.S. 50 years on will look very different from now and we need a national plan to get from here to there. Its good to hear a geologist at the center of this discussion.

Listen: After Big Storms: Rebuild Or No?

The Real Reason Behind The Santa Cruz Islands Earthquake

noreply@blogger.com (Suvrat Kher) — Thu, 07 Feb 2013 09:29:00 +0000

From Jesus and Mo..

And here is the less likely explanation.