That's Dr. Brian May To You!!

One of my favorite rockers Brian May of Queen (love his little guitar riffs!!)

is now Astrophysicist Dr. Brian May, Ph.D in interplanetary dust from Imperial College, London


Listen to Dr. May belt it out on NPR's Day to Day. He's also co-authored a new book titled Bang: A Complete History of the Universe. Might not sell as much as A Brief History of Time but it's a fair bet that many unread copies will sit atop bookshelves. I got all nostalgic and listened to A Night At The Opera. Lazing On A Sunday Afternoon, Death On Two Legs, I'm In Love With My Car...

Dr. May is now chancellor of John Moores University in Liverpool. What is it with Liverpool and great rockers?

Strange Climate Debate in Times

Last week came the news that scientists are predicting a decadal-scale plateau in temperatures or even a slight cooling of Europe and N. America probably related to shifting currents in the oceans. The long term forecast that mean global temperature will increase over the next century remains, but the research reminded us that global warming does not mean that temperatures on every square inch of the earth will increase in step, monotonously and uniformly. Dot Earth has a thoughtful post on whether we can use evidence of long-term risk of temperature increase and put in motion meaningful practical policy to reduce emissions of CO2 or will predictions about the short term variability of climate systems such as the coming cooling of Europe and N. America put the brakes on efforts to limit emissions. All current projections about India point to continued warming in the Indian subcontinent without any decadal-scale breathers.

Given this background the Times of India had a debate on climate change in its view and counter view format. The Times view was the consensus view that argued for continued action no matter how climate systems behave in the short term. I agree with this but was surprised to read the counter view. This was no subtle nuanced argument about complexities of climate systems and the economics of different policy options of combating global warming, but a full sucker punch in the face against the very notion of human-induced global warming. On second thoughts that such a polarized view was tabled should not have surprised me since the very format of the debate forces the counter viewer to take a completely opposite position no matter how ludicrous it might be. And ludicrous it was.

The argument was made not by a climate scientist- when will our media ever learn to engage experts- but by columnist Jug Suraiya! Now Mr. Suraiya is a well respected columnist but he is not a climate scientist and his lack of science training shows. He opens his argument not by referring to real science contradicting warming but by pointing out that the writer Michael Crichton has written a science fiction book that questions the human influence on global warming. I kid you not! Mr. Suraiya raises the bogey of a vast conspiracy involving tens of thousands of scientists, media, lawyers and NGO's all bent on getting their piece of the global warming funding pie. He then goes on to make some very strange remarks about the composition of the atmosphere essentially saying that the concentration of CO2 in the atmosphere compared with other gases is minuscule and that adding a little more presumable won't make a difference. He ignores the fact that while the relative proportion of CO2 compared with other gases is minuscule, CO2 along with water vapor are the major greenhouse gases and that calculations indicate that adding that "little more" CO2 is precisely what will overload the natural CO2 mass balance of the earth and cause warming. He then proceeds to dismiss the rise in surface temperatures of the earth as a sign of urban heat island effect. I frankly felt very irritated with the man. Does he really think that climate scientists are stupid and have not understood the heat island effect and not corrected for it and validated that correction? The terrestrial temperature measurements are also complimented by measurements of ocean temperatures which also have increased and those of the troposphere which satellite measurements show to have steadily increased too. Read too much Michael Crichton and you tend to forget the real data.

Mr. Suraiya finally regards the melting of glaciers and polar ice caps as natural inter-glacial phenomenon but then points out that the Greenland ice sheet has been growing for the last 6 thousand years. We are in an inter-glacial period and most of the glacial melting related to it took place in the first few thousand years of warming at the beginning of the Holocene period starting about 12 thousand years ago. Greenland ice sheet volume would have fluctuated as a response to the natural climate variability over the past few millennium and may even have grown a little over the last 6 thousand years, but what is important is the increased rates of glacial melting, both alpine glaciers and those in the Arctic and Antarctica that we observe today. For example current studies of the Greenland ice sheet indicate that net loss in ice volume of several glaciers has accelerated in the last few years. Climate scientists are afraid that there is a danger of continued decay of the Greenland ice sheet with attendant sea-level rise over the coming decades as Greenland and the Arctic ocean warms up. This is the point I think a lot of climate skeptics miss out on. It doesn't matter what natural trend existed over the last few thousand years, it is changes over the last 50 years and the next 100 years or so that are of importance and these changes in global temperatures and consequently sea-levels, the overwhelming evidence tells us are being caused by human activity.

I am all for debate on complex topics like climate change, global warming and societal response to it. But the debate should now move away from whether there is going to warming over the next century to how best to minimize it and adapt to it. And it's time that our media brings in climate and policy experts to talk about it.

Dino News: T. Rex ,Predictions, Media Muck Ups

Dinosaurs are undoubtedly the stars of palaeontology research if you go by media coverage of the field. Paleontologists who study foraminifers or graptolites may disagree but for the media Dino's are always newsworthy. No news about these creatures is small enough to cover. Dino's seem to occupy an iconic status among creatures long gone extinct. They do fascinate, more than any other beasts they bring visions of a primordial world that once was. Stephen Jay Gould wrote on many occasions how the Tyrannosaurus Rex exhibit at New York Museum of Natural History inspired him to become a paleontologist. His excellent collection of essays Bully for Brontosaurus has an affectionate tribute to Dino-mania. Two news reports on Dinosaurs in the last couple of weeks caught my eye.

Creationists often carp that evolutionary theory lacks predictive power. Ask a biologist they say how human evolution will proceed over the next 5 million years and there will be a shake of the head and a can't say for sure for an answer. If you cannot predict the future evolution of a species then evolutionary theory is not a true science. This line of argument is often persuasively sold by creationists to the layperson not familiar with the scientific method. It is true that it is not possible to forecast what specific evolutionary trajectory a particular lineage will take since there is contingency built into evolution. The process is very sensitive to starting conditions. Small initial variations between sister species may lead to large differences over time but on the other hand they may not. Unlike physical laws, biological "laws" are not universal in time and space. There are exceptions to just about every biological patterns and processes and this makes predicting long term evolutionary trends difficult. Moreover external events such as climatic shifts may push evolution this way or the other, disasters such as meteorite impacts may obliterate well adapted species and reorganize ecosystems. But in science prediction does not always mean foretelling future events. Especially in evolutionary theory a large part of prediction making deals with reconstructing events of the past, retro-dictions if you like. Which means predicting that certain biological patterns and properties will exist in nature given expectation of theory and complimentary data from another area of research. Based on anatomical comparisons between Dinosaurs and other vertebrates it is the consensus view today that birds are the closest living relatives of Dinosaurs. If gross morphology informs us such then so should individual molecules. A reasonable prediction would be that there would be greater DNA or protein sequence similarity between Dinosaurs and birds than between Dinosaurs and any other living vertebrate. And that is exactly the pattern that has been found in ancient proteins recovered from a 68 million year old T. rex bone. The analysis grouped T. rex closer to chickens and ostriches than to lizards and crocodiles. You can listen to the details in this NPR piece. This is how evolutionary theory gets strengthened. Predictions such as these are made every day in labs and tested. Lines of evidence from different fields converging on the same conclusion. Nothing earth shaking, no paradigm shifts or revolutions, just day to day science at work although in this case retrieving protein from a 68 million year old fossil was something special. But nearly 150 years of testing and validating predictions such as these is why evolution is such a strong theory.

Given the frequent coverage by media on dinosaurs and their relationship to birds I don't at all understand how Science Daily could have got it so wrong in another piece on dinosaurs. This one dealt with the absence of heat generating brown fat in lizards and birds. This is tissue that generates heat in mammals and a comparative molecular analysis suggests that the gene UCP1 responsible of this function arose in the common ancestor of mammals and birds. This is what the report said:

The ability to produce brown fat evolved in a common ancestor of birds and mammals, but the ability to generate heat was lost in the group that gave rise to birds and lizards after it separated from the mammalian lineage (the researchers found the lizard genome similarly lacks a UCP1 gene). This strongly implies that dinosaurs, which diverged from birds even later than lizards, also lacked brown fat.

Science Daily has got the evolution part all mixed up. The common ancestor of birds and mammals is the common ancestor of dinosaurs, lizards and mammals. See figure of vertebrate phylogeny below. Red indicates presence of UCP1 and black indicates its absence. Question mark indicate uncertainty on when exactly UCP1 was lost.


Source: BioMed Central

Birds are not ancestral to dinosaurs as the report implies but birds are highly derived dinosaurs. The best evidence suggests that they evolved from within the maniraptors, a group of small carnivorous dinosaurs. Birds lack UCP1 because dinosaurs lacked it and they (birds) inherited that condition and not the other way round.

Update: Just saw this in DNA. The Indian media is never far behind in copying the mistakes of others. DNA (April 28 08) pasting the same report came up with its own headline: Dinosaurs died as they failed to generate heat. The print edition went further and announced a new theory: New Theory on Dino's Extinction. The original research article did not approach the topic of extinction with a single condition answer and for good reason. End Cretaceous environmental changes must have affected organisms in various ways. Dinosaurs were varied in their size , shapes, diet and thermo regulation. It's unlikely the entire group would be affected in the same way by ecological changes. Absence of UCP1 and a lack of heat generating brown fat was a shared condition in lizards, non-avian dinosaurs and avian dinosaurs (birds). Only the non-avian dinosaurs went extinct. Any theory of dinosaur extinction has to explain this specificity since despite lacking UCP1 many ancient lizard and avian dinosaur (bird) species survived and proliferated. Many non-avian dinosaurs are thought to have had higher rates of metabolism than lizards and other reptiles so the answer to why dinosaurs went extinct has to account for that too.

Darwin: I Think I've Got It

Darwin has been in the news quite a lot past couple of weeks and not just because of the release of that misleading, "worse than stupid" movie Expelled.

The New York Botanical Garden has launched an exhibit named "Darwin's Garden: An Evolutionary Adventure" which highlights Darwin the botanist and his many works on plants. Cornelia Dean has a piece on this exhibit in the New York Times. The exhibit recreates portions of a typical British garden as Darwin would have seen through the window of his room and on loan from Cambridge and Harvard University are a selection of Darwin's notes, books and sketches on botanical topics. Dr. David Kohn the exhibit curator says about The Origin of Species and Darwin's work on plants:

Though most people associate that book and Darwin’s ideas generally with his voyage to the Galápagos and his study of finches there, his work with plants was far more central to his thinking

and

plants were the one group of organisms that he studied with most consistency and depth over the course of a long scientific career” of collecting, observing, experimenting and theorizing.

I knew reading Darwin historians that the finches of the Galapagos Island did not provide a eureka moment for Darwin and it took him some time after his return to London in 1836 to start putting together his thoughts on variation, adaptation and transmutation (evolution) into a coherent theory of evolution. I wasn't aware plants played a big role in this early thinking on evolution. But it makes sense since much of his observations on variation and the malleability of organisms relied on domesticated varieties and the effects of artificial selection. Plants would have made a good study material, easy to grow in your garden and manipulate to observe the effects of pollination and hybridization.

The exhibition opens Friday April 25th and runs through June 15th.

Also, Cambridge University has made available online more than 20,000 pages of documents, manuscripts, books and works of Charles Darwin. I went on the website and was lost. Where should one start exploring such an enormous quantity of material? I have settled on exploring -this is really a long term reading project- the Transmutation Notebooks (Notebook B, Notebook C, Notebook D, Notebook E), a series of notes Darwin complied during the period 1837-39 on some core ideas regarding the stability of species, common descent, extinction, variation, adaptation and natural selection. To say that the notebooks represent a "work in progress" has to be the greatest understatement of all. These writings contain the germs of ideas that changed biology and our understanding of life.

An example from Notebook B 1837:

Source: Darwin Online via NYtimes

The first sketch of the tree of life depicting evolutionary relationships and Darwin's rumination on common descent and the role of extinction in producing discrete gaps and degrees of relatedness between groups. There may not have been one big eureka moment for Darwin when all the pieces suddenly fell in place, but conceptualizing evolution as a branching process with a tree geometry must count as a breakthrough in his thinking, one of many "I've Got it" occasions, one piece of the puzzle clearer. The caption reads " I think", which is something the makers of the movie "Expelled" seem not to have done.

Those City Water Wells

Last week I came across a small report on groundwater levels in Pune and finally got down writing about it. The caption read: "Well" done! Water table has gone up in Pune. I am not sure how much significance to assign to this euphoric caption and particular findings detailed in the press report. One usual quibble I have regarding reports such as these is that a meaningful comparison and context is never given. Water table has gone up compared with what? The last measurement? A five year average? A ten year average ? What is the variation shown by the groundwater system over the last 100 years and how does this latest data point fit in? There are apparently some old observation wells that the Groundwater Survey and Development Agency (GSDA) monitors. This forms the basis of these periodic announcements of water table levels. The city has grown enormously over the last few decades and extrapolating from these few monitoring wells to the entire city does not seem to me a very sound idea. Basalt aquifers such as the ones that underlie Pune are quite heterogeneous in their groundwater transmissivity and storage capacities. What is happening to the water table in a few observation wells may not apply some distance away. Without understanding the variability of the system and its causes, simply reporting that the water table has gone up or gone down by a certain amount makes little sense.

The wells referred to in the report are shallow dug wells, which lots of old bungalows used to have when I was growing up in the 1970's. There are still some 5000 odd remaining according to the news report. I remember peering over the side to see how deep the wells were. The water table was shallow about 15-20 feet below surface and the wells always had plenty of water. But even then they were not being used as a drinking water source. Their use was for washing and for the garden. On Ananta Chaturdashi day many well owners used to let neighbors use the well for immersion of their Ganesh idol. It used to be quite a festive occasion. Over the last 3 decades or so their use as a water resource within the city has declined as the water has got more polluted. Still as a geologist I don't miss an opportunity to peer over the side. These dug wells tap the shallow groundwater system in the basalts. Image to the left below is a photo of a dug well I took a couple of days ago. The image to the right is a schematic which shows the hydrogeology of these wells (Source: ACWADAM).





















In the photo you can see that the well is lined. Below that level is the basalt rock which has a slab like appearance. That is due to horizontal sheet joints or fractures along which groundwater flows. Basalt is a volcanic crystalline rock which has a tight interlocking crystal fabric. Water is not stored and transmitted through the rock matrix i.e. spaces between crystals but along cracks and fractures that develop in the basalt. Vesicular amygdaloidal basalt is a type of basalt that has horizontal sheet joints. Another type of basalt known as compact basalt usually develops vertical joints. Basalts with horizontal sheet joints have higher transmissivity and storage capacity and yield more water than compact basalt. These controls are shown in the schematic in the figure to the right (above)

This shallow groundwater system within the city is underutilized today. The trend has been to fill up these wells as bungalows make way for bigger apartment complexes and to bypass the shallow system and tap the deeper aquifers using bore-wells. Many new apartment complexes have bore-wells and utilize the water for washing and the garden. There is an assumption that this deeper aquifer contains cleaner water but that might not always be true. As the graphic to the left shows (source: ACWADAM) deep aquifers are replenished through the shallow system by penetrating vertical fractures. There is a real chance of contamination of the deeper system as well and using that water without adequate treatment is a health risk.



The population of Pune metropolitan area today is around 3 million or so. The city is fortunate to have lots of big surface water reservoirs (Khadakvasala, Panchet, Varasgaon) and the water supply per person is about 2oo litres per day according to the Pune Municipal Corporation Env. Status Report 2004. These reservoirs have adequate capacity to meet projected water demands over the coming decades and the PMC claims to be building water supply infrastructure to supply a population of about 6 million by 2025. Besides surface water the Municipal Corporation keeps talking about using these groundwater aquifers as a supplemental water resource to be used for non-domestic purposes. Rain water harvesting, artificial recharge of aquifers, sustainability, these are the latest buzzwords the city government likes to throw around. But I see two problems for any sustainable use of these systems. The first is a lack of basic science. City officials admit that they don't have any rigorous quantitative estimates on how much water is there and how much extraction is possible given natural replenishment rates. The second problem has to do with how to regulate the use of this resource. Currently groundwater use is not regulated in India and allows the owner of the land to extract as much groundwater as needed. Without changes in the regulatory framework, there will be overexploitation and the danger of degradation of the groundwater system.