PZ Myers gets Expelled

PZ Myers who blogs at Pharyngula has an absolutely hilarious post on how he got expelled from a movie theater in Minneapolis. He along with a guest had gone to see the creationist propaganda movie Expelled. As he stood in line a policeman came up to him and told him that he was on a blacklist and had to leave immediately which Myers did. PZ Myers who teaches biology at University of Minnesota has been a nemesis of the creationist community, but what a silly infantile reaction to ban him from the movie! What is even funnier is that they allowed his guest to go in...

Small Humans and Science Outreach

One good place to follow science research is Science Friday on National Public Radio. Last week they had a interesting talk on newly discovered fossils of humans from the island of Palau. The unusual aspect of these fossils is that they most probably represent the remains of an extinct population of pygmy humans that inhabited that island about 2000-3000 years ago. Small body size is a common feature of hunter gatherer populations living in tropical habitats and these fossils show a body size comparable or slightly smaller than pygmy populations of S.E.Asia and Africa. The scientist in conversation Lee Berger gave quite a few insights into the phenomenon of island dwarfism which is an extreme reduction in body size as a response to living on resource poor islands where life spans are short and early reproductive maturity evolves at the expense of continued body size growth. I thought this topic would be of interest to Indians, since we have our own pygmy island populations in the Andaman islands. Recent genetic analysis suggests that these original inhabitants of the Andaman represent a population of great antiquity perhaps descendants of people who migrated out of Africa in the Late Pleistocene around 50,000 years ago and settled in the Andaman islands shortly thereafter. Their short stature is thought to have evolved independently of the African pygmies. The thought that a pygmy population living in another place went extinct is sobering given the current situation of the various Andamanese tribes such as the Onge. These people now number in their few hundreds and live in special reserve areas mostly out of contact from other island inhabitants. Anthropologists believe that such small statured human populations were once common all along the S.E. Asian islands from the Andaman to Malaysia to Philippines to Indonesia. Immigration of agriculturists in the past couple of thousand years have marginalized them. Only a few pygmy tribes remain today along these island chains. The Palau population may have been such an island outpost of small people.

Shifting tracks what struck me about this talk was how entertaining it was. Even someone with no special interest in anthropology will find that "the excitement of doing science" really comes through the enthusiastic give and take between host Ira Flatow and the guest Lee Berger. I feel this kind of a conversation about science is missing between Indian scientists and the public. Our scientists are by and large invisible. During school we used to meet them on that boring tiresome "science day" where hordes of kids are paraded through labs and given pep talks by all too grave looking scientists. Elsewhere they get invited occasionally on TV and in the print media, but the topics discussed are always too grandiloquent, India's moon mission, launch of a new satellite, general discussions on global warming. In newspapers too there is a lack of regular science columns where specific research topics or a specific piece of work carried out by Indian scientists in Indian labs is written about. Online editions now offer an opportunity to invite scientists or science journalists to start blogs but so far our media have not used this avenue. I am really not sure how much to blame the media for this. Science does not seem to attract most young Indians as an exciting career option and the lack of engagement of scientists by the media is probably a reflection of this. There may also be a perception that unless you are doing some earth shattering piece of research its not worth reporting on. But that is really not the point of a science conversation. The point is to engage the public and instill in them an interest in the practice of doing science. All discoveries big and small are interesting to the working scientist and programs such as Science Friday convey that excitement to listeners with great effectiveness. Besides mainstream media today there are avenues for Indian scientists to create their own audience primarily through their own blogs. This opportunity for science outreach still remains woefully unexploited by Indian scientists. I don't have a count of how may science faculty and science researchers blog but I suspect hardly any do. In Pune for example, there are several institutes of higher education and research, University of Pune, IUCAA, Indian Institute of Tropical Meteorology, National Chemical Laboratory but I have yet to discover a blog by a faculty or researcher from any of these places. What are other ways for Indian scientists to have a conversation about science with the public? An initial step may be University radio stations. These are essentially low power community radio stations. Mumbai and Delhi University have already started broadcasting and hopefully science will get some space. Individually their reach will remain local. But can a network of such University stations be set up with program sharing? Another way to get around the local coverage would be to set up attractive websites and provide online radio streaming and podcasts of programming. In general community radio may prove to be a really good tool for science outreach and our science institutions need to capitalize on the recent FM boom and be more proactive in using airwaves to promote science conversations with the public.

I've Never Been to the Grand Canyon

It's true, and I get a lot of ribbing from my friends about it. All those years studying and working in the U.S in geology and never been to the Grand Canyon?!! Conversations with people I meet on occasions also tend to be awkward:

Person: So, you're a geologist working in the U.S.
Me: Yes
Person: Very interesting topic. I have been to the Grand Canyon twice
Me: I've never been there
Person: No, but.....but.... you are a geologist. I mean what did you do?
Me: I spent all my free time in the southern Appalachian mountains
Person: Oh.... ya .... well....I guess..... nice rocks there too huh?

It's easy to see why geology and the Grand Canyon go together. Just take a look at this:

The deep gorge that the Colorado and ancestral rivers have incised exposes a geological section of rocks ranging in age from 2 billion years to about 200 million years. It's very unusual to have rocks representing such a long time period exposed in one place. For the layperson the fascination goes beyond whether the rocks are 2 billion years old or otherwise. The vastness of geological time, the relentless erosive power of rivers, insignificance of humans faced with nature on this scale, all these National Geographic style cliques fit well at the panorama tourists see before them. It must be an awe inspiring spectacle. I have to plan a trip soon.

The Grand Canyon was in the news last couple of weeks. One study showed that it is apparently older than the previous estimate of 6 million years. The new estimate suggests that rivers started incising the system of canyons about 17 million years ago. This the researchers arrived at by dating mineral deposits that form in caves, which were interpreted to mark the level of groundwater and by proxy the river. These caves are found at various levels along the canyon walls marking the deepening of the canyon as the river cut into it. The highest cave deposits were about 17 million years old and the lowest around 6 million years old. The finding has been disputed, the main argument against it being that caves can form without there being a river and there is no outwash, i.e debris deposited by the river that old in the western parts where the ancestral rivers first started incising into the Colorado plateau. According to the dissenters, the earlier caves were formed by groundwater systems without extensive surficial drainage network. Only later did the extensive river drainage form. I have to say the doubters have a point. For example large parts of Florida are pockmarked by surface and subsurface caves but not all of this system is associated with well defined river drainage networks. Groundwater has been eating away at the limestone. You can follow the debate here. The second piece of news is that water managers of the Colorado river systems have been flooding the Grand Canyon by releasing water from the Glen Canyon dam. This is being done to improve fish habitat. The flood of water around 41, 500 cubic feet a second will deepen the channel, deposit new sediment and enlarge sandbars. Not everyone is happy about this. You can read about this here.

I have been making a mental list of some of the very basic principles of geology that are elucidated in the Grand Canyon. I realized that about half the examples of the undergraduate first level lab I taught were taken from the Canyon geology.

1) Principle of gradualism: Geological processes of erosion and weathering gradually sculpt the crust into various geomorphological forms. John Wesley Powell, the geologist who first explored the canyon realized that the canyon has to be really old for the river to have the time to cut such a deep gorge. Gradualism does not mean that the rates of processes are constant. For example from about 2 million years ago the rates of incision of the canyon have decreased due to southwest U.S becoming arid and the river carrying less water than it used to.

2) Principle of Uniformitarianism: With the proper caveats the present can be the key to the past. If you walk along the beach and see the waves creating a ripple like pattern in the sand and then you see similar structures in ancient sandstone, you can infer that the sandstone was deposited in a beach like setting. The sedimentary rocks of the Grand Canyon have many such structures and they have been interpreted to have formed in specific settings by analogy to modern environments.

3) Principle of Correlation: Geological process taking place at one time may produce a rock record that is patchily distributed in space. Methods of correlation allow you to match rocks found at different places as being coeval or formed at the same time. This forms the basis of geological mapping. These principles are easy to teach using the Grand Canyons flat lying easy to trace rock layers.

4) Unconformities: These are surfaces that represent a gap in the geological rock record. Two episodes of rock formation may be separated by a period of non-deposition or erosion. Again plenty of examples in the Canyon section.

5) Discordant and intrusive relationships: Older rocks at the bottom, younger at the top. This is the principle of superposition vividly seen in canyon sections. But sometimes magma can intrude and cut across older rocks forming discordant structures. These are of great importance in establishing the sequence of events during geological mapping.

6) Fossils appear in evolutionary sequence: Young earth creationists claim that the canyon was cut very rapidly in a matter of days during the great flood. Sedimentological analysis has shown that rock layers were deposited gradually over time. Also, the sedimentary rocks contain fossils which appear in a sequence that is similar to fossil sequences all over the world. Materials dumped from flood waters would have jumbled up the sequence in different ways in different places on earth.

It is mid March already. My friend in New Jersey theorizes that the first batch of parents from India will be arriving to meet their children beginning early April. Apparently the first call of duty is a visit to the Niagara falls. It is almost a pilgrimage. Mom and Dad are dressed to kill, proudly looking on at their child's new Toyota. All summer long Indians visit that mammoth waterfall. I have met a few of them . They ask me: So, you are a geologist. We just saw the Niagara falls.

I admit sheepishly that I have never been there.

Mum Dad Gave Me Half My Happiness

An exceedingly silly and misleading headline from the Health and Science section of Times of India:

Half of our happiness lies in genes

A study showed that personality traits including those such as propensity to worry, sociability and some others which predispose a person to happiness are hereditary. The study was done using 900 twin pairs. The conclusion:

The researchers say that although happiness has its roots in our genes, around 50% of the differences between people in their life happiness is still down to external factors such as relationships, health and career.

The interpretation by media:

Therefore 50% of our happiness is in the genes. Notice I highlighted "our". Because herein lies the misunderstanding of the quantity 50%. The common sense notion of heredity is that parents pass on traits to their children. The common interpretation of this is that since personality traits may be inherited, this study shows that an individual inherits 50% of the capacity to be happy from his/her parents. This is simple untrue and a completely meaningless statement. What was been measured in the study using twin pairs is heritability, which is the proportion of variation of the trait in the sample population that is attributable to genetic differences between individuals. Heritability is a population concept. It says nothing about the role heredity plays in the development of the trait in an individual. So, a heritability measure of 0.5 does not mean that 50% of the trait in an individual is because of genes. In a study if we measure heritability of height to be 80% then it does not mean that about 4 feet 9 inches of the height of a 6 feet tall person is due to genes and the rest due to the environment. It simply means that 80% of the variation in height in the population may be attributable to genetic differences between individuals. This number can change with the sample studied. If you sample a population subjected to a wide variation in environmental conditions such as accessibility to good nutrition, sanitation etc, then the heritability measure of height will be much less, since more of the variation in height is explainable by the differences in environmental conditions faced by different individuals. In contrast if we measure heritability in a population that faces a more homogeneous environment, then any differences in height between individuals are more likely to be due to genetic differences and that sample will have a high heritability value for height. Heritability estimates by themselves do not say anything about the particular genes that contribute to that trait. Genes are not blueprints for traits. Genes and environment interact in complex ways during development to build the phenotype.

Yet the media never learns. The Times report was a copy and paste of a press release. Despite stating in the report that 50% of the differences between people.... there was no mention that what was actually measured in the study was heritability, let alone an attempt to explain the difference between heredity and heritability. I caught the last bit of a CNN report on TV and they too had a headline to the effect that 50% of human happiness is genetic, reinforcing the misconception that an individual inherits 50% of the capacity to be happy from parents.

I'm glad that the Times has a health and science section. But I am less that half happy at the awful reporting :-)

Global Warming, Corals, Faunal Turnovers

The Economist recently reported on some research which suggested that increasing atmospheric CO2 concentrations will lead to increasing amounts of CO2 getting dissolved in oceans, eventually dropping their pH by about half a unit by end of the century. Oceans absorb around 30% of annual CO2 emissions playing a big role in preventing a huge buildup of CO2 in the atmosphere. Currently the composition of the ocean is slightly alkaline but it will acidify if we do not reduce emissions soon. This may play havoc among marine organisms which secrete a skeleton of calcium carbonate. In acidic solutions the skeletons are likely to dissolve. Without its protective cover, many groups of marine organisms will perish.

I have spent a large part of my career studying limestones, some of them made up of ancient corals, so this story really caught my interest. Corals and reefs are pretty awesome ecosystems, and having seen many of them at close quarters in the Florida Keys, the news that there could be large scale degradation of these ecosystems is quite disturbing. Corals as a group have been around since the early Paleozoic. In the report, Andrew Knoll of Harvard Univ. points to the end Permian extinction event which is believed to have wiped out around 95% of marine species. He suggests that although the Permian extinction may have many causes, a significant cause was the eruption of the Siberian traps, a massive eruption of basaltic lava. This led an enormous increase in atmospheric CO2 levels, which in turn got absorbed in the oceans making them acidic. Knoll points out that there was a selectivity in which organisms did better than others during this "acid" crisis. Bivalves, gastropods and arthropods which had to ability to buffer their internal fluids from which the skeleton is precipitated resisted extinction, while groups such as the articulate brachiopods and corals which apparently did not have these buffering capabilities were wiped out in large numbers.

Throughout Phanerozoic history, biotas have shown compositional changes in their diversities. Below figure known as spindle diagram shows changes in diversities at the family taxonomic level in Bivalves, Gastropods, Articulate Brachiopods and Anthozoans (corals). C refers to Cambrian, P to end Permian mass extinction and K to end Cretaceous mass extinction.

Adapted from: On the Origin of Phyla

The patterns that Andrew Knoll pointed out are clearly seen. Bivalves and gastropods suffer a dent during the end Permian extinction event but their general history since their origin in early Paleozoic is one of increasing diversity. Brachiopods after an early diversification episode in the Paleozoic suffered large scale extinction during the end Permian and never recovered, some say because of competition from the more successful bivalves. Corals show a great volatility in diversity changes during the Paleozoic. They too suffer a crash in diversity end Permian but unlike Brachiopods recover and proliferate in the Mesozoic and again in the Cenozoic. Evolutionary paleontologists interested in long terms trends in biota compositions want to know why certain groups fail while others do well. The ability to internally buffer the chemistry of fluids may just be one such property of marine skeletal organisms on which biota composition gets sorted during times of environmental stress. That does not mean that buffering evolved to make organisms resistant to extinction. Evolution has no foresight. It cannot anticipate future extinction and make long term plans. Buffering must have evolved as a physiological adaptation that helped some organisms in the immediate term as against having some alternative body fluid chemistry. But it also ensured them long term success.

As it happened the Times of India had an editorial which although did not specifically go into changes in diversities through time gave a general account of ocean degradation including possible acidification. But there was some sloppy reporting as well. Here's what they had to say about ocean acidification

"The most vulnerable marine species are those that form shells, because a rising pH factor — which measures levels of acidity or alkali-nity in water — inhibits shell growth, even melts them."

High school chemistry! Did they mean rising hydrogen ion activity? That would translate to lowering of pH and acidification. But I doubt it. I think they just assumed that higher pH means higher acidity and so lower shell growth. Also shells dissolve in acids , they don't melt. Please get a science graduate to look over this slop before publishing.

But back to corals and the current trends in atmosphere CO2. Scientists believe that if pH does drop by half a unit by end century then most of southern ocean reefs may suffer extensive damage, even local extinction. As the figure shows, in the long term, corals as a group have proved to be quite resistant to extinction, surviving not just the end Permian event but also the end Cretaceous event with remarkably little loss in diversity and also later perturbations such as the Eocene Thermal maximum. The pattern suggests that there has been an overall decrease in coral extinction rates through the Phanerozoic. This trend has developed not by one group of corals gradually evolving adaptations that enabled it to resist extinction but through faunal turnovers, meaning replacement of one group or subtaxon of corals by another. Entire orders such as the Rugose and Tabulate corals which were important contributors to mid-late Paleozoic reefs have gone extinct, while others such as the Scleractinia persisted, proliferating in the Mesozoic and Cenozoic reef communities. This replacement has not been random but likely reflects species sorting on extinction rates. In subtaxons with high extinction rates, speciation could not replace lost species at an adequate rate. So over time subtaxons with lower extinction rates became more common while those with high extinction rates disappeared. Extinction rates is an example of a property a group of related species share. It is not a property that individuals possess and upon which natural selection acts on directly. Rather it is an effect of natural selection favoring features that improve individual reproductive fitness. For example, in some ecologic settings natural selection may favor individuals having the property of widespread larvae dispersal. This property will become characteristic of that species and its descendants. Clades with the property of wide dispersal of larvae resulting in a wide geographic range may be more resistant to extinction as compared with clades without this property. Over geologic time, wide larvae dispersing clades i.e. clades with lower extinction rates will replace clades with high extinction rates. I have used larvae dispersal as an example. I don't know if it applies to corals in particular, but such sorting on turnover rates has most likely taken place within corals. Some species of these low turnover or low volatility coral groups will survive this anticipated crisis and on a geological time scale may even proliferate. But that does not help us today. Evolutionary recovery over geological timescales is no consolation for humans whose priorities overlook the next 50-100 years. Ocean degradation and coral loss especially the reef building types will have a serious impact on marine biodiversity, since reefs shelter and provide a habitat to other diverse groups of organisms. It's hard to contemplate that the Lakshadweep islands and the Maldives may not have functioning living corals in a few decades. The time to save corals would be now.