Saturday, November 26, 2011

Terrible Obituary Of Lynn Margulis Of Symbiosis Fame

There is a really awful misrepresentation of evolution in a New York Times obituary for Lynn Margulis, the biologist who proposed that the eukaryotic cell originated through a symbiotic merger of  two free living bacterial cells. Life on earth is made of up one of two cell types, Prokaryotes or Eukaryotes. Eukaryotes are more complex. They contain their DNA in a nucleus and also possess organelles like mitochondria and chloroplasts which generate energy for cell metabolism.

At one time in the past, perhaps about a billion years ago, one prokaryotic bacterial cell engulfed another prokaryotic bacterial cell type. Instead of the engulfed cell being destroyed, the two evolved a partnership. The engulfed cell was perhaps good at certain tasks like burning food in the presence of oxygen. Over time this cell transferred most of its genes into the genome of the host cell and retained only a few needed for the specialized task of producing energy for cell metabolism. It evolved into the mitochondria. Lynn Margulis was ridiculed for proposing this but over time biologists have accepted this theory of the symbiotic origin of eukaryotes.

Here is a snippet from the obituary by Bruce Weber:

The hypothesis was a direct challenge to the prevailing neo-Darwinist belief that the primary evolutionary mechanism was random mutation.

Rather, Dr. Margulis argued that a more important mechanism was symbiosis; that is, evolution is a function of organisms that are mutually beneficial growing together to become one and reproducing. The theory undermined significant precepts of the study of evolution, underscoring the idea that evolution began at the level of micro-organisms long before it would be visible at the level of species.

I don't even know where to begin.

If there is any such thing as a neo-Darwinist "belief" then the mechanism of evolution in question is natural selection not random mutation. Mutations generate the variability on which natural selection acts.

And symbiosis doesn't underscore the idea that evolution began at the level of micro-organisms long before it would be visible at the level of species. What does that even mean? Very early life was a world of micro-organisms divided into many species and they evolved through a combination of natural selection and random genetic drift acting on random mutations. If a population of micro-organisms evolve then the species they belong to obviously also evolves! The micro-organisms may be of symbiotic origin or may not. The type of entity i.e. symbiotic or non-symbiotic has nothing to do with the mechanisms of evolution or whether evolution occurs through variations between individuals or variations between species. 

Another misconception I have often heard is that symbiosis means that complex cells and complexity in general evolved through a co-operative venture. So evolution is less about competition through natural selection and more about cooperation.

Again, this is a misunderstanding about the nature of evolution.

Sure, at one point in time two cells merged to form one cell...... But then what?

After the merger, there was just one or few of these novel cells in a population of other cell types. The merged cell was more efficient at extracting energy from the environment and reproduced more than other cells. Every round of reproduction threw out varieties of merged cells. Out of these, the more efficient symbiotic cells out-reproduced not just other non-symbiotic cell types but also slightly less efficient symbiotic cells. The symbiotic arrangement became more refined and over time the novel cell type proliferated and became the dominant cell type in that particular ecologic niche. Symbiosis and the cell structure and functionality that is recognized as eukaryote didn't instantly originate through a merger but evolved through natural selection. Eukaryotes became a common cell type by out-competing less efficient versions of itself and other non-symbiotic cell types. Cooperative ventures in life also evolve through competition.

So symbiosis doesn't undermine natural selection. Yes it can create novelty by bringing together different components within one individual, but that novelty if beneficial then evolves. It gets modified and refined and changes through natural selection and genetic drift.

Monday, November 21, 2011

Gold Boom Times In Elko Nevada

Geology and Livelihoods # 11

After Australia its time to go to Nevada. In a really engaging talk on Planet Money Robert Smith and Zoe Chace take a look at life in Elko, Nevada which is going through boom times due to the high demand for gold.

The motels are full, the brothels are full and high school girls want to start a truck repair business to support the mining community. Archaeologists are being hired to survey for ancient American Indian settlements before the machines start ripping the earth open. The town is cash rich.

and yet no money is being spent on long terms investments for the town. A history of busts seen all around Elko in numerous ghost towns is preventing that.

There is an Australian general manager of a mine who keeps hopping from one gold mine to another all over the world. For him its always been boom time. That's the difference between being undereducated and having a good education. The undereducated may well profit for a short time in local booms but when the mines run out they won't find high paying jobs elsewhere. For the better educated ..there is more flexibility in finding work.


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Thursday, November 17, 2011

A 200K Job In Australian Gold Mines

 Geology and Livelihoods # 10

The Wall Street Journal profiles  Mr. James Dinnison, a high school dropout from Western Australia who is currently earning $200,000 a year working underground in gold mines.

Here is an eye catcher:

Despite having earned roughly US$1 million since he started, he has no savings and doesn't apologize. "The mines are so dull, that when you get back here, everything is stimulation and excitement," he said. "The money I spend supports other businesses because of the [stuff] I blow it on."

Mr. Dinnison proudly calls himself a Cub—a Cashed-up Bogan, a bogan referring to Australian slang for an uneducated blue-collar worker. Books and documentaries are coming out about this group, exploring the country's unease with the thought that conspicuous consumption by undereducated people is what is helping to keep the country afloat.

....Mr. Dinnison hopes to be promoted to another underground job paying $1,400 a day, up from $800 a day.

Take that all you educated losers!

via  Geology News

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Thursday, November 10, 2011

Some Thoughts On The Evolution Of Dogs

Let me begin though with David W. Anthony's musings about the domestication of horses from his book The Horse The Wheel And Language:

Modern horses are derived from very few original wild males, and many, varied females.

In wild horse society there is a female hierarchy and mares are disposed to follow the lead of a dominant mare. Stallions on the other hand are more independent and react violently when confronted.

...A relatively docile and controllable mare could be found at the bottom of the pecking order in many wild horse bands, but a relatively docile and controllable stallion was an unusual individual - and one that had little hope of reproducing in the wild. Horse domestication might have depended on a lucky coincidence: the appearance of a relatively manageable and docile male in a place where humans could use him as the breeder of a domesticated bloodline.

From the horses perspective, humans were the only way he could get a girl. From the human's perspective, he was the only sire they wanted.

Well said!

Horse domestication depended on active selection of traits by humans from the very start. It may have been different for dogs at least in the earliest stages of human wolf interaction suggests naturalist  Mark Derr in an interview on Fresh Air. 

There are many hypothesis on how wolves got domesticated into dogs.

The puppy hypothesis suggests that abandoned wolf puppies were adopted by humans and then the more sociable and docile amongst them were allowed to breed. This involves selection pressures imposed by humans from the very start.

Then there is the garbage midden hypothesis. Wolves started hanging around human camp rubbish sites.  The key element in this hypothesis is that only wolves who were instinctively docile and perhaps not getting enough food in the wild engaged in this behavior. So there was a self selection for docile traits in the wolves who gradually got used to be near humans.

The third is the hunting band hypothesis. Humans began following wolves on hunts or maybe wolves started following humans on hunts.  These bands of wolves became socialized with humans and  isolated from other bands of wolves. Again it is possible that instinctively docile wolves were more likely to follow human hunts if the reward at the end was food which was hard to obtain otherwise. So there is an element of self selection in this hypothesis as well.

Mark Derr tilts towards this third hypothesis. To me, it hard to pick out the stronger contender. The three hypothesis are not mutually exclusive. The thing is that all three situations would have been a common occurrence. For example its reasonable to imagine a scenario whereby a docile male sifting through the garbage dump gets bold enough to latch on to a female adopted as a puppy and living amongst humans.

The three situations would have overlapped many times. Socialization could have occurred via all these three interactions. After that there would have been more severe direct intervention and selection by humans for traits like docility.

There are other interesting questions about dog domestication. For example, was there just one center of domestication or did domestication take place many times in different places? The Middle East is considered the likely place for dog domestication based on  arguments that the dogs from this region show more genetic variation pointing to a source population of greater antiquity. There also have been a case put forward for China being the place where dogs were first domesticated.

Considering the likelihood of repeated contact between wolves and humans there were probably many independent attempts to domesticate the wolf. Fossils of dogs and wolf-dog hybrids as old as 30 thousand years ago have been discovered from various place in the Middle East, Europe and Siberia suggesting multiple domestication attempts, perhaps successful ones.

What comes to my mind is how incredibly violent the initial process of domestication would have been. Wolf-dog pups and young adults not to the liking of humans in terms of their temperament and behavior and form would have been put to death often by a whack to the head.

As a dog lover I shudder at the thought.

Article On New Madrid Fault Zone Earthquake Risk

In Nature News Richard Monastersky has an informative article (open access)  on the New Madrid fault zone and the differing views between the USGS and other scientists on the risk of another big earthquake in that area. The New Madrid area in Missouri has been something of an enigma. Its lies far away from the present day plate boundaries and yet has suffered large earthquakes in the past couple of hundred years. Some scientists have suggested that faults which originated tens to hundreds of millions of years ago - when the New Madrid area was geologically more active -  may have strain stored in them.

These faults have been reactivated after the last ice age when the Mississippi river started eroding bedrock and  removing large amounts of sediment. The sudden removal of weight from above the faults may have altered stresses on faults on the verge of failing, resulting in the big earthquakes in the recent past.

The article focuses on the work of Northwestern University geophysicist Seth Stein who argues that on faults which have released strain in the recent past the risk of a big earthquake is quite low, a conclusion derived from GPS measurements which show that the crust is that area is not being warped at a rate that could be dangerous.  On the other hand he suggests that the earthquake activity could shift to an adjacent system of faults. According to him its best to view the entire region as one with interactive systems of faults with earthquake activity hopping from one zone to another over a time scale of hundreds to thousands of years.

This is a still a hypothesis but one for which Dr. Stein hopes to find evidence by expanding GPS measurements over larger regions around New Madrid.  The USGS disagrees with his risk assessment and the article brings together the different points of view.

Thursday, November 3, 2011

Field Photos: Driving Through A Basalt Countryside

The most prominent topographic feature of the Deccan volcanic province is the Western Ghat Escarpment that runs north south, roughly parallel to the west coast of India. The escarpment is the edge of a deeply dissected easterly tilted plateau, a result of Cenozoic crustal movement. Near Pune, several streams flowing eastwards through narrow valleys have been damned and the backwaters of these dams have some great views of a basalt landscape comprising deep valleys and spectacular exposures of basalt cliffs.

Last Sunday I drove with some friends along the backwaters of Mulshi dam. In the interactive embedded map below (Pune in south center) the western ghat escarpment is the arcuate north south ridge line on the left side of the image. You can count more than ten dams situated to the east which have flooded narrow valleys. If you pan north south you will see more reservoirs. The water is used to generate electricity and for urban and agricultural use.

View Larger Map

All pictures courtesy Bharat Parikh and Rajesh Sarde.

The countryside was lush. Wild grasses in full bloom.

A wide grassland meets distant peaks and ridges.

Steep basalt cliffs. Notice the layering of the lava flows.

The edge of the plateau is penetrated by fracture sets oriented in the NNW-SSE direction parallel to the coast and a NE-SW set. Some of these represent extensional stresses developed during rifting of India from Seychelles around 66 my to 65 my years ago and may have been conduits for the magmas. There are plenty of dykes intruding the lava pile oriented in a north south and north-east south-west direction. There are fracture sets too which may represent a later Cenozoic stress regime related to the uplift of the province. These provide a structural control on drainage.

The image below shows a north-east south-west oriented fracture set (red arrow) which has controlled the dissection of a deep valley. I call it Anil's valley in honor of my friend who told me about it. White arrows point to the NNW-SSE oriented lineaments. They may represent dykes or fractures.

 A view of Anil's valley. It is a box canyon with near vertical walls of basalt.

The main basalt flow type in this region are compound flows. These are made up of discrete blobs of lava that overlapped and coalesced with other blobs of lava to form a compound unit. During one eruptive episode several compound units may be stacked to form a thick lava pile.  These compound flows have weathered over time into a steep hummocky topography with domal summits accentuated by erosion along fractures. (Picture below taken on a previous field trip in February 2010).

A lonely road in the woods.

Bed load! A dry bouldery stream bed. Its just three weeks after the rains stopped and the streams in the upland areas are dry already. Small farming communities make by mostly through water in the monsoons and then rely on small springs to water their fields. Life gets quite hard here after the rains.

Food of a civilization. Yellow ripe paddy grown in the lowlands near the water source. Lava flows in the backdrop. You can smell the fresh rice as you pass by.

Until next time..