The layers of rock that you see have been dated to about 430 million years ago. This was an interesting time in our history. It is when our ocean-dwelling fish ancestors started incorporating a new invention into their bodies – bone. It was also the time when these ancestors (who would later give rise to amphibians, reptiles, birds and mammals) parted ways with the ancestors of some rather interesting characters. These were the Coelacanth and the Lungfish, the so-called ‘living fossils’ of the ocean.

Of course, there’s really no such thing as a living fossil, as Darwin was well aware when he coined this phrase. Every species alive today has been evolving for just as long as we have (and usually much longer, because evolution is measured in generations and not years). But the Coelacanth, and to a lesser extent the Lungfish, are the few cases where this phrase is appropriate. Fossil records and genetic comparisons bear out that Coelacanths have indeed not changed a whole lot for hundreds of millions of years. Our ancestors from this time may, at least superficially, have looked something like this.

In physics there is a concept known as spontaneous symmetry breaking, where a system that was initially symmetrical suddenly ends up in a non-symmetric state. Picture a ball precariously balanced at the top of a hill. There’s no way to know which valley it will roll down into, this is decided by tiny random fluctuations. But once the ball rolls down the hill, the symmetry is broken. You have to climb up the hill and look down at other valleys to figure out that symmetry was once there. Particle physicists are always on the lookout for these hidden symmetries. Unlike the case of balls on hills, the symmetries that physicists look for are not something that we can see. They are looking for symmetries in equations – in the language that nature uses to express herself.

In 1865, James Maxwell taught us that electricity and magnetism can be combined in a unified picture of light. We live in a world where the symmetry between electricity and magnetism is unbroken. In the twentieth century, the discovery of radioactivity suggested that there must be a new kind of interaction inside the atom, that was responsible for turning neutrons into protons. This was called the weak force, and it was thought to be fundamentally different from electromagnetism. By 1968, three physicists – Steven Weinberg, Abdus Salam and Sheldon Glashow – had worked out what was really going on.

It turns out that we live in a world with a broken symmetry between the electromagnetic and the weak force. They appear to us to be entirely different entities, but this is not really the case. There is a hidden symmetry manifest in the equations, and if you go back in time to the hot conditions of the early universe, this symmetry between light and radioactivity is restored. This kind of unification between seemingly disparate forces is what many particle physicists devote their lives to. By building advanced machines that can collide particles at immense energies, they are recreating the more symmetric conditions of our early universe. The journey of particle physics is, in many ways, a quest further back in time to seek out more symmetry in nature.

I think an analogous process takes place at smaller time scales. Three and a half billions years ago, we shared a common ancestor with all life on this planet. As we travel back in time from the present day to that point, the ancestors of more and more species start to meet up. It’s like travelling up a river from mouth to source – along the way you merge with different rivulets, streams, and distributaries. At every step of the way, we are discovering a more symmetrical state of life, of which we are all broken-symmetry manifestations.

And there are plenty of other changes along the way. The geology of the Earth is changing. As we travel back the hundreds of millions of years, the Earth goes through cycles of continents coming together and separating. Further back still, and the Earth is basically a molten hot ball of lava. Then our solar system begins to disassemble into a disc of dust, and the Sun diffuses into a nebulous cloud of hydrogen gas. Billions of years pass, as the galaxies too begin to crumble into gas. And then things start to get weird.

The universe goes through its dark ages, a time when it is too crowded with charges for light to be able to travel. Push further back still, are we are now very close to the source of this proverbial river. Just a fraction of a second away from the Big Bang, the universe is now going through a crunch of a scale that is impossible for our human minds to grasp. And after travelling back in time for 13.7 billion years, we arrive at a universe that’s unbelievably compact, hot, and unimaginably smooth – a state of ultimate symmetry. And before that, well.. the physicists are still working on it. We reach the limits of the current laws of physics.

What this timeless quest for symmetry teaches me is this – the world is fascinating at every scale. By learning more about nature, we are slowly climbing back up the hill. As we reach higher, we turn around to look back at the valley from where our quest began. What we see is home, but in a much richer and more informed context.

Have a great week, and happy exploring!

My previous musing: Plastic flowerpots and the mighty alphabet of the universe

Also, Wired Science has a nice interview today with Hans Fricke, a man who has spent more time with Coelacanths than anyone else.

And death is not just the end of the individual, it’s the end of a lineage. Organisms that die before they can reproduce deny their genes a road to the next generation. In this simple fact lies the engine of change. For example, genes that make a prey more camouflaged will end up increasing their reproductive success, whereas genes that make them more noticeable are not going to get very far. In this way, natural selection is driving prey to become better hiders, and predators to become better seekers.

Nowhere is this evolutionary race more evident than in the case of the peppered moth. This is a species of moth that is found all across England and Ireland. When people first studied them in the early 1800s, almost all the moths looked something like this:

As you can see (if you’re looking closely), the white and black speckles are effective camouflage. For ages, these moths have hidden on light colored trees and lichens. Over time, they have evolved this distinctive pattern to help them evade the notice of the birds that prey on them.

But just fifty years later, things were beginning to change. By the 1850s, moths of the same species had stumbled upon a new color. These new moths were called carbonaria after their carbon-black color, to distinguish them from their salt-and-pepper colored relatives with the dull name typica.

By the end of the nineteenth century, the change was drastic. In 1895, a study in Manchester showed that 95% of the peppered moths were now of the black type. So what was going here? What could cause such an incredible change in appearance in just a hundred years?

They key lies in a major event in the history of humanity that took place during the nineteenth century – the Industrial Revolution. During this time, a large number of factories were being built in England, and they burned a mind boggling amount of coal. From 1800 to 1900, annual coal production went up in the UK from about 10 million tonnes to 250 million tonnes.

This had a drastic effect on the environment. The trees in the woods between Manchester and London were covered in soot. And the increased levels of sulphur dioxide was killing the lichen. All of a sudden, the peppered moth was losing its camouflage. It stood out like a sore thumb against the sooty black barks of the trees, while the rare black form of the moth became an instant success.

In a new study in this week’s issue of the journal Science, researchers in Liverpool and the Czech Republic were able to trace down the genetic signatures of this extreme evolution. They did this by looking at the variation in letters of DNA between the 2 types of moths.

At the heart of the idea is sex. The genetic role of sex is to shuffle together different genomes in a population. This has the effect of creating more types of genomes, and thus increases diversity.

When the Industrial Revolution comes along, it paints the world of the moth black. Most of the genomes in the population get wiped out as they are no longer fit. A few rare ones contain a gene that protects their possessor by coloring them black. These genomes quickly begin to dominate in the population, and so there are now fewer kinds of genomes around – the diversity begins to plummet (think of 1895, when 95% of these moths were now black). This is known as a selective sweep, where a set of genes rapidly sweep through a population.

Over time, as these moths mate with others, the diversity builds back. But just as it takes many shuffles to completely randomize the order of cards in a deck, it takes many generations of sexual reproduction before all trace of the past is lost in the genome. By tracing down regions of the genome with unusually low diversity, we can uncover the signals of natural selection that must have acted on our ancestors. This method of detecting natural selection works best if the selection was strong (so that it wiped out the diversity), and if it happened recently (so that sex hasn’t had enough time to bring the diversity back).

This is just what the authors did. They first compared the genomes of 68 typica and 64 carbonaria moths (the offspring of two pairs of parents) and found that a particular region on one of the chromosomes was responsible for the difference in moth color. But this is a coarse-grained picture, as the region that they identified is over a million letters in length. The next step was to probe the diversity at a finer scale.

To do this, they looked at 6 variant letters of DNA that were spread out in this region, and measured how the carboneria and typica moths vary with respect to these letters. At each of these positions, there are 2 possibile letters that any moth can have. So if the genomes were properly shuffled with the maximum level of diversity, there would be 32 64 possible possible 6 letter words that could be formed here.[1] The spotted moths were found with many different words in this region, a sign of diversity. The black moths, on the other hand, all had small variations from just one sequence: CAGGTA. The scientists inferred that this must be the ancestral sequence of the black moths that thrived in the Industrial Revolution.

By comparing our DNA, we are actually looking back in time. We can use these techniques to infer the pressures that our distant ancestors faced. A cool example of this kind of DNA archeology is the story of lactose tolerance in humans.

Here’s a counter intuitive fact – mammals typically can not digest milk in adulthood. Of course, all mammals love milk as infants (that’s what gives them their name). That’s because they can produce a chemical called lactase, which breaks down the lactose in milk. But once infants reach the age of being weaned, the body switches off production of lactase. We all like to think of cats as cute pets that love a saucer of milk, but in reality this is more likely to give them indigestion and diarrhea. Lactose intolerance is not a disease, it’s actually the norm.

This makes sense from an evolutionary point of view. Milk is a nutrient rich food for infants, but it is costly for a mother to produce. At some point, the growing infant needs to move on, or it will become too great a burden for the mother. This digestive ‘switch’ in mammals ensures that this happens.[2]

So why is it that some us can digest milk? The answer takes us from one cultural revolution to another, to a time  8000 years ago when some of our ancestors had begun to rear cattle. This was happening in the Middle East and in Africa. Through sheer chance, anyone who had a mutation that disabled this lactase switch suddenly had an advantage over their peers. They had access to a reliable and nutrient rich source of food – milk from cattle.

The same process that changed the color of the moths is at work here. As was shown by a team led by Sarah Tishkoff in 2006, cattle herders in Africa and in the Middle East independently evolved different mutations that allowed them to drink milk, an example of what is called convergent evolution [3]. This is why lactose tolerance is very prevalent in Europeans. Many of their ancestors were cattle herders who originated in the Middle East. Similarly, northern Indians are more likely to be able to digest lactose than southern Indians, perhaps due to closer contact with the pastoral Sindhi tribes of north India.

And those of use who can digest milk carry the signs of this cultural revolution in our DNA. To date, the region surrounding the lactase gene has a remarkably low diversity in populations that descended from cattle herders.

We usually think of adaptations as occurring in response to changes from within nature. But I find it fascinating that our culture can also be a driving force of evolution. It has happened time and again, without our explicit knowledge of it. During the dawn of agriculture, we evolved wild grains into harvestable varieties like wheat and rice. In the birth of pastoralism, we modified our cattle to produce more milk, while also evolving ourselves to be able to consume it. And in the Industrial Revolution, our pollutants ended up driving evolution in moths.

As we look further out into space, we learn more about the origins of our universe. But at another extreme, by looking inwards to our DNA, we are also learning more about our place in it. We are unraveling the lives and cultures of our prehistoric ancestors, as well as the effect that we have had and continue to have on our surroundings.

Incidentally, the story of the moth has another surprising twist. Eventually the air quality improved in the UK, and the lichen began to grow back. The trees were restored to their lighter colors. And this meant that the carbonera moths have once again started to get noticed. They are now at a great disadvantage and have become extremely rare. In this way, the ebb and flow of genes are echoing the waves of cultural changes.

Footnotes

The kind of evolutionary genetics discussed in this article is the subject of my research. I have spent the last year and a half working on a project that studies how certain African pastoral tribes have evolved protection to their extreme diets, a case of culture and gene flow being intricately woven together.

[1] There are 2^6 = 32 64 combinations in all. The reason for there being 2 possible letters at these variant locations and not the usual 4 (A, C, T and G) has to do with biology. The variants arise through mutations (for example, an A gets flipped to a T) in somebody. It is incredibly unlikely that two mutations in the recent past (say, A to T and A to C) will occur at exactly the same place.

[2] However, if this lactase disabling switch was only useful to the mother, than it wouldn’t evolve. But such a switch also benefits her genes, as she can now invest the resources that she gains on caring for her offspring or on rearing more children.

[3] Incidentally, the peppered moth also occurs in North America, and there are reports that a similar adaptation towards darker moths arose along with the rise in pollution in the nineteenth century. If true, than this is another neat example of convergent evolution.

References

Van’t Hof AE, Edmonds N, Dalíková M, Marec F, & Saccheri IJ (2011). Industrial Melanism in British Peppered Moths Has a Singular and Recent Mutational Origin. Science (New York, N.Y.) PMID: 21493823

Tishkoff SA, Reed FA, Ranciaro A, Voight BF, Babbitt CC, Silverman JS, Powell K, Mortensen HM, Hirbo JB, Osman M, Ibrahim M, Omar SA, Lema G, Nyambo TB, Ghori J, Bumpstead S, Pritchard JK, Wray GA, & Deloukas P (2007). Convergent adaptation of human lactase persistence in Africa and Europe. Nature genetics, 39 (1), 31-40 PMID: 17159977

Image Credits

Creative Commons Licensed: Peppered moth (typica) by Andy Phillips. Black moth (carbonia) by naturalhistoryman. Cat and milk by Sunfox. Maasai herder Kamaika Kingi by Oxfam International.

Wikimedia Commons Licensed: Light and dark moth (typica and carbonia)

Indians today can hardly recall the last time that they saw a vulture. In the 1990s, these majestic birds were a common sight in the subcontinent, and would show up wherever there was exposed carrion. As a child, I remember marveling at vultures circling at impressive heights, probably looking back down at me with their incredible eyesight, their wings outstretched as they effortlessly hovered on columns of warm air.

But since the nineties, their numbers have been falling dramatically in India, Pakistan and Nepal. The scale is astonishing – for every thousand white-rumped vultures in 1990, only one is alive today. A similarly sad story holds for the Indian vulture and the slender-billed vulture. Together, all three Asian vultures are now listed as being critically endangered.

So what’s going on? It’s not that they are being hunted. For one thing, the killing of all wild animals in banned in India. But also, vultures have always provided a much valued ecological service. Most villagers dispose of dead animals by dumping the carrion. And they rely on the vultures to clean up.

Vultures have an undeservedly bad reputation. Because we associate carrion with disease, people believed that vultures spread diseases. But in fact, we now know that the opposite is true. Their powerfully corrosive stomach acids allow them to safely digest carrion that would be lethal to other scavengers, wiping out bacteria that can cause diseases like botulism and anthrax. They are the purgers of death and disease.

In their absence, populations of feral dogs have exploded, bringing with them the threat of rabies and human attacks. And if rats follow suit, India would face a new public health nightmare as it tries to control the spread of rodent-borne diseases like bubonic plague [1].

The absence of vultures is also having a cultural impact. The Zoroastrian Parsis in India have long maintained a tradition of sky burials. They leave their dead out on platforms for the vultures to consume, in order to avoid defiling earth, water, and fire with what they consider to be an unholy corpse [1]. These towers of silence, as they are known, would once attract many hundreds of vultures. Now they are eerily empty, forcing the Parsis to find new ways to deal with their dead.

So what is causing the mysterious collapse (often literally so) of vulture populations? It’s a daunting puzzle to solve, and in 2003 an international collaboration of scientists stepped up to the challenge. Their work [2] was supported by the US-based Peregrine fund and in collaboration with the Ornithological society of Pakistan. They discovered that most the dead vultures had pasty chalk-like deposits of uric acid crystals on their internal organs. This is a terrible disease called visceral gout, and is a sign of kidney failure.

But what was causing the kidney failure?

To solve this, the authors systematically began to rule out possible explanations, in a manner that would make an episode of CSI look like child’s play. They established that it wasn’t pesticides or heavy metal poisoning, nor nutritional deficiency or a bacterial or viral infection. Instead, they found that the occurrence of kidney failure was correlated with the presence of a single chemical called diclofenac. Within a few days of consuming contaminated carrion, the vultures would fall sick, begin to droop their necks severely, and then collapse. Sometimes they would fall right out of their perches.

In essence, we were unintentionally poisoning the vultures. Diclofenac is an anti-inflammatory drug that is used by livestock farmers in India to treat their cattle and water buffaloes. Studies have since identified a vulture-safe alternative. In a last ditch move to rescue the vultures, the India’s National Board for Wildlife recommended a ban on diclofenac in 2005. A year later, this resulted in a manufacturing ban on diclofenac for veterinary use, and it was two more years before it was made an imprisonable offense to produce, sell or use this drug for veterinary purposes in 2008. All the while the vulture numbers had been falling steadily.

So how effective has this ban been in rebuilding the vulture populations? This question was addressed by another international collaboration, in a study [3] published last week. This work was led by the Royal Society for the Protection of Birds in the UK, and the researchers hailed from institutes in the UK, Spain, and from wildlife conservation societies in India. They measured the concentration of diclofenac in 4500 liver samples from 21 locations across India, taken from carcasses before and after the ban on diclofenac.

Here’s what they found. When comparing 2004 (pre-ban) to 2008 (post-ban), the percentage of samples that were contaminated went down from 10.1% to 5.6%. The concentration of diclofenac in these contaminated carcasses had also gone down, by about a factor of 2.

The next question is, what does this mean for the vultures? Is this enough of a drop in contamination for them to start making a comeback? This is a tricky question because of the limited data and the many source of errors involved. The aim of this paper was to answer it.

They combined their measurements with available numbers for how much meat the average vulture eats, and how poisonous this chemical is to them. After a careful statistical analysis, they were able to estimate the overall effect on the white-rumped vultures. What they found is that in 2004, every meal that a vulture would eat had about a 1% chance of killing it. In 2006, this reduced to a quarter of a percent chance of death, per meal. Vultures eat about every 2-3 days, so over the course of the year these percentages begin to multiply.

Finally, the researchers plugged these numbers into a simulation to work out the rate at which the vultures are dying. In 2004, their results indicated that 80% of vultures were dying every year. By 2006, about 28% to 33% of them are dying every year. So the annual death rate has gone down to more than half what it was before the ban. They extrapolate that the death rate in 2007-2008 should be about 18%. Put another way, these odds amount to every vulture having to play an annual game of Russian roulette. And these are birds that are already critically endangered.

While the drop in death rates is encouraging, the researchers remained unconvinced that enough is being done to rescue the vultures. The fact that carcasses were contaminated well after the ban points to illegal use of diclofenac. For a critically endangered population, losing more than a sixth of your numbers every year is too heavy a toll to bear. In order for the vultures to stand a chance, the government still needs to focus its efforts on a stronger enforcement of the ban, as well as take on further conservation measures in parallel.

The story of the declining vultures is yet another reminder that ecosystems are fragile, interconnected and delicately balanced. Destroying a species can affect our own health, our environment, and even our culture in ways that are near impossible to predict.

If vultures vanish from the Indian subcontinent, it would certainly adversely affect the lives of its human inhabitants. We can try to put a dollar value on what the loss would cost us. Such cost versus benefit type of calculations can make a compelling case for rescuing endangered species and maintaining biodiversity.

Yet I have always felt that they miss an important part of the picture. There is another reason that we should value the vultures, that has less to do with economics and more to do with ethics. That reason is this: in our negligence, we would be responsible for the loss of these majestic birds, as well as the 3.5 billion years of evolutionary baggage that they have carried with them. And I’m not sure that we can put a price on that.

References

[1] Gross L (2006). Switching drugs for livestock may help save critically endangered Asian vultures. PLoS biology, 4 (3) PMID: 20076536

[2] Oaks JL, Gilbert M, Virani MZ, Watson RT, Meteyer CU, Rideout BA, Shivaprasad HL, Ahmed S, Chaudhry MJ, Arshad M, Mahmood S, Ali A, & Khan AA (2004). Diclofenac residues as the cause of vulture population decline in Pakistan. Nature, 427 (6975), 630-3 PMID: 14745453

[3] Cuthbert, R., Taggart, M., Prakash, V., Saini, M., Swarup, D., Upreti, S., Mateo, R., Chakraborty, S., Deori, P., & Green, R. (2011). Effectiveness of Action in India to Reduce Exposure of Gyps Vultures to the Toxic Veterinary Drug Diclofenac PLoS ONE, 6 (5) DOI: 10.1371/journal.pone.0019069

Image Credits

The header image is of an Indian vulture, courtesy B V Madhukar. The two images of the White-rumped vulture are taken by Umang Dutt. All three images are shared under the Creative Commons License.

The image of the Parsi Tower of Silence and the Vulture distribution map are from the Wikipedia Commons.