Semakau landfill "no dump"

Pulau Semakau has drawn international attention as the world's only landfill with a waiting list for visitors, as well as for its environmental credentials:

"... Semakau Landfill is the only active landfill that receives incinerated and industrial waste while supporting a thriving ecosystem, which includes more than 700 types of plants and animals and several endangered species."

Read more at the New York Times. The article also highlights some criticisms of the landfill, including the risk that waste might leak through to the sea, and the pollution caused by incinerators.

The mole's new thumb

Two instances of making do with what you have at hand.

With their huge hands, pointy snouts, and apparent lack of eyes, moles certainly appear to us as very peculiar creatures. These traits, however, are adaptations to a subterranean lifestyle. Those big front paws, in particular, are used for digging tunnels into the soil. Aside from being large relative to the rest of its body, the paws also have an elongated and enlarged radial sesamoid bone just beside the thumb. In some species of mole, this false 'thumb' (although it doesn't actually protrude as a distinct digit) is actually capable of some independent movement, spreading outwards to widen the hand.

This same wrist bone is also modified in giant pandas to form their peculiar 'thumb'. The panda uses its false thumb in feeding, to strip down the bamboo shoots that comprise its diet. (A photo of this in action can be found here.) This was the subject of a well-known essay by Stephen Jay Gould that later titled one of his published collections. As an example of what he called 'Tinkertoy evolution', it illustrates how evolution often makes do with existing structures to fulfill new functions. It is examples like these, which are less than perfect and highly contingent functional solutions, that break the illusion of a perfect world as posited by natural theology, and demonstrate evolution in action, he argued. (It's also the name of a popular evolution blog.) 

The case of the mole's 'thumb' also bears out this theme. Developmental biologists have recently found that Sox9, a gene involved in limb chondrification (the formation of cartilage tissue), is expressed in the region of the enlarged radial sesamoid during the development of the front paws of a mole embryo. This gene is also expressed in the 'normal' developing digits. However, the timing is different: it is expressed in that region of the wrist after Sox9 expressed has faded away in the normal digits. They compared this pattern of gene expression in embryos of the shrew, which are the closest relatives to moles, and did not find any Sox9 expression in the wrist at the same developmental stages.

Therefore, similar developmental mechanisms (the 'toolbox') have been co-opted to form the mole's false thumb, but their timing has been changed. That seems an easier option than to invent an entirely new set of tools.

Instances of obvious 'tinkering' such as this one make the messiness of evolution more apparent to us. Even structures of of evident perfection such as the eye (or eyes, since image-forming eyes have evolved multiple times) evolved by a long process of making do with existing structures to form new ones (clip from the BBC science show 'Bang Goes the Theory'). After all, isn't this just descent with modification, the very concept of biological evolution itself? Even at the level of genes and genomes, new genes often originate by duplication of existing genes (or even entire genomes, in the phenomenon of polyploidy) followed by divergence in function of these new copies from their originals. A whole book has recently been published on this subject.

What intrigues me is that the evolution of language also seems to have a similar pattern, and not just in terms of coining new words or borrowing vocabulary from other languages, but in the very grammatical structure of a language. Apparently 'perfect' systems like the Latin noun cases are actually the intermediate products of an ancient and on-going process of decay, accretion, and modification. A readable account is found in a popular-linguistics book I recently read, The Unfolding of Language.

Perhaps I'm straying too far from the original point of this post, and making a mountain out of a molehill, but the parallels to be found throughout the natural world and between the different sorts of evolution, biological and cultural, continue to fascinate me. Nature has immense and dizzying diversity, but that doesn't mean it has to be opaque to our understanding. 

Sources:

• BBC News story by Jennifer Carpenter
• C Mitgutsch et al. (2011) Circumventing the polydactyly 'constraint' - the mole's thumb. Biology Letters published online 13 July 2011. doi: 10.1098/rsbl.2011.0494

Indigenous peoples opposed to Indonesian carbon swap

Forest-dwelling communities in the Indonesian state of Kalimantan, on the island of Borneo, have expressed their objection to the REDD (Reducing Emissions from Deforestation and Degradation) agreements signed by Indonesia with other countries and non-governmental groups.

REDD schemes are designed to put an economic value on forested lands for biodiversity and ecosystems services, where previously the only ways to extract monetary value from them were logging and clearing land for agriculture. Under such schemes, many of which are bilateral, governments are paid money in exchange for preserving tracts of forest. (Example: UN-REDD programme in Indonesia)

To quote a forest reserve executive in Guyana: "We have a resource we would like to get money for. Either you pay us for biodiversity services or we will sell the forest to Malaysian logging companies." (source)

Indigenous peoples who claim customary use of forests have objected to them because they feel that their rights to the land have been overlooked in the process, displacing them from their livelihood and dwellings. It seems like there may be more than one indigenous organization making public statements against REDD programmes.

I've previously blogged about how deforested land is being 'swept under the carpet' due to poor oversight. Related concerns have been expressed about the tremendous potential for corruption that they bring. It seems obvious to state that corruption is possible when large sums of money are being given to a central government to pay for a rural commodity (ecosystem services) which is hard to define and which you can't take conventional delivery of.

Highlights of the Week

Some interesting news and articles from around the web for this week:

Cicadas are emerging en masse in the Midwestern United States after yet another 13-year cycle.
Cicadas are insects which are known for their loud and distinctive sounds produced by a mechanism called 'tymbalization' in their abdomens. Several species in the genus Magicicada in the US are called 'periodical cicadas' because they transition into the adult phase of their life cycle in a synchronized manner in cycles of 13 or 17 years. This summer the time has come for the emergence for the so-called brood XIX. These emergences happen in such numbers that early European settlers thought that the cicadas were the pestilential "locusts" of the Bible, and their carcasses litter forests in a deep crunchy layer. Find out more about cicadas at this website from the University of Michigan.

Mathematics and biology have a deep and subtle relationship. 
Viruses, for example, have self-assembling coats made up of protein subunits, which tile together in specific geometric forms. Disrupt these geometries, and one might be able to render a virus harmless.... Other fields of mathematics, such as chaos theory, can help in modeling natural phenomena such as plankton dynamics in the ocean. (I wish this essay was illustrated, though.)

How do flatworms regenerate their missing body parts?
The planarians (flatworms) are favorite classroom examples for regeneration because of their freakish ability to regenerate a complete worm when cut into multiple pieces. New research shows that cells in the worms called neoblasts, which can be thought of as analogous to stem cells in other animals, are pluripotent, meaning that they can develop into any cell type in the body. Researchers have also found some of the factors that determine whether a newly divided cell in a regenerating animal will develop into part of the head or the tail.

Where Do Petals Come From?

"From leaves, of course!" - would have been the answer given by Goethe, the German national poet and occasional scientist. He was one of the early proponents of the idea of homology, where two traits (which may be organs, limbs, tissues...) in two different species are said to be homologous if they are derived from the same organ in their common ancestor. Hence Goethe believed that "all plant is leaf", and that every part of the plant can be homologized with the leaves of the original, primeval Ur-plant.

We've come a long way since then. Floral development in particular has fascinated generations of botanists. Flowers comprise four parts, or 'whorls'–the sepals, petals, stamens, and carpel–listed from the outermost inwards. The sepals and petals, collectively called the perianth, are not always differentiated, and when they cannot they are called tepals. Non-flowering seed plants, or gymnosperms, such as pines, Ginkgo, and cycads, however, lack homologues to the perianth. Stamens and carpels, on the other hand, can be homologized to the male and female sexual organs of the gymnosperm cones (strobili). So where does the perianth come from?

Indonesian forest plan under threat?

Indonesia is a testbed for so-called 'cash for carbon' plans (Reduced Emissions from Deforestation and Forest Degradation, or REDD), where developing countries are given credits for reducing deforestation; this not only preserves valuable forest habitat for wildlife, but curbs carbon emissions from deforestation itself.

Greenpeace, however, has released a report that says Indonesia is planning to go ahead with massive forest clearance despite signing a new REDD agreement with Norway. According to the New York Times's coverage:

Greenpeace said that government documents show plans to bring 63 million hectares, or nearly 156 million acres, of land into production by 2030, including 80 percent of its peatland and half its forested orangutan habitat, to support expansion of industries including pulp, paper and palm oil.

At the same time, the group said, a push is on to rebrand the clearing of forests for plantations (which results in a net release of carbon into the atmosphere) as the replacement of degraded land with new trees (which takes carbon out of the atmosphere). This, they say, could effectively mean international funds would be subsidizing forest destruction. 

Tremendous disappointment, or 'more of the same'? How Indonesia handles this will certainly be watched closely. As with any current event it runs the risk of being swept under the carpet, or just sat upon until the media attention inevitably dissipates.

More coverage:

• Greenpeace's original report, titled 'Protection Money'.
• Blogger Chris Lang in REDD-Monitor gives a brief account of recent REDD-related developments in Indonesia.
• The REDD-ALERT website describing various REDD initiatives around the world.

D'Arcy Thompson at 150

Just as biologists are cleaning up the confetti from last year's big double anniversary of Charles Darwin and his Origin of Species, it's time to celebrate again. This year marks the 150th birthday of D'Arcy Wentworth Thompson, the Scottish polymath (a natural historian, linguist, classicist, physicist, mathematician...) whose most famous book, On Growth and Form (Google Books preview of the 1961 abridgement by J.T. Bonner, with an introduction by Stephen Jay Gould), pioneered the study of biomechanics and biomathematics.

Norman Borlaug

Norman Borlaug, "The Father of the Green Revolution" passed away at the age of 95 on Sept 12 2009. He was instrumental in developing and introducing semi-dwarf, high-yield, disease resistant wheat varieties. NY times wrote of him as "...the plant scientist who did more than anyone else in the 20th Century to teach the world to feed itself..."

He won the Nobel Peace Prize for agricultural innovation and the development of high-yield crops in 1970. The Green Revolution has been touted to have averted a world-wide famine in the late 20th century.

Excerpts of his speech during the Nobel Prize award ceremony showed how committed he was in using science for the betterment of mankind:

"Accordingly, I shall not dwell upon the personal honor, for I have not done so even within myself. Instead, I want to devote my remarks to commendation of the Nobel Committee which had the perspicacity and wisdom to recognize the actual and potential contributions of agricultural production to prosperity and peace among the nations and peoples of the world.

Obviously, I am personally honored beyond all dreams by my election. But the obligations imposed by the honor are far greater than the honor itself, both as concerns me personally and also the army of hunger fighters in which I voluntarily enlisted a quarter of a century ago for a lifetime term. I am acutely conscious of the fact that I am but one member of that vast army and so I want to share not only the present honor but also the future obligations with all my companions in arms, for the Green Revolution has not yet been won.

It is true that the tide of the battle against hunger has changed for the better during the past three years. But tides have a way of flowing and then ebbing again. We may be at high tide now, but ebb tide could soon set in if we become complacent and relax our efforts. For we are dealing with two opposing forces, the scientific power of food production and the biologic power of human reproduction.

Man has made amazing progress recently in his potential mastery of these two contending powers. Science, invention, and technology have given him materials and methods for increasing his food supplies substantially and sometimes spectacularly, as I hope to prove tomorrow in my first address as a newly decorated and dedicated Nobel Laureate. Man also has acquired the means to reduce the rate of human reproduction effectively and humanely. He is using his powers for increasing the rate and amount of food production. But he is not yet using adequately his potential for decreasing the rate of human reproduction. The result is that the rate of population increase exceeds the rate of increase in food production in some areas.

There can be no permanent progress in the battle against hunger until the agencies that fight for increased food production and those that fight for population control unite in a common effort. Fighting alone, they may win temporary skirmishes, but united they can win a decisive and lasting victory to provide food and other amenities of a progressive civilization for the benefit of all mankind.

Then, indeed, Alfred Nobel's efforts to promote Brotherhood between nations and their peoples will become a reality.

Let our wills say that it shall be so."

Further reading:

• "Agriculture pioneer Borlaug dies." BBC News, 13 Sep 2009.
• "Norman Borlaug, Plant Scientist Who Fought Famine, Dies at 95," by Justin Gillis. The New York Times, 13 Sep 2009.
• Wikipedia article: Norman Borlaug
• Norman Borlaug's Nobel Prize Speech: The Nobel Prize in Peace 1979, Norman Borlaug, nobelprize.org.
• "Norman Borlaugh and the high-yield dwarf spring wheat," by N. Sivasothi. Otterman speaks, 22 May 2005.

Singapore Ranked #1 in the World for....

... the wrong reason. Corey Bradshaw (Adelaide), Navjot Sodhi (NUS) and Giam Xingli (Princeton, formerly at NUS) have published a ranking of countries by environmental impact in PLoS ONE. When scaled for resource availability, Singapore comes out tops:

"The proportional index ranked Singapore, Korea, Qatar, Kuwait, Japan, Thailand, Bahrain, Malaysia, Philippines and Netherlands as having the highest proportional environmental impact, whereas Brazil, USA, China, Indonesia, Japan, Mexico, India, Russia, Australia and Peru had the highest absolute impact (i.e., total resource use, emissions and species threatened)."

(Figure source: PLoS ONE. Upper panel - proportional impact, lower panel - absolute impact.)

They claim that this study is robust, quantifiable, and looks only at the environmental impact, unlike previous rankings and data compilations.

More details from Bradshaw's personal blog, and the original paper.

(Thanks to Hann for heads-up)

Urban ecology: Revisiting weeds?

Urban landscapes seem very different from natural, 'pristine' landscapes, but many similar principles apply to understanding both of them. Those of us who are city-dwellers from birth, like most Singaporeans, have a very skewed vision of what urban vegetation 'should' be like, conditioned by heavily manicured and landscapes parks and plantings. We tend to look down on weeds and wildflowers as plant pests and ugly eyesores to be managed rather than celebrated. But weeds, or to use a more neutral term, 'spontaneous vegetation', have an important function in the urban environment, as Peter del Tredici argues.

Del Tredici is a scientist at the Arnold Arboretum and lecturer at the Harvard Graduate School of Design, and has just written a book titled Wild Urban Plants of the Northeast: A Field Guide, where he explains his philosophy of urban ecology in detail, along with descriptions of common species in the American Northeast. I attended a talk he gave in conjunction with a booksigning event, and was struck by how many of the things he observed about urban vegetation also applied to what we find in Singapore:

• Plants that thrive in urban open lots tend to be native to harsh environments. In the US, the 'Tree of Heaven' (Ailanthus altissima) is a cliff-dwelling species from East Asia and common in cities like Boston; in Singapore, Adinandra dumosa, which is common on wasteland, is actually native to limestone hills on the Peninsula.
  
• Bird-dispersed species with small seeds spread quickly and aggressively. Most of the successful species in urban landscapes are early successional species in 'nature'.
  
• The growth of spontaneous vegetation is inversely proportional to how wealthy the neighborhood is. In shrinking cities with declining economies, like Detroit, abandoned lots are being left to be grown over by wild grass and shrubs, and some companies even run pheasant hunts in the city because those birds are starting to colonize these spaces.
  
• Wayside trees planted for ornament and shade can escape and invade native habitats, displacing native species. Norway Maple is a big problem in Massachusetts, where it's illegal to plant this species, just like Albizzia might be in Singapore.
  

Ultimately what he argues for is a change of perspective - we can see these as ugly weeds, or we can incorporate them into our appreciation of the urban landscape, using and manipulating them to suit our needs. Even in their unmanaged form, urban wild plants provide many important services, not least among them shade and temperature regulation, soil consolidation, and even phytoremediation. With the economic downturn, less money is available for urban landscaping and planting, but if we can make use of these erstwhile invasive species, by weeding out the uglier and less cooperative species, making paths and borders, we could produce wild urban woodlands that enhance the urban experience, instead of detracting from it.

Looking at the plant list in his book, it is also striking how many of the species listed are actually common to both places. At the booksigning, he wrote in my copy that I "won't find any of these in Singapore," but at the genus or family level, there are quite a number of familiar names: Composites, Legumes, and Crucifers for sure, but also Euphorbiaceae, Scrophulariaceae, and Vitaceae. Familiar genera abounded especially among the grasses: Eragrostis, Digitaria, Poa. I'm sure someone has had similar thoughts before, but it would be instructive to look at the comparative community phylogenetics of weeds around the world - are certain groups of plants particularly predisposed to be successful in the urban landscape? If so we should start getting familiar with them, because these are the species that will be most familiar to most of the human population in time to come, if not already.

Are heart cells and mammal eggs regenerated?

Two of the dogmas that most biology students learn in school are that cardiac muscle is not renewed, and that women (and almost all female mammals) are born with their full complement of eggs - they can't make new ones. Two recent studies have shown that these dogmas may not be as clear cut as they originally seem to be.

The first of these studies (New York Times article) was carried out by a team at the Karolinska Instituet in Sweden. They wanted to see if any of the cardiac muscle cells in humans were formed after the person's birth. In biology, the classic method to do such a tracing experiment in animals is to feed the animals some sort of radioactive tracer, which would then become incorporated into the DNA of cells that are being formed during the period that the the radioactive tracer was being fed to the individual. Cells formed after that period would not have radioactive tracer in their DNA. Obviously there are ethical implications of feeding humans radioactive tracers, but the experiment has already been done on unwitting subjects at a global scale.

During the 1950s, Cold War powers tested nuclear bombs above ground, releasing significant and measurable quantities of carbon 14 into the atmosphere. Individuals born during that time would have incorporated this carbon 14 signal into their tissue. After the test ban treaty in 1963, carbon 14 levels gradually diminished, and this changed isotope ratio can be detected in DNA synthesized after that date. The team applied their method to heart muscle cells, and found that for individuals born before the test ban, some of their heart muscle cells had a lower carbon 14 isotope ratio, meaning that those cells were produced after that date - evidence for regeneration.

The second study was carried out at the Shanghai Jiaotong University, and involved mice and not humans (NY Times article, Science feature). They also used a really cool technique, but one which operates on a less grandiose scale. Before this study, the debate in the field was whether supposed female germline stem cells (FGSCs) in mouse ovaries thought to be responsible for generating new oöcytes were in fact capable of doing so. The method used to isolate the FGSCs is called immunomagnetic isolation. Antibodies to a protein found only on FGSC surfaces were raised, and coated onto magnetic particles. Therefore, a magnetic filter would be able to isolate the supposed FGSCs. After isolation, they were transformed with green fluorescent protein, and introduced into the ovaries of sterile mice. The sterile mice were then mated with normal males, and offspring, expressing green fluorescent protein, were produced. This demonstrates that ovaries possess stem cells that are capable of regenerating oöcytes. Given the similarity of mouse and human reproduction, it is possible that humans have similar capabilities.

In both cases, therapeutic applications are a long way off, but it is still intellectually exciting to be aware that what has long been "known" as fact is still open to reassessment by pure empirical work, showing that biology is still a young and growing field.

Birdsong and Human Speech

Speech and language seem to be uniquely human traits, which begs the question of how they arose. It turns out that a key regulatory gene controlling human speech, the FOXP2 (forkhead box transcription factor) gene, is also found in other animals, including songbirds. Knocking out these genes in humans (though accidental mutations) results in speech disorders associated with abnormalities in the basal ganglia, though exactly how they control the ability to speak is unknown. A team of German scientists used songbirds as a model for understanding the development of human speech. Instead of simply knocking out the gene, they used RNA interference to reduce FOXP2 levels in a specific area of the basal ganglia, known as Area X, in zebra finches, while they were in the stage of learning their song. This resulted in abnormal song patterns and provides a very persuasive example of how some genes can be directly linked to certain elements of behavior. However, note that the FOXP2 gene is a transcription factor gene that is part of the developmental toolkit, and so functions by regulating the expression of several other genes, so the actual pathway may be much more complicated that it first appears to be, so it would be misleading to simply call FOXP2 the 'speech gene'.