Archive for July, 2012

America in the time of AIDS…

This week the world descends on Washington DC, to discuss, evaluate, and get the state of the art of what is — without hyperbole — the disease of our times: HIV/AIDS; as the city prepares to host the International AIDS Conference (AIDS2012).

It is the cliché to think that sub-Saharan Africa, particularly southern Africa, typifies and exemplifies the problem we have and our struggle with HIV/AIDS. America hides an ugly truth about a disease that last year celebrated its 30th birthday (anniversary of the first case reports in the United States). Washington DC has an HIV infection rate of 3.2%. If it were a country it would rank 23rd out of 54 in percentage of people with HIV — placing it above the Democratic Republic of Congo, Ghana, and 30 other African countries, and just behind Nigeria.

In 1995, the number of new cases in black Americans overtook the number of new cases in white Americans and other ethnicities — and it’s been that way ever since. The District of Columbia, with a population of 600,000 odd inhabitants, has a rate of prevalence of HIV/AIDS among black males that far outweighs other ethnic groups, and even the total prevalence in other American cities.

With the number of cases around the world dropping, in general, in the US it has remained the same. If the problem in southern Africa is one of denialism… America’s problem is one of inequality. From the statistics you would be forgiven to think that poverty equals AIDS. Poverty does not equal AIDS. Inequality equals AIDS.

The problem seems systemic, being placed squarely on the shoulders of a city that has failed its population. The Globalpost writes “for years, the District had failed to do in-depth surveillance of the AIDS epidemic and had perceived it to a problem largely limited to the gay community and injectable drug users”.

On more than one occasion, when an American city is given the international stage in such a way, it only serves to highlight the disparities that exist in modern day America. When NATO descended on Chicago for a summit on peace and security, protesters took it as chance to outline the paradox. That the inequalities and injustices that the global community seeks to rid on the international stage are, more often than not, replicated and reflected at the local level. The developing world is everywhere. Especially, in the backyards of the most profitable and most developed.

More young people are killed in Chicago than any other city in America. Washington DC ranks the highest on all three measures of income inequality in the US. The stats don’t end there. Black unemployment rate as of this June was at 14.4%, compared to a national rate of 8.2%. Black America is only behind hispanics in terms of high-school dropouts. The mortality rate for black infants in Chicago is on a par with the West Bank. Black America’s life expectancy is definitely below that of White America.

Comparing the top ten causes of death between 1980 and 2007 among the African-American community, all the usual suspects are present — heart disease, cancer, diabetes, kidney disease and homicide. Some disproportionately affect Black America. Only HIV/AIDS was absent in 1980 and now in the top ten in 2007.

With around 7% of all African-American men in the District being HIV positive, there is renewed impetus to act. The situation is complicated. Trying to tease out what AIDS does to a community it is important to avoid separating AIDS from those other factors, systemic or otherwise, that also serve as contributing factors.

If I was to write this article one hundred times, I could focus on a hundred different facets of the disease — poverty, human rights, politics etc. Social and economic structures increase the vulnerability of populations who are at risk for or living with HIV/AIDS. The disease needs to be talked about in context of all other factors and dynamics of society. All facets that will be discussed at AIDS2012.

However, the fact still remains that the disease itself is an inherently social problem.

Sometime between 1888 and 1924, on a single occasion, the virus passed from a chimpanzee into a human somewhere in the Cameroonian rainforest. The virus spread and found its way to the town formerly known as Leopoldville (now Kinshasa). Today, as we enter the fourth decade of the disease, the central theme seems to be entanglement. Because of the way HIV is transmitted, the virus operates through the behaviour of host individuals, and thereby, amongst others, through their knowledge of infection and their beliefs about what is at stake.

During the conference activists will take to the streets of DC, lending their voices to the myriad of different themes, subjects, cases, burdens, problems, and questions on the matter of HIV/AIDS.

As the song goes… “a big disease with a little name”.

Originally appearing at Australian Science.

Image — sourcesource.

The extinction that is yet to come…

The Amazon rainforest contains a wider variety of plant and animal life than any other biome in the world. The region in its entirety is home to roughly 2.5 million insect species, tens of thousands of plants, and some 2000 birds and mammals. To date, at least 40,000 plant species, 2000 fishes, 1000 birds, 427 mammals, 428 amphibians, and 378 reptiles have been scientifically classified. The Brazilian Amazon harbors roughly 40% of the world’s tropical forest and a significant proportion of global biodiversity.

The numbers speak for themselves. However, over the past few years what we’re seeing is a biodiversity crisis in slow-motion. Those numbers are at risk. The largest drivers of which being climate change and habitat loss by deforestation.

Habitat loss results in species extinction, but not immediately. When habitats shrink it may take several generations after an initial impact before the last individual of a species is gone. Extinction against the clock and in slow motion.

Visualising how this occurs and estimating the impact has always been a problem for researchers. The question now is — how many species are headed for extinction as a result of past and future deforestation?

New research published today in Science describes cutting-edge statistical tools used to devise a novel strategy to estimate the expected number of local species extinctions as a function of the extent of habitat loss.

Researchers made predictions on the extent of the extinction damage based on four possible scenarios — two in which all parties comply and respect current environmental law and protected area networks; and two which rely on strong reductions and eliminations in current deforestation rates. A reflection of recent pledges by the Brazilian government and potential reductions in deforestation proposed in 2009. What researchers describe is an estimation of something much more serious than previous estimates.

Deforestation over the last three decades in some localities of the Amazon has already committed up to 8 species of amphibians, 10 species of mammals, and 20 species of birds to future extinction. Local regions will lose an average of nine vertebrate species and have a further 16 committed to extinction by 2050. The worst is yet to come it seems. More than 80% of local extinctions expected from historical deforestation have not yet happened.

An “extinction debt” — future biodiversity loss which have yet to be realized as a result of current or past habitat destruction — offers a time delay, the chance to save them… but it is a race against the clock. A window of opportunity for conservation, during which, researchers write, “it is possible to restore habitat or implement alternative measures to safeguard the persistence of species that are otherwise committed to extinction.

The fight for the heart of the Brazilian Amazon has already begun.

Brazil has a long-standing tradition of conserving its Amazon — or, at least, trying to be seen as conserving its Amazon. Up till now a mixture of firm legislation and strong-arm tactics ensured this. The Brazilian government has been known to use police raids to crack down on illegal deforesters. Currently, around 54% of Brazilian Amazon is under some form of environmental protection. Thanks, in no small part to the country’s half-century-old Forest Code.

The past few years, since the economic crisis, has seen political will erode and the Forest Code challenged. In today’s economic climate, reconciling income generation with sustainability is a difficult balance to maintain. The economist’s mantra, foregoing all for economic growth, has seen the Brazilian government pushing forth a rapid expansion of infrastructure in the Amazon, from the construction of vast hydroelectric power plants in the Amazon basin to agricultural expansions. Agriculture represents a significant proportion of Brazil’s GDP and there is pressure to open up more forest land to production.

Earlier this year, a bill seeking to overhaul the Forest Code was up for debate. As Rio+20 welcomed the world to debate the merits of development versus conservation Brazil herself was going through the same struggles.

Protected forest areas across the Brazil Amazon represents a cost of US$147 billion for Brazil (a number that includes the lost profits if they were to be opened up for a free-for-all as well as investments needed for their conservation). They cover a total area of 1.9 million km² and encompass just under half of the Amazon biome. It is hoped that this culture of conservation will continue and expand the total area.

In April of this year, the new forest code was approved, with many reservations from conservationists. The new code allows for a considerable reduction in reserve areas in the Amazon.

How this will affect the “extinction debt” is yet to be seen. Researchers acknowledge that their “best case scenario” (an end of deforestation scenario) “appeared feasible when first published in 2009 but appears much less so now in the face of recently voted changes to the Brazilian Forest Code that may weaken controls on deforestation rates.

The future of biodiversity in the Brazilian Amazon currently stands at a critical juncture. It seems the Amazon will continue to collect extinction debt for decades to come as we witness how the impact of present-day decision making policies by governments on future species extinctions.

[Images courtesy of Alexander Lees and William Laurance]

Originally appearing at Australian Science

Soares-Filho B, Moutinho P, Nepstad D, Anderson A, Rodrigues H, Garcia R, Dietzsch L, Merry F, Bowman M, Hissa L, Silvestrini R, & Maretti C (2010). Role of Brazilian Amazon protected areas in climate change mitigation. Proceedings of the National Academy of Sciences of the United States of America, 107 (24), 10821-6 PMID: 20505122

Ricketts TH, Soares-Filho B, da Fonseca GA, Nepstad D, Pfaff A, Petsonk A, Anderson A, Boucher D, Cattaneo A, Conte M, Creighton K, Linden L, Maretti C, Moutinho P, Ullman R, & Victurine R (2010). Indigenous lands, protected areas, and slowing climate change. PLoS biology, 8 (3) PMID: 20305712

Thesis word cloud… Part II

In Part I, somewhere at the hazy beginnings of this blog, I decided to reduce a lot of blood, sweat and tears, a large declaration of scientific effort into what was essentially a postcard.

In what was, at the time, a personal act of self-mutilation… I have decided to extend this gift of brevity to other theses. So Part II’s word cloud comes from a thesis entitled “Using metabolomic analyses to study mode of action of and resistance to Eflornithine in Trypanosoma brucei” from a baptised (through hell and fire) protégé. Read the whole thesis, it’s quite the page turner.

50,000 odd words, 317 pages, 65 figures, 13 tables, 6 chapters, and a Trebuchet font past the finish line…

Representing an entire thesis as word cloud is quite meaningless. As much as this act is a gross under-representation of what it’s like to write a thesis, or go through a PhD for that matter, it gets us to thinking about words.

‘aliquoted’ word or not a word? #phdthesischat

— Heather Doran (@hapsci) Juin 5, 2012

Specific words within our theses and the words we choose to describe the science that we do (god particle anyone?).

Writing about science, in whatever form, is a precise matter (as it should be). For a thesis, lofty ambitions and rhetoric, are for the most part, put aside in favour of exactitude.

“Outwith” is a word that occurs thrice within this thesis. And which was the topic of debate during the viva (so I hear).

As I write this I am reading that Jorge Cham over at PhD Comics is going one better… that is animating an entire thesis!

Super-villain watch…

How to make a volcano erupt on cue.

via Wired Science

Okay, so, how would I do it? First, I need to find a volcano ready to erupt that doesn’t erupt frequently (so that pressure is already building).

If you want an explosive volcanic eruption, you want to produce bubbles (and lots of them) by (1) decompressing the magma, causing gases to come out of solution; (2) crystallizing minerals to concentrate water/volatiles in the remaining magma or (3) heating the magma with a new intrusion. A release in pressure can be accomplished a number of ways, including the failure of the roof above the magma body (a volcanic landslide is a great way), the buoyant rise of the magma or through some less common factors like melting of a glacier (likely too slow a process to trigger a specific eruption), excessive precipitation to erode the volcano, changes in atmospheric pressure or maybe even Earth tides caused by the pull of the Sun and Moon (rare, mostly in already active volcanoes). Once you’ve produced bubbles, you need to concentrate them towards the top of the magma body, maybe through a earthquake — think about shaking an open bottle of soda with bubbles on the side: They all float to the top. However, in all these cases, you likely need a volcano that is “primed” to erupt — that is, one that has eruptible magma that just needs to be “tipped” into erupting.

Image — source

Previous super-villainary: part I and part II

Barack Obama doesn’t care about black people…

David Swerdlick, writing in The Root, says “there’s no shortage of folks who say that President Barack Obama — our first black president — hasn’t done enough for African Americans”. And he believes that’s exactly the way it should be. This was in response to Frederick Harris’ lamentations in The Washington Post on how he is still waiting for the first black President.

Outside the spire of political opinion commentary does this have any basis or warrant a closer look? Is it fair to claim that Barack Obama has ignored African Americans?

New published research explores race politics in America in more detail, and explores to what degree Obama’s election has signaled the end of racism in US politics. A number of experts in the field of critical race theory attempt to answer this question in a special issue of Qualitative Sociology: The Obamas and the New Politics of Race. With the 2012 US presidential election campaign in full swing, the meaning and significance of Barack Obama and his presidency are once again in the spotlight. Although, political commentators will tell you that much of the debate is likely to be consumed by healthcare.

Through the lens of Barack Obama’s presidency, what we see is something political commentators are missing. In an article entitled “Just another American story? The first Black First Family” Patricia Hill Collins shows – by highlighting their own ‘family stories’ during the 2008 campaign and in the post-election years – how the Obamas have been able to reintroduce race, gender, labour and equality into public policy discussions in a time when such debates are often deemed risky.

Michael Jeffries explores Obama himself as a figure of multi- and perhaps post-racialness in a paper entitled “Mutts like me: multiracial students’ perceptions of Barack Obama.” Exploring how other multiracial US citizens understand Obama’s racial identity, race and ‘race relations.’ In his interviews with multiracial students, Jefferies finds that respondents reject the concept of ‘post-racial idealism’ and do not view Obama’s election as signaling an end to racism. Instead, Obama is viewed predominantly as black rather than multiracial, even though his multiracial origins are acknowledged. Suggesting that racial schemas birthed by nineteenth century racial science continue to have a powerful effect in shaping popular perceptions of race today.

The election of Barack Obama – and his bid for re-election in November 2012 – allow us to consider how race and race relations have, or have not, changed — both in and outside of the electoral sphere.

Image — source

What had I twaught…

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