Catching up with Nature - Breathlessly!

Pitcher plant (courtesy :Wikipedia)

SLIPS Technologies Inc.  a company anchored at Cambridge , Massachusetts, is barely a year old. Unusually slippery surface of the pitcher  plant inspired a group of researchers and that is the genesis of this company.  SLIPS is the acronym for Slippery Liquid Infused Porous Surface. The concept of a slippery surface which repels everything and anything was proven and reported   in a  research paper published  Nature in 2011. And in fact we covered it here.  Now  SLIPS Technologies Inc  is all set to market their products. To quote from their website- omniphobic surface  with optical transparence, scratch resistance, self-repair and self-cleaning characteristics that can operate under extreme environmental conditions.  

So what is the chemistry? Teflon and teflon coated non-stick vessels are household word now.  SLIPS uses similar materials from the vast family of  perfluorohydrocarbons for surface modification.  For example for medical devices undergo a two step surface coating process.  First a mono layer of teflon  is chemically grafted onto the device surface, which is then impregnated with a layer of another liquid perfluorocarbon. Such treated surfaces are called TLP  surfaces. (Tethered -Liquid Perflurocarbon surface). The super slippery surface of TLP treated medical devices  doesn't encourage blood clotting because neither fibrin nor platelets can adhere to the surface. For the same reason nor can bacteria form biofilm.(1,2)
  

Lotus leaf in water -Courtesy: Wikipedia

Scientists also marvel at the water repellence (super hydrophobicity) and self cleaning properties of the lotus leaf.  Water droplets get tossed around on the leaf surface and often aggregate to form bigger droplets and with the slightest tilt  falls off the leaf. But while  being tossed around,  the droplet would have smeared  all the dirt on itself and thus gently wiped the surface clean. Studies have  revealed that wax coated micro/nano "pimples" on the leaf surface drive  this unique phenomena.  Lotus effect has been recreated and replicated  on nano patterned surfaces. 

Now  Lu et al have  added  another innovative dimension to this effort. Their research paper appeared in the 6th March issue of Science(3). Super hydrophobic surfaces so far developed are mechanically  fragile and their performance graph dip when contaminated with  oil.  Liu and team have come up with an elegant  solution in the form of a paint formulation. Titanium dioxide nano particles coated with perfluorooctyltriethoxysilane is dispersed in ethanol.  Any surface, big or small can be coated  with this paint. Multiple coating techniques can be adopted: spraying, dip-coating, spin coating, extrusion- you name it.  The assorted titanium nanoparticles in the paint film take on the role of the "surface pimples". For the paint film to  stick strongly to the surface, a suitable  adhesive can be added to the formulation.  The robustness of the film  even after repeated exposure rough weather such "40 abrasion cycles with  sand paper " has been demonstrated on surfaces of  glass, cotton wool, steel, and filter paper. 

On one count the lotus leaf and pitcher plant still score high : Breathability.  Hold your breath- we will soon be getting there.  

References: 

1. Bioinspired coating for medical devices repel blood and bacteria
2. Literally nothing will stick to this new slippery surface
3. Robust self-cleaning surfaces that function when exposed to either air or oil: Lu eta al  
Science Vol. 347, issue 6226, pp 1132-5, 2015. 

Luck Factor in Cancer !!!

Everything in the Universe is a fruit of chance and necessity.

Democritus,  in ancient Greece,  around 400 BC.

Not just philosophers, but scientists too have subscribed to this concept. Molecular biologist Jacques Monod  (Nobel laureate in Medicine and Biology 1965)  explained the significance and relevance of chance and necessity  in biology in his  book bearing the same title. It looks like even cancer could be a matter of chance. So far  two factors have been implicated in cancer: genetic predisposition and/or environmental factors. "Environmental factors" a huge black box, would contain  anything that is not genetic. For example  smoking, pollutants, pesticide, radiation, junk food, unhealthy life style.......runs into a long list.  In a recent issue of Science  Tomasetti and Vogelstein   suggest  that   there is a third factor- an element of chance (1). Based on a statistical analysis of available data, they state  that ".......only a third of the variation in cancer risk among tissues is attributable to environmental factors or inherited predispositions; vast majority of the rest, is due to "bad luck".  And they trace this   luck factor  to  the  random (stochastic- if you prefer a more scholarly term ) mutations during the normal process of DNA replication  in  healthy,  non cancerous stem cells. 

Little unsettling indeed. But  they present  supporting data.  It is known that   certain tissues are more prone to cancer than others. For example lung cancer is more common than pelvic bone cancer. Incidence of brain tumor in spite of the  protective  blood-brain barrier, is much higher  than that of the small intestine where epithelial cells constantly encounter more toxic chemistry. Within the food processing zone itself, large intestine is at much higher risk than either  stomach or small intestine.  Why this variation?   Are there missing factors?  That is the question Tomasetti, a mathematician and Vogelstein, a cancer geneticist, both at different institutions under the umbrella of Johns Hopkins Medical School, asked. 

They decided to focus on the stem cells in  selected  tissues. Stem cells have the power to self replicate and are responsible for the architectural  integrity of a given tissue. Recent studies have unraveled a lot of information about them.  As stem cells self replicate, random mutations which are not necessarily carcinogen induced can occur.  By simple reasoning, as frequency of cell divisions shoots up, so will  the probability of stochastic mutations. Mutations could be innocuous by themselves. But could  they spell danger  collectively? Could they  function as a defect/error that   leads to cancer?  Two parameters needed to be estimated for the statistical modeling of such a  situation. : (i)  the lifetime risk of   various tissues developing cancer and (ii)  lifetime number of stem cell divisions  in a given tissue. Tomasetti and Vogelstein selected 31 tissue types for which these two parameters were available. A correlation plot substantiated their hypothesis. Colorectal tissue which registered about  trillion stem cell divisions, had a high lifetime risk almost close to 1, while pelvis osteosarcoma  with just over a million stem cell divisions ranked low. 

Many researchers were quick to protest.(2). Main objection was to the statement "we show that these stochastic influences are in fact major contributors to cancer overall, often more important than either hereditary or external environmental factors". Was the process of collecting and  interpreting the data  statistically sound? Was the data skewed? Was the sample size and spread  sufficient? Genuine doubts. But more than anything I guess the scientific community is angered by the terminology "Bad Luck". 

During  a recent  interview the duo likened their conclusions to the   probability of a motor vehicle accident. Consider your body  to be a car;   the  make and model of the car define your genetic makeup.    Road, weather  conditions etc.  reflect  the environmental factors.  Even if your car is in top condition, and the weather perfect,  you can't  totally eliminate the probability of an accident. (In this  scenario there is no place for the "other" erratic  driver). You can only be careful to a limit,  beyond that it is chance.  

The message I got was this-  go for  regular  check up; early detection could minimize the risk factor.   

Tailpiece: Bad luck indeed!
The plan was to view moonlit  Taj Mahal ; but   unseasonal downpour intervened. Two views from our hotel balcony.

At dusk 

In daylight  

The usual 

References 

1. Variation in Cancer risk among tissues can be explained by the number of stem cell divisions.  C. Tomasetti and B. Vogekstein, Science 2 January 2015, vol. 347, issue 6217 pages 78-83. 

2. Letters : On Cancer risk :  Science 13 Feb. 2015 Vo;l. 347, issue 6223, pages 727-730

Privacy in Public Space ?

In his novel  Dans le cafe de la  jeunesse perdue   Patrick Modiano (Nobel Prize for literature 2014 ) sketches Louki .  Never wanting to attract attention, at Cafe Conde', she always  stayed in the background or hid herself among the crowd. But alas!  in the rare and random group photos taken in cafe,  she stands out because of her photogenic face. When she goes missing , Mr Caislly a detective  is put on the job to trace her.   At one point  Mr Caisley   feels morally bound to respect  Louki's right to remain untraced.  The story is set in the 1960's, when it was easy to remain hidden from public view. Fast forward to modern times. Do we have the privilege to remain anonymous? Can we wish to be among the "Forgotten People"? Well,   I may be  a total stranger to my next door neighbor but I leave digital footprints all over.   Mobile phone, credit cards, browsing habits. everything leaves a mark. Oh! No not just marks, I generate   a pattern of  my behavioral traits- restaurants I frequent, favorite holiday spots,   reading/browsing  habits, favorite cab service.......So much so that  often I receive  helpful prompts : here is a book you may like or We haven't seen you for so long........ Such personalized messages are just one part, I might have inadvertently checked a tiny box somewhere sometime to "be in the loop".  

But what about anonymized or ghost data? We are talking about  millions of such  digital footprints  devoid of users' identification marks.  Because of ease of data collection, consolidation, filtration and processing  such ghost data( or metadata) , constitute rich gold mine  for market research, R&D activities  and  also for meaningful studies in sociology behavioral science, public health, etc.  How harmless are such  ghost datasets ? Not quite that is what Anthony Tocker found out.  Curious brains can mix/ match/superimpose ghost data with other pieces of  information freely available in the public domain  and breathe life into skeletons.  For example when New York City Taxi and Limousine Commission put out rather innocuous details  of millions of trips  for the year 2013 on the web, (of course without   passenger details)  it was not at all difficult for Anthony Tockar   to couple trip info with freely available public domain data  and   thus de-anonymize the riders. As simple as  putting 2 and 2 together, but in a rather complex way.  

de Montjoye, at the   computational privacy  at the Massachusetts Institute of Technology, prefers to describe the process  as  Correlation Attack.  de Montjoye and his team decided to analyze credit card data in the same way. They collected  ghost data for credit card transactions over  a span of 3 months for  1.1 million people  and 10,000 shops  sans user name, sans  card number , sans shop name  and sans  time of transaction.    Armed with just the  details of   amount spent, shop type,  date stamp. and a code for each person, the team demonstrated that " 4 spatiotemporal  points are enough to uniquely reidentify  90% of individuals."  and  that " women are more identifiable than men in the credit card meta data." 

Efforts are on to fix such loopholes. Anonymous search engine duckduckgo doesn't capture user's ip address or store search history.  TrackMeNot  an add-on to Firefox or Chrome throws the tracker off the track and  into a Daedalian  labyrinth   with no Ariadne around to help. Researchers at Duke University have developed CacheCloak,  a program  which   camouflages mobile location.  Are we getting paranoid about our privacy?  Not necessarily. In my mobile contact list there are very few without a face; some have  uploaded their entire family! More interestingly there are monthly if not weekly updates.  Facebook too  tells the same  story; people are eager to talk about themselves, share their experiences- holidays, parties, workplace, constant updates...... Taking advantage of the millions of authenticated photos in their treasury, Facebook is all set to roll out DeepFace, a face recognition program, which can automatically tag a face with 97.25% accuracy. 

Perhaps  Digital Age has precipitated our eternal paradox: to  be unique and yet ordinary. 

Tailpiece:  

Stars, hide your fires;

Let not light see my black and deep desires                                                                           (Macbeth Act 1, Scene 4)

References:

.. 

1. Dans le Cafe de la jeunesse perdue : Patrick Modiano,  Gallimard 2007
2.Differential Privacy : The basics
3.Riding with the stars passenger privacy in the nyc taxicab dataset

4. Unique in Shopping mall : On the reidentifiability of credit card meta data 

de Montjoye et al Science 30 Jan. 2015, Vol. 347, issue 6221, pages 536-539
5. Hiding in plain sight, & Camouflaging searches in a sea of fake queries.
    Jia You  ibid page 500 & 502
6. Facebook will soon be able to ID you in any photo
6. Deep Face:Closing the gap to human level performance in face verification 

  

Inclusive Wealth Report 2012 & 2014.

Agricultural land, forest covers , high ranges and beaches are being lost to urbanization and development. This has a serious and direct  impact on the global ecological balance. For example a recent study states   that there is an increase in the atmospheric lightening over northern America due to global warming. Alarming indeed  because lightening triggers forest fires. The great barrier reef  that skirts the north eastern Australian coast  has been reduced by 50% over  the  last three decades.Among others coastal development and climate change are cited as reasons. Ocean warming has robbed coral off its color.  The great Himalayas,   prehistoric  Western Ghats, Amazonian forests and    mighty rivers are also facing threats.  Ecologists world over  believe we stand to lose much of our  natural heritage in our lifetime, if we don't take precautionary steps right away. While this may be a bit exaggerated, it is true that our natural wealth is being depleted.   We need to assess the instrumental value of our natural assets and then incorporate this  in the annual balance sheet- Just as the movable and immovable assets along with their depreciation show up in a company's  balance sheet. 

And therein lies the challenge. How do we compute  a nation's   wealth? In 2012 United Nations and World bank  brought together several like-minded agencies (UN University –International Human Dimensions Programme (UNU-IHDP) and the UN Environment Programme (UNEP), in collaboration with the UNESCOMahatma Gandhi Institute of Education for Peace and Sustainable Development (UNESCO-MGIEP), ASCENT Africa Sustainability Centre, the Malaysian Industry-Government Group for High Technology (MIGHT), Science to Action (S2A), the Ministry of Environment – Government of Japan, the UN University – Institute for the Advanced Study of Sustainability (UNU-IAS), and endorsed by the Science and Technology Alliance for Global Sustainability)  under one umbrella to crack this challenge- how to do national wealth accounting.   The team collected extensive data and devised a method to calculate  national wealth wherein natural wealth is a non-negotiabel term. The details of this exercise are contained in  the Inclusive Wealth Report 2012.  The report recognized three components  of the National wealth  as follows: 

Wealth =  Human Capital(HC)+ Produced Capital(PC)+ Natural Capital (NC)

While this empirical formula might seem naive it incorporates several layers of complexity behind the facade.  HC is computed taking into account education, skill-set, health etc.Computing  PC will be the easiest since it has a direct bearing on the GDP and  cover all products (industrial + agricultural, roads,buildings etc.)   NC, Natural wealth itself is viewed from three different angles: the intrinsic value, use value and optional value and assessed among other things in terms of irreversible uses and substitution possibilities and renewable resources.  Inclusive Wealth index (IWI) evaluated based on these premises falls below the GDP and HDI. IWR 2012 was also  the first step towards sensitizing governments  for the need for a cautious balance between growth rate and ecological integrity. 

IWR 2014 report is significant  is a jump forward from the 2012 report for several reasons. For example while  The 2012 reported covered 20 countries, the present report covers 140 countries. Its focus is the human capital; a    great national asset which could very easily turn into a liability.   The Human capital computation with   educational and health components as key changemakers  has received stringent scrutiny.  As Anantha Duraiappahin  states in the Preface of IWR 2014 -

 "We hope that policy-makers at the international, national, and state level will see the IWR 2014 as a useful tool, and as encouragement to take the steps necessary to close gaps in data and to utilize the inclusive wealth accounts presented in the report as guidance "  

Here is a snippet from the voluminous data in the report.  Since BRICS countries  will have a strong influence on the fate of  the world in years to come-by, I have just picked the details of the  BRICS group and thrown in western Europe and the USA and world data for comparison.   This for the 20 year period 1990-2010.     

While the results could be viewed through several filters ( single  or in combination), what stands out remarkable is way forward to  reach  a win-win situation. 
   
Reference : 

1.UNU-IHDP and UNEP (2014). Inclusive Wealth Report 2014. Measuring progress toward sustainability. Cambridge: Cambridge University Press.
2..UNU-IHDP and UNEP (2012). Inclusive Wealth Report 2014. Measuring progress toward sustainability. Cambridge: Cambridge University Press

Say that again, FRACKING ?

FRACKING  and Shale gas are  going to be increasingly in the News from now on. Shale is already present in the Oxford dictionary, but FRACKING  is yet to gain reputation to be admitted into the elite club.   In any case Fracking has gained popularity and assumed global importance because  that is how we  mine natural gas from shale deposits.   Obama has already declared that for the next 100 years America doesn't have to worry because "we have an abundance of natural gas". It is estimated that by 2040, about 50% of America's natural gas will be from Shale. 

  

Shale Gas Mining- Courtsey Wikipedia

Naturally then one asks  what is Shale?   It is a slate-like mineral deposit of limestone rich in sulfides  and carbonates of iron. Geologists call it Marcellus shale  (Utica or Upper Devonian shale also belong to this family).  These mineral deposits    hold large quantities of natural gas,in their pores and crevices.  in other words, natural gas is entrapped in  shale rock. It is not easy to pump out the gas. One needs to dig more than a kilometer  to reach the shale structure, and then  the structure tends to crack horizontally into layers making drilling difficult. Hydraulic  fracturing is  a specialized technique which uses a pressurized liquid to crack open the rock horizontally. A variety of fracturing liquids and gels  to suit the chemistry of the  rock type are used. Fracking is  an easier and more popular term  for hydraulic fracturing. Shale gas mining involves two steps:  first  step is to  drill straight down to reach the shale structure and then  drill  horizontally,  to take advantage of the layered structure of shale. One end of the well is sealed off and water (or any other fluid) is pumped under very high pressure to fracture the  rock.  This allows the interconnection of crevices spread over a large area. The gas is then mined out. 

In the US  West Virginia, Pennsylvania, New York, Texas, Arkansas  have already highly developed shale plays, (Plays mean fields). These plays collectively   " now supplies 385 million cubic metres of gas per day, more than  enough to supply half of the gas currently burned in US power plants.   And the US Energy Information Administration appears very confident  in its Annual Energy Outlook 2014.  The dream of cheap and abundant energy could soon come true. But as always there are skeptics. In a recent article in Nature says this could be just a wishful thinking. However  US dept. of Energy was quick to respond and allay the misgivings. 

Will shale gas remain a pipe dream? Let us wait and watch. 

References:

1. Hydrolic Fracturing 

2. The Gas Surge : Science 27 June 2014 (vo.344, Issue 6191, page 1464-1475

3. The Fracking Fallacy - M.Inman, Nature 4 Dec. 2014 (Vol.516, page 28-30)

4. US Dept. of Energy Responds

. 

On how plants keep Time.

Sun is THE MASTER CLOCK  for all  earthly beings, no doubt about that. (Of course having a clock and being punctual are two entirely different stories, we won't get into that now). We take a brief look at how living beings carry out their cellular functions punctually.  Mammals have a built-in super synchronizer  suprachiasmatic nucleus, (SCN) which coordinates and maintains a standard time for all cellular functions and set in motion the circadian rhythm. How do plants keep time? They directly receive their daily bread (via photosynsthesis) from the sun. But  apart from that   plants also have  short term and long term ( daily and seasonal ) rhythms. Some  flowers bloom with the early rays of Sun while others are literally  late bloomers; there are even those which spread their fragrance exclusively during the night. Mangoes and litchies arrive only in summer, while ripe oranges flood the markets  winter . So the question is do plants have a synchronizer? Or in other words, what is the SCN equivalent  in plants.?  Till now the general assumption has been that plants do have several built in  clocks but they all keep their own local time and are not exactly   synchronized. Sounds  a bit chaotic, but then there were no evidence to prove otherwise. And without proof scientists don't take decide one way or the other. 

20th November issue of Nature carries an interesting report by Endo et al  on the circadian clocks operative in plants. Endo and team proceeded to take a closer look at the  plant Arabidopsis thaliana. With a  short life span and  a  small genome (135mbp), arabidopsis thaliana is roughly  the vegetarian  equivalent of the guinea pig  in the lab. 
  

Endo et al sought answers at  molecular and genetic level on the circadian rhythms in arabidopsis thaliana.   The team  separately analysed three main cell lines in the leaf:  the epidermal cells on the surface ,  the   mesophyll cells underneath , which run  the photosynthesis factory and then the   vasculature cells  responsible for the plumbing system. This is important because, even when the solar factory is closed for the day, the plumbing system continues to do the logistics work  Endo and team  monitored the gene expression and  level of specific marker proteins  in vivo and also   in vitro for  these three types of tissues. It was  found that the mesophyll and vasculature clocks function independently but are not altogether uncoupled. Plants have two loops of cellular activity, the day loop and the night loop. The genes responsible for rhythmic behaviour in the mesophyll tissue are active during day time and those in the vasculature  tissues  report for duty during the evening hours. The day partollers must be leaving telltale signs for the night patrollers. The team also found that the vasculature clock has the upper hand and controls the physiological responses of the  plant as a whole. They suggest that the vasculature and mesophyll clocks are akin to the central and peripheral clocks in mammals  or evening and morning cells in drosophila
Tailpiece  
Acharya Jagadish Chandra Bose was one of the first to suggest  that plants have life and that they responded to various stimuli including light and dark cycles through  electrical impulses. In 1902  Bose compiled his  experiments, observations and conclusions   and published   Response in the living and non-living . This book  (currently  available  an e-book  in public domain, thanks to the Project Gutenberg),  carries complete details of the simple,  elegant and extensive  studies.

 References:

1. Response in the Living and the non-Living : J.C. Bose
2. Time specific clocks in Arabidopsis show assymmetric coupling.  Endo et al Nature,       20th Nov. 2014 p419-422.
3. Spontaneous spaciotemporal waves of gene expression from biological clocks in the leaf : Wenden B et al  Proc. Natl. Acad. Sci.(USA),109, 6757-6762 (2012)
4. The circadian clock in Arabidopsis is a simplified slave version of the clock in shoots.James, A.B. et al  Science 322, 1832-1835(2008)

Science and the Society : The TWAS-Lenovo Science Prize 2014

Sultanate of Oman hosted the 25th  annual meeting of The World Academy of Sciences (TWAS) at the capital city of Muscat from 26 till 28th of October. The venue was  one of the most scenic locations of Muscat, the Barr Al Jissa resort. 

 Quarraisha Abdool Karim 

This year, epidemiologist  Dr Quarraisha  Abdool Karim  was awarded   the  most prestigious TWAS-Lenovo Science Prize  for her relentless work in the area of HIV/AIDS prevention. Her research work  which  has few parrallels in terms of the socio-medical strategies and human impact has  helped set guidelines for patients infected with HIV  and doctors treating them.  It was in 1989 that Ms Karim joined  Aids Research Program of South African Medical Research Council' after obtaining a post graduate degree in Public Health  from Columbia University, USA. She soon realized that sociology is an integral part of epidemiology. She says "AIDS brought together two separate things for me; I saw the convergence between advocacy work and science ". The  extensive surveys she conducted in sub-Saharan Africa  brought to light not only the alarming statistics  but also  the plight of helpless and ignorant  adolescent girls    in a male dominated society.  Public health data showed that in South Africa alone an estimated 6.1 million people suffer from HIV infection, more than any other nation in the world. Women who are younger than 24 years are at  a greater risk than men in the same age group. Could there be a way to protect the women from HIV infection that didn't call for cooperation from their male partners? That is the question Karim and her team asked aloud. 

Tenofovir :courtsey Wikipedia

The team took a relook at   tenofovir an antiretroviral   drug used in HIV treatment   and developed it into a topical gel to be applied to genital areas.  In a study  spread over 3 years,  Karim and her team demonstrated that application of 1% tenofovir  gel  reduced infection in women by ~40%.   Follow up studies and mathematical modelling have indicated that tenofovir gel has the potential to  prevent millions of new infections. Currently  the gel is undergoing rigorous clinical trials. By the end of  2015  it would  move into licensing, manufacturing and distribution stage. 

Dr Karim is an associate professor of epidemiology at the Columbia University medical Center  and associate director of CAPRISA ( short for Centre for the AIDS program Research in South Africa).  The TWAS-Lenovo prize comes with a an award of 100,000 US$ provided by Lenovo.

Tailpiece: 

TWAS delegates were pleasantly surprised to  receive  a small (4cm long) Omani Khanjar  as memento . While fiddling with it,  it suddenly unleashed  a pendrive!

References: 

• Qurraisha Abdool Karim wins TWAS-Lenovo Prize 
• Globalization, Ethics, and AIDS Vaccines  Salim S. Abdool Karim-Science 23 June 2000: 2129

• Simon V, Ho DD, Abdool Karim Q HIV/AIDS epidemiology, pathogenesis, prevention, and treatment Lancet. 368 489-504 2006
• Woodsong C, Abdool Karim Q    A model to enhance informed consent: experiences from the HIV Prevention Trials Network American Journal of Public Health 95 412-419 2005
• Q.A Karim et al Effeciveness and Tenofovir Gel an antiretroviral microbicide for the prevention of HIV infection in Women Science 3 September 2010:1168-1174