Science – Page 2 – Metastable

US court settles bitter gene editing patent case

Posted on September 12, 2018 by newyesterday

On September 10, a US court settled an increasingly churlish patent dispute between two research institutions in the country, the University of California (UC) in Berkeley and the Broad Institute, Massachusetts, with great consequence for the commercial use of a powerful gene-editing technology called CRISPR-Cas9.

The dispute centred on CRISPR’s usability in two different kinds of biological lifeforms: prokaryotes and eukaryotes. UC had devised a way to edit the genetic makeup of prokaryotes using CRISPR in 2014. Broad followed a year later with a method to use CRISPR in eukaryotes. UC had subsequently contested the patentability of Broad’s method saying that it was a derivative of UC’s method and couldn’t be patented separately.

The court as well as the US patent office have disagreed and upheld Broad’s patent.

The following FAQ breaks the case down to its nuclear components and assesses the verdict’s implications and future courses of action.

What are CRISPR and CRISPR-Cas9?

CRISPR is a natural defensive mechanism that prokaryotes use to protect themselves against viruses. Prokaryotes are smaller, less complex lifeforms and include bacteria and archaea: they are unicellular, the cells lack a membrane as well as membrane-bound organelles. The bigger lifeforms are classified as eukaryotes, which are multicellular, whose cells have a membrane and the cells also contain membrane-bound organelles. Because of these and other differences (see here, p. 8), it wasn’t clear if a CRISPR system built for use in prokaryotes could be adapted by a person of reasonable skill for use in eukaryotes with a reasonable chance of success. This distinction is at the heart of the patents dispute.

CRISPR-Cas9 is essentially a technology that combines CRISPR with a protein called Cas9 to form a molecular tool. This tool can swim to a eukaryote’s DNA, pick out a specific section of the genes and snip it at both ends, removing it from the DNA sequence. Once the section is out, the DNA strand repairs itself to restore the genes. If the original section of genes was faulty (e.g. containing an undesirable mutation), then CRISPR-Cas9 can be used to remove it from the DNA and force the DNA strand to repair itself to a healthier version.

Researchers have already reported that they are close to using this technology to treat a debilitating condition called Duchenne muscular dystrophy.

Of course, there are other gene-editing technologies, including zing-finger nucleases and transcription activator-like effector nucleases, but CRISPR-Cas9 has proved to be more efficient, effective and easier to use. At the same time, a few concerns are starting to emergeabout unintended side-effects.

What was the case timeline?

The UC team, led by Jennifer Doudna, published a paper in August 2012 describing how an RNA-based system called CRISPR-Cas9 could be used to edit DNA in prokaryotic cells. Editing DNA is a lucrative prospect – then and now – because it allows us in theory to modify the fundamental constitution of biological life, curing debilitating illnesses as much as modifying crops. And what the UC team had found, together with Emmanuelle Charpentier, then of the University of Umea in Sweden, was the first tool that could achieve this. After their paper was published, the UC team filed a patent with the US Patent and Trademarks Office (USPTO) for the use of CRISPR in prokaryotes.

While UC’s patent was pending, a team led by Feng Zhang from the Broad Institute, setup by the Massachusetts Institute of Technology and Harvard University, Boston, published a paper in 2013 and then built a CRISPR system in 2014 that could work in eukaryotes. Zhang and co. then filed for an expedited patent that was granted in 2017. At this point, UC complained to the USPTO that the Broad patent infringed on its own – that, effectively, Zhang et al’s work was not patentably distinct from Doudna et al’s work. UC’s own patent for CRISPR use in prokaryotes was granted in early 2018.

In late 2017, the Patent Trial and Appeal Board (PTAB) of the USPTO upheld the Broad patent, effectively stating that the DNA-editing technologies used in prokaryotes and eukaryotes were “patentably distinct”. Specifically, it had ruled that there was no interference-in-fact, i.e. that UC’s general description of use of CRISPR in biological systems could not have anticipated, under reasonable circumstances, Broad’s more specific CRISPR invention for use in eukaryotes. An interference-in-fact check is pegged on a so called ‘obviousness review’. A 1966 SCOTUS case defines four factors using which it can be undertaken:

(1) the scope and content of the prior art; (2) the differences between the claims and the prior art; (3) the level of ordinary skill in the art; and (4) objective considerations of non-obviousness

UC decided to appeal the PTAB’s verdict with the US Court of Appeals of the Federal Circuit (CAFC). The latter came to its decision on September 10, ruling in favour of the USPTO and upholding the Broad patent.

What happens next?

A lot of things. Let’s classify them as financial, academic, legal and administrative.

Financial – Where there’s a patent, there’s money. However, there’s more money for Broad than for UC because almost all application of the CRISPR technology will happen in eukaryotes, a domain that includes humans and plants. And because the Broad patent has been upheld, this effectively means the UC patent can apply only to prokaryotes and not to eukaryotes.

Public attitudes to this affirmation were partly reflected in the share values of three companies intent on commercialising CRISPR tech: Crispr Therapeutics AG (cofounded by Charpentier) and Intellia Therapeutics have licenses with UC and their shares fell by 5.3% and 2.5% respectively; Editas Medicine Inc., which has licenses with Broad, climbed by 6.8%.

A review in 2017 stated that although “CRISPR IP ownership is claimed by at least seven different parties”, the Broad patent could be a “blocking patent” because of its ancestral nature. This is one reason why the Broad Institute has already issued 13 licenses, more than any of the other patent-holders. In all, the review estimated that the American gene-editing industry will be worth $3.5 billion by 2019, with CRISPR propelling biotechnology to the status of “second highest funded sector in the United States”.

Academic – The contest between UC and Broad has only worsened the mutual, and deleterious, embitterment between the institutions. In 2015, Broad launched an acrimonious campaign to turn public opinion in its favour, which included attempts to rewrite the history of DNA-editing research and present Zhang’s achievement in stronger light. The possibly most damaging thing Broad did was to quote UC’s Doudna herself as having expressed frustration and doubt about whether a CRISPR system for use in bacteria could be adapted for use in eukaryotic cells.

These quotes were used in Broad’s filings for the patent dispute, undermining UC’s case. However, scientists have argued that science is almost never free of frustration and that Doudna was also right to express doubt because that’s what any good scientist would do: lead with the uncertainty until something to the contrary could be demonstrated. However, Broad effectively penalised Doudna for being a good scientist – an action that Michael Eisen, a biologist in Doudna’s department at UC, has said is rooted in universities being able to profit from patents created with taxpayer dollars.

Legal – It’s important to recognise what UC has actually lost here. UC appealed the PTAB verdict, bringing it to the CAFC, who in turn ruled that the PTAB had not wronged in its conclusion. The judge did not reevaluate the evidence and did not hear arguments from the two parties; no new evidence was presented. The court only affirmed that UC, in the eyes of the law, did not have grounds to contend the PTAB verdict. A salient portion from the judgment follows, where the judge writes that some parts of the CRISPR/Cas9 system as used in prokaryotes could have been adapted for use in eukaryotes but that that’s besides the point (emphasis added):

UC expended substantial time and effort to convince this court that substantial evidence supports the view it would like us to adopt, namely, that a person of ordinary skill would have had a reasonable expectation of success in implementing the CRISPR-Cas9 system in eukaryotes. There is certainly evidence in the record that could support this position. The prior art contained a number of techniques that had been used for adapting prokaryotic systems for use in eukaryotic cells, obstacles adopting other prokaryotic systems had been overcome, and Dr. Carroll suggested using those techniques to implement CRISPR-Cas9 in eukaryotes. We are, however, an appellate body. We do not reweigh the evidence. It is not our role to ask whether substantial evidence supports fact-findings not made by the Board, but instead whether such evidence supports the findings that were in fact made. Here, we conclude that it does.

Therefore, this is a judgment of the law, not a judgment of the science.

According to Jacob Sherkow, a professor at the New York Law School, UC can either petition the CAFC for a rehearing or appeal to the Supreme Court. Sherkow added that neither strategy is likely to work because he doesn’t think “this case presents any *novel* legal issues” (emphasis in the original). This means UC will likely return to the patent office and attempt to “salvage what they can from their patent application”.

There is also another problem. To quote Chemical and Engineering News,

… it recently became clear that another CRISPR scientist, Virginijus Šikšnys of Vilnius University [Lithuania], filed a patent for CRISPR/Cas9 just weeks before UC Berkeley filed its patent in 2012. While UC Berkeley and Broad were entangled in their dispute, the Šikšnys patent was approved and made public, meaning that USPTO can now hold the Šikšnys patent against UC Berkeley. “That has the potential to sink whatever is left from Berkeley’s patent application,” Sherkow says.

Administrative – This part is confusing. In the US, the USPTO upheld the Broad patent in February 2017. But in Europe, the European Patent Office (EPO) ruled in favour of Doudna and Charpentier in March 2017. So depending on the jurisdiction, companies that want to commercialise CRISPR technology (for eukaryotes) will have to work with UC in Europe and the Broad Institute in the US. At least one company, DowDuPont, which is using CRISPR to engineer corn and soybean crops to be cultivable without pesticides, has purchased licenses with both institutions.

The different judgments arise from one difference in how the EPO and the USPTO evaluate ‘no interference-in-fact’. According to a May 2017 report by Sherkow, “In Europe, one is entitled to a broad patent on a new technique, if it demonstrates an ‘inventive step’ over prior methods, even if there [is] no guarantee that it will work for all of its claimed applications.” In the US, on the other hand, each “claimed application” has to be demonstrated and is separately patentable if one application doesn’t follow obviously from the previous. The EPO decision is open to challenge and Broad is likely to use the opportunity to do so.

By the way, the country with the second-most patents related to CRISPR is China, after the US. Chinese research institutions and industry players have been focusing mostly on knockout mechanisms of CRISPR, which control how undesirable genes in a DNA sequence are removed. To quote at length from the 2017 review,

The Chinese government has been actively involved in gene-editing funding. The National Natural Science Foundation of China (NNSF), invested $3.5 million in over 40 CRISPR projects during 2015. Through the NNSF and the National Basic Research Program, the Chinese government has funded the first use of CRISPR for the modification of human embryos. Additionally, Shenzhen Jinjia Color Printing Group Co., a public company, has pledged $0.5 million to fund Sun Yat-sen University for studying CRISPR in embryos.

What do scientists say?

Scientists’ reactions are still coming in, although no consensus is likely to emerge soon. In the meantime, awards make for a reasonable proxy to determine what scientists think is laudable. On this count, Doudna and Charpentier are clear leaders. Since 2014, Doudna has won 20 awards (excluding one from UNESCO), Charpentier has won dozens and Zhang, nine (although must be noted that Doudna and Charpentier have been scientists for longer than Zhang has). Doudna, Charpentier and Šikšnys were also jointly awarded the 2018 Kavli Prize in Nanoscience.

The Wire
September 11, 2018

Science

Criticism of ISRO

Posted on September 10, 2018 by newyesterday

The Statesman‘s editorial on India’s human spaceflight programme ends with the following line:

Only after placing the seventh and the last satellite in the NavIC system costing Rs 1,400 crore did ISRO realise the atomic clocks in the satellites had become dysfunctional, rendering the fleet a dud.

This line is wrong.

ISRO could not have realised some satellites in the constellation were having issues with their atomic clocks any earlier, so the ‘only’ is misplaced
Only two satellites out of seven were having issues with their clocks, and ISRO has made efforts to replace them.
The fleet was rendered unusable but that may not be fair to say given it was temporary. The dysfunctional instruments have been replaced and the constellation currently awaits operationalisation.

There may have been other issues with the IRNSS but the last line in the editorial wasn’t it.

Another example: many people are of the impression that Narendra Modi’s announcement on August 15, that India will launch a human into space by 2022, caught ISRO chairman K. Sivan by surprise. This is true – but it was only the announcement that caught Sivan by surprise, not the ambition itself. ISRO has been preparing for human spaceflight for over a decade now. It is certainly not the sort of ambition that can be prepared for and achieved in four years.

However, NewsBytes said:

Commenting on Modi’s announcement, ISRO chief K Sivan had then said, “It came as a big surprise to us.” Yet, the question is, should it have come as a big surprise to ISRO? Logic says no. ISRO, being the agency responsible for all of India’s space missions, should ideally have been consulted before lofty promises were made. But, Modi went ahead with it anyway. Given the lack of notice, ISRO is now engaged in frantic attempts to recruit astronauts, improve existing technology, and develop new technology to meet the deadline set by Modi.

I’m glad more newspersons are writing critically of ISRO. But space is a sector where there’s very little low-hanging fruit that can be plucked and juiced into a political analysis, so there’s a lot more work required to separate a critique of ISRO from chest-thumping and render the former meaningful.

Random thought: Facts can be assimilated into a bundle and bundles lend themselves to interpretation. Now, there’s bound to be a correlation between between the facts-to-interpretations (F-I) ratio and the correctness of news coverage. The larger the F-I ratio is, the more likely it is going to be find more small mistakes in multiple news reports (i.e. on the topic of those facts) and big mistakes in a few – i.e. bigger range. On the other hand, the smaller the F-I ratio is, there are likely to be fewer smaller as well as bigger mistakes – i.e. smaller range. Now, by comparing these two ranges across press coverage of a variety of technical subjects where quantitative answers are common (e.g. in physics but not in sociology), and using normalised values of F-I if necessary, would it be possible to elicit the relative strengths and weaknesses of the mainstream media among those subjects?

Featured image credit: Oleg Laptev/Unsplash.

Science

How do you determine the naturalness of homosexuality?

Posted on September 7, 2018 by newyesterday

“Homosexual carnal intercourse between two consenting adults” is legal in India now. It wasn’t for lack of reason or scientific data that the item of legislation that rendered sodomy illegal – Section 377 – had been retained for so long. Instead, it was more a question of whether sodomy offended public decency and morality. On September 6, the Supreme Court of India said no consensual sexual act between adults, whether of the same gender or otherwise, could be considered illegal or offensive to public decency or morality.

The US had this moment in 2003, but there, science did play a role. In the landmark case Lawrence v. Texas, the Supreme Court of the US was able to rule that homosexuality was not a sin against nature on the back of a growing body of evidence that homosexuality exists in nature. More broadly, science helped determine the construction of sexuality in human and non-human species and rescued it from the chokehold of religious ideals and the stigma it carried. CJI Dipak Misra and Justice A.M. Khanwilkar may not have laboured through the scientific evidence in their own judgment but the veins of rationalism are evident in their syntax. Consider this excerpt (from the full; emphasis added):

What nature gives is natural. That is called nature within. Thus, that part of the personality of a person has to be respected and not despised or looked down upon. The said inherent nature and the associated natural impulses in that regard are to be accepted. Non-acceptance of it by any societal norm or notion and punishment by law on some obsolete idea and idealism affects the kernel of the identity of an individual. Destruction of individual identity would tantamount to crushing of intrinsic dignity that cumulatively encapsulates the values of privacy, choice, freedom of speech and other expressions. It can be viewed from another angle. An individual in exercise of his choice may feel that he/she should be left alone but no one, and we mean, no one, should impose solitude on him/her.

From another part of the same judgment:

It is submitted on behalf of the petitioners and the intervenors that homosexuality, bisexuality and other sexual orientations are equally natural and reflective of expression of choice and inclination founded on consent of two persons who are eligible in law to express such consent and it is neither a physical nor a mental illness, rather they are natural variations of expression and free thinking process and to make it a criminal offence is offensive of the well established principles pertaining to individual dignity and decisional autonomy inherent in the personality of a person, a great discomfort to gender identity, destruction of the right to privacy which is a pivotal facet of Article 21 of the Constitution, unpalatable to the highly cherished idea of freedom and a trauma to the conception of expression of biological desire which revolves around the pattern of mosaic of true manifestation of identity. That apart, the phrase ‘order of nature’ is limited to the procreative concept that may have been conceived as natural by a systemic conservative approach and such limitations do not really take note of inborn traits or developed orientations or, for that matter, consensual acts which relate to responses to series of free exercise of assertions of one‘s bodily autonomy. … It is urged that the American Psychological Association has opined that sexual orientation is a natural condition and attraction towards the same sex or opposite sex are both naturally equal, the only difference being that the same sex attraction arises in far lesser numbers.

Many of these arguments hinge on what it means to be natural. But what is nature, and what is naturalness*? The Wikipedia article on homosexual behaviour among animals carries an instructive line in this regard, and vis-a-vis the tenet of peccatum contra naturam (Latin for “sin against nature”): “The observation of homosexual behaviour in animals can be seen as both an argument for and against the acceptance of homosexuality in humans.” It’s ‘for’ because if animals do it, then it’s natural; it’s ‘against’ because humans are not meant to be like other animals. It’s a ridiculous position to be in. I find a quote originally about economics to be useful here:

… if background conditions determine, in a way which in principle falls outside a theory, what counts as the events over which the theory ranges, the theory is at the mercy of changes in these conditions which at any moment can undermine the predictive power of the theory.

The philosopher Richard Norman had intended to develop a theory that could predict how much, rather what kind of, resistance certain technologies would meet from certain cultures based on what traditions each technology appeared to offend. He succeeded in that he was able to explain why some cultures struggled, and continue to struggle, with the acceptability of technologies like vitro fertilisation and contraception, and what the latter might have in common with homosexuality. He pegged it on background conditions. Russell Blackford, a philosopher at the University of Newcastle, Australia, summarised Norman’s thesis thus in a 2006 review (emphasis added)

According to Norman’s approach, anything that may threaten a culture’s basic assumptions about how ordinary human life works – especially assumptions about sex and its relationship with conception and birth, the development and rearing of children, the roles of men and women, the processes of ageing and death – is likely be disquieting to at least some people. For example, homosexual practices may seem to threaten a background condition that relates to sex and procreation. If there are recognised choices that include sexual acts with no possibility of pregnancy, then one of the background conditions has been lost.

Blackford writes in another part of the review (emphasis added):

Norman argues that the discomfort that some people feel about IVF and futuristic prospects such as that of biological immortality comes from a sense that important background conditions to choice – relating to procreation and death – are threatened. In this context, a “threat” to the background conditions seems to mean that certain conditions may no longer pertain. A sense that some background conditions are under threat can be expressed as a claim that nature is being interfered with. When such claims are made, nature is being equated with the background conditions recognised within the culture concerned. Norman, however, defends IVF on the basis that incremental changes to our own culture’s background conditions can be absorbed into our thinking.

However, given that the Bharatiya Janata Party has refused to issue a statement on the historic SC verdict, signalling its moral ambiguity (at the very least) on the subject, it seems unlikely that the party’s members – i.e. the country’s ministers – will be open to making incremental changes in their worldview to accommodate the naturalisation of “unnatural” sexual acts, so to speak.

*Not to be confused with the naturalness of particle physics, or maybe it is.

The Wire
September 7, 2018

Featured image credit: gagnonm1993/pixabay.

Science

Satire: Ducks in water could increase oxygen content

Posted on August 28, 2018 by newyesterday

According to Biplab Deb, the chief minister of Tripura, the oxygen content of water will increase if ducks swim in it. [Satire begins here] This is a sensational new discovery that has drastic implications for Earth’s future. The lawmaker’s thinking suggests it might have something to do with duck-farts.

There are thousands of water bodies around the world where masses of ducks have been swimming for tens of millions of years, and which could now be flush with oxygen. As a result, our planet now appears to be due for major bio-ecological changes as the abundance of oxygen is likely to spur cascading evolutionary effects.

In fact, it is being speculated that, in the aftermath of Deb’s confirmation, the sixth extinction of the Anthropocene epoch might just be halted in its tracks and forced to do a volte face; all it will take is lots of ducks. This might explain why oil companies in Texas are confident that their proposal to have the government erect a $12-billion ‘sea wall’ to protect their coastal facilities against rising water levels will be taken seriously.

At the same time, there also appears to be growing public resentment against scientists, with people wondering whether supposed researchers spending tax dollars might have kept this simple solution away from governments in an effort to maintain their self-importance. Major news publications like OneOp are reporting that this could be an urban naxal conspiracy and that a concerned ministry is expected to conduct raids soon. IndiaIndiaIndia reported that there’s a joke somewhere in here about going quack.

According to Indian Express, it appears Deb had also discovered that the ducks would recycle the oxygen in the water and prevent its molecules from going to waste. Thankfully for the minister as well as for the rest of us, oxygen molecules don’t affect the pH value of water, or we would also be confronted with a major acidity/salinity catastrophe. In all, it’s good news for everyone, including the people who will supply the 50,000 ducklings Deb says he will distribute among Tripura’s fisherfolk.

A senior scientist who didn’t wish to be named expressed surprise at the finding, and said he had applied for a grant to study the molecular chemistry of duck-farts. “I expect to hear back in five years,” he said. The same individual also expressed regret later. “We all had a chance to find this out before but we did not. It’s because we didn’t study the Vedas as thoroughly as we should have. Hopefully we will learn from this mistake. Om.”

NPMC

Featured image credit: Ryk Naves/Unsplash.

Science, Uncategorized

Absolute hot

Posted on August 25, 2018 by newyesterday

There’s only one absolute zero but there are multiple absolute ‘hots’, depending on the temperature at which various theories of physics break down. This is an interesting conception because, while absolute zero is very well-defined and perfectly understood, absolute hot simply stands for the exact opposite not in a physical sense but in an epistemological one: it is the temperature at which the object of study resembles something not understood at all. According to the short Wikipedia article on it, there are two well-known absolute hots:

Planck temperature – when the force of gravity becomes as strong as the other fundamental forces, leading to a system describable only by theories of quantum gravity, which don’t exist yet
Hagedorn temperature – when the system’s energy becomes so large that instead of heating up further, it begins to produce hadrons (particles made up of quarks and gluons, like protons and neutrons) or turns into a quark-gluon plasma

Over drinks yesterday with the physicist known as The Soufflé, he provided the example of a black hole. Thermodynamics stipulates that there is an upper limit to the amount of energy that can be packed into a given volume of space-time. So if you keep heating this volume even after it has breached its energy threshold, then it will transform into a black hole (by the rules of general relativity). For this system, its absolute hot will have been reached, and from the epistemological point of view, we don’t know the microscopic structure of black holes. So there.

However, it seems not all physical systems behave this way, i.e. become something unrecognisable beyond their absolute hot temperature. Quantum thermodynamics describes such systems as having negative temperatures on the kelvin scale. You are probably thinking it is simply colder than absolute zero – a forbidden state in classical thermodynamics – but this is not it. There seems to be a paradox here but it is more a cognitive illusion. That is, the paradox comes undone when you acknowledge the difference between energy and entropy.

The energy of a system is the theoretically maximum capacity it has to perform work. The entropy of the system is the amount of energy that cannot be used to do work, also interpreted as a degree of disorderliness. When a ‘conventional’ system is heated, its energy and entropy both increase. In a system with negative temperature, heating increases its energy while bringing its entropy down. In other words, a system with negative temperature becomes more energetic as well as is able to dedicate a larger fraction of that energy towards work at highertemperatures.

Such a system is believed to exist only when it can access quantum phenomena. More fundamentally, such a system is possible only if the number of high energy states it has are limited. In classical systems, which is anything that you can observe in your daily life, such as a pot of tea, objects can be heated as high a temperature as needed. But in the quantum realm, akin to what classical thermodynamics says about the birth of black holes – that its energy density became so high that space-time wrapped around the system – systems of elementary particles are often allowed to have possess only certain energies. As a result, even if the system is heated beyond its absolute hot, its energy can’t change, or at least there will be nothing to show for it.

While it was a monumentally drab subject in college, thermodynamics – as I have learnt since – can be endlessly fascinating the same way, say, the study of financial instruments can illuminate the pulse of capitalism. This is because thermodynamics – as in the study of heat, energy and entropy – encapsulates the physical pulse of the natural universe. You simply need to go where its laws take you to piece together many things about reality.

Of course, a thermodynamic view of the world may not always be the most useful way to study it. At the same time, there will almost always be a way to translate some theory of the world into thermodynamic equivalents. In that sense, the laws and rules of thermodynamics allow its practitioners to speak a kind of universal language the way Douglas Adams’s Babel fish does.

The most famous example of this in the popular conception of scientific research is the work of Stephen Hawking. Together with Jacob Bekenstein and others, Hawking used thermodynamic calculations to show (on paper) that black holes were mortal and in fact emitted radiation out into the universe, instead of sucking everything in. He also found that the total entropy contained inside a black hole – its overall disorderliness – was closely related to its surface area. This was in the 1970s, but the idea that there are opportunities to understand the insides of a black hole by studying its outsides is as profound today as it was then.

Science

'Weak charge' measurement holds up SM prediction

Posted on May 17, 2018 by newyesterday

Various dark matter detectors around the world, massive particle accelerators and colliders, powerful telescopes on the ground and in space all have their distinct agendas but ultimately what unites them is humankind’s quest to understand what the hell this universe is on about. There are unanswered questions in every branch of scientific endeavour that will keep us busy for millennia to come.

Among them, physics seems to be sufferingly uniquely, as it stumbles even as we speak through a ‘nightmare scenario’: the most sensitive measurements we have made of the physical reality around us, at the largest and smallest scales, don’t agree with what physicists have been able to work out on paper. Something’s gotta give – but scientists don’t know where or how they will find their answers.

The Qweak experiment at the Jefferson Lab, Virginia, is one of scores of experiments around the world trying to find a way out of the nightmare scenario. And Qweak is doing that by studying how the rate at which electrons scatter off a proton is affected by the electrons’ polarisation (a.k.a. spin polarisation: whether the spin of each electron is “left” or “right”).

Unlike instruments like the Large Hadron Collider, which are very big, operate at much higher energies, are expensive and are used to look for new particles hiding in spacetime, Qweak and others like it make ultra-precise measurements of known values, in effect studying the effects of particles both known and unknown on natural phenomena.

And if these experiments are able to find that these values deviate at some level from that predicted by the theory, physicists will have the break they’re looking for. For example, if Qweak is the one to break new ground, then physicists will have reason to suspect that the two nuclear forces of nature, simply called strong and weak, hold some secrets.

However, Qweak’s latest – and possibly its last – results don’t break new ground. In fact, they assert that the current theory of particle physics is correct, the same theory that physicists are trying to break free of.

Most of us are familiar with protons and electrons: they’re subatomic particles, carry positive and negative charges resp., and are the stuff of one chapter of high-school physics. What students of science find out quite later is that electrons are fundamental particles – they’re not made up of smaller particles – but protons are not. Protons are made up of quarks and gluons.

Interactions between electrons and quarks/gluons is mediated by two fundamental forces: the electromagnetic and the weak nuclear. The electromagnetic force is much stronger than the aptly named weak nuclear force. On the other hand, it is agnostic to the electron’s polarisation while the weak nuclear force is sensitive to it. In fact, the weak nuclear force is known to respond differently to left- and right-handed particles.

When electrons are bombarded at protons, the electrons are scattered off. Scientists at measure how often this happens and at what angle, together with the electrons’ polarisation – and try to find correlations between the two sets of data.

An illustration showing the expected outcomes when left- and right-handed electrons, visualised as mirror-images of each other, scatter off of a proton. Credit: doi:10.1038/s41586-018-0096-0

At Qweak, the electrons were accelerated to 1.16 GeV and bombarded at a tank of liquid hydrogen. A detector positioned near the tank picked up on electrons scattered at angles between 5.8º and 11.6º. By finely tuning different aspects of this setup, the scientists were able to up the measurement precision to 10 parts per billion.

For example, they were able to achieve a detection rate of 7 billion per second, a target luminosity of 1.7 x 10³⁹ cm^-2 s^-1 and provide a polarised beam of electrons at 180 µA – all considered high for an experiment of this kind.

The scientists were looking for patterns in the detector data that would tell them something about the proton’s weak charge: the strength with which it interacts with electrons via the weak nuclear force. (Its notation is Q_weak, hence the experiment’s name.)

At Qweak, they’re doing this by studying how the electrons are scattered versus their polarisation. The Standard Model (SM) of particle physics, the theory that physicists work with to understand the behaviour of elementary particles, predicts that the number of left- and right-handed electrons scattered should differ by one for every 10 million interactions. If this number is found to be bigger or smaller than usual when measured in the wild, then the Standard Model will be in trouble – much to physicists’ delight.

SM’s corresponding value for the proton’s weak charge is 0.0708. At Qweak, the value was measured to be 0.0719 ± 0.0045, i.e. between 0.0674 and 0.0764, completely agreeing with the SM prediction. Something’s gotta give – but it’s not going to be the proton’s weak charge for now.

Paper: Precision measurement of the weak charge of the proton

Featured image credit: Pexels/Unsplash.

Phone on a plane. Credit: Javier Cañada/Unsplash

Science

Myth of harmful cell phone radiation is good business for IndiGo

Posted on May 10, 2018 by newyesterday

When I fly, I always fly IndiGo. They’re not perfect but they and their services have become familiar, from their website (where I book my tickets) to when I exit the airport at my destination. The efficiency with which the IndiGo staff works – rather the economy of processes they follow – has seemed well thought-out. (For example, the air hostesses are sweet but the pilot also chips in over the intercom, keeping passengers updated about how high and fast they’re flying, etc.).

On my most recently flight, however, this facade of sanity was disturbed when I saw the following advertisement in their in-flight magazine:

You can see how that’d have gotten my goat. Indio strives to offer a highly optimised journey for the domestic traveller – including a healthy dose of pseudoscience. The funny thing is that the handheld extension plugged into the mobile phone has an electrical and electronic architecture similar to the one working inside the phone; the only difference is the absence of a signal receiver and emitter. It then follows that whatever radiation one is alleging the phone is serving as a hub of is all around us: if your phone is not on a call right now, some other phone in your vicinity surely is.

Cell phone radiation is not harmful because it is not ionising radiation. It’s that simple. Only ionising radiation can harm the body. It’s okay to want to protect yourself from threats but to believe your mobile phone is giving your head or your genitals cancer is stupid. On top of this, the product being advertised – aptly called the Phoni3 – promises to cut out 95% of the nonexistent harmful radiation. *facepalm* This is consumerism at the peak of its sway.

In fact, I’m curious why neither the makers of Phoni3 nor IndiGo saw fit to speak about background radiation. Did you know that the radiation your body is exposed to in the course of a six-hour flight is 444-times higher than the dose it receives if you live within 80 km of a nuclear power plant for a year? The reason we don’t panic is because even this elevated dose poses no danger to the human body. And the reason we don’t see an advertisement for lead-lined jackets or portable Faraday cages to wear/carry during air travel in the in-flight magazine is because it will be bad for business.

But anything short of hurting IndiGo can pass go. To wit, the following message is at the bottom of the same page containing the phone Phoni ad:

The government should ban advertisements for such products if only because, in this specific case, the Telecom Regulatory Authority of India (TRAI) has been working to dispel beliefs that cell phone radiation is harmful to the body. Unless the civil aviation authority bans such ads, TRAI’s efforts will be in vain. The IndiGo in-flight magazine is available for 180 passengers per flight of an Airbus A320, and the airline flies 131 such flights across the country a day (as of April 10, 2017). That’s more visibility than the TRAI can manage without significant effort.

Featured image credit: Javier Cañada/Unsplash.

Science

Performing with and without an audience

Posted on April 30, 2018 by newyesterday

My feeling is that as far as creativity is concerned, isolation is required. … The presence of others can only inhibit this process, since creation is embarrassing.

– Isaac Asimov (source)

Be it far from me to fall for a behavioural studies paper that’s not yet been replicated, and much farther to do so based on a university press release, but this one caught my attention because it suggests something completely opposite to my experience: “when there’s an audience, people’s performance improves”. Sure enough, four full paras into the piece there’s a qualification:

Vikram Chib, an assistant professor of biomedical engineering at Johns Hopkins … who has studied what happens in the brain when people choke under pressure, originally launched this project to investigate how performance suffers under social observation. But it quickly became clear that in certain situations, having an audience spurred people to do better, the same way it would if money was on the line. (emphasis added)

The situation in question involved 20 participants playing a videogame in front of an audience of two and, in a different ‘act’, in front of no audience at all. If a participant played the game better, he/she received a higher reward. Brain activity was monitored at all times using an fMRI machine.

You realise now that the press release’s headline is almost criminally wrong, considering it’s likely been vetted by some scientists if not those who conducted the study itself. It suggests that people’s performance improves in all circumstances; however, a videogame is nothing like writing, for example. In fact, you’d be hard-pressed to find someone who can write when they’re being watched. This is because writing isn’t a performance art whereas a videogame could be. And when executing a performance, having an audience helps.

According to Chib and the press release, this is the mechanism of action:

When participants knew an audience was watching, a part of the prefrontal cortex associated with social cognition, particularly the thoughts and intentions of others, activated along with another part of the cortex associated with reward. Together these signals triggered activity in the ventral striatum, an area of the brain that motivates action and motor skills.

While this is interesting, 20 people isn’t too much, the task is too simple and definitely not generalisable, and the audience is too small. Playing a videogame in front of two strangers (presumably) is nothing like playing a videogame in a room chock full of people, or when the stakes are higher. In fact, in real life, you’re almost certainly being judged if there’s an audience watching you as you conduct a task, and your stress levels are going to be far higher than when you’re playing something on your Xbox in front of two people.

A final quibble is more a wondering about the takeaway. The study seems to have focused on a very narrowly defined task while one of its authors – Chib – freely acknowledges its various shortcomings. Why weren’t these known issues addressed in the same paper instead of angling for a follow-up? I suspect future studies will also perform the same experiment multiple times with different kinds of tasks.

But if the audience was a lot bigger, and the stakes higher, the results could have gone the other way. “Here people with social anxiety tended to perform better,” Chib said, “but at some point, the size of the audience could increase the size of one’s anxiety but we still need to figure that out.”

Perhaps this is a case of someone trying to jack up their publication count.

Featured image credit: Skitterphoto/pixabay.

Science

The March for Science, ed. 2018

Posted on April 27, 2018 by newyesterday

K. VijayRaghavan, India’s new principal scientific advisor to the Government of India, has brought a lot of hope with him into the role as a result of his illustrious career as a biologist and former secretaryship with the Department of Biotechnology. Many stakeholders of the scientific establishment are already looking to him for positive changes in S&T policy, funding and administration in India under a government that, on matters of research and education, has focused on applications, translational research and actively ignored the spread of superstitious ideas in society.

In a recent interview, VijayRaghavan was asked about R&D funding in India. His response is worth noting against the backdrop of a ‘March for Science’ planned across India on April 14. As the interviewer reminds the reader, the 2018 Economic Survey bluntly acknowledged that India was underspending on research. This has also been one of the principal focus areas of the ‘March for Science’ organisers and participants: they have demanded that the Centre hike R&D spending to 3% and education spending to 10%, both as fractions of the GDP, apart from asking the government to stop the spread of superstitious beliefs.

Q: Getting funding for research is widely considered to be a prickly issue. The 2018 Economic Survey stated that India underspends on R&D. Is this a concern at the administration level?

A: These are wrongly posed questions, because it says that should magically the amount of funding go up, then science’s problems would be solved. Or that this is the key impediment. There’s no questions that there’s a correlation between increased R&D funding and innovation in many economies. South Korea is a striking example how high-tech R&D has resulted in transformation in their industries… Have we analysed, bottom-up, what Korea’s spending goes into and what we can learn from that and do afresh? Have we analysed our contest and learnt? …

Now interestingly, top-down this analysis has been done long ago. We as scientists, individuals and as journalists need to see that. The DST, and the DBT, the CSIR, the ICMR all have their plans should they get more resources. You can’t have a top-down articulation of how the resources can come and be used, unless that is also dynamically connected bottom-up.

When I look at 100 cases of why fund-flow is gridlocked, in about 70 cases, it’s poor institutional processes.

March for more than science

After the first Indian ‘March for Science’ happened in August 2017, the government showed no signs of having heard the participants’ claims, or even acknowledged the event. This was obviously jarring but it also prompted conversations about whether the march’s demands were entirely reasonable. Most news reports, include The Wire‘s, had focused on how this was the first outpouring of scientists, school-teachers and students, particularly at this scale. Scrutinising it deeply was taboo because there was some anxiety about jeopardising the need for such a march itself. However, ahead of the second march planned for April 14, it’s worth revisiting.

Sundar Sarukkai, the philosopher, had penned an oped the day after the 2017 march, asking scientists whether they had thought to climb down from their ivory towers and consider that the spread of superstitions in society under the Narendra Modi government may have been because of sociological and cultural reasons, and wasn’t simply a matter of spending more on R&D. Following a rebuttal from Rahul Siddharthan, Sarukkai clarified in The Wire:

Whenever ideal images are constructed (like ideal of woman, ideal of nation, etc.), one should be wary, since any such act is often driven by considerations of power. This ideal image of science too is used to establish science as a powerful agent within modern societies. The use of this ideal image to solve social problems related to caste, religion or hatred of any kind is a red herring. It is like using a hammer to fix a bulb. When we do that, it only means that we are not really interested in solving the problem (fixing the bulb) but more invested in using the method (the hammer) – irrespective of whether it is suitable for the task or not.

The terrible cases of lynching, hatred, oppression and misuse of religion must be unequivocally opposed. For those who are serious about that task, the solution is more important than the method used to achieve it. The categories of the ideal notion of science are applicable primarily to non-human systems. So even if they work well within such systems, there is no reason why they should do so within human systems.

A physicist said something similar to me around the time: that the old uncle preaching the benefits of homeopathy in his living room is doing so not because he doesn’t have access to scientific knowledge. That may be true but what’s more conspicuous by absence is someone in the same room challenging his views, communicating to him without being intimidating or patronising and having a discussion with him about what’s right, what’s wrong and the methods we use to tell the difference. Instead, focusing on making it easier for scientists to become and remain scientists alone will not take us closer to achieving the outcomes the ‘March for Science’ desires.

Sarukkai echoed this point in a comment to The Print: that scientists who march only for science are not doing anything useful, and that they must march against casteism and sexism as well (and social ills outside their labs). Without real change in these social contexts, it’s going to be near-impossible for those deemed less powerful by structures in place in these contexts to challenge the beliefs of those afforded more social authority. Ultimately, effecting such change is not going to be all about money – just as much as more money alone won’t solve anything, just as much as imploring the government to “fix” all these issues by itself will not work either.

This is where VijayRaghavan’s comments about R&D spending fit in. Before we throw more money in the general direction of supporting R&D, its Augean stables will have to be cleaned out and inefficiencies eliminated. One example, apropos VijayRaghavan’s comment about 70% of funds being gridlocked due to “poor institutional processes”, comes immediately to mind.

Sunil Mukhi, a theoretical physicist, wrote in 2008 that when he had been a member of the faculty at the Tata Institute of Fundamental Research, Mumbai, his station afford him a variety of privileges even as there was “no clear statement of our responsibility or duty to perform, and no consequences for failing to do so”. While he has since acknowledged a potential flaw in his suggested solution, the fact remains that many researchers often laze in prized research positions at well-funded institutes instead of also having to grapple with the teaching and mentorship load prevalent at state universities and colleges.

Additionally, though most people have directed their ire at the government for underfunding R&D, 55% of our R&D expenditure is from the public kitty. Among the ‘superpowers’, China is a distant second at less than 20%. So the marches for science should also ask the private sector to cough up more.

One for all

When the government pulled the financial carpet out from under the feet of the Council of Scientific and Industrial Research in 2014 and asked its 38 labs to “go fund themselves”, many scientists were aghast that the council was being handicapped even as more money was being funnelled into pseudo-research on cow urine. But there were also many other scientists who said that the CSIR had it coming, that – as a network of labs set up to facilitate applied and translational research – it was bloated, sluggish and ripe for a pruning. Perhaps similar audits, though with ample stakeholder consultations (not the RSS) and without drastic consequences, are due for the national scientific establishment as a whole.

As a corollary, it is also true that every march, protest or agitation undertaken against casteism, sexism, patriarchy, bigotry and zealotry can work in favour of the scientific establishment since what ‘they’ are fighting against is also what scientists, and science journalists, should be fighting against. Access to bonafide scientific ideas should not be solely through textbooks, news articles and freewheeling chats on Twitter. Instead, and irrespective of whether they become available, they should have the option to be availed through the many day-to-day interactions in which we confront structures of caste and class.

For example, there is no reason the person who cleans your toilet should not also cook your dinner. To institute this dumb restriction is to perpetuate caste/class divisions as well as to reject science in the form of hand-wash fluids. For another, there is no reason an employer shouldn’t let their domestic help use the toilet when they need to. However, the practice of expecting those who work in our homes to use separate toilets or be fired still persists, even in a society as ostensibly post-caste as West Bengal’s, demonstrating “the extent to which employer relations with domestic workers continue to be flavoured by caste” – as well as the extent to which we falsely attribute different human bodies with irrational biological threats.

These problems are also relevant to scientists, and must be solved before we can confront the bigger, and more nebulous, order of scientific temper in the country. However, such problems can’t be fixed by scientists and science alone.

It is worth reiterating that the ‘March for Science’ tomorrow is not a lost cause; far from it, in fact. The demand that 3% of GDP be spent on R&D is entirely valid – but it also needs to be accompanied by structural reforms to be completely meaningful. So the march, in effect, is an opportunity to examine the checks and balances of science’s administration in the country, the place of science in society, and introspect on our responsibility to confront a protean problem and not back down in the face of easy solutions. If the solution was as easy as ramping up spending on R&D and education, the problem would have been solved long ago.

The Wire, 13 April 2018.

Science

From comfortable summer wear to advanced geometry

Posted on April 16, 2018 by newyesterday

A friend of mine got harem pants and was talking about how much more comfortable they were than a lungi in Chennai’s current weather. A lungi is a long cylinder made of cloth (open at both ends of course) commonly worn by men in South India.

Five minutes later, our conversation included this statement:

2-manifolds with the same genus are homeomorphic.

Here’s how we got there, and a little more.

My friend’s a theoretical physicist. He works on string theory, which is a set of mathematical tools physicists use to solve problems about space and time.

To a physicist, a manifold is any surface. There are some specially defined manifolds that physicists use to understand how forces work.

For example, we’ve heard so much talk about Albert Einstein’s general theory of relativity, which describes how gravity works. When working with this theory, physicists assume that gravity is acting on the surface of the spacetime continuum. This surface is in the form of a so called Lorentzian manifold.

A numerical prefix to the manifold indicates the number of dimensions the surface has.

Say there’s an ant moving around on a sheet of paper. You can describe the ant’s position on the paper using two numbers: its distance from the length of the paper and its distance from the breadth.

For the ant, the surface it’s on has two dimensions – so it’s called a 2-manifold.

For humans, the surface of Earth is a 2-manifold. Humans can describe any point on Earth’s surface using two numbers: the latitude and the longitude coordinates.

Let’s take a slightly different shape called the torus.

A torus. Credit: Wikimedia Commons, CC BY-SA 3.0

A torus is a tube connected on itself, with a hole in the middle. Its surface is also a 2-manifold. According to the picture below, you can tell where you are on the torus by specifying the position of the red circle and your position on the red circle.

The surface of a torus. Credit: Wikimedia Commons

Now, let’s stick three toruses together like a fidget-spinner:

A triple torus. Credit: Wolfram Mathworld

Its surface is still a 2-manifold because you still need only two numbers to describe your position on it: the position of a circle moving across the entire triple torus and your position on the circle.

Both a normal torus and a triple torus are 2-manifolds. However, they have an important difference: one has one hole and the other, three. This difference is important to physicists who study manifolds.

The number of holes in an object, as far as the physicist is concerned, is called the genus. The normal torus has genus 1. The triple torus has genus 3. A sphere has genus 0.

Let’s revisit the statement from above:

2-manifolds with the same genus are homeomorphic.

If two solids are homeomorphic, then one solid can be deformed such that it forms the other solid. One example is a lungi and a torus.

So what my friend’s saying with his statement is that if two solids whose surfaces are 2-manifolds also have the same number of holes, then one solid can be deformed into the other.

A famous example of this is the torus and the coffee mug. Both their surfaces are 2-manifolds. Both of them have the same genus, 1. (The coffee mug’s opening at the top is not considered a hole because it is closed at the other end.)

This is where the conversation between my friend and myself took an interesting turn.

The reason 2-manifolds with the same genus are homeomorphic is because all of them can be constructed using a combination of objects shaped like a pair of pants.

A pair of pants in topology. Credit: Jean Raimbault/Wikimedia Commons, CC BY-SA 4.0

Mathematicians don’t have a different name for these objects. They are, in fact, called a pair of pants.

If you closed up the waist-rim of the pants and joined the two cuffs together, you’d get a normal torus. If you joined two pairs of pants by their waist-rims and joined the cuffs together at their respective ends. You’d get a double torus. Do this with three pairs of pants and you’d get a triple torus.

Some combination of these ‘pair of pants’ objects can be used to yield all the different kinds of 2-manifolds you can think of. So each pair of pants is like a nuclear unit, just like different combinations of protons and neutrons make up the nucleus of every different kind of atom in the world.

At this point, I proceeded to ask my friend about what kind of nuclear units make up 3-manifolds, surfaces on which you’d need three numbers to pinpoint your location.

He told me that it was a big unsolved problem in mathematics and physics, that mathematicians and physicists actually didn’t know.

The issue is with knowing how many different kinds of 3-manifolds there are. According to my friend, there could be millions upon millions – and that if you up came with a number, someone else would find a different 3-manifold that isn’t included in your set.

But there must be some way, some lead or indication of how we could go about it, I asked.

He said that mathematicians had been able to come up with a partial solution.

In our example, we used the genus as a differentiator. That is, 2-manifolds with different genuses were considered to be different kinds of 2-manifolds.

Instead, he said, mathematicians have used different differentiators other than genuses to describe the types of 3-manifolds.

They’ve found that if two 3-manifolds can be described by a fixed group of differentiators, then they may or may not be homeomorphic.

However, if two 3-manifolds can’t be described by the same group of differentiators, then they’re definitely nothomeomorphic.

It’s a sort of definition by exclusion, and that’s the best we have.

The Lorentzian manifold I mentioned above – the surface of the spacetime continuum on which gravity is thought to act – has four dimensions. It’s a 4-manifold. We have absolutely no idea how many types of 4-manifolds there are.

As I wonder on that, I’m going to get out my pair of pants, into my lungi and crash for the night. It’s so hot out here…