Category Archives: science

LaBiotechMap (a map of European biotechnology companies)

Thanks to Joachim Eeckhout of the LaBiotechMap team for contacting me regarding his and co-founder Philip Hemme’s European  biotechnology company map.

You can find the map here and for those who need an incentive to explore, here’s a bit of information and a few images from the site’s homepage to whet your interest,

It’s Elegant.

We spent time designing the map. And it’s apparent. Benefit from its unique user experience and finally enjoy surfing through Biotech companies.

It’s Focused.

Instead of gathering the universe of Biotech companies, we offer you a pre-selected galaxy. It results in the most coherent European Biotech Database.

It’s Smart.

Weekly updated, to keep you on track. Searchable, to directly reach your target. Sortable, for high precision.
In a word: Smart.

Here’s a screen capture or representation of the map,

LaBiotechMap

Here’s a screen capture or representation of the database search,

LaBiotechDatabase

Here’s more about the project from the FAQ (frequently asked questions) page,

What is our definition of a Biotech company?

Biotech is certainly one of the most difficult technological term to define.

For us, Biotech is not all life sciences, neither beer or cheese manufacturing. The gene editing revolution of the 80s gave birth to the term Biotechnology and is linked to the foundation of Genentech in California. Today, Biotechnology have a significant impact on the World by helping cure, feed and fuel people. Ground-breaking technologies includes for example gene therapy, biofuels, monoclonal antibodies, cell therapy and GMOs.

Which are our selection criteria?

Our selection criteria to enter for free on the map is to have raised or generated over €1M and to be innovative (spending high % of revenues in R&D and owning patents).

Can you help us improving it?

Yes, everybody can participate. You saw a company missing, a wrong information, an old information or something else? You can use our feedback page or send us a mail to contact-at-labiotechmap.com

Can people stop getting bored by surfing through Biotech companies?

We hope so.

Can I share the map if I like it?

We hope so.

They have a company blog on the website which doesn’t include any dates on the posts (sigh) but I believe their mention of launching the final version of the map in Munich (Munchen, Germany) is relatively recent,

Here we go, we launched the final version of LaBiotech Map in Munich in front of 30 CEOs during a brunch organized by the IZB cluster.

Creating a European Biotech Map may sound crazy, but we like challenges. We started working on it in September 2014 and launched a beta version beginning of November. Within 3 months, we received over 100 exciting feedback and more than 2000 people tried it out. …

I wish the founders and their team good luck with visualizing the biotech company scene in Europe.

Final note: this is not the only European map of its kind, there’s also France’s interactive nanotechnology map featured in my Feb. 4, 2013 posting.

Gender gaps in science and how statistics prove and disprove the finding

A Feb. 17, 2015 Northwestern University news release by Hilary Hurd Anyaso (also on EurekAlert) features research suggesting that parity in the numbers of men and women students pursuing science degrees is being achieved,

Scholars from diverse fields have long proposed that interlocking factors such as cognitive abilities, discrimination and interests may cause more women than men to leave the science, technology, engineering and mathematics (STEM) pipeline after entering college.

Now a new Northwestern University analysis has poked holes in the much referenced “leaky pipeline” metaphor.

The research shows that the bachelor’s-to-Ph.D. pipeline in science and engineering fields no longer leaks more women than men as it did in the past

Curt Rice, a professor at Norway’s University of Tromsø, has challenged the findings in a Feb. 18, 2015 post on his eponymous website (more about that later).

The news release goes on to describe how the research was conducted and the conclusions researchers drew from the data,

The researchers used data from two large nationally representative research samples to reconstruct a 30-year portrait of how bachelor’s-to-Ph.D. persistence rates for men and women have changed in the United States since the 1970s. For this study, the term STEM persistence rate refers to the proportion of students who earned a Ph.D. in a particular STEM field (e.g. engineering) among students who had earlier received bachelor’s degrees in that same field.

They were particularly surprised that the gender persistence gap completely closed in pSTEM fields (physical science, technology, engineering and mathematics) — the fields in which women are most underrepresented.

Among students earning pSTEM bachelor’s degrees in the 1970s, men were 1.6 to 1.7 times as likely as women to later earn a pSTEM Ph.D. However, this gap completely closed by the 1990s.

Men still outnumber women by approximately three to one among pSTEM Ph.D. earners. But those differences in representation are not explained by differences in persistence from the bachelor’s to Ph.D. degree, said David Miller, an advanced doctoral student in psychology at Northwestern and lead author of the study.

“Our analysis shows that women are overcoming any potential gender biases that may exist in graduate school or undergraduate mentoring about pursing graduate school,” Miller said. “In fact, the percentage of women among pSTEM degree earners is now higher at the Ph.D. level than at the bachelor’s, 27 percent versus 25 percent.”

Jonathan Wai, a Duke University Talent Identification Program research scientist and co-author of the study, said a narrowing of gender gaps makes sense given increased efforts to promote gender diversity in science and engineering.

“But a complete closing of the gap was unexpected, especially given recent evidence of gender bias in science mentoring,” Wai said.

Consequently, the widely used leaky pipeline metaphor is a dated description of gender differences in postsecondary STEM education, Wai added.

Other research shows that gaps in persistence rates are also small to nonexistent past the Ph.D., Miller said.

“For instance, in physical science and engineering fields, male and female Ph.D. holders are equally likely to earn assistant professorships and academic tenure,” Miller said.

The leaky pipeline metaphor is inaccurate for nearly all postsecondary pathways in STEM, Miller said, with two important exceptions.

“The Ph.D.-to-assistant-professor pipeline leaks more women than men in life science and economics,” he said. “Differences in those fields are large and important.”

The implications of the research, Miller said, are important in guiding research, resources and strategies to explain and change gender imbalances in science.

“The leaking pipeline metaphor could potentially direct thought and resources away from other strategies that could more potently increase women’s representation in STEM,” he said.

For instance, plugging leaks in the pipeline from the beginning of college to the bachelor’s degree would fail to substantially increase women’s representation among U.S. undergraduates in the pSTEM fields, Miller said.

Of concern, women’s representation among pSTEM bachelor’s degrees has been decreasing during the past decade, Miller noted. “Our analyses indicate that women’s representation at the Ph.D. level is starting to follow suit by declining for the first time in over 40 years,” he said.

“This recent decline at the Ph.D. level could likely mean that women’s progress at the assistant professor level might also slow down or reverse in future years, so these trends will need to be watched closely,” Wai said.

While the researchers are encouraged that gender gaps in doctoral persistence have closed, they stressed that accurately assessing and changing gender biases in science should remain an important goal for educators and policy makers.

Before moving on to Rice’s comments, here’s a link to and citation for the paper,

The bachelor’s to Ph.D. STEM pipeline no longer leaks more women than men: a 30-year analysis by David I. Miller and Jonathan Wai. Front. Psychol., 17 February 2015, doi: 10.3389/fpsyg.2015.00037

This paper is open access (at least for now).

Maybe the situation isn’t improving after all

Curt Rice’s response titled, The incontinent pipeline: it’s not just women leaving higher education, suggests this latest research has unmasked a problem (Note: Links have been removed),

Freshly published research gives a more nuanced picture. The traditional recitation of percentages at various points along the pipeline provides a snapshot. The new research is more like a time-lapse film.

Unfortunately, the new study doesn’t actually show a pipeline being tightened up to leak less. Instead, it shows a pipeline that is leaking even more! The convergence in persistence rates for men and women is not a result of an increase in the rate of women taking a PhD; it’s the result of a decline in the rate of men doing so. It’s as though the holes have gotten bigger — they used to be so small that only women slipped through, but now men slide out, too.

Rice believes  that this improvement is ‘relative improvement’ i.e. the improvement exists in relation to declining numbers of men, a statistic that Rice gives more weight to than the Northwestern researchers appear to have done. ‘Absolute improvement’ would mean that numbers of women studying in the field had improved while men’s numbers had held steady or improved for them too.

To be fair, the authors of the paper seem to have taken at least some of this decline in men’s numbers into account (from the research paper),,

Reasons for the convergences in persistence rates remain unclear. Sometimes the convergence was driven by declines in men’s rates (e.g., in mathematics/computer science), increases in women’s rates (e.g., in physical science), or both (e.g., in engineering). help account for the changes in persistence rates. …

Overenthusiasm in the news release

Unfortunately, the headline and bullet list of highlights suggest a more ebullient research conclusion than seems warranted by the actual research results.

Think again about gender gap in science
Bachelor’s-to-Ph.D. pipeline in science, engineering no longer ‘leaks’ more women than men, new 30-year analysis finds

Research shows dated ‘leaky pipeline’ assumptions about gender imbalances in science

  • Men outnumber women as Ph.D. earners in science but no longer in doctoral persistence
  • Dramatic increase of women in science at Ph.D., assistant professorship levels since 1970s, but recent decline since 2010 may be of concern for future supply of female scientists
  • Assessing inaccurate assumptions key to correcting gender biases in science

Here’s the researchers’ conclusion,

Overall, these results and supporting literature point to the need to understand gender differences at the bachelor’s level and below to understand women’s representation in STEM at the Ph.D. level and above. Women’s representation in computer science, engineering, and physical science (pSTEM) fields has been decreasing at the bachelor’s level during the past decade. Our analyses indicate that women’s representation at the Ph.D. level is starting to follow suit by declining for the first time in over 40 years (Figure 2). This recent decline may also cause women’s gains at the assistant professor level and beyond to also slow down or reverse in the next few years. Fortunately, however, pathways for entering STEM are considerably diverse at the bachelor’s level and below. For instance, our prior research indicates that undergraduates who join STEM from a non-STEM field can substantially help the U.S. meet needs for more well-trained STEM graduates (Miller et al., under review). Addressing gender differences at the bachelor’s level could have potent effects at the Ph.D. level, especially now that women and men are equally likely to later earn STEM Ph.D.’s after the bachelor’s.

The conclusion seems to contradict the researchers’ statements in the news release,

“But a complete closing of the gap was unexpected, especially given recent evidence of gender bias in science mentoring,” Wai said.

Consequently, the widely used leaky pipeline metaphor is a dated description of gender differences in postsecondary STEM education, Wai added.

Other research shows that gaps in persistence rates are also small to nonexistent past the Ph.D., Miller said.

Incomplete pipeline

Getting back to Rice, he notes the pipeline in the Northwestern paper is incomplete (Note: Links have been removed),

In addition to the dubious celebration of the decline of persistence rates of men, the new research article also looks at an incomplete pipeline. In particular, it leaves aside the important issue of which PhD institutions students get into. For young researchers moving towards academic careers, we know that a few high-prestige universities are responsible for training future faculty members at nearly all other research universities. Are women and men getting into those high prestige universities in the same numbers? Or do women go to lower prestige institutions?

Following on that thought about lower prestige institutions and their impact on your career, there’s a Feb. 23, 2015 article by Joel Warner and Aaron Clauset in Slate investigating the situation, which applies to both men and women,

The United States prides itself on offering broad access to higher education, and thanks to merit-based admissions, ample financial aid, and emphasis on diverse student bodies, our country can claim some success in realizing this ideal.

The situation for aspiring professors is far grimmer. Aaron Clauset, a co-author of this article, is the lead author of a new study published in Science Advances that scrutinized more than 16,000 faculty members in the fields of business, computer science, and history at 242 schools. He and his colleagues found, as the paper puts it, a “steeply hierarchical structure that reflects profound social inequality.” The data revealed that just a quarter of all universities account for 71 to 86 percent of all tenure-track faculty in the U.S. and Canada in these three fields. Just 18 elite universities produce half of all computer science professors, 16 schools produce half of all business professors, and eight schools account for half of all history professors.

Then, Warner and Clauset said this about gender bias,

Here’s further evidence that the current system isn’t merely sorting the best of the best from the merely good. Female graduates of elite institutions tend to slip 15 percent further down the academic hierarchy than do men from the same institutions, evidence of gender bias to go along with the bias toward the top schools.

I suggest reading the Slate article, Rice’s post, and, if you have time, the Northwestern University research paper.

Coda: All about Curt Rice

Finally, this is for anyone who’s unfamiliar with Curt Rice (from the About page on his website; Note: Links have been removed),

In addition to my work as a professor at the University of Tromsø, I have three other roles that are closely related to the content on this website. I was elected by the permanent faculty to sit on the university board, I lead Norway’s Committee on Gender Balance and Diversity in Research, and I am the head of the Board for Current Research Information System in Norway (CRIStin). In all of these roles, I work to pursue my conviction that research and education are essential to improving society, and that making universities better therefore has the potential to make societies better.

I’m currently writing a book on gender balance. Why do men and women have different career paths? Why should we care? How can we start to make things better? Why is improving gender balance not only the right thing to do, but also the smart thing to do? For a taste of my approach, grab a copy of my free ebook on gender equality.

Beyond this book project, I use my speaking and writing engagements to reach audiences on the topics that excite me the most: gender balance, open access, leadership issues and more. These interests have grown during the past decade while I’ve had the privilege to occupy what were then two brand new leadership positions at the University of Tromsø.

From 2009–2013, I served as the elected Vice Rector for Research & Development (prorektor for forskning og utvikling). Before that, from 2002–2008, I was the founding director of my university’s first Norwegian Center of Excellence, the Center for Advanced Study in Theoretical Linguistics (CASTL). Given the luxury of being able to define those positions, I was able to pursue my passion for improving academic life by working to enhance conditions for education and research.

I’m part of the European Science Foundation’s genderSTE COST action (Gender, Science, Technology and Environment); I helped create the BALANSE program at the Research Council of Norway, which is designed to increase the numbers of women at the highest levels of research organizations. I am on the Advisory Board of the European Commission project EGERA (Effective Gender Equality in Research and Academia); I was on the Science Leaders Panel of the genSET project, in which we advised the European Commission about gender in science; I am a member of the Steering Committee for the Gender Summits.

I also led a national task force on research-based education that issued many suggestions for Norwegian institutions.

Bypassing nanofabrication methods for colourful silver

A new technique developed by researchers at Northwestern University (Chicago, US) would be faster and cheaper than nanofabrication methods according to a Feb. 14, 2015 news item on Azonano,

Northwestern University researchers have created a new technique that can transform silver into any color of the rainbow. Their simple method is a fast, low-cost alternative to color filters currently used in electronic displays and monitors.

“Our technique doesn’t require expensive nanofabrication techniques or a lot of materials,” said Koray Aydin, assistant professor of electrical engineering and computer science at the McCormick School of Engineering. “And it can be completed in a half hour or so.”

A Feb. 12, 2015 Northwestern University news release (also on EurekAlert but dated Feb. 13, 2015), which originated the news item, provides more details about the research,

The filter’s secret lies within its “sandwich-like” structure. Aydin and his team created a three-layer design, where glass is wedged two thin layers of silver film. The silver layers are thin enough to allow optical light to pass through, which then transmits a certain color through the glass and reflects the rest of the visible spectrum. By changing the thickness of the glass, Aydin was able to filter and produce different colors.

“Controlling the thickness of the glass controls the color,” Aydin said. “This way, we can create any color desired.”

By making the bottom silver layer even thicker, Aydin found that the structure also acts as a color absorber because it traps light between the two metal layers. The team demonstrated a narrow bandwidth super absorber with 97 percent maximum absorption, which could have potential applications for optoelectric devices with controlled bandwidth, such as narrow-band photodetectors and light-emitting devices. The performance of Aydin’s structure is comparable to that of nanostructure-based devices but bypasses the complications of nanotechnology.

“People in the nanophotonics community are dealing with nanostructures, making nanoparticles, and using lithography or chemistry techniques,” he said. “That can be really challenging. We’re combatting that difficulty with a simple design.”

Aydin is also developing a similar structure out of aluminum and glass to filter or absorb ultraviolet spectrum. By controlling the thickness of the materials, he plans to design devices for other wavelengths of light.

Here’s a link to and a citation for the paper,

Large-Area, Lithography-Free Super Absorbers and Color Filters at Visible Frequencies Using Ultrathin Metallic Films by Zhongyang Li, Serkan Butun, and Koray Aydin. ACS Photonics, Article ASAP DOI: 10.1021/ph500410u Publication Date (Web): January 28, 2015
Copyright © 2015 American Chemical Society

This paper is behind a paywall.

Can the future influence the past? The answer is: mostly yes

The principles of quantum mechanics mystify me which, as it turns out, is the perfect place to start with the work featured in a Feb. 9, 2015 news item on ScienceDaily,

We’re so used to murder mysteries that we don’t even notice how mystery authors play with time. Typically the murder occurs well before the midpoint of the book, but there is an information blackout at that point and the reader learns what happened then only on the last page.

If the last page were ripped out of the book, physicist Kater Murch, PhD, said, would the reader be better off guessing what happened by reading only up to the fatal incident or by reading the entire book?

The answer, so obvious in the case of the murder mystery, is less so in world of quantum mechanics, where indeterminacy is fundamental rather than contrived for our reading pleasure.

A Feb. 13, 2015 Washington University at St. Louis (WUSTL) news release by Diana Lutz, which originated the news item, describes the research,

Even if you know everything quantum mechanics can tell you about a quantum particle, said Murch, an assistant professor of physics in Arts & Sciences at Washington University in St. Louis, you cannot predict with certainty the outcome of a simple experiment to measure its state. All quantum mechanics can offer are statistical probabilities for the possible results.

The orthodox view is that this indeterminacy is not a defect of the theory, but rather a fact of nature. The particle’s state is not merely unknown, but truly undefined before it is measured. The act of measurement itself that forces the particle to collapse to a definite state.

It’s as if what we did today, changed what we did yesterday. And as this analogy suggests, the experimental results have spooky implications for  time and causality—at least in microscopic world to which quantum mechanics applies.

Until recently physicists could explore the quantum mechanical properties of single particles only through thought experiments, because any attempt to observe them directly caused them to shed their mysterious quantum properties.

But in the 1980s and 1990s physicists invented devices that allowed them to measure these fragile quantum systems so gently that they don’t immediately collapse to a definite state.

The device Murch uses to explore quantum space is a simple superconducting circuit that enters quantum space when it is cooled to near absolute zero. Murch’s team uses the bottom two energy levels of this qubit, the ground state and an excited state, as their model quantum system. Between these two states, there are an infinite number of quantum states that are superpositions, or combinations, of the ground and excited states.

The quantum state of the circuit is detected by putting it inside a microwave box. A few microwave photons are sent into the box, where their quantum fields interact with the superconducting circuit. So when the photons exit the box they bear information about the quantum system.

Crucially, these “weak,” off-resonance measurements do not disturb the qubit, unlike “strong” measurements with photons that are resonant with the energy difference between the two states, which knock the circuit into one or the other state.

In Physical Review Letters, Murch describes a quantum guessing game played with the qubit.

“We start each run by putting the qubit in a superposition of the two states,” he said. “Then we do a strong measurement but hide the result, continuing to follow the system with weak measurements.”

They then try to guess the hidden result, which is their version of the missing page of the murder mystery.

“Calculating forward, using the Born equation that expresses the probability of finding the system in a particular state, your odds of guessing right are only 50-50,” Murch said. “But you can also calculate backward using something called an effect matrix. Just take all the equations and flip them around. They still work and you can just run the trajectory backward.

“So there’s a backward-going trajectory and a forward-going trajectory and if we look at them both together and weight the information in both equally, we get something we call a hindsight prediction, or “retrodiction.”

The shattering thing about the retrodiction is that it is 90 percent accurate. When the physicists check it against the stored measurement of the system’s earlier state it is right nine times out of 10.

Going from a 50% accuracy rate to 90% is quite amazing and according to the news release, this has many implications,

The quantum guessing game suggests ways to make both quantum computing and the quantum control of open systems, such as chemical reactions, more robust. But it also has implications for much deeper problems in physics.

For one thing, it suggests that in the quantum world time runs both backward and forward whereas in the classical world it only runs forward.

“I always thought the measurement would resolve the time symmetry in quantum mechanics,” Murch said. “If we measure a particle in a superposition of states and it collapses into one of two states, well, that sounds like a process that goes forward in time.”

But in the quantum guessing experiment, time symmetry has returned. The improved odds imply the measured quantum state somehow incorporates information from the future as well as the past. And that implies that time, notoriously an arrow in the classical world, is a double-headed arrow in the quantum world.

“It’s not clear why in the real world, the world made up of many particles, time only goes forward and entropy always increases,” Murch said. “But many people are working on that problem and I expect it will be solved in a few years,” he said.

In a world where time is symmetric, however, is there such a thing as cause and effect? To find out, Murch proposes to run a qubit experiment that would set up feedback loops (which are chains of cause and effect) and try to run them both forward and backward.

“It takes 20 or 30 minutes to run one of these experiments,” Murch said, “several weeks to process it, and a year to scratch our heads to see if we’re crazy or not.”

“At the end of the day,” he said, “I take solace in the fact that we have a real experiment and real data that we plot on real curves.”

Here are links to and citations for the Physical Review paper and an earlier version of the paper,

 Prediction and retrodiction for a continuously monitored superconducting qubit by D. Tan, S. Weber, I. Siddiqi, K. Mølmer, K. W. Murch. arXiv.org > quant-ph > arXiv:1409.0510 (Submitted on 1 Sep 2014 (v1), last revised 10 Nov 2014 (this version, v2))

I last mentioned Kater Murch and his work in a July 31, 2014 post titled: Paths of desire: quantum style.

Biophysics and molecular gastronomy (comme les français)

It’s a bit of a stretch as the presenter himself admits but there is a connection to be made between molecular gastronomy and biophysics according to a Feb. 9, 2015 news release on EurkeAlert,

Anyone who’s ever been to France knows it’s a country that celebrates its food and takes enormous pride in not only the taste, but also the appearance and the overall “joie de vivre” involved. So it should come as no surprise that scientific disciplines like biophysics are being embraced for their ability to reveal the underlying physical and chemical processes that occur during food preparation and consumption.

During the Biophysical Society’s 59th Annual Meeting in Baltimore, Md., Feb. 7-11, 2015, Christophe Lavelle, an expert in biophysics, epigenetics and food science who works for the National Museum of Natural History in Paris, France, will describe his research dedicated to gaining a deeper understanding of genome compaction within the cells in our bodies and the way it influences gene expression.

“While the link with cooking may not be immediately obvious, when you realize that not only are food transformations and gene expression both a matter of macromolecule structure and dynamics, but also that the types of food you choose to eat influence the expression of your genes, then you have two good reasons to be interested in molecular gastronomy and genome mechanics,” said Lavelle. [emphasis mine]

The study of molecular biology got its start in the 1930s when physicists and chemists became interested in exploring life at its most fundamental level. Forty years later, Hungarian physicist Nicolas Kurti exclaimed: “It is a sad reflection on our civilization that while we can and do measure the temperature in the atmosphere of Venus we do not know what goes on inside our soufflés.” [emphasis mine]

This paved the way for what Kurti and his French colleague Hervé This called “molecular gastronomy,” dedicated to the study of the physical and chemical processes involved in cooking and eating.

Kurti’s exclamation seems almost French or perhaps this devotion to food is an aspect of Hungarian culture heretofore unknown to me. In any event, the theme is developed somewhat further by Lavelle,

“Biophysics can be defined as an interdisciplinary science using concepts and methods of physics to study biological matter,” explains Lavelle. “So biophysics can naturally help us to understand what’s occurring when we cook.”

An egg white is 90 percent water, for example, but if you put it in the microwave for 10 seconds, although it remains 90 percent water its form changes enough so that you could bite into it. “There is obviously a lot of physics happening here,” Lavelle noted.

Another quick example that most of us know is that when you slice into an apple it quickly starts to turn brown. But to avoid this, you can sprinkle it with lemon juice. “This time, some chemistry is probably involved,” he said. “And since eggs, apples and lemon all come from nature, biology is obviously involved also!”

“These are just a few examples to introduce soft — and sometimes living — matter,” Lavelle pointed out. “Taking an interdisciplinary approach that combines biopolymer physics, thermodynamics, physiology and macromolecule biochemistry — among other subjects — can help us to better understand culinary phenomena and ultimately influence the way we cook and what we choose to eat.”

Food transformation and consumption phenomena also tend to generate puzzling questions, which Lavelle believes are actually “promising and appetizing” opportunities to raise interest in science and improve health among students and the general public.

The next step is to “merge human sciences with ‘hard’ sciences to reach a truly interdisciplinary knowledge of food — following the Brillat-Savarin definition of gastronomy as ‘the knowledge of all that relates to man as he eats,'” said Lavelle.

Sadly, it’s too late to attend Lavelle’s Feb. 9, 2015 presentation, “Delicious Biophysics: Cooking as a Prolific Support to Teach Biophysical Concepts”, at the 59th annual meeting of the Biophysical Society, Feb. 7 – 11, 2015.

‘Eve’ (robot/artificial intelligence) searches for new drugs

Following on today’s (Feb. 5, 2015) earlier post, The future of work during the age of robots and artificial intelligence, here’s a Feb. 3, 2015 news item on ScienceDaily featuring ‘Eve’, a scientist robot,

Eve, an artificially-intelligent ‘robot scientist’ could make drug discovery faster and much cheaper, say researchers writing in the Royal Society journal Interface. The team has demonstrated the success of the approach as Eve discovered that a compound shown to have anti-cancer properties might also be used in the fight against malaria.

A Feb. 4, 2015 University of Manchester press release (also on EurekAlert but dated Feb. 3, 2015), which originated the news item, gives a brief introduction to robot scientists,

Robot scientists are a natural extension of the trend of increased involvement of automation in science. They can automatically develop and test hypotheses to explain observations, run experiments using laboratory robotics, interpret the results to amend their hypotheses, and then repeat the cycle, automating high-throughput hypothesis-led research. Robot scientists are also well suited to recording scientific knowledge: as the experiments are conceived and executed automatically by computer, it is possible to completely capture and digitally curate all aspects of the scientific process.

In 2009, Adam, a robot scientist developed by researchers at the Universities of Aberystwyth and Cambridge, became the first machine to autonomously discover new scientific knowledge. The same team has now developed Eve, based at the University of Manchester, whose purpose is to speed up the drug discovery process and make it more economical. In the study published today, they describe how the robot can help identify promising new drug candidates for malaria and neglected tropical diseases such as African sleeping sickness and Chagas’ disease.

“Neglected tropical diseases are a scourge of humanity, infecting hundreds of millions of people, and killing millions of people every year,” says Professor Ross King, from the Manchester Institute of Biotechnology at the University of Manchester. “We know what causes these diseases and that we can, in theory, attack the parasites that cause them using small molecule drugs. But the cost and speed of drug discovery and the economic return make them unattractive to the pharmaceutical industry.

“Eve exploits its artificial intelligence to learn from early successes in her screens and select compounds that have a high probability of being active against the chosen drug target. A smart screening system, based on genetically engineered yeast, is used. This allows Eve to exclude compounds that are toxic to cells and select those that block the action of the parasite protein while leaving any equivalent human protein unscathed. This reduces the costs, uncertainty, and time involved in drug screening, and has the potential to improve the lives of millions of people worldwide.”

The press release goes on to describe how ‘Eve’ works,

Eve is designed to automate early-stage drug design. First, she systematically tests each member from a large set of compounds in the standard brute-force way of conventional mass screening. The compounds are screened against assays (tests) designed to be automatically engineered, and can be generated much faster and more cheaply than the bespoke assays that are currently standard. This enables more types of assay to be applied, more efficient use of screening facilities to be made, and thereby increases the probability of a discovery within a given budget.

Eve’s robotic system is capable of screening over 10,000 compounds per day. However, while simple to automate, mass screening is still relatively slow and wasteful of resources as every compound in the library is tested. It is also unintelligent, as it makes no use of what is learnt during screening.

To improve this process, Eve selects at random a subset of the library to find compounds that pass the first assay; any ‘hits’ are re-tested multiple times to reduce the probability of false positives. Taking this set of confirmed hits, Eve uses statistics and machine learning to predict new structures that might score better against the assays. Although she currently does not have the ability to synthesise such compounds, future versions of the robot could potentially incorporate this feature.

Steve Oliver from the Cambridge Systems Biology Centre and the Department of Biochemistry at the University of Cambridge says: “Every industry now benefits from automation and science is no exception. Bringing in machine learning to make this process intelligent – rather than just a ‘brute force’ approach – could greatly speed up scientific progress and potentially reap huge rewards.”

To test the viability of the approach, the researchers developed assays targeting key molecules from parasites responsible for diseases such as malaria, Chagas’ disease and schistosomiasis and tested against these a library of approximately 1,500 clinically approved compounds. Through this, Eve showed that a compound that has previously been investigated as an anti-cancer drug inhibits a key molecule known as DHFR in the malaria parasite. Drugs that inhibit this molecule are currently routinely used to protect against malaria, and are given to over a million children; however, the emergence of strains of parasites resistant to existing drugs means that the search for new drugs is becoming increasingly more urgent.

“Despite extensive efforts, no one has been able to find a new antimalarial that targets DHFR and is able to pass clinical trials,” adds Professor Oliver. “Eve’s discovery could be even more significant than just demonstrating a new approach to drug discovery.”

Here’s a link to and a citation for the paper,

Cheaper faster drug development validated by the repositioning of drugs against neglected tropical diseases by Kevin Williams, Elizabeth Bilsland, Andrew Sparkes, Wayne Aubrey, Michael Young, Larisa N. Soldatova, Kurt De Grave, Jan Ramon, Michaela de Clare, Worachart Sirawaraporn, Stephen G. Oliver, and Ross D. King. Journal of the Royal Society Interface March 2015 Volume: 12 Issue: 104 DOI: 10.1098/rsif.2014.1289 Published 4 February 2015

This paper is open access.

The quantum chemistry of nanomedicines

A Jan. 29, 2015 news item on Nanowerk provides an overview of the impact quantum chemical reactions may have on nanomedicines. Intriguingly, this line of query started with computations of white dwarf stars,

Quantum chemical calculations have been used to solve big mysteries in space. Soon the same calculations may be used to produce tomorrow’s cancer drugs.

Some years ago research scientists at the University of Oslo in Norway were able to show that the chemical bonding in the magnetic fields of small, compact stars, so-called white dwarf stars, is different from that on Earth. Their calculations pointed to a completely new bonding mechanism between two hydrogen atoms. The news attracted great attention in the media. The discovery, which in fact was made before astrophysicists themselves observed the first hydrogen molecules in white dwarf stars, was made by UiO’s Centre for Theoretical and Computational Chemistry. They based their work on accurate quantum chemical calculations of what happens when atoms and molecules are exposed to extreme conditions.

A Jan. 29, 2015 University of Oslo press release by Yngve Vogt, which originated the news item, offers a substantive description of molecules, electrons, and more for those of us whose last chemistry class is lost in the mists of time,

The research team is headed by Professor Trygve Helgaker, who for the last thirty years has taken the international lead on the design of a computer system for calculating quantum chemical reactions in molecules.

Quantum chemical calculations are needed to explain what happens to the electrons’ trajectories within a molecule.

Consider what happens when UV radiation sends energy-rich photons into your cells. This increases the energy level of the molecules. The outcome may well be that some of the molecules break up. This is exactly what happens when you sun-bathe.

“The extra energy will affect the behaviour of electrons and can destroy the chemical bonding within the molecule. This can only be explained by quantum chemistry. The quantum chemical models are used to produce a picture of the forces and tensions at play between the atoms and the electrons of a molecule, and of what is required for a molecule to dissociate,” says Trygve Helgaker.

The absurd world of the electrons

The quantum chemical calculations solve the Schrödinger equation for molecules. This equation is fundamental to all chemistry and describes the whereabouts of all electrons within a molecule. But here we need to pay attention, for things are really rather more complicated than that. Your high school physics teacher will have told you that electrons circle the atom. Things are not that simple, though, in the world of quantum physics. Electrons are not only particles, but waves as well. The electrons can be in many places at the same time. It’s impossible to keep track of their position. However, there is hope. Quantum chemical models describe the electrons’ statistical positions. In other words, they can establish the probable location of each electron.

The results of a quantum chemical calculation are often more accurate than what is achievable experimentally.

Among other things, the quantum chemical calculations can be used to predict chemical reactions. This means that the chemists will no longer have to rely on guesstimates in the lab. It is also possible to use quantum chemical calculations in order to understand what happens in experiments.

Enormous calculations

The calculations are very demanding.

“The Schrödinger equation is a highly complicated, partial differential equation, which cannot be accurately solved. Instead, we need to make do with heavy simulations”, says researcher Simen Kvaal.

The computations are so demanding that the scientists use one of the University’s fastest supercomputers.

“We are constantly stretching the boundaries of what is possible. We are restricted by the available machine capacity,” explains Helgaker.

Ten years ago it took two weeks to carry out the calculations for a molecule with 140 atoms. Now it can be done in two minutes.

“That’s 20,000 times faster than ten years ago. The computation process is now running 200 times faster because the computers have been doubling their speed every eighteen months. And the process is a further 100 times faster because the software has been undergoing constant improvement,” says senior engineer Simen Reine.

This year the research group has used 40 million CPU hours, of which twelve million were on the University’s supercomputer, which is fitted with ten thousand parallel processors. This allows ten thousand CPU hours to be over and done with in 60 minutes.

“We will always fill the computer’s free capacity. The higher the computational capacity, the bigger and more reliable the calculations.”

Thanks to ever faster computers, the quantum chemists are able to study ever larger molecules.

Today, it’s routine to carry out a quantum chemical calculation of what happens within a molecule of up to 400 atoms. By using simplified models it is possible to study molecules with several thousand atoms. This does, however, mean that some of the effects within the molecule are not being described in detail.

The researchers are now getting close to a level which enables them to study the quantum mechanics of living cells.

“This is exciting. The molecules of living cells may contain many hundred thousand atoms, but there is no need to describe the entire molecule using quantum mechanical principles. Consequently, we are already at a stage when we can help solve biological problems.”

There’s more from the press release which describes how this work could be applied in the future,

Hunting for the electrons of the insulin molecule

The chemists are thus able to combine sophisticated models with simpler ones. “This will always be a matter of what level of precision and detail you require. The optimal approach would have been to use the Schrödinger equation for everything.”

By way of compromise they can give a detailed description of every electron in some parts of the model, while in other parts they are only looking at average numbers.

Simen Reine has been using the team’s computer program, while working with Aarhus University [Finland], on a study of the insulin molecule. An insulin molecule consists of 782 atoms and 3,500 electrons.

“All electrons repel each other, while at the same time being pulled towards the atomic nuclei. The nuclei also repel each other. Nevertheless, the molecule remains stable. In order to study a molecule to a high level of precision, we therefore need to consider how all of the electrons move relative to one another. Such calculations are referred to as correlated and are very reliable.”

A complete correlated calculation of the insulin molecule takes nearly half a million CPU hours. If they were given the opportunity to run the program on the entire University’s supercomputer, the calculations would theoretically take two days.

“In ten years, we’ll be able to make these calculations in two minutes.”

Medically important

“Quantum chemical calculations can help describe phenomena at a level that may be difficult to access experimentally, but may also provide support for interpreting and planning experiments. Today, the calculations will be put to best use within the fields of molecular biology and biochemistry,” says Knut Fægri [vice-rector at the University of Oslo].

“Quantum chemistry is a fundamental theory which is important for explaining molecular events, which is why it is essential to our understanding of biological systems,” says [Associate Professor] Michele Cascella.

By way of an example, he refers to the analysis of enzymes. Enzymes are molecular catalysts that boost the chemical reactions within our cells.

Cascella also points to nanomedicines, which are drugs tasked with distributing medicine round our bodies in a much more accurate fashion.

“In nanomedicine we need to understand physical phenomena on a nano scale, forming as correct a picture as possible of molecular phenomena. In this context, quantum chemical calculations are important,” explains Michele Cascella.

Proteins and enzymes

Professor K. Kristoffer Andersson at the Department of Biosciences uses the simpler form of quantum chemical calculations to study the details of protein structures and the chemical atomic and electronic functions of enzymes.

“It is important to understand the chemical reaction mechanism, and how enzymes and proteins work. Quantum chemical calculations will teach us more about how proteins go about their tasks, step by step. We can also use the calculations to look at activation energy, i.e. how much energy is required to reach a certain state. It is therefore important to understand the chemical reaction patterns in biological molecules in order to develop new drugs,” says Andersson.

His research will also be useful in the search for cancer drugs. He studies radicals, which may be important to cancer. Among other things, he is looking at the metal ions function in proteins. These are ions with a large number of protons, neutrons and electrons.

Photosynthesis

Professor Einar Uggerud at the Department of Chemistry has uncovered an entirely new form of chemical bonding through sophisticated experiments and quantum chemical calculations.

Working with research fellow Glenn Miller, Professor Uggerud has found an unusually fragile key molecule, in a kite-shaped structure, consisting of magnesium, carbon and oxygen. The molecule may provide a new understanding of photosynthesis. Photosynthesis, which forms the basis for all life, converts CO2 into sugar molecules.

The molecule reacts so fast with water and other molecules that it has only been possible to study in isolation from other molecules, in a vacuum chamber.

“Time will tell whether the molecule really has an important connection with photosynthesis,” says Einar Uggerud.

I’m delighted with this explanation as it corrects my understanding of chemical bonds and helps me to better understand computational chemistry. Thank you University of Oslo and Yngve Vogt.

Finally, here’s a representation of an insulin molecule as understood by quantum computation,

QuantumInsulinMolecule

INSULIN: Working with Aarhus University, Simen Reine has calculated the tensions between the electrons and atoms of an insulin molecule. An insulin molecule consists of 782 atoms and 3,500 electrons. Illustration: Simen Reine-UiO

 

Atoms can be in two places at once

A Jan. 20, 2015 news item on Nanowerk offers a brief history of quantum mechanics,

Can a penalty kick simultaneously score a goal and miss? For very small objects, at least, this is possible: according to the predictions of quantum mechanics, microscopic objects can take different paths at the same time. The world of macroscopic objects follows other rules: the football always moves in a definite direction. But is this always correct? Physicists of the University of Bonn have constructed an experiment designed to possibly falsify this thesis. Their first experiment shows that Caesium atoms can indeed take two paths at the same time.

Almost 100 years ago physicists Werner Heisenberg, Max Born und Erwin Schrödinger created a new field of physics: quantum mechanics. Objects of the quantum world – according to quantum theory – no longer move along a single well-defined path. Rather, they can simultaneously take different paths and end up at different places at once.

A Jan. 20, 2015 Universität Bonn (University of Bonn) press release, which originated the news item, describes both the experiment and the thought process which led to the experiment,

At the level of atoms, it looks as if objects indeed obey quantum mechanical laws. Over the years, many experiments have confirmed quantum mechanical predictions. In our macroscopic daily experience, however, we witness a football flying along exactly one path; it never strikes the goal and misses at the same time.

“There are two different interpretations,” says Dr. Andrea Alberti of the Institute of Applied Physics of the University of Bonn. “Quantum mechanics allows superposition states of large, macroscopic objects. But these states are very fragile, even following the football with our eyes is enough to destroy the superposition and makes it follow a definite trajectory.”

But it could also be that footballs obey completely different rules than those applying for single atoms. “Let us talk about the macro-realistic view of the world,” Alberti explains. “According to this interpretation, the ball always moves on a specific trajectory, independent of our observation, and in contrast to the atom.”

In collaboration with Dr. Clive Emary of the University of Hull in the U.K., the Bonn team has come up with an experimental scheme that may help to answer this question. “The challenge was to develop a measurement scheme of the atoms’ positions which allows one to falsify macro-realistic theories,” adds Alberti.

The physicists describe their research in the journal “Physical Review X:” With two optical tweezers they grabbed a single Caesium atom and pulled it in two opposing directions. In the macro-realist’s world the atom would then be at only one of the two final locations. Quantum-mechanically, the atom would instead occupy a superposition of the two positions.

“We have now used indirect measurements to determine the final position of the atom in the most gentle way possible,” says the PhD student Carsten Robens. Even such an indirect measurement (see figure) significantly modified the result of the experiments. This observation excludes – falsifies, as Karl Popper would say more precisely – the possibility that Caesium atoms follow a macro-realistic theory. Instead, the experimental findings of the Bonn team fit well with an interpretation based on superposition states that get destroyed when the indirect measurement occurs. All that we can do is to accept that the atom has indeed taken different paths at the same time.

“This is not yet a proof that quantum mechanics hold for large objects,” cautions Alberti. “The next step is to separate the Caesium atom’s two positions by several millimetres. Should we still find the superposition in our experiment, the macro-realistic theory would suffer another setback.”

Here’s a link to and a citation for the paper,

Ideal negative measurements in quantum walks disprove theories based on classical trajectories by Carsten Robens, Wolfgang Alt, Dieter Meschede, Clive Emary, und Andrea Alberti. Physical Review X, 20.1.2015 (DOI: 10.1103/PhysRevX.5.011003)

This is an open access paper,

Part-time job at the Society for Canadian Women in Science and Technology (SCWIST)

The Vancouver-based Society for Canadian Women in Science and Technology (SCWIST) has a part-time, contract position available. From the SCWIST Coordinator – MS Infinity Program job page,

The Society for Canadian Women in Science and Technology (SCWIST) is a non-profit association that promotes, encourages and empowers women and girls in science, engineering and technology. Ms Infinity programs introduce girls to exciting career options and female role models in science and technology. Conferences and workshops with fun filled activities bring science alive. Girls are introduced to jobs from all areas of science and get the support they need when deciding how to take their interest in science further with e-mentor and role model programs.

POSITION OVERVIEW & KEY RESPONSIBILITIES

Title: Coordinator – MS Infinity Program
Type: Part-time contract (12 – 18 hours per week)
Start: ASAP
Application deadline: January 20, 2015
Reports to: Director of Outreach
Time Commitment:  This is a 6-month contract, to be renewed based on grant funding

Coordination and promotion of ms infinity programming:

  • Volunteer recruitment and management
  • Volunteer training, development and communication (quarterly e-newsletter)
  • Preparation of promotional material and marketing of the program
  • Organization of and communication with the ms infinity committee
  • Communication with workshop/ event/ conference organizers
  • Promotion of ms infinity offerings to SCWIST members
  • Assistance in workshop, event and conference organization
  • Research of new workshop and event possibilities to extend the reach of ms infinity
  • Development of new educational workshops
  • Grant application, reporting and budget management

Coordination of the e-mentoring program:

  • Program administration
  • Recruitment of mentors and mentees
  • Organization of discussion topics

Qualifications:

  • A degree in science or education
  • Experience in informal science education and program coordination
  • Positive, enthusiastic attitude
  • Ability to present the Society well in the science learning and promotion community
  • Strong organizational and communication skills
  • Self-motivated with attention to detail
  • Experience in event organization and management, as well as experience managing budgets
  • Excellent knowledge in MS Office and social media tools

Additional application information is on the job page.