September 22, 2018

Using virtual reality to study interactive molecular dynamics

Click on image to see video

Morales, A. (2018) How Virtual Reality Can Change The Way We See Our Molecular World, Forbes, 25 July

O’Connor, M. et al. (2018) Sampling molecular conformations and dynamics in a multiuser virtual reality framework, Science Advances, Vol. 4, No.6, 29 June

The problem

As the authors state in the article (O’Connor et al., 2018):

From a modeling perspective, the nanoscale represents an interesting domain, because the objects of study (for example, molecules) are invisible to the naked eye, and their behavior is governed by physical forces and interactions significantly different from those forces and interactions that we encounter during our day-to-day phenomenological experience. In domains like this, which are imperceptible to the naked eye, effective models are vital to provide the insight required to make research progress….

molecular systems typically have thousands of degrees of freedom. As a result, their motion is characterized by a complicated, highly correlated, and elegant many-body dynamical choreography, which is nonintuitive compared to the more familiar mechanics of objects that we encounter in the everyday physical world. Their combined complexity, unfamiliarity, and importance make molecules particularly interesting candidates for investigating the potential of new digital modeling paradigms.

Until recently, building dynamic models that operate not only in real time but also in three dimensions required not only specialized virtual reality equipment, but more importantly massive amounts of computing power to handle the visual representation and modelling of highly complex and dynamic molecular activity.

The solution

However, through the use of cloud computing and faster networks, building such models has now become a reality, enabling not only such models to be represented but allowing some degree of real-time manipulation by researchers in different locations but within the same time-frame – in other words, distance research and teaching. 

In the Department of Chemistry at the University of Bristol in the U.K., Dr. David Glowacki and his team in their VR laboratory have created an interactive molecular dynamics modelling tool in the form of Nano Simbox VR, which allows anyone to visit and play within the invisible molecular world. This was made possible through a partnership with Oracle which provided the researchers access to its Oracle Cloud Infrastructure with a grant from the Oracle Startup for Higher Education programme.

The main advantage of the use of a cloud platform is to allow the scaling up of modelling from simple to much more complex dynamic nano interactions and the synchronous sharing of the virtual reality experience with multiple users.

The Nano Simbox VR app allows several people to interact at once with the digital models. Users can download the framework and choose the Oracle data center (Frankfurt, Germany; Phoenix, Arizona; Ashburn, Virginia) nearest to them for minimal network latency. 

The main aim of this particular project is to provide an intuitive feeling of the way molecules operate in multiple dimensions to enable researchers and students to have a better understanding of how nano worlds operate.

The paper published by Glowacki and his team in Science Advances describes how the iMD VR app enabled researchers to

  • easily “grab” individual C60 atoms and manipulate their real-time dynamics to pass the C60 back and forth between each other.
  • take hold of a fully solvated benzylpenicillin ligand and interactively guide it to dock it within the active site of the TEM-1 β-lactamase enzyme (with both molecules fully flexible and dynamic) and generate the correct binding mode (33), a process that is important to understanding antimicrobial resistance
  • guide a methane molecule (CH4) through a carbon nanotube, changing the screw sense of an organic helicene molecule,
  • tie a knot in a small polypeptide [17-alanine (17-ALA)].

Glowacki’s team measured how quickly users were able to accomplish these tasks using the iMD VR app compared with other platforms, and found that in all applications the VR application led to faster mastery.

Comment

This is just one instance where VR is operating at the interface of research and teaching. In particular, its value lies in providing a deep, intuitive understanding of phenomena that are otherwise difficult if not impossible to visualise in other ways.

In some ways this reminds me of the impact of the first mathematics television programs developed by the UK Open University in the 1970s, which included simulations and models of mathematical formulae and processes. This enabled students who were often struggling with the abstract nature of numerical and algebraic calculations to understand in more concrete terms what the calculations and formulae meant.

This intuitive understanding is critical not only for deeper understanding but also for breakthroughs in research and applications of science. In other words, it is a great use of media in education. 

Full disclosure

One of the co-authors of the Science Advances paper is my son, Phil Bates, who is the Oracle Computing  cloud architect who suggested Oracle Cloud Infrastructure to Dr. Glowacki.

 

More developments in teaching science online

Screen shot from A101’s Virtual Reality of Human Anatomy (YouTube)

Matthews, D. (2018) Scepticism over Google plan to replace labs with virtual reality, Times Higher Education, June 7

The Harvard Gazette (2018) Virtual lab to extend reach of science education Harvard Gazette, June 6

It was interesting that I came across these two completely separate news announcements on the same day.

Google and Labster

The THE article is about a partnership between Google and the Danish virtual reality company, Labster. Among the 30 ‘virtual reality’ labs planned are ones allowing training in confocal microscopy, gene therapy and cytogenetics.

Arizona State University, one of the major online providers in the USA, will be the first institution to use the labs in VR this autumn, launching an online-only biological sciences degree. It has worked with Labster to develop the VR labs. Students will require access to their own VR headsets such as Google’s Daydream View, which costs US$99, used in combination with specific brands of smartphones. 

Harvard and Amgen

The second article from the Harvard Gazette announces a partnership between the Amgen Foundation and edX at Harvard University to establish a platform called LabXchange, ‘an online platform for global science education that integrates digital instruction and virtual lab experiences, while also connecting students, teachers, and researchers in a learning community based on sharing and collaboration.’ 

The term ‘virtual lab’ is used differently from the Google/Labster sense. Amgen, a major biotechnology company in the USA, is investing $6.5 million in grant funding to Harvard University to develop, launch and grow the LabXchange platform for teachers and students globally. LabXchange will include a variety of science content, such as simulated experiments, but more importantly it will provide an online network to connect students, researchers and instructors to enable ‘learning pathways’ to be built around the online materials.

Comment

It is interesting and perhaps somewhat unnerving to see commercial companies in the USA moving so strongly into online science teaching in partnership with leading universities.

Of course, the THE had to choose a snarky headline suggesting that you can’t teach science wholly online, rather than have the headline focus on the innovation itself. As with all innovation, the first steps are likely to be limited to certain kinds of online teaching or experiments, and in the end it will come down as much to economic factors as to academic validity. Can virtual labs and online science teaching scale economically better than campus-based courses and at the same quality or better?

More importantly I would expect that the technology will lead to new and exciting approaches not only to science teaching, but also to science research. Already some researchers are using virtual reality and mathematical modelling to explore variations in DNA sequences, for instance. Virtual and augmented reality in particular will lead to science being taught differently online than in physical labs, for different purposes.

At the same time, the two developments are very different. The Google/Labster/ASU partnership is pushing hard the technology boundaries in teaching science, using proprietal VR, whereas the Harvard/Amgen/edX partnership is more of a networked open educational resource, providing access to a wide range of online resources in science. Both these developments in turn are different from remote labs, which provide online access to controlling ‘real’ experimental equipment.

Lastly, both new developments are what I call ‘We’re gonna’ projects. They are announcements of projects that have yet to be delivered. It will be interesting to see how much the reality matches the hype in two year’s time. In the meantime, it’s good to see online learning being taken seriously in science teaching. The potential is fascinating.

How serious should we be about serious games in online learning?

An excerpt from the video game ‘Therapeutic Communication and Mental Health Assessment’ developed at Ryerson University

In the 2017 national survey of online learning in post-secondary education, and indeed in the Pockets of Innovation project, serious games were hardly mentioned as being used in Canadian universities or colleges. Yet there was evidence from the Chang School Talks in Toronto earlier this month that there is good reason to be taking serious games more seriously in online learning.

What are serious games?

The following definition from the Financial Times Lexicon is as good a definition as any:

Serious games are games designed for a purpose beyond pure entertainment. They use the motivation levers of game design – such as competition, curiosity, collaboration, individual challenge – and game media, including board games through physical representation or video games, through avatars and 3D immersion, to enhance the motivation of participants to engage in complex or boring tasks. Serious games are therefore used in a variety of professional situations such as education, training,  assessment, recruitment, knowledge management, innovation and scientific research. 

So serious games are not solely educational, nor necessarily online, but they can be both.

Why are serious games not used more in online learning?

Well, partly because some see serious games as an oxymoron. How can a game be serious? This may seem trivial, but many game designers fear that a focus on education risks killing the main element of a game, its fun. Similarly, many instructors fear that learning could easily be trivialised through games or that games can cover only a very limited part of what learning should be about – it can’t all be fun. 

Another more pragmatic reason is cost and quality. The best selling video games for instance cost millions of dollars to produce, on a scale similar to mainstream movies. What is the compelling business plan for educational games? And if games are produced cheaply, won’t the quality – in terms of production standards, narrative/plot, visuals, and learner engagement – suffer, thus making them unattractive for learners?

However, probably the main reason is that most educators simply do not know enough about serious games: what exists, how they can be used, nor how to design them. For this reason, the ChangSchoolTalks, organised each year by the School of Continuing Studies at Ryerson University, this year focused on serious games.

The conference

The conference, held on May 3rd in Toronto, consisted of nine key speakers who have had extensive experience with serious games, organised in three themes:

  • higher education
  • health care
  • corporate

The presentations were followed by a panel debate and question and answer session. The speakers were:

This proved to be an amazingly well-selected group of speakers on the topic. In one session run by Sylvester Arnab, he had the audience inventing a game within 30 seconds. Teams of two were given a range of  existing games or game concepts (such as Dictionary or Jeopardy) and a topic (such as international relations) and had up to two minutes to create an educational game. The winning team (in less than 30 seconds) required online students in political sciences to represent a country and suggest how they should respond to selected Tweets from Donald Trump.

I mentioned in an earlier blog that I suffered from such information overload from recent conferences that I had to go and lie down. It was at this conference where that happened! It has taken three weeks for me even to begin fully processing what I learned.

What did I learn?

Probably the most important thing is that there is a whole, vibrant world of serious games outside of education, and at the same time there are many possible and realistic applications for serious games in education, and particularly in online learning. So, yes, we should be taking serious games much more seriously in online learning – but we need to do it carefully and professionally.

The second lesson I learned is that excellent online serious games can be developed without spending ridiculous amounts of money (see some examples below). At the same time, there is a high degree of risk. There is no sure way of predicting in advance that a new game will be successful. Some low-cost simple games can work well; some expensively produced games can easily flop. This means careful testing and feedback during development.

For these and other reasons, research being conducted at Ryerson University and funded by eCampus Ontario is particularly important. Naza Djafarova and colleagues at Ryerson’s Chang School of Continuing Education are conducting research to develop a game design guide to enhance the process by which multidisciplinary teams, engaged in the pre-production stage, approach the design of a serious game. They have developed a process called the Art of Game Design methodology, for multidisciplinary teams involved in the design of serious games, and appraised in participatory workshops.

The Chang School has already developed a few prototype games, including:

  • Lake Devo, a virtual learning environment enabling online role-play activity in an educational context. Learners work synchronously, using visual, audio, and text elements to create avatars and interact in online role-play scenarios.
  • Skills Practice: A Home Visit that promotes the application of knowledge and skills related to establishing a therapeutic nurse-client relationship and completing a mental health assessment. Students assume the role of a community health nurse assigned to complete a home visit. Working with nurses and professors from George Brown College, Centennial College this project is working to establish a ‘virtual hospital’ with several serious games focused on maternity issues.

Thus serious games are a relatively high risk, high return activity for online learning. This requires building on best practices in games design, both within and outside education, sharing, and collaboration. However, as we move more and more towards skills development, experiential learning, and problem-solving, serious games will play an increasingly important role in online learning. Best to start now.

Open and remote labs from the UK Open University

The Open University’s remote access electron microscope set-up

On my recent visit to the UK Open University, I had the privilege of a guided tour of the Open University’s remote labs. These allow students to log on from anywhere and conduct experiments remotely. The tour was courtesy of Professor Nick Braithwaite, Associate Dean (Academic Excellence), Faculty of Science, Technology, Engineering & Mathematics.

Note that remote labs are somewhat different from simulated online experiments, where students interact by entering data or clicking and dragging on screen items. With remote labs, the equipment being operated is real, with the students actually controlling the equipment in real time as well as recording and interpreting data. 

The OpenScience Laboratory

The OpenScience Laboratory is a means of conducting authentic and rigorous investigations using real data and is globally available. It is an initiative of the Open University and the Wolfson Foundation. It includes:

  • Remote Experiments
  • Virtual instruments and interactive screen experiments
  • Online field investigations
  • 3D Immersive environments
  • Citizen Science
  • Research and development 

There are altogether more than 50 self-contained open educational resource modules in experimental science, in the OpenScience Laboratory, each taking somewhere between one to three hours of study to complete.

As an example, there is an experiment to identify what causes variation in species of heather on English moorland. It is a combination of an online video recorded on site in English moorland and guided student activities, such as taking simulated measurements and calculating and interpreting data. The video is divided in to 23 parts, showing how measurements are made in the field, how to calculate slope, water flow, and organic soil depth, and how to take simulated measurements, to test the hypothesis that different types of heather are associated with different levels of slope in moorlands. This took me a couple of hours to complete.

The heather hypothesis

The OpenSTEM labs

The Open STEM Labs are part of the OpenScience Laboratory project.

The OpenSTEM Labs connect students to state-of-the-art instrumentation and equipment for practical enquiries over the internet, where distance is no barrier and where access to equipment is available 24 hours a day.

Students and teachers access the equipment via a web browser through which they can view the experiment, send real-time control commands, monitor real-time performance and download data for subsequent analysis. Using remotely accessible hardware for laboratory and exploratory studies, ranging from electronics to chemical synthesis and from microscopes to telescopes, students are able to access the various instruments and other remote controlled resources virtually anytime from anywhere with an internet connection.

The new facilities are available to students studying Open University modules and may be available by subscription to other institutions of higher education.

Figure 1 below indicates the relationship between the Open Science Labs, OpenSTEM Labs and remote labs.

The Open University’s remote labs

Below are links to some of the diverse range of equipment available. Simply click on a link and this will take you to that experiment’s landing page, as seen by the OU’s students. Here you will then be able to access the equipment. Please note that you may have to book a session if all pieces of that equipment are being used by others. If you do book a session you should enter the experiment through the booking system at the allotted time. This will take you straight through to the equipment. (Not all these are currently operational at any one time and you may need to register first to get access).

The OU also has scanning electron microscopes, an auto-titrator, and a radio telescope available on request from those with direct experience of these curriculum areas. Please email OpenSTEM to arrange access and further briefing.

A student’s desktop view of the eye of a fly seen through the OU’s electron microscope. The student can manipulate the electron microscope to get different degrees of magnitude.

Many of the remote lab experiments are part of the Open University’s MSc in Space Science and Technology.  This includes student remote control of a model ‘Mars Rover’ operated in a mock-up of the surface of Mars.

The OU’s model of the Mars Rover

Comments

The Open University has added a new set of quality online resources in experimental science and technology to those currently offered by, among others:

I would welcome suggestions for other sources for high quality OER in experimental science and technology..

However, many more are still needed. We are still a long way from being able to build an entire high quality experimental science or technology curriculum with open educational resources. As well as increasing quantity, we need better quality resources that enable student activity and engagement, that include clearly understandable instructions, and that result in a high level of scientific inquiry. The Open University resources meet these standards, but not all other OER in this field do. Also there are issues of scalability. One needs enough students to justify the investment in software, production and equipment, especially for remote labs and quality simulations. Sharing of resources between institutions, and between departments within institutions, is therefore highly desirable.

Thus there is still a long way to go in this field, but progress is being made. If you teach science or engineering I recommend you look carefully at the Open University’s resources. It may stimulate you not only to integrate some of these resources into your own teaching, but also to create new resources for everyone.

Meeting the challenge of online degrees for the professions

 

Tina the Avatar from Drexel University’s nursing program. Tina not only responds to questions asked by students but can also be physically examined and will respond according to how she is being treated.

Chatlani, S. (2018) Navigating online professional degrees – potential and caution, Education Dive, March 21

In previous posts, I have pointed out the challenges of getting online qualifications recognised by professional associations, for instance:

The Chatlani article though shows how some institutions have worked with professional associations to obtain recognition.

Which institutions have received recognition from professional associations?

Chatlani looks at several institutions who have succeeded in getting their online professional degrees recognised. These include:

  • Syracuse University College of Law
  • Western Governors University College of Health Professions
  • Faulkner University’s Masters of Science in Counseling
  • The Santa Barbara & Ventura Colleges of Law

To these institutions I would add a couple of Canadian examples:

Some of these programs are not fully online, but are hybrid, with a good deal of online learning however.

How to get online professional degrees recognized

First, it ain’t easy. It’s no good just trying to convert your on-campus content into an online version. You have to do much more to satisfy professional associations – and quite rightly, in most cases.

The biggest challenge is providing a satisfactory online context for experiential learning: enabling students to apply what they have learned in an online environment that is ‘real’ enough to transfer to an actual workplace. Typical examples would be:

  • use of video, computer simulations, and augmented or virtual reality to teach procedures and/or motor (hands-on) skills
  • use of remote labs/equipment that students can manipulate online
  • ‘virtual’ offices, companies or workplace situations that mirror real companies and their work
  • online development of inter-personal skills through one-on-one online monitoring
  • use of synchronous as well as asynchronous delivery: Syracuse designed their law program so that 50% of each online course will be in real time with students and professors interacting just as they would in a residential program, with intense Socratic dialogue in real time
  • on-campus evaluation of specific skills, such as counselling, even if they are taught online.

In addition to providing appropriate experiential learning, there are general quality issues to be addressed:

  • secure validation of student identity and online assessment;
  • investment in ‘best practice’ online course design, which will involve using learning design and learning technology specialists;
  • opportunity for substantive interaction between faculty and students; 
  • close monitoring of student activities;
  • extensive training of faculty in online teaching.

This is rather a daunting list, even if not all of these requirements apply to all professional training.

Will it be enough?

One has to look to motive here for moving online. One motive is a scarcity of professionals (or more likely, a coming scarcity). This is one major reason for Queen’s University’s Bachelor in Mining Engineering. A shortage of professionals pushes up the costs of professionals and  a shortage of professionals may mean that there are unacceptable delays in court cases (as in Canada), for instance. Offering programs partly or wholly online enables those working or with families to study more flexibly and in the end results in a larger pool of professionals.

Another motive is cost: the cost of traditional, on-campus professional degrees is often so high that many who could benefit from such programs are just unable to afford it. The hope is that online programs can bring down the cost without losing quality.

Chatlani interviewed Christopher Chapman​, CEO of AccessLex Institute, a legal education advocacy group, who argued the hybrid degree option is necessary to make becoming a lawyer more accessible and possibly less expensive:

Truly experimentation in legal education is critical to the long-term future of the field and lawyers. This could allow for the development of better pedagogy and allow for scaling where schools may be able to eventually lower their price point.

However, often professional education does not necessarily scale easily as it may require fairly small class sizes if quality is to be maintained. This is not to say there are no economies of scale: once a simulation or a virtual reality environment is created, it can be used many times with many students, but this often means not only a heavy up-front investment, but also a sophisticated business model that allows for return on investment over several or even many years.

It is worth noting that none of the example institutions above are what might be called elite institutions, who have dominated education for professionals in law, medicine and engineering for many years, and whose alumni are often the ones who set accreditation requirements for the professional associations.

And this is the problem. It benefits existing professionals to limit the number of new professionals by making existing labour scarce. If the people who are responsible for accrediting educational programs for professional recognition benefit by keeping the market restricted and themselves come from elite institutions with no experience of online learning, then online professional programs become a huge risk for the departments planning to offer them and for the students who sign up for them.

The best approach is to ensure the support of the relevant professional associations before investing heavily in such programs. The worst case scenario is to spend lots of money on developing such programs only for students to find that they still cannot get a well paid professional job with their qualification.