Wednesday, June 5, 2019

CRISPR - The What, How and Why...

I gave a talk on CRISPR - A Gene editing tool under the auspices of Varahamihira Science Forum on 25th May 2019 at Tamil Virtual Academy, Kotturpuram, Chennai.

Background: There is so much excitement and apprehension about this in the scientific community. As a person who follows the developments in science and technology to the best of my ability, i wanted to know more about CRISPR and purchased Jeniffer Doudna's 'A Crack in Creation'.

Jeniffer Doudna is a leading figure in the CRISPR revolution and in 2012,  she along with Emmanuelle Charpentier were the first to propose that CRISPR/Cas9 enzymes from bacteria could be used for programmable editing of genomes.  

After reading the book and more articles , I understood why people were excited and apprehensive about CRISPR, all at the same time. Thought that it would be a good idea to talk about this to general public so more people are aware of what CRISPR is and why we , the general public, need to be aware of the technique , so we can make sense out of articles in news magazines or legislations/ guidelines government have come out with or may in the future.


CRISPR - What is it ? How does it work ? Why do we need this conversation ? 

Purpose of the talk was to provide a high level overview of CRISPR - a targeted gene editing technique , potential applications and the ethical questions that we as a society need to face. In the process answer the above questions.

Objective of the talk was to help the lay person make sense of CRISPR and better understand the news items, debates and articles surrounding the same. Through reference to articles and books, it also aims to be a launch pad for people who wants to explore CRISPR further.


Here is the video of the talk.

Here is a link to the presentation i used for the talk. It has got references to the data i shared in the talk and also mentions the books and links for further study.

I also thank Varahamihira Science Forum, a group that is doing yeomen service in popularising science to the common folks, for giving me this opportunity to talk about CRISPR and to all the people who attended the talk in person/ watched on youtube and came back to me with questions and suggestions.

Happy learning.

Wednesday, April 3, 2019

737-Max controversy, Bad Software and a lot more....

An employee walks down a stairway leading to a Boeing 737 MAX airplane on March 14, 2019, in Renton, Washington.*

Being in the software industry for more than 2 decades, i confidently say that Bad software is never a problem, but always a symptom of something more serious. 
In this case of 737-Max controversy, greed and a tendency to retain their market, whatever be the cost ( now it is 40 billion in the red and counting).
Here is a summary of what i understood. I recommend that the article as a must read.
  1. Airbus and Boeing are two major manufacturers and competitors 
  2. Introducing a new plane is an expensive and time consuming process. In addition to the time taken to design and build a plane ( which is typically more than a decade), FAA approval and pilot training all adds time and cost to the process
  3. AirBus introduces the Neo engine which is more fuel efficient and Boeing doesn’t have an equivalent offering in its portfolio
  4. Boeing’s design prevents them from replacing the existing engine with a more fuel efficient engine
  5. Best solution would have been to work on a newer Airplane
  6. Boeing is a major employer and has a powerful lobby in Washington
  7. Boeing goes ahead and decides to plug in a new engine to the existing 747 body though it kept talking about 5
  8. It is no longer the same plane and the aerodynamics are different. This plane has a different angle of attack
  9. But you can’t beat the laws of physics and a software is introduced to handle the complications introduced by step 7
  10. FAA is understaffed and important steps in validation and verification are done by Boeing themselves
  11. Also remember the pressure brought in by a company's loss looked upon as the country's loss
  12. Since everyone assumes it is the same plane design training is limited to what can be done on a tablet ( iPad )
  13. Pilots do complain, but it is overlooked 
  14. A cockpit light is introduced to warn pilots when the angle of attack sensors disagreed
  15. But then the light is made optional and costs 80,000 USD
  16. Lion Air and Ethiopian Airlines buy it without the light

The article explaining the 737-Max scandal can be read here.

* Image Source - the Vox article

Wednesday, March 27, 2019

“Feynman, Flexner and The Cluetrain Manifesto...” Notes from a conversation with my friend's son

Background: The kid’s parents are close friends for more than 20 years and i know the kid from the time he was born. While we were discussing  the Indian Origin Fields Medal Winner and were googling the youngest fields medal winner, the Kid joined us in our discussion. He is presently in his 11th standard and in a school where IIT-JEE preparation is part of the curriculum.  I enquired about this experience and he responded that there is lot of focus on just solving problems. He mentioned that the typical approach is ‘These are the steps and this is how you solve the problem and they don’t teach the principles behind the problem and don’t give it enough time. Even if we ask, there is no proper response’. And added that for some of the things he reads, he wondered why they are needed and how they were useful.

When  i mentioned couple of points from the conversation to other kids/ parents in the last 6 months, i decided to write it down before i  forget ;-)

What follows is a summary of  the conversation the parents, the kid and I had. It went on for nearly an hour. Have detailed out on the quotes and added references at the end, for further study.

Thanks to my friend for giving me permission to share this in public.

Preparing for Entrance Exams / Competitive Exams is a separate Skill set and is not the same as knowing the subject well. Competitive exams like IIT-JEE belong to this category and you should learn how to prepare and solve the problem in the time provided. It is a skill worth learning because that is how the exam is structured and it has to be handled accordingly. And it is not a bad skill to master. Don’t confuse it with knowing a subject well.

And when it comes to knowing about a certain subject/ idea in detail, you have to know that there is a vast difference between knowing something superficially and knowing it really well enough to talk about characteristics/ attributes/features/use. To quote Feynman, “we should know the difference between knowing the name of something and knowing it”.

When it comes to learning something, there is this concept of first principles. First principles are the fundamental building blocks of knowledge. If you understand the first principles of a concept , you will be able to break down even complex problems into basic elements and solve it .

To give you an example, if we, the Human race, are in a position where we will lose all knowledge gained so far, and can remember only one sentence, what do you think it will it be?

To quote from Feynman’s Lectures on Physics Vol-1, “If, in some cataclysm, all of scientific knowledge were to be destroyed, and only one sentence passed on to the next generation of creatures, what statement would contain the most information in the fewest words? I believe it is the atomic hypothesis that all things are made of atoms — little particles that move around in perpetual motion, attracting each other when they are a little distance apart, but repelling upon being squeezed into one another.In that one sentence, you will see, there is an enormous amount of information about the world, if just a little imagination and thinking are applied.”

You can use ideas like five Whys to put this into practice. So this is something that you have to think about, learn and put to use and will be useful during Research.

Also,  you should learn to connect what you already know to what you learn new.

If i mention Arjuna, would you connect it with Ambidextrous ? Remember , he is also known as Savyasachi or the one who can draw an bow with both hands. This is an additional data point that you remember about Arjuna, and it also helps to connect all the people who are ambidextrous.

The point here is that when you learn a new concept, try to link it to what you already know. Our brain works better when what we know is connected because . More synapses are formed,  brain is healthier and information retrieval is faster. Just as orphan table is useless in a database, facts/ information/ideas that are unconnected are of no use since they can’t be retrieved and hence can’t be put to use when needed..

Charlie Munger, Warren Buffet’s partner calls it a Lattice of Knowledge. This kind of learning takes time because it means constant shuffling around of what you know, whenever you acquire new knowledge. But believe me, it is worth the time spent.

You mentioned that you weren’t sure if some of the concepts / ideas that you learn is useful. Please understand that nothing in science is useless.  The people who came up with new inventions / discoveries didn’t care about whether it was useless or useful for human beings . they didn't do it for fame or money. They did it because they wanted to learn/ were curious and know. Simply put , driven by curiosity and passion.

Maxwell didn't do his work on electromagnetism because of money.  The radio, as Marconi built it, wouldn't have been possible without the work of Maxwell and Hertz. I recall a conversation between Abraham Flexner and George Eastman ( of the Kodak Company) where George Eastman mentioned Marconi as the most useful worker in science and Flexner countered that the building blocks for Radio were already in place due to the work done by Maxwell and Hertz and Marconi put them together. .

Flexner says that Maxwell and Hertz didn't have the use of the theoretical work in their mind and where driven only by curiosity. To quote Flexner, "...curiosity, which may or may not eventuate in something useful, is probably the outstanding characteristic of modern thinking. It is not new. It goes back to Galileo, Bacon, and to Sir Isaac Newton, and it must be absolutely unhampered. Institutions of learning should be devoted to the cultivation of curiosity and the less they are deflected by considerations of immediacy of application, the more likely they are to contribute not only to human welfare but to the equally important satisfaction of intellectual interest which may indeed be said to have become the ruling passion of intellectual life in modern times."

Faraday and Maxwell did all the groundwork for the amazing technological breakthroughs in the 20th century. But they didnt do all their work knowing/expecting such progress.

I recommend that you read Flexner’s classic essay ‘ The usefulness of useless things’ . He wrote this essay to define the Philosophy of the Institute of Advanced Studies, Princeton , New Jersey. If you can’t read the complete article , which i want you to read, please read my short notes on the article here.

In today’s world, being able to make connections between seemingly unrelated things is a highly sought after skill set. Just some time back, your dad mentioned that he was able to make progress in his research based on what he learnt from a conversation with a visiting professor. He didn’t know the in-depth details of the problem solved, but knew enough to make the connection between his area of research and the professor’s and ask if it helped progress in his own area of work.  Fortunately for him, it did.

This is typically an outcome of a knowledge that is a mix of deep expertise in one area and a broad skill sets and awareness. You can call this a T model of learning.   This kind of circles back to the lattice of knowledge idea. The links that we form become the key. The links don’t provide the answer, but leads us to people/ideas that help provide the answer.  It is like a chain and you may have to travel a single link or multiple links.

Remember, before the internet era, an expert was some one who knew lot of information on a topic. But the internet, has kind of levelled that. What you want to know is out there.  So knowing a lot about an area is no longer a big thing because however much you know, you still know only a thin slice. So this expertise , while still valued, is no longer as useful, as it was.

You may ask, what kind of expertise is useful then ? An useful expertise is to not necessarily know all the answers, but to know where and how to find them.  Wy go around carrying all the answers when you know where to find it ? So an Expert is the person who when you ask a question, will not just say , ‘i dont have the answer’ but can add, ‘ Think you can read that book, refer this web page or talk to this person to progress towards a solution’

To quote from this book called ‘The Cluetrain Manifesto’ , “ The new experts have value not by centralising information and control but by being great "pointers" to other people and to useful current information.”

And last but not the least, i see that writing skill doesn’t rank high in skill sets needed today. and today’s kids are hesitant to write by hand,  and that includes my son. Writing is an excellent way to structure and articulate your thoughts and you become better at shaping and presenting your ideas. It helps your thinking process. Please keep a journal and write about what you read, the books you read and your thoughts. You don’t have to necessarily publish it /  make it public. Share it with your parents, if you want, but do write.


Monday, March 4, 2019

From Modularity to Emergence - A Primer on the design and #Science of #Complex #Systems.

"Electrical networks, flocking birds, transportation hubs, weather patterns, commercial organisations, swarming robots... Increasingly, many of the systems that we want to engineer or understand are said to be ‘complex’. 

These systems are often considered to be intractable because of their unpredictability, non-linearity, interconnectivity, heterarchy and ‘emergence’. 

Such attributes are often framed as a problem, but can also be exploited to encourage systems to efficiently exhibit intelligent, robust, self-organising behaviours. 

But what does it mean to describe systems as complex? How do these complex systems differ from the more easily understood ‘modular’ systems that we are familiar with? What are the underlying similarities between different systems, whether modular or complex? 

Answering these questions is a first step in approaching the design and science of complexity. However, to do so, it is necessary to look beyond the specifics of any particular system or field of study. 

We need to consider the fundamental nature of systems, looking for a common way to view ostensibly different phenomena."

The document can be accessed here