Well here we are going on our third week of sheltering in place, but it is still possible to go outside and verify that the sky is not falling and the planetary orbits are still orbiting and still find time to study physics and virology online.
Last night, I went outside with my flimsy tripod and DSLR and verified that the sky has not fallen. Here we see the result of 3 minutes time to carry out the camera, setup and focus and take a photo of Venus close to the Moon. It would of normally just taken 2 minutes, but in this case I took an extra minute to see if I could get some trees in the foreground. Nope, couldn't be done; but here is the Moon and Venus in this 75 mm telephoto, 1/4 second DSLR exposure.
|The sky is not falling and the Moon and Venus are close to conjunction (Source: Palmia Observatory)|
So we just received word that our June tour of Transylvania and Ukraine has been officially cancelled. No need to search for vampire monsters when we are already under attack from virus monsters! This is a minor inconvenience for us compared to all of those who are out of work due to the pandemic. But we have been getting ready for continuation of our physicist wannabe journey and have three recommendations for ongoing study in our new isolated environments. The three video lecture series from Coursera are starting up again. You can watch the lectures at your own leisure, but if you want to participate in discussion with other students and do the homework, you probably should start now.
First up is a course on general relativity, which I tried to stagger through way back in 2016, which I guess was 4 BCV (Before Corona Virus)! Dr. Emil Akhmedow from the Russian Higher School of Economics University delivers again a very technical series of lectures. Check out the screenshot below and if the math scares you now, trust me he is just getting started. For me, this time around, I finally get what the hyperbolic diagram means about the case for constant acceleration. By the way, you will enjoy just watching how he appears to be able to write so well on the transparent blackboard!
|Dr. Emil Akhmedov lectures on General Relativity (Source: www.coursera.org)|
Next up is Professor Mike Brown, Caltech, who is also the same guy who helped kill Pluto, offers his course on the Science of the Solar System. This course is full of interesting topics and is much easier to understand and uses a lower level of mathematics.
|Professor Mike Brown, Caltech, talks about the science of the solar system (Source: www.coursera.org)|
Next up is Professor George Djorgovski, Caltech, who offers a course on the Evolving Universe. Here you will hear all about evolving galaxies and such. When I first took this course it was free, but it might cost a little bit now.
|Professor George Djorgovski ,Caltech, teaches course of the Evolving Universe (Source: www.coursera.org)|
Ok, we have time now to review some of the other scientific topics found in the ongoing Virology course. But first we should remind folks again about some weekly videos updating the current status of the coronavirus in the country and around the world. Enjoys Living in the Mountains, David, mentioned how much he likes the MedCram video series by Dr. Roger Seheult, as first mentioned here in the March 21 blog post. Thanks for that, David! You can check out the latest MedCram at:
In addition to the virology series of lectures by Dr. Vincent Racaniello, Columbia U., where he describes the established science of virology, he also provides a weekly update on the status of the spread and impact of the current pandemic on an internet production called "This Week in Virology." You can check out the latest episode at:
|Very informative weekly update from Columbia Professor of Virology (Source: Vincent Racaniello)|
And for up to date statistics you can check out the John Hopkins University Dashboard.
|Current status of worldwide coronavirus cases (Source: https://coronavirus.jhu.edu/map.html)|
So, check out those three mentioned sources for current information and handling of the pandemic. Now though, let's return to the science of virology and some interesting topics there. I found two interesting area to mention today. The first is about a problem that comes up when animals, such as mice are used to study the effects of viruses and vaccines, which is that mice are often no susceptible to many viruses.
|Humans and animals differ in viral susceptibility Columbia Professor of Virology (Source: Vincent Racaniello)|
If the animal does not have the receptor buried in its cellular membrane that the virus relies on to gain entry into the cell, that animal can't be used in testing. The virus only attacks living cells with the right kind of molecular receptor. Here you can see some examples of the types of molecular receptors in the cellular membrane. When a given receptor is activated by a molecule outside the cell, much like a lock and key, the cell responds by bringing the molecule inside the cell or by taking some other course of action. All of this is just natural requirements of the living cell.
|Membrane receptors, necessary for life, also enable viral entry into the cell Virology (Source: Vincent Racaniello)|
But it is possible now using enzymes, originally found in bacteria, to insert the molecular receptor, found in human cell, into the cells of the mouse or other animals. Here we see an example where the human receptor molecule that is also used by the polio virus to get inside the cell, is inserted into the mouse's cells. Now all the mice that have this work done are susceptible to polio and sadly, but thankfully for us, will contract the disease and can be used in research.
|Inserting the human polio virus receptor into mice from Columbia Professor of Virology (Source: Vincent Racaniello)|
So this lock and key concept and how the lock and key keep changing is part of the host-virus arms race. The receptors in the living cell membrane cannot easily be changed since they are necessary for the ongoing life processes of the cell. But some changes that don't interfere too much with cellular processes can be made which interferes with the viral entry into the cell. But, the virus is always evolving and changing and the arms race continues. At the same time, the human immune response in trying to ward off the viruses often causes additional risk itself because of inflammation and other effects.
|Viral host-virus arms race as described by Columbia Professor of Virology (Source: Vincent Racaniello)|
The second topic in the virology lectures that was especially interesting was the topic of evolution and viruses. This topic brings us right back to physics and information theory and the mathematics of combinatorics. For instance, in the last post we learned that the primers used in the PCR test were usually about 20 base pairs long. Now out of a virus of 29,000 base pairs, what is the likelihood that somewhere in all of those pair there will be not just one instance, the one that we are looking for, but two instances of that same combination used to make up the 20 base pairs? Well, my combinatorics theory is not the best but to me I see how you can calculate this probability. There are 29000 - 20 ways of arranging the 20 base pairs of the primer along the total length of 29000 base pairs and each one of them could be a valid condition. So, for every instance where the 20 base pairs is possible to be found there are 4 to the (29000 -20 ) power of ways that are completely compatible with that assumption. But the total 29,000 base pairs can be arranged in 4 to the 29,000 power. So after some calculation, diving numerator by denominator, I find that the odds of finding two identical arrangements that match the primer configuration are really quite low at about 2 times 10 to the minus 8. That is about 2 times out of a hundred billion. Maybe Math Whiz Dave can check my assumptions?
Ok, but we know for viruses, especially those based on RNA, like the current coronavirus and the common cold and flu, that RNA can mutate just by chance errors which happen much more that do viruses based on DNA because DNA replication has much more error correction built into the process. What will this mean for us? Well it means that we need to get the flu vaccine every year because the darn virus keep on mutating naturally just by errors that occur in the copying process. Yep, Darwin would have loved viruses because you can see mutation and evolution happening right in front of you in terms of days or years, not millions of years.
|Darwin had the insight to see evolution, but it would have been much easier with viruses (Source: Vincent Racaniello)|
In this slide we see the mutation rate expected for RNA viruses. This is why this type of virus makes it hard to develop a once and forever vaccine.
|Viral mutation rate for RNA based viruses as seen by Columbia Professor of Virology (Source: Vincent Racaniello)|
Here is an example for the influenza type virus mutation from 1918 to today. Also notice how the virus often comes from ducks and swine and then mutates to survive and multiply in humans.
|H1N1 virus mutation from 1918 to today and into the future (Source: Vincent Racaniello)|
The mutation rate in RNA viruses is so high that it is hard to make a vaccine that will work longer than a year. Check out the comparison between mutation rates for DNA based organisms, like humans, and that of RNA based viruses. The 2% difference in the genome between man and some earlier monkey ancestor took about 8 million years, but the same 2% difference in the virus's RNA can be seen in just 5 days. Wow, it is going to be hard to keep up with this mutation rate!
|Getting 2% change in genome for humans and viruses from Columbia Professor of Virology (Source: Vincent Racaniello)|
So what does this fast mutation and therefore possibly evolution of viruses mean? Here is where it gets interesting in that the probabilities coming from information theory and physics get together. The information content in bits for a typical virus in one mathematical sense exceeds the number of atoms in the whole universe. We have seen in previous papers and blog posts how information seems to be a very basic constituent in the universe and some physicists try to develop a consistent theory of how gravity and other forces comes about because of changes in information and entanglement. That is some pretty far out there stuff, but when you see how much information could be stored in the long stretches of viral RNA/DNA it is pretty amazing.
|More potential information in 10-kb viral genome than the number of atoms in the universe (Source: Vincent Racaniello)|
So how do we learn about mutation rates and look back in time to trace the origin of viruses? Well, mutation rates can be calculated based on chemical principles and sequences of virus genome, as well as other organisms, show how much change is needed to transition from one instance of a virus to another instance at a different time. So, this mutation rate serves as sort of a molecular clock. Astronomers are used to looking back in time from observations made today and biologists can look back in time by calculating and looking at fossils.
|Molecular clocks can trace the history of viruses (Source: Vincent Racaniello)|
So if we look far enough back in time what does that tell us about the origin of viruses? Well that is still an ongoing work but it is clear that viruses and living organisms seem to originate at about the same time. It could very well be that the first forms of life were based on RNA and viruses could have been an essential part of the beginning too. This slide shows some of the thoughts on the topic. Of course, if you are interested in these topics, be sure to check out the actual video lectures for more of the details.
|Origin of viruses as discussed by Columbia Professor of Virology (Source: Vincent Racaniello)|
Until next time, here from our burrow, stay sane, stay safe,