Category: random

Link to Science article re genomics of current outbreak

I keep a small notebook around with me to jot phone numbers, clinical data, and random ideas. It is a kind of fossil of the pre-digital age that persists. When someone finds my box of these notebooks, they will think my life was consumed by frustrated novel writing, grocery lists of esoteric food items, and vascular ailments. They would be correct. Here are my top ten thoughts about Ebola.

1.  Ebola is an RNA virus which likely has its origins in the most ancient recesses of life on earth. Likely during the prebiotic Hadean era, roughly a quarter billion years after earth solidified and liquid water started to coalesce into oceans, these molecules began replicating themselves within the primordial soup that made the whole planet a single cell, with chemical reaction times stretched over eons rather than seconds. When some of the molecules found shelter in enclosing the sea in a phospholipid bilayer, maybe some sudsy foam at the edge of an acid sea, these replicating molecules followed. The ribosome, transcription RNA, and other ribonucleotide based molecules in our cells are the friendly remnants of these molecules. Ebola is the stranger that comes to take life from our cells.
2.  This RNA world hypothesis is an idea first posited in the 80’s by Dr. Walter Gilbert, and RNA prefers an acidic, anaerobic environment, which is what is proffered once Ebola takes hold in the vasculature. The liver seems to be the place where Ebola’s fire ignites, and it offers the low oxygen, acidic environment that echoes the flavor of that primordial soup.
3.  Edema due to vascular leak results in eventual dehydration, and more anaerobic, acidic environs to run in. Patients who are well hydrated and kept euvolemic seem to do better per reports on the web. To this, I would add well oxygenated which would become harder to achieve with third spacing into the lung. Is there a role for active alkalinization. Patient’s who have filled their lungs with fluid -is there a way to push forward development of an oxygenator that is inserted into the central veins.
4.  Coherent light can cause particles of specific dimensions to resonate. Can this be a way of disrupting 80nm width virus particles? A light emitting catheter that uses laser energy to split virus particles while leaving other blood elements intact -for advance infections. Plasmonic resonance I believe it’s called.
5.  The current movement of Ebola patients out of general hospitals puts into sharp relief the importance of training and will in controlling difficult medical problems and the role of specialty centers of excellence. Medecins Sans Frontieres are able to achieve in a rude tent in the fever jungle what country club hospitals cannot. Generations of domination over infectious diseases has bred complacency as few remember polio quarantines and no one remembers the Spanish Flu pandemic of 1918. At Columbia P&S, in the student lounge, there was a plaque dedicated to the 20 medical students who died while caring for victims of that pandemic that took millions of lives. At that time 20 years ago, dying from an infectious disease seemed quaint and atavistic, just bad luck like dying from a plane crash or shark attack. Now, we’re not so sure.
6.  n=e^(qt) where q determines the rate of exponential growth. What is different about this outbreak compared to numerous others? The q may be different because of different factors but it starts with knowing the sequence of this Ebola compared to others. Also, the population density or temperature or inoculation may have been higher because of deforestation, climate change. Time will tell. The evidence thus far is that it is not airborne.
7.  The thing not often talked about in the Irish Potato Famine is the poor potato. Crowded into unending fields of monoculture, often by cloning via sprouting the “eyes” of the potato, it left it vulnerable to the potato blight. We are an unending field of monocultured humans when we look at cities of 10, 20, 30 million pressed back to front. Typically, human overpopulation is seen to be treatable through some combination of education, development, and draconian laws, because it is in our nature to be fruitful and multiply. Even plagues and wars fail to remove our reproductive drive. I feel least optimistic about this, and feel fraternity with the Irish Potato.
8.  Soap and water. Alkalinizing and oxidizing. Bleach. Peroxide. Alcohol? How do you kill something that is lifeless? We will be dealing with this for a long time but it won’t be like HIV. I have been stuck with needles from HIV+ patients and lived, and my biggest immediate fear then, even 10 years ago, was hepatitis, not HIV. This different.
9. Hackathons solve some hefty problems related to data security. We don’t have hackathons for these kind of medical and scientific problems. All the scientific disciplines have specialized to the point that its rare for people of different disciplines to synthesize and collaborate. I have socialize regularly with a physicist and live across the street from virologists. I had half a mind to bring them all together, and my physicist friend had the same thought. He works on plasmonic resonance -I won’t get into the math but at the size of nanoparticles, which are the size of Ebola virions, things resonate when hit with a particular frequency of light resulting in chemical changes. The problem is its too dangerous to work with Ebola directly, but the principles of phototherapy for example could be worked out in a model using plant RNA viruses -and we have a world leading lab here in Cleveland. Every university town in fact has the human capital to do something, but the way we have structured science and discovery works against multidisciplinary work. There should be a Cleveland Project, a Boston Project, a Berkeley Project, an Austin Project and so on. Let the hackathons begin.
10.  We survive as communities. The biggest lesson Zombie movies have for us is that the real monster is the unfriendly human. The other hidden lesson is that going it alone is unwise. We are evolved as social animals that hunt in packs and keep secure in numbers. That means we need each other more than ever before.