Microbiomes: The middle road to understanding

     "Western" medicine is excellent on the mechanics of the body -- replacing a hip, changing out a lens for the eye, insert a replacement cochlea, add an artificial replacement limb, and so forth. When it comes to working with the biochemistry of the body, it is more hit-and-miss and many discoveries have been serendipitous findings rather than the tail end of a focused search. Some aspects of interactions have been investigated and understood but, still, more from the point of view of mechanics -- receptacle points, chemical reactions, and enzymal subsystems.

     "Eastern" medicine has a longer history of treating the body, mind, and functioning as a holistic system -- recognizing that the mind (whatever that is), soul (whatever that is), and body all interact to make us live, react, and process life the way that we do. There is a tradition of building up longtime knowledge of the effects of various herbs, foods, and other substances with the way the body works. The manner in which such substances interact with the body are subsumed into spiritual, and traditional, teachings which often use words without specific "western" definitions.

     All approaches, and knowledge, can be of benefit.  Divisions between areas of knowledge are only useful for classification. "Western" medicine is becoming more interesting in energy aspects, such as chi. "Eastern" medicine is more allowing of the uses for engineering aspects of treating bodily ailments. Perhaps at some point, no divisions or classification will shine out.

     One area of development which is more in the "middle" of such development is research into the microbiomes of the body. As a recent "Gates Notes" blog indicated, a large percentage of our bodies are actually cells not directly part of the body. Most of such are beneficial and many are symbiotic. His blog emphasizes uses of pro- and prebiotics to help the microbiome in their tasks and provide a better symbiosis with the body. There are also books on microbiomes, a major tome of which is "I Contain Multitudes" by Ed Yong.

     Gates' blog emphasizes the role of the microbiome as applied to treatment of malnutrition. My own older blog on microbiomes (perhaps of interest to read, from May 25, 2015) covers some of the various important microbiomes -- including that on the skin which can provide a first point of defense for intruders into the body as well as the effect of the microbiomes may play with systemic diseases such as diabetes and asthma.

     I point out that a large problem with the transformation of our microbiomes is that manipulation can be very difficult to achieve. The upper digestive tract -- which should be the most direct route to the environment of the lower digestive tract, acting as a home for a major microbiome -- destroys most of any pre- or probiotics that try to enter via the route of ingestion. Substitution from the other direction (not necessarily for the squeamish) works much better but has the problem of being more of a "mallet" approach where it is not a manipulation but, rather, an attempt to conquer the old microbiome by a newer, hopefully healthier, microbiome.

     One side-effect of being aware of the existence of the microbiomes on, and inside, our bodies is that it has become much more obvious that it is wrong to say "kill all the bacteria" or "stop all the viruses". In fact, although antibiotics have been literal lifesavers to prevent major harm from bad bacteria, antibiotics may also contribute to more general illnesses (diabetes, arthritis, cancer, etc.) as a result of killing off helpful good bacteria.

     Note that there will never be ONE general population of microbiomes because each environment supports different situations. Someone who has rice as their principal food will support different creatures in their microbiome than someone who has wheat bread as their dominant food (and even different for those who have cola soft drinks as THEIR dominant calorie intake). A person living in near constant heat will have a different skin microbiome than someone who lives (or, with climate change, lived) in sub-freezing temperatures year-round.

     One of our challenges in this investigation is inventories. Just what viruses and bacteria are present in, and on, our bodies? What are their side-effects from living? What helps the good ones (which are typically dominant)? What hinders the specific bad ones (the methods we have do not discriminate well between beneficial inhabitants and those that are bad). We are aware that traditional uses of antibiotics are losing their usefulness as bacteria adapt to resist the medicines. Knowledge of our microbiomes will require us to understand well enough to tailor medicines against specific creatures rather than "all" creatures.

     After inventories -- knowing what, and what they do -- we need methods of manipulation. Pre-, pro-, and regular biotics might be encapsulated such that they only become vulnerable after the digestive process has completed its task of breaking down food into components. "Good" cultures could be maintained outside of the body and used to supplement existing microbiomes.

     Whatever emphasis is taken, our bodies ARE indeed houses for many. Some religious scriptures may refer to our bodies as temples and occupational spaces for the gods. We need good neighbors within our bodies as well as in the outside world between people. Finding methods of understanding these interior worlds of interacting cells may be as difficult as understanding of the outer world but both can be of great benefit and worth the effort;

Flattening that curve -- what does it mean?

[ Numbers are as accurate as possible at time of writing -- but continually changing]

     At this moment, much of the world is on "lockdown" -- isolated from one another and moving around only if a person is categorized as performing "essential" work or if a person must leave the house to perform an "essential" activity (obtain food, medicine, repair, ... as defined per state or country). An essential worker is a person who is performing that essential work.

     At the "front lines" are the medical workers, ambulance drivers, ERTs, and often police and fire department workers. Being at the front line means that you are being confronted, and working, with those who ARE sick -- not just someone who MIGHT be sick (which is about everyone). Others who are providing essential services -- grocery store workers, postal and delivery people, sanitation workers, truckers, agricultural and meat processing workers, pharmacists, people who work in take-out/curbside/delivery of food, and many others -- are interacting with people who might be sick. In some of these cases, because they are interacting with so many different people, their personal risk (and, indirectly, risk of their families and others with whom they may be in regular close contact) may be high.

     A total lockdown (nobody contacts anyone else), can stop the spread of a virus (in the current case, covid-19, but applicable to any viral pandemic). But such an absolute isolation would cause many deaths -- directly from the illness (not being able to go to a hospital) and indirectly from lack of food and other needed supplies. And testing would still be needed -- somehow -- to determine when it was safe to release the lockdown. Not an easy scenario and if you miss even one case before you ease the lockdown -- back to square one.

     So, we go towards the above, essential allowed, lockdowns. This cannot stop the spread of the virus but it can SLOOOOOW down the spread of the virus.

     Yes, until a vaccine is approved and administered, people will continue to get ill. Slowing down the spread is called "flattening the curve". The main reason for this is that if spread is allowed to go unchecked it will overwhelm the available healthcare system. The Center for Disease Control (CDC)  has the following diagram:

In simpler terms, the graph says that you want to delay the period at which you have the most active cases of people not being well AND you want that highest number of active cases to be as small as possible.

     Healthcare involves hospital space (beds), sufficient staff (doctors, nurses, administrative, ...), equipment (ventilators, masks, protection hoods, ...) and medicines. Overwhelming the capacity in any of these areas will put the "overflow" into danger mode. At that point, the staff will have to "triage" the infected people with treatment going to the most badly infected and the rest will have to hope to survive on their own.

     Much of the time, equipment and medicines are insufficient but there isn't much that a regular citizen can do about that situation. Staff, unfortunately, will fluctuate as people get sick and (hopefully) recover -- proper protective equipment can help with that. What people can best have an effect on is the number of infected cases -- and that can be done by reducing the chance of an infected person infecting other people.

     Hospital beds are easy to count, so lets use those numbers to determine the maximum "peak" of the curve that will not overwhelm the system. Note that lack of staff, equipment, and medicines may DECREASE the maximum that the healthcare system can handle.

     Let us say that, in my county, the hospitals have 617 beds (which should be close to accurate, according to noted average numbers of beds -- 1.9/1000 times 325 (my county has approximately 325,000 people)). Approximately 2/3 of those beds are already occupied at a given "normal" period of time. That leaves 207 beds available for emergency needs. If not too many health care workers get sick (such that we are unable to staff for a fully case load) then as long as the number of hospitalized cases stay under 207, it can be handled.

     One additional factor is what percentage of cases need to be hospitalized? All cases need to be identified and treated but not all require a hospital bed. Without universal, daily (or every two days), testing precise numbers are not possible -- because there is no way to know exactly how many people are infected. Some early reports indicated that MAYBE 1/5 of the cases need to be hospitalized. Therefore, a number greater than 1035 cases will overwhelm the number of hospital beds (1035 / 5 = 207) in my county. Recorded numbers (as of today) of cases for my county is 536 -- so we are not overwhelmed as of yet but our numbers continue to increase daily. We are still very much in danger.

     If we apply the same formulas to the situation in New York, we see (as of today) that there are approximately 270 hospital beds per 100,000 (2.7/1000). If 2/3 of these beds are already occupied, that leaves us with 90 beds per 100,000 As of today, there are 1302 cases per 100,000. 1/5 of 1302 is 260 expected hospitalized cases. We see that New York state has far exceeded the number of hospital beds (almost 3 times). And, New York may have 270 hospital beds per 100,000 for the STATE but hospital beds and cases are not equally spread out within the state. Thus, the New York City metro area is in much worse condition than what would be seen from the initial formula. That is why so many temporary hospital beds are being set up -- but just adding beds does not add equipment, medicine, or staff.

     What happens if we do exceed the number that can be handled? We can see that in areas of the country that have had cases rise out of control for too long. Death rates rise. In Italy, this has also happened. The same holds for cruise ships and other confined areas such as retirement homes.

     So, when can an "essentials only" lockdown be cleared? This is associated with the idea of "herd immunity" where the contagion factor (how easily the disease is passed along to others) is associated with how many people are no longer able to be infected (recovered or naturally immune or vaccinated). The contagion factor is improved by isolation and lockdown. There are too many factors involved for me to even venture a guess.

     In the Spanish Flu Pandemic (1918 through 1920), there were "waves" of infection. Lockdowns, followed by ease of restriction, followed by increasing infection, followed by lockdowns, followed by ease of restriction. Health care is potentially much better than in 1918 but many political and economic factors are involved with treatments and population restriction.

     As mentioned earlier, full accurate numbers are not available. We don't really know just how many people are, or have been, infected. We don't know how many people who have died and had their reasons marked down in error. But we do have ways to slow the rate of spread of infection and we have real world examples of what happens if the rate of infection overwhelms the healthcare available.

     Best of futures to all. Stay safe.

Computer Literacy 101 -- what are data?

All computers work with data. But, what are data? I say "what are data" because the word data is a plural one -- it is the plural of datum. However, almost no one ever uses the word datum and just about everyone treats data, grammatically, as singular. A datum is a single piece of information -- yes or no, it is raining or it is not raining, you have eaten breakfast or you have not eaten breakfast. You will note that a datum only indicates a yes/no or off/on, binary, condition. Most of the time, when we need information, it is really a collection of datum -- or data.

The same is true with computers -- they work on each individual datum but they pull them out of a pool of data. This data (I will use the conventional singular grammar here) is kept in storage, as I pointed out in a previous blog. It is then transferred from one storage area to the local RAM where the microprocessor can directly work with it.

Data is used by the microprocessor at many stages. The first stage, or startup (or bootup), is when the microprocessor first receives electricity. The actual hardware (the collection of semiconductor chips, and other discrete electronic components) is designed to start transferring data from a specific memory storage area and address. Often, this is address zero (0). This means that the microprocessor will transfer data from address 0 (the actual physical location, once again, depends on design of the hardware) to its working memory. It then executes the data -- it starts to perform specific operations based on the contents of that data that was at that address and then increments the address for the next instruction (usually by one -- unless the first instruction says something else) and then executes the operations for that address and on and on.

The next stage occurs once the registers (we talked about them in the storage blog) of the microprocessor have been filled with working data. At this stage, it is prepared to continue to execute instructions as it transfers them from memory. You can look at is as having two stages -- the first where the microprocessor "wakes up" with no specific contents in its registers and the second when the microprocessor has been initialized and can now proceed to work as the data tells it. Or, you can look at it as having three stages -- the first one the boot stage, the second is the startup stage where it is still getting ALL of the hardware connected to the computer ready to be used, and the third stage where any type of instructions can be executed because all of the hardware has been set up to be ready for use.

All of this works with the data. The data, for a general purpose microprocessor, is what makes it able to work differently each time it is turned on. For a specialized microprocessor, the incoming data starts the activities for which the microprocessor is designed.

Somehow, I managed to avoid the word program in this description but data are often split into two categories. Instruction data, or programs, are executable -- they contain instructions for the microprocessor while program data is used by the programs to produce more data. The difference between these categories of data is that instruction data does not change (unless someone specifically writes another program to change that instruction data -- the topic of viruses and software patches).

I'm going to swap the next two items on my original "computer literacy" list and talk about programs more in the next blog.