Sunday, August 4, 2024

Just some rambling, to get started writing more regularly (hopefully). We seem to be in a new world of problematic access to all our online apps and accounts. Everything requires two (or more) forms of confirmation, typically your password, and then often a random number generated and sent to your cell phone. The most bizarre in my case is when I access my gmail, or any other Google app, the followup confirmation goes to my phone's Youtube app. When anything goes wrong, or if you don't have your phone handy (or in the case of one work colleague, one doesn't have a smart phone), it can be very difficult, especially since none of these big companies has anything like direct customer service any more, just tons of often unhelpful suggestions on their help websites. One can do google searches for help from others, but the hits you get are usually out of order, and may relate to previous versions of the various software systems one is using. Of course, this is all necessary due to the high rate of hacking and identity theft we currently face. I say necessary, but of course the alternative would be to start doing things (like banking) in person again, at an actual place in the real world. Supposedly that is less efficient and more expensive, but we may be reaching the point where it becomes more efficient again, and possibly even less expensive if the big companies end up having to make regular payouts to customers who were hacked. We're not there yet, but it could happen. I'm no expert on network theory, but from my reading on this and complexity in general, it seems that there are multiple objectives in designing systems, which are sometimes in conflict with each other. For connection and information sharing purposes, networks need to be efficient. The best way to do that is via a "hub" structure, such as that used by Fedex, and even commercial airlines these days. Instead of having routes from everywhere to everywhere, which requires a lot of routes and therefore costly infrastructure, everything (and everyone) goes from the periphery to a hub, and then out again to a different site in the periphery. Such a structure is also robust to random failures or attacks, since a failure of any particular route only affects the peripheral site involved, but not really the hub. However, hub structures are way more vulnerable to targeted failures, or even random failures that occur at the hubs. When a hub is compromised, or even just fails randomly due to equipment problems, many more sites are involved, and potentially the entire network. We saw a recent example of that, where a non-malicious event, just implementation of a buggy software update, caused worldwide outages involving Microsoft, that took days to resolve and who knows at what cost. Even at a personal level the conflict between efficiency and security is evident. The easiest way to keep our (mental) lives simple would be to use the same password for all our accounts. Of course no sane knowledgeable person would do that these days. The next best thing is to have a super secure password manager, which itself tracks all our passwords, but we only need to remember how to access the one manager (I guess that is the same as a 'keychain', although I'm not sure). Myself, I don't use such a system, I'm not sure if such a manager could be safe enough. Maybe I could use it for all non-financial, i.e. social media and work-related, access, I'll consider it. But even so, at least in my case and probably yours, various sites I use require me to change my password on some schedule, whether annually, or less, or more frequently, and these are never in sync with each other. Every time I do a password update, I would have to update the manager. It's not clear if that would end up being easier. Of course, our personal computer web browsers will offer to save our passwords for us, and I do use that functionality. However I find that this is fairly buggy, so that when I change a password, and the browser invites me to update in its memory and I do, the next time I find that it did not in fact update. Also, the browser I use (Brave) recently managed to forget all my passwords, on both my desktop and laptop computers, and when I tried to manually re-add the passwords to the software manager one by one, they kept getting deleted every time I closed the software. But since then, it seems to be slowly re-remembering most of them. Very odd behavior indeed, and no obvious way to figure out what is going on. Wishing you safe travels in cyberspace!
Haven't checked here for a while. For some reason a bunch of old posts are now marked as only drafts. I just re-published them, but they show up with today's date so are way out of order. Just in case anything in them seems anachronistic, that's why!

Back to the classics

I have started studying the viola. It's ambitious, starting an instrument at a relatively advanced age. I have been playing other strings for years now, but nothing with a bow and nothing facing up - always facing out. So the strain on my left arm is significant. I'm trying to go slow and be patient, hopefully I'll increase the mobility over time. But I can pick out a simple tune in D major, which is a start. Bowing feels very natural. Also the viola uses the unusual alto clef, not that I read sheet music well anyway. But why not? I love the sound, it's my instrument for sure. Kind of rough and woolly, and in between. Violin is too high, cello is too awkward. It must be the greek thing - moderation in all things including pitch!

Northern migrations

I have to travel from Montreal to Ottawa for a short business trip. Without thinking much about it, I purchased an Air Canada round-trip ticket. Then a colleague reminded me that it's only a two hour drive, much shorter door-to-door than actually flying. I'm used to the idea that Canada is big! So big that no one could possibly drive from one major city to another in less than half a day. OK, I'm still learning about my adoptive country.

Speaking of Canada, it's time for us to initiate new crop programs, to create a more diverse agriculture. The huge (and successful?) canadian canola crop started as an experiment to provide alternative sources of oil during WWII. My personal favorites for development today are amaranth, a high protein grain, and kenaf, an attractive alternative to wood for paper production. Although I spend my professional life studying human biology for improving medicine, it's an unavoidable truth that we humans have multiplied exponentially and that there are now a lot of us. Keeping us all healthier longer won't be much use if we can't feed ourselves or maintain our supply of clean air and water. I drive a hybrid car, it's not a perfect solution by far, but the more of us that do, the stronger the message that people want a healthy environment for themselves and their children.

Oh, by the way, I cancelled my air flight to Ottawa for an AC credit, and am hitting the road.

personality type

I'm an ENFJ. That's a particular kind of personality type based on the Myers-Briggs classification scheme (check out Wikipedia for more on the scheme). First question, how reliable is the classification itself. The test involves lots of questions and redundancy, and seeing the outcome I'm reasonably comfortable with this typing.

E means extraverted. I do think a lot about other people though, how they might react to me, what they may be thinking about. If someone describes having a problem I tend to jump in with ideas or suggestions - which can be helpful but obviously not always. I sometimes jump in pre-emptively, to say that I know someone else who knows something or can help with whatever the person I'm talking with is talking about. Networking comes automatically to me.

N is for intuitive. This is a very particular sense of the word according to MB. It refers to the kind of information that is gathered and relied on, whether it's more sensory or more abstract and related to other similar information. I have a strong tendency to make connections between ideas, so that they validate each other. As a scientist (or even as a person) there always has to be validation by real observation, so it's not a matter of ignoring sensory input. But pure observation is overwhelming, I use patterns and schemes to organize it, and these come from internal reflection (as in intuition) but also as I said by cross-checking with other information. Ideally the different kinds of information are orthogonal, that is, based on really independent sources, so less likely to be purely coincidental.

F meens feeling, versus thinking (T). This too has to be understood within the language of the scheme, these aren't the common uses of the words. These have to do with paradigms of decision making. F tends to make decisions from within a situation, rather than from the outside. I'm not too clear about this one, for me to be an F seems a little bit contrary to also being an N. But for the afficianados of MB, there it is.

Finally, J means judging rather than perceiving. This seems to have to do with how one is perceived by others, as logical or more emotional and empathetic. My being a J here makes sense - although I think of myself as quite logical, I'm probably not really perceived that way by others (but feel free to comment!).

In any case, ENFJ types come with fairly specific description in the system. They are sensitive to others, they react to the general tone of a situation, and they are often organizers. In the Keirsey system, which is related to the MB system but focuses more on the practical implications, ENFJs are described as idealists, with a strong bent to being teachers. For sure I have a strong pedagogic streak, I love explaining things. That can be quite tedious if overdone or in the wrong social context. But when I give lectures I spend lots of time on the materials, and try to think about the information that I'm conveying as I want it to be perceived by my listeners.

It gets more interesting when you see how you match up with your partner. There are 16 MB types, so 256 different pairings of course. I don't think MB has something to say about each of these, but it's fun to make the comparisons ourselves.

That's all I have to say about that!

account management

How many accounts do you have? In my case, let's see, just at home I have my main email address, my previous email adddress which is still working even though we changed providers and don't have that service any more, my facebook account, my linkedin account, and my blog. These are just the personal ones, that doesn't include all the various banks and other financial and "home management" ones. At work - don't get me started. And if you're like me, many of them require regular changes of password for "security", but not on the same schedule of course. No one could remember all those changing passwords, so of course we all use shortcuts, common formulas, or even (heaven forbid) postit notes on our desks. My laptop tries valiantly to keep up, but it seems to be rather poor at it, since it tends to auto-fill in the wrong password for many sites I log on to, so I have to repeat it manually anyway. And then of course once you clean up your internet activities by deleting your temporary files, page history, and cookies, it's all gone the next time you fire up the browser. It's not that I prefer a world without computers, it's just that they do eat a fair amount of time for things that were supposedly easy, and also create new frustrations that require new coping mechanisms (besides throwing the mouse against the wall, that is).

I was going to write a nice blog about summer and the flowers in my garden, but it took 15 minutes to remember how to log onto this account since it appears to be irrevocably attached to my previous, not my current email address. This is not obvious because my current email address is there in my profile, but that's not the same as the one the account is formally linked to - and there seems no mechanism to update that, I think I would have to stop this blog and start another one. Arggh. Well, the flowers are very nice but more details will have to wait...

Genetics 101

Genetics is inescapable in the popular media these days. The Human Genome Project, the HapMap, personalized medicine, are buzzwords on a regular basis. But what are they really about, and what is or is not realistically feasible at the current time?

As everyone probably knows by now, the human genome consists of roughly 3 billion "bases" of information. This is packaged biochemically as long DNA molecules assembled into chromosomes. The human species has 23 pairs of chromosomes, 2 each of chromosome 1,2,3 etc up to chromosome 22; males have an X and a Y and females have two X chromosomes. In other words, except for the special properties of the X and Y, cells in our bodies have two complete copies of the genome. The chromosomes vary in length, chromosome 1 has around 300 million bases whereas chromosome 22 only about 50 million (very approximately).

Without getting into the details of DNA structure and chemistry, the computer analogy is fairly helpful. If DNA is a computer program for assembly of an organism, then the bases are like bits of information. As we write computer programs, the hardware ultimately sees each bit as either a 0 or 1, so there are two states - in contrast each base or bit of DNA can have 4 different states (chemically G, A, T or C).

Genes are simply segments of DNA sequence that encode particular activities. There is a lot of argument these days about the exact definition of a gene, and some slightly new-age holistic arguments that there are not actually any such things, but most working scientists still find it necessary to think of genes as real entities in nature. With the computer analogy, one can say that only a whole program has the ultimate information, but still programs can usually be helpfully broken down into segments of code, subroutines or even individual lines. In any case, the exact nature of a gene is not relevant to my train of thought here.

There is not actually one definable "human genome" sequence. Extensive experimental work has clearly shown that we each differ at millions of places in our DNA sequence - a place being defined as a particular element of the code that can usually be compared in two different individuals. Even more, since we each carry two copies of most of the chromosomes, one received from dad's sperm and one from mom's egg, those two are equally quite different. So internally we also carry two different bits of information at many millions of sites in our own genomes (with the exception of genetically identical twins, nature's clones). That is not to say that the human genome sequence as generated by the Human Genome Project is not real, it is simply a composite or consensus combined from different individual human sources.

It is clear that these millions of differences account for many of the physiological differences between individuals. Together they define the genetic component of biological individuality. There is of course a strong environmental component, it is not necessary for now to try and figure out how much of each is relevant to any particular trait such as height, eye color, disease susceptibility. The problem is, for any given DNA sequence variant, a G in one person but a T in another person (or on the two different copies of a particular chromosome in one person), what is the effect of that sequence variation on the physiology of that person. This in essence is the discipline of genetics: genetics is the study of genotype/phenotype causation. In practice it is very difficult, since there is simply so much DNA and so much variation, how can one possibly assign a cause/effect role to any particular variant and any particular physiological trait? I will start to address this in my next blog on the subject, but suffice for now to say that one starts with the simplest most straightforward examples, where many different kinds of evidence can be used to support a causal claim, and proceeds to more and more difficult examples where the evidence is far more tenuous and sometimes no more than speculation. This is how experimental science usually works, few genuine moments of absolute definitiveness and many moments of incremental growing certainty.