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.

Classical musings

I've recently read two related books on the subject of music (a major non-professional interest): This is Your Brain on Music (by Daniel Levitin) and Why Classical Music Still Matters (by Lawrence Kramer). More on the books themselves another time perhaps, but through reading them I've been led back to listening to a genre that I'd moved away from for many years. I'm discovering a new appreciation for the complexity of classical music, and in particular am for the first time enjoying music of smaller groups (soloists, duets, quartets). Right now I am enraptured by a string quartet by Dvorak, his "American", opus 96, in particular the second Lento movement. It opens with a sublime melody sung by the violin, repeated by the viola (or perhaps the second violin?) and then broken down, rearranged, modulated, re-assembled to various stages of (in)completion until it is fully re-stated at the close of the movement. It's ravishing. What is a "melody"? Why do some series of notes constitute one, whereas others though interesting and enjoyable do not? And when there is no obvious melody, why is it still sometimes great music?

Arthur Clarke wrote a story about a scientist who sets his computer to analyzing all the catchiest tunes in history, trying to identify a common element. The computer succeeds, and then constructs and plays out the ultimate catchy tune, an earworm that runs through the scientist's head excluding all other thought and input, making him a vegetable for life. Luckily for the world, the night custodian is tone-deaf and turns off the speakers before anyone else can enter the room. It's similar to the Monty Python sketch about the joke so funny that it makes you die laughing. The British army uses it as a weapon during WWII, after translating it into German with teams of translators, each working on only one word. Silliness, but still appreciating melody and humor seem to be universal and possibly defining human attributes.

Our photo here is one of the two housecats, Pepper. She shares some attributes with us that are not definingly human!

The lost science

Next time you're in a large bookstore, go to the science section and compare the number of different books offered by subject. You'll see a lot of biology (especially evolution), a lot of physics and astronomy, and a fair amount of mathematics and even earth science. But there will probably be little by way of chemistry. Perhaps several college study guides, and two or three popular books about oxygen, but that's it. For some time I have noticed this and pondered possible explanations. I suppose the large publishers have their reasons, but my suspicion is that chemistry is simply too messy. It is not intrinsically more difficult than any other science, or less difficult for that matter. But it seems to be harder to explain, in an interesting way at least, to a nonprofessional audience. The problems it deals with are not as fundamental as those of physics or mathematics. Nor are they are immediate as those of biology or earth science, where anyone has at least a chance of seeing the objects of study. Chemistry deals with the electronic interactions of atoms, that create infinite opportunities for new molecules from high temperature superconductors to new pharmaceuticals. But no one has ever really seen a molecule (except in indirect ways such as with electronic or atomic force microscopes). It is not easy to explain what a molecule actually is, since no one has directly seen an atom either. What are some objects we can see and hold, like iron bars or gold rings, elements (gold rings actually are not, they contain other metals to harden them, but in principle they could be), whereas others like salt or sugar are molecules? If you take one electron from a dangerously reactive metal (sodium) and give it to a poisonous gas (chlorine) you get table salt which is essential for us to live. To me that is amazing, but once you have said this, what else can be said without going into a lot of technical detail about orbitals and valences. Chemistry has many wonderful stories to tell. I loved Napoleon's Buttons, a book about many interesting chemicals, their discovery or synthesis or use. And I confess that from time to time I browse in Nature's Building Blocks, a book in which each chapter covers a different atomic element in detail. But these are compendia of stories, they do not have any clear flow. The history of chemistry does have such a clear chronological and intellectual flow, which has been recounted in numerous books. But such books tend to cover mostly the same ground repeatedly. Other than presenting new interesting molecules (like the nanocar, shown above on the right from a recent article), there does not seem to be anything new being said in popular literature about chemistry. This is a shame, as I doubt that it is true that there is nothing new worth saying. I call on literary chemists to tell us about their work.

Why do sudoku?

I've been a longtime afficionado of crossword puzzles. When I was younger I used to do the Sunday times with my mother, looking over her shoulder as she sat in her favorite chair in the living room. There was a wonderful sense of camaraderie as we worked together, complementing each other's knowledge so that we could usually complete a puzzle that neither of us could do alone. But for years I resisted the sudoku craze. There must have been multiple reasons: resisting the herd, preference for verbal not numeric puzzles for example. But for some unclear reason I recently tackled some easy ones in the local newspaper, and got hooked. From there it was an easy step to addicted. My stepson even bought me Sudoku for Dummies last Christmas. I've made my way through the sections from Easy to Tricky to Tough, but am currently stumped by Diabolical.

Sudoku is not really about math at all, it's pure logic - arbitrary symbols would work equally well though they would be much harder to track mentally. The harder puzzles involve longer chains of reasoning, or managing more alternatives in your head at once. But ultimately the satisfaction is probably the same as for other types of puzzles - the feeling of closure. In life, and certainly in the professional life of a research scientist, real closure comes infrequently and rarely with a definitive moment of "Aha!" Sudoku is to science as Woody Allen once said art is about life, we can make things come out better in one than they usually do in the other.

The photo has nothing to do with Sudoku, it's a selection of some of my exotic instruments from eastern and southern europe: turkish saz, oud, macedonian tambura, bulgarian tambura and dumbek. If I can figure out how to upload music I will hopefully add some samplers.

Opening the door

Well, this is my very first blog post. I have nothing special to say today, just hi! Lots more to come on science, music, politics...

A sucker for romance

I admit it, I'm a sucker for romantic comedy films - date flicks. I seem to have an endless capacity to watch new ones. Maybe a 19th century Englishman travels to the future and courts a 20th century woman in an unusual way (Kate and Leopold). Maybe two people fall in e-love (You've Got Mail). A socialite falls for a pesky journalist (The Philadelphia Story) or a scientist (Bringing up Baby), or a movie star with a nebbish (Notting Hill). The combinations are indeed endless. But in basic story line they are generally the same. As the old Jewish man complained deploring the theater: "First he wants and she doesn't want. Then she wants and he doesn't want. Then they both want and boom! down comes the curtain". If the story is so predictable, then how could anyone watch all these? (OK, Phila. Story does take an unexpected twist.) Not everyone can, I have friends who find the genre tedious, but at least some of us can, or Hollywood wouldn't keep making them.

I believe the answer is that we do in fact care about the details, the sometimes infinitesimal differences between the situations in each of these films. Finding a mate is one of the most essential biological drives, and whether we already have one in our lives or not, it's serious business. We need all the help we can get to find one, or keep the one we have. Seeing others succeed gives us ideas for our own lives - maybe silly ones, but no idea is too silly for some consideration in this critical activity.

I love the series of short documentary style interviews of couples in When Harry Met Sally - particularly the elderly chinese guy who went to great lengths to check out his intended bride before their arranged wedding. And there's the couple in Annie Hall, who tell Woody's character: "I'm shallow and have nothing to say"..."And I'm the same"; they've found each other. I was hiking once in southern Utah with my then current girlfriend, two eastern intellectual types enjoying the outdoors. We happened to cross paths with another couple, two blonde athletic waspy types in spotless white tennis clothes. We went our separate ways, but my friend and I looked at each and burst into simultaneous laughter. It was so...congruous. So the next time I see ads for a film in which a molecular geneticist falls head over heels for an artist he happens to meet on a ferry ride across the arctic, I'll be there. Or at least I'll see it when it hits the video stores.