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...
Sunday, August 4, 2024
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.
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.
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.
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.
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